Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 4 of 214
Found at i:1096283 original size:42 final size:43
Alignment explanation
Indices: 1096201--1096286 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
1096191 TAGCATAAGG
1096201 AAAAAAACTAAAATGACTAGAATACCCCTAGCATAATTTTTTT
1 AAAAAAACTAAAATGACTAGAATACCCCTAGCATAATTTTTTT
* * *
1096244 AAAAAAACTAAAATGACTAGAGTACCCTTAGCAT-TTTTTTTT
1 AAAAAAACTAAAATGACTAGAATACCCCTAGCATAATTTTTTT
1096286 A
1 A
1096287 GGTAGATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 8 0.20
43 32 0.80
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (43 bp):
AAAAAAACTAAAATGACTAGAATACCCCTAGCATAATTTTTTT
Found at i:1096449 original size:58 final size:57
Alignment explanation
Indices: 1096319--1096483 Score: 183
Period size: 58 Copynumber: 2.9 Consensus size: 57
1096309 TATTGTTATT
* * *
1096319 AAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATA-ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAACA
* * *
1096377 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAACA
* * *
1096434 AAATTCTTAATATAATTATTGTT--ATATGAATTTACTAAAATCATAATATA
1 AAATT-TTAATATAATTATTATTAAATAT-AATTTAATAAAATAAT-ATATA
1096484 TAATACTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
56 4 0.04
57 36 0.39
58 51 0.55
59 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAACA
Found at i:1098285 original size:13 final size:13
Alignment explanation
Indices: 1098267--1098291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1098257 GGACATGCAA
1098267 TAATGTAAGGCTG
1 TAATGTAAGGCTG
1098280 TAATGTAAGGCT
1 TAATGTAAGGCT
1098292 CCCTCGACAG
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:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
TAATGTAAGGCTG
Found at i:1099364 original size:16 final size:16
Alignment explanation
Indices: 1099336--1099390 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1099326 GCTTGATTCA
*
1099336 CTGTAAT-GAAATAGAG
1 CTGTAATAG-AATAAAG
1099352 CTGTAATAGAATAAAG
1 CTGTAATAGAATAAAG
* *
1099368 TTGCAATAGAATAAAG
1 CTGTAATAGAATAAAG
1099384 CTGTAAT
1 CTGTAAT
1099391 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
CTGTAATAGAATAAAG
Found at i:1102775 original size:70 final size:69
Alignment explanation
Indices: 1102693--1102825 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 69
1102683 GATTTAAAAA
** *
1102693 AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCTAAGATCGTTTAAAATT
1 AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCCTAAGATCGTTTAAAATT
1102758 TGGG
66 TGGG
* * *
1102762 AAAAATGGATCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCTTGAGATCGTTTAAAA
1 AAAAAAGG-TCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCCTAAGATCGTTTAAAA
1102826 CTTGAGTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 7 0.12
70 50 0.88
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (69 bp):
AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTCCTCATAATTCCTAAGATCGTTTAAAATT
TGGG
Found at i:1103285 original size:25 final size:23
Alignment explanation
Indices: 1103251--1103311 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
1103241 ATATGTGAAT
*
1103251 TATAAAATATATATAAATATATATA
1 TATAATATATATATAAA-ATATA-A
*
1103276 TATAATATATATTTTAAAATATAA
1 TATAATATATA-TATAAAATATAA
*
1103300 -AGAATATATATA
1 TATAATATATATA
1103312 AGTATGTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 1 0.03
25 15 0.48
26 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TATAATATATATATAAAATATAA
Found at i:1107352 original size:31 final size:29
Alignment explanation
Indices: 1107299--1107360 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
1107289 TTATAACTTG
*
1107299 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATAT-AAATATAAA
*
1107329 TTGTAAATATTTTTAAGTA-ATAAATATTAA
1 TTGTAAATA-TTTTAA-TATATAAATATAAA
1107359 TT
1 TT
1107361 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 18 0.64
31 8 0.29
32 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TTGTAAATATTTTAATATATAAATATAAA
Found at i:1108657 original size:43 final size:43
Alignment explanation
Indices: 1108430--1108641 Score: 293
Period size: 43 Copynumber: 4.9 Consensus size: 43
1108420 CGCTAAAGGT
* * ** *
1108430 CATGTTCTTTAGCGGCGC-TTAAAAACAAAACGCCGCTAAAGAA
1 CATGATCTTTAGCGGCGCTTTTATCAC-AAACGCCACTAAAGAA
* * *
1108473 CATGTTCTTTAGCGGCGC-TTTACTCATAAACGCCGCTAAAGAA
1 CATGATCTTTAGCGGCGCTTTTA-TCACAAACGCCACTAAAGAA
*
1108516 CATGATCTTTAGCAGCGCTTTTATCACAAACGCCACTAAAGAA
1 CATGATCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAA
* *
1108559 CATGATCTTTAGTGGCGCTTTCATCACAAACGCCACTAAAGAA
1 CATGATCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAA
1108602 CATGATCTTTAGCGGCGCTTTTATCACAAACGCCACTAAA
1 CATGATCTTTAGCGGCGCTTTTATCACAAACGCCACTAAA
1108642 AGTATGATTC
Statistics
Matches: 154, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 149 0.97
44 5 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
CATGATCTTTAGCGGCGCTTTTATCACAAACGCCACTAAAGAA
Found at i:1119850 original size:18 final size:17
Alignment explanation
Indices: 1119827--1119862 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1119817 TTGTTTTATC
*
1119827 CTTTTTCTTTTTCTTTTT
1 CTTTTT-TTTTTCCTTTT
1119845 CTTTTTTTTTTCCTTTT
1 CTTTTTTTTTTCCTTTT
1119862 C
1 C
1119863 CTTTGCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTTTTTTTCCTTTT
Found at i:1119866 original size:6 final size:6
Alignment explanation
Indices: 1119827--1119862 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1119817 TTGTTTTATC
*
1119827 CTTTTT CTTTTT CTTTTT CTTTTT -TTTTT CCTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
1119863 CTTTGCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:1119866 original size:18 final size:18
Alignment explanation
Indices: 1119825--1119866 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1119815 CGTTGTTTTA
1119825 TCCTTTTTCTTTTTCTTT
1 TCCTTTTTCTTTTTCTTT
*
1119843 TTCTTTTT-TTTTTCCTTT
1 TCCTTTTTCTTTTT-CTTT
1119861 TCCTTT
1 TCCTTT
1119867 GCTTGAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TCCTTTTTCTTTTTCTTT
Found at i:1124499 original size:29 final size:29
Alignment explanation
Indices: 1124444--1124500 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1124434 CTCTTTTTAA
* * *
1124444 AATACTAATGGTCAAATTAAACTAAAAAT
1 AATAATAAGGGTCAAATTAAACAAAAAAT
*
1124473 AATAATAAGGGTCAAATTGAA-AAAAAAT
1 AATAATAAGGGTCAAATTAAACAAAAAAT
1124501 GCAAACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (29 bp):
AATAATAAGGGTCAAATTAAACAAAAAAT
Found at i:1125330 original size:19 final size:18
Alignment explanation
Indices: 1125287--1125345 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1125277 TAACATCTCA
1125287 AAAAAT-TATAAAAACAT
1 AAAAATATATAAAAACAT
*
1125304 AAATAATATATAATAAACTT
1 AAA-AATATATAA-AAACAT
*
1125324 AAAAATATA-AACAAAAAT
1 AAAAATATATAA-AAACAT
1125342 AAAA
1 AAAA
1125346 CAAAACCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.09
18 13 0.37
19 11 0.31
20 8 0.23
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATATATAAAAACAT
Found at i:1125612 original size:3 final size:3
Alignment explanation
Indices: 1125604--1125633 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1125594 TATGTTACTA
1125604 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1125634 CATTTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1129466 original size:12 final size:12
Alignment explanation
Indices: 1129449--1129479 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1129439 AATGTTTAGG
1129449 CCTGCAATGAAT
1 CCTGCAATGAAT
1129461 CCTGCAATGAAT
1 CCTGCAATGAAT
1129473 CGCTGCA
1 C-CTGCA
1129480 GTGTCGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (12 bp):
CCTGCAATGAAT
Found at i:1138060 original size:30 final size:31
Alignment explanation
Indices: 1138017--1138078 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
1138007 GAATGGCTTG
*
1138017 GATATGCCTAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1138048 GATAT-CCAAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1138078 G
1 G
1138079 CCATATTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (31 bp):
GATATGCCAAGATGTTAATAATGTGTTTTGT
Found at i:1145916 original size:30 final size:30
Alignment explanation
Indices: 1145852--1145909 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1145842 GTGTATAATT
*
1145852 ATATCAAATCAAATTTATATATCAAATTAA
1 ATATTAAATCAAATTTATATATCAAATTAA
*
1145882 ATATTAAATCAAAATTTATGTAT-AAATT
1 ATATTAAATC-AAATTTATATATCAAATT
1145910 TGATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATTAAATCAAATTTATATATCAAATTAA
Found at i:1156384 original size:8 final size:9
Alignment explanation
Indices: 1156366--1156443 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
1156356 AAAATATTTT
1156366 AAAATTAAA
1 AAAATTAAA
1156375 AAAATTAAA
1 AAAATTAAA
**
1156384 AAAGTATT-TT
1 AAA--ATTAAA
1156394 AAAATTAAA
1 AAAATTAAA
1156403 AAAATTTAAA
1 AAAA-TTAAA
***
1156413 AAAAGTATTTT
1 AAAA-T-TAAA
1156424 AAAATTAAA
1 AAAATTAAA
1156433 AAAA-TAAA
1 AAAATTAAA
1156441 AAA
1 AAA
1156444 TAAAAATATT
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
8 10 0.19
9 21 0.40
10 14 0.26
11 8 0.15
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAATTAAA
Found at i:1156395 original size:28 final size:28
Alignment explanation
Indices: 1156370--1156443 Score: 123
Period size: 30 Copynumber: 2.6 Consensus size: 28
1156360 TATTTTAAAA
1156370 TTAAAAAAATTAAAAAAGTATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAA
1156398 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAA-TT-AAAAAAGTATTTTAAAA
1156428 TTAAAAAAA-TAAAAAA
1 TTAAAAAAATTAAAAAA
1156444 TAAAAATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.14
28 10 0.23
29 2 0.05
30 26 0.59
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (28 bp):
TTAAAAAAATTAAAAAAGTATTTTAAAA
Found at i:1169401 original size:6 final size:6
Alignment explanation
Indices: 1169390--1169430 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1169380 AGATTTCCAA
* * *
1169390 AAATGG AAATGG AAATGG AAATGA AAATGA AAATAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
1169431 TACAATTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:1169644 original size:25 final size:25
Alignment explanation
Indices: 1169572--1169645 Score: 103
Period size: 26 Copynumber: 2.9 Consensus size: 25
1169562 AATTTTCTCG
*
1169572 AAATTTTATTGGGGGTAAAATCGTCA
1 AAATTTTATT-GGGGTAAAATTGTCA
* *
1169598 AATTTTTATCGGGGGTAAAATTGTCA
1 AAATTTTAT-TGGGGTAAAATTGTCA
1169624 AAATTTTATTGGGGTAAAATTG
1 AAATTTTATTGGGGTAAAATTG
1169646 GGATGAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.29
26 30 0.71
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (25 bp):
AAATTTTATTGGGGTAAAATTGTCA
Found at i:1180315 original size:3 final size:3
Alignment explanation
Indices: 1180307--1180361 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1180297 TAATACAAGC
1180307 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1180355 TTA TTA T
1 TTA TTA T
1180362 AAACTTGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1183675 original size:97 final size:97
Alignment explanation
Indices: 1183501--1183678 Score: 245
Period size: 97 Copynumber: 1.8 Consensus size: 97
1183491 TTGAACATGT
** * *
1183501 GGTTACAAAATTGTGTTTTCATTATAAATTTGAGTAAATAGTTAATGAATTTTGTAGTTGTTGTA
1 GGTTACAAAACCGTGTTTTCATTATAAATTTGAGTAAATAATTAATGAATTTTGTAGTTGTTATA
*
1183566 AAATATTGTTATTTAGAACTTTCAGTGTGTTC
66 AAATATTATTATTTAGAACTTTCAGTGTGTTC
* *
1183598 GGTTACAAAACCGTGTTTTCATTA-AGAA-TTGAAGTAAATAATTTATGATTTTTGTAGTTGTTA
1 GGTTACAAAACCGTGTTTTCATTATA-AATTTG-AGTAAATAATTAATGAATTTTGTAGTTGTTA
1183661 TAACAA-ATTATTATTTAG
64 TAA-AATATTATTATTTAG
1183679 GGAGATACTT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
96 4 0.06
97 65 0.92
98 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (97 bp):
GGTTACAAAACCGTGTTTTCATTATAAATTTGAGTAAATAATTAATGAATTTTGTAGTTGTTATA
AAATATTATTATTTAGAACTTTCAGTGTGTTC
Found at i:1186908 original size:16 final size:15
Alignment explanation
Indices: 1186887--1186916 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1186877 CACAAAGACG
1186887 GTGGAACCAGTCCCAA
1 GTGGAACCA-TCCCAA
1186903 GTGGAACCATCCCA
1 GTGGAACCATCCCA
1186917 TGGTGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
GTGGAACCATCCCAA
Found at i:1187973 original size:18 final size:20
Alignment explanation
Indices: 1187933--1187973 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1187923 TTATTTTAAA
*
1187933 TTTTTTATATAGTATGTAGC
1 TTTTTTATATAGTATATAGC
1187953 TTTTTTAT-TAGTATATA-C
1 TTTTTTATATAGTATATAGC
1187971 TTT
1 TTT
1187974 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTTTATATAGTATATAGC
Found at i:1190240 original size:6 final size:6
Alignment explanation
Indices: 1190229--1190259 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1190219 TCAGCTTATC
1190229 CTAACA CTAACA CTAACA CTAACA CTAACA C
1 CTAACA CTAACA CTAACA CTAACA CTAACA C
1190260 CAATTTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CTAACA
Found at i:1194402 original size:19 final size:19
Alignment explanation
Indices: 1194374--1194410 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1194364 AAAATCATTT
* *
1194374 AAAAATAAATTTTTTTAAC
1 AAAAAAAAATATTTTTAAC
1194393 AAAAAAAAATATTTTTAA
1 AAAAAAAAATATTTTTAA
1194411 TTTACACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAAAAATATTTTTAAC
Found at i:1194963 original size:23 final size:25
Alignment explanation
Indices: 1194919--1194970 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1194909 GGTTCCTATT
1194919 TTTTTTTCATTTTGAGCAA-TTTAA
1 TTTTTTTCATTTTGAGCAATTTTAA
*
1194943 TTTTTTTC-TTTT-ATGCTATTTTAA
1 TTTTTTTCATTTTGA-GCAATTTTAA
1194967 TTTT
1 TTTT
1194971 AATTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 7 0.28
24 17 0.68
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTTTTTCATTTTGAGCAATTTTAA
Found at i:1195938 original size:11 final size:11
Alignment explanation
Indices: 1195922--1195957 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1195912 CAAAAATTAC
1195922 AAATTTTAAAA
1 AAATTTTAAAA
1195933 AAATTTTAAAAA
1 AAATTTT-AAAA
*
1195945 AAATTCTAAAA
1 AAATTTTAAAA
1195956 AA
1 AA
1195958 TATATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTTTAAAA
Found at i:1195946 original size:12 final size:12
Alignment explanation
Indices: 1195922--1195957 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1195912 CAAAAATTAC
1195922 AAATTTT-AAAA
1 AAATTTTAAAAA
1195933 AAATTTTAAAAA
1 AAATTTTAAAAA
*
1195945 AAATTCTAAAAA
1 AAATTTTAAAAA
1195957 A
1 A
1195958 TATATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATTTTAAAAA
Found at i:1197760 original size:28 final size:25
Alignment explanation
Indices: 1197693--1197767 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
1197683 AAATTTATTT
*
1197693 AAAAAAATTAAAA-TAATAAAAACTA
1 AAAAAAATAAAAACT-ATAAAAACTA
*
1197718 AAAAAAATAATAACTATAATAAACTA
1 AAAAAAATAAAAACTATAA-AAACTA
* *
1197744 AAAAGAAGTTAAAAACTAAAAAAA
1 AAAA-AA-ATAAAAACTATAAAAA
1197768 AAATTGGCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
25 15 0.37
26 11 0.27
27 5 0.12
28 10 0.24
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAAAAATAAAAACTATAAAAACTA
Found at i:1198279 original size:29 final size:29
Alignment explanation
Indices: 1198247--1198308 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1198237 CAACTTTTTA
*
1198247 TTTTATTTTATTTC-AATAAATCATTATAC
1 TTTTATTATA-TTCAAATAAATCATTATAC
**
1198276 TTTTATTATATTCAAATAAATTGTTATAC
1 TTTTATTATATTCAAATAAATCATTATAC
1198305 TTTT
1 TTTT
1198309 GAATCCCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTATTATATTCAAATAAATCATTATAC
Found at i:1201376 original size:16 final size:17
Alignment explanation
Indices: 1201350--1201383 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1201340 AAAATTCGAA
*
1201350 TGAGAAAATTATTTAAT
1 TGAGAAAATTAATTAAT
1201367 TGAG-AAATTAATTAAT
1 TGAGAAAATTAATTAAT
1201383 T
1 T
1201384 TAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TGAGAAAATTAATTAAT
Found at i:1203160 original size:24 final size:23
Alignment explanation
Indices: 1203124--1203169 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1203114 TAAATAAATA
*
1203124 AATAGATAATAAAAAAATAATAAC
1 AATAAATAATAAAAAAA-AATAAC
* *
1203148 AATAAATAGTAAAATAAAATAA
1 AATAAATAATAAAAAAAAATAA
1203170 ATAGATGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (23 bp):
AATAAATAATAAAAAAAAATAAC
Found at i:1207801 original size:31 final size:31
Alignment explanation
Indices: 1207766--1207836 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1207756 AGTGACCAAA
* *
1207766 ATGAAAATTATTTTTGACG-GTAGTGCCTAAG
1 ATGAAAATTATTTGT-AAGAGTAGTGCCTAAG
* *
1207797 ATGAAAATGATTTGTAAGAGTAGTGCTTAAG
1 ATGAAAATTATTTGTAAGAGTAGTGCCTAAG
1207828 ATGAAAATT
1 ATGAAAATT
1207837 TTTAGTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (31 bp):
ATGAAAATTATTTGTAAGAGTAGTGCCTAAG
Found at i:1214999 original size:34 final size:34
Alignment explanation
Indices: 1214956--1215021 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1214946 AGTAAAATAT
* *
1214956 TTTTCGTAAAATGGTTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
1214989 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
1215022 CTAGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1216679 original size:3 final size:3
Alignment explanation
Indices: 1216671--1216697 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1216661 AATAGAATAG
1216671 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1216698 AAAATTAGAT
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):
TTA
Found at i:1222785 original size:13 final size:15
Alignment explanation
Indices: 1222761--1222794 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1222751 TTTAATTTTC
1222761 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
1222775 AAAATTT-AAAAATA
1 AAAATTTCAAAAATA
1222789 AAAATT
1 AAAATT
1222795 ACATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:1222830 original size:30 final size:29
Alignment explanation
Indices: 1222790--1222909 Score: 95
Period size: 30 Copynumber: 4.1 Consensus size: 29
1222780 TTAAAAATAA
*
1222790 AAATTACATTTTGACCCCTAAATTTTTCCT
1 AAATTTCATTTTGACCCCTAAATTTTT-CT
*
1222820 AAATTTCATTTTGACCCTTAAACTTTCTT-T
1 AAATTTCATTTTGACCCCTAAA-TTT-TTCT
* * * *
1222850 AAATTTCACTTAGATCCCTAAA-CTTTCATT
1 AAATTTCATTTTGACCCCTAAATTTTTC--T
**
1222880 AAATTTCATTTT-AATCCTAAA-TTTTCT
1 AAATTTCATTTTGACCCCTAAATTTTTCT
1222907 AAA
1 AAA
1222910 AATTACATTT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
27 6 0.08
28 1 0.01
29 11 0.15
30 50 0.68
31 3 0.04
32 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (29 bp):
AAATTTCATTTTGACCCCTAAATTTTTCT
Found at i:1223174 original size:10 final size:10
Alignment explanation
Indices: 1223155--1223204 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1223145 TTTTTCGAAG
*
1223155 GAAAAAAGAA
1 GAAAAGAGAA
1223165 GAAAAGAGAA
1 GAAAAGAGAA
1223175 GAAAAGAGAA
1 GAAAAGAGAA
* *
1223185 -AGAGGAGAA
1 GAAAAGAGAA
1223194 GAAAAGA-AA
1 GAAAAGAGAA
1223203 GA
1 GA
1223205 GTACCAGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:1223205 original size:17 final size:19
Alignment explanation
Indices: 1223158--1223200 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1223148 TTCGAAGGAA
1223158 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
1223176 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
1223195 AAAAGA
1 AAAAGA
1223201 AAGAGTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:1223276 original size:3 final size:3
Alignment explanation
Indices: 1223270--1223320 Score: 84
Period size: 3 Copynumber: 16.3 Consensus size: 3
1223260 GTGTAGGAGG
1223270 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AG-A AGA AGA
1223317 AGA A
1 AGA A
1223321 AGAAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1223609 original size:15 final size:15
Alignment explanation
Indices: 1223591--1223673 Score: 94
Period size: 15 Copynumber: 5.2 Consensus size: 15
1223581 AAAAGGAGAG
*
1223591 AAAGAAAAAATAAAA
1 AAAGAAAAAAGAAAA
*
1223606 AAAGAAAGAAGAAAA
1 AAAGAAAAAAGAAAA
*
1223621 AAAGAAAAGAGAAAA
1 AAAGAAAAAAGAAAA
1223636 AAAGGAAAAAAGGGAAAA
1 AAA-GAAAAAA--GAAAA
1223654 AGAAGAAAAAAAGAAAA
1 A-AAG-AAAAAAGAAAA
1223671 AAA
1 AAA
1223674 AGAGTTTCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
15 29 0.50
16 8 0.14
17 6 0.10
18 7 0.12
19 8 0.14
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:1223625 original size:8 final size:8
Alignment explanation
Indices: 1223591--1223673 Score: 82
Period size: 8 Copynumber: 10.4 Consensus size: 8
1223581 AAAAGGAGAG
1223591 AAAG-AAA
1 AAAGAAAA
*
1223598 AAATAAAA
1 AAAGAAAA
1223606 AAAG-AAA
1 AAAGAAAA
*
1223613 GAAGAAAA
1 AAAGAAAA
1223621 AAAG-AAA
1 AAAGAAAA
*
1223628 AGAGAAAA
1 AAAGAAAA
1223636 AAAGGAAAA
1 AAA-GAAAA
*
1223645 AAGGGAAAA
1 AA-AGAAAA
1223654 AGAAGAAAA
1 A-AAGAAAA
1223663 AAAGAAAA
1 AAAGAAAA
1223671 AAA
1 AAA
1223674 AGAGTTTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
7 15 0.24
8 27 0.44
9 19 0.31
10 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1223643 original size:9 final size:9
Alignment explanation
Indices: 1223625--1223675 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
1223615 AGAAAAAAAG
1223625 AAAAGAGAAA
1 AAAAG-GAAA
1223635 AAAAGGAAA
1 AAAAGGAAA
*
1223644 AAAGGGAAA
1 AAAAGGAAA
1223653 AAGAA-GAAA
1 AA-AAGGAAA
*
1223662 AAAAGAAAA
1 AAAAGGAAA
1223671 AAAAG
1 AAAAG
1223676 AGTTTCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 2 0.06
9 28 0.78
10 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAGGAAA
Found at i:1224255 original size:20 final size:22
Alignment explanation
Indices: 1224218--1224261 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1224208 AATTTTGTGT
*
1224218 AAAAAAATCCAGTGTTTTCAAAA
1 AAAAAAATCCAGT-TTTCCAAAA
1224241 AAAAAAATCCA-TTTTCCAAAA
1 AAAAAAATCCAGTTTTCCAAAA
1224262 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAAAAATCCAGTTTTCCAAAA
Found at i:1224299 original size:17 final size:17
Alignment explanation
Indices: 1224257--1224419 Score: 150
Period size: 17 Copynumber: 9.4 Consensus size: 17
1224247 ATCCATTTTC
* *
1224257 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
1224275 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
1224293 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
* *
1224309 CAAAAATTTCCGTATTT
1 CAAAAATTTTCGTGTTT
1224326 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
1224344 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
1224361 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
1224379 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
1224396 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
1224414 CAAAAA
1 CAAAAA
1224420 AAAATCTCGT
Statistics
Matches: 118, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
16 15 0.13
17 50 0.42
18 41 0.35
19 12 0.10
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:1224419 original size:35 final size:34
Alignment explanation
Indices: 1224257--1224419 Score: 159
Period size: 35 Copynumber: 4.7 Consensus size: 34
1224247 ATCCATTTTC
* * * * *
1224257 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTATTT
1224293 CAAAAATTTTC--GTTTTCAAAAATTTCCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTATTT
*
1224326 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTATTT
** * *
1224361 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTATTT
**
1224396 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
1224420 AAAATCTCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 21 0.20
34 9 0.08
35 61 0.58
36 12 0.11
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTATTT
Found at i:1224432 original size:38 final size:37
Alignment explanation
Indices: 1224380--1224507 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 37
1224370 TCTTGTTTTC
*
1224380 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTCGTGTTTTCAAAA
* *
1224419 AAAAATCTCGTGTTTCATAAATTTT-G-GTTTTTAAAA
1 AAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAA
* * * *
1224455 AAATAT-T-ATGTGTTAAAATTCTCGTGTTTTCAAAA
1 AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA
1224490 CAAGAAATTCTCGTGTTT
1 -AA-AAA-TCTCGTGTTT
1224508 CAATCGGATC
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
33 6 0.09
34 6 0.09
35 10 0.14
36 16 0.23
37 4 0.06
38 14 0.20
39 9 0.13
40 4 0.06
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (37 bp):
AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA
Found at i:1234963 original size:9 final size:9
Alignment explanation
Indices: 1234949--1234995 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
1234939 GACAATCTTC
1234949 AAAATTATA
1 AAAATTATA
1234958 AAAATT-TA
1 AAAATTATA
*
1234966 GAAATTAT-
1 AAAATTATA
1234974 AAAA-TATA
1 AAAATTATA
1234982 AAAATTATA
1 AAAATTATA
1234991 TAAAA
1 -AAAA
1234996 ATAAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 3 0.09
8 14 0.44
9 11 0.34
10 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:1235001 original size:17 final size:16
Alignment explanation
Indices: 1234949--1235016 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
1234939 GACAATCTTC
*
1234949 AAAATTATAAAAATTTA
1 AAAATTATAAAAA-ATA
* *
1234966 GAAATTATAAAATATA
1 AAAATTATAAAAAATA
1234982 AAAATTATATAAAAAT-
1 AAAATTATA-AAAAATA
*
1234998 AAAATGA-AAAAAATA
1 AAAATTATAAAAAATA
1235013 AAAA
1 AAAA
1235017 AAATATTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 16 0.37
17 16 0.37
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATTATAAAAAATA
Found at i:1235036 original size:21 final size:22
Alignment explanation
Indices: 1235012--1235054 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1235002 TGAAAAAAAT
*
1235012 AAAAAAAATA-TTTACTTTTTA
1 AAAAAAAATATTTTAATTTTTA
*
1235033 AAAAAAATTATTTTAATTTTTA
1 AAAAAAAATATTTTAATTTTTA
1235055 TAATTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAAAAATATTTTAATTTTTA
Found at i:1235377 original size:56 final size:58
Alignment explanation
Indices: 1235245--1235427 Score: 174
Period size: 56 Copynumber: 3.2 Consensus size: 58
1235235 GAAATGTTAG
* * * * * * *
1235245 GGACTAACTTGGACAAAAAAAATT-AAACTCGAAGGTGGGAACAATTGTCAAGTTTAA
1 GGACTAACTTGGAAAAAAAAAATTCAAACCCTAATGTGGAAACAATTATCAAGTTCAA
* * * * *
1235302 GGACTAATTTGG-GAAAAAAAGTTCAAGCCCTAATGT-GAAATAATTATCAAGTTCAA
1 GGACTAACTTGGAAAAAAAAAATTCAAACCCTAATGTGGAAACAATTATCAAGTTCAA
* * *
1235358 GGACTAACTTGAAACAAAAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAA
1 GGACTAACTTG---GAAAAAAAAAATTCAAACCCTAATGTGGAAACAATTATCAAGTTCAA
*
1235419 AGACTAACT
1 GGACTAACT
1235428 CAAACAACAA
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
56 35 0.35
57 19 0.19
60 20 0.20
61 26 0.26
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (58 bp):
GGACTAACTTGGAAAAAAAAAATTCAAACCCTAATGTGGAAACAATTATCAAGTTCAA
Found at i:1235433 original size:60 final size:60
Alignment explanation
Indices: 1235315--1235434 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
1235305 CTAATTTGGG
* * * * *
1235315 AAAAAAAGTTCAAGCCCTAATGTGAAATAATTATCAAGTTCAAGGACTAACTTGAAACAA
1 AAAAAAAATTCAAACCCTAATGTGAAACAATTATCAAGTTCAAAGACTAACTTCAAACAA
* *
1235375 AAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAAAGACTAAC-TCAAACAA
1 AAAAAAAATTCAAACCCTAATGT-GAAACAATTATCAAGTTCAAAGACTAACTTCAAACAA
1235435 CAAACTTTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
60 27 0.52
61 25 0.48
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (60 bp):
AAAAAAAATTCAAACCCTAATGTGAAACAATTATCAAGTTCAAAGACTAACTTCAAACAA
Found at i:1236808 original size:20 final size:20
Alignment explanation
Indices: 1236783--1236832 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1236773 TGGCTTAAAA
1236783 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1236803 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1236820 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1236833 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1241447 original size:20 final size:20
Alignment explanation
Indices: 1241422--1241471 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1241412 TGGCTTAAAA
1241422 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1241442 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1241459 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1241472 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1242081 original size:16 final size:17
Alignment explanation
Indices: 1242050--1242082 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1242040 TAAAATTTTA
1242050 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
1242068 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
1242083 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:1242369 original size:16 final size:16
Alignment explanation
Indices: 1242348--1242378 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1242338 AATATTTATT
*
1242348 ATTTTATTAATATTAA
1 ATTTTATTAAAATTAA
1242364 ATTTTATTAAAATTA
1 ATTTTATTAAAATTA
1242379 TTATTTTATA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATTAAAATTAA
Found at i:1242929 original size:24 final size:24
Alignment explanation
Indices: 1242884--1242931 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1242874 TTTCGTTTCT
*
1242884 CTTTTTATTTTGCTTTCTTTTTAC
1 CTTTTTATTTTACTTTCTTTTTAC
*
1242908 CTTTTTATTTTATTTTACTTTTTA
1 CTTTTTATTTTACTTT-CTTTTTA
1242932 TTTTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (24 bp):
CTTTTTATTTTACTTTCTTTTTAC
Found at i:1242930 original size:17 final size:18
Alignment explanation
Indices: 1242902--1242938 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
1242892 TTTGCTTTCT
1242902 TTTTACCTTTTTATTTTA
1 TTTTACCTTTTTATTTTA
1242920 TTTTA-CTTTTTATTTTA
1 TTTTACCTTTTTATTTTA
1242937 TT
1 TT
1242939 GTTGCAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTACCTTTTTATTTTA
Found at i:1248731 original size:57 final size:57
Alignment explanation
Indices: 1248598--1248740 Score: 162
Period size: 57 Copynumber: 2.4 Consensus size: 57
1248588 AATTGACGGT
*
1248598 AAAAAGGATCTAGCTCGGACGGGTGATCCTATCCTGATATAACCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGAT-C--T--TGATATAACCCTCCCGAAGAATATGTGTG
* * *
1248661 AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAGCCGTCTCGAAGAATATGTG-G
1 AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAACCCTCCCGAAGAATATGTGTG
* *
1248717 AAAATGGATTTAGCCCGGACGGGT
1 AAAA-AGATCTAGCCCGGACGGGT
1248741 AATCCGAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
56 5 0.07
57 41 0.56
59 1 0.01
61 1 0.01
62 20 0.27
63 5 0.07
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAACCCTCCCGAAGAATATGTGTG
Found at i:1253457 original size:20 final size:20
Alignment explanation
Indices: 1253403--1253458 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
1253393 TCCAATTTAA
** *
1253403 AATTTTAAGGTTTTTTTATC
1 AATTTTAATATTTTTATATC
*
1253423 -ATATTT-ATATCTTTATATC
1 AAT-TTTAATATTTTTATATC
1253442 AATTTTAATATTTTTAT
1 AATTTTAATATTTTTAT
1253459 GATTTCTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (20 bp):
AATTTTAATATTTTTATATC
Found at i:1254971 original size:59 final size:59
Alignment explanation
Indices: 1254902--1255021 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
1254892 TTAATGAAAA
1254902 ATAGAAAAAAAATCTTAAAAAATTTAAATTGATTTATAATGATAATTTTTTATATCTTT
1 ATAGAAAAAAAATCTTAAAAAATTTAAATTGATTTATAATGATAATTTTTTATATCTTT
1254961 ATAGAAAAAAAATCTTAAAAAATTTAAATTGATTTATAATGATAATTTTTTATATCTTT
1 ATAGAAAAAAAATCTTAAAAAATTTAAATTGATTTATAATGATAATTTTTTATATCTTT
1255020 AT
1 AT
1255022 GATGATTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (59 bp):
ATAGAAAAAAAATCTTAAAAAATTTAAATTGATTTATAATGATAATTTTTTATATCTTT
Found at i:1261172 original size:24 final size:24
Alignment explanation
Indices: 1261140--1261187 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1261130 TGCACCTGCC
1261140 TTGGCTTGCGAGTCTGCTAACAAA
1 TTGGCTTGCGAGTCTGCTAACAAA
1261164 TTGGCTTGCGAGTCTGCTAACAAA
1 TTGGCTTGCGAGTCTGCTAACAAA
1261188 ATATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (24 bp):
TTGGCTTGCGAGTCTGCTAACAAA
Found at i:1262541 original size:97 final size:95
Alignment explanation
Indices: 1262432--1262644 Score: 304
Period size: 96 Copynumber: 2.2 Consensus size: 95
1262422 GTTTTATATG
*
1262432 ATTTTTTCTTAAAAACCCTAAATACTAAACTCC-AATCTAATTTTTTTAAAATTTATAATTAATT
1 ATTTTTTCTTAAAAACCCTAAACACTAAAC-CCTAATCTAA-TTTTTTAAAATTTATAATTAATT
* * *
1262496 TACTCAAGTAACCCTGAACCCTAATTTATTTA
64 TAATCAAGAAACCCTAAACCCTAATTTATTTA
*
1262528 ATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTT
1 A-TTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTT
* * *
1262593 AATTAAGAAACCTTAAACCCTTATTTATTTA
65 AATCAAGAAACCCTAAACCCTAATTTATTTA
*
1262624 ATTTTTCCTT-AAAACCCTAAA
1 ATTTTTTCTTAAAAACCCTAAA
1262645 ATTTAAAAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
94 10 0.10
95 8 0.08
96 53 0.50
97 34 0.32
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (95 bp):
ATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTA
ATCAAGAAACCCTAAACCCTAATTTATTTA
Found at i:1262843 original size:40 final size:40
Alignment explanation
Indices: 1262752--1262848 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
1262742 CAACGTAGAC
* * *
1262752 ACAAAGCGCTCCCTCAAGGAAGCGTTTTCTATCCATGTGG
1 ACAAAGCGCTTCCTTAAGGAAGCGTTTTCTATCCACGTGG
* * * *
1262792 ACAAAGTGCTTCCTTGAGGAAGCGTTTTTTGTCCACGTGG
1 ACAAAGCGCTTCCTTAAGGAAGCGTTTTCTATCCACGTGG
1262832 ACAAAGCGCTTCCTTAA
1 ACAAAGCGCTTCCTTAA
1262849 AAAAGTGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (40 bp):
ACAAAGCGCTTCCTTAAGGAAGCGTTTTCTATCCACGTGG
Found at i:1262859 original size:40 final size:40
Alignment explanation
Indices: 1262752--1262859 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
1262742 CAACGTAGAC
* * ** * * *
1262752 ACAAAGCGCTCCCTCAAGGAAGCGTTTTCTATCCATGTGG
1 ACAAAGCGCTTCCTTAAAAAAGCGTTTTTTGTCCACGTGG
* * **
1262792 ACAAAGTGCTTCCTTGAGGAAGCGTTTTTTGTCCACGTGG
1 ACAAAGCGCTTCCTTAAAAAAGCGTTTTTTGTCCACGTGG
*
1262832 ACAAAGCGCTTCCTTAAAAAAGTGTTTT
1 ACAAAGCGCTTCCTTAAAAAAGCGTTTT
1262860 CTTGCTCTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (40 bp):
ACAAAGCGCTTCCTTAAAAAAGCGTTTTTTGTCCACGTGG
Found at i:1266940 original size:44 final size:44
Alignment explanation
Indices: 1266844--1267173 Score: 238
Period size: 44 Copynumber: 7.6 Consensus size: 44
1266834 TTTTAATCCA
* * *
1266844 CTCCACTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * * *
1266887 CTTCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTTAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * * *
1266931 CTCCACTGTAACCTCAGGGAGATAAAATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--ACTTCTTTGATCTG
* ** * *
1266977 TTCCACTGTAATCTCAGGGAGATAAGA-C--CTGATGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACTTCTTTGATCTG
* * * *
1267018 CTCTACTGTAA-CTTCAGAGAGATAAGA--T-C--CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTACTTCTTTGATCTG
* * *
1267057 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * *
1267101 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--ACTTCTTTGATCTG
*
1267147 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
1267174 CCTGTATAAT
Statistics
Matches: 223, Mismatches: 47, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
39 25 0.11
40 3 0.01
41 31 0.14
43 22 0.10
44 69 0.31
45 3 0.01
46 67 0.30
47 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTACTTCTTTGATCTG
Found at i:1282086 original size:1 final size:1
Alignment explanation
Indices: 1282080--1282124 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
1282070 CTCTCCAAAG
1282080 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1282125 AGAAAGCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1292271 original size:17 final size:17
Alignment explanation
Indices: 1292249--1292282 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1292239 CCTCGAAAAG
*
1292249 CGGTTGTTTTTAATAAA
1 CGGTTGATTTTAATAAA
*
1292266 CGGTTGATTTTATTAAA
1 CGGTTGATTTTAATAAA
1292283 ACAACAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
CGGTTGATTTTAATAAA
Found at i:1302009 original size:19 final size:20
Alignment explanation
Indices: 1301970--1302014 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1301960 TGTAATTTTC
1301970 TATA-TTTTATTAAATTGTA
1 TATATTTTTATTAAATTGTA
*
1301989 TA-ATTTTTA-TAAATTCTTA
1 TATATTTTTATTAAATT-GTA
1302008 TATATTT
1 TATATTT
1302015 GAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 7 0.32
19 11 0.50
20 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTTTTATTAAATTGTA
Found at i:1310370 original size:20 final size:21
Alignment explanation
Indices: 1310336--1310383 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1310326 ATTTTAGATT
1310336 TTTTTAATAAATATTTTGAAA
1 TTTTTAATAAATATTTTGAAA
* *
1310357 TTTTTAA-AATTATTTTGATTA
1 TTTTTAATAAATATTTTGA-AA
1310378 TTTTTA
1 TTTTTA
1310384 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTTAATAAATATTTTGAAA
Found at i:1310500 original size:18 final size:18
Alignment explanation
Indices: 1310473--1310507 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1310463 CAATCTATCG
*
1310473 TTTGAGTTATTCAAATTA
1 TTTGAATTATTCAAATTA
*
1310491 TTTGAATTATTCGAATT
1 TTTGAATTATTCAAATT
1310508 GTGAAATTCA
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:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTATTCAAATTA
Found at i:1312088 original size:24 final size:26
Alignment explanation
Indices: 1312061--1312110 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
1312051 CAGTAAATAT
*
1312061 ATATATTTTTTAA-AAATTT-TAAAA
1 ATATATTATTTAATAAATTTGTAAAA
1312085 ATATATTATTTAATAAATTTGTAAAA
1 ATATATTATTTAATAAATTTGTAAAA
1312111 TAAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 6 0.26
26 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATATATTATTTAATAAATTTGTAAAA
Found at i:1312114 original size:13 final size:13
Alignment explanation
Indices: 1312096--1312126 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1312086 TATATTATTT
*
1312096 AATAAATTTGTAA
1 AATAAATTTATAA
1312109 AATAAATTTATAA
1 AATAAATTTATAA
1312122 AATAA
1 AATAA
1312127 GGTGCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AATAAATTTATAA
Found at i:1315690 original size:18 final size:19
Alignment explanation
Indices: 1315666--1315708 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1315656 TATTAAAAAT
*
1315666 TAAAAATTACAAAATATTA
1 TAAAAATAACAAAATATTA
*
1315685 -AAAAATAACTAAATATTA
1 TAAAAATAACAAAATATTA
1315703 TAAAAA
1 TAAAAA
1315709 GTTAATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAACAAAATATTA
Found at i:1316419 original size:30 final size:28
Alignment explanation
Indices: 1316362--1316419 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1316352 CATACATTTG
**
1316362 GAATTTGTCCATATACTTTTATTTTTAA
1 GAATTTGTCCATATACTTTTAGATTTAA
*
1316390 GAATTTAGTCCATCTACTTTTTAGATTTAA
1 GAATTT-GTCCATATAC-TTTTAGATTTAA
1316420 AAATGCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (28 bp):
GAATTTGTCCATATACTTTTAGATTTAA
Found at i:1317275 original size:73 final size:73
Alignment explanation
Indices: 1317131--1317394 Score: 295
Period size: 72 Copynumber: 3.6 Consensus size: 73
1317121 ACTGCTCATG
* * * *
1317131 ATTTTAATGTCGAAAATTTGGTCACAAACAAATTGAATAGTTGTGACCATTCATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGGT-ACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1317196 TTGCTTACA
65 TTGCTTACA
* * * * * * *
1317205 ATTTTAGTGTCGACAATATGGTACAAA-AAAATGAATAATTATGACCATTTATATTTATAAAAAA
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGT-CACAA
**
1317269 TTGCTTATG
65 TTGCTTACA
** *
1317278 A-TTTAGTGTAAAAAATTTGGCCACAAACAAAAT-AATAATTGTGACCATTTATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGG-TACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1317341 TTGCTTACA
65 TTGCTTACA
* *
1317350 ATTTTAGTGTCGAAAATTTAG-ACAAA-AAAATTTAATAATTGTGAC
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAA-TGAATAATTGTGAC
1317395 AACTTTGTAA
Statistics
Matches: 156, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
70 4 0.03
71 6 0.04
72 63 0.40
73 59 0.38
74 24 0.15
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (73 bp):
ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAAT
TGCTTACA
Found at i:1321774 original size:18 final size:17
Alignment explanation
Indices: 1321752--1321794 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1321742 GAACTTTTAT
1321752 TAAAATAAAAAAAATTA
1 TAAAATAAAAAAAATTA
* *
1321769 TAAAAATACAGAAAA-TA
1 T-AAAATAAAAAAAATTA
1321786 TAAAATAAA
1 TAAAATAAA
1321795 TTGTAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 4 0.18
18 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAAAAATTA
Found at i:1322089 original size:16 final size:17
Alignment explanation
Indices: 1322059--1322091 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1322049 TAGTTAATTA
1322059 ATTTTCTTTAAATATTT
1 ATTTTCTTTAAATATTT
*
1322076 ATTTT-TTTATATATTT
1 ATTTTCTTTAAATATTT
1322092 TTTAATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTCTTTAAATATTT
Found at i:1322465 original size:29 final size:30
Alignment explanation
Indices: 1322423--1322494 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 30
1322413 TTTTAATATT
* *
1322423 TTTTTGTATTTTTTTA-ATAAATATTAAAT-A
1 TTTTTATATTTTTATATA-AAAT-TTAAATAA
*
1322453 TTTTCTATA-TTTTATATAAAATTTTAATAA
1 TTTT-TATATTTTTATATAAAATTTAAATAA
1322483 TTTTTATATTTT
1 TTTTTATATTTT
1322495 CTCCCTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
29 9 0.26
30 22 0.63
31 4 0.11
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTATATTTTTATATAAAATTTAAATAA
Found at i:1334841 original size:44 final size:44
Alignment explanation
Indices: 1334791--1334878 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
1334781 TTTTATAAAC
* * * *
1334791 TACATTTTATAGTTATTTTATTTTAGTTATCTATACTATTATTT
1 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1334835 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1334879 AAGGTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (44 bp):
TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
Found at i:1336117 original size:26 final size:26
Alignment explanation
Indices: 1336065--1336122 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1336055 ATTTTTGTTT
* **
1336065 TTTTTATTGATTTTACATTCTTTAAA
1 TTTTTATTGATTTTAAATGATTTAAA
1336091 TTTTTATTGA-TTTAAATGATTTCAAA
1 TTTTTATTGATTTTAAATGATTT-AAA
1336117 TATTTT
1 T-TTTT
1336123 TTACTTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 14 0.52
27 4 0.15
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (26 bp):
TTTTTATTGATTTTAAATGATTTAAA
Found at i:1338736 original size:46 final size:46
Alignment explanation
Indices: 1338686--1338778 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1338676 ATCAAAATGA
1338686 ATCCCCAAAAAATACAGGTACCAAAGTGGACTTAGTTACCAAGTTC
1 ATCCCCAAAAAATACAGGTACCAAAGTGGACTTAGTTACCAAGTTC
1338732 ATCCCCAAAAAATACAGGTACCAAAGTGGACTTAGTTACCAAGTTC
1 ATCCCCAAAAAATACAGGTACCAAAGTGGACTTAGTTACCAAGTTC
1338778 A
1 A
1338779 AGGGCCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (46 bp):
ATCCCCAAAAAATACAGGTACCAAAGTGGACTTAGTTACCAAGTTC
Found at i:1351602 original size:63 final size:63
Alignment explanation
Indices: 1351524--1351652 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
1351514 TCCAACTGAG
* * * *
1351524 TATGTTCCGCTAACTATTATGTAACTGCTGTAACTCTAATTAAGTTGCGTGCACATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
* * ** *
1351587 TATGTTCCGTTAACTATTATGTAACCGCTGTAGCACAAATGAAGTTGTTTGCGCATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
1351650 TAT
1 TAT
1351653 CAAGAAGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (63 bp):
TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
Found at i:1352183 original size:16 final size:16
Alignment explanation
Indices: 1352162--1352194 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1352152 AGATCGGTCT
*
1352162 TTCTAGCACCATTCTC
1 TTCTAGCAACATTCTC
1352178 TTCTAGCAACATTCTC
1 TTCTAGCAACATTCTC
1352194 T
1 T
1352195 ATCGTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCTAGCAACATTCTC
Found at i:1354636 original size:58 final size:58
Alignment explanation
Indices: 1354498--1354640 Score: 214
Period size: 59 Copynumber: 2.4 Consensus size: 58
1354488 TGGCTTGCGA
* *
1354498 TTGCGGTTGCTTTTAGTGCCCAAACAAATTCAATCCTTGACATGCTGGTTCTTGTGAC
1 TTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTACTTGTGAC
* * * * *
1354556 TTGTGGTTTACTTTTAGTGCCAAAACAAATTTAATCCTTGACATGCTGGTAGTTGTGGC
1 TTGCGG-TTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTACTTGTGAC
1354615 TTGCGGTTGCTTTTAGTGCCAAAACA
1 TTGCGGTTGCTTTTAGTGCCAAAACA
1354641 TAGCAACTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
58 24 0.32
59 51 0.68
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (58 bp):
TTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTACTTGTGAC
Found at i:1354735 original size:26 final size:26
Alignment explanation
Indices: 1354682--1354737 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1354672 AATGTCACAC
* *
1354682 ATTTTGAAGCTTCATTTTCTTTGATT
1 ATTTTGAAGCTTCAATTTCTATGATT
*
1354708 ATTTTGAA-CTTCAATTTCATATGCTT
1 ATTTTGAAGCTTCAATTTC-TATGATT
1354734 ATTT
1 ATTT
1354738 CAGATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTTTGAAGCTTCAATTTCTATGATT
Found at i:1355203 original size:18 final size:17
Alignment explanation
Indices: 1355175--1355209 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1355165 ATTATTAAGA
*
1355175 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1355192 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1355210 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1355256 original size:120 final size:120
Alignment explanation
Indices: 1355121--1355346 Score: 443
Period size: 120 Copynumber: 1.9 Consensus size: 120
1355111 TAAGTATTGT
*
1355121 AGTATTATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1355186 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
1355241 AGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1355306 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1355347 TAAATATGAT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 105 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
Found at i:1355323 original size:18 final size:17
Alignment explanation
Indices: 1355295--1355329 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1355285 ATTATTAAGA
*
1355295 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1355312 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1355330 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1355559 original size:44 final size:45
Alignment explanation
Indices: 1355494--1355584 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1355484 ACCTCTATTC
* * *
1355494 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1355538 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1355583 CA
1 CA
1355585 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1355586 original size:16 final size:16
Alignment explanation
Indices: 1355565--1355633 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
1355555 GATTAGCTAT
1355565 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1355581 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1355598 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
1355614 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
1355630 TACA
1 TACA
1355634 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1355607 original size:33 final size:32
Alignment explanation
Indices: 1355565--1355633 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
1355555 GATTAGCTAT
1355565 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
1355598 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1355630 TACA
1 TACA
1355634 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1358494 original size:3 final size:3
Alignment explanation
Indices: 1358486--1358553 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1358476 AGAATGGCAA
1358486 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
1358534 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
1358554 ATGTGTTCCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1358948 original size:21 final size:21
Alignment explanation
Indices: 1358922--1358964 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1358912 GGTTCGCTGT
*
1358922 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
1358943 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
1358964 A
1 A
1358965 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:1358964 original size:16 final size:16
Alignment explanation
Indices: 1358945--1358977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1358935 TGTATTGGAT
*
1358945 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
1358961 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
1358977 T
1 T
1358978 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:1359022 original size:45 final size:44
Alignment explanation
Indices: 1358956--1359050 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
1358946 GGATTAGAGG
* *
1358956 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
1359001 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
1359045 TGTAAT
1 TGTAAT
1359051 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:1359233 original size:18 final size:17
Alignment explanation
Indices: 1359212--1359246 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1359202 TTATTATTTA
*
1359212 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1359230 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1359247 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1359240 original size:28 final size:27
Alignment explanation
Indices: 1359170--1359242 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1359160 TTTATTATCA
*
1359170 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
1359198 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
1359225 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
1359243 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:1359320 original size:77 final size:77
Alignment explanation
Indices: 1359238--1359465 Score: 227
Period size: 77 Copynumber: 3.1 Consensus size: 77
1359228 ATATATAATT
1359238 TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
1 TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
1359303 GATTAATATCAA
66 GATTAATATCAA
* * * * * *
1359315 TAATAAATAAT-TTAATCATATTTAAACA-TAA-TTATTAT--TAAA-TA---TATTTTAA--TT
1 TAATAAA-ATTCTTAAT-A-A-TT-AGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTT
*
1359369 AA-AATATATAAT-T---
61 AATAAGAT-TAATATCAA
1359382 TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
1 TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
1359447 GATTAATATCAA
66 GATTAATATCAA
1359459 TAATAAA
1 TAATAAA
1359466 TAATTTAATC
Statistics
Matches: 115, Mismatches: 14, Indels: 44
0.66 0.08 0.25
Matches are distributed among these distances:
63 3 0.03
64 4 0.03
65 6 0.05
66 3 0.03
67 16 0.14
68 2 0.02
70 5 0.04
71 15 0.13
73 15 0.13
74 5 0.04
76 2 0.02
77 23 0.20
78 3 0.03
79 6 0.05
80 4 0.03
81 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (77 bp):
TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
GATTAATATCAA
Found at i:1359359 original size:144 final size:144
Alignment explanation
Indices: 1359131--1359546 Score: 769
Period size: 144 Copynumber: 2.9 Consensus size: 144
1359121 ATGATTATTG
*
1359131 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATT-TTATTTAAATTTTAATAAGATTA---A-TATCAATAATAAATAATTTAATCATATTTAA
*
1359196 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
61 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
1359261 AGAAATTTGTTTTGGTAAA
126 AGAAATTTGTTTTGGTAAA
1359280 TTATTTTATTTAAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
1 TTATTTTATTTAAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
1359345 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAA
1359410 TTTGTTTTGGTAAA
131 TTTGTTTTGGTAAA
1359424 TTATTTTATTTAAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
1 TTATTTTATTTAAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
1359489 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1359547 ATATTCTTAT
Statistics
Matches: 265, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
144 236 0.89
145 1 0.00
148 23 0.09
149 5 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (144 bp):
TTATTTTATTTAAATTTTAATAAGATTAATATCAATAATAAATAATTTAATCATATTTAAACATA
ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAA
TTTGTTTTGGTAAA
Found at i:1359377 original size:18 final size:17
Alignment explanation
Indices: 1359356--1359390 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1359346 TTATTATTAA
*
1359356 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1359374 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1359391 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1359521 original size:18 final size:17
Alignment explanation
Indices: 1359500--1359534 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1359490 TTATTATTAA
*
1359500 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1359518 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1359535 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1399477 original size:105 final size:103
Alignment explanation
Indices: 1399284--1399477 Score: 271
Period size: 105 Copynumber: 1.9 Consensus size: 103
1399274 CCGAATTGAC
* *
1399284 GAGGATGTAAGTGATGGTAATTTTTAAATCTGTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
1 GAGGAGGTAAGTGATGGTAATTTCTAAATCTGTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
**
1399349 AAAGATAAGGTAATTATTAATGAACATATGGAACTGGT
66 AAAGATAAACTAATTATTAATGAACATATGGAACTGGT
* ** * *
1399387 GAGGAGGTAAGTGATGGTAGTTTCTGGATCTTTAAAGAATTCAAGTGTGTTTATTTTGCTTGTGA
1 GAGGAGGTAAGTGATGGTAATTTCTAAATCTGTAAAGAATTCAA--GTGTTTACTTTGCTTGTGA
* *
1399452 GTAAATATAAACTACTTATTAATGAA
64 GTAAAGATAAACTAATTATTAATGAA
1399478 GAGCGCATCA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 38 0.49
105 40 0.51
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (103 bp):
GAGGAGGTAAGTGATGGTAATTTCTAAATCTGTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
AAAGATAAACTAATTATTAATGAACATATGGAACTGGT
Found at i:1400814 original size:29 final size:29
Alignment explanation
Indices: 1400788--1400844 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1400778 TCCTTTTTCA
* *
1400788 TTTTTTAATAAATGACCCAATATTTTTAC
1 TTTTTGAATAAATAACCCAATATTTTTAC
* *
1400817 TTTTTGCATAAATAACCCAATATGTTTA
1 TTTTTGAATAAATAACCCAATATTTTTA
1400845 TGTTTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTTTGAATAAATAACCCAATATTTTTAC
Found at i:1401790 original size:4 final size:4
Alignment explanation
Indices: 1401781--1401808 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1401771 CATGAGAGTA
1401781 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1401809 AGGTGGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:1406949 original size:20 final size:18
Alignment explanation
Indices: 1406920--1406974 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
1406910 GTGTGATGTG
1406920 TTTTTT-AATTTATTTAAT
1 TTTTTTAAATTTATTT-AT
1406938 TTATTTTAAATTTATTGTAT
1 TT-TTTTAAATTTATT-TAT
*
1406958 TTTTTAAATATTTATTT
1 TTTTTTAA-ATTTATTT
1406975 TAAAGACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.06
19 10 0.31
20 19 0.59
21 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTAAATTTATTTAT
Found at i:1410896 original size:29 final size:28
Alignment explanation
Indices: 1410838--1410897 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1410828 GATTTCGCGG
1410838 AAAATGGCCCATTCCGGTAAATAATTAAA
1 AAAATGGCCCATTCCGGTAAATAA-TAAA
* * * *
1410867 AAAGTGGCCTATTTCGGTAAATTA-AAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
1410894 AAAA
1 AAAA
1410898 GGTTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 6 0.23
29 20 0.77
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:1420029 original size:20 final size:20
Alignment explanation
Indices: 1420006--1420045 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1419996 TAATTTAGCC
*
1420006 ATTTTTATTTTTATTTTAAT
1 ATTTTTATTTTTAATTTAAT
*
1420026 ATTTTTGTTTTTAATTTAAT
1 ATTTTTATTTTTAATTTAAT
1420046 TGTTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTTATTTTTAATTTAAT
Found at i:1422989 original size:44 final size:43
Alignment explanation
Indices: 1422912--1422995 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 43
1422902 TATGCCCTTG
* *
1422912 ATAATTTTTAAAATTAATTATTTAAACCATAATTATATTTTTCT
1 ATAATTTTTAAAATTAAATATTCAAACCATAATTA-ATTTTTCT
*
1422956 ATAATTTTTAAAATTAAATATTCAAA-TAGTAATTAATTTT
1 ATAATTTTTAAAATTAAATATTCAAACCA-TAATTAATTTT
1422996 GTTCTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 6 0.17
44 30 0.83
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (43 bp):
ATAATTTTTAAAATTAAATATTCAAACCATAATTAATTTTTCT
Found at i:1426859 original size:20 final size:20
Alignment explanation
Indices: 1426834--1426883 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1426824 TGGCTTAAAA
1426834 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1426854 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1426871 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1426884 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1431498 original size:20 final size:20
Alignment explanation
Indices: 1431473--1431522 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1431463 TGGCTTAAAA
1431473 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1431493 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1431510 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1431523 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1434871 original size:72 final size:72
Alignment explanation
Indices: 1434754--1434937 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
1434744 ACAACTTGAC
*
1434754 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1434819 ACTAACA
66 ACTAACA
1434826 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1434891 ACTAACA
66 ACTAACA
1434898 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1434938 AATAATAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:1434946 original size:3 final size:3
Alignment explanation
Indices: 1434938--1434969 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1434928 ATTACATCCA
1434938 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1434970 AACATGTGAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1439303 original size:72 final size:72
Alignment explanation
Indices: 1439186--1439369 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
1439176 ACAACTTGAC
*
1439186 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1439251 ACTAACA
66 ACTAACA
1439258 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1439323 ACTAACA
66 ACTAACA
1439330 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1439370 AATAATAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:1439378 original size:3 final size:3
Alignment explanation
Indices: 1439370--1439410 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1439360 ATTACATCCA
1439370 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1439411 AACATGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1442797 original size:30 final size:30
Alignment explanation
Indices: 1442761--1442821 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1442751 ATCATGATCA
*
1442761 AAATTCACCAGTTGATATAGCACAGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
* *
1442791 AAATTCACGAGTTGATATAACACGGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
1442821 A
1 A
1442822 TTTGGAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (30 bp):
AAATTCACCAGTTGATATAACACAGAACTT
Found at i:1454076 original size:17 final size:17
Alignment explanation
Indices: 1454054--1454152 Score: 90
Period size: 17 Copynumber: 5.5 Consensus size: 17
1454044 AAAAAGTATT
1454054 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
1454071 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTTAAAA
*
1454088 GTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
***
1454105 TTAAAAAATAATAAAAAAGTA
1 TT-AAAAAT-ATTTTAAA--A
1454126 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
1454145 TTAAAAAT
1 TTAAAAAT
1454153 TTAAAAAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
17 38 0.59
18 6 0.09
19 6 0.09
21 6 0.09
22 6 0.09
23 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:1454133 original size:40 final size:39
Alignment explanation
Indices: 1454042--1454151 Score: 158
Period size: 34 Copynumber: 2.9 Consensus size: 39
1454032 TTTTAGAAAT
*
1454042 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
1 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
*
1454081 TTAAAAAG-----TAAAAATATTTTAAAATTAAAAAATAA
1 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-AA
1454116 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
1 TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
1454152 TTTAAAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
34 24 0.39
35 8 0.13
39 7 0.11
40 23 0.37
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
TAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
Done.