Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011271.1 Kokia drynarioides strain JFW-HI SEQ_126250, 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: 19208
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:4718 original size:17 final size:17
Alignment explanation
Indices: 4696--4739 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
4686 TAAACTTATA
*
4696 AATTAATTGCTTA-ACTT
1 AATTAATTACTTAGA-TT
4713 AATTAATTACTTATGATT
1 AATTAATTACTTA-GATT
4731 AATTAATTA
1 AATTAATTA
4740 ATTGTTCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 12 0.50
18 11 0.46
19 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (17 bp):
AATTAATTACTTAGATT
Found at i:5198 original size:19 final size:20
Alignment explanation
Indices: 5149--5198 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
5139 GTCTGAGGAT
5149 TAAATTGAAAAAATTAAAAA
1 TAAATTGAAAAAATTAAAAA
* * *
5169 T-TATTGGAAAAATTTAAAA
1 TAAATTGAAAAAATTAAAAA
5188 TAAATT-AAAAA
1 TAAATTGAAAAA
5199 TAACATTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (20 bp):
TAAATTGAAAAAATTAAAAA
Found at i:7612 original size:18 final size:18
Alignment explanation
Indices: 7571--7686 Score: 139
Period size: 17 Copynumber: 6.6 Consensus size: 18
7561 CCATACTCTC
7571 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
7589 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
*
7606 TTTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAA
7623 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
7641 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
* *
7658 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
7676 TTTAAAGTTTA
1 TTTAAA-TTTA
7687 AAATAAATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
17 44 0.53
18 36 0.43
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:7628 original size:7 final size:6
Alignment explanation
Indices: 7603--7688 Score: 56
Period size: 6 Copynumber: 14.5 Consensus size: 6
7593 ATTTGTTTAA
* *
7603 AAATTT AAATTT --GTTT AAAATTT AAATTT -ATTTT AAAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT -AAATTT AAATTT
* * *
7650 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAAGTTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA-TTT AAA
7689 ATAAATAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
4 3 0.05
5 12 0.20
6 29 0.48
7 17 0.28
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:7628 original size:35 final size:35
Alignment explanation
Indices: 7571--7686 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 35
7561 CCATACTCTC
* *
7571 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAGTTTAAAATTAAATTTATTTAAAAA
*
7606 TTTAAATTT-GTTTAAAATTTAAATTTATTTTAAAA
1 TTTAAATTTAGTTTAAAA-TTAAATTTATTTAAAAA
* ** * **
7641 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTAGTTTAAAATTAAATTTATTTAAAAA
7676 TTTAAAGTTTA
1 TTTAAA-TTTA
7687 AAATAAATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 7 0.10
35 54 0.77
36 9 0.13
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTAGTTTAAAATTAAATTTATTTAAAAA
Found at i:7661 original size:24 final size:24
Alignment explanation
Indices: 7620--7666 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7610 AATTTGTTTA
*
7620 AAATTTAAATTTATTTTAAAATTT
1 AAATTTAAATTTAGTTTAAAATTT
7644 AAATTT-AATTTAAGTTTAAAATT
1 AAATTTAAATTT-AGTTTAAAATT
7667 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):
AAATTTAAATTTAGTTTAAAATTT
Found at i:8357 original size:18 final size:19
Alignment explanation
Indices: 8323--8364 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
8313 AAAACGTTTC
*
8323 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
8342 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
8360 AATAA
1 AATAA
8365 TAACACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:8466 original size:7 final size:7
Alignment explanation
Indices: 8441--8479 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
8431 TTTATATTAG
8441 TAATAA-
1 TAATAAT
8447 TAAT-AT
1 TAATAAT
8453 TAATAAT
1 TAATAAT
*
8460 TATTAAT
1 TAATAAT
8467 TAATAAT
1 TAATAAT
8474 TAATAA
1 TAATAA
8480 AAAAGGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:8873 original size:22 final size:22
Alignment explanation
Indices: 8834--8890 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
8824 AAACCGTGTA
* *
8834 GATCTAG-GCTAGATCTGGTTT
1 GATCTAGCCCTAGAGCTGGTTT
8855 GATCTAGCCCTAGAGCTGGTTT
1 GATCTAGCCCTAGAGCTGGTTT
8877 GATCTAGCCCTAGA
1 GATCTAGCCCTAGA
8891 TCTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (22 bp):
GATCTAGCCCTAGAGCTGGTTT
Found at i:9727 original size:29 final size:29
Alignment explanation
Indices: 9698--9976 Score: 211
Period size: 29 Copynumber: 9.6 Consensus size: 29
9688 CTAAACTTTT
* *
9698 TAAAAATTACCATTTTACCCTTGAACTTT
1 TAAAAATTACCATTTTACCCTCGAACTTC
* *
9727 TAAAAA-TCCCAATTTTGA-CCTCAAACGTTC
1 TAAAAATTACC-ATTTT-ACCCTCGAAC-TTC
9757 TAAAAATTACCATTTTTACCC-CTGAACTTC
1 TAAAAATTACCA-TTTTACCCTC-GAACTTC
* * *
9787 CAAATA-TCCCATTTTTGACCC-CGAACCTTC
1 TAAAAATTACCA-TTTT-ACCCTCGAA-CTTC
* *
9817 AAAAAATTACCA-TTTACCCCCGAACTTC
1 TAAAAATTACCATTTTACCCTCGAACTTC
* **
9845 CAAAAA-CCCCATTTTTGACCC-CGAACCTTC
1 TAAAAATTACCA-TTTT-ACCCTCGAA-CTTC
*
9875 TAAAAATTACCATTTTACCTTCGAACTTC
1 TAAAAATTACCATTTTACCCTCGAACTTC
**
9904 TAAAAA-CCCCATTTTGACCC-CGAACCTTC
1 TAAAAATTACCATTTT-ACCCTCGAA-CTTC
9933 TAAAAATTACCATTTTACCCTCGAACTTC
1 TAAAAATTACCATTTTACCCTCGAACTTC
* *
9962 CAAAAA-TCCCATTTT
1 TAAAAATTACCATTTT
9977 TGACTCCGAA
Statistics
Matches: 203, Mismatches: 26, Indels: 43
0.75 0.10 0.16
Matches are distributed among these distances:
27 3 0.01
28 35 0.17
29 82 0.40
30 64 0.32
31 19 0.09
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (29 bp):
TAAAAATTACCATTTTACCCTCGAACTTC
Found at i:9857 original size:58 final size:59
Alignment explanation
Indices: 9698--9991 Score: 414
Period size: 58 Copynumber: 5.0 Consensus size: 59
9688 CTAAACTTTT
* ** * * * *
9698 TAAAAATTACCATTTTACCCTTGAACTTTTAAAAATCCCAATTTTGACCTCAAACGTTC
1 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
*
9757 TAAAAATTACCATTTTTACCC-CTGAACTTCCAAATATCCCATTTTTGACCCCGAACCTTC
1 TAAAAATTACCA-TTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
* * *
9817 AAAAAATTACCA-TTTACCCCCGAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTC
1 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
* * *
9875 TAAAAATTACCATTTTACCTTCGAACTTCTAAAAACCCCA-TTTTGACCCCGAACCTTC
1 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
*
9933 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTC
1 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
9992 CCCAAAACTA
Statistics
Matches: 211, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
58 108 0.51
59 54 0.26
60 49 0.23
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
Found at i:13452 original size:18 final size:18
Alignment explanation
Indices: 13429--13467 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13419 ACCGAGTCTA
* *
13429 GAAACACCCTTTGACTAC
1 GAAACACACTTTGAATAC
13447 GAAACACACTTTGAATAC
1 GAAACACACTTTGAATAC
13465 GAA
1 GAA
13468 GGAACAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (18 bp):
GAAACACACTTTGAATAC
Found at i:16391 original size:23 final size:23
Alignment explanation
Indices: 16363--16417 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
16353 CGTCCATCAT
16363 TGCTGACT-AGACCTTCTAGAAGC
1 TGCTGACTGA-ACCTTCTAGAAGC
16386 TGCTGACTGAACCTTCTAGAAGC
1 TGCTGACTGAACCTTCTAGAAGC
16409 TGCTGACTG
1 TGCTGACTG
16418 GATGCCACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (23 bp):
TGCTGACTGAACCTTCTAGAAGC
Done.