Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004446.1 Kokia drynarioides strain JFW-HI SEQ_117847, 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: 60887
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:489 original size:27 final size:26
Alignment explanation
Indices: 433--489 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
423 ATTGACCTAT
* * ** *
433 TGACCCGACTCGTTACTTTGACTTGT
1 TGACCAGAATCGTTACTTTGACCCGA
459 TGACCAGAATCGTTGACTTTGACCCGA
1 TGACCAGAATCGTT-ACTTTGACCCGA
486 TGAC
1 TGAC
490 TCGACCCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (26 bp):
TGACCAGAATCGTTACTTTGACCCGA
Found at i:1007 original size:464 final size:464
Alignment explanation
Indices: 139--1071 Score: 1812
Period size: 464 Copynumber: 2.0 Consensus size: 464
129 ATATTATGTC
139 TAAAATGGACATTTTATTTCTCAAAAGCACTTTTTGACAGCAATACCAAACACTCAAATATTAAA
1 TAAAATGGACATTTTATTTCTCAAAAGCACTTTTTGACAGCAATACCAAACACTCAAATATTAAA
* *
204 CAAAAGCACTTCTCAAAAGTCCTTTTCTACTGTACTTTTTAAAAACTCTTTTCAAAAGCAATGCT
66 CAAAAGCACTTCCCAAAAGTCCTTTTCTACCGTACTTTTTAAAAACTCTTTTCAAAAGCAATGCT
269 AAACTAGCCCAAAGGCCCAACCTTAGCAACCATTTTCAACTTTGGTTTAACCTAATTGTGCAAGC
131 AAACTAGCCCAAAGGCCCAACCTTAGCAACCATTTTCAACTTTGGTTTAACCTAATTGTGCAAGC
334 CCAATGCCCAAAACCACGACCCATTTGTGAACTTGAACCGAACCGGCCCAACTCAAACCGAACTT
196 CCAATGCCCAAAACCACGACCCATTTGTGAACTTGAACCGAACCGGCCCAACTCAAACCGAACTT
399 GACTTGTTGACTTTGACCATTAACATTGACCTATTGACCCGACTCGTTACTTTGACTTGTTGACC
261 GACTTGTTGACTTTGACCATTAACATTGACCTATTGACCCGACTCGTTACTTTGACTTGTTGACC
*
464 AGAATCGTTGACTTTGACCCGATGACTCGACCCATTAACTTTGATCGTACAGATTCTGAATCTAC
326 AGAATCGTTGACTTCGACCCGATGACTCGACCCATTAACTTTGATCGTACAGATTCTGAATCTAC
*
529 AGTCCGTTTCATCAAATTCTAACCCGAAAGCCCCGTTTTAGATATTTGCAATTATTTTTATATTC
391 AGTCCGTTTCATCAAATTCGAACCCGAAAGCCCCGTTTTAGATATTTGCAATTATTTTTATATTC
594 AGTAATTTT
456 AGTAATTTT
603 TAAAATGGACATTTTATTTCTCAAAAGCACTTTTTGACAGCAATACCAAACACTCAAATATTAAA
1 TAAAATGGACATTTTATTTCTCAAAAGCACTTTTTGACAGCAATACCAAACACTCAAATATTAAA
668 CAAAAGCACTTCCCAAAAGTCCTTTTCTACCGTACTTTTTAAAAACTCTTTTCAAAAGCAATGCT
66 CAAAAGCACTTCCCAAAAGTCCTTTTCTACCGTACTTTTTAAAAACTCTTTTCAAAAGCAATGCT
733 AAACTAGCCCAAAGGCCCAACCTTAGCAACCATTTTCAACTTTGGTTTAACCTAATTGTGCAAGC
131 AAACTAGCCCAAAGGCCCAACCTTAGCAACCATTTTCAACTTTGGTTTAACCTAATTGTGCAAGC
*
798 CCAATGCCCAAAACCACGACCCATTTGTGAACTTGAACCGAACCGGCCCAACTCAAATCGAACTT
196 CCAATGCCCAAAACCACGACCCATTTGTGAACTTGAACCGAACCGGCCCAACTCAAACCGAACTT
863 GACTTGTTGACTTTGACCATTAACATTGACCTATTGACCCGACTCGTTACTTTGACTTGTTGACC
261 GACTTGTTGACTTTGACCATTAACATTGACCTATTGACCCGACTCGTTACTTTGACTTGTTGACC
*
928 AGAATCGTTGACTTCGACCCGATGACTCGACCCATTAACTTTGATCGTACATATTCTGAATCTAC
326 AGAATCGTTGACTTCGACCCGATGACTCGACCCATTAACTTTGATCGTACAGATTCTGAATCTAC
993 AGTCCGTTTCATCAAATTCGAACCCGAAAGCCCCGTTTTAGATATTTGCAATTATTTTTATATTC
391 AGTCCGTTTCATCAAATTCGAACCCGAAAGCCCCGTTTTAGATATTTGCAATTATTTTTATATTC
1058 AGTAATTTT
456 AGTAATTTT
1067 TAAAA
1 TAAAA
1072 AAAGTGGATA
Statistics
Matches: 463, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
464 463 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (464 bp):
TAAAATGGACATTTTATTTCTCAAAAGCACTTTTTGACAGCAATACCAAACACTCAAATATTAAA
CAAAAGCACTTCCCAAAAGTCCTTTTCTACCGTACTTTTTAAAAACTCTTTTCAAAAGCAATGCT
AAACTAGCCCAAAGGCCCAACCTTAGCAACCATTTTCAACTTTGGTTTAACCTAATTGTGCAAGC
CCAATGCCCAAAACCACGACCCATTTGTGAACTTGAACCGAACCGGCCCAACTCAAACCGAACTT
GACTTGTTGACTTTGACCATTAACATTGACCTATTGACCCGACTCGTTACTTTGACTTGTTGACC
AGAATCGTTGACTTCGACCCGATGACTCGACCCATTAACTTTGATCGTACAGATTCTGAATCTAC
AGTCCGTTTCATCAAATTCGAACCCGAAAGCCCCGTTTTAGATATTTGCAATTATTTTTATATTC
AGTAATTTT
Found at i:1506 original size:22 final size:22
Alignment explanation
Indices: 1477--1534 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
1467 TTTTATATGG
*
1477 AATT-TTGAATTGAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
1498 AATTATTGAATTAAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
1520 AATTATTGAATTAAA
1 AATTATTGAATTAAA
1535 AGTTAGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
AATTATTGAATTAAAGAATTTT
Found at i:3522 original size:13 final size:13
Alignment explanation
Indices: 3504--3529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3494 GATATCGATC
3504 ATCGAAGTACAGT
1 ATCGAAGTACAGT
3517 ATCGAAGTACAGT
1 ATCGAAGTACAGT
3530 TCTGATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
ATCGAAGTACAGT
Found at i:8624 original size:21 final size:21
Alignment explanation
Indices: 8594--8647 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
8584 GATTTTGGTT
*
8594 GTATCAGTAGTTGCT-TATTAA
1 GTATCGGTAGTTG-TATATTAA
8615 GTATCGGTAGTTGTATATTAA
1 GTATCGGTAGTTGTATATTAA
*
8636 ATATCGGTAGTT
1 GTATCGGTAGTT
8648 CTGTCCGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (21 bp):
GTATCGGTAGTTGTATATTAA
Found at i:11233 original size:3 final size:3
Alignment explanation
Indices: 11225--11277 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
11215 TAAGTAGTGA
11225 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11273 AAT AA
1 AAT AA
11278 AACTTGTGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12435 original size:23 final size:23
Alignment explanation
Indices: 12397--12473 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
12387 ACATTAGCGC
12397 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCACTGTGTGT
* * *
12420 GCGTACTGATTCGCACTATATGT
1 GCTTACTGATTCGCACTGTGTGT
* *
12443 GCTTACTGATTTGCACTGTGTAT
1 GCTTACTGATTCGCACTGTGTGT
12466 GCTTACTG
1 GCTTACTG
12474 TTTCCCCAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (23 bp):
GCTTACTGATTCGCACTGTGTGT
Found at i:14709 original size:26 final size:27
Alignment explanation
Indices: 14680--14740 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
14670 ACTCGATTGG
*
14680 TTGACTTTGA-CCATTGACCCGACCTA
1 TTGACTTTGATCAATTGACCCGACCTA
**
14706 TTGACTTTGATCAATTGTTCCGACCTA
1 TTGACTTTGATCAATTGACCCGACCTA
14733 TTGACTTT
1 TTGACTTT
14741 CACTTTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (27 bp):
TTGACTTTGATCAATTGACCCGACCTA
Found at i:17796 original size:19 final size:20
Alignment explanation
Indices: 17772--17814 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
17762 AAATCAAATT
17772 ATATTAAA-TTAAAATGTAA
1 ATATTAAATTTAAAATGTAA
* *
17791 ATATTAAATTTCAAATTTAA
1 ATATTAAATTTAAAATGTAA
17811 ATAT
1 ATAT
17815 AATAGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATTAAATTTAAAATGTAA
Found at i:18720 original size:16 final size:16
Alignment explanation
Indices: 18696--18737 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
18686 TGAAACCACA
*
18696 TATATATATGTATATG
1 TATACATATGTATATG
18712 TATACATATGTATATG
1 TATACATATGTATATG
18728 TATACATATG
1 TATACATATG
18738 AATCCATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (16 bp):
TATACATATGTATATG
Found at i:21748 original size:95 final size:94
Alignment explanation
Indices: 21535--21738 Score: 225
Period size: 95 Copynumber: 2.1 Consensus size: 94
21525 AATCAAATAT
* * *
21535 ACATTAATTTAAATAATTTAACAATTGAAATTATTTCTTCACTCATGAAGGTTAATACAGTGGGG
1 ACATTTATATAAATAATTTAA-AATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGTGGGG
* * * ** * *
21600 GAGTTCTAATTACTTATTAAATTTCGAATAT
65 GAGGTCTAATGACTTATCAAA-TTAAAAAAA
*
21631 ACATTTATTTAAATAATTTAAAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGTGGGGG
1 ACATTTATATAAATAATTTAAAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGTGGGGG
*
21696 AGGGT-T-ATGGACTTCTCCAAA-TAAAAAAA
66 A-GGTCTAAT-GACTTAT-CAAATTAAAAAAA
*
21725 ATATTTATATAAAT
1 ACATTTATATAAAT
21739 GTAATTAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
94 18 0.19
95 50 0.54
96 25 0.27
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (94 bp):
ACATTTATATAAATAATTTAAAATTGAAATTATTTCTTCACTCATAAAGGTTAATACAGTGGGGG
AGGTCTAATGACTTATCAAATTAAAAAAA
Found at i:21843 original size:22 final size:22
Alignment explanation
Indices: 21818--21859 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21808 AAAATAAAAA
*
21818 TTAATATATGATAATTTTAATT
1 TTAATATATGATAAATTTAATT
*
21840 TTAATATTTGATAAATTTAA
1 TTAATATATGATAAATTTAA
21860 AACTCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAATATATGATAAATTTAATT
Found at i:22373 original size:30 final size:30
Alignment explanation
Indices: 22337--22401 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
22327 CAACTTAACA
* *
22337 AACAAATGTCTCTAAAATAGTAAAAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
*
22367 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
22397 AACAA
1 AACAA
22402 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAAAAAAATT
Found at i:25061 original size:6 final size:7
Alignment explanation
Indices: 25046--25071 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25036 AAAAATTATT
25046 AAAATAA
1 AAAATAA
25053 AAAATAA
1 AAAATAA
25060 AAAATAA
1 AAAATAA
25067 AAAAT
1 AAAAT
25072 TATATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:25080 original size:16 final size:16
Alignment explanation
Indices: 25034--25080 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
25024 AAGAAGATTG
25034 TAAAAAATTAT-TAAAA
1 TAAAAAATTATAT-AAA
*
25050 TAAAAAA-TA-AAAAA
1 TAAAAAATTATATAAA
25064 TAAAAAATTATATAAA
1 TAAAAAATTATATAAA
25080 T
1 T
25081 TATATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.38
15 4 0.15
16 12 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAAATTATATAAA
Found at i:25183 original size:24 final size:23
Alignment explanation
Indices: 25142--25192 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
25132 GAAAAATATT
*
25142 AATAAATTAACAAAATATTATAAA
1 AATAAATTAACAAAATATGA-AAA
*
25166 AATAAATT-CCAAATATATGAAAA
1 AATAAATTAACAAA-ATATGAAAA
25189 AATA
1 AATA
25193 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAATTAACAAAATATGAAAA
Found at i:29330 original size:59 final size:59
Alignment explanation
Indices: 29191--29323 Score: 180
Period size: 59 Copynumber: 2.3 Consensus size: 59
29181 TGTGTGTTTG
* *
29191 GCTCGTGTGACCACTACACCTTAAATAGCAAAACAATATCCACACACAGTCTGGCACAC
1 GCTCGTGTGACCACTACACCTTAAATAGCAAAACAATAGCCACACACAGTCTGACACAC
* * * *
29250 G-TCTGTGTGTCCACTACACCTTAATTCAG-AAAACAGTAGCCACACACGGTCTGACACAC
1 GCTC-GTGTGACCACTACACCTTAAAT-AGCAAAACAATAGCCACACACAGTCTGACACAC
29309 GCTCGTGTGACCACT
1 GCTCGTGTGACCACT
29324 GTACCTTGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 2 0.03
59 58 0.91
60 4 0.06
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.21
Consensus pattern (59 bp):
GCTCGTGTGACCACTACACCTTAAATAGCAAAACAATAGCCACACACAGTCTGACACAC
Found at i:42404 original size:26 final size:26
Alignment explanation
Indices: 42375--42443 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
42365 TAAACAACAA
* *
42375 TTTTCAAAATAATTTTTCATAAGCACT
1 TTTTCAAAACAATTTTT-AAAAGCACT
**
42402 TTTTCCTAACAATTTTTAAAAGCAC-
1 TTTTCAAAACAATTTTTAAAAGCACT
*
42427 TTTTCAAAAGAATTTTT
1 TTTTCAAAACAATTTTT
42444 TTTTTTTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
25 14 0.40
26 7 0.20
27 14 0.40
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.45
Consensus pattern (26 bp):
TTTTCAAAACAATTTTTAAAAGCACT
Found at i:42443 original size:13 final size:13
Alignment explanation
Indices: 42375--42443 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
42365 TAAACAACAA
*
42375 TTTTCAAAATAAT
1 TTTTCAAAAGAAT
* *
42388 TTTTCATAAGCACT
1 TTTTCAAAAG-AAT
** *
42402 TTTTCCTAACAAT
1 TTTTCAAAAGAAT
* *
42415 TTTT-AAAAGCAC
1 TTTTCAAAAGAAT
42427 TTTTCAAAAGAAT
1 TTTTCAAAAGAAT
42440 TTTT
1 TTTT
42444 TTTTTTTTGT
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
12 7 0.17
13 24 0.59
14 10 0.24
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.45
Consensus pattern (13 bp):
TTTTCAAAAGAAT
Found at i:42444 original size:26 final size:27
Alignment explanation
Indices: 42375--42444 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 27
42365 TAAACAACAA
* * *
42375 TTTTCAAAATAATTTTTCATAAGCACT
1 TTTTCAAAACAATTTTTTAAAAGCACT
**
42402 TTTTCCTAACAA-TTTTTAAAAGCAC-
1 TTTTCAAAACAATTTTTTAAAAGCACT
*
42427 TTTTCAAAAGAATTTTTT
1 TTTTCAAAACAATTTTTT
42445 TTTTTTTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 9 0.26
26 16 0.47
27 9 0.26
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTTCAAAACAATTTTTTAAAAGCACT
Found at i:43326 original size:16 final size:16
Alignment explanation
Indices: 43305--43335 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43295 ATGAAGCCAT
43305 AGTAAGAGTGTAAGAA
1 AGTAAGAGTGTAAGAA
43321 AGTAAGAGTGTAAGA
1 AGTAAGAGTGTAAGA
43336 CAATTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (16 bp):
AGTAAGAGTGTAAGAA
Found at i:49302 original size:24 final size:24
Alignment explanation
Indices: 49281--49329 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
49271 ACCAAAAAGC
49281 AGAAGCAA-TATTTGAGAGAAAACA
1 AGAA-CAAGTATTTGAGAGAAAACA
* *
49305 AGAACAAGTTTTTGAGAGAGAACA
1 AGAACAAGTATTTGAGAGAAAACA
49329 A
1 A
49330 AACTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.18
Consensus pattern (24 bp):
AGAACAAGTATTTGAGAGAAAACA
Found at i:49515 original size:455 final size:455
Alignment explanation
Indices: 48664--49576 Score: 1709
Period size: 455 Copynumber: 2.0 Consensus size: 455
48654 AACCCTTTAA
*
48664 GGCCTATATAAACAGTCTTTTTAAGACAGATTCACCCTCTCCTAGGTGTTAAATAATTTTTGGAC
1 GGCCTATATAAACAGTCTCTTTAAGACAGATTCACCCTCTCCTAGGTGTTAAATAATTTTTGGAC
48729 GTCTATCTCCCAGGATACAACAATAATCAATTACCAAAAGTAGCACAAAATTTGTAACAGGAGAA
66 GTCTATCTCCCAGGATACAACAATAATCAATTACCAAAAGTAGCACAAAATTTGTAACAGGAGAA
48794 TGCTAACCAAGCATCTTTTATCACCAAAAAGCAAAAGCAATATTTGAGAGAAAACAAGAACAAGT
131 TGCTAACCAAGCATCTTTTATCACCAAAAAGCAAAAGCAATATTTGAGAGAAAACAAGAACAAGT
48859 TTTTGAGAGAAAACAAAACTTGTTTCTTTTACTCTTGATATGTAAAATGAAATGAAAAGTGAGCT
196 TTTTGAGAGAAAACAAAACTTGTTTCTTTTACTCTTGATATGTAAAATGAAATGAAAAGTGAGCT
*
48924 ATTTATAGTGAAAATTTCATTAAACAGTTTCATTTAATTTAAAACAAAACATTATGAATGGAGAG
261 ATTTATAGTGAAAATTTCATGAAACAGTTTCATTTAATTTAAAACAAAACATTATGAATGGAGAG
48989 TTACAAAATAATGTTTGGTAAGTTATAAAAATGGTGAGTTACAAAAAATTAAAACAAAATAAAGC
326 TTACAAAATAATGTTTGGTAAGTTATAAAAATGGTGAGTTACAAAAAATTAAAACAAAATAAAGC
*
49054 TATAGTAACTGCCTTTGGAAGGCCAAAGGACAGTTCTGTGTTGAAAAGAAAAAAATATTTAAAAG
391 TATAGTAACTGCCTTTGGAAGGCCAAAGGACAGTTCTGTGTAGAAAAGAAAAAAATATTTAAAAG
* *
49119 GGCCTATATAAACAGTCTCTTTAAGACAGGTTCACCCTCTCTTAGGTGTTAAATAATTTTTGGAC
1 GGCCTATATAAACAGTCTCTTTAAGACAGATTCACCCTCTCCTAGGTGTTAAATAATTTTTGGAC
49184 GTCTATCTCCCAGGATACAACAATAATCAATTACCAAAAGTAGCACAAAATTTGTAACAGGAGAA
66 GTCTATCTCCCAGGATACAACAATAATCAATTACCAAAAGTAGCACAAAATTTGTAACAGGAGAA
* *
49249 TGCTAACCAAGCCTCTTTTATCACCAAAAAGCAGAAGCAATATTTGAGAGAAAACAAGAACAAGT
131 TGCTAACCAAGCATCTTTTATCACCAAAAAGCAAAAGCAATATTTGAGAGAAAACAAGAACAAGT
*
49314 TTTTGAGAGAGAACAAAACTTGTTTCTTTTACTCTTGATATGTAAAATGAAATGAAAAGTGAGCT
196 TTTTGAGAGAAAACAAAACTTGTTTCTTTTACTCTTGATATGTAAAATGAAATGAAAAGTGAGCT
* *
49379 ATTTATAGTGAAATTTTCATGAAACAGTTTCATTTAATTTAAAACAAAACATTATGATTGGAGAG
261 ATTTATAGTGAAAATTTCATGAAACAGTTTCATTTAATTTAAAACAAAACATTATGAATGGAGAG
*
49444 TTACAAAATAATGTTTGGTAAGTTATAAAAATGGTGAGTTACAAAAAATTAAAATAAAATAAAGC
326 TTACAAAATAATGTTTGGTAAGTTATAAAAATGGTGAGTTACAAAAAATTAAAACAAAATAAAGC
* *
49509 TATAGTAACTGCCTTTGGAAGGTCAAAGGACAGTTCTGTGTAGAAAAGAAAAAAATATTTAAATG
391 TATAGTAACTGCCTTTGGAAGGCCAAAGGACAGTTCTGTGTAGAAAAGAAAAAAATATTTAAAAG
49574 GGC
1 GGC
49577 TACAAATTTT
Statistics
Matches: 445, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
455 445 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (455 bp):
GGCCTATATAAACAGTCTCTTTAAGACAGATTCACCCTCTCCTAGGTGTTAAATAATTTTTGGAC
GTCTATCTCCCAGGATACAACAATAATCAATTACCAAAAGTAGCACAAAATTTGTAACAGGAGAA
TGCTAACCAAGCATCTTTTATCACCAAAAAGCAAAAGCAATATTTGAGAGAAAACAAGAACAAGT
TTTTGAGAGAAAACAAAACTTGTTTCTTTTACTCTTGATATGTAAAATGAAATGAAAAGTGAGCT
ATTTATAGTGAAAATTTCATGAAACAGTTTCATTTAATTTAAAACAAAACATTATGAATGGAGAG
TTACAAAATAATGTTTGGTAAGTTATAAAAATGGTGAGTTACAAAAAATTAAAACAAAATAAAGC
TATAGTAACTGCCTTTGGAAGGCCAAAGGACAGTTCTGTGTAGAAAAGAAAAAAATATTTAAAAG
Found at i:51453 original size:26 final size:26
Alignment explanation
Indices: 51416--51524 Score: 96
Period size: 26 Copynumber: 4.2 Consensus size: 26
51406 AGATCATACG
*
51416 AGCCGAGT-CAGTAAATCGCTCTTACA
1 AGCC-AGTACAGTATATCGCTCTTACA
* *
51442 AGCCAGTACAGTATGTCGCTTTTACA
1 AGCCAGTACAGTATATCGCTCTTACA
* * * *
51468 AGCTAATACAATATGTCGCTCTTACGA
1 AGCCAGTACAGTATATCGCTCTTAC-A
** *
51495 A-CCAGTGTAGTATATTGCTCTTACA
1 AGCCAGTACAGTATATCGCTCTTACA
51520 AGCCA
1 AGCCA
51525 ATATCGCTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
25 5 0.08
26 59 0.89
27 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (26 bp):
AGCCAGTACAGTATATCGCTCTTACA
Found at i:51577 original size:18 final size:18
Alignment explanation
Indices: 51538--51598 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
51528 TCGCTTTTAC
* *
51538 GAGCCAATATTGTTCCAAT
1 GAGCCAATA-TGCTCAAAT
*
51557 GAGCCAATATGCTCGAAT
1 GAGCCAATATGCTCAAAT
* *
51575 GAGCCAGTATGCTCAAAC
1 GAGCCAATATGCTCAAAT
51593 GAGCCA
1 GAGCCA
51599 GTAATGCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 28 0.76
19 9 0.24
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (18 bp):
GAGCCAATATGCTCAAAT
Found at i:51599 original size:18 final size:18
Alignment explanation
Indices: 51557--51606 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
51547 TTGTTCCAAT
* * *
51557 GAGCCAATATGCTCGAAT
1 GAGCCAGTATGCTCAAAC
51575 GAGCCAGTATGCTCAAAC
1 GAGCCAGTATGCTCAAAC
51593 GAGCCAGTAATGCT
1 GAGCCAGT-ATGCT
51607 ATTCCTTCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (18 bp):
GAGCCAGTATGCTCAAAC
Found at i:57022 original size:3 final size:3
Alignment explanation
Indices: 57014--57038 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57004 AGAGAGAGAG
57014 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
57039 TCATCCGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Done.