Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 4 of 211
Found at i:1111691 original size:41 final size:41
Alignment explanation
Indices: 1111524--1111702 Score: 120
Period size: 41 Copynumber: 4.5 Consensus size: 41
1111514 ATCAAAGAAT
* **
1111524 AAATTAGTTCTATTAAAAATT-TCATCAATTTCTACGGTTAA
1 AAATTAGTTCTATTAAAAATTAT-ATCAATTTCCAATGTTAA
* * *
1111565 AAATTAGTTCTA-TAAAAA--AAATCAATTTCTAATATTAA
1 AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
* * ** * * * * *
1111603 AAATTGGTTCTATTCATTATTATACGCTAGTT-CAAAG--AGC
1 AAATTAGTTCTATTAAAAATTATA-TCAATTTCCAATGTTA-A
* *
1111643 AAATTAGTTCTATTAAAAATTCTATCAATTTCCACTGTTAA
1 AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
*
1111684 AAATTAGTTCTATAAAAAA
1 AAATTAGTTCTATTAAAAA
1111703 ATAGTTTAAT
Statistics
Matches: 101, Mismatches: 28, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
38 26 0.26
39 8 0.08
40 28 0.28
41 34 0.34
42 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (41 bp):
AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
Found at i:1118158 original size:32 final size:32
Alignment explanation
Indices: 1118119--1118189 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1118109 TATGGGTTAT
*
1118119 ACAACAAACACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1118151 ACAACAAAAACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1118183 ACAACAA
1 ACAACAA
1118190 TAATTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (32 bp):
ACAACAAAAACATATTTAAAACTCAAAACCCA
Found at i:1119000 original size:18 final size:18
Alignment explanation
Indices: 1118979--1119022 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1118969 TTTTATATAA
* *
1118979 AAATAAATTTAATACATT
1 AAATAAATTAAAAACATT
*
1118997 AAATAAATTAAAAATATT
1 AAATAAATTAAAAACATT
1119015 AAATAAAT
1 AAATAAAT
1119023 GTTTTCTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAATTAAAAACATT
Found at i:1119001 original size:9 final size:9
Alignment explanation
Indices: 1118979--1119022 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1118969 TTTTATATAA
1118979 AAATAAATT
1 AAATAAATT
* *
1118988 TAATACATT
1 AAATAAATT
1118997 AAATAAATT
1 AAATAAATT
1119006 AAA-AATATT
1 AAATAA-ATT
1119015 AAATAAAT
1 AAATAAAT
1119023 GTTTTCTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 25 0.86
10 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATAAATT
Found at i:1123496 original size:27 final size:27
Alignment explanation
Indices: 1123464--1123529 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 27
1123454 TAAGTTTTGG
1123464 GTTTAATTAATTTTTTTAAAATTAAGA
1 GTTTAATTAATTTTTTTAAAATTAAGA
* *
1123491 GTTTAATCAGAATTTTTTTAAAATTGAGA
1 GTTTAAT--TAATTTTTTTAAAATTAAGA
*
1123520 TTTTAATTAA
1 GTTTAATTAA
1123530 AAATTTTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 9 0.27
29 24 0.73
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (27 bp):
GTTTAATTAATTTTTTTAAAATTAAGA
Found at i:1123535 original size:30 final size:29
Alignment explanation
Indices: 1123472--1123571 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
1123462 GGGTTTAATT
* *
1123472 AATTTTTTTAAAATTAAGAGTTTAATCAG
1 AATTTTTTTAAAATTAAGAGTTTAATAAA
* *
1123501 AATTTTTTTAAAATTGAGATTTTAATTAAA
1 AATTTTTTTAAAATTAAGAGTTTAA-TAAA
*** ** *
1123531 AATTTTGAGAAAATTGTGAGATTAAT-AA
1 AATTTTTTTAAAATTAAGAGTTTAATAAA
*
1123559 AATCTTTTTAAAA
1 AATTTTTTTAAAA
1123572 AACAAGAGAC
Statistics
Matches: 56, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 11 0.20
29 24 0.43
30 21 0.38
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (29 bp):
AATTTTTTTAAAATTAAGAGTTTAATAAA
Found at i:1125802 original size:51 final size:52
Alignment explanation
Indices: 1125747--1125845 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
1125737 TATTTGAAAA
* *
1125747 AAATTAAAC-TATGAAGCCAAG-TTCACGTACCTAATTGGACAA-AAAAATATC
1 AAATTAAACAT-TGAAACCAAGATT-ACGTACCTAACTGGACAATAAAAATATC
* *
1125798 AAATTAAACATTGAAACTAAGATTAGGTACCTAACTGGACAATAAAAA
1 AAATTAAACATTGAAACCAAGATTACGTACCTAACTGGACAATAAAAA
1125846 AAAACTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 33 0.80
52 8 0.20
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.23
Consensus pattern (52 bp):
AAATTAAACATTGAAACCAAGATTACGTACCTAACTGGACAATAAAAATATC
Found at i:1126587 original size:16 final size:17
Alignment explanation
Indices: 1126566--1126598 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1126556 TATATTTATT
1126566 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
1126582 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
1126599 AATACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:1126638 original size:22 final size:21
Alignment explanation
Indices: 1126590--1126645 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1126580 AATTTTAAAA
* **
1126590 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAATTTTTGG
1126611 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTTGG
1126634 TATTTATTAAAA
1 TATTT-TTAAAA
1126646 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 15 0.52
23 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTGG
Found at i:1130658 original size:35 final size:36
Alignment explanation
Indices: 1130619--1130697 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
1130609 TTTGCCCAGA
1130619 CCCGGCCCGAGAAAAAA-TCACAAGCCCGGGCCCGG
1 CCCGGCCCGAGAAAAAATTCACAAGCCCGGGCCCGG
*
1130654 CCCGGCCCGGGAAAAAATTCACAAGCCCGGGCCCGG
1 CCCGGCCCGAGAAAAAATTCACAAGCCCGGGCCCGG
1130690 CCCGGCCC
1 CCCGGCCC
1130698 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 16 0.38
36 26 0.62
ACGTcount: A:0.24, C:0.43, G:0.29, T:0.04
Consensus pattern (36 bp):
CCCGGCCCGAGAAAAAATTCACAAGCCCGGGCCCGG
Found at i:1130747 original size:21 final size:21
Alignment explanation
Indices: 1130702--1130743 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1130692 CGGCCCATTT
1130702 TTATTTTAAAAAATTAAAAAAA
1 TTATTTT-AAAAATTAAAAAAA
1130724 TTATTTT-AAAATTAAAAAAA
1 TTATTTTAAAAATTAAAAAAA
1130744 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.65
22 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATTTTAAAAATTAAAAAAA
Found at i:1130777 original size:31 final size:30
Alignment explanation
Indices: 1130709--1130767 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1130699 TTTTTATTTT
* *
1130709 AAAAAATTAAAAAAATTATTTTAAAATTAA
1 AAAAAATTAAAAAAAGTATTTTAAAAATAA
1130739 AAAAAATTAAAAAAAGTATTTTAAAAATA
1 AAAAAATTAAAAAAAGTATTTTAAAAATA
1130768 TTGTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (30 bp):
AAAAAATTAAAAAAAGTATTTTAAAAATAA
Found at i:1130783 original size:39 final size:38
Alignment explanation
Indices: 1130719--1130824 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 38
1130709 AAAAAATTAA
* * *
1130719 AAAAATTATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTGTAAAATT-TAAAAAA-TAAAAAAAGTA-TGT
1130761 AAAAATATTGTAAAATTTAAAAAATAAAAAAAGTATGT
1 AAAAATATTGTAAAATTTAAAAAATAAAAAAAGTATGT
* **
1130799 AAAAATATTTTAAAATAAAAAAAATA
1 AAAAATATTGTAAAATTTAAAAAATA
1130825 TTTATTATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 25 0.43
39 11 0.19
40 6 0.10
41 11 0.19
42 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (38 bp):
AAAAATATTGTAAAATTTAAAAAATAAAAAAAGTATGT
Found at i:1148782 original size:14 final size:14
Alignment explanation
Indices: 1148763--1148793 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1148753 GTTATCTGTG
1148763 TATTCGTATTTGGT
1 TATTCGTATTTGGT
1148777 TATTCGTATTTGGT
1 TATTCGTATTTGGT
1148791 TAT
1 TAT
1148794 CCGTGTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.19, T:0.58
Consensus pattern (14 bp):
TATTCGTATTTGGT
Found at i:1161498 original size:23 final size:23
Alignment explanation
Indices: 1161468--1161513 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1161458 AGTGTGATTT
*
1161468 AATTTGAGAATTTGGACCATATC
1 AATTTGAGAATATGGACCATATC
1161491 AATTTGAGAATATGGACCATATC
1 AATTTGAGAATATGGACCATATC
1161514 TATAACTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (23 bp):
AATTTGAGAATATGGACCATATC
Found at i:1170443 original size:21 final size:21
Alignment explanation
Indices: 1170398--1170443 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1170388 AATGATAATT
* *
1170398 TAAATATTAAAATAAAAAAAT
1 TAAATATCAAAATAAAAAAAG
* *
1170419 TAAATATCAAAATAGAAATAG
1 TAAATATCAAAATAAAAAAAG
1170440 TAAA
1 TAAA
1170444 ATTTAATTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAATATCAAAATAAAAAAAG
Found at i:1173755 original size:2 final size:2
Alignment explanation
Indices: 1173750--1173786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1173740 TTTTTTTAAA
1173750 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1173787 AATCTATCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1177112 original size:3 final size:3
Alignment explanation
Indices: 1177104--1177131 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1177094 AAAATAAGTA
1177104 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1177132 AGAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1180525 original size:26 final size:28
Alignment explanation
Indices: 1180476--1180528 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1180466 GATAATCATA
1180476 ATTAATATATCAATAAATAAAATTTTAT
1 ATTAATATATCAATAAATAAAATTTTAT
* *
1180504 ATTAA-ATAT-AATAATTACAATTTTA
1 ATTAATATATCAATAAATAAAATTTTA
1180529 AAGTATGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 4 0.17
28 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATATATCAATAAATAAAATTTTAT
Found at i:1183816 original size:3 final size:3
Alignment explanation
Indices: 1183808--1183832 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1183798 GCTAAAAAGA
1183808 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1183833 CTTCTTTTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1185247 original size:30 final size:31
Alignment explanation
Indices: 1185213--1185275 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1185203 ATAAAATGGC
1185213 CATTGAACTA-TTAAAAGTTTTTATTTAAAT
1 CATTGAACTATTTAAAAGTTTTTATTTAAAT
*
1185243 CATTGACCTATTTAAAAGTTTTTATTTAAAT
1 CATTGAACTATTTAAAAGTTTTTATTTAAAT
1185274 CA
1 CA
1185276 CTTGGATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (31 bp):
CATTGAACTATTTAAAAGTTTTTATTTAAAT
Found at i:1186998 original size:3 final size:3
Alignment explanation
Indices: 1186992--1187021 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1186982 AGAAGAAGAA
*
1186992 GAT GAT GAT GAT GAT GAA GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1187022 ATTGTGGATT
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:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:1187571 original size:25 final size:25
Alignment explanation
Indices: 1187507--1187573 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1187497 CCACAAAATT
1187507 AGAAGTTTATAATTTAATTTCTTAAA
1 AGAA-TTTATAATTTAATTTCTTAAA
* * *
1187533 AGAATTTAAAATTTTATTTCTCTCAA
1 AGAATTTATAATTTAATTTCT-TAAA
*
1187559 A-AATTTATGATTTAA
1 AGAATTTATAATTTAA
1187574 AATGGGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 26 0.76
26 8 0.24
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
AGAATTTATAATTTAATTTCTTAAA
Found at i:1191668 original size:21 final size:21
Alignment explanation
Indices: 1191647--1191691 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1191637 ACTCGTTTTA
1191647 TACATTTTTAATATATTATTAT
1 TACATTTTT-ATATATTATTAT
**
1191669 TTTATTTTTATATATTA-TAT
1 TACATTTTTATATATTATTAT
1191689 TAC
1 TAC
1191692 TAGTTACTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TACATTTTTATATATTATTAT
Found at i:1201181 original size:13 final size:11
Alignment explanation
Indices: 1201153--1201187 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1201143 TTTAATAAAA
1201153 TTATAATTTTT
1 TTATAATTTTT
1201164 TTATAAATTTTGT
1 TTAT-AATTTT-T
1201177 TTATAATTTTT
1 TTATAATTTTT
1201188 ATGATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:1204712 original size:27 final size:28
Alignment explanation
Indices: 1204682--1204735 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
1204672 TAAGCACTCG
1204682 TAAATATAGTCAAAT-ATATATTATTGT
1 TAAATATAGTCAAATAATATATTATTGT
*
1204709 TAAATATAGTTAAATAAATATATTATT
1 TAAATATAGTCAAAT-AATATATTATT
1204736 ATCGAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
TAAATATAGTCAAATAATATATTATTGT
Found at i:1204743 original size:29 final size:27
Alignment explanation
Indices: 1204683--1204744 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
1204673 AAGCACTCGT
* *
1204683 AAATATAGTCAAATATATATTATTGTT
1 AAATATAGTCAAATATATATTATTATC
*
1204710 AAATATAGTTAAATAAATATATTATTATC
1 AAATATAGTCAAAT--ATATATTATTATC
*
1204739 GAATAT
1 AAATAT
1204745 TATGTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
29 16 0.55
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATATAGTCAAATATATATTATTATC
Found at i:1218866 original size:20 final size:20
Alignment explanation
Indices: 1218830--1218867 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1218820 AGCTTTCAAT
1218830 AAAATATTTATTATAATTTA
1 AAAATATTTATTATAATTTA
*
1218850 AAAATCTTTCATT-TAATT
1 AAAATATTT-ATTATAATT
1218868 ATATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATTTATTATAATTTA
Found at i:1221065 original size:18 final size:18
Alignment explanation
Indices: 1221038--1221073 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
1221028 TCTTTTTTCT
1221038 TTTTAGTTTTAC-TTTAA
1 TTTTAGTTTTACATTTAA
1221055 TTTTAGCTTTTACATTTAA
1 TTTTAG-TTTTACATTTAA
1221074 AACTTATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTAGTTTTACATTTAA
Found at i:1221862 original size:47 final size:47
Alignment explanation
Indices: 1221809--1221906 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
1221799 GAGTCATGTA
1221809 TCTTAATTGTTGGGGTCAAGGATGAGGATTTTGACTTGTTCTTCGGC
1 TCTTAATTGTTGGGGTCAAGGATGAGGATTTTGACTTGTTCTTCGGC
1221856 TCTTAATTGTTGGGGTCAAGGATGAGGATTTTGACTTGTTCTTCGGC
1 TCTTAATTGTTGGGGTCAAGGATGAGGATTTTGACTTGTTCTTCGGC
1221903 TCTT
1 TCTT
1221907 TTTTTTTCGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (47 bp):
TCTTAATTGTTGGGGTCAAGGATGAGGATTTTGACTTGTTCTTCGGC
Found at i:1222607 original size:15 final size:16
Alignment explanation
Indices: 1222589--1222619 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1222579 TATAATAAAA
1222589 AGTTTTAAG-ATTTTT
1 AGTTTTAAGTATTTTT
1222604 AGTTTTAAGTATTTTT
1 AGTTTTAAGTATTTTT
1222620 CAGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (16 bp):
AGTTTTAAGTATTTTT
Found at i:1222793 original size:7 final size:7
Alignment explanation
Indices: 1222781--1222805 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1222771 AAAATAAGAT
1222781 AAATTTA
1 AAATTTA
1222788 AAATTTA
1 AAATTTA
1222795 AAATTTA
1 AAATTTA
1222802 AAAT
1 AAAT
1222806 AATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:1233781 original size:142 final size:141
Alignment explanation
Indices: 1233505--1233785 Score: 438
Period size: 142 Copynumber: 2.0 Consensus size: 141
1233495 ATTTGATACC
* * * *
1233505 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAAAATTAGGCACGGCATAGCCAGCAAATC
1 TTAAGCAAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
** *
1233570 AGTTCTTAACCTCTCATTTGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAT
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
1233635 TTCAATTAACT
131 TTCAATTAACT
* *
1233646 TTAAGCAAAGTTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCAAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCC-AGCAAA
* *
1233710 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCA
1233775 ACTTCAATTAA
129 ACTTCAATTAA
1233786 AACTAGCTTA
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 13 0.10
142 112 0.88
143 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCAAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
TTCAATTAACT
Found at i:1234570 original size:24 final size:24
Alignment explanation
Indices: 1234537--1234614 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
1234527 ATTTATATTA
1234537 TTTTTA-ATTTAATATTTAATAAT
1 TTTTTATATTTAATATTTAATAAT
* *
1234560 TTTTTATATTTTATACTTATTATAA-
1 TTTTTATATTTAATA-TT-TAATAAT
*
1234585 -TTTTATATATAATTATCTTAAT-AT
1 TTTTTATATTTAA-TAT-TTAATAAT
1234609 TTTTTA
1 TTTTTA
1234615 ATGTTTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
23 7 0.16
24 21 0.49
25 10 0.23
26 5 0.12
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTATATTTAATATTTAATAAT
Found at i:1234604 original size:26 final size:26
Alignment explanation
Indices: 1234555--1234604 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1234545 TTAATATTTA
* *
1234555 ATAATTTTTTATATTTTATACTTATT
1 ATAATTTTATATATATTATACTTATT
1234581 ATAATTTTATATATAATTAT-CTTA
1 ATAATTTTATATAT-ATTATACTTA
1234605 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATAATTTTATATATATTATACTTATT
Found at i:1237324 original size:6 final size:6
Alignment explanation
Indices: 1237313--1237389 Score: 136
Period size: 6 Copynumber: 12.8 Consensus size: 6
1237303 CTCTAAACAG
*
1237313 TACATA TACATA TACATA TACATA TACATG TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
1237361 TACATG TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACATA TACAT
1237390 GAAGGTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:1241705 original size:26 final size:26
Alignment explanation
Indices: 1241667--1241718 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1241657 TTACTATGAA
1241667 AATAATAAAGGTTAAAATACAAACACT
1 AATAATAAAGGTTAAAAT-CAAACACT
* *
1241694 AATAA-AAAGGTTGAAATCTAACACT
1 AATAATAAAGGTTAAAATCAAACACT
1241719 TAGACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (26 bp):
AATAATAAAGGTTAAAATCAAACACT
Found at i:1243733 original size:14 final size:16
Alignment explanation
Indices: 1243708--1243745 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1243698 TTAAAATTCA
1243708 AAAAATACATT-AATT
1 AAAAATACATTAAATT
1243723 AAAAATA-ATTAAATT
1 AAAAATACATTAAATT
1243738 -AAAATACA
1 AAAAATACA
1243746 AAAACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATACATTAAATT
Found at i:1259869 original size:122 final size:123
Alignment explanation
Indices: 1259599--1259860 Score: 314
Period size: 122 Copynumber: 2.1 Consensus size: 123
1259589 ATTAGGCAAG
* * * * * * *
1259599 AGATTTTTGAATTTGGGTCAGATCGAATTGACTTAAATTCGAATTAGACATTCCCATTGATTGAA
1 AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
* * *
1259664 ATACTCTTCTAACCTTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGGATGA
66 ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAATAA
* * * * *
1259722 A-ACTTTTAAATTTGGATAAGATCAAACTAACTTGAATTCGAATTAAACATTCTCATTAATTAAA
1 AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
* * ** *
1259786 ATACTC-TCTAACCCTTT-AAGTTTGATCTAAAGTTATAAAAATCAAACTTTGAATAAA
66 ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAAT-AA
1259843 AGATTTTTGAATTTGGGT
1 AGATTTTTGAATTTGGGT
1259861 TATTTCAAAT
Statistics
Matches: 114, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
120 31 0.27
121 12 0.11
122 70 0.61
123 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (123 bp):
AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAATAA
Found at i:1260793 original size:16 final size:16
Alignment explanation
Indices: 1260763--1260802 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1260753 TATTGTTAAC
*
1260763 ATATTAATAATATATA
1 ATATAAATAATATATA
1260779 ATA-AAATATATATATA
1 ATATAAATA-ATATATA
1260795 ATATAAAT
1 ATATAAAT
1260803 CAGTTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATAATATATA
Found at i:1264574 original size:16 final size:16
Alignment explanation
Indices: 1264553--1264583 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1264543 TTTATTCAGA
*
1264553 TCATTTCATGTTTAAG
1 TCATTTCAGGTTTAAG
1264569 TCATTTCAGGTTTAA
1 TCATTTCAGGTTTAA
1264584 ATTATTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
TCATTTCAGGTTTAAG
Found at i:1264590 original size:16 final size:16
Alignment explanation
Indices: 1264552--1264590 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1264542 ATTTATTCAG
*
1264552 ATCATTTCATGTTTAA
1 ATCATTTCAGGTTTAA
*
1264568 GTCATTTCAGGTTTAA
1 ATCATTTCAGGTTTAA
*
1264584 ATTATTT
1 ATCATTT
1264591 TGGGCTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (16 bp):
ATCATTTCAGGTTTAA
Found at i:1265606 original size:31 final size:31
Alignment explanation
Indices: 1265571--1265631 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1265561 CTCAATGACA
*
1265571 TAAATAAAAACTTTTGAATAGTTTACTGATT
1 TAAATAAAAACTTTTGAATAATTTACTGATT
* *
1265602 TAAATGAAAACTTTTGAATAATTTAGTGAT
1 TAAATAAAAACTTTTGAATAATTTACTGAT
1265632 CATTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (31 bp):
TAAATAAAAACTTTTGAATAATTTACTGATT
Found at i:1269271 original size:25 final size:25
Alignment explanation
Indices: 1269237--1269287 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1269227 ATCAGCTATA
1269237 ACGATTAAATTTTAAAAGTTTCATG
1 ACGATTAAATTTTAAAAGTTTCATG
1269262 ACGATTAAATTTTAAAAGTTTCATG
1 ACGATTAAATTTTAAAAGTTTCATG
1269287 A
1 A
1269288 TTACCATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (25 bp):
ACGATTAAATTTTAAAAGTTTCATG
Found at i:1274246 original size:17 final size:18
Alignment explanation
Indices: 1274207--1274247 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1274197 TTTTATAAAT
1274207 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGATA
1274225 TGTGAATTA-ATATTGA-A
1 TGTGAATTATAT-TTGATA
1274242 TGTGAA
1 TGTGAA
1274248 AGGAAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (18 bp):
TGTGAATTATATTTGATA
Found at i:1274498 original size:23 final size:23
Alignment explanation
Indices: 1274471--1274591 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
1274461 AGTGTTATTG
1274471 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1274493 ATTCAGTGGTAGCTACGGTTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
1274517 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1274540 TTCAGTGGTAGCTAC-GCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1274562 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1274585 ATCAGTG
1 ATCAGTG
1274592 TGGCATTTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
22 20 0.23
23 66 0.76
24 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1274577 original size:45 final size:46
Alignment explanation
Indices: 1274471--1274591 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
1274461 AGTGTTATTG
* *
1274471 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1274517 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTAC-GCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
1274562 ATCAGTGGTAACTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
1274592 TGGCATTTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
45 34 0.48
46 37 0.52
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:1278630 original size:26 final size:25
Alignment explanation
Indices: 1278579--1278663 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
1278569 GGGGTCAAAT
* **
1278579 TAAATTATATATTTT-TTATGATAA
1 TAAATTAAATATTTTATTATTTTAA
1278603 TAAATTAAATTATTTTATTATTTTAA
1 TAAATTAAA-TATTTTATTATTTTAA
* * *
1278629 TAATTTATATA-TTTATAACTTTTAA
1 TAAATTAAATATTTTATTA-TTTTAA
*
1278654 AAAATTAAAT
1 TAAATTAAAT
1278664 TAAAATTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 14 0.29
25 21 0.43
26 14 0.29
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAATTAAATATTTTATTATTTTAA
Found at i:1278631 original size:29 final size:28
Alignment explanation
Indices: 1278575--1278632 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1278565 TTTAGGGGTC
1278575 AAATTAAATTATATATTTTTTATGATAAT
1 AAATTAAATTATATATTTTTTA-GATAAT
*
1278604 AAATTAAATTATTTTATTATTTTA-ATAAT
1 AAATTAAATTA-TATATT-TTTTAGATAAT
1278633 TTATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 16 0.62
30 5 0.19
31 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AAATTAAATTATATATTTTTTAGATAAT
Found at i:1278881 original size:13 final size:13
Alignment explanation
Indices: 1278863--1278907 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1278853 AAGGGAAAAT
1278863 AATAAAATATTTG
1 AATAAAATATTTG
**
1278876 AATAAAATAAAT-
1 AATAAAATATTTG
1278888 AATAAAATATTTG
1 AATAAAATATTTG
1278901 AATAAAA
1 AATAAAA
1278908 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
AATAAAATATTTG
Found at i:1278917 original size:25 final size:25
Alignment explanation
Indices: 1278859--1278907 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1278849 TTAAAAGGGA
1278859 AAATAATAAAATATTTGAATAAAAT
1 AAATAATAAAATATTTGAATAAAAT
1278884 AAATAATAAAATATTTGAATAAAA
1 AAATAATAAAATATTTGAATAAAA
1278908 AGAGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATAAAATATTTGAATAAAAT
Found at i:1280623 original size:31 final size:31
Alignment explanation
Indices: 1280574--1280706 Score: 112
Period size: 31 Copynumber: 4.4 Consensus size: 31
1280564 AAAAAAGATT
*
1280574 AGATACCAAATTAAGAAAAAGAGTCAAGTTC
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
* * * * *
1280605 AGGTACCAGATTAGGAAAACGTGTCAAGTTT
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
* * * *
1280636 GGGTACCAAATT-GGACCAAAA-A--AAAGTTT
1 AGATACCAAATTAGGA--AAAAGAGTCAAGTTC
* *
1280665 AGATACCAAATTAGGAAAACGTGTCAAGTTC
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
1280696 AGATACCAAAT
1 AGATACCAAAT
1280707 GTCATAAATT
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.04
29 16 0.20
30 6 0.08
31 51 0.65
32 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (31 bp):
AGATACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:1281076 original size:51 final size:51
Alignment explanation
Indices: 1280972--1281083 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
1280962 TGTTGCGAGC
* * * **
1280972 TAAATTTGTT-AATCAAGATGAAATTGACATAATGTGTAAATATTGTGGGT
1 TAAATTTGTTAAATCAAGATGAAATTAACAAAATGTGTAAATATTGAGCAT
*
1281022 TAAATTTGTTAAATCAATAT-AGAATTAACAAAATGTGTAAACT-TTGAGCAT
1 TAAATTTGTTAAATCAAGATGA-AATTAACAAAATGTGTAAA-TATTGAGCAT
1281073 TAAATTTGTTA
1 TAAATTTGTTA
1281084 TTATACCAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 11 0.21
51 41 0.77
52 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (51 bp):
TAAATTTGTTAAATCAAGATGAAATTAACAAAATGTGTAAATATTGAGCAT
Found at i:1288800 original size:107 final size:107
Alignment explanation
Indices: 1288660--1288868 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 107
1288650 AAAGCTACCA
* * *
1288660 TCTTTACCCGTCGGTGATAAAAAAGACAAAATTGAACAATTAGATAACCCAAAAAATATTTACTA
1 TCTTTACCCGTCGATAATAAAAAAGACAAAATTGAACAATTAGATAACCAAAAAAATATTTACTA
* *
1288725 ACAATATGACCAAA-TTTTTTTTTACTAATAGCTGGATAACC
66 ACAAGATGACCAAATTTTTTTTTTACTAATAACTGGATAACC
* * * * *
1288766 TCTTTACCTGTCGATAATTAAAAAAGACAGAATTGAACAGTTAGATCACTAAAAAAATATTTACT
1 TCTTTACCCGTCGATAA-TAAAAAAGACAAAATTGAACAATTAGATAACCAAAAAAATATTTACT
* *
1288831 AACTAGATGATCAAATTTTTTTTTTACTAATAACTGGA
65 AACAAGATGACCAAATTTTTTTTTTACTAATAACTGGA
1288869 AAACTATTAC
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 14 0.16
107 54 0.61
108 21 0.24
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (107 bp):
TCTTTACCCGTCGATAATAAAAAAGACAAAATTGAACAATTAGATAACCAAAAAAATATTTACTA
ACAAGATGACCAAATTTTTTTTTTACTAATAACTGGATAACC
Found at i:1306313 original size:3 final size:3
Alignment explanation
Indices: 1306305--1306329 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1306295 CTTTCTTTAC
1306305 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1306330 GAATGCTTCT
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:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1311378 original size:47 final size:47
Alignment explanation
Indices: 1311327--1311421 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1311317 ATAATTATGG
1311327 TAAGTTTAATTTTATTTATTTACAGTCCCTCTATAGATAAATATATA
1 TAAGTTTAATTTTATTTATTTACAGTCCCTCTATAGATAAATATATA
1311374 TAAGTTTAATTTTATTTATTTACAGTCCCTCTATAGATAAATATATA
1 TAAGTTTAATTTTATTTATTTACAGTCCCTCTATAGATAAATATATA
1311421 T
1 T
1311422 TTTAATTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (47 bp):
TAAGTTTAATTTTATTTATTTACAGTCCCTCTATAGATAAATATATA
Found at i:1318105 original size:137 final size:135
Alignment explanation
Indices: 1317798--1318191 Score: 483
Period size: 137 Copynumber: 2.9 Consensus size: 135
1317788 AGAACAAACA
* * * * * * *
1317798 AAAACCGACGATTAGCAGAGAAGAGAGAACAACTTCGAACGCTGGGAACCACTTCAAAGTTATCG
1 AAAAGCGAAGATTAGCAGAGAAGAGAGAACAACTTCG-ACGCTCGTAATCACTACAAAGCTATCG
* * **
1317863 AAATTCGATCAAACGAAC-TTCATAATTCGGCTATAAAACAACCATCCATCAC---CCAAAAAAA
65 AAATTCGATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAAAA
1317924 AAATTC
130 AAATTC
* * * *
1317930 AAAAGC-AACGGTTAGCAAAGAAGAGAGAACAATTTCGACGCTCGTAATCACTCCAAAGCTATCG
1 AAAAGCGAA-GATTAGCAGAGAAGAGAGAACAACTTCGACGCTCGTAATCACTACAAAGCTATCG
*
1317994 AAATTCGATCAAACGAACTTTCATAATTCGACTATAAAACAATGATCCATCACAAAAAAAAAAAA
65 AAATTCGATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCAC-AAAAAAAAAAA
1318059 AGAAATTC
129 A-AAATTC
* * *
1318067 AAAAGCGAAGATTAGCAGAGCAGAGAGAACAACTTCGACGCTCGTAATCACTACAAATCTATCTA
1 AAAAGCGAAGATTAGCAGAGAAGAGAGAACAACTTCGACGCTCGTAATCACTACAAAGCTATCGA
* * ** * * *
1318132 AATTTGATCAAACGAACTTGCATAACCCGACTATTAAACAACGATCTATCACCAAAAAAA
66 AATTCGATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAA
1318192 TTCAAAAAAC
Statistics
Matches: 224, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
131 41 0.18
132 61 0.27
136 14 0.06
137 106 0.47
138 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (135 bp):
AAAAGCGAAGATTAGCAGAGAAGAGAGAACAACTTCGACGCTCGTAATCACTACAAAGCTATCGA
AATTCGATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAAAAA
AATTC
Found at i:1323702 original size:60 final size:60
Alignment explanation
Indices: 1323603--1323720 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
1323593 GAAAATAGTG
* * * * * * *
1323603 AAGAAGTGAGTTATGGGAGTATTCTCTAGTCAATGTGGGATTAAAATTAATTTTTTAAGA
1 AAGAAGTGAGCTATGGAAGTATTATATAGCCAATGTGGGATTAAAATGAAATTTTTAAGA
* *
1323663 AAGAAGTGGGCTATGGAAGTATTATATAGCCAATTTGGGATTAAAATGAAATTTTTAA
1 AAGAAGTGAGCTATGGAAGTATTATATAGCCAATGTGGGATTAAAATGAAATTTTTAA
1323721 TAAAAATAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (60 bp):
AAGAAGTGAGCTATGGAAGTATTATATAGCCAATGTGGGATTAAAATGAAATTTTTAAGA
Found at i:1331956 original size:21 final size:20
Alignment explanation
Indices: 1331927--1331965 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1331917 AATTTAATAA
*
1331927 AATTTAATTAATAATTTTTTC
1 AATTGAATT-ATAATTTTTTC
*
1331948 AATTGAATTTTAATTTTT
1 AATTGAATTATAATTTTT
1331966 AAATATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTGAATTATAATTTTTTC
Found at i:1331987 original size:22 final size:21
Alignment explanation
Indices: 1331957--1331998 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1331947 CAATTGAATT
*
1331957 TTAATTTTTAAATATGAAAATA
1 TTAAATTTTAAA-ATGAAAATA
*
1331979 TTAAATTTTAAAATTAAAAT
1 TTAAATTTTAAAATGAAAAT
1331999 TAAAGAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAATTTTAAAATGAAAATA
Found at i:1342375 original size:4 final size:4
Alignment explanation
Indices: 1342368--1342394 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1342358 AAGAAAGACA
1342368 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1342395 ATGAAACGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1342617 original size:8 final size:8
Alignment explanation
Indices: 1342604--1342631 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1342594 AAAAATAGAA
1342604 TAAAATTT
1 TAAAATTT
1342612 TAAAATTT
1 TAAAATTT
1342620 TAAAATTT
1 TAAAATTT
1342628 TAAA
1 TAAA
1342632 TATGACAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TAAAATTT
Found at i:1347681 original size:11 final size:11
Alignment explanation
Indices: 1347665--1347732 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
1347655 TCCTCTCTTA
1347665 AATTTCCTCTC
1 AATTTCCTCTC
*
1347676 AATTTCCTCTA
1 AATTTCCTCTC
*
1347687 AATTTGCTCTC
1 AATTTCCTCTC
*
1347698 AATTTGCTCTC
1 AATTTCCTCTC
* *
1347709 AAATTCCTTCTA
1 AATTTCC-TCTC
1347721 AATTT-CTCTC
1 AATTTCCTCTC
1347731 AA
1 AA
1347733 ATTCATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
10 5 0.10
11 36 0.75
12 7 0.15
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (11 bp):
AATTTCCTCTC
Found at i:1347691 original size:22 final size:22
Alignment explanation
Indices: 1347658--1347735 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
1347648 AAACTAATCC
*
1347658 TCTCTTAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
*
1347680 TC-CTCTAAATTTGCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
*
1347702 TGCTCTCAAA-TTCCTTCTAAATT
1 T-CTCTCAAATTTCC-TCTCAATT
1347725 TCTCTCAAATT
1 TCTCTCAAATT
1347736 CATATTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.04
22 29 0.62
23 13 0.28
24 3 0.06
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:1347702 original size:33 final size:33
Alignment explanation
Indices: 1347665--1347732 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1347655 TCCTCTCTTA
*
1347665 AATTTCCTCTCAATTTCC-TCTAAATTTGCTCTC
1 AATTTCCTCTCAAATTCCTTCTAAATTT-CTCTC
*
1347698 AATTTGCTCTCAAATTCCTTCTAAATTTCTCTC
1 AATTTCCTCTCAAATTCCTTCTAAATTTCTCTC
1347731 AA
1 AA
1347733 ATTCATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (33 bp):
AATTTCCTCTCAAATTCCTTCTAAATTTCTCTC
Found at i:1347734 original size:11 final size:11
Alignment explanation
Indices: 1347658--1347735 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
1347648 AAACTAATCC
*
1347658 TCTCTTAAATT
1 TCTCTCAAATT
1347669 TCCTCTC-AATT
1 T-CTCTCAAATT
1347680 TC-CTCTAAATT
1 TCTCTC-AAATT
1347691 TGCTCTC-AATT
1 T-CTCTCAAATT
1347702 TGCTCTCAAATT
1 T-CTCTCAAATT
*
1347714 CCT-TCTAAATT
1 TCTCTC-AAATT
1347725 TCTCTCAAATT
1 TCTCTCAAATT
1347736 CATATTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 36 0.64
12 11 0.20
13 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:1347793 original size:51 final size:51
Alignment explanation
Indices: 1347694--1347793 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
1347684 CTAAATTTGC
* *
1347694 TCTCAATTTGCTCTCAAATTCCTTCTAAATTTCTCTCAAATTCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCTAAATTCCTCTCAAATCCATATTTAA
* * *
1347745 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTCCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-TAAATTCCTCTCAAATCCATATTT
1347794 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCTAAATTCCTCTCAAATCCATATTTAA
Found at i:1349595 original size:18 final size:18
Alignment explanation
Indices: 1349568--1349602 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1349558 CAGGTGCGTT
* *
1349568 CCCTAGCCCTTTTATGTA
1 CCCTAACCCTTATATGTA
1349586 CCCTAACCCTTATATGT
1 CCCTAACCCTTATATGT
1349603 TTCCTTTTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.34, G:0.09, T:0.37
Consensus pattern (18 bp):
CCCTAACCCTTATATGTA
Found at i:1350166 original size:14 final size:14
Alignment explanation
Indices: 1350149--1350197 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1350139 TTAATTGACA
1350149 AACCTTAAACCCTT
1 AACCTTAAACCCTT
*
1350163 AACCTAAAAACCC-T
1 AACCT-TAAACCCTT
*
1350177 AACCCT-AACCCTT
1 AACCTTAAACCCTT
1350190 AA-CTTAAA
1 AACCTTAAA
1350198 AATCGTAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
12 7 0.25
13 5 0.18
14 10 0.36
15 6 0.21
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCTTAAACCCTT
Found at i:1350182 original size:21 final size:21
Alignment explanation
Indices: 1350177--1350303 Score: 155
Period size: 21 Copynumber: 6.0 Consensus size: 21
1350167 TAAAAACCCT
1350177 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* * *
1350198 AATCGTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
*
1350219 AACCCTAAACCCTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAA
* * * *
1350241 AACCGTAGCCCTTAAATAAAA
1 AACCCTAACCCTTAACTTAAA
* *
1350262 AACCCTAACACTTAAGTTAAA
1 AACCCTAACCCTTAACTTAAA
1350283 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
1350304 TATAATTTGA
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 68 0.79
22 18 0.21
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:1350188 original size:27 final size:27
Alignment explanation
Indices: 1350156--1350209 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1350146 ACAAACCTTA
1350156 AACCCTTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
* * *
1350183 AACCCTTAACTTAAAAATCGTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
1350210 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.22
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCCT
Found at i:1350233 original size:43 final size:42
Alignment explanation
Indices: 1350177--1350303 Score: 173
Period size: 43 Copynumber: 3.0 Consensus size: 42
1350167 TAAAAACCCT
*
1350177 AACCCTAACCCTTAACTTAAAAATCGTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAAAACCGTAACCCTTAAATTAAA
* * *
1350219 AACCCTAAACCCTTAACTTTAAAACCGTAGCCCTTAAATAAAA
1 AACCCT-AACCCTTAACTTAAAAACCGTAACCCTTAAATTAAA
* * * *
1350262 AACCCTAACACTTAAGTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCGTAACCCTTAAATTAAA
1350304 TATAATTTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 35 0.48
43 38 0.52
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (42 bp):
AACCCTAACCCTTAACTTAAAAACCGTAACCCTTAAATTAAA
Found at i:1353249 original size:28 final size:28
Alignment explanation
Indices: 1353218--1353282 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1353208 ATTTAAGAAA
*
1353218 TAAATATAATATATATAAATTAA-AATAT
1 TAAA-ATAATATAAATAAATTAACAATAT
*
1353246 TAAAATAAATTTAAATAAATTAACAATAT
1 TAAAAT-AATATAAATAAATTAACAATAT
1353275 TAAAATAA
1 TAAAATAA
1353283 GTTGAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 20 0.61
29 11 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAATAATATAAATAAATTAACAATAT
Found at i:1353273 original size:29 final size:28
Alignment explanation
Indices: 1353232--1353310 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
1353222 TATAATATAT
*
1353232 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
*
1353260 ATAAATTAACAATATTAAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
1353289 ATGAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
1353311 TCTGAAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 10 0.22
29 35 0.78
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:1353654 original size:3 final size:3
Alignment explanation
Indices: 1353640--1353695 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1353630 CAATGATAGC
* * * *
1353640 AAT AAT AGT AAT AAT ATT AAT AAT AAT GAA- AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
1353685 AAT TAT AAT AA
1 AAT AAT AAT AA
1353696 CAACAACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.93
4 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1359695 original size:31 final size:32
Alignment explanation
Indices: 1359657--1359717 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
1359647 CATGTTAAGC
1359657 ACATGTGTCCATAATCTTGTA-CATTTGGTTA
1 ACATGTGTCCATAATCTTGTATCATTTGGTTA
*
1359688 ACATGTGTCCATACTCTTGTATCATTTGGT
1 ACATGTGTCCATAATCTTGTATCATTTGGT
1359718 CAGGTGAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (32 bp):
ACATGTGTCCATAATCTTGTATCATTTGGTTA
Found at i:1362033 original size:11 final size:11
Alignment explanation
Indices: 1362017--1362084 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
1362007 TCCTCTCTTA
1362017 AATTTCCTCTC
1 AATTTCCTCTC
*
1362028 AATTTCCTCTA
1 AATTTCCTCTC
*
1362039 AATTTGCTCTC
1 AATTTCCTCTC
*
1362050 AATTTGCTCTC
1 AATTTCCTCTC
* *
1362061 AAATTCCTTCTA
1 AATTTCC-TCTC
1362073 AATTT-CTCTC
1 AATTTCCTCTC
1362083 AA
1 AA
1362085 ATTCATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
10 5 0.10
11 36 0.75
12 7 0.15
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (11 bp):
AATTTCCTCTC
Found at i:1362043 original size:22 final size:22
Alignment explanation
Indices: 1362010--1362087 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
1362000 AAACTAATCC
*
1362010 TCTCTTAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
*
1362032 TC-CTCTAAATTTGCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
*
1362054 TGCTCTCAAA-TTCCTTCTAAATT
1 T-CTCTCAAATTTCC-TCTCAATT
1362077 TCTCTCAAATT
1 TCTCTCAAATT
1362088 CATATTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.04
22 29 0.62
23 13 0.28
24 3 0.06
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:1362054 original size:33 final size:33
Alignment explanation
Indices: 1362017--1362084 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1362007 TCCTCTCTTA
*
1362017 AATTTCCTCTCAATTTCC-TCTAAATTTGCTCTC
1 AATTTCCTCTCAAATTCCTTCTAAATTT-CTCTC
*
1362050 AATTTGCTCTCAAATTCCTTCTAAATTTCTCTC
1 AATTTCCTCTCAAATTCCTTCTAAATTTCTCTC
1362083 AA
1 AA
1362085 ATTCATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (33 bp):
AATTTCCTCTCAAATTCCTTCTAAATTTCTCTC
Found at i:1362086 original size:11 final size:11
Alignment explanation
Indices: 1362010--1362087 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
1362000 AAACTAATCC
*
1362010 TCTCTTAAATT
1 TCTCTCAAATT
1362021 TCCTCTC-AATT
1 T-CTCTCAAATT
1362032 TC-CTCTAAATT
1 TCTCTC-AAATT
1362043 TGCTCTC-AATT
1 T-CTCTCAAATT
1362054 TGCTCTCAAATT
1 T-CTCTCAAATT
*
1362066 CCT-TCTAAATT
1 TCTCTC-AAATT
1362077 TCTCTCAAATT
1 TCTCTCAAATT
1362088 CATATTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 36 0.64
12 11 0.20
13 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:1362145 original size:51 final size:51
Alignment explanation
Indices: 1362046--1362145 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
1362036 CTAAATTTGC
* *
1362046 TCTCAATTTGCTCTCAAATTCCTTCTAAATTTCTCTCAAATTCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCTAAATTCCTCTCAAATCCATATTTAA
* * *
1362097 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTCCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-TAAATTCCTCTCAAATCCATATTT
1362146 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCTAAATTCCTCTCAAATCCATATTTAA
Found at i:1363983 original size:18 final size:18
Alignment explanation
Indices: 1363957--1363995 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1363947 AGGTGCGTTC
* *
1363957 CCTAGCCCTTTTATGTAT
1 CCTAACCCTTATATGTAT
*
1363975 CCTAACCCTTATATGTTT
1 CCTAACCCTTATATGTAT
1363993 CCT
1 CCT
1363996 TTTCCGAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.31, G:0.08, T:0.44
Consensus pattern (18 bp):
CCTAACCCTTATATGTAT
Found at i:1364609 original size:82 final size:83
Alignment explanation
Indices: 1364514--1364682 Score: 297
Period size: 83 Copynumber: 2.0 Consensus size: 83
1364504 AATTTTATAA
1364514 TTAAATGCATAATTTAATTGACAAACCTT-AACCCTTAACCTAAAAACCCTAACCCTAACCCTTA
1 TTAAATGCATAATTTAATTGACAAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAACCCTTA
1364578 ACTTAAAAATCGT-GACCC
66 ACTTAAAAATCGTAG-CCC
* *
1364596 TTAAATGCATAATTTAATTGACAAACCTTAAACCCTTAACCTAAAAACCTTAACCCTAACCTTTA
1 TTAAATGCATAATTTAATTGACAAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAACCCTTA
1364661 ACTTAAAAATCGTAGCCC
66 ACTTAAAAATCGTAGCCC
1364679 TTAA
1 TTAA
1364683 GTTAAAAACC
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
82 29 0.35
83 53 0.64
84 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (83 bp):
TTAAATGCATAATTTAATTGACAAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAACCCTTA
ACTTAAAAATCGTAGCCC
Found at i:1364643 original size:22 final size:20
Alignment explanation
Indices: 1364618--1364657 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1364608 TTTAATTGAC
1364618 AAACCTTAAACCCTTAACCTAA
1 AAACCTT-AACCC-TAACCTAA
1364640 AAACCTTAACCCTAACCT
1 AAACCTTAACCCTAACCT
1364658 TTAACTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACCTTAACCCTAACCTAA
Found at i:1364679 original size:27 final size:27
Alignment explanation
Indices: 1364626--1364679 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1364616 ACAAACCTTA
*
1364626 AACCCTTAACCTAAAAACCTTAACCCT
1 AACCCTTAACCTAAAAACCGTAACCCT
* * * *
1364653 AACCTTTAACTTAAAAATCGTAGCCCT
1 AACCCTTAACCTAAAAACCGTAACCCT
1364680 TAAGTTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.39, C:0.31, G:0.04, T:0.26
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCGTAACCCT
Found at i:1364722 original size:21 final size:21
Alignment explanation
Indices: 1364647--1364773 Score: 137
Period size: 21 Copynumber: 6.0 Consensus size: 21
1364637 TAAAAACCTT
*
1364647 AACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* * * *
1364668 AATCGTAGCCCTTAAGTTAAA
1 AACCCTAACCCTTAACTTAAA
*
1364689 AACCCTAAACCCTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAA
* * *
1364711 AACCATAACCCTTAAATAAAA
1 AACCCTAACCCTTAACTTAAA
* *
1364732 AACCCTAACACTTAAGTTAAA
1 AACCCTAACCCTTAACTTAAA
*
1364753 AACCTTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
1364774 TATAATTTGA
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
21 67 0.80
22 17 0.20
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:1367692 original size:28 final size:28
Alignment explanation
Indices: 1367661--1367753 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
1367651 ATTTAAGAAA
* *
1367661 TAAATATAATATATATAAATTTA-AATAT
1 TAAA-ATAATATAAATAAATTAACAATAT
*
1367689 TAAAATAAATTTAAATAAATTAACAATAT
1 TAAAAT-AATATAAATAAATTAACAATAT
*
1367718 TAAAATAAGT-TGAAATAAATTAA-AGATGT
1 TAAAATAA-TAT-AAATAAATTAACA-ATAT
1367747 TAAAATA
1 TAAAATA
1367754 TCTATATAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.04
28 21 0.38
29 33 0.59
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAATAATATAAATAAATTAACAATAT
Found at i:1367716 original size:29 final size:28
Alignment explanation
Indices: 1367675--1367753 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
1367665 TATAATATAT
* *
1367675 ATAAATTTAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
*
1367703 ATAAATTAACAATATTAAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
*
1367732 ATAAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
1367754 TCTATATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 9 0.20
29 36 0.80
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:1368068 original size:9 final size:9
Alignment explanation
Indices: 1368056--1368090 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1368046 ATAATATTAT
1368056 CAATAATAG
1 CAATAATAG
1368065 CAATAATAG
1 CAATAATAG
*
1368074 TAATAATAG
1 CAATAATAG
*
1368083 TAATAATA
1 CAATAATA
1368091 ATGAAAGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (9 bp):
CAATAATAG
Found at i:1368072 original size:3 final size:3
Alignment explanation
Indices: 1368066--1368121 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1368056 CAATAATAGC
* * * *
1368066 AAT AAT AGT AAT AAT AGT AAT AAT AAT GAA- AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
1368111 AAT TAT AAT AA
1 AAT AAT AAT AA
1368122 CAACAACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.93
4 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1368821 original size:15 final size:14
Alignment explanation
Indices: 1368801--1368834 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1368791 TCAAAATTCC
1368801 TCTTTTCCTTTTTTT
1 TCTTTT-CTTTTTTT
1368816 TCTTTTCTTTTTTT
1 TCTTTTCTTTTTTT
1368830 T-TTTT
1 TCTTTT
1368835 ATCTCCCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:1378722 original size:13 final size:13
Alignment explanation
Indices: 1378704--1378728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1378694 TTCATCCCCA
1378704 CAATTAGGATAAG
1 CAATTAGGATAAG
1378717 CAATTAGGATAA
1 CAATTAGGATAA
1378729 TCATATTATA
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:0.08, G:0.20, T:0.24
Consensus pattern (13 bp):
CAATTAGGATAAG
Found at i:1403187 original size:3 final size:3
Alignment explanation
Indices: 1403179--1403221 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1403169 ATCACATGTT
1403179 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1403222 GGATGTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1403298 original size:73 final size:73
Alignment explanation
Indices: 1403221--1403406 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
1403211 ATTATTATTA
* *
1403221 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1403286 ATTTTAAG
66 ATTTTAAG
1403294 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1403359 ATTTTAAG
66 ATTTTAAG
1403367 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1403407 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.40
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
ATTTTAAG
Found at i:1407630 original size:3 final size:3
Alignment explanation
Indices: 1407622--1407659 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1407612 ATCACATGTT
1407622 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1407660 TGGATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1407741 original size:73 final size:73
Alignment explanation
Indices: 1407660--1407845 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
1407650 TATTATTATT
* *
1407660 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1407725 ATTTTAAG
66 ATTTTAAG
1407733 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
1407798 ATTTTAAG
66 ATTTTAAG
1407806 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1407846 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.40
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGAGGTGATTT
ATTTTAAG
Found at i:1410043 original size:32 final size:32
Alignment explanation
Indices: 1410007--1410067 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1409997 ATGTTAAGCA
*
1410007 CATGTGTCCATAATCTTTTATCATTTGGTTAG
1 CATGTGTCCATAATCTTGTATCATTTGGTTAG
1410039 CATGTGTCCATAATCTTGTATCATTTGGT
1 CATGTGTCCATAATCTTGTATCATTTGGT
1410068 AAGGTGAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (32 bp):
CATGTGTCCATAATCTTGTATCATTTGGTTAG
Found at i:1410286 original size:15 final size:15
Alignment explanation
Indices: 1410266--1410296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1410256 GTCATGTAAG
*
1410266 TGAAAGGTCAAGAGT
1 TGAAAGATCAAGAGT
1410281 TGAAAGATCAAGAGT
1 TGAAAGATCAAGAGT
1410296 T
1 T
1410297 ATATTGTTTT
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:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (15 bp):
TGAAAGATCAAGAGT
Found at i:1410485 original size:17 final size:17
Alignment explanation
Indices: 1410452--1410490 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1410442 TAAGCTTTTG
1410452 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
1410469 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
1410486 ATTTT
1 ATTTT
1410491 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:1411257 original size:15 final size:16
Alignment explanation
Indices: 1411231--1411260 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1411221 TGGAGATCGA
1411231 GAAAATGGTCGTGGTG
1 GAAAATGGTCGTGGTG
1411247 GAAAA-GGTCGTGGT
1 GAAAATGGTCGTGGT
1411261 CAAGAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.07, G:0.43, T:0.23
Consensus pattern (16 bp):
GAAAATGGTCGTGGTG
Found at i:1414639 original size:15 final size:15
Alignment explanation
Indices: 1414619--1414649 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1414609 GTCATGTAAG
1414619 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
1414634 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
1414649 T
1 T
1414650 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:1414839 original size:17 final size:17
Alignment explanation
Indices: 1414806--1414844 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1414796 TAAGCTTTTG
1414806 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
1414823 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
1414840 ATTTT
1 ATTTT
1414845 CCACAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:1423274 original size:35 final size:35
Alignment explanation
Indices: 1423231--1423304 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
1423221 GAACTAAGTT
1423231 ACATTACATCAACTAAAAATACAAAATGAAACAAA
1 ACATTACATCAACTAAAAATACAAAATGAAACAAA
1423266 ACATTACATCAACTAAAAATACAAAATGAAACAAA
1 ACATTACATCAACTAAAAATACAAAATGAAACAAA
1423301 ACAT
1 ACAT
1423305 GCTTGTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (35 bp):
ACATTACATCAACTAAAAATACAAAATGAAACAAA
Found at i:1429353 original size:21 final size:22
Alignment explanation
Indices: 1429327--1429373 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1429317 CTCTGCTCAA
*
1429327 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1429348 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1429370 ACTC
1 ACTC
1429374 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1439048 original size:21 final size:22
Alignment explanation
Indices: 1439019--1439065 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1439009 CAGAAGGAGT
*
1439019 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1439041 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1439062 GAGT
1 GAGT
1439066 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1445793 original size:23 final size:23
Alignment explanation
Indices: 1445767--1445821 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1445757 AATTAAAAAG
1445767 ATGAAAGCAT-TATAACTACCATT
1 ATGAAAGCATAT-TAACTACCATT
* *
1445790 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAACTACCATT
1445813 ATGAAAGCA
1 ATGAAAGCA
1445822 AAAGATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (23 bp):
ATGAAAGCATATTAACTACCATT
Found at i:1445854 original size:59 final size:59
Alignment explanation
Indices: 1445762--1445877 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
1445752 TTAATAATTA
1445762 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
* * * *
1445821 AAAAGATTAAAGCATTATAGCTATCATTATGAAAGCATATTAGCTATTATTATGAAA
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAA
1445878 CCAAGGTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (59 bp):
AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
Found at i:1445857 original size:23 final size:23
Alignment explanation
Indices: 1445829--1445877 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1445819 GCAAAAGATT
1445829 AAAGCAT-TATAGCTATCATTATG
1 AAAGCATAT-TAGCTATCATTATG
*
1445852 AAAGCATATTAGCTATTATTATG
1 AAAGCATATTAGCTATCATTATG
1445875 AAA
1 AAA
1445878 CCAAGGTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (23 bp):
AAAGCATATTAGCTATCATTATG
Found at i:1447877 original size:37 final size:37
Alignment explanation
Indices: 1447835--1448029 Score: 264
Period size: 37 Copynumber: 5.0 Consensus size: 37
1447825 GGTAGTTTTA
1447835 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
1447872 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* *
1447909 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
1447946 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAA---GT-G
*
1447987 CTTCAGCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 -----GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1448029 G
1 G
1448030 TAGCCTAGCT
Statistics
Matches: 142, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 104 0.73
40 2 0.01
41 1 0.01
42 1 0.01
43 2 0.01
46 32 0.23
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:1447926 original size:74 final size:78
Alignment explanation
Indices: 1447799--1448029 Score: 290
Period size: 74 Copynumber: 2.9 Consensus size: 78
1447789 TTTGAGTACT
* *
1447799 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGG-AG--CT--CTACACTTATCTGATCAAGTGACAAAGT
1447864 GATAAGTGGCTACACTTA
61 GATAAGTGGCTACACTTA
*
1447882 TCTGATCAAGAGACAAAGTGATAAGT-G-G-T-TACACTTATCTGATCAAGAGACAAAGTGATAA
1 TCTGATCAAGAGACAAAGTGATAAGTGGAGCTCTACACTTATCTGATCAAGTGACAAAGTGATAA
1447943 GTGGCTACACTTA
66 GTGGCTACACTTA
* * *
1447956 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGGCAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGG-AGC-T---CTACACTTATCTGATCAAGTGACAAAGT
1448021 GATAAGTGG
61 GATAAGTGG
1448030 TAGCCTAGCT
Statistics
Matches: 133, Mismatches: 6, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
74 68 0.51
75 1 0.01
77 2 0.02
79 1 0.01
80 1 0.01
82 1 0.01
83 59 0.44
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (78 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGAGCTCTACACTTATCTGATCAAGTGACAAAGTGATAA
GTGGCTACACTTA
Found at i:1448055 original size:45 final size:46
Alignment explanation
Indices: 1447946--1448069 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
1447936 GTGATAAGTG
* *
1447946 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
1447992 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
1448037 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1448070 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:1453185 original size:23 final size:23
Alignment explanation
Indices: 1453157--1453208 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1453147 AAAGCAAAAG
1453157 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
1453180 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
1453203 ATGAAA
1 ATGAAA
1453209 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:1453185 original size:59 final size:59
Alignment explanation
Indices: 1453093--1453208 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
1453083 TTAATAATTA
*
1453093 AAAAGATGAAAGTATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
* * *
1453152 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGCATATTAGCTATTATTATGAAA
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAA
1453209 CCAAGTTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (59 bp):
AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
Found at i:1457394 original size:24 final size:23
Alignment explanation
Indices: 1457328--1457401 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
1457318 AAAAAGGGGT
*
1457328 GATAAATAATAATGAAATAATAATA
1 GATAAATAA-AATG-AATAATAATG
*
1457353 GATAACA-AAATATCAATAATAATG
1 GATAA-ATAAA-ATGAATAATAATG
1457377 GCATAAATAAAATGAATAACTAATG
1 G-ATAAATAAAATGAATAA-TAATG
1457402 AAAGAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
24 19 0.46
25 21 0.51
26 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.26
Consensus pattern (23 bp):
GATAAATAAAATGAATAATAATG
Found at i:1457739 original size:25 final size:27
Alignment explanation
Indices: 1457711--1457765 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
1457701 AAATACCAAT
1457711 AAATTTAAACAAAAAT-TA-ACTATTA
1 AAATTTAAACAAAAATATAGACTATTA
* *
1457736 AAA--TATACAAAGATATAGACTATTA
1 AAATTTAAACAAAAATATAGACTATTA
1457761 AAATT
1 AAATT
1457766 GTGAAATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 9 0.38
24 2 0.08
25 13 0.54
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (27 bp):
AAATTTAAACAAAAATATAGACTATTA
Found at i:1457745 original size:23 final size:25
Alignment explanation
Indices: 1457719--1457764 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1457709 ATAAATTTAA
1457719 ACAAAAAT-TA-ACTATTAAAATAT
1 ACAAAAATATAGACTATTAAAATAT
*
1457742 ACAAAGATATAGACTATTAAAAT
1 ACAAAAATATAGACTATTAAAAT
1457765 TGTGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 2 0.10
25 11 0.55
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (25 bp):
ACAAAAATATAGACTATTAAAATAT
Found at i:1464524 original size:141 final size:141
Alignment explanation
Indices: 1464270--1464552 Score: 548
Period size: 141 Copynumber: 2.0 Consensus size: 141
1464260 GAGTTTATGA
1464270 TATTTGAGGTTTGAATCCTATTCTGTGCATTTACTTTCTAGACTTTATATAAAAACGAAAGGGTA
1 TATTTGAGGTTTGAATCCTATTCTGTGCATTTACTTTCTAGACTTTATATAAAAACGAAAGGGTA
1464335 AATTATGGAAATGGTCCTTTTGTCTTATTTTGTTCACCTCTGAAACAAAATTTTATTTCTTCCAT
66 AATTATGGAAATGGTCCTTTTGTCTTATTTTGTTCACCTCTGAAACAAAATTTTATTTCTTCCAT
1464400 TGGCATTTGGC
131 TGGCATTTGGC
*
1464411 TATTTGAGGTTTGAATCCTATTCTGTGCATTTACTTTCTAGACTTTATATAAAAGCGAAAGGGTA
1 TATTTGAGGTTTGAATCCTATTCTGTGCATTTACTTTCTAGACTTTATATAAAAACGAAAGGGTA
*
1464476 AATTATGGAAATGGTCCTTTTGTCTTATTTTGTTCACCTCTGAAACAAAATTTTATTTGTTCCAT
66 AATTATGGAAATGGTCCTTTTGTCTTATTTTGTTCACCTCTGAAACAAAATTTTATTTCTTCCAT
1464541 TGGCATTTGGC
131 TGGCATTTGGC
1464552 T
1 T
1464553 GCAATGCTTG
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (141 bp):
TATTTGAGGTTTGAATCCTATTCTGTGCATTTACTTTCTAGACTTTATATAAAAACGAAAGGGTA
AATTATGGAAATGGTCCTTTTGTCTTATTTTGTTCACCTCTGAAACAAAATTTTATTTCTTCCAT
TGGCATTTGGC
Found at i:1471038 original size:17 final size:17
Alignment explanation
Indices: 1471018--1471072 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1471008 ACTAAAATAT
1471018 TCATTCTATTAACAAAA
1 TCATTCTATTAACAAAA
*
1471035 TCATATC-ATTAA-AATAT
1 TCAT-TCTATTAACAA-AA
1471052 TCATTCTATTAACAAAA
1 TCATTCTATTAACAAAA
1471069 TCAT
1 TCAT
1471073 AAAAAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.38
Consensus pattern (17 bp):
TCATTCTATTAACAAAA
Found at i:1471038 original size:34 final size:34
Alignment explanation
Indices: 1471000--1471073 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 34
1470990 CTTTTATTGG
1471000 ATCATACCACTAAAATATTCATTCTATTAACAAA
1 ATCATACCACTAAAATATTCATTCTATTAACAAA
* *
1471034 ATCATATCATTAAAATATTCATTCTATTAACAAA
1 ATCATACCACTAAAATATTCATTCTATTAACAAA
1471068 ATCATA
1 ATCATA
1471074 AAAAACTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (34 bp):
ATCATACCACTAAAATATTCATTCTATTAACAAA
Found at i:1471397 original size:34 final size:36
Alignment explanation
Indices: 1471350--1471418 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 36
1471340 TGGAAAAAAT
* *
1471350 ATTTTATTGAAAACATA-TAAATTTAA-TTTAATTTA
1 ATTTTATTAAAAACATAGT-AACTTAATTTTAATTTA
1471385 ATTTT-TTAAAAACATAGTAACTTAATTTTAATTT
1 ATTTTATTAAAAACATAGTAACTTAATTTTAATTT
1471419 TGAATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTTTATTAAAAACATAGTAACTTAATTTTAATTTA
Done.