Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008797.1 Kokia drynarioides strain JFW-HI SEQ_123480, 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: 77985
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27 TTATGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25218 original size:32 final size:32
Alignment explanation
Indices: 25182--25247 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
25172 TAGTAGAACT
25182 GGTTTATTCTTGTTTGATAGCTTCACAAATTG
1 GGTTTATTCTTGTTTGATAGCTTCACAAATTG
25214 GGTTTATTCTTGTTTGATAGCTTCACAAATTG
1 GGTTTATTCTTGTTTGATAGCTTCACAAATTG
25246 GG
1 GG
25248 GTATTTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (32 bp):
GGTTTATTCTTGTTTGATAGCTTCACAAATTG
Found at i:29494 original size:17 final size:17
Alignment explanation
Indices: 29461--29494 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29451 TTTTAAATTG
* *
29461 TGTAACTTGTTCTTTTT
1 TGTAACTTGTGCATTTT
29478 TGTAACTTGTGCATTTT
1 TGTAACTTGTGCATTTT
29495 GTTACTAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (17 bp):
TGTAACTTGTGCATTTT
Found at i:39273 original size:108 final size:111
Alignment explanation
Indices: 39151--39358 Score: 260
Period size: 117 Copynumber: 1.8 Consensus size: 111
39141 TTAAGATATG
* * * *
39151 TGTACATTTTAATACATTTGTGTA-T-TC-TTTTTCATTTTCAATAGATCGCATTTTCCATAAAT
1 TGTACATTTCAATACAATTGTGTACTCTCTTTTTTCATTTTCAATACATCGCATTTTACATAAAT
39213 TATTATAATTATTTAATTTTACCATAATTCTTAAGAATTAAATAGC
66 TATTATAATTATTTAATTTTACCATAATTCTTAAGAATTAAATAGC
* ** *
39259 TGTACGTTTCAATACAATTGTGTACTCTCTTTTTTTTTTTTCATTTTCAATACATCTTATTTTAT
1 TGTACATTTCAATACAATTGTGTACTCTC------TTTTTTCATTTTCAATACATCGCATTTTAC
*
39324 ATAAATTTTTATAATTATTTAATTTTACCATAATT
60 ATAAATTATTATAATTATTTAATTTTACCATAATT
39359 ATAGATGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
108 21 0.26
109 1 0.01
110 2 0.02
117 58 0.71
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (111 bp):
TGTACATTTCAATACAATTGTGTACTCTCTTTTTTCATTTTCAATACATCGCATTTTACATAAAT
TATTATAATTATTTAATTTTACCATAATTCTTAAGAATTAAATAGC
Found at i:43739 original size:41 final size:42
Alignment explanation
Indices: 43672--43788 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 42
43662 CACATAAATA
* * *
43672 AAGCGTCGCTAATGCTCTGACTTTTAGCGA-CGTTTTTTCAT
1 AAGCGTCGCTAATACTCTGACCTTTAGCGAGCGCTTTTTCAT
* *
43713 AAGCGTCGCTAGTACTCTAACCTTTAGC-AGCGCTTTTTCAT
1 AAGCGTCGCTAATACTCTGACCTTTAGCGAGCGCTTTTTCAT
*
43754 AAGCGCCGCTAATACTCTGACCTTTAGCG-GCGCTT
1 AAGCGTCGCTAATACTCTGACCTTTAGCGAGCGCTT
43789 ATGATGTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.02
41 65 0.98
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (42 bp):
AAGCGTCGCTAATACTCTGACCTTTAGCGAGCGCTTTTTCAT
Found at i:50608 original size:23 final size:23
Alignment explanation
Indices: 50578--50623 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
50568 AGCCACTACA
50578 GGTTCTGTTCTACGGCTGGAAGC
1 GGTTCTGTTCTACGGCTGGAAGC
*
50601 GGTTCTGTTCTATGGCTGGAAGC
1 GGTTCTGTTCTACGGCTGGAAGC
50624 CTGGAACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.35, T:0.33
Consensus pattern (23 bp):
GGTTCTGTTCTACGGCTGGAAGC
Found at i:54479 original size:6 final size:7
Alignment explanation
Indices: 54462--54505 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
54452 GTCAAAGGTA
54462 AAAAAAC
1 AAAAAAC
54469 AAAAAAC
1 AAAAAAC
54476 AAAAAAC
1 AAAAAAC
54483 AAAAAAC
1 AAAAAAC
54490 -AAAAAC
1 AAAAAAC
54496 -AAAAAC
1 AAAAAAC
54502 AAAA
1 AAAA
54506 CATGAGGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.33
7 24 0.67
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:60405 original size:128 final size:128
Alignment explanation
Indices: 60177--60562 Score: 610
Period size: 128 Copynumber: 3.0 Consensus size: 128
60167 TAGGAATAAC
* *
60177 ATATATTTGTTAAATCACAATGCATGTCTTCTGCAATCCATTGTTAAATTACTATGATTTGTATC
1 ATATATTTGTTAAATCACAATGCATGTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATC
*
60242 ACTGGCCTTTCTTACATCACAAAGGAACGTCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
66 ACTGGCCTTTCTTACAGCACAAAGGAACGTCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
*
60305 ATATATTTGTTAAATCACAATGCATGTCTTCTGTAATCCACTATTAAATTACTATGATTTGTATC
1 ATATATTTGTTAAATCACAATGCATGTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATC
** *
60370 ACTGGTTTTTCTTACAGCACAAAGGAACATCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
66 ACTGGCCTTTCTTACAGCACAAAGGAACGTCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
* * *
60433 ATATATTTGTTAAATCACAATACATGTCTTTTGTAATCTACTGTTAAATTACTATGATTTGTATC
1 ATATATTTGTTAAATCACAATGCATGTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATC
* * * * * * * *
60498 AGTGACCTGTCTTAGAGCACAAAGGAACGTCCAAAGCTTCTGAACCATTAATGGTAGCTAAAT
66 ACTGGCCTTTCTTACAGCACAAAGGAACGTCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
60561 AT
1 AT
60563 TTACATATCT
Statistics
Matches: 236, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 236 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (128 bp):
ATATATTTGTTAAATCACAATGCATGTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATC
ACTGGCCTTTCTTACAGCACAAAGGAACGTCCAAAGTTTTTGAACCATTAATAGTAGCCAAAT
Done.