Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 85 of 193
Found at i:28151409 original size:49 final size:49
Alignment explanation
Indices: 28151343--28151838 Score: 155
Period size: 49 Copynumber: 10.2 Consensus size: 49
28151333 TGGCTTTAAT
*
28151343 CTATCCCTTTTTAGTTTTCGGGTGTTAGGTCCA-CTGTTGCGACTTCAAC
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATC-GTTGCGACTTCAAC
* * * * ** * *
28151392 CTATCCCTCTTTGGTTTTAAGGTGTAATATCTATCGTTGCGACTTCAAT
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * ** *
28151441 CTTTCTCTTTTTAGTTTTAGGGTGTTAGGTCTATCGTTATGAGTTCAAC
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * * * * * * * * * *
28151490 TTATCCCTCTTCAATTTTAAGGTGTAAGATCCGTCGATACGGCTTCAAT
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * * ** * * ** * *
28151539 CT-TCCCATATTCGATTTTAAGGTGTTAAATCCGTCTTTTTGGCTTCAAT
1 CTATCCCTTTTTAG-TTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * * ** * * *
28151588 CTATCCCTATTT-GATTTTAGGGTGATAAGTTCGCCTTTACGGCTTCAAC
1 CTATCCCTTTTTAG-TTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * * * * * * *
28151637 CTATCCCTCTTCAATTTTAAGGTGTAAGATCCGTCGTTACGACTTTAACC
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAA-C
* * * * * *
28151687 CT-TTCCTCTTT-GATTTT-GAGGTGTTAGGT-CTTCCATTACGGCTTCAAC
1 CTATCCCTTTTTAG-TTTTAG-GGTGTTAGGTCCAT-CGTTGCGACTTCAAC
* * *** * * * ** *
28151735 CTATCCCTCTTCAGTTTTAATATGTAAGATCTATTATTGCGACTTCAAT
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
* * * * *
28151784 CTTTCCC--TATAGTTTTAGGGTGTTAGGTCCGTCATTACGACTTCAAC
1 CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
28151831 CTATCCCT
1 CTATCCCT
28151839 CTTCAATTTT
Statistics
Matches: 323, Mismatches: 111, Indels: 27
0.70 0.24 0.06
Matches are distributed among these distances:
47 34 0.11
48 10 0.03
49 267 0.83
50 12 0.04
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (49 bp):
CTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTGCGACTTCAAC
Found at i:28151451 original size:98 final size:98
Alignment explanation
Indices: 28151340--28151516 Score: 239
Period size: 98 Copynumber: 1.8 Consensus size: 98
28151330 TCGTGGCTTT
* * *
28151340 AATCTATCCCTTTTTAGTTTTCGGGTGTTAGGTCCA-CTGTTGCGACTTCAACCTATCCCTCTTT
1 AATCTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATC-GTTACGACTTCAACCTATCCCTCTTC
**
28151404 GGTTTTAAGGTGTAATATCTATCGTTGCGACTTC
65 AATTTTAAGGTGTAATATCTATCGTTGCGACTTC
* * * * * *
28151438 AATCTTTCTCTTTTTAGTTTTAGGGTGTTAGGTCTATCGTTATGAGTTCAACTTATCCCTCTTCA
1 AATCTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTACGACTTCAACCTATCCCTCTTCA
28151503 ATTTTAAGGTGTAA
66 ATTTTAAGGTGTAA
28151517 GATCCGTCGA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
98 66 0.99
99 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (98 bp):
AATCTATCCCTTTTTAGTTTTAGGGTGTTAGGTCCATCGTTACGACTTCAACCTATCCCTCTTCA
ATTTTAAGGTGTAATATCTATCGTTGCGACTTC
Found at i:28151536 original size:98 final size:96
Alignment explanation
Indices: 28151309--28151541 Score: 236
Period size: 98 Copynumber: 2.4 Consensus size: 96
28151299 CCGTCTTTAG
* * * *
28151309 TTTTAAGGTGTTAGATCCGCTTCGT-GGCTTTAATCTATCCCTTTTTAGTTTTCGGGTGTTAGGT
1 TTTTAAGGTGTAAGATCCG--TCGTCGGCTTCAATCTTTCCCTTTTTAGTTTTAGGGTGTTAGGT
* ***
28151373 CCACTGTTGCGACTTCAACCTATCCCTCTTTGG
64 CCACTGTTACGACTTCAACCTATCCCTCTTCAA
* ** * *
28151406 TTTTAAGGTGTAATATCTATCGTTGCGACTTCAATCTTTCTCTTTTTAGTTTTAGGGTGTTAGGT
1 TTTTAAGGTGTAAGATCCGTCG-T-CGGCTTCAATCTTTCCCTTTTTAGTTTTAGGGTGTTAGGT
* * * *
28151471 CTA-TCGTTATGAGTTCAACTTATCCCTCTTCAA
64 CCACT-GTTACGACTTCAACCTATCCCTCTTCAA
28151504 TTTTAAGGTGTAAGATCCGTCGATACGGCTTCAATCTT
1 TTTTAAGGTGTAAGATCCGTCG-T-CGGCTTCAATCTT
28151542 CCCATATTCG
Statistics
Matches: 109, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
95 3 0.03
96 1 0.01
97 16 0.15
98 89 0.82
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (96 bp):
TTTTAAGGTGTAAGATCCGTCGTCGGCTTCAATCTTTCCCTTTTTAGTTTTAGGGTGTTAGGTCC
ACTGTTACGACTTCAACCTATCCCTCTTCAA
Found at i:28151536 original size:147 final size:145
Alignment explanation
Indices: 28151382--28151710 Score: 340
Period size: 147 Copynumber: 2.2 Consensus size: 145
28151372 TCCACTGTTG
* * * *
28151382 CGACTTCAACCTATCCCTCTTTGGTTTTAAGGTGTAATATCTATCGTTGCGACTTCAATCTTTCT
1 CGACTTCAACCT-TCCCTCTTTGATTTTAAGGTGTAA-ATCCATCGTTGCGACTTCAATCTATCC
* * * * * *
28151447 CT-TTTTAGTTTTAGGGTG-TTAGGTCTATCGTTATGAG-TTCAACTTATCCCTCTTCAATTTTA
64 CTATTTGA-TTTTAGGGTGATAAGTTC-ACCGTTACG-GCTTCAACCTATCCCTCTTCAATTTTA
28151509 AGGTGTAAGATCCGTCGATA
126 AGGTGTAAGATCCGTCGATA
* * * * * * ** *
28151529 CGGCTTCAATCTTCCCATATTCGATTTTAAGGTGTTAAATCCGTCTTTTTGGCTTCAATCTATCC
1 CGACTTCAACCTTCCC-TCTTTGATTTTAAGGTG-TAAATCCATCGTTGCGACTTCAATCTATCC
* *
28151594 CTATTTGATTTTAGGGTGATAAGTTCGCCTTTACGGCTTCAACCTATCCCTCTTCAATTTTAAGG
64 CTATTTGATTTTAGGGTGATAAGTTCACCGTTACGGCTTCAACCTATCCCTCTTCAATTTTAAGG
*
28151659 TGTAAGATCCGTCGTTA
129 TGTAAGATCCGTCGATA
* * *
28151676 CGACTTTAACCCTTTCCTCTTTGATTTTGAGGTGT
1 CGACTTCAA-CCTTCCCTCTTTGATTTTAAGGTGT
28151711 TAGGTCTTCC
Statistics
Matches: 147, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
146 6 0.04
147 124 0.84
148 17 0.12
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (145 bp):
CGACTTCAACCTTCCCTCTTTGATTTTAAGGTGTAAATCCATCGTTGCGACTTCAATCTATCCCT
ATTTGATTTTAGGGTGATAAGTTCACCGTTACGGCTTCAACCTATCCCTCTTCAATTTTAAGGTG
TAAGATCCGTCGATA
Found at i:28151870 original size:49 final size:49
Alignment explanation
Indices: 28151484--28151926 Score: 305
Period size: 49 Copynumber: 9.1 Consensus size: 49
28151474 TCGTTATGAG
* *
28151484 TTCAACTTATCCCTCTTCAATTTTAAGGTGTAAGATCCGTCGA-TACGGC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCG-CTATTACGGC
* * * **
28151533 TTCAATCT-TCCCATATTCGATTTTAAGGTGTTAA-ATCCGTCT-TTTTGGC
1 TTCAACCTATCCC-TCTTCAATTTTAAGGTG-TAAGATCCG-CTATTACGGC
* * ** * *
28151582 TTCAATCTATCCCTATTTGATTTTAGGGTGATAAG-TTCGCCT-TTACGGC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTG-TAAGATCCG-CTATTACGGC
* *
28151631 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCG-TCGTTACGAC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCT-ATTACGGC
* * ** * * * ** *
28151680 TTTAACCCT-TTCCTCTTTGATTTTGAGGTGTTAGGTCTTCCATTACGGC
1 TTCAA-CCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGC
* ** *** * *
28151729 TTCAACCTATCCCTCTTCAGTTTTAATATGTAAGATCTATTATTGCGAC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGC
* * * * * * * *
28151778 TTCAATCTTTCCCT-AT-AGTTTTAGGGTGTTAGGTCCG-TCATTACGAC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCT-ATTACGGC
*
28151825 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGT
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGC
* * * * *
28151874 TTCAATCTTTCCCTCTTCAATTTTAAGGTGTTAGATCCACCATTACGGC
1 TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGC
28151923 TTCA
1 TTCA
28151927 TCTATCTATT
Statistics
Matches: 305, Mismatches: 74, Indels: 30
0.75 0.18 0.07
Matches are distributed among these distances:
46 1 0.00
47 34 0.11
48 13 0.04
49 246 0.81
50 11 0.04
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (49 bp):
TTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCTATTACGGC
Found at i:28160584 original size:28 final size:29
Alignment explanation
Indices: 28160552--28160632 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
28160542 TTAATAACAT
*
28160552 AATAAATATATAATTATAGTATTAAAT-A-
1 AATAAATATATAATTATAGTAAT-AATGAC
*
28160580 AATAACA-ATATAATCATAGTAATAATGAC
1 AATAA-ATATATAATTATAGTAATAATGAC
*
28160609 AATAAATAT-TAATTA-ATTAATAAT
1 AATAAATATATAATTATAGTAATAAT
28160633 ATAAGAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
27 11 0.24
28 26 0.58
29 8 0.18
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (29 bp):
AATAAATATATAATTATAGTAATAATGAC
Found at i:28161418 original size:25 final size:24
Alignment explanation
Indices: 28161359--28161420 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
28161349 ATTTTATTCC
* * *
28161359 AAAAAATTCT-TCTTTGAACAATA
1 AAAAAATTCTCCCTCTGAACAAAA
28161382 AAAAAA-TC-CCCTCTGAACAAAAA
1 AAAAAATTCTCCCTCTGAAC-AAAA
28161405 AAAAAATTCTCCCTCT
1 AAAAAATTCTCCCTCT
28161421 TACATTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 9 0.28
23 15 0.47
24 2 0.06
25 6 0.19
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (24 bp):
AAAAAATTCTCCCTCTGAACAAAA
Found at i:28164302 original size:22 final size:22
Alignment explanation
Indices: 28164240--28164302 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
28164230 AAAAAATAAA
*
28164240 ATGAATAGTGAGA-TCTCTAGC
1 ATGAATAGTGAGATTCTCTGGC
* * * *
28164261 ATGAACAGTAATATTTTCTGGC
1 ATGAATAGTGAGATTCTCTGGC
28164283 ATGAATAGTGAGATTCTCTG
1 ATGAATAGTGAGATTCTCTG
28164303 ACAATATTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (22 bp):
ATGAATAGTGAGATTCTCTGGC
Found at i:28164322 original size:90 final size:91
Alignment explanation
Indices: 28164224--28164403 Score: 260
Period size: 91 Copynumber: 2.0 Consensus size: 91
28164214 AGATATTCCC
* *
28164224 TGCAAGAAAAAATAAAATGAATAGTGAGA-TCTCT-AGCATGAACAGTAATATTTTC-TGGCATG
1 TGCAAGAAAAAACAAAATGAATAGTGAGATTCTCTGA-CATGAACAGTAATA-TTCCATGGCATG
28164286 AATAGTGAGATTCTCT-GACAATATTCTT
64 AATAGTGAGATTCTCTAG-CAATATTCTT
* *
28164314 TGCAAGAAAAAACAAAATGAATAGTGAGATTCTCTGATATGAACAGTGATATTCCATGGCATGAA
1 TGCAAGAAAAAACAAAATGAATAGTGAGATTCTCTGACATGAACAGTAATATTCCATGGCATGAA
*
28164379 TAGTGAGATTTTCTAGCAATATTCT
66 TAGTGAGATTCTCTAGCAATATTCT
28164404 CTTGTAATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
90 31 0.38
91 48 0.59
92 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (91 bp):
TGCAAGAAAAAACAAAATGAATAGTGAGATTCTCTGACATGAACAGTAATATTCCATGGCATGAA
TAGTGAGATTCTCTAGCAATATTCTT
Found at i:28173730 original size:59 final size:59
Alignment explanation
Indices: 28173658--28173887 Score: 236
Period size: 59 Copynumber: 3.9 Consensus size: 59
28173648 AATCGGGATC
* * * *
28173658 AAAAATGAGATTTTTGGAAGTT-TAGGGGTAAAAATATATTTTTTTGAAGTTTTAGGGTT
1 AAAAATGAAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTTGGAAGTTTTAGGGTT
* **
28173717 -AAAATGGAAA-TTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTT
1 AAAAAT-GAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTT
* ** * * *
28173775 AAAAATGGAATTTTTGGTTGTTTG-GGAGTAAAAATGTAATTTTTGGAAG-TTTCGAGGTT
1 AAAAATGAAATTTTTGGAAGTTCGAGG-GTAAAAATATAATTTTTGGAAGTTTTAG-GGTT
* *
28173834 AAAAATGTAATTTTGGAGAAGTTCGAGGGTAAAAATATAATTTTTGGACAGTTT
1 AAAAATGAAATTTTTG-GAAGTTCGAGGGTAAAAATATAATTTTTGGA-AGTTT
28173888 AGAGACTTTC
Statistics
Matches: 142, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
58 53 0.37
59 59 0.42
60 24 0.17
61 4 0.03
62 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (59 bp):
AAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTT
Found at i:28173780 original size:30 final size:29
Alignment explanation
Indices: 28173658--28173887 Score: 219
Period size: 29 Copynumber: 7.8 Consensus size: 29
28173648 AATCGGGATC
*
28173658 AAAAATG-AGATTTTTGGAAGTTTAGGGGT
1 AAAAATGTA-ATTTTTGGAAGTTTGGGGGT
* * * **
28173687 AAAAATATATTTTTTTGAAGTTTTAGGGT
1 AAAAATGTAATTTTTGGAAGTTTGGGGGT
* * * * *
28173716 TAAAATGGAAATTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTGGGGGT
28173745 AAAAATGTAATTTTTGGAAGTTTGGGGGTT
1 AAAAATGTAATTTTTGGAAGTTTGGGGG-T
* ** *
28173775 AAAAATGGAATTTTTGGTTGTTTGGGAGT
1 AAAAATGTAATTTTTGGAAGTTTGGGGGT
* *
28173804 AAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGTAATTTTTGGAAGTTT-GGGGGT
* * *
28173834 AAAAATGTAATTTTGGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTG-GAAGTTTGGGGGT
*
28173864 AAAAATATAATTTTTGGACAGTTT
1 AAAAATGTAATTTTTGGA-AGTTT
28173888 AGAGACTTTC
Statistics
Matches: 162, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
29 89 0.55
30 67 0.41
31 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTGGGGGT
Found at i:28175834 original size:6 final size:6
Alignment explanation
Indices: 28175825--28175896 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
28175815 TCAAAACAAC
** *
28175825 TTTAAA TTTAAA -ACAAA TTTAAA TTTAAAA ATT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
28175872 TTTATAAA TTTAGAA --TAAA TTTAAA
1 -TT-TAAA TTTA-AA TTTAAA TTTAAA
28175897 ATCAAAAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 26 0.50
7 11 0.21
8 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:28175861 original size:18 final size:17
Alignment explanation
Indices: 28175811--28175871 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
28175801 GAATTATTCC
* *
28175811 AAATTCAAAACAACTTT
1 AAATTTAAAACAAATTT
28175828 AAATTTAAAACAAATTT
1 AAATTTAAAACAAATTT
28175845 AAATTTAAAA-ATTAATTT
1 AAATTTAAAACA--AATTT
28175863 AAATTTAAA
1 AAATTTAAA
28175872 TTTATAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.03
17 25 0.62
18 14 0.35
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTAAAACAAATTT
Found at i:28182959 original size:28 final size:29
Alignment explanation
Indices: 28182927--28182990 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 29
28182917 AATTTTAATA
28182927 TTAAAATTATTTTAAAA-AATATAAATTT
1 TTAAAATTATTTTAAAATAATATAAATTT
* *
28182955 TTAAAATTATTTTAAAATTATTTAAATTT
1 TTAAAATTATTTTAAAATAATATAAATTT
28182984 TTAAAAT
1 TTAAAAT
28182991 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAATTATTTTAAAATAATATAAATTT
Found at i:28183310 original size:22 final size:22
Alignment explanation
Indices: 28183282--28183325 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28183272 TAGATGAGTT
28183282 TAGTATTTTCCCAAGAAACAAA
1 TAGTATTTTCCCAAGAAACAAA
**
28183304 TAGTATTTTCCTGAGAAACAAA
1 TAGTATTTTCCCAAGAAACAAA
28183326 CGTACGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (22 bp):
TAGTATTTTCCCAAGAAACAAA
Found at i:28185492 original size:9 final size:9
Alignment explanation
Indices: 28185472--28185508 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28185462 TATAATTTGA
*
28185472 TATTCGACT
1 TATTCGAAT
*
28185481 TATTCAAAT
1 TATTCGAAT
28185490 TATTCGAAT
1 TATTCGAAT
28185499 TATTCGAAT
1 TATTCGAAT
28185508 T
1 T
28185509 TGAAAAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28188019 original size:30 final size:30
Alignment explanation
Indices: 28187968--28188282 Score: 295
Period size: 30 Copynumber: 10.5 Consensus size: 30
28187958 TGCTCGAGGG
* * *
28187968 TAAAATGGTGATTTTT-GGAAGTTTAGGGGC
1 TAAAAT-GTAATTTTTAAGAAGTTTAGGGGT
* *
28187998 AAAAATGTAATTTTTAAGAAGTTTAAGGGT
1 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
* * ** *
28188028 CAAAATATAATTTTGGAGCAGTTTAGGGGT
1 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
* * *
28188058 CAAAATGTAATTTTT-GGAAAGTTTATGGGT
1 TAAAATGTAATTTTTAAG-AAGTTTAGGGGT
* *
28188088 TAAAATGTAA-TTTTAAAAATTTTAGGGGT
1 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
* * *
28188117 TAAAATGTATTTTTTGAGAAGTTTAAGGGT
1 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
*
28188147 TAAAATCTAATTTTGT-AGAAGTTT-GAGGGT
1 TAAAATGTAATTTT-TAAGAAGTTTAG-GGGT
28188177 TAAAATGTAATTTTT-AGAAAGTTTTA-GGGT
1 TAAAATGTAATTTTTAAG-AAG-TTTAGGGGT
* * *
28188207 TAAATTATAATTTTTGAA-AAGTTTAAGGGT
1 TAAAATGTAATTTTT-AAGAAGTTTAGGGGT
28188237 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
1 TAAAATGTAATTTTTAAGAAGTTTAGGGGT
* *
28188267 TAAAATATATTTTTTA
1 TAAAATGTAATTTTTA
28188283 GATAGTTCAG
Statistics
Matches: 235, Mismatches: 37, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
29 41 0.17
30 189 0.80
31 4 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.41
Consensus pattern (30 bp):
TAAAATGTAATTTTTAAGAAGTTTAGGGGT
Found at i:28188063 original size:60 final size:59
Alignment explanation
Indices: 28187986--28188280 Score: 333
Period size: 60 Copynumber: 4.9 Consensus size: 59
28187976 TGATTTTTGG
** * *
28187986 AAGTTTAGGGGCAAAAATGTAATTTTTAAGAAGTTTAAGGGTCAAAATATAATTTTGGAG
1 AAGTTTAGGGGTTAAAATGTAATTTTT-AGAAGTTTAAGGGTTAAAATATAATTTTGGAA
* * * * * *
28188046 CAGTTTAGGGGTCAAAATGTAATTTTTGGAAAGTTTATGGGTTAAAATGTAATTTT-AAA
1 AAGTTTAGGGGTTAAAATGTAATTTTTAG-AAGTTTAAGGGTTAAAATATAATTTTGGAA
* * * * *
28188105 AATTTTAGGGGTTAAAATGTATTTTTTGAGAAGTTTAAGGGTTAAAATCTAATTTTGTAG
1 AAGTTTAGGGGTTAAAATGTAATTTTT-AGAAGTTTAAGGGTTAAAATATAATTTTGGAA
* * *
28188165 AAGTTT-GAGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAATTATAATTTTTGAA
1 AAGTTTAG-GGGTTAAAATGTAATTTTTAG-AAGTTTAAGGGTTAAAATATAATTTTGGAA
* * *
28188225 AAGTTTAAGGGTTAAAATGTAATTTTTAAGAAGTTTAGGGGTTAAAATATATTTTT
1 AAGTTTAGGGGTTAAAATGTAATTTTT-AGAAGTTTAAGGGTTAAAATATAATTTT
28188281 TAGATAGTTC
Statistics
Matches: 197, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
59 52 0.26
60 143 0.73
61 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (59 bp):
AAGTTTAGGGGTTAAAATGTAATTTTTAGAAGTTTAAGGGTTAAAATATAATTTTGGAA
Found at i:28188284 original size:90 final size:88
Alignment explanation
Indices: 28187964--28188282 Score: 365
Period size: 90 Copynumber: 3.6 Consensus size: 88
28187954 TAGATGCTCG
* * ** *
28187964 AGGG-TAAAATGGTGATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTTAAGAAGTTTAAGGGT
1 AGGGTTAAAAT-GTAATTTTTAGAAGTTTAGGGGTTAAAATGTAATTTTTAA-AAGTTTTAGGGT
* * *
28188028 CAAAATATAATTTTGGAGCAGTTTA
64 TAAAATATAATTTTTGAGAAGTTTA
* * * * *
28188053 GGGGTCAAAATGTAATTTTTGGAAAGTTTATGGGTTAAAATGTAA-TTTTAAAAATTTTAGGGGT
1 AGGGTTAAAATGTAATTTTTAG-AAGTTTAGGGGTTAAAATGTAATTTTTAAAAGTTTTA-GGGT
* *
28188117 TAAAATGTATTTTTTGAGAAGTTTA
64 TAAAATATAATTTTTGAGAAGTTTA
*
28188142 AGGGTTAAAATCTAATTTTGTAGAAGTTT-GAGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGG
1 AGGGTTAAAATGTAATTTT-TAGAAGTTTAG-GGGTTAAAATGTAATTTTTA-AAAGTTTTAGGG
* *
28188206 TTAAATTATAATTTTTGAAAAGTTTA
63 TTAAAATATAATTTTTGAGAAGTTTA
* *
28188232 AGGGTTAAAATGTAATTTTTAAGAAGTTTAGGGGTTAAAATATATTTTTTA
1 AGGGTTAAAATGTAATTTTT-AGAAGTTTAGGGGTTAAAATGTAATTTTTA
28188283 GATAGTTCAG
Statistics
Matches: 195, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
88 6 0.03
89 80 0.41
90 100 0.51
91 9 0.05
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (88 bp):
AGGGTTAAAATGTAATTTTTAGAAGTTTAGGGGTTAAAATGTAATTTTTAAAAGTTTTAGGGTTA
AAATATAATTTTTGAGAAGTTTA
Found at i:28189993 original size:6 final size:6
Alignment explanation
Indices: 28189979--28190074 Score: 51
Period size: 6 Copynumber: 16.2 Consensus size: 6
28189969 GTTTAAAACC
* *
28189979 ATTTCAA ATTTAA ATTTAA ACTTAA A-ATAA A--TAA ATTTAA ATTTCAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
* * * *
28190026 A--TAA ATTTAA ATTAAAACA ATTTAA ACTTAA A-ATAA ATTTAA AATTAA
1 ATTTAA ATTTAA ATT--TA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
28190074 A
1 A
28190075 AGTTTGATCT
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
4 7 0.10
5 9 0.12
6 43 0.60
7 8 0.11
8 1 0.01
9 4 0.06
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (6 bp):
ATTTAA
Found at i:28190009 original size:17 final size:16
Alignment explanation
Indices: 28190007--28190075 Score: 86
Period size: 17 Copynumber: 4.2 Consensus size: 16
28189997 AACTTAAAAT
*
28190007 AAATAAATTTAAATTTC
1 AAATAAATTTAAA-TTA
28190024 AAATAAATTTAAATTA
1 AAATAAATTTAAATTA
*
28190040 AAA-CAATTTAAACTTA
1 AAATAAATTTAAA-TTA
28190056 AAATAAATTTAAAATTA
1 AAATAAATTT-AAATTA
28190073 AAA
1 AAA
28190076 GTTTGATCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.17
16 11 0.24
17 24 0.52
18 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAAATTTAAATTA
Found at i:28190015 original size:21 final size:21
Alignment explanation
Indices: 28189989--28190031 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28189979 ATTTCAAATT
28189989 TAAATTTAAACTTAAAATAAA
1 TAAATTTAAACTTAAAATAAA
* *
28190010 TAAATTTAAATTTCAAATAAA
1 TAAATTTAAACTTAAAATAAA
28190031 T
1 T
28190032 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTTAAACTTAAAATAAA
Found at i:28190048 original size:32 final size:31
Alignment explanation
Indices: 28189971--28190075 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 31
28189961 AAAATTAAGT
* *
28189971 TTAAAACCATTTCAAATTTAAATTTAAACTTAAA
1 TTAAAACAATTT-AAATTTAAA--TAAATTTAAA
*
28190005 ATAAATA-AATTTAAATTTCAAATAAATTTAAA
1 TTAAA-ACAATTTAAATTT-AAATAAATTTAAA
*
28190037 TTAAAACAATTTAAACTTAAAATAAATTTAAAA
1 TTAAAACAATTTAAA-TTTAAATAAATTT-AAA
28190070 TTAAAA
1 TTAAAA
28190076 GTTTGATCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
31 1 0.02
32 31 0.51
33 17 0.28
34 11 0.18
35 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (31 bp):
TTAAAACAATTTAAATTTAAATAAATTTAAA
Found at i:28190051 original size:21 final size:20
Alignment explanation
Indices: 28189989--28190045 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 20
28189979 ATTTCAAATT
*
28189989 TAAATTTAAACTTAAAATAAA
1 TAAATTTAAA-TTAAAACAAA
*
28190010 TAAATTTAAATT---TCAAA
1 TAAATTTAAATTAAAACAAA
28190027 TAAATTTAAATTAAAACAA
1 TAAATTTAAATTAAAACAA
28190046 TTTAAACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 15 0.50
20 5 0.17
21 10 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATTTAAATTAAAACAAA
Found at i:28190735 original size:86 final size:86
Alignment explanation
Indices: 28190584--28190752 Score: 189
Period size: 86 Copynumber: 2.0 Consensus size: 86
28190574 TTGTTTCATT
* * * * *
28190584 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
1 GATTTGGTACACTTATCTGTATCTCATCAGGAAGATGACCACATCACTTGCTTCAATCCACTTCT
** *
28190649 CTGTATCTCATCAGGAAGACG
66 CAATACCTCATCAGGAAGACG
* ** * *
28190670 GATTTGGTCCACTTATCTGTATCTCATCAGGAAGATGACCATTTTA-TTGCTTCGA-CCTACTTT
1 GATTTGGTACACTTATCTGTATCTCATCAGGAAGATGACCACATCACTTGCTTCAATCC-AC-TT
28190733 CTCAATACCTCATCAGGAAG
64 CTCAATACCTCATCAGGAAG
28190753 CTGGGGTTCG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
84 2 0.03
85 8 0.12
86 58 0.85
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (86 bp):
GATTTGGTACACTTATCTGTATCTCATCAGGAAGATGACCACATCACTTGCTTCAATCCACTTCT
CAATACCTCATCAGGAAGACG
Found at i:28190816 original size:210 final size:209
Alignment explanation
Indices: 28190455--28191038 Score: 918
Period size: 210 Copynumber: 2.8 Consensus size: 209
28190445 TTTTACTAGA
* * * * * * **
28190455 AAGACGGATTTGGTTCACTTCTCTGTGTCTTATAAGGACGACGATCGCTTTATTGCTTCGATCC-
1 AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGA-CCT
* * * *
28190519 GCTTCTTAGTATCTCATCAGGATGCTGGGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTTCATT
65 GCTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTGTTTCATT
28190584 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
130 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
28190649 CTGTATCTCATCAGG
195 CTGTATCTCATCAGG
* * *
28190664 AAGACGGATTTGGTCCACTTATCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTA
1 AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTG
*
28190729 CTTTCTCAATACCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTGTTTCATT
66 C-TTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTGTTTCATT
* * *
28190794 GTTTTGGTATACTTCTCTGTATCTCATCAAGAAAATGACCGCATCACTTGTTTTAATCCACTTCT
130 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
28190859 CTGTATCTCATCAGG
195 CTGTATCTCATCAGG
*
28190874 AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACTTG
1 AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTG
**
28190939 CTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAAGTTTTCGCTCATATTGAGCCTTACTTCATT
66 CTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAAG-TTTCGCTCATATTGAGCCTTGTTTCATT
* *
28191004 GATTTGGTATACTTCTTTGTGTCTCATCAGGAAGA
130 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
28191039 CGGATTTTAT
Statistics
Matches: 341, Mismatches: 31, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
208 2 0.01
209 86 0.25
210 253 0.74
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (209 bp):
AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTGCTTCGACCTG
CTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTGTTTCATTG
ATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTC
TGTATCTCATCAGG
Found at i:28192054 original size:45 final size:46
Alignment explanation
Indices: 28191988--28192076 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
28191978 TCATCTTGAT
*
28191988 TTTTTTAAAATCGAGACGCCCTTTTGCG-GGTTTCATCTCAATCCC
1 TTTTTTAAAATCGAGACGCCCTTTTACGAGGTTTCATCTCAATCCC
* * **
28192033 TTTTTTAGAATCG-GTATGCCCTTTTACGATTTTTCATCTCAATC
1 TTTTTTAAAATCGAG-ACGCCCTTTTACGAGGTTTCATCTCAATC
28192077 TTTTTTTCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.03
45 23 0.62
46 13 0.35
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (46 bp):
TTTTTTAAAATCGAGACGCCCTTTTACGAGGTTTCATCTCAATCCC
Found at i:28194857 original size:11 final size:11
Alignment explanation
Indices: 28194841--28194907 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
28194831 TGCTTTGAAA
*
28194841 TTAAATTTATT
1 TTAAATTTAAT
28194852 TTAAATTTAAT
1 TTAAATTTAAT
*
28194863 TTAAGTTTGAAT
1 TTAAATTT-AAT
28194875 TT-AATTTAAAT
1 TTAAATTT-AAT
28194886 TT-AATATT-AT
1 TTAAAT-TTAAT
28194896 TGTAAATTTAAT
1 T-TAAATTTAAT
28194908 GTCCATTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.06
11 32 0.68
12 12 0.26
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:28194861 original size:17 final size:17
Alignment explanation
Indices: 28194838--28194906 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
28194828 ATTTGCTTTG
* *
28194838 AAATTAAATTT-ATTTT
1 AAATTTAATTTAAATTT
*
28194854 AAATTTAATTTAAGTTT
1 AAATTTAATTTAAATTT
*
28194871 GAATTTAATTTAAATTT
1 AAATTTAATTTAAATTT
28194888 -AATATT-ATTGTAAATTT
1 AAAT-TTAATT-TAAATTT
28194905 AA
1 AA
28194907 TGTCCATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
16 16 0.36
17 28 0.62
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTAATTTAAATTT
Found at i:28194863 original size:5 final size:5
Alignment explanation
Indices: 28194839--28194890 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
28194829 TTTGCTTTGA
* *
28194839 AATTA AATTT ATTTT AAATTT AATTT AAGTTT GAATTT AATTT AAATTT
1 AATTT AATTT AATTT -AATTT AATTT AA-TTT -AATTT AATTT -AATTT
28194888 AAT
1 AAT
28194891 ATTATTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 23 0.57
6 15 0.38
7 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:28194903 original size:28 final size:28
Alignment explanation
Indices: 28194841--28194907 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
28194831 TGCTTTGAAA
*
28194841 TTAAATTTATTTTAAATTTAATTTAAGT
1 TTAAATTTAATTTAAATTTAATTTAAGT
*
28194869 TTGAATTTAATTTAAATTTAATATT-A-T
1 TTAAATTTAATTTAAATTTAAT-TTAAGT
28194896 TGTAAATTTAAT
1 T-TAAATTTAAT
28194908 GTCCATTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TTAAATTTAATTTAAATTTAATTTAAGT
Found at i:28196892 original size:29 final size:29
Alignment explanation
Indices: 28196830--28197083 Score: 209
Period size: 29 Copynumber: 8.8 Consensus size: 29
28196820 GGAGGTCTCT
* * *
28196830 AAACTATCTAAAAATTACATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCA-TTTTAACCTCA
*
28196860 AAACTTCC-AAAATTCCATTCTTAACCCCA
1 AAACTTCCAAAAATTCCATT-TTAACCTCA
* *
28196889 AAACTTCCAAAAATTACATTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTAACCTCA
* * *
28196918 AAATTTCC-AAAATTTCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTAACCTCA
* *
28196947 TAACTTCCAAAAATTACATTTTAACC-CA
1 AAACTTCCAAAAATTCCATTTTAACCTCA
* *
28196975 AAATTTCCAAAAATTTCATTTTTAACCTC-
1 AAACTTCCAAAAATTCCA-TTTTAACCTCA
* *
28197004 GAACTTCCAAAAATTCCATTTTTAACCTTA
1 AAACTTCCAAAAATTCCA-TTTTAACCTCA
* * *
28197034 AAACTTTC-AAAATTACCATTTT-ACCCCC
1 AAACTTCCAAAAATT-CCATTTTAACCTCA
*
28197062 AAA-TGTCCAAAAATCCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
28197084 TAATCCTAAT
Statistics
Matches: 184, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.02
28 54 0.29
29 94 0.51
30 33 0.18
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTAACCTCA
Found at i:28196929 original size:58 final size:59
Alignment explanation
Indices: 28196830--28197086 Score: 253
Period size: 58 Copynumber: 4.4 Consensus size: 59
28196820 GGAGGTCTCT
* * * *
28196830 AAACTATCTAAAAATTACATTTTTACCCTC-AAACTTCCAAAATTCCATTCTTAACCCCA
1 AAACT-TCCAAAAATTACATTTTTAACCTCAAAATTTCCAAAATTCCATTTTTAACCCCA
* * * *
28196889 AAACTTCCAAAAATTACA-TTTTAACCTCGAAATTTCCAAAATTTCATTTTTGACCTCA
1 AAACTTCCAAAAATTACATTTTTAACCTCAAAATTTCCAAAATTCCATTTTTAACCCCA
* * *
28196947 TAACTTCCAAAAATTACA-TTTTAACC-CAAAATTTCCAAAAATTTCATTTTTAACCTC-
1 AAACTTCCAAAAATTACATTTTTAACCTCAAAATTTCC-AAAATTCCATTTTTAACCCCA
* * * *
28197004 GAACTTCCAAAAATTCCATTTTTAACCTTAAAACTTT-CAAAATTACCA-TTTT-ACCCCC
1 AAACTTCCAAAAATTACATTTTTAACCTCAAAA-TTTCCAAAATT-CCATTTTTAACCCCA
**
28197062 AAA-TGTCCAAAAATCCCATTTTTAA
1 AAACT-TCCAAAAATTACATTTTTAA
28197087 TCCTAATTTT
Statistics
Matches: 173, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
57 39 0.23
58 119 0.69
59 12 0.07
60 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTAACCTCAAAATTTCCAAAATTCCATTTTTAACCCCA
Found at i:28197017 original size:87 final size:85
Alignment explanation
Indices: 28196830--28197086 Score: 277
Period size: 87 Copynumber: 2.9 Consensus size: 85
28196820 GGAGGTCTCT
* * *
28196830 AAACTATCTAAAAATTACATTTTTACCCTCAAACTTCCAAAATTCCATTCTTAACCCCAAAACTT
1 AAACT-TCCAAAAATTACATTTTTA-CCTCAAACTTCCAAAATTACATT-TTAA-CCCAAAATTT
28196895 CCAAAAATTACA-TTTTAACCTCG
62 CCAAAAATTACATTTTTAACCTCG
* *
28196918 AAATTTCC-AAAATTTCATTTTTGACCTCATAACTTCCAAAAATTACATTTTAACCCAAAATTTC
1 AAACTTCCAAAAATTACATTTTT-ACCTCA-AACTTCC-AAAATTACATTTTAACCCAAAATTTC
*
28196982 CAAAAATTTCATTTTTAACCTCG
63 CAAAAATTACATTTTTAACCTCG
* * * * * *
28197005 -AACTTCCAAAAATTCCATTTTTAACCTTAAAACTTTCAAAATTACCATTTTACCCCCAAATGTC
1 AAACTTCCAAAAATTACATTTTT-ACC-TCAAACTTCCAAAATTA-CATTTTAACCCAAAATTTC
**
28197069 CAAAAATCCCATTTTTAA
63 CAAAAATTACATTTTTAA
28197087 TCCTAATTTT
Statistics
Matches: 146, Mismatches: 16, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
86 51 0.35
87 79 0.54
88 16 0.11
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (85 bp):
AAACTTCCAAAAATTACATTTTTACCTCAAACTTCCAAAATTACATTTTAACCCAAAATTTCCAA
AAATTACATTTTTAACCTCG
Found at i:28197247 original size:29 final size:28
Alignment explanation
Indices: 28197160--28197229 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
28197150 AAATTTTCCT
*
28197160 AAAATTATCC-TTTTATCCCC-AAGAGTCC
1 AAAATTA-CCATTTTACCCCCGAA-AGTCC
28197188 AAAATTACCATTTTACCCCCGAAAGTCC
1 AAAATTACCATTTTACCCCCGAAAGTCC
28197216 AAAATTACCATTTT
1 AAAATTACCATTTT
28197230 GGCCCCCGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAAAGTCC
Found at i:28209345 original size:17 final size:17
Alignment explanation
Indices: 28209341--28209431 Score: 92
Period size: 17 Copynumber: 5.0 Consensus size: 17
28209331 AAAATAAATT
*
28209341 TAAATTTAAAGTTAAAA
1 TAAATTTAAATTTAAAA
28209358 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
28209375 TAAATTTAAATTTAAATTTAA
1 TAAATTTAAATTT-AA---AA
* *
28209396 AACCAATTTAAACTTAAAA
1 TA--AATTTAAATTTAAAA
*
28209415 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
28209432 GTTTGATCTA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
17 43 0.68
18 2 0.03
19 3 0.05
21 3 0.05
22 2 0.03
23 10 0.16
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28209346 original size:6 final size:6
Alignment explanation
Indices: 28209320--28209396 Score: 88
Period size: 6 Copynumber: 13.2 Consensus size: 6
28209310 GTTTAAAACC
* * *
28209320 ATTTCAA ATTTAA A-ATAA ATTTAA ATTTAA AGTTAA A-ATAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
28209367 ATTTAA A-ATAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
28209397 ACCAATTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
5 12 0.20
6 44 0.73
7 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:28209407 original size:23 final size:23
Alignment explanation
Indices: 28209320--28209396 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
28209310 GTTTAAAACC
28209320 ATTTCAAATTTAAAATAAATTTAA
1 ATTT-AAATTTAAAATAAATTTAA
*
28209344 ATTTAAAGTTAAAATAAATTTAA
1 ATTTAAATTTAAAATAAATTTAA
* *
28209367 ATTTAAA-ATAAATTTAAATTTAA
1 ATTTAAATTTAAA-ATAAATTTAA
28209390 ATTTAAA
1 ATTTAAA
28209397 ACCAATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
22 4 0.08
23 41 0.84
24 4 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTTAAATTTAAAATAAATTTAA
Found at i:28209412 original size:23 final size:23
Alignment explanation
Indices: 28209320--28209413 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
28209310 GTTTAAAACC
*
28209320 ATTTCAAATTTAAAATAAATTTAA
1 ATTT-AAATTTAAAACAAATTTAA
*
28209344 ATTTAAAGTT---A-AAA--TAA
1 ATTTAAATTTAAAACAAATTTAA
*
28209361 ATTTAAATTTAAAATAAATTTAA
1 ATTTAAATTTAAAACAAATTTAA
*
28209384 ATTTAAATTTAAAACCAATTTAA
1 ATTTAAATTTAAAACAAATTTAA
*
28209407 ACTTAAA
1 ATTTAAA
28209414 ATAAATTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
17 12 0.20
19 3 0.05
20 2 0.03
21 3 0.05
23 35 0.59
24 4 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (23 bp):
ATTTAAATTTAAAACAAATTTAA
Found at i:28209430 original size:40 final size:40
Alignment explanation
Indices: 28209288--28209430 Score: 198
Period size: 40 Copynumber: 3.6 Consensus size: 40
28209278 ATTTTGGACT
* *
28209288 TTTAAACTAAATTTAAAATTAAGTTTAAAACC-ATTTCAAA
1 TTTAAAATAAATTTAAAATTAAATTTAAAACCAATTT-AAA
* * **
28209328 TTTAAAATAAATTTAAATTTAAAGTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAAATTAAATTTAAAACCAATTTAAA
*
28209368 TTTAAAATAAATTTAAATTTAAATTTAAAACCAATTTAAA
1 TTTAAAATAAATTTAAAATTAAATTTAAAACCAATTTAAA
*
28209408 CTTAAAATAAATTTAAAATTAAA
1 TTTAAAATAAATTTAAAATTAAA
28209431 AGTTTGATCT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
40 87 0.96
41 4 0.04
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (40 bp):
TTTAAAATAAATTTAAAATTAAATTTAAAACCAATTTAAA
Found at i:28214921 original size:30 final size:29
Alignment explanation
Indices: 28214834--28215055 Score: 230
Period size: 30 Copynumber: 7.4 Consensus size: 29
28214824 AAATTAAAAA
* *
28214834 TTTTGGAAAGTTTGATGGCCAAATTTCA-AAT
1 TTTTGGAAAGTTTG-GGGCCAAA--ACATAAT
* * *
28214865 TTTTGCAAAGTTTGGGGTCGAAACATAAT
1 TTTTGGAAAGTTTGGGGCCAAAACATAAT
*
28214894 TTGTGGAAAGTTTGGTGGCCAAAACATAAT
1 TTTTGGAAAGTTTGG-GGCCAAAACATAAT
*
28214924 TTTTGGAAAGTTTAGGGGCCAAGACATAAT
1 TTTTGGAAAGTTT-GGGGCCAAAACATAAT
* * *
28214954 TTTTGGAATGTTAGGGGGCTAAAACATAAT
1 TTTTGGAAAGTT-TGGGGCCAAAACATAAT
* *
28214984 TTTTGGAAAGTTTGAGGGCTAAAATATAAT
1 TTTTGGAAAGTTTG-GGGCCAAAACATAAT
**
28215014 TTTTGGAAAGTTTGGAGGTTAAAACATAAT
1 TTTTGGAAAGTTTGG-GGCCAAAACATAAT
*
28215044 TTTTAGAAAGTT
1 TTTTGGAAAGTT
28215056 CAGGGGTTAA
Statistics
Matches: 164, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 129 0.79
31 15 0.09
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTTGGGGCCAAAACATAAT
Found at i:28215067 original size:60 final size:59
Alignment explanation
Indices: 28214862--28215077 Score: 218
Period size: 60 Copynumber: 3.6 Consensus size: 59
28214852 CCAAATTTCA
* * * * * * *
28214862 AATTTTTGCAAAGTTTGGGG-TCGAAACATAATTTGTGGAAAGTTTGGTGGCCAAAACAT
1 AATTTTTGGAAAGTTAGGGGCT-AAAATATAATTTTTGGAAAGTTTGGAGGCTAAAACAT
* * * * * *
28214921 AATTTTTGGAAAGTTTAGGGGCCAAGACATAATTTTTGGAATGTTAGGGGGCTAAAACAT
1 AATTTTTGGAAAG-TTAGGGGCTAAAATATAATTTTTGGAAAGTTTGGAGGCTAAAACAT
* *
28214981 AATTTTTGGAAAGTTTGAGGGCTAAAATATAATTTTTGGAAAGTTTGGAGGTTAAAACAT
1 AATTTTTGGAAAGTTAG-GGGCTAAAATATAATTTTTGGAAAGTTTGGAGGCTAAAACAT
* * *
28215041 AATTTTTAGAAAGTTCAGGGGTTAAAAATAGAATTTT
1 AATTTTTGGAAAGTT-AGGGGCT-AAAATATAATTTT
28215078 GAAGAGTTCA
Statistics
Matches: 130, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
59 15 0.12
60 102 0.78
61 13 0.10
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (59 bp):
AATTTTTGGAAAGTTAGGGGCTAAAATATAATTTTTGGAAAGTTTGGAGGCTAAAACAT
Found at i:28215078 original size:60 final size:58
Alignment explanation
Indices: 28214831--28215078 Score: 205
Period size: 60 Copynumber: 4.1 Consensus size: 58
28214821 ATCAAATTAA
* * * * * *
28214831 AAATTTTGGAAAGTTT-GATGGCCAAATTTCA-AATTTTTGCAAAGTTTGGGGTCGAAACAT
1 AAATTTTGGAAAGTTTGGA-GGCTAAA--ACATAATTTTTGGAAAGTTAGGGG-CTAAAAAT
* * * *
28214891 -AATTTGTGGAAAGTTTGGTGGCCAAAACATAATTTTTGGAAAGTTTAGGGGCCAAGACAT
1 AAATTT-TGGAAAGTTTGGAGGCTAAAACATAATTTTTGGAAAG-TTAGGGGCTAA-AAAT
* * * * *
28214951 AATTTTTGGAATGTTAGGGGGCTAAAACATAATTTTTGGAAAGTTTGAGGGCTAAAATAT
1 AAATTTTGGAAAGTTTGGAGGCTAAAACATAATTTTTGGAAAGTTAG-GGGCTAAAA-AT
* * * *
28215011 AATTTTTGGAAAGTTTGGAGGTTAAAACATAATTTTTAGAAAGTTCAGGGGTTAAAAAT
1 AAATTTTGGAAAGTTTGGAGGCTAAAACATAATTTTTGGAAAGTT-AGGGGCTAAAAAT
28215070 AGAATTTTG
1 A-AATTTTG
28215079 AAGAGTTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
58 2 0.01
59 27 0.17
60 122 0.78
61 6 0.04
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (58 bp):
AAATTTTGGAAAGTTTGGAGGCTAAAACATAATTTTTGGAAAGTTAGGGGCTAAAAAT
Found at i:28215078 original size:90 final size:90
Alignment explanation
Indices: 28214885--28215078 Score: 227
Period size: 90 Copynumber: 2.2 Consensus size: 90
28214875 TTTGGGGTCG
*
28214885 AAACAT-AATTTGTGGAAAGTTTGGTGGCCAAAACATAATTTTTGGAAAGTTTAGGGGCCAAGAC
1 AAACATAAATTT-TGGAAAGTTTGGTGGCCAAAACATAATTTTTGGAAAGTTTAGGGGCCAAAAC
* *
28214949 ATAATTTTTGGAATGTTAGGGGGCTA
65 ATAATTTTTAGAAAGTTAGGGGGCTA
* * * **
28214975 AAACATAATTTTTGGAAAGTTTGAG-GGCTAAAATATAATTTTTGGAAAGTTT-GGAGGTTAAAA
1 AAACATAAATTTTGGAAAGTTTG-GTGGCCAAAACATAATTTTTGGAAAGTTTAGG-GGCCAAAA
*
28215038 CATAATTTTTAGAAAGTTCA-GGGGTTA
64 CATAATTTTTAGAAAGTT-AGGGGGCTA
28215065 AAA-ATAGAATTTTG
1 AAACATA-AATTTTG
28215079 AAGAGTTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
89 5 0.06
90 78 0.88
91 6 0.07
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (90 bp):
AAACATAAATTTTGGAAAGTTTGGTGGCCAAAACATAATTTTTGGAAAGTTTAGGGGCCAAAACA
TAATTTTTAGAAAGTTAGGGGGCTA
Found at i:28215086 original size:30 final size:30
Alignment explanation
Indices: 28214914--28215087 Score: 97
Period size: 30 Copynumber: 5.8 Consensus size: 30
28214904 TTTGGTGGCC
* * * **
28214914 AAAACATAATTTTTGGAAAGTTTAGGGGCC
1 AAAACATAAATTTTAGAAAGTTCAGGGGTT
* * * * *
28214944 AAGACATAATTTTTGGAATGTT-AGGGGGCT
1 AAAACATAAATTTTAGAAAGTTCA-GGGGTT
* * * *
28214974 AAAACATAATTTTTGGAAAGTT-TGAGGGCT
1 AAAACATAAATTTTAGAAAGTTCAG-GGGTT
* * * *
28215004 AAAATATAATTTTTGGAAAGTT-TGGAGGTT
1 AAAACATAAATTTTAGAAAGTTCAGG-GGTT
*
28215034 AAAACATAATTTTTAGAAAGTTCAGGGGTT
1 AAAACATAAATTTTAGAAAGTTCAGGGGTT
28215064 AAAA-ATAGAATTTT-GAAGAGTTCA
1 AAAACATA-AATTTTAGAA-AGTTCA
28215088 AGGACCTTAT
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.07
30 115 0.91
31 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAACATAAATTTTAGAAAGTTCAGGGGTT
Found at i:28216804 original size:14 final size:14
Alignment explanation
Indices: 28216785--28216823 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
28216775 TTAAAATTAC
28216785 TAAAATTATTTTTT
1 TAAAATTATTTTTT
*
28216799 TAAAATATAATTTTT
1 TAAAAT-TATTTTTT
*
28216814 TAAATTTATT
1 TAAAATTATT
28216824 AAATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAAATTATTTTTT
Found at i:28217610 original size:39 final size:39
Alignment explanation
Indices: 28217560--28217636 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
28217550 ATGATGATTA
*
28217560 TAATTTTAAATAATTTTAA-AACTTTTATATTTTAAAAAT
1 TAATTTAAAATAATTTTAATAA-TTTTATATTTTAAAAAT
28217599 TAATTTAAAATAATTTTAATAATTTTATATTTTAAAAA
1 TAATTTAAAATAATTTTAATAATTTTATATTTTAAAAA
28217637 AAATTAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 34 0.94
40 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
TAATTTAAAATAATTTTAATAATTTTATATTTTAAAAAT
Found at i:28218206 original size:46 final size:46
Alignment explanation
Indices: 28218126--28219375 Score: 904
Period size: 46 Copynumber: 27.4 Consensus size: 46
28218116 TCCCATGATT
* *
28218126 GGGGTAAGAGATTGGATGGTATCTTCAATCTGCCCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * * * * *
28218172 GGGGTAAAAGATTAGATGGTGGCTTTAATTTG-CCCT-AT-A-ATC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
*
28218214 GGGGTAAGAA-ATTGGATAGTATGTCTTCAA-CTTGCCCCTCTTGACTTA
1 GGGGTAA-AAGATTGGAT-G-GTGTCTTCAATC-TGCCCCTCTTGACTTA
* * *
28218262 GAGGTAAAAGATTGGATGGTGATGTTTTCAATCTGCCTCTCTTGACTTA
1 GGGGTAAAAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* * * * * *
28218311 GGGGTAAAAGATTGGATGATGACTTCAATTTG-CCC-CATG--GTC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * *
28218353 GGGGTAAGAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * * * *
28218399 AGGGTAAAAGATTGGATAGTGGCTTCAATTTG-TCC-CATGA-TT-
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * *
28218441 -GGGTAAGAA-ATTGGATAGTATCTCTTCAATTTGCCCCTCTTAACTTA
1 GGGGTAA-AAGATTGGAT-G-GTGTCTTCAATCTGCCCCTCTTGACTTA
* *
28218488 GGGGTTAAAGATTGGATGGTAATGTCTTCAATCTGCCTC-CTTGACTTA
1 GGGGTAAAAGATTGGATGG---TGTCTTCAATCTGCCCCTCTTGACTTA
* * * * * * * *
28218536 GGGGTAAAAGATCGGATGATGACTTCAATTTG-ACC-CATG--GTC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* *
28218578 GGGGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * * *
28218624 GAGGTAAAAGATTAGATGGTGGCTTCAATCTG-CCC-CATGA--TC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
*
28218666 GGGGTAAGAA-ATTAGATAGTGATGTCTTCAATCTGCCCCTCTTGACTTA
1 GGGGTAA-AAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* * *
28218715 GGGGTAAAAGATTGGATAGTGATATCTTCAATCTTCCCCTCTTAACTTA
1 GGGGTAAAAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* * * *
28218764 GGGGTAAAAGATTGGATGATAG-CTTCAATCTG--CCTCAT-A-GTC
1 GGGGTAAAAGATTGGATGGT-GTCTTCAATCTGCCCCTCTTGACTTA
* * *
28218806 GAGGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * * *
28218852 GAGGTAAAAGATTAGATGGTGGCTTCAATCTG-CCCT-ATGA--TC
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
28218894 GGGGTAAGAA-ATTGGATAGTGATGTCTTCAATCTGCCCCTCTTGACTTA
1 GGGGTAA-AAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* * *
28218943 GAGGTAAAAGATTGGATAGTGATGTCTTCAATCTTCCCCTCTTAACTTA
1 GGGGTAAAAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
** * * *
28218992 GGGGTAAAAGATTGGATAATAG-CTTCAATCTG--CCTCAT-A-GTC
1 GGGGTAAAAGATTGGATGGT-GTCTTCAATCTGCCCCTCTTGACTTA
* * * *
28219034 GAGGTAAGAGATTGGATGGTGTCTTCAATCTACTCCTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* * * * *
28219080 GGGGTAAAAGATTAGATGGTGGCTTCAATTTG-CCC-CATGA-TCA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* *
28219123 -AGGTAAGAA-ATTGAATAGTGATGTCTTCAATCTGCCCCTCTTGACTTA
1 GGGGTAA-AAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* **
28219171 GGGGTAAAAGATTGGATGGTGACTTCAATCTGCCTTTCTTGACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
**
28219217 GGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCATCTCTTGACTTA
1 GGGGTAAAAGATTGGAT-G-G-TGTCTTCAATCTGCCCCTCTTGACTTA
* * * **** *
28219266 GGGGTAAAAGATTGGGTGATGGCTTCAATCTTTTGCTCTTAACTTA
1 GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
* *
28219312 GGGGTAAAAGATTGGATGGTAG-GTTCAA-CTTGCCCTTCTTGACTTA
1 GGGGTAAAAGATTGGATGGT-GTCTTCAATC-TGCCCCTCTTGACTTA
** *
28219358 AAGGTAAAAGATTAGATG
1 GGGGTAAAAGATTGGATG
28219376 ATGATGTAAC
Statistics
Matches: 946, Mismatches: 183, Indels: 150
0.74 0.14 0.12
Matches are distributed among these distances:
41 15 0.02
42 160 0.17
43 35 0.04
44 63 0.07
45 73 0.08
46 289 0.31
47 21 0.02
48 65 0.07
49 224 0.24
50 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (46 bp):
GGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCTCTTGACTTA
Found at i:28218425 original size:88 final size:88
Alignment explanation
Indices: 28218259--28219328 Score: 486
Period size: 88 Copynumber: 11.8 Consensus size: 88
28218249 CCCTCTTGAC
* * * *
28218259 TTAGAGGTAAAAGATTGGATGGTGATGTTTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGATT
1 TTAGGGGTAAAAGATTGGATGGT-A--TCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATT
* *
28218324 GGAT-GATGACTTCAATTTGCCCCATG
63 GGATAG-TGGCTTCAATCTGCCCCATG
* * * *
28218350 GTCGGGGTAAGAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAAGGGTAAAAGATTGGA
1 TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGA
* *
28218415 TAGTGGCTTCAATTTGTCCCATG
66 TAGTGGCTTCAATCTGCCCCATG
* * * * *
28218438 ATT--GGGTAAGAA-ATTGGATAGTATCTCTTCAATTTGCCCCTCTTAACTTAGGGGTTAAAGAT
1 -TTAGGGGTAA-AAGATTGGATGGTA--TCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGAT
* * *
28218500 TGGATGGTAATGTCTTCAATCTGCCTCCTTG
62 TGGA---TAGTGGCTTCAATCTGCC-CCATG
* * * * * * *
28218531 ACTTAGGGGTAAAAGATCGGATGATGA-CTTCAATTTGA--CC-CATG--GTCGGGGTAAGAGAT
1 --TTAGGGGTAAAAGATTGGATGGT-ATCTTCAATCT-ACCCCTCTTGACTTAGGGGTAAAAGAT
* * * *
28218590 TGGATGGTGTCTTCAATCTACCCCTCTTG
62 TGGATAGTGGCTTCAATCT-GCCC-CATG
* * ** * * *
28218619 ACTTAGAGGTAAAAGATTAGATGGTGGCTTCAATCT-GCCC-CATGA--TCGGGGTAAGAA-ATT
1 --TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAA-AAGATT
* *
28218679 AGATAGTGATGTCTTCAATCTGCCCCTCTTG
63 GGATAGTG--G-CTTCAATCTG-CCC-CATG
* *
28218710 ACTTAGGGGTAAAAGATTGGATAGTGATATCTTCAATCTTCCCCTCTTAACTTAGGGGTAAAAGA
1 --TTAGGGGTAAAAGATTGGAT-G-G-TATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGA
* *
28218775 TTGGAT-GATAGCTTCAATCTGCCTCATAG
61 TTGGATAG-TGGCTTCAATCTGCCCCAT-G
* * * * * *
28218804 -TCGAGGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGA
1 TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGA
* *
28218868 TGGTGGCTTCAATCTGCCCTATG
66 TAGTGGCTTCAATCTGCCCCATG
* * * * *
28218891 ATCGGGGTAAGAA-ATTGGATAGTGATGTCTTCAATCTGCCCCTCTTGACTTAGAGGTAAAAGAT
1 TTAGGGGTAA-AAGATTGGAT-G-G-TATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGAT
* **
28218955 TGGATAGTGATGTCTTCAATCTTCCCCTCTTAAC
62 TGGATAGTG--G-CTTCAATC-TGCCC-C--ATG
** * * * * * * *
28218989 TTAGGGGTAAAAGATTGGATAATAGCTTCAATCT--GCCTCAT-A-GTCGAGGTAAGAGATTGGA
1 TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGA
* * * *
28219050 TGGTGTCTTCAATCTACTCCTCTTG
66 TAGTGGCTTCAATCTGC-CC-CATG
* ** ** * * *
28219075 ACTTAGGGGTAAAAGATTAGATGGTGGCTTCAAT-TTGCCC-CATGA-TCA-AGGTAAGAA-ATT
1 --TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAA-AAGATT
* *
28219135 GAATAGTGATGTCTTCAATCTGCCCCTCTTG
63 GGATAGTG--G-CTTCAATCTG-CCC-CATG
* **
28219166 ACTTAGGGGTAAAAGATTGGATGGTGA-CTTCAATCTGCCTTTCTTGACTTAGGGGTAAAAGATT
1 --TTAGGGGTAAAAGATTGGATGGT-ATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATT
* * *
28219230 GGATGGTGATGTCTTCAATCTGCATCTCTTG
63 GGATAGTG--G-CTTCAATCTGC--CCCATG
* * ** **** *
28219261 ACTTAGGGGTAAAAGATTGGGTGATGGCTTCAATCTTTTGCTCTTAACTTAGGGGTAAAAGATTG
1 --TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTG
28219326 GAT
64 GAT
28219329 GGTAGGTTCA
Statistics
Matches: 778, Mismatches: 131, Indels: 136
0.74 0.13 0.13
Matches are distributed among these distances:
87 34 0.04
88 244 0.31
89 47 0.06
90 18 0.02
91 184 0.24
92 21 0.03
93 19 0.02
94 37 0.05
95 119 0.15
96 18 0.02
97 6 0.01
98 31 0.04
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (88 bp):
TTAGGGGTAAAAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGA
TAGTGGCTTCAATCTGCCCCATG
Found at i:28218531 original size:137 final size:138
Alignment explanation
Indices: 28218224--28219370 Score: 672
Period size: 137 Copynumber: 8.4 Consensus size: 138
28218214 GGGGTAAGAA
* * * * *
28218224 ATTGGATAGTATGTCTTCAA-CTTGCCCCTCTTGACTTAGAGGTAAAAGATTGGATGGTGATGTT
1 ATTGGATGGTATGTCTTCAATC-TGCCTC-CTTGACTTAGGGGTAAAAGATTGGATAGTG--G-C
* * * * *
28218288 TTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGATTGGAT-GATGACTTCAATTTG-CCC-CATG
61 TTCAATTTGCC-CTCATGACTTA-GGGTAAAAGATTGGATAGATGTCTTCAATCTGCCCCTCTTG
* *
28218350 --GTCGGGG-TAAGAG
124 ACTTAGGGGTTAA-AG
* * *
28218363 ATTGGATGGTA--TCTTCAATCTACCCCTCTTGACTTAAGGGTAAAAGATTGGATAGTGGCTTCA
1 ATTGGATGGTATGTCTTCAATCTGCCTC-CTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCA
* * * *
28218426 ATTTGTCC-CATGA-TT-GGGTAAGAA-ATTGGATAGTATCTCTTCAATTTGCCCCTCTTAACTT
65 ATTTGCCCTCATGACTTAGGGTAA-AAGATTGGATAG-ATGTCTTCAATCTGCCCCTCTTGACTT
28218487 AGGGGTTAAAG
128 AGGGGTTAAAG
* *
28218498 ATTGGATGGTAATGTCTTCAATCTGCCTCCTTGACTTAGGGGTAAAAGATCGGAT-GATGACTTC
1 ATTGGATGGT-ATGTCTTCAATCTGCCTCCTTGACTTAGGGGTAAAAGATTGGATAG-TGGCTTC
* * ** * * *
28218562 AATTTGACC-CATG-GTCGGGGTAAGAGATTGGAT-GGTGTCTTCAATCTACCCCTCTTGACTTA
64 AATTTGCCCTCATGACTTAGGGTAAAAGATTGGATAGATGTCTTCAATCTGCCCCTCTTGACTTA
* *
28218624 GAGGTAAAAG
129 GGGGTTAAAG
* * * * *
28218634 ATTAGATGG--TGGCTTCAATCTGCC-CCATGA--TCGGGGTAAGAA-ATTAGATAGTGATGTCT
1 ATTGGATGGTATGTCTTCAATCTGCCTCCTTGACTTAGGGGTAA-AAGATTGGATAGTG--G-CT
* * * *
28218693 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATAGTGATATCTTCAATCTTCCCCTCTT
62 TCAATTTG-CCCTCATGACTTA-GGGTAAAAGATTGGATA--GATGTCTTCAATCTGCCCCTCTT
* *
28218758 AACTTAGGGGTAAAAG
123 GACTTAGGGGTTAAAG
* * * * * * * *
28218774 ATTGGATGATA-G-CTTCAATCTGCCT-CAT-A-GTCGAGGTAAGAGATTGGATGGTGTCTTCAA
1 ATTGGATGGTATGTCTTCAATCTGCCTCCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAA
** * * * * * *
28218834 TCTACCCCTCTTGACTTAGAGGTAAAAGATTAGAT-GGTGGCTTCAATCTG-CCCT-ATGA--TC
66 T-TTGCCCTCATGACTTAG-GGTAAAAGATTGGATAGATGTCTTCAATCTGCCCCTCTTGACTTA
*
28218894 GGGG-TAAGAA
129 GGGGTTAA-AG
* * *
28218904 ATTGGATAGTGATGTCTTCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGATAGTGATGTC
1 ATTGGATGGT-ATGTCTTCAATCTGCCTC-CTTGACTTAGGGGTAAAAGATTGGATAGTG--G-C
* * * *
28218969 TTCAATCTTCCCCTCTTAACTTAGGGGTAAAAGATTGGATA-ATAG-CTTCAATCTG--CCTCAT
61 TTCAAT-TTGCCCTCATGACTTA-GGGTAAAAGATTGGATAGAT-GTCTTCAATCTGCCCCTCTT
* * *
28219030 -A-GTCGAGG-TAAGAG
123 GACTTAGGGGTTAA-AG
* * *
28219044 ATTGGATGG--TGTCTTCAATCT-ACTCCTCTTGACTTAGGGGTAAAAGATTAGATGGTGGCTTC
1 ATTGGATGGTATGTCTTCAATCTGCCT-C-CTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTC
* * *
28219106 AATTTGCCC-CATGA-TCAAGGTAAGAA-ATTGAATAGTGATGTCTTCAATCTGCCCCTCTTGAC
64 AATTTGCCCTCATGACTTAGGGTAA-AAGATTGGATA--GATGTCTTCAATCTGCCCCTCTTGAC
*
28219168 TTAGGGGTAAAAG
126 TTAGGGGTTAAAG
* * *
28219181 ATTGGATGG--TGACTTCAATCTGCCTTTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCT
1 ATTGGATGGTATGTCTTCAATCTGCC-TCCTTGACTTAGGGGTAAAAGATTGGATAGTG--G-CT
* * * * * **** *
28219244 TCAATCTGCATCTCTTGACTTAGGGGTAAAAGATTGGGT-GATGGCTTCAATCTTTTGCTCTTAA
62 TCAATTTGC-CCTCATGACTTA-GGGTAAAAGATTGGATAGATGTCTTCAATCTGCCCCTCTTGA
*
28219308 CTTAGGGGTAAAAG
125 CTTAGGGGTTAAAG
* * **
28219322 ATTGGATGGTA-G-GTTCAA-CTTGCCCTTCTTGACTTAAAGGTAAAAGATT
1 ATTGGATGGTATGTCTTCAATC-TG-CCTCCTTGACTTAGGGGTAAAAGATT
28219371 AGATGATGAT
Statistics
Matches: 811, Mismatches: 121, Indels: 150
0.75 0.11 0.14
Matches are distributed among these distances:
129 15 0.02
130 44 0.05
131 22 0.03
132 19 0.02
133 59 0.07
134 29 0.04
135 29 0.04
136 49 0.06
137 250 0.31
138 30 0.04
139 18 0.02
140 151 0.19
141 75 0.09
142 7 0.01
143 4 0.00
144 10 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (138 bp):
ATTGGATGGTATGTCTTCAATCTGCCTCCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAA
TTTGCCCTCATGACTTAGGGTAAAAGATTGGATAGATGTCTTCAATCTGCCCCTCTTGACTTAGG
GGTTAAAG
Found at i:28218831 original size:228 final size:229
Alignment explanation
Indices: 28218128--28219252 Score: 1666
Period size: 228 Copynumber: 5.0 Consensus size: 229
28218118 CCATGATTGG
* * *
28218128 GGTAAGAGATTGGATGGTATCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTAGATGGTG
1 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
* * *
28218193 GCTTTAATTTGCCCTATAATCGGGGTAAGAAATTGGATAGT-ATGTCTTCAA-CTTGCCCCTCTT
66 GCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATC-TGCCCCTCTT
* *
28218256 GACTTAGAGGTAAAAGATTGGATGGTGATGTTTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAG
130 GACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAG
* * * *
28218321 ATTGGATGAT-GACTTCAATTTGCCCCATGGTCGG
195 ATTGGATGATAGACTTCAATCTGCCTCATAGTCGA
* * *
28218355 GGTAAGAGATTGGATGGTATCTTCAATCTACCCCTCTTGACTTA-AGGGTAAAAGATTGGATAGT
1 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGA-GGTAAAAGATTAGATGGT
* * * *
28218419 GGCTTCAATTTGTCCCATGAT-TGGGTAAGAAATTGGATAGT-ATCTCTTCAATTTGCCCCTCTT
65 GGCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTT
* * *
28218482 AACTTAGGGGTTAAAGATTGGATGGTAATGTCTTCAATCTGCCTC-CTTGACTTAGGGGTAAAAG
130 GACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAG
* * * *
28218546 ATCGGATGAT-GACTTCAATTTGACC-CATGGTCGG
195 ATTGGATGATAGACTTCAATCTG-CCTCATAGTCGA
28218580 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
1 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
* *
28218645 GCTTCAATCTGCCCCATGATCGGGGTAAGAAATTAGATAGTGATGTCTTCAATCTGCCCCTCTTG
66 GCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTTG
* * * * *
28218710 ACTTAGGGGTAAAAGATTGGATAGTGATATCTTCAATCTTCCCCTCTTAACTTAGGGGTAAAAGA
131 ACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGA
28218775 TTGGATGATAG-CTTCAATCTGCCTCATAGTCGA
196 TTGGATGATAGACTTCAATCTGCCTCATAGTCGA
28218808 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
1 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
* *
28218873 GCTTCAATCTGCCCTATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTTG
66 GCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTTG
* * * * *
28218938 ACTTAGAGGTAAAAGATTGGATAGTGATGTCTTCAATCTTCCCCTCTTAACTTAGGGGTAAAAGA
131 ACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGA
*
28219003 TTGGATAATAG-CTTCAATCTGCCTCATAGTCGA
196 TTGGATGATAGACTTCAATCTGCCTCATAGTCGA
* *
28219036 GGTAAGAGATTGGATGGTGTCTTCAATCTACTCCTCTTGACTTAGGGGTAAAAGATTAGATGGTG
1 GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
** *
28219101 GCTTCAATTTGCCCCATGATCAAGGTAAGAAATTGAATAGTGATGTCTTCAATCTGCCCCTCTTG
66 GCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTTG
*
28219166 ACTTAGGGGTAAAAGATTGGATGGTGA---CTTCAATCTGCCTTTCTTGACTTAGGGGTAAAAGA
131 ACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGA
* *
28219228 TTGGATGGTGATGTCTTCAATCTGC
196 TTGGATGAT-A-GACTTCAATCTGC
28219253 ATCTCTTGAC
Statistics
Matches: 828, Mismatches: 58, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
225 165 0.20
226 100 0.12
227 137 0.17
228 425 0.51
229 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (229 bp):
GGTAAGAGATTGGATGGTGTCTTCAATCTACCCCTCTTGACTTAGAGGTAAAAGATTAGATGGTG
GCTTCAATTTGCCCCATGATCGGGGTAAGAAATTGGATAGTGATGTCTTCAATCTGCCCCTCTTG
ACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTGCCTCTCTTGACTTAGGGGTAAAAGA
TTGGATGATAGACTTCAATCTGCCTCATAGTCGA
Found at i:28219555 original size:95 final size:95
Alignment explanation
Indices: 28219434--28219768 Score: 478
Period size: 96 Copynumber: 3.5 Consensus size: 95
28219424 TTGTTACCTA
* * * *
28219434 TTTTGACCCACTTTTTTGTATCTCATCAGGAAGAT-GGGTTTGAAGTTTCGCTCCACTCCATTGT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCGCTCCACTCCACTGT
* *
28219498 AACCTAAGGGACATTGAGCTCTGCTTTATTG
66 AACCTAA-GGACGTTGAGCTCTGCTTCATTG
* * *
28219529 TTTTGATCCATTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTTTCGCTGCACTCCACTGT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCGCTCCACTCCACTGT
28219594 AACCTCAAGGACGTTGAGCTCTGCTTCATTG
66 AACCT-AAGGACGTTGAGCTCTGCTTCATTG
* * *
28219625 TTTTGATCCACTTCTCTGTATTTCATCA-GAAGGATGGGGTTTGAAGTTTCACTCTACTCCACTG
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAA-GATGGGGTTTGAAGTTTCGCTCCACTCCACTG
* *
28219689 TAACCCCAAGGACGTTGAGCTCTACTTCA-TG
65 TAA-CCTAAGGACGTTGAGCTCTGCTTCATTG
*
28219720 TTTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTT
28219769 TGTTGTAATT
Statistics
Matches: 217, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
95 79 0.36
96 134 0.62
97 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (95 bp):
TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCGCTCCACTCCACTGT
AACCTAAGGACGTTGAGCTCTGCTTCATTG
Found at i:28220778 original size:18 final size:18
Alignment explanation
Indices: 28220755--28220793 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28220745 CATCTTGACC
28220755 TTCCCTTATCT-TTTTCTT
1 TTCCCTT-TCTCTTTTCTT
*
28220773 TTCCCTTTTTCTTTTCTT
1 TTCCCTTTCTCTTTTCTT
28220791 TTC
1 TTC
28220794 TCTCTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCCCTTTCTCTTTTCTT
Found at i:28220782 original size:13 final size:13
Alignment explanation
Indices: 28220764--28220788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28220754 CTTCCCTTAT
28220764 CTTTTTCTTTTCC
1 CTTTTTCTTTTCC
28220777 CTTTTTCTTTTC
1 CTTTTTCTTTTC
28220789 TTTTCTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTTCTTTTCC
Found at i:28221730 original size:8 final size:8
Alignment explanation
Indices: 28221717--28221777 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
28221707 GACCTTTTTC
28221717 TTTTTCTT
1 TTTTTCTT
28221725 TTTTTCTT
1 TTTTTCTT
*
28221733 TCTTTCTT
1 TTTTTCTT
*
28221741 TCTTTCTT
1 TTTTTCTT
*
28221749 TTTCCTCTT
1 TTT-TTCTT
28221758 TTTTT-TT
1 TTTTTCTT
**
28221765 TTTACCTT
1 TTTTTCTT
28221773 TTTTT
1 TTTTT
28221778 ACACATCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 5 0.12
8 31 0.72
9 7 0.16
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:28221736 original size:4 final size:4
Alignment explanation
Indices: 28221719--28221749 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
28221709 CCTTTTTCTT
*
28221719 TTTC TTTT TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
28221750 TTCCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:28225629 original size:12 final size:12
Alignment explanation
Indices: 28225612--28225657 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
28225602 TCTCGTCATT
28225612 TGTTCTTGCAAC
1 TGTTCTTGCAAC
*
28225624 TGTTCTTGCAAT
1 TGTTCTTGCAAC
** *
28225636 TGAGCTTGCATC
1 TGTTCTTGCAAC
28225648 TGTTCTTGCA
1 TGTTCTTGCA
28225658 TATCTCTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (12 bp):
TGTTCTTGCAAC
Found at i:28227942 original size:29 final size:30
Alignment explanation
Indices: 28227898--28228036 Score: 112
Period size: 30 Copynumber: 4.7 Consensus size: 30
28227888 GGTCAAAATG
* **
28227898 AAATTTTGA-AAAGTTCGA-GGCCAAATTT
1 AAATTTTTAGAAAGTTCGAGGGCCAAACAT
*
28227926 AAATTTTTAGAAAGTTC-ATGGGTCGAAACAT
1 AAATTTTTAGAAAGTTCGA-GGG-CCAAACAT
28227957 -AATTTTTAGAAAGTTCGAGGGCCAAAACAT
1 AAATTTTTAGAAAGTTCGAGGGCC-AAACAT
* * * *
28227987 -AATTTTTGGGAAGTTTGAGTGCCAAAACAT
1 AAATTTTTAGAAAGTTCGAGGGCC-AAACAT
*
28228017 -AATTTTTAAAAAGTTC-AGGG
1 AAATTTTTAGAAAGTTCGAGGG
28228037 GTCAAAAATA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
28 9 0.10
29 11 0.12
30 65 0.71
31 6 0.07
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (30 bp):
AAATTTTTAGAAAGTTCGAGGGCCAAACAT
Found at i:28227963 original size:30 final size:30
Alignment explanation
Indices: 28227927--28228043 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
28227917 GCCAAATTTA
* *
28227927 AATTTTTAGAAAGTTCATGGGTCGAAACAT
1 AATTTTTAGAAAGTTCATGGGCCAAAACAT
28227957 AATTTTTAGAAAGTTCGA-GGGCCAAAACAT
1 AATTTTTAGAAAGTTC-ATGGGCCAAAACAT
* *
28227987 AATTTTTGGGAAGTT--TGAGTGCCAAAACAT
1 AATTTTTAGAAAGTTCATG-G-GCCAAAACAT
* * *
28228017 AATTTTTAAAAAGTTCAGGGGTCAAAA
1 AATTTTTAGAAAGTTCATGGGCCAAAA
28228044 ATAGAATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 67 0.93
31 2 0.03
32 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (30 bp):
AATTTTTAGAAAGTTCATGGGCCAAAACAT
Found at i:28228757 original size:2 final size:2
Alignment explanation
Indices: 28228752--28228777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28228742 TAAAAAATGA
28228752 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28228778 GTAGATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28229961 original size:30 final size:30
Alignment explanation
Indices: 28229925--28229990 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
28229915 ATTAATAAAA
*
28229925 ATAAAAATAGACTTTAACTTTTCAAAAATC
1 ATAAAAATAGAATTTAACTTTTCAAAAATC
** * * *
28229955 ATAAAAATTTAATTTAATTTTTTAAAAATT
1 ATAAAAATAGAATTTAACTTTTCAAAAATC
28229985 ATAAAA
1 ATAAAA
28229991 TATAAACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (30 bp):
ATAAAAATAGAATTTAACTTTTCAAAAATC
Found at i:28231460 original size:21 final size:21
Alignment explanation
Indices: 28231409--28231467 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
28231399 GGTTAAATTC
28231409 TTAAATCAAA-TAATAATAAAA
1 TTAAATCAAACTAATAA-AAAA
* *
28231430 -TAATTTAAACTAATAAAAAA
1 TTAAATCAAACTAATAAAAAA
* *
28231450 TTAACTCAAACAAATAAA
1 TTAAATCAAACTAATAAA
28231468 CAGAATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAATCAAACTAATAAAAAA
Found at i:28231488 original size:24 final size:24
Alignment explanation
Indices: 28231450--28231501 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28231440 TAATAAAAAA
28231450 TTAACTCAAACAAATAAACAGAAT
1 TTAACTCAAACAAATAAACAGAAT
* * *
28231474 TTAACTGAAATAAATAAATAGAAT
1 TTAACTCAAACAAATAAACAGAAT
28231498 TTAA
1 TTAA
28231502 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.27
Consensus pattern (24 bp):
TTAACTCAAACAAATAAACAGAAT
Found at i:28232761 original size:22 final size:21
Alignment explanation
Indices: 28232736--28232776 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28232726 ACTTTTCTTT
*
28232736 TTCTTTTTTCATTCTCTTCTAC
1 TTCTATTTTCATTC-CTTCTAC
*
28232758 TTCTATTTTCCTTCCTTCT
1 TTCTATTTTCATTCCTTCT
28232777 CCATTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCTATTTTCATTCCTTCTAC
Found at i:28234743 original size:15 final size:15
Alignment explanation
Indices: 28234723--28234760 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
28234713 TCTATCAATT
28234723 CATGCATGTTTATAG
1 CATGCATGTTTATAG
28234738 CATGCATGTTTATAG
1 CATGCATGTTTATAG
28234753 CATGCATG
1 CATGCATG
28234761 CATTCATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (15 bp):
CATGCATGTTTATAG
Found at i:28238582 original size:15 final size:16
Alignment explanation
Indices: 28238557--28238588 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28238547 AATACATTCC
28238557 ATATCCATCATGCATA
1 ATATCCATCATGCATA
28238573 ATAT-CATCATGCATA
1 ATATCCATCATGCATA
28238588 A
1 A
28238589 CTGATTCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (16 bp):
ATATCCATCATGCATA
Found at i:28251577 original size:49 final size:49
Alignment explanation
Indices: 28251357--28252130 Score: 567
Period size: 49 Copynumber: 15.8 Consensus size: 49
28251347 TCGAGGAAAT
* * * * *
28251357 ATGAAGATTTGAAGGGAAAGGTTAAGGCTGTAACGGCGAATCCGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * *
28251406 ATGAA-ATGTGATGGGAAAGGTTGAGGCCGCAATGGCTAACCTGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * * * * * **
28251454 GTAAAAGATGTGATGGCAAAGATTGAGACCACAACGGTGAATTCGGTACC
1 AT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * *
28251504 AT-AAAATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGATACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * *
28251552 ATGAAGATTTAAAGGGAAAAGTTGAGGCCGTAACGGCGAACCCGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * ** * * * *
28251601 ATAAAAGATGTGATGGG-AAGGATTGAGGGTGTAATGGCGAATCCGATACC
1 AT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC
* * * ***
28251651 ATGAAGATGCGACGGGAAAGGTTGAGGTCGCAACGATAAACCCGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * * **
28251700 ATGAAGATTTGAAGGGAAAAGTTAAGGTCGTAACGGCGAACTTGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* ** * ** *
28251749 TTAGAAGATGTGATTGGAAAGATTGAGGCCGCAACGATGAATCCGGTACC
1 AT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * **
28251799 ATGAA-ATGTGATGGGAAAGGTTGAGGTCACAATAGCGAACCCGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * *
28251847 ATGAAGATTTAAAGGGAAAGGTTAAGGCCGCAACGACGAACCCGGTACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * ** * *
28251896 TTAGAAGATGTGATA-GG-AAGGATTGAGGCTGCAACGGTAAATCCGATACC
1 AT-GAAGATGTGA-AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC
* ** * * * *
28251946 ATGAAGATGCGATTGGAAAAGTTGAGGCCACAACGGCAAACCCGGCACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * * **
28251995 ATAAAGATTTGAAGGGAAAGGTTGAGGCTGCAATGGTGAACCCGACACC
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * *
28252044 TTAAAAGATG-GATGAG-AAGGATTGAGGCCGCAACGGCGAATCCGGTACC
1 AT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC
* * *
28252093 ATGAA-ATATGATGGGAAAGGTTGAGGCTGCAACGGCGA
1 ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGA
28252131 GTCTTATACC
Statistics
Matches: 555, Mismatches: 153, Indels: 35
0.75 0.21 0.05
Matches are distributed among these distances:
47 2 0.00
48 141 0.25
49 262 0.47
50 149 0.27
51 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (49 bp):
ATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
Found at i:28251651 original size:147 final size:147
Alignment explanation
Indices: 28251370--28252128 Score: 784
Period size: 147 Copynumber: 5.2 Consensus size: 147
28251360 AAGATTTGAA
* * * * * * * *
28251370 GGGAAAGGTTAAGGCTGTAACGGCGAATCCGGTACCATGAA-ATGTGATGGGAAAGGTTGAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* * * * * * * * *
28251434 GCAATGGCTAACCTGGTACCGTAAAAGATGTGATGGCAAAGATTGAGACCACAACGGTGAATTCG
66 GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
28251499 GTACCATAAAATGTGAT
131 GTACCATAAAATGTGAT
* ** * *
28251516 GGGAAAGGTTGAGGCCGCAATGGTGAACCCGATACCATGAAGATTTAAAGGGAAAAGTTGAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* * ** * * *
28251581 GTAACGGCGAACCCGGTACCATAAAAGATGTGATGGGAAGGATTGAGGGTGTAATGGCGAATCCG
66 GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
* * * *
28251646 ATACCATGAAGATGCGAC
131 GTACCAT-AAAATGTGAT
* ** * * * *
28251664 GGGAAAGGTTGAGGTCGCAACGATAAACCCGGTACCATGAAGATTTGAAGGGAAAAGTTAAGGTC
1 GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* ** * * * *
28251729 GTAACGGCGAACTTGGTACCTTAGAAGATGTGATTGGAAAGATTGAGGCCGCAACGATGAATCCG
66 GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
*
28251794 GTACCATGAAATGTGAT
131 GTACCATAAAATGTGAT
* * ** * *
28251811 GGGAAAGGTTGAGGTCACAATAGCGAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTAAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* * * * *
28251876 GCAACGACGAACCCGGTACCTTAGAAGATGTGATAGGAAGGATTGAGGCTGCAACGGTAAATCCG
66 GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
* * *
28251941 ATACCATGAAGATGCGAT
131 GTACCAT-AAAATGTGAT
* * * * * * *
28251959 TGGAAAAGTTGAGGCCACAACGGCAAACCCGGCACCATAAAGATTTGAAGGGAAAGGTTGAGGCT
1 GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* * ** * *
28252024 GCAATGGTGAACCCGACACCTTAAAAGATG-GATGAGAAGGATTGAGGCCGCAACGGCGAATCCG
66 GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
* *
28252088 GTACCATGAAATATGAT
131 GTACCATAAAATGTGAT
*
28252105 GGGAAAGGTTGAGGCTGCAACGGC
1 GGGAAAGGTTGAGGCCGCAACGGC
28252129 GAGTCTTATA
Statistics
Matches: 502, Mismatches: 108, Indels: 6
0.81 0.18 0.01
Matches are distributed among these distances:
146 60 0.12
147 234 0.47
148 208 0.41
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.18
Consensus pattern (147 bp):
GGGAAAGGTTGAGGCCGCAACGGCAAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
GCAACGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCG
GTACCATAAAATGTGAT
Found at i:28251989 original size:295 final size:293
Alignment explanation
Indices: 28251388--28252119 Score: 946
Period size: 295 Copynumber: 2.5 Consensus size: 293
28251378 TTAAGGCTGT
* * * * *
28251388 AACGGCGAATCCGGTACCATGAA-ATGTGATGGGAAAGGTTGAGGCCGCAATGGCTAACCTGGTA
1 AACGGCAAACCCGGTACCATGAAGATTTGAAGGGAAAGGTTGAGG-CGCAATGGCGAACCTGGTA
* * * * *
28251452 CCGTAAAAGATGTGATGGCAAAGATTGAGACCACAACGGTGAATTCGGTACCATAAAATGTGATG
65 CCTTAAAAGATGTGATGG-AAAGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGTGATG
* * * *
28251517 GGAAAGGTTGAGGCCGCAATGGTGAACCCGATACCATGAAGATTTAAAGGGAAAAGTTGAGGCCG
129 GGAAAGGTTGAGGCCACAATAGCGAACCCGATACCATGAAGATTTAAAGGGAAAAGTTAAGGCCG
* * * * * * *
28251582 TAACGGCGAACCCGGTACCATAAAAGATGTGATGGGAAGGATTGAGGGTGTAATGGCGAATCCGA
194 CAACGACGAACCCGGTACCATAAAAGATGTGATAGGAAGGATTGAGGCTGCAACGGCAAATCCGA
* * *
28251647 TACCATGAAGATGCGACGGGAAAGGTTGAGGTCGC
259 TACCATGAAGATGCGACGGGAAAAGTTGAGGCCAC
** * * * * *
28251682 AACGATAAACCCGGTACCATGAAGATTTGAAGGGAAAAGTTAAGGTCGTAACGGCGAACTTGGTA
1 AACGGCAAACCCGGTACCATGAAGATTTGAAGGGAAAGGTTGAGG-CGCAATGGCGAACCTGGTA
* *
28251747 CCTTAGAAGATGTGATTGGAAAGATTGAGGCCGCAACGATGAATCCGGTACCATGAAATGTGATG
65 CCTTAAAAGATGTGA-TGGAAAGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGTGATG
* * *
28251812 GGAAAGGTTGAGGTCACAATAGCGAACCCGGTACCATGAAGATTTAAAGGGAAAGGTTAAGGCCG
129 GGAAAGGTTGAGGCCACAATAGCGAACCCGATACCATGAAGATTTAAAGGGAAAAGTTAAGGCCG
* * *
28251877 CAACGACGAACCCGGTACCTTAGAAGATGTGATAGGAAGGATTGAGGCTGCAACGGTAAATCCGA
194 CAACGACGAACCCGGTACCATAAAAGATGTGATAGGAAGGATTGAGGCTGCAACGGCAAATCCGA
**
28251942 TACCATGAAGATGCGATTGGAAAAGTTGAGGCCAC
259 TACCATGAAGATGCGACGGGAAAAGTTGAGGCCAC
* * * * **
28251977 AACGGCAAACCCGGCACCATAAAGATTTGAAGGGAAAGGTTGAGGCTGCAATGGTGAACCCGACA
1 AACGGCAAACCCGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGC-GCAATGGCGAACCTGGTA
* * *
28252042 CCTTAAAAGATG-GATGAGAAGGATTGAGGCCGCAACGGCGAATCCGGTACCATGAAATATGATG
65 CCTTAAAAGATGTGATG-GAAAGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGTGATG
28252106 GGAAAGGTTGAGGC
129 GGAAAGGTTGAGGC
28252120 TGCAACGGCG
Statistics
Matches: 373, Mismatches: 61, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
293 2 0.01
294 78 0.21
295 290 0.78
296 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (293 bp):
AACGGCAAACCCGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCGCAATGGCGAACCTGGTAC
CTTAAAAGATGTGATGGAAAGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGTGATGGG
AAAGGTTGAGGCCACAATAGCGAACCCGATACCATGAAGATTTAAAGGGAAAAGTTAAGGCCGCA
ACGACGAACCCGGTACCATAAAAGATGTGATAGGAAGGATTGAGGCTGCAACGGCAAATCCGATA
CCATGAAGATGCGACGGGAAAAGTTGAGGCCAC
Found at i:28252490 original size:77 final size:78
Alignment explanation
Indices: 28252372--28252577 Score: 272
Period size: 77 Copynumber: 2.7 Consensus size: 78
28252362 GAAGATTTCG
* * * * * *
28252372 ATCTCTTACCCCGATG-GTGGGACAGATCACAATCATTCGATCTTTTACCCTAAATTTGGGATAG
1 ATCTCTTACCCCGA-GCCTAGGACAGATTACAACCATTCGATCTTTTACCCCAAACTTGGGATAG
*
28252436 ATCACCATCAGCAA
65 ATCACCATCAACAA
* *
28252450 ATCTCTTACCCCGAGCCTAGG-CAGATTGCAACCATTCGATCTTTTACCCCAAGCTTGGGATAGA
1 ATCTCTTACCCCGAGCCTAGGACAGATTACAACCATTCGATCTTTTACCCCAAACTTGGGATAGA
*
28252514 TCACCATCAACCA
66 TCACCATCAACAA
** *
28252527 ATCTCTTACCCCGAGCCTAGGACAGATTACAGTCATTTGATCTTTTACCCC
1 ATCTCTTACCCCGAGCCTAGGACAGATTACAACCATTCGATCTTTTACCCC
28252578 GAGCCTGAGG
Statistics
Matches: 112, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
77 70 0.62
78 42 0.38
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTAGGACAGATTACAACCATTCGATCTTTTACCCCAAACTTGGGATAGA
TCACCATCAACAA
Found at i:28252653 original size:78 final size:78
Alignment explanation
Indices: 28252566--28252732 Score: 185
Period size: 78 Copynumber: 2.1 Consensus size: 78
28252556 CAGTCATTTG
* * * *
28252566 ATCTTTTACCCCGAGCCT-GAGGCATATTGCAACCATTCGATCTTTTA-CCGCGATCATGGGGCA
1 ATCTCTTACCCCGAG-ATAGAGGCAGATTGCAACCATCCGATCTTTTATCC-CGATCATGGGGCA
* * *
28252629 AATCACCATCAGCCA
64 AATCACAACCACCCA
* * * * *
28252644 ATCTCTTACCCCGCGATAGGGGTAGATTGTAACCATCCGATCTTTTATCCCGATCATGGGGCAGA
1 ATCTCTTACCCCGAGATAGAGGCAGATTGCAACCATCCGATCTTTTATCCCGATCATGGGGCAAA
*
28252709 TCACAACCACCCG
66 TCACAACCACCCA
28252722 ATCTCTTACCC
1 ATCTCTTACCC
28252733 TGACCATAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
77 1 0.01
78 71 0.96
79 2 0.03
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGATAGAGGCAGATTGCAACCATCCGATCTTTTATCCCGATCATGGGGCAAA
TCACAACCACCCA
Found at i:28252686 original size:117 final size:116
Alignment explanation
Indices: 28252450--28252696 Score: 280
Period size: 117 Copynumber: 2.1 Consensus size: 116
28252440 CCATCAGCAA
* * * *
28252450 ATCTCTTACCCCGAGCCTAGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTGGGATAGAT
1 ATCTTTTACCCCGAGCCTAGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCATGGGACAAAT
* ** **
28252515 CACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGTCATTTG
66 CACCATCAACCAATCTCTTACCCCGAGCATAGGACAGATTACAACCATCCG
* * * * *
28252566 ATCTTTTACCCCGAGCCTGAGGCATATTGCAACCATTCGATCTTTTACCGCGATCATGGGGCAAA
1 ATCTTTTACCCCGAGCCT-AGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCATGGGACAAA
* * ** **
28252631 TCACCATCAGCCAATCTCTTACCCCGCG-ATAGGGGTAGATTGTAACCATCCG
65 TCACCATCAACCAATCTCTTACCCCGAGCATA-GGACAGATTACAACCATCCG
*
28252683 ATCTTTTATCCCGA
1 ATCTTTTACCCCGA
28252697 TCATGGGGCA
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
116 19 0.18
117 89 0.82
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (116 bp):
ATCTTTTACCCCGAGCCTAGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCATGGGACAAAT
CACCATCAACCAATCTCTTACCCCGAGCATAGGACAGATTACAACCATCCG
Found at i:28252787 original size:39 final size:39
Alignment explanation
Indices: 28252450--28252787 Score: 146
Period size: 39 Copynumber: 8.7 Consensus size: 39
28252440 CCATCAGCAA
* * ** *
28252450 ATCTCTTACCCCGAGCCT-AGGCAGATTGCAACCATTCG
1 ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
* * * * * * * * *
28252488 ATCTTTTACCCCAAGCTTG-GGATAGATCACCATCAACCA
1 ATCTCTTACCCCGATCATGAGG-CAGATCACAACCATCCG
* * * ** **
28252527 ATCTCTTACCCCGAGCCT-AGGACAGATTACAGTCATTTG
1 ATCTCTTACCCCGATCATGAGG-CAGATCACAACCATCCG
* * * * ** *
28252566 ATCTTTTACCCCGAGCCTGAGGCATATTGCAACCATTCG
1 ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
* * * * * * * *
28252605 ATCTTTTACCGCGATCATGGGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
* * ***
28252644 ATCTCTTACCCCG--CGATAGGGGTAGATTGTAACCATCCG
1 ATCTCTTACCCCGATC-AT-GAGGCAGATCACAACCATCCG
* * * *
28252683 ATCTTTTATCCCGATCATGGGGCAGATCACAACCACCCG
1 ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
* * * * * *
28252722 ATCTCTTACCCTGACCATAAGACAGATCACAGCCATCCA
1 ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
28252761 ATCTCTTACCCCGATCATGAGGCAGAT
1 ATCTCTTACCCCGATCATGAGGCAGAT
28252788 TATAGTTATC
Statistics
Matches: 220, Mismatches: 72, Indels: 15
0.72 0.23 0.05
Matches are distributed among these distances:
37 1 0.00
38 19 0.09
39 194 0.88
40 5 0.02
41 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGATCATGAGGCAGATCACAACCATCCG
Found at i:28253463 original size:204 final size:204
Alignment explanation
Indices: 28252834--28253809 Score: 1403
Period size: 204 Copynumber: 4.8 Consensus size: 204
28252824 GACGAGATGT
* * * * * *
28252834 AGAGAAGCGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAACGGATTAAAACAAGTGATGTG
1 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
*
28252899 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATAAAGCTCAATGTGAGTGAAACAT
66 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
* * *
28252964 CAAACCCTATCTTCCTGATGAGATACAGAGAAATGGGTCAAAGCAATAAAGAGGTCGTCTTCCTG
131 CAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCGTCTTCCTG
*
28253029 ATGAAATAT
196 ATGAAATAC
28253038 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
1 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
* *
28253103 ATCATCTTCCTGATGACATACAGAGAAGTAGACCAAATCGATGAAGCTC--------TGAAACAT
66 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
* * **
28253160 CAAACCCCATC-TTCTTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAAAGGTTATCTTCCT
131 CAAACCCCATCTTTC-TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCGTCTTCCT
28253224 GATGAAATAC
195 GATGAAATAC
* * * * *
28253234 AGAGAAGTGGACCAAATCCGTCTTCCTGATGAGGTACATAGAAGTGCATTAAAACAAGTGATGCG
1 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
*
28253299 GTCACCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
66 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
* *
28253364 CAAACCCCATCTTTCTAATGAGATACAGAGAAGTGGGTCAAATCAATAAAGAGGTCGTCTTCCTG
131 CAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCGTCTTCCTG
28253429 ATGAAATAC
196 ATGAAATAC
* * *
28253438 AGAGAAGTGGACCAAATCTGTCTTCCTAATGAGATACAGAGAAACGGATTAAAACAAGTGATACG
1 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
* * *
28253503 GTCACCTTCCTGATGAGATACAGAGAAGTAGAGCAAATCGATGAAGCTCAATGTGAATGAAACAT
66 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
* * * * *
28253568 TAAACCCCATCTTTCTGATGAGATTCAAAAAAGTGAGTCAAAGCAATAAAGAGGTCGTCTTCCTG
131 CAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCGTCTTCCTG
28253633 ATGAAATAC
196 ATGAAATAC
* * * * *
28253642 AGAGAAGCGGACCAAATCCGTCTTCCTAATGAGATATAGATAAGCGGATTAAAACAAGCGATGCA
1 AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
* * * *
28253707 GTCATCTTCCTGGTGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTTAGTGTGAGAGA
66 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGAT-----GAAGCTCAATGTGAGTGA
* * *
28253772 AACTTCAAACCTCATCTTCCTGATGAGATACAGAGAAG
126 AACATCAAACCCCATCTTTCTGATGAGATACAGAGAAG
28253810 AAGATTAAGA
Statistics
Matches: 687, Mismatches: 70, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
195 2 0.00
196 177 0.26
204 460 0.67
205 3 0.00
209 45 0.07
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (204 bp):
AGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCG
GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCTCAATGTGAGTGAAACAT
CAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCGTCTTCCTG
ATGAAATAC
Found at i:28255368 original size:29 final size:29
Alignment explanation
Indices: 28255325--28255519 Score: 112
Period size: 29 Copynumber: 6.6 Consensus size: 29
28255315 CCCTATTTTC
* *
28255325 TTTCAAAAATCACATTTTTACCCAAAACTT
1 TTTCAAAAATTACATTTTGACCCAAAAC-T
*
28255355 TTTC-AAAATTACATTTTGACCCTAGAACT
1 TTTCAAAAATTACATTTTGACCC-AAAACT
* * *
28255384 TTGCAAAAATTATATTTTGACCCCTAAACT
1 TTTCAAAAATTACATTTTGA-CCCAAAACT
* * *
28255414 TTCCAAAAATTATATTTCT-ACCCCAAACT
1 TTTCAAAAATTACATTT-TGACCCAAAACT
** * ** *
28255443 TCGCCAAAATCCCATTTCGACCTC-AAACT
1 TTTCAAAAATTACATTTTGACC-CAAAACT
* * **
28255472 TTTCCAAAATTATGATTTT-ACCCTCGAA-T
1 TTTCAAAAATTA-CATTTTGACCC-AAAACT
28255501 TTCTCAAAAATTACATTTT
1 TT-TCAAAAATTACATTTT
28255520 TACCTTCGAA
Statistics
Matches: 130, Mismatches: 25, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.01
29 66 0.51
30 59 0.45
31 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTCAAAAATTACATTTTGACCCAAAACT
Found at i:28255391 original size:59 final size:57
Alignment explanation
Indices: 28255324--28255519 Score: 157
Period size: 59 Copynumber: 3.4 Consensus size: 57
28255314 GCCCTATTTT
* *
28255324 CTTT-CAAAAATCACATTTTTACCCAAAACTTTTTCAAAATTACATTTTGACCCTAGAA
1 CTTTGCAAAAATCACATTTTGACCC-AAACTTTTCCAAAATTACATTTT-ACCCTAGAA
* * * *
28255382 CTTTGCAAAAATTATATTTTGACCCCTAAAC-TTTCCAAAAATTATATTTCTACCCCA-AA
1 CTTTGCAAAAATCACATTTTGA-CCC-AAACTTTTCC-AAAATTACATTT-TACCCTAGAA
* * * * * *
28255441 CTTCGCCAAAATCCCATTTCGACCTCAAACTTTTCCAAAATTATGATTTTACCCTCGAA
1 CTTTGCAAAAATCACATTTTGACC-CAAACTTTTCCAAAATTA-CATTTTACCCTAGAA
* *
28255500 -TTTCTCAAAAATTACATTTT
1 CTTT-GCAAAAATCACATTTT
28255520 TACCTTCGAA
Statistics
Matches: 107, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
58 24 0.22
59 59 0.55
60 23 0.21
61 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (57 bp):
CTTTGCAAAAATCACATTTTGACCCAAACTTTTCCAAAATTACATTTTACCCTAGAA
Found at i:28255537 original size:29 final size:30
Alignment explanation
Indices: 28255327--28255598 Score: 152
Period size: 30 Copynumber: 9.2 Consensus size: 30
28255317 CTATTTTCTT
* ** *
28255327 TCAAAAATCACATTTTTACCC-AAAACTTTT
1 TCAAAAATTACATTTTTACCCTCGAAC-TTC
* *
28255357 TC-AAAATTACATTTTGACCCTAGAACTT-
1 TCAAAAATTACATTTTTACCCTCGAACTTC
* * *
28255385 TGCAAAAATTATATTTTGACCC-CTAAACTT-
1 T-CAAAAATTACATTTTTACCCTC-GAACTTC
* * *
28255415 TCCAAAAATTATATTTCTACCC-CAAACTTC
1 T-CAAAAATTACATTTTTACCCTCGAACTTC
* * ** ** * *
28255445 GCCAAAATCCCATTTCGA-CCTCAAACTTT
1 TCAAAAATTACATTTTTACCCTCGAACTTC
* * *
28255474 TCCAAAATTATGA-TTTTACCCTCGAATTTC
1 TCAAAAATTA-CATTTTTACCCTCGAACTTC
* *
28255504 TCAAAAATTACATTTTTACCTTCGAACGTC
1 TCAAAAATTACATTTTTACCCTCGAACTTC
* *
28255534 -CAAAAATCAAATTTTTTACCCTCGAACTTC
1 TCAAAAATTACA-TTTTTACCCTCGAACTTC
* *
28255564 TAAAAAATTACA-TTTTACGCTCGAACTTC
1 TCAAAAATTACATTTTTACCCTCGAACTTC
28255593 -CAAAAA
1 TCAAAAA
28255599 CCCAAACTTT
Statistics
Matches: 192, Mismatches: 39, Indels: 24
0.75 0.15 0.09
Matches are distributed among these distances:
28 8 0.04
29 80 0.42
30 96 0.50
31 8 0.04
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
TCAAAAATTACATTTTTACCCTCGAACTTC
Found at i:28255570 original size:60 final size:59
Alignment explanation
Indices: 28255487--28255598 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 59
28255477 AAAATTATGA
* *
28255487 TTTTACCCTCGAATTTCTCAAAAATTACATTTTTAC-CTTCGAACGTCCAAAAATCAAATT
1 TTTTACCCTCGAACTTCTAAAAAATTACA-TTTTACGC-TCGAACGTCCAAAAATCAAATT
*
28255547 TTTTACCCTCGAACTTCTAAAAAATTACATTTTACGCTCGAACTTCCAAAAA
1 TTTTACCCTCGAACTTCTAAAAAATTACATTTTACGCTCGAACGTCCAAAAA
28255599 CCCAAACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
59 20 0.42
60 28 0.58
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (59 bp):
TTTTACCCTCGAACTTCTAAAAAATTACATTTTACGCTCGAACGTCCAAAAATCAAATT
Found at i:28255672 original size:29 final size:28
Alignment explanation
Indices: 28255603--28255690 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
28255593 CAAAAACCCA
* *
28255603 AACTTTCAAAAATCACATTTTT-CCCCG
1 AACTTTCCAAAATTACATTTTTACCCCG
* *
28255630 AACTTCCCAAAATTACATTTTTACCCCT
1 AACTTTCCAAAATTACATTTTTACCCCG
* *
28255658 AACCTTTCCAAAATTACATTTTAACCCCA
1 AA-CTTTCCAAAATTACATTTTTACCCCG
28255687 AACT
1 AACT
28255691 CTTCGAAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 19 0.37
28 8 0.15
29 25 0.48
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.33
Consensus pattern (28 bp):
AACTTTCCAAAATTACATTTTTACCCCG
Found at i:28255838 original size:15 final size:15
Alignment explanation
Indices: 28255811--28255869 Score: 68
Period size: 14 Copynumber: 4.0 Consensus size: 15
28255801 TGATTCATGA
28255811 TTCGTAT-TTTATTT
1 TTCGTATATTTATTT
*
28255825 TTCTTATATTTA-TT
1 TTCGTATATTTATTT
*
28255839 TTCGTATATTTATTCA
1 TTCGTATATTTATT-T
*
28255855 TTCGTATAATTATTT
1 TTCGTATATTTATTT
28255870 GTGCTTGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 19 0.51
15 5 0.14
16 13 0.35
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.64
Consensus pattern (15 bp):
TTCGTATATTTATTT
Found at i:28255868 original size:30 final size:28
Alignment explanation
Indices: 28255811--28255869 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
28255801 TGATTCATGA
* * *
28255811 TTCGTATTTTATTTTTCTTATATTTATT
1 TTCGTATTTTATTATTCGTATAATTATT
28255839 TTCGTATATTTATTCATTCGTATAATTATT
1 TTCGTAT-TTTATT-ATTCGTATAATTATT
28255869 T
1 T
28255870 GTGCTTGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.27
29 6 0.23
30 13 0.50
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.64
Consensus pattern (28 bp):
TTCGTATTTTATTATTCGTATAATTATT
Found at i:28256545 original size:12 final size:12
Alignment explanation
Indices: 28256528--28256552 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28256518 ATTTTCGAGA
28256528 CCTATTTATTTT
1 CCTATTTATTTT
28256540 CCTATTTATTTT
1 CCTATTTATTTT
28256552 C
1 C
28256553 TCAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (12 bp):
CCTATTTATTTT
Found at i:28256913 original size:20 final size:20
Alignment explanation
Indices: 28256870--28256912 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28256860 CATCGGTACC
28256870 AAAATTATGAAAGAAATATA
1 AAAATTATGAAAGAAATATA
28256890 AAAATTAT--AAGAAAATATA
1 AAAATTATGAAAG-AAATATA
28256909 AAAA
1 AAAA
28256913 AATGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATTATGAAAGAAATATA
Found at i:28259974 original size:22 final size:21
Alignment explanation
Indices: 28259949--28259998 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
28259939 ATCAAAATAA
28259949 TAATTTTAAAATATTTTAATTT
1 TAATTTTAAAATATTTT-ATTT
*
28259971 TAATTTTAAATTATTTTATTT
1 TAATTTTAAAATATTTTATTT
28259992 TGAATTT
1 T-AATTT
28259999 GTTGTTAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TAATTTTAAAATATTTTATTT
Found at i:28264303 original size:263 final size:263
Alignment explanation
Indices: 28263301--28266833 Score: 4565
Period size: 264 Copynumber: 13.6 Consensus size: 263
28263291 AATAATATGA
28263301 CTATAGAAAAAATAT-AAAATTACAAATATAAAATTTTGTTTATATAATGAAGATATTTT-AAAA
1 CTATAGAAAAAATATAAAAATTACAAATAT-AAATTTTGTTTATATAATGAAGATATTTTAAAAA
* * * *
28263364 ATTGGGAGGGTGA-GCCTCTCTTGCCTTCAATGACTATCTATCTACGGAAACATGCATTTAATAA
65 ATTGGGAGGGTGAGGCC-CT-TTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAA
* * *
28263428 AATCAATTTACTTTATTTATATTACACGAGAAAAGAATGGGTAAAAGGATGATACTGAAATTTTT
128 AATCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTT
* * * *
28263493 ATCCACTACCATCCTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATCTGCTTGATAATCAA
193 GTCCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAA
*
28263558 TGGTGG
258 GGGTGG
* *
28263564 CTATAG-AAAAATATAAAAATTACAAATATAAATTTTATTTATATAATAAAGATA-TTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* **
28263627 TTGAGAGGGTGAGGCCCTTTCGCCTTCAATGACTATCCACCTATAGAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAGGCCCTTT-GCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* *
28263692 TCGATTTATTTTACTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* * *
28263757 CCACTACCATCCTATCTTAATTTTATGTCTCATTTGAACTCCATGTATTTGCTTAATAGTCAAGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
28263822 GTGG
260 GTGG
* *
28263826 CTATAGAAAAAAAATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAATA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
** * * * * * *
28263891 TTTAGAGGGTAAAGCCCCCTTGCCTTCAATGAGTATCCACTTACGGAAACATATATTTATTAAAA
66 TTGGGAGGGT-GAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* **
28263956 TCAATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATGTTGAAATTTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* * * *
28264021 CTACTACCATCCTATCTTAATTTTATGTCTCATTTGAACTCTGTGTATTTGCTTGATAATCAAGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
*
28264086 GTGA
260 GTGG
* *
28264090 CTATAGAAAAAATATAAAAATTACAAATATAAAATTTATTTATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
*
28264155 TTGGGAGGGAGAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
66 TTGGGAGGGTGAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
*
28264220 CGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAAGATGATACTGAAATTTTTGTC
131 CGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGTC
28264285 CACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
196 CACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
28264350 TGG
261 TGG
*
28264353 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTACATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* * * **
28264418 TTGGGTGGGTGAAGCCCCCTTGCCTTCAATGACTATCCACCTAAAGAAACATGTATTTATTAAAA
66 TTGGGAGGGTG-AGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
28264483 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* * ** * *
28264548 CCACCACCATCCTATCTTAATTTTATACCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGA
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
28264613 GTGG
260 GTGG
*
28264617 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTAAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTT-TAAAAA
* * * *
28264682 ATTTAGAAGGGTGGGGCCCTTTGCCTTCAATGACTA-CTCACCTACGAAAACATGTATTTATTAA
65 A-TTGGGAGGGTGAGGCCCTTTGCCTTCAATGACTATC-CACCTACGGAAACATGTATTTATTAA
* * * *
28264746 ATTCGATTTACTTTATTTATATTGCACGAGGAAAGAATTGATAAAAGGATGATAATGAAATTTTT
128 AATCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTT
* * * * *
28264811 GTCCACTACCATCCTATCTTAATTTTATGCCTAATTTGATCTTCGTGTATTTGCTTGATAGTCAA
193 GTCCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAA
28264876 GGGTGG
258 GGGTGG
*
28264882 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTAATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
*
28264947 TTGGGAGGGTGAGACCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAG-GCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* * * *
28265012 TCGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAGAAATTTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
*
28265077 CTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
28265142 GTGG
260 GTGG
* * *
28265146 CTATAGAAAAAAAAAAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAATA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* * * * * *
28265211 TTGGGAGGGTAAAGCCCCATTGCCTTTAATGAGTATCCACTTACGGAAACATGTATTTATTAAAA
66 TTGGGAGGGT-GAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* **
28265276 TCAATTTACTTTA--TATATTGCACGAGGAAAGAATGGGTAAAAGGATGATGTTGAAATTTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* * * *
28265339 CTACTACCATCCTATCTTAATTTTATGTCTCATTTGAACTCTGTGTATTTGCTTGATAATCAAGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
* *
28265404 TTGA
260 GTGG
* *
28265408 CTATAGAAAAAATATAAAAATTACAAATATAAAATTT-ATTATATAATGAAGATA--TTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* *
28265470 TTGGGAGGGTGAGGCCCCTTGCCTTCAATGACTATCCACCTACGGAAACATATATTTATTAAAAT
66 TTGGGAGGGTGAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
*
28265535 CGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAAGATGATACTGAAATTTTTGTC
131 CGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGTC
* * *
28265600 CACTACCTTCCTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAAGG
196 CACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
28265665 TGG
261 TGG
*
28265668 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTACATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* * **
28265733 TTGGGAGGGTGAAGCCCCCTTGCCTTCAATGACTATCCACCTAAAGAAACATGTATTTATTAAAA
66 TTGGGAGGGTG-AGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* * ** * * *
28265798 TCGATTTACTTTATGTATATTGCACGAGGAAAGAATGAG--ACTGCCATCCCAT-CT-TAATTTT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAG-GAT--GATACTGAAATTTT
* * *** * * * * *
28265859 ATG--C-CT--TAT-TTAAAC-TCCGTGTAT-T-TGC--TTGATAGTCAAG-G--GTGGC-T-AT
192 -TGTCCACTACCATCTT-ATCTTAATTTTATGTCT-CATTTGA-ACTC-CGTGTATTTGCTTGAT
**
28265908 AG--AA----AA
252 AGTCAAGGGTGG
** * * *
28265914 AAATA-TAAAAAT-TACAAA-TA-TAAT------TTTGTTTATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
28265969 TTGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAGG-CCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* * * ** *
28266034 TCGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* *
28266099 CTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
28266164 GTGG
260 GTGG
*
28266168 CTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* * *
28266233 TTGGGAGGGTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAGG-CCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* ** * * *
28266297 TCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGG--ACTGCCATCCCAT-CT-TAATTTT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAG-GAT--GATACTGAAATTTT
* * *** * * * * *
28266358 ATG--C-CT--TAT-TTAAAC-TCCGTGTAT-T-TGC--TTGATAGTCAAG-G--GTGGC-T-AT
192 -TGTCCACTACCATCTT-ATCTTAATTTTATGTCT-CATTTGA-ACTC-CGTGTATTTGCTTGAT
**
28266407 AG--AA----AA
252 AGTCAAGGGTGG
** * * *
28266413 AAATA-TAAAAAT-TACAAA-TA-TAAT------TTTGTTTATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
28266468 TTGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAGG-CCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
* * * ** *
28266533 TCGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGT
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGT
* *
28266598 CTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGG
195 CCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGG
28266663 GTGG
260 GTGG
28266667 CTATAGAAAAAATATAAAAA-TACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
1 CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
* * *
28266731 TTGGGAGGGTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAAAA
66 TTGGGAGGGTGAGG-CCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAA
*
28266795 TCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGG
130 TCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGG
28266834 ACTGCCATCC
Statistics
Matches: 2853, Mismatches: 308, Indels: 219
0.84 0.09 0.06
Matches are distributed among these distances:
235 57 0.02
236 206 0.07
237 14 0.00
238 4 0.00
239 4 0.00
241 11 0.00
242 19 0.01
243 13 0.00
244 21 0.01
245 17 0.01
246 9 0.00
247 2 0.00
248 8 0.00
249 1 0.00
250 4 0.00
251 4 0.00
252 5 0.00
253 4 0.00
254 13 0.00
255 21 0.01
256 20 0.01
257 15 0.01
258 72 0.03
259 20 0.01
260 147 0.05
261 40 0.01
262 445 0.16
263 480 0.17
264 926 0.32
265 243 0.09
266 8 0.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (263 bp):
CTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAA
TTGGGAGGGTGAGGCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
CGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATTTTTGTC
CACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
TGG
Found at i:28267186 original size:498 final size:500
Alignment explanation
Indices: 28263763--28267588 Score: 5543
Period size: 498 Copynumber: 7.5 Consensus size: 500
28263753 TTGTCCACTA
* * * * * *
28263763 CCATCCTATCTTAATTTTATGTCTCATTTGAACTCCATGTATTTGCTTAATAGTCAAGGGTGGCT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
* *
28263828 ATAGAAAAAAAATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAATATT
66 ATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATT
** * * * * * *
28263893 TAGAGGGTAAAGCCCCCTTGCCTTCAATGAGTATCCACTTACGGAAACATATATTTATTAAAATC
131 GGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAATC
* * ***
28263958 AATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATGTTGAAATTTTTGTCT
196 GATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTCT
* * *
28264023 ACTACCATCCTATCTTAATTTTATGTCTCATTTGAACTCTGTGTATTTGCTTGATAATCAAGGGT
261 ACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGGT
* * * *
28264088 GACTATAGAAAAAATATAAAAATTACAAATATAAAATTTATTTATATAATGAAGATATTTTAAAA
326 GGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAA
* * * *
28264153 AATTGGGAGGGAGAGG-CCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAA
391 AATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAA
*
28264217 AATCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAAGATGATACTGAAATTTTT
456 AATCGATTTACTTTATGTATATTGCACGAGGAAAGAAT--G------G--G--AC---------T
28264282 G
500 G
* * *
28264283 TCCACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAG
1 -CCA-T-CC--C--ATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAG
*
28264348 GGTGGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTACATAATGAAGATATTTTA
59 GGTGGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTA
* * * **
28264413 AAAAATTGGGTGGGTGAAGCCCCCTTGCCTTCAATGACTATCCACCTAAAGAAACATGTATTTAT
124 AAAAATTGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTAT
* *
28264478 TAAAATCGATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAGGATGATACTGAAATT
189 TAAAATCGATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATT
* * * ** *
28264543 TTTGTCCACCACCATCCTATCTTAATTTTATACCTCATTTAAACTCCGTGTATTTGCTTGATAGT
254 TTTGTCTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGT
* *
28264608 CAAGAGTGGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATAT
319 CAAGGGTGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATAT
* * * * *
28264673 TTAAAAAAAATTTAGAAGGGTG-GGGCCCTTTGCCTTCAATGACTA-CTCACCTACGAAAACATG
384 TT-TAAAAAA-TTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCT-ACCTACGAAAACATG
* *
28264736 TATTTATTAAATTCGATTTACTTTATTTATATTGCACGAGGAAAGAATTGATAAAAGGATGATAA
446 TATTTATTAAAATCGATTTACTTTATGTATATTGCACGAGGAAAG-A---AT-----G--G----
*
28264801 TGAAATTTTTG
496 -G--A---CTG
* * * *
28264812 TCCACTACCATCCTATCTTAATTTTATGCCTAATTTGATCTTCGTGTATTTGCTTGATAGTCAAG
1 -CCA-T--C--CC-ATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAG
*
28264877 GGTGGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTAATATAATGAAGATATTTTA
59 GGTGGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTA
*
28264942 AAAAATTGGGAGGGTGAGACCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTAT
124 AAAAATTGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTAT
* *
28265007 TAAAATCGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAGAAATT
189 TAAAATCGATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATT
28265072 TTTGTCTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGT
254 TTTGTCTACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGT
*
28265137 CAAGGGTGGCTATAGAAAAAA-AAAAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATA
319 CAAGGGTGGCTATAGAAAAAATATAAAAAA-TACAAATATAAATTTTGTTTATATAATGAAGATA
* * * * * * * * *
28265201 TTTTAAAATATTGGGAGGGTAAAGCCCCATTGCCTTTAATGAGTATCCACTTACGGAAACATGTA
383 TTTTAAAAAATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTA
*
28265266 TTTATTAAAATCAATTTACTTTA--TATATTGCACGAGGAAAGAATGGGTAAAAGGATGATGTTG
448 TTTATTAAAATCGATTTACTTTATGTATATTGCAC-------G-A--GG--AAA-GA--ATG--G
*
28265329 AAATTTTTGTCTACTA
496 --------G---ACTG
* * * * * * * *
28265345 CCATCCTATCTTAATTTTATGTCTCATTTGAACTCTGTGTATTTGCTTGATAATCAAGGTTGACT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
* *
28265410 ATAGAAAAAATATAAAAATTACAAATATAAAATTT-ATTATATAATGAAGATA--TTAAAAAATT
66 ATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATT
*
28265472 GGGAGGGTGAGGCCCC-TTGCCTTCAATGACTATCCACCTACGGAAACATATATTTATTAAAATC
131 GGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAATC
* * * *
28265536 GATTTACTTTATTTATATTGCACGAGGAAAGAATGGGTAAAAAGATGATACTGAAATTTTTGTCC
196 GATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTCT
* * *
28265601 ACTACCTTCCTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAAGGT
261 ACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGGT
* *
28265666 GGCTATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTACATAATGAAGATATTTTAAAA
326 GGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAA
* * *
28265731 AATTGGGAGGGTGAAGCCCCCTTGCCTTCAATGACTATCCACCTA-AAGAAACATGTATTTATTA
391 AATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGA-AAACATGTATTTATTA
*
28265795 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGAGACTG
455 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
28265841 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
28265906 ATAGAAAAAAATATAAAAATTACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAAT
66 ATAG-AAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAAT
28265970 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
130 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
* * * *
28266035 CGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTC
195 CGATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTC
*
28266100 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGGG
260 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
28266165 TGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
325 TGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
28266230 AAATTGGGAGGGTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
390 AAATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
28266294 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
455 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
28266340 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
28266405 ATAGAAAAAAATATAAAAATTACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAAT
66 ATAG-AAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAAT
28266469 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
130 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
* * * *
28266534 CGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTC
195 CGATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTC
*
28266599 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGGG
260 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
28266664 TGGCTATAGAAAAAATAT-AAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
325 TGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
28266728 AAATTGGGAGGGTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
390 AAATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
28266792 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
455 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
28266838 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
28266903 ATAGAAAAAA-ATATAAAATTACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAAT
66 ATAGAAAAAATATA-AAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAAT
28266966 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
130 TGGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAAT
* * * *
28267031 CGATTTATTTTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTC
195 CGATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTC
*
28267096 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGGG
260 TACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGG
28267161 TGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
325 TGGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAA
28267226 AAATTGGGAGGGTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
390 AAATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTA
28267290 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
455 AAATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
28267336 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
1 CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
28267401 ATAGAAAAAATATAAAAATTACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAATT
66 ATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATT
* * *
28267465 GGGAGGGTAAAGCCCC-TTGCCTTTAATGACTATCCACCTACGGAAACATGTATTTATTAAAATC
131 GGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAATC
* * * *
28267529 GATTTACTTTATTTATATTGCACGAGGAAAGATTGGATAAAAGGATGATACTGAAATTTT
196 GATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTT
28267589 ATGAAATTTA
Statistics
Matches: 3080, Mismatches: 166, Indels: 142
0.91 0.05 0.04
Matches are distributed among these distances:
496 72 0.02
497 407 0.13
498 520 0.17
499 453 0.15
500 251 0.08
509 3 0.00
511 2 0.00
512 3 0.00
514 2 0.00
516 1 0.00
517 1 0.00
521 3 0.00
522 294 0.10
523 33 0.01
524 10 0.00
525 15 0.00
526 94 0.03
527 359 0.12
528 74 0.02
529 443 0.14
530 3 0.00
531 1 0.00
532 9 0.00
533 4 0.00
534 1 0.00
535 8 0.00
536 5 0.00
537 4 0.00
538 4 0.00
539 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (500 bp):
CCATCCCATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCT
ATAGAAAAAATATAAAAATTACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATT
GGGAGGGTGAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAATC
GATTTACTTTATTTATATTGCACGAGAAAAGAATGGGTAAAAGGATGATACAGAAATTTTTGTCT
ACTACCATCTTATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCAAGGGT
GGCTATAGAAAAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAA
AATTGGGAGGGTGAGGCCCCCTTGCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAA
AATCGATTTACTTTATGTATATTGCACGAGGAAAGAATGGGACTG
Found at i:28267314 original size:263 final size:263
Alignment explanation
Indices: 28266845--28267331 Score: 843
Period size: 263 Copynumber: 1.9 Consensus size: 263
28266835 CTGCCATCCC
*
28266845 ATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
1 ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
*
28266910 AAAATATAAAATTACAAATATAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGGT
66 AAAATATAAAAATACAAATATAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGGT
* * *
28266975 GAGGCCCCTTTGCCTTCAATGACTATCCACCTACGGAAACATGTATTTATTAAAATCGATTTATT
131 GAGGCCCCCTTGCCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTACT
*
28267040 TTATTTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTCTACTACCAT
196 TTATGTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTCTACTACCAT
28267105 CTT
261 CTT
* * *
28267108 ATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGGGTGGCTATAG-AA
1 ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
28267172 AAAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGG
66 AAAATAT-AAAAATACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGG
*
28267237 GTGAGGCCCCCTT-CCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAAAATCGATTTA
129 GTGAGGCCCCCTTGCCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTA
*
28267301 CTTTATGTATATTGCACGAGGAAAGAATGGG
194 CTTTATGTATATTGCACGAGAAAAGAATGGG
28267332 ACTGCCATCC
Statistics
Matches: 211, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
262 9 0.04
263 148 0.70
264 54 0.26
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (263 bp):
ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
AAAATATAAAAATACAAATATAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGGT
GAGGCCCCCTTGCCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTACT
TTATGTATATTGCACGAGAAAAGAATGGGTGAAAGGATGATACAAAAAATTTTGTCTACTACCAT
CTT
Found at i:28267523 original size:234 final size:235
Alignment explanation
Indices: 28267108--28267560 Score: 784
Period size: 234 Copynumber: 1.9 Consensus size: 235
28267098 CTACCATCTT
* * *
28267108 ATCTTAATTTTATGTCTCATTTGAACTCCGTGTATTTGCTTGATAGTCATGGGTGGCTATAGAAA
1 ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
28267173 AAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGG
66 AAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGG
* * *
28267238 TGAGGCCCCCTTCCTTCAATGACTATCTACCTACGAAAACATGTATTTATTAAAATCGATTTACT
131 TAAAGCCCCCTTCCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTACT
28267303 TTATGTATATTGCACGAGGAAAGAATGGGACTGCCATCCC
196 TTATGTATATTGCACGAGGAAAGAATGGGACTGCCATCCC
*
28267343 ATCTTAATTTTATGCCTTATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
1 ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
*
28267408 AAATATAAAAATTACAAATAT-AATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGG
66 AAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGG
* *
28267472 TAAAG-CCCCTTGCCTTTAATGACTATCCACCTACGGAAACATGTATTTATTAAAATCGATTTAC
131 TAAAGCCCCCTT-CCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTAC
*
28267536 TTTATTTATATTGCACGAGGAAAGA
195 TTTATGTATATTGCACGAGGAAAGA
28267561 TTGGATAAAA
Statistics
Matches: 206, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
233 6 0.03
234 119 0.58
235 81 0.39
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (235 bp):
ATCTTAATTTTATGCCTCATTTAAACTCCGTGTATTTGCTTGATAGTCAAGGGTGGCTATAGAAA
AAATATAAAAAATACAAATATAAATTTTGTTTATATAATGAAGATATTTTAAAAAATTGGGAGGG
TAAAGCCCCCTTCCTTCAATGACTATCCACCTACGAAAACATGTATTTATTAAAATCGATTTACT
TTATGTATATTGCACGAGGAAAGAATGGGACTGCCATCCC
Found at i:28267808 original size:32 final size:29
Alignment explanation
Indices: 28267753--28267850 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 29
28267743 TTAAAAGCTG
*
28267753 AAATTTTTTTAGGGCCCCTTAAAAACTGAAA
1 AAATATTTTT-GGG-CCCTTAAAAACTGAAA
* *
28267784 AAATAAATTTTTGGGCTCCTTAAAAGCTG-GA
1 AAAT--ATTTTTGGGC-CCTTAAAAACTGAAA
* *
28267815 AAATTTTTTTGGACCCTTAAAAACT-AAA
1 AAATATTTTTGGGCCCTTAAAAACTGAAA
28267843 AAA-ATTTT
1 AAATATTTT
28267851 GGACCAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
27 4 0.07
28 14 0.25
29 8 0.15
31 10 0.18
32 14 0.25
33 5 0.09
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (29 bp):
AAATATTTTTGGGCCCTTAAAAACTGAAA
Found at i:28267832 original size:28 final size:28
Alignment explanation
Indices: 28267743--28267836 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 28
28267733 ATTAGGCTCT
*
28267743 TTAAAAGCT-G-AAATTTTTTTAGGGCCCC
1 TTAAAAGCTGGAAAATTTTTTT--GGACCC
* * * *
28267771 TTAAAAACTGAAAAAATAAATTTTTGGGCTCC
1 TTAAAAGCTG-GAAAAT--TTTTTTGGAC-CC
28267803 TTAAAAGCTGGAAAATTTTTTTGGACCC
1 TTAAAAGCTGGAAAATTTTTTTGGACCC
28267831 TTAAAA
1 TTAAAA
28267837 ACTAAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 16 0.31
29 8 0.15
31 12 0.23
32 11 0.21
33 5 0.10
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (28 bp):
TTAAAAGCTGGAAAATTTTTTTGGACCC
Found at i:28269503 original size:36 final size:37
Alignment explanation
Indices: 28269434--28269504 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 37
28269424 AATGTCACTA
*
28269434 CATGAGCACTTCTAGATTTCGCCCAAAACTGTCGCCT
1 CATGAGCACTTCCAGATTTCGCCCAAAACTGTCGCCT
28269471 CATGAGCACTTCCAGA-TT-GCACCAAAACTGTCGC
1 CATGAGCACTTCCAGATTTCGC-CCAAAACTGTCGC
28269505 TACAGGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 2 0.06
36 15 0.47
37 15 0.47
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (37 bp):
CATGAGCACTTCCAGATTTCGCCCAAAACTGTCGCCT
Found at i:28272657 original size:17 final size:17
Alignment explanation
Indices: 28272637--28272674 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28272627 AATTGTCCCA
28272637 GCATTTTTATTGTAACT
1 GCATTTTTATTGTAACT
*
28272654 GCATTTTTATTGTCACT
1 GCATTTTTATTGTAACT
28272671 GCAT
1 GCAT
28272675 CTACATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (17 bp):
GCATTTTTATTGTAACT
Found at i:28273823 original size:26 final size:26
Alignment explanation
Indices: 28273787--28273839 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
28273777 ACTCAAGAGC
*
28273787 GTCGCTGCATGAACATGTCTAGAATT
1 GTCGCTGCATGAACATGTCCAGAATT
*
28273813 GTCGCTGCATGAACGTGTCCAGAATT
1 GTCGCTGCATGAACATGTCCAGAATT
28273839 G
1 G
28273840 CGCCAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (26 bp):
GTCGCTGCATGAACATGTCCAGAATT
Found at i:28286825 original size:39 final size:39
Alignment explanation
Indices: 28286771--28287111 Score: 309
Period size: 39 Copynumber: 8.7 Consensus size: 39
28286761 AGTGATCAAA
* *
28286771 ATACTGAACTAGCAGTGACACTGTAAACACTACGAAGTT
1 ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
* * * *
28286810 ATACTAAACAAGCAGTGACACTGTAAACATTGCGAAACT
1 ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
* * * *
28286849 ATACTGAACTTGCAGTGACTCTGTAAACACTGTGAAACT
1 ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
* * * **
28286888 ATATTGAACT-GACAGTAACACTGTAAACAATGCGAAATT
1 ATACTGAACTAG-CAGTGACACTGTAAACACTGCGAAGCT
* * *
28286927 ATACTGAAC-AGACAGTGACATTGTAAACATTGTGAAGCT
1 ATACTGAACTAG-CAGTGACACTGTAAACACTGCGAAGCT
* *
28286966 ATACCG-ACTTAGCAGTGACACTATAAACACTGCGAAGCT
1 ATACTGAAC-TAGCAGTGACACTGTAAACACTGCGAAGCT
* *
28287005 ATAAC-G-ACTTAACAGTGACACTATAAACACTGCGAAGCT
1 AT-ACTGAAC-TAGCAGTGACACTGTAAACACTGCGAAGCT
* * *
28287044 ATACCG-ACTTAGCAGTGACAGTGTAAACACTGC-AATGTT
1 ATACTGAAC-TAGCAGTGACACTGTAAACACTGCGAA-GCT
* * * *
28287083 ATTCTGAACTGGCAATGATACTGTAAACA
1 ATACTGAACTAGCAGTGACACTGTAAACA
28287112 TCGCATGACA
Statistics
Matches: 253, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
38 7 0.03
39 240 0.95
40 6 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (39 bp):
ATACTGAACTAGCAGTGACACTGTAAACACTGCGAAGCT
Found at i:28288469 original size:136 final size:136
Alignment explanation
Indices: 28288225--28288497 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
28288215 AGTGGAGACT
28288225 AAACAATAATGAAATTTGTAAACCAACCTTGGGAGGAGTTGCATACTGCACAAGCTAAGATTTCA
1 AAACAATAATGAAATTTGTAAACCAACCTTGGGAGGAGTTGCATACTGCACAAGCTAAGATTTCA
28288290 GTAAAAAATAAAATAAGAAAATAGTAGTGTCATGCATTCCGAGCACAATTTCTACAGACTTGACG
66 GTAAAAAATAAAATAAGAAAATAGTAGTGTCATGCATTCCGAGCACAATTTCTACAGACTTGACG
28288355 TGCAGG
131 TGCAGG
28288361 AAACAATAATGAAATTTGTAAACCAACCTTGGGAGGAGTTGCATACTGCACAAGCTAAGATTTCA
1 AAACAATAATGAAATTTGTAAACCAACCTTGGGAGGAGTTGCATACTGCACAAGCTAAGATTTCA
28288426 GTAAAAAATAAAATAAGAAAATAGTAGTGTCATGCATTCCGAGCACAATTTCTACAGACTTGACG
66 GTAAAAAATAAAATAAGAAAATAGTAGTGTCATGCATTCCGAGCACAATTTCTACAGACTTGACG
28288491 TGCAGG
131 TGCAGG
28288497 A
1 A
28288498 TTCTTCCTCC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (136 bp):
AAACAATAATGAAATTTGTAAACCAACCTTGGGAGGAGTTGCATACTGCACAAGCTAAGATTTCA
GTAAAAAATAAAATAAGAAAATAGTAGTGTCATGCATTCCGAGCACAATTTCTACAGACTTGACG
TGCAGG
Found at i:28296407 original size:178 final size:178
Alignment explanation
Indices: 28296105--28296455 Score: 546
Period size: 178 Copynumber: 2.0 Consensus size: 178
28296095 GTTATCCACC
*
28296105 ATATTGAAGGAGGAATTTCACCACCAAAAGAATTCTAGATTGCTATAGCTCCATATTGGAAGGGG
1 ATATTGAAGGAGGAATTTCACCACCAAAAGAATTCTAGATCGCTATAGCTCCATATTGGAAGGGG
28296170 ACACAAGTTACAGAAAAAAGACAGAAATTACAGAAAAGAAAAAAATGTAATCGCAACAAACAAAC
66 ACACAAGTTACAGAAAAAAGACAGAAATTACAGAAAAGAAAAAAATGTAATCGCAACAAACAAAC
*
28296235 AATTGTTTGAGCAGCGTAAGACATGCTTAAAAAACAAGTAATTTCACT
131 AATTGTTTGAGAAGCGTAAGACATGCTTAAAAAACAAGTAATTTCACT
* * *
28296283 ATATTGAAGGAGGCATTTCACCACCAAGAGAATTCTAGATCGCTATAGCTCGATA-TGGAA-GGG
1 ATATTGAAGGAGGAATTTCACCACCAAAAGAATTCTAGATCGCTATAGCTCCATATTGGAAGGGG
** * *
28296346 ACACAAGTTACAGAAAAAATGGTGAGAAATTACAGGAAAAG-AAAAGATGTAATCTCAACAAACA
66 ACACAAGTTACAGAAAAAA--GACAGAAATTACA-GAAAAGAAAAAAATGTAATCGCAACAAACA
* * *
28296410 AATACTTGTTTGAGAAGCGTAAGACATGCTTAAAAAACCAGTAATT
128 AACAATTGTTTGAGAAGCGTAAGACATGCTTAAAAAACAAGTAATT
28296456 GACAATGCAG
Statistics
Matches: 158, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
176 22 0.14
177 5 0.03
178 125 0.79
179 6 0.04
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.22
Consensus pattern (178 bp):
ATATTGAAGGAGGAATTTCACCACCAAAAGAATTCTAGATCGCTATAGCTCCATATTGGAAGGGG
ACACAAGTTACAGAAAAAAGACAGAAATTACAGAAAAGAAAAAAATGTAATCGCAACAAACAAAC
AATTGTTTGAGAAGCGTAAGACATGCTTAAAAAACAAGTAATTTCACT
Found at i:28307424 original size:24 final size:24
Alignment explanation
Indices: 28307392--28307439 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28307382 ATTAATTAGC
28307392 CTATCAGCCTATGATTCTGTAACA
1 CTATCAGCCTATGATTCTGTAACA
28307416 CTATCAGCCTATGATTCTGTAACA
1 CTATCAGCCTATGATTCTGTAACA
28307440 AAGACTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (24 bp):
CTATCAGCCTATGATTCTGTAACA
Found at i:28312111 original size:24 final size:23
Alignment explanation
Indices: 28312052--28312112 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
28312042 GTCTTGATAG
* *
28312052 ATATCTATTTAAT-AAAATATTT
1 ATATATATTTAATAAAAATATAT
28312074 ATATA-ATTTCTAATAAAAATATAT
1 ATATATA-TT-TAATAAAAATATAT
28312098 ATATATATTATAATA
1 ATATATATT-TAATA
28312113 CGTATAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 4 0.12
24 20 0.62
25 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATATATTTAATAAAAATATAT
Found at i:28316475 original size:24 final size:24
Alignment explanation
Indices: 28316448--28316493 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28316438 TAAGATGACT
28316448 ATATAAAAAAAATTAATAAATAAA
1 ATATAAAAAAAATTAATAAATAAA
* * *
28316472 ATATGAATAAAATTATTAAATA
1 ATATAAAAAAAATTAATAAATA
28316494 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
ATATAAAAAAAATTAATAAATAAA
Found at i:28316656 original size:17 final size:18
Alignment explanation
Indices: 28316634--28316675 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28316624 CCCAATGAGA
*
28316634 TAAATTTGGTTTTAAA-T
1 TAAATTTGATTTTAAATT
28316651 TAAATTT-ATTTTAAATT
1 TAAATTTGATTTTAAATT
28316668 TAAATTTG
1 TAAATTTG
28316676 CACAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTGATTTTAAATT
Found at i:28317515 original size:16 final size:16
Alignment explanation
Indices: 28317477--28317522 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
28317467 GTTAACAAAT
28317477 ATTTTAATAATAATAA
1 ATTTTAATAATAATAA
*
28317493 ATATTAATAATAAT-A
1 ATTTTAATAATAATAA
28317508 ATGTTTAATATATAA
1 AT-TTTAATA-ATAA
28317523 AAAAAGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 3 0.12
16 19 0.73
17 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTTTAATAATAATAA
Found at i:28318709 original size:28 final size:28
Alignment explanation
Indices: 28318678--28318947 Score: 176
Period size: 29 Copynumber: 9.4 Consensus size: 28
28318668 CAAAAATTAT
* *
28318678 ATTTTGACCCCGAAC-TTCAGAAAATTCC
1 ATTTTAACCCCGAACTTTC-TAAAATTCC
* **
28318706 ATTTTTGACCCTAAACTTTCTAAAATTCC
1 A-TTTTAACCCCGAACTTTCTAAAATTCC
* * *
28318735 ATTTTAACCCCGAAACTTCCAAAAATTACT
1 ATTTTAACCCCG-AACTTTCTAAAATT-CC
**
28318765 ATTTTAACCCTAAACTTTCTAAAATTCC
1 ATTTTAACCCCGAACTTTCTAAAATTCC
28318793 ATTTTAACCCCG-A-TTTCATCAAAAATTACC
1 ATTTTAACCCCGAACTTTC-T--AAAATT-CC
* * * *
28318823 ATTTT-ACCCTCGTATTTTCCAAAATCCC
1 ATTTTAACCC-CGAACTTTCTAAAATTCC
**
28318851 ATTTTAACCCTAAACTTTCTAAAATTCC
1 ATTTTAACCCCGAACTTTCTAAAATTCC
28318879 ATTTTAACCCCG-A-TTTCATAAAAAATTACC
1 ATTTTAACCCCGAACTTTC-T--AAAATT-CC
* * * *
28318909 ATTTT-ACCCTCGTATTTTCCAAAATCCC
1 ATTTTAACCC-CGAACTTTCTAAAATTCC
28318937 ATTTTTAACCC
1 A-TTTTAACCC
28318948 TAAATTTTCC
Statistics
Matches: 193, Mismatches: 28, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
26 8 0.04
27 4 0.02
28 52 0.27
29 83 0.43
30 36 0.19
31 2 0.01
32 8 0.04
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTTTAACCCCGAACTTTCTAAAATTCC
Found at i:28318777 original size:58 final size:56
Alignment explanation
Indices: 28318678--28318888 Score: 212
Period size: 58 Copynumber: 3.7 Consensus size: 56
28318668 CAAAAATTAT
* *
28318678 ATTTTGACCCCGAACTT-CAGAAAATTCCATTTTTGACCCTAAACTTTCTAAAATTCC
1 ATTTTAACCCCGAACTTCCA-AAAATTCCA-TTTTAACCCTAAACTTTCTAAAATTCC
*
28318735 ATTTTAACCCCGAAACTTCCAAAAATTACTATTTTAACCCTAAACTTTCTAAAATTCC
1 ATTTTAACCCCG-AACTTCCAAAAATT-CCATTTTAACCCTAAACTTTCTAAAATTCC
* ** * * *
28318793 ATTTTAACCCCG-ATTTCATCAAAAATTACCATTTT-ACCCTCGTATTTTCCAAAATCCC
1 ATTTTAACCCCGAACTTC--CAAAAATT-CCATTTTAACCCT-AAACTTTCTAAAATTCC
** * *
28318851 ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCC
1 ATTTTAACCCCGAACTTCCAAAAATTCCATTTTAACCC
28318889 CGATTTCATA
Statistics
Matches: 131, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
56 11 0.08
57 27 0.21
58 86 0.66
59 7 0.05
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (56 bp):
ATTTTAACCCCGAACTTCCAAAAATTCCATTTTAACCCTAAACTTTCTAAAATTCC
Found at i:28318874 original size:86 final size:86
Alignment explanation
Indices: 28318765--28318971 Score: 360
Period size: 86 Copynumber: 2.4 Consensus size: 86
28318755 AAAAATTACT
*
28318765 ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCATCAAAAATTACCATTTTAC
1 ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCATAAAAAATTACCATTTTAC
28318830 CCTCGTATTTTCCAAAATCCC
66 CCTCGTATTTTCCAAAATCCC
28318851 ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCATAAAAAATTACCATTTTAC
1 ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCATAAAAAATTACCATTTTAC
28318916 CCTCGTATTTTCCAAAATCCC
66 CCTCGTATTTTCCAAAATCCC
* * *
28318937 ATTTTTAACCCTAAATTTTCCCAAAATTACATTTT
1 A-TTTTAACCCTAAACTTT-CTAAAATTCCATTTT
28318972 TGCCTTCGAG
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 86 0.75
87 16 0.14
88 13 0.11
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (86 bp):
ATTTTAACCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCATAAAAAATTACCATTTTAC
CCTCGTATTTTCCAAAATCCC
Found at i:28330990 original size:201 final size:200
Alignment explanation
Indices: 28330633--28331084 Score: 613
Period size: 201 Copynumber: 2.3 Consensus size: 200
28330623 AGTAGTTCAA
* * *
28330633 CAAAAC-AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAC
1 CAAAACAAGCGAGGCGATCATCTTCCTAATGAGATACAAAGAAGAATACCAACTCAACGCTCAAC
* * * *
28330697 ACGAGCCAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAATG
66 ACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAG
* * * * *
28330762 GTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCTTGAGGAGATCCAGAGAAG
131 GTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTACCTGAGGAGATCCAGAGAAA
28330827 CGAAT
196 CGAAT
* *
28330832 CAAAACAAGCGAGGCGATCATCTTCCTAATGAGATATAAAGAAGAATACCAGCTCAACGCTCAA-
1 CAAAACAAGCGAGGCGATCATCTTCCTAATGAGATACAAAGAAGAATACCAACTCAACGCTCAAC
* *
28330896 ACGCAAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCATGTCGAAGCAATAAAA
66 ACG--AGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* *
28330961 AGGTTAGCTTCCTGATGAGACATAGAGAAGTGGACCAAATTCGTCTACCTGAGGTGATCCAGAGA
129 AGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTACCTGAGGAGATCCAGAGA
28331026 AACGAAT
194 AACGAAT
* * * * * * * *
28331033 TAAAAC-AGATGATCGCGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCA
1 CAAAACAAG-CGA-GGCGATCATCTTCCTAATGAGATACAAAGAAGAATACCA
28331085 GATCAATGAA
Statistics
Matches: 221, Mismatches: 27, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
199 9 0.04
200 54 0.24
201 126 0.57
202 32 0.14
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (200 bp):
CAAAACAAGCGAGGCGATCATCTTCCTAATGAGATACAAAGAAGAATACCAACTCAACGCTCAAC
ACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAG
GTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTACCTGAGGAGATCCAGAGAAA
CGAAT
Found at i:28331441 original size:17 final size:18
Alignment explanation
Indices: 28331419--28331461 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
28331409 GCCCAATGAG
*
28331419 ATAAATTTGGTTTTAAA-
1 ATAAATTTGATTTTAAAT
28331436 ATAAATTT-ATTTTAAAT
1 ATAAATTTGATTTTAAAT
*
28331453 TTAAATTTG
1 ATAAATTTG
28331462 TACAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
ATAAATTTGATTTTAAAT
Found at i:28331495 original size:17 final size:17
Alignment explanation
Indices: 28331432--28331495 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
28331422 AATTTGGTTT
*
28331432 TAAA-ATAAATTTATTT
1 TAAATATAAATTTATTA
* *
28331448 TAAATTTAAATTT-GTA
1 TAAATATAAATTTATTA
* * *
28331464 CAAAATTTAAGTTTATTA
1 -TAAATATAAATTTATTA
28331482 TAAATATAAATTTA
1 TAAATATAAATTTA
28331496 AAATTAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 5 0.14
17 29 0.81
18 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATATAAATTTATTA
Found at i:28333499 original size:28 final size:28
Alignment explanation
Indices: 28333459--28333646 Score: 87
Period size: 29 Copynumber: 6.6 Consensus size: 28
28333449 TGAGCTGTCC
** *
28333459 AAAAATTATATTTTGACCCCGAACTTCA
1 AAAAATTCCATTTTTACCCCGAACTTCA
* * **
28333487 AAAAATTCCATTTTTTACCTCAAACTTTT
1 AAAAATTCCA-TTTTTACCCCGAACTTCA
* *
28333516 CAAAATTCCATTTTTACCTCGAAACTTCCA
1 AAAAATTCCATTTTTACCCCG-AACTT-CA
* * * **
28333546 AAATAA--CTATTTTGACCCCAAACTTTT
1 AAA-AATTCCATTTTTACCCCGAACTTCA
* * * * *
28333573 CAAAATTCCATTTTTAACCCTAATTTTCC
1 AAAAATTCCATTTTTACCCCGAA-CTTCA
28333602 AAAAATTACCA-TTTTACCCTCGAACTTTC-
1 AAAAATT-CCATTTTTACCC-CGAAC-TTCA
* *
28333631 CAAAATCCCATTTTTA
1 AAAAATTCCATTTTTA
28333647 AACCCGATTT
Statistics
Matches: 117, Mismatches: 32, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 38 0.32
29 62 0.53
30 11 0.09
31 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCCGAACTTCA
Found at i:28333549 original size:57 final size:57
Alignment explanation
Indices: 28333476--28333646 Score: 163
Period size: 57 Copynumber: 3.0 Consensus size: 57
28333466 ATATTTTGAC
*
28333476 CCCG-AACTTCAAAAAATTCCATTTTTTACCTCAAACTTTTCAAAATTCCATTTTTA
1 CCCGAAACTTCCAAAAATTCCATTTTTTACCTCAAACTTTTCAAAATTCCATTTTTA
** * *
28333532 CCTCGAAACTTCC-AAAATAAC-TATTTTGACCCCAAACTTTTCAAAATTCCATTTTTAA
1 CC-CGAAACTTCCAAAAATTCCAT-TTTTTACCTCAAACTTTTCAAAATTCCATTTTT-A
* ** * * *
28333590 CCCTAATTTTCCAAAAATTACCA--TTTTACCCTCGAACTTTCCAAAATCCCATTTTTA
1 CCCGAAACTTCCAAAAATT-CCATTTTTTA-CCTCAAACTTTTCAAAATTCCATTTTTA
28333647 AACCCGATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
56 3 0.03
57 51 0.55
58 37 0.40
59 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (57 bp):
CCCGAAACTTCCAAAAATTCCATTTTTTACCTCAAACTTTTCAAAATTCCATTTTTA
Found at i:28333557 original size:29 final size:28
Alignment explanation
Indices: 28333488--28333646 Score: 126
Period size: 29 Copynumber: 5.5 Consensus size: 28
28333478 CGAACTTCAA
* *
28333488 AAAATTCCATTTTTTACCTCAAACTTTTC
1 AAAATACCA-TTTTTACCTCAAACTTTCC
*
28333517 AAAATTCCATTTTTACCTCGAAAC-TTCC
1 AAAATACCATTTTTACCTC-AAACTTTCC
* * * *
28333545 AAAATAACTATTTTGACCCCAAACTTTTC
1 AAAAT-ACCATTTTTACCTCAAACTTTCC
* * *
28333574 AAAATTCCATTTTTAACC-CTAATTTTCC
1 AAAATACCATTTTT-ACCTCAAACTTTCC
*
28333602 AAAAATTACCA-TTTTACCCTCGAACTTTCC
1 -AAAA-TACCATTTTTA-CCTCAAACTTTCC
*
28333632 AAAATCCCATTTTTA
1 AAAATACCATTTTTA
28333647 AACCCGATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
28 40 0.38
29 53 0.50
30 12 0.11
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATACCATTTTTACCTCAAACTTTCC
Found at i:28333607 original size:86 final size:87
Alignment explanation
Indices: 28333467--28333636 Score: 215
Period size: 86 Copynumber: 2.0 Consensus size: 87
28333457 CCAAAAATTA
* *
28333467 TATTTTGACCCCGAACTTCAAAAAATTCCATTTTTTACCTCAAACTTTTCAAAATT-CCATTTTT
1 TATTTTGACCCCAAACTTCAAAAAATTCCATTTTTAACCTCAAACTTTTCAAAATTACCA-TTTT
28333531 A-CCTCGAAAC-TTCCAAAATAAC
65 ACCCTCG-AACTTTCCAAAATAAC
*** *
28333553 TATTTTGACCCCAAACTTTTCAAAATTCCATTTTTAACC-CTAA-TTTTCCAAAAATTACCATTT
1 TATTTTGACCCCAAACTTCAAAAAATTCCATTTTTAACCTCAAACTTTT-C-AAAATTACCATTT
28333616 TACCCTCGAACTTTCCAAAAT
64 TACCCTCGAACTTTCCAAAAT
28333637 CCCATTTTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
84 4 0.05
85 4 0.05
86 48 0.66
87 17 0.23
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (87 bp):
TATTTTGACCCCAAACTTCAAAAAATTCCATTTTTAACCTCAAACTTTTCAAAATTACCATTTTA
CCCTCGAACTTTCCAAAATAAC
Found at i:28333635 original size:58 final size:58
Alignment explanation
Indices: 28333499--28333733 Score: 218
Period size: 59 Copynumber: 4.1 Consensus size: 58
28333489 AAATTCCATT
* ** * *
28333499 TTTTA-CCTCAAACTTTTCAAAATTCCATTTTT-ACCTCGAAACTTCC-AAAATAACTA
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACC-CGAATTTTCCAAAAATTACCA
* *
28333555 TTTTGACCC-CAAACTTTTCAAAATTCCATTTTTAACCCTAATTTTCCAAAAATTACCA
1 TTTT-ACCCTCAAACTTTCCAAAATTCCATTTTTAACCCGAATTTTCCAAAAATTACCA
* *
28333613 TTTTACCCTCGAACTTTCCAAAATCCCATTTTTAAACCCG-A-TTTCATCAAAAATTACCA
1 TTTTACCCTCAAACTTTCCAAAATTCCATTTTT-AACCCGAATTTTC--CAAAAATTACCA
* * * *
28333672 CTTTACCCTCGAA-TATTCTAAAA-TCCTATTTTTAACCCCGAATTTTCCCAAAATTA-CA
1 TTTTACCCTCAAACT-TTCCAAAATTCC-ATTTTTAA-CCCGAATTTTCCAAAAATTACCA
28333730 TTTT
1 TTTT
28333734 TGCCCCCGAG
Statistics
Matches: 152, Mismatches: 14, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
56 4 0.03
57 40 0.26
58 49 0.32
59 54 0.36
60 1 0.01
61 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCGAATTTTCCAAAAATTACCA
Found at i:28333733 original size:29 final size:28
Alignment explanation
Indices: 28333512--28333733 Score: 98
Period size: 29 Copynumber: 7.7 Consensus size: 28
28333502 TACCTCAAAC
* * *
28333512 TTTT-CAAAATTCCATTTTTACCTCGAA
1 TTTTCCAAAATTACATTTTAACCCCGAA
** * * *
28333539 ACTTCCAAAATAACTATTTTGACCCCAAA
1 TTTTCCAAAATTAC-ATTTTAACCCCGAA
* *
28333568 CTTTT-CAAAATTCCATTTTTAA-CCCTAA
1 -TTTTCCAAAATTACA-TTTTAACCCCGAA
28333596 TTTTCCAAAAATTACCATTTT-ACCCTCGAA
1 TTTTCC-AAAATTA-CATTTTAACCC-CGAA
* ** *
28333626 CTTTCCAAAATCCCATTTTTAAACCCG-A
1 TTTTCCAAAATTACA-TTTTAACCCCGAA
* *
28333654 TTTCATCAAAAATTACCACTTT-ACCCTCGAA
1 TTT--TCCAAAATTA-CATTTTAACCC-CGAA
* * *
28333685 TATTCTAAAATCCTA-TTTTTAACCCCGAA
1 TTTTCCAAAAT--TACATTTTAACCCCGAA
28333714 TTTTCCCAAAATTACATTTT
1 TTTT-CCAAAATTACATTTT
28333734 TGCCCCCGAG
Statistics
Matches: 142, Mismatches: 32, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
27 6 0.04
28 22 0.15
29 70 0.49
30 37 0.26
31 7 0.05
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTTCCAAAATTACATTTTAACCCCGAA
Found at i:28339429 original size:26 final size:26
Alignment explanation
Indices: 28339393--28339444 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28339383 ATCCTGGGTG
28339393 TAATTCTGGACACGTTCATGCAGCGA
1 TAATTCTGGACACGTTCATGCAGCGA
* *
28339419 TAATTTTGGACATGTTCATGCAGCGA
1 TAATTCTGGACACGTTCATGCAGCGA
28339445 CATTCCTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (26 bp):
TAATTCTGGACACGTTCATGCAGCGA
Found at i:28339595 original size:37 final size:37
Alignment explanation
Indices: 28339554--28339624 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
28339544 ATTCCTGTGG
* * *
28339554 CGACAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGA
1 CGACAATTTTGGGCGCAATCTAGAAGTGCTCATGCGA
*
28339591 CGACAATTTTGTGCGCAATCTAGAAGTGCTCATG
1 CGACAATTTTGGGCGCAATCTAGAAGTGCTCATG
28339625 TAGCGACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (37 bp):
CGACAATTTTGGGCGCAATCTAGAAGTGCTCATGCGA
Found at i:28339632 original size:37 final size:36
Alignment explanation
Indices: 28339553--28339632 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
28339543 TATTCCTGTG
* * * *
28339553 GCGACAGTTTTGGGTGCAATCTGGAAGTGCTCATGC
1 GCGACAATTTTGGGCGCAATCTAGAAGTGCTCATGA
*
28339589 GACGACAATTTTGTGCGCAATCTAGAAGTGCTCATGTA
1 G-CGACAATTTTGGGCGCAATCTAGAAGTGCTCATG-A
28339627 GCGACA
1 GCGACA
28339633 TTAGTAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 1 0.03
37 35 0.95
38 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (36 bp):
GCGACAATTTTGGGCGCAATCTAGAAGTGCTCATGA
Found at i:28342147 original size:43 final size:43
Alignment explanation
Indices: 28342025--28342157 Score: 178
Period size: 43 Copynumber: 3.1 Consensus size: 43
28342015 GTACCAGATT
* * * * * **
28342025 GTGTGTGTATACTATATTGGGACACACAGACGTGTATCAGACC
1 GTGTGTGTATACTGTCTTGGGACACGCAGGCATGTGCCAGACC
*
28342068 GTGTGTGTATACTGTCTT-GGACAAGCAGGCATGTGCCAGACC
1 GTGTGTGTATACTGTCTTGGGACACGCAGGCATGTGCCAGACC
*
28342110 GTGTGTGTATACTGTCTTGGGACACGCGGGCATGTGCCAGACC
1 GTGTGTGTATACTGTCTTGGGACACGCAGGCATGTGCCAGACC
28342153 GTGTG
1 GTGTG
28342158 AATACACTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 36 0.46
43 43 0.54
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (43 bp):
GTGTGTGTATACTGTCTTGGGACACGCAGGCATGTGCCAGACC
Found at i:28350668 original size:23 final size:24
Alignment explanation
Indices: 28350620--28350668 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28350610 AGTGACACTT
*
28350620 ATTTAATTAATTTGTATTTTTATC
1 ATTTAATTAATTAGTATTTTTATC
28350644 ATTTAATT-ATTAGTAATTTTT-TC
1 ATTTAATTAATTAGT-ATTTTTATC
28350667 AT
1 AT
28350669 AATTTATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTAATTAATTAGTATTTTTATC
Found at i:28352619 original size:39 final size:39
Alignment explanation
Indices: 28352561--28352788 Score: 164
Period size: 39 Copynumber: 5.8 Consensus size: 39
28352551 AGTGATCAAA
* * *
28352561 ATACTGAACT-GATAGTGACATTGTAAACAGTACGAAACT
1 ATACTGAACTAG-CAGTGACACTGTAAACACTACGAAACT
* *
28352600 ATATTGAACTAGCAGTGACATTGTAAACACTACGAAACT
1 ATACTGAACTAGCAGTGACACTGTAAACACTACGAAACT
* * *
28352639 ATGCTGAGC-AGACAGTGACACTGTAAACACTACGAAGCT
1 ATACTGAACTAG-CAGTGACACTGTAAACACTACGAAACT
* * * **
28352678 ATACCG-ACTTAGCAGTGACGCTGTAAACACTGC-AATGTT
1 ATACTGAAC-TAGCAGTGACACTGTAAACACTACGAA-ACT
* * * * *
28352717 ATTCTGAACT-GACGGTGACACTATAAACATTAC-ACGACT
1 ATACTGAACTAG-CAGTGACACTGTAAACACTACGA-AACT
* *
28352756 ATAACTGAA-TAGTAGTGACATTGTAAACACTAC
1 AT-ACTGAACTAGCAGTGACACTGTAAACACTAC
28352789 TAGAACATTA
Statistics
Matches: 149, Mismatches: 30, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
38 6 0.04
39 132 0.89
40 11 0.07
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (39 bp):
ATACTGAACTAGCAGTGACACTGTAAACACTACGAAACT
Found at i:28352735 original size:78 final size:78
Alignment explanation
Indices: 28352564--28352788 Score: 197
Period size: 78 Copynumber: 2.9 Consensus size: 78
28352554 GATCAAAATA
* * * ** *
28352564 CTGAACTGATAGTGACATTGTAAACAGTACGAAACTATATTGAACTAGCAGTGACATTGTAAACA
1 CTGAACTGACAGTGACACTGTAAACACTACGAAACTATACCGAACTAGCAGTGACACTGTAAACA
28352629 CTACGAAACTATG
66 CTACGAAACTATG
* * * *
28352642 CTGAGCAGACAGTGACACTGTAAACACTACGAAGCTATACCG-ACTTAGCAGTGACGCTGTAAAC
1 CTGAACTGACAGTGACACTGTAAACACTACGAAACTATACCGAAC-TAGCAGTGACACTGTAAAC
* ** *
28352706 ACTGC-AATGTTATT
65 ACTACGAA-ACTATG
* * * * * * *
28352720 CTGAACTGACGGTGACACTATAAACATTAC-ACGACTATAACTGAA-TAGTAGTGACATTGTAAA
1 CTGAACTGACAGTGACACTGTAAACACTACGA-AACTAT-ACCGAACTAGCAGTGACACTGTAAA
28352783 CACTAC
64 CACTAC
28352789 TAGAACATTA
Statistics
Matches: 116, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
77 5 0.04
78 107 0.92
79 3 0.03
80 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (78 bp):
CTGAACTGACAGTGACACTGTAAACACTACGAAACTATACCGAACTAGCAGTGACACTGTAAACA
CTACGAAACTATG
Done.