Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011229.1 Kokia drynarioides strain JFW-HI SEQ_126207, 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: 16353
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:2647 original size:24 final size:24
Alignment explanation
Indices: 2621--2706 Score: 118
Period size: 24 Copynumber: 3.5 Consensus size: 24
2611 GATTAATAAG
*
2621 AGTTTAACTGAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAA
**
2645 AGTTTATTTGAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
* *
2669 AGTTTAATTGAACCAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
2693 AGTTTAACTCGAAA
1 AGTTTAACT-GAAA
2707 AATATTTCTC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 51 0.94
25 3 0.06
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:2886 original size:3 final size:3
Alignment explanation
Indices: 2878--2903 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2868 GGGTCGCTTA
2878 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2904 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:7664 original size:6 final size:6
Alignment explanation
Indices: 7655--7719 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
7645 TATTTCTAAT
* * *
7655 TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA -TTCAT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
7701 TTT-AG TTTAAA TTTGAAA T
1 TTTAAA TTTAAA TTT-AAA T
7720 AATTTTAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
5 11 0.23
6 32 0.68
7 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:7681 original size:23 final size:23
Alignment explanation
Indices: 7655--7704 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
7645 TATTTCTAAT
*
7655 TTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCACTTTAAATTTAAA
*
7678 TTTAAATTCATTTTAAATTTAAA
1 TTTAAATTCACTTTAAATTTAAA
7701 TTTA
1 TTTA
7705 GTTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAATTCACTTTAAATTTAAA
Found at i:7691 original size:34 final size:34
Alignment explanation
Indices: 7651--7734 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
7641 GATTTATTTC
*
7651 TAATTTTAAATTT-ACTTTAAATTTAAATTT-AAA
1 TAATTTTAAATTTAAATTT-AATTTAAATTTGAAA
* *
7684 TTCATTTTAAATTTAAATTTAGTTTAAATTTGAAA
1 -TAATTTTAAATTTAAATTTAATTTAAATTTGAAA
*
7719 TAATTTTAAACTTAAA
1 TAATTTTAAATTTAAA
7735 ACTTTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 36 0.84
35 7 0.16
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (34 bp):
TAATTTTAAATTTAAATTTAATTTAAATTTGAAA
Found at i:7714 original size:11 final size:11
Alignment explanation
Indices: 7655--7704 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
7645 TATTTCTAAT
*
7655 TTTAAATTTAC
1 TTTAAATTTAA
7666 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
7678 TTTAAATTCAT
1 TTTAAATTTAA
7689 TTTAAATTTAAA
1 TTTAAATTT-AA
7701 TTTA
1 TTTA
7705 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:7726 original size:17 final size:17
Alignment explanation
Indices: 7651--7734 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
7641 GATTTATTTC
**
7651 TAATTTTAAATTTACTT
1 TAATTTTAAATTTAAAT
*
7668 TAAATTTAAATTTAAAT
1 TAATTTTAAATTTAAAT
*
7685 TCATTTTAAATTTAAAT
1 TAATTTTAAATTTAAAT
* *
7702 TTAGTTTAAATTTGAAA-
1 TAATTTTAAATTT-AAAT
*
7719 TAATTTTAAACTTAAA
1 TAATTTTAAATTTAAA
7735 ACTTTAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
16 3 0.05
17 50 0.89
18 3 0.05
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTTTAAATTTAAAT
Found at i:9623 original size:30 final size:29
Alignment explanation
Indices: 9524--9866 Score: 240
Period size: 30 Copynumber: 11.6 Consensus size: 29
9514 TCCCTTAAAT
* **
9524 TTCCAAAAATCACGA-TTTAACCCTTAAAC
1 TTCCAAAAATCAC-ATTTTGACCCTCGAAC
* * * * *
9553 TTTCCAAAAATTATATTTTGACCCCCAAAATT
1 -TTCCAAAAATCACATTTTGACCCTC-GAA-C
9585 TTCC-AAAATCACATTTTGACCCTCGAAC
1 TTCCAAAAATCACATTTTGACCCTCGAAC
*
9613 TTCACAAAAATTACATTTTTG-CCCTCGAAC
1 TTC-CAAAAATCACA-TTTTGACCCTCGAAC
* *
9643 TTTCCATAAATTACATTTT-ACCCTCGAAC
1 -TTCCAAAAATCACATTTTGACCCTCGAAC
* *
9672 TTCCAAAAAATCACAGTTTGA-TCTCGAAAC
1 TTCC-AAAAATCACATTTTGACCCTCG-AAC
* * *
9702 TTTCAAAAATTACATTTTTACCCTCGAAC
1 TTCCAAAAATCACATTTTGACCCTCGAAC
* *
9731 TTCCAAAAATTCTA-TTTTTGACCC-CAAAAC
1 TTCCAAAAA-TC-ACATTTTGACCCTC-GAAC
* * *
9761 TTCTAAAAATTACATCTTT-ACCCTCAAAC
1 TTCCAAAAATCACAT-TTTGACCCTCGAAC
9790 TTCCAAAAATTC-CATTTTTGA-CCTCGAAAC
1 TTCCAAAAA-TCACA-TTTTGACCCTCG-AAC
* * *
9820 TTCCAAAAATTACATTTTTACCCCCGAAC
1 TTCCAAAAATCACATTTTGACCCTCGAAC
9849 TTCCAAAAATTC-CATTTT
1 TTCCAAAAA-TCACATTTT
9867 TAACATGAAA
Statistics
Matches: 251, Mismatches: 37, Indels: 51
0.74 0.11 0.15
Matches are distributed among these distances:
28 8 0.03
29 108 0.43
30 119 0.47
31 16 0.06
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATCACATTTTGACCCTCGAAC
Found at i:9681 original size:59 final size:59
Alignment explanation
Indices: 9523--9901 Score: 357
Period size: 59 Copynumber: 6.4 Consensus size: 59
9513 GTCCCTTAAA
* * ** * * * *
9523 TTTCCAAAAATCACGATTTAACCCTTAAACTTTCCAAAAATTATA-TTTTGACCCCCAAAAT
1 TTTCCAAAAATTAC-ATTTTACCCTCGAAC-TTCCAAAAATTACATTTTTGA-CCTCGAAAC
* *
9584 TTTCC-AAAATCACATTTTGACCCTCGAACTTCACAAAAATTACATTTTTGCCCTCG-AAC
1 TTTCCAAAAATTACATTTT-ACCCTCGAACTTC-CAAAAATTACATTTTTGACCTCGAAAC
* * * *
9643 TTTCCATAAATTACATTTTACCCTCGAACTTCCAAAAAATCACA-GTTTGATCTCGAAAC
1 TTTCCAAAAATTACATTTTACCCTCGAACTTCC-AAAAATTACATTTTTGACCTCGAAAC
* *
9702 TTT-CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATT-CTATTTTTGACCCCAAAAC
1 TTTCCAAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTAC-ATTTTTGACCTCGAAAC
* * *
9761 -TTCTAAAAATTACATCTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCGAAAC
1 TTTCCAAAAATTACAT-TTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTCGAAAC
* * * *
9820 -TTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACAT-GAAAAC
1 TTTCCAAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTCG-AAAC
*
9879 TTT-C-AAAATTACCCTTTTACCCT
1 TTTCCAAAAATTA-CATTTTACCCT
9902 AGATGTCCCA
Statistics
Matches: 271, Mismatches: 31, Indels: 35
0.80 0.09 0.10
Matches are distributed among these distances:
57 1 0.00
58 45 0.17
59 171 0.63
60 44 0.16
61 10 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (59 bp):
TTTCCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTCGAAAC
Found at i:9867 original size:29 final size:29
Alignment explanation
Indices: 9585--9868 Score: 301
Period size: 29 Copynumber: 9.7 Consensus size: 29
9575 CCCCAAAATT
* *
9585 TTCC-AAAATCACATTTTGACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
9613 TTCACAAAAATTACATTTTTGCCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
*
9643 TTTCCATAAATTACA-TTTTACCCTCGAAC
1 -TTCCAAAAATTACATTTTTACCCTCGAAC
* * * *
9672 TTCCAAAAAATCACAGTTTGA-TCTCGAAAC
1 TTCC-AAAAATTACATTTTTACCCTCG-AAC
*
9702 TTTCAAAAATTACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
9731 TTCCAAAAATT-CTATTTTTGACCC-CAAAAC
1 TTCCAAAAATTAC-ATTTTT-ACCCTC-GAAC
* * *
9761 TTCTAAAAATTACATCTTTACCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
9790 TTCCAAAAATTCCATTTTTGA-CCTCGAAAC
1 TTCCAAAAATTACATTTTT-ACCCTCG-AAC
*
9820 TTCCAAAAATTACATTTTTACCCCCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
9849 TTCCAAAAATTCCATTTTTA
1 TTCCAAAAATTACATTTTTA
9869 ACATGAAAAC
Statistics
Matches: 216, Mismatches: 25, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
28 8 0.04
29 110 0.51
30 94 0.44
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCGAAC
Done.