Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009430.1 Kokia drynarioides strain JFW-HI SEQ_124137, 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: 104905
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5829 original size:30 final size:31
Alignment explanation
Indices: 5790--5852 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
5780 CATTTAACAC
* *
5790 AACAGTCACTCAACTT-T-GAAAACGTGACAA
1 AACAATCACTAAACTTATCGAAAA-GTGACAA
*
5820 AACAATCACTAAAGTTATCGAAAAGTGACAA
1 AACAATCACTAAACTTATCGAAAAGTGACAA
5851 AA
1 AA
5853 TAGTCCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.46
31 10 0.36
32 5 0.18
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (31 bp):
AACAATCACTAAACTTATCGAAAAGTGACAA
Found at i:13567 original size:19 final size:18
Alignment explanation
Indices: 13539--13576 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
13529 CAAATTACAA
13539 AAAAAATCAAAATATTTAT
1 AAAAAATCAAAA-ATTTAT
*
13558 AAAAATTCAAAAATTTAT
1 AAAAAATCAAAAATTTAT
13576 A
1 A
13577 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATCAAAAATTTAT
Found at i:16245 original size:3 final size:3
Alignment explanation
Indices: 16226--16282 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
16216 TCCTCTTTTA
* *
16226 TTC TGC TTC TGC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
16274 TTC GTC TTC
1 TTC TTC TTC
16283 AGCTACAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:28828 original size:21 final size:21
Alignment explanation
Indices: 28804--28846 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28794 TGTTCGTTTA
28804 TTTAACTTTTGTTGTGTTGTT
1 TTTAACTTTTGTTGTGTTGTT
** *
28825 TTTATTTTTTGTTTTGTTGTT
1 TTTAACTTTTGTTGTGTTGTT
28846 T
1 T
28847 GGAATGGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.02, G:0.16, T:0.74
Consensus pattern (21 bp):
TTTAACTTTTGTTGTGTTGTT
Found at i:59688 original size:23 final size:23
Alignment explanation
Indices: 59655--59698 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
59645 CCTTTTCAAA
*
59655 ATGATAGAATTATATATTAATAT
1 ATGATAAAATTATATATTAATAT
*
59678 ATGATAAAATTATATTTTAAT
1 ATGATAAAATTATATATTAAT
59699 TTTTCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
ATGATAAAATTATATATTAATAT
Found at i:66435 original size:56 final size:56
Alignment explanation
Indices: 66349--66458 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
66339 ATTGTTCACG
66349 TATCCATGTGTTCTGATTTTACCTTTTAAGAGATTCAAAATAAATTTTAGCGATCA
1 TATCCATGTGTTCTGATTTTACCTTTTAAGAGATTCAAAATAAATTTTAGCGATCA
* *
66405 TATCCATGTGTTTTGATTTTACCTTTTAAGATATTCAAAATAAATTTTAGCGAT
1 TATCCATGTGTTCTGATTTTACCTTTTAAGAGATTCAAAATAAATTTTAGCGAT
66459 TAATTATGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (56 bp):
TATCCATGTGTTCTGATTTTACCTTTTAAGAGATTCAAAATAAATTTTAGCGATCA
Found at i:75152 original size:71 final size:69
Alignment explanation
Indices: 75020--75157 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 69
75010 ATGCCGATCA
* *
75020 TTGAATCTCAAAAGTGTGTAAATTTCTTTCTTTACTATTTCATTAAGTGATTTTGAACGCCTTTT
1 TTGAATCTCAAAAGTGTGTAAATTACTTTCTTTACTATTTCATGAAGTGATTTTGAACGCCTTTT
75085 ATCG
66 ATCG
* *
75089 TTGAATCTCAAAAGTGTGTAAAATTACTTTCTTTTACTGTTTCATGAATTGATTTT-AATCGCCT
1 TTGAATCTCAAAAGTGTGT-AAATTACTTTC-TTTACTATTTCATGAAGTGATTTTGAA-CGCCT
75153 TTTAT
63 TTTAT
75158 GGAGTTAGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
69 19 0.31
70 12 0.19
71 31 0.50
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (69 bp):
TTGAATCTCAAAAGTGTGTAAATTACTTTCTTTACTATTTCATGAAGTGATTTTGAACGCCTTTT
ATCG
Found at i:93813 original size:5 final size:5
Alignment explanation
Indices: 93803--93838 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
93793 GAGATAGAAT
93803 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
93839 ATATTTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
TCGAA
Found at i:97461 original size:24 final size:24
Alignment explanation
Indices: 97428--97475 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
97418 ATACAAGCAA
97428 AAAAAAAAAATTAGTATTAAAAAT
1 AAAAAAAAAATTAGTATTAAAAAT
* * *
97452 AAAAATAAAATTATTATTATAAAT
1 AAAAAAAAAATTAGTATTAAAAAT
97476 CCGAGCCGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAAAAAAATTAGTATTAAAAAT
Found at i:104641 original size:106 final size:106
Alignment explanation
Indices: 104487--104698 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
104477 AGTGTAGTAG
104487 CTATCCAATTTTTAAGAGAAATGCATTCATACTTGTCTTGGAGGAGAAAGAAAATGGACATTAGT
1 CTATCCAATTTTTAAGAGAAATGCATTCATACTTGTCTTGGAGGAGAAAGAAAATGGACATTAGT
104552 GTTAAATACAAGTGATTAAGGTAAGAAAGTTAAACTCCTCT
66 GTTAAATACAAGTGATTAAGGTAAGAAAGTTAAACTCCTCT
104593 CTATCCAATTTTTAAGAGAAATGCATTCATACTTGTCTTGGAGGAGAAAGAAAATGGACATTAGT
1 CTATCCAATTTTTAAGAGAAATGCATTCATACTTGTCTTGGAGGAGAAAGAAAATGGACATTAGT
104658 GTTAAATACAAGTGATTAAGGTAAGAAAGTTAAACTCCTCT
66 GTTAAATACAAGTGATTAAGGTAAGAAAGTTAAACTCCTCT
104699 TTAAATACAT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (106 bp):
CTATCCAATTTTTAAGAGAAATGCATTCATACTTGTCTTGGAGGAGAAAGAAAATGGACATTAGT
GTTAAATACAAGTGATTAAGGTAAGAAAGTTAAACTCCTCT
Done.