Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013238.1 Kokia drynarioides strain JFW-HI SEQ_128257, 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: 7403
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:240 original size:22 final size:22
Alignment explanation
Indices: 215--258 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
205 TAAAAAAAAA
*
215 CAGATCTAGGTCTAGAT-CAAAC
1 CAGATCTA-GCCTAGATCCAAAC
237 CAGATCTAGCCTAGATCCAAAC
1 CAGATCTAGCCTAGATCCAAAC
259 GGTTTTCNNN
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (22 bp):
CAGATCTAGCCTAGATCCAAAC
Found at i:534 original size:17 final size:17
Alignment explanation
Indices: 512--546 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
502 ATTAATATTA
512 TTATTATTAAAAAATAT
1 TTATTATTAAAAAATAT
*
529 TTATTATTAATAAATAT
1 TTATTATTAAAAAATAT
546 T
1 T
547 ATGAAAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTATTAAAAAATAT
Found at i:534 original size:20 final size:19
Alignment explanation
Indices: 505--542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
495 TAATATTATT
*
505 AATATTATTATTATTAAAA
1 AATATTATTATTAATAAAA
524 AATATTTATTATTAATAAA
1 AATA-TTATTATTAATAAA
543 TATTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTATTATTAATAAAA
Found at i:537 original size:3 final size:3
Alignment explanation
Indices: 481--520 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
471 TTTTCGTTTT
* *
481 TTA TTA TTA TTCA TTA ATA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
521 AAAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:655 original size:31 final size:32
Alignment explanation
Indices: 595--661 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 32
585 TACTGCCATC
595 TATTATTAATATTATTCTTATTAACTAATAT-
1 TATTATTAATATTATTCTTATTAACTAATATG
*
626 TATTATTAATATT-TT-TTACTGTAATTAATATG
1 TATTATTAATATTATTCTTA-T-TAACTAATATG
658 TATT
1 TATT
662 TAAAACGCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.09
30 3 0.09
31 22 0.69
32 4 0.12
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (32 bp):
TATTATTAATATTATTCTTATTAACTAATATG
Found at i:1358 original size:35 final size:34
Alignment explanation
Indices: 1319--1393 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
1309 AGCCTTATTT
* *
1319 AAATTTATAGTAATTTTAAATTTGAAAATAAATTA
1 AAATTTAAAGTAAATTTAAA-TTGAAAATAAATTA
* *
1354 AAATTTAAATTAAATTTAAATTGAAAATAAATTT
1 AAATTTAAAGTAAATTTAAATTGAAAATAAATTA
1388 AAATTT
1 AAATTT
1394 TTAAACAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 19 0.53
35 17 0.47
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (34 bp):
AAATTTAAAGTAAATTTAAATTGAAAATAAATTA
Found at i:1359 original size:18 final size:18
Alignment explanation
Indices: 1315--1426 Score: 113
Period size: 18 Copynumber: 6.4 Consensus size: 18
1305 TTTTAGCCTT
* *
1315 ATTTAAATTT-ATAGTAA
1 ATTTAAATTTGAAAATAA
*
1332 TTTTAAATTTGAAAATAA
1 ATTTAAATTTGAAAATAA
* *
1350 ATTAAAATTT-AAATTAA
1 ATTTAAATTTGAAAATAA
1367 ATTTAAA-TTGAAAATAA
1 ATTTAAATTTGAAAATAA
** *
1384 ATTTAAATTTTTAAACAA
1 ATTTAAATTTGAAAATAA
* *
1402 ATTTAATTTTTAAAATAA
1 ATTTAAATTTGAAAATAA
1420 ATTTAAA
1 ATTTAAA
1427 GGGAGTTTGG
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
16 2 0.03
17 34 0.44
18 41 0.53
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTTAAATTTGAAAATAA
Found at i:1363 original size:6 final size:6
Alignment explanation
Indices: 1315--1393 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
1305 TTTTAGCCTT
* * * * *
1315 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
1362 A-TTAA ATTTAA ATTGAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1394 TTAAACAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
5 13 0.24
6 38 0.70
7 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:1370 original size:11 final size:12
Alignment explanation
Indices: 1347--1393 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
1337 AATTTGAAAA
1347 TAAATTAAAATT
1 TAAATTAAAATT
1359 TAAATT-AAATT
1 TAAATTAAAATT
1370 TAAATTGAAAA--
1 TAAATT-AAAATT
*
1381 TAAATTTAAATT
1 TAAATTAAAATT
1393 T
1 T
1394 TTAAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 3 0.10
11 17 0.57
12 7 0.23
13 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TAAATTAAAATT
Found at i:2090 original size:201 final size:204
Alignment explanation
Indices: 1737--2175 Score: 575
Period size: 201 Copynumber: 2.2 Consensus size: 204
1727 TTGACTTGAC
* * * *
1737 CTTCTTCTCAATATCTCATCAGGAAAATGACCGCGTCGCTTGTTTCAATCCGCTTCTCTTTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAAATGACCACATCGCTTGTTTCAATCCGCTTCTCTGTATCT
* *
1802 AATCAGGAAGACGAATTTGGTTTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTT
66 AATCAGGAAGACGAATTTGGTTGACTTCTCAGTATCTCATCAGGAAGCTAACCATCTATTGCTTT
* * *
1867 CACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGAAAATTTCGCTCG-TTT-CG-A-GCC
131 CACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTCGCTCGCTTTGCGTAGGCC
1928 TCATTTGGGT
196 TCATTT-GGT
* * *
1938 CTTCTTCTCAGTGTCTCATCAGGAGAATGATCACATCGCTTGTTTCAATCCGCTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAAATGACCACATCGCTTGTTTCAATCCGCTTCTCTGTATCT
* * ** * *
2003 CATCAGGAAGACGAATTTGGTTGACTTTTTTGTATCTTATCAGGAAGCTAACCGTCTATTGC-TT
66 AATCAGGAAGACGAATTTGGTTGACTTCTCAGTATCTCATCAGGAAGCTAACCATCTATTGCTTT
* * *
2067 CGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAG
131 C-ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTCGCTCGCTTT--GCGTAG
*
2132 GCCTGATTTGGT
193 GCCTCATTTGGT
* *
2144 CTTCTTCTCAGCATCTCA-CTAGGAAGATGACC
1 CTTCTTCTCAGTATCTCATC-AGGAAAATGACC
2176 GCGTCGTTTG
Statistics
Matches: 203, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
200 3 0.01
201 157 0.77
202 3 0.01
205 3 0.01
206 29 0.14
207 8 0.04
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (204 bp):
CTTCTTCTCAGTATCTCATCAGGAAAATGACCACATCGCTTGTTTCAATCCGCTTCTCTGTATCT
AATCAGGAAGACGAATTTGGTTGACTTCTCAGTATCTCATCAGGAAGCTAACCATCTATTGCTTT
CACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTCGCTCGCTTTGCGTAGGCC
TCATTTGGT
Done.