Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 30 of 135
Found at i:11928282 original size:100 final size:99
Alignment explanation
Indices: 11927933--11928272 Score: 338
Period size: 100 Copynumber: 3.4 Consensus size: 99
11927923 GGTTAGGGTT
* * * *
11927933 AGGGTTAGGGTTTTTAAGTTAAGTGTTTAGGGTTTTTAAGTT-AAAGGTTAGGGTTTTTAAGTTA
1 AGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTTTAAGTTA
* * ** * *
11927997 AGGGTTAGAGTTTAGGGTTTAGG-GCTAAGAGTTT
66 AGGGTTAGGGTTTAGAGTTTAGGTTTTTA-AGTTA
* *
11928031 TGGGTTGAGAGGTTTTTCAGTTAAGTCAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTT
1 AGGGTT-A-AGG--TTT---TTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTT
11928096 TAAGTTAAGGGTTAGGGTTT--AG----GGTTTTTAAGTTAA
59 TAAGTTAAGGGTTAGGGTTTAGAGTTTAGGTTTTTAAGTT-A
* *
11928132 AAGTTTAAGGTTTTTAAGTTAAGGGTTAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTTT
1 AGGGTTAAGGTTTTTAAGTT-A-----AGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTTT
11928197 AAGTTAAGGGTTAGGGTTTAGAGTTTATGGTTTTTAAGTTA
60 AAGTTAAGGGTTAGGGTTTAGAGTTTA-GGTTTTTAAGTTA
11928238 AGGGTT-AGGATTTTTAAGTTAAGGGTTTAGGGTTT
1 AGGGTTAAGG-TTTTTAAGTTAAGGGTTTAGGGTTT
11928273 GTCAATTAAA
Statistics
Matches: 200, Mismatches: 18, Indels: 46
0.76 0.07 0.17
Matches are distributed among these distances:
94 6 0.03
95 1 0.00
97 3 0.01
98 5 0.03
99 4 0.02
100 80 0.40
101 5 0.03
102 5 0.03
104 1 0.00
105 31 0.16
106 47 0.23
107 12 0.06
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (99 bp):
AGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAAGGTTTTTAAGTTA
AGGGTTAGGGTTTAGAGTTTAGGTTTTTAAGTTA
Found at i:11928535 original size:21 final size:21
Alignment explanation
Indices: 11928511--11928555 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11928501 TTGTCTAGCT
*
11928511 TCCGGCGACGG-TTGTGGTTCC
1 TCCGGCG-CGGATTCTGGTTCC
*
11928532 TCCGGCGGGGATTCTGGTTCC
1 TCCGGCGCGGATTCTGGTTCC
11928553 TCC
1 TCC
11928556 AGTAGGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.04, C:0.31, G:0.36, T:0.29
Consensus pattern (21 bp):
TCCGGCGCGGATTCTGGTTCC
Found at i:11929684 original size:20 final size:20
Alignment explanation
Indices: 11929647--11929684 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11929637 ATTATTTTTA
*
11929647 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
11929667 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
11929685 TACTTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:11930615 original size:14 final size:14
Alignment explanation
Indices: 11930582--11930608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11930572 TACGATTTAA
11930582 AAATTTTTTTAAAT
1 AAATTTTTTTAAAT
11930596 AAATTTTTTTAAA
1 AAATTTTTTTAAA
11930609 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATTTTTTTAAAT
Found at i:11930662 original size:51 final size:51
Alignment explanation
Indices: 11930618--11930717 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
11930608 AATTATTTAA
*
11930618 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AAGAAATTGAGAGCAAATTGAGATT
* * *
11930669 AAATATGGATTTAAGAGAGATTTAGAAAGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAAGAAATTGAGAGCAAATTGAGA
11930718 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAAGAAATTGAGAGCAAATTGAGATT
Found at i:11931493 original size:65 final size:66
Alignment explanation
Indices: 11931368--11931495 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 66
11931358 TAAAAAACGG
* ** *
11931368 TTTTTACATGAAAAAAAGTAATTACTAAAATAAAATAAAAACAAATTATTTCCAATAATGTATCG
1 TTTTTACATGAAAAAAAGTAATTACGAAAATAAAATAAAAACAAATTATTTAAAAGAATGTATCG
11931433 T
66 T
* * *
11931434 TTTTTACATG-AAAAAATTAATTACGAAAATAAAATAAAAATAAATTGTTTAAAAGAATGTAT
1 TTTTTACATGAAAAAAAGTAATTACGAAAATAAAATAAAAACAAATTATTTAAAAGAATGTAT
11931496 TATTTTAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
65 45 0.82
66 10 0.18
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (66 bp):
TTTTTACATGAAAAAAAGTAATTACGAAAATAAAATAAAAACAAATTATTTAAAAGAATGTATCG
T
Found at i:11931531 original size:17 final size:17
Alignment explanation
Indices: 11931496--11931528 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11931486 AAGAATGTAT
*
11931496 TATTTTAAAGACAATAA
1 TATTTTAAAGAAAATAA
11931513 TATTTT-AAGAAAATAA
1 TATTTTAAAGAAAATAA
11931529 ATAAAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (17 bp):
TATTTTAAAGAAAATAA
Found at i:11931637 original size:8 final size:8
Alignment explanation
Indices: 11931622--11931696 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
11931612 TTATTATTTA
11931622 TATA-TTT
1 TATAGTTT
11931629 TATAGTTT
1 TATAGTTT
11931637 TAT-GATTT
1 TATAG-TTT
11931645 TATA-TTT
1 TATAGTTT
11931652 TATTAG---
1 TA-TAGTTT
11931658 T-TAGTTT
1 TATAGTTT
11931665 TATA--TT
1 TATAGTTT
11931671 TATA-TTT
1 TATAGTTT
11931678 TATAGTTT
1 TATAGTTT
*
11931686 TATAATTT
1 TATAGTTT
11931694 TAT
1 TAT
11931697 TTTATTTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 21
0.72 0.01 0.27
Matches are distributed among these distances:
4 3 0.05
6 7 0.12
7 17 0.30
8 29 0.52
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (8 bp):
TATAGTTT
Found at i:11931683 original size:21 final size:22
Alignment explanation
Indices: 11931622--11931701 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 22
11931612 TTATTATTTA
*
11931622 TATATTTTATAGTTTTATGATTT
1 TATATTTTATAGTTTTAT-AATT
*
11931645 TATATTTTATTAGTTAGTTTTATATT
1 TATATTTTA-TAGTT--TTATA-ATT
11931671 TATATTTTATAGTTTTATAATT
1 TATATTTTATAGTTTTATAATT
11931693 T-TATTTTAT
1 TATATTTTAT
11931702 TTAATAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 8 0.16
22 4 0.08
23 13 0.26
24 5 0.10
25 6 0.12
26 14 0.28
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TATATTTTATAGTTTTATAATT
Found at i:11932117 original size:30 final size:32
Alignment explanation
Indices: 11932066--11932128 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
11932056 AAATATACAT
*
11932066 ATTATCAAAACATTAAAAAAATTATAATTATA
1 ATTATCAAAAAATTAAAAAAATTATAATTATA
*
11932098 ATTAT-AAAAAATT-AAAAAATTGTAATTATA
1 ATTATCAAAAAATTAAAAAAATTATAATTATA
11932128 A
1 A
11932129 AAATAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 17 0.59
31 7 0.24
32 5 0.17
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (32 bp):
ATTATCAAAAAATTAAAAAAATTATAATTATA
Found at i:11932135 original size:30 final size:31
Alignment explanation
Indices: 11932072--11932136 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
11932062 ACATATTATC
* **
11932072 AAAACATTAAAAAAATTATAATTATAATTAT
1 AAAAAATTAAAAAAATTATAATTATAAAAAT
*
11932103 AAAAAATT-AAAAAATTGTAATTATAAAAAT
1 AAAAAATTAAAAAAATTATAATTATAAAAAT
11932133 AAAA
1 AAAA
11932137 CAACTCAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (31 bp):
AAAAAATTAAAAAAATTATAATTATAAAAAT
Found at i:11932188 original size:27 final size:27
Alignment explanation
Indices: 11932153--11932208 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
11932143 AACCATTTTT
11932153 TATAAAATA-AAATA-AAATTATGAAAAC
1 TATAAAATATAAATATAAA-TAT-AAAAC
11932180 TATAAAATATAAATATAAATATAAAAC
1 TATAAAATATAAATATAAATATAAAAC
11932207 TA
1 TA
11932209 ACTAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 8 0.30
29 3 0.11
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (27 bp):
TATAAAATATAAATATAAATATAAAAC
Found at i:11932257 original size:19 final size:19
Alignment explanation
Indices: 11932221--11932256 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11932211 TAATAAAGTA
*
11932221 TAAAAACATATTATAAAAC
1 TAAAAAAATATTATAAAAC
11932240 TAAAAAAATA-TATAAAA
1 TAAAAAAATATTATAAAA
11932257 AAAAGAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAAAAAATATTATAAAAC
Found at i:11934981 original size:246 final size:242
Alignment explanation
Indices: 11934549--11934993 Score: 565
Period size: 246 Copynumber: 1.8 Consensus size: 242
11934539 TTTGAGATAG
* *
11934549 TGTGATAAGATGAGGTTGCTTTTCTCAACTTATAATGATCCCCTAACCTTTTAACCTGAATTCTT
1 TGTGATAAGATGAGGTTGCTTTCCTCAACTTATAATGATCCCCTAACCTGTTAACCTGAATTCTT
* * * *
11934614 TTATCCATTATTGTTAGATCTGCTAGAGACATGTTTTCTTTTTTTTTTGTCCCTGCATTCTTTTC
66 TTATCCATTATTGTTAGATCTGCTAGAGACAAGTTTCCTTTTTTTTTTATCCCTACATTCTTTTC
* * * * * *
11934679 TTTTTTTTATTACACCTTTTATCTTATTAAAAATGGAAAAGCAAACTTACTTCAAGCTCTGAGCT
131 TTTTTTTGATTA-ACCTTCTATCTTAATAAAAATGCAAAAGAAAACATACTTCAAGCTCTGAGCT
11934744 ATAAGAGGAATATTCGTAAGGATACTTTATCATTCTAATTGTGGTCAT
195 ATAAGAGGAATATTCGTAAGGATACTTTATCATTCTAATTGTGGTCAT
* * * * *
11934792 TGTGATAAGATGAGGTTGGTTTCCTCCAGTTATAAATGAT-CCCTCCACCTGTTAGCCCT-AATT
1 TGTGATAAGATGAGGTTGCTTTCCTCAACTTAT-AATGATCCCCT-AACCTGTTA-ACCTGAA-T
* * * *
11934855 TCTTTTTCTCCATTATTGTTAGATCTGCTTGTGACAAGCTGTTCCTTTTTTCTTTTATCCCTACG
62 TC-TTTTATCCATTATTGTTAGATCTGCTAGAGACAAG-T-TTCCTTTTTT-TTTTATCCCTACA
* * *
11934920 TTCTTTTC-TTTTTTGCTT-ATCTTCTATCTTAATAAAAATGCAAAAGAAAACATAGTTCAAGCT
123 TTCTTTTCTTTTTTTGATTAACCTTCTATCTTAATAAAAATGCAAAAGAAAACATACTTCAAGCT
11934983 CTGAGCTATAA
188 CTGAGCTATAA
11934994 TTTGATAAAT
Statistics
Matches: 170, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
243 33 0.19
244 15 0.09
245 6 0.04
246 80 0.47
247 1 0.01
248 17 0.10
249 18 0.11
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (242 bp):
TGTGATAAGATGAGGTTGCTTTCCTCAACTTATAATGATCCCCTAACCTGTTAACCTGAATTCTT
TTATCCATTATTGTTAGATCTGCTAGAGACAAGTTTCCTTTTTTTTTTATCCCTACATTCTTTTC
TTTTTTTGATTAACCTTCTATCTTAATAAAAATGCAAAAGAAAACATACTTCAAGCTCTGAGCTA
TAAGAGGAATATTCGTAAGGATACTTTATCATTCTAATTGTGGTCAT
Found at i:11938360 original size:112 final size:111
Alignment explanation
Indices: 11938157--11938380 Score: 358
Period size: 112 Copynumber: 2.0 Consensus size: 111
11938147 AATTCTAAGA
11938157 TCATTTGAATTTATCATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
1 TCATTTGAATTTATCATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
11938222 TCATCAAATCATGATTGCAGCCAAAATGTCACTATATTTAGTAAAT
66 TCATCAAATCATGATTGCAGCCAAAATGTCACTATATTTAGTAAAT
* * * *
11938268 TCATTTGCATTTATCCTTGTGAGCACAGCTTTGATCTTTGTAGTTTATTTATTTTTCATCCTACC
1 TCATTTGAATTTATCATTGTGAGCAAAGCTTTGATCTTT-TAGTTTATTTATTTGTCATCCTACC
* * ** *
11938333 ATCATCAAATCTTGATTGTAGTTAAAATTTCACTATATTTAGTAAAT
65 ATCATCAAATCATGATTGCAGCCAAAATGTCACTATATTTAGTAAAT
11938380 T
1 T
11938381 AAAATTTTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 36 0.35
112 67 0.65
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (111 bp):
TCATTTGAATTTATCATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
TCATCAAATCATGATTGCAGCCAAAATGTCACTATATTTAGTAAAT
Found at i:11955293 original size:15 final size:15
Alignment explanation
Indices: 11955275--11955305 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11955265 ATTTTAAAAA
*
11955275 TGGGCCGGGCCGGGC
1 TGGGCCGGGCCAGGC
11955290 TGGGCCGGGCCAGGC
1 TGGGCCGGGCCAGGC
11955305 T
1 T
11955306 TATGATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.32, G:0.55, T:0.10
Consensus pattern (15 bp):
TGGGCCGGGCCAGGC
Found at i:11960144 original size:46 final size:46
Alignment explanation
Indices: 11960074--11960161 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
11960064 GACAGTCGGC
* * *
11960074 CACGGTTCAATGGGAAATTGTATTTTTAATCGTAAAATGGATTCGT
1 CACGGTTCAATGGGAAATTATATTTTAAACCGTAAAATGGATTCGT
* *
11960120 CACGGTTCAAT-GGAAGGTTATATTTTAAACCTTAAAATGGAT
1 CACGGTTCAATGGGAA-ATTATATTTTAAACCGTAAAATGGAT
11960162 CAATAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 4 0.11
46 32 0.89
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (46 bp):
CACGGTTCAATGGGAAATTATATTTTAAACCGTAAAATGGATTCGT
Found at i:11977999 original size:12 final size:12
Alignment explanation
Indices: 11977982--11978006 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11977972 GCAGTAGCCC
11977982 CAGTACCAGCAG
1 CAGTACCAGCAG
11977994 CAGTACCAGCAG
1 CAGTACCAGCAG
11978006 C
1 C
11978007 GATAGTGGCT
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:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CAGTACCAGCAG
Found at i:11985889 original size:1 final size:1
Alignment explanation
Indices: 11985885--11985914 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
11985875 CCCCCCCCTC
11985885 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11985915 CATTCAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12012454 original size:2 final size:2
Alignment explanation
Indices: 12012447--12012482 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12012437 AGACTCTCAT
12012447 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12012483 TATATATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12024502 original size:20 final size:20
Alignment explanation
Indices: 12024474--12024514 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12024464 ATTAGGTGAT
* *
12024474 TAAATGACTTAATTAATAAA
1 TAAAGGACTTAAATAATAAA
12024494 TAAAGGACTTAAATAATAAA
1 TAAAGGACTTAAATAATAAA
12024514 T
1 T
12024515 GTACCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAGGACTTAAATAATAAA
Found at i:12025377 original size:17 final size:17
Alignment explanation
Indices: 12025342--12025378 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12025332 ATATATGTTC
*
12025342 TATTGTTGGAATTAAAT
1 TATTGTTGGAAATAAAT
*
12025359 TATTGTTGGAAATATAT
1 TATTGTTGGAAATAAAT
12025376 TAT
1 TAT
12025379 CGAATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAAATAAAT
Found at i:12025559 original size:19 final size:21
Alignment explanation
Indices: 12025522--12025565 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
12025512 TTTTACTTTT
12025522 TGTTCAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTACGAGCTTC
12025543 TGTTCAGCT-TT-CGAGCTTC
1 TGTTCAGCTCTTACGAGCTTC
12025562 TGTT
1 TGTT
12025566 GGTGTATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.43
Consensus pattern (21 bp):
TGTTCAGCTCTTACGAGCTTC
Found at i:12025805 original size:18 final size:17
Alignment explanation
Indices: 12025784--12025827 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12025774 ATGATGGTAC
*
12025784 ATGATATATTGATATGTA
1 ATGATATATTGAAATG-A
*
12025802 ATGATATATTGAAATGG
1 ATGATATATTGAAATGA
12025819 ATGATATAT
1 ATGATATAT
12025828 GTATATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGATATATTGAAATGA
Found at i:12033769 original size:105 final size:105
Alignment explanation
Indices: 12033587--12033780 Score: 266
Period size: 105 Copynumber: 1.8 Consensus size: 105
12033577 AATGTTTAAA
*** **
12033587 TGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGACACCTTGA
1 TGTAAGACCATAGCCCAGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
**
12033652 ACGTAAGACCATGGTTGGACCATGGCAGTATAAATACATC
66 ACGTAAGACCATGGCAGGACCATGGCAGTATAAATACATC
* *
12033692 TGTAAGACCATAGCCCAGCTATGGCATTTTGATGATAAGACCATAACTAGGG-TATGACA-CTAC
1 TGTAAGACCATAGCCCAGCTATGGCATTTTAATGAAAAGACCATAACT-GGGTTATGACACCT-C
*
12033755 AAATGTAAGACCATGGCAGGACCATG
64 AAACGTAAGACCATGGCAGGACCATG
12033781 CCAATACATG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 2 0.03
105 72 0.94
106 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (105 bp):
TGTAAGACCATAGCCCAGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
ACGTAAGACCATGGCAGGACCATGGCAGTATAAATACATC
Found at i:12034442 original size:19 final size:19
Alignment explanation
Indices: 12034418--12034457 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12034408 AGTATAGGTT
12034418 AATGTCAAAATGAGTGAGA
1 AATGTCAAAATGAGTGAGA
12034437 AATGTCAAAATGAGTGAGA
1 AATGTCAAAATGAGTGAGA
12034456 AA
1 AA
12034458 AGTGGCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (19 bp):
AATGTCAAAATGAGTGAGA
Found at i:12035395 original size:22 final size:22
Alignment explanation
Indices: 12035368--12035409 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12035358 CTGTTTTAGA
*
12035368 AATAATATTAATTTTAATATAT
1 AATAATATTAATATTAATATAT
*
12035390 AATAATATTTATATTAATAT
1 AATAATATTAATATTAATAT
12035410 TTTTCTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAATATTAATATTAATATAT
Found at i:12036802 original size:4 final size:4
Alignment explanation
Indices: 12036793--12036964 Score: 344
Period size: 4 Copynumber: 43.0 Consensus size: 4
12036783 ATAATTCAAT
12036793 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
12036841 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
12036889 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
12036937 TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA
12036965 ACACTCATAC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 168 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:12037549 original size:21 final size:21
Alignment explanation
Indices: 12037519--12037589 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
12037509 CTGAACAGAA
* *
12037519 GAACAAAAGCTCGAAAGAGCT
1 GAACAAAAGCTCGTAAGAGTT
*
12037540 GAACAGAAGCTCGTAAGAGTT
1 GAACAAAAGCTCGTAAGAGTT
12037561 GAACAAAAGCTCGTAAGAGTT
1 GAACAAAAGCTCGTAAGAGTT
12037582 GAACAAAA
1 GAACAAAA
12037590 ACTCATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.14
Consensus pattern (21 bp):
GAACAAAAGCTCGTAAGAGTT
Found at i:12044061 original size:21 final size:21
Alignment explanation
Indices: 12044037--12044189 Score: 102
Period size: 21 Copynumber: 7.3 Consensus size: 21
12044027 ACATACAAGA
12044037 AATTATGAAAGAGAGAAGCAG
1 AATTATGAAAGAGAGAAGCAG
* * **
12044058 AATTATCAGCAG-GTCAAG-AG
1 AATTATGA-AAGAGAGAAGCAG
12044078 AAATTATGAAAGAGAGAAGCAG
1 -AATTATGAAAGAGAGAAGCAG
* * **
12044100 AATTATCAGCAG-GTCAAG-AG
1 AATTATGA-AAGAGAGAAGCAG
12044120 AAATTATGAAAGAGAGAAGCAG
1 -AATTATGAAAGAGAGAAGCAG
* * **
12044142 AATTATCAGCAG-GTCAAG-AG
1 AATTATGA-AAGAGAGAAGCAG
12044162 AAATTATGAAAGAGAGAAGCAG
1 -AATTATGAAAGAGAGAAGCAG
12044184 AATTAT
1 AATTAT
12044190 CAGCAGGTCA
Statistics
Matches: 96, Mismatches: 24, Indels: 24
0.67 0.17 0.17
Matches are distributed among these distances:
20 12 0.12
21 72 0.75
22 12 0.12
ACGTcount: A:0.48, C:0.08, G:0.25, T:0.18
Consensus pattern (21 bp):
AATTATGAAAGAGAGAAGCAG
Found at i:12044081 original size:42 final size:42
Alignment explanation
Indices: 12044034--12044204 Score: 342
Period size: 42 Copynumber: 4.1 Consensus size: 42
12044024 ATAACATACA
12044034 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
1 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
12044076 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
1 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
12044118 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
1 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
12044160 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
1 AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
12044202 AGA
1 AGA
12044205 TTAGCCCAAA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 129 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.16
Consensus pattern (42 bp):
AGAAATTATGAAAGAGAGAAGCAGAATTATCAGCAGGTCAAG
Found at i:12050300 original size:24 final size:21
Alignment explanation
Indices: 12050273--12050325 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
12050263 TACAAACAAC
12050273 AATATAATAACAAGTATTCTATAA
1 AATATAATAA-AA-TATTCTA-AA
*
12050297 AATATAATAAAATATTTTAAA
1 AATATAATAAAATATTCTAAA
12050318 AATA-AATA
1 AATATAATA
12050326 TATAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 6 0.21
23 2 0.07
24 10 0.36
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
AATATAATAAAATATTCTAAA
Found at i:12050468 original size:23 final size:24
Alignment explanation
Indices: 12050419--12050471 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12050409 CATTAACATG
* *
12050419 AAAAAAATGTTACCTAACTACTTTT
1 AAAAAAACGTTACCTAACTA-TCTT
*
12050444 AAAAAAACGTTATCTAACT-TCTT
1 AAAAAAACGTTACCTAACTATCTT
12050467 AAAAA
1 AAAAA
12050472 GGAAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
25 17 0.68
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAAAAACGTTACCTAACTATCTT
Found at i:12051142 original size:57 final size:57
Alignment explanation
Indices: 12051081--12051281 Score: 152
Period size: 57 Copynumber: 3.3 Consensus size: 57
12051071 ATGTTTTTCT
* *
12051081 TAAATTAGTCTTTAAATTTAGTAATTGCTTTTATATTATGATTTGAATTTTTTTATC
1 TAAATTAATCTATAAATTTAGTAATTGCTTTTATATTATGATTTGAATTTTTTTATC
* * * * * * **
12051138 TAAATTAATCTATAAACTTGGCAATCATTCTATGTATTTTTATATATAATTAAAATATAAAATGT
1 TAAATTAATCTATAAATTTAGTAAT--TGC----T-TTTATAT-TATGATTTGAAT-T----T-T
12051203 TTT-TC
52 TTTATC
* *
12051208 TTAAATTAGTCTTTAAATTTAGTAATTGCTTTTATATTATGATTTGAATTTTTTTATC
1 -TAAATTAATCTATAAATTTAGTAATTGCTTTTATATTATGATTTGAATTTTTTTATC
12051266 TAAATTAATCTATAAA
1 TAAATTAATCTATAAA
12051282 CTTGGCAATC
Statistics
Matches: 106, Mismatches: 22, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
57 38 0.36
58 3 0.03
59 2 0.02
62 1 0.01
63 10 0.09
64 12 0.11
65 10 0.09
66 1 0.01
69 2 0.02
70 3 0.03
71 24 0.23
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.51
Consensus pattern (57 bp):
TAAATTAATCTATAAATTTAGTAATTGCTTTTATATTATGATTTGAATTTTTTTATC
Found at i:12051205 original size:128 final size:129
Alignment explanation
Indices: 12051043--12051300 Score: 509
Period size: 128 Copynumber: 2.0 Consensus size: 129
12051033 ATTCGGTAAT
12051043 TATTTTTATATTATAATTAAAATATAAAATGTTTTTCTTAAATTAGTCTTTAAATTTAGTAATTG
1 TATTTTTATATTATAATTAAAATATAAAATGTTTTTCTTAAATTAGTCTTTAAATTTAGTAATTG
12051108 CTTTTATATTATGATTTGAATTTTTTTATCTAAATTAATCTATAAACTTGGCAATCATTCTATG
66 CTTTTATATTATGATTTGAATTTTTTTATCTAAATTAATCTATAAACTTGGCAATCATTCTATG
12051172 TATTTTTATA-TATAATTAAAATATAAAATGTTTTTCTTAAATTAGTCTTTAAATTTAGTAATTG
1 TATTTTTATATTATAATTAAAATATAAAATGTTTTTCTTAAATTAGTCTTTAAATTTAGTAATTG
12051236 CTTTTATATTATGATTTGAATTTTTTTATCTAAATTAATCTATAAACTTGGCAATCATTCTATG
66 CTTTTATATTATGATTTGAATTTTTTTATCTAAATTAATCTATAAACTTGGCAATCATTCTATG
12051300 T
1 T
12051301 TAAAGTCTAA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 119 0.92
129 10 0.08
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (129 bp):
TATTTTTATATTATAATTAAAATATAAAATGTTTTTCTTAAATTAGTCTTTAAATTTAGTAATTG
CTTTTATATTATGATTTGAATTTTTTTATCTAAATTAATCTATAAACTTGGCAATCATTCTATG
Found at i:12055836 original size:2 final size:2
Alignment explanation
Indices: 12055831--12055859 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12055821 GTGTGTGTGT
12055831 GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12055860 CCTGCTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12058122 original size:3 final size:3
Alignment explanation
Indices: 12058114--12058149 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
12058104 CTCTCGCTCC
* *
12058114 TAA TAA TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12058150 GGTACATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12058259 original size:3 final size:3
Alignment explanation
Indices: 12058251--12058305 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
12058241 AAGATGAAAC
*
12058251 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12058297 TAA TAA TAA
1 TAA TAA TAA
12058306 AGAAAAGAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12063279 original size:86 final size:86
Alignment explanation
Indices: 12063130--12063302 Score: 301
Period size: 86 Copynumber: 2.0 Consensus size: 86
12063120 GGATTGTTCA
* * * *
12063130 ACTGTACCAAGTTTAGTGAGTTCACTAGTTATGTAGATGTCATATTGTGATATGCGGTGTGCTCA
1 ACTGTACCAAGTTTAGTGAGTTCACTAATTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
12063195 TGGTATGACCCTGCATATAGC
66 TGGTATGACCCTGCATATAGC
12063216 ACTGTACCAAGTTTAGTGAGTTCACTAATTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
1 ACTGTACCAAGTTTAGTGAGTTCACTAATTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
*
12063281 TGGTATGACGCTGCATATAGC
66 TGGTATGACCCTGCATATAGC
12063302 A
1 A
12063303 GGAACCTAGT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (86 bp):
ACTGTACCAAGTTTAGTGAGTTCACTAATTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
TGGTATGACCCTGCATATAGC
Found at i:12072898 original size:31 final size:31
Alignment explanation
Indices: 12072863--12072926 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
12072853 CATTCTTTAC
12072863 AAAATCGAGACTCTGGTAGATTTCTATGACT
1 AAAATCGAGACTCTGGTAGATTTCTATGACT
12072894 AAAATCGAGACTCTGGTAGATTTCTATGACT
1 AAAATCGAGACTCTGGTAGATTTCTATGACT
12072925 AA
1 AA
12072927 CTTTCCTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (31 bp):
AAAATCGAGACTCTGGTAGATTTCTATGACT
Found at i:12078806 original size:7 final size:7
Alignment explanation
Indices: 12078789--12078817 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12078779 ACATGGCTGG
12078789 AAAAT-A
1 AAAATAA
12078795 AAAATAA
1 AAAATAA
12078802 AAAATAA
1 AAAATAA
12078809 AAAATAA
1 AAAATAA
12078816 AA
1 AA
12078818 GCGCAAGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:12080752 original size:12 final size:12
Alignment explanation
Indices: 12080732--12080772 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
12080722 TTTAAGTTTG
*
12080732 ATTTAATATTCA
1 ATTTGATATTCA
12080744 ATTTGATATTCA
1 ATTTGATATTCA
12080756 ATTT--T-TTCA
1 ATTTGATATTCA
12080765 ATTTGATA
1 ATTTGATA
12080773 CTTGAGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 8 0.32
10 1 0.04
11 1 0.04
12 15 0.60
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (12 bp):
ATTTGATATTCA
Found at i:12083176 original size:259 final size:259
Alignment explanation
Indices: 12082717--12083235 Score: 1004
Period size: 259 Copynumber: 2.0 Consensus size: 259
12082707 CCCATTGGCA
* *
12082717 GTTTGGTCAAACATTCACCGGCAAGAATTTCCGAGTTTGATAAATATGTGTTTTTTTTTTTTGAC
1 GTTTGGTCAAACATTCACCGCCAAAAATTTCCGAGTTTGATAAATATGTGTTTTTTTTTTTTGAC
12082782 GATTTGGAGGAAGGAACAACCAATTTGCAAAAGAAAAACTTATTAACCCCAAGAGTGAAAAAAAA
66 GATTTGGAGGAAGGAACAACCAATTTGCAAAAGAAAAACTTATTAACCCCAAGAGTGAAAAAAAA
12082847 CTTTAGCAGTAGAAACGAAAAAAAAATACAAGTTCCCCGCCATGATCCATTTCCATTTCTACTCT
131 CTTTAGCAGTAGAAACGAAAAAAAAATACAAGTTCCCCGCCATGATCCATTTCCATTTCTACTCT
12082912 TATTTTCTTTTGGGTTTCGACTTTTTAACCAGTATTGACCCTTTTTAGTCGTAAAGAGACGAAG
196 TATTTTCTTTTGGGTTTCGACTTTTTAACCAGTATTGACCCTTTTTAGTCGTAAAGAGACGAAG
12082976 GTTTGGTCAAACATTCCACCGCCAAAAATTTCCGAGTTTGATAAATATGTG-TTTTTTTTTTTGA
1 GTTTGGTCAAACATT-CACCGCCAAAAATTTCCGAGTTTGATAAATATGTGTTTTTTTTTTTTGA
12083040 CGATTTGGAGGAAGGAACAACCAATTTGCAAAAGAAAAACTTATTAACCCCAAGAGTGAAAAAAA
65 CGATTTGGAGGAAGGAACAACCAATTTGCAAAAGAAAAACTTATTAACCCCAAGAGTGAAAAAAA
12083105 ACTTTAGCAGTAGAAACGAAAAAAAAATACAAGTTCCCCGCCATGATCCATTTCCATTTCTACTC
130 ACTTTAGCAGTAGAAACGAAAAAAAAATACAAGTTCCCCGCCATGATCCATTTCCATTTCTACTC
12083170 TTATTTTCTTTTGGGTTTCGACTTTTTAACCAGTATTGACCCTTTTTAGTCGTAAAGAGACGAAG
195 TTATTTTCTTTTGGGTTTCGACTTTTTAACCAGTATTGACCCTTTTTAGTCGTAAAGAGACGAAG
12083235 G
1 G
12083236 GCAAATGTGT
Statistics
Matches: 257, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
259 224 0.87
260 33 0.13
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (259 bp):
GTTTGGTCAAACATTCACCGCCAAAAATTTCCGAGTTTGATAAATATGTGTTTTTTTTTTTTGAC
GATTTGGAGGAAGGAACAACCAATTTGCAAAAGAAAAACTTATTAACCCCAAGAGTGAAAAAAAA
CTTTAGCAGTAGAAACGAAAAAAAAATACAAGTTCCCCGCCATGATCCATTTCCATTTCTACTCT
TATTTTCTTTTGGGTTTCGACTTTTTAACCAGTATTGACCCTTTTTAGTCGTAAAGAGACGAAG
Found at i:12090891 original size:20 final size:19
Alignment explanation
Indices: 12090847--12090896 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
12090837 TCATATTAAT
*
12090847 TTTTTATTTTAAAAATTTA
1 TTTTTATTTTAAAAATTGA
**
12090866 GATTTATTTTAATAAATTGA
1 TTTTTATTTTAA-AAATTGA
12090886 TTTTTATTTTA
1 TTTTTATTTTA
12090897 TAACTTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTATTTTAAAAATTGA
Found at i:12091485 original size:20 final size:20
Alignment explanation
Indices: 12091460--12091500 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12091450 TTCAAAATTT
*
12091460 ATATTTTAAAAAAATTATAA
1 ATATTTCAAAAAAATTATAA
*
12091480 ATATTTCAAAAAAATTCTAA
1 ATATTTCAAAAAAATTATAA
12091500 A
1 A
12091501 AATATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTTCAAAAAAATTATAA
Found at i:12104509 original size:17 final size:16
Alignment explanation
Indices: 12104487--12104529 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
12104477 ACATTACTAA
12104487 TATAAAATTTTATAAAT
1 TATAAAATTTT-TAAAT
*
12104504 TATAAAATATTTAAAT
1 TATAAAATTTTTAAAT
*
12104520 GA-AAAATTTT
1 TATAAAATTTT
12104530 CCATTTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TATAAAATTTTTAAAT
Found at i:12106391 original size:23 final size:22
Alignment explanation
Indices: 12106356--12106398 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12106346 GACATGAGTA
12106356 AATTAGAGCTGAAACAAAAAAAC
1 AATTAGAGCTG-AACAAAAAAAC
* *
12106379 AATTGGAGTTGAACAAAAAA
1 AATTAGAGCTGAACAAAAAA
12106399 GGCCTACTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (22 bp):
AATTAGAGCTGAACAAAAAAAC
Found at i:12119675 original size:104 final size:106
Alignment explanation
Indices: 12119410--12119659 Score: 371
Period size: 106 Copynumber: 2.4 Consensus size: 106
12119400 CATTGTTAAA
* *
12119410 TAAAATTAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAA
1 TAAAA-TAAATTTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAA
* **
12119475 TCTAATCATAAATTACTAACAAAATAACTATAAAATTATTAT
65 TCAAATCATAAATTACTAACAAAATAACTATAAAAACATTAT
*** *
12119517 TATTTTAAATTTACATTACTAAAAAATCACAAAACCCTAAACTAAACACTAACAATTTATA-AA-
1 TAAAATAAATTTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAAT
*
12119580 CAAATCATAAATTACTAACAAAATAACTATAAAAACATTTT
66 CAAATCATAAATTACTAACAAAATAACTATAAAAACATTAT
*
12119621 TAAAAT-ATTTTACATTACTAAAAAATCACAAAACACTAA
1 TAAAATAAATTTACATTACTAAAAAATCACAAAACACTAA
12119660 CATAAATTAC
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
103 31 0.24
104 40 0.31
105 2 0.02
106 53 0.41
107 2 0.02
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (106 bp):
TAAAATAAATTTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAAT
CAAATCATAAATTACTAACAAAATAACTATAAAAACATTAT
Found at i:12119685 original size:12 final size:12
Alignment explanation
Indices: 12119670--12119694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12119660 CATAAATTAC
12119670 TAACAAAATAAT
1 TAACAAAATAAT
12119682 TAACAAAATAAT
1 TAACAAAATAAT
12119694 T
1 T
12119695 TTACATTAAT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TAACAAAATAAT
Found at i:12119737 original size:59 final size:63
Alignment explanation
Indices: 12119622--12119746 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 63
12119612 AAACATTTTT
* *
12119622 AAAATATTTTACATTACTAAAAAATCACAAAACACTAACATAAATTACTAACAAAATAATTAAC
1 AAAATATTTTACATTAATAAAAAATCACAAAACAC-AACATAAATCACTAACAAAATAATTAAC
12119686 AAAATAATTTTACATTAATAAAAAATCAC-AAA-AC-ACA-AAA-CACTAACAAAATAATTAAC
1 AAAAT-ATTTTACATTAATAAAAAATCACAAAACACAACATAAATCACTAACAAAATAATTAAC
12119745 AA
1 AA
12119747 TTTATAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
59 20 0.34
60 3 0.05
61 3 0.05
63 2 0.03
64 8 0.14
65 22 0.38
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (63 bp):
AAAATATTTTACATTAATAAAAAATCACAAAACACAACATAAATCACTAACAAAATAATTAAC
Found at i:12120715 original size:27 final size:26
Alignment explanation
Indices: 12120684--12120751 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 26
12120674 CGTTCCGGGT
12120684 TCGGGTCCTTTAGAAAGAGGGTTCATG
1 TCGGGTCCTTT-GAAAGAGGGTTCATG
* *
12120711 TCGGGTCCGATTGAGAGAGGGTTCATG
1 TCGGGTCC-TTTGAAAGAGGGTTCATG
12120738 TCGGGTCCTCTTGA
1 TCGGGTCCT-TTGA
12120752 TAATACTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (26 bp):
TCGGGTCCTTTGAAAGAGGGTTCATG
Found at i:12125378 original size:121 final size:122
Alignment explanation
Indices: 12125240--12125487 Score: 410
Period size: 121 Copynumber: 2.0 Consensus size: 122
12125230 GAAAAAATAC
*
12125240 AAAAAAAACTAACACAAAAATTATTAGTCATATATTAGATATTCTAGACTACAGTGGTATTTCAG
1 AAAAAAAACTAACACAAAAATTATTAGTCATATATTAGATACTCTAGACTACAGTGGTATTTCAG
*
12125305 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTGCATATT
66 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTACATATT
* * *
12125362 AAAAAAAACCT-A-ACAAATATTATTAGTCATATATTAGATACTCTAGATTATAGTGGTATTTCA
1 AAAAAAAA-CTAACACAAAAATTATTAGTCATATATTAGATACTCTAGACTACAGTGGTATTTCA
*
12125425 GTTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTGCCTTTTACATATT
65 GTTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTACATATT
*
12125483 CAAAA
1 AAAAA
12125488 GCAAAACATC
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
121 107 0.91
122 9 0.08
123 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (122 bp):
AAAAAAAACTAACACAAAAATTATTAGTCATATATTAGATACTCTAGACTACAGTGGTATTTCAG
TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTACATATT
Found at i:12132549 original size:5 final size:5
Alignment explanation
Indices: 12132539--12132563 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12132529 ATTAGGTTTC
12132539 TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT
12132564 GAAGGAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGATT
Found at i:12143849 original size:13 final size:13
Alignment explanation
Indices: 12143831--12143855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12143821 GCAGATTTGC
12143831 TTTTGAAAAATAT
1 TTTTGAAAAATAT
12143844 TTTTGAAAAATA
1 TTTTGAAAAATA
12143856 ATGTGGAAAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAAATAT
Found at i:12154011 original size:34 final size:34
Alignment explanation
Indices: 12153965--12154033 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
12153955 CTCGTAAAGG
*
12153965 TTGGAAGCTGGTCGGAGTATCATCACACTATCCC
1 TTGGAAGCTGGTCGGAGTATCACCACACTATCCC
* *
12153999 TTGGAAGTTGGTCGGAGTATCACCGCACTATCCC
1 TTGGAAGCTGGTCGGAGTATCACCACACTATCCC
12154033 T
1 T
12154034 CAGCTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (34 bp):
TTGGAAGCTGGTCGGAGTATCACCACACTATCCC
Found at i:12157381 original size:27 final size:26
Alignment explanation
Indices: 12157343--12157394 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
12157333 ATATTTTGTA
**
12157343 AAAATATTATTATGTTAATAATTTATG
1 AAAATATTATTAAATTAA-AATTTATG
12157370 AAAAT-TTAATTAAATTAAAATTTAT
1 AAAATATT-ATTAAATTAAAATTTAT
12157395 ATAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AAAATATTATTAAATTAAAATTTATG
Found at i:12157403 original size:17 final size:17
Alignment explanation
Indices: 12157370--12157417 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
12157360 ATAATTTATG
*
12157370 AAAATTTA-ATTAAATT
1 AAAATTTATATAAAATT
12157386 AAAATTTATATAAAATT
1 AAAATTTATATAAAATT
*
12157403 AAAATTTTTATAAAA
1 AAAATTTATATAAAA
12157418 AATTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTTATATAAAATT
Found at i:12157414 original size:19 final size:17
Alignment explanation
Indices: 12157381--12157422 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
12157371 AAATTTAATT
*
12157381 AAATTAAAATTTATATA
1 AAATTAAAATTTATAAA
12157398 AAATTAAAATTTTTATAAA
1 AAATTAAAA--TTTATAAA
12157417 AAATTA
1 AAATTA
12157423 TATATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
19 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAAAATTTATAAA
Found at i:12175302 original size:20 final size:20
Alignment explanation
Indices: 12175265--12175302 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12175255 TCCTAAATTG
* *
12175265 CTTATTTATAAGATTATTTT
1 CTTATTTATAAAACTATTTT
12175285 CTTATTTATAAAACTATT
1 CTTATTTATAAAACTATT
12175303 ATTTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (20 bp):
CTTATTTATAAAACTATTTT
Found at i:12175623 original size:16 final size:18
Alignment explanation
Indices: 12175586--12175625 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
12175576 AATATTAAAT
*
12175586 TTTAATAATAAAAAAGGA
1 TTTAATAATAAAAAAGAA
12175604 -TTAA-AATAAAAAA-AA
1 TTTAATAATAAAAAAGAA
12175619 TTTAATA
1 TTTAATA
12175626 TGAATGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.05
16 13 0.68
17 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TTTAATAATAAAAAAGAA
Found at i:12175859 original size:24 final size:25
Alignment explanation
Indices: 12175827--12175873 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12175817 GGAAGAGTGA
12175827 TTAAAATATTAA-ATTTTAATAACG
1 TTAAAATATTAATATTTTAATAACG
* *
12175851 TTAACATATTAATATTTTTATAA
1 TTAAAATATTAATATTTTAATAA
12175874 TTTACTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
TTAAAATATTAATATTTTAATAACG
Found at i:12185832 original size:20 final size:21
Alignment explanation
Indices: 12185809--12185862 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
12185799 CATTTAAGCT
*
12185809 TTAAAATTTTAAATTA-ATTA
1 TTAAAAATTTAAATTAGATTA
* **
12185829 TTAAAAACTTATGTTAGATTA
1 TTAAAAATTTAAATTAGATTA
12185850 TTAAAAATTTAAA
1 TTAAAAATTTAAA
12185863 AATGGTAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TTAAAAATTTAAATTAGATTA
Found at i:12191390 original size:2 final size:2
Alignment explanation
Indices: 12191385--12191422 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12191375 AACAAAAAAT
12191385 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12191423 CTTTGCCTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12192594 original size:19 final size:21
Alignment explanation
Indices: 12192566--12192604 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12192556 CGTATCAAAT
*
12192566 AAATACCTTTTTA-TTAATTA
1 AAATACCTTTGTAGTTAATTA
12192586 AAATA-CTTTGTAGTTAATT
1 AAATACCTTTGTAGTTAATT
12192605 TGTTAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATACCTTTGTAGTTAATTA
Found at i:12192948 original size:19 final size:19
Alignment explanation
Indices: 12192920--12192969 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
12192910 TACATAATTT
*
12192920 ATATTTTAAAAAA-TATTAA
1 ATATTATAAAAAATTATT-A
12192939 ATATTATAAAAAATTATTA
1 ATATTATAAAAAATTATTA
*
12192958 ATATGATAAAAA
1 ATATTATAAAAA
12192970 TAATTTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATATTATAAAAAATTATTA
Found at i:12194091 original size:151 final size:151
Alignment explanation
Indices: 12193930--12194231 Score: 586
Period size: 151 Copynumber: 2.0 Consensus size: 151
12193920 AATATATTAT
12193930 AAAAAAAAATTTGGCCATAACTTTAGAATTTTAGTATTTAAATATTTTTTTATAACTTTATAAAA
1 AAAAAAAAATTTGGCCATAACTTTAGAATTTTAGTATTTAAATATTTTTTTATAACTTTATAAAA
12193995 CACAAATTGTTTCTATAATGATTTTTTTAGAATTTATAATATAAATTTATTTTGTCATAACCATC
66 CACAAATTGTTTCTATAATGATTTTTTTAGAATTTATAATATAAATTTATTTTGTCATAACCATC
*
12194060 ACAACTATTGGTACAGATTTA
131 ACAAATATTGGTACAGATTTA
12194081 AAAAAAAAATTTGGCCATAACTTTAGAATTTTAGTATTTAAATATTTTTTTATAACTTTATAAAA
1 AAAAAAAAATTTGGCCATAACTTTAGAATTTTAGTATTTAAATATTTTTTTATAACTTTATAAAA
12194146 CACAAATTGTTTCTATAATGATTTTTTTAGAATTTATAATATAAATTTATTTTGTCATAACCATC
66 CACAAATTGTTTCTATAATGATTTTTTTAGAATTTATAATATAAATTTATTTTGTCATAACCATC
*
12194211 CCAAATATTGGTACAGATTTA
131 ACAAATATTGGTACAGATTTA
12194232 TGCTTATAAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (151 bp):
AAAAAAAAATTTGGCCATAACTTTAGAATTTTAGTATTTAAATATTTTTTTATAACTTTATAAAA
CACAAATTGTTTCTATAATGATTTTTTTAGAATTTATAATATAAATTTATTTTGTCATAACCATC
ACAAATATTGGTACAGATTTA
Found at i:12196003 original size:28 final size:29
Alignment explanation
Indices: 12195946--12196006 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
12195936 AAATCAGTTC
***
12195946 ATTTCCGTAATTTTTTTAAATTTTGATTT
1 ATTTCCGTAATTTTTTTAAAAAATGATTT
*
12195975 ATTTCCGTAA-TTTTTTAAAAAATGCTTT
1 ATTTCCGTAATTTTTTTAAAAAATGATTT
12196003 ATTT
1 ATTT
12196007 AGTTGTGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (29 bp):
ATTTCCGTAATTTTTTTAAAAAATGATTT
Found at i:12217812 original size:3 final size:3
Alignment explanation
Indices: 12217804--12217828 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12217794 AAGTAATACC
12217804 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
12217829 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12218563 original size:3 final size:3
Alignment explanation
Indices: 12218555--12218593 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12218545 NNNNNNNNNN
12218555 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12218594 TTTTTATTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12219145 original size:21 final size:22
Alignment explanation
Indices: 12219119--12219173 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
12219109 AACAGCGGTG
12219119 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
12219140 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
12219161 GCGGTGAGATTAG
1 GCGGTGAGATTAG
12219174 AAACAGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:12223693 original size:15 final size:15
Alignment explanation
Indices: 12223673--12223712 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
12223663 TCACCGATCC
*
12223673 ACCTCCACTGTCAAG
1 ACCTCCACCGTCAAG
12223688 ACCTCCACCGTCAAG
1 ACCTCCACCGTCAAG
12223703 ACCTCCACCG
1 ACCTCCACCG
12223713 ATCTACCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.25, C:0.47, G:0.12, T:0.15
Consensus pattern (15 bp):
ACCTCCACCGTCAAG
Found at i:12226559 original size:46 final size:46
Alignment explanation
Indices: 12226492--12226642 Score: 196
Period size: 46 Copynumber: 3.5 Consensus size: 46
12226482 ATAAGTATAG
12226492 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
12226538 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
12226574 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
12226620 CACTTATCACTTTATCTCTTGAT
1 CACTTATCACTTTTTCACTTGAT
12226643 TAGAAGTACT
Statistics
Matches: 89, Mismatches: 6, Indels: 20
0.77 0.05 0.17
Matches are distributed among these distances:
36 28 0.31
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 49 0.55
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:12226579 original size:36 final size:36
Alignment explanation
Indices: 12226538--12226610 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
12226528 CTAAAGCTAC
*
12226538 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
12226574 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
12226610 C
1 C
12226611 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:12226615 original size:82 final size:82
Alignment explanation
Indices: 12226478--12226642 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
12226468 ATCCGGCGTT
12226478 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
12226543 ATCACTTTGTCTCTTGA
66 ATCACTTTATCTCTTGA
*
12226560 TCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
12226625 ATCACTTTATCTCTTGA
66 ATCACTTTATCTCTTGA
12226642 T
1 T
12226643 TAGAAGTACT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
ATCACTTTATCTCTTGA
Found at i:12230896 original size:673 final size:675
Alignment explanation
Indices: 12229681--12230929 Score: 1648
Period size: 673 Copynumber: 1.8 Consensus size: 675
12229671 TATTCAAAAT
* *
12229681 TTTATTTTTTGGTCACCACACGTTAAATTACTAATGGAAAAATAACTCGAAAACTTTTAAAATTG
1 TTTATTTTTTGGTCACCACACATTAAATTACTAATGGAAAAATAAATCGAAAACTTTTAAAATTG
* * *
12229746 ACATAATAACAACTTTAACCTTCAATATTTATAATCATCTCAATTTATTATTGATTCAAAAAAAA
66 ACATAATAACAACTTTAACCTTCAACATTTATAATCATCTCAAATTAATATTGATTC----AAAA
* *
12229811 AAAAAAACAATCATCAACATTTGCACATTGTGTAATTTAGTTTTTTTTTTGTTTACAATTTTACA
127 AAAAAAACAATCATCAACATTTGCACATTGTGTAATTTAG--TATTTTTTGTTTACAAGTTTACA
* * * * *
12229876 TTTTATTTGTGACATCAAAGGTTAATTTTAAAATAATGAGAAAATATAAAAATTATTATATTAGA
190 TTTTATTTGTAACATCAAAGGTTAATTTTAAAATAATAAAAAAATATAAAAATTATCATATTAAA
* * *
12229941 TTTGTTTGGTGTTTTCATTTTTGACATATTTCTAGTCAAATTTAATCAATAAATTAAACATAGAA
255 TTTGTTTGGTGTTTCCATTTTTGACATATTTCTAATCAAAATTAATCAATAAATTAAACATAGAA
* * *
12230006 TTGCGTTACACTGAGGACAACATGACACCACATCAACTCAAATGCTTGTACCATCATTCTCAAAC
320 TTGCATTACACCGAGGACAACATCACACCACATCAACTCAAATGCTTGTACCATCATTCTCAAAC
*
12230071 AACACTACCAACTCAGTAGATGGCTTGTCATAATCAATAATAACCAAGTTCAAGTGATCACCATA
385 AACACTACCAACTCAGTAGATGGCTTGACATAATCAATAATAACCAAGTTCAAGTGATCACCATA
* * * * * *
12230136 CGCCAATTTAGCATTTTTAATTGCTACTCCATTCACCTTATCATAAATGTATATAATAAAGCTTG
450 CGCCAATTTAGCAATTTTAATTGCTACTCCATTCACCTCACCAGAAATGTATATAACAAACCTTG
* *
12230201 AATTTTGTTTTAAAAAATAAAAGTTTTAAAGAATGTAAATTTATTTT-TCATAGAATGACGTTAC
515 AATTTTATTTTAAAAAATAAAAGTTTCAAAGAATGTAAATTTATTTTCT-ATAGAATGACGTTAC
12230265 CTTGGGACCACTCAACATCCTTGAAGAAAAATAAGGGTAAATTATATTTCATTATCTAACTATGA
579 CTTGGGACCACTCAACATCCTTGAAGAAAAATAAGGGTAAATTATATTTCATTATCTAACTATGA
12230330 AAAATTATAAAATAATCATCCAACTAATCGGC
644 AAAATTATAAAATAATCATCCAACTAATCGGC
* * *
12230362 TTTATTTTTTTGGTCATCACCCATTAAATTACTAATGGAAAAATAAATCGACAACTTTTAAAATT
1 TTTA-TTTTTTGGTCACCACACATTAAATTACTAATGGAAAAATAAATCGAAAACTTTTAAAATT
** * * * **
12230427 GGTATAATAATAACTTTAA-CTCTCAACATTTTTAATCATGTCAAATTAATATTGA-TC-CCAAA
65 GACATAATAACAACTTTAACCT-TCAACATTTATAATCATCTCAAATTAATATTGATTCAAAAAA
* ** *
12230489 CAAATTAATCATCAACATTTGCACATTGTGTAATTT-G-ATTTTTT-TTTAC-AGTTTACTTTTT
129 AAAAACAATCATCAACATTTGCACATTGTGTAATTTAGTATTTTTTGTTTACAAGTTTACATTTT
* * * * *
12230550 ATTTGTAACATCGAGGGTTAATTTTTAAATAAATAAAAAAATATGAAAATTATCATCTTGAAATT
194 ATTTGTAACATCAAAGGTTAATTTTAAAAT-AATAAAAAAATATAAAAATTATCATATT-AAATT
** * *
12230615 T-TTT-GTGTTTCCA-TTTTGGTATA-TTCTCAATCAAAATTAGTCAATAAATTAATCATAGAAT
257 TGTTTGGTGTTTCCATTTTTGACATATTTCT-AATCAAAATTAATCAATAAATTAAACATAGAAT
* * *
12230676 TGCATTACACCGATGG-CAAGATCACACCACATCAACTCAACTGCTTGTACCATCATTCTCTAAC
321 TGCATTACACCGA-GGACAACATCACACCACATCAACTCAAATGCTTGTACCATCATTCTCAAAC
* * * *
12230740 AACATTACCAACTCAGTAGGTGGGTCT-ACATATATCATTAATAATCACCAAGTTCAAG-GAATC
385 AACACTACCAACTCAGTAGATGGCT-TGACATA-ATC---AATAATAACCAAGTTCAAGTG-ATC
* * * *
12230803 ACCATATGCCAATTTATCAATTTT-ATCTGTTACTCCATTCACCTCACCAGAAATGTATTTAACA
444 ACCATACGCCAATTTAGCAATTTTAAT-TGCTACTCCATTCACCTCACCAGAAATGTATATAACA
*
12230867 AACCTTGAATTTTATTTTAAAAAATAAAAGTTTCAAATAATGTAAATTTATTTTCTATAGAAT
508 AACCTTGAATTTTATTTTAAAAAATAAAAGTTTCAAAGAATGTAAATTTATTTTCTATAGAAT
12230930 TATGTTACAT
Statistics
Matches: 492, Mismatches: 62, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
668 4 0.01
669 118 0.24
670 50 0.10
671 31 0.06
672 14 0.03
673 130 0.26
674 1 0.00
675 1 0.00
676 36 0.07
681 8 0.02
682 99 0.20
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (675 bp):
TTTATTTTTTGGTCACCACACATTAAATTACTAATGGAAAAATAAATCGAAAACTTTTAAAATTG
ACATAATAACAACTTTAACCTTCAACATTTATAATCATCTCAAATTAATATTGATTCAAAAAAAA
AAACAATCATCAACATTTGCACATTGTGTAATTTAGTATTTTTTGTTTACAAGTTTACATTTTAT
TTGTAACATCAAAGGTTAATTTTAAAATAATAAAAAAATATAAAAATTATCATATTAAATTTGTT
TGGTGTTTCCATTTTTGACATATTTCTAATCAAAATTAATCAATAAATTAAACATAGAATTGCAT
TACACCGAGGACAACATCACACCACATCAACTCAAATGCTTGTACCATCATTCTCAAACAACACT
ACCAACTCAGTAGATGGCTTGACATAATCAATAATAACCAAGTTCAAGTGATCACCATACGCCAA
TTTAGCAATTTTAATTGCTACTCCATTCACCTCACCAGAAATGTATATAACAAACCTTGAATTTT
ATTTTAAAAAATAAAAGTTTCAAAGAATGTAAATTTATTTTCTATAGAATGACGTTACCTTGGGA
CCACTCAACATCCTTGAAGAAAAATAAGGGTAAATTATATTTCATTATCTAACTATGAAAAATTA
TAAAATAATCATCCAACTAATCGGC
Found at i:12233154 original size:530 final size:531
Alignment explanation
Indices: 12232143--12233203 Score: 2115
Period size: 530 Copynumber: 2.0 Consensus size: 531
12232133 CAAAAAATAG
12232143 AGAGAATTATTAAAATTATTTAAATTTTTTGTAAAAAATATTATAATTTTAAAAAAAATATATTA
1 AGAGAATTATTAAAATTATTTAAATTTTTTGTAAAAAATATTATAATTTTAAAAAAAATATATTA
12232208 AAAATTAATTAAATTTTGACATGGCAATTCATGTGTAAGTCTATGTCAGCAAAGTTAATATTTGT
66 AAAATTAATTAAATTTTGACATGGCAATTCATGTGTAAGTCTATGTCAGCAAAGTTAATATTTGT
12232273 TTTCTTTTTTATTTATATTAGAGTGATTTGACAAAAAAAAACACTAAAGTCAAAAAGGTAAAAGA
131 TTTCTTTTTTATTTATATTAGAGTGATTTGACAAAAAAAAACACTAAAGTCAAAAAGGTAAAAGA
12232338 AGTGAAAAATAAAATGAATGACTAAAATAATTTTTTGTTTAAGTTTAGAAGGCTAAATAAATCAT
196 AGTGAAAAATAAAATGAATGACTAAAATAATTTTTTGTTTAAGTTTAGAAGGCTAAATAAATCAT
12232403 CATACCATTATCTTATTGGGCTATCTTATCATGGTTGTGTTAGTCCAGTAGCTGGAGCTGCATGT
261 CATACCATTATCTTATTGGGCTATCTTATCATGGTTGTGTTAGTCCAGTAGCTGGAGCTGCATGT
12232468 TCCCCTAACTGCCAACTTTAAATCACCAGCCCTAAAAATACATAACCGCTGTCACTTGTAAACCA
326 TCCCCTAACTGCCAACTTTAAATCACCAGCCCTAAAAATACATAACCGCTGTCACTTGTAAACCA
12232533 TGCCAAAACCTTAGCTCGCCTTCTTTTTTGTATCCTCACTCGGAGCACAGACGCGGCCGCTAATT
391 TGCCAAAACCTTAGCTCGCCTTCTTTTTTGTATCCTCACTCGGAGCACAGACGCGGCCGCTAATT
12232598 TTGCTTTCAGGTAAAGTATATCAAGTCAGCTCTTTAAATTTCATCTTTGTTATGAATTTTATGCT
456 TTGCTTTCAGGTAAAGTATATCAAGTCAGCTCTTTAAATTTCATCTTTGTTATGAATTTTATGCT
12232663 CTACTTATTTA
521 CTACTTATTTA
12232674 AGAGAATTA-TAAAATTATTTAAATTTTTTGTAAAAAATATTATAATTTTAAAAAAAATATATTA
1 AGAGAATTATTAAAATTATTTAAATTTTTTGTAAAAAATATTATAATTTTAAAAAAAATATATTA
12232738 AAAATTAATTAAATTTTGACATGGCAATTCATGTGTAAGTCTATGTCAGCAAAGTTAATATTTGT
66 AAAATTAATTAAATTTTGACATGGCAATTCATGTGTAAGTCTATGTCAGCAAAGTTAATATTTGT
12232803 TTTCTTTTTTATTTATATTAGAGTGATTTGACAAAAAAAAACACTAAAGTCAAAAAGGTAAAAGA
131 TTTCTTTTTTATTTATATTAGAGTGATTTGACAAAAAAAAACACTAAAGTCAAAAAGGTAAAAGA
12232868 AGTGAAAAATAAAATGAATGACTAAAATAATTTTTTGTTTAAGTTTAGAAGGCTAAATAAATCAT
196 AGTGAAAAATAAAATGAATGACTAAAATAATTTTTTGTTTAAGTTTAGAAGGCTAAATAAATCAT
12232933 CATACCATTATCTTATTGGGCTATCTTATCATGGTTGTGTTAGTCCAGTAGCTGGAGCTGCATGT
261 CATACCATTATCTTATTGGGCTATCTTATCATGGTTGTGTTAGTCCAGTAGCTGGAGCTGCATGT
12232998 TCCCCTAACTGCCAACTTTAAATCACCAGCCCTAAAAATACATAACCGCTGTCACTTGTAAACCA
326 TCCCCTAACTGCCAACTTTAAATCACCAGCCCTAAAAATACATAACCGCTGTCACTTGTAAACCA
12233063 TGCCAAAACCTTAGCTCGCCTTCTTTTTTGTATCCTCACTCGGAGCACAGACGCGGCCGCTAATT
391 TGCCAAAACCTTAGCTCGCCTTCTTTTTTGTATCCTCACTCGGAGCACAGACGCGGCCGCTAATT
12233128 TTGCTTTCAGGTAAAGTATATCAAGTCAGCTCTTTAAATTTCATCTTTGTTATGAATTTTATGCT
456 TTGCTTTCAGGTAAAGTATATCAAGTCAGCTCTTTAAATTTCATCTTTGTTATGAATTTTATGCT
12233193 CTACTTATTTA
521 CTACTTATTTA
12233204 TTTATTTCTT
Statistics
Matches: 530, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
530 521 0.98
531 9 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (531 bp):
AGAGAATTATTAAAATTATTTAAATTTTTTGTAAAAAATATTATAATTTTAAAAAAAATATATTA
AAAATTAATTAAATTTTGACATGGCAATTCATGTGTAAGTCTATGTCAGCAAAGTTAATATTTGT
TTTCTTTTTTATTTATATTAGAGTGATTTGACAAAAAAAAACACTAAAGTCAAAAAGGTAAAAGA
AGTGAAAAATAAAATGAATGACTAAAATAATTTTTTGTTTAAGTTTAGAAGGCTAAATAAATCAT
CATACCATTATCTTATTGGGCTATCTTATCATGGTTGTGTTAGTCCAGTAGCTGGAGCTGCATGT
TCCCCTAACTGCCAACTTTAAATCACCAGCCCTAAAAATACATAACCGCTGTCACTTGTAAACCA
TGCCAAAACCTTAGCTCGCCTTCTTTTTTGTATCCTCACTCGGAGCACAGACGCGGCCGCTAATT
TTGCTTTCAGGTAAAGTATATCAAGTCAGCTCTTTAAATTTCATCTTTGTTATGAATTTTATGCT
CTACTTATTTA
Found at i:12246465 original size:33 final size:33
Alignment explanation
Indices: 12246418--12246482 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
12246408 ATAGGATTAC
12246418 CAGCCATTCTTTTAACATGTTCAAAGTAACTAT
1 CAGCCATTCTTTTAACATGTTCAAAGTAACTAT
* * *
12246451 CAGCCATT-TCTTTAACATTTTCCAGGTAACTA
1 CAGCCATTCT-TTTAACATGTTCAAAGTAACTA
12246483 AAACTAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (33 bp):
CAGCCATTCTTTTAACATGTTCAAAGTAACTAT
Found at i:12249727 original size:26 final size:26
Alignment explanation
Indices: 12249662--12249727 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
12249652 ATAAAACCAA
* *
12249662 ACTTTTTAAAAGTACTTCTCAAAAAC
1 ACTTTTCAAAAGCACTTCTCAAAAAC
* * * * **
12249688 ATTTTTCCACAGCATTTCTCAAAAGT
1 ACTTTTCAAAAGCACTTCTCAAAAAC
12249714 ACTTTTCAAAAGCA
1 ACTTTTCAAAAGCA
12249728 ATTAAAAACT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAAC
Found at i:12253343 original size:3 final size:3
Alignment explanation
Indices: 12253335--12253359 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12253325 CCATTTCACT
12253335 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
12253360 CTCTATCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12254687 original size:21 final size:23
Alignment explanation
Indices: 12254661--12254715 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
12254651 TAAGATATTG
*
12254661 AAAAAATAACA-AGAAAATA-TA
1 AAAAAATAACAGAAAAAATAGTA
12254682 AAAAAATAACAGTAAAAAATAGTA
1 AAAAAATAACAG-AAAAAATAGTA
12254706 AAAAAA-AACA
1 AAAAAATAACA
12254716 TATTCGGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 11 0.37
23 11 0.37
24 8 0.27
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (23 bp):
AAAAAATAACAGAAAAAATAGTA
Found at i:12255033 original size:22 final size:20
Alignment explanation
Indices: 12254986--12255036 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
12254976 TTCGACATCC
12254986 TTAAATT-ATAAATATTTTT
1 TTAAATTGATAAATATTTTT
*
12255005 TTCAAATTGATATATAATTTATT
1 TT-AAATTGATAAAT-ATTT-TT
12255028 TTAAATTGA
1 TTAAATTGA
12255037 ATCCTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 5 0.19
21 5 0.19
22 11 0.41
23 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
TTAAATTGATAAATATTTTT
Found at i:12266494 original size:2 final size:2
Alignment explanation
Indices: 12266487--12266516 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12266477 CAATAGCCTG
12266487 AT AT 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 AT AT
12266517 GATGCCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12273367 original size:43 final size:43
Alignment explanation
Indices: 12273287--12273368 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
12273277 TTATTTTTAA
* *
12273287 AATTTTTTAGTGCCGTCACTTCACATGGTGTGGCCAAAATTTG
1 AATTTTTTAGTCCCGTCACTTCACATGGTGTGACCAAAATTTG
** *
12273330 AATTTTTTAGTCCCGTCACTTCATGTGGTGTTACCAAAA
1 AATTTTTTAGTCCCGTCACTTCACATGGTGTGACCAAAA
12273369 ACAGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (43 bp):
AATTTTTTAGTCCCGTCACTTCACATGGTGTGACCAAAATTTG
Found at i:12278319 original size:85 final size:86
Alignment explanation
Indices: 12278212--12278379 Score: 320
Period size: 85 Copynumber: 2.0 Consensus size: 86
12278202 AAAAACTATA
*
12278212 CCATATATTAAAATTTATATAGAATAAATTATTTTGGAATTAAATAATTACAATAAACTATAATT
1 CCATATATTAAAATTTATATAGAATAAATTATTTTGAAATTAAATAATTACAATAAACTATAATT
12278277 AAATGAAACCAACATGAAATC
66 AAATGAAACCAACATGAAATC
12278298 CCATATA-TAAAATTTATATAGAATAAATTATTTTGAAATTAAATAATTACAATAAACTATAATT
1 CCATATATTAAAATTTATATAGAATAAATTATTTTGAAATTAAATAATTACAATAAACTATAATT
12278362 AAATGAAACCAACATGAA
66 AAATGAAACCAACATGAA
12278380 TATATGCAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 74 0.91
86 7 0.09
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.33
Consensus pattern (86 bp):
CCATATATTAAAATTTATATAGAATAAATTATTTTGAAATTAAATAATTACAATAAACTATAATT
AAATGAAACCAACATGAAATC
Found at i:12279629 original size:2 final size:2
Alignment explanation
Indices: 12279622--12279647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12279612 ATTCTTCCTC
12279622 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
12279648 GATGTGCCTT
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:12281150 original size:28 final size:27
Alignment explanation
Indices: 12281031--12281139 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 27
12281021 AATTTTGAAG
* * *
12281031 TACATATTTTTAAGTAT-AAAATGCAA
1 TACAAATTTTTAATTATAAAAATGTAA
* ** *
12281057 TGCACGTTTTTAATTTATAAAATTGTAA
1 TACAAATTTTTAA-TTATAAAAATGTAA
* *
12281085 TACAAATTTTTTAATAATAAAAATGCAA
1 TACAAA-TTTTTAATTATAAAAATGTAA
12281113 TACAAATTTTTAATTATAAAAATGTAA
1 TACAAATTTTTAATTATAAAAATGTAA
12281140 CCCATAATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
26 10 0.15
27 22 0.33
28 27 0.41
29 7 0.11
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (27 bp):
TACAAATTTTTAATTATAAAAATGTAA
Found at i:12281152 original size:27 final size:27
Alignment explanation
Indices: 12281063--12281150 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
12281053 GCAATGCACG
* * * *
12281063 TTTTTAATTTATAAAATTGTAATACAAA
1 TTTTTAA-TAATAAAAATGCAACACAAA
*
12281091 TTTTTTAATAATAAAAATGCAATACAAA
1 -TTTTTAATAATAAAAATGCAACACAAA
* * *
12281119 TTTTTAATTATAAAAATGTAACCCATAA
1 TTTTTAATAATAAAAATGCAACACA-AA
12281147 TTTT
1 TTTT
12281151 AAACATTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 21 0.41
28 23 0.45
29 7 0.14
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTTTAATAATAAAAATGCAACACAAA
Found at i:12295729 original size:50 final size:50
Alignment explanation
Indices: 12295667--12295821 Score: 193
Period size: 50 Copynumber: 3.1 Consensus size: 50
12295657 GTCACATCGT
* *
12295667 GACATACTGTTTTGGCCTCGTCAAGACGATGGAGTCTCTCGTCGTGCCGA
1 GACATACTGTTTTGGCCTCGTCAAGACGACGGAGTCTCTCGTCATGCCGA
* * *
12295717 GACATACTGTTTTGGCCTCGTCGAGACGACGGAGTCTCTCTTCATGCCGT
1 GACATACTGTTTTGGCCTCGTCAAGACGACGGAGTCTCTCGTCATGCCGA
* * * * * * * *
12295767 GGCATACTATTTTGGCCTTGTCAAGATGACGGTGTCTTTCGTCACGCCGT
1 GACATACTGTTTTGGCCTCGTCAAGACGACGGAGTCTCTCGTCATGCCGA
12295817 GACAT
1 GACAT
12295822 TATAAGTCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (50 bp):
GACATACTGTTTTGGCCTCGTCAAGACGACGGAGTCTCTCGTCATGCCGA
Found at i:12296975 original size:42 final size:41
Alignment explanation
Indices: 12296925--12297115 Score: 195
Period size: 42 Copynumber: 4.5 Consensus size: 41
12296915 TGGCACACAT
12296925 AGTGCATCATCGATTAAACCGAAGCAATCATATTGGCATGTA
1 AGTGCATCATCGA-TAAACCGAAGCAATCATATTGGCATGTA
* * * *
12296967 AGTGCATCATTGGATAAACCGAAGCAATTATACTGGCAAGTA
1 AGTGCATCA-TCGATAAACCGAAGCAATCATATTGGCATGTA
* * *
12297009 AGTGCATCATCGGATATACCGAATCAATCATATTGGCACGTA
1 AGTGCATCATC-GATAAACCGAAGCAATCATATTGGCATGTA
* ** * *
12297051 AGTGCATCATCGGGTGTATCGAAGAAAAT-ATATTGGCATGTA
1 AGTGCATCATC-GATAAACCGAAG-CAATCATATTGGCATGTA
* *
12297093 AGTGCGTCATCGGCTAAACCGAA
1 AGTGCATCATC-GATAAACCGAA
12297116 ATGTATACTT
Statistics
Matches: 125, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 118 0.94
43 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (41 bp):
AGTGCATCATCGATAAACCGAAGCAATCATATTGGCATGTA
Found at i:12297074 original size:84 final size:84
Alignment explanation
Indices: 12296925--12297115 Score: 240
Period size: 84 Copynumber: 2.3 Consensus size: 84
12296915 TGGCACACAT
* *
12296925 AGTGCATCATC-GATTAAACCGAAGCAATCATATTGGCATGTAAGTGCATCATTGGATAAACCGA
1 AGTGCATCATCGGA-TAAACCGAAGCAATCATATTGGCACGTAAGTGCATCATCGGATAAACCGA
* *
12296989 AGCAATTATACTGGCAAGTA
65 AGAAAATATACTGGCAAGTA
* * * ** *
12297009 AGTGCATCATCGGATATACCGAATCAATCATATTGGCACGTAAGTGCATCATCGGGTGTATCGAA
1 AGTGCATCATCGGATAAACCGAAGCAATCATATTGGCACGTAAGTGCATCATCGGATAAACCGAA
* *
12297074 GAAAATATATTGGCATGTA
66 GAAAATATACTGGCAAGTA
* *
12297093 AGTGCGTCATCGGCTAAACCGAA
1 AGTGCATCATCGGATAAACCGAA
12297116 ATGTATACTT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 89 0.98
85 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (84 bp):
AGTGCATCATCGGATAAACCGAAGCAATCATATTGGCACGTAAGTGCATCATCGGATAAACCGAA
GAAAATATACTGGCAAGTA
Found at i:12298722 original size:5 final size:5
Alignment explanation
Indices: 12298712--12298737 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12298702 TGAGCATTCG
12298712 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
12298738 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:12306183 original size:20 final size:21
Alignment explanation
Indices: 12306143--12306190 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
12306133 TACAATTTCT
12306143 CTTAAGAATTTTACCCAAAAC
1 CTTAAGAATTTTACCCAAAAC
*
12306164 CTTAAGATTTTTACCC-AAAC
1 CTTAAGAATTTTACCCAAAAC
12306184 CTTAAGA
1 CTTAAGA
12306191 CTCAATCCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (21 bp):
CTTAAGAATTTTACCCAAAAC
Found at i:12306605 original size:21 final size:20
Alignment explanation
Indices: 12306562--12306617 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
12306552 AAACACAATT
**
12306562 TATCGATACTTGGTAAAAGG
1 TATCGATACTTTTTAAAAGG
*
12306582 TATCGATACTTTTTGAAAATG
1 TATCGATACTTTTT-AAAAGG
*
12306603 TATCAATACTTTTTA
1 TATCGATACTTTTTA
12306618 TAATTAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (20 bp):
TATCGATACTTTTTAAAAGG
Found at i:12307293 original size:21 final size:20
Alignment explanation
Indices: 12307269--12307312 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
12307259 AACTTGTTTT
12307269 AAAACTCTTTTAACATGATTG
1 AAAACTCTTTTAAC-TGATTG
*
12307290 AAAA-TTTTTTAACTGAATTG
1 AAAACTCTTTTAACTG-ATTG
12307310 AAA
1 AAA
12307313 CCATTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 4 0.19
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (20 bp):
AAAACTCTTTTAACTGATTG
Found at i:12308272 original size:14 final size:14
Alignment explanation
Indices: 12308253--12308279 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12308243 ATATTAATTG
12308253 TTATTATTATTATA
1 TTATTATTATTATA
12308267 TTATTATTATTAT
1 TTATTATTATTAT
12308280 GAAATAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:12309041 original size:22 final size:24
Alignment explanation
Indices: 12309013--12309056 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
12309003 TATGGCAAGA
12309013 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGCTAGAAAAGTAAGTATG
12309035 AATTAAGCTAGAAAAGTAAGTA
1 AATTAAGCTAGAAAAGTAAGTA
12309057 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTAAGCTAGAAAAGTAAGTATG
Found at i:12309333 original size:21 final size:21
Alignment explanation
Indices: 12309309--12309350 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12309299 ATGGGACATT
12309309 TAAAGTAAGGTAAGTAATAAC
1 TAAAGTAAGGTAAGTAATAAC
*
12309330 TAAAGTAAGGTAGGTAATAAC
1 TAAAGTAAGGTAAGTAATAAC
12309351 ATTTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (21 bp):
TAAAGTAAGGTAAGTAATAAC
Found at i:12309363 original size:25 final size:24
Alignment explanation
Indices: 12309304--12309371 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 24
12309294 TAATCATGGG
12309304 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAGTAATA
*
12309328 AC---TAAAGTAAGGTAGGTAATA
1 ACATTTAAAGTAAGGTAAGTAATA
*
12309349 ACATTTGAAATTAA-GTAAG-AATA
1 ACATTT-AAAGTAAGGTAAGTAATA
12309372 TGTGTGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 20 0.54
23 4 0.11
24 7 0.19
25 6 0.16
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (24 bp):
ACATTTAAAGTAAGGTAAGTAATA
Found at i:12309677 original size:27 final size:26
Alignment explanation
Indices: 12309619--12309677 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
12309609 ATCTAATGCC
**
12309619 TTATTGGTGTGTTTGGGAGGATATAA
1 TTATTGGTGTGTTAAGGAGGATATAA
* *
12309645 TATATTGGTGTGTTAATGAGGATTTATA
1 T-TATTGGTGTGTTAAGGAGGATATA-A
12309673 TTATT
1 TTATT
12309678 CCGGGTGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 24 0.89
28 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (26 bp):
TTATTGGTGTGTTAAGGAGGATATAA
Found at i:12327542 original size:40 final size:39
Alignment explanation
Indices: 12327483--12327559 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
12327473 CGGTGTTGCG
* * *
12327483 ACATCTAATATTCAGTGTTGCAACATTGGGCTATGTCGTT
1 ACATCCAACATTCAATGTTGCAACATT-GGCTATGTCGTT
*
12327523 ACATCCAACATTCAATGTTGCAACATTGGCTTTGTCG
1 ACATCCAACATTCAATGTTGCAACATTGGCTATGTCG
12327560 CGACATTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 9 0.27
40 24 0.73
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (39 bp):
ACATCCAACATTCAATGTTGCAACATTGGCTATGTCGTT
Found at i:12336189 original size:20 final size:18
Alignment explanation
Indices: 12336160--12336200 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
12336150 TTTTTTCAAC
12336160 TTTAAGGAAAAACCTAGTT
1 TTTAAGG-AAAACCTAGTT
12336179 TTTAGAGGAAAACCTAGTT
1 TTTA-AGGAAAACCTAGTT
12336198 TTT
1 TTT
12336201 TTACAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTAAGGAAAACCTAGTT
Found at i:12343579 original size:41 final size:41
Alignment explanation
Indices: 12343522--12343602 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
12343512 GAAAAAAATC
12343522 TTTTTTTTTCTTTCCAATAATTTACTCAAATAAATGAATGA
1 TTTTTTTTTCTTTCCAATAATTTACTCAAATAAATGAATGA
12343563 TTTTTTTTTCTTTCCAATAATTTACTCAAATAAATGAATG
1 TTTTTTTTTCTTTCCAATAATTTACTCAAATAAATGAATG
12343603 GTTCAACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.49
Consensus pattern (41 bp):
TTTTTTTTTCTTTCCAATAATTTACTCAAATAAATGAATGA
Found at i:12353325 original size:3 final size:3
Alignment explanation
Indices: 12353317--12353346 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12353307 ACTCCCGCTA
*
12353317 CTG CTG CTG CTG CTG CTG CTG CCG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
12353347 TGAATCGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (3 bp):
CTG
Found at i:12356488 original size:41 final size:40
Alignment explanation
Indices: 12356443--12356521 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
12356433 GAGACACTGG
* *
12356443 GTGTCAATTTACTACTTCGGATATATTCGATGAGACATTCA
1 GTGTCAATTTACTACTTCGAAT-TATCCGATGAGACATTCA
* *
12356484 GTGTCAATTTATTACTTCGAATTATCCGATGAGGCATT
1 GTGTCAATTTACTACTTCGAATTATCCGATGAGACATT
12356522 GGGTGCCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 14 0.41
41 20 0.59
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (40 bp):
GTGTCAATTTACTACTTCGAATTATCCGATGAGACATTCA
Found at i:12361226 original size:13 final size:13
Alignment explanation
Indices: 12361210--12361242 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12361200 AATGGAATAA
12361210 AAATAATATAAAC-
1 AAATAA-ATAAACG
12361223 AAATAAATAAACG
1 AAATAAATAAACG
12361236 AAATAAA
1 AAATAAA
12361243 AAGCAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAATAAACG
Found at i:12362729 original size:40 final size:40
Alignment explanation
Indices: 12362683--12362762 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
12362673 CTATTTCAAA
* *
12362683 TTCACTTTTGATTCAAT-CACAATTCA-ATTCAATTTCACTT
1 TTCACTTTTCAATCAATACACAATTCAGA-T-AATTTCACTT
*
12362723 TTCACTTTTCAATCAATACACAGTTCAGATAATTTCACTT
1 TTCACTTTTCAATCAATACACAATTCAGATAATTTCACTT
12362763 CGATTCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 25 0.71
41 9 0.26
42 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (40 bp):
TTCACTTTTCAATCAATACACAATTCAGATAATTTCACTT
Found at i:12363522 original size:12 final size:12
Alignment explanation
Indices: 12363507--12363537 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12363497 TTCTCTTTTA
12363507 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
12363519 TTTTTCTTTCGC
1 TTTTTCTTTCCC
12363531 TTTTTCT
1 TTTTTCT
12363538 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:12366900 original size:42 final size:43
Alignment explanation
Indices: 12366819--12366900 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
12366809 AATACATACG
***
12366819 GTGGAGAGTTTCCTACATCAAAGGGTCATATATGTATAACCTT
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
* *
12366862 GTGGAGAGTTTCCTACATC-AAGGGTCATTTCCCAATAAC
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAAC
12366901 ATAAGCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 15 0.44
43 19 0.56
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
Found at i:12380759 original size:20 final size:20
Alignment explanation
Indices: 12380734--12380773 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12380724 AGCCTATGTG
12380734 AAAGTTTCTGATACTAATAT
1 AAAGTTTCTGATACTAATAT
12380754 AAAGTTTCTGATACTAATAT
1 AAAGTTTCTGATACTAATAT
12380774 GCCAATTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAGTTTCTGATACTAATAT
Found at i:12383875 original size:21 final size:21
Alignment explanation
Indices: 12383849--12383889 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12383839 AATATGATTT
12383849 TAATATTTTATG-ATTATAATG
1 TAATATTTTA-GCATTATAATG
12383870 TAATATTTTAGCATTATAAT
1 TAATATTTTAGCATTATAAT
12383890 TTTTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TAATATTTTAGCATTATAATG
Found at i:12383913 original size:3 final size:3
Alignment explanation
Indices: 12383905--12383929 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12383895 ATAAATTAAA
12383905 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
12383930 CGAGGAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12390124 original size:27 final size:25
Alignment explanation
Indices: 12390073--12390124 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
12390063 TTTGGATAAT
**
12390073 AATAATATATATCTTTTCTGATTAA
1 AATAATATATATCTTTTAGGATTAA
*
12390098 AATATATATTATATCTTTTAGGTTTAA
1 AATA-ATA-TATATCTTTTAGGATTAA
12390125 CATGAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 15 0.68
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (25 bp):
AATAATATATATCTTTTAGGATTAA
Found at i:12390317 original size:3 final size:3
Alignment explanation
Indices: 12390309--12390340 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12390299 CTCCAAAAAT
12390309 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12390341 GTAGATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12393794 original size:2 final size:2
Alignment explanation
Indices: 12393787--12393815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12393777 ATGTTGACAG
12393787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12393816 AAGCCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12394823 original size:18 final size:18
Alignment explanation
Indices: 12394767--12394823 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
12394757 ATTAAGAAAC
12394767 TAAAAATTAGACTATAAA
1 TAAAAATTAGACTATAAA
* * *
12394785 TATATATT-GA-TA-AAT
1 TAAAAATTAGACTATAAA
12394800 TAAAAATTAGACTATAAA
1 TAAAAATTAGACTATAAA
12394818 TAAAAA
1 TAAAAA
12394824 CTTGTAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
17 4 0.13
18 14 0.47
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAAATTAGACTATAAA
Found at i:12395304 original size:16 final size:17
Alignment explanation
Indices: 12395278--12395324 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
12395268 TTCATGGTAT
12395278 ATTTT-TAATTTA-AAA
1 ATTTTATAATTTATAAA
*
12395293 TTTTTATAATTTATAAA
1 ATTTTATAATTTATAAA
*
12395310 ATTTTA-AATTAATAA
1 ATTTTATAATTTATAA
12395325 CGATAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATAATTTATAAA
Found at i:12396112 original size:19 final size:19
Alignment explanation
Indices: 12396080--12396145 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
12396070 TTAATTTTAA
12396080 TTTTTCAATATTATTTAATAT
1 TTTTTC-AT-TTATTTAATAT
*
12396101 TTTTTCATTTATGTAAT-T
1 TTTTTCATTTATTTAATAT
* *
12396119 TTAATTCATTTTTATTTTATAT
1 TT-TTTCA--TTTATTTAATAT
12396141 TTTTT
1 TTTTT
12396146 TATAACAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 3 0.08
19 12 0.33
20 2 0.06
21 16 0.44
22 3 0.08
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTCATTTATTTAATAT
Found at i:12398215 original size:92 final size:92
Alignment explanation
Indices: 12398065--12398673 Score: 1200
Period size: 92 Copynumber: 6.6 Consensus size: 92
12398055 CAACATTGAT
12398065 TTTTTAAAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTT
1 TTTTT-AAA-ATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTT
12398130 AAATATTTTAATAGTAATTTATTTTTATA
64 AAATATTTTAATAGTAATTTATTTTTATA
12398159 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
12398224 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
12398251 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
12398316 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
12398343 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
12398408 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
12398435 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
12398500 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
12398527 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
12398592 ATATTTTAATAGTAATTTATTTTTATA
66 ATATTTTAATAGTAATTTATTTTTATA
12398619 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAA
1 TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAA
12398674 NNNNNNNNNN
Statistics
Matches: 515, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
92 507 0.98
93 3 0.01
94 5 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (92 bp):
TTTTTAAAATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTAA
ATATTTTAATAGTAATTTATTTTTATA
Found at i:12403972 original size:127 final size:128
Alignment explanation
Indices: 12403740--12404015 Score: 337
Period size: 127 Copynumber: 2.2 Consensus size: 128
12403730 TAAGGCCAAA
* * * * *
12403740 CAGGAAATACTGT-AGAAAAATAGCATCCACGTGAGAGTTTTTTTCATCAATTTTACTGACAGTC
1 CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAGAGCTTTTTCCATCAATTTTACTGACAGTC
*
12403804 CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAGAACCGTCTTCTCAAAATTATT-ATTT
66 CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAAAACCGTCTTCTCAAAATTATTCATTT
* *
12403866 CAGGAACTACTGTAAAAAAAAGAGCGTCCACGTG-GTAGCTTTTTCCAGT-AATTTTGCTGACAG
1 CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAG-AGCTTTTTCCA-TCAATTTTACTGACAG
* ** * * *
12403929 TGCATCCTGCTTGAAGTGTTTTTTACATTATCTT-TTCAAAACCGTCTTCTCAAAATTATTCTTT
64 TCCATCCTGCTTGAAGCATTTTTGACACTAT-TTATTCAAAACCGTCTTCTCAAAATTATTCATT
12403993 T
128 T
**
12403994 CATAAACTACTGTAGAAAAAAA
1 CAGGAACTACTGTA-AAAAAAA
12404016 AACAAAAGTT
Statistics
Matches: 128, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
126 13 0.10
127 90 0.70
128 18 0.14
129 7 0.05
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (128 bp):
CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAGAGCTTTTTCCATCAATTTTACTGACAGTC
CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAAAACCGTCTTCTCAAAATTATTCATTT
Found at i:12404111 original size:34 final size:32
Alignment explanation
Indices: 12404067--12404182 Score: 115
Period size: 34 Copynumber: 3.5 Consensus size: 32
12404057 CTAAACACAA
*
12404067 AATTATTTAAAAAAACTAACCCATAATTTAATT
1 AATTTTTTAAAAAAACTAACCC-TAATTTAATT
**
12404100 AATTTTCTTAAAAATCCTAATCCCTAATTTAATT
1 AATTTT-TTAAAAAAACTAA-CCCTAATTTAATT
*** * *
12404134 AATTTATTTAAAATCTCAAAAACCTAATTTAATT
1 AATTT-TTTAAAAAAAC-TAACCCTAATTTAATT
12404168 AATTTTTTAAAAAAA
1 AATTTTTTAAAAAAA
12404183 TCTTAAACCT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 12 0.18
34 50 0.74
35 6 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (32 bp):
AATTTTTTAAAAAAACTAACCCTAATTTAATT
Done.