Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001080.1 Kokia drynarioides strain JFW-HI SEQ_112336, 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: 19542
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2487 original size:30 final size:29
Alignment explanation
Indices: 2453--2743 Score: 230
Period size: 30 Copynumber: 9.7 Consensus size: 29
2443 TTGACCCTCG
*
2453 AACTTCTCCAAAATTACATTTTAACCCTCA
1 AACTT-TCCAAAATTACATTTTAACCCTTA
* * *
2483 AACTTTACAAAAATCACATTTTGACCCTTA
1 AACTTT-CCAAAATTACATTTTAACCCTTA
* *
2513 AACTTATCCAAAAATGCATTTTAACCCTTA
1 AACTT-TCCAAAATTACATTTTAACCCTTA
* * * * *
2543 AAGTTTCCTAAAGTCACATTTCAACCCCTA
1 AACTTTCC-AAAATTACATTTTAACCCTTA
* *
2573 AACTTTCTAAAAATTACATTTTAACCCCTA
1 AACTTTC-CAAAATTACATTTTAACCCTTA
* * *
2603 AACTTTTCTAAAAAATT-TATTTTGACTCC-TA
1 AAC-TTTC--CAAAATTACATTTTAAC-CCTTA
*
2634 AACTTCTCCAAAATTACATTTTTACCCTTA
1 AACTT-TCCAAAATTACATTTTAACCCTTA
* *
2664 AACTTTTCCAAAATTATATTTTGAGCCCTTA
1 AAC-TTTCCAAAATTACATTTT-AACCCTTA
* *
2695 AATTTTCCAAAA-TA-TTTTTAACCCTTA
1 AACTTTCCAAAATTACATTTTAACCCTTA
* *
2722 AATTTTTCTAAAATTACATTTT
1 AA-CTTTCCAAAATTACATTTT
2744 GATCCCAAAT
Statistics
Matches: 211, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
27 9 0.04
28 13 0.06
29 16 0.08
30 135 0.64
31 29 0.14
32 9 0.04
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTAACCCTTA
Found at i:2507 original size:60 final size:59
Alignment explanation
Indices: 2433--2771 Score: 278
Period size: 60 Copynumber: 5.7 Consensus size: 59
2423 GTACAAAAAT
* * * *
2433 AAATCACACTTTGACCCTCGAACTTCTCCAAAATTACATTTTAACCCTCAAACTTTACAA
1 AAATCACATTTTGACCCT-AAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAA
* * * * * *
2493 AAATCACATTTTGACCCTTAAACTTATCCAAAAATGCATTTTAACCCTTAAAGTTTCCTA
1 AAATCACATTTTGACCC-TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAA
* ** * *
2553 AAGTCACATTTCAACCCCTAAACTT-TCTAAAAATTACATTTTAACCCCTAAACTTTTCTAAA
1 AAATCACATTTTGA-CCCTAAACTTCTC-CAAAATTACATTTTAACCCTTAAACTTTTC--AA
** * *
2615 AAAT-TTATTTTGACTCCTAAACTTCTCCAAAATTACATTTTTACCCTTAAACTTTTCCA
1 AAATCACATTTTGAC-CCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAA
* * * * * *
2674 AAATTATATTTTGAGCCCTTAAA-TTTTCCAAAA-TA-TTTTTAACCCTTAAATTTTTCTA
1 AAATCACATTTTGA-CCC-TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAA
* ** *
2732 AAATTACATTTTGATCCC-AAA-TTCTCTGAAATTTCATTTT
1 AAATCACATTTTGA-CCCTAAACTTCTCCAAAATTACATTTT
2772 TTGACCGCTG
Statistics
Matches: 226, Mismatches: 41, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
56 10 0.04
57 1 0.00
58 39 0.17
59 9 0.04
60 111 0.49
61 50 0.22
62 6 0.03
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
AAATCACATTTTGACCCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAA
Found at i:2677 original size:91 final size:90
Alignment explanation
Indices: 2453--2743 Score: 279
Period size: 91 Copynumber: 3.2 Consensus size: 90
2443 TTGACCCTCG
* * * *
2453 AACTTCTCCAAAATTACATTTTAACCCTCAAACTTTACAAAAATCACATTTTGACCCTTAAACTT
1 AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTT
* * **
2518 ATCCAAAAATGCATTTTAACCCTTA
66 TTCAAAAAATTTATTTTAACCCTTA
* * * * * *
2543 AAGTT-TCCTAAAGTCACATTTCAACCCCTAAAC-TTTCTAAAAATTACATTTTAACCCCTAAAC
1 AACTTCTCC-AAAATTACATTTTAACCCTTAAACTTTTC-AAAAATTACATTTTAACCCTTAAAC
*
2606 TTTTCTAAAAAATTTATTTTGACTCC-TA
64 TTTTC-AAAAAATTTATTTTAAC-CCTTA
* * * *
2634 AACTTCTCCAAAATTACATTTTTACCCTTAAACTTTTCCAAAATTATATTTTGAGCCCTTAAA-T
1 AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTT-AACCCTTAAACT
* *
2698 TTTC-CAAAATAT-TTTTAACCCTTA
65 TTTCAAAAAATTTATTTTAACCCTTA
* * *
2722 AATTTTTCTAAAATTACATTTT
1 AACTTCTCCAAAATTACATTTT
2744 GATCCCAAAT
Statistics
Matches: 162, Mismatches: 31, Indels: 18
0.77 0.15 0.09
Matches are distributed among these distances:
87 2 0.01
88 27 0.17
89 12 0.07
90 49 0.30
91 55 0.34
92 17 0.10
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (90 bp):
AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTT
TTCAAAAAATTTATTTTAACCCTTA
Found at i:6950 original size:27 final size:27
Alignment explanation
Indices: 6912--6970 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
6902 AAAATGATAA
*
6912 TATGATTGATTCGACTAATAACCTTAT
1 TATGATTGATTCGACTAATAACCTGAT
* *
6939 TATGATTGATTCGGCTAATAATCTGAT
1 TATGATTGATTCGACTAATAACCTGAT
6966 TATGA
1 TATGA
6971 CAATATTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
TATGATTGATTCGACTAATAACCTGAT
Found at i:7559 original size:23 final size:23
Alignment explanation
Indices: 7533--7587 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
7523 ACAGAAAACA
* *
7533 TTTAATTTATAGATCTTATTTAT
1 TTTAATTTATAAATCTTAATTAT
* *
7556 TTTAATTTTTAAATTTTAATTAT
1 TTTAATTTATAAATCTTAATTAT
*
7579 TTTGATTTA
1 TTTAATTTA
7588 AAAGGGTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTAATTTATAAATCTTAATTAT
Found at i:19059 original size:15 final size:15
Alignment explanation
Indices: 19041--19100 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
19031 TGGCTTGTCA
19041 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
*
19056 TCTTTGGATTTGTT-G
1 TCTTTTGATTT-TTCG
* *
19071 TCTTTTGATTTGTCA
1 TCTTTTGATTTTTCG
19086 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
19101 CCATTGACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 34 0.92
16 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.63
Consensus pattern (15 bp):
TCTTTTGATTTTTCG
Done.