Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015153.1 Kokia drynarioides strain JFW-HI SEQ_130197, 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: 800050
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 392 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:644313 original size:26 final size:25
Alignment explanation
Indices: 644262--644310 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
644252 CAGATTCGGT
644262 GAAAAAAAAAAGAAAAGTAAAGAAAG
1 GAAAAAAAAAAGAAAAG-AAAGAAAG
*
644288 GAAAAATAAAAGAAAA-AAAGAAA
1 GAAAAAAAAAAGAAAAGAAAGAAA
644311 AAGGAGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (25 bp):
GAAAAAAAAAAGAAAAGAAAGAAAG
Found at i:672511 original size:27 final size:29
Alignment explanation
Indices: 672479--672542 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
672469 TATATATTAT
672479 ATATATAGGCGTCTAAAGTTTGTTAAATA
1 ATATATAGGCGTCTAAAGTTTGTTAAATA
* *
672508 ATATAATATGTGTCTAAAGTTTGTTAAATA
1 ATAT-ATAGGCGTCTAAAGTTTGTTAAATA
672538 ATATA
1 ATATA
672543 AATATGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (29 bp):
ATATATAGGCGTCTAAAGTTTGTTAAATA
Found at i:672523 original size:30 final size:31
Alignment explanation
Indices: 672489--672551 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
672479 ATATATAGGC
672489 GTCTAAAGTTTGTTAAATAATAT-AATATGT
1 GTCTAAAGTTTGTTAAATAATATAAATATGT
672519 GTCTAAAGTTTGTTAAATAATATAAATATGT
1 GTCTAAAGTTTGTTAAATAATATAAATATGT
672550 GT
1 GT
672552 ACTGTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (31 bp):
GTCTAAAGTTTGTTAAATAATATAAATATGT
Found at i:673608 original size:21 final size:22
Alignment explanation
Indices: 673579--673620 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
673569 AAAAATAACA
673579 AATAAATAAAA-TAAACAAAAC
1 AATAAATAAAATTAAACAAAAC
* *
673600 AATACATAAAATTAAATAAAA
1 AATAAATAAAATTAAACAAAA
673621 GCGAGAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (22 bp):
AATAAATAAAATTAAACAAAAC
Found at i:673908 original size:47 final size:46
Alignment explanation
Indices: 673870--673968 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 46
673860 TAATAATTAG
673870 ATAAATAAACAAAAAAATAAAAAATTAAATG-CTAAAATAAACAAATAA
1 ATAAATAAAC-AAAAAATAAAAAATTAAATGTC-AAAAT-AACAAATAA
* * * *
673918 ATAACTAAACAAAAAATCAATAATTAAATGTCAAAATAAGCAAGTAA
1 ATAAATAAACAAAAAATAAAAAATTAAATGTCAAAATAA-CAAATAA
673965 ATAA
1 ATAA
673969 TAATAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
46 2 0.04
47 33 0.73
48 10 0.22
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.20
Consensus pattern (46 bp):
ATAAATAAACAAAAAATAAAAAATTAAATGTCAAAATAACAAATAA
Found at i:673972 original size:3 final size:3
Alignment explanation
Indices: 673964--673992 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
673954 TAAGCAAGTA
673964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
673993 ATGAACTCTG
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:674729 original size:27 final size:27
Alignment explanation
Indices: 674699--674783 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
674689 TGCCAAGTTT
*
674699 GGTTCGCTAGTGTGTTTGGCAAGCTAG
1 GGTTCGCTAGTGTGTTTGGCGAGCTAG
**
674726 GGTTCATTAGTGTGTTTGGCGAGCTAG
1 GGTTCGCTAGTGTGTTTGGCGAGCTAG
* * **
674753 GGTTTGCCAGTGCATTTGGCGAGCTAG
1 GGTTCGCTAGTGTGTTTGGCGAGCTAG
674780 GGTT
1 GGTT
674784 TGCCAGGTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.14, C:0.14, G:0.38, T:0.34
Consensus pattern (27 bp):
GGTTCGCTAGTGTGTTTGGCGAGCTAG
Found at i:675350 original size:26 final size:26
Alignment explanation
Indices: 675312--675392 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 26
675302 TTACTACTAA
* * *
675312 TGTCACTGTATGAGCATGTCCAAAAT
1 TGTCACTGCATGAGCATGTCTAGAAT
* *
675338 TGTCGCTGCATGAACATGT-TAGAAT
1 TGTCACTGCATGAGCATGTCTAGAAT
*
675363 TGTCATTGCATGAGCATGTCTAGAAT
1 TGTCACTGCATGAGCATGTCTAGAAT
675389 TGTC
1 TGTC
675393 GCCGCATTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 20 0.43
26 26 0.57
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (26 bp):
TGTCACTGCATGAGCATGTCTAGAAT
Found at i:684287 original size:17 final size:18
Alignment explanation
Indices: 684267--684307 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
684257 ACATTTTAAC
* *
684267 TGTCATTGCATTTGCA-T
1 TGTCATTACATTTCCATT
684284 TGTCATTACATTTCCATT
1 TGTCATTACATTTCCATT
684302 TGTCAT
1 TGTCAT
684308 GGTATTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.49
Consensus pattern (18 bp):
TGTCATTACATTTCCATT
Found at i:685325 original size:26 final size:26
Alignment explanation
Indices: 685287--685352 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
685277 TTACTACTAA
* *
685287 TGTCGTTGTATGAGCATGTCCAAAAT
1 TGTCGCTGCATGAGCATGTCCAAAAT
** * * *
685313 TGTCGCTGCATGAATATTTCTAGAAT
1 TGTCGCTGCATGAGCATGTCCAAAAT
685339 TGTCGCTGCATGAG
1 TGTCGCTGCATGAG
685353 TACGTCTAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (26 bp):
TGTCGCTGCATGAGCATGTCCAAAAT
Found at i:685360 original size:26 final size:26
Alignment explanation
Indices: 685310--685366 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
685300 GCATGTCCAA
**
685310 AATTGTCGCTGCATGAATATTTCTAG
1 AATTGTCGCTGCATGAATACGTCTAG
*
685336 AATTGTCGCTGCATGAGTACGTCTAG
1 AATTGTCGCTGCATGAATACGTCTAG
685362 AATTG
1 AATTG
685367 CATCCAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (26 bp):
AATTGTCGCTGCATGAATACGTCTAG
Found at i:688625 original size:41 final size:43
Alignment explanation
Indices: 688402--688675 Score: 378
Period size: 43 Copynumber: 6.5 Consensus size: 43
688392 ACTTGATATT
*
688402 TAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* **
688445 TAAAAGAAAGACTCA-GTCTCTAGTTGAGCATGAGAATTTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
*
688487 TAAAAGGAAGACTCGTGTCTCGGGTTGAGCATGAGAATTTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
*
688530 TAAAAGGAAGACTCGTGTCTCGGGTTGAGCATGAGAATTTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* * *
688573 TAAAAGGAAGACTCATGTCTCGAGATGAGAATGAG-A-TTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* * * * *
688614 TTAAAGGAAGACTCATGTCTCGGGATGAGAACGA-TA-TTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
*
688655 TTAAAGGAAGACTCATGTCTC
1 TAAAAGGAAGACTCATGTCTC
688676 AAAATGAGCG
Statistics
Matches: 214, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
41 63 0.29
42 39 0.18
43 112 0.52
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (43 bp):
TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
Found at i:688759 original size:40 final size:40
Alignment explanation
Indices: 688706--688787 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
688696 GTTTAAAATT
* * * * *
688706 GAAGACTTATGACTCGGTAGAGCATTAGAGTGATTAAAAG
1 GAAGAATTATGACTCGATAAACCATAAGAGTGATTAAAAG
* *
688746 GAAGAATTGTGACTCGATAAACCATAAGATTGATTAAAAG
1 GAAGAATTATGACTCGATAAACCATAAGAGTGATTAAAAG
688786 GA
1 GA
688788 GCACTTATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (40 bp):
GAAGAATTATGACTCGATAAACCATAAGAGTGATTAAAAG
Found at i:695753 original size:43 final size:43
Alignment explanation
Indices: 695700--695847 Score: 210
Period size: 43 Copynumber: 3.5 Consensus size: 43
695690 ACTCGATATT
*
695700 TAAATGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* * *
695743 TAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAAAATTTATG
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* *
695786 TAAAAGGAAGACTCATGTCTCGGGATGAGAATGAG-A-TTATA
1 TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
* *
695827 TTAAAGGAAGAATCATGTCTC
1 TAAAAGGAAGACTCATGTCTC
695848 AAAATGAGCG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.24
42 1 0.01
43 70 0.74
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (43 bp):
TAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTATA
Found at i:700360 original size:17 final size:17
Alignment explanation
Indices: 700334--700383 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
700324 ACTAACACTA
*
700334 AAATGTAATGACAATGG
1 AAATGCAATGACAATGG
**
700351 AAATGCAATGGTAATGG
1 AAATGCAATGACAATGG
*
700368 AAATGCACTGACAATG
1 AAATGCAATGACAATG
700384 TTTACTAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATGG
Found at i:722484 original size:18 final size:17
Alignment explanation
Indices: 722437--722487 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
722427 TATAGATATG
722437 ATTTTTATTTTATTATTTC
1 ATTTTT-TTTTATT-TTTC
**
722456 ATTTTAGTTTATTTTTC
1 ATTTTTTTTTATTTTTC
722473 ATCTTTTTTTTATTT
1 AT-TTTTTTTTATTT
722488 GTTTAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTTTTTTTTATTTTTC
Found at i:726560 original size:12 final size:12
Alignment explanation
Indices: 726543--726572 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
726533 ATACACGGCT
726543 GTGTGACAAATC
1 GTGTGACAAATC
*
726555 GTGTGACAAGTC
1 GTGTGACAAATC
726567 GTGTGA
1 GTGTGA
726573 ACATACGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (12 bp):
GTGTGACAAATC
Found at i:727581 original size:27 final size:27
Alignment explanation
Indices: 727547--727600 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
727537 ATATTTAAGA
*
727547 AGTCATTAGTATCGTATTAAAATTTGG
1 AGTCATTAGTATCGCATTAAAATTTGG
727574 AGTCATTAGTATCGCATTAAAATTTGG
1 AGTCATTAGTATCGCATTAAAATTTGG
727601 TGACGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
AGTCATTAGTATCGCATTAAAATTTGG
Found at i:729014 original size:19 final size:19
Alignment explanation
Indices: 728990--729029 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
728980 CTCTGAAGTG
**
728990 ATATTGGCTTTTAAGAGCA
1 ATATTGGCTCGTAAGAGCA
729009 ATATTGGCTCGTAAGAGCA
1 ATATTGGCTCGTAAGAGCA
729028 AT
1 AT
729030 TTACTGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (19 bp):
ATATTGGCTCGTAAGAGCA
Found at i:729097 original size:35 final size:35
Alignment explanation
Indices: 729056--729148 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 35
729046 TAAGAACTAA
*
729056 AAATTACTGGGAATCTTGAAGAGCTTGTATGAGTT
1 AAATTACTGGGAATCTTGAAGAGCTCGTATGAGTT
*
729091 AAATTACTGGGAATCTTGAAGAACTCGTATGAGTT
1 AAATTACTGGGAATCTTGAAGAGCTCGTATGAGTT
* *
729126 AAATCACT-GGAAGACTTGAAGAG
1 AAATTACTGGGAA-TCTTGAAGAG
729149 ATCTACTGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 4 0.08
35 48 0.92
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (35 bp):
AAATTACTGGGAATCTTGAAGAGCTCGTATGAGTT
Found at i:730905 original size:25 final size:25
Alignment explanation
Indices: 730877--730951 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
730867 TAGAAATTTA
* *
730877 GCTCTTATGAGCCAAATAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
* *
730902 GCTCTTACGAGCCAGACAGGATATC
1 GCTCTTACGAGCCAAACAGAATATC
* * *
730927 ACTCTTACGAGCCAGACAGGATATC
1 GCTCTTACGAGCCAAACAGAATATC
730952 TTTATCGTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATATC
Found at i:733220 original size:29 final size:28
Alignment explanation
Indices: 733155--733220 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
733145 GACATGTGAC
733155 AAAAATATAAAAAAAATAAAAATTAATA
1 AAAAATATAAAAAAAATAAAAATTAATA
** * **
733183 AAAGTTATAAAAATAATTAAATTTTAATA
1 AAAAATATAAAAA-AAATAAAAATTAATA
733212 AAAAATATA
1 AAAAATATA
733221 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAAATATAAAAAAAATAAAAATTAATA
Found at i:733295 original size:28 final size:29
Alignment explanation
Indices: 733264--733323 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
733254 AAAAATCGCA
* * *
733264 AAAAAAT-ATAAAAAAGTATAAAATTTAT
1 AAAAAATAAAAAAAAACTATAAAATGTAT
*
733292 -AAAAATAAAAAAAAACTATACAATGTAT
1 AAAAAATAAAAAAAAACTATAAAATGTAT
733320 AAAA
1 AAAA
733324 TAATTCCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (29 bp):
AAAAAATAAAAAAAAACTATAAAATGTAT
Found at i:733602 original size:28 final size:29
Alignment explanation
Indices: 733560--733629 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
733550 TATACTTTTT
* * *
733560 TTTACAATTTCTAATAAATTTTAA-ATATA
1 TTTATAATTTTTAATAAAATTTAATA-ATA
*
733589 TTTAT-ATTTTTAATAAAATTTAATAATT
1 TTTATAATTTTTAATAAAATTTAATAATA
733617 TTTATAATTTTTA
1 TTTATAATTTTTA
733630 CTGATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 23 0.66
29 12 0.34
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTATAATTTTTAATAAAATTTAATAATA
Found at i:733629 original size:19 final size:19
Alignment explanation
Indices: 733558--733629 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
733548 TTTATACTTT
* *
733558 TTTTTACAATTTCTAATAA
1 TTTTTATAATTTTTAATAA
*
733577 ATTTTA-AATATATTT-AT-A
1 TTTTTATAAT-T-TTTAATAA
**
733595 TTTTTAATAAAATTTAATAA
1 TTTTT-ATAATTTTTAATAA
733615 TTTTTATAATTTTTA
1 TTTTTATAATTTTTA
733630 CTGATTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 11 0.28
19 19 0.47
20 10 0.25
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTATAATTTTTAATAA
Found at i:737016 original size:67 final size:67
Alignment explanation
Indices: 736908--737041 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
736898 ACGATTTCTT
*
736908 CCCTCTTGGTAGTTTTACCAAGTCCCATGTCTTCTACTGAACGAGTGCTTCCAATTCAACCTACA
1 CCCTCTTGGTAGTTTTACCAAGACCCATGTCTTCTACTGAACGAGTGCTTCCAATTCAACCTACA
736973 TG
66 TG
736975 CCCTCTTGGTAGTTTTACCAAGACCCATGTCTTCTACTGAACGAGTGCTTCCAATTCAACCTACA
1 CCCTCTTGGTAGTTTTACCAAGACCCATGTCTTCTACTGAACGAGTGCTTCCAATTCAACCTACA
737040 TG
66 TG
737042 GCATTCTTCC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (67 bp):
CCCTCTTGGTAGTTTTACCAAGACCCATGTCTTCTACTGAACGAGTGCTTCCAATTCAACCTACA
TG
Found at i:740418 original size:17 final size:16
Alignment explanation
Indices: 740393--740426 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
740383 ATCAATTATG
740393 CTTAAATTTTTATATTT
1 CTTAAATTTTTA-ATTT
*
740410 CTTATATTTTTAATTT
1 CTTAAATTTTTAATTT
740426 C
1 C
740427 ACCCAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTAAATTTTTAATTT
Found at i:742171 original size:22 final size:22
Alignment explanation
Indices: 742141--742189 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
742131 CAGAGAAGCA
*
742141 AAGATAAAATGGTCCAAACTAG
1 AAGACAAAATGGTCCAAACTAG
742163 AAGACAAAATGGTCCAAACTAG
1 AAGACAAAATGGTCCAAACTAG
742185 AAGAC
1 AAGAC
742190 CATTCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (22 bp):
AAGACAAAATGGTCCAAACTAG
Found at i:751348 original size:20 final size:18
Alignment explanation
Indices: 751301--751350 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
751291 CAAGATAAAC
751301 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
751318 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
751338 ATTAAATTAATAT
1 ATTAAATTAATAT
751351 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 8 0.29
18 2 0.07
19 3 0.11
20 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:751352 original size:25 final size:26
Alignment explanation
Indices: 751313--751361 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
751303 TAAATTAAAT
751313 TTAATATTAAGATAATCACT-TTAATA
1 TTAATATTAAGATAAT-ACTATTAATA
*
751339 TTAA-ATTAATATAATACTATTAA
1 TTAATATTAAGATAATACTATTAA
751362 AATAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
TTAATATTAAGATAATACTATTAATA
Found at i:751374 original size:37 final size:37
Alignment explanation
Indices: 751333--751409 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
751323 GATAATCACT
*
751333 TTAATATTAAATT-AATA-T-AATACTATTAAAATAAGTA
1 TTAAT-TTAAATTCAATATTAAAT-CTATTAAAACAA-TA
*
751370 TTAATTTTAATTCAATATTAAATCTATTAAAACAATA
1 TTAATTTAAATTCAATATTAAATCTATTAAAACAATA
751407 TTA
1 TTA
751410 TTTTTGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 6 0.17
37 14 0.40
38 12 0.34
39 3 0.09
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (37 bp):
TTAATTTAAATTCAATATTAAATCTATTAAAACAATA
Found at i:754149 original size:33 final size:34
Alignment explanation
Indices: 754107--754172 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
754097 CTGCTCCGAT
754107 AGCCAAGACTAACTATATCCTCAAAT-GAATTGG
1 AGCCAAGACTAACTATATCCTCAAATGGAATTGG
*
754140 AGCCAAGACTAACTATATCCTCAATTGGAATTG
1 AGCCAAGACTAACTATATCCTCAAATGGAATTG
754173 TATACAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (34 bp):
AGCCAAGACTAACTATATCCTCAAATGGAATTGG
Found at i:756717 original size:41 final size:41
Alignment explanation
Indices: 756650--756929 Score: 239
Period size: 41 Copynumber: 6.9 Consensus size: 41
756640 GTTTTCTCAT
* * * *
756650 AAACACCGTAAAAGGTAAGAGTATTAGCAGCATTTATGACA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTTATGAGA
756691 AAACGCCGCAAAAGGTAAGAGCATTAGC-G-ATGTTTATGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCA--TTTATGAGA
* * *
756732 AAACGCCGC-AACGGTAAGAGCATTA-CTGACATTTATAAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAG-CATTTATGAGA
** * * *
756772 AAACGTTGCAAAAGGTCAGAGCATTAGCAACGTTTATGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTTATGAGA
* * * **
756813 AAAAGTCGCAAAAGGTAAGAGCATTAGCGGTGTTTATGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTTATGAGA
* * * **
756854 AAACGCCACAAAAGGGAAGAGCATTAGCGGTGTTTAT-AGGAA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTTATGA-G-A
* * * *
756896 AAACACCGCTAAAGGTTA-AGCAATAGCAGCATTT
1 AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTT
756930 TCCCATAAAC
Statistics
Matches: 197, Mismatches: 33, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
39 2 0.01
40 33 0.17
41 146 0.74
42 16 0.08
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTAAGAGCATTAGCAGCATTTATGAGA
Found at i:756765 original size:81 final size:81
Alignment explanation
Indices: 756659--756929 Score: 271
Period size: 82 Copynumber: 3.3 Consensus size: 81
756649 TAAACACCGT
* *
756659 AAAAGGTAAGAGTATTAGCAGCATTTATGACAAAACGCCGCAAAAGGTAAGAGCATTAGCGATGT
1 AAAAGGTAAGAGCATTAGC-GCATTTATGAGAAAACGCCGCAAAAGGTAAGAGCATTAGCGATGT
*
756724 TTATGAGAAAACGCCGC
65 TTATGAGAAAAAGCCGC
* * ** * * *
756741 -AACGGTAAGAGCATTA-CTGACATTTATAAGAAAACGTTGCAAAAGGTCAGAGCATTAGCAACG
1 AAAAGGTAAGAGCATTAGC-G-CATTTATGAGAAAACGCCGCAAAAGGTAAGAGCATTAGCGATG
*
756804 TTTATGAGAAAAAGTCGC
64 TTTATGAGAAAAAGCCGC
** * * *
756822 AAAAGGTAAGAGCATTAGCGGTGTTTATGAGAAAACGCCACAAAAGGGAAGAGCATTAGCGGTGT
1 AAAAGGTAAGAGCATTAGC-GCATTTATGAGAAAACGCCGCAAAAGGTAAGAGCATTAGCGATGT
*
756887 TTAT-AGGAAAAACACCGC
65 TTATGA-GAAAAA-GCCGC
* * *
756905 TAAAGGTTA-AGCAATAGCAGCATTT
1 AAAAGGTAAGAGCATTAGC-GCATTT
756930 TCCCATAAAC
Statistics
Matches: 151, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
80 2 0.01
81 67 0.44
82 70 0.46
83 12 0.08
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (81 bp):
AAAAGGTAAGAGCATTAGCGCATTTATGAGAAAACGCCGCAAAAGGTAAGAGCATTAGCGATGTT
TATGAGAAAAAGCCGC
Found at i:756835 original size:122 final size:123
Alignment explanation
Indices: 756659--756879 Score: 336
Period size: 122 Copynumber: 1.8 Consensus size: 123
756649 TAAACACCGT
* * *
756659 AAAAGGTAAGAGTATTAGCAGCATTTATGACAAAACGCCGCAAAAGGTAAGAGCATTAGCGATGT
1 AAAAGGTAAGAGCATTAGCAACATTTATGACAAAAAGCCGCAAAAGGTAAGAGCATTAGCGATGT
* * *
756724 TTATGAGAAAACGCCGC-AACGGTAAGAGCATTACTGACATTTATAAGAAAACGTTGC
66 TTATGAGAAAACGCCACAAAAGGGAAGAGCATTACTGACATTTATAAGAAAACGTTGC
* * * * *
756781 AAAAGGTCAGAGCATTAGCAACGTTTATGAGAAAAAGTCGCAAAAGGTAAGAGCATTAGCGGTGT
1 AAAAGGTAAGAGCATTAGCAACATTTATGACAAAAAGCCGCAAAAGGTAAGAGCATTAGCGATGT
756846 TTATGAGAAAACGCCACAAAAGGGAAGAGCATTA
66 TTATGAGAAAACGCCACAAAAGGGAAGAGCATTA
756880 GCGGTGTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
122 73 0.84
123 14 0.16
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (123 bp):
AAAAGGTAAGAGCATTAGCAACATTTATGACAAAAAGCCGCAAAAGGTAAGAGCATTAGCGATGT
TTATGAGAAAACGCCACAAAAGGGAAGAGCATTACTGACATTTATAAGAAAACGTTGC
Found at i:758406 original size:41 final size:40
Alignment explanation
Indices: 758361--758449 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
758351 AGGGGTTAAG
*** *
758361 CAATAGCGACATTTATGGGAAAAACGCCGCAAAAGGTAAAT
1 CAATAGCGACATTT-TCCCAAAAACACCGCAAAAGGTAAAT
* * *
758402 CAATAGCGACGTTTTCCCATAAACACCGTAAAAGGTAAAT
1 CAATAGCGACATTTTCCCAAAAACACCGCAAAAGGTAAAT
758442 CAATAGCG
1 CAATAGCG
758450 GCGTTTACGA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 28 0.68
41 13 0.32
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (40 bp):
CAATAGCGACATTTTCCCAAAAACACCGCAAAAGGTAAAT
Found at i:759374 original size:16 final size:16
Alignment explanation
Indices: 759353--759387 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
759343 CGATAGCGGA
759353 AGCATTTTAGGTGTAT
1 AGCATTTTAGGTGTAT
759369 AGCATTTTAGGTGTAT
1 AGCATTTTAGGTGTAT
759385 AGC
1 AGC
759388 TTCAAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (16 bp):
AGCATTTTAGGTGTAT
Found at i:761093 original size:34 final size:34
Alignment explanation
Indices: 761045--761156 Score: 116
Period size: 34 Copynumber: 3.0 Consensus size: 34
761035 ACTTATTTAA
*
761045 TTAAATATTTAATTATTAAAAACAATCCAAATAT
1 TTAATTATTTAATTATTAAAAACAATCCAAATAT
* *
761079 TTAATTATTTAATTATTAAAAATAACTCAAATATGAATTTTAT
1 TTAATTATTTAATTATTAAAAACAA-TC---CA--AA---TAT
761122 TTAATTATTTAATTATTAAAAACAATCCAAATAT
1 TTAATTATTTAATTATTAAAAACAATCCAAATAT
761156 T
1 T
761157 CGATTCAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
34 27 0.42
35 2 0.03
37 2 0.03
38 1 0.02
39 1 0.02
40 2 0.03
42 2 0.03
43 27 0.42
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (34 bp):
TTAATTATTTAATTATTAAAAACAATCCAAATAT
Found at i:764632 original size:13 final size:13
Alignment explanation
Indices: 764614--764639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
764604 CAAGCAGCTC
764614 TAACCTAACTTGT
1 TAACCTAACTTGT
764627 TAACCTAACTTGT
1 TAACCTAACTTGT
764640 CACCGCATCT
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
TAACCTAACTTGT
Found at i:765683 original size:20 final size:20
Alignment explanation
Indices: 765658--765695 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
765648 CATCCTTTTC
*
765658 ATTTGTTTATTTTTTAACCA
1 ATTTGTTCATTTTTTAACCA
765678 ATTTGTTCATTTTTTAAC
1 ATTTGTTCATTTTTTAAC
765696 ATAGTGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTGTTCATTTTTTAACCA
Found at i:767331 original size:14 final size:15
Alignment explanation
Indices: 767295--767333 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
767285 GAGAGACCAT
*
767295 AAAAGTATTTTAAAG
1 AAAAATATTTTAAAG
767310 AAAGAATATTTT-AAG
1 AAA-AATATTTTAAAG
767325 AAAAATATT
1 AAAAATATT
767334 AGCCTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAAATATTTTAAAG
Found at i:768450 original size:43 final size:43
Alignment explanation
Indices: 768347--768434 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
768337 CAGCTTCAAA
*
768347 ATATGATGAAAATGTTTTAGTAAAATCAATCGTAGAATTCATC
1 ATATGATGAAAATGTTTTAGTAAAATCAATCGTAGAATCCATC
768390 ATATGATGAAAATGTTTTAGTAAAATCAATCGTAGAATCCATC
1 ATATGATGAAAATGTTTTAGTAAAATCAATCGTAGAATCCATC
768433 AT
1 AT
768435 CTTAGACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
ATATGATGAAAATGTTTTAGTAAAATCAATCGTAGAATCCATC
Found at i:768742 original size:43 final size:43
Alignment explanation
Indices: 768645--768742 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
768635 TTTGTTAATG
* *
768645 TTAGCGGCGTTTGTGGGAAAAACGCCTCTAAAGAACATGTTAT
1 TTAGCGGCGTTAGTGGGAAAAACGCCACTAAAGAACATGTTAT
* * * * *
768688 ATAGCGACGTTAGTGGGAAAAATGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTAGTGGGAAAAACGCCACTAAAGAACATGTTAT
*
768731 TTAGTGGCGTTA
1 TTAGCGGCGTTA
768743 TCTTTAGCGG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTAGTGGGAAAAACGCCACTAAAGAACATGTTAT
Found at i:775838 original size:21 final size:20
Alignment explanation
Indices: 775800--775839 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
775790 TTTCCCTTGC
* *
775800 TTTATTTCTTTTACTTTAAT
1 TTTATTTCTTTAAATTTAAT
775820 TTTATGTTCTTTAAATTTAA
1 TTTAT-TTCTTTAAATTTAA
775840 AACCCAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTATTTCTTTAAATTTAAT
Found at i:777816 original size:18 final size:18
Alignment explanation
Indices: 777785--777819 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
777775 ACTTATTCAG
* *
777785 TTTCTTCTTTCCTTTAGC
1 TTTCTACTTCCCTTTAGC
777803 TTTCTACTTCCCTTTAG
1 TTTCTACTTCCCTTTAG
777820 AGGATAAGGG
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:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTCTACTTCCCTTTAGC
Found at i:780683 original size:17 final size:17
Alignment explanation
Indices: 780661--780696 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
780651 ATATAACACT
780661 ATTAAGATAAATATTAA
1 ATTAAGATAAATATTAA
* *
780678 ATTAAGTTTAATATTAA
1 ATTAAGATAAATATTAA
780695 AT
1 AT
780697 CTATTAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTAAGATAAATATTAA
Found at i:780997 original size:19 final size:20
Alignment explanation
Indices: 780973--781010 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
780963 CTCCACTAGT
*
780973 TTTTGGG-TCTTGGTCCCAG
1 TTTTGGGCTCTTGGACCCAG
780992 TTTTGGGCTCTTGGACCCA
1 TTTTGGGCTCTTGGACCCA
781011 ATTTACTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.08, C:0.24, G:0.29, T:0.39
Consensus pattern (20 bp):
TTTTGGGCTCTTGGACCCAG
Done.