Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008482.1 Kokia drynarioides strain JFW-HI SEQ_123157, 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: 7567
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Found at i:1485 original size:17 final size:18
Alignment explanation
Indices: 1446--1495 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
1436 AGGTATACCC
1446 ATTATTTATGAAATTGAA
1 ATTATTTATGAAATTGAA
* *
1464 ATTATTTATGAAGTT-TA
1 ATTATTTATGAAATTGAA
*
1481 ATTATTTATGCAATT
1 ATTATTTATGAAATT
1496 ATTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (18 bp):
ATTATTTATGAAATTGAA
Found at i:1643 original size:26 final size:26
Alignment explanation
Indices: 1605--1685 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
1595 CCTAAACACT
* * *
1605 AAAACCCCTATCAATAGCCGGCATTA
1 AAAATCCCAATCAATGGCCGGCATTA
1631 AAAATCCCAATCAATGGCCGGCATTA
1 AAAATCCCAATCAATGGCCGGCATTA
* *
1657 AAAATCCCCATCAATGGCCGGCAGTA
1 AAAATCCCAATCAATGGCCGGCATTA
1683 AAA
1 AAA
1686 GTCCACCATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (26 bp):
AAAATCCCAATCAATGGCCGGCATTA
Found at i:2708 original size:28 final size:28
Alignment explanation
Indices: 2663--2717 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2653 AAAAAAAATT
* *
2663 AAAAAATTCATAATAATTTTTAAATTTC
1 AAAAAATTCATAAAAATTTTAAAATTTC
* *
2691 AAAATATTTATAAAAATTTTAAAATTT
1 AAAAAATTCATAAAAATTTTAAAATTT
2718 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAAAATTCATAAAAATTTTAAAATTTC
Found at i:2738 original size:25 final size:26
Alignment explanation
Indices: 2697--2747 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2687 TTTCAAAATA
*
2697 TTTATAAAAATT-TTAAAATTTATATT
1 TTTATAAAAATTATAAAAATTT-TATT
2723 TTTA-AAAAATTATAAAAATTTTATT
1 TTTATAAAAATTATAAAAATTTTATT
2748 AAAAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTATAAAAATTATAAAAATTTTATT
Found at i:4949 original size:61 final size:61
Alignment explanation
Indices: 4803--4950 Score: 154
Period size: 61 Copynumber: 2.4 Consensus size: 61
4793 GTTTACATGT
* * * *
4803 TCTATCAATTTGGTCATAAATATAAAAAAGTCAACAAATTTAGCCGTCAATGTTTACAAAA
1 TCTATCAATTTAGTCATAAATCTAAAAAAGTCAACAAATTTAGCCCTCAATATTTACAAAA
* * * * * * * *
4864 TTTGTCATTTTAGTTATAATTCTAAAAAAGATTAATAAATTTGGCCCTC-ATATTTACAAAA
1 TCTATCAATTTAGTCATAAATCTAAAAAAG-TCAACAAATTTAGCCCTCAATATTTACAAAA
* *
4925 TCTATCAATTTAGTCCTAACTCTAAA
1 TCTATCAATTTAGTCATAAATCTAAA
4951 CAATTTTTAA
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
61 54 0.79
62 14 0.21
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (61 bp):
TCTATCAATTTAGTCATAAATCTAAAAAAGTCAACAAATTTAGCCCTCAATATTTACAAAA
Found at i:7445 original size:20 final size:20
Alignment explanation
Indices: 7422--7459 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7412 GAGTAAAAGT
7422 TTTAAAAAAATAAGAAAATA
1 TTTAAAAAAATAAGAAAATA
*
7442 TTTAAAAAAATCAGAAAA
1 TTTAAAAAAATAAGAAAA
7460 CCCTCGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
TTTAAAAAAATAAGAAAATA
Done.