Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004712.1 Kokia drynarioides strain JFW-HI SEQ_118282, 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: 45470
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:9380 original size:31 final size:31
Alignment explanation
Indices: 9345--9418 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
9335 CTTAACAGAC
** *
9345 CAATGAATTAAATAAAAACTTTTGAATAGTT
1 CAATGAATTAAATAAAAACTTTCAAATAATT
*
9376 CAATGACTTAAATAAAAACTTTCAAATAATT
1 CAATGAATTAAATAAAAACTTTCAAATAATT
9407 CAATG-ATTAAAT
1 CAATGAATTAAAT
9419 TGTAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (31 bp):
CAATGAATTAAATAAAAACTTTCAAATAATT
Found at i:18889 original size:31 final size:31
Alignment explanation
Indices: 18829--18925 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
18819 AAAAATTTTT
**
18829 TTAAA-AAGAAAAATTT-AATAGCTTAGTGAC
1 TTAAATAA-AAAAATTTAAATAATTTAGTGAC
* ** *
18859 TTAAATAGAAACTTTTGAATAATTTAGTGAC
1 TTAAATAAAAAAATTTAAATAATTTAGTGAC
*
18890 TTAAATAAAAAAATTTAAATAATTTAATGAC
1 TTAAATAAAAAAATTTAAATAATTTAGTGAC
18921 -TAAAT
1 TTAAAT
18926 TATAATTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 16 0.29
31 39 0.71
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (31 bp):
TTAAATAAAAAAATTTAAATAATTTAGTGAC
Found at i:28594 original size:25 final size:25
Alignment explanation
Indices: 28566--28613 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28556 ATCCTTAGTT
*
28566 TTTAATCTAATTTA-ATTGATAATAG
1 TTTAAT-TAATTTATATTCATAATAG
*
28591 TTTAATTTATTTATATTCATAAT
1 TTTAATTAATTTATATTCATAAT
28614 TTTATTGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTAATTAATTTATATTCATAATAG
Found at i:29549 original size:13 final size:13
Alignment explanation
Indices: 29517--29549 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29507 CCTGGTAAGT
29517 TTTTTTTCCTTTA
1 TTTTTTTCCTTTA
*
29530 CTTTTTTCCTTTA
1 TTTTTTTCCTTTA
29543 TTTTTTT
1 TTTTTTT
29550 TAATCGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTCCTTTA
Found at i:38550 original size:306 final size:307
Alignment explanation
Indices: 38032--38630 Score: 834
Period size: 306 Copynumber: 2.0 Consensus size: 307
38022 CATTGTCGTG
* *
38032 TTCTTATTGAGATCTTGTCATGAGAGTGATTTCATCATATGGTAGTCAATATTTATAATGAATAA
1 TTCTTATTGAGATCTTGTCATGAGAGTGATTTCATCATATGATAGCCAATATTTATAATGAATAA
* * * *
38097 AAAGGAGTAGGTAATTAATATGTATTTGGAACCACGAGTTTTATTAAATATGAGGAAACATTTGA
66 AAAAGAGAAGATAATTAATATGTATTTGGAACCACGAGTTTTATTAAATACGAGGAAACATTTGA
* * * * * *
38162 TACGTGAACGACATAGCTTTATTACCTGTTCTTATTTTCTAGTAACTCCCCCGTAACAATGGCGT
131 TACATGAAAGACATAACTTTAGTACCTATTCTTATTTTCTAGTAACTCCCCCG-AACAATGACGT
* * *
38227 AAAAGCTTTTGGTAATTTACACCACGACCTCTCCTTAC-AATGTTTTGCCCAAACAATC-T-TTT
195 AAAAACTTTTAGTAATTTACACCACGACCTCT--TTACAAATGTCTTGCCCAAACAATCTTATTT
*
38289 TT-TTTTTAATAAGAA-TCTTCAATTCATTCGGAGGTCCTCCATTGTTGCT
258 TTCTTTTTAATAAGAACT-TTCAATTAATTCGGAGGTCCTCCATTGTTGCT
* * *
38338 TTCTTGTTGAGATTTTGTCATGAGAGTGATTTCATCATATGATAGCCAATATTTGTAATGAATAA
1 TTCTTATTGAGATCTTGTCATGAGAGTGATTTCATCATATGATAGCCAATATTTATAATGAATAA
* *
38403 AAAAGAGAAGATAATTAATA-GATATTTGGAACCACGAGTTTTATTCAATACGAGGAAATATTTG
66 AAAAGAGAAGATAATTAATATG-TATTTGGAACCACGAGTTTTATTAAATACGAGGAAACATTTG
* **
38467 ATACATGAAAGACATAACTTTAGTACCTATTTTTATTTTCTAGTGGCTCCTCCC-AACAATGACG
130 ATACATGAAAGACATAACTTTAGTACCTATTCTTATTTTCTAGTAACTCC-CCCGAACAATGACG
* * *
38531 TAAAAAACTTTTAGTAATTTACACCATGACCTCTTTCCAAATGTCTTGTCCAAACAATCTTATTT
194 T-AAAAACTTTTAGTAATTTACACCACGACCTCTTTACAAATGTCTTGCCCAAACAATCTTATTT
*
38596 TTCTTTTTAATAAGAACTTTCAATTAATTCTGAGG
258 TTCTTTTTAATAAGAACTTTCAATTAATTCGGAGG
38631 CTCGCCTTCT
Statistics
Matches: 257, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
304 3 0.01
305 29 0.11
306 188 0.73
307 8 0.03
308 28 0.11
309 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (307 bp):
TTCTTATTGAGATCTTGTCATGAGAGTGATTTCATCATATGATAGCCAATATTTATAATGAATAA
AAAAGAGAAGATAATTAATATGTATTTGGAACCACGAGTTTTATTAAATACGAGGAAACATTTGA
TACATGAAAGACATAACTTTAGTACCTATTCTTATTTTCTAGTAACTCCCCCGAACAATGACGTA
AAAACTTTTAGTAATTTACACCACGACCTCTTTACAAATGTCTTGCCCAAACAATCTTATTTTTC
TTTTTAATAAGAACTTTCAATTAATTCGGAGGTCCTCCATTGTTGCT
Found at i:40739 original size:20 final size:20
Alignment explanation
Indices: 40711--40870 Score: 74
Period size: 20 Copynumber: 8.0 Consensus size: 20
40701 GGAAGAAAGC
*
40711 AAAACAAAACAAAGTAATAT
1 AAAATAAAACAAAGTAATAT
* * *
40731 AAAATAAAAGAAAATAACAT
1 AAAATAAAACAAAGTAATAT
* * *
40751 AAAACAAAATAAAGTAA-AGC
1 AAAATAAAACAAAGTAATA-T
* **
40771 AAAATAATACAAAACAA-A-
1 AAAATAAAACAAAGTAATAT
** * *
40789 ACAAGGAAAAGCAAAGCAAGAT
1 A-AAATAAAA-CAAAGTAATAT
* * *
40811 AAAATAAAGCAAAGCAAAAT
1 AAAATAAAACAAAGTAATAT
**
40831 AAAATAAAGTAAAGTAATAT
1 AAAATAAAACAAAGTAATAT
** *
40851 AAAGCAAAGCAAAGTAATAT
1 AAAATAAAACAAAGTAATAT
40871 TGACATACAT
Statistics
Matches: 108, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
18 1 0.01
19 6 0.06
20 94 0.87
21 6 0.06
22 1 0.01
ACGTcount: A:0.68, C:0.09, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAATAAAACAAAGTAATAT
Found at i:40763 original size:30 final size:30
Alignment explanation
Indices: 40706--40789 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
40696 GTTTCGGAAG
* * ** *
40706 AAAGCAAAACAAAACAAAGTAATATAAAAT
1 AAAGCAAAATAACACAAAACAAAATAAAAT
* *
40736 AAAAG-AAAATAACATAAAACAAAATAAAGT
1 -AAAGCAAAATAACACAAAACAAAATAAAAT
*
40766 AAAGCAAAATAATACAAAACAAAA
1 AAAGCAAAATAACACAAAACAAAA
40790 CAAGGAAAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 4 0.09
30 35 0.81
31 4 0.09
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.12
Consensus pattern (30 bp):
AAAGCAAAATAACACAAAACAAAATAAAAT
Found at i:40788 original size:15 final size:14
Alignment explanation
Indices: 40732--40789 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
40722 AAGTAATATA
*
40732 AAATAAAAGAAAAT
1 AAATAAAACAAAAT
40746 AACATAAAACAAAAT
1 AA-ATAAAACAAAAT
*
40761 AAAGTAAAGCAAAAT
1 AAA-TAAAACAAAAT
*
40776 AATACAAAACAAAA
1 AA-ATAAAACAAAA
40790 CAAGGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.08
15 33 0.89
16 1 0.03
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (14 bp):
AAATAAAACAAAAT
Found at i:40800 original size:30 final size:30
Alignment explanation
Indices: 40736--40803 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
40726 AATATAAAAT
* *
40736 AAAAG-AAAATAACATAAAACAAAATAAAG
1 AAAAGCAAAATAACACAAAACAAAACAAAG
* * *
40765 TAAAGCAAAATAATACAAAACAAAACAAGG
1 AAAAGCAAAATAACACAAAACAAAACAAAG
40795 AAAAGCAAA
1 AAAAGCAAA
40804 GCAAGATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.72, C:0.10, G:0.09, T:0.09
Consensus pattern (30 bp):
AAAAGCAAAATAACACAAAACAAAACAAAG
Found at i:40839 original size:15 final size:15
Alignment explanation
Indices: 40811--40858 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
40801 AAAGCAAGAT
**
40811 AAAATAAAGCAAAGC
1 AAAATAAAATAAAGC
*
40826 AAAATAAAATAAAGT
1 AAAATAAAATAAAGC
* *
40841 AAAGTAATATAAAGC
1 AAAATAAAATAAAGC
40856 AAA
1 AAA
40859 GCAAAGTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (15 bp):
AAAATAAAATAAAGC
Done.