Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_pilon, whole genome shotgun sequence
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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 26
Found at i:1192014 original size:31 final size:31
Alignment explanation
Indices: 1191979--1192040 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1191969 GTCATACATG
*
1191979 TACTAACTAAATTT-TTTCTTTTGTTTGTGTA
1 TACTAACT-AATTTCTTTATTTTGTTTGTGTA
*
1192010 TACTAACTTATTTCGTTTATTTTGTTTGTGT
1 TACTAACTAATTTC-TTTATTTTGTTTGTGT
1192041 CATTTTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 8 0.30
32 15 0.56
ACGTcount: A:0.19, C:0.10, G:0.11, T:0.60
Consensus pattern (31 bp):
TACTAACTAATTTCTTTATTTTGTTTGTGTA
Found at i:1193496 original size:28 final size:28
Alignment explanation
Indices: 1193465--1193533 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
1193455 AAATCAACTT
* *
1193465 AGAGAGAAAATAAAAGACAAAGAAACAA
1 AGAGAAAAAATAAAAGAAAAAGAAACAA
**
1193493 AGAGAAAAAAGCAAAGAAAAAGAAACAA
1 AGAGAAAAAATAAAAGAAAAAGAAACAA
1193521 AGAGAAAAAATAA
1 AGAGAAAAAATAA
1193534 GAAAAGGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (28 bp):
AGAGAAAAAATAAAAGAAAAAGAAACAA
Found at i:1193507 original size:14 final size:13
Alignment explanation
Indices: 1193467--1193530 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
1193457 ATCAACTTAG
*
1193467 AGAGAAAATA-AA
1 AGAGAAAAAACAA
*
1193479 AGACAAAGAAACAA
1 AGAGAAA-AAACAA
1193493 AGAGAAAAAAGCAA
1 AGAGAAAAAA-CAA
*
1193507 AGAAAAAGAAACAA
1 AGAGAAA-AAACAA
1193521 AGAGAAAAAA
1 AGAGAAAAAA
1193531 TAAGAAAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 6 0.14
13 8 0.19
14 26 0.60
15 3 0.07
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (13 bp):
AGAGAAAAAACAA
Found at i:1193544 original size:15 final size:15
Alignment explanation
Indices: 1193526--1193554 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1193516 AACAAAGAGA
1193526 AAAAATAAGAAAAGG
1 AAAAATAAGAAAAGG
1193541 AAAAATAAGAAAAG
1 AAAAATAAGAAAAG
1193555 TAAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAATAAGAAAAGG
Found at i:1193563 original size:18 final size:17
Alignment explanation
Indices: 1193526--1193595 Score: 81
Period size: 18 Copynumber: 4.1 Consensus size: 17
1193516 AACAAAGAGA
1193526 AAAAATAAGAAAAG--G
1 AAAAATAAGAAAAGAAG
1193541 AAAAATAAGAAAAGTAAG
1 AAAAATAAGAAAAG-AAG
*
1193559 AAAAATAACAAAAGAAG
1 AAAAATAAGAAAAGAAG
* *
1193576 AAAAAAGAAGACAAGAAG
1 -AAAAATAAGAAAAGAAG
1193594 AA
1 AA
1193596 CATGCAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 14 0.30
17 5 0.11
18 28 0.60
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAATAAGAAAAGAAG
Found at i:1195253 original size:130 final size:130
Alignment explanation
Indices: 1195052--1195326 Score: 338
Period size: 130 Copynumber: 2.1 Consensus size: 130
1195042 ATCGCGTAAT
* * * ** *
1195052 AACCGTGTCAT-CCATCGACCAGACCTCCTCATCACGTAGGAGTTGTGCCACCCCTGATAACCAG
1 AACCGTGTCATCCCCT-AACCAGACCTCCTCATCACGCAGGAGCCGTGCCACCCCTGATAAACAG
* * * *
1195116 CAGTCCTCATCACGTAGAAACCGTGTTATCATTTCTAAAGATGGAATATCGTCCTCATCACGTAG
65 CAGTCCTCATCACGTAGAAACCGTGTTATCATTCCTAAAGATGGAATATCATCATCATCAAGTAG
*
1195181 G
130 A
* * * *
1195182 AACTGTGTCATCCCCTAACCAGACCTCCTTATCACGCAGGAGCCGTGTCACCCCTGATAAACGGT
1 AACCGTGTCATCCCCTAACCAGACCTCCTCATCACGCAGGAGCCGTGCCACCCCTGATAAACAG-
* * * * *
1195247 CA-TCCTCATCACGTAGGAACTGTGTTATCATTCCTAAAGATGGCATGTTATCATCATCAAGTAG
65 CAGTCCTCATCACGTAGAAACCGTGTTATCATTCCTAAAGATGGAATATCATCATCATCAAGTAG
1195311 A
130 A
1195312 AACCGTGTCATCCCC
1 AACCGTGTCATCCCC
1195327 ATCACGTAGG
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
130 117 0.96
131 5 0.04
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (130 bp):
AACCGTGTCATCCCCTAACCAGACCTCCTCATCACGCAGGAGCCGTGCCACCCCTGATAAACAGC
AGTCCTCATCACGTAGAAACCGTGTTATCATTCCTAAAGATGGAATATCATCATCATCAAGTAGA
Found at i:1195330 original size:25 final size:25
Alignment explanation
Indices: 1195301--1195351 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1195291 ATGTTATCAT
1195301 CATCAAGTAGAAACCGTGTCATCCC
1 CATCAAGTAGAAACCGTGTCATCCC
* *
1195326 CATCACGTAGGAACCGTGTCATCCC
1 CATCAAGTAGAAACCGTGTCATCCC
1195351 C
1 C
1195352 CGACCAGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (25 bp):
CATCAAGTAGAAACCGTGTCATCCC
Found at i:1195459 original size:155 final size:155
Alignment explanation
Indices: 1195171--1195481 Score: 426
Period size: 155 Copynumber: 2.0 Consensus size: 155
1195161 ATATCGTCCT
* * * *
1195171 CATCACGTAGGAACTGTGTCATCCCCTAACCAGACCTCCTTATCACGCAGGAGCCGTGTCACCCC
1 CATCACGTAGGAACCGTGTCATCCCCCAACCAGACCTCCTCATCACGCAGGAACCGTGTCACCCC
* * * * * *
1195236 TGATAAACGGTCATCCTCATCACGTAGGAACTGTGTTATCATTCCTAAAGATGGCATGTTATCAT
66 TGATAAACAGCCATCCTCATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCATGTCATCAT
1195301 CATCA-AGTAGAAACCGTGTCATCCC
131 CATCACA-TAGAAACCGTGTCATCCC
* * *
1195326 CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCATGTAGGAACCGTGTCACCCC
1 CATCACGTAGGAACCGTGTCATCCCCCAACCAGACCTCCTCATCACGCAGGAACCGTGTCACCCC
* * * * * *
1195391 TGATAACCAGCCGTCTTCATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCTTGTCGTCCT
66 TGATAAACAGCCATCCTCATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCATGTCATCAT
*
1195456 CATCACATAGGAACCGTGTCATCCC
131 CATCACATAGAAACCGTGTCATCCC
1195481 C
1 C
1195482 GACCAGACCT
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
155 134 0.99
156 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (155 bp):
CATCACGTAGGAACCGTGTCATCCCCCAACCAGACCTCCTCATCACGCAGGAACCGTGTCACCCC
TGATAAACAGCCATCCTCATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCATGTCATCAT
CATCACATAGAAACCGTGTCATCCC
Found at i:1195512 original size:39 final size:39
Alignment explanation
Indices: 1195326--1195597 Score: 156
Period size: 42 Copynumber: 6.5 Consensus size: 39
1195316 GTGTCATCCC
1195326 CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
1 CATCACGTAGGAACCGTGTCAT-CCCCGACCAGACCTCCT
* *
1195366 CATCATGTAGGAACCGTGTCA-CCCCTGATAACCAG-CCGTCTT
1 CATCACGTAGGAACCGTGTCATCCCC-G---ACCAGACC-TCCT
* * ** ** * *
1195408 CATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCTTGTCGTCCT
1 CATCACGTAGGAAC--CG-TGTCA-TCC--CCGA---CCAGACCTCCT
*
1195456 CATCACATAGGAACCGTGTCATCCCCGACCAGACCTCCT
1 CATCACGTAGGAACCGTGTCATCCCCGACCAGACCTCCT
* * * *
1195495 CATCACGTTGGAGCCGTGTCA-CCCCTGATAATCAG-CCGTACT
1 CATCACGTAGGAACCGTGTCATCCCC-G---ACCAGACC-TCCT
* * *
1195537 CATCATGTAGGAATCGTGTCATCCTCCGACTAGACCTCCT
1 CATCACGTAGGAACCGTGTCATCC-CCGACCAGACCTCCT
*
1195577 CATCACGTAGGAGCCGTGTCA
1 CATCACGTAGGAACCGTGTCA
1195598 CCCATGATAA
Statistics
Matches: 173, Mismatches: 35, Indels: 48
0.68 0.14 0.19
Matches are distributed among these distances:
38 8 0.05
39 27 0.16
40 44 0.25
41 6 0.03
42 46 0.27
43 3 0.02
44 7 0.04
45 9 0.05
46 2 0.01
47 2 0.01
48 18 0.10
49 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (39 bp):
CATCACGTAGGAACCGTGTCATCCCCGACCAGACCTCCT
Found at i:1195608 original size:211 final size:213
Alignment explanation
Indices: 1195326--1195766 Score: 609
Period size: 211 Copynumber: 2.1 Consensus size: 213
1195316 GTGTCATCCC
* *
1195326 CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCATGTAGGAACCGTGTCACCCC
1 CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAACCGTGTCACCCA
* * * * *
1195391 TGATAACCAGCCGTCTTCATCACGTAGAAACTGCGTTATCATTCCAAAAGATGGCTTGTC-GTCC
66 TGATAACCAACCGTCCTCATCACGTAAAAACTGCGTTATCATTCCAAAAGATGGATT-ACAGTCC
* *
1195455 TCATCACATAGGAACCGTGTCATCCCC-GACCAGACCTCCTCATCACGTTGGAGCCGTGTCACCC
130 TCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCACCACGTAGGAGCCGTGTCACCC
*
1195519 CT-GATAATCAGCCGTACT
195 CTAGATAACCAGCCGTACT
* * * * *
1195537 CATCATGTAGGAATCGTGTCATCCTCCGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACCCA
1 CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAACCGTGTCACCCA
* * * * **
1195602 TGATAACCAACTGTCCTCATTATGTAAAAACTGTGTTATCATTCTTAAAGATGGATTACAGTCCT
66 TGATAACCAACCGTCCTCATCACGTAAAAACTGCGTTATCATTCCAAAAGATGGATTACAGTCCT
*
1195667 CATCACGTAGGAACCGTGTCATCCCCAGACCAGACCTCCTCACCACGTAGGAGCCGTGTCACCCC
131 CATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCACCACGTAGGAGCCGTGTCACCCC
* *
1195732 TAGATAACCAGTCGTCCT
196 TAGATAACCAGCCGTACT
** *
1195750 CATTGCATAGGAACCGT
1 CATCACGTAGGAACCGT
1195767 TTTATCACCA
Statistics
Matches: 198, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
210 1 0.01
211 135 0.68
212 37 0.19
213 25 0.13
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (213 bp):
CATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAACCGTGTCACCCA
TGATAACCAACCGTCCTCATCACGTAAAAACTGCGTTATCATTCCAAAAGATGGATTACAGTCCT
CATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCACCACGTAGGAGCCGTGTCACCCC
TAGATAACCAGCCGTACT
Found at i:1195621 original size:82 final size:81
Alignment explanation
Indices: 1195450--1195627 Score: 248
Period size: 82 Copynumber: 2.2 Consensus size: 81
1195440 GATGGCTTGT
** *
1195450 CGTCCTCATCACATAGGAACCGTGTCATCCCCGACCAGACCTCCTCATCACGTTGGAGCCGTGTC
1 CGTCCTCATCATGTAGGAACCGTGTCATCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
* * *
1195515 ACCCCTGATAATCAGC
66 ACCCATGATAACCAAC
* * *
1195531 CGTACTCATCATGTAGGAATCGTGTCATCCTCCGACTAGACCTCCTCATCACGTAGGAGCCGTGT
1 CGTCCTCATCATGTAGGAACCGTGTCATCC-CCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
1195596 CACCCATGATAACCAAC
65 CACCCATGATAACCAAC
* *
1195613 TGTCCTCATTATGTA
1 CGTCCTCATCATGTA
1195628 AAAACTGTGT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 26 0.31
82 58 0.69
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (81 bp):
CGTCCTCATCATGTAGGAACCGTGTCATCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTC
ACCCATGATAACCAAC
Found at i:1197634 original size:30 final size:30
Alignment explanation
Indices: 1197506--1197633 Score: 118
Period size: 29 Copynumber: 4.3 Consensus size: 30
1197496 TTATTTGTAA
* *
1197506 TTGCTATTTTAGTCCTCTGAGTTTCTATTT
1 TTGCTATTTTAGTCCTCTAAGTTTATATTT
*
1197536 TTTCTA-TTTAGTCCAT-TAAGTTTATATTT
1 TTGCTATTTTAGTCC-TCTAAGTTTATATTT
* * * * *
1197565 TT-CTATTTTAGCCCTTTAAATGTATGTTT
1 TTGCTATTTTAGTCCTCTAAGTTTATATTT
* * *
1197594 TTGCAATTTTGGTCCTCTAAGTTTCTATTT
1 TTGCTATTTTAGTCCTCTAAGTTTATATTT
*
1197624 TTGCAATTTT
1 TTGCTATTTT
1197634 GTTCCCTTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.05
29 40 0.51
30 35 0.44
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGCTATTTTAGTCCTCTAAGTTTATATTT
Found at i:1206121 original size:20 final size:21
Alignment explanation
Indices: 1206088--1206133 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1206078 CACAGCGAAA
*
1206088 GGATTGATCATTTTTTAAAAG
1 GGATCGATCATTTTTTAAAAG
**
1206109 GGATCGATC-TTTTTTGGAAG
1 GGATCGATCATTTTTTAAAAG
1206129 GGATC
1 GGATC
1206134 AATTCGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (21 bp):
GGATCGATCATTTTTTAAAAG
Found at i:1212145 original size:18 final size:19
Alignment explanation
Indices: 1212122--1212160 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1212112 TCAATAAATT
1212122 ACATAAACCC-TAATTTGA
1 ACATAAACCCATAATTTGA
1212140 ACATAAACCCAATAATTTGA
1 ACATAAACCC-ATAATTTGA
1212160 A
1 A
1212161 ATCTTTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (19 bp):
ACATAAACCCATAATTTGA
Found at i:1219464 original size:30 final size:27
Alignment explanation
Indices: 1219404--1219475 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 27
1219394 TAAATATGTG
* * *
1219404 TCATTATTATTAAATCATTGCCTTATA
1 TCATTATTATTAAATCATAGCATTAAA
1219431 TCATTATTATTAAATCAATAAGTCATTAAA
1 TCATTATTATTAAATC-AT-AG-CATTAAA
1219461 TCATTATTATTAAAT
1 TCATTATTATTAAAT
1219476 AAAATTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.41
28 2 0.05
29 1 0.03
30 20 0.51
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (27 bp):
TCATTATTATTAAATCATAGCATTAAA
Found at i:1219561 original size:31 final size:31
Alignment explanation
Indices: 1219514--1219575 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1219504 GTTTAAATTG
* * *
1219514 ATATTTAAAAATATTCATTCAAATAGAAATA
1 ATATTTAAAAACATTCATCCAAATACAAATA
*
1219545 ATATTTACAAACATTCATCCAAATACAAATA
1 ATATTTAAAAACATTCATCCAAATACAAATA
1219576 TGCAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (31 bp):
ATATTTAAAAACATTCATCCAAATACAAATA
Found at i:1221584 original size:18 final size:18
Alignment explanation
Indices: 1221543--1221580 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1221533 TTATTTTTAC
* *
1221543 TTTAATTGCTTTTACTTA
1 TTTAATCGCGTTTACTTA
1221561 TTTAATCGCGTTTA-TTA
1 TTTAATCGCGTTTACTTA
1221578 TTT
1 TTT
1221581 TAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTAATCGCGTTTACTTA
Found at i:1223815 original size:39 final size:40
Alignment explanation
Indices: 1223772--1223952 Score: 206
Period size: 39 Copynumber: 4.5 Consensus size: 40
1223762 TAAAAAAATC
*
1223772 ACTCAACAATATCATTTAACAAAAAATATATGT-AATTAA
1 ACTCAACAATATCATTTAACAAAAAATATATGTAAAATAA
* * * * *
1223811 ACTCAACAACATCATTTAACAGAACAATACGAGGTAAAATATT
1 ACTCAACAATATCATTTAACA-AAAAATA-TATGTAAAATA-A
* * *
1223854 ACTCAACGATATCATTTAACAAAAAATATTTGT-AAATGA
1 ACTCAACAATATCATTTAACAAAAAATATATGTAAAATAA
* *
1223893 ACTCAACAATATCATTTAACAAAAAATATTTGT-AAATTA
1 ACTCAACAATATCATTTAACAAAAAATATATGTAAAATAA
*
1223932 ACTCAATAATATCATTTAACA
1 ACTCAACAATATCATTTAACA
1223953 TAACAATACG
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 77 0.64
40 10 0.08
41 5 0.04
42 10 0.08
43 19 0.16
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (40 bp):
ACTCAACAATATCATTTAACAAAAAATATATGTAAAATAA
Found at i:1223876 original size:82 final size:83
Alignment explanation
Indices: 1223740--1223913 Score: 278
Period size: 82 Copynumber: 2.1 Consensus size: 83
1223730 CTGATATACA
1223740 CATTTAACAGAACAATACGAGGTAAAAAAATCACTCAACAATATCATTTAACAAAAAATATATGT
1 CATTTAACAGAACAATACGAGGTAAAAAAATCACTCAACAATATCATTTAACAAAAAATATATGT
*
1223805 AATTAAACTCAACAACAT
66 AAATAAACTCAACAACAT
* * * *
1223823 CATTTAACAGAACAATACGAGGT-AAAATATTACTCAACGATATCATTTAACAAAAAATATTTGT
1 CATTTAACAGAACAATACGAGGTAAAAAAATCACTCAACAATATCATTTAACAAAAAATATATGT
* *
1223887 AAATGAACTCAACAATAT
66 AAATAAACTCAACAACAT
1223905 CATTTAACA
1 CATTTAACA
1223914 AAAAATATTT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 61 0.73
83 23 0.27
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (83 bp):
CATTTAACAGAACAATACGAGGTAAAAAAATCACTCAACAATATCATTTAACAAAAAATATATGT
AAATAAACTCAACAACAT
Found at i:1225914 original size:3 final size:3
Alignment explanation
Indices: 1225908--1225932 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1225898 ACTACTAAAA
1225908 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1225933 GAAATCAAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1229188 original size:33 final size:33
Alignment explanation
Indices: 1229147--1229212 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1229137 TTGCAGAGTG
*
1229147 AACCAACTCAAACTTGTTTTCAACACCCCCATC
1 AACCAACTCAAACTTGTTTTCAACACCCACATC
*
1229180 AACCAACTCCAACTTGTTTTCAACACCCACATC
1 AACCAACTCAAACTTGTTTTCAACACCCACATC
1229213 GCATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.39, G:0.03, T:0.24
Consensus pattern (33 bp):
AACCAACTCAAACTTGTTTTCAACACCCACATC
Found at i:1232685 original size:32 final size:33
Alignment explanation
Indices: 1232656--1232718 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1232646 TATCACCTCC
* *
1232656 AAGGTTTGATCATCTTCAATTGGTGCACCTCTA
1 AAGGTTTAATCATCTTCAAATGGTGCACCTCTA
*
1232689 AAGTTTTAATCATCTTCAAATGGTGCACCT
1 AAGGTTTAATCATCTTCAAATGGTGCACCT
1232719 GCAACTGCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (33 bp):
AAGGTTTAATCATCTTCAAATGGTGCACCTCTA
Found at i:1245870 original size:119 final size:121
Alignment explanation
Indices: 1245593--1245875 Score: 394
Period size: 120 Copynumber: 2.4 Consensus size: 121
1245583 TAATATTAAT
* * * *
1245593 GACCATTTAATTCACAATGACAGAAACTTTTCAGTGATGTGTCACTTTAATTCAGTGATACATCA
1 GACCATTTAATGCACAATGACAGAAACTTTTCAGTGATATATCACTTCAATTCAGTGATACATCA
* * *
1245658 TACCATTGAATAATGTTTTTGACCAATGTTTTAATGAAAAACGTCATTTTCTCATA
66 TACCATTGAATAATGTTTTTGACCAATGCTTTAATGAAAAACGTCATTTCCTCAAA
* *
1245714 GA-CATTTAATGCACAATGACAGAAACTTTTCAATGATATATCACTTCAATTCAGTGATATATCA
1 GACCATTTAATGCACAATGACAGAAACTTTTCAGTGATATATCACTTCAATTCAGTGATACATCA
* * * *
1245778 -ATCCATTGAATGATGTTTTT-ACCAATGCTTTAATG-GAAATGTCCTTTCCTCAAA
66 TA-CCATTGAATAATGTTTTTGACCAATGCTTTAATGAAAAACGTCATTTCCTCAAA
* *
1245832 GACCATTTAATGAACAATGATAGAAACTTTTCAGTGATATATCA
1 GACCATTTAATGCACAATGACAGAAACTTTTCAGTGATATATCA
1245876 GACCATTTAA
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
118 16 0.11
119 53 0.37
120 73 0.51
121 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (121 bp):
GACCATTTAATGCACAATGACAGAAACTTTTCAGTGATATATCACTTCAATTCAGTGATACATCA
TACCATTGAATAATGTTTTTGACCAATGCTTTAATGAAAAACGTCATTTCCTCAAA
Found at i:1250327 original size:57 final size:56
Alignment explanation
Indices: 1250263--1250379 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 56
1250253 AGTTTATGAA
*
1250263 TTAATTTAGAATGGAGTTTTGTTTTTTTGAAGAAAAATAT-AAAAATATTTTTAAAAC
1 TTAATTTAGAATGGAGTTTTG-TGTTTTGAAGAAAAATATAAAAAATA-TTTTAAAAC
* * *
1250320 TTAATTTAGAATGGAGTTTTGTGTTTTGAATACAGATATAAAAAATATTTTAAAAC
1 TTAATTTAGAATGGAGTTTTGTGTTTTGAAGAAAAATATAAAAAATATTTTAAAAC
1250376 TTAA
1 TTAA
1250380 AGTGTATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
56 27 0.49
57 28 0.51
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.43
Consensus pattern (56 bp):
TTAATTTAGAATGGAGTTTTGTGTTTTGAAGAAAAATATAAAAAATATTTTAAAAC
Found at i:1250373 original size:56 final size:57
Alignment explanation
Indices: 1250263--1250379 Score: 175
Period size: 56 Copynumber: 2.1 Consensus size: 57
1250253 AGTTTATGAA
*
1250263 TTAATTTAGAATGGAGTTTTGTTTTTTTGAAGAAAAATATAAAAATATTTTTAAAAC
1 TTAATTTAGAATGGAGTTTTGTTGTTTTGAAGAAAAATATAAAAATATTTTTAAAAC
* * *
1250320 TTAATTTAGAATGGAGTTTTG-TGTTTTGAATACAGATATAAAAA-ATATTTTAAAAC
1 TTAATTTAGAATGGAGTTTTGTTGTTTTGAAGAAAAATATAAAAATAT-TTTTAAAAC
1250376 TTAA
1 TTAA
1250380 AGTGTATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 2 0.04
56 32 0.58
57 21 0.38
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.43
Consensus pattern (57 bp):
TTAATTTAGAATGGAGTTTTGTTGTTTTGAAGAAAAATATAAAAATATTTTTAAAAC
Found at i:1252364 original size:19 final size:17
Alignment explanation
Indices: 1252342--1252387 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1252332 GAAGATGATG
1252342 AGAAGAAATAAAGAAATAA
1 AGAAGAAATAAAG-AA-AA
1252361 AGAAG-AA-AAAGAAAA
1 AGAAGAAATAAAGAAAA
*
1252376 AGAAAAAATAAA
1 AGAAGAAATAAA
1252388 TAATTGGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 6 0.25
16 4 0.17
17 7 0.29
18 2 0.08
19 5 0.21
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AGAAGAAATAAAGAAAA
Found at i:1253431 original size:17 final size:17
Alignment explanation
Indices: 1253409--1253444 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1253399 TGATTCAGGC
1253409 ATGTGGTATGGAGGTAT
1 ATGTGGTATGGAGGTAT
*
1253426 ATGTGGTATTGAGGTAT
1 ATGTGGTATGGAGGTAT
1253443 AT
1 AT
1253445 TCGCCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (17 bp):
ATGTGGTATGGAGGTAT
Found at i:1260071 original size:20 final size:21
Alignment explanation
Indices: 1260046--1260097 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1260036 TTTTCCCAAT
*
1260046 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1260066 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1260087 TCGCAATGCGA
1 TCGCAATGCGA
1260098 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1260111 original size:20 final size:20
Alignment explanation
Indices: 1260086--1260199 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1260076 AATTGGGAAA
*
1260086 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1260106 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
1260126 ATCGCAATGCTATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1260147 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1260167 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1260187 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1260200 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1260130 original size:61 final size:61
Alignment explanation
Indices: 1260083--1260199 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1260073 GCGAATTGGG
* * * * * *
1260083 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCTATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1260144 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1260200 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1260756 original size:19 final size:19
Alignment explanation
Indices: 1260718--1260784 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1260708 TTCGAGAATG
1260718 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1260738 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1260757 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1260776 AAAATCGCA
1 AAAATCGCA
1260785 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1260802 original size:19 final size:19
Alignment explanation
Indices: 1260780--1260945 Score: 109
Period size: 20 Copynumber: 9.1 Consensus size: 19
1260770 GAAACCAAAA
*
1260780 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1260799 TCGCGTTGAGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1260818 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* * *
1260838 TCACGTTGCGA---TCGTC
1 TCGCGTTGCGATTTTCATT
* **
1260854 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1260871 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1260885 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1260904 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1260924 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1260944 TC
1 TC
1260946 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
14 16 0.14
16 6 0.05
17 6 0.05
18 1 0.01
19 36 0.32
20 47 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1260826 original size:20 final size:19
Alignment explanation
Indices: 1260789--1260845 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1260779 ATCGCATTGC
1260789 GATTTTCATTTCGCGTTGA
1 GATTTTCATTTCGCGTTGA
* *
1260808 GATTTTTATTTCGCGGTTGC
1 GATTTTCATTTCGC-GTTGA
*
1260828 GATTTTCATTTCACGTTG
1 GATTTTCATTTCGCGTTG
1260846 CGATCGTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGA
Found at i:1260870 original size:33 final size:32
Alignment explanation
Indices: 1260833--1260920 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 32
1260823 GTTGCGATTT
* *
1260833 TCATTTCACGTTGCGATCGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATC-TCTCGTCGCGATAG
*
1260866 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGA-TCTCTCGTCGCGATAG
1260899 TCATTTCCGCGTTGCGAT-TCTC
1 TCATTT-CGCGTTGCGATCTCTC
1260921 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 4 0.08
33 34 0.68
34 12 0.24
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (32 bp):
TCATTTCGCGTTGCGATCTCTCGTCGCGATAG
Found at i:1263027 original size:42 final size:42
Alignment explanation
Indices: 1262947--1263069 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1262937 GCCCGACTCG
* * * ** * *
1262947 CCTATCATCCCTCAAGAGTCCACTCATATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1262989 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
1263031 ACTGTCATT-GTTGAAGAAGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AG-AGTCCCCTCCCACCGTTCAAGAG
1263070 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.93
43 3 0.04
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:1264447 original size:14 final size:14
Alignment explanation
Indices: 1264428--1264463 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1264418 ATTGTTTAAT
*
1264428 TGATTTGTAAAGGG
1 TGATTTGTAAAAGG
*
1264442 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1264456 TGATTTGT
1 TGATTTGT
1264464 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1264646 original size:19 final size:20
Alignment explanation
Indices: 1264602--1264646 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1264592 GCAACGAGAG
1264602 AATT-GCAACGCGAAAATGA
1 AATTCGCAACGCGAAAATGA
* *
1264621 AAATCGCAACGCG-AAATTA
1 AATTCGCAACGCGAAAATGA
1264640 AATTCGC
1 AATTCGC
1264647 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTCGCAACGCGAAAATGA
Found at i:1264664 original size:19 final size:19
Alignment explanation
Indices: 1264642--1264792 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1264632 CGAAATTAAA
1264642 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
1264661 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1264676 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1264694 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1264708 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1264727 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1264742 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1264760 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1264779 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1264793 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1264688 original size:33 final size:32
Alignment explanation
Indices: 1264646--1264772 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1264636 ATTAAATTCG
*
1264646 CGTTGCGATTTTCATTTCGTATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1264679 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1264712 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1264745 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1264773 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1264722 original size:66 final size:66
Alignment explanation
Indices: 1264639--1264771 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1264629 ACGCGAAATT
* *
1264639 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1264704 G
66 G
*
1264705 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1264770 G
66 G
1264771 A
1 A
1264772 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1267082 original size:12 final size:12
Alignment explanation
Indices: 1267065--1267089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1267055 TCTTCGGGGA
1267065 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1267077 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1267089 C
1 C
1267090 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1267298 original size:24 final size:24
Alignment explanation
Indices: 1267264--1267317 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1267254 CTGAAACATC
*
1267264 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAG
*
1267288 ATCAAAGTCCGGATATTGACCAAG
1 ATCAAAATCCGGATATTGACCAAG
1267312 ATCAAA
1 ATCAAA
1267318 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAG
Found at i:1267331 original size:24 final size:24
Alignment explanation
Indices: 1267280--1267331 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1267270 ATCCGTGTAT
* * *
1267280 TGACCAATATCAAAGTCCGGATAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1267304 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1267328 TGAC
1 TGAC
1267332 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1268402 original size:20 final size:20
Alignment explanation
Indices: 1268377--1268433 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1268367 ATTCATTTGA
*
1268377 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1268397 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1268417 TTATCGCAACGAGAAAA
1 CTATCGCAACGAGAAAA
1268434 CGTTGCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1268460 original size:19 final size:19
Alignment explanation
Indices: 1268436--1268484 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1268426 CGAGAAAACG
1268436 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1268455 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1268474 TTGCGATTTTC
1 TTGCGATTTTC
1268485 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1268620 original size:14 final size:14
Alignment explanation
Indices: 1268601--1268637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1268591 CATCAATTAA
1268601 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1268615 ACAAATCATCTTTT
1 ACAAATCAACATTT
1268629 ACAAATCAA
1 ACAAATCAA
1268638 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1270542 original size:20 final size:19
Alignment explanation
Indices: 1270507--1270573 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1270497 GAAACTTAAA
1270507 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1270526 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1270546 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1270565 ATCGCAACG
1 ATCGCAACG
1270574 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1270581 original size:14 final size:14
Alignment explanation
Indices: 1270562--1270619 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1270552 ATGCGAAATG
1270562 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1270576 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1270592 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1270608 AAAATCGCAACG
1 AAAATCGCAACG
1270620 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1270604 original size:32 final size:33
Alignment explanation
Indices: 1270546--1270624 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1270536 GGAAATGGCT
*
1270546 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1270579 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1270611 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1270625 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1270672 original size:14 final size:14
Alignment explanation
Indices: 1270653--1270710 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1270643 TTTCATTTCG
1270653 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1270667 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1270683 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1270699 CGTTGCGATTTT
1 CGTTGCGATTTT
1270711 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1270717 original size:33 final size:33
Alignment explanation
Indices: 1270636--1270726 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1270626 ACAAATCGCA
*
1270636 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1270669 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1270701 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1270727 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1270762 original size:20 final size:20
Alignment explanation
Indices: 1270711--1270754 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1270701 TTGCGATTTT
*
1270711 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1270730 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1270750 CATTT
1 CATTT
1270755 TCGTGTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1271273 original size:18 final size:18
Alignment explanation
Indices: 1271247--1271291 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1271237 GTCGATCAGA
*
1271247 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1271265 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1271283 TGATGGCTC
1 TGATGGCTC
1271292 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1272636 original size:20 final size:20
Alignment explanation
Indices: 1272611--1272648 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1272601 AATAGTTTCT
1272611 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1272631 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1272649 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1272942 original size:22 final size:22
Alignment explanation
Indices: 1272912--1272955 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1272902 GATGGAGATA
*
1272912 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1272934 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1272956 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1273168 original size:20 final size:20
Alignment explanation
Indices: 1273143--1273236 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1273133 GATTATGTAT
1273143 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1273163 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1273183 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1273204 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1273224 TATCGCATTGCGA
1 TATCGCGTTGCGA
1273237 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1273237 original size:20 final size:20
Alignment explanation
Indices: 1273123--1273237 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1273113 CGCTTTGAAA
*
1273123 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1273144 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1273164 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1273184 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1273205 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1273225 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1273238 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1273255 original size:21 final size:21
Alignment explanation
Indices: 1273226--1273318 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
1273216 ATAGTCAGTA
1273226 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1273247 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1273267 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
1273288 TCACGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1273308 TCGCATTGCGA
1 TCGCATTGCGA
1273319 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1273256 original size:41 final size:41
Alignment explanation
Indices: 1273165--1273299 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1273155 AAAGTCAGTA
* * * ** *
1273165 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1273205 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1273247 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
1273288 TCACGTTGCGAT
1 TCGCGTTGCGAT
1273300 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1273300 original size:41 final size:41
Alignment explanation
Indices: 1273226--1273318 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1273216 ATAGTCAGTA
*
1273226 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1273267 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1273308 TCGCATTGCGA
1 TCGCATTGCGA
1273319 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
Found at i:1278589 original size:2 final size:2
Alignment explanation
Indices: 1278584--1278610 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1278574 TGGTTATATA
1278584 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1278611 TAAGGATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1282536 original size:3 final size:3
Alignment explanation
Indices: 1282528--1282552 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1282518 AAATGTTATA
1282528 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
1282553 ATAATAATAA
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:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:1282557 original size:3 final size:3
Alignment explanation
Indices: 1282551--1282582 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1282541 GTAGTAGTAG
1282551 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1282583 GATTAATAAG
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):
TAA
Found at i:1283157 original size:139 final size:138
Alignment explanation
Indices: 1282791--1283193 Score: 576
Period size: 138 Copynumber: 2.9 Consensus size: 138
1282781 ATTTGAAGAA
* * * ** * *
1282791 AACACGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGGTGACACTGCTCTTACGTGATGAG
1 AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGATGCGGCTCCTACGTGATGAG
* * *
1282856 GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGGGGACGTCTAGCCTTCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTTTAGGGATAA
*
1282921 ATTGAGAT
131 ATTGACAT
* * * * *
1282929 AACACAGTTTCTACATGATGAGGAAGTCTGGCTATCTAAGGATGATGCGACTTCTACGTGATGAG
1 AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGATGCGGCTCCTACGTGATGAG
1282994 GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTTTAGGGATAA
1283059 ATTGGACAT
131 ATT-GACAT
* * *
1283068 AACA-TGATTCCTACGTGATGAGGACGTCTGGTTATCTAAGGATGATGCGGCTCCTACGTGTTGA
1 AACACAG-TTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGATGCGGCTCCTACGTGATGA
* *
1283132 GGAGATCTGGTCGATGGATGACATTGTTCCTATGTGATGAGGA-AGTCTAGCCATCTTTAGGG
65 GGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACA-TCTAGCCATCTTTAGGG
1283194 TTAATTTGTT
Statistics
Matches: 236, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
138 120 0.51
139 116 0.49
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (138 bp):
AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGATGCGGCTCCTACGTGATGAG
GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTTTAGGGATAA
ATTGACAT
Found at i:1283454 original size:37 final size:37
Alignment explanation
Indices: 1283325--1283447 Score: 149
Period size: 37 Copynumber: 3.3 Consensus size: 37
1283315 CTTAAGGAAG
* *
1283325 ACTATCTCAAGTGAGACGAAATTTGTTTTTAAGAGAA
1 ACTATCTCAAGCGAGACGAAATTTGTTTTCAAGAGAA
* * * *
1283362 ACTGTCTCAAGCGAGACAAAATTTGTATTTCGAGGGAAA
1 ACTATCTCAAGCGAGACGAAATTTGT-TTTCAAGAG-AA
1283401 ACTATCTCAAGCGAGACGAAACTTTG-TTTCAAGAGAA
1 ACTATCTCAAGCGAGACGAAA-TTTGTTTTCAAGAGAA
*
1283438 ACAATCTCAA
1 ACTATCTCAA
1283448 AGGAGACAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 34 0.47
38 13 0.18
39 21 0.29
40 4 0.06
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (37 bp):
ACTATCTCAAGCGAGACGAAATTTGTTTTCAAGAGAA
Found at i:1290913 original size:95 final size:95
Alignment explanation
Indices: 1290691--1290892 Score: 255
Period size: 95 Copynumber: 2.1 Consensus size: 95
1290681 ACTGCTGTGG
* * * * * * * *
1290691 GTATCGATACCAAGAGAAAGGTATCGATACCA-AAGATTCCAGAATGTCGAAATGGTATTGATAC
1 GTATCGATACCAAGATAAAGGTATCGATACTATGA-ATTACAAAATATAGAAATGGTATCGATAC
1290755 TGAAAGAGAGTATCGATACCATAGTATAGAA
65 TGAAAGAGAGTATCGATACCATAGTATAGAA
* * *
1290786 GTATCGATTCTAAGATAAAGGTATCGATACTATGAATTACAAAATATAGAAATGGTATCGATATT
1 GTATCGATACCAAGATAAAGGTATCGATACTATGAATTACAAAATATAGAAATGGTATCGATACT
* *
1290851 GAAAGGGTGTATC-AGTACCATAGTATAGAA
66 GAAAGAGAGTATCGA-TACCATAGTATAGAA
1290881 GTATCGATACCA
1 GTATCGATACCA
1290893 TGGTAGGGGT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 88 0.98
96 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (95 bp):
GTATCGATACCAAGATAAAGGTATCGATACTATGAATTACAAAATATAGAAATGGTATCGATACT
GAAAGAGAGTATCGATACCATAGTATAGAA
Found at i:1291364 original size:45 final size:45
Alignment explanation
Indices: 1291313--1291432 Score: 197
Period size: 45 Copynumber: 2.7 Consensus size: 45
1291303 TAAACGAATA
1291313 CATAAATGAAATGCATAACAGTGCATTATCGGA-AAGAAAGGATGC
1 CATAAATGAAATGCATAACAGTGCATTATC-GACAAGAAAGGATGC
* * *
1291358 CATAAATGAAATGCATAACGGTGCACTATCGACATGAAAGGATGC
1 CATAAATGAAATGCATAACAGTGCATTATCGACAAGAAAGGATGC
1291403 CATAAATGAAATGCATAACAGTGCATTATC
1 CATAAATGAAATGCATAACAGTGCATTATC
1291433 TGTAATACCC
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
44 2 0.03
45 67 0.97
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACAGTGCATTATCGACAAGAAAGGATGC
Found at i:1292906 original size:81 final size:81
Alignment explanation
Indices: 1292771--1293253 Score: 745
Period size: 81 Copynumber: 6.0 Consensus size: 81
1292761 TATTTTAAAA
* * * *
1292771 TAAAAGATTAAATGTCTAGTTGTGCATTTGACATAAAGTTGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1292836 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
1292852 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1292917 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
1292933 TAAAAGATTAAATGCCTAGCTGTACATTTGACAGAAAGCTGTCAATCATGCCAGTTAGCTGAAAG
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1292998 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1293014 TAAAAGATTAAATGCATAGTTGTGCATTTGACAGAAATGTTTCAATCATGCCATTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1293079 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
1293095 TAAAAGATTAAATGTCTAGCTATGCATTTGACAGAAAGGTGTCAATCATG-CAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1293159 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
1293175 TAAAAAATTAAATGCCTAACTGTACATTTGGCAGAAAGGT-TCCAATAATACAAGTTAGATGAAA
1 TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGT-CAATCATGCCAGTTAGATGAAA
*
1293239 GGTTAAATATCTTTG
65 GGTTAAATACCTTTG
1293254 GGATGAAAGA
Statistics
Matches: 368, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
79 1 0.00
80 69 0.19
81 298 0.81
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1293379 original size:49 final size:49
Alignment explanation
Indices: 1293286--1293380 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
1293276 CTGTTCTTTT
* *** *
1293286 TGGCAGAAAAGTGCCATTAATGCAAGATAGATGCCTAATGGTGCATTTC
1 TGGCAGAAAAGTGCCACTAATGCAAGATAGATGAAGAATAGTGCATTTC
*
1293335 TGGCAG-AAAGCTGCCACTAATGCAAGTTAGATGAAGAATAGTGCAT
1 TGGCAGAAAAG-TGCCACTAATGCAAGATAGATGAAGAATAGTGCAT
1293381 AATTGGCATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 4 0.10
49 35 0.90
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (49 bp):
TGGCAGAAAAGTGCCACTAATGCAAGATAGATGAAGAATAGTGCATTTC
Found at i:1293388 original size:49 final size:47
Alignment explanation
Indices: 1293285--1293394 Score: 112
Period size: 49 Copynumber: 2.2 Consensus size: 47
1293275 ACTGTTCTTT
* *** * *
1293285 TTGGCAGAAAAGTGCCATTAATGCAAGATAGATGCCTAATGGTGCATT
1 TTGGCAG-AAAGTGCCACTAATGCAAGATAGATGAAGAATAGTGCATA
*
1293333 TCTGGCAGAAAGCTGCCACTAATGCAAGTTAGATGAAGAATAGTGCATAA
1 T-TGGCAGAAAG-TGCCACTAATGCAAGATAGATGAAGAATAGTGCAT-A
1293383 TTGGCATGAAAG
1 TTGGCA-GAAAG
1293395 GATGCCACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
48 5 0.10
49 40 0.78
50 6 0.12
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (47 bp):
TTGGCAGAAAGTGCCACTAATGCAAGATAGATGAAGAATAGTGCATA
Found at i:1294361 original size:46 final size:45
Alignment explanation
Indices: 1294143--1294358 Score: 261
Period size: 45 Copynumber: 4.8 Consensus size: 45
1294133 AAATGGGTGT
* * **
1294143 TACATTATCGGCATGAATGGATGTTATAAATGAAATGCATAACGG
1 TACATTATTGGCATGAAAGGATGCCATAAATGAAATGCATAACGG
* * * *
1294188 TACATTATCGGCATGTAATGATGCCATAAATGAAATGCATAATGG
1 TACATTATTGGCATGAAAGGATGCCATAAATGAAATGCATAACGG
* *
1294233 TACATTATTGGCATGAAAAGATTCCATAAATGAAATGCATAACGG
1 TACATTATTGGCATGAAAGGATGCCATAAATGAAATGCATAACGG
* * * *
1294278 TGCATTATTGGCATGAAAGGATGCCATAAATAAAAATACATAATGG
1 TACATTATTGGCATGAAAGGATGCCATAAAT-GAAATGCATAACGG
* ** *
1294324 TGCATTATAAGCATGAACGGATGCCATAAATGAAA
1 TACATTATTGGCATGAAAGGATGCCATAAATGAAA
1294359 ATAAAGAATA
Statistics
Matches: 149, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 110 0.74
46 39 0.26
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (45 bp):
TACATTATTGGCATGAAAGGATGCCATAAATGAAATGCATAACGG
Found at i:1300500 original size:21 final size:21
Alignment explanation
Indices: 1300476--1300533 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1300466 TTCGATGAAC
* *
1300476 AGTATTGATACTGATGCAATT
1 AGTATCGATACTGATGAAATT
1300497 AGTATCGATACTGATGAAATT
1 AGTATCGATACTGATGAAATT
*
1300518 AGTATCGATATTGATG
1 AGTATCGATACTGATG
1300534 TGGGTATCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
AGTATCGATACTGATGAAATT
Found at i:1300655 original size:95 final size:95
Alignment explanation
Indices: 1300537--1300738 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 95
1300527 ATTGATGTGG
** * * **
1300537 GTATCGATACCAAATGAAAGGTATCGATACCAGGGATTCCAGAATGTTGAAATGGTATTGATACT
1 GTATCGATACCAAATGAAAGGTATCGATACCAGAAATTACAGAATGTAGAAATGGTATCAATACT
1300602 AAAAGGAAGTATCGGTACCATAGTATAGAA
66 AAAAGGAAGTATCGGTACCATAGTATAGAA
* * * *
1300632 GTATCGATACTAAGAT-AAAGGTATTGATACCATAAATTACATAATGTAGAAATGGTATCAATAC
1 GTATCGATACCAA-ATGAAAGGTATCGATACCAGAAATTACAGAATGTAGAAATGGTATCAATAC
* ***
1300696 TGAAAGGGTTTATCGGTACCATAGTATAGAA
65 TAAAAGGAAGTATCGGTACCATAGTATAGAA
1300727 GTATCGATACCA
1 GTATCGATACCA
1300739 TGGTAGGGGT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 89 0.98
96 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (95 bp):
GTATCGATACCAAATGAAAGGTATCGATACCAGAAATTACAGAATGTAGAAATGGTATCAATACT
AAAAGGAAGTATCGGTACCATAGTATAGAA
Found at i:1301210 original size:45 final size:45
Alignment explanation
Indices: 1301159--1301395 Score: 330
Period size: 45 Copynumber: 5.2 Consensus size: 45
1301149 AAAACGAATA
*
1301159 CATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
* * *
1301204 CATAAATGAAATGTATAACGGTGCATTATCAGAATGAAAGGATTC
1 CATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
* *
1301249 CATAAATGAAACGCATAACGGTGCATTATCAGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
* * * *
1301294 CATAAATGAAATGCATAACGGTGCATTATCGGTAAGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
* * * * *
1301339 AATAAATAAAAATGCATAATGGTGCATTATAAGCATGAACGGATGC
1 CATAAAT-GAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
1301385 CATAAATGAAA
1 CATAAATGAAA
1301396 ATAAAGAATA
Statistics
Matches: 167, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 131 0.78
46 36 0.22
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.24
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGC
Found at i:1306004 original size:3 final size:3
Alignment explanation
Indices: 1305996--1306039 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1305986 AATTAAAATG
*
1305996 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1306040 GCCTAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1309032 original size:41 final size:42
Alignment explanation
Indices: 1308985--1309073 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 42
1308975 TTTTTATAGT
* *
1308985 GGTGTTTTTTC-AACAACGCCGCAAAATAATAGTAATTTAGC
1 GGTGTTTTCTCAAAAAACGCCGCAAAATAATAGTAATTTAGC
* * *
1309026 GGTG-TTTCTCAAAAAACGCCGTAATATAGTAGTAATTTAGC
1 GGTGTTTTCTCAAAAAACGCCGCAAAATAATAGTAATTTAGC
1309067 GGTGTTT
1 GGTGTTT
1309074 ATAAGGTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 5 0.12
41 34 0.83
42 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (42 bp):
GGTGTTTTCTCAAAAAACGCCGCAAAATAATAGTAATTTAGC
Found at i:1309071 original size:82 final size:82
Alignment explanation
Indices: 1308891--1309073 Score: 183
Period size: 82 Copynumber: 2.2 Consensus size: 82
1308881 ACCACAAAAT
* ** * * * *
1308891 GATACTTTAGCGGCATTTTTCCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATAGA
1 GATAATTTAGCGGTGTTTTTCCAACAAACGCCGCAAAAGAATAGTAATTTAGCGGCGTTTATACA
1308956 AAAAACGCCGTTATAGA
66 AAAAACGCCGTTATAGA
** * * * * *
1308973 GATTTTTATAGTGGTGTTTTTTCAAC-AACGCCGCAAAATAATAGTAATTTAGCGGTGTTTCT-C
1 GATAATT-TAGCGGTGTTTTTCCAACAAACGCCGCAAAAGAATAGTAATTTAGCGGCGTTTATAC
1309036 AAAAAACGCCGTAATATAGTA
65 AAAAAACGCCGT--TATAG-A
1309057 G-TAATTTAGCGGTGTTT
1 GATAATTTAGCGGTGTTT
1309074 ATAAGGTTGT
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
81 12 0.15
82 45 0.56
83 22 0.27
84 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (82 bp):
GATAATTTAGCGGTGTTTTTCCAACAAACGCCGCAAAAGAATAGTAATTTAGCGGCGTTTATACA
AAAAACGCCGTTATAGA
Found at i:1309754 original size:22 final size:22
Alignment explanation
Indices: 1309723--1309775 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1309713 GTGTTTTTCC
*
1309723 GCTTTCGAATAGGAAAATAATA
1 GCTTTTGAATAGGAAAATAATA
*
1309745 GCTTTTGAATAGGAAAATATTA
1 GCTTTTGAATAGGAAAATAATA
1309767 GCTTTTGAA
1 GCTTTTGAA
1309776 AACATGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (22 bp):
GCTTTTGAATAGGAAAATAATA
Found at i:1316109 original size:20 final size:19
Alignment explanation
Indices: 1316084--1316144 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 19
1316074 TTTTGGTGTA
*
1316084 GAGGGAATCGATCTCCCCCT
1 GAGGGAACCGAT-TCCCCCT
1316104 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
1316125 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1316145 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
21 2 0.06
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:1316153 original size:21 final size:21
Alignment explanation
Indices: 1316127--1316166 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1316117 CCCCCTTTGA
*
1316127 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1316148 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1316167 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1318906 original size:20 final size:20
Alignment explanation
Indices: 1318881--1318931 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1318871 CACTTAGGGA
* *
1318881 ACCGATTCCCCATAGTGGGT
1 ACCGATTCCCCAAAGGGGGT
1318901 ACCGATTCCCCAAAGGGGGT
1 ACCGATTCCCCAAAGGGGGT
1318921 ACCGATTCCCC
1 ACCGATTCCCC
1318932 CCACGCTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCAAAGGGGGT
Found at i:1321073 original size:18 final size:18
Alignment explanation
Indices: 1321050--1321086 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1321040 TATCGTTCCT
1321050 AACCTTGTCCACCAGCGC
1 AACCTTGTCCACCAGCGC
1321068 AACCTTGTCCACCAGCGC
1 AACCTTGTCCACCAGCGC
1321086 A
1 A
1321087 GCCTCACGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.16
Consensus pattern (18 bp):
AACCTTGTCCACCAGCGC
Found at i:1323076 original size:39 final size:39
Alignment explanation
Indices: 1323033--1323158 Score: 243
Period size: 39 Copynumber: 3.2 Consensus size: 39
1323023 CCGCAAGAAG
1323033 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
1 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
1323072 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
1 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
1323111 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
1 AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
*
1323150 AATCAATTG
1 AATCTATTG
1323159 CTAATTATGT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (39 bp):
AATCTATTGAGGTACTATATTGAACTTAATAATAAATAA
Found at i:1323498 original size:18 final size:17
Alignment explanation
Indices: 1323470--1323506 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
1323460 AGTGGTTTTG
1323470 TTTGTTTGTTGTCTTAT
1 TTTGTTTGTTGTCTTAT
1323487 TTTGTATTGTTGTCTTAT
1 TTTGT-TTGTTGTCTTAT
1323505 TT
1 TT
1323507 CATTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTGTCTTAT
Found at i:1330304 original size:43 final size:43
Alignment explanation
Indices: 1330074--1330298 Score: 193
Period size: 44 Copynumber: 5.2 Consensus size: 43
1330064 ATAACATAGT
* *
1330074 TATTGCGGCGTTTGTGTGAAAAACT-CCGCTAAATATCAACAAC
1 TATTGCGGCGTTTGT-TGAAAAAATGCCGCTAAATATCAACACC
* * * * *
1330117 TATTGCGGCATTTGTGAGAAAAAACGTCGCTAAATATCAAAACC
1 TATTGCGGCGTTTGT-TGAAAAAATGCCGCTAAATATCAACACC
** * ** * **
1330161 TATTGCTTCGTTTGTT-AAAAAACGCCGCTAAACCTTATTACC
1 TATTGCGGCGTTTGTTGAAAAAATGCCGCTAAATATCAACACC
* * * * **
1330203 TATTGCGGCGCTTGTGGGAAAAATGCCACTAAACCTCAACACC
1 TATTGCGGCGTTTGTTGAAAAAATGCCGCTAAATATCAACACC
* * *
1330246 TATTGCGACGTTTTTTAGAAAAAATACCGCTAAATATCAACACC
1 TATTGCGGCGTTTGTT-GAAAAAATGCCGCTAAATATCAACACC
1330290 TATTGCGGC
1 TATTGCGGC
1330299 ATTTTTTTTA
Statistics
Matches: 142, Mismatches: 37, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
42 32 0.23
43 53 0.37
44 57 0.40
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
TATTGCGGCGTTTGTTGAAAAAATGCCGCTAAATATCAACACC
Found at i:1331127 original size:21 final size:21
Alignment explanation
Indices: 1331082--1331127 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1331072 CAATTGACTA
*
1331082 TCAGATCAATTGTTTTTCGGT
1 TCAGATCAATTGTTTTTCGGG
*
1331103 TCAGATCAGTTGATTTTT-GGG
1 TCAGATCAATTG-TTTTTCGGG
1331124 TCAG
1 TCAG
1331128 GTTGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (21 bp):
TCAGATCAATTGTTTTTCGGG
Found at i:1331473 original size:16 final size:16
Alignment explanation
Indices: 1331454--1331487 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1331444 TTTTGTTCAC
*
1331454 GTTACTTTCGGTTCGG
1 GTTACTTTCGATTCGG
*
1331470 GTTATTTTCGATTCGG
1 GTTACTTTCGATTCGG
1331486 GT
1 GT
1331488 CAAATTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.15, G:0.29, T:0.47
Consensus pattern (16 bp):
GTTACTTTCGATTCGG
Found at i:1340952 original size:21 final size:22
Alignment explanation
Indices: 1340926--1340966 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1340916 CCAGGACAGG
1340926 GAGTATCGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
*
1340947 GAGTATCGGTACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
1340967 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:1346022 original size:14 final size:16
Alignment explanation
Indices: 1345993--1346024 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1345983 CGTTTGTGAA
1345993 CGTTCGATTATATGTT
1 CGTTCGATTATATGTT
1346009 CGTTC-ATT-TATGTT
1 CGTTCGATTATATGTT
1346023 CG
1 CG
1346025 AACAGGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
CGTTCGATTATATGTT
Found at i:1347907 original size:3 final size:3
Alignment explanation
Indices: 1347899--1347957 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
1347889 AAGGTCGATA
1347899 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1347947 AAG AGAG AAG A
1 AAG A-AG AAG A
1347958 GAACCAAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1349662 original size:43 final size:44
Alignment explanation
Indices: 1349600--1349699 Score: 166
Period size: 44 Copynumber: 2.3 Consensus size: 44
1349590 CAGCATGCAG
* *
1349600 AATCATGTTAAGAAATGAAATTG-TTGAAACAAAGTTTGAAGAA
1 AATCATGTTAAGCAATGAAATTGTTTGAAACAAAATTTGAAGAA
*
1349643 AATCATGTTAAGCATTGAAATTGTTTGAAACAAAATTTGAAGAA
1 AATCATGTTAAGCAATGAAATTGTTTGAAACAAAATTTGAAGAA
1349687 AATCATGTTAAGC
1 AATCATGTTAAGC
1349700 GATGTGTTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 21 0.40
44 32 0.60
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (44 bp):
AATCATGTTAAGCAATGAAATTGTTTGAAACAAAATTTGAAGAA
Found at i:1349992 original size:21 final size:21
Alignment explanation
Indices: 1349912--1350008 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
1349902 AATAATTCTC
* * *
1349912 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCCT
* * * *
1349933 TTTATGAAGAGGTTAAGCCCT
1 TTCATCAAAAGGTTAAGTCCT
** *
1349954 TTCATCAAAAGGAGAAGTCTT
1 TTCATCAAAAGGTTAAGTCCT
*
1349975 TTAATCAAAAGGTTAAGTCCT
1 TTCATCAAAAGGTTAAGTCCT
*
1349996 TTCATCGAAAGGT
1 TTCATCAAAAGGT
1350009 CTTAACCTTT
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCCT
Found at i:1352988 original size:21 final size:21
Alignment explanation
Indices: 1352937--1352991 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1352927 TTATGAAAGC
1352937 CCTTTCATCAAAAGGAGAAGT
1 CCTTTCATCAAAAGGAGAAGT
** * **
1352958 ATTTTAATCAAAAGGTTAAGT
1 CCTTTCATCAAAAGGAGAAGT
1352979 CCTTTCATCAAAA
1 CCTTTCATCAAAA
1352992 CGTCTTAACC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (21 bp):
CCTTTCATCAAAAGGAGAAGT
Found at i:1354194 original size:11 final size:11
Alignment explanation
Indices: 1354178--1354206 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1354168 TCAGCAAAAG
1354178 CAGGAAGGAAA
1 CAGGAAGGAAA
1354189 CAGGAAGGAAA
1 CAGGAAGGAAA
1354200 CAGGAAG
1 CAGGAAG
1354207 CCAAACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.38, T:0.00
Consensus pattern (11 bp):
CAGGAAGGAAA
Found at i:1355836 original size:25 final size:25
Alignment explanation
Indices: 1355796--1355873 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 25
1355786 AATCCTAAAG
*
1355796 TATA-AATACTAA-TAATAATTAAT
1 TATATAATAATAATTAATAATTAAT
1355819 TATATAATAATAATTAATAATTAA-
1 TATATAATAATAATTAATAATTAAT
*
1355843 -AGCATAA-AAT-ATTAA-AATTAAT
1 TA-TATAATAATAATTAATAATTAAT
1355865 TATCATAAT
1 TAT-ATAAT
1355874 CCGAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 6 0.13
22 5 0.11
23 13 0.29
24 11 0.24
25 10 0.22
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (25 bp):
TATATAATAATAATTAATAATTAAT
Found at i:1357781 original size:185 final size:182
Alignment explanation
Indices: 1357378--1357804 Score: 490
Period size: 185 Copynumber: 2.3 Consensus size: 182
1357368 GGGTTACTTT
* * * * * * * * **
1357378 ACTACTCTTCCGTGAAGGTTAAATTCG-AGACTAGAATACTTTACTACTCTTTCATG-AGACTTC
1 ACTACTCTTCCGTGAAGATCAGATTCGAAG-TTGGAATACTTCACTACTCTTCCGTGAAGGTTTC
* * *
1357441 ATACTTTGCTAAAAAATCTGTTCCACTACTCTTCCGTAGAGAGCGAATTTTGATTTTACTTTTGC
65 ATACTTTGCTAAAAAATCTGTTCCACAACTCTTCCGTAGAGAGCAAATTTTGATCTTACTTTTGC
*
1357506 TTCACTACTATTTCATGAAGGCTGAGGATGATAAACTTAAGAAGAATCTGTTTC
130 TTCACTACTATTTCATGAAGGCTGA-GATGATAAACTTAAGAAGAATATGTTTC
* *
1357560 ACTACTCTTCCGTGAAGATCATATTCGAAGTTGGAATACTTCACTACTTTTCCGTGAAGGTTTCA
1 ACTACTCTTCCGTGAAGATCAGATTCGAAGTTGGAATACTTCACTACTCTTCCGTGAAGGTTTCA
* * *
1357625 TACTTTGCTGAAAAATCTGTTCCACAACTCTTCCGTGGAGAGCAAATTTTGATCTTGCTTGTGCT
66 TACTTTGCTAAAAAATCTGTTCCACAACTCTTCCGTAGAGAGCAAATTTTGATCTTAC-T-T--T
* * **
1357690 CCTGCTTCACTACT-CTTCTGTGAAGGCTGA-A-GA-CGACTTAAGAAGAATATGTTTC
127 --TGCTTCACTACTATTTC-ATGAAGGCTGAGATGATAAACTTAAGAAGAATATGTTTC
* *
1357745 ACTACTCTTCCGTGAAGATCAGATTTGATA-TTGGAATCCTTCACTACTCTTCCGTGAAGG
1 ACTACTCTTCCGTGAAGATCAGATTCGA-AGTTGGAATACTTCACTACTCTTCCGTGAAGG
1357805 ATGAATTAAC
Statistics
Matches: 209, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
182 44 0.21
183 60 0.29
184 1 0.00
185 74 0.35
186 3 0.01
187 2 0.01
188 3 0.01
189 22 0.11
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (182 bp):
ACTACTCTTCCGTGAAGATCAGATTCGAAGTTGGAATACTTCACTACTCTTCCGTGAAGGTTTCA
TACTTTGCTAAAAAATCTGTTCCACAACTCTTCCGTAGAGAGCAAATTTTGATCTTACTTTTGCT
TCACTACTATTTCATGAAGGCTGAGATGATAAACTTAAGAAGAATATGTTTC
Found at i:1357874 original size:20 final size:20
Alignment explanation
Indices: 1357862--1358136 Score: 379
Period size: 20 Copynumber: 13.8 Consensus size: 20
1357852 ACCCAAAGGA
*
1357862 TTTACAAATGACCCGAAGGC
1 TTTACAAATGACCCGGAGGC
*
1357882 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1357902 TTTACAAATGACCCGAAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1357922 TTTACAAATTACCTGGAGGT
1 TTTACAAATGACCCGGAGGC
*
1357942 TTTACAAATAACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1357962 TTCACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1357982 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
1358002 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1358022 TTGATAAATTACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1358042 TTTATAAATGACCCAGTGGC
1 TTTACAAATGACCCGGAGGC
*
1358062 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
1358082 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1358102 TTTACAAATGACCCGGAAGC
1 TTTACAAATGACCCGGAGGC
*
1358122 TTTACAATTGACCCG
1 TTTACAAATGACCCG
1358137 AAAATAATTT
Statistics
Matches: 227, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 227 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (20 bp):
TTTACAAATGACCCGGAGGC
Found at i:1366326 original size:18 final size:18
Alignment explanation
Indices: 1366293--1366328 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1366283 CTTGCTGGAA
*
1366293 TTGGGCCTGGACTGGTTG
1 TTGGGCCTGAACTGGTTG
*
1366311 TTGGGCCTGAATTGGTTG
1 TTGGGCCTGAACTGGTTG
1366329 CATGGCTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.14, G:0.42, T:0.36
Consensus pattern (18 bp):
TTGGGCCTGAACTGGTTG
Found at i:1370537 original size:8 final size:8
Alignment explanation
Indices: 1370495--1370538 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1370485 TTATATATAT
1370495 TTATTTTA
1 TTATTTTA
1370503 -TATTTTA
1 TTATTTTA
1370510 TTATTGTT-
1 TTATT-TTA
1370518 TTATGTTTA
1 TTAT-TTTA
1370527 TTATTTTA
1 TTATTTTA
1370535 TTAT
1 TTAT
1370539 CCATTTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.22
8 18 0.56
9 7 0.22
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:1370538 original size:17 final size:16
Alignment explanation
Indices: 1370495--1370538 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1370485 TTATATATAT
1370495 TTATTTTA-TATTTTA
1 TTATTTTATTATTTTA
1370510 TTATTGTT-TTATGTTTA
1 TTATT-TTATTAT-TTTA
1370527 TTATTTTATTAT
1 TTATTTTATTAT
1370539 CCATTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 13 0.52
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (16 bp):
TTATTTTATTATTTTA
Found at i:1370545 original size:25 final size:23
Alignment explanation
Indices: 1370493--1370546 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
1370483 TGTTATATAT
**
1370493 ATTTATTTTATATTTTATTATTG
1 ATTTATTTTATATTTTATTATCC
*
1370516 TTTTATGTTTATTATTTTATTATCC
1 ATTTAT-TTTA-TATTTTATTATCC
1370541 ATTTAT
1 ATTTAT
1370547 CTAGTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 16 0.64
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTATTTTATATTTTATTATCC
Found at i:1371042 original size:3 final size:3
Alignment explanation
Indices: 1371034--1371060 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1371024 GTCATGAAAA
1371034 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1371061 GACACCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1372369 original size:20 final size:20
Alignment explanation
Indices: 1372310--1372427 Score: 130
Period size: 20 Copynumber: 5.9 Consensus size: 20
1372300 CGTTGCGATT
*
1372310 TTCTGACTATCGCAATGCTA
1 TTCTGACTATCGCAATGCGA
* * * *
1372330 ATATGTA-AATCACAATGCGA
1 TTCTG-ACTATCGCAATGCGA
* *
1372350 TTATGACTATCGCAACGCGA
1 TTCTGACTATCGCAATGCGA
*
1372370 TTCTGACTATCGCAATGAGA
1 TTCTGACTATCGCAATGCGA
*
1372390 TTCTGACTGTCGCAATGCGA
1 TTCTGACTATCGCAATGCGA
*
1372410 TGCTGACTATCGCAATGC
1 TTCTGACTATCGCAATGC
1372428 ATTTTCAAAG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.98
21 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (20 bp):
TTCTGACTATCGCAATGCGA
Found at i:1372631 original size:22 final size:22
Alignment explanation
Indices: 1372606--1372648 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1372596 GGCGACATCC
1372606 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1372628 GTCCCCATCTCTGACGAAATC
1 GTCCCCATCTCCGACGAAATC
1372649 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1373058 original size:20 final size:20
Alignment explanation
Indices: 1373033--1373085 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1373023 CGATTTTAGT
1373033 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
1373053 TTCGCGTTGCAATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
1373073 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1373086 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1374840 original size:18 final size:18
Alignment explanation
Indices: 1374817--1374867 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1374807 TTTACTCGTA
1374817 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1374835 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
1374853 ATTTCAGTTAGATTA
1 ATTTCACTTAGATTA
1374868 CTTAGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1375039 original size:20 final size:20
Alignment explanation
Indices: 1375014--1375061 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1375004 TAGTTTACTT
1375014 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
1375034 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
1375054 TCGCAACG
1 TCGCAACG
1375062 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1375132 original size:20 final size:19
Alignment explanation
Indices: 1375104--1375170 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1375094 GCGATTCTCT
*
1375104 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
1375124 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
1375144 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
1375162 TGTTGCGAT
1 CGTTGCGAT
1375171 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.29
19 1 0.02
20 29 0.69
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:1377180 original size:14 final size:14
Alignment explanation
Indices: 1377161--1377222 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1377151 TTGCTTGTTT
1377161 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1377175 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1377189 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1377204 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1377218 TAATT
1 -AATT
1377223 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1377194 original size:28 final size:29
Alignment explanation
Indices: 1377163--1377217 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1377153 GCTTGTTTAA
*
1377163 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
1377191 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
1377218 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:1377346 original size:20 final size:20
Alignment explanation
Indices: 1377321--1377374 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1377311 AGGTACACTT
*
1377321 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
1377341 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
1377361 TCGCAATGCGAAAG
1 TCGCAACGCGAAAG
1377375 TCAATTCGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:1377410 original size:20 final size:20
Alignment explanation
Indices: 1377367--1377553 Score: 199
Period size: 20 Copynumber: 9.7 Consensus size: 20
1377357 AAAATCGCAA
*
1377367 TGCGAAAGTC-AATTCGCGT
1 TGCGATAGTCAAATTCGCGT
* * *
1377386 TGCGATAGTCTAATACGCTT
1 TGCGATAGTCAAATTCGCGT
*
1377406 TGCGAT--T----TTCTCGT
1 TGCGATAGTCAAATTCGCGT
* * * *
1377420 TGTGATAGTCGAATACCCGT
1 TGCGATAGTCAAATTCGCGT
* **
1377440 TGCGATAATCAAATTCATGT
1 TGCGATAGTCAAATTCGCGT
1377460 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
1377480 TGCGATAGTCAAATTTGCGT
1 TGCGATAGTCAAATTCGCGT
1377500 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
1377520 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCGCGT
*
1377540 TGCGATATTCAAAT
1 TGCGATAGTCAAAT
1377554 AAATGTGTAA
Statistics
Matches: 140, Mismatches: 21, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
14 9 0.06
16 1 0.01
18 1 0.01
19 9 0.06
20 120 0.86
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGCGT
Found at i:1380041 original size:24 final size:24
Alignment explanation
Indices: 1380007--1380060 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1379997 CTGAAACATC
1380007 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1380031 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1380055 ATCAAA
1 ATCAAA
1380061 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1380928 original size:20 final size:20
Alignment explanation
Indices: 1380882--1380994 Score: 113
Period size: 20 Copynumber: 5.5 Consensus size: 20
1380872 AAATTCAGCG
*
1380882 TTGCGACAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
1380902 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
1380922 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
1380942 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
1380962 TTGCAATAGTCGGAAAATCGCA
1 TTGCGATAGTC--ATAATCGCA
1380984 TTGCGATAGTC
1 TTGCGATAGTC
1380995 GGAAAATTGC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
19 1 0.01
20 62 0.77
21 1 0.01
22 17 0.21
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:1380985 original size:22 final size:22
Alignment explanation
Indices: 1380957--1381001 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1380947 ATTTACATAT
1380957 TCGCATTGCAATAGTCGGAAAA
1 TCGCATTGCAATAGTCGGAAAA
*
1380979 TCGCATTGCGATAGTCGGAAAA
1 TCGCATTGCAATAGTCGGAAAA
1381001 T
1 T
1381002 TGCAACACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (22 bp):
TCGCATTGCAATAGTCGGAAAA
Found at i:1385631 original size:4 final size:4
Alignment explanation
Indices: 1385610--1385661 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
1385600 AAAATTAATG
* * *
1385610 TAAA TAAA TGAA TAAAA TAAA TTAAT TAAT TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA T-AAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1385660 TA
1 TA
1385662 CTAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 36 0.86
5 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:1385644 original size:17 final size:17
Alignment explanation
Indices: 1385610--1385661 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1385600 AAAATTAATG
* * *
1385610 TAAATAAATGAATAAAA
1 TAAATTAATTAATTAAA
1385627 TAAATTAATTAATTAAA
1 TAAATTAATTAATTAAA
* *
1385644 TAAA-TAAATAAATAAA
1 TAAATTAATTAATTAAA
1385660 TA
1 TA
1385662 CTAAATGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAATTAATTAATTAAA
Found at i:1386861 original size:83 final size:82
Alignment explanation
Indices: 1386773--1386937 Score: 267
Period size: 83 Copynumber: 2.0 Consensus size: 82
1386763 ATATACATGC
* * *
1386773 ATACATCAGTAATATCCAAGCGATAAATTAGGTAAATTTCAAATTTAATATTCAAGGAAGTTATG
1 ATACATCAGTAATATCCAAGCGATAAATTAGGTAAATTCCAAATTAAATATTCAAGGAAGTTATA
1386838 CTTGTCTTATATATATAT
66 CTTGTCTTATATA-ATAT
* *
1386856 ATACATCAGTAATATCCAAGTGATAAATTAGGTAAATTCCAAATTAAATATTCAAGGAAGTTCTA
1 ATACATCAGTAATATCCAAGCGATAAATTAGGTAAATTCCAAATTAAATATTCAAGGAAGTTATA
*
1386921 CTTGTCTTCTATAATAT
66 CTTGTCTTATATAATAT
1386938 GCTAAATGGA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 4 0.05
83 72 0.95
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (82 bp):
ATACATCAGTAATATCCAAGCGATAAATTAGGTAAATTCCAAATTAAATATTCAAGGAAGTTATA
CTTGTCTTATATAATAT
Found at i:1389338 original size:26 final size:27
Alignment explanation
Indices: 1389308--1389359 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
1389298 ATTTTTGGGT
*
1389308 TGCTCTCTGTCTCCT-CTCGGTTTTTC
1 TGCTCTCTGTATCCTCCTCGGTTTTTC
*
1389334 TGCTCTCTGTATCCTCCTTGGTTTTT
1 TGCTCTCTGTATCCTCCTCGGTTTTT
1389360 TGCAGGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.02, C:0.31, G:0.15, T:0.52
Consensus pattern (27 bp):
TGCTCTCTGTATCCTCCTCGGTTTTTC
Found at i:1389749 original size:3 final size:3
Alignment explanation
Indices: 1389743--1389778 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1389733 TAATAAATAA
1389743 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
1389779 ATAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Done.