Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009774.1 Kokia drynarioides strain JFW-HI SEQ_124495, 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: 9695
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Found at i:8688 original size:201 final size:201
Alignment explanation
Indices: 8343--8882 Score: 911
Period size: 201 Copynumber: 2.7 Consensus size: 201
8333 TTAAGCCTAC
* * *
8343 GCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGC
1 GCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCGAGCCGAAGC
8408 AATAAAAGGTTAGCTTCCTGAT-ACGATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAAGGTTAGCTTCCTGATGA-GATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGAT
*
8472 ATAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGCAGAAGACCC
130 ACAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGCAGAAGACCC
8537 AAACGAG
195 AAACGAG
*
8544 GCTCAAAGCGAGCAAAATCTTCGAACCCGAGCTTCCTGATGAGACACTGAGAAGCGAGCCGAAGC
1 GCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCGAGCCGAAGC
*
8609 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATA
*
8674 CAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGGAGAAGACCCA
131 CAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGCAGAAGACCCA
8739 AACGAG
196 AACGAG
* * * **
8745 GCTCAAAGCGAGCAAAATCTTTGAACCCCAACTTCCTGATGAGACACTGAGAAGCAAGTGGAAGC
1 GCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCGAGCCGAAGC
* * * *
8810 AATAAATGGTTAGCTTCCTAATGAAATACTGGGAAGTGAATCAAATTCGTCTTCCTGATGAGATA
66 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATA
*
8875 CGGAGAAG
131 CAGAGAAG
8883 TGAACAAAAT
Statistics
Matches: 319, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
201 318 1.00
202 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (201 bp):
GCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCGAGCCGAAGC
AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGAGTTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGCAGAAGACCCA
AACGAG
Found at i:8864 original size:37 final size:37
Alignment explanation
Indices: 8823--8912 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 37
8813 AAATGGTTAG
* *
8823 CTTCCTAATGAAATACTGG-GAAGTGAATC-AAATTCGT
1 CTTCCTGATGAGATAC-GGAGAAGTGAA-CAAAATTCGT
8860 CTTCCTGATGAGATACGGAGAAGTGAACAAAATTCGT
1 CTTCCTGATGAGATACGGAGAAGTGAACAAAATTCGT
8897 CTTCCTGATGAGATAC
1 CTTCCTGATGAGATAC
8913 AAAGAAGCGG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 46 0.94
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (37 bp):
CTTCCTGATGAGATACGGAGAAGTGAACAAAATTCGT
Found at i:9045 original size:237 final size:236
Alignment explanation
Indices: 8622--9117 Score: 746
Period size: 237 Copynumber: 2.1 Consensus size: 236
8612 AAAAGGTTAG
* * *
8622 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
1 CTTCCTGATGAGATACAGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAGT
*
8687 TGAAACAAACGACGCAGTCATCTTCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCAAA
66 TGAAACAAACGACGCAGCCATCTTCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCAAA
8752 GCGAGCAAAATCTTTGAACCCCAACTTCCTGATGAGACACTGAGAAGCAAGTGGAAGCAATAAAT
131 GCGAGCAAAATCTTTGAACCCCAACTTCCTGATGAGACACTGAGAAGCAAGTGGAAGC--TAAAT
*
8817 GGTTAGCTTCCTAATGAAATACTGGGAAGTGAATCAAATTCGT
194 GGTTAGCTTCCTAATGAAATACTGGGAAGTGAACCAAATTCGT
*
8860 CTTCCTGATGAGATACGGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAAAGAAGCG-GA
1 CTTCCTGATGAGATACAGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAG-
* * * * * *
8924 TTGAAAC-GATGATG-GGACCATCTTTCTTATGAGACACTGAGGAGAAGACCCAAACGAGGCTCA
65 TTGAAACAAACGACGCAG-CCATCTTCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCA
* * * *
8987 AAGTGAGCAAAATCTTTGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTGGAAGCTAAAT
129 AAGCGAGCAAAATCTTTGAACCCCAACTTCCTGATGAGACACTGAGAAGCAAGTGGAAGCTAAAT
* * * *
9052 GGTTAGCTTCTTGATGAGATATTGGGAAGTGAACCAAATTCGT
194 GGTTAGCTTCCTAATGAAATACTGGGAAGTGAACCAAATTCGT
*
9095 CTTCCTGATGAGATTCAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
9118 CGGATTGAAA
Statistics
Matches: 235, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
235 64 0.27
236 1 0.00
237 104 0.44
238 66 0.28
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (236 bp):
CTTCCTGATGAGATACAGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAGT
TGAAACAAACGACGCAGCCATCTTCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCAAA
GCGAGCAAAATCTTTGAACCCCAACTTCCTGATGAGACACTGAGAAGCAAGTGGAAGCTAAATGG
TTAGCTTCCTAATGAAATACTGGGAAGTGAACCAAATTCGT
Found at i:9521 original size:18 final size:18
Alignment explanation
Indices: 9480--9578 Score: 121
Period size: 18 Copynumber: 5.6 Consensus size: 18
9470 TCATATTCCC
9480 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
9498 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
9515 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
9533 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
* *
9550 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
9568 TTTAAAGTTTA
1 TTTAAA-TTTA
9579 AAATAAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
17 29 0.43
18 36 0.53
19 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:9539 original size:24 final size:24
Alignment explanation
Indices: 9512--9558 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9502 ATTTGTTTAA
*
9512 AAATTTAAATTT-ATTTTAAAATTT
1 AAATTT-AATTTAAGTTTAAAATTT
9536 AAATTTAATTTAAGTTTAAAATT
1 AAATTTAATTTAAGTTTAAAATT
9559 ATTTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATTTAATTTAAGTTTAAAATTT
Found at i:9558 original size:36 final size:36
Alignment explanation
Indices: 9480--9579 Score: 125
Period size: 35 Copynumber: 2.8 Consensus size: 36
9470 TCATATTCCC
*
9480 TTTAAATTTATTTTAAAA-TTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAAAATTTAAATTTAATTT-AAAA
*
9515 TTTAAATTTATTTTAAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAATTTAAATTTAATTTAAAA
* *
9550 TTTAAAATTATTTTCAAATTTAAAGTTTAA
1 TTTAAATTTATTTTAAAATTTAAA-TTTAA
9580 AATAAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 42 0.72
36 13 0.22
37 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (36 bp):
TTTAAATTTATTTTAAAATTTAAATTTAATTTAAAA
Done.