Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015208.1 Kokia drynarioides strain JFW-HI SEQ_130252, 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: 339328
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 467 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:285590 original size:23 final size:22
Alignment explanation
Indices: 285536--285595 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
285526 GAATTTATTT
* *
285536 TTAAATTTAAATATATTTTAAG
1 TTAAATTTAAATTTATTTTAAC
*
285558 TTGAAGTTTAAATTTATTTTAAAC
1 TT-AAATTTAAATTTATTTT-AAC
285582 TTAAATTT-AATTTA
1 TTAAATTTAAATTTA
285596 AGTTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.25
23 20 0.62
24 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAAATTTAAATTTATTTTAAC
Found at i:285596 original size:40 final size:41
Alignment explanation
Indices: 285520--285599 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
285510 GATTTATCTT
* * *
285520 AAGTTTGAATTTATTTTTAAATTTAAATATATTTTAAGTTG
1 AAGTTTAAATTTATTTTTAAACTTAAATATAATTTAAGTTG
*
285561 AAGTTTAAATTTA-TTTTAAACTTAAATTTAATTTAAGTT
1 AAGTTTAAATTTATTTTTAAACTTAAATATAATTTAAGTT
285600 TAAATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 23 0.66
41 12 0.34
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (41 bp):
AAGTTTAAATTTATTTTTAAACTTAAATATAATTTAAGTTG
Found at i:286287 original size:19 final size:19
Alignment explanation
Indices: 286265--286301 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
286255 TAAAAAAGAA
*
286265 AAATGATAATAATAATAAT
1 AAATGATAATAAAAATAAT
*
286284 AAATGTTAATAAAAATAA
1 AAATGATAATAAAAATAA
286302 AAAAGAAAAA
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:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATGATAATAAAAATAAT
Found at i:287387 original size:30 final size:30
Alignment explanation
Indices: 287286--287446 Score: 83
Period size: 29 Copynumber: 5.5 Consensus size: 30
287276 CTTAAATTTT
*
287286 CAAAAA-TCCCATTTTTG-CCTCGAAACTCC
1 CAAAAATTACCATTTTTGCCCTCG-AACTCC
* * * *
287315 CAAAAATTA--AGTTTTTACCC-CAAATTTC
1 CAAAAATTACCA-TTTTTGCCCTCGAACTCC
*
287343 CAAAAAAT-CTCATTTTTGCCCTCGAACTCC
1 CAAAAATTAC-CATTTTTGCCCTCGAACTCC
* *
287373 CAAAAATTACCA-TTTTACCC-CCATA-TCTC
1 CAAAAATTACCATTTTTGCCCTCGA-ACTC-C
* * * *
287402 CAAAAATTA-CAATTTTGACCTTGAACTTTC
1 CAAAAATTACCATTTTTGCCCTCGAAC-TCC
287432 C-AAAATTACCATTTT
1 CAAAAATTACCATTTT
287447 ACCTCGAATG
Statistics
Matches: 98, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
28 18 0.18
29 52 0.53
30 26 0.27
31 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
CAAAAATTACCATTTTTGCCCTCGAACTCC
Found at i:287389 original size:58 final size:56
Alignment explanation
Indices: 287279--287449 Score: 175
Period size: 58 Copynumber: 3.0 Consensus size: 56
287269 TTTACCTCTT
* * ***
287279 AAATTTTCAAAAATCCCATTTTTGCCTCGAAACTCCCAAAAATTAAGTTTTTACCCC
1 AAATTTCCAAAAATCTCATTTTTGCCTCG-AACTCCCAAAAATTACCATTTTACCCC
287336 AAATTTCCAAAAAATCTCATTTTTGCCCTCGAACTCCCAAAAATTACCATTTTACCCCC
1 AAATTTCC-AAAAATCTCATTTTTG-CCTCGAACTCCCAAAAATTACCATTTTA-CCCC
* * * * *
287395 ATATCTCCAAAAAT-TACAATTTTGACCTTGAACTTTCC-AAAATTACCATTTTACC
1 AAATTTCCAAAAATCT-CATTTTTG-CCTCGAAC-TCCCAAAAATTACCATTTTACC
287450 TCGAATGTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
57 10 0.10
58 70 0.71
59 18 0.18
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (56 bp):
AAATTTCCAAAAATCTCATTTTTGCCTCGAACTCCCAAAAATTACCATTTTACCCC
Found at i:287436 original size:29 final size:28
Alignment explanation
Indices: 287404--287503 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 28
287394 CATATCTCCA
287404 AAAATTACAATTTTGACCTTGAACTTTCC
1 AAAATTACAATTTT-ACCTTGAACTTTCC
* * **
287433 AAAATTACCATTTTACCTCGAA-TGTTTA
1 AAAATTACAATTTTACCTTGAACT-TTCC
* *
287461 AAAATTACAATTTTAACTCTAAACTTTCC
1 AAAATTACAATTTTACCT-TGAACTTTCC
*
287490 AAAATTACCATTTT
1 AAAATTACAATTTT
287504 TAACCCTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.02
28 25 0.44
29 30 0.53
30 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTACAATTTTACCTTGAACTTTCC
Found at i:287486 original size:57 final size:58
Alignment explanation
Indices: 287375--287503 Score: 172
Period size: 57 Copynumber: 2.2 Consensus size: 58
287365 CGAACTCCCA
* *
287375 AAAATTACCATTTTACCCCCATATCTCCAAAAATTACAATTTTGACCTTGAACTTTCC
1 AAAATTACCATTTTACCCCCATATCTCCAAAAATTACAATTTTAACCTTAAACTTTCC
* * * **
287433 AAAATTACCATTTTACCTCGA-ATGTTTAAAAATTACAATTTTAA-CTCTAAACTTTCC
1 AAAATTACCATTTTACCCCCATATCTCCAAAAATTACAATTTTAACCT-TAAACTTTCC
287490 AAAATTACCATTTT
1 AAAATTACCATTTT
287504 TAACCCTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 2 0.03
57 42 0.67
58 19 0.30
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCATATCTCCAAAAATTACAATTTTAACCTTAAACTTTCC
Found at i:287507 original size:30 final size:29
Alignment explanation
Indices: 287425--287535 Score: 107
Period size: 28 Copynumber: 3.8 Consensus size: 29
287415 TTTGACCTTG
* *
287425 AACTTTCCAAAATTACCATTTTACCTCGA
1 AACTTTCCAAAATTACCATTTTAACTCTA
** * *
287454 ATGTTT-AAAAATTACAATTTTAACTCTA
1 AACTTTCCAAAATTACCATTTTAACTCTA
*
287482 AACTTTCCAAAATTACCATTTTTAACCCTA
1 AACTTTCCAAAATTACCA-TTTTAACTCTA
** *
287512 AACTTTTTAAAAATTATCATTTTA
1 AAC-TTTCCAAAATTACCATTTTA
287536 CCCCCGAACA
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 22 0.34
29 13 0.20
30 18 0.28
31 12 0.18
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (29 bp):
AACTTTCCAAAATTACCATTTTAACTCTA
Found at i:287533 original size:31 final size:29
Alignment explanation
Indices: 287457--287534 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
287447 ACCTCGAATG
* *
287457 TTTAAAAATTACAATTTTAACTCTAAACT
1 TTTAAAAATTACATTTTTAACCCTAAACT
**
287486 TTCCAAAATTACCATTTTTAACCCTAAACTT
1 TTTAAAAATTA-CATTTTTAACCCTAAAC-T
287517 TTTAAAAATTATCATTTT
1 TTTAAAAATTA-CATTTT
287535 ACCCCCGAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 9 0.22
30 15 0.38
31 16 0.40
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (29 bp):
TTTAAAAATTACATTTTTAACCCTAAACT
Found at i:287553 original size:29 final size:28
Alignment explanation
Indices: 287518--287658 Score: 122
Period size: 29 Copynumber: 4.9 Consensus size: 28
287508 CCTAAACTTT
*
287518 TTAAAAATTATCATTTTACCCCCGAACA
1 TTAAAAATTATCATTTTACCCCCGAACG
* * * **
287546 TTAAAAAATTACCATTTTGCCCTCGAGTG
1 TT-AAAAATTATCATTTTACCCCCGAACG
* *
287575 TCTAAAAATTATCGTTTTACCCTCGAACG
1 T-TAAAAATTATCATTTTACCCCCGAACG
* **
287604 CTCAAAAATTATCATTTTACCCCCGAGTG
1 -TTAAAAATTATCATTTTACCCCCGAACG
*
287633 TCTAAAAATTA-CTGTTTTACCCCCGA
1 T-TAAAAATTATC-ATTTTACCCCCGA
287659 TCATCCCAAA
Statistics
Matches: 90, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.04
29 84 0.93
30 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (28 bp):
TTAAAAATTATCATTTTACCCCCGAACG
Found at i:287595 original size:58 final size:58
Alignment explanation
Indices: 287519--287740 Score: 213
Period size: 58 Copynumber: 3.9 Consensus size: 58
287509 CTAAACTTTT
* * *
287519 TAAAAATTATCATTTTACCCCCGAACATTAAAAAATTACCATTTTGCCCTCGAGTGTC
1 TAAAAATTATCGTTTTACCCCCGAACATTCAAAAATTACCATTTTGCCCCCGAGTGTC
* ** * *
287577 TAAAAATTATCGTTTTACCCTCGAACGCTCAAAAATTATCATTTTACCCCCGAGTGTC
1 TAAAAATTATCGTTTTACCCCCGAACATTCAAAAATTACCATTTTGCCCCCGAGTGTC
* * ***
287635 TAAAAATTA-CTGTTTTACCCCCGATCATCCCAAAAA-TACCATTTTG-CCCC-AACATC
1 TAAAAATTATC-GTTTTACCCCCGAACAT-TCAAAAATTACCATTTTGCCCCCGAGTGTC
* * ** *
287691 TAAAAATTA-CATTTTTCCCATGAAC-TTCCAAAAATTATCATTTTGCCCCC
1 TAAAAATTATCGTTTTACCCCCGAACATT-CAAAAATTACCATTTTGCCCCC
287741 AAGCATCCAA
Statistics
Matches: 134, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
54 7 0.05
55 19 0.14
56 17 0.13
57 5 0.04
58 80 0.60
59 6 0.04
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.32
Consensus pattern (58 bp):
TAAAAATTATCGTTTTACCCCCGAACATTCAAAAATTACCATTTTGCCCCCGAGTGTC
Found at i:287749 original size:29 final size:29
Alignment explanation
Indices: 287520--287755 Score: 121
Period size: 29 Copynumber: 8.2 Consensus size: 29
287510 TAAACTTTTT
**
287520 AAAAATTATCATTTTACCCCCGAA-CATTA
1 AAAAATTATCATTTTACCCCC-AAGCATCC
* * * * ** *
287549 AAAAATTACCATTTTGCCCTCGAGTGTCT
1 AAAAATTATCATTTTACCCCCAAGCATCC
* *
287578 AAAAATTATCGTTTTACCCTCGAACGC-T-C
1 AAAAATTATCATTTTACCC-CCAA-GCATCC
* ** *
287607 AAAAATTATCATTTTACCCCCGAGTGTCT
1 AAAAATTATCATTTTACCCCCAAGCATCC
* * *
287636 AAAAATTA-CTGTTTTACCCCCGATCATCCC
1 AAAAATTATC-ATTTTACCCCCAAGCAT-CC
* * *
287666 AAAAA-TACCATTTT-GCCCCAA-CATCT
1 AAAAATTATCATTTTACCCCCAAGCATCC
* ** *
287692 AAAAATTA-CATTTTTCCCATGAA-CTTCC
1 AAAAATTATCATTTTACCC-CCAAGCATCC
*
287720 AAAAATTATCATTTTGCCCCCAAGCATCC
1 AAAAATTATCATTTTACCCCCAAGCATCC
287749 AAAAATT
1 AAAAATT
287756 GCATTTTTGA
Statistics
Matches: 155, Mismatches: 39, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
26 12 0.08
27 8 0.05
28 25 0.16
29 100 0.65
30 9 0.06
31 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (29 bp):
AAAAATTATCATTTTACCCCCAAGCATCC
Found at i:289673 original size:22 final size:22
Alignment explanation
Indices: 289601--289675 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
289591 TATACTTTCT
289601 TTTCATTTTA-ATAATTTATATTA
1 TTTCATTTTATAT-ATTTA-ATTA
* ** *
289624 TGTTTATATTTAATATATTTTCTGA
1 T-TTCAT-TTT-ATATATTTAATTA
289649 TTTCATTTTATATATTTAATTA
1 TTTCATTTTATATATTTAATTA
289671 TTTCA
1 TTTCA
289676 CATATATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
22 15 0.38
23 4 0.10
24 8 0.20
25 6 0.15
26 5 0.12
27 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTCATTTTATATATTTAATTA
Found at i:292626 original size:18 final size:18
Alignment explanation
Indices: 292605--292656 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
292595 TTGAACTTTA
*
292605 TTTAATATTTTTATAAAT
1 TTTAATATTTTTACAAAT
292623 TTTAATAATGTTTTACAAAT
1 TTTAAT-AT-TTTTACAAAT
*
292643 TTATAATTTTTTTA
1 TT-TAATATTTTTA
292657 AAGGAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 12 0.41
21 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTAATATTTTTACAAAT
Found at i:292631 original size:21 final size:18
Alignment explanation
Indices: 292607--292654 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
292597 GAACTTTATT
*
292607 TAATATTTTTATAAATTTTAA
1 TAAT-TTTTTACAAA-TTT-A
*
292628 TAATGTTTTACAAATTTA
1 TAATTTTTTACAAATTTA
292646 TAATTTTTT
1 TAATTTTTT
292655 TAAAGGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 8 0.33
21 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TAATTTTTTACAAATTTA
Found at i:295384 original size:7 final size:7
Alignment explanation
Indices: 295372--295396 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
295362 AAGATTAAAA
295372 AATTAAT
1 AATTAAT
295379 AATTAAT
1 AATTAAT
295386 AATTAAT
1 AATTAAT
295393 AATT
1 AATT
295397 TTTTAAAATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTAAT
Found at i:297140 original size:20 final size:20
Alignment explanation
Indices: 297102--297140 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
297092 TATAAAAATA
*
297102 ATTATTTTTATTTACTTTAG
1 ATTATTTTTAGTTACTTTAG
297122 ATTATATTTTAGTTA-TTTA
1 ATTAT-TTTTAGTTACTTTA
297141 TGTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTATTTTTAGTTACTTTAG
Found at i:299823 original size:21 final size:19
Alignment explanation
Indices: 299786--299824 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
299776 ATAGTACTAA
*
299786 TATATTAATTTTTTTAATT
1 TATATTAATTTTGTTAATT
299805 TATATTAACTTATTGTTAAT
1 TATATTAA-TT-TTGTTAAT
299825 AATATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TATATTAATTTTGTTAATT
Found at i:300740 original size:15 final size:15
Alignment explanation
Indices: 300716--300747 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
300706 TAAGTGCACC
300716 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
*
300731 TTTTTTTTTTCTTTT
1 TTTTTCTTTTCTTTT
300746 TT
1 TT
300748 CAAATAGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTCTTTTCTTTT
Found at i:301326 original size:5 final size:5
Alignment explanation
Indices: 301316--301340 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
301306 TATCTTGAAA
301316 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
301341 CTGTTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:301747 original size:20 final size:18
Alignment explanation
Indices: 301714--301778 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
301704 GTGTTATTTG
* *
301714 TTTTTTTTTTAAATTTAA
1 TTTTTTTTTAAAAATTAA
301732 TTTTATTTTTAAAAATTAA
1 TTTT-TTTTTAAAAATTAA
*
301751 TGATTTTTTTTAAGAATTAA
1 T--TTTTTTTTAAAAATTAA
301771 TTTCTTTT
1 TTT-TTTT
301779 CCACTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.15
19 17 0.43
20 14 0.35
21 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTTTTTTAAAAATTAA
Found at i:301778 original size:19 final size:17
Alignment explanation
Indices: 301715--301778 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 17
301705 TGTTATTTGT
*
301715 TTTTTTTTTAAATTTAA
1 TTTTTTTTTAAAATTAA
301732 TTTTATTTTTAAAAATTAA
1 TTTT-TTTTT-AAAATTAA
301751 TGATTTTTTTTAAGAATTAA
1 T--TTTTTTTTAA-AATTAA
*
301771 TTTCTTTT
1 TTTTTTTT
301779 CCACTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 4 0.10
18 11 0.28
19 10 0.25
20 12 0.30
21 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTTTTTAAAATTAA
Found at i:302319 original size:20 final size:20
Alignment explanation
Indices: 302280--302319 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
302270 TCAAACTTAT
*
302280 TATTAAGGTTAGTTTTAAAA
1 TATTAAGGTTAGTTTAAAAA
302300 TATTAAGGTTAGTTTAAAAA
1 TATTAAGGTTAGTTTAAAAA
302320 ATAATATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (20 bp):
TATTAAGGTTAGTTTAAAAA
Found at i:308280 original size:5 final size:5
Alignment explanation
Indices: 308268--308315 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
308258 ATCTGCTTGG
* * * *
308268 AAGAA AGGAA AGGAA AGGAA AGGAA AAGAA AAGAA AAGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
308316 CAACCCTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:308290 original size:15 final size:15
Alignment explanation
Indices: 308268--308315 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
308258 ATCTGCTTGG
*
308268 AAGAAAGGAAAGGAA
1 AAGAAAGGAAAAGAA
*
308283 AGGAAAGGAAAAGAA
1 AAGAAAGGAAAAGAA
*
308298 AAGAAAAGAAAAGAA
1 AAGAAAGGAAAAGAA
308313 AAG
1 AAG
308316 CAACCCTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAGAAAGGAAAAGAA
Found at i:319814 original size:28 final size:28
Alignment explanation
Indices: 319782--319844 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
319772 AAATTTCTTT
319782 ACTTCTAATTTAGCACAGAAGATTATAA
1 ACTTCTAATTTAGCACAGAAGATTATAA
* * * *
319810 ACTTCTAGTTTGGGAGAGAAGATTATAA
1 ACTTCTAATTTAGCACAGAAGATTATAA
319838 ACTTCTA
1 ACTTCTA
319845 GTCATACACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (28 bp):
ACTTCTAATTTAGCACAGAAGATTATAA
Found at i:325616 original size:23 final size:23
Alignment explanation
Indices: 325590--325634 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
325580 TTCAAAATTT
*
325590 ATATTTAAAAAAAAAATCTAAAA
1 ATATATAAAAAAAAAATCTAAAA
*
325613 ATATATAAAAAAAAAATTTAAA
1 ATATATAAAAAAAAAATCTAAA
325635 TTTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
ATATATAAAAAAAAAATCTAAAA
Found at i:327064 original size:30 final size:29
Alignment explanation
Indices: 327012--327083 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
327002 ATTATTTGTT
327012 TTTTTATTATTTATTATATAATAT-TTAAA
1 TTTTTATT-TTTATTATATAATATATTAAA
* **
327041 TTTTTATTTTTATTTTAACTAATATATTCTA
1 TTTTTATTTTTATTAT-A-TAATATATTAAA
*
327072 TTTTAATTTTTA
1 TTTTTATTTTTA
327084 AAAATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.19
29 9 0.25
30 6 0.17
31 14 0.39
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTATTTTTATTATATAATATATTAAA
Found at i:327233 original size:20 final size:19
Alignment explanation
Indices: 327208--327251 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
327198 ACATATTTTA
*
327208 ATTTTAAAATTGTCAAATAT
1 ATTTT-AAATTATCAAATAT
*
327228 ATTTT-AATTATCAAGTAT
1 ATTTTAAATTATCAAATAT
327246 ATTTTA
1 ATTTTA
327252 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 16 0.76
20 5 0.24
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTTAAATTATCAAATAT
Found at i:327241 original size:18 final size:18
Alignment explanation
Indices: 327215--327251 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
327205 TTAATTTTAA
*
327215 AATTGTCAAATATATTTT
1 AATTATCAAATATATTTT
*
327233 AATTATCAAGTATATTTT
1 AATTATCAAATATATTTT
327251 A
1 A
327252 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTATCAAATATATTTT
Found at i:327913 original size:37 final size:37
Alignment explanation
Indices: 327853--327939 Score: 156
Period size: 37 Copynumber: 2.4 Consensus size: 37
327843 TATAATCACC
* *
327853 TTAATCTTTTTCTCCATCTCCACCAAACACAATATCA
1 TTAACCTTTATCTCCATCTCCACCAAACACAATATCA
327890 TTAACCTTTATCTCCATCTCCACCAAACACAATATCA
1 TTAACCTTTATCTCCATCTCCACCAAACACAATATCA
327927 TTAACCTTTATCT
1 TTAACCTTTATCT
327940 TCTTCGAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (37 bp):
TTAACCTTTATCTCCATCTCCACCAAACACAATATCA
Found at i:331856 original size:31 final size:32
Alignment explanation
Indices: 331790--331865 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
331780 AGTCACGCAA
*
331790 GTTGCATTTACAAGAGTTGCAGTCACATAAACT
1 GTTGCATTTACAAGAGCTGCAGTCACA-AAACT
*
331823 GTTGCATTTACATG-GACTGCAGTCAC-AAACT
1 GTTGCATTTACAAGAG-CTGCAGTCACAAAACT
331854 GTTGCATTTACA
1 GTTGCATTTACA
331866 CAAACCACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 17 0.43
32 1 0.03
33 22 0.55
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (32 bp):
GTTGCATTTACAAGAGCTGCAGTCACAAAACT
Found at i:331877 original size:31 final size:32
Alignment explanation
Indices: 331809--331877 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
331799 ACAAGAGTTG
*** **
331809 CAGTCACATAAACTGTTGCATTTACATGGACTG
1 CAGTCACA-AAACTGTTGCATTTACACAAACCA
331842 CAGTCAC-AAACTGTTGCATTTACACAAACCA
1 CAGTCACAAAACTGTTGCATTTACACAAACCA
331873 CAGTC
1 CAGTC
331878 GCACAAGCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 24 0.77
33 7 0.23
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (32 bp):
CAGTCACAAAACTGTTGCATTTACACAAACCA
Found at i:331895 original size:30 final size:30
Alignment explanation
Indices: 331856--331926 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
331846 CACAAACTGT
331856 TGCATTTACACAAACCACAGTCGCACAAGC
1 TGCATTTACACAAACCACAGTCGCACAAGC
* ** ** *
331886 TGTATTTACACGGATTACAGTCGCACGAGC
1 TGCATTTACACAAACCACAGTCGCACAAGC
331916 TGCATTTACAC
1 TGCATTTACAC
331927 TGATTGCAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (30 bp):
TGCATTTACACAAACCACAGTCGCACAAGC
Found at i:331937 original size:30 final size:30
Alignment explanation
Indices: 331872--331955 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
331862 TACACAAACC
* *
331872 ACAGTCGCACAAGCTGTATTTACACGGATT
1 ACAGTCGCACGAGCTGCATTTACACGGATT
*
331902 ACAGTCGCACGAGCTGCATTTACACTGATT
1 ACAGTCGCACGAGCTGCATTTACACGGATT
* * *
331932 GCAGTCGCACGAACTACATTTACA
1 ACAGTCGCACGAGCTGCATTTACA
331956 AGAAGGCAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (30 bp):
ACAGTCGCACGAGCTGCATTTACACGGATT
Found at i:332210 original size:12 final size:12
Alignment explanation
Indices: 332193--332222 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
332183 TGTTACGAAA
332193 CAAAACAAATAG
1 CAAAACAAATAG
*
332205 CAAAACAAATAT
1 CAAAACAAATAG
332217 CAAAAC
1 CAAAAC
332223 TCATAATACC
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:0.67, C:0.20, G:0.03, T:0.10
Consensus pattern (12 bp):
CAAAACAAATAG
Found at i:333308 original size:6 final size:6
Alignment explanation
Indices: 333265--333304 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
333255 GATGCAATGA
*
333265 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGAG AAGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGG
333305 AGAAAGAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:333456 original size:17 final size:17
Alignment explanation
Indices: 333431--333464 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
333421 TTTTCCCGTA
*
333431 TTTGTAAAATAATTTAC
1 TTTGGAAAATAATTTAC
*
333448 TTTGGAAAATCATTTAC
1 TTTGGAAAATAATTTAC
333465 AACCAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (17 bp):
TTTGGAAAATAATTTAC
Found at i:338334 original size:23 final size:23
Alignment explanation
Indices: 338257--338424 Score: 77
Period size: 23 Copynumber: 7.5 Consensus size: 23
338247 TAAACGGAAC
* *
338257 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* * *
338279 AAACATATAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
338301 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
338327 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
338347 --AC--TGAGCACACAAAATGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
338366 AATCAGAGAGTACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
338389 AATAACAGAAAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
338414 AAACAGAGAGC
1 AAACAGAGAGC
338425 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 25, Indels: 29
0.66 0.16 0.18
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 16 0.15
23 38 0.36
24 2 0.02
25 25 0.24
26 8 0.08
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Done.