Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015257.1 Kokia drynarioides strain JFW-HI SEQ_130302, 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: 576078
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 879 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:358127 original size:3 final size:3
Alignment explanation
Indices: 358119--358154 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
358109 AAGTAATGTG
*
358119 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
358155 GTTAGATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:358754 original size:31 final size:33
Alignment explanation
Indices: 358719--358782 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
358709 AAAAAAATGA
358719 AGAAAAAAT-C-AAATGAAACACAATAATTATG
1 AGAAAAAATACAAAATGAAACACAATAATTATG
*
358750 AGAAAAAATAACAAAATGAAACTCAATAATTAT
1 AGAAAAAAT-ACAAAATGAAACACAATAATTAT
358783 AGGAATAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.31
33 1 0.03
34 19 0.66
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.20
Consensus pattern (33 bp):
AGAAAAAATACAAAATGAAACACAATAATTATG
Found at i:377123 original size:18 final size:19
Alignment explanation
Indices: 377100--377143 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
377090 AAATAAGTTG
377100 TTATTAA-AATTTAAAATA
1 TTATTAACAATTTAAAATA
*
377118 TTATTAACGACTTTAAAATA
1 TTATTAAC-AATTTAAAATA
*
377138 TCATTA
1 TTATTA
377144 CGTGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
TTATTAACAATTTAAAATA
Found at i:377633 original size:18 final size:18
Alignment explanation
Indices: 377610--377651 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
377600 TTTTTAGTCG
377610 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
377628 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
377646 TAATTA
1 TAATTA
377652 GAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:380870 original size:24 final size:26
Alignment explanation
Indices: 380828--380879 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
380818 ATTTAATTTT
*
380828 AATTAAAAATTATTTAAAAT-TCATAA
1 AATTAAAAATTATTAAAAATAT-ATAA
380854 AATT-AAAA-TATTAAAAATATATAA
1 AATTAAAAATTATTAAAAATATATAA
380878 AA
1 AA
380880 CCAACGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 15 0.62
25 5 0.21
26 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AATTAAAAATTATTAAAAATATATAA
Found at i:381095 original size:20 final size:20
Alignment explanation
Indices: 381070--381107 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
381060 GATGTCCTTT
381070 CATTGATTCCTCCTAAATTG
1 CATTGATTCCTCCTAAATTG
**
381090 CATTGATTTGTCCTAAAT
1 CATTGATTCCTCCTAAAT
381108 ATTTCATTTC
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:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (20 bp):
CATTGATTCCTCCTAAATTG
Found at i:381638 original size:25 final size:23
Alignment explanation
Indices: 381597--381642 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
381587 CCAATTAGGG
381597 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
381620 AATTATTTTTTTAGAATTTAATT
1 AATTA-TTATTTAG-ATTTAATT
381643 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:383914 original size:22 final size:22
Alignment explanation
Indices: 383889--383936 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
383879 AGGTACTTAA
383889 TCTTCATTTTTTAGCTTTAATC
1 TCTTCATTTTTTAGCTTTAATC
* * *
383911 TCTTCGTTTTTTATCTTTAATT
1 TCTTCATTTTTTAGCTTTAATC
383933 TCTT
1 TCTT
383937 GGGTTCCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.04, T:0.65
Consensus pattern (22 bp):
TCTTCATTTTTTAGCTTTAATC
Found at i:398592 original size:2 final size:2
Alignment explanation
Indices: 398585--398613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
398575 GGCCCTTCTA
398585 CT 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 CT C
398614 AGCTGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:403308 original size:69 final size:68
Alignment explanation
Indices: 403228--403367 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 68
403218 CTCTTTGTTA
* * *
403228 TTAGCACTGTGTGTGCTCTCTG-A-CTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACT
1 TTAGCACTGTGTGTGCTCTCTGTACCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT-AGTACT
403291 CTCTGT
63 CTCTGT
*
403297 TTAGCACTGTGTGTGCTCTCTGTTACCCAGTACTTATGTGCTCTCTGTTAGTACTTTAGTACTCT
1 TTAGCACTGTGTGTGCTCTCTG-TACCCAGCACTTATGTGCTCTCTGTTAGTACTTTAGTACTCT
403362 CTGT
65 CTGT
403366 TT
1 TT
403368 GTTCCGTATA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
69 35 0.55
70 10 0.16
71 14 0.22
72 5 0.08
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (68 bp):
TTAGCACTGTGTGTGCTCTCTGTACCCAGCACTTATGTGCTCTCTGTTAGTACTTTAGTACTCTC
TGT
Found at i:403319 original size:23 final size:23
Alignment explanation
Indices: 403192--403320 Score: 134
Period size: 23 Copynumber: 5.5 Consensus size: 23
403182 GAACACTAGC
* *
403192 GTGCTCTTTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
*
403214 CGTGCTCTTTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCACTGTGT
** *
403240 GTGCTCTCTGACTAGCACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* * *
403263 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
403286 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
403309 GTGCTCTCTGTT
1 GTGCTCTCTGTT
403321 ACCCAGTACT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 71 0.78
24 1 0.01
25 16 0.18
26 3 0.03
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:403349 original size:21 final size:21
Alignment explanation
Indices: 403239--403364 Score: 85
Period size: 23 Copynumber: 5.5 Consensus size: 21
403229 TAGCACTGTG
* *
403239 TGTGCTCTCTGACTAGCACTTT
1 TGTGCTCTCTGATTAGTAC-TT
403261 GTGTGCTCTCTGATTAGTACTT
1 -TGTGCTCTCTGATTAGTACTT
* *
403283 TGTGTACTCTCTGTTTAGCACTGT
1 TGTG--CTCTCTGATTAGTACT-T
403307 GTGTGCTCTCTG-TTACCCAGTACTT
1 -TGTGCTCTCTGATT----AGTACTT
403332 ATGTGCTCTCTG-TTAGTACTT
1 -TGTGCTCTCTGATTAGTACTT
*
403353 TAGTACTCTCTG
1 T-GTGCTCTCTG
403365 TTTGTTCCGT
Statistics
Matches: 87, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.01
21 20 0.23
22 4 0.05
23 38 0.44
24 1 0.01
25 18 0.21
26 5 0.06
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (21 bp):
TGTGCTCTCTGATTAGTACTT
Found at i:407747 original size:3 final size:3
Alignment explanation
Indices: 407739--407775 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
407729 TTTATCTTGC
407739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
407776 CGTTAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:412669 original size:22 final size:21
Alignment explanation
Indices: 412643--412685 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
412633 TTTAAAAAGT
412643 TATTAGATTAAAAAAAATTAAA
1 TATTA-ATTAAAAAAAATTAAA
*
412665 TATTATTTAAAAAAAATTAAA
1 TATTAATTAAAAAAAATTAAA
412686 AGCATACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TATTAATTAAAAAAAATTAAA
Found at i:412905 original size:5 final size:5
Alignment explanation
Indices: 412895--412927 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
412885 GAAACATCTG
*
412895 AATTT AATTT AATTT AATTT -TTTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
412928 CTATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
AATTT
Found at i:413132 original size:17 final size:18
Alignment explanation
Indices: 413093--413133 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
413083 AATTCTCATT
*
413093 TATTAAA-AATATTATTA
1 TATTAAATAAAATTATTA
413110 -ATTAAATAAAATT-TTA
1 TATTAAATAAAATTATTA
413126 TATTAAAT
1 TATTAAAT
413134 TTGAGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTAAATAAAATTATTA
Found at i:416490 original size:103 final size:104
Alignment explanation
Indices: 416250--416538 Score: 393
Period size: 103 Copynumber: 2.8 Consensus size: 104
416240 TTCATTTAAA
* * ** * * * *
416250 ACTCACAATGACA-TATAGTCATCGAACCTTCTGTTCTGTAAAGGAACTCATGTACTCACGATAA
1 ACTCACGATGACACT-TAGTCATCGAACCTTATAATCCGTAAAGG-ATTCATTTACTCACGATGA
416314 CACTTAGTCATCGGACCTCACAATCCGTAAAGGATTCATAT
64 CACTTAGTCATCGGACCTCACAATCCGTAAAGGATTCATAT
* * * * *
416355 ACTCATGATGACACTTAGCCATCGGACTTTATAATCCGTAAAGGATTCATTTACTCACGATGATA
1 ACTCACGATGACACTTAGTCATCGAACCTTATAATCCGTAAAGGATTCATTTACTCACGATGACA
* * * *
416420 CTTAGTCATCGGACTTCATAATCCGTACA-GATTCATTT
66 CTTAGTCATCGGACCTCACAATCCGTAAAGGATTCATAT
416458 ACTCACGATGACACTTAGTCATCGAACCTTATAATCCGTAAAGGATTCATTTACTCACGATGACA
1 ACTCACGATGACACTTAGTCATCGAACCTTATAATCCGTAAAGGATTCATTTACTCACGATGACA
416523 CTTAGTCATCGGACCT
66 CTTAGTCATCGGACCT
416539 TTATCATTTA
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
103 83 0.52
104 43 0.27
105 33 0.21
106 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (104 bp):
ACTCACGATGACACTTAGTCATCGAACCTTATAATCCGTAAAGGATTCATTTACTCACGATGACA
CTTAGTCATCGGACCTCACAATCCGTAAAGGATTCATAT
Found at i:416539 original size:52 final size:52
Alignment explanation
Indices: 416250--416539 Score: 370
Period size: 52 Copynumber: 5.6 Consensus size: 52
416240 TTCATTTAAA
* * * ** * * *
416250 ACTCACAATGACA-TATAGTCATCGAACCTTCTGTTCTGTAAAGGAACTCATGT
1 ACTCACGATGACACT-TAGTCATCGGACCTTATAATCCGTAAAGG-ATTCATTT
* * * *
416303 ACTCACGATAACACTTAGTCATCGGACCTCACAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATTT
* * *
416355 ACTCATGATGACACTTAGCCATCGGACTTTATAATCCGTAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATTT
* *
416407 ACTCACGATGATACTTAGTCATCGGA-CTTCATAATCCGTACA-GATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTT-ATAATCCGTAAAGGATTCATTT
*
416458 ACTCACGATGACACTTAGTCATCGAACCTTATAATCCGTAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATTT
416510 ACTCACGATGACACTTAGTCATCGGACCTT
1 ACTCACGATGACACTTAGTCATCGGACCTT
416540 TATCATTTAC
Statistics
Matches: 206, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
51 46 0.22
52 126 0.61
53 33 0.16
54 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (52 bp):
ACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCATTT
Found at i:421823 original size:13 final size:14
Alignment explanation
Indices: 421800--421828 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
421790 TATCTAATTT
421800 AAAAATACTTAAAA
1 AAAAATACTTAAAA
421814 AAAAAT-CTTAAAA
1 AAAAATACTTAAAA
421827 AA
1 AA
421829 TATTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATACTTAAAA
Found at i:425629 original size:2 final size:2
Alignment explanation
Indices: 425622--425656 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
425612 TCAGCTCAGG
*
425622 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
425657 GCATGTCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:432680 original size:11 final size:11
Alignment explanation
Indices: 432664--432689 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
432654 GAATAATAAA
432664 AATATTATTTT
1 AATATTATTTT
432675 AATATTATTTT
1 AATATTATTTT
432686 AATA
1 AATA
432690 GTATATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTATTTT
Found at i:440398 original size:61 final size:61
Alignment explanation
Indices: 440299--440421 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
440289 CTAACTAAAA
* *
440299 TTTTCTCTCCACGTCTCTGCAACCCCCTGCTACTATTTTTTCCCGACAACTGCTTTGCTAT
1 TTTTCTCTCCACGTCTCTACAACCCCCTGCTACCATTTTTTCCCGACAACTGCTTTGCTAT
* * * * *
440360 TTTTCTCTTCACGTCTCTACAATCCCCTGCTGCCATTTTTTCCCGGCAATTGCTTTGCTAT
1 TTTTCTCTCCACGTCTCTACAACCCCCTGCTACCATTTTTTCCCGACAACTGCTTTGCTAT
440421 T
1 T
440422 CAATTGTTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (61 bp):
TTTTCTCTCCACGTCTCTACAACCCCCTGCTACCATTTTTTCCCGACAACTGCTTTGCTAT
Found at i:443774 original size:18 final size:18
Alignment explanation
Indices: 443741--443792 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
443731 GTTTATATTC
*
443741 TTTTATATATTTTTTAGAT
1 TTTTATA-AATTTTTAGAT
*
443760 TTCTTA-AAATTTTTATAT
1 TT-TTATAAATTTTTAGAT
443778 TTTTATAAATATTTT
1 TTTTATAAAT-TTTT
443793 TTTAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
18 15 0.54
19 7 0.25
20 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATAAATTTTTAGAT
Found at i:448988 original size:14 final size:11
Alignment explanation
Indices: 448949--448976 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
448939 ATCATTTCGC
448949 TATTATATTGT
1 TATTATATTGT
448960 TATTATATTGT
1 TATTATATTGT
448971 TATTAT
1 TATTAT
448977 TACTTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (11 bp):
TATTATATTGT
Found at i:449175 original size:14 final size:15
Alignment explanation
Indices: 449143--449175 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
449133 AATGTATTTG
449143 ATATATTATATTTTT
1 ATATATTATATTTTT
449158 -TATATT-TATTTTT
1 ATATATTATATTTTT
449171 ATATA
1 ATATA
449176 AAAATAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATATTATATTTTT
Found at i:454291 original size:30 final size:30
Alignment explanation
Indices: 454250--454307 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
454240 TTAACTGTCA
* *
454250 AGTGACTTAAATAAAAAATTTTAAATAGTT
1 AGTGACATAAATAAAAAAATTTAAATAGTT
454280 AGTGACATAAATAAAAAAATTTAAATAG
1 AGTGACATAAATAAAAAAATTTAAATAG
454308 CTCATGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.31
Consensus pattern (30 bp):
AGTGACATAAATAAAAAAATTTAAATAGTT
Found at i:462020 original size:30 final size:31
Alignment explanation
Indices: 461985--462067 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
461975 TTTAAATTTT
*
461985 AATAATAAAATAATCACTTATTTT-TTAAAA
1 AATAATAAAATAATCACTTATTTTATCAAAA
*
462015 AATAAT-AAATCCATCA-TTAATTTTATCAAAA
1 AATAATAAAAT-AATCACTT-ATTTTATCAAAA
*
462046 AATAATAAATTAATCACTTATT
1 AATAATAAAATAATCACTTATT
462068 AATATTTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 6 0.14
30 15 0.34
31 18 0.41
32 5 0.11
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (31 bp):
AATAATAAAATAATCACTTATTTTATCAAAA
Found at i:462733 original size:14 final size:14
Alignment explanation
Indices: 462714--462755 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
462704 GACTAGAGTT
462714 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
462728 AAG--AAAAAGAAA
1 AAGAAAAAAAGAAA
* *
462740 AAGAATATAAGAAA
1 AAGAAAAAAAGAAA
462754 AA
1 AA
462756 ACGGATAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:462734 original size:5 final size:6
Alignment explanation
Indices: 462719--462755 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
462709 GAGTTAAGAA
462719 AAAAAG AAAAAG AAAAAG AAAAAG AATATAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-A-AAG AAAAA
462756 ACGGATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.76
7 2 0.07
8 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:466652 original size:2 final size:2
Alignment explanation
Indices: 466645--466674 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
466635 TACAGTACAG
*
466645 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466675 TCATGTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:467565 original size:18 final size:18
Alignment explanation
Indices: 467542--467577 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
467532 AACAATAAAC
*
467542 CAATTACCGAATTCGCAA
1 CAATTACCAAATTCGCAA
467560 CAATTACCAAATTCGCAA
1 CAATTACCAAATTCGCAA
467578 TTGTGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (18 bp):
CAATTACCAAATTCGCAA
Found at i:473341 original size:13 final size:13
Alignment explanation
Indices: 473309--473346 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
473299 AAACTTTAAA
473309 TTTTAAATAT-TT
1 TTTTAAATATATT
*
473321 TTCATAAATATATT
1 TT-TTAAATATATT
473335 TTTTAAATATAT
1 TTTTAAATATAT
473347 ATATTTCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 16 0.73
14 4 0.18
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:473591 original size:21 final size:20
Alignment explanation
Indices: 473567--473658 Score: 73
Period size: 18 Copynumber: 4.5 Consensus size: 20
473557 TTTCTAAAAT
473567 TAAAATACTTTTAATTTTTTA
1 TAAAATA-TTTTAATTTTTTA
473588 T-AAA-ATTTTAATTTTTTA
1 TAAAATATTTTAATTTTTTA
* * *
473606 TATATTATTTTCACTTTTTTA
1 TAAAATATTTT-AATTTTTTA
*
473627 TAATTATATATTTTAGA-ATTTTA
1 TAA--A-ATATTTTA-ATTTTTTA
473650 TAAAATATT
1 TAAAATATT
473659 ATTTTTATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 14 0.25
19 2 0.04
20 13 0.23
21 12 0.21
23 10 0.18
24 6 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (20 bp):
TAAAATATTTTAATTTTTTA
Found at i:473609 original size:20 final size:20
Alignment explanation
Indices: 473575--473628 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
473565 ATTAAAATAC
473575 TTTTAA-TTTTT-TATAAAA
1 TTTTAATTTTTTATATAAAA
**
473593 TTTTAATTTTTTATATATTA
1 TTTTAATTTTTTATATAAAA
*
473613 TTTTCACTTTTTTATA
1 TTTT-AATTTTTTATA
473629 ATTATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 9 0.30
21 10 0.33
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATTTTTTATATAAAA
Found at i:473632 original size:20 final size:19
Alignment explanation
Indices: 473575--473633 Score: 75
Period size: 18 Copynumber: 3.1 Consensus size: 19
473565 ATTAAAATAC
*
473575 TTTTAATTTTTTATAA-AA
1 TTTTAATTTTTTATAATTA
473593 TTTTAATTTTTTATATATTA
1 TTTTAATTTTTTATA-ATTA
*
473613 TTTTCACTTTTTTATAATTA
1 TTTT-AATTTTTTATAATTA
473633 T
1 T
473634 ATATTTTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.42
19 1 0.03
20 10 0.28
21 10 0.28
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATTTTTTATAATTA
Found at i:480180 original size:17 final size:18
Alignment explanation
Indices: 480159--480214 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
480149 ATATTTTGAA
480159 AAATATATAAAAAATTAT
1 AAATATATAAAAAATTAT
**
480177 -AATATA-AAAATTTTAT
1 AAATATATAAAAAATTAT
*
480193 AAATTTAT-AAAAATATAT
1 AAATATATAAAAAAT-TAT
480211 AAAT
1 AAAT
480215 GACTAAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 8 0.27
17 15 0.50
18 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATATAAAAAATTAT
Found at i:482375 original size:22 final size:22
Alignment explanation
Indices: 482350--482393 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
482340 AATTTTTAAA
482350 AAATATTTATATTATAT-TATTT
1 AAATATTTA-ATTATATATATTT
*
482372 AAATATTTAATTTTATATATTT
1 AAATATTTAATTATATATATTT
482394 TTATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATATTTAATTATATATATTT
Found at i:482415 original size:25 final size:24
Alignment explanation
Indices: 482361--482416 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
482351 AATATTTATA
482361 TTATATTATTTAAATATTTAATTT
1 TTATATTATTTAAATATTTAATTT
**
482385 TATATATT-TTTATTTATTTAAACTTT
1 T-TATATTATTTAAATATTT-AA-TTT
482411 TTATAT
1 TTATAT
482417 AGTTATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 10 0.37
25 13 0.48
26 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATTATTTAAATATTTAATTT
Found at i:484415 original size:2 final size:2
Alignment explanation
Indices: 484408--484438 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
484398 TCCTTTGTAC
484408 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
484439 TGGAGGGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:486055 original size:24 final size:23
Alignment explanation
Indices: 486002--486056 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
485992 ATTTTTTTTT
486002 ATTTTAGTTTTTAATTATCCATTA
1 ATTTTA-TTTTTAATTATCCATTA
* *
486026 AATTTATTTTTAATATTATCTA-TA
1 ATTTTATTTTT-A-ATTATCCATTA
486050 ATTTTAT
1 ATTTTAT
486057 ATTTGGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
25 7 0.27
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTATTTTTAATTATCCATTA
Found at i:509938 original size:36 final size:36
Alignment explanation
Indices: 509898--509971 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
509888 AAAAAGTTTA
509898 AGAGAGTTGGGTGATAGTTTGCTCGTGTGATTCATC
1 AGAGAGTTGGGTGATAGTTTGCTCGTGTGATTCATC
*
509934 AGAGAGTTGGGTGATAGTTTGCTCGTGTGGTTCATC
1 AGAGAGTTGGGTGATAGTTTGCTCGTGTGATTCATC
509970 AG
1 AG
509972 GTGAATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.11, G:0.35, T:0.35
Consensus pattern (36 bp):
AGAGAGTTGGGTGATAGTTTGCTCGTGTGATTCATC
Found at i:511453 original size:6 final size:6
Alignment explanation
Indices: 511442--511467 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
511432 ATAAGAAATG
511442 TTTAAT TTTAAT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TT
511468 CTAAATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:513657 original size:22 final size:23
Alignment explanation
Indices: 513608--513658 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
513598 ACCCAACAGG
* *
513608 GTACCCAATAATGAAAACCCCAC
1 GTACCTAATAATAAAAACCCCAC
* *
513631 ATACCTAATAATAAAAACCCGA-
1 GTACCTAATAATAAAAACCCCAC
513653 GTACCT
1 GTACCT
513659 CTGAGTCTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (23 bp):
GTACCTAATAATAAAAACCCCAC
Found at i:514209 original size:15 final size:15
Alignment explanation
Indices: 514189--514226 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
514179 TGATAAAGTG
*
514189 AAAAATTAAGTGCTA
1 AAAAATTAAGTACTA
*
514204 AAAAA-TAATTACTA
1 AAAAATTAAGTACTA
514218 AAAAATTAA
1 AAAAATTAA
514227 ATGTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (15 bp):
AAAAATTAAGTACTA
Found at i:515865 original size:30 final size:30
Alignment explanation
Indices: 515829--515963 Score: 213
Period size: 30 Copynumber: 4.6 Consensus size: 30
515819 AACAACTACA
515829 ACAACAACAATGGCTACACCACAAGTAAGT
1 ACAACAACAATGGCTACACCACAAGTAAGT
515859 ACAACAACAATGGCTACACCACAAGTAAGT
1 ACAACAACAATGGCTACACCACAAGTAAGT
** * *
515889 ACAACAACAATGGCTACA--AGGA-CAACT
1 ACAACAACAATGGCTACACCACAAGTAAGT
515916 ACAACAACAATGGCTACACCACAAGTAAGT
1 ACAACAACAATGGCTACACCACAAGTAAGT
515946 ACAACAACAATGGCTACA
1 ACAACAACAATGGCTACA
515964 AGGACAACTA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
27 21 0.22
28 2 0.02
29 2 0.02
30 69 0.73
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (30 bp):
ACAACAACAATGGCTACACCACAAGTAAGT
Found at i:515925 original size:57 final size:57
Alignment explanation
Indices: 515858--516039 Score: 298
Period size: 57 Copynumber: 3.2 Consensus size: 57
515848 CACAAGTAAG
515858 TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
1 TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
515915 TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
1 TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
** * * *
515972 TACAACAACAATGGCTACA--AGGA-CAACTACAACAACAATGGCTACAATGACAAC
1 TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
516026 TACAACAACAATGG
1 TACAACAACAATGG
516040 GTATGAGACA
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
54 42 0.35
55 2 0.02
57 76 0.63
ACGTcount: A:0.48, C:0.26, G:0.14, T:0.13
Consensus pattern (57 bp):
TACAACAACAATGGCTACACCACAAGTAAGTACAACAACAATGGCTACAAGGACAAC
Found at i:515975 original size:27 final size:27
Alignment explanation
Indices: 515888--516039 Score: 232
Period size: 27 Copynumber: 5.5 Consensus size: 27
515878 CACAAGTAAG
515888 TACAACAACAATGGCTACAAGGACAAC
1 TACAACAACAATGGCTACAAGGACAAC
** * *
515915 TACAACAACAATGGCTACACCACAAGTAAG
1 TACAACAACAATGGCTACA--AGGA-CAAC
515945 TACAACAACAATGGCTACAAGGACAAC
1 TACAACAACAATGGCTACAAGGACAAC
515972 TACAACAACAATGGCTACAAGGACAAC
1 TACAACAACAATGGCTACAAGGACAAC
*
515999 TACAACAACAATGGCTACAATGACAAC
1 TACAACAACAATGGCTACAAGGACAAC
516026 TACAACAACAATGG
1 TACAACAACAATGG
516040 GTATGAGACA
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
27 88 0.78
28 2 0.02
29 2 0.02
30 21 0.19
ACGTcount: A:0.48, C:0.26, G:0.14, T:0.12
Consensus pattern (27 bp):
TACAACAACAATGGCTACAAGGACAAC
Found at i:515980 original size:30 final size:29
Alignment explanation
Indices: 515820--516039 Score: 210
Period size: 27 Copynumber: 7.7 Consensus size: 29
515810 TACGGGAACA
*
515820 ACAACTACAACAACAACAATGGCTAC-ACC
1 ACAACTA-AACAACAACAATGGCTACAACG
* *
515849 ACAAGTAAGTACAACAACAATGGCTAC-ACC
1 ACAACTAA--ACAACAACAATGGCTACAACG
* *
515879 ACAAGTAAGTACAACAACAATGGCTACAAGG
1 ACAACTAA--ACAACAACAATGGCTACAACG
*
515910 ACAACT--ACAACAACAATGGCTAC-ACC
1 ACAACTAAACAACAACAATGGCTACAACG
* *
515936 ACAAGTAAGTACAACAACAATGGCTACAAGG
1 ACAACTAA--ACAACAACAATGGCTACAACG
*
515967 ACAACT--ACAACAACAATGGCTACAAGG
1 ACAACTAAACAACAACAATGGCTACAACG
*
515994 ACAACT--ACAACAACAATGGCTACAATG
1 ACAACTAAACAACAACAATGGCTACAACG
516021 ACAACT--ACAACAACAATGG
1 ACAACTAAACAACAACAATGG
516040 GTATGAGACA
Statistics
Matches: 172, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
26 6 0.03
27 83 0.48
28 1 0.01
29 6 0.03
30 64 0.37
31 12 0.07
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.12
Consensus pattern (29 bp):
ACAACTAAACAACAACAATGGCTACAACG
Found at i:516009 original size:12 final size:12
Alignment explanation
Indices: 515967--516036 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 12
515957 GGCTACAAGG
515967 ACAACTACAACA
1 ACAACTACAACA
**
515979 ACAATGGCTACAAGG
1 ACAA---CTACAACA
515994 ACAACTACAACA
1 ACAACTACAACA
**
516006 ACAATGGCTACAATG
1 ACAA---CTACAACA
516021 ACAACTACAACA
1 ACAACTACAACA
516033 ACAA
1 ACAA
516037 TGGGTATGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
12 24 0.55
15 20 0.45
ACGTcount: A:0.51, C:0.27, G:0.10, T:0.11
Consensus pattern (12 bp):
ACAACTACAACA
Found at i:517896 original size:31 final size:30
Alignment explanation
Indices: 517835--517905 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 30
517825 ATGATTTTAT
*
517835 AATTATTATAATTATTTTTTAAGAATATAA
1 AATTATTAAAATTATTTTTTAAGAATATAA
*
517865 AATTATTAAAATTATTTTTT-TGAAATAATAA
1 AATTATTAAAATTATTTTTTAAG-AAT-ATAA
517896 AATTATTAAA
1 AATTATTAAA
517906 TAATTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.03
30 22 0.59
31 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AATTATTAAAATTATTTTTTAAGAATATAA
Found at i:519140 original size:20 final size:20
Alignment explanation
Indices: 519101--519140 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
519091 TGATTCAAAA
* *
519101 GTTAGGGTTTAGTTTTTTTT
1 GTTAGGGTTTAATTTGTTTT
*
519121 GTTAGTGTTTAATTTGTTTT
1 GTTAGGGTTTAATTTGTTTT
519141 AATTTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (20 bp):
GTTAGGGTTTAATTTGTTTT
Found at i:519156 original size:17 final size:18
Alignment explanation
Indices: 519128--519161 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
519118 TTTGTTAGTG
519128 TTTAATTTGTTTTAATTT
1 TTTAATTTGTTTTAATTT
519146 TTTAA-TTGTTTTAATT
1 TTTAATTTGTTTTAATT
519162 GTGGGTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTAATTTGTTTTAATTT
Found at i:519157 original size:9 final size:9
Alignment explanation
Indices: 519128--519163 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
519118 TTTGTTAGTG
519128 TTTAATTTGT
1 TTTAA-TTGT
519138 TTTAATT-T
1 TTTAATTGT
519146 TTTAATTGT
1 TTTAATTGT
519155 TTTAATTGT
1 TTTAATTGT
519164 GGGTCCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 12 0.48
10 5 0.20
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TTTAATTGT
Found at i:519208 original size:18 final size:18
Alignment explanation
Indices: 519177--519225 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
519167 TCCCAAATTT
**
519177 TTTAAATTTTTTTTAAAA
1 TTTAAATTAATTTTAAAA
* *
519195 TTTTAATTAATTTTTAAA
1 TTTAAATTAATTTTAAAA
*
519213 TTTAAATTTATTT
1 TTTAAATTAATTT
519226 ACTGATATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTAATTTTAAAA
Found at i:522388 original size:16 final size:17
Alignment explanation
Indices: 522352--522391 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
522342 CCAACCAACC
522352 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAATGA
522369 GAAAAAGAAAGAAAA-G-
1 GAAAAAGAAA-AAAATGA
522385 GAAAAAG
1 GAAAAAG
522392 GAATGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAAAAAATGA
Found at i:529574 original size:63 final size:63
Alignment explanation
Indices: 529475--529600 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
529465 CAGTCTTTTG
529475 AAACCACGTCGATACTTGTAAGAAGGGTTGATTTGAAAAACAAGTATAAAAACATATATCTGT
1 AAACCACGTCGATACTTGTAAGAAGGGTTGATTTGAAAAACAAGTATAAAAACATATATCTGT
529538 AAACCACGTCGATACTTGTAAGAAGGGTTGATTTGAAAAACAAGTATAAAAACATATATCTGT
1 AAACCACGTCGATACTTGTAAGAAGGGTTGATTTGAAAAACAAGTATAAAAACATATATCTGT
529601 CGCCTGTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (63 bp):
AAACCACGTCGATACTTGTAAGAAGGGTTGATTTGAAAAACAAGTATAAAAACATATATCTGT
Found at i:534318 original size:35 final size:32
Alignment explanation
Indices: 534239--534319 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 32
534229 TGTTATAAAC
534239 ATATTTAAAAT--AAATAAATAAATAAAAATA
1 ATATTTAAAATAAAAATAAATAAATAAAAATA
* **
534269 GTATTTACCA-AAAAATAAATAAATAAAAATA
1 ATATTTAAAATAAAAATAAATAAATAAAAATA
534300 ATATACATTAAAATAAAAAT
1 ATAT---TTAAAATAAAAAT
534320 TTAGTTTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
30 7 0.18
31 22 0.56
34 4 0.10
35 6 0.15
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (32 bp):
ATATTTAAAATAAAAATAAATAAATAAAAATA
Found at i:540282 original size:7 final size:7
Alignment explanation
Indices: 540266--540296 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
540256 AATGGATGTA
540266 GAACAAT
1 GAACAAT
*
540273 GAACAGT
1 GAACAAT
540280 GAACAAT
1 GAACAAT
540287 GAACAAT
1 GAACAAT
540294 GAA
1 GAA
540297 GACCACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (7 bp):
GAACAAT
Found at i:540636 original size:37 final size:36
Alignment explanation
Indices: 540578--540647 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
540568 AAAAAAATTC
* *
540578 TATTTTTATAATTTTAGATTTT-TAATATATTTATTT
1 TATTTTTAAAATTTTAAATTTTAT-ATATATTTATTT
540614 TATTTTATAAAATTTTAAATTTTATATATATTTA
1 TATTTT-TAAAATTTTAAATTTTATATATATTTA
540648 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 6 0.20
37 23 0.77
38 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (36 bp):
TATTTTTAAAATTTTAAATTTTATATATATTTATTT
Found at i:540659 original size:21 final size:21
Alignment explanation
Indices: 540635--540674 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
540625 ATTTTAAATT
540635 TTATATATATTTAATAAAAAA
1 TTATATATATTTAATAAAAAA
* *
540656 TTATATATTTTTATTAAAA
1 TTATATATATTTAATAAAA
540675 TGCCACCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATATATATTTAATAAAAAA
Found at i:540866 original size:17 final size:17
Alignment explanation
Indices: 540846--540887 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
540836 CTCCCTTGAC
*
540846 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
540863 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
540880 CTTATAAC
1 CTT-TAAC
540888 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:540871 original size:24 final size:24
Alignment explanation
Indices: 540826--540873 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
540816 ATGGATGTTC
*
540826 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
540850 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
540874 CATATTCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:544760 original size:17 final size:17
Alignment explanation
Indices: 544725--544766 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
544715 CTCTCTTAAC
*
544725 CTTTAACCTTCTTTCTT
1 CTTTAACCTTCTTTATT
544742 CTTTAACCTT-TTATATT
1 CTTTAACCTTCTT-TATT
544759 CTTGTAAC
1 CTT-TAAC
544767 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 16 0.73
18 4 0.18
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.55
Consensus pattern (17 bp):
CTTTAACCTTCTTTATT
Found at i:549785 original size:47 final size:47
Alignment explanation
Indices: 549718--549811 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
549708 CAATTGGAGC
549718 AAAATACTTGAAGGCTAGCGTGAAGAATGAAGCATGGTGTTGGCACA
1 AAAATACTTGAAGGCTAGCGTGAAGAATGAAGCATGGTGTTGGCACA
549765 AAAATACTTGAAGGCTAGCGTGAAGAATGAAGCATGGTGTTGGCACA
1 AAAATACTTGAAGGCTAGCGTGAAGAATGAAGCATGGTGTTGGCACA
549812 TGAAATTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (47 bp):
AAAATACTTGAAGGCTAGCGTGAAGAATGAAGCATGGTGTTGGCACA
Found at i:572431 original size:26 final size:25
Alignment explanation
Indices: 572375--572425 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
572365 AGGACTATTT
*
572375 TATGTGGAAGTCCATGAAGGCTATC
1 TATGTGGAAGTCCATGAAGACTATC
572400 TATGTGGAAAGTCCACT-AAGACTATC
1 TATGTGG-AAGTCCA-TGAAGACTATC
572426 GTTGTGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 15 0.65
27 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (25 bp):
TATGTGGAAGTCCATGAAGACTATC
Found at i:573352 original size:14 final size:14
Alignment explanation
Indices: 573333--573362 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
573323 TTACAAACCC
573333 AATCAAATAACCTA
1 AATCAAATAACCTA
573347 AATCAAATAACCTA
1 AATCAAATAACCTA
573361 AA
1 AA
573363 CACTAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (14 bp):
AATCAAATAACCTA
Found at i:573368 original size:21 final size:20
Alignment explanation
Indices: 573344--573384 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
573334 ATCAAATAAC
573344 CTAAATCAAATAACCTAAACA
1 CTAAATCAAAT-ACCTAAACA
* *
573365 CTAAATCCAATTCCTAAACA
1 CTAAATCAAATACCTAAACA
573385 AACTCAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (20 bp):
CTAAATCAAATACCTAAACA
Done.