Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014803.1 Kokia drynarioides strain JFW-HI SEQ_129845, 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: 24793
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7334 original size:29 final size:29
Alignment explanation
Indices: 7292--7781 Score: 346
Period size: 29 Copynumber: 16.5 Consensus size: 29
7282 CTAAACTATT
* *
7292 CAAAAATTACATTTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * * *
7321 CAAAAAATCCATTTTCGACCTCGAAACTTC
1 CAAAAATTCCATTTT-TACCCCCAAACTTC
*
7351 CAAAAATTCCATTTTTACCACCGAAACTTC
1 CAAAAATTCCATTTTTACC-CCCAAACTTC
* *
7381 CTAAAATTCCATTTTTTCCCCCAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * **
7410 CTAAAATTCCATTTTCACCCCTGAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * *
7439 AAAAAATTCCATTTTTGA-CCCCAAGATTGTT
1 CAAAAATTCCATTTTT-ACCCCCAA-ACT-TC
* **
7470 CAAAAATTACATTTTTGACCCAAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* * * *
7500 AAAAAATCCCA-TTTTACCCACCGAACTTT
1 CAAAAATTCCATTTTTACCC-CCAAACTTC
* *
7529 CAAAAATTCCATTTTCACCCACAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
7558 CAAAAATTCCATTTTTGACCCCAAAAACTTC
1 CAAAAATTCCATTTTT-ACCCC-CAAACTTC
*
7589 CAAAAATTCCATTTTTACCCCCAAACCTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * * *
7618 CAAAATTTACATTTTTGACCCCAAAACTTT
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* * * * * *
7648 TAAAAATTATCA-TTGTGCCCTCGAA-TGTC
1 CAAAAATT-CCATTTTTACCCCCAAACT-TC
* *
7677 CAAAAATTCCATTTTTAACCTCGAAAC-TC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* * *
7706 TC-AAAATTACCCTTTTTACCCTCGAA-TGTC
1 -CAAAAATT-CCATTTTTACCCCCAAACT-TC
* * * *
7736 TAAAAATTCCATTTTTAACCCCGAGCTTTC
1 CAAAAATTCCATTTTTACCCCCAAAC-TTC
*
7766 CCAAAATTACCATTTT
1 CAAAAATT-CCATTTT
7782 GCCCCCGATA
Statistics
Matches: 356, Mismatches: 81, Indels: 46
0.74 0.17 0.10
Matches are distributed among these distances:
28 7 0.02
29 168 0.47
30 125 0.35
31 52 0.15
32 4 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCAAACTTC
Found at i:7593 original size:119 final size:116
Alignment explanation
Indices: 7284--7726 Score: 383
Period size: 119 Copynumber: 3.7 Consensus size: 116
7274 GGAGGTCCCT
* * * * * *
7284 AAACTATTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAAATCCATTTTCGACCTCGAAACT
1 AAACT-TTCAAAAATTCCATTTTCA-CCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACT
** ** * *
7349 TCCAAAAATTCCATTTTTACCACCGAAACTTCCTAAAATTCCATTTTTTCCCCC
64 TCCAAAAATTCCATTTTTACC-CAAAAACTTCAAAAAATCCCATTTTTACCCCC
* * * * *
7403 AAACTTCCTAAAATTCCATTTTCACCCCTGAACTTCAAAAAATTCCATTTTTGACCCCAAGATTG
1 AAACTTTCAAAAATTCCATTTTCACCCC-GAACTTCCAAAAATTCCATTTTTGACCCCAAAACT-
* *
7468 TTCAAAAATTACATTTTTGACCCAAAAACTTCAAAAAATCCCA-TTTTACCCACC
64 TCCAAAAATTCCATTTTT-ACCCAAAAACTTCAAAAAATCCCATTTTTACCC-CC
* *
7522 GAACTTTCAAAAATTCCATTTTCACCCACAAACTTCCAAAAATTCCATTTTTGACCCCAAAAACT
1 AAACTTTCAAAAATTCCATTTTCACCC-CGAACTTCCAAAAATTCCATTTTTGACCCC-AAAACT
** * * * ** *
7587 TCCAAAAATTCCATTTTTACCCCCAAACCTCCAAAATTTACATTTTTGACCCCA
64 TCCAAAAATTCCATTTTTACCCAAAAACTTCAAAAAATCCCATTTTT-ACCCCC
* * * * * * *
7641 AAACTTTTAAAAATTATCATTGTGC-CCTCGAA-TGTCCAAAAATTCCATTTTTAACCTCGAAAC
1 AAACTTTCAAAAATT-CCATT-TTCACCCCGAACT-TCCAAAAATTCCATTTTTGACCCCAAAAC
*
7704 -TCTC-AAAATTACCCTTTTTACCC
63 TTC-CAAAAATT-CCATTTTTACCC
7727 TCGAATGTCT
Statistics
Matches: 265, Mismatches: 46, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
117 12 0.05
118 84 0.32
119 149 0.56
120 18 0.07
121 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (116 bp):
AAACTTTCAAAAATTCCATTTTCACCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
CAAAAATTCCATTTTTACCCAAAAACTTCAAAAAATCCCATTTTTACCCCC
Found at i:7704 original size:59 final size:59
Alignment explanation
Indices: 7556--7757 Score: 176
Period size: 59 Copynumber: 3.4 Consensus size: 59
7546 CCCACAAACT
* * * * * **
7556 TCCAAAAATTCCATTTTTGACCCCAAAAACTTCCAAAAATT--CCATTTTTACCCCCAAACC
1 TCCAAAAATTCCATTTTTAACCCC-AAAAC-TCTAAAAATTACCCA-TTGTACCCTCGAATG
* * * * * *
7616 TCCAAAATTTACATTTTTGACCCCAAAACTTTTAAAAATTA-TCATTGTGCCCTCGAATG
1 TCCAAAAATTCCATTTTTAACCCCAAAAC-TCTAAAAATTACCCATTGTACCCTCGAATG
* * * * *
7675 TCCAAAAATTCCATTTTTAACCTCGAAACTCTCAAAATTACCCTTTTTACCCTCGAATG
1 TCCAAAAATTCCATTTTTAACCCCAAAACTCTAAAAATTACCCATTGTACCCTCGAATG
*
7734 TCTAAAAATTCCATTTTTAACCCC
1 TCCAAAAATTCCATTTTTAACCCC
7758 GAGCTTTCCC
Statistics
Matches: 116, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
58 9 0.08
59 83 0.72
60 24 0.21
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAACCCCAAAACTCTAAAAATTACCCATTGTACCCTCGAATG
Found at i:22513 original size:71 final size:72
Alignment explanation
Indices: 22423--22562 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 72
22413 TTGTTTCTGT
* * *
22423 TCTGTTTTCTTTGCATTTTTCGA-TTTTTCCTGGGTTTTGTACTACTTCAATAGCTGGTAAATGT
1 TCTGGTTTCTTTGCATTTTTCGATTTTTTCCTGGGTTTTGTACAAATTCAATAGCTGGTAAATGT
22487 TATTTGA
66 TATTTGA
* * * * *
22494 TCTGGTTTCTTTGCATTTTTGGATTTTTTTTCCTTGGTTTTTTACAAATTCGATTGCTGGTAAAT
1 TCTGGTTTCTTTGCATTTTTCGA--TTTTTTCCTGGGTTTTGTACAAATTCAATAGCTGGTAAAT
22559 GTTA
64 GTTA
22563 ATTACTTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 21 0.36
74 37 0.64
ACGTcount: A:0.16, C:0.13, G:0.17, T:0.54
Consensus pattern (72 bp):
TCTGGTTTCTTTGCATTTTTCGATTTTTTCCTGGGTTTTGTACAAATTCAATAGCTGGTAAATGT
TATTTGA
Done.