Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010076.1 Kokia drynarioides strain JFW-HI SEQ_124854, 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: 93030
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:536 original size:17 final size:17
Alignment explanation
Indices: 514--633 Score: 125
Period size: 17 Copynumber: 6.7 Consensus size: 17
504 TTGGACATTT
514 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
531 TAAATTTAAATTTCAAATAA
1 TAAATTTAAATTT---ATAA
551 CTTTAAATTTAAATTTATAA
1 ---TAAATTTAAATTTATAA
571 TAAATTTAAATTTCA-AA
1 TAAATTTAAATTT-ATAA
*
588 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
* * *
605 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
622 TAAATTCAAATT
1 TAAATTTAAATT
634 CCAATAGACC
Statistics
Matches: 90, Mismatches: 5, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
16 1 0.01
17 67 0.74
18 1 0.01
20 8 0.09
23 13 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:538 original size:23 final size:23
Alignment explanation
Indices: 512--588 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
502 AATTGGACAT
512 TTTAAATTTAAATTTATAATAAA
1 TTTAAATTTAAATTTATAATAAA
* *
535 TTTAAA--T---TTCA-AATAAC
1 TTTAAATTTAAATTTATAATAAA
552 TTTAAATTTAAATTTATAATAAA
1 TTTAAATTTAAATTTATAATAAA
575 TTTAAATTTCAAAT
1 TTTAAATTT-AAAT
589 AAATTTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
17 11 0.26
18 3 0.07
19 1 0.02
21 1 0.02
22 3 0.07
23 20 0.47
24 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAATTTAAATTTATAATAAA
Found at i:556 original size:34 final size:34
Alignment explanation
Indices: 514--633 Score: 141
Period size: 34 Copynumber: 3.4 Consensus size: 34
504 TTGGACATTT
514 TAAATTTAAATTTATAATAAATTTAAATTTCAAATAA
1 TAAATTTAAATTTATAATAAATTTAAATTTC--A-AA
551 CTTTAAATTTAAATTTATAATAAATTTAAATTTCAAA
1 ---TAAATTTAAATTTATAATAAATTTAAATTTCAAA
* * * *
588 TAAATTTAAATTTAAAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAATTTAAATTTCAAA
*
622 TAAATTCAAATT
1 TAAATTTAAATT
634 CCAATAGACC
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 41 0.55
37 2 0.03
38 1 0.01
40 31 0.41
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAATTTAAATTTCAAA
Found at i:556 original size:40 final size:40
Alignment explanation
Indices: 512--603 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
502 AATTGGACAT
*
512 TTTAAATTTAAATTTATAATAAATTTAAATTTCAAATAAC
1 TTTAAATTTAAATTTATAATAAATTTAAATTTCAAATAAA
552 TTTAAATTTAAATTTATAATAAATTTAAATTTCAAATAAA
1 TTTAAATTTAAATTTATAATAAATTTAAATTTCAAATAAA
592 TTTAAATTTAAA
1 TTTAAATTTAAA
604 ATAAACTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (40 bp):
TTTAAATTTAAATTTATAATAAATTTAAATTTCAAATAAA
Found at i:591 original size:11 final size:10
Alignment explanation
Indices: 520--598 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 10
510 ATTTTAAATT
520 TAAATTTATAA
1 TAAATTTA-AA
531 TAAATTTAAA
1 TAAATTTAAA
*
541 T---TTCAAA
1 TAAATTTAAA
*
548 TAACTTTAAA
1 TAAATTTAAA
558 TTTAAATTTATAA
1 --TAAATTTA-AA
571 TAAATTTAAA
1 TAAATTTAAA
*
581 T---TTCAAA
1 TAAATTTAAA
588 TAAATTTAAA
1 TAAATTTAAA
598 T
1 T
599 TTAAAATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
7 12 0.22
10 17 0.31
11 16 0.30
12 7 0.13
13 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:597 original size:23 final size:23
Alignment explanation
Indices: 531--603 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
521 AAATTTATAA
*
531 TAAATTTAAATTTCAAATAACTT
1 TAAATTTAAATTTCAAATAAATT
554 TAAATTTAAATTT---AT-AA--
1 TAAATTTAAATTTCAAATAAATT
571 TAAATTTAAATTTCAAATAAATT
1 TAAATTTAAATTTCAAATAAATT
594 TAAATTTAAA
1 TAAATTTAAA
604 ATAAACTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 13 0.30
19 1 0.02
20 4 0.09
21 2 0.05
23 23 0.53
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTTAAATTTCAAATAAATT
Found at i:605 original size:7 final size:6
Alignment explanation
Indices: 512--633 Score: 84
Period size: 6 Copynumber: 21.3 Consensus size: 6
502 AATTGGACAT
*
512 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAC TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
558 TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * * * *
604 -ATAAA CTTAAT TTTAAA -ATAAA TTCAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
634 CCAATAGACC
Statistics
Matches: 92, Mismatches: 10, Indels: 28
0.71 0.08 0.22
Matches are distributed among these distances:
4 9 0.10
5 14 0.15
6 59 0.64
7 10 0.11
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:3296 original size:15 final size:14
Alignment explanation
Indices: 3265--3297 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3255 AGTTGAGTTC
3265 TTTTATTTTTATAA
1 TTTTATTTTTATAA
3279 TTTTATTTTT-TAA
1 TTTTATTTTTATAA
3292 TATTTA
1 T-TTTA
3298 AAATAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTTTATAA
Found at i:5073 original size:13 final size:14
Alignment explanation
Indices: 5049--5082 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
5039 ATTTGTCAAC
5049 TTTTTATTATTATTTA
1 TTTTTATTATTA--TA
5065 TTTTTATTATTATA
1 TTTTTATTATTATA
5079 TTTT
1 TTTT
5083 ATAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
16 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTATTATTATA
Found at i:5266 original size:20 final size:18
Alignment explanation
Indices: 5220--5261 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5210 TGATTCCACC
5220 AAATATAAAATATATATTT
1 AAAT-TAAAATATATATTT
*
5239 AAATTAAATTATATATTT
1 AAATTAAAATATATATTT
5257 AAATT
1 AAATT
5262 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTAAAATATATATTT
Found at i:5612 original size:16 final size:17
Alignment explanation
Indices: 5591--5623 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5581 ATAAAAAAAA
5591 TATTTTTAAG-TCTTTT
1 TATTTTTAAGATCTTTT
*
5607 TATTTTTCAGATCTTTT
1 TATTTTTAAGATCTTTT
5624 AGTATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (17 bp):
TATTTTTAAGATCTTTT
Found at i:9527 original size:99 final size:99
Alignment explanation
Indices: 9332--9519 Score: 322
Period size: 99 Copynumber: 1.9 Consensus size: 99
9322 TACTTTATAT
*
9332 AGGTATAGTACAAAGTTGAAAAAGAAATACGGGATTGGGATATGGGCTCCAAACTGCCACGACAT
1 AGGTATAGTACAAAGTTGAAAAAGAAATACGGGATTGGGATATGGGATCCAAACTGCCACGACAT
* *
9397 ACGCACAGGGTTAATGAAATGTATCAAACCTCAC
66 ACACACAGGGATAATGAAATGTATCAAACCTCAC
*
9431 AGGTATAGTACAAAGTTGAAAAAGAAATACGGGATTGGGATATGGGATCCAAACTGCCATGACAT
1 AGGTATAGTACAAAGTTGAAAAAGAAATACGGGATTGGGATATGGGATCCAAACTGCCACGACAT
* *
9496 GCACACAGGGATAATGAAGTGTAT
66 ACACACAGGGATAATGAAATGTAT
9520 TGAACCTCCT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 83 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (99 bp):
AGGTATAGTACAAAGTTGAAAAAGAAATACGGGATTGGGATATGGGATCCAAACTGCCACGACAT
ACACACAGGGATAATGAAATGTATCAAACCTCAC
Found at i:10491 original size:25 final size:25
Alignment explanation
Indices: 10426--10493 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
10416 CAAAATTAAA
10426 TTAAATT-A-AACAAAACAAATAAT
1 TTAAATTAATAACAAAACAAATAAT
* *
10449 ATATAA-TAATTACTAAAA-AAATAATT
1 TTA-AATTAATAAC-AAAACAAATAA-T
10475 TTAAATTAATAACAAAACA
1 TTAAATTAATAACAAAACA
10494 TTTTCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 14 0.41
26 14 0.41
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (25 bp):
TTAAATTAATAACAAAACAAATAAT
Found at i:10668 original size:16 final size:16
Alignment explanation
Indices: 10647--10678 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10637 AACAACAACA
*
10647 AAACTTTCTTTTCTTT
1 AAACTTACTTTTCTTT
10663 AAACTTACTTTTCTTT
1 AAACTTACTTTTCTTT
10679 CTCTCCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (16 bp):
AAACTTACTTTTCTTT
Found at i:12785 original size:23 final size:23
Alignment explanation
Indices: 12738--12786 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12728 TTACATCCAA
* *
12738 ATACAATTTTAAAAATTATTTTT
1 ATACAATTATAAAAATTATTATT
12761 ATACAAGTTATAAAAATTA-TATT
1 ATACAA-TTATAAAAATTATTATT
12784 ATA
1 ATA
12787 AGCATAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
ATACAATTATAAAAATTATTATT
Found at i:16683 original size:17 final size:17
Alignment explanation
Indices: 16661--16699 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16651 AGGTGGAGAA
*
16661 CTTGTTCGTTGA-AAGTT
1 CTTGTTCGTAGAGAA-TT
16678 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
16695 CTTGT
1 CTTGT
16700 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:18225 original size:16 final size:15
Alignment explanation
Indices: 18183--18225 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
18173 ATAATTAAAG
18183 ATTTTATATT-ATTA
1 ATTTTATATTAATTA
*
18197 ATTTAATATTTAATTA
1 ATTTTATA-TTAATTA
18213 ATTTTCATATTAA
1 ATTTT-ATATTAA
18226 GGCTTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.29
15 2 0.08
16 12 0.50
17 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTATATTAATTA
Found at i:18806 original size:21 final size:21
Alignment explanation
Indices: 18782--18823 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18772 ATCTCACGAA
18782 TATAAT-ATCTAATATTATTTT
1 TATAATAAT-TAATATTATTTT
*
18803 TATAATAATTAATCTTATTTT
1 TATAATAATTAATATTATTTT
18824 CACCGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAATAATTAATATTATTTT
Found at i:28741 original size:6 final size:6
Alignment explanation
Indices: 28730--28761 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28720 CATACCTCAT
*
28730 TTCCTC TTCCTC TTCCTC TTCCTC GTCCTC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
28762 TCACGGCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (6 bp):
TTCCTC
Found at i:29322 original size:24 final size:24
Alignment explanation
Indices: 29294--29355 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
29284 GTAGTTGTGG
* *
29294 TGCTTGTGCTAATAATGGTGGCGC
1 TGCTTGTGCTAACAATGATGGCGC
* * *
29318 TGCTTGTGCTGACAATGATTGCGG
1 TGCTTGTGCTAACAATGATGGCGC
29342 TGCTTGTGCTAACA
1 TGCTTGTGCTAACA
29356 CAGGTTGTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.34
Consensus pattern (24 bp):
TGCTTGTGCTAACAATGATGGCGC
Found at i:33500 original size:16 final size:16
Alignment explanation
Indices: 33470--33499 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33460 ATATTTTTTA
33470 AAAAGCCCCAAAAAAT
1 AAAAGCCCCAAAAAAT
33486 AAAA-CCCCAAAAAA
1 AAAAGCCCCAAAAAA
33500 AAAGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.27, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAGCCCCAAAAAAT
Found at i:34159 original size:2 final size:2
Alignment explanation
Indices: 34152--34182 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34142 TAGTATTTTA
*
34152 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34183 AAATGTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41739 original size:11 final size:11
Alignment explanation
Indices: 41719--41750 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41709 AGATTTAATT
41719 AATTTAGTAAG
1 AATTTAGTAAG
*
41730 AATTTCGTAAG
1 AATTTAGTAAG
41741 AATTTAGTAA
1 AATTTAGTAA
41751 TTTTAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (11 bp):
AATTTAGTAAG
Found at i:43982 original size:20 final size:21
Alignment explanation
Indices: 43953--43991 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
43943 CCCGAATTTT
43953 AAAATCTTAAAA-AAAAATTA
1 AAAATCTTAAAATAAAAATTA
*
43973 AAAATTTTAAAATAAAAAT
1 AAAATCTTAAAATAAAAAT
43992 AAAGAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATCTTAAAATAAAAATTA
Found at i:44436 original size:27 final size:27
Alignment explanation
Indices: 44362--44425 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
44352 CCGCCACCAA
* **
44362 AACCCGAACCACCAGCGGAAACGCCAC
1 AACCCGAACCACCGGAAGAAACGCCAC
* *
44389 AACCTGAACCACCGGAAGAAATGCCAC
1 AACCCGAACCACCGGAAGAAACGCCAC
44416 AACCCGAACC
1 AACCCGAACC
44426 GGCGGCTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.41, G:0.17, T:0.03
Consensus pattern (27 bp):
AACCCGAACCACCGGAAGAAACGCCAC
Found at i:44569 original size:24 final size:24
Alignment explanation
Indices: 44538--44620 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
44528 TGTTCAAACA
44538 TATGCTCCGACATATCCTCCAATT
1 TATGCTCCGACATATCCTCCAATT
* * ** **
44562 TATACTCCGACGTATGCC-GGAACA
1 TATGCTCCGACATAT-CCTCCAATT
*
44586 TATGCTCCGACCTATCCTCCAATT
1 TATGCTCCGACATATCCTCCAATT
44610 TATGCTCCGAC
1 TATGCTCCGAC
44621 GTACGCTACA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
23 2 0.04
24 41 0.91
25 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.29
Consensus pattern (24 bp):
TATGCTCCGACATATCCTCCAATT
Found at i:51011 original size:20 final size:20
Alignment explanation
Indices: 50961--51028 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
50951 GAAATGCAAG
50961 TTTCTTATAAAATTACTGAA
1 TTTCTTATAAAATTACTGAA
* * *
50981 TTTTTTTATAACATTATTGAA
1 -TTTCTTATAAAATTACTGAA
* *
51002 TCTCTTATAATATTACTGAA
1 TTTCTTATAAAATTACTGAA
51022 TTTCTTA
1 TTTCTTA
51029 CTTGGAATCC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTCTTATAAAATTACTGAA
Found at i:58006 original size:22 final size:21
Alignment explanation
Indices: 57979--58019 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
57969 AAATAATTAA
*
57979 TCGACCTTCGACCGAATTAAGT
1 TCGACCATCGACCG-ATTAAGT
58001 TCGACCATCGACCGATTAA
1 TCGACCATCGACCGATTAA
58020 CCGAATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
TCGACCATCGACCGATTAAGT
Found at i:58370 original size:40 final size:41
Alignment explanation
Indices: 58296--58372 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
58286 AGAAAATTGG
* * **
58296 AATTTCTCATTAAATCTTTCAAATGTTTTTAATTTTTTGAT
1 AATTTCTCATTAAATCTTTAAAATATTTGAAATTTTTTGAT
*
58337 AATTT-TCGTTAAATCTTTAAAATATTTGAAATTTTT
1 AATTTCTCATTAAATCTTTAAAATATTTGAAATTTTT
58373 AATTAGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 26 0.84
41 5 0.16
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (41 bp):
AATTTCTCATTAAATCTTTAAAATATTTGAAATTTTTTGAT
Found at i:59981 original size:30 final size:31
Alignment explanation
Indices: 59947--60004 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
59937 CTAATTATTT
**
59947 AAATAAAAA-TTTTAAATAATTTAATAACTC
1 AAATAAAAACTTCAAAATAATTTAATAACTC
59977 AAATAAAAACTTCAAAATAATTTAATAA
1 AAATAAAAACTTCAAAATAATTTAATAA
60005 TTATAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (31 bp):
AAATAAAAACTTCAAAATAATTTAATAACTC
Found at i:69637 original size:56 final size:56
Alignment explanation
Indices: 69549--69665 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 56
69539 AATGGTGATT
* * *
69549 GTTTTAATTTTAACCCGAAAAAAGCACGTAAAAAGTATGAAAGCATTCTATTTTGA
1 GTTTTAATTTTAACCCGAAAAAAGCACATAAAAAGCAAGAAAGCATTCTATTTTGA
* **
69605 GTTTTACA-TTTAACCTGAAAAAAGCACATAAAAAGCAAGAAAGTGTTCTATTTTGA
1 GTTTTA-ATTTTAACCCGAAAAAAGCACATAAAAAGCAAGAAAGCATTCTATTTTGA
69661 GTTTT
1 GTTTT
69666 GCCTCGAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 53 0.98
57 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (56 bp):
GTTTTAATTTTAACCCGAAAAAAGCACATAAAAAGCAAGAAAGCATTCTATTTTGA
Found at i:69782 original size:13 final size:13
Alignment explanation
Indices: 69766--69796 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
69756 TACTAAAAGG
69766 TTAAGAGTTGAAT
1 TTAAGAGTTGAAT
69779 TTAAGAGTTGAAT
1 TTAAGAGTTGAAT
69792 TTAAG
1 TTAAG
69797 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (13 bp):
TTAAGAGTTGAAT
Found at i:74539 original size:3 final size:3
Alignment explanation
Indices: 74531--74639 Score: 69
Period size: 3 Copynumber: 37.0 Consensus size: 3
74521 TGTTATGATC
* * * * *
74531 ATT ATT ATT AAT AAT AAT AAT AAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *** * * * **
74579 ATT CTT TTT CCC ATT -TT AAT GTT ATA AAC A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74625 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
74640 CTTTTTCCCA
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
2 3 0.03
3 83 0.97
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:74640 original size:58 final size:58
Alignment explanation
Indices: 74554--74668 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
74544 ATAATAATAA
74554 TATTATTATTATTATTATTATTATTATTCTTTTTCCCATTTTAATGTTATAAACATAT
1 TATTATTATTATTATTATTATTATTATTCTTTTTCCCATTTTAATGTTATAAACATAT
74612 TATTATTATTATTATTATTATTATTATTCTTTTTCCCATTTTAATGTTATAAACATA
1 TATTATTATTATTATTATTATTATTATTCTTTTTCCCATTTTAATGTTATAAACATA
74669 CTTTTTCATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (58 bp):
TATTATTATTATTATTATTATTATTATTCTTTTTCCCATTTTAATGTTATAAACATAT
Found at i:85435 original size:52 final size:52
Alignment explanation
Indices: 85373--85479 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
85363 TGGTAAGGAC
85373 TAAGCATAGCATTGTCACATCTTCCCCGCACCAGGGCCACATAATCATCAAG
1 TAAGCATAGCATTGTCACATCTTCCCCGCACCAGGGCCACATAATCATCAAG
*
85425 TAAGCATAGCATTGTCACATCTTCCCTGCACCAGGGCCACATAATCATCAAG
1 TAAGCATAGCATTGTCACATCTTCCCCGCACCAGGGCCACATAATCATCAAG
85477 TAA
1 TAA
85480 TTGAGTGGGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (52 bp):
TAAGCATAGCATTGTCACATCTTCCCCGCACCAGGGCCACATAATCATCAAG
Found at i:91551 original size:31 final size:31
Alignment explanation
Indices: 91515--91573 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
91505 CATTTTAATG
* * *
91515 ACTTAAATAAAAACTTTTGAATACTTTATTA
1 ACTTAAATAAAAAATTTCGAATAATTTATTA
91546 ACTTAAATAAAAAATTTCGAATAATTTA
1 ACTTAAATAAAAAATTTCGAATAATTTA
91574 GCGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCGAATAATTTATTA
Found at i:92943 original size:4 final size:4
Alignment explanation
Indices: 92923--92992 Score: 79
Period size: 4 Copynumber: 17.2 Consensus size: 4
92913 AAATAAACGG
* * *
92923 GAAA AAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAA GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
92973 GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
92993 GTAATGTGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
3 3 0.05
4 45 0.82
5 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Done.