Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013587.1 Kokia drynarioides strain JFW-HI SEQ_128614, 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: 110612
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:4300 original size:13 final size:13
Alignment explanation
Indices: 4282--4309 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4272 CATTATTCAC
4282 TTATTATTATCAA
1 TTATTATTATCAA
4295 TTATTATTATCAA
1 TTATTATTATCAA
4308 TT
1 TT
4310 CGTTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTATCAA
Found at i:8309 original size:15 final size:16
Alignment explanation
Indices: 8285--8317 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8275 AGAAGAGGGA
8285 GAAAGAGAAAAAGAAG
1 GAAAGAGAAAAAGAAG
*
8301 GAAAG-GAAAGAGAAG
1 GAAAGAGAAAAAGAAG
8316 GA
1 GA
8318 TAAAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAGAAAAAGAAG
Found at i:9940 original size:15 final size:16
Alignment explanation
Indices: 9915--9945 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9905 CATCGAAATC
9915 TCCATCTAATGCTGGA
1 TCCATCTAATGCTGGA
9931 TCCA-CTAATGCTGGA
1 TCCATCTAATGCTGGA
9946 AGATCCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (16 bp):
TCCATCTAATGCTGGA
Found at i:13713 original size:5 final size:5
Alignment explanation
Indices: 13698--13728 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
13688 ACTAATTTTA
13698 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
13729 TGACCAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17277 original size:10 final size:10
Alignment explanation
Indices: 17262--17290 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
17252 ATAAAAATTT
17262 AAAAATTAAA
1 AAAAATTAAA
17272 AAAAA-TAAA
1 AAAAATTAAA
17281 AAAAATTAAA
1 AAAAATTAAA
17291 TGAAAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:23611 original size:25 final size:25
Alignment explanation
Indices: 23558--23604 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
23548 ATTGGATCCA
23558 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
23583 AATTAAA-TCTAAACA-ATAATTT
1 AATTAAATTCTAAAAAGATAATTT
23605 CCTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:26454 original size:31 final size:31
Alignment explanation
Indices: 26417--26487 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
26407 TATATCATTG
* * *
26417 TATTAAATCATTTAACTATCATTTATTATTA
1 TATTAAATCATTTAAATATAATTTATAATTA
* *
26448 TATTAAATTATTTAAATATAATTTGTAATTA
1 TATTAAATCATTTAAATATAATTTATAATTA
26479 TATTTAAAT
1 TA-TTAAAT
26488 TTTTGTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (31 bp):
TATTAAATCATTTAAATATAATTTATAATTA
Found at i:26699 original size:13 final size:13
Alignment explanation
Indices: 26681--26707 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26671 ATTCTACTTG
26681 TCAAAAATATTTT
1 TCAAAAATATTTT
26694 TCAAAAATATTTT
1 TCAAAAATATTTT
26707 T
1 T
26708 TTAAGGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAAAAATATTTT
Found at i:26765 original size:31 final size:29
Alignment explanation
Indices: 26729--26807 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
26719 AATTTAAAAT
*
26729 TATACATGAATTTTAATTCAATGTGCAATTG
1 TATACATGAATTTTAATT-AA-GTGCAATTA
* *
26760 TATACATGAATTTTAATTTAGTGTAATTA
1 TATACATGAATTTTAATTAAGTGCAATTA
*
26789 TACACATGAAATTTTAATT
1 TATACATG-AATTTTAATT
26808 GTGGTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 18 0.42
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (29 bp):
TATACATGAATTTTAATTAAGTGCAATTA
Found at i:38426 original size:23 final size:21
Alignment explanation
Indices: 38390--38433 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
38380 CATTATTTTG
* *
38390 AAATTGAAAGAATAATTCAAAAC
1 AAATTAAAAAAAT-ATT-AAAAC
38413 AAATTAAAAAAATATTAAAAC
1 AAATTAAAAAAATATTAAAAC
38434 CTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATTAAAAAAATATTAAAAC
Found at i:44665 original size:31 final size:32
Alignment explanation
Indices: 44611--44670 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
44601 CAATTTAAAC
*
44611 ACTTAACGTTTTAGATCATTTCTATTTTGATT
1 ACTTAACGTTTTAGATCACTTCTATTTTGATT
**
44643 ACTT-ACGTTTTAGATTGCTTCTATTTTG
1 ACTTAACGTTTTAGATCACTTCTATTTTG
44671 GTAACTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.53
Consensus pattern (32 bp):
ACTTAACGTTTTAGATCACTTCTATTTTGATT
Found at i:45106 original size:14 final size:13
Alignment explanation
Indices: 45087--45116 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45077 AAATGTTAAC
*
45087 AAAAAAAAAAGGA
1 AAAAAAAAAAAGA
45100 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
45113 AAAA
1 AAAA
45117 GCTTCTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:45830 original size:31 final size:31
Alignment explanation
Indices: 45792--45854 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
45782 AACTAGAGAC
* * *
45792 TATCTAAAATGTTAGTAACTAAAATAGAAAT
1 TATCTAAAACGTTAATAACTAAAATAAAAAT
*
45823 TATCTAAAACGTTAATAACTAAATTAAAAAT
1 TATCTAAAACGTTAATAACTAAAATAAAAAT
45854 T
1 T
45855 TTCATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.33
Consensus pattern (31 bp):
TATCTAAAACGTTAATAACTAAAATAAAAAT
Found at i:50372 original size:19 final size:20
Alignment explanation
Indices: 50326--50372 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
50316 TATGGAAAAA
* *
50326 TTAAGTTTAAGATAATTTTT
1 TTAATTTTAAAATAATTTTT
* *
50346 TGAGTTTTAAAAT-ATTTTT
1 TTAATTTTAAAATAATTTTT
50365 TTAATTTT
1 TTAATTTT
50373 TAATTTATGA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (20 bp):
TTAATTTTAAAATAATTTTT
Found at i:50373 original size:20 final size:20
Alignment explanation
Indices: 50326--50375 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
50316 TATGGAAAAA
*
50326 TTAAG-TTTAAGATAATTTT
1 TTAAGTTTTAAAATAATTTT
* *
50345 TTGAGTTTTAAAATATTTTT
1 TTAAGTTTTAAAATAATTTT
*
50365 TTAATTTTTAA
1 TTAAGTTTTAA
50376 TTTATGAGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTAAGTTTTAAAATAATTTT
Found at i:59032 original size:13 final size:13
Alignment explanation
Indices: 58989--59057 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 13
58979 TCAAGAATAT
58989 TTTTAATATTTAAA
1 TTTTAAT-TTTAAA
*
59003 TATTTAATGTTATAA
1 T-TTTAATTTTA-AA
*
59018 TTTTATTTTTAAA
1 TTTTAATTTTAAA
* *
59031 -TTTAAATTTAATG
1 TTTTAATTTTAA-A
*
59044 TTTTTATTTTAAA
1 TTTTAATTTTAAA
59057 T
1 T
59058 AAACATAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
12 9 0.21
13 3 0.07
14 21 0.50
15 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TTTTAATTTTAAA
Found at i:59044 original size:32 final size:35
Alignment explanation
Indices: 58986--59054 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 35
58976 AAATCAAGAA
58986 TATTTTTAATATTTAAATATTTAATGTTATAATTT
1 TATTTTTAATATTTAAATATTTAATGTTATAATTT
* *
59021 TATTTTTAA-ATTT-AA-ATTTAATGTTTTTATTT
1 TATTTTTAATATTTAAATATTTAATGTTATAATTT
59053 TA
1 TA
59055 AATAAACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 17 0.53
33 2 0.06
34 4 0.12
35 9 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (35 bp):
TATTTTTAATATTTAAATATTTAATGTTATAATTT
Found at i:69259 original size:2 final size:2
Alignment explanation
Indices: 69219--69245 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69209 TAAATAACTT
69219 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 T
69246 GAATATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76048 original size:21 final size:22
Alignment explanation
Indices: 76024--76066 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
76014 ATTTTACTTC
76024 ATTATA-TTTTAAATAGATTTT
1 ATTATATTTTTAAATAGATTTT
76045 ATTATATTTTTTAAATAGATTT
1 ATTATA-TTTTTAAATAGATTT
76067 AACGATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
ATTATATTTTTAAATAGATTTT
Found at i:77468 original size:103 final size:104
Alignment explanation
Indices: 77338--77524 Score: 245
Period size: 103 Copynumber: 1.8 Consensus size: 104
77328 CCAGCATCCA
* * *
77338 AAAAAAATATGTTTAAATCTGAAAAAAATA-ATGTCAGTCATTGGGTGCG-AAACA-CCTAAAAA
1 AAAAAAATATGTTTAAATCTGAAAAAAA-AGATGTAAGTCATTAGGTG-GTAAACACCCGAAAAA
77400 AATATTTTTAAATCTGAAAAAAGCTATTGGGTGGTAAACAT
64 AATATTTTTAAATCTGAAAAAAGCTATTGGGTGGTAAACAT
* * * * * *
77441 AAAAAAATATTTTTATATTTGAGAAAAAAGGTGTAAGTCATTAGGTGGTAAACACCCGGAAAAAA
1 AAAAAAATATGTTTAAATCTGAAAAAAAAGATGTAAGTCATTAGGTGGTAAACACCCGAAAAAAA
*
77506 TATTTTTAAATTTGAAAAA
66 TATTTTTAAATCTGAAAAA
77525 GGTGGTGTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
102 2 0.03
103 43 0.61
104 26 0.37
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (104 bp):
AAAAAAATATGTTTAAATCTGAAAAAAAAGATGTAAGTCATTAGGTGGTAAACACCCGAAAAAAA
TATTTTTAAATCTGAAAAAAGCTATTGGGTGGTAAACAT
Found at i:77510 original size:58 final size:57
Alignment explanation
Indices: 77442--77580 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 57
77432 GGTAAACATA
* ** * *
77442 AAAAAATATTTTTATATTTGAGAAAA-AAGGTGTAAGTCATTAGG-TGGTAAACACCC
1 AAAAAATATTTTTAAATTTGAGAAAAGAAGGTGTAAACCATT-GGATAGCAAACACCC
**
77498 GGAAAAAATATTTTTAAATTTGA-AAAAGGTGGTGTAAACCATTGGATAGCAAACACCC
1 --AAAAAATATTTTTAAATTTGAGAAAAGAAGGTGTAAACCATTGGATAGCAAACACCC
*
77556 AAAAAATATTTTTAAATCTGAGAAA
1 AAAAAATATTTTTAAATTTGAGAAA
77581 TCTGTAGGCC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
56 20 0.29
57 9 0.13
58 41 0.59
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (57 bp):
AAAAAATATTTTTAAATTTGAGAAAAGAAGGTGTAAACCATTGGATAGCAAACACCC
Found at i:78218 original size:7 final size:7
Alignment explanation
Indices: 78206--78230 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
78196 AAATATATAA
78206 AAATATT
1 AAATATT
78213 AAATATT
1 AAATATT
78220 AAATATT
1 AAATATT
78227 AAAT
1 AAAT
78231 TAAAATAACA
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:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:78685 original size:16 final size:17
Alignment explanation
Indices: 78645--78678 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
78635 ATCTATGCCC
* *
78645 AATTGAAATGGTTTATT
1 AATTAAAATGGCTTATT
78662 AATTAAAATGGCTTATT
1 AATTAAAATGGCTTATT
78679 TTTAAAAATA
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:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
AATTAAAATGGCTTATT
Found at i:84629 original size:28 final size:28
Alignment explanation
Indices: 84589--84679 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 28
84579 GATATCCAAT
84589 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
*
84617 TTACTCCTTGTTGACCCAAAGGTCATAATGCTC
1 TTACTCCCTGTTGACCCAAAGGTC---ATG--C
84650 ATTTTACTCCCTGTTGACCCAAAGGTCATG
1 ---TTACTCCCTGTTGACCCAAAGGTCATG
84680 ATGCTCATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
28 23 0.43
31 3 0.06
33 4 0.08
36 23 0.43
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:84665 original size:36 final size:36
Alignment explanation
Indices: 84617--84714 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
84607 AAGGTCATGC
*
84617 TTACTCCTTGTTGACCCAAAGGTCATAATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATAATGCTCATT
*
84653 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATAATGCTCATT
*
84689 TTACTTCCTGTTGACCCAAAGGTCAT
1 TTACTCCCTGTTGACCCAAAGGTCAT
84715 GCCTGTTACC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGGTCATAATGCTCATT
Found at i:88390 original size:20 final size:20
Alignment explanation
Indices: 88357--88395 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
88347 ATTTATAACA
*
88357 TAAATATCATTTATATAAAAT
1 TAAATATCAATTAT-TAAAAT
88378 TAAATA-CAATTATTAAAA
1 TAAATATCAATTATTAAAA
88396 ACAGTATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATCAATTATTAAAAT
Found at i:93196 original size:17 final size:18
Alignment explanation
Indices: 93159--93193 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
93149 TTTTGAGAAT
93159 TATTTTTAGAATAAAAAA
1 TATTTTTAGAATAAAAAA
93177 TATTTTTA-AGATAAAAA
1 TATTTTTAGA-ATAAAAA
93194 TATCACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TATTTTTAGAATAAAAAA
Found at i:96462 original size:25 final size:25
Alignment explanation
Indices: 96427--96477 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
96417 TTTGGTGGAG
*
96427 CATTAGGGATCCTTACCAACTCACC
1 CATTAGAGATCCTTACCAACTCACC
96452 CATTAGAGATCCTTACCAACTCACC
1 CATTAGAGATCCTTACCAACTCACC
96477 C
1 C
96478 TCCTATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.37, G:0.10, T:0.24
Consensus pattern (25 bp):
CATTAGAGATCCTTACCAACTCACC
Found at i:99015 original size:17 final size:17
Alignment explanation
Indices: 98985--99028 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
98975 AAAGAAAAAA
*
98985 TAAAAAAATTATATTCTT
1 TAAAAAAATAATATT-TT
99003 TAAAAAAA-AATATTTT
1 TAAAAAAATAATATTTT
*
99019 CAAAAAAATA
1 TAAAAAAATA
99029 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 6 0.26
18 8 0.35
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAAAATAATATTTT
Found at i:99025 original size:14 final size:13
Alignment explanation
Indices: 99006--99037 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
98996 TATTCTTTAA
99006 AAAAAAATATTTT
1 AAAAAAATATTTT
99019 CAAAAAAATATTTT
1 -AAAAAAATATTTT
99033 AAAAA
1 AAAAA
99038 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAAATATTTT
Found at i:104261 original size:21 final size:21
Alignment explanation
Indices: 104203--104264 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
104193 TTTTACCTAT
* * *
104203 AATCTTGAATCTTAAACTTTA
1 AATCTTGAACCCTGAACTTTA
*
104224 AATCTCGAATCCC-GAACTTTA
1 AATCTTGAA-CCCTGAACTTTA
104245 AATCTTGAACCCTGAACTTT
1 AATCTTGAACCCTGAACTTT
104265 GAACCCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.09
21 30 0.88
22 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.35
Consensus pattern (21 bp):
AATCTTGAACCCTGAACTTTA
Found at i:106298 original size:29 final size:30
Alignment explanation
Indices: 106265--106323 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
106255 TCACGTGCGT
*
106265 AATTGCAC-CAAATTAAAGTTCATGTATAC
1 AATTGCACGCAAATCAAAGTTCATGTATAC
*
106294 AATTGCACGTTAAATCAAAGTTCATGTATA
1 AATTGCACG-CAAATCAAAGTTCATGTATA
106324 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (30 bp):
AATTGCACGCAAATCAAAGTTCATGTATAC
Done.