Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015044.1 Kokia drynarioides strain JFW-HI SEQ_130088, 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: 61578
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:526 original size:29 final size:28
Alignment explanation
Indices: 487--1097 Score: 437
Period size: 29 Copynumber: 21.0 Consensus size: 28
477 GAAGGTCCCT
* *
487 AAACTGTCCAAAAATTCCGTTTTCACCCTC
1 AAACT-TCCAAAAATTCCATTTTGACCC-C
* * *
517 GAACTTCCAAAAA-CCCTATTTTTGACCTCA
1 AAACTTCCAAAAATTCC-A-TTTTGACC-CC
* * *
547 AAACTTTCAAAAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTGACCC-C
* * *
576 GAACTTCCAAAAATTCCATTTTGATCCG
1 AAACTTCCAAAAATTCCATTTTGACCCC
* *
604 AAACTCCCAAAAATTCC-TTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTGACCC-C
*
632 AAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCA-TTTTGACCCC
* * *
661 AAAACTCCCAAAAATTCTATTTTCACCCCC
1 -AAACTTCCAAAAATTCCATTTTGA-CCCC
* * * *
691 GAACTTCCAAAAA-CCTCATTTTTTACTCCA
1 AAACTTCCAAAAATTC-CA-TTTTGAC-CCC
* *
721 AAACTCCCAAAAATTCCATTTTCACCCCC
1 AAACTTCCAAAAATTCCATTTTGA-CCCC
* *
750 GAACTTCC-AAAA-TCTCATTTTTACCCC
1 AAACTTCCAAAAATTC-CATTTTGACCCC
* *
777 AAAACTCCCAAAAATTCCATTTTTACCCC
1 -AAACTTCCAAAAATTCCATTTTGACCCC
**
806 TAAACTTCCAAAAACCCCATTTTTGACCCC
1 -AAACTTCCAAAAATTCCA-TTTTGACCCC
* * *
836 AAAACTCCCAAAAATTCTATTTTCACCCCC
1 -AAACTTCCAAAAATTCCATTTTGA-CCCC
**
866 AAACTTCCAAAAACCCCATTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTGACCCC
* * *
894 GAAACTCCCAAAAATTCTATTTTCACCCCC
1 -AAACTTCCAAAAATTCCATTTTGA-CCCC
**
924 AAACTTCCAAAAACCCCATTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTGACCCC
* * *
952 AAAACTCCCAAAAATTCTATTTTTACCCC
1 -AAACTTCCAAAAATTCCATTTTGACCCC
*
981 TAAACTTCCAAAAATTCCATTTTGACCTCG
1 -AAACTTCCAAAAATTCCATTTTGACC-CC
* *
1011 AAACTTCCAAAAAAATCTATTTCT-ACCCCC
1 AAACTTCC-AAAAATTCCATTT-TGA-CCCC
*
1041 GAACTTCCAAAAA-TCTCATCTTTGACCCC
1 AAACTTCCAAAAATTC-CAT-TTTGACCCC
* * *
1070 GAAGCCTCTAAAAATTACCATTTT-ACCC
1 -AAACTTCCAAAAATT-CCATTTTGACCC
1098 TCGGATGTCC
Statistics
Matches: 457, Mismatches: 90, Indels: 69
0.74 0.15 0.11
Matches are distributed among these distances:
27 13 0.03
28 61 0.13
29 232 0.51
30 140 0.31
31 10 0.02
32 1 0.00
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.29
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTGACCCC
Found at i:562 original size:59 final size:58
Alignment explanation
Indices: 494--1069 Score: 646
Period size: 59 Copynumber: 9.9 Consensus size: 58
484 CCTAAACTGT
* * * * *
494 CCAAAAATTCCGTTTTCACCCTCGAACTTCCAAAAACCCTATTTTTGACCTCAAAACTT
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAACCC-ATTTTTGACCCCAAAACTC
* * * * * * * *
553 TCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGA-TCCGAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAACTC
* *
610 CCAAAAATTCC-TTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAACTC
* * * *
668 CCAAAAATTCTATTTTCACCCCCGAACTTCCAAAAACCTCATTTTTTACTCCAAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAACC-CATTTTTGACCCCAAAACTC
* * *
727 CCAAAAATTCCATTTTCACCCCCGAACTTCCAAAATCTCATTTTT-ACCCCAAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAACCCATTTTTGACCCCAAAACTC
* *
784 CCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAACCCCATTTTTGACCCCAAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAACTC
* *
843 CCAAAAATTCTATTTTCACCCCCAAACTTCCAAAAACCCCA-TTTTGACCCCGAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAACTC
*
901 CCAAAAATTCTATTTTCACCCCCAAACTTCCAAAAACCCCA-TTTTGACCCCAAAACTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAACTC
* * * * * *
959 CCAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATTCCA-TTTTGACCTCGAAACTTC
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCCAAAAC-TC
* * * * * *
1018 CAAAAAAATCTA-TTTCTACCCCCGAACTTCCAAAAATCTCATCTTTGACCCC
1 CCAAAAATTCCATTTTC-ACCCCCAAACTTCCAAAAA-CCCATTTTTGACCCC
1070 GAAGCCTCTA
Statistics
Matches: 457, Mismatches: 50, Indels: 19
0.87 0.10 0.04
Matches are distributed among these distances:
56 27 0.06
57 64 0.14
58 167 0.37
59 189 0.41
60 10 0.02
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (58 bp):
CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAACCCATTTTTGACCCCAAAACTC
Found at i:805 original size:116 final size:117
Alignment explanation
Indices: 494--1069 Score: 698
Period size: 116 Copynumber: 4.9 Consensus size: 117
484 CCTAAACTGT
* * * * **
494 CCAAAAATTCCGTTTTCACCCTCGAACTTCCAAAAA-CCCTATTTTTGACCTCAAAACTTTCAAA
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCC-ATTTTT-ACCCCAAAACTCCCAAA
* * * *
558 AATTCTATTTTTACCCTCGAACTTCCAAAAA-TTCCA-TTTTGA-TCCGAAACTC
64 AATTCTATTTTTACCCCCGAACTTCCAAAAACCT-CATTTTTGACCCCAAAACTC
* *
610 CCAAAAATTCC-TTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTCCCAAAA
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACTCCCAAAA
* * *
674 ATTCTATTTTCACCCCCGAACTTCCAAAAACCTCATTTTTTACTCCAAAACTC
65 ATTCTATTTTTACCCCCGAACTTCCAAAAACCTCATTTTTGACCCCAAAACTC
* *
727 CCAAAAATTCCATTTTCACCCCCGAACTTCC-AAAATCTCATTTTTACCCCAAAACTCCCAAAAA
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACTCCCAAAAA
* ** *
791 TTCCATTTTTACCCCTAAACTTCCAAAAACCCCATTTTTGACCCCAAAACTC
66 TTCTATTTTTACCCCCGAACTTCCAAAAACCTCATTTTTGACCCCAAAACTC
* * * *
843 CCAAAAATTCTATTTTCACCCCCAAACTTCCAAAAACCCCATTTTGACCCCGAAACTCCCAAAAA
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACTCCCAAAAA
* * *
908 TTCTATTTTCACCCCCAAACTTCCAAAAACCCCA-TTTTGACCCCAAAACTC
66 TTCTATTTTTACCCCCGAACTTCCAAAAACCTCATTTTTGACCCCAAAACTC
* * * * * * * *
959 CCAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAA
1 CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAAC-TCCCAAAA
* * * *
1024 AATCTATTTCTACCCCCGAACTTCCAAAAATCTCATCTTTGACCCC
65 ATTCTATTTTTACCCCCGAACTTCCAAAAACCTCATTTTTGACCCC
1070 GAAGCCTCTA
Statistics
Matches: 409, Mismatches: 43, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
115 74 0.18
116 181 0.44
117 129 0.32
118 25 0.06
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (117 bp):
CCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACTCCCAAAAA
TTCTATTTTTACCCCCGAACTTCCAAAAACCTCATTTTTGACCCCAAAACTC
Found at i:1097 original size:59 final size:57
Alignment explanation
Indices: 494--1160 Score: 605
Period size: 59 Copynumber: 11.4 Consensus size: 57
484 CCTAAACTGT
* * * * *
494 CCAAAAATTCCGTTTTCACCCTCGAACTTCCAAAAA-CCCTATTTTTGACCTCAAAACTT
1 CCAAAAATTCCATTTT-ACCCCCGAACTTCCAAAAATCTC-A-TTTTGACCCCAAAACTC
* * * * *
553 TCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAAT-TCCATTTTGA-TCCGAAACTC
1 CCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCT-CATTTTGACCCCAAAACTC
* * * *
610 CCAAAAATTCCTTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTC
1 CCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATCTCA-TTTTGACCCCAAAACTC
* * * *
668 CCAAAAATTCTATTTTCACCCCCGAACTTCCAAAAACCTCATTTTTTACTCCAAAACTC
1 CCAAAAATTCCATTTT-ACCCCCGAACTTCCAAAAATCTCA-TTTTGACCCCAAAACTC
*
727 CCAAAAATTCCATTTTCACCCCCGAACTTCC-AAAATCTCATTTTTACCCCAAAACTC
1 CCAAAAATTCCATTTT-ACCCCCGAACTTCCAAAAATCTCATTTTGACCCCAAAACTC
** * *
784 CCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAACCCCATTTTTGACCCCAAAACTC
1 CCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCTCA-TTTTGACCCCAAAACTC
* * * * *
843 CCAAAAATTCTATTTTCACCCCCAAACTTCCAAAAACCCCATTTTGACCCCGAAACTC
1 CCAAAAATTCCATTTT-ACCCCCGAACTTCCAAAAATCTCATTTTGACCCCAAAACTC
* * * *
901 CCAAAAATTCTATTTTCACCCCCAAACTTCCAAAAACCCCATTTTGACCCCAAAACTC
1 CCAAAAATTCCATTTT-ACCCCCGAACTTCCAAAAATCTCATTTTGACCCCAAAACTC
* ** * *
959 CCAAAAATTCTATTTTTACCCCTAAACTTCCAAAAAT-TCCATTTTGACCTCGAAACTTC
1 CCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCT-CATTTTGACCCCAAAAC-TC
* * * * *
1018 CAAAAAAATCTATTTCTACCCCCGAACTTCCAAAAATCTCATCTTTGACCCCGAAGC-C
1 CCAAAAATTCCATTT-TACCCCCGAACTTCCAAAAATCTCAT-TTTGACCCCAAAACTC
* * * * * *
1076 TCTAAAAATTACCATTTTACCCTCGGA-TGTCCAAAAA-CTCCAATTTTGATCTCGAAACTC
1 -CCAAAAATT-CCATTTTACCCCCGAACT-TCCAAAAATCT-C-ATTTTGACCCCAAAACTC
* *
1136 TC-AAAATTACCCTTTTACCCCCGAA
1 CCAAAAATT-CCATTTTACCCCCGAA
1161 TGTCTAAAAA
Statistics
Matches: 526, Mismatches: 59, Indels: 47
0.83 0.09 0.07
Matches are distributed among these distances:
56 25 0.05
57 61 0.12
58 196 0.37
59 218 0.41
60 26 0.05
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (57 bp):
CCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATCTCATTTTGACCCCAAAACTC
Found at i:1641 original size:96 final size:96
Alignment explanation
Indices: 1476--1661 Score: 236
Period size: 96 Copynumber: 1.9 Consensus size: 96
1466 AAAGCTTTAA
* * * * **
1476 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTCACTAGGTGCAATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTCTGAAAATTTGCGCCTTAACTCACTAGGTACAACC
1541 TTTCTTCAAATCGAA-ATAATCGAATGCCCTT
66 TTTCTTCAAATC-AAGATAATCGAATGCCCTT
* *
1572 AATCGAGGCAATGTT-TCCTTATCTTCG-GTTCTG-AAATATTGCGCCTTAACTTACTAGGTACA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTCTGAAAAT-TTGCGCCTTAACTCACTAGGTACA
1634 ACCTTTCTTCAAATCAAGATAATCGAAT
63 ACCTTTCTTCAAATCAAGATAATCGAAT
1662 ATCTTTTTCG
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
95 7 0.09
96 67 0.86
97 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTCTGAAAATTTGCGCCTTAACTCACTAGGTACAACC
TTTCTTCAAATCAAGATAATCGAATGCCCTT
Found at i:6613 original size:103 final size:103
Alignment explanation
Indices: 6505--6711 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
6495 CTAATATACA
6505 TATATGTGGGGGGATTTTTCAAAGTTTTTGGAAGAAGATTTTTTATCAGAGAAAAAGATGGAAGG
1 TATATGTGGGGGGATTTTTCAAAGTTTTTGGAAGAAGATTTTTTATCAGAGAAAAAGATGGAAGG
6570 GAGGGAGAAGGCTATGGAATCATTACTATGAAAGGCTG
66 GAGGGAGAAGGCTATGGAATCATTACTATGAAAGGCTG
6608 TATATGTGGGGGGATTTTTCAAAGTTTTTGGAAGAAGATTTTTTATCAGAGAAAAAGATGGAAGG
1 TATATGTGGGGGGATTTTTCAAAGTTTTTGGAAGAAGATTTTTTATCAGAGAAAAAGATGGAAGG
6673 GAGGGAGAAGGCTATGGAATCATTACTATGAAAGGCTG
66 GAGGGAGAAGGCTATGGAATCATTACTATGAAAGGCTG
6711 T
1 T
6712 GTGGAAGAAG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (103 bp):
TATATGTGGGGGGATTTTTCAAAGTTTTTGGAAGAAGATTTTTTATCAGAGAAAAAGATGGAAGG
GAGGGAGAAGGCTATGGAATCATTACTATGAAAGGCTG
Found at i:12343 original size:14 final size:13
Alignment explanation
Indices: 12326--12360 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
12316 TTCTCCTCAG
12326 TTTTTCTTCTTTTT
1 TTTTTCTT-TTTTT
12340 TTTTTC-TTTTTT
1 TTTTTCTTTTTTT
12352 TTTTTCTTT
1 TTTTTCTTT
12361 AAAAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.55
13 3 0.15
14 6 0.30
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:12349 original size:10 final size:11
Alignment explanation
Indices: 12326--12360 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12316 TTCTCCTCAG
*
12326 TTTTTCTTCTT
1 TTTTTTTTCTT
12337 TTTTTTTTCTTT
1 TTTTTTTTC-TT
12349 TTTTTTTTCTT
1 TTTTTTTTCTT
12360 T
1 T
12361 AAAAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:49574 original size:32 final size:32
Alignment explanation
Indices: 49538--49601 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
49528 GAGCTTACTT
49538 AACTTTGGCGATTTTCTTTTATACACGTTAAA
1 AACTTTGGCGATTTTCTTTTATACACGTTAAA
*
49570 AACTTTGGCGATTTTCTTTTCTACACGTTAAA
1 AACTTTGGCGATTTTCTTTTATACACGTTAAA
49602 CGTCCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (32 bp):
AACTTTGGCGATTTTCTTTTATACACGTTAAA
Found at i:58291 original size:2 final size:2
Alignment explanation
Indices: 58279--58308 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58269 CTTTTAACAT
*
58279 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58309 ACACCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Done.