Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008926.1 Kokia drynarioides strain JFW-HI SEQ_123617, 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: 41440
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1622 original size:14 final size:14
Alignment explanation
Indices: 1599--1639 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1589 CTAAAATTCA
1599 AACATTGAA-CTCTG
1 AACATTGAACCT-TG
*
1613 AACCTTGAACCTTG
1 AACATTGAACCTTG
1627 AACATTGAACCTT
1 AACATTGAACCTT
1640 AGACTCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (14 bp):
AACATTGAACCTTG
Found at i:1728 original size:22 final size:22
Alignment explanation
Indices: 1678--1728 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
1668 ACAAATGGGC
* *
1678 TCAGGGTATAAGGTTTAAGGTT
1 TCAGGGTTTAAGGTTTAAGGAT
*
1700 TTA-GGTTTCAAGGTTT-AGGAT
1 TCAGGGTTT-AAGGTTTAAGGAT
1721 TCAGGGTT
1 TCAGGGTT
1729 CATGGTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.24, C:0.06, G:0.31, T:0.39
Consensus pattern (22 bp):
TCAGGGTTTAAGGTTTAAGGAT
Found at i:4561 original size:30 final size:30
Alignment explanation
Indices: 4526--4583 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4516 TTAGTAAAAG
* *
4526 TAAAATTTCACTTTGATCCTTTAAAAATAA
1 TAAAATTTCAATTTAATCCTTTAAAAATAA
* *
4556 TAAAATTTTAATTTAATCTTTTAAAAAT
1 TAAAATTTCAATTTAATCCTTTAAAAAT
4584 TACACTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAAATTTCAATTTAATCCTTTAAAAATAA
Found at i:14275 original size:34 final size:34
Alignment explanation
Indices: 14232--14307 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
14222 ATTTCATCAA
14232 ACAAAGTCACAGCATGAGAAATCTTACTTCGATT
1 ACAAAGTCACAGCATGAGAAATCTTACTTCGATT
*
14266 ACAAAGTCACAGCATGAGAAATCTTACTTCGGTT
1 ACAAAGTCACAGCATGAGAAATCTTACTTCGATT
14300 ACAAAGTC
1 ACAAAGTC
14308 CATTGATCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (34 bp):
ACAAAGTCACAGCATGAGAAATCTTACTTCGATT
Found at i:40178 original size:96 final size:95
Alignment explanation
Indices: 40010--40182 Score: 258
Period size: 96 Copynumber: 1.8 Consensus size: 95
40000 TTTTTGGGGA
* *
40010 AAGGGCATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAATAAGTTAAGACGCAATATTTCA
1 AAGGGCATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATATTTCA
40075 AAATCGAAGATAATGAAACGTTGCCTCGGTT
66 AAATCGAA-ATAATGAAACGTTGCCTCGGTT
* * * *
40106 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTCG
1 AAGGGCATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATATTTC-
*
40170 AAACTCGAAATAA
65 AAAATCGAAATAA
40183 AAGAATATTA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
95 9 0.13
96 60 0.87
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (95 bp):
AAGGGCATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATATTTCA
AAATCGAAATAATGAAACGTTGCCTCGGTT
Found at i:40566 original size:60 final size:59
Alignment explanation
Indices: 40492--40841 Score: 434
Period size: 59 Copynumber: 5.9 Consensus size: 59
40482 TTTGGAAAAA
* * *
40492 TTCGAGGTCAAAAATGGGATTTTTAGAAGTTTTGGGGTAAAAATAGAATTTTTGAAGGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAGGT
* * * *
40551 TTTGGGGTAAAAAAATGGGATTTTTGGAAATTTGGGGGTAAAAATGGAATTTTTGAAGGT
1 TTCGGGGT-CAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAGGT
* * *
40611 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTTAAGGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAGGT
* * * *
40670 TTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGAGGGTAAAAATAGGATTTTTTGGAA-GT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATA-GAATTTTT-GAAGGT
* * * * * * *
40730 TTTGGGGTCAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATAGAAATTTTAAAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAGGT
* * *
40789 TTCAGGGAT-AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAAAATTTTT
1 TTC-GGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTT
40842 CAACAATTTA
Statistics
Matches: 253, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
58 2 0.01
59 144 0.57
60 105 0.42
61 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGAAGGT
Found at i:40652 original size:119 final size:119
Alignment explanation
Indices: 40492--40841 Score: 445
Period size: 119 Copynumber: 2.9 Consensus size: 119
40482 TTTGGAAAAA
* * * *
40492 TTCGAGGTCAAAAATGGGATTTTTAGAAGTTTTGGGGTAAAAATAGAATTTTTGAAGGTTTTGGG
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTAAAGGTTTCGGG
*
40557 GTAAAAAAATGGGATTTTTGGAAATTTGGGGGTAAAAATGGAATTTTT-GAAGGT
66 GTAAAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAA-GT
* * *
40611 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTTAAGGTTTCGAG
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTAAAGGTTTCGGG
* * * *
40676 GT-CAAAAATAGGATTTTTGGAAGTTTGAGGGTAAAAATAGGATTTTTTGGAAGT
66 GTAAAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAAT-GGAATTTTTGGAAGT
* * * * * * * *
40730 TTTGGGGTCAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATAGAAATTTTAAAAGTTTCAGG
1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTAAAGGTTTCGGG
* * **
40795 G-ATAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATAAAATTTTT
66 GTAAAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTT
40842 CAACAATTTA
Statistics
Matches: 199, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
118 38 0.19
119 158 0.79
120 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (119 bp):
TTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTAAAGGTTTCGGG
GTAAAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
Done.