Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015269.1 Kokia drynarioides strain JFW-HI SEQ_130314, 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: 664642
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 122 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:571339 original size:10 final size:10
Alignment explanation
Indices: 571324--571356 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
571314 AAATAATTTT
571324 AAAATTATAA
1 AAAATTATAA
571334 AAAATT-TAAA
1 AAAATTAT-AA
571344 AAAATTATAA
1 AAAATTATAA
571354 AAA
1 AAA
571357 TTCAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTATAA
Found at i:572755 original size:20 final size:21
Alignment explanation
Indices: 572730--572774 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
572720 TATTCACTAA
572730 TTAATT-TT-ATAATAGATATT
1 TTAATTCTTGATAATA-ATATT
572750 TTAATTCCTTGATAATAATATT
1 TTAATT-CTTGATAATAATATT
572772 TTA
1 TTA
572775 TTTCAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
TTAATTCTTGATAATAATATT
Found at i:573593 original size:19 final size:20
Alignment explanation
Indices: 573571--573610 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
573561 AATATTTACT
573571 TTAATAT-TATCTATTAAAA
1 TTAATATATATCTATTAAAA
*
573590 TTAATATAATATCTCTTAAAA
1 TTAATAT-ATATCTATTAAAA
573611 ACTCAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATATATATCTATTAAAA
Found at i:580775 original size:13 final size:13
Alignment explanation
Indices: 580757--580781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580747 GAAGATGGAA
580757 GTTTTTTGTTTTT
1 GTTTTTTGTTTTT
580770 GTTTTTTGTTTT
1 GTTTTTTGTTTT
580782 GCGAAATGTT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
GTTTTTTGTTTTT
Found at i:593697 original size:15 final size:15
Alignment explanation
Indices: 593675--593708 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
593665 TTTTCACAAT
*
593675 TTATTTTTATTTTCTA
1 TTATTTTAATTTT-TA
593691 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
593706 TTA
1 TTA
593709 AAAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTAATTTTTA
Found at i:594294 original size:32 final size:32
Alignment explanation
Indices: 594255--594319 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
594245 GTACATTATT
*
594255 AAAACTAATCCAATTGTTGATAAAAACATATA
1 AAAACTAATACAATTGTTGATAAAAACATATA
594287 AAAACTAATACAATTGTTGATAAAAACATATA
1 AAAACTAATACAATTGTTGATAAAAACATATA
594319 A
1 A
594320 GCTTGAACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (32 bp):
AAAACTAATACAATTGTTGATAAAAACATATA
Found at i:594997 original size:26 final size:27
Alignment explanation
Indices: 594968--595025 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
594958 AAATTGAAAA
* *
594968 TAATCATTACCTAT-AAAAATTTAGGG
1 TAATCATTAACTATAAAAAAGTTAGGG
594994 TAAT--TTAACTATAAAAAAGTTAGGG
1 TAATCATTAACTATAAAAAAGTTAGGG
595019 TGAATCA
1 T-AATCA
595026 CCCCATTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
24 7 0.27
25 12 0.46
26 7 0.27
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (27 bp):
TAATCATTAACTATAAAAAAGTTAGGG
Found at i:597427 original size:24 final size:24
Alignment explanation
Indices: 597399--597445 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
597389 AACAAATATA
597399 CTAATAAATG-TCAAATATATTATG
1 CTAATAAATGCT-AAATATATTATG
597423 CTAATAAATGCTAAATATATTAT
1 CTAATAAATGCTAAATATATTAT
597446 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATG
Found at i:597455 original size:24 final size:24
Alignment explanation
Indices: 597411--597462 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
597401 AATAAATGTC
* * *
597411 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAAAAAATACT
*
597435 AAATATATTATATTAAAAAATACT
1 AAATATATTATACTAAAAAATACT
597459 AAAT
1 AAAT
597463 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAAAAAATACT
Found at i:602352 original size:18 final size:18
Alignment explanation
Indices: 602329--602369 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
602319 CTCCTCGGCT
602329 CCCGAGA-CCGCTCCTCTA
1 CCCGAGATCC-CTCCTCTA
*
602347 CCCGAGATCCCTCCTCTT
1 CCCGAGATCCCTCCTCTA
602365 CCCGA
1 CCCGA
602370 AGCACTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.15, C:0.51, G:0.15, T:0.20
Consensus pattern (18 bp):
CCCGAGATCCCTCCTCTA
Found at i:602786 original size:2 final size:2
Alignment explanation
Indices: 602779--602805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
602769 AAATAAATAA
602779 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
602806 AACAAAGAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:603831 original size:29 final size:29
Alignment explanation
Indices: 603739--603832 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 29
603729 TGTTTTGTTC
* * *
603739 AAAAATTATATTTAAACCCCTAAACTTTT
1 AAAAATCACATTTTAACCCCTAAACTTTT
* * **
603768 CAAAAATGATATTTTAACCCCTAATTTTTT
1 -AAAAATCACATTTTAACCCCTAAACTTTT
* *
603798 TAAAATCACATTTTTA-CCCTAAACTTTCT
1 AAAAATCACATTTTAACCCCTAAACTTT-T
603827 AAAAAT
1 AAAAAT
603833 TTATTTTCCT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
28 9 0.17
29 18 0.35
30 25 0.48
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.39
Consensus pattern (29 bp):
AAAAATCACATTTTAACCCCTAAACTTTT
Found at i:624611 original size:29 final size:28
Alignment explanation
Indices: 624542--624611 Score: 63
Period size: 29 Copynumber: 2.4 Consensus size: 28
624532 CTCGGGGAGC
** *
624542 AAATGGTAATTTTGGATTTTTGGGG--CA
1 AAATGG-AATTTTGGAAGTTTGGGGTTAA
624569 AAATGGTAATTTTTGGAAAGTTTGGGGTTAA
1 AAATGG-AA-TTTTGG-AAGTTTGGGGTTAA
624600 AAATGGAATTTT
1 AAATGGAATTTT
624612 TAGACATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.25
28 6 0.17
29 12 0.33
30 2 0.06
31 7 0.19
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.40
Consensus pattern (28 bp):
AAATGGAATTTTGGAAGTTTGGGGTTAA
Found at i:624612 original size:30 final size:29
Alignment explanation
Indices: 624568--625020 Score: 315
Period size: 29 Copynumber: 15.4 Consensus size: 29
624558 TTTTTGGGGC
624568 AAAATGGTAATTTTTGGAAAGTTTGGGGTTA
1 AAAATGG-AATTTTTGG-AAGTTTGGGGTTA
* *
624599 AAAATGGAATTTTTAGACA-TTATAGGG--A
1 AAAATGGAATTTTTGGA-AGTT-TGGGGTTA
* * * * **
624627 AAAAGGGTAA-ATTT-GAGAGTTCCGAGGTCG
1 AAAATGG-AATTTTTGGA-AGTT-TGGGGTTA
* *
624657 AAAATGGAGTTTTTGGACA-TCTGGGCG-T-
1 AAAATGGAATTTTTGGA-AGTTTGGG-GTTA
* * *
624685 AAAATGGTAATTTTTGAAAGTTTCGGGATCA
1 AAAATGG-AATTTTTGGAAGTTT-GGGGTTA
* * **
624716 AAAATGGAAATTTTGGAGGTTCAAGGG-TA
1 AAAATGGAATTTTTGGAAGTT-TGGGGTTA
* *
624745 AATATGGAATTTTTGGAAGTTTCGAGGTT-
1 AAAATGGAATTTTTGGAAGTTT-GGGGTTA
*
624774 AAAATGGAATTTTTGGAAGTTCGAGGG-T-
1 AAAATGGAATTTTTGGAAGTTTG-GGGTTA
* * *
624802 AAAATAGAATTTTTAGAAGTTTGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTGGGGTTA
* *
624831 AAAATAGAATTTTTGGAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTTA
* *
624860 AAAATGGAATTGTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGTTA
624890 AAAATGGAATTTTTGGAAGTTTGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTTA
* *
624919 AAAATGGAATTTTTGTAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGTTA
**
624949 AAAATGGAATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAATTTTTGGAAG-TTTGGGGTTA
* *
624979 AAAATGGAATTTTTGAAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTTA
*
625008 AAAATGTAATTTT
1 AAAATGGAATTTT
625021 CAAAAAATTT
Statistics
Matches: 334, Mismatches: 61, Indels: 56
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.01
28 45 0.13
29 145 0.43
30 122 0.37
31 17 0.05
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTTA
Found at i:624730 original size:59 final size:56
Alignment explanation
Indices: 624542--625020 Score: 355
Period size: 59 Copynumber: 8.2 Consensus size: 56
624532 CTCGGGGAGC
** * * *
624542 AAATGGTAA-TTTTGGATTTTTGGGGCAAAATGGTAATTTTTGGAAAGTTTGGGGTTAA
1 AAATGG-AATTTTTGGAAGTTTGGGGTAAAATGG-AATTTTT-GAAAGTTTCGGGTCAA
* * * * * * * *
624600 AAATGGAATTTTTAGACA-TTATAGGGAAAAAGGGTAA-ATTTGAGAGTTCCGAGGTCGA
1 AAATGGAATTTTTGGA-AGTT-TGGGGTAAAATGG-AATTTTTGAAAGTTTCG-GGTCAA
* *
624658 AAATGGAGTTTTTGGACA-TCTGGGCGTAAAATGGTAATTTTTGAAAGTTTCGGGATCAA
1 AAATGGAATTTTTGGA-AGTTTGGG-GTAAAATGG-AATTTTTGAAAGTTTCGGG-TCAA
* * ** * *
624717 AAATGGAAATTTTGGAGGTTCAAGGGTAAATATGGAATTTTTGGAAGTTTCGAGGT-TA
1 AAATGGAATTTTTGGAAGTT-TGGGGTAAA-ATGGAATTTTTGAAAGTTTCG-GGTCAA
* * *
624775 AAATGGAATTTTTGGAAGTTCGAGGGTAAAATAGAATTTTT-AGAAGTTT-GAGGTTAA
1 AAATGGAATTTTTGGAAGTTTG-GGGTAAAATGGAATTTTTGA-AAGTTTCG-GGTCAA
* * * * *
624832 AAATAGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTGTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTG-GGGT-AAAATGGAATTTTTGAAAG-TTTCGGGTCAA
* *
624891 AAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGTAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTG-GGGT-AAAATGGAATTTTTGAAAG-TTTCGGGTCAA
624950 AAATGGAATTTTTGGAAGTTTTGGGGTCGAAAATGGAATTTTTGAAAG-TTCGAGGGT-AA
1 AAATGGAATTTTTGGAAG-TTTGGGGT--AAAATGGAATTTTTGAAAGTTTC--GGGTCAA
*
625009 AAATGTAATTTT
1 AAATGGAATTTT
625021 CAAAAAATTT
Statistics
Matches: 350, Mismatches: 49, Indels: 43
0.79 0.11 0.10
Matches are distributed among these distances:
56 5 0.01
57 55 0.16
58 93 0.27
59 162 0.46
60 35 0.10
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (56 bp):
AAATGGAATTTTTGGAAGTTTGGGGTAAAATGGAATTTTTGAAAGTTTCGGGTCAA
Found at i:624753 original size:29 final size:29
Alignment explanation
Indices: 624685--625020 Score: 351
Period size: 29 Copynumber: 11.4 Consensus size: 29
624675 ATCTGGGCGT
* *
624685 AAAATGGTAATTTTTGAAAGTTTCG-GGATCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
* * *
624716 AAAATGGAAATTTTGGAGGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
624745 AATATGGAATTTTTGGAAGTTTCGA-GGTT
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
624774 AAAATGGAATTTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * * *
624802 AAAATAGAATTTTTAGAAGTTTGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
624831 AAAATAGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
624860 AAAATGGAATTGTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
624890 AAAATGGAATTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
624919 AAAATGGAATTTTTGTAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
624949 AAAATGGAATTTTTGGAAGTTTTG-GGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
624979 AAAATGGAATTTTTGAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
625008 AAAATGTAATTTT
1 AAAATGGAATTTT
625021 CAAAAAATTT
Statistics
Matches: 266, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
28 29 0.11
29 133 0.50
30 97 0.36
31 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:625762 original size:25 final size:24
Alignment explanation
Indices: 625717--625763 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
625707 TGCCAGAAGG
*
625717 TAAAAACTGCTTTTTTTTTTCTTT
1 TAAAAACTCCTTTTTTTTTTCTTT
625741 TAAAAAC-CCTTTTATTTCTTTCT
1 TAAAAACTCCTTTT-TTT-TTTCT
625764 CTTTTGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.57
Consensus pattern (24 bp):
TAAAAACTCCTTTTTTTTTTCTTT
Found at i:626921 original size:16 final size:16
Alignment explanation
Indices: 626902--626954 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
626892 TTTTTTGGAC
* *
626902 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
626918 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
626935 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
626952 TTT
1 TTT
626955 AAAGCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:626938 original size:17 final size:17
Alignment explanation
Indices: 626922--627056 Score: 144
Period size: 17 Copynumber: 7.6 Consensus size: 17
626912 ATTAAGTTTT
* *
626922 AAATCAATTTAAATTTT
1 AAATAAATTTAAATTTA
*
626939 AATTAAATTTAAATTTA
1 AAATAAATTTAAATTTA
**
626956 AAGCAAATTTAAATTTAAA
1 AAATAAATTTAAATTT--A
*
626975 AAACAAATTTAAATTTAAA
1 AAATAAATTTAAATTT--A
626994 AAATAAATTTAAATTTAAA
1 AAATAAATTTAAATTT--A
627013 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTTA
*
627030 AAATAAATTTAAATTAA
1 AAATAAATTTAAATTTA
*
627047 AAATACATTT
1 AAATAAATTT
627057 GAATCAATTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
17 54 0.50
19 53 0.50
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:626939 original size:33 final size:34
Alignment explanation
Indices: 626927--627044 Score: 65
Period size: 38 Copynumber: 3.3 Consensus size: 34
626917 GTTTTAAATC
* ** * **
626927 AATTTAAATTTTAATTAAATTTAAATTTAAAGCA
1 AATTTAAATTTAAAGCAAATTTAAATTTTAATTA
* * *
626961 AATTTAAATTTAAAAAACAAATTTAAATTTAAAAAATA
1 AATTTAAATTT--AAAGCAAATTTAAATTT--TAATTA
** * *
626999 AATTTAAATTTAAAAAATAAATTTAAATTTAAAATA
1 AATTTAAATTT--AAAGCAAATTTAAATTTTAATTA
627035 AATTTAAATT
1 AATTTAAATT
627045 AAAAATACAT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
34 11 0.15
36 30 0.41
38 33 0.45
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (34 bp):
AATTTAAATTTAAAGCAAATTTAAATTTTAATTA
Found at i:626942 original size:6 final size:6
Alignment explanation
Indices: 626927--627044 Score: 89
Period size: 6 Copynumber: 19.7 Consensus size: 6
626917 GTTTTAAATC
* **
626927 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
*** ** **
626974 AAAACA AATTTA AATTTAA AAAATA AATTTA AATTTAA AAAATA AATTTA
1 AATTTA AATTTA AATTT-A AATTTA AATTTA AATTT-A AATTTA AATTTA
*
627024 AATTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATT
627045 AAAAATACAT
Statistics
Matches: 84, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
5 11 0.13
6 62 0.74
7 11 0.13
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:626946 original size:11 final size:11
Alignment explanation
Indices: 626930--627047 Score: 57
Period size: 11 Copynumber: 10.5 Consensus size: 11
626920 TTAAATCAAT
*
626930 TTAAATTTTAA
1 TTAAATTTAAA
626941 TTAAATTTAAA
1 TTAAATTTAAA
**
626952 TTTAAA-GCAAA
1 -TTAAATTTAAA
626963 TTTAAATTTAAA
1 -TTAAATTTAAA
*
626975 --AAA--CAAA
1 TTAAATTTAAA
626982 TTTAAATTTAAAAA
1 -TTAAATTT--AAA
*
626996 ATAAATTTAAA
1 TTAAATTTAAA
**
627007 TTTAAAAAATAAA
1 -TT-AAATTTAAA
627020 TTTAAATTTAAA
1 -TTAAATTTAAA
*
627032 ATAAATTTAAA
1 TTAAATTTAAA
627043 TTAAA
1 TTAAA
627048 AATACATTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
7 3 0.04
9 3 0.04
10 3 0.04
11 36 0.44
12 16 0.20
13 17 0.21
14 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:626983 original size:19 final size:19
Alignment explanation
Indices: 626942--627049 Score: 154
Period size: 19 Copynumber: 5.9 Consensus size: 19
626932 AAATTTTAAT
*
626942 TAAATTTAAATTT--AAAG
1 TAAATTTAAATTTAAAAAA
*
626959 CAAATTTAAATTTAAAAAA
1 TAAATTTAAATTTAAAAAA
*
626978 CAAATTTAAATTTAAAAAA
1 TAAATTTAAATTTAAAAAA
626997 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTTAAAAAA
627016 TAAATTTAAATTT--AAAA
1 TAAATTTAAATTTAAAAAA
627033 TAAATTTAAA-TTAAAAA
1 TAAATTTAAATTTAAAAA
627050 TACATTTGAA
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
16 2 0.02
17 26 0.31
18 3 0.04
19 53 0.63
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (19 bp):
TAAATTTAAATTTAAAAAA
Found at i:627786 original size:158 final size:158
Alignment explanation
Indices: 627574--627914 Score: 423
Period size: 158 Copynumber: 2.2 Consensus size: 158
627564 CTTCGACCTG
**
627574 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCTAGCGTGAGTTTGTTT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCTAGCGTGAGTTTAATT
* * * *
627639 TGGTATTCTTCTCAATTTTTCATCAAGAAGATGATCGTATCCCTTACTTCAATCCGCTTCTCTGT
66 TGGTATTCTTCTCAATATCTCATCAAGAAGATGACCGCATCCCTTACTTCAATCCGCTTCTCTGT
627704 ATCTCATCAGGAAGACGAATTTGGTCCA
131 ATCTCATCAGGAAGACGAATTTGGTCCA
* * * ** * * *
627732 CTTCTCGGTATCTCATCAGGAAGTTGGGGTTTGAAGATTTTTTCGCGT-TGAGCGTGGGTTTAAT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCT-AGCGTGAGTTTAAT
* * *** * * ** *
627796 TTGGTCTTCTTCTCAGTATCTCATTGGGAAGGTGACCGCATCGCTTGTTTCAATCCGCTTCTTTG
65 TTGGTATTCTTCTCAATATCTCATCAAGAAGATGACCGCATCCCTTACTTCAATCCGCTTCTCTG
*
627861 TATCTCATCAGGAAGACGAATTTGGTTCA
130 TATCTCATCAGGAAGACGAATTTGGTCCA
* *
627890 CTTCTTAGTATCTTATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
627915 AACCATTTTA
Statistics
Matches: 153, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
157 1 0.01
158 152 0.99
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (158 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCTAGCGTGAGTTTAATT
TGGTATTCTTCTCAATATCTCATCAAGAAGATGACCGCATCCCTTACTTCAATCCGCTTCTCTGT
ATCTCATCAGGAAGACGAATTTGGTCCA
Found at i:639801 original size:96 final size:96
Alignment explanation
Indices: 639627--639808 Score: 228
Period size: 96 Copynumber: 1.9 Consensus size: 96
639617 AAGGATGTTC
* ** * * *
639627 GATTATCTTGATTTGAAGAAAGGTTGCACCTATTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTTGATTTGAAAAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAA
*
639692 TAAGGAAACATTGCCTCGATTATGAGTATTT
66 TAAAGAAACATTGCCTCGATTATGAGTATTT
639723 GATTAT-TTCGATTTGAAAAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC-A
1 GATTATCTT-GATTTGAAAAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGA
*
639785 AAATAAA-AGAATATTGCCTCGATT
63 AAATAAAGA-AACATTGCCTCGATT
639809 CAAAGTTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
95 4 0.05
96 68 0.92
97 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (96 bp):
GATTATCTTGATTTGAAAAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAA
TAAAGAAACATTGCCTCGATTATGAGTATTT
Found at i:640188 original size:58 final size:57
Alignment explanation
Indices: 640143--640285 Score: 178
Period size: 58 Copynumber: 2.4 Consensus size: 57
640133 AGAGTTTTGG
* * *
640143 GGTCGAAAATGAAAATTTTGGAGGTTTAAGGGTAAAAATGGAATTTTTGGAAGTTTCAA
1 GGTCAAAAATG-AAATTTTGGAAGTTCAAGGGTAAAAATGGAA-TTTTGGAAGTTTCAA
* * *
640202 GGTTAAAAATGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGTCAAAAATGAAATTTTGGAAGTTCAAGGGTAAAAATGGAA-TTTTGGAAGTTTCAA
* *
640260 GGTCAAAAATAGAATTTTTGGGAGTT
1 GGTCAAAAAT-GAAATTTTGGAAGTT
640286 TCGAGGTCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 52 0.70
59 22 0.30
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (57 bp):
GGTCAAAAATGAAATTTTGGAAGTTCAAGGGTAAAAATGGAATTTTGGAAGTTTCAA
Found at i:640211 original size:30 final size:30
Alignment explanation
Indices: 640148--640328 Score: 203
Period size: 30 Copynumber: 6.2 Consensus size: 30
640138 TTTGGGGTCG
* * * *
640148 AAAATGAAAATTTTGGAGGTTT-AAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
* *
640177 AAAATGGAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
*
640207 AAAAT-GAAATTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
640235 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
* *
640265 AAAATAGAATTTTTGGGAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGT-A
**
640295 AAAATTAAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
640324 AAAAT
1 AAAAT
640329 ATAATTTTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
28 13 0.10
29 57 0.43
30 64 0.48
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGGTA
Found at i:641501 original size:21 final size:22
Alignment explanation
Indices: 641469--641516 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
641459 TTTTAAAAAA
641469 TATTATTTATTACTGTTGTTAC
1 TATTATTTATTACTGTTGTTAC
*
641491 TATTA-TTATTACTGTTGTTAT
1 TATTATTTATTACTGTTGTTAC
641512 TATTA
1 TATTA
641517 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (22 bp):
TATTATTTATTACTGTTGTTAC
Found at i:642243 original size:33 final size:34
Alignment explanation
Indices: 642198--642296 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 34
642188 TGTATTTGTT
* * *
642198 TTTAAACTTTTAATTTAA-TTAAGTTTTAAATCAAA
1 TTTAAA-TTTTAATTAAATTTAA-ATTTAAAGCAAA
642233 -TTAAATTTTAATTAAATTTAAATTTAAAGCAAA
1 TTTAAATTTTAATTAAATTTAAATTTAAAGCAAA
* *
642266 TTTAAATTTAAAAGATAAATTTAAATTTAAA
1 TTTAAATTT-TAA-TTAAATTTAAATTTAAA
642297 AATACATTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
33 20 0.36
34 17 0.31
35 2 0.04
36 16 0.29
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTAAATTTTAATTAAATTTAAATTTAAAGCAAA
Found at i:642253 original size:6 final size:6
Alignment explanation
Indices: 642233--642296 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
642223 TTAAATCAAA
* ** *
642233 TTAAAT TTTAA- TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAAAG
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT
*
642280 ATAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
642297 AATACATTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 7 0.16
6 34 0.76
7 4 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:642253 original size:17 final size:17
Alignment explanation
Indices: 642198--642293 Score: 70
Period size: 17 Copynumber: 5.5 Consensus size: 17
642188 TGTATTTGTT
*
642198 TTTAAACTTTTAATTTAA
1 TTTAAA-TTTTAATTAAA
* *
642216 -TTAAGTTTTAAATCAAA
1 TTTAAATTTT-AATTAAA
642233 -TTAAATTTTAATTAAA
1 TTTAAATTTTAATTAAA
* **
642249 TTTAAATTTAAAGCAAA
1 TTTAAATTTTAATTAAA
* *
642266 TTTAAATTTAAAAGATAAA
1 TTTAAATTT-TAA-TTAAA
642285 TTTAAATTT
1 TTTAAATTT
642294 AAAAATACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.16
17 39 0.61
18 3 0.05
19 12 0.19
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAATTTTAATTAAA
Found at i:642287 original size:19 final size:18
Alignment explanation
Indices: 642245--642297 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
642235 AAATTTTAAT
642245 TAAATTTAAATTT-AAAG
1 TAAATTTAAATTTAAAAG
*
642262 CAAATTTAAATTTAAAAG
1 TAAATTTAAATTTAAAAG
642280 ATAAATTTAAATTTAAAA
1 -TAAATTTAAATTTAAAA
642298 ATACATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 16 0.50
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAG
Found at i:652284 original size:30 final size:30
Alignment explanation
Indices: 652244--652309 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
652234 CCGACTTGGA
652244 TATATTATGTTATAAAAATAATTATAT-TAAT
1 TATA-TATGTTA-AAAAATAATTATATATAAT
* * *
652275 TATATATGTTAAATAATTATTATATATATT
1 TATATATGTTAAAAAATAATTATATATAAT
652305 TATAT
1 TATAT
652310 TAAATCACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.39
30 15 0.48
31 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
TATATATGTTAAAAAATAATTATATATAAT
Found at i:657265 original size:3 final size:3
Alignment explanation
Indices: 657257--657281 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
657247 TTTATTTATT
657257 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
657282 CAAAGTGGTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:657501 original size:18 final size:18
Alignment explanation
Indices: 657478--657535 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
657468 AATATTGAAT
* * *
657478 ATTTTTTTAGTTTATTCG
1 ATTTTTTTAATTTAATCA
657496 ATTTTTTTAATTTAATCA
1 ATTTTTTTAATTTAATCA
* *
657514 ATTTTTCT-ATTTAATCT
1 ATTTTTTTAATTTAATCA
657531 ATTTT
1 ATTTT
657536 AAATTGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTTTTAATTTAATCA
Found at i:657705 original size:23 final size:23
Alignment explanation
Indices: 657643--657710 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 23
657633 CTATTAAAAT
657643 TTAATACTCTTAAAAGCCCAAACCCA
1 TTAATA-TC-TAAAA-CCCAAACCCA
*
657669 TTAATATTTAAAACCCAATACCCA
1 TTAATATCTAAAACCCAA-ACCCA
657693 TTAATATCT-AAACCCAAA
1 TTAATATCTAAAACCCAAA
657711 TTGATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.03
23 13 0.33
24 18 0.46
25 1 0.03
26 6 0.15
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (23 bp):
TTAATATCTAAAACCCAAACCCA
Found at i:663709 original size:2 final size:2
Alignment explanation
Indices: 663702--663726 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
663692 CAACAATACT
663702 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
663727 TTGATGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:664613 original size:23 final size:23
Alignment explanation
Indices: 664554--664613 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
664544 TAACCATGAT
* *
664554 AAAATTTTAA-TTTAATATTTTA
1 AAAATTATAATTTTAATATTGTA
* *
664576 AAATTTAT-ATCTTTACTATTGTA
1 AAAATTATAAT-TTTAATATTGTA
664599 AAAATTATAATTTTA
1 AAAATTATAATTTTA
664614 TTTCTATCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 6 0.20
23 21 0.70
24 2 0.07
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
AAAATTATAATTTTAATATTGTA
Done.