Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002098.1 Kokia drynarioides strain JFW-HI SEQ_114017, 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: 2943
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Found at i:1819 original size:201 final size:201
Alignment explanation
Indices: 1526--2031 Score: 664
Period size: 201 Copynumber: 2.5 Consensus size: 201
1516 GTTCAAAGCA
* *
1526 AGCAAAATCTTCGAACCCCAGCTTCCTGA-GAAGATACTGAGAAGCAGGTCGAAGCAATAAAAGG
1 AGCAAAATCTTTGAACCCCAGCTTCCTGATG-AGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
*
1590 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTC-TCCTTCCTG-ATGAGATATAGAGAA
65 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT-CTTCC-GAATGAGATACAGAGAA
*
1653 GAGAGTTGAAACAAACTACGCG-G-TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
128 GAGAATTGAAACAAAC-A-GCGAGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGA
**
1716 GGCTCAAAGTG
191 GGCTCAAAACG
1727 AGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
1 AGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * * * * * * * *
1792 TAGCTTCCTAATGAGGTATTCAGAAGTGAACTAAATTCGTCTTTCGAATGAGATACGGAGGAGCG
66 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCGAATGAGATACAGAGAAGAG
* *
1857 AATTGAAACAAACAGCGATGTAATTATCTTCCTGATGAGGCACTGAGAAGAAGACCCAAACGAGG
131 AATTGAAACAAACAGCGA-G--ATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGG
1922 CTCAAAACG
193 CTCAAAACG
* ** * * *
1931 AGC-AAATCTTTGAACCCCCGCTTCCTGATGAGACGTTGAGAAGCAGGTCAAAGCCATAAAGTGG
1 AGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA-AGG
* *
1995 TTAGCTCCCTGATGAGATACAGAGAAGTGAACCAAAT
65 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAAT
2032 CCTGATGAAA
Statistics
Matches: 266, Mismatches: 30, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
199 3 0.01
200 2 0.01
201 125 0.47
202 2 0.01
203 52 0.20
204 82 0.31
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (201 bp):
AGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCGAATGAGATACAGAGAAGAG
AATTGAAACAAACAGCGAGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTC
AAAACG
Found at i:2465 original size:17 final size:18
Alignment explanation
Indices: 2442--2536 Score: 85
Period size: 17 Copynumber: 5.6 Consensus size: 18
2432 CCAAACTCCC
2442 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
2460 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
2477 TTTAAATTTATTTT----
1 TTTAAATTTATTTTAAAA
* *
2491 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
* *
2508 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
*
2526 TTTAAAATTAT
1 TTTAAATTTAT
2537 CATAAATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
14 13 0.20
17 27 0.42
18 24 0.38
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:2527 original size:49 final size:49
Alignment explanation
Indices: 2442--2536 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
2432 CCAAACTCCC
* * * *
2442 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAATTTAAATTTATTTT
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATTTT
** **
2491 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAATTTAAAATTAT
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTAT
2537 CATAAATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (49 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATTTT
Found at i:2545 original size:17 final size:18
Alignment explanation
Indices: 2508--2550 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2498 TTAATTTAAG
**
2508 TTTAAAATTATTTTCAAA
1 TTTAAAATTATCATCAAA
2526 TTTAAAATTATCAT-AAA
1 TTTAAAATTATCATCAAA
2543 TTTAAAAT
1 TTTAAAAT
2551 AAATAAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATTATCATCAAA
Done.