Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006691.1 Hibiscus syriacus cultivar Beakdansim tig00016637_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: 1195339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:857 original size:21 final size:23
Alignment explanation
Indices: 807--858 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
797 ATTCCCCTGT
807 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
830 AGGGGGAATCGGTT-CCC-TCAG
1 GGGGGGAATCGGTTCCCCTTCAA
851 GGGGGGAA
1 GGGGGGAA
859 GTTCCCTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.17
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:4633 original size:22 final size:21
Alignment explanation
Indices: 4591--4630 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4581 GAGTTTGTTT
*
4591 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4612 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4631 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:6869 original size:30 final size:30
Alignment explanation
Indices: 6835--6895 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
6825 AAATCGTTTG
6835 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
6865 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
6895 G
1 G
6896 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:32138 original size:27 final size:26
Alignment explanation
Indices: 32100--32151 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
32090 TAATAAAAAC
* *
32100 ATATATTGTTAGTGTTTATTATTCAAA
1 ATATATTGTTAG-GTTGATTAATCAAA
*
32127 ATATATTTTTAGGTTGATTAATCAA
1 ATATATTGTTAGGTTGATTAATCAA
32152 TATCAGACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (26 bp):
ATATATTGTTAGGTTGATTAATCAAA
Found at i:42170 original size:25 final size:26
Alignment explanation
Indices: 42096--42202 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 26
42086 TTTTAAAATT
* * *
42096 AATTACCAATATAGCACCATTTTCAAA
1 AATTACAAAAATAGCA-CTTTTTCAAA
*
42123 ATATTTACTAAAAT-GTCACTTTTTCAAA
1 A-A-TTACAAAAATAG-CACTTTTTCAAA
*
42151 AATTACAAAAATAGCA-TTTTTAAAA
1 AATTACAAAAATAGCACTTTTTCAAA
* *
42176 AAATACAAAAATAGCACCCTTTTCAAA
1 AATTACAAAAATAGCA-CTTTTTCAAA
42203 TTAATTCCCA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
25 23 0.35
26 11 0.17
27 10 0.15
28 12 0.18
29 10 0.15
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.32
Consensus pattern (26 bp):
AATTACAAAAATAGCACTTTTTCAAA
Found at i:42283 original size:18 final size:18
Alignment explanation
Indices: 42260--42298 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42250 CTCGGTCAAC
* * *
42260 GGTCAATGGGTCGTGTCG
1 GGTCAACGGGTAGGGTCG
42278 GGTCAACGGGTAGGGTCG
1 GGTCAACGGGTAGGGTCG
42296 GGT
1 GGT
42299 TGTAACCGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.15, G:0.49, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTAGGGTCG
Found at i:46665 original size:18 final size:18
Alignment explanation
Indices: 46639--46673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46629 TCGAAAGGAC
*
46639 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
46657 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
46674 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:49352 original size:12 final size:12
Alignment explanation
Indices: 49293--49352 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
49283 CGGAAATCAA
*
49293 AACAAAATTCAG
1 AACAGAATTCAG
*
49305 AACA-TATATCAG
1 AACAGAAT-TCAG
*
49317 AACAGAATCCAG
1 AACAGAATTCAG
*
49329 ATA-AGAAATCAG
1 A-ACAGAATTCAG
49341 AACAGAATTCAG
1 AACAGAATTCAG
49353 GTCATGTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.08
12 32 0.84
13 3 0.08
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:49387 original size:24 final size:24
Alignment explanation
Indices: 49307--49389 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
49297 AAATTCAGAA
* *
49307 CATATATCAGAACAGAA-TCCAGAT
1 CATAAATCAGAACAGAATTCAAG-T
* * *
49331 AAGAAATCAGAACAGAATTCAGGT
1 CATAAATCAGAACAGAATTCAAGT
** *
49355 CATGTATCAGAACATAATTCAAGT
1 CATAAATCAGAACAGAATTCAAGT
49379 CGA-AAATCAGA
1 C-ATAAATCAGA
49390 TAAAATATTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
24 40 0.91
25 4 0.09
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (24 bp):
CATAAATCAGAACAGAATTCAAGT
Found at i:52365 original size:19 final size:19
Alignment explanation
Indices: 52337--52388 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
52327 ACCAGTTTGA
52337 CCGGTCTGAACCGGATTGG
1 CCGGTCTGAACCGGATTGG
* * *
52356 CCGGTATGAATCGGTTTGG
1 CCGGTCTGAACCGGATTGG
52375 CCGGTCTGAACCGG
1 CCGGTCTGAACCGG
52389 GTTGACTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (19 bp):
CCGGTCTGAACCGGATTGG
Found at i:52426 original size:17 final size:17
Alignment explanation
Indices: 52404--52438 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52394 CTAGTCTGAC
*
52404 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGGTGA
52421 CCGACCCGACCCGGTGA
1 CCGACCCGACCCGGTGA
52438 C
1 C
52439 ATTTTGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.26, T:0.09
Consensus pattern (17 bp):
CCGACCCGACCCGGTGA
Found at i:52572 original size:19 final size:19
Alignment explanation
Indices: 52544--52609 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
52534 ACCAGTTTGA
52544 CCGGTCTGAACCGGATTGG
1 CCGGTCTGAACCGGATTGG
* * *
52563 CCGGTATGAATCGGTTTGG
1 CCGGTCTGAACCGGATTGG
* *
52582 CCGGTCTGAACCGGGTTGA
1 CCGGTCTGAACCGGATTGG
*
52601 CTGGTCTGA
1 CCGGTCTGA
52610 CCCGACCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (19 bp):
CCGGTCTGAACCGGATTGG
Found at i:52645 original size:17 final size:17
Alignment explanation
Indices: 52611--52645 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52601 CTGGTCTGAC
*
52611 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGGTGA
*
52628 CCGACCCGACTCGGTGA
1 CCGACCCGACCCGGTGA
52645 C
1 C
52646 ATTTTGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.46, G:0.26, T:0.11
Consensus pattern (17 bp):
CCGACCCGACCCGGTGA
Found at i:52645 original size:207 final size:207
Alignment explanation
Indices: 52289--52700 Score: 788
Period size: 207 Copynumber: 2.0 Consensus size: 207
52279 CGCTGCCCCT
52289 GCGGGTGGGGGAGTTCCGAATTGAGAGGTGATGTTATGACCAGTTTGACCGGTCTGAACCGGATT
1 GCGGGTGGGGGAGTTCCGAATTGAGAGGTGATGTTATGACCAGTTTGACCGGTCTGAACCGGATT
52354 GGCCGGTATGAATCGGTTTGGCCGGTCTGAACCGGGTTGACTAGTCTGACCCGACCCGACCCGTT
66 GGCCGGTATGAATCGGTTTGGCCGGTCTGAACCGGGTTGACTAGTCTGACCCGACCCGACCCGTT
* *
52419 GACCGACCCGACCCGGTGACATTTTGGGAAATATTTTGAAAAATGTGACATTCTTGGAAATATTT
131 GACCGACCCGACCCGGTGACATTTTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTT
52484 TGAAAGAGGTCA
196 TGAAAGAGGTCA
52496 GCGGGTGGGGGAGTTCCGAATTGAGAGGTGATGTTATGACCAGTTTGACCGGTCTGAACCGGATT
1 GCGGGTGGGGGAGTTCCGAATTGAGAGGTGATGTTATGACCAGTTTGACCGGTCTGAACCGGATT
*
52561 GGCCGGTATGAATCGGTTTGGCCGGTCTGAACCGGGTTGACTGGTCTGACCCGACCCGACCCGTT
66 GGCCGGTATGAATCGGTTTGGCCGGTCTGAACCGGGTTGACTAGTCTGACCCGACCCGACCCGTT
*
52626 GACCGACCCGACTCGGTGACATTTTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTT
131 GACCGACCCGACCCGGTGACATTTTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTT
52691 TGAAAGAGGT
196 TGAAAGAGGT
52701 GACATTCTGG
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 201 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (207 bp):
GCGGGTGGGGGAGTTCCGAATTGAGAGGTGATGTTATGACCAGTTTGACCGGTCTGAACCGGATT
GGCCGGTATGAATCGGTTTGGCCGGTCTGAACCGGGTTGACTAGTCTGACCCGACCCGACCCGTT
GACCGACCCGACCCGGTGACATTTTGGGAAATATTTTGAAAAAGGTGACATTCTGGGAAATATTT
TGAAAGAGGTCA
Found at i:52772 original size:29 final size:29
Alignment explanation
Indices: 52640--52773 Score: 196
Period size: 29 Copynumber: 4.6 Consensus size: 29
52630 GACCCGACTC
* *
52640 GGTGACATTTTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAATTATTTTGAAAAA
* *
52669 GGTGACATTCTGGGAAATATTTTGAAAGA
1 GGTGACATTCTGGGAATTATTTTGAAAAA
52698 GGTGACATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAATTATTTTGAAAAA
* *
52727 GGTAACATTCTGAGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAATTATTTTGAAAAA
* *
52756 TGTGACATTTTGGGAATT
1 GGTGACATTCTGGGAATT
52774 TTCGAATGTA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (29 bp):
GGTGACATTCTGGGAATTATTTTGAAAAA
Found at i:53967 original size:20 final size:20
Alignment explanation
Indices: 53942--53980 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53932 AATTTCTGAA
53942 CTACTACTCA-TTTATTGTAT
1 CTACTA-TCATTTTATTGTAT
*
53962 CTACTATGATTTTATTGTA
1 CTACTATCATTTTATTGTA
53981 CTATTGGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (20 bp):
CTACTATCATTTTATTGTAT
Found at i:58940 original size:17 final size:16
Alignment explanation
Indices: 58894--58940 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
58884 CAAAAAACAT
* *
58894 AAAATATGACTTTTCG
1 AAAATTTGACTTTTCA
*
58910 AAAATTTAACTTTTCA
1 AAAATTTGACTTTTCA
58926 AAAACTTTGACTTTT
1 AAAA-TTTGACTTTT
58941 AGGTTAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (16 bp):
AAAATTTGACTTTTCA
Found at i:64798 original size:17 final size:16
Alignment explanation
Indices: 64752--64798 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
64742 CAAAAAACAT
* *
64752 AAAATATGACTTTTCG
1 AAAATTTGACTTTTCA
*
64768 AAAATTTAACTTTTCA
1 AAAATTTGACTTTTCA
64784 AAAACTTTGACTTTT
1 AAAA-TTTGACTTTT
64799 AGGTTAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (16 bp):
AAAATTTGACTTTTCA
Found at i:70203 original size:15 final size:16
Alignment explanation
Indices: 70174--70205 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
70164 GCGTAATGTA
70174 TTAAAAAATAGAAATT
1 TTAAAAAATAGAAATT
70190 TTAAAAAATA-AAATT
1 TTAAAAAATAGAAATT
70205 T
1 T
70206 ATTGACTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAAAAATAGAAATT
Found at i:77273 original size:14 final size:15
Alignment explanation
Indices: 77238--77270 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
77228 CCGAAATACA
77238 GAAATCAGATATCAG
1 GAAATCAGATATCAG
77253 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
77268 GAA
1 GAA
77271 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:78099 original size:30 final size:29
Alignment explanation
Indices: 78055--78225 Score: 222
Period size: 30 Copynumber: 5.9 Consensus size: 29
78045 CTAAAATAAT
78055 ACCTTTTT--AATTAAATTCCCAAAATAGC
1 ACCTTTTTCGAATT-AATTCCCAAAATAGC
*
78083 ACCTTTTTCGAATTAAATTCCCAATATAGC
1 ACCTTTTTCGAATT-AATTCCCAAAATAGC
*
78113 ACCTTTTTCAAATTAAATTCCCAAAATAGC
1 ACCTTTTTCGAATT-AATTCCCAAAATAGC
** * *
78143 ACCCATTTCGAAATAATTCCCAAAATAGG
1 ACCTTTTTCGAATTAATTCCCAAAATAGC
**
78172 ACCCGTTTCGAATTAATTCCCAAAATAGC
1 ACCTTTTTCGAATTAATTCCCAAAATAGC
78201 ACC-TTTTCGAATTAATTCCCAAAAT
1 ACCTTTTTCGAATTAATTCCCAAAAT
78226 TTCACCCGGT
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
28 29 0.22
29 43 0.33
30 57 0.44
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (29 bp):
ACCTTTTTCGAATTAATTCCCAAAATAGC
Found at i:78293 original size:27 final size:27
Alignment explanation
Indices: 78239--78293 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
78229 ACCCGGTCAA
* * *
78239 CGGTCAACGGGTCGGGTCGAGTCGGGT
1 CGGTCAACGGATCGGGTCGAGACCGGT
78266 CGGTCAACGGATCGGGTCG-GAACCGGT
1 CGGTCAACGGATCGGGTCGAG-ACCGGT
78293 C
1 C
78294 AAACCGGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.15, C:0.25, G:0.44, T:0.16
Consensus pattern (27 bp):
CGGTCAACGGATCGGGTCGAGACCGGT
Found at i:86481 original size:22 final size:22
Alignment explanation
Indices: 86451--86504 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
86441 CCGATAGTGA
*
86451 ATTGGAACACATATCCAAATCC
1 ATTGCAACACATATCCAAATCC
86473 ATTGCAACACATATCCAAATCC
1 ATTGCAACACATATCCAAATCC
86495 ATTGCAACAC
1 ATTGCAACAC
86505 GATTCTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (22 bp):
ATTGCAACACATATCCAAATCC
Found at i:88445 original size:53 final size:53
Alignment explanation
Indices: 88365--88475 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
88355 TAAATATCTT
88365 AGAATCTTTAGTGGAGAAGAAACACTATTATATTCGACAACAACTACATGGAA
1 AGAATCTTTAGTGGAGAAGAAACACTATTATATTCGACAACAACTACATGGAA
*
88418 AGAATCTTTAGTGGAGAAGAAACACTATTGTATTCGACAACAACTACATGGAA
1 AGAATCTTTAGTGGAGAAGAAACACTATTATATTCGACAACAACTACATGGAA
88471 AGAAT
1 AGAAT
88476 TGATATTGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (53 bp):
AGAATCTTTAGTGGAGAAGAAACACTATTATATTCGACAACAACTACATGGAA
Found at i:89560 original size:24 final size:24
Alignment explanation
Indices: 89533--89625 Score: 150
Period size: 24 Copynumber: 3.9 Consensus size: 24
89523 ACATGATTCG
89533 GGTCAAGTATCATATCAGAATCCA
1 GGTCAAGTATCATATCAGAATCCA
89557 GGTCAAGTATCATATCAGAATCCA
1 GGTCAAGTATCATATCAGAATCCA
*
89581 GGTCAAGTATCAAATCAGAATCCA
1 GGTCAAGTATCATATCAGAATCCA
* * *
89605 TGTCAGGTATCATAACAGAAT
1 GGTCAAGTATCATATCAGAAT
89626 TCAAATCGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
GGTCAAGTATCATATCAGAATCCA
Found at i:100612 original size:32 final size:31
Alignment explanation
Indices: 100576--100648 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
100566 GCCACGGGGT
* *
100576 CTACCTAAGAACACATCTTAGGGCCGCAGGGC
1 CTACCTAAGAA-ACATCTCAGGGCCGCAGAGC
** ** *
100608 CTACCCGAGAATGATCTCAGGGCCGTAGAGC
1 CTACCTAAGAAACATCTCAGGGCCGCAGAGC
100639 CTACCTAAGA
1 CTACCTAAGA
100649 GTCATATTAG
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (31 bp):
CTACCTAAGAAACATCTCAGGGCCGCAGAGC
Found at i:104539 original size:14 final size:14
Alignment explanation
Indices: 104499--104541 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
104489 GTCAACACCG
104499 GTCAACGGTCAATGTA
1 GTCAACGGTCAA--TA
* *
104515 ATCAACAGTCAATA
1 GTCAACGGTCAATA
104529 GTCAACGGTCAAT
1 GTCAACGGTCAAT
104542 GGGTCGAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (14 bp):
GTCAACGGTCAATA
Found at i:106694 original size:24 final size:24
Alignment explanation
Indices: 106667--106775 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
106657 ATATAAAAAA
*
106667 ATCAAAACATG-ATTCAGGTCAAGT
1 ATCAAAACA-GAATCCAGGTCAAGT
* *
106691 ATCATATCAGAATCCAGGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * *
106715 AT-AAGATCAAAATCCAAGTCAAGT
1 ATCAA-AACAGAATCCAGGTCAAGT
* ** *
106739 ATCAAATCAGAATCCATATCAGGT
1 ATCAAAACAGAATCCAGGTCAAGT
*
106763 ATCATAACAGAAT
1 ATCAAAACAGAAT
106776 TCAAATCGGA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 66 0.94
25 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAAGT
Found at i:110407 original size:32 final size:32
Alignment explanation
Indices: 110368--110434 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
110358 GATACAAAAT
*
110368 AATTTAATTCAAATC-TC-TAAATTATTTTTAAA
1 AATTTAA-T-AAATCTTCTTAAATGATTTTTAAA
*
110400 AATTTAATAAATCTTCTTAAATGATTTTTCAA
1 AATTTAATAAATCTTCTTAAATGATTTTTAAA
110432 AAT
1 AAT
110435 CCATCACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 5 0.16
31 3 0.10
32 23 0.74
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.46
Consensus pattern (32 bp):
AATTTAATAAATCTTCTTAAATGATTTTTAAA
Found at i:119102 original size:69 final size:69
Alignment explanation
Indices: 119012--119158 Score: 215
Period size: 69 Copynumber: 2.1 Consensus size: 69
119002 GTCAAATGAT
* *
119012 AAAGACAGGGAAGGAACGTCTTTGCCGGTATGGACTGAAGCTTCGGACAGTTGAAGATGA-GCAA
1 AAAGAGAGGGAAGGAACGTCTTTACCGGTATGGACTGAAGCTTCGGACAGTTGAAGAT-ATGCAA
*
119076 CTGAG
65 CTCAG
* * * *
119081 AAAGAGAGGGAAGGAATGTCTTTACTGGTATGGACTGAAGCTTCGGACAGTTGTAGATATTCAAC
1 AAAGAGAGGGAAGGAACGTCTTTACCGGTATGGACTGAAGCTTCGGACAGTTGAAGATATGCAAC
119146 TCAG
66 TCAG
119150 AAAGAGAGG
1 AAAGAGAGG
119159 TGAGGTGTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
68 1 0.01
69 69 0.99
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (69 bp):
AAAGAGAGGGAAGGAACGTCTTTACCGGTATGGACTGAAGCTTCGGACAGTTGAAGATATGCAAC
TCAG
Found at i:123647 original size:17 final size:17
Alignment explanation
Indices: 123613--123654 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
123603 CATTTCCCTT
* *
123613 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
123629 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
123646 TCGTTCGAG
1 TCTTTCGAG
123655 CAGCAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:128060 original size:11 final size:11
Alignment explanation
Indices: 128044--128068 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
128034 CATGTAAAAC
128044 ATTTAACACTT
1 ATTTAACACTT
128055 ATTTAACACTT
1 ATTTAACACTT
128066 ATT
1 ATT
128069 CTTCTCCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTAACACTT
Found at i:130384 original size:20 final size:20
Alignment explanation
Indices: 130309--130392 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
130299 AACAGAACCC
*
130309 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
130328 CTGTGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGAATCGATT-CCC-T
* *
130351 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
130372 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
130392 C
1 C
130393 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
20 28 0.54
21 5 0.10
22 3 0.06
23 14 0.27
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:134233 original size:22 final size:21
Alignment explanation
Indices: 134191--134230 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
134181 GAGTTTGTTT
*
134191 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
134212 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
134231 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:141001 original size:3 final size:3
Alignment explanation
Indices: 140995--141043 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
140985 CTTTTTTCCT
*
140995 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
141043 T
1 T
141044 ATATACTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:141070 original size:27 final size:26
Alignment explanation
Indices: 140998--141105 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 26
140988 TTTTCCTTTA
* *
140998 TTATTATTATTA-TTATTATTATTATTA
1 TTATTATT-TTACTTATTA-TATTTTTT
141025 TTATTATTATTATCATTATATATACTTTTTT
1 TTATTATT-TTA-C-TTAT-TATA-TTTTTT
*
141056 TT-TTATTTTACTTATTGTATTTTTT
1 TTATTATTTTACTTATTATATTTTTT
*
141081 TTATTTTTTTATCTATATTATATTT
1 TTATTATTTTA-CT-TATTATATTT
141106 ATCTTGTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
25 8 0.12
26 10 0.15
27 18 0.26
28 10 0.15
29 3 0.04
30 11 0.16
31 8 0.12
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (26 bp):
TTATTATTTTACTTATTATATTTTTT
Found at i:141090 original size:26 final size:27
Alignment explanation
Indices: 141041--141105 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
141031 TTATTATCAT
141041 TATA-TATACTTTTTTTTTTATTTTA-C
1 TATATTATA-TTTTTTTTTTATTTTATC
* *
141067 T-TATTGTATTTTTTTTATTTTTTTATC
1 TATATTATATTTTTTTT-TTATTTTATC
141094 TATATTATATTT
1 TATATTATATTT
141106 ATCTTGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 10 0.31
26 11 0.34
27 2 0.06
28 9 0.28
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (27 bp):
TATATTATATTTTTTTTTTATTTTATC
Found at i:141137 original size:6 final size:6
Alignment explanation
Indices: 141122--141228 Score: 55
Period size: 6 Copynumber: 18.3 Consensus size: 6
141112 TTTACCTTTC
* * * * *
141122 TTTTAT TTTT-T ATTT-T CTTTAT CTTTA- TTTTAT TTTTAT ATATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * * *
141167 TTTTCAC TTTT-C TTTCAT TTTTAT TTTTGT TTTT-T TCTTTA- TCTTAT
1 TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT
141214 TTTTAT GTTTTAT TT
1 TTTTAT -TTTTAT TT
141229 CTTTTTATCT
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
5 21 0.27
6 47 0.59
7 11 0.14
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:141137 original size:59 final size:54
Alignment explanation
Indices: 141073--141214 Score: 135
Period size: 59 Copynumber: 2.5 Consensus size: 54
141063 TTACTTATTG
* * *
141073 TATTTTTTTTATTTTTTTATCTATATTATATTTATCTTGTTTACCTTTCTTTTATTTTT
1 TATTTTTTTT-TTTTTTTATCT-TATTATATATAT-TT-TTCACCTTTCTTTCA-TTTT
*
141132 TATTTTCTTTATCTTTATTTTAT-TT-TTATATATATTTTTCACTTTTCTTTCATTTT
1 TATTTT-TTT-T-TTT-TTTTATCTTATTATATATATTTTTCACCTTTCTTTCATTTT
141188 TATTTTTGTTTTTTTCTTTATCTTATT
1 TATTTTT-TTTTTTT-TTTATCTTATT
141215 TTTATGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
53 1 0.01
54 8 0.11
55 4 0.06
56 14 0.20
57 12 0.17
58 2 0.03
59 15 0.21
60 4 0.06
61 5 0.07
62 6 0.08
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.73
Consensus pattern (54 bp):
TATTTTTTTTTTTTTTTATCTTATTATATATATTTTTCACCTTTCTTTCATTTT
Found at i:141159 original size:11 final size:11
Alignment explanation
Indices: 141122--141260 Score: 54
Period size: 11 Copynumber: 12.3 Consensus size: 11
141112 TTTACCTTTC
141122 TTTTATTTT-T
1 TTTTATTTTAT
141132 TATTT-TCTTTAT
1 T-TTTAT-TTTAT
*
141144 CTTTATTTTAT
1 TTTTATTTTAT
*
141155 TTTTATATATAT
1 TTTTAT-TTTAT
*
141167 TTTTCACTTTT-C
1 TTTT-A-TTTTAT
*
141179 TTTCATTTTTAT
1 TTTTA-TTTTAT
* *
141191 TTTTGTTTTTT
1 TTTTATTTTAT
*
141202 TCTTTATCTTAT
1 T-TTTATTTTAT
141214 TTTTATGTTTTAT
1 TTTTA--TTTTAT
*
141227 TTCT-TTTTAT
1 TTTTATTTTAT
* * *
141237 CTTTGTTTCAT
1 TTTTATTTTAT
*
141248 TTGT-TTTTAT
1 TTTTATTTTAT
141258 TTT
1 TTT
141261 CTTTAGTTTT
Statistics
Matches: 94, Mismatches: 23, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
10 17 0.18
11 41 0.44
12 24 0.26
13 11 0.12
14 1 0.01
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:141242 original size:46 final size:46
Alignment explanation
Indices: 141122--141249 Score: 127
Period size: 47 Copynumber: 2.8 Consensus size: 46
141112 TTTACCTTTC
* * *
141122 TTTTATTTTTTATTT-TCTTTATCTTTATTTTATTTTTATATATAT
1 TTTTATCTTTTATTTCTTTTTATCTTTGTTTTATTTTTATATATAT
* * * *
141167 TTTTCA-CTTTTCTTTCATTTTTATTTTTGTTTTTTTCTTTATCT-TAT
1 TTTT-ATCTTTTATTTC-TTTTTATCTTTGTTTTATT-TTTATATATAT
* *
141214 TTTTATGTTTTATTTCTTTTTATCTTTGTTTCATTT
1 TTTTATCTTTTATTTCTTTTTATCTTTGTTTTATTT
141250 GTTTTTATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
45 12 0.18
46 18 0.27
47 30 0.45
48 6 0.09
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (46 bp):
TTTTATCTTTTATTTCTTTTTATCTTTGTTTTATTTTTATATATAT
Found at i:144151 original size:98 final size:95
Alignment explanation
Indices: 143890--144152 Score: 303
Period size: 95 Copynumber: 2.7 Consensus size: 95
143880 AGATTATAAT
* * **
143890 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTATTGCAATTGGTTAAACGCCCCGACTTTA
1 ATTATA-ATATAAAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
** *
143955 TGGATAAGATTTAGCTAGCCTGATAAAGACG
65 TGGATAAGATCCAGCTAGCCTGATAAAGACA
* * * * *
143986 ATTATAATATAAAATAAAACTTGAGTTGTCCCTCTAGAGAAATTAGTTAAACGCCCTGGCTTTAT
1 ATTATAATATAAAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
* * **
144051 GGATAATATCCAGCTAGTCTGATAAAGGTA
66 GGATAAGATCCAGCTAGCCTGATAAAGACA
* * *
144081 ATTATAATATCTATACAATGATA-TTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGACT
1 ATTATAATA--TA-A-AATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACT
144145 TTATGGAT
62 TTATGGAT
144153 TCAACTAGCC
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
95 82 0.59
96 6 0.04
97 2 0.01
98 44 0.32
99 5 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (95 bp):
ATTATAATATAAAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
GGATAAGATCCAGCTAGCCTGATAAAGACA
Found at i:145552 original size:21 final size:21
Alignment explanation
Indices: 145519--145568 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
145509 CGAAACAATG
145519 CAACTTACACAACATTGGATTT
1 CAACTT-CACAACATTGGATTT
145541 CAACTTCACAACATTGGATTT
1 CAACTTCACAACATTGGATTT
145562 CAA-TTCA
1 CAACTTCA
145569 AAGCTCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 4 0.14
21 18 0.64
22 6 0.21
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (21 bp):
CAACTTCACAACATTGGATTT
Found at i:145847 original size:60 final size:61
Alignment explanation
Indices: 145686--145847 Score: 229
Period size: 62 Copynumber: 2.7 Consensus size: 61
145676 TTTACTCAAG
* * *
145686 ATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTTACTC
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTCGTGAAACATAC-C
* *
145748 ATTGGATTTCAACCTCACGACGAAGGATATCCAGCTCAAAACCAATTTCGTGAAACAATA-C
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTCGTGAAAC-ATACC
* *
145809 -TTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAA
145848 GATCAACTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
60 35 0.39
61 1 0.01
62 52 0.58
63 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (61 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTCGTGAAACATACC
Found at i:146197 original size:61 final size:62
Alignment explanation
Indices: 146069--146239 Score: 231
Period size: 61 Copynumber: 2.8 Consensus size: 62
146059 TGAACTCGAA
* *
146069 GTGAAACTTACTCAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTTAAAACCAATTTG
1 GTGAAACTTACTC---ATTGGATTTCAACTTCACGACGAAGGATATCCAACGTAAAACCAATTTG
*
146134 GTGAAACTTACTCATTGGATTTCAACTTCATGACGAAGG-TATCCAACGTAAAACCAATTTG
1 GTGAAACTTACTCATTGGATTTCAACTTCACGACGAAGGATATCCAACGTAAAACCAATTTG
* ** *
146195 GTGAAAC--AATCCCTGGATTTCAACTTCACGATGAAGGATATCCAA
1 GTGAAACTTACTCATTGGATTTCAACTTCACGACGAAGGATATCCAA
146240 TTGAAAGCTC
Statistics
Matches: 97, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
59 25 0.26
60 7 0.07
61 28 0.29
62 24 0.25
65 13 0.13
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (62 bp):
GTGAAACTTACTCATTGGATTTCAACTTCACGACGAAGGATATCCAACGTAAAACCAATTTG
Found at i:146551 original size:86 final size:85
Alignment explanation
Indices: 146297--146587 Score: 370
Period size: 85 Copynumber: 3.4 Consensus size: 85
146287 TAGCCCAGTG
* * *
146297 CAACATAACTCAAGGCGAAAAGGGTTATCTGTCATCAAAGACCTTCGAGTTCGATTACACTCAGC
1 CAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
146362 TCAAAGGCACATCTAATTTA
66 TCAAAGGCACATCAAATTTA
* * * * * *
146382 TATA-ATAACTCAAGGCGATAAGGGTTATCTGTCAACCAAGGCCTTTGAGTTCAATTAC-TCTCA
1 CA-ACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAT-TCA
*
146445 ACTCAAAGGCACATCAAATTTA
64 GCTCAAAGGCACATCAAATTTA
* * * *
146467 CAGCATAGCTCAAGGCGAGAAGGGTTATATATCAACAAAAGACCTTCGAGTTCGATTACATTCAG
1 CAACATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAG
* *
146532 CTCAGAGGCATATCAAATTTA
65 CTCAAAGGCACATCAAATTTA
* *
146553 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAA
1 CAACATAACTCAAGGCGAGAAGGGTTATCTGTCAA
146588 AAAAAAAACT
Statistics
Matches: 174, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
85 101 0.58
86 72 0.41
87 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
CAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGCACATCAAATTTA
Found at i:150850 original size:20 final size:20
Alignment explanation
Indices: 150813--150851 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
150803 AGATTGAGTG
* * *
150813 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
150833 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
150852 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:151034 original size:21 final size:21
Alignment explanation
Indices: 151008--151047 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
150998 CAGAACCCCA
*
151008 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
151029 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
151048 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:151076 original size:20 final size:21
Alignment explanation
Indices: 151030--151090 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
151020 TTCCCCTGTG
151030 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
151053 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
151073 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
151091 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:154767 original size:21 final size:20
Alignment explanation
Indices: 154725--154768 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
154715 TCAAGAGAAG
*
154725 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
154745 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
154766 TTT
1 TTT
154769 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:158204 original size:20 final size:18
Alignment explanation
Indices: 158179--158218 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
158169 ATATTTCCAC
*
158179 TTTTCTTTCATTTTCATTTT
1 TTTTCTTT-ATCTT-ATTTT
158199 TTTTCTTTATCTTATTTT
1 TTTTCTTTATCTTATTTT
158217 TT
1 TT
158219 ATGTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTATCTTATTTT
Found at i:159729 original size:13 final size:13
Alignment explanation
Indices: 159711--159735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
159701 AGAGAGAACA
159711 AAAAAAGAAAATC
1 AAAAAAGAAAATC
159724 AAAAAAGAAAAT
1 AAAAAAGAAAAT
159736 TGAGAAAGAG
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:0.80, C:0.04, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAAGAAAATC
Found at i:163408 original size:697 final size:698
Alignment explanation
Indices: 162062--163452 Score: 2534
Period size: 697 Copynumber: 2.0 Consensus size: 698
162052 GGTGGGACAG
* * *
162062 CTATAGGGGTTGAGATGAGTCCTTCCTTCAGCTCTTGAAATGATACAACGCAACTATCATCAAGG
1 CTATAAGGGCTGAGATGAGTCCTTCCTTCAGCTCTTGAAATGATACAACACAACTATCATCAAGG
162127 AGAAAGGGTTGATTTTACTACAGTAGAGTACACAAGGGATTAGATATCTTGAAAAAAATACTTAA
66 AGAAAGGGTTGATTTTACTACAGTAGAGTACACAAGGGATTAGATATCTTGAAAAAAATACTTAA
*
162192 TGGATCTTCGATAGAATCCAACATGCCCTATAAAGCTTCGAACTCCTTTGGCTGTAGTGGGAGGA
131 TGGATCTTCGATAGAATCCAAAATGCCCTATAAAGCTTCGAACTCCTTTGGCTGTAGTGGGAGGA
162257 GACAGTTTCTCGATCACTTTAATTTTAGATTGGTCCACCTCAAAGACCTTTTTTGAGATTTTGAG
196 GACAGTTTCTCGATCACTTTAATTTTAGATTGGTCCACCTCAAAGACCTTTTTTGAGATTTTGAG
*
162322 TCCTAAAATAGTTCTCTCGGACACCATAAAGTGACACTTCTCCTAGTTCATAACCAAATATACTT
261 TCCTAAAATAGTTCTCTCGGACACCATAAAGTGACACTTCTCCCAGTTCATAACCAAATATACTT
*
162387 TCTCGTACCTCTTAAGCACATTTTCCATATTGCGAAGGCATAAGTTGAAATTATCGCTAGAGACC
326 TCTCGTACCTCTTAAGCACATTTTCCATATTGCGAAGGAATAAGTTGAAATTATCGCTAGAGACC
*
162452 AAGAAATAATCCATGAAAATATCCAAAACTTCTTCTACTATGTCCGAGAAGATGGCTAGCATGCA
391 AAGAAATAATCCATGAAAATATCCAAAACTTCTTCTACCATGTCCGAGAAGATGGCTAGCATGCA
* *
162517 CCTTTGAAATATGGCTGGTGTATTGCATAACCGGAAATGTATCATTCTAAAGGTGTAGGTTTCAT
456 CCTTTGAAATATGGATGGTGTATTGCATAACCGGAAATGTATCATTCTAAAGGCGTAGGTTTCAT
* *
162582 AAAGACAAGTAAAAATTGTCTTCTCTTGGTCTTTGAATGCTATAGCAATTTGGTTGTAGCCCGAA
521 AAAGACAAGTAAAAATTGTCTTCTCTTGGTCTTTGAATGCTATAGCAATCTGGTTGTAGACCGAA
*
162647 TATCTATCAAGAAAATAATAAAATGGTTTGCCTGCCAACCGGTCCAATATTTGATCGATGAAAGG
586 TATCTATCAAGAAAATAATAAAATGGTTTGCCTGCCAACCGGTCCAATATTTGACCGATGAAAGG
* *
162712 AATGGAATTGGTCATTTTAGTGTCCTTGCTAAGATTCCTATAGTACAA
651 AATGAAAATGGTCATTTTAGTGTCCTTGCTAAGATTCCTATAGTACAA
162760 CTATAAGGGCTGAGATGAGTCCTTCCTTCAGCTCTTGAAATGATACAACACAACTATCATCAAGG
1 CTATAAGGGCTGAGATGAGTCCTTCCTTCAGCTCTTGAAATGATACAACACAACTATCATCAAGG
* *
162825 AGAAAGGGTTGATTTTACTGCAGTAGAGTACACAAGGGATTAGATATCTTG-AAAAAGTACTTAA
66 AGAAAGGGTTGATTTTACTACAGTAGAGTACACAAGGGATTAGATATCTTGAAAAAAATACTTAA
*
162889 TGGATCTTCGATAGAATCCAAAATGCCCTATAAAGCTTCGAATTCCTTTGGCTGTAGTGGGAGGA
131 TGGATCTTCGATAGAATCCAAAATGCCCTATAAAGCTTCGAACTCCTTTGGCTGTAGTGGGAGGA
* *
162954 GACAGTTTCTCGATCACTTTAATTTTAGCTTGGTCCACCTCAATGACCTTTTTTGAGATTTTGAG
196 GACAGTTTCTCGATCACTTTAATTTTAGATTGGTCCACCTCAAAGACCTTTTTTGAGATTTTGAG
* *
163019 TCCTAAAATAGTTTTCTCGGACACCATAAAGTGACACTTCTCCCAGTTCATAACCAAATCTACTT
261 TCCTAAAATAGTTCTCTCGGACACCATAAAGTGACACTTCTCCCAGTTCATAACCAAATATACTT
163084 TCTCGTACCTCTTAAGCACATTTTCCATATTGCGAAGGAATAAGTTGAAATTATCGCTAGAGACC
326 TCTCGTACCTCTTAAGCACATTTTCCATATTGCGAAGGAATAAGTTGAAATTATCGCTAGAGACC
163149 AAGAAATAATCCATGAAAATATCCAAAACTTCTTCTACCATG-CTCGAGAAGATGGCTAGCATGC
391 AAGAAATAATCCATGAAAATATCCAAAACTTCTTCTACCATGTC-CGAGAAGATGGCTAGCATGC
*
163213 ACCTTTGAAATATTGATGGTGTATTGCATAACCGGAAATGTATCATTCTAAAGGCGTAGGTTTCA
455 ACCTTTGAAATATGGATGGTGTATTGCATAACCGGAAATGTATCATTCTAAAGGCGTAGGTTTCA
163278 TAAAGACAAGTAAAAATTGTCTTCTCTTGGTCTTTGAATGCTATAGCAATCTGGTTGTAGACCGA
520 TAAAGACAAGTAAAAATTGTCTTCTCTTGGTCTTTGAATGCTATAGCAATCTGGTTGTAGACCGA
* *
163343 ATATCTATCAAGAAAGTAATAAAATGGTTTGCCTGCCAACTGGTCCAATATTTGACCGATGAAAG
585 ATATCTATCAAGAAAATAATAAAATGGTTTGCCTGCCAACCGGTCCAATATTTGACCGATGAAAG
*
163408 GAATGAAAATGGTCATTTTAGTGTCCTTGTTAAGATTCCTATAGT
650 GAATGAAAATGGTCATTTTAGTGTCCTTGCTAAGATTCCTATAGT
163453 CCATGCATAT
Statistics
Matches: 667, Mismatches: 25, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
696 1 0.00
697 554 0.83
698 112 0.17
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (698 bp):
CTATAAGGGCTGAGATGAGTCCTTCCTTCAGCTCTTGAAATGATACAACACAACTATCATCAAGG
AGAAAGGGTTGATTTTACTACAGTAGAGTACACAAGGGATTAGATATCTTGAAAAAAATACTTAA
TGGATCTTCGATAGAATCCAAAATGCCCTATAAAGCTTCGAACTCCTTTGGCTGTAGTGGGAGGA
GACAGTTTCTCGATCACTTTAATTTTAGATTGGTCCACCTCAAAGACCTTTTTTGAGATTTTGAG
TCCTAAAATAGTTCTCTCGGACACCATAAAGTGACACTTCTCCCAGTTCATAACCAAATATACTT
TCTCGTACCTCTTAAGCACATTTTCCATATTGCGAAGGAATAAGTTGAAATTATCGCTAGAGACC
AAGAAATAATCCATGAAAATATCCAAAACTTCTTCTACCATGTCCGAGAAGATGGCTAGCATGCA
CCTTTGAAATATGGATGGTGTATTGCATAACCGGAAATGTATCATTCTAAAGGCGTAGGTTTCAT
AAAGACAAGTAAAAATTGTCTTCTCTTGGTCTTTGAATGCTATAGCAATCTGGTTGTAGACCGAA
TATCTATCAAGAAAATAATAAAATGGTTTGCCTGCCAACCGGTCCAATATTTGACCGATGAAAGG
AATGAAAATGGTCATTTTAGTGTCCTTGCTAAGATTCCTATAGTACAA
Found at i:170162 original size:5 final size:5
Alignment explanation
Indices: 170152--170182 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
170142 AGGATTGGTA
170152 ATTTT ATTTT ATTTAT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTT-T ATTTT ATTTT ATTTT
170183 TATCTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:181365 original size:21 final size:21
Alignment explanation
Indices: 181340--181382 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
181330 CATCATGGTC
181340 TTTGTGGAAGCCATGAAATCT
1 TTTGTGGAAGCCATGAAATCT
* * *
181361 TTTGTTGAGGCCATGAATTCT
1 TTTGTGGAAGCCATGAAATCT
181382 T
1 T
181383 GCAATGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (21 bp):
TTTGTGGAAGCCATGAAATCT
Found at i:186829 original size:28 final size:27
Alignment explanation
Indices: 186798--186857 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
186788 GGCTTAGAAA
*
186798 TATTTTAGGTCATTTTACACTTTAGGGG
1 TATTTTA-GTCATTTTACAATTTAGGGG
* *
186826 TATTCTAGTCATTTTATAATTTAGGGG
1 TATTTTAGTCATTTTACAATTTAGGGG
*
186853 CATTT
1 TATTT
186858 CTATAAATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (27 bp):
TATTTTAGTCATTTTACAATTTAGGGG
Found at i:187782 original size:15 final size:14
Alignment explanation
Indices: 187762--187815 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
187752 AAGTCAACGG
187762 GTTGACTCAGACCGA
1 GTTGACTCAGA-CGA
*
187777 GTTGACT-AGGACGG
1 GTTGACTCA-GACGA
*
187791 GTTGACTCAGATTGA
1 GTTGACTCAGA-CGA
187806 GTTGACTCAG
1 GTTGACTCAG
187816 TGACTCGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:189759 original size:13 final size:13
Alignment explanation
Indices: 189743--189767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
189733 AAGCGAGAAG
189743 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
189756 AAGAAAAAGAAA
1 AAGAAAAAGAAA
189768 GAAAACGAAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:192083 original size:190 final size:190
Alignment explanation
Indices: 191754--192106 Score: 440
Period size: 190 Copynumber: 1.9 Consensus size: 190
191744 TAATATTAAA
* * *
191754 TCTCATAGGACTTGTATCTTAGAAAACTCAATCTAGTCTTTATTAGGATAGTTTCTCTAGAAACC
1 TCTCATAGGACTTGTATCCTAGAAAACTCAATATAGTCTTTATTAAGATAGTTTCTCTAGAAACC
* * * ** * * *
191819 TCAATTTAGTCTTTATAAATATTGTTCCCCGTAGAATCTCATTCTTGATATTCTTAGGACATGTA
66 TCAATTTAGACTTTATAAATATCGTTCCACAAAGAACCTCATTCTTGATATTATTAAGACATGTA
* *
191884 TCATAGAAAACTCACTCTTATCGTGTTTAAGATTGTTCCCCAAGGAACCTCAATCTTGAC
131 TCATAGAAAACTCAATCTTATCGTGCTTAAGATTGTTCCCCAAGGAACCTCAATCTTGAC
* * * * * *
191944 TCTCTTAGGACTTGTATCCTAGAAAGCTTAATATAGTCTTTCTTAAGATCGTTTGTCTAGAAACC
1 TCTCATAGGACTTGTATCCTAGAAAACTCAATATAGTCTTTATTAAGATAGTTTCTCTAGAAACC
* * *
192009 TCAATTT-GACATTTTTAAA-AGTCGTTCCACAAAGAACCTCATTCTTGATTTTATTAAGACGTG
66 TCAATTTAGAC-TTTATAAATA-TCGTTCCACAAAGAACCTCATTCTTGATATTATTAAGACATG
* * * *
192072 TCTCTTAGAAAACTCAATCTTGTCTTGCTTAAGAT
129 TATCATAGAAAACTCAATCTTATCGTGCTTAAGAT
192107 GGTTTAACTG
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
189 3 0.02
190 132 0.98
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (190 bp):
TCTCATAGGACTTGTATCCTAGAAAACTCAATATAGTCTTTATTAAGATAGTTTCTCTAGAAACC
TCAATTTAGACTTTATAAATATCGTTCCACAAAGAACCTCATTCTTGATATTATTAAGACATGTA
TCATAGAAAACTCAATCTTATCGTGCTTAAGATTGTTCCCCAAGGAACCTCAATCTTGAC
Found at i:193002 original size:66 final size:65
Alignment explanation
Indices: 192926--193051 Score: 146
Period size: 66 Copynumber: 1.9 Consensus size: 65
192916 AGATTGTTTT
* * *
192926 TCTTAAAAC-AAATTTCGTTTCACTTGAGACAGTCTCCCTTAAAACACAAATATTTGAAATTGTT
1 TCTTAAAACAAAATTT-ATCTCACTTAAGACAGTCTCCCTTAAAACACAAAT-TTTGAAATTGTT
192990 CC
64 CC
* * * * * *
192992 TCTTGAAACAAAATTTATCTCACTTAAGATAGTTTTCCTTGAAATACAAATTTTGAAATT
1 TCTTAAAACAAAATTTATCTCACTTAAGACAGTCTCCCTTAAAACACAAATTTTGAAATT
193052 ATTTCACTCC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
65 9 0.18
66 35 0.70
67 6 0.12
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (65 bp):
TCTTAAAACAAAATTTATCTCACTTAAGACAGTCTCCCTTAAAACACAAATTTTGAAATTGTTCC
Found at i:203817 original size:26 final size:26
Alignment explanation
Indices: 203787--203848 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
203777 TTTACAAAGT
**
203787 AAAACCCAAACCTAAATACCTGACCC
1 AAAACCCAAACCTAAATACCCAACCC
*
203813 AAAACCC-AACCTTAATACCCAACCC
1 AAAACCCAAACCTAAATACCCAACCC
*
203838 AGAACCCAAAC
1 AAAACCCAAAC
203849 TAGACTCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.47, C:0.40, G:0.03, T:0.10
Consensus pattern (26 bp):
AAAACCCAAACCTAAATACCCAACCC
Found at i:206872 original size:38 final size:39
Alignment explanation
Indices: 206830--206914 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
206820 ACATTTGTCA
* * * *
206830 TAATATTTTTTGTTAAAACTA-AAATTTTATGAAGAATG
1 TAATATTTTCTGTTAAAACCAGAAATATTATAAAGAATG
***
206868 TAATATTTTCTGTTGGCACCAGAAATATTATAAAGAATG
1 TAATATTTTCTGTTAAAACCAGAAATATTATAAAGAATG
206907 TAATATTT
1 TAATATTT
206915 CAGGTTGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (39 bp):
TAATATTTTCTGTTAAAACCAGAAATATTATAAAGAATG
Found at i:208466 original size:59 final size:59
Alignment explanation
Indices: 208357--208469 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
208347 AGTTTGAAAC
* * * *
208357 TGAAATGTTTAAGAGTTTGAGGACTAATTTAGAACGATAGCCATAGTTTAAGGATAAAA
1 TGAAATGTTTAAAAGTTTAAGGACCAATTTAGAACGATAGCCATAATTTAAGGATAAAA
* *
208416 TGAAATGTTTAAAAGTTTAAGGACCAATTTAGAATGA-AGGTCATAATTTAAGGA
1 TGAAATGTTTAAAAGTTTAAGGACCAATTTAGAACGATA-GCCATAATTTAAGGA
208470 CGTGAGATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (59 bp):
TGAAATGTTTAAAAGTTTAAGGACCAATTTAGAACGATAGCCATAATTTAAGGATAAAA
Found at i:210873 original size:2 final size:2
Alignment explanation
Indices: 210866--210893 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
210856 AGATACATAC
210866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210894 GCATGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212257 original size:10 final size:10
Alignment explanation
Indices: 212244--212303 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
212234 TAATAAAATT
212244 TAAAATTTTA
1 TAAAATTTTA
**
212254 TAAAAAATTA
1 TAAAATTTTA
212264 TTAAAATTATTAA
1 -TAAAATT-TT-A
*
212277 AAGAAATTTTA
1 TA-AAATTTTA
212288 -AAAATTTTA
1 TAAAATTTTA
212297 TAAAATT
1 TAAAATT
212304 CAAAAACTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 8 0.20
10 15 0.38
11 6 0.15
12 5 0.12
13 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TAAAATTTTA
Found at i:212269 original size:21 final size:20
Alignment explanation
Indices: 212238--212301 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
212228 AATATTTAAT
212238 AAAA-TTTAAAATTTTATAA
1 AAAATTTTAAAATTTTATAA
212257 AAAATTATTAAAATTATTA-AA
1 AAAATT-TTAAAATT-TTATAA
212278 AGAAATTTTAAAAATTTTATAA
1 A-AAATTTT-AAAATTTTATAA
212300 AA
1 AA
212302 TTCAAAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.10
20 1 0.03
21 17 0.44
22 17 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATTTTAAAATTTTATAA
Found at i:212360 original size:29 final size:30
Alignment explanation
Indices: 212328--212395 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
212318 TAATAAATTT
* *
212328 AAATTTTAAA-AAATATTTGTAAAA-TATTA
1 AAATTATAAATAAA-ATTTATAAAACTATTA
*
212357 AAATTATAAATTAAATTTATAAAACTATTA
1 AAATTATAAATAAAATTTATAAAACTATTA
212387 AAACTTATA
1 AAA-TTATA
212396 GTTTATAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 18 0.55
30 10 0.30
31 5 0.15
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
AAATTATAAATAAAATTTATAAAACTATTA
Found at i:212440 original size:9 final size:9
Alignment explanation
Indices: 212426--212450 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
212416 TCAATATAGC
212426 TTTTAATAT
1 TTTTAATAT
212435 TTTTAATAT
1 TTTTAATAT
212444 TTTTAAT
1 TTTTAAT
212451 TTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:230570 original size:82 final size:81
Alignment explanation
Indices: 230317--230629 Score: 398
Period size: 80 Copynumber: 3.9 Consensus size: 81
230307 TGTAAATCCT
* * *
230317 TACGGACCTAAGGATAT-CTTGGGTAGGGCCCAAGGTATTTCCTTAGGTTGGTT-CCTTTTGTTG
1 TACGGATCTAAGGATATCCTTGGGTA-GACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGTTG
230380 TGTGCTTAAGGTAACCC
65 TGTGCTTAAGGTAACCC
* * * * * *
230397 TACGAATCTAATGATGTCTTTAGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCC-TTTGTTGT
1 TACGGATCTAAGGATATCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGTTGT
*
230461 GTGCATAAGGTAACCC
66 GTGCTTAAGGTAACCC
* * *
230477 TACGGATCTAAGGATACCCTTGGGTAGTCCCAAGGTATATCCTTAGATTGGTTCCCTTTTTGTTG
1 TACGGATCTAAGGATATCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCC-TTTTGTTG
230542 TGTGCTTAAGGTAACCC
65 TGTGCTTAAGGTAACCC
* ** * **
230559 TATGGATCTAAGGATATCCTTGACTAGACCTCAAGGTATATCCTTAGGTTGGCTCCCCTTTTACT
1 TACGGATCTAAGGATATCCTTGGGTAGACC-CAAGGTATATCCTTAGGTTGG-TTCCCTTTTGTT
230624 GTGTGC
64 GTGTGC
230630 CGAGGGAAGC
Statistics
Matches: 199, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
80 108 0.54
81 8 0.04
82 48 0.24
83 31 0.16
84 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (81 bp):
TACGGATCTAAGGATATCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGTTGT
GTGCTTAAGGTAACCC
Found at i:234449 original size:31 final size:31
Alignment explanation
Indices: 234408--234535 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
234398 AGAACCTCGG
* * *
234408 AAACTATCCATAGGTCCCGAAGAACCTAGGT
1 AAACTGTCCATATGTCCCGAAGAACATAGGT
* ** *
234439 AAACTGTCCATATGTTCCTTAGAATATAGGT
1 AAACTGTCCATATGTCCCGAAGAACATAGGT
*
234470 ATACTGTCCATATGTCCCGAA-AGACATAGGT
1 AAACTGTCCATATGTCCCGAAGA-ACATAGGT
* ** * *
234501 AATTCTGTCCATATGTTTCGTAGAATATAGGT
1 AA-ACTGTCCATATGTCCCGAAGAACATAGGT
234533 AAA
1 AAA
234536 GCCTTGACTC
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
30 1 0.01
31 49 0.65
32 24 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
AAACTGTCCATATGTCCCGAAGAACATAGGT
Found at i:234528 original size:63 final size:62
Alignment explanation
Indices: 234414--234533 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
234404 TCGGAAACTA
* *
234414 TCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAATATAGGTATACTG
1 TCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAATATAGGTATACTG
* * *
234476 TCCATATGTCCCGAA-AGACATAGGTAATTCTGTCCATATGTTTCGTAGAATATAGGTA
1 TCCATAGGTCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAATATAGGTA
234534 AAGCCTTGAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 23 0.45
63 27 0.53
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (62 bp):
TCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAATATAGGTATACTG
Found at i:234531 original size:32 final size:32
Alignment explanation
Indices: 234434--234534 Score: 118
Period size: 31 Copynumber: 3.2 Consensus size: 32
234424 CCGAAGAACC
*
234434 TAGGTAA-ACTGTCCATATGTTCCTTAGAATA
1 TAGGTAATACTGTCCATATGTTCCGTAGAATA
* * *
234465 TAGGT-ATACTGTCCATATGTCCCG-AAAGACA
1 TAGGTAATACTGTCCATATGTTCCGTAGA-ATA
* *
234496 TAGGTAATTCTGTCCATATGTTTCGTAGAATA
1 TAGGTAATACTGTCCATATGTTCCGTAGAATA
234528 TAGGTAA
1 TAGGTAA
234535 AGCCTTGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 3 0.05
31 27 0.47
32 25 0.44
33 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (32 bp):
TAGGTAATACTGTCCATATGTTCCGTAGAATA
Found at i:241897 original size:15 final size:15
Alignment explanation
Indices: 241877--241907 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
241867 TTAATTATAA
241877 TATTAAATTTTAATT
1 TATTAAATTTTAATT
241892 TATTAAATTTTAATT
1 TATTAAATTTTAATT
241907 T
1 T
241908 TAATTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTAAATTTTAATT
Found at i:242064 original size:13 final size:12
Alignment explanation
Indices: 242046--242075 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
242036 AAAAAATATA
242046 TATTAATTATTAT
1 TATTAATTATT-T
242059 TATTAATTATTT
1 TATTAATTATTT
242071 TATTA
1 TATTA
242076 GATTTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTAATTATTT
Found at i:247144 original size:14 final size:12
Alignment explanation
Indices: 247110--247137 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
247100 CAAAACGAAG
247110 AAAAAAAGAGAA
1 AAAAAAAGAGAA
247122 AAAAAAAGAGAA
1 AAAAAAAGAGAA
247134 AAAA
1 AAAA
247138 GACAAGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:249755 original size:38 final size:37
Alignment explanation
Indices: 249638--249768 Score: 135
Period size: 37 Copynumber: 3.5 Consensus size: 37
249628 AGAGACAAAT
* *
249638 TTTTTCTTAAAATCAAAATTTT-TCTCGC-TAGAGAGAA
1 TTTTTCTTAAAAAC-AAATTTTGTCTCGCTTA-AGACAA
* *
249675 TTTTTCTTAAAAAACAAATTTTGTCTTGCTTGAGAC-A
1 TTTTTCTT-AAAAACAAATTTTGTCTCGCTTAAGACAA
* *
249712 GTTTTCTCTAAAAACAAATTTTGTCACGCTTAAGACAA
1 TTTTTCT-TAAAAACAAATTTTGTCTCGCTTAAGACAA
*
249750 TTTTTC-TCAAAACAAATTT
1 TTTTTCTTAAAAACAAATTT
249769 CATCTCACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
36 12 0.15
37 46 0.58
38 20 0.25
39 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (37 bp):
TTTTTCTTAAAAACAAATTTTGTCTCGCTTAAGACAA
Found at i:249784 original size:36 final size:36
Alignment explanation
Indices: 249599--249788 Score: 132
Period size: 37 Copynumber: 5.1 Consensus size: 36
249589 TTTGAAATTG
** * * *
249599 TTTTTCTCGAAACAAAGTGTCGTCTCACTAGAGACAAA
1 TTTTTCTAAAAACAAA-TTTCGTCTCGCTTGAGAC-AA
* * * *
249637 TTTTTTCTTAAAATCAAAATTT-TTCTCGCTAGAGAGAA
1 -TTTTTC-TAAAAAC-AAATTTCGTCTCGCTTGAGACAA
* * *
249675 TTTTTCTTAAAAAACAAATTTTGTCTTGCTTGAGACAG
1 TTTTTC-T-AAAAACAAATTTCGTCTCGCTTGAGACAA
* * *
249713 TTTTCTCTAAAAACAAATTTTGTCACGCTTAAGACAA
1 TTTT-TCTAAAAACAAATTTCGTCTCGCTTGAGACAA
* * *
249750 TTTTTCTCAAAACAAATTTCATCTCACTTGAGAC-A
1 TTTTTCTAAAAACAAATTTCGTCTCGCTTGAGACAA
249785 TTTT
1 TTTT
249789 CCTTTGAGAT
Statistics
Matches: 123, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
35 5 0.04
36 24 0.20
37 43 0.35
38 23 0.19
39 19 0.15
40 6 0.05
41 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTTTCTAAAAACAAATTTCGTCTCGCTTGAGACAA
Found at i:250032 original size:31 final size:31
Alignment explanation
Indices: 249992--250102 Score: 87
Period size: 31 Copynumber: 3.4 Consensus size: 31
249982 CTTGAGACAA
* *
249992 TTTCTCTTGAAAGAAAAAATCTTTGAGTCTG
1 TTTCCCTTGAAAAAAAAAATCTTTGAGTCTG
**** * *
250023 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-AAA----AAAATCT-TTGAGTCTG
*
250060 TTTCTCTTGAAAAAAAAAATCTTTGAGTCTG
1 TTTCCCTTGAAAAAAAAAATCTTTGAGTCTG
250091 TTTCCCTTGAAA
1 TTTCCCTTGAAA
250103 CAAAGTTTTG
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
31 29 0.50
32 5 0.09
36 6 0.10
37 18 0.31
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCCCTTGAAAAAAAAAATCTTTGAGTCTG
Found at i:250037 original size:68 final size:67
Alignment explanation
Indices: 249959--250171 Score: 363
Period size: 68 Copynumber: 3.1 Consensus size: 67
249949 GATTATCTCT
249959 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAAGAAAAAATCTTTGAGTCTGT
1 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAA-AAAAAATCTTTGAGTCTGT
250024 TTC
65 TTC
*
250027 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAAAATCTTTGAGTCTGT
1 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG-AAAAAAAAATCTTTGAGTCTGT
250092 TTC
65 TTC
* * * *
250095 CCTTGAAACAAAGTTTTGTCACTCTTGGGACAATTTCTCTTGAAACAAAAGTCTTTGAGTCTGTT
1 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAAAAAAAATCTTTGAGTCTGTT
250160 TC
66 TC
250162 CCTTGAAACA
1 CCTTGAAACA
250172 CAAACATTGA
Statistics
Matches: 138, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
67 33 0.24
68 102 0.74
69 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (67 bp):
CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAAAAAAAATCTTTGAGTCTGTT
TC
Found at i:250069 original size:37 final size:37
Alignment explanation
Indices: 249960--250143 Score: 122
Period size: 37 Copynumber: 5.3 Consensus size: 37
249950 ATTATCTCTC
*
249960 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCT
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
* *** * * *
249997 CTTGAAAGAAA-----AAATCT-TTGAGTCTGTTTCC
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
250028 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
**** * * *
250065 CTTGAAA-AAA----AAAATCT-TTGAGTCTGTTTCC
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
* * *
250096 CTTGAAACAAAGTTTTGTCACTCTTGGGACAATTTCT
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
250133 CTTGAAACAAA
1 CTTGAAACAAA
250144 AGTCTTTGAG
Statistics
Matches: 103, Mismatches: 32, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
31 38 0.37
32 9 0.09
36 8 0.08
37 48 0.47
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (37 bp):
CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
Found at i:250167 original size:30 final size:28
Alignment explanation
Indices: 250128--250201 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
250118 CTTGGGACAA
* * **
250128 TTTCTCTTGAAACAAAAGTCTTTGAGTCTG
1 TTTCCCTTGAAACAAAA--CATTGAGAATG
250158 TTTCCCTTGAAACACAAACATTGAGAATG
1 TTTCCCTTGAAACA-AAACATTGAGAATG
250187 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
250202 GTTTTTCTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 22 0.56
30 13 0.33
31 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (28 bp):
TTTCCCTTGAAACAAAACATTGAGAATG
Found at i:250483 original size:134 final size:133
Alignment explanation
Indices: 250238--250584 Score: 448
Period size: 134 Copynumber: 2.6 Consensus size: 133
250228 TTGAAACATT
* * * *
250238 ATCCCTAAAGATGGCTAGCTGTCCTCATCACGTAGGAACCATGTCATCCACTGACCATATCTCCT
1 ATCCCTAAAGATGGCCAACTATCCTCATCACGTAGGAACCATGTCATCCACCGACCATATCTCCT
* * * *
250303 CATCGCGTAGGAGACGCGTCAACCTTAGGTAACCAACCGTCCTCATCGCGTAGAAA-CTGTGTTA
66 CATCACGTAGGAG-CGCATCAACCTTAGATAACCAACCGTCCTCATCACGTAGAAATC-GTGTTA
250367 TCATC
129 TCATC
* * * * * *
250372 ATCCCTAAAGATGGTCAATTATCC-CTATCACATAAGAACCATGTCATCCACCGACCAAATTTCC
1 ATCCCTAAAGATGGCCAACTATCCTC-ATCACGTAGGAACCATGTCATCCACCGACCATATCTCC
* *
250436 TCATCACGTAGGAGCTGCATCAACCTTAGATAACC-ACCTGTCTTCATCACGTAGGAATCGTGTT
65 TCATCACGTAGGAGC-GCATCAACCTTAGATAACCAACC-GTCCTCATCACGTAGAAATCGTGTT
250500 ATCATC
128 ATCATC
* * * *
250506 ATCCTTAAAGATGGCCAACTGTCCTCATCACGTAGGAATCGTGTCATCCACCGACCATATCTCCT
1 ATCCCTAAAGATGGCCAACTATCCTCATCACGTAGGAACCATGTCATCCACCGACCATATCTCCT
250571 CATCACGTAGGAGC
66 CATCACGTAGGAGC
250585 AGCGTCATCA
Statistics
Matches: 182, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
133 5 0.03
134 175 0.96
135 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.25
Consensus pattern (133 bp):
ATCCCTAAAGATGGCCAACTATCCTCATCACGTAGGAACCATGTCATCCACCGACCATATCTCCT
CATCACGTAGGAGCGCATCAACCTTAGATAACCAACCGTCCTCATCACGTAGAAATCGTGTTATC
ATC
Found at i:250781 original size:3 final size:3
Alignment explanation
Indices: 250768--250806 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
250758 CTAACAAAAA
250768 TAT TAAT TAT TAT TAT TAT TAT TAT TAAT TAT TA- TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA
250807 CATTTTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 25 0.76
4 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:254904 original size:16 final size:16
Alignment explanation
Indices: 254879--254943 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
254869 TAATAAATAA
*
254879 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
254895 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
254911 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
254927 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
254943 A
1 A
254944 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:254908 original size:10 final size:10
Alignment explanation
Indices: 254875--254949 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
254865 CATTTAATAA
*
254875 ATAAACGAAT
1 ATAAACGAAC
254885 ATAAACGAAC
1 ATAAACGAAC
254895 ----ACGAAC
1 ATAAACGAAC
254901 ATAAACGAAC
1 ATAAACGAAC
** *
254911 ACGAAC-ATAA
1 ATAAACGA-AC
254921 ATGAACACGAAC
1 AT-AA-ACGAAC
254933 ATAAACGAAC
1 ATAAACGAAC
254943 ATAAACG
1 ATAAACG
254950 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:256062 original size:24 final size:24
Alignment explanation
Indices: 256022--256082 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
256012 GATTGGGTTA
* *
256022 AACATAAAT-GAATGAACATAAGTG
1 AACAT-AATCGAACGAACATAAATG
256046 AACATAATCGAACGAACATAAATG
1 AACATAATCGAACGAACATAAATG
*
256070 AACATAACCGAAC
1 AACATAATCGAAC
256083 ATAACCGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.09
24 30 0.91
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.16
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAATG
Found at i:256075 original size:34 final size:34
Alignment explanation
Indices: 256032--256100 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
256022 AACATAAATG
** *
256032 AATGAACATAAGTGAACATAATCGAACGAACATA
1 AATGAACATAACCGAACATAACCGAACGAACATA
256066 AATGAACATAACCGAACATAACCGAACGAACATA
1 AATGAACATAACCGAACATAACCGAACGAACATA
256100 A
1 A
256101 CCGAACGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.54, C:0.19, G:0.13, T:0.14
Consensus pattern (34 bp):
AATGAACATAACCGAACATAACCGAACGAACATA
Found at i:256106 original size:10 final size:10
Alignment explanation
Indices: 256058--256092 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
256048 CATAATCGAA
*
256058 CGAACATAAA
1 CGAACATAAC
*
256068 TGAACATAAC
1 CGAACATAAC
256078 CGAACATAAC
1 CGAACATAAC
256088 CGAAC
1 CGAAC
256093 GAACATAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (10 bp):
CGAACATAAC
Found at i:257747 original size:23 final size:23
Alignment explanation
Indices: 257716--257779 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
257706 ATAAGAATAA
* *
257716 TTCTATTTTTGTTATACGTTTTT
1 TTCTATTTTTGTGACACGTTTTT
*
257739 TTCTGTTTTTGTGACACG-TTTT
1 TTCTATTTTTGTGACACGTTTTT
* * *
257761 TTATACTTTTATGACACGT
1 TTCTATTTTTGTGACACGT
257780 ATTCTCATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (23 bp):
TTCTATTTTTGTGACACGTTTTT
Found at i:259892 original size:18 final size:18
Alignment explanation
Indices: 259865--259901 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
259855 GTCACAACCC
259865 GACCCAACCCGTTGACCT
1 GACCCAACCCGTTGACCT
*
259883 GACCCGACCCGTTGACCT
1 GACCCAACCCGTTGACCT
259901 G
1 G
259902 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (18 bp):
GACCCAACCCGTTGACCT
Found at i:262392 original size:12 final size:12
Alignment explanation
Indices: 262355--262393 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
262345 ATCTGATACT
262355 TGACATGGATTC
1 TGACATGGATTC
*
262367 TGATAT-GATATC
1 TGACATGGAT-TC
262379 TGACATGGATTC
1 TGACATGGATTC
262391 TGA
1 TGA
262394 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:262471 original size:24 final size:24
Alignment explanation
Indices: 262343--262454 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
262333 ATTTGAATTA
262343 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
262367 TGATATGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
262391 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
262415 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
262439 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
262455 GTGAATTATG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:264853 original size:18 final size:18
Alignment explanation
Indices: 264830--264867 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
264820 AAATCATTAT
264830 AAATACTAAATAAATAGA
1 AAATACTAAATAAATAGA
264848 AAATACTAAATAAATAGA
1 AAATACTAAATAAATAGA
264866 AA
1 AA
264868 GAGGAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATACTAAATAAATAGA
Found at i:267180 original size:26 final size:25
Alignment explanation
Indices: 267151--267207 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
267141 TAAATAAATT
*
267151 AATATATAGAAAAAATTAAATATTAA
1 AATAAATA-AAAAAATTAAATATTAA
* * *
267177 AATAAAATAATAAATTTAAGTATTAA
1 AAT-AAATAAAAAAATTAAATATTAA
267203 AATAA
1 AATAA
267208 TAATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
AATAAATAAAAAAATTAAATATTAA
Found at i:267184 original size:13 final size:13
Alignment explanation
Indices: 267162--267214 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
267152 ATATATAGAA
*
267162 AAAATTAAATATT
1 AAAATAAAATATT
*
267175 AAAATAAAATAAT
1 AAAATAAAATATT
* * *
267188 AAATTTAAGTATT
1 AAAATAAAATATT
267201 AAAATAATAATATT
1 AAAATAA-AATATT
267215 TTTAAAATCA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
13 25 0.83
14 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAAATAAAATATT
Found at i:267465 original size:18 final size:17
Alignment explanation
Indices: 267442--267479 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
267432 AATACACGAA
267442 AAAATATATAAAAAATTT
1 AAAATATA-AAAAAATTT
*
267460 AAAATATAAAAGAATTT
1 AAAATATAAAAAAATTT
267477 AAA
1 AAA
267480 TTTTTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATATAAAAAAATTT
Found at i:267468 original size:16 final size:17
Alignment explanation
Indices: 267447--267479 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
267437 ACGAAAAAAT
267447 ATATAAAA-AATTTAAA
1 ATATAAAAGAATTTAAA
267463 ATATAAAAGAATTTAAA
1 ATATAAAAGAATTTAAA
267480 TTTTTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
ATATAAAAGAATTTAAA
Found at i:271919 original size:5 final size:5
Alignment explanation
Indices: 271909--271934 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
271899 TACGGGTAGC
271909 CCGAT CCGAT CCGAT CCGAT CCGAT C
1 CCGAT CCGAT CCGAT CCGAT CCGAT C
271935 TCAGATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CCGAT
Found at i:273178 original size:13 final size:13
Alignment explanation
Indices: 273160--273189 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
273150 GACGGTCAAC
273160 GGTCAACGGGTCG
1 GGTCAACGGGTCG
273173 GGTCAACGGGTCG
1 GGTCAACGGGTCG
273186 GGTC
1 GGTC
273190 GGGTTGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:275315 original size:24 final size:24
Alignment explanation
Indices: 275288--275416 Score: 109
Period size: 24 Copynumber: 5.4 Consensus size: 24
275278 TATATCAAAA
*
275288 ATCAAAACATAAAT-CAAGTCAAGT
1 ATCAAATCA-AAATCCAAGTCAAGT
* *
275312 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
275336 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* * * *
275360 ATCAGATCAGAATCTATGTC-AGAT
1 ATCAAATCAAAATCCAAGTCAAG-T
* * *
275384 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
*
275408 ATCAGATCA
1 ATCAAATCA
275417 GAATTCAAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 6 0.06
24 85 0.91
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Found at i:275417 original size:24 final size:24
Alignment explanation
Indices: 275305--275420 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
275295 CATAAATCAA
* * *
275305 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
275329 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
275353 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
275377 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
275401 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
275421 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:275436 original size:48 final size:48
Alignment explanation
Indices: 275336--275438 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 48
275326 CAGGTCAAGT
** *
275336 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
275384 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
275432 ATCAGAT
1 ATCAGAT
275439 AAAATATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 2 0.04
48 47 0.96
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:277909 original size:15 final size:15
Alignment explanation
Indices: 277889--277935 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
277879 GGTCAACGAC
277889 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
*
277904 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
*
277919 GGTC--GAGTCAACG
1 GGTCAACAGTCAACG
277932 GGTC
1 GGTC
277936 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:277930 original size:13 final size:13
Alignment explanation
Indices: 277896--277936 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
277886 GACGGTCAAC
*
277896 AGTCAACGGGTCA
1 AGTCAACGGGTCG
277909 ACGGTCAACGGGTCG
1 A--GTCAACGGGTCG
277924 AGTCAACGGGTCG
1 AGTCAACGGGTCG
277937 GGTCGGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.15
Consensus pattern (13 bp):
AGTCAACGGGTCG
Found at i:277940 original size:18 final size:18
Alignment explanation
Indices: 277917--277970 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
277907 CAACGGTCAA
*
277917 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
277935 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
277953 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
277971 TGTGACCGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:282169 original size:60 final size:61
Alignment explanation
Indices: 282055--282184 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 61
282045 GTATAATTTG
* * * * *
282055 GGATGAAATTGAAATTTTTAAAAAGTTTGAGGACCAATTTAGAATAAAAGTCATAGTTTAA
1 GGATGAAAATGAAATTGTTAAAAAGATTGAAGACCAATTTAGAATAAAAGTCATAGTGTAA
* * ** *
282116 GGATGAAAATGAAA-TGTTCAAAAGATTGAAGACTAATTTAGAATCATTA-TCATAGTGTAT
1 GGATGAAAATGAAATTGTTAAAAAGATTGAAGACCAATTTAGAAT-AAAAGTCATAGTGTAA
282176 GGAT-AAAAT
1 GGATGAAAAT
282185 TGGTATATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
59 5 0.09
60 38 0.66
61 15 0.26
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (61 bp):
GGATGAAAATGAAATTGTTAAAAAGATTGAAGACCAATTTAGAATAAAAGTCATAGTGTAA
Found at i:284709 original size:26 final size:26
Alignment explanation
Indices: 284657--284710 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
284647 AAATTTTGGG
*
284657 TTTTTAAAAATAAAAATAAAATTAAA
1 TTTTTAAAAATAAAAATAAAATAAAA
* *
284683 TTTTTTAAAATAAAATTTAAAA-AAAA
1 TTTTTAAAAATAAAA-ATAAAATAAAA
284709 TT
1 TT
284711 ATAAACATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTTTTAAAAATAAAAATAAAATAAAA
Found at i:285101 original size:3 final size:3
Alignment explanation
Indices: 285095--285127 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
285085 ATATTATTAT
*
285095 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
285128 CATATGTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:288485 original size:59 final size:59
Alignment explanation
Indices: 288343--288485 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 59
288333 TATGGTTGAA
* *
288343 TTATACAAATGATTCCTCGACTATAGAATATTATTTTGTTGACCCCTCTAATTATTAAAAG
1 TTATA-AAATGATT-CTCGACTATAGAATATTATTTTGTTGACACCTCTAACTATTAAAAG
* * * * * * *
288404 TTATGAAATGGTTCTCTAACTATAG-GTATTATTTTGTTGA-ATCTCATGACTATTAAGAG
1 TTATAAAATGATTCTC-GACTATAGAATATTATTTTGTTGACACCTC-TAACTATTAAAAG
288463 TTATAAAATGATTACTCGACTAT
1 TTATAAAATGATT-CTCGACTAT
288486 TTATATGTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
58 3 0.04
59 43 0.64
60 17 0.25
61 4 0.06
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (59 bp):
TTATAAAATGATTCTCGACTATAGAATATTATTTTGTTGACACCTCTAACTATTAAAAG
Found at i:292469 original size:11 final size:11
Alignment explanation
Indices: 292455--292480 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
292445 TTATATATTT
292455 TTTATTTCATA
1 TTTATTTCATA
292466 TTTATTTCATA
1 TTTATTTCATA
292477 TTTA
1 TTTA
292481 AATAGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATTTCATA
Found at i:300630 original size:29 final size:28
Alignment explanation
Indices: 300568--300637 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
300558 ACAAAATATG
*
300568 AAAATAAA-TAAAATGTAGGTCTAAATT
1 AAAATAAATTAAAATGCAGGTCTAAATT
*
300595 AAAATAAATTAAAATTGCATGGTC-AACTT
1 AAAATAAATTAAAA-TGCA-GGTCTAAATT
*
300624 AAAATAAATAAAAA
1 AAAATAAATTAAAA
300638 ACATATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 8 0.22
28 5 0.14
29 20 0.54
30 4 0.11
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.27
Consensus pattern (28 bp):
AAAATAAATTAAAATGCAGGTCTAAATT
Found at i:301990 original size:3 final size:3
Alignment explanation
Indices: 301982--302024 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
301972 TAAAGCCTGA
301982 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
302025 TTAAATGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:302614 original size:134 final size:134
Alignment explanation
Indices: 302224--303181 Score: 875
Period size: 134 Copynumber: 7.1 Consensus size: 134
302214 ATTCTTCAGG
*
302224 GAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAA-ACGAA
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGA-G-A
* * * *
302288 GGG-TTTGTTTCACTTCTTCTTGAGGGAAAATCAGTTATGGGGACGTTGATTCATTCCATTGTCA
64 GGGATATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCA
*
302352 -TTCAGG
129 CTT-AGA
* * * * *
302358 GAAGATTGAATCTAGGCAG-CTTGTTCCACTGTTACCCA-GGAATATCAACTCTTGAAAGAGGGG
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
** * * * * * *
302421 GATATGTTTTGCGTCTTTTTTTTTATTTTATGAAAAATCAGATATGGGGATGTTGATTCATTCCA
66 GATATG--TT-C--C--ACTTCTT-CTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCA
* *
302486 CTGACACTTATA
123 CTGTCACTTAGA
* * ** * * * *
302498 GAAGATTGAATCGAGGTAGACTTATTTAACTTTTACTCAGGGAATATCAAATCCTAAAATAGAGG
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
* * ** *
302563 GATCTGTTCCACTTCTTCCT-ATGGGAAAATCAGATATGGGGACGTTGATTCATTTTACTATC-C
66 GATATGTTCCACTTCTTCTTGA-GGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCAC
*
302626 TTTAGG
130 -TTAGA
* * * * *
302632 GAAGATTAAATCGAGGCAAACTTGTTCCACTGTTACTCAGGTAATATAAAATCTTGAAAGAGAGG
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
* * * * * *
302697 GGTATGTTTCGCTTCTTCTTGAGGGAAAATTAGATATGGGGACATTGATTAATTCCACTGTC-CT
66 GATATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACT
302761 TCA-A
131 T-AGA
* *
302765 GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGAG
1 -GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAG
* * ** * * * *
302830 AGATCTGTTCTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGTCGTTGATTTATTCTACTGTCAC
65 GGATATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCAC
* *
302895 TCAGG
130 TTAGA
* * * *
302900 GAAGATTGAATCAAGGTAGACTTGTTCCACTATTACTCATGGAATATCGAATCTTGAAAGAGAGG
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
* * ** * * *
302965 GATCTATTCTGCTTCTTCTTAAGGGAAAATCAGATCTGGAGG-CGTTGATTCATTCCACTTTTCA
66 GATATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGG-GGACGTTGATTCATTCCAC-TGTCA
* *
303029 -ATAGG
129 CTTAGA
* * * *
303034 GAAAATTGAATCGAGGCAGACTTGTTCCACTGTTACTCATGGAATATCAAAT-ATGAAAGAGAGG
1 GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
* * * * ** *
303098 GATATGTTCCA-TTGCTTCTTGAGAGAAACTTAGATCTGGAAATC-TTGATTCATTCCACTATC-
66 GATATGTTCCACTT-CTTCTTGAGGGAAAATCAGATATGGGGA-CGTTGATTCATTCCACTGTCA
*
303160 CTTCAGG
129 CTT-AGA
*
303167 GAAGATTGATTCGAG
1 GAAGATTGAATCGAG
303182 TTCGATTCGC
Statistics
Matches: 671, Mismatches: 126, Indels: 55
0.79 0.15 0.06
Matches are distributed among these distances:
131 3 0.00
132 28 0.04
133 91 0.14
134 430 0.64
135 13 0.02
137 2 0.00
139 5 0.01
140 58 0.09
141 16 0.02
142 25 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (134 bp):
GAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAAGAGAGG
GATATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACT
TAGA
Found at i:302828 original size:268 final size:268
Alignment explanation
Indices: 302223--303175 Score: 1015
Period size: 268 Copynumber: 3.5 Consensus size: 268
302213 TATTCTTCAG
* *
302223 GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAA-ACGA
1 GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATA-G-
* * * * *
302287 AGGG-TTTGTTTCACTTCTTCTTGAGGGAAAATCAGTTATGGGGACGTTGATTCATTCCATTGTC
64 AGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCTACTGTC
* * * * *
302351 ATTCAGGGAAGATTGAATCTAGGC-AGCTTGTTCCACTGTTACCCAGGAATATCAACTCTTGAAA
129 CTTCAGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGGAATATCAAATCTTGAAA
* * * * *
302415 GAG-GGGGATATGTTTTGCGTCTTTTTTTTTATTTTATGAAAAATCAGATATGGGGATGTTGATT
194 GAGAGGGG-TATG-TTT-CG-C-TTCTTCTTA----AGGGAAAATCAGATATGGGGACGTTGATT
*
302479 CATTCCACTGACACTT-ATA
250 CATTCCACTGTC-CTTCATA
* ** * * *
302498 -GAAGATTGAATCGAGGTAGACTTATTTAACTTTTACTCAGGGAATATCAAATCCTAAAATAGAG
1 GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGAG
* * *
302562 GGATCTGTTCCACTTCTTCCT-ATGGGAAAATCAGATATGGGGACGTTGATTCATTTTACTATCC
66 GGATCTGTTCCACTTCTTCTTGA-GGGAAAATCAGATATGGGGACGTTGATTCATTCTACTGTCC
* * * *
302626 TTTAGGGAAGATTAAATCGAGGCAAACTTGTTCCACTGTTACTCAGGTAATATAAAATCTTGAAA
130 TTCAGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGG-AATATCAAATCTTGAAA
* * * *
302691 GAGAGGGGTATGTTTCGCTTCTTCTTGAGGGAAAATTAGATATGGGGACATTGATTAATTCCACT
194 GAGAGGGGTATGTTTCGCTTCTTCTTAAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACT
302756 GTCCTTCA-A
259 GTCCTTCATA
302765 GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGAG
1 GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGAG
* ** * * *
302830 AGATCTGTTCTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGTCGTTGATTTATTCTACTGTCAC
66 GGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCTACTGTC-C
* * * *
302895 -TCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTATTACTCATGGAATATCGAATCTTGAAA
130 TTCAGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCA-GGAATATCAAATCTTGAAA
* *
302959 GAGA-GGG-ATCTATTCTGCTTCTTCTTAAGGGAAAATCAGATCTGGAGG-CGTTGATTCATTCC
194 GAGAGGGGTATGT-TTC-GCTTCTTCTTAAGGGAAAATCAGATATGG-GGACGTTGATTCATTCC
303021 ACT-T--TTCAATA
256 ACTGTCCTTC-ATA
* * * * * *
303032 GGGAAAATTGAATCGAGGCAGACTTGTTCCACTGTTACTCATGGAATATCAAAT-ATGAAAGAGA
1 -GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGA
* * * * * ** * *
303096 GGGATATGTTCCA-TTGCTTCTTGAGAGAAACTTAGATCTGGAAATC-TTGATTCATTCCACTAT
65 GGGATCTGTTCCACTT-CTTCTTGAGGGAAAATCAGATATGGGGA-CGTTGATTCATTCTACTGT
303159 CCTTCAGGGAAGATTGA
128 CCTTCAGGGAAGATTGA
303176 TTCGAGTTCG
Statistics
Matches: 578, Mismatches: 80, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
265 3 0.01
266 7 0.01
267 80 0.14
268 293 0.51
269 6 0.01
272 6 0.01
273 6 0.01
274 126 0.22
275 25 0.04
276 22 0.04
277 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (268 bp):
GGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAAATAGAG
GGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCTACTGTCCT
TCAGGGAAGATTGAATCAAGGCAAACTTGTTCCACTGTTACTCAGGAATATCAAATCTTGAAAGA
GAGGGGTATGTTTCGCTTCTTCTTAAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGT
CCTTCATA
Found at i:303036 original size:402 final size:401
Alignment explanation
Indices: 302221--303181 Score: 1085
Period size: 402 Copynumber: 2.4 Consensus size: 401
302211 ACTATTCTTC
* *
302221 AGGGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAA-AC
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA-GGAATATCAAATCTTGAAAGA-
* * * * *
302285 GAAGGGTTTGTTTCACTTCTTCTTGAGGGAAAATCAGTTATGGGGACGTTGATTCATTCCATTGT
64 GAGGGGTATGTTTC-CTTCTTCTTGAGGGAAAATTAGATATGGGGAC-TTGATTCATTCCACTGT
* * * * *
302350 CATTCAGGGAAGATTGAATCTAGGCAGCTTGTTCCACTGTTACCCAGGAATATCAACTCTTGAAA
127 CCTTCAGGGAAGATTGAATCGAGGCAGCTTATTCCACTATTACCCAGGAATATCAAATCTTGAAA
* * * * * * *
302415 GAGGGGGATATGTTTTGCGTCTTTTTTTTTATTTTATGAAAAATCAGATATGGGGATGTTGATTC
192 GAGAGAGATATGTTCT-CGTC---TTTCTTACTTGAGGAAAAATCAGATATGGGGATGTTGATTC
* * * * *
302480 ATTCCACTGACACTTATAGAAGATTGAATCGAGGTAGACTTATTTAACTTTTACTCAGGGAATAT
253 ATTCCACTGACACTCAGAGAAGATTGAATCAAGGTAGACTTATTCAACTATTACTCAGGGAATAT
* * *
302545 CAAATCCTAAAATAGAGGGATCTGTTCCACTTCTTCCTATGGGAAAATCAGATATGGGGACGTTG
318 CAAATCCTAAAAGAGAGGGATCTATTCCACTTCTTCCTAAGGGAAAATCAGATATGGGGACGTTG
** **
302610 ATTCATTTTACTATCCTTT
383 ATTCATTCCACTATCCAAT
* * *
302629 AGGGAAGATTAAATCGAGGCAAACTTGTTCCACTGTTACTCAGGTAATATAAAATCTTGAAAGAG
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGG-AATATCAAATCTTGAAAGAG
*
302694 AGGGGTATGTTTCGCTTCTTCTTGAGGGAAAATTAGATATGGGGACATTGATTAATTCCACTGTC
65 AGGGGTATGTTTC-CTTCTTCTTGAGGGAAAATTAGATATGGGGAC-TTGATTCATTCCACTGTC
* *
302759 CTTCAAGGAAGATTGAATCGAGGCAGACTTATTCCACTATTACTCAGGGAATATCAAATCTTGAA
128 CTTCAGGGAAGATTGAATCGAGGCAG-CTTATTCCACTATTACCCA-GGAATATCAAATCTTGAA
* * * * *
302824 ATAGAGAGATCTGTTCT-G-C-TTCTT-CTTGAGGGAAAATCAGATCTGGGG-TCGTTGATTTAT
191 AGAGAGAGATATGTTCTCGTCTTTCTTACTTGAGGAAAAATCAGATATGGGGAT-GTTGATTCAT
* * * * * * *
302884 TCTACTGTCACTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTATTACTCATGGAATATCG
255 TCCACTGACACTCAGAGAAGATTGAATCAAGGTAGACTTATTCAACTATTACTCAGGGAATATCA
* * ** * *
302949 AATCTTGAAAGAGAGGGATCTATTCTGCTTCTTCTTAAGGGAAAATCAGATCTGGAGG-CGTTGA
320 AATCCTAAAAGAGAGGGATCTATTCCACTTCTTCCTAAGGGAAAATCAGATATGG-GGACGTTGA
* *
303013 TTCATTCCACTTTTCAAT
384 TTCATTCCACTATCCAAT
* *
303031 AGGGAAAATTGAATCGAGGCAGACTTGTTCCACTGTTACTCATGGAATATCAAAT-ATGAAAGAG
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA-GGAATATCAAATCTTGAAAGAG
* * * * ** *
303095 AGGGATATG-TTCCATTGCTTCTTGAGAGAAACTTAGATCTGGAAATCTTGATTCATTCCACTAT
65 AGGGGTATGTTTCC-TT-CTTCTTGAGGGAAAATTAGATATGGGGA-CTTGATTCATTCCACTGT
*
303159 CCTTCAGGGAAGATTGATTCGAG
127 CCTTCAGGGAAGATTGAATCGAG
303182 TTCGATTCGC
Statistics
Matches: 469, Mismatches: 74, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
399 1 0.00
400 5 0.01
401 76 0.16
402 194 0.41
403 8 0.02
407 3 0.01
408 136 0.29
409 17 0.04
410 29 0.06
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (401 bp):
AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAATATCAAATCTTGAAAGAGA
GGGGTATGTTTCCTTCTTCTTGAGGGAAAATTAGATATGGGGACTTGATTCATTCCACTGTCCTT
CAGGGAAGATTGAATCGAGGCAGCTTATTCCACTATTACCCAGGAATATCAAATCTTGAAAGAGA
GAGATATGTTCTCGTCTTTCTTACTTGAGGAAAAATCAGATATGGGGATGTTGATTCATTCCACT
GACACTCAGAGAAGATTGAATCAAGGTAGACTTATTCAACTATTACTCAGGGAATATCAAATCCT
AAAAGAGAGGGATCTATTCCACTTCTTCCTAAGGGAAAATCAGATATGGGGACGTTGATTCATTC
CACTATCCAAT
Found at i:304961 original size:13 final size:12
Alignment explanation
Indices: 304945--305054 Score: 62
Period size: 11 Copynumber: 9.8 Consensus size: 12
304935 TTCCTTATTC
304945 TATTTCTTATCTA
1 TATTTCTT-TCTA
*
304958 TATTTTCTTTCTT
1 TA-TTTCTTTCTA
*
304971 TA-TT-TTTCTT
1 TATTTCTTTCTA
*
304981 TATTT-TTTCTT
1 TATTTCTTTCTA
*
304992 TATTT-TTTCTT
1 TATTTCTTTCTA
305003 TATTT-TTTCCT-
1 TATTTCTTT-CTA
305014 T-TTTCTTTCT-
1 TATTTCTTTCTA
305024 T-TTTCTTTTCT-
1 TATTTC-TTTCTA
*
305035 T-TTTCTTTCTT
1 TATTTCTTTCTA
305046 TATTTCTTT
1 TATTTCTTT
305055 TTTCAAACGT
Statistics
Matches: 89, Mismatches: 1, Indels: 15
0.85 0.01 0.14
Matches are distributed among these distances:
10 23 0.26
11 44 0.49
12 9 0.10
13 7 0.08
14 6 0.07
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTCTTTCTA
Found at i:304989 original size:11 final size:11
Alignment explanation
Indices: 304965--305050 Score: 108
Period size: 11 Copynumber: 8.0 Consensus size: 11
304955 CTATATTTTC
304965 TTTCTTTA-TT
1 TTTCTTTATTT
304975 TTTCTTTATTT
1 TTTCTTTATTT
304986 TTTCTTTATTT
1 TTTCTTTATTT
304997 TTTCTTTATTT
1 TTTCTTTATTT
*
305008 TTTCCTTT-TTC
1 TTT-CTTTATTT
305019 TTTCTTT-TTCT
1 TTTCTTTATT-T
*
305030 TTTCTTT-TTC
1 TTTCTTTATTT
305040 TTTCTTTATTT
1 TTTCTTTATTT
305051 CTTTTTTCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
10 21 0.31
11 43 0.63
12 4 0.06
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTATTT
Found at i:304991 original size:21 final size:21
Alignment explanation
Indices: 304942--305050 Score: 114
Period size: 22 Copynumber: 5.0 Consensus size: 21
304932 ATTTTCCTTA
* *
304942 TTCTATTTCTTATCTATATTTTCT
1 TTCTTTTTCTT-TCTTTA-TTT-T
304966 TTCTTTATT-TTTCTTTATTTT
1 TTCTTT-TTCTTTCTTTATTTT
*
304987 TTCTTTATTTTTTCTTTATTTT
1 TTCTTT-TTCTTTCTTTATTTT
305009 TTCCTTTTTCTTTCTTT-TTCTT
1 TT-CTTTTTCTTTCTTTATT-TT
305031 TTCTTTTTCTTTCTTTATTT
1 TTCTTTTTCTTTCTTTATTT
305051 CTTTTTTCAA
Statistics
Matches: 77, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
21 27 0.35
22 32 0.42
23 9 0.12
24 7 0.09
25 2 0.03
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (21 bp):
TTCTTTTTCTTTCTTTATTTT
Found at i:305001 original size:50 final size:49
Alignment explanation
Indices: 304933--305057 Score: 123
Period size: 50 Copynumber: 2.5 Consensus size: 49
304923 CCCTTTTCAA
*
304933 TTTTCCTTATTCTATTTCTTATCTATATTT-TCTTTCTTTATTTTTCTTTAT-T
1 TTTTCTTTATT-TATTTCTTAT-T-T-TTTCTCTTTCTTTATTTTTCTTT-TCT
* *
304985 TTTTCTTTATTT-TTTCTTTATTTTTTCCTTTTTCTTTCTTTTTCTTTTCT
1 TTTTCTTTATTTATTTC-TTATTTTTT-CTCTTTCTTTATTTTTCTTTTCT
*
305035 TTTTCTTTCTTTATTTCTT-TTTT
1 TTTTCTTTATTTATTTCTTATTTT
305058 CAAACGTGGT
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
48 3 0.05
49 6 0.09
50 36 0.56
51 9 0.14
52 10 0.16
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (49 bp):
TTTTCTTTATTTATTTCTTATTTTTTCTCTTTCTTTATTTTTCTTTTCT
Found at i:305021 original size:40 final size:40
Alignment explanation
Indices: 304973--305058 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 40
304963 TCTTTCTTTA
*
304973 TTTTTCTTTATTTTTTCTTTAT-TTTTTCTTTATTT-TTTCC
1 TTTTTCTTT-CTTTTTCTTT-TCTTTTTCTTTATTTATTTCC
* *
305013 TTTTTCTTTCTTTTTCTTTTCTTTTTCTTTCTTTATTTCT
1 TTTTTCTTTCTTTTTCTTTTCTTTTTCTTTATTTATTTCC
305053 TTTTTC
1 TTTTTC
305059 AAACGTGGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 21 0.51
40 19 0.46
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (40 bp):
TTTTTCTTTCTTTTTCTTTTCTTTTTCTTTATTTATTTCC
Done.