Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000306.1 Kokia drynarioides strain JFW-HI SEQ_111067, 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: 68506
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1865 original size:231 final size:220
Alignment explanation
Indices: 1457--1947 Score: 616
Period size: 227 Copynumber: 2.2 Consensus size: 220
1447 CAAAATCTTG
* * * *
1457 TATATATGAACTAGAAGATC---AAACATCACTAGAACTCCTTCACTATGTATGCACTATGAACT
1 TATATATGAACTAGAAGATCAATAAACATCACTAGCACTCCATCACTATGCATGAACTATGAACT
* * *
1519 TACCATTGTTATATTTTGCTACTAAAATCTACACCTGAAACAAATTACAGCTTCATTTCAAATTT
66 TACCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGCTTCATTCCAAATTC
* * **
1584 TAAACTTTCTCAAATAGTTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAAAATTAGCC
131 AAAACTTTCTCAAATAGGTTCCATTCAAACACTCATATGATACTAATCAAGTT--AAAATTAGAA
* *
1649 AAA-AAACTTCAAAACATTATATATATATA
194 AAAGAAACAT-AAAA-AAT-TATATATATA
*
1678 TATATATGAACTAGAAGATCAATAAAGCATCACTAGCACTCCATCACTATGCATGAATTATGAAC
1 TATATATGAACTAGAAGATCAATAAA-CATCACTAGCACTCCATCACTATGCATGAACTATGAAC
* * *
1743 TTAGCCATTGTTATATTTTACTACTAAAATCTACACCTGAACCTGATATAAATTACAGTTTTATT
65 TTA-CCATTGTTATATTTTACTACTAAAATCTACACCTG-A----A-ACAAATTACAGCTTCATT
* *
1808 CCAAGTTCAAAAC-TTCTCAAATAGGTTCCATTCAAACTCTCATATGATA-TCAATCAAGTTAAA
123 CCAAATTCAAAACTTTCTCAAATAGGTTCCATTCAAACACTCATATGATACT-AATCAAGTTAAA
*
1871 TTTAGAAAAAGAAACATAAAAAATTATATATATA
187 ATTAGAAAAAGAAACATAAAAAATTATATATATA
*
1905 TATATATGAACTAGAAGATCAATAAAACATCACTATCACTCCA
1 TATATATGAACTAGAAGATCAAT-AAACATCACTAGCACTCCA
1948 CTAAGTATGA
Statistics
Matches: 235, Mismatches: 21, Indels: 22
0.85 0.08 0.08
Matches are distributed among these distances:
221 20 0.09
224 3 0.01
225 36 0.15
226 34 0.14
227 49 0.21
228 5 0.02
229 14 0.06
230 6 0.03
231 44 0.19
232 24 0.10
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (220 bp):
TATATATGAACTAGAAGATCAATAAACATCACTAGCACTCCATCACTATGCATGAACTATGAACT
TACCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGCTTCATTCCAAATTC
AAAACTTTCTCAAATAGGTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAATTAGAAAA
AGAAACATAAAAAATTATATATATA
Found at i:7897 original size:47 final size:47
Alignment explanation
Indices: 7806--7903 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 47
7796 CTCTATGATG
* * * *
7806 ATTTTATTTAAATCAAAATAATTTAATTGAATTTTAAAGATTAA-TA
1 ATTTTATTTAAATAAAAAAAATTTAACTAAATTTTAAAGATTAATTA
**
7852 ATTTTATTTAAATAAAAAAAAGTTTAACTAAATTTTAAATTTTAATTA
1 ATTTTATTTAAATAAAAAAAA-TTTAACTAAATTTTAAAGATTAATTA
7900 ATTT
1 ATTT
7904 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
46 19 0.43
47 19 0.43
48 6 0.14
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (47 bp):
ATTTTATTTAAATAAAAAAAATTTAACTAAATTTTAAAGATTAATTA
Found at i:8767 original size:60 final size:60
Alignment explanation
Indices: 8693--8814 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
8683 AATACTTAAG
8693 TTACAATAGTTGCCGACAGTCGCATTATTAAAGTGATAAAATTATTGTACGTTGATTTCT
1 TTACAATAGTTGCCGACAGTCGCATTATTAAAGTGATAAAATTATTGTACGTTGATTTCT
*
8753 TTACAGTAGTTGCCGACAGTCGCATTATTAAAGTGATAAAATTATTGTACGTTGATTTCT
1 TTACAATAGTTGCCGACAGTCGCATTATTAAAGTGATAAAATTATTGTACGTTGATTTCT
8813 TT
1 TT
8815 TACATGTGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (60 bp):
TTACAATAGTTGCCGACAGTCGCATTATTAAAGTGATAAAATTATTGTACGTTGATTTCT
Found at i:18037 original size:32 final size:34
Alignment explanation
Indices: 17989--18053 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
17979 TAATAAAAGT
17989 AAAATTATATTTTAATTGTTTAAAAATGATAAAA
1 AAAATTATATTTTAATTGTTTAAAAATGATAAAA
* * *
18023 AAAATTA-A-TTTAATTTTTTAAAGATTATAAA
1 AAAATTATATTTTAATTGTTTAAAAATGATAAA
18054 GATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.71
33 1 0.04
34 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (34 bp):
AAAATTATATTTTAATTGTTTAAAAATGATAAAA
Found at i:19787 original size:21 final size:20
Alignment explanation
Indices: 19740--19788 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
19730 TTTTAGTTTT
**
19740 ATTTTGTTTATTTAACTGTTA
1 ATTTT-TTTATTTAACACTTA
*
19761 AATTTTTTATTTAATCACTTA
1 ATTTTTTTATTTAA-CACTTA
19782 ATTTTTT
1 ATTTTTT
19789 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (20 bp):
ATTTTTTTATTTAACACTTA
Found at i:29037 original size:30 final size:30
Alignment explanation
Indices: 29001--29059 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28991 GTTTACATTT
*
29001 CAGTCTCTCAATTTTAAAAATATGACAAAA
1 CAGTCTCTCAACTTTAAAAATATGACAAAA
*
29031 CAGTCTCTCAACTTTGAAAATATGACAAA
1 CAGTCTCTCAACTTTAAAAATATGACAAA
29060 GTAGTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (30 bp):
CAGTCTCTCAACTTTAAAAATATGACAAAA
Found at i:33402 original size:42 final size:42
Alignment explanation
Indices: 33306--33705 Score: 317
Period size: 42 Copynumber: 9.7 Consensus size: 42
33296 GGGAACAGAT
* * *
33306 CAAATGGTAACAAAGAGCTTGAAC-GAGCCTAT-GGGAACTGAC
1 CAAAGGGTCACAAAGAGCTTG-CCTGAGCCTATAGGG-ACTGAC
** * * * * *
33348 CGGAGGGGCACCAAGAACCTGCCTGAGTCTATAGGGACTGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
* * * * *
33390 CAGAGGGTCACCAAGAACTTGCCTGAGCCTATGGGGAATGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
** *
33432 CAAAGTATCACAAAGAGCTTGCCTGAGCCTATCGGGACTGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
*
33474 CAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
*
33516 CAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
* *
33558 CAGA-GG-------GA-CTTGCCTGAGCCTAT-GGAAACTGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGG-GACTGAC
* ** *
33591 CAGAGGGTCACCGAG-GACTTGCCTGAGCCTATGGGGACTGAC
1 CAAAGGGTCACAAAGAG-CTTGCCTGAGCCTATAGGGACTGAC
* * * * * *
33633 CAAAGTGTCCCAAAGACCTTGCCTAAGCCAAT-GGAGACCGAC
1 CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGG-GACTGAC
* ** *
33675 CAACGCATCACAAAGA-CTTTGCCCGAGCCTA
1 CAAAGGGTCACAAAGAGC-TTGCCTGAGCCTA
33706 CGGAGATTGG
Statistics
Matches: 296, Mismatches: 45, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
32 2 0.01
33 25 0.08
34 4 0.01
41 6 0.02
42 254 0.86
43 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (42 bp):
CAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGAC
Found at i:33575 original size:33 final size:33
Alignment explanation
Indices: 33533--33597 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
33523 TCACAAAGAG
*
33533 CTTGCCTGAGCCTATAGG-GACTGACCAGAGGGA
1 CTTGCCTGAGCCTAT-GGAAACTGACCAGAGGGA
33566 CTTGCCTGAGCCTATGGAAACTGACCAGAGGG
1 CTTGCCTGAGCCTATGGAAACTGACCAGAGGG
33598 TCACCGAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18
Consensus pattern (33 bp):
CTTGCCTGAGCCTATGGAAACTGACCAGAGGGA
Found at i:33614 original size:75 final size:75
Alignment explanation
Indices: 33491--33634 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 75
33481 TCACAAAGAG
* *
33491 CTTGCCTGAGCCTATAGGGACTGACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
1 CTTGCCTGAGCCTATAGGAACTGACCAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
33556 ACCAGAGGGA
66 ACCAGAGGGA
* ** *
33566 CTTGCCTGAGCCTAT-GGAAACTGACCAGAGGGTCACCGAG-GACTTGCCTGAGCCTATGGGGAC
1 CTTGCCTGAGCCTATAGG-AACTGACCAAAGGGTCACAAAGAG-CTTGCCTGAGCCTATAGGGAC
33629 TGACCA
64 TGACCA
33635 AAGTGTCCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
74 3 0.05
75 58 0.95
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (75 bp):
CTTGCCTGAGCCTATAGGAACTGACCAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
ACCAGAGGGA
Found at i:33640 original size:159 final size:159
Alignment explanation
Indices: 33406--33705 Score: 392
Period size: 159 Copynumber: 1.9 Consensus size: 159
33396 GTCACCAAGA
* *
33406 ACTTGCCTGAGCCTATGGGGAATGACCAAAGTATCACAAAGAGCTTGCCTGAGCCTATCGGGACT
1 ACTTGCCTGAGCCTATGGGAAATGACCAAAGGATCACAAAGAGCTTGCCTGAGCCTATCGGGACT
* * * * **
33471 GACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGG-GACTGACCAAAGTGTCACAAAGAGC-
66 GACCAAAGTGTCACAAAGACCTTGCCTAAGCCAAT-GGAGACCGACCAAAGCATCACAAAGA-CT
*
33534 TTGCCTGAGCCTATAGGGACTGACCAGAGGG
129 TTGCCCGAGCCTATAGGGACTGACCAGAGGG
* * ** *
33565 ACTTGCCTGAGCCTAT-GGAAACTGACCAGAGGGTCACCGAG-GACTTGCCTGAGCCTATGGGGA
1 ACTTGCCTGAGCCTATGGGAAA-TGACCAAAGGATCACAAAGAG-CTTGCCTGAGCCTATCGGGA
* *
33628 CTGACCAAAGTGTCCCAAAGACCTTGCCTAAGCCAATGGAGACCGACCAACGCATCACAAAGACT
64 CTGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCGACCAAAGCATCACAAAGACT
33693 TTGCCCGAGCCTA
129 TTGCCCGAGCCTA
33706 CGGAGATTGG
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
158 8 0.07
159 113 0.93
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (159 bp):
ACTTGCCTGAGCCTATGGGAAATGACCAAAGGATCACAAAGAGCTTGCCTGAGCCTATCGGGACT
GACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCGACCAAAGCATCACAAAGACTTT
GCCCGAGCCTATAGGGACTGACCAGAGGG
Found at i:33655 original size:117 final size:117
Alignment explanation
Indices: 33449--33661 Score: 313
Period size: 117 Copynumber: 1.8 Consensus size: 117
33439 TCACAAAGAG
* *
33449 CTTGCCTGAGCCTATCGGGACTGACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
1 CTTGCCTGAGCCTATCGGAACTGACCAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
* *
33514 ACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGGGA
66 ACCAAAGTGTCACAAAGACCTTGCCTAAGCCTATAGGGACTGACCAGAGGGA
* ** *
33566 CTTGCCTGAGCCTAT-GGAAACTGACCAGAGGGTCACCGAG-GACTTGCCTGAGCCTATGGGGAC
1 CTTGCCTGAGCCTATCGG-AACTGACCAAAGGGTCACAAAGAG-CTTGCCTGAGCCTATAGGGAC
*
33629 TGACCAAAGTGTCCCAAAGACCTTGCCTAAGCC
64 TGACCAAAGTGTCACAAAGACCTTGCCTAAGCC
33662 AATGGAGACC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
116 3 0.04
117 82 0.96
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (117 bp):
CTTGCCTGAGCCTATCGGAACTGACCAAAGGGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTG
ACCAAAGTGTCACAAAGACCTTGCCTAAGCCTATAGGGACTGACCAGAGGGA
Found at i:39951 original size:19 final size:19
Alignment explanation
Indices: 39927--39964 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39917 AATTTAATCC
39927 TCGTACTTCATAAAAAGCT
1 TCGTACTTCATAAAAAGCT
39946 TCGTACTTCATAAAAAGCT
1 TCGTACTTCATAAAAAGCT
39965 AATAGATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
TCGTACTTCATAAAAAGCT
Found at i:40819 original size:19 final size:18
Alignment explanation
Indices: 40797--40832 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
40787 TAAAAATTCA
40797 TAAAAAGTATAAAAAAAAC
1 TAAAAA-TATAAAAAAAAC
40816 TAAAAATATAAAAAAAA
1 TAAAAATATAAAAAAAA
40833 TCATTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
TAAAAATATAAAAAAAAC
Found at i:42077 original size:26 final size:28
Alignment explanation
Indices: 42029--42087 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
42019 TGCGATGCAA
42029 TTTAAATTGACCCAAATTATATATAAT-T
1 TTTAAATTGACCCAAATTATATAT-ATCT
42057 TTTAAATTGACCCAAA-T-TATATATCT
1 TTTAAATTGACCCAAATTATATATATCT
42083 TTTAA
1 TTTAA
42088 CAATTTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 2 0.07
26 11 0.37
27 1 0.03
28 16 0.53
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTAAATTGACCCAAATTATATATATCT
Found at i:54176 original size:8 final size:8
Alignment explanation
Indices: 54163--54197 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
54153 CACTTTTATT
54163 AATTTTAA
1 AATTTTAA
54171 AATTTTTAA
1 AA-TTTTAA
*
54180 AATTTTTA
1 AATTTTAA
54188 AATTTTAA
1 AATTTTAA
54196 AA
1 AA
54198 GACTAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
AATTTTAA
Found at i:54177 original size:9 final size:9
Alignment explanation
Indices: 54165--54197 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
54155 CTTTTATTAA
54165 TTTTAAAAT
1 TTTTAAAAT
54174 TTTTAAAAT
1 TTTTAAAAT
54183 TTTT-AAA-
1 TTTTAAAAT
54190 TTTTAAAA
1 TTTTAAAA
54198 GACTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.17
8 6 0.26
9 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:54183 original size:17 final size:16
Alignment explanation
Indices: 54163--54197 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
54153 CACTTTTATT
54163 AATTTTAAAATTTTTAA
1 AATTTTAAAA-TTTTAA
*
54180 AATTTTTAAATTTTAA
1 AATTTTAAAATTTTAA
54196 AA
1 AA
54198 GACTAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTTAAAATTTTAA
Found at i:55626 original size:20 final size:19
Alignment explanation
Indices: 55577--55629 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
55567 ATAAAAGAGT
* *
55577 AAATTAAGTTTT-TTATTA
1 AAATTAATTTTTATTATAA
*
55595 AAATATATTTTTTATTAATAA
1 AAAT-TAATTTTTATT-ATAA
55616 AAATTAATTTTTAT
1 AAATTAATTTTTAT
55630 ATGACACATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 11 0.39
21 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AAATTAATTTTTATTATAA
Found at i:56609 original size:12 final size:12
Alignment explanation
Indices: 56592--56617 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56582 TCCTTCAACA
56592 CCGCCACCTCCG
1 CCGCCACCTCCG
56604 CCGCCACCTCCG
1 CCGCCACCTCCG
56616 CC
1 CC
56618 TCCTGCAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.69, G:0.15, T:0.08
Consensus pattern (12 bp):
CCGCCACCTCCG
Found at i:56859 original size:141 final size:141
Alignment explanation
Indices: 56605--56903 Score: 492
Period size: 141 Copynumber: 2.1 Consensus size: 141
56595 CCACCTCCGC
* * **
56605 CGCCACCTCCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGTTGTTGGCCGG
1 CGCCACCGCCGCCTCCTGCACCTGCATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGG
*
56670 AAAGACAATGTGAATAATACTCAGAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCC
66 AAAGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCC
56735 TCAGCCAGTAA
131 TCAGCCAGTAA
* *
56746 CGCCACCGCCGTCTCCTGCACCTG-ATTATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGTCG
1 CGCCACCGCCGCCTCCTGCACCTGCA-TATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCG
** *
56810 GAAAGGGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAACTGAGTCTCCGGCTC
65 GAAAGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTC
56875 CTCAGCCAGTAA
130 CTCAGCCAGTAA
56887 CGCCACCGCCGCCTCCT
1 CGCCACCGCCGCCTCCT
56904 CCGCCTCGAC
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
140 1 0.01
141 145 0.99
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (141 bp):
CGCCACCGCCGCCTCCTGCACCTGCATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGG
AAAGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCC
TCAGCCAGTAA
Found at i:58187 original size:5 final size:5
Alignment explanation
Indices: 58177--58211 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
58167 AAAGTGGTGG
58177 ATACA ATACA ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA ATACA ATACA
58212 TAGGGGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATACA
Found at i:62411 original size:15 final size:14
Alignment explanation
Indices: 62378--62408 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
62368 AAAATATAAT
62378 AAATAGTTTTAGTA
1 AAATAGTTTTAGTA
62392 AAATAGTTTTAGTA
1 AAATAGTTTTAGTA
62406 AAA
1 AAA
62409 ATATATTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (14 bp):
AAATAGTTTTAGTA
Found at i:62417 original size:14 final size:15
Alignment explanation
Indices: 62378--62419 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
62368 AAAATATAAT
*
62378 AAATAGTTTTAGT-A
1 AAATAGTATTAGTAA
*
62392 AAATAGTTTTAGTAA
1 AAATAGTATTAGTAA
62407 AAATA-TATTAGTA
1 AAATAGTATTAGTA
62420 GTTACTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (15 bp):
AAATAGTATTAGTAA
Found at i:64614 original size:16 final size:16
Alignment explanation
Indices: 64576--64607 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64566 GTTTTATTAT
64576 TAAAA-AAAA-TTAAA
1 TAAAATAAAATTTAAA
64590 TAAAATAAAATTTAAA
1 TAAAATAAAATTTAAA
64606 TA
1 TA
64608 GATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAATAAAATTTAAA
Found at i:65619 original size:148 final size:148
Alignment explanation
Indices: 65351--65646 Score: 558
Period size: 148 Copynumber: 2.0 Consensus size: 148
65341 TTGACTCATC
65351 AACATTGATTACTCATTTAATATAGTTGTTTATTTTTTCTATAAATATAAATATAAATTATTTTT
1 AACATTGATTACTCATTTAATATAGTTGTTTATTTTTTCTATAAATATAAATATAAATTATTTTT
* *
65416 GGCCCAATAATTGAACTTGCAAACCATACCAGCACGTAATTTAATATCTTTCCTATGAAATACCG
66 GGCCCAATAATTGAACTTGCAAACCACACCAGCACGTAATTTAATATCTTTCCTATGAAATACCA
65481 AACATACAC-TTAAATGTT
131 AACATACACGTT-AATGTT
65499 AACATTGATTACTCATTTAATATAGTTGTTTATTTTTTCTATAAATATAAATATAAATTATTTTT
1 AACATTGATTACTCATTTAATATAGTTGTTTATTTTTTCTATAAATATAAATATAAATTATTTTT
65564 GGCCCAATAATTGAACTTGCAAACCACACCAGCACGTAATTTAATATCTTTCCTATGAAATACCA
66 GGCCCAATAATTGAACTTGCAAACCACACCAGCACGTAATTTAATATCTTTCCTATGAAATACCA
65629 AACATACACGTTAATGTT
131 AACATACACGTTAATGTT
65647 CTTTAGACAA
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
148 143 0.99
149 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (148 bp):
AACATTGATTACTCATTTAATATAGTTGTTTATTTTTTCTATAAATATAAATATAAATTATTTTT
GGCCCAATAATTGAACTTGCAAACCACACCAGCACGTAATTTAATATCTTTCCTATGAAATACCA
AACATACACGTTAATGTT
Found at i:68366 original size:2 final size:2
Alignment explanation
Indices: 68361--68388 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
68351 TATAAAAAAA
68361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68389 TTACAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.