Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 94 of 187
Found at i:28059548 original size:14 final size:16
Alignment explanation
Indices: 28059517--28059549 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28059507 ATAATGCATT
28059517 AAACCACATAACACCA
1 AAACCACATAACACCA
28059533 AAACCAC-TAA-ACCA
1 AAACCACATAACACCA
28059547 AAA
1 AAA
28059550 TGATATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.61, C:0.33, G:0.00, T:0.06
Consensus pattern (16 bp):
AAACCACATAACACCA
Found at i:28061272 original size:16 final size:16
Alignment explanation
Indices: 28061253--28061285 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28061243 AGAATTTATT
28061253 TTAAAAT-TTATTTAAA
1 TTAAAATATT-TTTAAA
28061269 TTAAAATATTTTTAAA
1 TTAAAATATTTTTAAA
28061285 T
1 T
28061286 GTATTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATATTTTTAAA
Found at i:28062957 original size:19 final size:19
Alignment explanation
Indices: 28062929--28062968 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28062919 AGTTCTAATA
*
28062929 TTTTTTAATA-AATTTTCAC
1 TTTTTAAATATAATTTT-AC
28062948 TTTTTAAATATAATTTTAC
1 TTTTTAAATATAATTTTAC
28062967 TT
1 TT
28062969 ATATCTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAAATATAATTTTAC
Found at i:28063282 original size:31 final size:31
Alignment explanation
Indices: 28063234--28063292 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
28063224 TTTCCCCGTG
28063234 TTTTTATTAGGGCTTTTAAG-GTTTATTAGGA
1 TTTTTATTAGGGCTTTT-AGTGTTTATTAGGA
28063265 TTTTTAATTAGGG-TTTTAGTGTTTATTA
1 TTTTT-ATTAGGGCTTTTAGTGTTTATTA
28063293 TTTATGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 2 0.08
31 17 0.65
32 7 0.27
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (31 bp):
TTTTTATTAGGGCTTTTAGTGTTTATTAGGA
Found at i:28065147 original size:54 final size:54
Alignment explanation
Indices: 28065043--28065208 Score: 156
Period size: 67 Copynumber: 2.9 Consensus size: 54
28065033 TATTTATCAC
* *
28065043 GATAAATATTAGATTAAATTTAATATTAAATCTTATTAAAATAATATAAATGTA
1 GATAAATATTAAATTAAATTTAATATTAAATCTCATTAAAATAATATAAATGTA
* *
28065097 GATAAATATTAAATTAAATTTAATATTAAGATCATCACTTTAATATTAAATTATAAAATACTATT
1 GATAAATATTAAATTAAATTTAATATTAA-ATC-TCA--TTAA-AAT-AA-TAT--AA-A-T-GT
28065162 AA
54 -A
*
28065164 GATAAGTATTAAATTAAATTTAATATTAAA-CT-ATTAAAATAATAT
1 GATAAATATTAAATTAAATTTAATATTAAATCTCATTAAAATAATAT
28065209 TATTTTTTGA
Statistics
Matches: 93, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
54 28 0.30
55 3 0.03
56 2 0.02
58 7 0.08
59 4 0.04
60 4 0.04
61 7 0.08
63 3 0.03
64 2 0.02
65 2 0.02
66 2 0.02
67 29 0.31
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (54 bp):
GATAAATATTAAATTAAATTTAATATTAAATCTCATTAAAATAATATAAATGTA
Found at i:28073412 original size:62 final size:62
Alignment explanation
Indices: 28073315--28073441 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
28073305 ACTTAGTCGC
*
28073315 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACCTCCTAAA
1 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTATCCATCAATACCTCCTAAA
28073377 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTATCCATCAATACCTCCTAAA
1 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTATCCATCAATACCTCCTAAA
28073439 ATA
1 ATA
28073442 CCGTATCCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (62 bp):
ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTATCCATCAATACCTCCTAAA
Found at i:28075565 original size:13 final size:13
Alignment explanation
Indices: 28075520--28075577 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 13
28075510 TAGAACACGG
*
28075520 AAAAAATTTTAAT
1 AAAAAATATTAAT
**
28075533 AAAAAA-ATTTCT
1 AAAAAATATTAAT
*
28075545 TAAAAATATTAAT
1 AAAAAATATTAAT
*
28075558 AAAAAATA-GAAT
1 AAAAAATATTAAT
28075570 AAAAAATA
1 AAAAAATA
28075578 GAATTTGGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 19 0.53
13 17 0.47
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAAAATATTAAT
Found at i:28075570 original size:12 final size:12
Alignment explanation
Indices: 28075555--28075581 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28075545 TAAAAATATT
28075555 AATAAAAAATAG
1 AATAAAAAATAG
28075567 AATAAAAAATAG
1 AATAAAAAATAG
28075579 AAT
1 AAT
28075582 TTGGATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
AATAAAAAATAG
Found at i:28075682 original size:31 final size:32
Alignment explanation
Indices: 28075612--28075684 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
28075602 AGCAAAAAAT
** **
28075612 TAAGAGAGAATTTGAGAGATTTTTGAGAGTTGA
1 TAAGAGA-AATTTGAGAGATTTAAGAGAGTAAA
*
28075645 T-TGAGAAATTTGAGAGATTTAAGAGAG-AAA
1 TAAGAGAAATTTGAGAGATTTAAGAGAGTAAA
28075675 TAAGAGAAAT
1 TAAGAGAAAT
28075685 GTAAGAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.06
31 26 0.79
32 4 0.12
33 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (32 bp):
TAAGAGAAATTTGAGAGATTTAAGAGAGTAAA
Found at i:28079505 original size:21 final size:23
Alignment explanation
Indices: 28079453--28079505 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
28079443 AAAAAATTGT
*
28079453 TGTTAGTTTTAACAAGTTTTTTA
1 TGTTAGTTTTAACAAGTTTTATA
* *
28079476 TTTTTGTTTT-AC-AGTTTTATA
1 TGTTAGTTTTAACAAGTTTTATA
28079497 TGTTAGTTT
1 TGTTAGTTT
28079506 GCGCTTTGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 15 0.60
22 2 0.08
23 8 0.32
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (23 bp):
TGTTAGTTTTAACAAGTTTTATA
Found at i:28087759 original size:17 final size:17
Alignment explanation
Indices: 28087737--28087769 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28087727 ATATTTAATA
28087737 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
28087754 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
28087770 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:28088679 original size:9 final size:9
Alignment explanation
Indices: 28088662--28088697 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
28088652 TGAGTTTTCG
28088662 AATTCGAAT
1 AATTCGAAT
*
28088671 AACTCGAAT
1 AATTCGAAT
28088680 AATTCGAAT
1 AATTCGAAT
28088689 AATTCGAAT
1 AATTCGAAT
28088698 GTCAAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28089116 original size:20 final size:20
Alignment explanation
Indices: 28089077--28089116 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28089067 TTATTCCCCA
* *
28089077 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTCTCACCCT
*
28089097 AAACTTTTTCTTCTCACCCT
1 AAACTTTTTATTCTCACCCT
28089117 TTACTCTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTCTCACCCT
Found at i:28089812 original size:18 final size:20
Alignment explanation
Indices: 28089785--28089828 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28089775 GGTATCATAT
*
28089785 ATTT-ATTCAT-ATTTTTC-
1 ATTTAATTCATAATTTTACG
28089802 ATTTAATTCATAATTTTACG
1 ATTTAATTCATAATTTTACG
28089822 ATTTAAT
1 ATTTAAT
28089829 CCATTTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 6 0.26
20 7 0.30
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTAATTCATAATTTTACG
Found at i:28100628 original size:26 final size:25
Alignment explanation
Indices: 28100572--28100647 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
28100562 ATGAATTTTC
* * *
28100572 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATGAGGGTAAAATTG
*
28100597 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28100623 TCAAAATTTTATTG-GGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28100648 AGATGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 21 0.48
26 23 0.52
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATGAGGGTAAAATTG
Found at i:28100646 original size:25 final size:25
Alignment explanation
Indices: 28100572--28100647 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
28100562 ATGAATTTTC
** * *
28100572 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATTGGGGTAAAATTG
* *
28100597 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTATTG-GGGTAAAATTG
28100623 TCAAAATTTTATTGGGGTAAAATTG
1 TCAAAATTTTATTGGGGTAAAATTG
28100648 AGATGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATTGGGGTAAAATTG
Found at i:28111310 original size:59 final size:59
Alignment explanation
Indices: 28111244--28111362 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
28111234 GCATTTTCAA
28111244 TTTAGTAAATTGAATTTTATAACTCAGTGAATCCATGCCTATTTTATCCTTAATTTTGC
1 TTTAGTAAATTGAATTTTATAACTCAGTGAATCCATGCCTATTTTATCCTTAATTTTGC
*
28111303 TTTAGTAAATTGAATTTTATAACTCAGTGAATCCATGCCTATTTTATCGTTAATTTTGC
1 TTTAGTAAATTGAATTTTATAACTCAGTGAATCCATGCCTATTTTATCCTTAATTTTGC
28111362 T
1 T
28111363 ATCTTTTTGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (59 bp):
TTTAGTAAATTGAATTTTATAACTCAGTGAATCCATGCCTATTTTATCCTTAATTTTGC
Found at i:28113141 original size:12 final size:12
Alignment explanation
Indices: 28113125--28113156 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28113115 CGCTTCTTTA
28113125 CTTACTTACTTG
1 CTTACTTACTTG
*
28113137 TTTACTTACTTG
1 CTTACTTACTTG
28113149 CTTACTTA
1 CTTACTTA
28113157 AATAACTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (12 bp):
CTTACTTACTTG
Found at i:28113507 original size:50 final size:53
Alignment explanation
Indices: 28113453--28113597 Score: 161
Period size: 50 Copynumber: 2.7 Consensus size: 53
28113443 TTGTCATATT
* * *
28113453 GGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCT-T-ATCTC-
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTATAACCTCA
* * * *
28113503 GGTGCCAACGCCCTGTCCCAGACATGGTCTTATATGGGACCTCTCATAACCTCAA
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT-ATAACCTC-A
* *
28113558 TGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
28113598 TCTCATTCCC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 38 0.49
52 1 0.01
53 4 0.05
56 35 0.45
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.25
Consensus pattern (53 bp):
GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTATAACCTCA
Found at i:28115135 original size:46 final size:47
Alignment explanation
Indices: 28115033--28115135 Score: 172
Period size: 47 Copynumber: 2.2 Consensus size: 47
28115023 ATTGTTTTCA
*
28115033 AGTTATTGCATCGACAACCATCCTCACAATTTGTCTTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTGTATTATTTATATCT
* *
28115080 AGTTATTGCATCGATAACTATCCTCACAATTT-TATTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTGTATTATTTATATCT
28115126 AGTTATTGCA
1 AGTTATTGCA
28115136 CCAACATTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 23 0.43
47 30 0.57
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (47 bp):
AGTTATTGCATCGACAACCATCCTCACAATTTGTATTATTTATATCT
Found at i:28142767 original size:22 final size:22
Alignment explanation
Indices: 28142739--28142800 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
28142729 TTTATTGTTC
28142739 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
28142761 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
28142783 AGCCATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
28142801 TAACATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:28151349 original size:20 final size:21
Alignment explanation
Indices: 28151326--28151369 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
28151316 GTAAACGTAT
28151326 TTTTTTAT-TTTTAAATTTAA
1 TTTTTTATATTTTAAATTTAA
*
28151346 -TTTTTATATTTTAATTTTAA
1 TTTTTTATATTTTAAATTTAA
28151366 TTTT
1 TTTT
28151370 GAGACTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTATATTTTAAATTTAA
Found at i:28151378 original size:20 final size:20
Alignment explanation
Indices: 28151335--28151381 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28151325 TTTTTTTATT
* * *
28151335 TTTAAATTTAATTTTTATAT
1 TTTAAATTTAATTTTGAGAC
*
28151355 TTTAATTTTAATTTTGAGAC
1 TTTAAATTTAATTTTGAGAC
28151375 TTTAAAT
1 TTTAAAT
28151382 CTCTATACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAAATTTAATTTTGAGAC
Found at i:28151615 original size:20 final size:21
Alignment explanation
Indices: 28151565--28151619 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
28151555 ATAAAACCAT
**
28151565 AAAAATAAAATAAATATTTTA
1 AAAAATAAAATTTATATTTTA
28151586 AAAAATTAAAATTTAT-TTTTA
1 AAAAA-TAAAATTTATATTTTA
28151607 AAAAAT-AAATTTA
1 AAAAATAAAATTTA
28151620 AAATTTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.23
20 1 0.03
21 15 0.48
22 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATAAAATTTATATTTTA
Found at i:28151927 original size:16 final size:17
Alignment explanation
Indices: 28151893--28151930 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28151883 CGGTTCAAAT
* *
28151893 AAAATAAAATATTTTTA
1 AAAATAAAATAATTATA
28151910 AAAATAAAA-AATTATA
1 AAAATAAAATAATTATA
28151926 AAAAT
1 AAAAT
28151931 TGATTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAAAATAATTATA
Found at i:28152190 original size:17 final size:18
Alignment explanation
Indices: 28152154--28152195 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28152144 ATCTTTAAAA
28152154 TTCAAAAATAAAAAATAT
1 TTCAAAAATAAAAAATAT
* *
28152172 TTTAAAAATATAAAA-AT
1 TTCAAAAATAAAAAATAT
28152189 TTCAAAA
1 TTCAAAA
28152196 TTCAATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TTCAAAAATAAAAAATAT
Found at i:28153806 original size:21 final size:21
Alignment explanation
Indices: 28153770--28153826 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28153760 AGCTACAGAA
* * *
28153770 TTCTACTAGTAGAACTGAAAG
1 TTCTACTAATATAACTCAAAG
* * *
28153791 TTCTACTGATATAACTCTAGG
1 TTCTACTAATATAACTCAAAG
28153812 TTCTACTAATATAAC
1 TTCTACTAATATAAC
28153827 CCGGACTTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (21 bp):
TTCTACTAATATAACTCAAAG
Found at i:28157775 original size:30 final size:29
Alignment explanation
Indices: 28157737--28157793 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
28157727 GCAATATCAC
* *
28157737 ACATAAATTTTGATTTTATGTAATTTTAT
1 ACATAAATTTTAATTTGATGTAATTTTAT
*
28157766 ACATGAAATTTTAATTTGATTTAATTTT
1 ACAT-AAATTTTAATTTGATGTAATTTT
28157794 CAAAAATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (29 bp):
ACATAAATTTTAATTTGATGTAATTTTAT
Found at i:28158458 original size:17 final size:17
Alignment explanation
Indices: 28158438--28158473 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28158428 TGGAGCATGA
*
28158438 TTGAAAACCAAGTTTGG
1 TTGAAAACCAAATTTGG
28158455 TTGAAAACCAAATTTGG
1 TTGAAAACCAAATTTGG
28158472 TT
1 TT
28158474 CAGTTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (17 bp):
TTGAAAACCAAATTTGG
Found at i:28163851 original size:2 final size:2
Alignment explanation
Indices: 28163846--28163883 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
28163836 ATTTTTATTT
28163846 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28163884 TATGAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28163854 original size:17 final size:17
Alignment explanation
Indices: 28163845--28163883 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
28163835 TATTTTTATT
28163845 TTATATATATATATATA
1 TTATATATATATATATA
28163862 TTATATATATATATATA
1 TTATATATATATATATA
28163879 -TATAT
1 TTATAT
28163884 TATGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATATATATATATA
Found at i:28163856 original size:19 final size:19
Alignment explanation
Indices: 28163841--28163881 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28163831 AATATATTTT
*
28163841 TATTTTATATATATATATA
1 TATTATATATATATATATA
28163860 TATTATATATATATATATA
1 TATTATATATATATATATA
28163879 TAT
1 TAT
28163882 ATTATGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATATATATATATATA
Found at i:28163896 original size:21 final size:21
Alignment explanation
Indices: 28163846--28163886 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28163836 ATTTTTATTT
28163846 TATATATATATATATATTATA
1 TATATATATATATATATTATA
28163867 TATATATATATATATATTAT
1 TATATATATATATATATTAT
28163887 GAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATATATATATATATTATA
Found at i:28164302 original size:21 final size:21
Alignment explanation
Indices: 28164287--28164335 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
28164277 TTTATTTATT
28164287 AAAATAATAATTTTATAAATA
1 AAAATAATAATTTTATAAATA
28164308 AAAATAATAATTTTATAAAT-
1 AAAATAATAATTTTATAAATA
28164328 AAAATAAT
1 AAAATAAT
28164336 TTAAGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATAATTTTATAAATA
Found at i:28164863 original size:15 final size:14
Alignment explanation
Indices: 28164828--28164870 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
28164818 GTTTGTGAGT
*
28164828 TTTTTTATAAAAATA
1 TTTTTTAT-AAATTA
28164843 TTTTTTATAAATTA
1 TTTTTTATAAATTA
28164857 TTATTTTAATAAAT
1 TT-TTTT-ATAAAT
28164871 AAATTTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 12 0.48
16 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTTATAAATTA
Found at i:28164990 original size:14 final size:14
Alignment explanation
Indices: 28164966--28165001 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
28164956 ATCGAAAATA
28164966 TGAATTTTTAATTTT
1 TGAA-TTTTAATTTT
*
28164981 TTAATTTTAATTTT
1 TGAATTTTAATTTT
28164995 TGAATTT
1 TGAATTT
28165002 GTAAGAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
TGAATTTTAATTTT
Found at i:28165969 original size:21 final size:19
Alignment explanation
Indices: 28165935--28165973 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
28165925 TTAAAAATTA
28165935 TAAAATTATTTAAATTATT
1 TAAAATTATTTAAATTATT
28165954 TAAAATATATTTTAAATTAT
1 TAAAAT-TA-TTTAAATTAT
28165974 ATTATTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATTATTTAAATTATT
Found at i:28168281 original size:23 final size:21
Alignment explanation
Indices: 28168225--28168285 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
28168215 ATCAGTATAT
28168225 GACACATAAGTGCCT-AAAAC
1 GACACATAAGTGCCTGAAAAC
* *
28168245 GACACACGAGGTGCCTGAAATAC
1 GACACA-TAAGTGCCTGAAA-AC
28168268 GACACATAAAGTGCCTGA
1 GACACAT-AAGTGCCTGA
28168286 TTGGCAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 7 0.21
22 3 0.09
23 17 0.52
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (21 bp):
GACACATAAGTGCCTGAAAAC
Found at i:28169212 original size:18 final size:19
Alignment explanation
Indices: 28169191--28169226 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28169181 ATTATTTATC
28169191 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
28169209 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
28169227 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:28169235 original size:19 final size:18
Alignment explanation
Indices: 28169195--28169237 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
28169185 TTTATCTAAT
*
28169195 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
28169213 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
28169232 AAATAT
1 AAATAT
28169238 AAATATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:28170991 original size:21 final size:21
Alignment explanation
Indices: 28170965--28171023 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
28170955 CAAACACGCT
28170965 CGTGTGTCCAAAACACAAGCC
1 CGTGTGTCCAAAACACAAGCC
* * *** * *
28170986 CGTGTGGCTAAGGGACATGGC
1 CGTGTGTCCAAAACACAAGCC
28171007 CGTGTGTCCAAAACACA
1 CGTGTGTCCAAAACACA
28171024 CGCAAGTGTG
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (21 bp):
CGTGTGTCCAAAACACAAGCC
Found at i:28176380 original size:16 final size:16
Alignment explanation
Indices: 28176359--28176395 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
28176349 TTTTATAAAA
28176359 GATGCTTGGATAAATT
1 GATGCTTGGATAAATT
28176375 GATGCTTGGATAAATT
1 GATGCTTGGATAAATT
28176391 GATGC
1 GATGC
28176396 AGATGCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (16 bp):
GATGCTTGGATAAATT
Found at i:28178677 original size:382 final size:381
Alignment explanation
Indices: 28178176--28178892 Score: 1281
Period size: 382 Copynumber: 1.9 Consensus size: 381
28178166 AGCAGAGGAG
**
28178176 CACCCCCCATGTGCCGCTTCAACGTCGGAGTCCCCAACCATCTAGTTTTGATCGGAATTAACGAG
1 CACCCCCCATGTGCCGCTTCAACGTCGGAGTCCCCAACCATCTAGTTCCGATCGGAATTAACGAG
* * *
28178241 GGGTTCGACGGCAGACTTAACCAAGTACGGGCTCTTCCCCTTTTTTATTTTGTTACCCAGTTTAT
66 GGGCTCGACAGCAGACTTAACCAAGTACGGGCTCTTCCCCTTTTTTATTTTGTTACCCAGATTAT
* *
28178306 GAAAAATAAATCCAAAGAAAAAAGAAAGATAATAAAGAAGAGGAAAAAGGAAGATCGGAATCAGA
131 GAAAAACAAATCCAAAGAAAAAAGAAAAATAATAAAGAAGAGGAAAAAGGAAGATCGGAATCAGA
*
28178371 AATCACCTCCAAAGTATGCTATATTTGTTATTTTTTTGAAAGTTTTTTTCTGTATCCTTGTATTG
196 AATCACCTCCAAAGTATGCTATATTTGCTATTTTTTTGAAAG-TTTTTTCTGTATCCTTGTATTG
*
28178436 ATGTTGTGTCTAGTTACAAATTCTGGAAAATGGCTTTATAGTCGAAGATAAAACGAAATAAAAAA
260 ATGTTGTGTCTAGTTACAAATTCTGGAAAATGGCTTTATAGCCGAAGATAAAACGAAATAAAAAA
28178501 TACCACCAAAACGACGCCGTTTTGAAACCATTGCCTCGACATCAAACGACGTCGGAC
325 TACCACCAAAACGACGCCGTTTTGAAACCATTGCCTCGACATCAAACGACGTCGGAC
* *
28178558 CACCCCCCATGTGCCGCTTCAACGTCGGAGTCCCCAACCATCTGGTTCCGATCGGAATTAACTAG
1 CACCCCCCATGTGCCGCTTCAACGTCGGAGTCCCCAACCATCTAGTTCCGATCGGAATTAACGAG
* * * *
28178623 GGGCTCGACAGCGGACTTAACCAGGTATGGGCTCTTCCCCTTTTTTATTTTGTTACTCAGATTAT
66 GGGCTCGACAGCAGACTTAACCAAGTACGGGCTCTTCCCCTTTTTTATTTTGTTACCCAGATTAT
28178688 GAAAAACAAATCCAAAGAAAAAAGAAAAATAATAAAGAAGAGGAAAAAGGAAGATCGGAATCAGA
131 GAAAAACAAATCCAAAGAAAAAAGAAAAATAATAAAGAAGAGGAAAAAGGAAGATCGGAATCAGA
*
28178753 AATCACCTCTAAAGTATGCTATATTTGCTATTTTTTTGAAAGTTTTTTCTGTATCCTTGTATTGA
196 AATCACCTCCAAAGTATGCTATATTTGCTATTTTTTTGAAAGTTTTTTCTGTATCCTTGTATTGA
28178818 TGTTGTGTCTAGTTACAAATTCTGGAAAATGGCTTTATAGCCGAAGATAAAACGAAATAAAAAAT
261 TGTTGTGTCTAGTTACAAATTCTGGAAAATGGCTTTATAGCCGAAGATAAAACGAAATAAAAAAT
28178883 ACCACCAAAA
326 ACCACCAAAA
28178893 TATATTTCGC
Statistics
Matches: 319, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
381 97 0.30
382 222 0.70
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (381 bp):
CACCCCCCATGTGCCGCTTCAACGTCGGAGTCCCCAACCATCTAGTTCCGATCGGAATTAACGAG
GGGCTCGACAGCAGACTTAACCAAGTACGGGCTCTTCCCCTTTTTTATTTTGTTACCCAGATTAT
GAAAAACAAATCCAAAGAAAAAAGAAAAATAATAAAGAAGAGGAAAAAGGAAGATCGGAATCAGA
AATCACCTCCAAAGTATGCTATATTTGCTATTTTTTTGAAAGTTTTTTCTGTATCCTTGTATTGA
TGTTGTGTCTAGTTACAAATTCTGGAAAATGGCTTTATAGCCGAAGATAAAACGAAATAAAAAAT
ACCACCAAAACGACGCCGTTTTGAAACCATTGCCTCGACATCAAACGACGTCGGAC
Found at i:28179823 original size:21 final size:18
Alignment explanation
Indices: 28179783--28179836 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
28179773 GGAAAGTTCA
* *
28179783 ATATTATTATTTTTAATAT
1 ATATAATTATATTTAA-AT
28179802 ATATAATTATATATTAAAT
1 ATATAATTATAT-TTAAAT
28179821 ATATAATTATATTTAA
1 ATATAATTATATTTAA
28179837 TAAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATAATTATATTTAAAT
Found at i:28184531 original size:20 final size:20
Alignment explanation
Indices: 28184506--28184549 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28184496 ATATTTTAAA
*
28184506 TAAATTT-ATTTTTTATTATC
1 TAAATTTAATATTTT-TTATC
28184526 TAAATTTAATATTTTTTATC
1 TAAATTTAATATTTTTTATC
28184546 TAAA
1 TAAA
28184550 CTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAATTTAATATTTTTTATC
Found at i:28184555 original size:22 final size:21
Alignment explanation
Indices: 28184516--28184561 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
28184506 TAAATTTATT
*
28184516 TTTTATTATCTAAATTTAATA
1 TTTTATTATCTAAATTTAAAA
28184537 TTTT-TTATCTAAACTTTTAAAA
1 TTTTATTATCTAAA--TTTAAAA
28184559 TTT
1 TTT
28184562 CGAGCAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 9 0.41
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATTATCTAAATTTAAAA
Found at i:28188717 original size:165 final size:165
Alignment explanation
Indices: 28188445--28188772 Score: 620
Period size: 165 Copynumber: 2.0 Consensus size: 165
28188435 CTCGATAAGA
28188445 AACTTACTTACAACTTTAGACTTTTCTATCCGCTTTTTCTTATCCTTACATTTTGGAGGATCCTT
1 AACTTACTTACAACTTTAGACTTTTCTATCCGCTTTTTCTTATCCTTACATTTTGGAGGATCCTT
*
28188510 GAGTTGTTCGTTTACGTACGTTCTTTCGTGCGAGTTGTAACACGATCCCCATTACTTTTTCTGGT
66 GAGTTGTTCGTTTACGTACGTTCTTTCGTACGAGTTGTAACACGATCCCCATTACTTTTTCTGGT
28188575 TAACATTCAAGTTTTTCCTTTTGTAAAATTTACTT
131 TAACATTCAAGTTTTTCCTTTTGTAAAATTTACTT
*
28188610 AACTTACTTACAACTTTATACTTTTCTATCCGCTTTTTCTTATCCTTACATTTTGGAGGATCCTT
1 AACTTACTTACAACTTTAGACTTTTCTATCCGCTTTTTCTTATCCTTACATTTTGGAGGATCCTT
*
28188675 GAGTTGTTCGTTTACGTACGTTTTTTCGTACGAGTTGTAACACGATCCCCATTACTTTTTCTGGT
66 GAGTTGTTCGTTTACGTACGTTCTTTCGTACGAGTTGTAACACGATCCCCATTACTTTTTCTGGT
*
28188740 TAACTTTCAAGTTTTTCCTTTTGTAAAATTTAC
131 TAACATTCAAGTTTTTCCTTTTGTAAAATTTAC
28188773 CTGACGCTAT
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 159 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (165 bp):
AACTTACTTACAACTTTAGACTTTTCTATCCGCTTTTTCTTATCCTTACATTTTGGAGGATCCTT
GAGTTGTTCGTTTACGTACGTTCTTTCGTACGAGTTGTAACACGATCCCCATTACTTTTTCTGGT
TAACATTCAAGTTTTTCCTTTTGTAAAATTTACTT
Found at i:28193241 original size:28 final size:28
Alignment explanation
Indices: 28193209--28193268 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
28193199 TTTTTATTTA
*
28193209 TTTATT-TATTATTATTATTTTTATGATT
1 TTTATTATATTATTA-TATTATTATGATT
* * *
28193237 TTTATTATCTTGTTATATTATTATTATT
1 TTTATTATATTATTATATTATTATGATT
28193265 TTTA
1 TTTA
28193269 AAAAATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTATTATATTATTATATTATTATGATT
Found at i:28197940 original size:16 final size:16
Alignment explanation
Indices: 28197916--28197957 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
28197906 CAAATTTTTC
28197916 AAAAA-AAAAAG-AAA
1 AAAAAGAAAAAGCAAA
28197930 GAAAAAGAAAAAGCAAA
1 -AAAAAGAAAAAGCAAA
28197947 AAAAAGAAAAA
1 AAAAAGAAAAA
28197958 AGGAGAGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.20
16 17 0.68
17 3 0.12
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGCAAA
Found at i:28199329 original size:42 final size:43
Alignment explanation
Indices: 28199264--28199418 Score: 161
Period size: 43 Copynumber: 3.6 Consensus size: 43
28199254 AGATTGCAGA
*
28199264 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAG
1 TCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAG
* * * * * **
28199307 TC-TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAG
1 TCTTATCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCCCCAG
*
28199349 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAG
1 -TCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAG
* * * *
28199393 CCTTATCTCCCTGAGTAGCAGCGGAG
1 TCTTATCTCCCTAAGCAGCAGTGGAG
28199419 TAGGTTAAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
42 28 0.32
43 31 0.36
44 28 0.32
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.24
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAG
Found at i:28199389 original size:86 final size:87
Alignment explanation
Indices: 28199238--28199648 Score: 357
Period size: 86 Copynumber: 4.7 Consensus size: 87
28199228 CCTGTATTGA
* * *
28199238 CAGCGAAGTAGATTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCC
1 CAGCGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCC
*
28199303 CCAGTC-TATCTCCCTGAGCAG
66 CCAGCCTTATCTCCCTGAGCAG
* *
28199324 CAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCC
1 CAGCGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCC
*
28199389 CCAGCCTTATCTCCCTGAGTAG
66 CCAGCCTTATCTCCCTGAGCAG
* * * * *
28199411 CAGCGGAGTAGGTTAAAAAAATTGTAGATATTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA
1 CAGCGGAGTAGGTT--GAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGT
* * ** **
28199476 CACTAGCCTTGCCTCCCTCG-GTGG
64 CCCCAGCCTTATCTCCCT-GAGCAG
* * * ** * * * * *
28199500 CAGCGGAGCAGGCT-AAAGATAGCAGATCTTGCCTCCCTGTA-CTGACAGTGAAGCAGATCGAAA
1 CAGCGGAGTAGGTTGAAA-ATTGCAGATCTTATCTCCCT-AAGCAG-TAGTGGAGCAGATCGAAG
*** **
28199563 AAACCAATCTTATCTCCCTG-GACAG
63 TCCCCAGCCTTATCTCCCTGAG-CAG
* * ** ***
28199588 CAGTGGAATAGGTT-AAAATTATAGATCTTATCTCCCTAAGCAGTAGCATAGCAGATCGAAG
1 CAGCGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
28199649 ACACTAGCCT
Statistics
Matches: 260, Mismatches: 56, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
86 82 0.32
87 63 0.24
88 42 0.16
89 72 0.28
90 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (87 bp):
CAGCGGAGTAGGTTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCC
CCAGCCTTATCTCCCTGAGCAG
Found at i:28199667 original size:174 final size:174
Alignment explanation
Indices: 28199428--28199771 Score: 598
Period size: 174 Copynumber: 2.0 Consensus size: 174
28199418 GTAGGTTAAA
* ** *
28199428 AAAATTGTAGATATTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCTTGCCTCCC
1 AAAATTATAGATATTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGACACTAGCCTTGCCTCCC
*
28199493 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTGACAGTGAAGCAGAT
66 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTAACAGTGAAGCAGAT
28199558 CGAAAAAACCAATCTTATCTCCCTGGACAGCAGTGGAATAGGTT
131 CGAAAAAACCAATCTTATCTCCCTGGACAGCAGTGGAATAGGTT
* *
28199602 AAAATTATAGATCTTATCTCCCTAAGCAGTAGCATAGCAGATCGAAGACACTAGCCTTGCCTCCC
1 AAAATTATAGATATTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGACACTAGCCTTGCCTCCC
* *
28199667 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCTTGTACTAACAGTGAAGTAGAT
66 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTAACAGTGAAGCAGAT
*
28199732 CGAAAAAACCAATCTTATCTCCCTGGTCAGCAGTGGAATA
131 CGAAAAAACCAATCTTATCTCCCTGGACAGCAGTGGAATA
28199772 ATTTGAGGAT
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 160 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (174 bp):
AAAATTATAGATATTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGACACTAGCCTTGCCTCCC
TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTAACAGTGAAGCAGAT
CGAAAAAACCAATCTTATCTCCCTGGACAGCAGTGGAATAGGTT
Found at i:28199971 original size:218 final size:218
Alignment explanation
Indices: 28199568--28199989 Score: 634
Period size: 218 Copynumber: 1.9 Consensus size: 218
28199558 CGAAAAAACC
* *
28199568 AATCTTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTATAGATCTTATCTCCCTAAGCAGTA
1 AATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTA
*
28199633 GCATAGCAGATCGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCGGAGCAGGCTAAAGATAGCA
66 GCAGAGCAGATCGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCGGAGCAGGCTAAAGATAGCA
* *
28199698 GATCTTGCCTCCTTGTACTAACAGTGAAGTAGATCGAAAAAACCAATCTTATCTCCCTGG-TCAG
131 GATCTTGCCTCCTTGTACTAACAGTGAAGCAGATCGAAAAAACCAATCCTATCTCCCTGGAT-AG
28199762 CAGTGGAATAATTTGAGGATTGAG
195 CAGTGGAATAATTTGAGGATTGAG
*
28199786 AATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTA
1 AATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTA
* * * *
28199851 GCGGAGCAGATCGAAGACACTAGCCTTGCCT-CCTTGGTGGCAGCGGAGCATGTTAAAGATAGCA
66 GCAGAGCAGATCGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCGGAGCAGGCTAAAGATAGCA
* * ***** *
28199915 GATCTTGCCTTCC-TGTACTGATAGTGAAGCAGATCGAAGATTGTGAATCCTATCTCCTTGGATA
131 GATCTTGCC-TCCTTGTACTAACAGTGAAGCAGATCGAA-AAAACCAATCCTATCTCCCTGGATA
28199979 GCAGTGGAATA
194 GCAGTGGAATA
28199990 GATTAAAAAT
Statistics
Matches: 183, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
217 61 0.33
218 121 0.66
219 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (218 bp):
AATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTA
GCAGAGCAGATCGAAGACACTAGCCTTGCCTCCCTCGGTGGCAGCGGAGCAGGCTAAAGATAGCA
GATCTTGCCTCCTTGTACTAACAGTGAAGCAGATCGAAAAAACCAATCCTATCTCCCTGGATAGC
AGTGGAATAATTTGAGGATTGAG
Found at i:28200019 original size:175 final size:174
Alignment explanation
Indices: 28199779--28200131 Score: 519
Period size: 175 Copynumber: 2.0 Consensus size: 174
28199769 ATAATTTGAG
* *
28199779 GATTGAGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTA
1 GATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGATTAAAATTACAGATCTTATCTCCCTA
* * * * * *
28199844 AGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCTTGGTGGC-AGCGGAGCATGTTAAA
66 AGCAGTAGCAGAGCAAATCGAAGACACCAGCCTTGCCTCCCTGG-GGCAAACGGAGCAGGTTAAA
* *
28199908 GATAGCAGATCTTGCCTTCCTGTACTGATAGTGAAGCAGATCGAA
130 GATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
* * *
28199953 GATTGTGAATCCTATCTCCTTGGATAGCAGTGGAATAGATTAAAAATTACAGATCTTATCTCCCT
1 GATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGATT-AAAATTACAGATCTTATCTCCCT
* * * *
28200018 AAGCAGTAGCAGAGCAAATCGAAGATACCAGCCTTGCCTCCCTGGGTCATAATGGAGCAGGTTGA
65 AAGCAGTAGCAGAGCAAATCGAAGACACCAGCCTTGCCTCCCTGGGGCA-AACGGAGCAGGTTAA
28200083 AGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
129 AGATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
28200129 GAT
1 GAT
28200132 ACCAGCCTTA
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
174 38 0.24
175 63 0.40
176 58 0.36
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (174 bp):
GATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGATTAAAATTACAGATCTTATCTCCCTA
AGCAGTAGCAGAGCAAATCGAAGACACCAGCCTTGCCTCCCTGGGGCAAACGGAGCAGGTTAAAG
ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
Found at i:28200146 original size:175 final size:173
Alignment explanation
Indices: 28199791--28200316 Score: 560
Period size: 176 Copynumber: 3.0 Consensus size: 173
28199781 TTGAGAATCC
* *
28199791 TATCTCCCTGGACAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGA
1 TATCTCCCTGGATAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAGA
* * * * * * *
28199856 GCAGATCGAAGACACTAGCCTTGCCTCCTTGGTGGC-AGCGGAGCATGTTAAAGATAGCAGATCT
66 GCAGATCGAAGATACCAGCCTTGCCTCCCTGG-GTCTAGTGGAGCAGGTTGAAGATAGCAGATCT
* * *** *
28199920 TGCCTTCCTGTACTGATAGTGAAGCAGATCGAAGATTGTGAATCC-
130 TGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGA-T-ACCAGCCT
* * *
28199965 TATCTCCTTGGATAGCAGTGGAATAGATTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
1 TATCTCCCTGGATAGTAGTGGAATAGGTT-AAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
* *
28200030 AGCAAATCGAAGATACCAGCCTTGCCTCCCTGGGTCATAATGGAGCAGGTTGAAGATAGCAGATC
65 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTC-TAGTGGAGCAGGTTGAAGATAGCAGATC
28200095 TTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCT
129 TTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCT
* * ** * * ** * *
28200140 TATCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGA-TAGCAAATCTTGCCTTCCTGTACCGACAGT
1 TATCTCCCTGGATAGTAGTGGAATAGGTT-AAAATTA-CAGATCTTATC-TCC-CTA-AG-CAGT
* * *
28200204 -G-A-AGTAGATCGAAGATACCAACCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGC
60 AGCAGAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGG-TCTAGTGGAGCAGGTTGAAGATAGC
* * * * *
28200266 AGATCTTGCCTTTCTGCACCAACAGTGAAGCAGATCAAAGACACCAGCCT
124 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCT
28200316 T
1 T
28200317 GCTTCCCTGG
Statistics
Matches: 298, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
174 32 0.11
175 97 0.33
176 159 0.53
177 4 0.01
178 2 0.01
179 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (173 bp):
TATCTCCCTGGATAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAGA
GCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTCTAGTGGAGCAGGTTGAAGATAGCAGATCTT
GCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCT
Found at i:28200184 original size:88 final size:88
Alignment explanation
Indices: 28200030--28200370 Score: 495
Period size: 88 Copynumber: 3.9 Consensus size: 88
28200020 GCAGTAGCAG
* ** *
28200030 AGCAAATCGAAGATACCAGCCTTGCCTCCCTGGGTCATAATGGAGCAGGTTGAAGATAGCAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
28200095 TTGCCTTCCTGTACCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
** *
28200118 AGCAGATCGAAGATACCAGCCTTATCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
28200183 TTGCCTTCCTGTACCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
* *
28200206 AGTAGATCGAAGATACCAACCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
* * *
28200271 TTGCCTTTCTGCACCAACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
* * * * * *
28200294 AGCAGATCAAAGACACCAGCCTTGCTTCCCTGGGTTGT-GCGGAGCAGGCTGAAGATAGTAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
* *
28200358 TTGTCTTCATGTA
66 TTGCCTTCCTGTA
28200371 TTAGCATGAA
Statistics
Matches: 226, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
87 32 0.14
88 194 0.86
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (88 bp):
AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
TTGCCTTCCTGTACCGACAGTGA
Found at i:28200274 original size:44 final size:44
Alignment explanation
Indices: 28200050--28200276 Score: 170
Period size: 44 Copynumber: 5.2 Consensus size: 44
28200040 AGATACCAGC
* *
28200050 CTTGCCTCCCTGGGTCATAATGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGAT
* *** * * * * * *
28200094 CTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCTGGGTCG-TAGTGGAGCAGGTTGAAGATAGCAGAT
** * *
28200138 CTTATCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAAAT
1 CTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGAT
* *** * * * * * * *
28200182 CTTGCCTTCCTGTACCGACAGTGAAGTAGATCGAAGATACCA-AC
1 CTTGCCTCCCTGGGTCG-TAGTGGAGCAGGTTGAAGATAGCAGAT
*
28200226 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGAT
28200270 CTTGCCT
1 CTTGCCT
28200277 TTCTGCACCA
Statistics
Matches: 127, Mismatches: 52, Indels: 8
0.68 0.28 0.04
Matches are distributed among these distances:
43 37 0.29
44 53 0.42
45 37 0.29
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGAT
Found at i:28200408 original size:44 final size:44
Alignment explanation
Indices: 28200353--28200586 Score: 290
Period size: 44 Copynumber: 5.3 Consensus size: 44
28200343 TGAAGATAGT
*
28200353 AGATCTTGTCTTCATGTATTAGCATGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
*** ** * *
28200397 AGATCTTGTCTTCCCATATTGGTGGTAAAGTAGATCGAAGA-AAGC
1 AGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCAAAGATAA-C
* * *
28200442 AAATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGGTAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
* * ** *
28200486 AGATCTTGTCTTCACGTATTGGCGTGAAGTAGATTGAAGATGAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
*
28200530 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
28200574 AGATCTTGTCTTC
1 AGATCTTGTCTTC
28200587 CCATACTAGT
Statistics
Matches: 155, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
44 121 0.78
45 34 0.22
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
Found at i:28200453 original size:89 final size:90
Alignment explanation
Indices: 28200355--28200614 Score: 391
Period size: 88 Copynumber: 2.9 Consensus size: 90
28200345 AAGATAGTAG
* *
28200355 ATCTTGTCTTCATGTATTAGCATGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATATTGGT
1 ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATATTGGT
*
28200420 GGTAAAGTAGATCGAAGAAAG-CAA
66 GGTGAAGTAGATCGAAGAAAGACAA
* * *
28200444 ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGGTAGCAGATCTTGTCTTCACGTATTGG-
1 ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATATTGGT
* * * *
28200508 CGTGAAGTAGATTGAAG-ATGACAG
66 GGTGAAGTAGATCGAAGAAAGACAA
* *
28200532 ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTAGT
1 ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATATTGGT
28200597 GGTGAAGTAGATCGAAGA
66 GGTGAAGTAGATCGAAGA
28200615 TCACATCTAG
Statistics
Matches: 151, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
87 2 0.01
88 75 0.50
89 74 0.49
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (90 bp):
ATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATATTGGT
GGTGAAGTAGATCGAAGAAAGACAA
Found at i:28200556 original size:88 final size:89
Alignment explanation
Indices: 28200344--28200614 Score: 366
Period size: 89 Copynumber: 3.1 Consensus size: 89
28200334 GGAGCAGGCT
* * * *
28200344 GAAGATAGTAGATCTTGTCTTCATGTATTAGCATGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
* *
28200409 CCCATATTGGTGGTAAAGTAGATC
66 CACATATTGGTCGTAAAGTAGATC
* *
28200433 GAAGAAAGCAAATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGGTAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
* * *
28200498 CACGTATTGG-CGTGAAGTAGATT
66 CACATATTGGTCGTAAAGTAGATC
*
28200521 GAAG-ATGACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
1 GAAGAAAG-CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
* * * * *
28200585 TCCCATACTAGTGGTGAAGTAGATC
65 TCACATATTGGTCGTAAAGTAGATC
28200610 GAAGA
1 GAAGA
28200615 TCACATCTAG
Statistics
Matches: 159, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
87 2 0.01
88 75 0.47
89 82 0.52
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (89 bp):
GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
CACATATTGGTCGTAAAGTAGATC
Found at i:28205705 original size:18 final size:18
Alignment explanation
Indices: 28205682--28205717 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28205672 ACAACATCTT
28205682 TAACATCGCCTTCCTCTA
1 TAACATCGCCTTCCTCTA
28205700 TAACATCGCCTTCCTCTA
1 TAACATCGCCTTCCTCTA
28205718 AGGTACGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.06, T:0.33
Consensus pattern (18 bp):
TAACATCGCCTTCCTCTA
Found at i:28207421 original size:22 final size:22
Alignment explanation
Indices: 28207396--28207438 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28207386 TAAAATAGGG
28207396 ATGGTATCGCAATATCGAAGGT
1 ATGGTATCGCAATATCGAAGGT
* *
28207418 ATGGTATCGCGATATTGAAGG
1 ATGGTATCGCAATATCGAAGG
28207439 CAGACCACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (22 bp):
ATGGTATCGCAATATCGAAGGT
Found at i:28209201 original size:34 final size:34
Alignment explanation
Indices: 28209158--28209226 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28209148 CAAGATACTT
28209158 AGCATCAATTTAACAGATTTACAAGTGAATTGAA
1 AGCATCAATTTAACAGATTTACAAGTGAATTGAA
28209192 AGCATCAATTTAACAGATTTACAAGTGAATTGAA
1 AGCATCAATTTAACAGATTTACAAGTGAATTGAA
28209226 A
1 A
28209227 ACCAAGACCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (34 bp):
AGCATCAATTTAACAGATTTACAAGTGAATTGAA
Found at i:28209241 original size:34 final size:33
Alignment explanation
Indices: 28209169--28209242 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
28209159 GCATCAATTT
* ***
28209169 AACAGATTTACAAGTGAATTGAAAGCATCAATTT
1 AACAGATTTACAAGTGAATTGAAACCA-CAACCG
28209203 AACAGATTTACAAGTGAATTGAAAACCA-AGACCG
1 AACAGATTTACAAGTGAATTG-AAACCACA-ACCG
28209237 AACAGA
1 AACAGA
28209243 AACCTAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 1 0.03
34 28 0.82
35 5 0.15
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (33 bp):
AACAGATTTACAAGTGAATTGAAACCACAACCG
Found at i:28216301 original size:27 final size:26
Alignment explanation
Indices: 28216271--28216460 Score: 107
Period size: 27 Copynumber: 7.1 Consensus size: 26
28216261 ACATAAGGCC
28216271 ATAACAGTCATTTTATCTCCTA-GGGGT
1 ATAACAGTCATTTTA-C-CCTAGGGGGT
*
28216298 ATAACAATCATTTTACCCTATGGGGGT
1 ATAACAGTCATTTTACCCTA-GGGGGT
**
28216325 ATTTCAGTCATTTTACCCTATGGGGGT
1 ATAACAGTCATTTTACCCTA-GGGGGT
***
28216352 ATTTTAGTCATTTT-CCCTATGGGGGT
1 ATAACAGTCATTTTACCCTA-GGGGGT
** * * *
28216378 ATTTCGGTTATTTTACCCTATTGGGGT
1 ATAACAGTCATTTTACCCTA-GGGGGT
**** *
28216405 ATTTTGGTCATTTTACCTTATGGGGGT
1 ATAACAGTCATTTTACCCTA-GGGGGT
** *
28216432 ATTTC-GATCATTTTACCCTATAGGGGT
1 ATAACAG-TCATTTTACCCTA-GGGGGT
28216459 AT
1 AT
28216461 TTTTGTTATT
Statistics
Matches: 143, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
25 4 0.03
26 25 0.17
27 114 0.80
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (26 bp):
ATAACAGTCATTTTACCCTAGGGGGT
Found at i:28216461 original size:27 final size:27
Alignment explanation
Indices: 28216304--28216583 Score: 325
Period size: 27 Copynumber: 10.4 Consensus size: 27
28216294 GGGTATAACA
28216304 ATCATTTTACCCTATGGGGGTATTTC-
1 ATCATTTTACCCTATGGGGGTATTTCG
*
28216330 AGTCATTTTACCCTATGGGGGTATTT-T
1 A-TCATTTTACCCTATGGGGGTATTTCG
28216357 AGTCATTTT-CCCTATGGGGGTATTTCG
1 A-TCATTTTACCCTATGGGGGTATTTCG
* * * *
28216384 GTTATTTTACCCTATTGGGGTATTTTG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
28216411 GTCATTTTACCTTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
28216438 ATCATTTTACCCTATAGGGGTATTTTTG
1 ATCATTTTACCCTATGGGGGTA-TTTCG
* *
28216466 -TTATTTTACCCTATGGGGTTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
** * *
28216492 GCCATTTTACCCTATGAGGGTATTTTG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
28216519 ATCATTTTACCTTATTGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
28216546 ATCATTTTACCCTATAGGGGTATTTTG
1 ATCATTTTACCCTATGGGGGTATTTCG
*
28216573 GTCATTTTACC
1 ATCATTTTACC
28216584 TATTTTGGGG
Statistics
Matches: 216, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
26 27 0.12
27 185 0.86
28 4 0.02
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
ATCATTTTACCCTATGGGGGTATTTCG
Found at i:28216584 original size:54 final size:54
Alignment explanation
Indices: 28216305--28216583 Score: 393
Period size: 54 Copynumber: 5.2 Consensus size: 54
28216295 GGTATAACAA
* *
28216305 TCATTTTACCCTATGGGGGTATTTC-AGTCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTATAGGGGTATTTTGG
* * *
28216359 TCATTTT-CCCTATGGGGGTATTTCGGTTATTTTACCCTATTGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGG
* *
28216412 TCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTTG
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGG
* * ** *
28216466 TTATTTTACCCTATGGGGTTATTTCGGCCATTTTACCCTAT-GAGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAG-GGGTATTTTGG
* *
28216520 TCATTTTACCTTATTGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGG
28216574 TCATTTTACC
1 TCATTTTACC
28216584 TATTTTGGGG
Statistics
Matches: 198, Mismatches: 23, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
53 49 0.25
54 148 0.75
55 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.46
Consensus pattern (54 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTTGG
Found at i:28222015 original size:45 final size:46
Alignment explanation
Indices: 28221930--28222017 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
28221920 GAATGAATAT
*
28221930 AAATAGAGAAATGGAAAACATTAAAAAATGATTATGGTTTTCTTTG
1 AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCTTTG
* *** *
28221976 AAATAGAGAAAT-GAAATCATTTGGAAATGAATGTGGTTTTCT
1 AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCT
28222018 CAAAATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 24 0.67
46 12 0.33
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (46 bp):
AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCTTTG
Found at i:28223806 original size:18 final size:18
Alignment explanation
Indices: 28223770--28223807 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28223760 AATATATATT
* *
28223770 TTAAAATATTTTAATTAA
1 TTAAAATATTTAAAATAA
28223788 TTAAAATATTTAAAATAA
1 TTAAAATATTTAAAATAA
28223806 TT
1 TT
28223808 GAGATCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATATTTAAAATAA
Found at i:28224556 original size:26 final size:26
Alignment explanation
Indices: 28224508--28224558 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
28224498 AGCCCGGCCC
* *
28224508 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTTAAAATAAAAAATAAAAAATT
28224534 ATTTTTAAAATAAAAAAATAAAAAA
1 ATTTTTAAAAT-AAAAAATAAAAAA
28224559 AATTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTTTTAAAATAAAAAATAAAAAATT
Found at i:28228929 original size:34 final size:35
Alignment explanation
Indices: 28228885--28228951 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28228875 CAGTAAAATA
28228885 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
28228919 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
28228952 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:28234435 original size:21 final size:22
Alignment explanation
Indices: 28234393--28234435 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
28234383 TACTTCAAAC
*
28234393 CTTTCAAACATCTTAGAAAATT
1 CTTTCAAACATCTTACAAAATT
28234415 CTTT-AAACA-CTTACAATAATT
1 CTTTCAAACATCTTACAA-AATT
28234436 TTGCAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (22 bp):
CTTTCAAACATCTTACAAAATT
Found at i:28235384 original size:34 final size:34
Alignment explanation
Indices: 28235341--28235410 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
28235331 AATTGTTGTG
28235341 TTCATTGTTCTATATTTTCTTCTAGCTTTCTTAA
1 TTCATTGTTCTATATTTTCTTCTAGCTTTCTTAA
28235375 TTCATTGTTCTATATTTTCTTCTAGCTTTCTTAA
1 TTCATTGTTCTATATTTTCTTCTAGCTTTCTTAA
28235409 TT
1 TT
28235411 TAAAACAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (34 bp):
TTCATTGTTCTATATTTTCTTCTAGCTTTCTTAA
Found at i:28239115 original size:26 final size:27
Alignment explanation
Indices: 28239086--28239169 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 27
28239076 TGTAAATTAA
*
28239086 TAATAATAAATAAT-TT-AATCATATTT
1 TAATAATAAATAATATTAAAT-ATAATT
28239112 TAAT-AT-AATAATTATTAAATATAATT
1 TAATAATAAATAA-TATTAAATATAATT
28239138 TAATAA-AAATAATGA-T--ATATAATT
1 TAATAATAAATAAT-ATTAAATATAATT
28239162 TAATAATA
1 TAATAATA
28239170 TTCTTAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
24 19 0.38
25 4 0.08
26 17 0.34
27 10 0.20
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
TAATAATAAATAATATTAAATATAATT
Found at i:28239143 original size:24 final size:24
Alignment explanation
Indices: 28239116--28239183 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
28239106 ATATTTTAAT
28239116 ATAATAATTATTAAATATAATTTA
1 ATAATAATTATTAAATATAATTTA
* * * *
28239140 ATAAAAATAATGATATATAATTTA
1 ATAATAATTATTAAATATAATTTA
*
28239164 ATAAT-ATTCTT-AATATAATT
1 ATAATAATTATTAAATATAATT
28239184 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 8 0.23
23 3 0.09
24 24 0.69
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
ATAATAATTATTAAATATAATTTA
Found at i:28252162 original size:28 final size:28
Alignment explanation
Indices: 28252131--28252190 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
28252121 TTTAATCTCT
28252131 TAGGGGGTATAAC-AGTCATTTTACCCTA
1 TAGGGGGTATAACTA-TCATTTTACCCTA
**
28252159 TA-GGGGTATTTCTATCATTTTACCCTA
1 TAGGGGGTATAACTATCATTTTACCCTA
28252186 T-GGGG
1 TAGGGG
28252191 ACATTTCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (28 bp):
TAGGGGGTATAACTATCATTTTACCCTA
Found at i:28252176 original size:27 final size:26
Alignment explanation
Indices: 28252146--28252343 Score: 181
Period size: 27 Copynumber: 7.4 Consensus size: 26
28252136 GGTATAACAG
28252146 TCATTTTACCCTATAGGGGTATTTCTA
1 TCATTTTACCCTAT-GGGGTATTTCTA
* *
28252173 TCATTTTACCCTATGGGGACATTTCGA
1 TCATTTTACCCTATGGGG-TATTTCTA
28252200 TCATTTTACCCT-TGGGTGTATTT-TGA
1 TCATTTTACCCTATGGG-GTATTTCT-A
28252226 TCGA-TTTACCCTATGGGGGTATTTCGT-
1 TC-ATTTTACCCTAT-GGGGTATTTC-TA
* *
28252253 TCAATTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTCTA
* *
28252280 TCATTTTACCCTAGAGGGGTATTTCGA
1 TCATTTTACCCTA-TGGGGTATTTCTA
* * *
28252307 TCATTTTATCGTATTGGGGTATTT-TGG
1 TCATTTTACCCTA-TGGGGTATTTCT-A
28252334 TCATTTTACC
1 TCATTTTACC
28252344 TATTTTGAGG
Statistics
Matches: 144, Mismatches: 14, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
26 25 0.17
27 114 0.79
28 4 0.03
29 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (26 bp):
TCATTTTACCCTATGGGGTATTTCTA
Found at i:28252209 original size:54 final size:53
Alignment explanation
Indices: 28252146--28252343 Score: 233
Period size: 54 Copynumber: 3.7 Consensus size: 53
28252136 GGTATAACAG
**
28252146 TCATTTTACCCTATAGGGGTATTTCT-ATCATTTTACCCTATGGGGACATTTCGA
1 TCATTTTACCCTAT-GGGGTATTT-TGATCATTTTACCCTATGGGGGTATTTCGA
*
28252200 TCATTTTACCCT-TGGGTGTATTTTGATCGA-TTTACCCTATGGGGGTATTTCGT
1 TCATTTTACCCTATGGG-GTATTTTGATC-ATTTTACCCTATGGGGGTATTTCGA
* *
28252253 TCAATTTACCCTATGAGGGTATTTCGATCATTTTACCCTA-GAGGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTTGATCATTTTACCCTATG-GGGGTATTTCGA
* * *
28252307 TCATTTTATCGTATTGGGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTA-TGGGGTATTTTGATCATTTTACC
28252344 TATTTTGAGG
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
52 4 0.03
53 43 0.34
54 74 0.59
55 4 0.03
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (53 bp):
TCATTTTACCCTATGGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGA
Found at i:28252346 original size:80 final size:80
Alignment explanation
Indices: 28252146--28252343 Score: 231
Period size: 80 Copynumber: 2.5 Consensus size: 80
28252136 GGTATAACAG
28252146 TCATTTTACCCTATAGGGGTATTTCT-ATCATTTTACCCTATGGGGACATTTCGATCATTTTACC
1 TCATTTTACCCTATAGGGGTATTT-TGATCATTTTACCCTATGGGGACATTTCGATCATTTTACC
* * *
28252210 CTTGGGTGTATTTTGA
65 CTAGGGGGTATTTCGA
* * * * *
28252226 TCGA-TTTACCCTATGGGGGTATTTCGTTCAATTTACCCTATGAGGG-TATTTCGATCATTTTAC
1 TC-ATTTTACCCTATAGGGGTATTTTGATCATTTTACCCTATG-GGGACATTTCGATCATTTTAC
28252289 CCTAGAGGGGTATTTCGA
64 CCTAG-GGGGTATTTCGA
* * * *
28252307 TCATTTTATCGTATTGGGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTATAGGGGTATTTTGATCATTTTACC
28252344 TATTTTGAGG
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
80 56 0.57
81 43 0.43
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (80 bp):
TCATTTTACCCTATAGGGGTATTTTGATCATTTTACCCTATGGGGACATTTCGATCATTTTACCC
TAGGGGGTATTTCGA
Found at i:28254639 original size:25 final size:25
Alignment explanation
Indices: 28254582--28254718 Score: 101
Period size: 25 Copynumber: 5.5 Consensus size: 25
28254572 TAGTACTTCA
*
28254582 CCACAAAGGCTT-TCACA-AGATTAG
1 CCACAAAGGCTTCTCAGATA-ATTAG
*
28254606 CCACAAAGGCTTCTCAGATTA-TACG
1 CCACAAAGGCTTCTCAGATAATTA-G
*
28254631 CCACAAAGGCTTTTCTCA-A-CATTAG
1 CCACAAAGGC--TTCTCAGATAATTAG
*
28254656 CAACAAAGGCTTC-CTAGATAA-TACG
1 CCACAAAGGCTTCTC-AGATAATTA-G
* *
28254681 CCACAAAGGCTTTTCACA-AGATTAG
1 CCACAAAGGCTTCTCAGATA-ATTAG
28254706 CCACAAAGGCTTC
1 CCACAAAGGCTTC
28254719 CTAGGTAACC
Statistics
Matches: 91, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.01
23 4 0.04
24 18 0.20
25 56 0.62
26 6 0.07
27 6 0.07
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (25 bp):
CCACAAAGGCTTCTCAGATAATTAG
Found at i:28254664 original size:50 final size:50
Alignment explanation
Indices: 28254582--28254722 Score: 223
Period size: 50 Copynumber: 2.8 Consensus size: 50
28254572 TAGTACTTCA
*
28254582 CCACAAAGGC-TTTCACAAGATTAGCCACAAAGGCTT-CTCAGATTATACG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCT-AGATAATACG
* * *
28254631 CCACAAAGGCTTTTCTCAACATTAGCAACAAAGGCTTCCTAGATAATACG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAGATAATACG
28254681 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAG
28254723 GTAACCTGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
49 10 0.12
50 71 0.86
51 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (50 bp):
CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAGATAATACG
Found at i:28261508 original size:18 final size:18
Alignment explanation
Indices: 28261468--28261509 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28261458 GTGTGTGCTT
* *
28261468 ATGTGGGCCCGTACGCCC
1 ATGTGGGCCCGCACACCC
*
28261486 GTGTGGGCCCGCACACCC
1 ATGTGGGCCCGCACACCC
28261504 ATGTGG
1 ATGTGG
28261510 CCCACTCGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.36, G:0.36, T:0.17
Consensus pattern (18 bp):
ATGTGGGCCCGCACACCC
Found at i:28279088 original size:21 final size:21
Alignment explanation
Indices: 28279062--28279110 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28279052 CATTTTTTCT
** *
28279062 AATCTCACTGCTACAATATCC
1 AATCTCACCACTACAATAACC
*
28279083 AATCTCACCACTACAATAACT
1 AATCTCACCACTACAATAACC
28279104 AATCTCA
1 AATCTCA
28279111 TCGCCACTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.33, G:0.02, T:0.27
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:28285124 original size:78 final size:78
Alignment explanation
Indices: 28284986--28285131 Score: 204
Period size: 78 Copynumber: 1.9 Consensus size: 78
28284976 ATTCGCTAGC
*
28284986 TGAGATCCAACATAAATTGCGGATTCTTGAAAACATGAGTGAGAAACATCAAATTCTTATTTAGC
1 TGAGATCCAACATAAATTGCGGATTCTCGAAAACATGAGTGAGAAACATCAAATTCTTATTTAGC
28285051 GATCCGTGGTGGT
66 GATCCGTGGTGGT
* * * * * * *
28285064 TGAGATCCAACATAAATTGTGGATTCTCGACATCTTGAGTGAGTAGCATCGAA-TCATTATTTAG
1 TGAGATCCAACATAAATTGCGGATTCTCGAAAACATGAGTGAGAAACATCAAATTC-TTATTTAG
28285128 CGAT
65 CGAT
28285132 GGCTAAGATC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
77 2 0.03
78 57 0.97
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (78 bp):
TGAGATCCAACATAAATTGCGGATTCTCGAAAACATGAGTGAGAAACATCAAATTCTTATTTAGC
GATCCGTGGTGGT
Found at i:28297017 original size:67 final size:68
Alignment explanation
Indices: 28296927--28297095 Score: 180
Period size: 67 Copynumber: 2.5 Consensus size: 68
28296917 TTTTTTCTCA
* * * *
28296927 GCAGACTATCTTTATTGTCATAGTCAAGCTATGGACTTACACAGCACACCCCAT-ATTTAATGTC
1 GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATGATTTAATGTC
28296991 ATG
66 ATG
* * * * * *
28296994 GTAGACTATATTTGTTGCCATAGTCGAGCAATGGACTTACATAGTACACCACATGTTTTAATGTC
1 GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATGATTTAATGTC
*
28297059 CTG
66 ATG
** * *
28297062 GCAGACTCCATTGGTTGGCATAGTCTAA-CTATGG
1 GCAGACTATATTTGTTGCCATAGTC-AAGCTATGG
28297096 TCCTATACCT
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
67 45 0.55
68 36 0.44
69 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (68 bp):
GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATGATTTAATGTC
ATG
Found at i:28297221 original size:27 final size:27
Alignment explanation
Indices: 28297135--28297228 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
28297125 GTCACGATGA
* * * *
28297135 ACTATCCCGTGTTTGCTGTCCCAACGG
1 ACTATCCCATGTTTACTATCCCAACAG
* * * * * *
28297162 ACTATCCTATGTTTATTCTCTCGACAA
1 ACTATCCCATGTTTACTATCCCAACAG
*
28297189 AGTATCCCATGTTTACTATCCCAACAG
1 ACTATCCCATGTTTACTATCCCAACAG
*
28297216 ACTATCTCATGTT
1 ACTATCCCATGTT
28297229 ATTGTTTCAG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (27 bp):
ACTATCCCATGTTTACTATCCCAACAG
Found at i:28298804 original size:25 final size:25
Alignment explanation
Indices: 28298758--28298805 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28298748 CACTTTGTTG
* *
28298758 GCTCACACATAACCACTTACATAGA
1 GCTCACACATAACAACTCACATAGA
* *
28298783 GCTCACATATCACAACTCACATA
1 GCTCACACATAACAACTCACATA
28298806 TTCCACAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.33, G:0.06, T:0.21
Consensus pattern (25 bp):
GCTCACACATAACAACTCACATAGA
Found at i:28299014 original size:51 final size:51
Alignment explanation
Indices: 28298955--28299457 Score: 499
Period size: 51 Copynumber: 10.1 Consensus size: 51
28298945 TTTGCTTATA
* ** * * *
28298955 GAACTTAATATAATCAGCACGCACATACTTTTTTTAGATAGTTAACACATT
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * *
28299006 GAACTTAATATAATCAACACGCACACACTTGTTTTAGACAATTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * *
28299057 GAACTTAATATTATCAACACGCACATACTTTGTTTAGACAGTTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * * * *
28299108 GAGCTTAATATAATTAGCACGCACATACTTGGTTTAGATAGTTCACACATA
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * * * *
28299159 GAACTTAATATAACCAGCATGCACATACCTGGTTTAGACAATTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * * *
28299210 GAACTTAATATAATCAACATGCACATACTTTGTTTAGATAGTTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * * * *
28299261 GAGCTTAATATAATTAACACACACATACTTGGTTTAGACAATTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* ** * * *
28299312 AAACTTAATATAATCAGTACACACATACTTTGTTTAGATAGTTCACAC-T-
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* * * *
28299361 --A--TAAT-CAAT--ACA--CATATACTTTGTTTAGATAGTTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
* ** * * *
28299403 GAACTTAATATAATTAGTACGCACACACTTAGTTTAGACAGTTCACAAAT-
1 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
28299453 GAACT
1 GAACT
28299458 CTTCCTTGTG
Statistics
Matches: 377, Mismatches: 64, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
40 26 0.07
41 1 0.00
42 1 0.00
44 4 0.01
45 4 0.01
46 4 0.01
47 4 0.01
49 1 0.00
50 6 0.02
51 326 0.86
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (51 bp):
GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
Found at i:28299203 original size:153 final size:150
Alignment explanation
Indices: 28298958--28299457 Score: 597
Period size: 153 Copynumber: 3.3 Consensus size: 150
28298948 GCTTATAGAA
* ** * * * *
28298958 CTTAATATAATCAGCACGCACATACTTTTTTTAGATAGTTAACACATTGAACTTAATATAATCAA
1 CTTAATATAATTAGCACGCACATACTTGGTTTAGACAGTTCACA-AATGAACTTAATATAATCAG
* *
28299023 CACGCACACACTTGTTTTAGACAATTCACACATGGAACTTAATATTATCAACACGCACATACTTT
65 CACGCACATACTTGGTTTAGACAATTCACACATGGAACTTAATA-TATCAACA-GCACATACTTT
*
28299088 GTTTAGACAGTTCACAAATGGAG
128 GTTTAGATAGTTCACAAATGGAG
* * *
28299111 CTTAATATAATTAGCACGCACATACTTGGTTTAGATAGTTCACACATAGAACTTAATATAACCAG
1 CTTAATATAATTAGCACGCACATACTTGGTTTAGACAGTTCACAAAT-GAACTTAATATAATCAG
* *
28299176 CATGCACATACCTGGTTTAGACAATTCACACATGGAACTTAATATAATCAACATGCACATACTTT
65 CACGCACATACTTGGTTTAGACAATTCACACATGGAACTTAATAT-ATCAACA-GCACATACTTT
28299241 GTTTAGATAGTTCACAAATGGAG
128 GTTTAGATAGTTCACAAATGGAG
* * *
28299264 CTTAATATAATTAACACACACATACTTGGTTTAGACAATTCACAAATGAAACTTAATATAATCAG
1 CTTAATATAATTAGCACGCACATACTTGGTTTAGACAGTTCACAAATG-AACTTAATATAATCAG
* * * * * *
28299329 TACACACATACTTTGTTTAGATAGTTCACAC-T---A--TAATCA-AT--ACA-CATATACTTTG
65 CACGCACATACTTGGTTTAGACAATTCACACATGGAACTTAAT-ATATCAACAGCACATACTTTG
* *
28299384 TTTAGATAGTTCACACATGGAA
129 TTTAGATAGTTCACAAATGGAG
* * *
28299406 CTTAATATAATTAGTACGCACACACTTAGTTTAGACAGTTCACAAATGAACT
1 CTTAATATAATTAGCACGCACATACTTGGTTTAGACAGTTCACAAATGAACT
28299458 CTTCCTTGTG
Statistics
Matches: 307, Mismatches: 36, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
141 4 0.01
142 72 0.23
144 3 0.01
146 2 0.01
147 4 0.01
148 1 0.00
149 1 0.00
152 4 0.01
153 216 0.70
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (150 bp):
CTTAATATAATTAGCACGCACATACTTGGTTTAGACAGTTCACAAATGAACTTAATATAATCAGC
ACGCACATACTTGGTTTAGACAATTCACACATGGAACTTAATATATCAACAGCACATACTTTGTT
TAGATAGTTCACAAATGGAG
Found at i:28299380 original size:40 final size:40
Alignment explanation
Indices: 28299320--28299399 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
28299310 TGAAACTTAA
*
28299320 TATAATCAGTACACACATACTTTGTTTAGATAGTTCACAC
1 TATAATCAATACACACATACTTTGTTTAGATAGTTCACAC
*
28299360 TATAATCAATACACATATACTTTGTTTAGATAGTTCACAC
1 TATAATCAATACACACATACTTTGTTTAGATAGTTCACAC
28299400 ATGGAACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (40 bp):
TATAATCAATACACACATACTTTGTTTAGATAGTTCACAC
Found at i:28299438 original size:91 final size:91
Alignment explanation
Indices: 28299269--28299449 Score: 245
Period size: 91 Copynumber: 2.0 Consensus size: 91
28299259 TGGAGCTTAA
*
28299269 TATAATTAACACACACATACTTGGTTTAGACAATTCACAAATGAAACTTAATATAATCAGTACAC
1 TATAATCAACACACACATACTTGGTTTAGACAATTCACAAATGAAACTTAATATAATCAGTACAC
* * *
28299334 ACATACTTTGTTTAGATAGTTCACAC
66 ACACACTTAGTTTAGACAGTTCACAC
* * * * * * * * *
28299360 TATAATCAATACACATATACTTTGTTTAGATAGTTCACACATGGAACTTAATATAATTAGTACGC
1 TATAATCAACACACACATACTTGGTTTAGACAATTCACAAATGAAACTTAATATAATCAGTACAC
28299425 ACACACTTAGTTTAGACAGTTCACA
66 ACACACTTAGTTTAGACAGTTCACA
28299450 AATGAACTCT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (91 bp):
TATAATCAACACACACATACTTGGTTTAGACAATTCACAAATGAAACTTAATATAATCAGTACAC
ACACACTTAGTTTAGACAGTTCACAC
Found at i:28300167 original size:42 final size:42
Alignment explanation
Indices: 28300011--28300275 Score: 356
Period size: 42 Copynumber: 6.3 Consensus size: 42
28300001 GTGTCGCTAA
* * *
28300011 CTTTTGCGGCGCTTTTCCACAAATGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTTCACAAACGCCGCTATAGATCAAGAC
* * * **
28300053 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAAACCGTGAC
1 CTTTAGCGGCGCTTTT-TCACAAACGCCGCTATAGATCAAGAC
* * *
28300096 CTTTAGCGGCGC-TTTTCCCAAACGCCGCTATAGATCAGGAT
1 CTTTAGCGGCGCTTTTTCACAAACGCCGCTATAGATCAAGAC
*
28300137 CTTTAGCGGTGCTTTTTCACAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTTCACAAACGCCGCTATAGATCAAGAC
*
28300179 CTTTAGCGGCGC-TTTTCGACAAACGCCGCTATAGATCAAGAT
1 CTTTAGCGGCGCTTTTTC-ACAAACGCCGCTATAGATCAAGAC
* *
28300221 CTTTAGCGGCGCTTTTTCACAAACGTCGCTATAGAACAA-AC
1 CTTTAGCGGCGCTTTTTCACAAACGCCGCTATAGATCAAGAC
28300262 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
28300276 CTCATAAAAC
Statistics
Matches: 197, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
41 50 0.25
42 109 0.55
43 38 0.19
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTTCACAAACGCCGCTATAGATCAAGAC
Found at i:28305530 original size:41 final size:41
Alignment explanation
Indices: 28305469--28305627 Score: 246
Period size: 41 Copynumber: 3.9 Consensus size: 41
28305459 TCAATTCGGG
* *
28305469 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGACCCGAGT
1 ATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGACCCGAGC
* *
28305510 ATTAGCGGCACTTTTCCAAAAACACCGATAAAGACCCGAGC
1 ATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGACCCGAGC
*
28305551 ATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGACCCGAGC
* **
28305592 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGACC
1 ATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGACC
28305628 TACAAGGTCA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTCCAAAAACACCGCTAAAGACCCGAGC
Found at i:28306316 original size:12 final size:12
Alignment explanation
Indices: 28306299--28306362 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
28306289 AAACTTAATC
28306299 AATTTAATATTA
1 AATTTAATATTA
28306311 AATTTAATA-TA
1 AATTTAATATTA
*
28306322 ATATTT-ATCTTGATA
1 A-ATTTAAT-AT--TA
28306337 AATATT-ATATTA
1 AAT-TTAATATTA
28306349 AATTTAATATTA
1 AATTTAATATTA
28306361 AA
1 AA
28306363 CTATTAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
11 7 0.16
12 26 0.60
14 3 0.07
15 7 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (12 bp):
AATTTAATATTA
Found at i:28312347 original size:25 final size:25
Alignment explanation
Indices: 28312244--28312355 Score: 102
Period size: 25 Copynumber: 4.5 Consensus size: 25
28312234 GTACATGTAT
* *
28312244 GCTCATACGAGCTGTA-AACAGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
28312268 GCTCCT-CTGAGCTGAATAATGGTAA
1 GCTCATAC-GAGCTGAATAACGGTAA
* * * * *
28312293 GCTCCTCCAAGCTAAATAATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
28312318 GCTCATACGAGCTGAGTAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
28312343 GCTCATAAGAGCT
1 GCTCATACGAGCT
28312356 AAAATTGGTA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.01
24 12 0.17
25 58 0.81
26 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:28312420 original size:74 final size:74
Alignment explanation
Indices: 28312340--28312487 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
28312330 TGAGTAACGG
*
28312340 TAAGCTCATAAGAGCTAAAATTGGTAACCCTAATGGCATGTCATTTGTATCCTACGAATTCCTAA
1 TAAGCTCATAAGAGCTAAAATTGGTAACCCTAATGACATGTCATTTGTATCCTACGAATTCCTAA
28312405 GGTTCAAAC
66 GGTTCAAAC
*
28312414 TAAGCTCATAAGAGCTGAAATTGGTAACCCTAATGACATGTCATTTGTATCCTACGAATTCCTAA
1 TAAGCTCATAAGAGCTAAAATTGGTAACCCTAATGACATGTCATTTGTATCCTACGAATTCCTAA
28312479 GGTTCAAAC
66 GGTTCAAAC
28312488 GGGGTTCGGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (74 bp):
TAAGCTCATAAGAGCTAAAATTGGTAACCCTAATGACATGTCATTTGTATCCTACGAATTCCTAA
GGTTCAAAC
Found at i:28319096 original size:50 final size:50
Alignment explanation
Indices: 28318985--28319231 Score: 241
Period size: 50 Copynumber: 4.8 Consensus size: 50
28318975 ATTTGGGTAA
28318985 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* * *
28319041 AGAGGTCCCATGTAAGACCATGTCTGGGAGATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
28319091 AGAGGTCACC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
28319141 AGA-ACTCCTATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
28319190 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28319232 TGTTATTATC
Statistics
Matches: 162, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
49 40 0.25
50 76 0.47
51 2 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28319647 original size:84 final size:84
Alignment explanation
Indices: 28319506--28319679 Score: 348
Period size: 84 Copynumber: 2.1 Consensus size: 84
28319496 TTTGGTTATT
28319506 ATTATTTGTGTTTAATGTTGCTATTTATTTACTTGTAAAATTACTAATCATTATGCTTACTTTGC
1 ATTATTTGTGTTTAATGTTGCTATTTATTTACTTGTAAAATTACTAATCATTATGCTTACTTTGC
28319571 TTATTTTCTTTTATATAGC
66 TTATTTTCTTTTATATAGC
28319590 ATTATTTGTGTTTAATGTTGCTATTTATTTACTTGTAAAATTACTAATCATTATGCTTACTTTGC
1 ATTATTTGTGTTTAATGTTGCTATTTATTTACTTGTAAAATTACTAATCATTATGCTTACTTTGC
28319655 TTATTTTCTTTTATATAGC
66 TTATTTTCTTTTATATAGC
28319674 ATTATT
1 ATTATT
28319680 AATCAAAGTC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.55
Consensus pattern (84 bp):
ATTATTTGTGTTTAATGTTGCTATTTATTTACTTGTAAAATTACTAATCATTATGCTTACTTTGC
TTATTTTCTTTTATATAGC
Found at i:28319683 original size:45 final size:45
Alignment explanation
Indices: 28319545--28319684 Score: 132
Period size: 45 Copynumber: 3.2 Consensus size: 45
28319535 TACTTGTAAA
28319545 ATTACTAATCATTATGCTTACTTTGCTTATTTTCTTTTATATAGC
1 ATTACTAATCATTATGCTTACTTTGCTTATTTTCTTTTATATAGC
* ** ** * * * *
28319590 ATTATTTGTGTTTAATG-TTGCTAT--TTATTTACTTGTA-A-A--
1 ATTACTAATCATT-ATGCTTACTTTGCTTATTTTCTTTTATATAGC
28319629 ATTACTAATCATTATGCTTACTTTGCTTATTTTCTTTTATATAGC
1 ATTACTAATCATTATGCTTACTTTGCTTATTTTCTTTTATATAGC
*
28319674 ATTATTAATCA
1 ATTACTAATCA
28319685 AAGTCGGGGA
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
38 3 0.04
39 13 0.19
41 12 0.18
42 2 0.03
43 12 0.18
45 23 0.34
46 3 0.04
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (45 bp):
ATTACTAATCATTATGCTTACTTTGCTTATTTTCTTTTATATAGC
Found at i:28321876 original size:25 final size:25
Alignment explanation
Indices: 28321840--28321897 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
28321830 GTTGTAAACA
* *
28321840 GTAAGCTTCTCCGAGCTGAATAACG
1 GTAAGCTCCTCCGAGCTAAATAACG
28321865 GTAAGCTCCTCCGAGCTAAATAACG
1 GTAAGCTCCTCCGAGCTAAATAACG
28321890 GTAAGCTC
1 GTAAGCTC
28321898 ATAAGAGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (25 bp):
GTAAGCTCCTCCGAGCTAAATAACG
Found at i:28321905 original size:25 final size:25
Alignment explanation
Indices: 28321852--28321911 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
28321842 AAGCTTCTCC
* * **
28321852 GAGCTGAATAACGGTAAGCTCCTCC
1 GAGCTAAATAACGGTAAGCTCATAA
28321877 GAGCTAAATAACGGTAAGCTCATAA
1 GAGCTAAATAACGGTAAGCTCATAA
28321902 GAGCTGAAAT
1 GAGCT-AAAT
28321912 CGGTAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
GAGCTAAATAACGGTAAGCTCATAA
Found at i:28323104 original size:22 final size:22
Alignment explanation
Indices: 28323079--28323146 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
28323069 AGGTAAGTTC
28323079 GTATATTTATATGTTTTAAATT
1 GTATATTTATATGTTTTAAATT
* *
28323101 G--TATTTATTGAGGTAATTAAATT
1 GTATATTTA-T-ATGT-TTTAAATT
*
28323124 GTATATTTATATATTTTAAATT
1 GTATATTTATATGTTTTAAATT
28323146 G
1 G
28323147 AATTATAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 12 0.33
23 10 0.28
24 1 0.03
25 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (22 bp):
GTATATTTATATGTTTTAAATT
Found at i:28323397 original size:25 final size:25
Alignment explanation
Indices: 28323310--28323422 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
28323300 GACACACCAT
* **
28323310 AGCTCGTATGAGCTTCCCGATTTGC
1 AGCTCGTATGAGCTTACCGATTCAC
* *
28323335 AGCTCGTGA-GAGCTTACCAATTCTC
1 AGCTCGT-ATGAGCTTACCGATTCAC
*
28323360 AACTCGTATGAGCTTACCGATTCAC
1 AGCTCGTATGAGCTTACCGATTCAC
* * *
28323385 AGCTCGTGA-GAGCATATCGATTCAT
1 AGCTCGT-ATGAGCTTACCGATTCAC
*
28323410 AGCTCATATGAGC
1 AGCTCGTATGAGC
28323423 ATATATGTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 2 0.03
25 68 0.94
26 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCAC
Found at i:28323420 original size:50 final size:50
Alignment explanation
Indices: 28323307--28323422 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
28323297 GCGGACACAC
* ** *
28323307 CATAGCTCGTATGAGCTTCCCGATTTGCAGCTCGTGAGAGCTTACCAATT
1 CATAGCTCGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCAATT
* * *
28323357 C-TCAACTCGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATATCGATT
1 CAT-AGCTCGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCAATT
*
28323407 CATAGCTCATATGAGC
1 CATAGCTCGTATGAGC
28323423 ATATATGTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.02
50 53 0.96
51 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
CATAGCTCGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCAATT
Found at i:28328341 original size:13 final size:13
Alignment explanation
Indices: 28328323--28328349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28328313 CCAAGAATCC
28328323 AGAGCTTATACAG
1 AGAGCTTATACAG
28328336 AGAGCTTATACAG
1 AGAGCTTATACAG
28328349 A
1 A
28328350 AAATTTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (13 bp):
AGAGCTTATACAG
Found at i:28330954 original size:50 final size:50
Alignment explanation
Indices: 28330877--28330983 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
28330867 ATCATAGTTG
* * ** * *
28330877 GTATGAGCTTCCCGATTTGCAGCTCGTGAGAGCTTACCAATTCTTAACTC
1 GTATGAGCTTACCGACTCACAGCTCGTGAGAGCATACCAATTCATAACTC
* *
28330927 GTATGAGCTTACCGACTCACAGGTCGTGAGAGCATACCAATTCATAGCTC
1 GTATGAGCTTACCGACTCACAGCTCGTGAGAGCATACCAATTCATAACTC
28330977 GTATGAG
1 GTATGAG
28330984 AATATATGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (50 bp):
GTATGAGCTTACCGACTCACAGCTCGTGAGAGCATACCAATTCATAACTC
Found at i:28330978 original size:25 final size:25
Alignment explanation
Indices: 28330897--28330978 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
28330887 CCCGATTTGC
*
28330897 AGCTCGTGAGAGCTTACCAATTCTT
1 AGCTCGTGAGAGCTTACCAATTCAT
* * * *
28330922 AACTCGT-ATGAGCTTACCGACTCAC
1 AGCTCGTGA-GAGCTTACCAATTCAT
* *
28330947 AGGTCGTGAGAGCATACCAATTCAT
1 AGCTCGTGAGAGCTTACCAATTCAT
28330972 AGCTCGT
1 AGCTCGT
28330979 ATGAGAATAT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
24 1 0.02
25 41 0.95
26 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCTCGTGAGAGCTTACCAATTCAT
Found at i:28335689 original size:18 final size:18
Alignment explanation
Indices: 28335663--28335707 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
28335653 GCAATAAAAA
28335663 AATGTTTTG-AAATTGAAT
1 AATGTTTTGTAAA-TGAAT
*
28335681 AATGATTTGTAAATGAAT
1 AATGTTTTGTAAATGAAT
28335699 AATGTTTTG
1 AATGTTTTG
28335708 GAAACAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
AATGTTTTGTAAATGAAT
Found at i:28338086 original size:13 final size:13
Alignment explanation
Indices: 28338056--28338094 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28338046 TTTACTCTCA
* *
28338056 ATTTTACAAAAAG
1 ATTTTACTAAAAT
*
28338069 GTTTTACTAAAAT
1 ATTTTACTAAAAT
28338082 ATTTTACTAAAAT
1 ATTTTACTAAAAT
28338095 TGTGGTTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (13 bp):
ATTTTACTAAAAT
Found at i:28345890 original size:10 final size:10
Alignment explanation
Indices: 28345877--28345918 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
28345867 TTTAAATCTT
*
28345877 TTTTTCTTCA
1 TTTTTATTCA
28345887 TTTTTATT-A
1 TTTTTATTCA
*
28345896 TTTTTTTTCA
1 TTTTTATTCA
28345906 TTTTTATTC-
1 TTTTTATTCA
28345915 TTTT
1 TTTT
28345919 AAAACGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:28345905 original size:19 final size:20
Alignment explanation
Indices: 28345876--28345918 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
28345866 TTTTAAATCT
28345876 TTTTTTCTTCATTTTTATTA
1 TTTTTTCTTCATTTTTATTA
*
28345896 TTTTTT-TTCATTTTTATTC
1 TTTTTTCTTCATTTTTATTA
28345915 TTTT
1 TTTT
28345919 AAAACGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTCATTTTTATTA
Found at i:28347337 original size:107 final size:108
Alignment explanation
Indices: 28347098--28347524 Score: 587
Period size: 107 Copynumber: 4.0 Consensus size: 108
28347088 TTTATTCAGA
* * * *
28347098 TAAAATTTTCAAAATAAGGTAATATTTTGCATTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCT
1 TAAAACTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCT
* * *
28347163 GGATTTC-ACTTTTTTCGTTCGACCAAATAGGTAAAATATCCTTT
66 GGGTTTCGA--TTTTTCGTTCAACCAAATAGCTAAAATATCCTTT
* * * *
28347207 TAAAA-TTTCAAAATAAGGTAATATTTTGCGTTTAGAAATTCGAGAAAACATGCCCTAACATGCT
1 TAAAACTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCT
28347271 GGGTTTCGATTTTTCGTTCAACCAAATAGCTAAAATATCCTTT
66 GGGTTTCGATTTTTCGTTCAACCAAATAGCTAAAATATCCTTT
* * *
28347314 TAAAA-TTTCAAAATAAGGCAATATTTTACGTTTTGGCAATTCGAGAAAACGTGCCCTAACGCGC
1 TAAAACTTTCAAAATAAGGCAATATTTTGCG-TTTGGAAATTCGAGAAAACGTGCCCTAACGTGC
* *
28347378 T-GGTTTCGATTTTTCGCTCGACCAAATAGCTAAAATATCC-TT
65 TGGGTTTCGATTTTTCGTTCAACCAAATAGCTAAAATATCCTTT
** *
28347420 TAAAACTTTCAAAATAAAACAATATTTTGCGTTTGGAAATTCGAGAAAACGTACCCTAACGTGCT
1 TAAAACTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCT
* * *
28347485 GGGTTTCGATTTCTCGTTAAACCAAATAGC-CAAATATCCT
66 GGGTTTCGATTTTTCGTTCAACCAAATAGCTAAAATATCCT
28347525 CTTATACCTT
Statistics
Matches: 285, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
106 46 0.16
107 144 0.51
108 89 0.31
109 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (108 bp):
TAAAACTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCT
GGGTTTCGATTTTTCGTTCAACCAAATAGCTAAAATATCCTTT
Found at i:28348982 original size:19 final size:19
Alignment explanation
Indices: 28348941--28348985 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28348931 TCTTTTTCTT
28348941 TTGCATT-CATTCCATGCA
1 TTGCATTACATTCCATGCA
*
28348959 TTGCATTACATTGCAT-CA
1 TTGCATTACATTCCATGCA
28348977 TATGCATTA
1 T-TGCATTA
28348986 GAGTTTCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (19 bp):
TTGCATTACATTCCATGCA
Found at i:28366848 original size:8 final size:9
Alignment explanation
Indices: 28366828--28366852 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28366818 CATAAATTTT
28366828 AAAAATTCA
1 AAAAATTCA
28366837 AAAAATTCA
1 AAAAATTCA
28366846 AAAAATT
1 AAAAATT
28366853 ATTCTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATTCA
Found at i:28372788 original size:38 final size:38
Alignment explanation
Indices: 28372737--28372812 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
28372727 GCTCTCTCTC
28372737 AACTAGGAGATTGATTTTTCTATTAAATAAGTATTATT
1 AACTAGGAGATTGATTTTTCTATTAAATAAGTATTATT
28372775 AACTAGGAGATTGATTTTTCTATTAAATAAGTATTATT
1 AACTAGGAGATTGATTTTTCTATTAAATAAGTATTATT
28372813 TGTATTCTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (38 bp):
AACTAGGAGATTGATTTTTCTATTAAATAAGTATTATT
Found at i:28377245 original size:10 final size:9
Alignment explanation
Indices: 28377214--28377238 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28377204 AAAAACGATT
28377214 AAAAAATAG
1 AAAAAATAG
28377223 AAAAAATAG
1 AAAAAATAG
28377232 AAAAAAT
1 AAAAAAT
28377239 TATAAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (9 bp):
AAAAAATAG
Found at i:28377432 original size:19 final size:18
Alignment explanation
Indices: 28377389--28377432 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28377379 ATTATAATTC
*
28377389 TTTAAAAAATTTTAAAAA
1 TTTAAAAAATATTAAAAA
*
28377407 TTATAAAATATATTAAAAA
1 TT-TAAAAAATATTAAAAA
28377426 TATTAAA
1 T-TTAAA
28377433 TCTGACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 19 0.86
20 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAAATATTAAAAA
Found at i:28378007 original size:18 final size:19
Alignment explanation
Indices: 28377965--28378007 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28377955 TATAAACTTC
28377965 TATTTATAATTTATTAGAA
1 TATTTATAATTTATTAGAA
* * *
28377984 TTTTTAT-ATTTTTTATAA
1 TATTTATAATTTATTAGAA
28378002 TATTTA
1 TATTTA
28378008 AAAAAATTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTATAATTTATTAGAA
Found at i:28387858 original size:30 final size:30
Alignment explanation
Indices: 28387824--28387880 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28387814 CTTACTTTTT
28387824 TACTTT-CTCCCCAAAACTTTTACTCCCTCC
1 TACTTTCCT-CCCAAAACTTTTACTCCCTCC
28387854 TACTTTCCTCCCAAAACTTTTACTCCC
1 TACTTTCCTCCCAAAACTTTTACTCCC
28387881 CTTCTATCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (30 bp):
TACTTTCCTCCCAAAACTTTTACTCCCTCC
Found at i:28394508 original size:11 final size:11
Alignment explanation
Indices: 28394437--28394508 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
28394427 ATTCCAAATA
*
28394437 TAATATTATTT
1 TAATATTAATT
28394448 TAATA-T-ATT
1 TAATATTAATT
28394457 TAATATTAAATT
1 TAATATT-AATT
* *
28394469 AAATATTTATCT
1 TAATATTAAT-T
*
28394481 TAATAGT-ATT
1 TAATATTAATT
28394491 T--TATTAATT
1 TAATATTAATT
28394500 TAATATTAA
1 TAATATTAA
28394509 AGTAATTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
8 3 0.06
9 11 0.23
10 4 0.08
11 15 0.31
12 15 0.31
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Done.