Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012932.1 Kokia drynarioides strain JFW-HI SEQ_127950, 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: 23521
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:171 original size:12 final size:12
Alignment explanation
Indices: 156--199 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
146 GTTCCCTTTT
156 TATTATTATTAA
1 TATTATTATTAA
*
168 TATTTTTATTAA
1 TATTATTATTAA
* *
180 TATTAATAATAA
1 TATTATTATTAA
*
192 TTTTATTA
1 TATTATTA
200 ATACCTACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:175 original size:18 final size:18
Alignment explanation
Indices: 152--202 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
142 TTTAGTTCCC
*
152 TTTTTATTATTATTAATA
1 TTTTTATTAATATTAATA
170 TTTTTATTAATATTAATAA
1 TTTTTATTAATATTAAT-A
189 TAATTTTATTAATA
1 T--TTTTATTAATA
203 CCTACTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.55
19 2 0.07
21 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATTAATATTAATA
Found at i:189 original size:21 final size:21
Alignment explanation
Indices: 159--202 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
149 CCCTTTTTAT
* *
159 TATTATTAATATTTTTATTAA
1 TATTAATAATAATTTTATTAA
180 TATTAATAATAATTTTATTAA
1 TATTAATAATAATTTTATTAA
201 TA
1 TA
203 CCTACTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATAATAATTTTATTAA
Found at i:888 original size:17 final size:17
Alignment explanation
Indices: 868--977 Score: 123
Period size: 17 Copynumber: 6.4 Consensus size: 17
858 ATTTATTTAT
* *
868 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
885 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
903 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
920 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
937 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
955 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTAAAATAAA
972 TTTAAA
1 TTTAAA
978 ATGAGTTTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 49 0.63
18 28 0.36
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:913 original size:6 final size:6
Alignment explanation
Indices: 868--945 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
858 ATTTATTTAT
* * *
868 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
915 -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
946 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:924 original size:11 final size:11
Alignment explanation
Indices: 886--944 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
876 TATAATAATT
886 TTAAATTTGAAA
1 TTAAATTT-AAA
*
898 ATAAATTTAAA
1 TTAAATTTAAA
909 CTTAAA-TTAAA
1 -TTAAATTTAAA
920 TTTAAATTTAAA
1 -TTAAATTTAAA
*
932 ATAAATTTAAA
1 TTAAATTTAAA
943 TT
1 TT
945 TTTAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:925 original size:52 final size:52
Alignment explanation
Indices: 868--977 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
858 ATTTATTTAT
* * * * *
868 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
** *
920 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATCCTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
972 TTTAAA
1 TTTAAA
978 ATGAGTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
Found at i:956 original size:35 final size:35
Alignment explanation
Indices: 868--977 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
858 ATTTATTTAT
* *
868 TTTAAATTTAT-AATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAATTT-AAAATAAA
*
903 TTTAAA--CTTAAATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTTTAAA-TAAATTTAAATTTAAAATAAA
* *
937 TTTAAATTTTTAAACAAATTT-AATCCTAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAAT-TTAAAATAAA
972 TTTAAA
1 TTTAAA
978 ATGAGTTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 19 0.30
35 39 0.61
36 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTAAATTTTTAAATAAATTTAAATTTAAAATAAA
Found at i:1700 original size:205 final size:206
Alignment explanation
Indices: 1396--1772 Score: 596
Period size: 205 Copynumber: 1.8 Consensus size: 206
1386 AGAAAGATGG
* * * * * * *
1396 ATTTGGTTCACTTCTCTGTATCTCATCAGGGAGCTATCTACTTTATTGCTTCTACCTGATTCTTA
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACTACTTTATTGCTTCGACCTGATTCTCA
* *
1461 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGAGTTTGATTTGGTCTT
66 GTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGGGCGTGAGTTTGATTTGGTCTT
*
1526 CTTCTCAGTATCTTATCAGGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTTTGTATCTCAT
131 CTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTTTGTATCTCAT
1591 CAGGAAGACAA
196 CAGGAAGACAA
* *
1602 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAAC-CCTTTATTGCTTCGCCCT-ACTTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACTACTTTATTGCTTCGACCTGA-TTCTC
* *
1665 CGTATCTCATCAGGAAGTTGGGATTCGAAGATTTGCTCACATCGGGCGTGAGTTTGATTTGGTCT
65 AGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGGGCGTGAGTTTGATTTGGTCT
*
1730 TCTTCTCAGTATCTCATCAGGAAGATGTCTGCATCGTTTGTTT
130 TCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTT
1773 TGTGGATTGT
Statistics
Matches: 155, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
204 1 0.01
205 121 0.78
206 33 0.21
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (206 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACTACTTTATTGCTTCGACCTGATTCTCA
GTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGGGCGTGAGTTTGATTTGGTCTT
CTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTTTGTATCTCAT
CAGGAAGACAA
Found at i:13348 original size:28 final size:28
Alignment explanation
Indices: 13304--13361 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
13294 AGACTTTTCA
13304 GATTCTCGAGGGCAAAATGGTAATTTTG
1 GATTCTCGAGGGCAAAATGGTAATTTTG
13332 GATTCTCG-GGGCAAAAATGGTAATTTTG
1 GATTCTCGAGGGC-AAAATGGTAATTTTG
13360 GA
1 GA
13362 AAATTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.31
Consensus pattern (28 bp):
GATTCTCGAGGGCAAAATGGTAATTTTG
Found at i:13476 original size:18 final size:17
Alignment explanation
Indices: 13452--13563 Score: 143
Period size: 17 Copynumber: 6.4 Consensus size: 17
13442 CCAAACTCCC
13452 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
13470 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
13488 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
13505 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
13522 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
13539 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
13557 TTTAAAT
1 TTTAAAT
13564 AAAGCTAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
17 46 0.57
18 34 0.43
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13496 original size:6 final size:6
Alignment explanation
Indices: 13485--13563 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
13475 ATTTGTTTAA
* * *
13485 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
13531 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAAT
13564 AAAGCTAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
5 17 0.29
6 38 0.64
7 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:13504 original size:11 final size:11
Alignment explanation
Indices: 13505--13560 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
13495 TTATTTTAAA
13505 TTTAAATTTAT
1 TTTAAATTTAT
* *
13516 TTTGAATTTAAA
1 TTTAAATTT-AT
*
13528 TTT-AATTTAAG
1 TTTAAATTT-AT
13539 TTTAAATTTAT
1 TTTAAATTTAT
13550 TTTCAAATTTA
1 TTT-AAATTTA
13561 AATAAAGCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:13511 original size:23 final size:23
Alignment explanation
Indices: 13485--13563 Score: 56
Period size: 23 Copynumber: 3.4 Consensus size: 23
13475 ATTTGTTTAA
* *
13485 AAATTTAAATTTATTTTAAATTT
1 AAATTTAAATTTAATTTAAGTTT
* *
13508 AAATTT-ATTTTGAATTTAAATTT
1 AAATTTAAATTT-AATTTAAGTTT
* *
13531 -AATTTAAGTTTAAATTT-ATTTT
1 AAATTTAAATTT-AATTTAAGTTT
13553 CAAATTTAAAT
1 -AAATTTAAAT
13564 AAAGCTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 13 0.28
23 25 0.54
24 8 0.17
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (23 bp):
AAATTTAAATTTAATTTAAGTTT
Found at i:15408 original size:29 final size:29
Alignment explanation
Indices: 15373--15640 Score: 185
Period size: 29 Copynumber: 9.2 Consensus size: 29
15363 CCTAAACTTT
15373 CAAAAATCCCATTTTTGACCCGAACCTTC
1 CAAAAATCCCATTTTTGACCCGAACCTTC
** ** *
15402 TGAAAATTACAATTTT-ACCCTCGAA-CTTC
1 CAAAAATCCCATTTTTGA-CC-CGAACCTTC
* *
15431 CAAAAATCCCATTTTTGACTCGAACCTTTT
1 CAAAAATCCCATTTTTGACCCGAACC-TTC
* * * *
15461 GAAAATTACCA-TTTT-ACACTGAA-CTTC
1 CAAAAATCCCATTTTTGAC-CCGAACCTTC
15488 CAAAAATCCCATTTTTGACCTCGAACCTTC
1 CAAAAATCCCATTTTTGACC-CGAACCTTC
* ***
15518 CAAAAATTACCATTTTACCCCCGAA-CTTC
1 CAAAAA-TCCCATTTTTGACCCGAACCTTC
*
15547 CAAAAATCCCATGTTTGACCCCGAACCTTTC
1 CAAAAATCCCATTTTTGA-CCCGAACC-TTC
* * * *
15578 GAAAATTACCA-TTTT-ACCCTGGAA-CTTT
1 CAAAAATCCCATTTTTGACCC--GAACCTTC
*
15606 CAAAAATCCCATTTTTGACTCCGAACCTTT
1 CAAAAATCCCATTTTTGAC-CCGAACCTTC
15636 CAAAA
1 CAAAA
15641 CCACCATTTT
Statistics
Matches: 180, Mismatches: 39, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
27 10 0.06
28 33 0.18
29 67 0.37
30 47 0.26
31 23 0.13
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (29 bp):
CAAAAATCCCATTTTTGACCCGAACCTTC
Found at i:15439 original size:58 final size:58
Alignment explanation
Indices: 15367--15634 Score: 387
Period size: 59 Copynumber: 4.6 Consensus size: 58
15357 AAGGTCCCTA
* *
15367 AACTTTCAAAAATCCCATTTTTGACCCGAACCTTCTGAAAATTACAATTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTGACCCGAACCTTCTGAAAATTACCATTTTACCCTCG
* * *
15425 AACTTCCAAAAATCCCATTTTTGACTCGAACCTTTTGAAAATTACCATTTTACACT-G
1 AACTTCCAAAAATCCCATTTTTGACCCGAACCTTCTGAAAATTACCATTTTACCCTCG
** *
15482 AACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCTGAAAATTACCATTTTACCCTCG
* *
15541 AACTTCCAAAAATCCCATGTTTGACCCCGAACCTT-TCGAAAATTACCATTTTACCCTGG
1 AACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCT-GAAAATTACCATTTTACCCTCG
*
15600 AACTTTCAAAAATCCCATTTTTGACTCCGAACCTT
1 AACTTCCAAAAATCCCATTTTTGAC-CCGAACCTT
15635 TCAAAACCAC
Statistics
Matches: 187, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
57 26 0.14
58 77 0.41
59 82 0.44
60 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTGACCCGAACCTTCTGAAAATTACCATTTTACCCTCG
Found at i:16570 original size:30 final size:29
Alignment explanation
Indices: 16531--16734 Score: 154
Period size: 30 Copynumber: 6.9 Consensus size: 29
16521 GAGGTTCAAA
*
16531 GGTAAAAATGAAATTTTTGAAAGTTTCGG
1 GGTAAAAATGAAATTTTTGGAAGTTTCGG
* **
16560 GATAAAAAATGGCATTTTTGGAAG-TTCGGG
1 GGT-AAAAATGAAATTTTTGGAAGTTTC-GG
16590 GGTAAAAAT-AGAATTTTTGGAAGTTTCGG
1 GGTAAAAATGA-AATTTTTGGAAGTTTCGG
*
16619 GGTCAAAAAT-AGGATTTTTGGAAG-TTCGAG
1 GGT-AAAAATGA-AATTTTTGGAAGTTTCG-G
* * **
16649 GGTAAAAATGGAATTTTTGAAAGTTTTAG
1 GGTAAAAATGAAATTTTTGGAAGTTTCGG
*
16678 GGT--CAATGATAGGATTTTTGGAAG-TTCGGG
1 GGTAAAAATGA-A--ATTTTTGGAAGTTTC-GG
16708 GGTAAAAAT-AGAATTTTTGGACAGTTT
1 GGTAAAAATGA-AATTTTTGGA-AGTTT
16735 AGGGACCTCT
Statistics
Matches: 139, Mismatches: 20, Indels: 30
0.74 0.11 0.16
Matches are distributed among these distances:
27 4 0.03
28 1 0.01
29 62 0.45
30 65 0.47
31 4 0.03
32 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGTAAAAATGAAATTTTTGGAAGTTTCGG
Found at i:16606 original size:59 final size:58
Alignment explanation
Indices: 16531--16726 Score: 270
Period size: 59 Copynumber: 3.3 Consensus size: 58
16521 GAGGTTCAAA
*
16531 GGTAAAAAT-GAAATTTTTGAAAGTTTCGGGATAAAAAAT-GGCATTTTTGGAAGTTCGGG
1 GGTAAAAATAG-AATTTTTGAAAGTTTCGGG-TCAAAAATAGG-ATTTTTGGAAGTTCGGG
* *
16590 GGTAAAAATAGAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGAG
1 GGTAAAAATAGAATTTTTGAAAGTTTC-GGGTCAAAAATAGGATTTTTGGAAGTTCGGG
* * **
16649 GGTAAAAATGGAATTTTTGAAAGTTTTAGGGTCAATGATAGGATTTTTGGAAGTTCGGG
1 GGTAAAAATAGAATTTTTGAAAG-TTTCGGGTCAAAAATAGGATTTTTGGAAGTTCGGG
16708 GGTAAAAATAGAATTTTTG
1 GGTAAAAATAGAATTTTTG
16727 GACAGTTTAG
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
59 114 0.93
60 9 0.07
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
GGTAAAAATAGAATTTTTGAAAGTTTCGGGTCAAAAATAGGATTTTTGGAAGTTCGGG
Found at i:18340 original size:6 final size:6
Alignment explanation
Indices: 18314--18376 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
18304 ATTTATTTAT
* *
18314 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
18360 TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
18377 ATTTTAAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.02
5 11 0.23
6 33 0.70
7 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:18352 original size:17 final size:17
Alignment explanation
Indices: 18332--18376 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
18322 TATAATAATT
18332 TTAAATTTAAACTTAAA
1 TTAAATTTAAACTTAAA
*
18349 TTAAATTTAAATTTAAA
1 TTAAATTTAAACTTAAA
*
18366 ATAAATTTAAA
1 TTAAATTTAAA
18377 ATTTTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAACTTAAA
Found at i:18357 original size:23 final size:23
Alignment explanation
Indices: 18314--18365 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
18304 ATTTATTTAT
* *
18314 TTTAAATTTATAATAATTTTAAA
1 TTTAAACTTATAATAAATTTAAA
18337 TTTAAACTTA-AATTAAATTTAAA
1 TTTAAACTTATAA-TAAATTTAAA
18360 TTTAAA
1 TTTAAA
18366 ATAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAACTTATAATAAATTTAAA
Found at i:18408 original size:17 final size:16
Alignment explanation
Indices: 18333--18410 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 16
18323 ATAATAATTT
* *
18333 TAAATTTAAACTTAAAT
1 TAAATTT-AATTTAAAA
18350 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTAAAA
*
18367 TAAATTTAAAATTTTAAA
1 TAAATTT--AATTTAAAA
* *
18385 CAAATTTAATCCTAAAA
1 TAAATTTAAT-TTAAAA
18402 TAAATTTAA
1 TAAATTTAA
18411 AATGAGTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 3 0.06
17 34 0.65
18 15 0.29
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:22977 original size:17 final size:18
Alignment explanation
Indices: 22943--22978 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22933 TGAATTTCTA
22943 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
22961 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
22978 T
1 T
22979 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Done.