Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015140.1 Kokia drynarioides strain JFW-HI SEQ_130184, 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: 233467
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 1111 characters in sequence are not A, C, G, or T
Found at i:8777 original size:16 final size:16
Alignment explanation
Indices: 8756--8798 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
8746 CTTTTTCAGG
8756 TCATTTTAAATTTGAA
1 TCATTTTAAATTTGAA
*
8772 TCATTTCAAGA-TTGAA
1 TCATTTTAA-ATTTGAA
*
8788 TTATTTTAAAT
1 TCATTTTAAAT
8799 CTAAATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (16 bp):
TCATTTTAAATTTGAA
Found at i:17440 original size:24 final size:26
Alignment explanation
Indices: 17394--17443 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
17384 GCTTAGTAGA
17394 AATTTAATTTCTACTTTTATTTTTAAT
1 AATTTAATTTCTA-TTTTATTTTTAAT
17421 AATTTAATTT-T-TTTTATTTTTAA
1 AATTTAATTTCTATTTTATTTTTAA
17444 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (26 bp):
AATTTAATTTCTATTTTATTTTTAAT
Found at i:17446 original size:22 final size:25
Alignment explanation
Indices: 17393--17449 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
17383 TGCTTAGTAG
17393 AAATTTAATTTCTACTTTTATTTTTA
1 AAATTTAATTTCTA-TTTTATTTTTA
17419 ATAATTTAATTT-T-TTTTATTTTT-
1 A-AATTTAATTTCTATTTTATTTTTA
17442 AAATTTAA
1 AAATTTAA
17450 AAATCTCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 10 0.33
26 2 0.07
27 10 0.33
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
AAATTTAATTTCTATTTTATTTTTA
Found at i:19221 original size:31 final size:31
Alignment explanation
Indices: 19184--19263 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
19174 TGACTCCAAA
* *
19184 AAGTTTAAGTACCAACTTA-AAAAAATGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAA-GTGTC
* *
19215 AAGTTTAGGTATCAAATTAGAAATAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
*
19246 AAGTTTAGGTACTAAATT
1 AAGTTTAGGTACCAAATT
19264 GAACCAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 37 0.88
32 5 0.12
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
Found at i:26518 original size:15 final size:17
Alignment explanation
Indices: 26494--26525 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26484 GGGGTTATTA
26494 AAATTATTG-TTATTTT
1 AAATTATTGTTTATTTT
26510 AAATT-TTGTTTATTTT
1 AAATTATTGTTTATTTT
26526 CACCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
AAATTATTGTTTATTTT
Found at i:39522 original size:237 final size:236
Alignment explanation
Indices: 39103--39578 Score: 726
Period size: 237 Copynumber: 2.0 Consensus size: 236
39093 ATACGGAAGA
39103 AATAGAAAATAAGCTCATTTCCCTTTTCATTGCCGGCTCCAAATTAGAGAAAATGCTAATACATT
1 AATAGAAAATAAGCTCATTTCCCTTTTCATTGCCGGCTCCAAATTAGAGAAAATGCTAATACATT
* *
39168 TGACTACTTCGTCAGTTGTAAAAAAGCAGGAGTGAATCTTGTAATGACTTTATGCTACATTAGTC
66 TGACTACTTCGTCAGTGGTAAAAAAGCAGGAGTGAATCTTGTAATAACTTTATGCTACATTAGTC
** * * *
39233 AGTTTTCGCGAGAATTGTAGGAGGGGAAGAAAGGCAAGGAAAATTTCATTAAAAGAAC-TGTAAG
131 AGTTTTCGCGAGAATCATAGAAGGGGAAGAAAGGCAAGGAAAATTGCATTAAAAGAACAT-CAAG
39297 GAAGCCATTCCAATGAGTTTTTCATTAAGG-GGTGAAGTGATAC
195 GAAGCCATTCCAATGAG-TTTTCATTAAGGAGG-GAAGTGATAC
** *
39340 AATAGAAAATAAAG-TCATTTCTTTTTTCATTGCTGGCTCCAAATTAGAGAAAATGCTAATACAT
1 AATAGAAAAT-AAGCTCATTTCCCTTTTCATTGCCGGCTCCAAATTAGAGAAAATGCTAATACAT
* * **
39404 TTTACTATCTT-GTTAGTGGTAAAAAAGCAGGAGTGTGTCTTGTAATAACTTTATGCTACATTAG
65 TTGACTA-CTTCGTCAGTGGTAAAAAAGCAGGAGTGAATCTTGTAATAACTTTATGCTACATTAG
* * *
39468 TCAGTTTTCGTGAGAATCATAGAAGGGGAAGGAAGGCAAGGAAGATTGCATTAAAAGAACATCAA
129 TCAGTTTTCGCGAGAATCATAGAAGGGGAAGAAAGGCAAGGAAAATTGCATTAAAAGAACATCAA
39533 GGAAGCCATTCCAATGAGTTTTCATTAAGGAGGGAAGTGATAC
194 GGAAGCCATTCCAATGAGTTTTCATTAAGGAGGGAAGTGATAC
39576 AAT
1 AAT
39579 TTGGTGTTTT
Statistics
Matches: 218, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
236 25 0.11
237 186 0.85
238 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (236 bp):
AATAGAAAATAAGCTCATTTCCCTTTTCATTGCCGGCTCCAAATTAGAGAAAATGCTAATACATT
TGACTACTTCGTCAGTGGTAAAAAAGCAGGAGTGAATCTTGTAATAACTTTATGCTACATTAGTC
AGTTTTCGCGAGAATCATAGAAGGGGAAGAAAGGCAAGGAAAATTGCATTAAAAGAACATCAAGG
AAGCCATTCCAATGAGTTTTCATTAAGGAGGGAAGTGATAC
Found at i:43223 original size:1 final size:1
Alignment explanation
Indices: 43217--43241 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43207 ACTGTTAAGA
43217 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
43242 AAAATTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54456 original size:22 final size:22
Alignment explanation
Indices: 54422--54475 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
54412 GAAAATGATA
* *
54422 ATAATC-CATAAATGAAATAAG
1 ATAATCACAAAAATAAAATAAG
54443 ATAATCACAAAAATAAAATAAG
1 ATAATCACAAAAATAAAATAAG
*
54465 ATAATTACAAA
1 ATAATCACAAA
54476 TCAAAGTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (22 bp):
ATAATCACAAAAATAAAATAAG
Found at i:55529 original size:18 final size:18
Alignment explanation
Indices: 55506--55542 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
55496 AGTTCTTTTC
55506 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
55524 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
55542 T
1 T
55543 AGATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:55535 original size:23 final size:23
Alignment explanation
Indices: 55501--55544 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
55491 AAGACAGTTC
55501 TTTTCTTTCTATTA-TATTAGTA
1 TTTTCTTTCTATTAGTATTAGTA
55523 TTTTCTATTCTATTAGTATTAG
1 TTTTCT-TTCTATTAGTATTAG
55545 ATTAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTCTTTCTATTAGTATTAGTA
Found at i:72572 original size:5 final size:5
Alignment explanation
Indices: 72559--72615 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
72549 CTGCGAAACC
* *
72559 AAAAG AAAAT AAAAG AACAA- AAATG AAAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AA-AAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
72609 -AAAG AAA
1 AAAAG AAA
72616 GTGAAAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 9 0.21
5 28 0.65
6 6 0.14
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:72605 original size:9 final size:9
Alignment explanation
Indices: 72585--72615 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
72575 ACAAAAATGA
72585 AAAAGAAAAG
1 AAAAG-AAAG
72595 AAAAGAAAG
1 AAAAGAAAG
72604 AAAAGAAAG
1 AAAAGAAAG
72613 AAA
1 AAA
72616 GTGAAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:72607 original size:26 final size:25
Alignment explanation
Indices: 72559--72611 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
72549 CTGCGAAACC
*
72559 AAAAGAAAATAAAAGAACAAAAATGA
1 AAAAGAAAAGAAAAGAACAAAAA-GA
72585 AAAAGAAAAGAAAAGAA-AGAAAAGA
1 AAAAGAAAAGAAAAGAACA-AAAAGA
72610 AA
1 AA
72612 GAAAGTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAGAAAAGAACAAAAAGA
Found at i:72721 original size:18 final size:17
Alignment explanation
Indices: 72689--72722 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
72679 GGCGTGAAAA
*
72689 CAAAATTGGCTTAAATG
1 CAAAATTGCCTTAAATG
72706 CAAAATTGACCTTAAAT
1 CAAAATTG-CCTTAAAT
72723 TGTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
CAAAATTGCCTTAAATG
Found at i:74525 original size:23 final size:25
Alignment explanation
Indices: 74474--74526 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
74464 TTTTTTATTT
74474 ATTAAAATTTTTTTATATAGTTATC
1 ATTAAAATTTTTTTATATAGTTATC
*
74499 -TTAATATTTTTTT-TAT-GTT-TAC
1 ATTAAAATTTTTTTATATAGTTAT-C
74521 ATTAAA
1 ATTAAA
74527 GTAATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 4 0.17
23 7 0.29
24 12 0.50
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTAAAATTTTTTTATATAGTTATC
Found at i:77574 original size:10 final size:9
Alignment explanation
Indices: 77528--77596 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
77518 AATATTTTTT
77528 AAAATTATA
1 AAAATTATA
*
77537 AAACATGATTA
1 AAA-ATTA-TA
77548 AAAATTATA
1 AAAATTATA
77557 AAAATTATA
1 AAAATTATA
*
77566 AAATTTTATA
1 AAA-ATTATA
*
77576 ATAAAATA-A
1 A-AAATTATA
*
77585 AAAATGATA
1 AAAATTATA
77594 AAA
1 AAA
77597 GTCATTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.08
9 23 0.48
10 14 0.29
11 7 0.15
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:77588 original size:37 final size:37
Alignment explanation
Indices: 77547--77618 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
77537 AAACATGATT
* *
77547 AAAAATTATAAAAATTA-TAAAATTTTATAATAAAATA
1 AAAAATGATAAAAATCATTAAAA-TTTATAATAAAATA
* *
77584 AAAAATGATAAAAGTCATTAAAATTTATATTAAAA
1 AAAAATGATAAAAATCATTAAAATTTATAATAAAA
77619 ATTTGAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 25 0.83
38 5 0.17
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (37 bp):
AAAAATGATAAAAATCATTAAAATTTATAATAAAATA
Found at i:77690 original size:15 final size:15
Alignment explanation
Indices: 77672--77723 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
77662 TTAAATACTG
77672 AATTTTTTACTATTC
1 AATTTTTTACTATTC
* * *
77687 AATTTTATAAGC-ACTG
1 AATTTT-TTA-CTATTC
77703 AATTTTTTACTATTC
1 AATTTTTTACTATTC
77718 AATTTT
1 AATTTT
77724 ATAAGCACTG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 16 0.57
16 10 0.36
17 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (15 bp):
AATTTTTTACTATTC
Found at i:77703 original size:31 final size:31
Alignment explanation
Indices: 77668--77738 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
77658 AAAATTAAAT
77668 ACTGAATTTTTTACTATTCAATTTTATAAGC
1 ACTGAATTTTTTACTATTCAATTTTATAAGC
77699 ACTGAATTTTTTACTATTCAATTTTATAAGC
1 ACTGAATTTTTTACTATTCAATTTTATAAGC
77730 ACTGAATTT
1 ACTGAATTT
77739 ATATTATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (31 bp):
ACTGAATTTTTTACTATTCAATTTTATAAGC
Found at i:77708 original size:16 final size:16
Alignment explanation
Indices: 77687--77738 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
77677 TTTACTATTC
77687 AATTTTATAAGCACTG
1 AATTTTATAAGCACTG
* * *
77703 AATTTT-TTA-CTATTC
1 AATTTTATAAGC-ACTG
77718 AATTTTATAAGCACTG
1 AATTTTATAAGCACTG
77734 AATTT
1 AATTT
77739 ATATTATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.37
16 15 0.56
17 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (16 bp):
AATTTTATAAGCACTG
Found at i:83093 original size:14 final size:14
Alignment explanation
Indices: 83071--83103 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
83061 ACAATTTCAC
*
83071 TATTATGTTGTTAT
1 TATTTTGTTGTTAT
83085 TATTTTGTTGTTAT
1 TATTTTGTTGTTAT
83099 TATTT
1 TATTT
83104 GGATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TATTTTGTTGTTAT
Found at i:90094 original size:20 final size:20
Alignment explanation
Indices: 90069--90108 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
90059 TTAAGCTAAC
*
90069 TTTTAAGAGAAAAAAATCTT
1 TTTTAAGACAAAAAAATCTT
*
90089 TTTTAAGACATAAAAATCTT
1 TTTTAAGACAAAAAAATCTT
90109 CTCATATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTTAAGACAAAAAAATCTT
Found at i:101023 original size:22 final size:23
Alignment explanation
Indices: 100972--101031 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
100962 TTTAATTTAG
* *
100972 TATTTT-ATAATTTATAAAATTT
1 TATTTTAATAATTAATAAAATTA
**
100994 TAAATTAATAA-TAATAAAATTA
1 TATTTTAATAATTAATAAAATTA
101016 TATTTTAATCAATTAA
1 TATTTTAAT-AATTAA
101032 AAATGATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 20 0.69
23 6 0.21
24 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTTAATAATTAATAAAATTA
Found at i:101030 original size:30 final size:30
Alignment explanation
Indices: 100996--101053 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
100986 TAAAATTTTA
* *
100996 AATTAATAATAATAA-AATTATATTTTAATC
1 AATTAAAAATAATAATAATT-TAATTTAATC
*
101026 AATTAAAAATGATAATAATTTAATTTAA
1 AATTAAAAATAATAATAATTTAATTTAA
101054 CCCTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
AATTAAAAATAATAATAATTTAATTTAATC
Found at i:109724 original size:23 final size:24
Alignment explanation
Indices: 109698--109743 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
109688 GAATTAAAAA
*
109698 TTATAATTAATTA-AAAAGAATTC
1 TTATAATTAATGATAAAAGAATTC
*
109721 TTATATTTAATGATAAAAGAATT
1 TTATAATTAATGATAAAAGAATT
109744 ATTGGGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (24 bp):
TTATAATTAATGATAAAAGAATTC
Found at i:118456 original size:20 final size:19
Alignment explanation
Indices: 118427--118466 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
118417 AAATCATCAC
118427 TTTTTAAAATTTTAAATAAA
1 TTTTTAAAATTTTAAA-AAA
*
118447 TTTTTTAAATTTTAAAAAA
1 TTTTTAAAATTTTAAAAAA
118466 T
1 T
118467 AATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATTTTAAAAAA
Found at i:120026 original size:30 final size:31
Alignment explanation
Indices: 119970--120036 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
119960 AAAATAATAT
119970 TGAATTATTCAAAATTTTTCATTTAAGTCAC
1 TGAATTATTCAAAATTTTTCATTTAAGTCAC
120001 TGAATTATTCGAAAA-TTTT-ATTTAAGTCAC
1 TGAATTATTC-AAAATTTTTCATTTAAGTCAC
*
120031 TAAATT
1 TGAATT
120037 GTTAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 16 0.47
31 14 0.41
32 4 0.12
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.45
Consensus pattern (31 bp):
TGAATTATTCAAAATTTTTCATTTAAGTCAC
Found at i:123572 original size:21 final size:20
Alignment explanation
Indices: 123552--123588 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
123542 TAATATTATT
123552 TTCAAA-AAAAATCTAATTA
1 TTCAAACAAAAATCTAATTA
*
123571 TTCAAACAAACATCTAAT
1 TTCAAACAAAAATCTAAT
123589 GTTCACGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
TTCAAACAAAAATCTAATTA
Found at i:124792 original size:24 final size:26
Alignment explanation
Indices: 124754--124802 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
124744 TCTACGTGGG
124754 CATAATCTCTCATAT-TCATCATTTAT
1 CATAATCTCTCATATATCA-CATTTAT
124780 CATAAT-T-TCATATATCACATTTA
1 CATAATCTCTCATATATCACATTTA
124803 CATTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 12 0.55
25 4 0.18
26 6 0.27
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTAT
Found at i:126526 original size:9 final size:9
Alignment explanation
Indices: 126512--126536 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
126502 CTTATAACAC
126512 AATTCTAAT
1 AATTCTAAT
126521 AATTCTAAT
1 AATTCTAAT
126530 AATTCTA
1 AATTCTA
126537 CTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTCTAAT
Found at i:133807 original size:28 final size:29
Alignment explanation
Indices: 133776--133835 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
133766 AATTAATACA
133776 ATTTTAAACTT-AAATTA-AAAAGATGAGT
1 ATTTTAAACTTAAAATTAGAAAA-ATGAGT
*
133804 ATTTTAAATTTAAAATTAGAAAAATGAGT
1 ATTTTAAACTTAAAATTAGAAAAATGAGT
133833 ATT
1 ATT
133836 AACTCTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.34
29 15 0.52
30 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTTTAAACTTAAAATTAGAAAAATGAGT
Found at i:134526 original size:21 final size:22
Alignment explanation
Indices: 134493--134534 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
134483 GGATAAAGCA
*
134493 AGGGAAATGGAAGGAAAAGAGG
1 AGGGAAATCGAAGGAAAAGAGG
*
134515 AGGG-AATCGAAGGGAAAGAG
1 AGGGAAATCGAAGGAAAAGAG
134535 AACAAAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.48, C:0.02, G:0.45, T:0.05
Consensus pattern (22 bp):
AGGGAAATCGAAGGAAAAGAGG
Found at i:135314 original size:210 final size:210
Alignment explanation
Indices: 134952--135582 Score: 1190
Period size: 210 Copynumber: 3.0 Consensus size: 210
134942 AGGTCAAGAA
134952 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
1 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
* * *
135017 AAAGAAACAAGTTACCGAAAGTGAAGCCATTGAAGGGACAGATACAGATAAGAGTCGAAGAAGGG
66 AAGGAAACAAGTTACTGAAAGTGAAGCCATTGAAGGGACATATACAGATAAGAGTCGAAGAAGGG
135082 CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
131 CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
135147 GAAGAAGAAGAGCCT
196 GAAGAAGAAGAGCCT
135162 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
1 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
135227 AAGGAAACAAGTTACTGAAAGTGAAGCCATTGAAGGGACATATACAGATAAGAGTCGAAGAAGGG
66 AAGGAAACAAGTTACTGAAAGTGAAGCCATTGAAGGGACATATACAGATAAGAGTCGAAGAAGGG
*
135292 CGAAAAATGGGTCTTCGGGAATGAATGAGTCGGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
131 CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
*
135357 GAAGAAGAGGAGCCT
196 GAAGAAGAAGAGCCT
*
135372 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGTATGCAAAGAAACGAGGAAGGGGTAGGCC
1 GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
* *
135437 AAGGAAACAAGCTACTGAAAGTGAAGCCATTGAAGGGACATACACAGATAAGAGTCGAAGAAGGG
66 AAGGAAACAAGTTACTGAAAGTGAAGCCATTGAAGGGACATATACAGATAAGAGTCGAAGAAGGG
135502 CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
131 CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
135567 GAAGAAGAAGAGCCT
196 GAAGAAGAAGAGCCT
135582 G
1 G
135583 TGCCTGGTTC
Statistics
Matches: 411, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 411 1.00
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.19
Consensus pattern (210 bp):
GATGGTTTTATTAGTGAGAATGGTGATAATACGGTGCATGCAAAGAAACGAGGAAGGGGTAGGCC
AAGGAAACAAGTTACTGAAAGTGAAGCCATTGAAGGGACATATACAGATAAGAGTCGAAGAAGGG
CGAAAAATGGGTCTTCGGGAATGAATGAGTCAGAAAATTTGGTTAAGCCCTTAAGGGTTCCCGGG
GAAGAAGAAGAGCCT
Found at i:149973 original size:6 final size:6
Alignment explanation
Indices: 149964--149991 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
149954 GGCTGTTCTC
149964 GTTCCT GTTCCT GTTCCT GTTCCT GTTC
1 GTTCCT GTTCCT GTTCCT GTTCCT GTTC
149992 TTGTCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (6 bp):
GTTCCT
Found at i:157666 original size:19 final size:19
Alignment explanation
Indices: 157638--157674 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
157628 ATAAATGCTT
*
157638 AACTTATCTAAATGTTTTA
1 AACTTATCTAAATATTTTA
*
157657 AACTTCTCTAAATATTTT
1 AACTTATCTAAATATTTT
157675 TCGCTCTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (19 bp):
AACTTATCTAAATATTTTA
Found at i:160561 original size:16 final size:16
Alignment explanation
Indices: 160538--160593 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
160528 CGTTTAGTTC
160538 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
160554 GTTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
160570 GCTGTAATGGAATAGTA
1 GCTGTAATGGAATAG-A
160587 -CTGTAAT
1 GCTGTAAT
160594 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 34 0.97
17 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:160798 original size:58 final size:56
Alignment explanation
Indices: 160736--160900 Score: 172
Period size: 58 Copynumber: 2.8 Consensus size: 56
160726 TTTTAGTTAG
160736 ATAATTATTGTTATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATA
1 ATAATTATT-TTATTAAATTTTAATATA-ATTATTATTAAATATAATTTAAT-AAAATA
* * * * *
160794 ATAATTAATTTAATTATATTTTAACATAATTATTATTAAATACAATATAATAAAATA
1 ATAATT-ATTTTATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAATA
* *
160851 AT-ATATAATTTAATAACATTTTTAATATAATTATTATTAAAATATGAATT
1 ATAAT-TATTTTATTAA-A-TTTTAATATAATTATTATT-AAATAT-AATT
160901 AGTAAAAGTT
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
56 8 0.09
57 10 0.11
58 58 0.66
59 9 0.10
60 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (56 bp):
ATAATTATTTTATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAATA
Found at i:176372 original size:19 final size:19
Alignment explanation
Indices: 176348--176386 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
176338 TTTAAAATTT
176348 AAATATTCAAAAAATAAAA
1 AAATATTCAAAAAATAAAA
* *
176367 AAATATTTAAAAAGTAAAA
1 AAATATTCAAAAAATAAAA
176386 A
1 A
176387 TTTTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATATTCAAAAAATAAAA
Found at i:178212 original size:14 final size:12
Alignment explanation
Indices: 178182--178206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
178172 ATTGTATTAA
178182 AAATTTTAATAT
1 AAATTTTAATAT
178194 AAATTTTAATAT
1 AAATTTTAATAT
178206 A
1 A
178207 TCAATTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTTAATAT
Found at i:178602 original size:15 final size:17
Alignment explanation
Indices: 178581--178621 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
178571 AAACTCTTTA
178581 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
178597 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
178613 AAAATTATA
1 AAAATTATA
178622 TTTCTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:178854 original size:23 final size:25
Alignment explanation
Indices: 178811--178856 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
178801 TGTGCTAATC
178811 AAATATATTCTATTATATTTATTCA
1 AAATATATTCTATTATATTTATTCA
*
178836 AAATATATT-TTTTAT-TTTATT
1 AAATATATTCTATTATATTTATT
178857 ATATTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATATTCTATTATATTTATTCA
Found at i:181520 original size:29 final size:32
Alignment explanation
Indices: 181478--181540 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 32
181468 TATTTATAAC
*
181478 TTTTAAAAAATTAAATTA-AATTTT-T-ATTA
1 TTTTAAAAAATTAAAGTATAATTTTATCATTA
**
181507 TTTTAAAATGTTAAAGTATAATTTTATCATTA
1 TTTTAAAAAATTAAAGTATAATTTTATCATTA
181539 TT
1 TT
181541 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.54
30 6 0.21
31 1 0.04
32 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTTAAAAAATTAAAGTATAATTTTATCATTA
Found at i:185722 original size:112 final size:112
Alignment explanation
Indices: 185601--185824 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
185591 AGCTGGCCAA
185601 ATAGGTTTTTTTTTTTAAGAATTAGGGAAATAGGTAAATTTTGGAGAGAGTATGAAAAACGTGCC
1 ATAGGTTTTTTTTTTTAAGAATTAGGGAAATAGGTAAATTTTGGAGAGAGTATGAAAAACGTGCC
185666 TAATTGAATGCGTTTTTTGCACAATTGACAGGAAAGTTCGTTCAGTT
66 TAATTGAATGCGTTTTTTGCACAATTGACAGGAAAGTTCGTTCAGTT
185713 ATAGGTTTTTTTTTTTAAGAATTAGGGAAATAGGTAAATTTTGGAGAGAGTATGAAAAACGTGCC
1 ATAGGTTTTTTTTTTTAAGAATTAGGGAAATAGGTAAATTTTGGAGAGAGTATGAAAAACGTGCC
185778 TAATTGAATGCGTTTTTTGCACAATTGACAGGAAAGTTCGTTCAGTT
66 TAATTGAATGCGTTTTTTGCACAATTGACAGGAAAGTTCGTTCAGTT
185825 GAACGAGTTT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (112 bp):
ATAGGTTTTTTTTTTTAAGAATTAGGGAAATAGGTAAATTTTGGAGAGAGTATGAAAAACGTGCC
TAATTGAATGCGTTTTTTGCACAATTGACAGGAAAGTTCGTTCAGTT
Found at i:212709 original size:13 final size:14
Alignment explanation
Indices: 212683--212729 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
212673 TGAAGTAACA
212683 ATTTTTTAATAATT
1 ATTTTTTAATAATT
212697 ATTTTTTAA-AATT
1 ATTTTTTAATAATT
* *
212710 AATATTATAAATAATT
1 -AT-TTTTTAATAATT
212726 ATTT
1 ATTT
212730 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 7 0.25
16 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTTAATAATT
Found at i:213240 original size:30 final size:30
Alignment explanation
Indices: 213172--213256 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
213162 GATTAAATCA
* * *
213172 AAATTAAAGTTTCAAGTATATATTTTAACT
1 AAATTAAAGTTTCAAGTATATAATTGAACC
* * *
213202 ATAATTAAAGTTTCACGTGTATAATTGCACC
1 A-AATTAAAGTTTCAAGTATATAATTGAACC
* *
213233 AAATTAAAG-TTCATGTATAAAATT
1 AAATTAAAGTTTCAAGTATATAATT
213257 ATACATGAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 12 0.27
30 9 0.20
31 24 0.53
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATAATTGAACC
Found at i:214150 original size:20 final size:20
Alignment explanation
Indices: 214127--214169 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
214117 ATGTTGATCG
* *
214127 ATGATGTGACATGTTAATTA
1 ATGATATGACAAGTTAATTA
*
214147 ATGATATGATAAGTTAATTA
1 ATGATATGACAAGTTAATTA
214167 ATG
1 ATG
214170 TTGACCCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGATATGACAAGTTAATTA
Found at i:214637 original size:29 final size:28
Alignment explanation
Indices: 214597--214659 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
214587 AAATTATATA
*
214597 TTTTTAACAATTTTTCAAT-TTTTAAGAT
1 TTTTTAACAATTTAT-AATATTTTAAGAT
* *
214625 TTTTTTACGAATTTATAATATTTTAATAT
1 TTTTTAAC-AATTTATAATATTTTAAGAT
214654 TTTTTA
1 TTTTTA
214660 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTTAACAATTTATAATATTTTAAGAT
Found at i:214657 original size:9 final size:9
Alignment explanation
Indices: 214538--214668 Score: 51
Period size: 9 Copynumber: 14.3 Consensus size: 9
214528 CTGTTTGTTA
214538 TAATAATTTT
1 TAAT-ATTTT
214548 TAAT-TTTT
1 TAATATTTT
*
214556 TAAAATTAATT
1 TAATATT--TT
214567 TAATATTTTT
1 TAATA-TTTT
214577 TAA-A-TTT
1 TAATATTTT
* * *
214584 TAAAAATTA
1 TAATATTTT
214593 T-ATATTTT
1 TAATATTTT
*
214601 TAACAATTTT
1 TAA-TATTTT
214611 TCAAT-TTTT
1 T-AATATTTT
* *
214620 AAGATTTTTT
1 TA-ATATTTT
*
214630 TACGA-ATTTA
1 TA--ATATTTT
214640 TAATA-TTT
1 TAATATTTT
214648 TAATATTTT
1 TAATATTTT
*
214657 TTATATTTT
1 TAATATTTT
214666 TAA
1 TAA
214669 ATAAAATTTA
Statistics
Matches: 92, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
7 6 0.07
8 22 0.24
9 27 0.29
10 25 0.27
11 10 0.11
12 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (9 bp):
TAATATTTT
Found at i:214750 original size:17 final size:17
Alignment explanation
Indices: 214729--214772 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
214719 TTTTACCAGT
214729 TTTTTAATT-TTAAATA
1 TTTTTAATTATTAAATA
214745 TCTTTTACAATTATTAAATA
1 T-TTTT--AATTATTAAATA
214765 TTTTTAAT
1 TTTTTAAT
214773 GATTTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 7 0.29
19 8 0.33
20 8 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATTATTAAATA
Found at i:214756 original size:19 final size:19
Alignment explanation
Indices: 214734--214770 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
214724 CCAGTTTTTT
214734 AATT-TTAAATATCTTTTAC
1 AATTATTAAATAT-TTTTAC
214753 AATTATTAAATATTTTTA
1 AATTATTAAATATTTTTA
214771 ATGATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTATTAAATATTTTTAC
Found at i:216647 original size:3 final size:3
Alignment explanation
Indices: 216639--216663 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
216629 ATTCTTTTCA
216639 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
216664 TCAATATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:216999 original size:16 final size:15
Alignment explanation
Indices: 216968--217018 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
216958 TAATTTTATC
*
216968 ATTTT-TAATTTAAA
1 ATTTTATAAATTAAA
216982 ATTTTATAAATTATAA
1 ATTTTATAAATTA-AA
* *
216998 ATTGTCTAAATTAAA
1 ATTTTATAAATTAAA
217013 ATTTTA
1 ATTTTA
217019 CCATTTTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 5 0.17
15 12 0.40
16 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTTATAAATTAAA
Found at i:231800 original size:16 final size:15
Alignment explanation
Indices: 231779--231808 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
231769 AAGAAAGAAA
231779 GAAGAAGGAAGAAGGG
1 GAAGAAGG-AGAAGGG
231795 GAAGAAGGAGAAGG
1 GAAGAAGGAGAAGG
231809 AAAAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGG
Found at i:232197 original size:20 final size:21
Alignment explanation
Indices: 232155--232199 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
232145 TAATTTACTT
232155 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
232176 TAATTTTATTTTGTTA-TTAG
1 TAATTTAATTTTGTTAGTTAG
232196 TAAT
1 TAAT
232200 AGTATGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:232493 original size:30 final size:28
Alignment explanation
Indices: 232457--232567 Score: 89
Period size: 30 Copynumber: 3.8 Consensus size: 28
232447 TAAACCTAGC
232457 TAATTAATTACTAAAATATAATATAAAAAA
1 TAATTAATTA-TAAAA-ATAATATAAAAAA
* *****
232487 TAATTAATTATCAAAATAATAT-TCTCT
1 TAATTAATTATAAAAATAATATAAAAAA
*
232514 TCATATTATTTATCAAAATATAATATAAAAAA
1 T-A-ATTAATTAT-AAAA-ATAATATAAAAAA
*
232546 TAATTAATTATGAAAATAATAT
1 TAATTAATTATAAAAATAATAT
232568 CCCTATCATA
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
27 1 0.02
28 15 0.25
29 15 0.25
30 21 0.34
31 8 0.13
32 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (28 bp):
TAATTAATTATAAAAATAATATAAAAAA
Found at i:232502 original size:16 final size:16
Alignment explanation
Indices: 232483--232565 Score: 52
Period size: 16 Copynumber: 5.5 Consensus size: 16
232473 TATAATATAA
232483 AAAATAATTAATTATC
1 AAAATAATTAATTATC
*
232499 AAAATAA-T-ATTCTC
1 AAAATAATTAATTATC
*** *
232513 TTCAT-ATTATTTATC
1 AAAATAATTAATTATC
*
232528 AAAAT-A-TAA-TATAA
1 AAAATAATTAATTAT-C
*
232542 AAAATAATTAATTATG
1 AAAATAATTAATTATC
232558 AAAATAAT
1 AAAATAAT
232566 ATCCCTATCA
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
13 4 0.08
14 15 0.31
15 9 0.18
16 18 0.37
17 3 0.06
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (16 bp):
AAAATAATTAATTATC
Found at i:232567 original size:59 final size:59
Alignment explanation
Indices: 232459--232591 Score: 205
Period size: 59 Copynumber: 2.3 Consensus size: 59
232449 AACCTAGCTA
* * *
232459 ATTAATTACTAAAATATAATATAAAAAATAATTAATTATCAAAATAATATTCTCT-TCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATA-TCCCTATCAT
* *
232518 ATTATTTATCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCTATCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCTATCAT
232577 ATTATTTACCAAAAT
1 ATTATTTACCAAAAT
232592 GATACAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 4 0.06
59 63 0.94
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (59 bp):
ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCTATCAT
Done.