Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006967.1 Kokia drynarioides strain JFW-HI SEQ_121573, 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: 158710
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:11777 original size:23 final size:23
Alignment explanation
Indices: 11740--11783 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11730 TATTAAAAAT
**
11740 ATAATATAAGTATAAATATTTTA
1 ATAATATAAACATAAATATTTTA
*
11763 ATAATATAAACATAATTATTT
1 ATAATATAAACATAAATATTT
11784 ATTTATATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAATATAAACATAAATATTTTA
Found at i:12355 original size:16 final size:17
Alignment explanation
Indices: 12334--12367 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12324 TTATTGGTAT
12334 AAATTTAATACT-AATA
1 AAATTTAATACTGAATA
*
12350 AAATTTAGTACTGAATA
1 AAATTTAATACTGAATA
12367 A
1 A
12368 CCCCATACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
AAATTTAATACTGAATA
Found at i:13788 original size:13 final size:13
Alignment explanation
Indices: 13770--13795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13760 TATCTGTTGG
13770 TAAACAAATTATA
1 TAAACAAATTATA
13783 TAAACAAATTATA
1 TAAACAAATTATA
13796 GCAGAAAACT
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACAAATTATA
Found at i:19947 original size:37 final size:37
Alignment explanation
Indices: 19923--20031 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
19913 GCCCAAATAT
*
19923 ACCGACACGAAGCCTACTAGGCACACAGCCTGAAAAC
1 ACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAAC
* * *
19960 ACCGGCACGAAGCCTACTGGGCACAAAACCTGAAAAC
1 ACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAAC
* *
19997 ACCGGCACGAAGCCTACTAGGCACAAAACCTGAAA
1 ACCGACACGAAGCCTACTAGGCACAAAGCCTGAAA
20032 TTTTAGATGC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.39, C:0.33, G:0.20, T:0.08
Consensus pattern (37 bp):
ACCGACACGAAGCCTACTAGGCACAAAGCCTGAAAAC
Found at i:19973 original size:21 final size:21
Alignment explanation
Indices: 19949--20011 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19939 CTAGGCACAC
19949 AGCCTGAAAACACCGGCACGA
1 AGCCTGAAAACACCGGCACGA
** *
19970 AGCCT----AC-TGGGCACAA
1 AGCCTGAAAACACCGGCACGA
*
19986 AACCTGAAAACACCGGCACGA
1 AGCCTGAAAACACCGGCACGA
20007 AGCCT
1 AGCCT
20012 ACTAGGCACA
Statistics
Matches: 29, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
20 2 0.07
21 15 0.52
ACGTcount: A:0.37, C:0.33, G:0.22, T:0.08
Consensus pattern (21 bp):
AGCCTGAAAACACCGGCACGA
Found at i:28343 original size:16 final size:16
Alignment explanation
Indices: 28318--28357 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28308 CAAATAAGTC
*
28318 AATATATTATATTAAT
1 AATATTTTATATTAAT
*
28334 AATATTTTATCTTAAT
1 AATATTTTATATTAAT
*
28350 GATATTTT
1 AATATTTT
28358 TATGTATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
AATATTTTATATTAAT
Found at i:28499 original size:37 final size:37
Alignment explanation
Indices: 28447--28522 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
28437 CAACCACAAC
28447 AACAGTTCCCAATCCCCAGCC-TGATTTAGATTACGAT
1 AACAGTTCCCAAT-CCCAGCCTTGATTTAGATTACGAT
* *
28484 AACAGCTTCCC-ATCCCAGCCTTGGTTTAGATTATGAT
1 AACAG-TTCCCAATCCCAGCCTTGATTTAGATTACGAT
28521 AA
1 AA
28523 TCATGTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.20
37 23 0.66
38 5 0.14
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (37 bp):
AACAGTTCCCAATCCCAGCCTTGATTTAGATTACGAT
Found at i:31391 original size:14 final size:14
Alignment explanation
Indices: 31372--31399 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31362 GTTTAATGAG
31372 GGGTTTGCACTTTT
1 GGGTTTGCACTTTT
31386 GGGTTTGCACTTTT
1 GGGTTTGCACTTTT
31400 CTGTAAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (14 bp):
GGGTTTGCACTTTT
Found at i:37417 original size:30 final size:30
Alignment explanation
Indices: 37361--37418 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
37351 TTCGATATTT
*
37361 TAATAATTACATTTCTAATATATTTTTAAC
1 TAATAATTACATCTCTAATATATTTTTAAC
37391 TAATAAATTACATCT-TAATCAT-TTTTTA
1 TAAT-AATTACATCTCTAAT-ATATTTTTA
37419 TTAACAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (30 bp):
TAATAATTACATCTCTAATATATTTTTAAC
Found at i:47375 original size:20 final size:20
Alignment explanation
Indices: 47347--47417 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
47337 ATTTTGGTGC
* *
47347 TGTTTTTTTACTGTTTTGAT
1 TGTTATTTTACTGTTTTGGT
* *
47367 TGTTATTTTTTGCTTTTTTGTGT
1 TGTTA--TTTTACTGTTTTG-GT
47390 TGTT-TTTTACTGTTTTGGT
1 TGTTATTTTACTGTTTTGGT
*
47409 TATTATTTT
1 TGTTATTTT
47418 CGTGTTATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 5 0.12
20 19 0.47
22 11 0.28
23 5 0.12
ACGTcount: A:0.08, C:0.04, G:0.15, T:0.72
Consensus pattern (20 bp):
TGTTATTTTACTGTTTTGGT
Found at i:47375 original size:22 final size:21
Alignment explanation
Indices: 47350--47417 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
47340 TTGGTGCTGT
47350 TTTTTTACTGTTTTGATTGTTA
1 TTTTTTACTGTTTTG-TTGTTA
* * *
47372 TTTTTTGCTTTTTTG-TGTTG
1 TTTTTTACTGTTTTGTTGTTA
*
47392 TTTTTTACTGTTTTGGTTATTA
1 TTTTTTACTGTTTT-GTTGTTA
47414 TTTT
1 TTTT
47418 CGTGTTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 16 0.43
21 1 0.03
22 20 0.54
ACGTcount: A:0.09, C:0.04, G:0.15, T:0.72
Consensus pattern (21 bp):
TTTTTTACTGTTTTGTTGTTA
Found at i:47662 original size:27 final size:26
Alignment explanation
Indices: 47605--47674 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
47595 ATAAAAAAAT
* * *
47605 TTAATGTATTTTAAATTTATTTATTTT
1 TTAATGT-TTTTAAATGTATTTATATA
*
47632 TTAATGTTTTTAAGTGTATTTGATATA
1 TTAATGTTTTTAAATGTATTT-ATATA
*
47659 TTAATAATTTTTAAAT
1 TTAAT-GTTTTTAAAT
47675 TTGTTGTATG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 12 0.34
27 15 0.43
28 8 0.23
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (26 bp):
TTAATGTTTTTAAATGTATTTATATA
Found at i:52466 original size:24 final size:24
Alignment explanation
Indices: 52438--52488 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
52428 ATAAATAATC
* *
52438 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
52462 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
52486 TTT
1 TTT
52489 GAGTGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:54444 original size:24 final size:24
Alignment explanation
Indices: 54416--54466 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
54406 AGAAATAATC
* * *
54416 TTTCAGTTAAATTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
*
54440 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
54464 TTT
1 TTT
54467 GAGTCAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:57040 original size:22 final size:22
Alignment explanation
Indices: 56998--57059 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
56988 ATTTCGGCAC
*
56998 TTCTATTTTCTATT-TTTTTAA
1 TTCTATTTTCTTTTATTTTTAA
57019 TTCTATTTTCTTTTATTTTTAA
1 TTCTATTTTCTTTTATTTTTAA
*
57041 TTCT-GTTTCTTTTATTTTT
1 TTCTATTTTCTTTTATTTTT
57060 CCTCAGATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
TTCTATTTTCTTTTATTTTTAA
Found at i:68727 original size:24 final size:24
Alignment explanation
Indices: 68700--68750 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
68690 AATTTGACTC
* *
68700 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
68724 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
68748 AAA
1 AAA
68751 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:71702 original size:39 final size:39
Alignment explanation
Indices: 71648--71722 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
71638 ACTCGTTGTT
71648 TATACGGATCGATCTTCAACAAAATTATTTTAATTTAAA
1 TATACGGATCGATCTTCAACAAAATTATTTTAATTTAAA
71687 TATACGGATCGATCTTCAACAAAATTATTTTAATTT
1 TATACGGATCGATCTTCAACAAAATTATTTTAATTT
71723 CATTTAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (39 bp):
TATACGGATCGATCTTCAACAAAATTATTTTAATTTAAA
Found at i:74653 original size:6 final size:6
Alignment explanation
Indices: 74603--74649 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
74593 CCAAAAGGAT
* *
74603 AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC AAAAAC AAAGAT AAAGA
1 AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC AAAGA
74650 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.70, C:0.13, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAGAC
Found at i:74663 original size:18 final size:18
Alignment explanation
Indices: 74603--74661 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
74593 CCAAAAGGAT
*
74603 AAAGACAAAGACAAAGAC
1 AAAGACAAAGACAAAAAC
74621 AAAGACAAAGACAAAAAC
1 AAAGACAAAGACAAAAAC
* * *
74639 AAAGATAAAGATAAAAAT
1 AAAGACAAAGACAAAAAC
74657 AAAGA
1 AAAGA
74662 TAGAGAGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAGACAAAGACAAAAAC
Found at i:87470 original size:6 final size:6
Alignment explanation
Indices: 87459--87486 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
87449 GTGGCACGAC
87459 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
87487 ATCATCGCTC
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:104312 original size:16 final size:18
Alignment explanation
Indices: 104286--104328 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
104276 TAAACAACAA
*
104286 AATATTACAAT-TTTAAT
1 AATATTACAATATTAAAT
104303 AATA-TACAATATTAAAT
1 AATATTACAATATTAAAT
*
104320 AATCTTACA
1 AATATTACA
104329 TTCTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 4 0.18
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATTACAATATTAAAT
Found at i:107107 original size:23 final size:25
Alignment explanation
Indices: 107080--107125 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
107070 AACCAGCTGA
*
107080 TTTATTA-A-ATTTTTTTTAATAAT
1 TTTATTATAGATTTTTTATAATAAT
107103 TTTATTATAGATTTTTTATAATA
1 TTTATTATAGATTTTTTATAATA
107126 TCTGTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 1 0.05
25 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTATTATAGATTTTTTATAATAAT
Found at i:108546 original size:25 final size:28
Alignment explanation
Indices: 108485--108541 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
108475 ATTTTTAGAG
*
108485 TATGATCCTATTAAATTTGGTTATTTAT
1 TATGATCTTATTAAATTTGGTTATTTAT
108513 TATGATCTTATTAAATTTGGTTATTTAT
1 TATGATCTTATTAAATTTGGTTATTTAT
108541 T
1 T
108542 GTCTTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (28 bp):
TATGATCTTATTAAATTTGGTTATTTAT
Found at i:108739 original size:19 final size:19
Alignment explanation
Indices: 108717--108761 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
108707 TTATATTAGG
108717 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
108736 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
108755 ATTTAAT
1 ATTTAAT
108762 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:109568 original size:15 final size:16
Alignment explanation
Indices: 109550--109579 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
109540 CTTTCCTATT
109550 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
109565 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
109580 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:109572 original size:22 final size:22
Alignment explanation
Indices: 109545--109605 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
109535 TTCGACTTTC
109545 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
109567 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
109589 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
109606 TCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:109606 original size:22 final size:22
Alignment explanation
Indices: 109559--109605 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
109549 TTTCTATTTC
*
109559 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
109581 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
109602 TTTT
1 TTTT
109606 TCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:115424 original size:8 final size:8
Alignment explanation
Indices: 115400--115464 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
115390 GATGAATCAT
115400 TAAAAATTA
1 TAAAAA-TA
*
115409 TAAGAATA
1 TAAAAATA
115417 TAAAAATA
1 TAAAAATA
115425 TTAAAAATA
1 -TAAAAATA
* *
115434 TTAAAATG
1 TAAAAATA
*
115442 CAAAAATA
1 TAAAAATA
115450 TATAAAA-A
1 TA-AAAATA
115458 TAAAAAT
1 TAAAAAT
115465 TTTGATTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
7 4 0.09
8 24 0.53
9 17 0.38
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (8 bp):
TAAAAATA
Found at i:115433 original size:17 final size:17
Alignment explanation
Indices: 115398--115506 Score: 59
Period size: 17 Copynumber: 6.5 Consensus size: 17
115388 GTGATGAATC
*
115398 ATTAAAAATTATAAGAAT
1 ATTAAAAA-TATAAAAAT
115416 A-TAAAAATATTAAAAAT
1 ATTAAAAATA-TAAAAAT
**
115433 ATT-AAAATGCAAAAAT
1 ATTAAAAATATAAAAAT
115449 A-TATAAAA-ATAAAAAT
1 ATTA-AAAATATAAAAAT
** ** *
115465 -TTTGATTTATTAAAAT
1 ATTAAAAATATAAAAAT
*
115481 -TTAGAAAATATTAAAAT
1 ATTA-AAAATATAAAAAT
115498 ATTAAAAAT
1 ATTAAAAAT
115507 TATTTTAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.03
16 25 0.36
17 37 0.54
18 5 0.07
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (17 bp):
ATTAAAAATATAAAAAT
Found at i:115498 original size:8 final size:8
Alignment explanation
Indices: 115413--115508 Score: 54
Period size: 8 Copynumber: 11.9 Consensus size: 8
115403 AAATTATAAG
*
115413 AATATAAA
1 AATATTAA
115421 AATATTAAA
1 AATATT-AA
115430 AATATTAA
1 AATATTAA
***
115438 AATGCAAA
1 AATATTAA
115446 AATATATAA
1 AATAT-TAA
*
115455 AA-ATAAA
1 AATATTAA
* *
115462 AATTTTGA
1 AATATTAA
**
115470 TTTATTAA
1 AATATTAA
115478 AAT-TTAGAA
1 AATATT--AA
115487 AATATTAA
1 AATATTAA
115495 AATATTAA
1 AATATTAA
115503 AA-ATTA
1 AATATTA
115509 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 17, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
7 10 0.15
8 36 0.55
9 17 0.26
10 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (8 bp):
AATATTAA
Found at i:116163 original size:15 final size:14
Alignment explanation
Indices: 116142--116182 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
116132 ATTGATTATG
116142 AATTAAAATAAATT
1 AATTAAAATAAATT
*
116156 ATATTAAAATTAATT
1 A-ATTAAAATAAATT
*
116171 AATTAAACTAAA
1 AATTAAAATAAA
116183 ACCCCACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAAATAAATT
Found at i:119182 original size:27 final size:30
Alignment explanation
Indices: 119111--119186 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
119101 TTTTCATTAT
*
119111 TAATAAATAT-TTTATATAAATTTGATAGA
1 TAATAAATATATTTATATAAATTTGATAAA
119140 -AATAACATATTGATTTA-A-AAA-TTGATAAA
1 TAATAA-ATA-T-ATTTATATAAATTTGATAAA
119169 TAATAAATATATTTATAT
1 TAATAAATATATTTATAT
119187 CGATAATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
27 5 0.13
28 7 0.18
29 13 0.33
30 9 0.23
31 1 0.03
32 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (30 bp):
TAATAAATATATTTATATAAATTTGATAAA
Found at i:119230 original size:16 final size:17
Alignment explanation
Indices: 119211--119243 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
119201 TTATATCAAC
*
119211 AAAATATTAAT-TATAA
1 AAAATATAAATATATAA
119227 AAAATATAAATATATAA
1 AAAATATAAATATATAA
119244 TCACTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATAAATATATAA
Found at i:133445 original size:31 final size:30
Alignment explanation
Indices: 133378--133444 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
133368 ATTATTTATT
*
133378 ATTTTTATAATTTTTAAAAGATTAAATTAA
1 ATTTTTATAATTTTTAAAAGATTAAAGTAA
* * *
133408 ATTTTTATTATTTTTAAGAGGGTTAAAGTATA
1 ATTTTTATAATTTTTAA-AAGATTAAAGTA-A
133440 ATTTT
1 ATTTT
133445 ACTTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 16 0.52
31 9 0.29
32 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAGATTAAAGTAA
Found at i:133602 original size:18 final size:18
Alignment explanation
Indices: 133579--133614 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
133569 AAAATTCTAA
133579 TTTTATA-AATAAATATTT
1 TTTTATACAATAAA-ATTT
133597 TTTTATACAATAAAATTT
1 TTTTATACAATAAAATTT
133615 GAATGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATACAATAAAATTT
Found at i:139255 original size:2 final size:2
Alignment explanation
Indices: 139248--139280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
139238 TGAATTTTGT
139248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
139281 TAACTTACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140490 original size:5 final size:5
Alignment explanation
Indices: 140461--140489 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
140451 GGTTATCTAC
140461 CAAAA CAAAA CAAAA CAAAA CAAAA -AAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
140490 AGGCGTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:143235 original size:28 final size:29
Alignment explanation
Indices: 143174--143237 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
143164 AAATTTAAAA
** *
143174 AAATAAAAAGATTAAATTTCTATAAATAC
1 AAATAAATGGATTAAATTTCTAAAAATAC
143203 AAATAAATGGATTAAA-TTCTAAAAATAC
1 AAATAAATGGATTAAATTTCTAAAAATAC
*
143231 TAATAAA
1 AAATAAA
143238 CAAGAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATAAATGGATTAAATTTCTAAAAATAC
Found at i:150717 original size:25 final size:25
Alignment explanation
Indices: 150689--150737 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
150679 TGACATTTAT
150689 AAATACTTATAATTT-ATTATAAAAG
1 AAATACTTATAATTTAATT-TAAAAG
*
150714 AAATATTTATAATTTAATTTAAAA
1 AAATACTTATAATTTAATTTAAAA
150738 TTATTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATACTTATAATTTAATTTAAAAG
Found at i:151675 original size:7 final size:7
Alignment explanation
Indices: 151663--151687 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
151653 CATGAACCCT
151663 AAACTCA
1 AAACTCA
151670 AAACTCA
1 AAACTCA
151677 AAACTCA
1 AAACTCA
151684 AAAC
1 AAAC
151688 CGAACCCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACTCA
Found at i:151845 original size:17 final size:18
Alignment explanation
Indices: 151823--151856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
151813 ATGTTTATAA
151823 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
151840 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
151857 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Done.