Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014414.1 Kokia drynarioides strain JFW-HI SEQ_129452, 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: 101275
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:1702 original size:21 final size:23
Alignment explanation
Indices: 1669--1710 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1659 TAAAAAAACG
*
1669 GATCTAGGTCTAGAT-CAAACCA
1 GATCTAGGCCTAGATCCAAACCA
1691 GATCTA-GCCTAGATCCAAAC
1 GATCTAGGCCTAGATCCAAAC
1711 GGTTTTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (23 bp):
GATCTAGGCCTAGATCCAAACCA
Found at i:2647 original size:17 final size:16
Alignment explanation
Indices: 2625--2687 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
2615 TGGACTTTTC
2625 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
2642 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
2659 TAAACTTAAATTTAAAA
1 TAAA-TTTAATTTTAAA
*
2676 TAAATTCAATTT
1 TAAATTTAATTT
2688 CCAACGGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.17
17 25 0.62
18 8 0.20
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:2942 original size:22 final size:21
Alignment explanation
Indices: 2898--2943 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2888 AACATTTTCA
*
2898 TTTAATATTTTGTTCAATGTC
1 TTTAATATTTTGATCAATGTC
2919 TTTAATATTTGTGCATC-ATGTC
1 TTTAATATTT-TG-ATCAATGTC
2941 TTT
1 TTT
2944 TAAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 10 0.45
23 2 0.09
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTAATATTTTGATCAATGTC
Found at i:6090 original size:19 final size:19
Alignment explanation
Indices: 6048--6090 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
6038 CAAATCTAAC
**
6048 AATTTTTAGAATTATTTTT
1 AATTTTTAGAATTATTTAG
* *
6067 TATTTTTATAATTATTTAG
1 AATTTTTAGAATTATTTAG
6086 AATTT
1 AATTT
6091 ATCTTTGCTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
AATTTTTAGAATTATTTAG
Found at i:11935 original size:33 final size:33
Alignment explanation
Indices: 11893--11959 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
11883 AAGTGATAAA
11893 ATATGTATAGTTCAGAAGCCAAATCATGAAATT
1 ATATGTATAGTTCAGAAGCCAAATCATGAAATT
11926 ATATGTATAGTTCAGAAGCCAAATCATGAAATT
1 ATATGTATAGTTCAGAAGCCAAATCATGAAATT
11959 A
1 A
11960 ACTTATTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (33 bp):
ATATGTATAGTTCAGAAGCCAAATCATGAAATT
Found at i:14928 original size:26 final size:26
Alignment explanation
Indices: 14899--14977 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 26
14889 CAATTTGTGA
14899 TTAAATATCTATCTTTGTAATTGTTT
1 TTAAATATCTATCTTTGTAATTGTTT
* * ** **
14925 TT-AAT-TTTA-CTTAGTTTTTGTGA
1 TTAAATATCTATCTTTGTAATTGTTT
14948 TTAAATATCTATCTTTGTAATTGTTT
1 TTAAATATCTATCTTTGTAATTGTTT
14974 TTAA
1 TTAA
14978 TTTTACTTAG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
23 11 0.29
24 6 0.16
25 6 0.16
26 15 0.39
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (26 bp):
TTAAATATCTATCTTTGTAATTGTTT
Found at i:14954 original size:49 final size:49
Alignment explanation
Indices: 14892--14991 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
14882 TACTTCACAA
14892 TTTGTGATTAAATATCTATCTTTGTAATTGTTTTTAATTTTACTTAGTT
1 TTTGTGATTAAATATCTATCTTTGTAATTGTTTTTAATTTTACTTAGTT
14941 TTTGTGATTAAATATCTATCTTTGTAATTGTTTTTAATTTTACTTAGTT
1 TTTGTGATTAAATATCTATCTTTGTAATTGTTTTTAATTTTACTTAGTT
14990 TT
1 TT
14992 ATATGCTGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.60
Consensus pattern (49 bp):
TTTGTGATTAAATATCTATCTTTGTAATTGTTTTTAATTTTACTTAGTT
Found at i:20375 original size:19 final size:19
Alignment explanation
Indices: 20333--20375 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
20323 CAAATCTAAT
**
20333 AATTTTTATAATTATTTCT
1 AATTTTTATAATTATTTAA
*
20352 TATTTTTATAATTATTTAA
1 AATTTTTATAATTATTTAA
20371 AATTT
1 AATTT
20376 ATCTTTGCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTATAATTATTTAA
Found at i:30511 original size:17 final size:18
Alignment explanation
Indices: 30477--30511 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30467 ATATATATAT
*
30477 ATATTAAATTCTTTAATA
1 ATATTAAAATCTTTAATA
30495 ATATTAAAATC-TTAATA
1 ATATTAAAATCTTTAATA
30512 TACATTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTAAAATCTTTAATA
Found at i:37570 original size:25 final size:25
Alignment explanation
Indices: 37536--37585 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
37526 ACTCTCAGAA
37536 AGCAAAATCCAACAGCTGTGTGGTT
1 AGCAAAATCCAACAGCTGTGTGGTT
37561 AGCAAAATCCAACAGCTGTGTGGTT
1 AGCAAAATCCAACAGCTGTGTGGTT
37586 CTTACTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
AGCAAAATCCAACAGCTGTGTGGTT
Found at i:47065 original size:23 final size:25
Alignment explanation
Indices: 47039--47084 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
47029 CCAATTAAGG
47039 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
47062 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
47085 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:47376 original size:157 final size:156
Alignment explanation
Indices: 47091--47400 Score: 453
Period size: 157 Copynumber: 2.0 Consensus size: 156
47081 AATTTGGATC
* *
47091 CAACTACAGATTTCCATGTATTATAACTAGGAGATGGAGTGATATGAATAGGCACTTTCAATTTT
1 CAACTACAGATTTCCATGTATTATAAATAGGAGATAGAGTGATATGAATAGGCACTTTCAATTTT
* * *
47156 CGGTAACATCCTCCATTCCCCAAATCCAAACCGTCAGAGATTATTGAAGGAAACAACTGAAGAAA
66 CGGTAAAATCCTCCACTCCCCAAATCCAAACCGTCAGAGATTATTGAAGAAAACAACTGAAGAAA
*
47221 CACCATAGAAGTCGTCTTTGAAGAAA
131 CACCATAGAAGTCATCTTTGAAGAAA
* *
47247 CAACTAGAGATTTTCATGTATTATAAATA-GAGGATAGAGTGATATGAATTAGGCACTTTCAATT
1 CAACTACAGATTTCCATGTATTATAAATAGGA-GATAGAGTGATATGAA-TAGGCACTTTCAATT
** * * * *
47311 TTTTGTAAAATTCTCCACTCTCCAAA-CTCAAGCCGTCAGAGATTATTGAAGAAAACAATTGAAG
64 TTCGGTAAAATCCTCCACTCCCCAAATC-CAAACCGTCAGAGATTATTGAAGAAAACAACTGAAG
47375 AAACACCATAGAAGTCATCTTTGAAG
128 AAACACCATAGAAGTCATCTTTGAAG
47401 CAAATTTCCA
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
155 2 0.01
156 42 0.31
157 93 0.68
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (156 bp):
CAACTACAGATTTCCATGTATTATAAATAGGAGATAGAGTGATATGAATAGGCACTTTCAATTTT
CGGTAAAATCCTCCACTCCCCAAATCCAAACCGTCAGAGATTATTGAAGAAAACAACTGAAGAAA
CACCATAGAAGTCATCTTTGAAGAAA
Found at i:49297 original size:25 final size:23
Alignment explanation
Indices: 49269--49314 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
49259 GTTGGATCCA
49269 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
49294 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
49315 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:50411 original size:26 final size:25
Alignment explanation
Indices: 50360--50422 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
50350 CACTTTTGTC
*
50360 TTTTTTTTTTCTTTTTTTTCAATTT
1 TTTTTTTTTTCTATTTTTTCAATTT
*
50385 TTTTATTTTTTC-ATTTTTTCGACTTT
1 TTTT-TTTTTTCTATTTTTTC-AATTT
50411 TTTCTTTCTTTT
1 TTT-TTT-TTTT
50423 TTTTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 11 0.34
26 16 0.50
27 5 0.16
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTTCTATTTTTTCAATTT
Found at i:53658 original size:17 final size:17
Alignment explanation
Indices: 53636--53672 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
53626 CTTAGCCAGC
53636 GAAAAATATTTTAATAA
1 GAAAAATATTTTAATAA
*
53653 GAAAAATATTTTACTAA
1 GAAAAATATTTTAATAA
53670 GAA
1 GAA
53673 CTTCTCAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (17 bp):
GAAAAATATTTTAATAA
Found at i:55401 original size:25 final size:23
Alignment explanation
Indices: 55373--55418 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
55363 GTTGGATCCA
55373 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
55398 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
55419 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:56137 original size:23 final size:25
Alignment explanation
Indices: 56111--56156 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56101 CCAATTAGGG
56111 AATTA-TTGTTTAG-ATTTAATTCT
1 AATTATTTGTTTAGAATTTAATTCT
*
56134 AATTATTTTTTTAGAATTTAATT
1 AATTATTTGTTTAGAATTTAATT
56157 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
AATTATTTGTTTAGAATTTAATTCT
Found at i:56762 original size:25 final size:25
Alignment explanation
Indices: 56733--56783 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
56723 AATGCGACAA
56733 TAGGGGTTTTAATTAGAAAGAAATT
1 TAGGGGTTTTAATTAGAAAGAAATT
56758 TAGGGGTTTTAATTAGAAAGAAATT
1 TAGGGGTTTTAATTAGAAAGAAATT
56783 T
1 T
56784 CAATTAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (25 bp):
TAGGGGTTTTAATTAGAAAGAAATT
Found at i:57256 original size:6 final size:6
Alignment explanation
Indices: 57247--57321 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
57237 TAATTTAGCC
* * * * **
57247 ATTTTT ATTTTT ATTTTC ATTTTTT GTTTTT AATTTA ATTTTT ACATTT
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
57296 ACTTTT A-TTTT A-TTTT A-TTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
57322 ATAGGTTCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
5 15 0.27
6 37 0.66
7 4 0.07
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:57263 original size:5 final size:5
Alignment explanation
Indices: 57249--57323 Score: 55
Period size: 5 Copynumber: 14.2 Consensus size: 5
57239 ATTTAGCCAT
* * *
57249 TTTTA TTTTTA TTTTCA TTTT- TTGTT- TTTAA TTTAA TTTTTA CATTTA
1 TTTTA -TTTTA TTTT-A TTTTA TT-TTA TTTTA TTTTA -TTTTA -TTTTA
57297 CTTTTA TTTTA TTTTA TTTTA TTTTA T
1 -TTTTA TTTTA TTTTA TTTTA TTTTA T
57324 AGGTTCTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
4 3 0.05
5 34 0.57
6 23 0.38
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:57276 original size:19 final size:19
Alignment explanation
Indices: 57248--57289 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57238 AATTTAGCCA
* *
57248 TTTTTATTTTTATTTTCAT
1 TTTTTATTTTTAATTTAAT
*
57267 TTTTTGTTTTTAATTTAAT
1 TTTTTATTTTTAATTTAAT
57286 TTTT
1 TTTT
57290 ACATTTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTATTTTTAATTTAAT
Found at i:58946 original size:22 final size:20
Alignment explanation
Indices: 58913--58953 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
58903 TTTATGTTTT
58913 AAAAAATGAAAAAAAAAATC
1 AAAAAATGAAAAAAAAAATC
58933 AAAAAATTGTAAAAAAAAAAT
1 AAAAAA-TG-AAAAAAAAAAT
58954 TAATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAAATC
Found at i:58981 original size:12 final size:11
Alignment explanation
Indices: 58961--59014 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 11
58951 AATTAATATA
58961 TTTATTTTCAT
1 TTTATTTTCAT
58972 TTTCATTTTCAAT
1 TTT-ATTTTC-AT
58985 TTTATTTT-AT
1 TTTATTTTCAT
*
58995 TTTAGTTTTAAT
1 TTTA-TTTTCAT
59007 TTTATTTT
1 TTTATTTT
59015 AATTATGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.15
11 11 0.28
12 17 0.44
13 5 0.13
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTTTCAT
Found at i:58993 original size:5 final size:5
Alignment explanation
Indices: 58961--59015 Score: 56
Period size: 5 Copynumber: 9.8 Consensus size: 5
58951 AATTAATATA
58961 TTTAT TTTCAT TTTCAT TTTCAAT TTTAT TTTAT TTTAGT TTTAAT TTTAT
1 TTTAT TTT-AT TTT-AT TTT--AT TTTAT TTTAT TTTA-T TTT-AT TTTAT
59012 TTTA
1 TTTA
59016 ATTATGCACT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 20 0.44
6 19 0.42
7 6 0.13
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:62183 original size:933 final size:933
Alignment explanation
Indices: 60377--62221 Score: 3100
Period size: 933 Copynumber: 2.0 Consensus size: 933
60367 TTGTTAATTC
*
60377 TGACTAAGGCAAGTGCACCTATCAATTAATAGTATAGTTACGGAGAGCACAAATATCGTTCCCAC
1 TGACTAAGACAAGTGCACCTATCAATTAATAGTATAGTTACGGAGAGCACAAATATCGTTCCCAC
* *
60442 GAGGACTAAAAATACTAGTAATAGTTGCTTTCTATTATTTAACCGATCGAATAGAGTGATTGTTT
66 GAGGACTAAAAATACTAGTAATAGTTGCTTTCTATTATCTAACCGATCAAATAGAGTGATTGTTT
* *
60507 TAAACTAAATTTAACTAAATTAATAAACTAAAAGTGCGACAAAGAATAAAACAAGAAATAACAAG
131 TAAACTAAACTTAACTAAATTAATAAACTAAAAGTACGACAAAGAATAAAACAAGAAATAACAAG
* *
60572 TGTTTTAATACCAAGAAGCAAACAATACTCAGGAAAGACTCCACCTAGATTTCATCTACCATTAT
196 TGTTTTAATACCAAGAAGCAAACAATACCCAGGAAAGACTCAACCTAGATTTCATCTACCATTAT
* * * * *
60637 TATTCTGAATTAAGCAATTTATTCACTTAGTATTTTGATTCATAGAAATCCCTAAATTATGCTAA
261 CATTCTAAATTAAGCAATTTATTCACTTAGTATTTTAATCCATAAAAATCCCTAAATTATGCTAA
*
60702 TACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAGTTGAAATTTCTTTCGAATTAA
326 TACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATTTCTTTCGAATTAA
* * *
60767 AATCCCTATTGTCGCATTAATTCGATCTATGGATTCCCCTATTAGATTTGATTCTAATCCGGTAA
391 AACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAGATTTGATTCTAATCCGATAA
* *
60832 ATTTATGTTGTCCTATTTCTAGGATTGCATGCAACTCCACTCAATTATGCTAGATCTACTCTTAA
456 ATTTATATCGTCCTATTTCTAGGATTGCATGCAACTCCACTCAATTATGCTAGATCTACTCTTAA
** * *
60897 ACAGGATTTATTCCTCCTTTGATTTAAGCACGTCAAACAAGAATTAATATCTCAAAAATACTAAA
521 ACAGGATCAATTCCTCCTCTGATTTAAGCACATCAAACAAGAATTAATATCTCAAAAATACTAAA
* *
60962 TCAAGAAATAAGCACACATAATTGAGAACAAAATTTAAGTATTTATTGTGTAAAATCAGAAATCA
586 TCAAGAAATAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTGCGTAAAATCAGAAATCA
61027 AATGACAAAATTCATCCTAGAGTTCATCTCCCCTAAGTATTTAGGAATTTAGTTCATGCTAATAA
651 AATGACAAAATTCATCCTAGAGTTCATCTCCCCTAAGTATTTAGGAATTTAGTTCATGCTAATAA
* * * *
61092 ATGGAAACATCTTAAAGATAATATAATCACAAGATAAAGAGAAACTCATAGTAAAATCAAATGAA
716 ATGAAAACATCTCAAAGATAATATAACCACAAGATAAAGAGAAACTCATAGTAAAATCAAAAGAA
* * *
61157 TTTAGAAAGAGGTCTTCAATCTTCGTGGAAATCGACTTCAAAGACAGCTTCTATGTTGTTTTTTC
781 TTTAGAAAAAGGTCTTCAATCTTCGTGAAAATCGACTTCAAAGACAGCTTCTATGGTGTTTTTTC
*
61222 AGTTGTTTCCTTCAATAATCTCTGACAGCTTGAATTTGGGGAATGGAGGATGTTACCGAAAATTG
846 AGTTGTTTCCTTCAATAATCTCTGACAGCTTGAATTTGAGGAATGGAGGATGTTACCGAAAATTG
61287 GAAGTCAAACCTAACTAAAAATA
911 GAAGTCAAACCTAACTAAAAATA
* *
61310 TGACTAAGACAAGTGCACCTATCAATTAATAGTATAGTTACGGTGAGCACAGATATCGTTCCCAC
1 TGACTAAGACAAGTGCACCTATCAATTAATAGTATAGTTACGGAGAGCACAAATATCGTTCCCAC
61375 GAGGACTAAAAATACTAGTAATAGTTGCTTTCTATTATCTAACCGATCAAATAGAGTGATTGTTT
66 GAGGACTAAAAATACTAGTAATAGTTGCTTTCTATTATCTAACCGATCAAATAGAGTGATTGTTT
*
61440 TAAACTAAACTTAACTAAATTAATAAACTAAAAGTACGACAAAGAATAAAATAAGAAATAACAAG
131 TAAACTAAACTTAACTAAATTAATAAACTAAAAGTACGACAAAGAATAAAACAAGAAATAACAAG
* * * * *
61505 TGTTTTAATACTAAGAAGCAAATAATACCCAGTAAAGACTCAACCTAGATTTCATCTGCTATTAT
196 TGTTTTAATACCAAGAAGCAAACAATACCCAGGAAAGACTCAACCTAGATTTCATCTACCATTAT
* *
61570 CATTCTAAATTAAGCAATTTATTCACTTAGTATTTTAATCCGTAAAAATCCCTAAATTATGTTAA
261 CATTCTAAATTAAGCAATTTATTCACTTAGTATTTTAATCCATAAAAATCCCTAAATTATGCTAA
* * *
61635 TACCTCTATTCAAGCATAAAATCAACTGACTCTAGGTTGATTAATTGATATTTCTTTCTAATTAA
326 TACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATTTCTTTCGAATTAA
* * *
61700 AACCCCTATTATCGTATTAATTCGATCTATGGATTCTCCTATTAGATTTGATTCTAATCCGATAG
391 AACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAGATTTGATTCTAATCCGATAA
*
61765 TTTTATATCGTCCTATTTCTAGGATTGCATGCAACTCCACTCAATTATGCTAGATCTACTCTTAA
456 ATTTATATCGTCCTATTTCTAGGATTGCATGCAACTCCACTCAATTATGCTAGATCTACTCTTAA
* *
61830 ACAGTG-TCAATTCCTCCTCTGATTTAAGCACATCAAACAAGATTTAATATCTCAAGAATACTAA
521 ACAG-GATCAATTCCTCCTCTGATTTAAGCACATCAAACAAGAATTAATATCTCAAAAATACTAA
* * *
61894 ATCAAGAATTAATCACATATAATTGAGAACAAAATCTAAGTATTTATTGCGTAAAATCAGAAATC
585 ATCAAGAAATAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTGCGTAAAATCAGAAATC
* *
61959 AAATGACAGAATTCATCCTA-AGGTTCATCTCCCCTAGGTATTTAGGAATTTAGTTCATGCTAAT
650 AAATGACAAAATTCATCCTAGA-GTTCATCTCCCCTAAGTATTTAGGAATTTAGTTCATGCTAAT
*
62023 AAATGAAAACATCTCAAAGATAATATAACCACAAGATGAAGAGAAACTCATAGTAAAATCAAAAG
714 AAATGAAAACATCTCAAAGATAATATAACCACAAGATAAAGAGAAACTCATAGTAAAATCAAAAG
* **
62088 AATTTAGAAAAAGGTCTTCAATCTTCGTGAAAATCGGCTTCAAAGATGGCTTCTATGGTGTTTTT
779 AATTTAGAAAAAGGTCTTCAATCTTCGTGAAAATCGACTTCAAAGACAGCTTCTATGGTGTTTTT
* *
62153 TTAGTTGTTTCCTTCAATAATCTCTGACAGCTTGGATTTGAGGAATGGAGGATGTTACCGAAAAT
844 TCAGTTGTTTCCTTCAATAATCTCTGACAGCTTGAATTTGAGGAATGGAGGATGTTACCGAAAAT
62218 TGGA
909 TGGA
62222 TGTGCCTATT
Statistics
Matches: 848, Mismatches: 62, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
932 1 0.00
933 846 1.00
934 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (933 bp):
TGACTAAGACAAGTGCACCTATCAATTAATAGTATAGTTACGGAGAGCACAAATATCGTTCCCAC
GAGGACTAAAAATACTAGTAATAGTTGCTTTCTATTATCTAACCGATCAAATAGAGTGATTGTTT
TAAACTAAACTTAACTAAATTAATAAACTAAAAGTACGACAAAGAATAAAACAAGAAATAACAAG
TGTTTTAATACCAAGAAGCAAACAATACCCAGGAAAGACTCAACCTAGATTTCATCTACCATTAT
CATTCTAAATTAAGCAATTTATTCACTTAGTATTTTAATCCATAAAAATCCCTAAATTATGCTAA
TACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATTTCTTTCGAATTAA
AACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAGATTTGATTCTAATCCGATAA
ATTTATATCGTCCTATTTCTAGGATTGCATGCAACTCCACTCAATTATGCTAGATCTACTCTTAA
ACAGGATCAATTCCTCCTCTGATTTAAGCACATCAAACAAGAATTAATATCTCAAAAATACTAAA
TCAAGAAATAAGCACACATAATTGAGAACAAAATCTAAGTATTTATTGCGTAAAATCAGAAATCA
AATGACAAAATTCATCCTAGAGTTCATCTCCCCTAAGTATTTAGGAATTTAGTTCATGCTAATAA
ATGAAAACATCTCAAAGATAATATAACCACAAGATAAAGAGAAACTCATAGTAAAATCAAAAGAA
TTTAGAAAAAGGTCTTCAATCTTCGTGAAAATCGACTTCAAAGACAGCTTCTATGGTGTTTTTTC
AGTTGTTTCCTTCAATAATCTCTGACAGCTTGAATTTGAGGAATGGAGGATGTTACCGAAAATTG
GAAGTCAAACCTAACTAAAAATA
Found at i:64180 original size:21 final size:21
Alignment explanation
Indices: 64163--64202 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
64153 TTCATAATTA
64163 AAAT-AAAATTAAAAATAAAAT
1 AAATGAAAA-TAAAAATAAAAT
64184 AAATGAAAATAAAAATAAA
1 AAATGAAAATAAAAATAAA
64203 TATACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATGAAAATAAAAATAAAAT
Found at i:64192 original size:16 final size:15
Alignment explanation
Indices: 64174--64203 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
64164 AATAAAATTA
64174 AAAATAAAATAAATG
1 AAAATAAAATAAATG
64189 AAAATAAAAATAAAT
1 AAAAT-AAAATAAAT
64204 ATACTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAAATG
Found at i:64244 original size:18 final size:18
Alignment explanation
Indices: 64210--64243 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64200 AAATATACTA
64210 ATTTTTTTTTGAATTTTG
1 ATTTTTTTTTGAATTTTG
64228 ATTTTTTTTT-AATTTT
1 ATTTTTTTTTGAATTTT
64244 TTTTGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
ATTTTTTTTTGAATTTTG
Found at i:65990 original size:24 final size:24
Alignment explanation
Indices: 65955--66035 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
65945 AATATTCCAG
65955 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
* * *
65979 TTAAATTTTGTTTGTTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
66003 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
66027 TCAAACTCT
1 TTAAACTCT
66036 TATTAGTCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:88603 original size:20 final size:19
Alignment explanation
Indices: 88580--88629 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
88570 TGTGATATAG
88580 TATTATATAATGAAATAATA
1 TATTATATAA-GAAATAATA
* * *
88600 TATTTTATAAGTATTAATA
1 TATTATATAAGAAATAATA
88619 TATATATATAA
1 TAT-TATATAA
88630 CTATTATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TATTATATAAGAAATAATA
Found at i:88642 original size:20 final size:20
Alignment explanation
Indices: 88595--88635 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
88585 TATAATGAAA
* *
88595 TAATATAT-TTTATAAGTAT
1 TAATATATATATATAACTAT
88614 TAATATATATATATAACTAT
1 TAATATATATATATAACTAT
88634 TA
1 TA
88636 TCATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATATATATATATAACTAT
Found at i:88919 original size:30 final size:30
Alignment explanation
Indices: 88858--88927 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
88848 AGGTTATAAT
* * *
88858 TAGTTTATTTTTCATTTGGGTAGTAATGAG
1 TAGTTTATTTTTCATTTGGATAATAAAGAG
*
88888 TAGTTTATTTTTCGTTTGGATAATAAAGAG
1 TAGTTTATTTTTCATTTGGATAATAAAGAG
88918 TAAG-TTATTT
1 T-AGTTTATTT
88928 GACTTTTGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (30 bp):
TAGTTTATTTTTCATTTGGATAATAAAGAG
Done.