Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015322.1 Kokia drynarioides strain JFW-HI SEQ_130368, 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: 397318
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 459 characters in sequence are not A, C, G, or T
Found at i:431 original size:15 final size:15
Alignment explanation
Indices: 413--483 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
403 TTTTGGGTAG
413 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
* *
428 TTTGTATTTGGGTCA
1 TTTGTAATTGGGCCA
* *
443 TCTGTAACTGGGCCA
1 TTTGTAATTGGGCCA
* *
458 TTTATTATTGGGCCA
1 TTTGTAATTGGGCCA
473 TTTGTAATTGG
1 TTTGTAATTGG
484 ACTTTGTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:537 original size:17 final size:16
Alignment explanation
Indices: 515--593 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
505 TTGGACTTTC
515 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
532 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
549 TGAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
566 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
582 TAAATTCAATTT
1 TAAATTTAATTT
594 CCAATAAGTC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
16 16 0.31
17 29 0.57
18 6 0.12
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:555 original size:34 final size:33
Alignment explanation
Indices: 515--593 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
505 TTGGACTTTC
* *
515 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
* *
549 TGAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
582 TAAATTCAATTT
1 TAAATTTAATTT
594 CCAATAAGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 12 0.32
34 26 0.68
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:3470 original size:667 final size:667
Alignment explanation
Indices: 2279--3627 Score: 2434
Period size: 667 Copynumber: 2.0 Consensus size: 667
2269 TCCACCAAAA
2279 AATTAA-TTTTTTTAATCCTATGGCTAATGTGACATGTTGATAATGCAAATATTTTTGGCTCTAT
1 AATTAATTTTTTTTAATCCTATGGCTAATGTGACATGTTGATAATGCAAATATTTTTGGCTCTAT
*
2343 CAATTTTTACTATTTATTTTAGCTCATTTACGTATTTTTGTAATTATTCAAAATTTTAAGATTAT
66 CAATTTTTACTATTCATTTTAGCTCATTTACGTATTTTTGTAATTATTCAAAATTTTAAGATTAT
* *
2408 TTTTTTTATAGAAAAAGCCAAATTAACTTGATATGTGGTATGGTTTTTTTTTTTTTGGTGAATGA
131 TTTTTTTATAGAAAAAGCCAAATTAACCTGATATGTGGTATGGATTTTTTTTTTTTGGTGAATGA
* * * * *
2473 TATGTGGTATAGTTTTTATTTTCTCAAGTTGAAAGATACATTTAATGTTTTTGGCTTGTCGAATC
196 TATGTGATATAGTTTCTATTTTCTCAAGTTAAAAGATACATTTAATGTTTTTGGCCTGTCAAATC
2538 ACGAATATACATTATTGTCGGCAACATATGTTTCACGAGTTAAAACATGACGTGAACTGATGCAC
261 ACGAATATACATTATTGTCGGCAACATATGTTTCACGAGTTAAAACATGACGTGAACTGATGCAC
*
2603 ATTAATTATTAAAAAATGTGCCACTATTCCCTACGTGGTTGCCCCAGGCATCATCCAGTTGTAGT
326 ATTAATTATTAAAAAATGTGCCACTATTCCCTACGTGATTGCCCCAGGCATCATCCAGTTGTAGT
*
2668 CAAACTTTAATATTTTCAAAAAATATTTGGCTTTTTTTATGAAAACAAAGTTGAAAGTATTAATT
391 CAAACTTTAATATTTTCAAAAAATATTTGGCTTTTTTTATGAAAACAAAATTGAAAGTATTAATT
* * *
2733 AATTAATTAGAAAATATTTGAACCATAAATTACTTTAAAAAATATCCATTTTCTACGGTAAAAGT
456 AATTAATTAGAAAACATTTGAACCATAAATTACTTTAAAAAATATCCATTTGCTACGGTAAAAAT
2798 CGATGCGGCACCATTTTCTTGGCCTAATCACTAGCCAATCATCAATTTTGAAAAAGAAGAATTAT
521 CGATGCGGCACCATTTTCTTGGCCTAATCACTAGCCAATCATCAATTTTGAAAAAGAAGAATTAT
2863 TTTTGCCGCCATATTCATATGTATTTTTCAAAATATCAATGAAAAATATGAATATTCACTGTAAA
586 TTTTGCCGCCATATTCATATGTATTTTTCAAAATATCAATGAAAAATATGAATATTCACTGTAAA
2928 TAAAAAAATATTTTTGT
651 TAAAAAAATATTTTTGT
*
2945 AATTAATTTTTTTTAATCCTATGGCTAATGTGACATGTTGATAATGCAAATATTTTTTGCTCTAT
1 AATTAATTTTTTTTAATCCTATGGCTAATGTGACATGTTGATAATGCAAATATTTTTGGCTCTAT
3010 CAATTTTTACTATTCATTTTAGCTCATTTACGTATTTTTGTAATTATTCAAAATTTTAAGATTA-
66 CAATTTTTACTATTCATTTTAGCTCATTTACGTATTTTTGTAATTATTCAAAATTTTAAGATTAT
3074 TTTTTTTATAGAAAAAGCCAAATTAACCTGATATGTGGTAT-GATTTTTTTTTTTTGGTGAATGA
131 TTTTTTTATAGAAAAAGCCAAATTAACCTGATATGTGGTATGGATTTTTTTTTTTTGGTGAATGA
3138 TATGTGATATAGTTTCTATTTTCTCAAGTTAAAAGATACATTTAATGTTTTTGGCCTGTCAAATC
196 TATGTGATATAGTTTCTATTTTCTCAAGTTAAAAGATACATTTAATGTTTTTGGCCTGTCAAATC
*
3203 ACGAATATACATTATTGTCGGCAACATATGTTTCACGAGTTAAAACATGACGTGAATTGATGCAC
261 ACGAATATACATTATTGTCGGCAACATATGTTTCACGAGTTAAAACATGACGTGAACTGATGCAC
* * * * *
3268 ATTAATTATTGAAAATATGTGTCACTATTTCCTACGTGATTGCCTCCATGCATCATCCAGTTGTC
326 ATTAATTATT-AAAAAATGTGCCACTATTCCCTACGTGATTGCC-CCAGGCATCATCCAGTTGTA
* *
3333 GTCAAATTTTAATATTTTCAAAAAATATTTGGCTTTTTTTATGAAAACAAAATTGAAAGTATTCA
389 GTCAAACTTTAATATTTTCAAAAAATATTTGGCTTTTTTTATGAAAACAAAATTGAAAGTATTAA
*
3398 TTAATTAATTAGAAAACATTTGAACCATAAATTATTTTAAAAAATATCCATTTGCTACGGTAAAA
454 TTAATTAATTAGAAAACATTTGAACCATAAATTACTTTAAAAAATATCCATTTGCTACGGTAAAA
*
3463 ATCGATGCGGCACCATTTTCTTGGCCTAATCACTAGCTAATCATCAATTTTGAAAAAGAAGAATT
519 ATCGATGCGGCACCATTTTCTTGGCCTAATCACTAGCCAATCATCAATTTTGAAAAAGAAGAATT
*
3528 ATTTTTGCCGTCATATTCATATGTATTTTTCAAAATATCAATGAAAAATATGAATATTCACTGTA
584 ATTTTTGCCGCCATATTCATATGTATTTTTCAAAATATCAATGAAAAATATGAATATTCACTGTA
3593 AATAAAAAAATATTTTTGT
649 AATAAAAAAATATTTTTGT
3612 AATTAATTTTTTTTAA
1 AATTAATTTTTTTTAA
3628 AAAATATTTA
Statistics
Matches: 655, Mismatches: 25, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
665 156 0.24
666 75 0.11
667 424 0.65
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (667 bp):
AATTAATTTTTTTTAATCCTATGGCTAATGTGACATGTTGATAATGCAAATATTTTTGGCTCTAT
CAATTTTTACTATTCATTTTAGCTCATTTACGTATTTTTGTAATTATTCAAAATTTTAAGATTAT
TTTTTTTATAGAAAAAGCCAAATTAACCTGATATGTGGTATGGATTTTTTTTTTTTGGTGAATGA
TATGTGATATAGTTTCTATTTTCTCAAGTTAAAAGATACATTTAATGTTTTTGGCCTGTCAAATC
ACGAATATACATTATTGTCGGCAACATATGTTTCACGAGTTAAAACATGACGTGAACTGATGCAC
ATTAATTATTAAAAAATGTGCCACTATTCCCTACGTGATTGCCCCAGGCATCATCCAGTTGTAGT
CAAACTTTAATATTTTCAAAAAATATTTGGCTTTTTTTATGAAAACAAAATTGAAAGTATTAATT
AATTAATTAGAAAACATTTGAACCATAAATTACTTTAAAAAATATCCATTTGCTACGGTAAAAAT
CGATGCGGCACCATTTTCTTGGCCTAATCACTAGCCAATCATCAATTTTGAAAAAGAAGAATTAT
TTTTGCCGCCATATTCATATGTATTTTTCAAAATATCAATGAAAAATATGAATATTCACTGTAAA
TAAAAAAATATTTTTGT
Found at i:12121 original size:16 final size:15
Alignment explanation
Indices: 12102--12173 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 15
12092 ATCTGAATAT
12102 AAAATAATTTGAACTC
1 AAAA-AATTTGAACTC
*
12118 AAAAAATTTAAACTC
1 AAAAAATTTGAACTC
* * *
12133 GAAAGAATCTGAACTTG
1 -AAAAAATTTGAAC-TC
* * *
12150 TAAAAATTTAAATTC
1 AAAAAATTTGAACTC
12165 AAAAAATTT
1 AAAAAATTT
12174 AAATCTTAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
15 19 0.45
16 22 0.52
17 1 0.02
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.31
Consensus pattern (15 bp):
AAAAAATTTGAACTC
Found at i:12131 original size:15 final size:15
Alignment explanation
Indices: 12102--12176 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
12092 ATCTGAATAT
*
12102 AAAATAATTTGAACTC
1 AAAA-AATTTAAACTC
12118 AAAAAATTTAAACTC
1 AAAAAATTTAAACTC
* * * *
12133 GAAAGAATCTGAACTTG
1 -AAAAAATTTAAAC-TC
* *
12150 TAAAAATTTAAATTC
1 AAAAAATTTAAACTC
12165 AAAAAATTTAAA
1 AAAAAATTTAAA
12177 TCTTAAATAA
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 22 0.49
16 22 0.49
17 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (15 bp):
AAAAAATTTAAACTC
Found at i:31312 original size:23 final size:24
Alignment explanation
Indices: 31278--31322 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
31268 CTAATTAAAT
*
31278 TTTATAAATATTTAATATTTATTG
1 TTTATAAATATTTAAAATTTATTG
31302 TTTA-AAATATTTAAAATTTAT
1 TTTATAAATATTTAAAATTTAT
31323 ATTTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTATAAATATTTAAAATTTATTG
Found at i:31760 original size:69 final size:69
Alignment explanation
Indices: 31680--31817 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
31670 ACATTCAAAT
31680 CTTAAATCAAAATTTTCAAAAATACTTTTCCATAGCACTTTTCTAAAATAATGTTAAATTAGCCC
1 CTTAAATCAAAATTTTCAAAAATACTTTTCCATAGCACTTTTCTAAAATAATGTTAAATTAGCCC
31745 TTAG
66 TTAG
31749 CTTAAATCAAAATTTTCAAAAATACTTTTCCATAGCACTTTTCTAAAATAATGTTAAATTAGCCC
1 CTTAAATCAAAATTTTCAAAAATACTTTTCCATAGCACTTTTCTAAAATAATGTTAAATTAGCCC
31814 TTAG
66 TTAG
31818 TAGAGTGCAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (69 bp):
CTTAAATCAAAATTTTCAAAAATACTTTTCCATAGCACTTTTCTAAAATAATGTTAAATTAGCCC
TTAG
Found at i:36201 original size:2 final size:2
Alignment explanation
Indices: 36194--36221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36184 CCAAAGCAAC
36194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36222 GTGAAAGGAA
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):
TA
Found at i:49036 original size:22 final size:24
Alignment explanation
Indices: 49011--49054 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
49001 ATTATATTCA
49011 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
49033 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
49055 TATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:58328 original size:2 final size:2
Alignment explanation
Indices: 58323--58349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58313 TTTTCATGAA
58323 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
58350 CTTCTGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:63842 original size:3 final size:3
Alignment explanation
Indices: 63834--63895 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
63824 TATCAACATA
* * * * *
63834 AAT AAT AAT AAT AAT GAT GAT GAT GAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
63882 GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
63896 GCAAGCAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:64258 original size:3 final size:3
Alignment explanation
Indices: 64243--64273 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
64233 GAGAAGGGAC
*
64243 ACA ACA TCA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
64274 AAAGCTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.32, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:65947 original size:33 final size:33
Alignment explanation
Indices: 65910--66012 Score: 77
Period size: 33 Copynumber: 3.0 Consensus size: 33
65900 TATCTTAGTA
65910 TTATTTAAGTATATATTTTTTAATTTTTTTTAT
1 TTATTTAAGTATATATTTTTTAATTTTTTTTAT
* * *
65943 TTATTGGAA-AATAT-TTATTTTAA-TGTTTTTAGT
1 TTATT-TAAGTATATATT-TTTTAATTTTTTTTA-T
* *
65976 GTATTTTATGTATTATATTTTTTAAATTTATTTTTAT
1 TTA-TTTAAGTA-TATATTTTTT-AATTT-TTTTTAT
66013 ATTAAAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
32 9 0.17
33 19 0.37
34 5 0.10
35 7 0.13
36 4 0.08
37 2 0.04
38 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (33 bp):
TTATTTAAGTATATATTTTTTAATTTTTTTTAT
Found at i:74461 original size:64 final size:64
Alignment explanation
Indices: 74360--74483 Score: 230
Period size: 64 Copynumber: 1.9 Consensus size: 64
74350 CAACGCACTC
*
74360 GAATCCACGTCTTCCTGCATTAATAATAATATTCATTTCAATTGAGTTAAAACTTAATTGGCAG
1 GAATCCACATCTTCCTGCATTAATAATAATATTCATTTCAATTGAGTTAAAACTTAATTGGCAG
*
74424 GAATCCACATCTTCCTGTATTAATAATAATATTCATTTCAATTGAGTTAAAACTTAATTG
1 GAATCCACATCTTCCTGCATTAATAATAATATTCATTTCAATTGAGTTAAAACTTAATTG
74484 ACAAAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (64 bp):
GAATCCACATCTTCCTGCATTAATAATAATATTCATTTCAATTGAGTTAAAACTTAATTGGCAG
Found at i:87282 original size:29 final size:29
Alignment explanation
Indices: 87231--87297 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
87221 TCCCTATGCA
* * *
87231 TCCATATTATTCCAGTAATTAAACTTTTT
1 TCCATATTATTCCAATAAATAAAATTTTT
* *
87260 TTCATATTATTTCAATAAATAAAATTTTT
1 TCCATATTATTCCAATAAATAAAATTTTT
87289 TCCATATTA
1 TCCATATTA
87298 ATCCCAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.49
Consensus pattern (29 bp):
TCCATATTATTCCAATAAATAAAATTTTT
Found at i:87962 original size:26 final size:27
Alignment explanation
Indices: 87933--87984 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
87923 TGTGTTTAAA
* *
87933 TTTTAATT-AATTTTTAAATGTAATTT
1 TTTTAATTAAATTGTTAAATATAATTT
*
87959 TTTTATTTAAATTGTTAAATATAATT
1 TTTTAATTAAATTGTTAAATATAATT
87985 AAAATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTAATTAAATTGTTAAATATAATTT
Found at i:113276 original size:17 final size:17
Alignment explanation
Indices: 113254--113290 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
113244 AGGTGGAGAA
* *
113254 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
113271 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
113288 CTT
1 CTT
113291 TTCAAGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:116518 original size:3 final size:3
Alignment explanation
Indices: 116510--116539 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
116500 AAGCTCCTTG
116510 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
116540 AAAGTTAATT
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:117675 original size:4 final size:4
Alignment explanation
Indices: 117666--117690 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
117656 TATGATGGCC
117666 CCAT CCAT CCAT CCAT CCAT CCAT C
1 CCAT CCAT CCAT CCAT CCAT CCAT C
117691 TCATGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (4 bp):
CCAT
Found at i:133137 original size:28 final size:27
Alignment explanation
Indices: 133105--133160 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 27
133095 CCACTGCTAA
133105 TTTAATCTAATAAAAAAAACAATATTAG
1 TTTAAT-TAATAAAAAAAACAATATTAG
133133 --T--TTAATAAAAAAAACAATATTAG
1 TTTAATTAATAAAAAAAACAATATTAG
133156 TTTAA
1 TTTAA
133161 ATTTGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
23 21 0.88
24 1 0.04
25 1 0.04
26 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (27 bp):
TTTAATTAATAAAAAAAACAATATTAG
Found at i:133142 original size:23 final size:23
Alignment explanation
Indices: 133112--133160 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
133102 TAATTTAATC
133112 TAATAAAAAAAACAATATTAGTT
1 TAATAAAAAAAACAATATTAGTT
133135 TAATAAAAAAAACAATATTAGTT
1 TAATAAAAAAAACAATATTAGTT
133158 TAA
1 TAA
133161 ATTTGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
TAATAAAAAAAACAATATTAGTT
Found at i:153921 original size:24 final size:24
Alignment explanation
Indices: 153885--153930 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
153875 CATAGACGTG
* *
153885 GTAAAAATATAAACATAAATTGTA
1 GTAAAAATATAAAAAAAAATTGTA
153909 GTAAAAA-AGTAAAAAAAAATTG
1 GTAAAAATA-TAAAAAAAAATTG
153931 GAAAATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (24 bp):
GTAAAAATATAAAAAAAAATTGTA
Found at i:160364 original size:24 final size:25
Alignment explanation
Indices: 160319--160367 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
160309 TTCATTTTGA
* **
160319 ATTTTTTGTGTTGTTGTTGGTGTGG
1 ATTTTTTGTGTTGCTGAGGGTGTGG
160344 ATTTTTTG-GTTGCTGAGGGTGTGG
1 ATTTTTTGTGTTGCTGAGGGTGTGG
160368 TGAGGATGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.06, C:0.02, G:0.39, T:0.53
Consensus pattern (25 bp):
ATTTTTTGTGTTGCTGAGGGTGTGG
Found at i:161206 original size:18 final size:18
Alignment explanation
Indices: 161179--161213 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
161169 TGAATTTTAC
*
161179 AATTTGAATAACTCGAAT
1 AATTTAAATAACTCGAAT
*
161197 AATTTAAATAATTCGAA
1 AATTTAAATAACTCGAA
161214 AAATAAATTG
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:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (18 bp):
AATTTAAATAACTCGAAT
Found at i:161361 original size:18 final size:21
Alignment explanation
Indices: 161338--161382 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
161328 TTTATATTTT
161338 AAAAAATATAAA-AAT-TA-A
1 AAAAAATATAAATAATATATA
*
161356 AAAAAATCTAAATAATATATA
1 AAAAAATATAAATAATATATA
161377 AAAAAA
1 AAAAAA
161383 AAAGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 3 0.13
20 2 0.09
21 7 0.30
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAATATAAATAATATATA
Found at i:166234 original size:6 final size:6
Alignment explanation
Indices: 166190--166232 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
166180 AGGAGTAAAA
166190 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTTCC C-CTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC-TCC CTCTCC C
166233 CCATTCCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:168195 original size:18 final size:17
Alignment explanation
Indices: 168122--168210 Score: 60
Period size: 16 Copynumber: 5.0 Consensus size: 17
168112 TAATCTTAAT
*
168122 TATAAAAATTATAAAAAA
1 TATAAATATTA-AAAAAA
*
168140 -A-AAATATTTCAAAAAA
1 TATAAATA-TTAAAAAAA
168156 TCATAAATATTAAAATGTAAA
1 T-ATAAATATTAAAA---AAA
168177 TATAAATTATTAAAAAAA
1 TATAAA-TATTAAAAAAA
168195 T-TAAA-ATTTAAAAAAA
1 TATAAATA-TTAAAAAAA
168211 AAATACAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
15 1 0.02
16 19 0.32
17 7 0.12
18 10 0.17
19 5 0.08
20 5 0.08
21 12 0.20
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (17 bp):
TATAAATATTAAAAAAA
Found at i:177146 original size:210 final size:211
Alignment explanation
Indices: 176783--177205 Score: 627
Period size: 210 Copynumber: 2.0 Consensus size: 211
176773 AAGAAGTTTG
* *
176783 TAGTCTTGATTGCTAGTTCAGTTTCCCGATAATAGTAGCGCTCAAGAAATAACATTTTGAGAGAT
1 TAGTCTTGATTGCTAGTTCAGTTTCCCGATAATAGTAGCGCTCAAGAAATAACATTGTGAGAGAA
*
176848 CAGGATGGTGCATATGATTCTTAACAAACCAACCAGTATACAGCACCAAAGCAAGATGAATATTC
66 CAGGATGGTGCATATGATTCTTAACAAACCAACCAGTATACAGCACCAAAGCAAGATGAAAATTC
* *
176913 GATATTGTAACTAAAGAATTTTCATATGATGTCCTAGTTTACGAAAGACAGAAGAGTAGGTTTAA
131 AATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACGAAAGACAGAAGAGTAGGTTTAA
176978 TATTGTTCAACTTCCA
196 TATTGTTCAACTTCCA
* * * * * * *
176994 TAGTCTTGATTGCTGGTTCAGTTTTCTGATATTGGTAGGGCTTAAGAAATAACATTGT-AGA-AA
1 TAGTCTTGATTGCTAGTTCAGTTTCCCGATAATAGTAGCGCTCAAGAAATAACATTGTGAGAGAA
* * * * * *
177057 CAAGGGTGGTGCATATGATTCCTT-ACAAACCATCCAGTATACTGCACCGAATCAAGGTGAAAAT
66 C-AGGATGGTGCATATGATT-CTTAACAAACCAACCAGTATACAGCACCAAAGCAAGATGAAAAT
* *
177121 TCAATATTGTGACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTT
129 TCAATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACGAAAGACAGAAGAGTAGGTTT
177186 AATATTGTTCAACTTCCA
194 AATATTGTTCAACTTCCA
177204 TA
1 TA
177206 AAGAAGCCTG
Statistics
Matches: 190, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
209 2 0.01
210 135 0.71
211 53 0.28
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (211 bp):
TAGTCTTGATTGCTAGTTCAGTTTCCCGATAATAGTAGCGCTCAAGAAATAACATTGTGAGAGAA
CAGGATGGTGCATATGATTCTTAACAAACCAACCAGTATACAGCACCAAAGCAAGATGAAAATTC
AATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACGAAAGACAGAAGAGTAGGTTTAA
TATTGTTCAACTTCCA
Found at i:181564 original size:20 final size:20
Alignment explanation
Indices: 181539--181576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
181529 TAAAATTTAA
181539 ATAATTTTCTATAATTATGT
1 ATAATTTTCTATAATTATGT
* *
181559 ATAATTTTGTATACTTAT
1 ATAATTTTCTATAATTAT
181577 TTAAGAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
ATAATTTTCTATAATTATGT
Found at i:191277 original size:100 final size:100
Alignment explanation
Indices: 191104--191310 Score: 414
Period size: 100 Copynumber: 2.1 Consensus size: 100
191094 CGTTCCCACA
191104 ATAAAAACATACGAGTTTTCTTTCCATCTTGTTACCTTTGTGTTGTTCTATTAGATGTTGCAACA
1 ATAAAAACATACGAGTTTTCTTTCCATCTTGTTACCTTTGTGTTGTTCTATTAGATGTTGCAACA
191169 TGATTTACATTAACATGCCCAACCTTTCCACAAGG
66 TGATTTACATTAACATGCCCAACCTTTCCACAAGG
191204 ATAAAAACATACGAGTTTTCTTTCCATCTTGTTACCTTTGTGTTGTTCTATTAGATGTTGCAACA
1 ATAAAAACATACGAGTTTTCTTTCCATCTTGTTACCTTTGTGTTGTTCTATTAGATGTTGCAACA
191269 TGATTTACATTAACATGCCCAACCTTTCCACAAGG
66 TGATTTACATTAACATGCCCAACCTTTCCACAAGG
191304 ATAAAAA
1 ATAAAAA
191311 AACATGTTTT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 107 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (100 bp):
ATAAAAACATACGAGTTTTCTTTCCATCTTGTTACCTTTGTGTTGTTCTATTAGATGTTGCAACA
TGATTTACATTAACATGCCCAACCTTTCCACAAGG
Found at i:193947 original size:12 final size:12
Alignment explanation
Indices: 193930--193954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
193920 TATATATGGA
193930 CGAATGACGATG
1 CGAATGACGATG
193942 CGAATGACGATG
1 CGAATGACGATG
193954 C
1 C
193955 AGCCAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (12 bp):
CGAATGACGATG
Found at i:195442 original size:43 final size:43
Alignment explanation
Indices: 195394--195480 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
195384 AAATTTAAAC
195394 TCATTATCAAGTTGAATTCCTTAGGAGTAATGGTAACTATAAG
1 TCATTATCAAGTTGAATTCCTTAGGAGTAATGGTAACTATAAG
195437 TCATTATCAAGTTGAATTCCTTAGGAGTAATGGTAACTATAAG
1 TCATTATCAAGTTGAATTCCTTAGGAGTAATGGTAACTATAAG
195480 T
1 T
195481 TATTGGAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (43 bp):
TCATTATCAAGTTGAATTCCTTAGGAGTAATGGTAACTATAAG
Found at i:196716 original size:14 final size:14
Alignment explanation
Indices: 196697--196727 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
196687 TTTGTTAGAA
*
196697 TTTATTTTCTTTAT
1 TTTATTTGCTTTAT
196711 TTTATTTGCTTTAT
1 TTTATTTGCTTTAT
196725 TTT
1 TTT
196728 TCAATTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTTGCTTTAT
Found at i:202913 original size:9 final size:8
Alignment explanation
Indices: 202899--202927 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
202889 CTGGGCTAGG
202899 TTTTTTTA
1 TTTTTTTA
202907 TTTTTTTA
1 TTTTTTTA
202915 -TTTTTTA
1 TTTTTTTA
202922 TTTTTT
1 TTTTTT
202928 ATGATGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:202918 original size:6 final size:7
Alignment explanation
Indices: 202900--202929 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
202890 TGGGCTAGGT
202900 TTTTTTA
1 TTTTTTA
202907 TTTTTTTA
1 -TTTTTTA
202915 TTTTTTA
1 TTTTTTA
202922 TTTTTTA
1 TTTTTTA
202929 T
1 T
202930 GATGACTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:203582 original size:2 final size:2
Alignment explanation
Indices: 203575--203610 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
203565 TTACAGAAAC
203575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203611 CTACACTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222731 original size:39 final size:39
Alignment explanation
Indices: 222687--222763 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
222677 AAAAGTCCCA
* *
222687 TATCACATATTCAACAATAAACTTAGAAAAATTAAGAGG
1 TATCACACATTCAACAACAAACTTAGAAAAATTAAGAGG
*
222726 TATCACACATTCAACGACAAACTTAGAAAAATTAAGAG
1 TATCACACATTCAACAACAAACTTAGAAAAATTAAGAG
222764 TTAGATTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (39 bp):
TATCACACATTCAACAACAAACTTAGAAAAATTAAGAGG
Found at i:233659 original size:21 final size:22
Alignment explanation
Indices: 233609--233659 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
233599 CTATTTTTTA
233609 TTTA-TTTTAATTCTGTTTTCT
1 TTTATTTTTAATTCTGTTTTCT
233630 TTTATTTTTAATTCTG-TTTCT
1 TTTATTTTTAATTCTGTTTTCT
233651 TTTATTTTT
1 TTTATTTTT
233660 CTTCAGATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTATTTTTAATTCTGTTTTCT
Found at i:233659 original size:22 final size:23
Alignment explanation
Indices: 233604--233659 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 23
233594 TACATCTATT
233604 TTTTATTTATTTTAATTCTGTTTTC
1 TTTTA-TT-TTTTAATTCTGTTTTC
233629 TTTTA-TTTTTAATTCTG-TTTC
1 TTTTATTTTTTAATTCTGTTTTC
233650 TTTTATTTTT
1 TTTTATTTTT
233660 CTTCAGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.30
22 15 0.50
23 1 0.03
25 5 0.17
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTTAATTCTGTTTTC
Found at i:234651 original size:22 final size:22
Alignment explanation
Indices: 234620--234670 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
234610 TATCTATTTA
*
234620 TTCTT-TTCTTTTTTTCCTTTC
1 TTCTTATTCTTCTTTTCCTTTC
*
234641 TTCTTATTCTTCTTTTCTTTTC
1 TTCTTATTCTTCTTTTCCTTTC
*
234663 ATCTTATT
1 TTCTTATT
234671 GCCCTTCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.73
Consensus pattern (22 bp):
TTCTTATTCTTCTTTTCCTTTC
Found at i:236134 original size:86 final size:87
Alignment explanation
Indices: 236033--236225 Score: 221
Period size: 87 Copynumber: 2.2 Consensus size: 87
236023 TAAAAAATCT
* * **
236033 TCAAA-CTTTCTCAAAAAAAATAATTAAGT-CTTTTTTTTTTGCACTC-ATTCGAAAACTTGAAC
1 TCAAACCTTT-TCAAAAAAAACAATTAAATCCTTACTTTTTTGCACTCAATT-GAAAACTTGAAC
236095 TTTCAAAATGCATCAAAAAGACCC
64 TTTCAAAATGCATCAAAAAGACCC
* *** *
236119 TCAAACCTTTTCAAAAAAAGCAATTAAATCCTTACTTTTTTGCACTCAATTGGGTATTTGAACTT
1 TCAAACCTTTTCAAAAAAAACAATTAAATCCTTACTTTTTTGCACTCAATTGAAAACTTGAACTT
* **
236184 TTAAAATGCATCAAAAAGACTT
66 TCAAAATGCATCAAAAAGACCC
* *
236206 TCGAACTTTTTCAAAAAAAA
1 TCAAACCTTTTCAAAAAAAA
236226 AAAAAGCAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
86 21 0.24
87 65 0.73
88 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (87 bp):
TCAAACCTTTTCAAAAAAAACAATTAAATCCTTACTTTTTTGCACTCAATTGAAAACTTGAACTT
TCAAAATGCATCAAAAAGACCC
Found at i:236333 original size:20 final size:19
Alignment explanation
Indices: 236310--236362 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
236300 AAATTTTAAT
236310 AAAAAATATTAAAA-CTTAGA
1 AAAAAATATTAAAATCTT--A
*
236330 AAAAAATATAAAAATCTTA
1 AAAAAATATTAAAATCTTA
*
236349 AAAATATATTAAAA
1 AAAAAATATTAAAA
236363 AAATTGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
20 13 0.45
21 3 0.10
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAAATATTAAAATCTTA
Found at i:236334 original size:19 final size:20
Alignment explanation
Indices: 236300--236362 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
236290 AAATATGATT
*
236300 AAATTTTAATAAAAAATATTA
1 AAATCTTAA-AAAAAATATTA
*
236321 AAA-CTTAGAAAAAAATATAA
1 AAATCTTA-AAAAAAATATTA
*
236341 AAATCTT-AAAAATATATTA
1 AAATCTTAAAAAAAATATTA
236360 AAA
1 AAA
236363 AAATTGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 13 0.36
20 16 0.44
21 7 0.19
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATCTTAAAAAAAATATTA
Found at i:236407 original size:27 final size:27
Alignment explanation
Indices: 236361--236476 Score: 76
Period size: 28 Copynumber: 4.2 Consensus size: 27
236351 AATATATTAA
* *
236361 AAAAATTGTAAAATTTTATAAAAATCAT
1 AAAAATTATAAAA-TATATAAAAATCAT
*
236389 AAAAATTATAAAATATATAGAAAT-AT
1 AAAAATTATAAAATATATAAAAATCAT
* * *
236415 AAAATTTTATAAAGTAGTA-AGAAAATTAT
1 AAAA-ATTATAAAATA-TATA-AAAATCAT
* * *
236444 ACAAAA-TATAAAGAAATATAAAATTCGT
1 A-AAAATTATAAA-ATATATAAAAATCAT
236472 AAAAA
1 AAAAA
236477 AAAATTAAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
26 6 0.09
27 23 0.33
28 32 0.46
29 5 0.07
30 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (27 bp):
AAAAATTATAAAATATATAAAAATCAT
Found at i:236415 original size:17 final size:19
Alignment explanation
Indices: 236376--236419 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
236366 TTGTAAAATT
236376 TTATAAAA-ATCATAAAAA
1 TTATAAAATATCATAAAAA
*
236394 TTATAAAATAT-ATAGAAA
1 TTATAAAATATCATAAAAA
236412 -TATAAAAT
1 TTATAAAAT
236420 TTTATAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
TTATAAAATATCATAAAAA
Found at i:236488 original size:48 final size:45
Alignment explanation
Indices: 236388--236488 Score: 103
Period size: 48 Copynumber: 2.2 Consensus size: 45
236378 ATAAAAATCA
* * * ** *
236388 TAAAAATTATAAAATATATAGAAATATAAAATTTTATAAAGTAGT
1 TAAAAATTATAAAATATAAAGAAATATAAAATTGTAAAAAAAAAT
*
236433 AAGAAAATTATACAAAATATAAAGAAATATAAAATTCGTAAAAAAAAAT
1 TA-AAAATTAT--AAAATATAAAGAAATATAAAATT-GTAAAAAAAAAT
236482 TAAAAAT
1 TAAAAAT
236489 GATCATACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
45 1 0.02
46 8 0.18
48 27 0.61
49 8 0.18
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (45 bp):
TAAAAATTATAAAATATAAAGAAATATAAAATTGTAAAAAAAAAT
Found at i:236794 original size:18 final size:18
Alignment explanation
Indices: 236773--236814 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
236763 ATTTTAGTTT
*
236773 TTTAT-ATTTTTATTAAAA
1 TTTATAATTTTT-CTAAAA
236791 TTTAATAATTTTTCTAAAA
1 TTT-ATAATTTTTCTAAAA
236810 TTTAT
1 TTTAT
236815 TGTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTCTAAAA
Found at i:246861 original size:74 final size:74
Alignment explanation
Indices: 246764--246901 Score: 204
Period size: 74 Copynumber: 1.9 Consensus size: 74
246754 ATAACAATCG
* * *
246764 ATTTTTGGGAGAGCTATAGTATATATACAAAGGGGGAAATTGCAAAAATCTTAAACCTTAGGGGA
1 ATTTTTCGGAGAGCCATAGTATATATACAAAGGGCGAAATTGCAAAAATCTTAAACCTTAGGGGA
246829 CCTACTTAT
66 CCTACTTAT
* * * * *
246838 ATTTTTCGGAGGGCCATAGTATATCTACAAAGGGCTAAATTGCAAAAATTTTAAACCTTGGGGG
1 ATTTTTCGGAGAGCCATAGTATATATACAAAGGGCGAAATTGCAAAAATCTTAAACCTTAGGGG
246902 GCCATGGGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (74 bp):
ATTTTTCGGAGAGCCATAGTATATATACAAAGGGCGAAATTGCAAAAATCTTAAACCTTAGGGGA
CCTACTTAT
Found at i:250958 original size:3 final size:3
Alignment explanation
Indices: 250950--250978 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
250940 AAATGCACAA
250950 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
250979 AAGGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:254670 original size:25 final size:26
Alignment explanation
Indices: 254623--254672 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
254613 TAACTAATTT
* *
254623 AACTTTATTTTTAATTATGTTAATAA
1 AACTTAATTTTTAATTATATTAATAA
254649 AACTTAATTTTTAATTA-ATTAATA
1 AACTTAATTTTTAATTATATTAATA
254673 TTTTTACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (26 bp):
AACTTAATTTTTAATTATATTAATAA
Found at i:262643 original size:17 final size:17
Alignment explanation
Indices: 262621--262655 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
262611 CATAGATTTC
262621 TGTGGAATTGCTTTATG
1 TGTGGAATTGCTTTATG
*
262638 TGTGGAATTGGTTTATG
1 TGTGGAATTGCTTTATG
262655 T
1 T
262656 ATCTTGCCCT
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:0.03, G:0.31, T:0.49
Consensus pattern (17 bp):
TGTGGAATTGCTTTATG
Found at i:265612 original size:47 final size:47
Alignment explanation
Indices: 265542--265637 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
265532 CAAGAAGCAA
*
265542 TCTAAATGAATTACATAAGGTATACAGTAAATTTTGATTTGATTATT
1 TCTAAATGAATTACATAACGTATACAGTAAATTTTGATTTGATTATT
265589 TCTAAATGAATTACATAACGTATACAGTAAATTTTGATTTGATTATT
1 TCTAAATGAATTACATAACGTATACAGTAAATTTTGATTTGATTATT
265636 TC
1 TC
265638 GCAGCTTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (47 bp):
TCTAAATGAATTACATAACGTATACAGTAAATTTTGATTTGATTATT
Found at i:273737 original size:5 final size:5
Alignment explanation
Indices: 273721--273750 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
273711 GATAAATTAG
273721 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
273751 CAATTAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:275702 original size:3 final size:3
Alignment explanation
Indices: 275694--275721 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
275684 GATGGAGCAT
275694 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
275722 AGGATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:283200 original size:78 final size:78
Alignment explanation
Indices: 283071--283228 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
283061 ATGATGCATG
283071 TATTCAAGTTTATACATCTGAACCTACTGTCAGGTTCCTTCTTCTAAGTGTTATATTTTTACTTA
1 TATTCAAGTTTATACATCTGAACCTACTGTCAGGTTCCTTCTTCTAAGTGTTATATTTTTACTTA
283136 TATTATTAAGCGA
66 TATTATTAAGCGA
283149 TATTCAAGTTTATACATCTGAACCTACTGTCAGGTTCCTTCTTCTAAGTGTTATATTTTTACTTA
1 TATTCAAGTTTATACATCTGAACCTACTGTCAGGTTCCTTCTTCTAAGTGTTATATTTTTACTTA
283214 TATTATTAAGCGA
66 TATTATTAAGCGA
283227 TA
1 TA
283229 GTTTGGTTGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (78 bp):
TATTCAAGTTTATACATCTGAACCTACTGTCAGGTTCCTTCTTCTAAGTGTTATATTTTTACTTA
TATTATTAAGCGA
Found at i:289099 original size:113 final size:117
Alignment explanation
Indices: 288896--289129 Score: 377
Period size: 113 Copynumber: 2.0 Consensus size: 117
288886 TGTATAACTC
* * *
288896 GAATGTTTTAGTTGGTAGCTATTTTTAGCAGTTGCTTACTAGAGTTAAGTTGGGTTCATATTTAT
1 GAATGTTTCACTTGGTAGCTATTTTTAGCAGTTGCTTACT--A-TAAAGTTGGGTTCATATTTAT
288961 GTTGGTCAATGACGGTTTAAGAGGGGTGTCGTGAATAGGT-G-GTGATTGAAATT
63 GTTGGTCAATGACGGTTTAAGAGGGGTGTCGTGAATAGGTGGTGTGATTGAAATT
289014 GAATGTTTCACTTGGTAGCTATTTTTAGCAGTTGCTTA-T-TAAAGTTGGGTTCATATTTATGTT
1 GAATGTTTCACTTGGTAGCTATTTTTAGCAGTTGCTTACTATAAAGTTGGGTTCATATTTATGTT
*
289077 GGTCAATGACTGTTTAAGAGGGGTGTCGTGAATAGGTGGTGTGATTGAAATT
66 GGTCAATGACGGTTTAAGAGGGGTGTCGTGAATAGGTGGTGTGATTGAAATT
289129 G
1 G
289130 TAAAATTTAA
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
113 59 0.54
114 1 0.01
115 13 0.12
117 1 0.01
118 36 0.33
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (117 bp):
GAATGTTTCACTTGGTAGCTATTTTTAGCAGTTGCTTACTATAAAGTTGGGTTCATATTTATGTT
GGTCAATGACGGTTTAAGAGGGGTGTCGTGAATAGGTGGTGTGATTGAAATT
Found at i:293603 original size:17 final size:16
Alignment explanation
Indices: 293565--293607 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
293555 TTAATTTTTT
*
293565 TAAAATTTATAAAGATA
1 TAAAA-TTATAAAAATA
293582 T-AAATTATAAAAATAA
1 TAAAATTATAAAAAT-A
293598 TAAAATTATA
1 TAAAATTATA
293608 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 5 0.22
17 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAATTATAAAAATA
Found at i:295827 original size:30 final size:31
Alignment explanation
Indices: 295774--295836 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
295764 ATGTAGTAAT
295774 TAATTATTTTTTAAAATTAAAAAAAAAATCA
1 TAATTATTTTTTAAAATTAAAAAAAAAATCA
295805 TAATTATTTTTTAAAATT-AAAAAAAAATCA
1 TAATTATTTTTTAAAATTAAAAAAAAAATCA
295835 TA
1 TA
295837 CTTTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
TAATTATTTTTTAAAATTAAAAAAAAAATCA
Found at i:298968 original size:11 final size:11
Alignment explanation
Indices: 298933--298968 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
298923 TTTTGTTATC
298933 ATTTTACTATT
1 ATTTTACTATT
*
298944 ATGTTACTATT
1 ATTTTACTATT
*
298955 ATTTTATTATT
1 ATTTTACTATT
298966 ATT
1 ATT
298969 GTTTGCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:301981 original size:7 final size:7
Alignment explanation
Indices: 301969--301998 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
301959 AATTTTTTGA
301969 AATTTTT
1 AATTTTT
301976 AATTTTT
1 AATTTTT
301983 AATTTTT
1 AATTTTT
*
301990 AAATTTT
1 AATTTTT
301997 AA
1 AA
301999 AAAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
AATTTTT
Found at i:312938 original size:10 final size:10
Alignment explanation
Indices: 312923--312952 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
312913 GTAAGACATA
312923 TTATAAATAT
1 TTATAAATAT
312933 TTATAAATA-
1 TTATAAATAT
312942 TTATAAATAT
1 TTATAAATAT
312952 T
1 T
312953 AAGCAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTATAAATAT
Found at i:312945 original size:9 final size:9
Alignment explanation
Indices: 312920--312953 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
312910 TTGGTAAGAC
312920 ATATTATAA
1 ATATTATAA
312929 ATATTTATAA
1 ATA-TTATAA
312939 ATATTATAA
1 ATATTATAA
312948 ATATTA
1 ATATTA
312954 AGCAATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATTATAA
Found at i:318011 original size:19 final size:20
Alignment explanation
Indices: 317976--318017 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
317966 ACATTTCATG
317976 TTTTATAAAATTATTTA-AT
1 TTTTATAAAATTATTTATAT
*
317995 TTTTA-AAAATGTTTTTATAT
1 TTTTATAAAAT-TATTTATAT
318015 TTT
1 TTT
318018 AAATAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 10 0.50
20 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTATAAAATTATTTATAT
Found at i:318157 original size:20 final size:20
Alignment explanation
Indices: 318132--318172 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
318122 CCTTTCCAAA
*
318132 TTTTAAGCAATTCTTTTATG
1 TTTTAAGCAATTCTTTCATG
* *
318152 TTTTAAGTATTTCTTTCATG
1 TTTTAAGCAATTCTTTCATG
318172 T
1 T
318173 ATTACAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTTAAGCAATTCTTTCATG
Found at i:322139 original size:15 final size:16
Alignment explanation
Indices: 322119--322152 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
322109 TTAAAAATTC
*
322119 AAAATTAA-AATTAAA
1 AAAATTAACAAATAAA
322134 AAAATTAACAAATAAA
1 AAAATTAACAAATAAA
322150 AAA
1 AAA
322153 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATTAACAAATAAA
Found at i:322754 original size:21 final size:19
Alignment explanation
Indices: 322700--322759 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
322690 TTTTCTTTAA
** *
322700 ATTATTTTATTTATAAGACT
1 ATTATTTTATAAATAA-ATT
322720 ATTATTTTATAAATACAATT
1 ATTATTTTATAAATA-AATT
322740 ATTATTTTAATAAATAAATT
1 ATTATTTT-ATAAATAAATT
322760 TCATACTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATTTTATAAATAAATT
Found at i:326929 original size:27 final size:27
Alignment explanation
Indices: 326899--326974 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
326889 CATCGATATG
* * *
326899 AATTTAAAAAAAAGAAGTGAAATAAAA
1 AATTGAAAAAAAACAAGTAAAATAAAA
* *
326926 AATTGAAAAGAAACAATTAAAATAAAA
1 AATTGAAAAAAAACAAGTAAAATAAAA
326953 AA-TGAAAACAAAA-AAGATAAAA
1 AATTGAAAA-AAAACAAG-TAAAA
326975 GAGGGAACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.20
27 32 0.80
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (27 bp):
AATTGAAAAAAAACAAGTAAAATAAAA
Found at i:326960 original size:13 final size:13
Alignment explanation
Indices: 326918--326967 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
326908 AAAAGAAGTG
326918 AAATAAAAAATTGA
1 AAATAAAAAA-TGA
* * *
326932 AAAGAAACAATTA
1 AAATAAAAAATGA
326945 AAATAAAAAATGA
1 AAATAAAAAATGA
*
326958 AAACAAAAAA
1 AAATAAAAAA
326968 GATAAAAGAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (13 bp):
AAATAAAAAATGA
Found at i:327131 original size:25 final size:25
Alignment explanation
Indices: 327103--327155 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
327093 GAGAAAAGAA
* *
327103 AAGAGAATAACAAATGTGAAACATT
1 AAGAGAATAACAAATATGAAAAATT
*
327128 AAGAGAATAATAAATATGAAAAATT
1 AAGAGAATAACAAATATGAAAAATT
327153 AAG
1 AAG
327156 GTTTGAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (25 bp):
AAGAGAATAACAAATATGAAAAATT
Found at i:327807 original size:16 final size:16
Alignment explanation
Indices: 327783--327817 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
327773 TCAATATAAT
*
327783 AAAGGGATAAATATTA
1 AAAGAGATAAATATTA
*
327799 AAAGAGATAAATTTTA
1 AAAGAGATAAATATTA
327815 AAA
1 AAA
327818 TTATACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (16 bp):
AAAGAGATAAATATTA
Found at i:328687 original size:20 final size:19
Alignment explanation
Indices: 328662--328701 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
328652 GAATTTTATA
328662 TTTTATTAAATTTTAATTTT
1 TTTTATT-AATTTTAATTTT
* *
328682 TTTTATTGATTTTTATTTT
1 TTTTATTAATTTTAATTTT
328701 T
1 T
328702 ATCATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATTAATTTTAATTTT
Found at i:329430 original size:24 final size:24
Alignment explanation
Indices: 329363--329432 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 24
329353 GATGGAAATT
* *
329363 AAATTATATATTTTTATGGTATTAA
1 AAATT-TATATTTTTATGATTTTAA
* *
329388 AAATATA-AATTTTA--ATTTTAA
1 AAATTTATATTTTTATGATTTTAA
*
329409 TAATTTATATTTTTATGATTTTAA
1 AAATTTATATTTTTATGATTTTAA
329433 GAGAATTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
23 6 0.17
24 9 0.26
25 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
AAATTTATATTTTTATGATTTTAA
Found at i:334338 original size:15 final size:17
Alignment explanation
Indices: 334303--334340 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
334293 GAATGAAAAG
*
334303 AAAATTGAAAGAGTAGA
1 AAAATAGAAAGAGTAGA
334320 AAAATAGAAAGA-T-GA
1 AAAATAGAAAGAGTAGA
334335 AAAATA
1 AAAATA
334341 CAATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (17 bp):
AAAATAGAAAGAGTAGA
Found at i:337663 original size:29 final size:28
Alignment explanation
Indices: 337625--337679 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
337615 GCGTACCAAA
*
337625 GGATTGGGACTTGGAAATTAGAATAAAAG
1 GGATTGGGACGTGGAAATTA-AATAAAAG
337654 GGATTGGGACGTGGAAATTAAATAAA
1 GGATTGGGACGTGGAAATTAAATAAA
337680 TGCTAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.42, C:0.04, G:0.31, T:0.24
Consensus pattern (28 bp):
GGATTGGGACGTGGAAATTAAATAAAAG
Found at i:339235 original size:76 final size:76
Alignment explanation
Indices: 339136--339286 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
339126 TGGTTCTCAC
339136 CATAAAGGATATCATTGTTTGTTACCAACTGGTAAAATTATAGTGTGTATTTGATGAGTTTAGGT
1 CATAAAGGATATCATTGTTTGTTACCAACTGGTAAAATTATAGTGTGTATTTGATGAGTTTAGGT
339201 TTCTGTTTCCT
66 TTCTGTTTCCT
339212 CATAAAGGATATCATTGTTTGTTACCAACTGGTAAAATTATAGTGTGTATTTGATGAGTTTAGGT
1 CATAAAGGATATCATTGTTTGTTACCAACTGGTAAAATTATAGTGTGTATTTGATGAGTTTAGGT
339277 TTCTGTTTCC
66 TTCTGTTTCC
339287 AAAGGAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (76 bp):
CATAAAGGATATCATTGTTTGTTACCAACTGGTAAAATTATAGTGTGTATTTGATGAGTTTAGGT
TTCTGTTTCCT
Found at i:340164 original size:20 final size:20
Alignment explanation
Indices: 340097--340166 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
340087 ATATAAAATA
* *
340097 TAAAATAAACTTAAAAACAT
1 TAAAACAAATTTAAAAACAT
*
340117 TAAAACAAACATTAAAAA-A-
1 TAAAACAAA-TTTAAAAACAT
340136 T-AAACAAATTTAAAATACAT
1 TAAAACAAATTTAAAA-ACAT
340156 TAAAA-AAATTT
1 TAAAACAAATTT
340167 TATATTAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
17 6 0.14
18 8 0.19
19 2 0.05
20 16 0.38
21 10 0.24
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAACAAATTTAAAAACAT
Found at i:340298 original size:21 final size:20
Alignment explanation
Indices: 340266--340309 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
340256 AAAATAGTAA
*
340266 AAACACATAAAAATAACATCC
1 AAACAC-TAAAAATAACAACC
340287 AAACAAC-AAAAATAACAACC
1 AAAC-ACTAAAAATAACAACC
340307 AAA
1 AAA
340310 ATAGCAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 15 0.71
21 4 0.19
22 2 0.10
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.09
Consensus pattern (20 bp):
AAACACTAAAAATAACAACC
Found at i:340305 original size:12 final size:12
Alignment explanation
Indices: 340288--340416 Score: 103
Period size: 12 Copynumber: 11.3 Consensus size: 12
340278 ATAACATCCA
340288 AACAACAAAAAT
1 AACAACAAAAAT
*
340300 AACAACCAAAAT
1 AACAACAAAAAT
* **
340312 AGCAGTAAAAAT
1 AACAACAAAAAT
*
340324 AACAGC-AAAAT
1 AACAACAAAAAT
*
340335 AACGAC--AAA-
1 AACAACAAAAAT
340344 AACAAC--AAA-
1 AACAACAAAAAT
*
340353 AACAACAAAAAC
1 AACAACAAAAAT
340365 AACAACAAAAAT
1 AACAACAAAAAT
**
340377 AACAGTAAAAAT
1 AACAACAAAAAT
*
340389 AGCAACAAAAA-
1 AACAACAAAAAT
340400 AAGCAACAAAAAT
1 AA-CAACAAAAAT
340413 AACA
1 AACA
340417 GTATCAAAAC
Statistics
Matches: 95, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
9 14 0.15
10 3 0.03
11 13 0.14
12 63 0.66
13 2 0.02
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:340344 original size:23 final size:22
Alignment explanation
Indices: 340292--340416 Score: 60
Period size: 23 Copynumber: 5.5 Consensus size: 22
340282 CATCCAAACA
*
340292 ACAAAAATAACAACCAAAATAGC
1 ACAAAAATAAC-ACCAAAATAAC
* *
340315 AGTAAAAATAACAGCAAAATAAC
1 A-CAAAAATAACACCAAAATAAC
* *
340338 GACAAAAACAACA--AAAA-CA-
1 -ACAAAAATAACACCAAAATAAC
* *
340357 ACAAAAACAACAACAAAAATAAC
1 ACAAAAATAAC-ACCAAAATAAC
* * * *
340380 AGTAAAAATAGCAACAAAAAAAGC
1 A-CAAAAATAACACCAAAATAA-C
340404 AACAAAAATAACA
1 -ACAAAAATAACA
340417 GTATCAAAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
18 11 0.14
19 1 0.01
20 1 0.01
21 8 0.10
22 1 0.01
23 27 0.35
24 27 0.35
25 1 0.01
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.07
Consensus pattern (22 bp):
ACAAAAATAACACCAAAATAAC
Found at i:340362 original size:65 final size:66
Alignment explanation
Indices: 340287--340416 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 66
340277 AATAACATCC
* * * * * *
340287 AAACAACAAAAATAACAACCAAAATAGCAGTAAAAATAACAGCAAAATAA-CGACAAAAACAACA
1 AAACAACAAAAACAACAACAAAAATAACAGTAAAAATAACAACAAAAAAAGCAACAAAAACAACA
340351 A
66 A
* *
340352 AAACAACAAAAACAACAACAAAAATAACAGTAAAAATAGCAACAAAAAAAGCAACAAAAATAACA
1 AAACAACAAAAACAACAACAAAAATAACAGTAAAAATAACAACAAAAAAAGCAACAAAAACAACA
340417 GTATCAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
65 44 0.79
66 12 0.21
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (66 bp):
AAACAACAAAAACAACAACAAAAATAACAGTAAAAATAACAACAAAAAAAGCAACAAAAACAACA
A
Found at i:340380 original size:9 final size:9
Alignment explanation
Indices: 340339--340369 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
340329 CAAAATAACG
340339 ACAAAAACA
1 ACAAAAACA
340348 ACAAAAACA
1 ACAAAAACA
340357 ACAAAAACA
1 ACAAAAACA
340366 ACAA
1 ACAA
340370 CAAAAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (9 bp):
ACAAAAACA
Found at i:340459 original size:34 final size:36
Alignment explanation
Indices: 340359--340471 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
340349 CAAAAACAAC
* * *
340359 AAAAACAACAACAAAAATAACAGTA--AAAATAGCAA
1 AAAAACAGCAACAAAAATAACAG-ACCAAAACAGTAA
* *
340394 CAAAAAAAGCAACAAAAATAACAGTATCAAAACAGTAA
1 -AAAAACAGCAACAAAAATAACAG-ACCAAAACAGTAA
*
340432 AAAAACAGCATC-AAAATAACA-ACCAAAACAGTAA
1 AAAAACAGCAACAAAAATAACAGACCAAAACAGTAA
340466 AAAAAC
1 AAAAAC
340472 CAAAACAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
34 18 0.26
36 32 0.47
37 10 0.15
38 8 0.12
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (36 bp):
AAAAACAGCAACAAAAATAACAGACCAAAACAGTAA
Found at i:340486 original size:16 final size:17
Alignment explanation
Indices: 340452--340487 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
340442 TCAAAATAAC
*
340452 AACCAAAACAGTAAAAA
1 AACCAAAACAATAAAAA
340469 AACCAAAACAATAAAAA
1 AACCAAAACAATAAAAA
340486 AA
1 AA
340488 TAACACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.17, G:0.03, T:0.06
Consensus pattern (17 bp):
AACCAAAACAATAAAAA
Found at i:340487 original size:51 final size:48
Alignment explanation
Indices: 340421--340553 Score: 142
Period size: 51 Copynumber: 2.7 Consensus size: 48
340411 ATAACAGTAT
* *
340421 CAAAACAGTAAAAAAACAGCATCAAAATAACAACCAAAACAGTAAA-AAAAC
1 CAAAACAGTAAAAAAA-AGCACCAAAATAACAA--AAAACA-AAAACAAAAC
* * *
340472 CAAAACAATAAAAAAATAACACCAAAATAGCAAAAAACAAAAACCAAAAC
1 CAAAACAGTAAAAAAA-AGCACCAAAATAACAAAAAACAAAAA-CAAAAC
* *
340522 CAAAACAGTAAAAAAAAGCACTAAAACAACAA
1 CAAAACAGTAAAAAAAAGCACCAAAATAACAA
340554 TATAATTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 3 0.04
49 18 0.26
50 20 0.29
51 28 0.41
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (48 bp):
CAAAACAGTAAAAAAAAGCACCAAAATAACAAAAAACAAAAACAAAAC
Found at i:340517 original size:22 final size:21
Alignment explanation
Indices: 340464--340521 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
340454 CCAAAACAGT
*
340464 AAAAAAACCAAAACAATAAAA
1 AAAAAAACCAAAACAACAAAA
* * *
340485 AAATAACACCAAAATAGCAAAA
1 AAA-AAAACCAAAACAACAAAA
340507 AACAAAAACCAAAAC
1 AA-AAAAACCAAAAC
340522 CAAAACAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.10
22 25 0.86
23 1 0.03
ACGTcount: A:0.74, C:0.19, G:0.02, T:0.05
Consensus pattern (21 bp):
AAAAAAACCAAAACAACAAAA
Found at i:346407 original size:39 final size:39
Alignment explanation
Indices: 346364--346440 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
346354 AAGTGATATT
*
346364 TAAATTCATTAATATTATAATATGTAAAATATATAAACA
1 TAAATTCATTAATATTATAATATATAAAATATATAAACA
* * *
346403 TAAATTTATTAATATTATACTATATGAAATATATAAAC
1 TAAATTCATTAATATTATAATATATAAAATATATAAAC
346441 TTTAAGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (39 bp):
TAAATTCATTAATATTATAATATATAAAATATATAAACA
Found at i:350285 original size:17 final size:16
Alignment explanation
Indices: 350265--350306 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
350255 TTTTTAATCC
350265 ATATATTTTAATTTTT
1 ATATATTTTAATTTTT
* *
350281 AATATAATTTGATTTTT
1 -ATATATTTTAATTTTT
350298 ATAT-TTTTA
1 ATATATTTTA
350307 TAACGTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 3 0.14
16 4 0.19
17 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
ATATATTTTAATTTTT
Found at i:351338 original size:21 final size:21
Alignment explanation
Indices: 351297--351337 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
351287 ATTCACTATC
*
351297 ATTATCATACTAATTTAAAAT
1 ATTATCATACTAATATAAAAT
*
351318 ATTATCAATATTAATATAAA
1 ATTATC-ATACTAATATAAA
351338 TTTAATGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTATCATACTAATATAAAAT
Found at i:357371 original size:10 final size:9
Alignment explanation
Indices: 357348--357403 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
357338 TATAAGAATA
357348 TTCTTTT-T
1 TTCTTTTAT
357356 TTCTTTTAT
1 TTCTTTTAT
357365 GTTCTTTTAAT
1 -TTCTTTT-AT
357376 TT-TTTT-T
1 TTCTTTTAT
357383 TTCTTTT-T
1 TTCTTTTAT
357391 TT-TTTTAT
1 TTCTTTTAT
357399 TTCTT
1 TTCTT
357404 CTACTTCTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.17
8 17 0.40
9 7 0.17
10 9 0.21
11 2 0.05
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (9 bp):
TTCTTTTAT
Found at i:370021 original size:6 final size:6
Alignment explanation
Indices: 370012--370073 Score: 115
Period size: 6 Copynumber: 10.3 Consensus size: 6
370002 CCTGATTCTG
370012 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
1 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
*
370060 ATACTA AAACTA AT
1 ATACTA ATACTA AT
370074 TTGACCACGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:378818 original size:38 final size:38
Alignment explanation
Indices: 378766--378851 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
378756 AAATTTAAAT
* *
378766 TTAAAAA-AATAATCTTATTTG-ATTCAAAATAAAATAA
1 TTAAAAATTATAATCTTATTTGCA-TCAAAATAAAAAAA
378803 TTAAAAATTATAATCTTATTTGCATCAAAATAAAAAAA
1 TTAAAAATTATAATCTTATTTGCATCAAAATAAAAAAA
*
378841 TAAAATAATTA
1 TTAAA-AATTA
378852 AATTAAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 7 0.16
38 30 0.70
39 6 0.14
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (38 bp):
TTAAAAATTATAATCTTATTTGCATCAAAATAAAAAAA
Found at i:386608 original size:95 final size:95
Alignment explanation
Indices: 386459--386656 Score: 292
Period size: 95 Copynumber: 2.1 Consensus size: 95
386449 TTTTTATCTA
* **
386459 TATTATTAATAAAACTCTTAATTGAATTGATGTCATGGGTTAATCAGAAATCACCTCGATTAAGA
1 TATTATTAATAAAACTCTTAATTGAATTGATGTCACGAATTAATCAGAAATCACCTCGATTAAGA
* *
386524 AATGACTAATATATCATTTTATTAAATGAT
66 AATGACTAATAAACCATTTTATTAAATGAT
*
386554 TATTATTAATAAAATTCTTAATTGAATTGATGTCACGAATTAA-CTA-AATATCACCTCGATTAA
1 TATTATTAATAAAACTCTTAATTGAATTGATGTCACGAATTAATC-AGAA-ATCACCTCGATTAA
*
386617 GAAATGACTAATAAACCATTTTATTGAATGAT
64 GAAATGACTAATAAACCATTTTATTAAATGAT
*
386649 TACTATTA
1 TATTATTA
386657 TTACTGAGGT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
94 3 0.03
95 90 0.97
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (95 bp):
TATTATTAATAAAACTCTTAATTGAATTGATGTCACGAATTAATCAGAAATCACCTCGATTAAGA
AATGACTAATAAACCATTTTATTAAATGAT
Found at i:394618 original size:17 final size:17
Alignment explanation
Indices: 394553--394629 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 17
394543 AACTTTTTTT
*
394553 TTTTTAATATTTTAGTAA
1 TTTTTAATATTTTTGT-A
394571 CTTTTT-ATATTTATATTGT-
1 -TTTTTAATA-TT-T-TTGTA
*
394590 TTTTTTAT-TTTTTGTA
1 TTTTTAATATTTTTGTA
*
394606 TTTTTAATATTTTTATA
1 TTTTTAATATTTTTGTA
*
394623 ATTTTAA
1 TTTTTAA
394630 ATACTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
15 4 0.08
16 8 0.17
17 15 0.31
18 8 0.17
19 9 0.19
20 1 0.02
21 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTAATATTTTTGTA
Found at i:394618 original size:18 final size:17
Alignment explanation
Indices: 394572--394619 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
394562 TTTTAGTAAC
394572 TTTTTATATTTATATTGT-
1 TTTTTATATTT-T-TTGTA
394590 TTTTT-TATTTTTTGTA
1 TTTTTATATTTTTTGTA
394606 TTTTTAATATTTTT
1 TTTTT-ATATTTTT
394620 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.15
16 6 0.22
17 5 0.19
18 12 0.44
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTATATTTTTTGTA
Found at i:394626 original size:18 final size:18
Alignment explanation
Indices: 394553--394638 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
394543 AACTTTTTTT
394553 TTTTTAATA-TTTTAGTAA
1 TTTTTAATATTTTTA-TAA
* **
394571 CTTTTT-ATATTTATATTG
1 -TTTTTAATATTTTTATAA
* *
394589 TTTTT-TTATTTTT-TGTA
1 TTTTTAATATTTTTAT-AA
394606 TTTTTAATATTTTTATAA
1 TTTTTAATATTTTTATAA
*
394624 TTTTAAATACTTTTT
1 TTTTTAATA-TTTTT
394639 TTGGAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.02
17 17 0.32
18 20 0.38
19 15 0.28
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTAATATTTTTATAA
Found at i:394627 original size:26 final size:26
Alignment explanation
Indices: 394538--394627 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
394528 TTAAATGTGA
*
394538 TTTATAACTTTTTTTTTTTTAATA-T
1 TTTATAACTTTTTTATTTTTAATATT
* * *
394563 TTTAGTAACTTTTTATATTTATATTGTT
1 TTTA-TAACTTTTT-TATTTTTAATATT
* *
394591 TTT-TTATTTTTTGTATTTTTAATATT
1 TTTATAACTTTTT-TATTTTTAATATT
394617 TTTATAA-TTTT
1 TTTATAACTTTT
394628 AAATACTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
25 4 0.08
26 33 0.66
27 9 0.18
28 4 0.08
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.71
Consensus pattern (26 bp):
TTTATAACTTTTTTATTTTTAATATT
Found at i:396089 original size:40 final size:40
Alignment explanation
Indices: 395972--396121 Score: 178
Period size: 41 Copynumber: 3.7 Consensus size: 40
395962 GTTTATGTCA
* * * * *
395972 AAGCGCCGCTAAAGGTCACAGTATTCGCGACGCTTTCCTAT
1 AAGCGCCGCTAAAGGTCA-GGCATTAGCGACACTTTCCCAT
*
396013 AAGCGCCGCTAAAGGTCAAGACATTAGCGACACTTTCCCAT
1 AAGCGCCGCTAAAGGTC-AGGCATTAGCGACACTTTCCCAT
396054 AAGCGCCGCTAAAGGTCAGGCATTAGC-AGCACTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGCATTAGCGA-CACTTTCCCAT
* *
396094 AAGCGTCGCTTAA-GTCAGGTCATTAGCG
1 AAGCGCCGCTAAAGGTCAGG-CATTAGCG
396122 GCGCTTTCGC
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 7 0.07
40 38 0.40
41 50 0.52
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
AAGCGCCGCTAAAGGTCAGGCATTAGCGACACTTTCCCAT
Found at i:396245 original size:41 final size:41
Alignment explanation
Indices: 396188--396329 Score: 189
Period size: 41 Copynumber: 3.5 Consensus size: 41
396178 CAGGGTATTA
* * **
396188 GCTAAAAGTCAGGGCATTAACGATGCTTTCCTATAAATGCC
1 GCTAAAGGTCAGGGCATTAGCGATGCTTTCCTATAAGCGCC
*
396229 GCTAAAGGTTAGGGCATTAGCGATGCTTTCCTATAAGCGCC
1 GCTAAAGGTCAGGGCATTAGCGATGCTTTCCTATAAGCGCC
* *
396270 GTTAAAGGTCAGGGCATTAGCGGCT-CTTTTCC-ATAAGCGCC
1 GCTAAAGGTCAGGGCATTAGC-GATGC-TTTCCTATAAGCGCC
396311 GCTAAAGGTCAGGGCATTA
1 GCTAAAGGTCAGGGCATTA
396330 CCGGCGCTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 83 0.92
42 7 0.08
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
GCTAAAGGTCAGGGCATTAGCGATGCTTTCCTATAAGCGCC
Found at i:397282 original size:17 final size:17
Alignment explanation
Indices: 397255--397294 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
397245 ATAAATTCTA
*
397255 AATAGACTAAATATAAAT
1 AATA-ACTAAATAAAAAT
397273 AATAACTAAATAAAAAT
1 AATAACTAAATAAAAAT
397290 AATAA
1 AATAA
397295 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAACTAAATAAAAAT
Done.