Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004230.1 Kokia drynarioides strain JFW-HI SEQ_117491, 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: 2375
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Found at i:538 original size:17 final size:17
Alignment explanation
Indices: 501--597 Score: 104
Period size: 17 Copynumber: 5.6 Consensus size: 17
491 CAAATTTCTG
501 ATAATTTTAAATTTGAAA
1 ATAATTTTAAATTT-AAA
* *
519 ATAATTTTGAACTTAAA
1 ATAATTTTAAATTTAAA
*
536 ATAAATTTAAATTTAAA
1 ATAATTTTAAATTTAAA
* *
553 ATAAATTTAAATTTTAA
1 ATAATTTTAAATTTAAA
* * *
570 ACAAATTTAATTTTAAA
1 ATAATTTTAAATTTAAA
*
587 ATAAATTTAAA
1 ATAATTTTAAA
598 GGGAGTTTGG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
17 56 0.82
18 12 0.18
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAATTTTAAATTTAAA
Found at i:576 original size:34 final size:34
Alignment explanation
Indices: 506--597 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 34
496 TTCTGATAAT
* * *
506 TTTAAATTTGAAAATAATTTTGAACTTAAAATAAA
1 TTTAAATTT-AAAATAAATTTAAACTTAAAACAAA
* *
541 TTTAAATTTAAAATAAATTTAAATTTTAAACAAA
1 TTTAAATTTAAAATAAATTTAAACTTAAAACAAA
*
575 TTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
598 GGGAGTTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 42 0.82
35 9 0.18
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAACTTAAAACAAA
Found at i:1637 original size:205 final size:203
Alignment explanation
Indices: 1009--1680 Score: 809
Period size: 206 Copynumber: 3.3 Consensus size: 203
999 TTTCATCAGG
* * * * * *
1009 ATTTGGTTCACTTCTCTGTATCTCATGAGGGAGCTAACCACTTTATGGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACC-GTTTATTGCTCCGACCTGCTTCTCA
* * * * * *
1074 GCGTCTCATCAGGAAGCTGGGGCTCGAAGATTTGCTCATTTTGAGCCT-CGTTTG---GGTATTC
65 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAGCGTGGGTTTGATTGGT-TTC
* * ** * * *
1135 TTCTCAGTGTCACATCAGGAAGATGACCGCGTCGTTTGTTTCAA-CTCGCTTCTTTGTATCTCAT
129 TTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATC-CGCTTCTCTGTATCTCAC
*
1199 CAGGAAGGCGA
193 CAGGAAGACGA
* * *
1210 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGACCTGCTTCTCAG
* * * *
1275 TATCTTC-TCAGGAAGCTGGGGTTCGAAGATTTTG-TTCGCTTTGAGCGTGGATTCGATTTGGTT
66 TGTC-TCATCAGGAAGCTGGGGTTCGAAGA-TTTGCTT-ACTTTGAGCGTGGGTTTGA-TTGGTT
* ** *
1338 CTCTTCCCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATCAACTTCTCTGTATCTT
127 -TCTTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATCCGCTTCTCTGTATCTC
1403 ACCAGGAAGACGA
191 ACCAGGAAGACGA
* *
1416 ATTTGGTTTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATCTGCTTCTCAG
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGACCTGCTTCTCAG
* * *
1481 TGTCTCATCAGGAAGCTGGGATTCGAAGACTTGCTTACTTCGAGCGTGGGTTTGACTTGGTCTTC
66 TGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAGCGTGGGTTTGA-TTGGT-TTC
* * * * **
1546 TTCTCAGTATCTCGTCAAGAAGATGACCATATAGCTTGTTTCAATCCGCTTCTCCATATCTCACC
129 TTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATCCGCTTCTCTGTATCTCACC
*
1611 AGGAAGATGA
194 AGGAAGACGA
*
1621 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATCTGCTT
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGACCTGCTT
1681 TAAGCTGGGA
Statistics
Matches: 406, Mismatches: 52, Indels: 22
0.85 0.11 0.05
Matches are distributed among these distances:
200 48 0.12
201 50 0.12
202 3 0.01
205 151 0.37
206 153 0.38
207 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (203 bp):
ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGACCTGCTTCTCAG
TGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAGCGTGGGTTTGATTGGTTTCTT
CTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATCCGCTTCTCTGTATCTCACCAG
GAAGACGA
Found at i:2285 original size:27 final size:27
Alignment explanation
Indices: 2253--2312 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2243 TCAAAAATTT
* *
2253 TATTAAGAAGAGGATCAAAAGAAGCAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
* *
2280 TATTAAAAAGATGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
2307 TCATTA
1 T-ATTA
2313 GTTGAAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAAGAAACAA
Done.