Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013399.1 Kokia drynarioides strain JFW-HI SEQ_128424, 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: 26749
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:228 original size:29 final size:29
Alignment explanation
Indices: 194--586 Score: 274
Period size: 29 Copynumber: 13.4 Consensus size: 29
184 GTCCCTAAAC
194 CTTCCAAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
* *
223 CTTCCAAAAA-TCCCATTTTTGA-CCTCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
* *
252 TCTTCC-AAAATTACTATTTTACCCCAGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* * * *
281 CTTTCAAAAA-T-CTCATTTTTAACCTCAAA
1 CTTCCAAAAATTAC-CA-TTTTACCCCCGAA
** *
310 TCTTCCAAAAATTATTATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
*
340 CTTCCAAAAA-T-CTCATTTTTGA-CCCCAAA
1 CTTCCAAAAATTAC-CA-TTTT-ACCCCCGAA
*
369 TCTTCCAAAAATTACTATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* *
399 CTTCCAAAAA-TCCCATTTTTAACCCCGAA
1 CTTCCAAAAATTACCA-TTTTACCCCCGAA
** *
428 CCTTCTTAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* ** **
458 CTTCCAACAA-T-CTCATTTTTGGCCTTGAA
1 CTTCCAAAAATTAC-CA-TTTTACCCCCGAA
* *
487 TCTTCCAAAAATTACTATTTTCCCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
*
517 -TTCACAAAAA-T-CTCATTTTTAGCCCCGAA
1 CTTC-CAAAAATTAC-CA-TTTTACCCCCGAA
*
546 TCTTCCAAAAATTACCATTTTACCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
576 CTTCCAAAAAT
1 CTTCCAAAAAT
587 CCTATTTTTG
Statistics
Matches: 283, Mismatches: 48, Indels: 66
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.01
28 24 0.08
29 133 0.47
30 104 0.37
31 16 0.06
32 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:350 original size:59 final size:59
Alignment explanation
Indices: 194--595 Score: 522
Period size: 59 Copynumber: 6.8 Consensus size: 59
184 GTCCCTAAAC
* * * *
194 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
* * * *
253 CTTCC-AAAATTACTATTTTACCCCAGAACTTTCAAAAATCTCATTTTTAACCTCAAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
* * * *
311 CTTCCAAAAATTATTATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
* *
370 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
** * * * ** **
429 CTTCTTAAAATTACCATTTTACCCCCAAACTTCCAACAATCTCATTTTTGGCCTTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
* *
488 CTTCCAAAAATTACTATTTTCCCCCCGAA-TTCACAAAAATCTCATTTTTAGCCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTC-CAAAAATCTCATTTTTAACCCCGAAT
* *
547 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATC-CTATTTTT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTC-ATTTTT
596 GATTCCGAAC
Statistics
Matches: 298, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
58 56 0.19
59 239 0.80
60 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCGAAT
Found at i:440 original size:118 final size:118
Alignment explanation
Indices: 191--597 Score: 577
Period size: 118 Copynumber: 3.5 Consensus size: 118
181 GAGGTCCCTA
* *
191 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
* * * *
256 CC-AAAATTACTATTTTACCCCAGAACTTTCAAAAATCTCATTTTTAACCTCA
66 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCG
* ** * *
308 AATCTTCCAAAAATTATTATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
*
373 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG
66 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCG
** * * *
426 AACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCAACAATCTCATTTTTGGCCTTGAATCTT
1 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
* *
491 CCAAAAATTACTATTTTCCCCCCGAA-TTCACAAAAATCTCATTTTTAGCCCCG
66 CCAAAAATTACTATTTTACCCCCGAACTTC-CAAAAATCTCATTTTTAACCCCG
* * *
544 AATCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATC-CTATTTTTGA
1 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTC-ATTTTTGA
598 TTCCGAACAT
Statistics
Matches: 255, Mismatches: 32, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
117 64 0.25
118 191 0.75
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (118 bp):
AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATCTT
CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCG
Found at i:978 original size:96 final size:96
Alignment explanation
Indices: 866--1052 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 96
856 TTTAATATCA
* ** * **
866 AGGCAATATTCTTTTAT-TTCGAGTTTCGAAA-ATTTGCGCCTTAACTCACTAAGTGCAATTTTT
1 AGGCAATATTCTTTTATCTTCGA-TTACGAAATA-TTGCAACTTAACTCACTAAGTACAACCTTT
*
929 CTTCAAATCGA-AGTAATCGAATAACCTTAATCG
64 CTTCAAATCGAGA-TAATCAAATAACCTTAATCG
* * *
962 AGGCAATATTTTTTTATCTTCGATTACGAAATATTGCAACTTAACTTACTAGGTACAACCTTTCT
1 AGGCAATATTCTTTTATCTTCGATTACGAAATATTGCAACTTAACTCACTAAGTACAACCTTTCT
*
1027 TCAAATCGAGATAATCAAATATCCTT
66 TCAAATCGAGATAATCAAATAACCTT
1053 CTCGCAAAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
96 70 0.91
97 7 0.09
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (96 bp):
AGGCAATATTCTTTTATCTTCGATTACGAAATATTGCAACTTAACTCACTAAGTACAACCTTTCT
TCAAATCGAGATAATCAAATAACCTTAATCG
Found at i:6355 original size:10 final size:10
Alignment explanation
Indices: 6340--6431 Score: 75
Period size: 9 Copynumber: 9.4 Consensus size: 10
6330 TCTGTAGCAA
6340 AAAAAATTAT
1 AAAAAATTAT
6350 AAAAAA-TAT
1 AAAAAATTAT
* *
6359 TAAAAATTAGAA
1 AAAAAATT--AT
6371 AAAAAATTAT
1 AAAAAATTAT
*
6381 -AAAAATTGT
1 AAAAAATTAT
* *
6390 AAAAAAATGT
1 AAAAAATTAT
*
6400 -AAAATTTAT
1 AAAAAATTAT
*
6409 AAAAAATCAT
1 AAAAAATTAT
6419 -AAAAATTAT
1 AAAAAATTAT
6428 AAAA
1 AAAA
6432 TGCATAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 30 0.47
10 26 0.41
12 8 0.12
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:6363 original size:9 final size:9
Alignment explanation
Indices: 6340--6445 Score: 50
Period size: 10 Copynumber: 11.0 Consensus size: 9
6330 TCTGTAGCAA
6340 AAAAAATTAT
1 AAAAAA-TAT
6350 AAAAAATATT
1 AAAAAATA-T
* *
6360 AAAAATTAGAA
1 AAAAA--ATAT
6371 AAAAAATTAT
1 AAAAAA-TAT
* *
6381 AAAAATTGT
1 AAAAAATAT
*
6390 AAAAAAATGT
1 -AAAAAATAT
**
6400 AAAATTTAT
1 AAAAAATAT
6409 AAAAAATCAT
1 AAAAAAT-AT
*
6419 AAAAATTAT
1 AAAAAATAT
***
6428 AAAATGCAT
1 AAAAAATAT
6437 AAAAAATAT
1 AAAAAATAT
6446 CATTTAACCA
Statistics
Matches: 71, Mismatches: 19, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
9 30 0.42
10 34 0.48
11 5 0.07
12 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:6365 original size:19 final size:20
Alignment explanation
Indices: 6341--6431 Score: 98
Period size: 19 Copynumber: 4.7 Consensus size: 20
6331 CTGTAGCAAA
6341 AAAAATTATAAAAAATAT-T
1 AAAAATTATAAAAAATATAT
* *
6360 AAAAATTAGAAAAAAAATTAT
1 AAAAATTATAAAAAATA-TAT
* *
6381 AAAAATTGTAAAAAA-ATGT
1 AAAAATTATAAAAAATATAT
* *
6400 AAAATTTATAAAAAAT-CAT
1 AAAAATTATAAAAAATATAT
6419 AAAAATTATAAAA
1 AAAAATTATAAAA
6432 TGCATAAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 43 0.73
20 2 0.03
21 14 0.24
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (20 bp):
AAAAATTATAAAAAATATAT
Found at i:6586 original size:10 final size:9
Alignment explanation
Indices: 6546--6596 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
6536 ACATGTGACG
*
6546 AAAAATGAT
1 AAAAATTAT
6555 AAAAA--AT
1 AAAAATTAT
*
6562 AAAAATAAAT
1 AAAAAT-TAT
6572 AAAAATTAT
1 AAAAATTAT
6581 AGAAAATTAT
1 A-AAAATTAT
6591 AAAAAT
1 AAAAAT
6597 ACTTCCTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 7 0.19
9 13 0.35
10 17 0.46
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6757 original size:29 final size:30
Alignment explanation
Indices: 6716--6775 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
6706 TTTTATATAT
* * *
6716 TTTATAATTTTTTTCTAATTTT-TAATAAAA
1 TTTATAATATTTTTAT-ATTTTATAAAAAAA
6746 TTTA-AATATTTTTATATTTTATAAAAAAA
1 TTTATAATATTTTTATATTTTATAAAAAAA
6775 T
1 T
6776 ATAATAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 17 0.65
30 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTATAATATTTTTATATTTTATAAAAAAA
Found at i:6758 original size:30 final size:29
Alignment explanation
Indices: 6678--6771 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
6668 CTTACAACTC
* *
6678 TATAAAATTTTATATTTTTTTTGTATATTTT
1 TATAAAA-TTTA-AATTTTTTTCTATATTTT
* *
6709 TATATATTTTATAATTTTTTTCTA-ATTTT
1 TATAAAATTTA-AATTTTTTTCTATATTTT
*
6738 TAATAAAATTTAAA-TATTTT-TATA-TTT
1 T-ATAAAATTTAAATTTTTTTCTATATTTT
6765 TATAAAA
1 TATAAAA
6772 AAATATAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 6 0.11
27 6 0.11
28 6 0.11
29 8 0.15
30 23 0.43
31 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TATAAAATTTAAATTTTTTTCTATATTTT
Found at i:9601 original size:20 final size:19
Alignment explanation
Indices: 9574--9614 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
9564 ACTTAATCAC
9574 TTTAATATTAAATATAATA
1 TTTAATATTAAATATAATA
*
9593 TTTATATATTAAATTTAATA
1 TTTA-ATATTAAATATAATA
9613 TT
1 TT
9615 AAATCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATATTAAATATAATA
Found at i:9704 original size:20 final size:18
Alignment explanation
Indices: 9657--9705 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
9647 GTAGATAAAC
9657 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
9674 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
9694 ATTAAATTAATA
1 ATTAAATTAATA
9706 AAATACTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:12256 original size:9 final size:9
Alignment explanation
Indices: 12242--12272 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12232 GAATTTTACA
12242 ATTCGAATG
1 ATTCGAATG
12251 ATTCGAATG
1 ATTCGAATG
*
12260 ATTCGAATA
1 ATTCGAATG
12269 ATTC
1 ATTC
12273 AAATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (9 bp):
ATTCGAATG
Found at i:12277 original size:9 final size:9
Alignment explanation
Indices: 12241--12279 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
12231 TGAATTTTAC
12241 AATTCGAAT
1 AATTCGAAT
*
12250 GATTCGAAT
1 AATTCGAAT
*
12259 GATTCGAAT
1 AATTCGAAT
*
12268 AATTCAAAT
1 AATTCGAAT
12277 AAT
1 AAT
12280 AAATTGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15950 original size:18 final size:18
Alignment explanation
Indices: 15927--15964 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
15917 TAATATAATT
15927 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
15945 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
15963 TT
1 TT
15965 TGAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:17286 original size:33 final size:33
Alignment explanation
Indices: 17244--17352 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
17234 TCATGGTCCT
* * * *
17244 ACTACGGTCTTACATTCATAATGCCATAACCCA
1 ACTATGGTCTTACATTCAGAATGTCATAGCCCA
*
17277 ATTATGGTCTTAACA-TCAGAAT-TCATAGCCCA
1 ACTATGGTCTT-ACATTCAGAATGTCATAGCCCA
17309 ACTATGGTCTTATCATT-AGAATGTCATAGCCCA
1 ACTATGGTCTTA-CATTCAGAATGTCATAGCCCA
*
17342 ACTATAGTCTT
1 ACTATGGTCTT
17353 CCATATATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
31 1 0.02
32 25 0.38
33 36 0.55
34 3 0.05
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (33 bp):
ACTATGGTCTTACATTCAGAATGTCATAGCCCA
Found at i:19714 original size:6 final size:6
Alignment explanation
Indices: 19703--19771 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
19693 GACCCAAATC
* *
19703 AAATTT AAATTT AAATTT -ATTTT AAATTT AAATTT --ATTGT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT
*
19749 AAGTTT AAATTT --ATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
19772 CTAATGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 37 0.73
7 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:19726 original size:17 final size:17
Alignment explanation
Indices: 19706--19755 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
19696 CCAAATCAAA
19706 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
19723 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* * *
19740 TGTAAAATTAAGTTTA
1 TTTAAATTTAAATTTA
19756 AATTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:19750 original size:23 final size:22
Alignment explanation
Indices: 19724--19767 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
19714 TAAATTTATT
19724 TTAAATTTAAATTTATTGTAAAA
1 TTAAATTTAAATTTATT-TAAAA
*
19747 TTAAGTTTAAATTTATTTAAA
1 TTAAATTTAAATTTATTTAAA
19768 TTTACTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TTAAATTTAAATTTATTTAAAA
Found at i:20403 original size:11 final size:11
Alignment explanation
Indices: 20387--20427 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
20377 ATGAGGCATT
20387 TAATAAATAAA
1 TAATAAATAAA
20398 TAATAAATATAA
1 TAATAAATA-AA
20410 TAAT-AATAAAA
1 TAATAAAT-AAA
20421 TAATAAA
1 TAATAAA
20428 GAGTTGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:21577 original size:4 final size:4
Alignment explanation
Indices: 21559--21597 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
21549 AAGGAAAAAA
*
21559 AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AA
21598 GGAAGAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:21605 original size:7 final size:7
Alignment explanation
Indices: 21593--21646 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
21583 GAAAGAAAGA
21593 AAGAAGG
1 AAGAAGG
21600 AAGAAGG
1 AAGAAGG
21607 AAGAAGG
1 AAGAAGG
21614 AAGAAGG
1 AAGAAGG
21621 AA-AA-G
1 AAGAAGG
*
21626 AAG-GGG
1 AAGAAGG
21632 AAGAAGG
1 AAGAAGG
21639 -AGAAGG
1 AAGAAGG
21645 AA
1 AA
21647 AAAAATGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 3 0.07
6 12 0.29
7 26 0.63
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:21616 original size:18 final size:18
Alignment explanation
Indices: 21589--21646 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
21579 GAAAGAAAGA
*
21589 AAGAAAGAAGGAAGAAGG
1 AAGAAGGAAGGAAGAAGG
21607 AAGAAGGAA-GAAGGAA--
1 AAGAAGGAAGGAA-GAAGG
21623 AAGAAGG--GGAAGAAGG
1 AAGAAGGAAGGAAGAAGG
21639 -AGAAGGAA
1 AAGAAGGAA
21647 AAAAATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 7 0.21
17 3 0.09
18 11 0.33
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (18 bp):
AAGAAGGAAGGAAGAAGG
Found at i:21807 original size:18 final size:18
Alignment explanation
Indices: 21784--21818 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21774 GAAAGAAAAG
21784 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
21802 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
21819 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:22032 original size:20 final size:21
Alignment explanation
Indices: 21991--22033 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21981 TACTTTAATT
21991 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
22012 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
22032 TA
1 TA
22034 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:22793 original size:16 final size:15
Alignment explanation
Indices: 22748--22797 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
22738 TAAACCTAGC
22748 TAATTAATTATCAAAA
1 TAATTAATTA-CAAAA
*
22764 T-A-TAATATAAAAAA
1 TAATTAAT-TACAAAA
22778 TAATTAATTACCAAAA
1 TAATTAATTA-CAAAA
22794 TAAT
1 TAAT
22798 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATTAATTACAAAA
Found at i:24176 original size:43 final size:43
Alignment explanation
Indices: 24094--24178 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
24084 ATTAACATGT
* *
24094 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* * *
24137 TAAATTTTATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
24179 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:24881 original size:45 final size:45
Alignment explanation
Indices: 24746--24882 Score: 211
Period size: 45 Copynumber: 3.0 Consensus size: 45
24736 GCATAGCTCA
24746 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
24791 CCCAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * *
24836 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
24881 TC
1 TC
24883 TATTCCTCCC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.18
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:25169 original size:27 final size:27
Alignment explanation
Indices: 25139--25217 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
25129 TTTCATAATA
* *
25139 TTAAATCCAAAAACCTAAACCCTAAAC
1 TTAAAACCATAAACCTAAACCCTAAAC
* * *
25166 TTAAAACCCTAATCATAAACCCTAAAC
1 TTAAAACCATAAACCTAAACCCTAAAC
*
25193 TTAAAACCATAAACCTTAAATCCTA
1 TTAAAACCATAAACC-TAAACCCTA
25218 TACAAAAACA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 34 0.81
28 8 0.19
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (27 bp):
TTAAAACCATAAACCTAAACCCTAAAC
Found at i:25172 original size:14 final size:14
Alignment explanation
Indices: 25155--25212 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
25145 CCAAAAACCT
25155 AAACCCTAAACTTA
1 AAACCCTAAACTTA
* *
25169 AAACCCTAATCAT-
1 AAACCCTAAACTTA
25182 AAACCCTAAACTTA
1 AAACCCTAAACTTA
*
25196 AAACCATAAACCTTA
1 AAACCCTAAA-CTTA
25211 AA
1 AA
25213 TCCTATACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.30
14 20 0.54
15 6 0.16
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCCTAAACTTA
Found at i:26224 original size:23 final size:23
Alignment explanation
Indices: 26194--26239 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
26184 TTGAGACCAT
26194 TGCCACCGCTCCATGGTACCCAA
1 TGCCACCGCTCCATGGTACCCAA
26217 TGCCACCGCTCCATGGTACCCAA
1 TGCCACCGCTCCATGGTACCCAA
26240 CCACTCGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.17
Consensus pattern (23 bp):
TGCCACCGCTCCATGGTACCCAA
Done.