Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009646.1 Kokia drynarioides strain JFW-HI SEQ_124364, 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: 115745
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:469 original size:23 final size:23
Alignment explanation
Indices: 438--513 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
428 CGCTAGCGCA
* *
438 CTTATTGTTTCGCACTTTGTGTG
1 CTTACTGTTTCGCACTTCGTGTG
*
461 CTTACTGTTTCGTACTTCGTGTG
1 CTTACTGTTTCGCACTTCGTGTG
*
484 CTTACTGTTTCGCACCTCGTGTG
1 CTTACTGTTTCGCACTTCGTGTG
*
507 CCTACTG
1 CTTACTG
514 ATTTGCGCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.45
Consensus pattern (23 bp):
CTTACTGTTTCGCACTTCGTGTG
Found at i:547 original size:22 final size:22
Alignment explanation
Indices: 502--572 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
492 TTCGCACCTC
* *
502 GTGTGCCTACTGATTTGCGCTGT
1 GTGTGCCTATTGA-TTGCACTGT
*
525 GTGTGCCTATTGATTGCATTGT
1 GTGTGCCTATTGATTGCACTGT
*
547 GTGTGTCTATTGGATTGCACTGT
1 GTGTGCCTATT-GATTGCACTGT
570 GTG
1 GTG
573 CTTACTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 17 0.40
23 25 0.60
ACGTcount: A:0.11, C:0.15, G:0.31, T:0.42
Consensus pattern (22 bp):
GTGTGCCTATTGATTGCACTGT
Found at i:2372 original size:65 final size:65
Alignment explanation
Indices: 2276--2409 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
2266 TCAATATCAA
2276 ACCAAGATATAAAAGTGTAGAACAATGAAGTCATGAAGATATATTAATTTAAATCAAATCAAACT
1 ACCAAGATATAAAAGTGTAGAACAATGAAGTCATGAAGATATATTAATTTAAATCAAATCAAACT
2341 ACCAAGATATAAAAGTGTAGAACAATGAAGTCATGAAGATATATTAATTTAAATCAAATCAAACT
1 ACCAAGATATAAAAGTGTAGAACAATGAAGTCATGAAGATATATTAATTTAAATCAAATCAAACT
2406 ACCA
1 ACCA
2410 CCCATGCAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (65 bp):
ACCAAGATATAAAAGTGTAGAACAATGAAGTCATGAAGATATATTAATTTAAATCAAATCAAACT
Found at i:2383 original size:32 final size:32
Alignment explanation
Indices: 2279--2383 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
2269 ATATCAAACC
2279 AAGATATAAAAGTGTAGAACAATGAAGTCATG
1 AAGATATAAAAGTGTAGAACAATGAAGTCATG
* * * * **
2311 AAGATATATTAA-TTTA-AATCAAATCAA-ACTACC
1 AAGATATA-AAAGTGTAGAA-C-AATGAAGTC-ATG
2344 AAGATATAAAAGTGTAGAACAATGAAGTCATG
1 AAGATATAAAAGTGTAGAACAATGAAGTCATG
2376 AAGATATA
1 AAGATATA
2384 TTAATTTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
31 2 0.04
32 29 0.54
33 21 0.39
34 2 0.04
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (32 bp):
AAGATATAAAAGTGTAGAACAATGAAGTCATG
Found at i:3780 original size:33 final size:33
Alignment explanation
Indices: 3740--3802 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
3730 CTGTTAATTA
*
3740 AAAGATCTATTTTTTATGATTTAATTATTCCTT
1 AAAGATCTAATTTTTATGATTTAATTATTCCTT
3773 AAAGATCTAATTTTTATGATTTAATTATTC
1 AAAGATCTAATTTTTATGATTTAATTATTC
3803 TTTTTAATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.52
Consensus pattern (33 bp):
AAAGATCTAATTTTTATGATTTAATTATTCCTT
Found at i:6762 original size:20 final size:19
Alignment explanation
Indices: 6732--6769 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
6722 GCTGAAACCA
6732 AACAAAACAATAAAAGAAG
1 AACAAAACAATAAAAGAAG
6751 AACAAGAACAATAAAAGAA
1 AACAA-AACAATAAAAGAA
6770 ATGGAGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.05
Consensus pattern (19 bp):
AACAAAACAATAAAAGAAG
Found at i:7139 original size:20 final size:19
Alignment explanation
Indices: 7099--7139 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
7089 AAGCCTAAAG
*
7099 TTCTCTCTTTCTTGTTACT
1 TTCTCTCTTTCTTGTGACT
*
7118 TTCTCTTCTTTCTTGTGCCT
1 TTCTC-TCTTTCTTGTGACT
7138 TT
1 TT
7140 ATATTGGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.02, C:0.27, G:0.07, T:0.63
Consensus pattern (19 bp):
TTCTCTCTTTCTTGTGACT
Found at i:7481 original size:16 final size:16
Alignment explanation
Indices: 7456--7488 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7446 CCTCCAACGT
*
7456 GACCGGTTAAATGACA
1 GACCGATTAAATGACA
7472 GACCGATTAAATGACA
1 GACCGATTAAATGACA
7488 G
1 G
7489 GTCATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (16 bp):
GACCGATTAAATGACA
Found at i:7718 original size:4 final size:4
Alignment explanation
Indices: 7698--7772 Score: 61
Period size: 4 Copynumber: 19.5 Consensus size: 4
7688 AATATAATTC
* *
7698 ATAA AT-A ATAA ACAA ATAA AT-A ATAA ATAA A-AA TATAT ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA
* *
7744 TTAA AT-- ATAA ATAT ATAA ATAAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATAA AT
7773 GCACAAACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
2 2 0.04
3 8 0.14
4 41 0.73
5 5 0.09
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:7755 original size:24 final size:23
Alignment explanation
Indices: 7713--7760 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
7703 TAATAAACAA
7713 ATAAATAATAAATAAAAATATAT
1 ATAAATAATAAATAAAAATATAT
*
7736 ATAAATAATTAAATATAAATATAT
1 ATAAATAA-TAAATAAAAATATAT
7760 A
1 A
7761 AATAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATAATAAATAAAAATATAT
Found at i:10708 original size:22 final size:21
Alignment explanation
Indices: 10674--10714 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10664 TATGATGTTT
10674 TTAAGTTCAGATTTTATTATGA
1 TTAAGTTCAGA-TTTATTATGA
**
10696 TTAAGTTGTGATTTATTAT
1 TTAAGTTCAGATTTATTAT
10715 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (21 bp):
TTAAGTTCAGATTTATTATGA
Found at i:28184 original size:31 final size:31
Alignment explanation
Indices: 28133--28191 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
28123 ATAGTAGATT
* *
28133 TTAATATTTGATATTTAAATTTGTTTTTGATA
1 TTAATATTTAATATTCAAA-TTGTTTTTGATA
28165 TTAA-ATTTAATATTCAAATTGTTTTTG
1 TTAATATTTAATATTCAAATTGTTTTTG
28192 GTCCAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 12 0.48
32 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (31 bp):
TTAATATTTAATATTCAAATTGTTTTTGATA
Found at i:29318 original size:20 final size:20
Alignment explanation
Indices: 29293--29336 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
29283 ATTTAACCAT
29293 ATATGAAAGTTTACTTTTGA
1 ATATGAAAGTTTACTTTTGA
29313 ATATGAAAGTTTACTTTTGA
1 ATATGAAAGTTTACTTTTGA
29333 ATAT
1 ATAT
29337 TCAAAGTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
ATATGAAAGTTTACTTTTGA
Found at i:29344 original size:21 final size:20
Alignment explanation
Indices: 29293--29344 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
29283 ATTTAACCAT
*
29293 ATATGAAAGTTTACTTTTGA
1 ATATCAAAGTTTACTTTTGA
*
29313 ATATGAAAGTTTACTTTTGA
1 ATATCAAAGTTTACTTTTGA
29333 ATATTCAAAGTT
1 ATA-TCAAAGTT
29345 CCAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (20 bp):
ATATCAAAGTTTACTTTTGA
Found at i:34483 original size:12 final size:12
Alignment explanation
Indices: 34444--34484 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
34434 TCGAGTACTT
*
34444 GAACCCGAACCC
1 GAACCTGAACCC
* *
34456 GAACCTGAATCT
1 GAACCTGAACCC
34468 GAACCTGAACCC
1 GAACCTGAACCC
34480 GAACC
1 GAACC
34485 CAGCTGCTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.34, C:0.39, G:0.17, T:0.10
Consensus pattern (12 bp):
GAACCTGAACCC
Found at i:35544 original size:72 final size:72
Alignment explanation
Indices: 35455--35598 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
35445 CATTCTGGCC
35455 AAAAGGAAAACTATTTTTTTTAATAAAAAAACCCTTATTTCATTGGCTTTTGCTCACTTCTAGAG
1 AAAAGGAAAACTATTTTTTTTAATAAAAAAACCCTTATTTCATTGGCTTTTGCTCACTTCTAGAG
35520 TAATTGA
66 TAATTGA
35527 AAAAGGAAAACTATTTTTTTTAATAAAAAAACCCTTATTTCATTGGCTTTTGCTCACTTCTAGAG
1 AAAAGGAAAACTATTTTTTTTAATAAAAAAACCCTTATTTCATTGGCTTTTGCTCACTTCTAGAG
35592 TAATTGA
66 TAATTGA
35599 GGCAATATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (72 bp):
AAAAGGAAAACTATTTTTTTTAATAAAAAAACCCTTATTTCATTGGCTTTTGCTCACTTCTAGAG
TAATTGA
Found at i:38636 original size:104 final size:104
Alignment explanation
Indices: 38456--38664 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
38446 GAATTTCTAC
*
38456 TTTAGTCAATCCGTACAGAAAAATTCTTCTAAGTTTCCCCTTCTTTGCTGCTTGACAGTTTCGAC
1 TTTAGCCAATCCGTACAGAAAAATTCTTCTAAGTTTCCCCTTCTTTGCTGCTTGACAGTTTCGAC
38521 CTTGCTTTACTAAAAATTAATTATCTATTAGTACAGGGT
66 CTTGCTTTACTAAAAATTAATTATCTATTAGTACAGGGT
38560 TTTAGCCAATCCGTACAGAAAAATTCTTCTAAGTTTCCCCTTCTTTGCTGCTTGACAGTTTCGAC
1 TTTAGCCAATCCGTACAGAAAAATTCTTCTAAGTTTCCCCTTCTTTGCTGCTTGACAGTTTCGAC
*
38625 CTTGCTTTACTAAAAATTAATTATCTATTAGTATAGGGT
66 CTTGCTTTACTAAAAATTAATTATCTATTAGTACAGGGT
38664 T
1 T
38665 CGGATGATGT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (104 bp):
TTTAGCCAATCCGTACAGAAAAATTCTTCTAAGTTTCCCCTTCTTTGCTGCTTGACAGTTTCGAC
CTTGCTTTACTAAAAATTAATTATCTATTAGTACAGGGT
Found at i:39673 original size:23 final size:23
Alignment explanation
Indices: 39641--39684 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39631 ACTATCATTT
39641 TTTAAATAAAATAATAATAAATA
1 TTTAAATAAAATAATAATAAATA
* *
39664 TTTAAGTAAAATATTAATAAA
1 TTTAAATAAAATAATAATAAA
39685 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TTTAAATAAAATAATAATAAATA
Found at i:39677 original size:13 final size:11
Alignment explanation
Indices: 39645--39687 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
39635 TCATTTTTTA
*
39645 AATAAAATAAT
1 AATAAAATATT
39656 AAT-AAATATTT
1 AATAAAATA-TT
39667 AAGTAAAATATT
1 AA-TAAAATATT
39679 AATAAAATA
1 AATAAAATA
39688 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:40277 original size:14 final size:14
Alignment explanation
Indices: 40258--40284 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40248 GTCATCTAAG
40258 TGAAATTTCACATA
1 TGAAATTTCACATA
40272 TGAAATTTCACAT
1 TGAAATTTCACAT
40285 CATCTCGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TGAAATTTCACATA
Found at i:41649 original size:69 final size:69
Alignment explanation
Indices: 41533--41674 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
41523 CAATGGCAAC
**
41533 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACAAGAGAATCCTTCATAGTACTT-
1 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACAAGAGAATCAGTCATAGTACTTA
41597 CTACT
66 C-ACT
* * *
41602 TTCAACTGCGTCCATGGTTGGTGAATCCTCATCCAACACTACTAGAGAATCAGTCATAGTACTTA
1 TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACAAGAGAATCAGTCATAGTACTTA
41667 CACT
66 CACT
41671 TTCA
1 TTCA
41675 TCCAGAACAG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (69 bp):
TTCAACTGCATCCATGGTTGGTGAATCCTCATCCAACACCACAAGAGAATCAGTCATAGTACTTA
CACT
Found at i:46364 original size:20 final size:20
Alignment explanation
Indices: 46312--46364 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
46302 GCGAATAATT
*
46312 TAATCAAACTTAAAATAAGA
1 TAATCAAACTTGAAATAAGA
* * *
46332 AAATCAAATTTGAAATTAGA
1 TAATCAAACTTGAAATAAGA
*
46352 TAATTAAACTTGA
1 TAATCAAACTTGA
46365 TAGTGGAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (20 bp):
TAATCAAACTTGAAATAAGA
Found at i:47450 original size:11 final size:11
Alignment explanation
Indices: 47421--47489 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
47411 TACAATATCT
*
47421 AAAATAACAAC
1 AAAATAATAAC
47432 AAAATAATAAC
1 AAAATAATAAC
*
47443 AATATAATAAC
1 AAAATAATAAC
* * *
47454 GAAATGATAAT
1 AAAATAATAAC
**
47465 AAAACCATGAA-
1 AAAATAAT-AAC
47476 AAAA-AATAAC
1 AAAATAATAAC
47486 AAAA
1 AAAA
47490 GTAAACAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
9 2 0.04
10 6 0.13
11 36 0.78
12 2 0.04
ACGTcount: A:0.70, C:0.10, G:0.04, T:0.16
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:63553 original size:20 final size:21
Alignment explanation
Indices: 63530--63579 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
63520 GAATCTTTTA
63530 TTTCCTTTAAATTTTC-CCTT
1 TTTCCTTTAAATTTTCTCCTT
* *
63550 TTTCCTTT-TATTTTCTTCTT
1 TTTCCTTTAAATTTTCTCCTT
*
63570 TTTCTTTTAA
1 TTTCCTTTAA
63580 GAGAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCCTTTAAATTTTCTCCTT
Found at i:66543 original size:109 final size:110
Alignment explanation
Indices: 66398--66616 Score: 395
Period size: 110 Copynumber: 2.0 Consensus size: 110
66388 TAGAATAAAT
*
66398 GTTCAATCCTACAAAATGCATAAAAAAATATTCATCAAC-GTTAAAGACGTGCATGATAGGCCCA
1 GTTCAATCCTACAAAATGCATAAAAAAATATTCATCAACGGTTAAAGACGTGCATGATAAGCCCA
66462 TTTATTTATACATTCAATCAATACAAGATTGTTACGCTTTAACAG
66 TTTATTTATACATTCAATCAATACAAGATTGTTACGCTTTAACAG
* *
66507 GTTCAATCTTACAAAATGCATAAAAAAATATTCATCAACGGTTAAATACGTGCATGATAAGCCCA
1 GTTCAATCCTACAAAATGCATAAAAAAATATTCATCAACGGTTAAAGACGTGCATGATAAGCCCA
*
66572 TTTATTTATACATTCAATCAATACAAGGTTGTTACGCTTTAACAG
66 TTTATTTATACATTCAATCAATACAAGATTGTTACGCTTTAACAG
66617 ATACTCTATT
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
109 38 0.36
110 67 0.64
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (110 bp):
GTTCAATCCTACAAAATGCATAAAAAAATATTCATCAACGGTTAAAGACGTGCATGATAAGCCCA
TTTATTTATACATTCAATCAATACAAGATTGTTACGCTTTAACAG
Found at i:67969 original size:23 final size:21
Alignment explanation
Indices: 67943--68026 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 21
67933 AATATATTTG
*
67943 TAAAATAATATTTAAAAATAAC
1 TAAAATAATAATTAAAAA-AAC
* *
67965 ATAAATTAATAATTACAAAAAC
1 -TAAAATAATAATTAAAAAAAC
67987 TAAAAATTCAATAATTAAAAAAA-
1 T-AAAA-T-AATAATTAAAAAAAC
* *
68010 TAAAATAAAAACTAAAA
1 TAAAATAATAATTAAAA
68027 TTCAAATAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
20 9 0.18
21 2 0.04
22 10 0.20
23 17 0.33
24 13 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAATAATAATTAAAAAAAC
Found at i:67999 original size:24 final size:22
Alignment explanation
Indices: 67944--68014 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
67934 ATATATTTGT
* *
67944 AAAA-TAATATTTAAAAATAACA
1 AAAATTAATAATTAAAAA-AATA
* *
67966 TAAATTAATAATTACAAAAACTA
1 AAAATTAATAATTA-AAAAAATA
67989 AAAATTCAATAATTAAAAAAATA
1 AAAATT-AATAATTAAAAAAATA
68012 AAA
1 AAA
68015 TAAAAACTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 3 0.08
23 25 0.62
24 12 0.30
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATTAATAATTAAAAAAATA
Found at i:73859 original size:5 final size:5
Alignment explanation
Indices: 73851--73876 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
73841 TTTTTTTTAA
73851 TCACC TCACC TCACC TCACC TCACC T
1 TCACC TCACC TCACC TCACC TCACC T
73877 AAGTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.58, G:0.00, T:0.23
Consensus pattern (5 bp):
TCACC
Found at i:75071 original size:16 final size:17
Alignment explanation
Indices: 75052--75091 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
75042 TTAATCTTTT
75052 TAAAATT-ATAAAA--A
1 TAAAATTAATAAAATGA
75066 TATAAATTAATAAAATGA
1 TA-AAATTAATAAAATGA
75084 TAAAATTA
1 TAAAATTA
75092 CATTATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 5 0.23
16 6 0.27
17 6 0.27
18 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTAATAAAATGA
Found at i:75076 original size:30 final size:31
Alignment explanation
Indices: 75017--75076 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
75007 TATTTTGATT
*
75017 TTTTTAAAAATAAAAAAAAATTAATTTAATC
1 TTTTTAAAAATAAAAAAAAATTAAATTAATC
* * *
75048 TTTTTAAAATTATAAAAATA-TAAATTAAT
1 TTTTTAAAAATAAAAAAAAATTAAATTAAT
75077 AAAATGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTTAAAAATAAAAAAAAATTAAATTAATC
Found at i:75364 original size:168 final size:170
Alignment explanation
Indices: 75174--75488 Score: 417
Period size: 168 Copynumber: 1.8 Consensus size: 170
75164 TAAAAAGCAA
* * *
75174 AAATATTCTGCATTAACCATTAATGGGCTGGCA-GGGACTGCC-CTTAAAA-T-GAAACAAATT-
1 AAATATTCTACATTAACCATTAATGGGCTGGCAGGGGACTGCCAC-TAAAATTAAAAAAAAATTC
75234 ATTTAAATTATTTAAAATTTTAATTAATAAAAAACAAAATTATATTTT-ATTTTTTTTTAAAAAT
65 ATTTAAATTATTTAAAATTTTAATTAAT-AAAAACAAAATTATATTTTGA--TTTTTTTAAAAAT
*
75298 GATAAAAATTTAATTTAAATATGTTTTGGGTACAGTAAAAATAG
127 AATAAAAATTTAATTTAAATATGTTTTGGGTACAGTAAAAATAG
*
75342 AAATATTCTACATTAACCATTAATGGGCTGGCAGGGGGCTGCCACTAAAATTAAAAAAAAAAAAT
1 AAATATTCTACATTAACCATTAATGGGCTGGCAGGGGACTGCCACTAAAATT---AAAAAAAAAT
** * * **
75407 TCATTTAGGTTTTTTAAAATTTTAATTAGTAAAAGTAAAATTATATTTTGATTTTTTTAAAAATA
63 TCATTTAAATTATTTAAAATTTTAATTAATAAAAACAAAATTATATTTTGATTTTTTTAAAAATA
*
75472 ATAAAATTTTAATTTAA
128 ATAAAAATTTAATTTAA
75489 TCCTTTAAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
168 32 0.25
169 13 0.10
170 2 0.02
173 29 0.23
174 25 0.20
175 25 0.20
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (170 bp):
AAATATTCTACATTAACCATTAATGGGCTGGCAGGGGACTGCCACTAAAATTAAAAAAAAATTCA
TTTAAATTATTTAAAATTTTAATTAATAAAAACAAAATTATATTTTGATTTTTTTAAAAATAATA
AAAATTTAATTTAAATATGTTTTGGGTACAGTAAAAATAG
Found at i:75519 original size:30 final size:30
Alignment explanation
Indices: 75462--75519 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
75452 TTTTGATTTT
* *
75462 TTTAAAAATAATAAAATTTTAATTTAATCC
1 TTTAAAAATAATAAAATTATAAGTTAATCC
*
75492 TTTAAAAATTATAAAGA-TATAAGTTAAT
1 TTTAAAAATAATAAA-ATTATAAGTTAAT
75520 AAAATGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TTTAAAAATAATAAAATTATAAGTTAATCC
Found at i:85289 original size:16 final size:16
Alignment explanation
Indices: 85268--85306 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
85258 CGACTCACTC
*
85268 TATAACAATCA-TTCTT
1 TATAACAAT-ATTTCAT
85284 TATAACAATATTTCAT
1 TATAACAATATTTCAT
85300 TATAACA
1 TATAACA
85307 GTCAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAACAATATTTCAT
Found at i:85546 original size:22 final size:20
Alignment explanation
Indices: 85507--85547 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
85497 GATTTTTATA
*
85507 TAAAAATATTTTATTAAATG
1 TAAAAATATTTTAATAAATG
85527 TAAATAATATTTTTAATAAAT
1 TAAA-AATA-TTTTAATAAAT
85548 AAAATTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAAAAATATTTTAATAAATG
Found at i:85552 original size:21 final size:21
Alignment explanation
Indices: 85511--85552 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
85501 TTTATATAAA
* *
85511 AATATTTTATTAAATGTAAAT
1 AATATTTTAATAAATGAAAAT
85532 AATATTTTTAATAAAT-AAAAT
1 AATA-TTTTAATAAATGAAAAT
85553 TACATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATATTTTAATAAATGAAAAT
Found at i:85629 original size:14 final size:15
Alignment explanation
Indices: 85586--85633 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
85576 ATATAATTTA
85586 AATATTATTAATTATT
1 AATATTATTAATTA-T
85602 AATATTATTAAATTAT
1 AATATTATT-AATTAT
85618 AATATT-TTAATTAT
1 AATATTATTAATTAT
85632 AA
1 AA
85634 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.26
15 2 0.06
16 16 0.52
17 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATTAATTAT
Found at i:85639 original size:14 final size:15
Alignment explanation
Indices: 85579--85641 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
85569 ATTAAAGATA
85579 TAATT-TAAATATTAT
1 TAATTATAAATATT-T
*
85594 TAATTATTAATATTAT
1 TAATTATAAATATT-T
85610 TAAATTAT-AATATTT
1 T-AATTATAAATATTT
85625 TAATTATAAAT-TTT
1 TAATTATAAATATTT
85639 TAA
1 TAA
85642 AAAAATCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 12 0.27
15 10 0.23
16 16 0.36
17 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAAATATTT
Found at i:88548 original size:35 final size:35
Alignment explanation
Indices: 88509--88577 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
88499 AAAAAATTAT
*
88509 ATTGTTGTTATGA-TACTGTTTTTTTTACTGTTTTG
1 ATTGTTGTT-TGATTACTGTTTTTGTTACTGTTTTG
**
88544 ATTGTTGTTTGATTGTTGTTTTTGTTACTGTTTT
1 ATTGTTGTTTGATTACTGTTTTTGTTACTGTTTT
88578 TGTTGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.12, C:0.04, G:0.19, T:0.65
Consensus pattern (35 bp):
ATTGTTGTTTGATTACTGTTTTTGTTACTGTTTTG
Found at i:88554 original size:11 final size:11
Alignment explanation
Indices: 88540--88564 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
88530 TTTTTACTGT
88540 TTTGATTGTTG
1 TTTGATTGTTG
88551 TTTGATTGTTG
1 TTTGATTGTTG
88562 TTT
1 TTT
88565 TTGTTACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (11 bp):
TTTGATTGTTG
Found at i:88566 original size:24 final size:22
Alignment explanation
Indices: 88539--88599 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
88529 TTTTTTACTG
*
88539 TTTTGATTGTTGTTTGATTGTTGT
1 TTTTGATTGTT-TTTG-TTGTTAT
*
88563 TTTTGTTACTGTTTTTGTTGTTAT
1 TTTTG--ATTGTTTTTGTTGTTAT
88587 TTTTG-TTGTTTTT
1 TTTTGATTGTTTTT
88600 AATATTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 7 0.22
24 16 0.50
25 4 0.12
26 5 0.16
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.72
Consensus pattern (22 bp):
TTTTGATTGTTTTTGTTGTTAT
Found at i:88584 original size:35 final size:33
Alignment explanation
Indices: 88525--88633 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 33
88515 GTTATGATAC
*
88525 TGTTTTTTTTACTG-TTTTGATTGTTGTTTGATTGT
1 TGTTTTTATTACTGTTTTTG-TTGTT-TTTG-TTGT
*
88560 TGTTTTTGTTACTGTTTTTGTTGTTATTT-TTGT
1 TGTTTTTATTACTGTTTTTGTTGTT-TTTGTTGT
* * *
88593 TGTTTTTAATATTGTTTTGCTGTTATTTTTGTTGT
1 TGTTTTTATTACTGTTTT--TGTTGTTTTTGTTGT
88628 TGTTTT
1 TGTTTT
88634 GGTTGTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
33 19 0.30
34 3 0.05
35 37 0.58
36 5 0.08
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71
Consensus pattern (33 bp):
TGTTTTTATTACTGTTTTTGTTGTTTTTGTTGT
Found at i:88589 original size:12 final size:12
Alignment explanation
Indices: 88551--88646 Score: 58
Period size: 12 Copynumber: 8.2 Consensus size: 12
88541 TTGATTGTTG
*
88551 TTTGATTGTTGTT
1 TTTG-TTGTTATT
** *
88564 TTTGTTACTGTT
1 TTTGTTGTTATT
88576 TTTGTTGTTATT
1 TTTGTTGTTATT
88588 TTTGTTGTT-TT
1 TTTGTTGTTATT
* *
88599 TAATATTG----T
1 T-TTGTTGTTATT
*
88608 TTTGCTGTTATT
1 TTTGTTGTTATT
*
88620 TTTGTTGTTGTT
1 TTTGTTGTTATT
*
88632 TTGGTTGTTATT
1 TTTGTTGTTATT
88644 TTT
1 TTT
88647 TATGATTGTC
Statistics
Matches: 63, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
8 3 0.05
9 2 0.03
11 3 0.05
12 51 0.81
13 4 0.06
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (12 bp):
TTTGTTGTTATT
Found at i:88611 original size:32 final size:32
Alignment explanation
Indices: 88525--88628 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 32
88515 GTTATGATAC
** *
88525 TGTTTTTTTTACTGTTTTGATTGTTGTTTGATTGT
1 TGTTTTTAATACTGTTTTG-TTGTTATTT--TTGT
**
88560 TGTTTTTGTTACTGTTTTTGTTGTTATTTTTGT
1 TGTTTTTAATACTG-TTTTGTTGTTATTTTTGT
* *
88593 TGTTTTTAATATTGTTTTGCTGTTATTTTTGT
1 TGTTTTTAATACTGTTTTGTTGTTATTTTTGT
88625 TGTT
1 TGTT
88629 GTTTTGGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 21 0.34
33 15 0.24
35 21 0.34
36 5 0.08
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (32 bp):
TGTTTTTAATACTGTTTTGTTGTTATTTTTGT
Found at i:88622 original size:24 final size:24
Alignment explanation
Indices: 88590--88655 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
88580 TTGTTATTTT
* *
88590 TGTTGTTTTTAATATTGTTTT-GC
1 TGTTATTTTTTATATTGTTTTGGC
* *
88613 TGTTATTTTTGT-TGTTGTTTTGGT
1 TGTTATTTTT-TATATTGTTTTGGC
88637 TGTTATTTTTTATGATTGT
1 TGTTATTTTTTAT-ATTGT
88656 CATTTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 18 0.53
24 12 0.35
25 4 0.12
ACGTcount: A:0.11, C:0.02, G:0.20, T:0.68
Consensus pattern (24 bp):
TGTTATTTTTTATATTGTTTTGGC
Found at i:105531 original size:3 final size:3
Alignment explanation
Indices: 105523--105569 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
105513 AGGGAAATTA
105523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
105570 CCTGAAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:107028 original size:8 final size:8
Alignment explanation
Indices: 107015--107046 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
107005 ACTCTGCTTC
107015 TTCTTTTT
1 TTCTTTTT
107023 TTC--TTT
1 TTCTTTTT
107029 TTCTTTTT
1 TTCTTTTT
107037 TTCTTTTT
1 TTCTTTTT
107045 TT
1 TT
107047 TTTGCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:107034 original size:14 final size:14
Alignment explanation
Indices: 107015--107049 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
107005 ACTCTGCTTC
107015 TTCTTTTTTTCTTT
1 TTCTTTTTTTCTTT
107029 TTCTTTTTTTCTTT
1 TTCTTTTTTTCTTT
107043 TT-TTTTT
1 TTCTTTTT
107050 GCTTCTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTCTTTTTTTCTTT
Done.