Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000278.1 Kokia drynarioides strain JFW-HI SEQ_111028, 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: 4546
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Found at i:863 original size:27 final size:25
Alignment explanation
Indices: 830--915 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 25
820 ATATTAATAA
830 ATTAAAAATCAGAAATTTATAAAAATT
1 ATTAAAAATCA-AAA-TTATAAAAATT
*
857 ATTAAAATATTAAAATTATAGAAAATT
1 ATTAAAA-ATCAAAATTATA-AAAATT
884 A--AAATAAGTCAAAAATTATAAAAATTT
1 ATTAAA-AA-TC-AAAATTATAAAAA-TT
911 ATTAA
1 ATTAA
916 GAATTTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
25 4 0.08
26 11 0.22
27 29 0.59
28 3 0.06
29 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (25 bp):
ATTAAAAATCAAAATTATAAAAATT
Found at i:886 original size:16 final size:17
Alignment explanation
Indices: 851--888 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
841 GAAATTTATA
851 AAAATTATTAAAATATT
1 AAAATTATTAAAATATT
868 AAAATTA-TAGAAA-ATT
1 AAAATTATTA-AAATATT
884 AAAAT
1 AAAAT
889 AAGTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATTATTAAAATATT
Found at i:936 original size:9 final size:9
Alignment explanation
Indices: 846--936 Score: 64
Period size: 9 Copynumber: 10.0 Consensus size: 9
836 AATCAGAAAT
846 TTATAAAAA
1 TTATAAAAA
*
855 TTATTAAAA
1 TTATAAAAA
*
864 -TATTAAAA
1 TTATAAAAA
872 TTATAGAAAA
1 TTATA-AAAA
882 TTA-AAATAA
1 TTATAAA-AA
* *
891 GT-CAAAAA
1 TTATAAAAA
899 TTATAAAAA
1 TTATAAAAA
*
908 TTTATTAAGAA
1 -TTA-TAAAAA
919 TT-TATAAAA
1 TTATA-AAAA
928 TTATAAAAA
1 TTATAAAAA
937 AACCATTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
8 15 0.23
9 32 0.48
10 14 0.21
11 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1285 original size:26 final size:27
Alignment explanation
Indices: 1256--1327 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
1246 AACTATATTT
*
1256 TTTATATTTTATCAAATTTT-AATAAC
1 TTTATATTTTATAAAATTTTAAATAAC
*
1282 TTTATAGTTTTCTAATAAGTTTTAAATAAC
1 TTTATA-TTTTATAA-AA-TTTTAAATAAC
1312 TTT-T-TTTTATAAAATT
1 TTTATATTTTATAAAATT
1328 CTATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.05
26 8 0.21
27 13 0.33
28 2 0.05
29 5 0.13
30 9 0.23
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTATATTTTATAAAATTTTAAATAAC
Found at i:1606 original size:22 final size:22
Alignment explanation
Indices: 1573--1638 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
1563 TTTATAAATA
* *
1573 TTTAATCG-ATTTTTTTATTTT
1 TTTAATAGTATTTTTTTATCTT
1594 TTTAATAGTATTTTTTTTTTATCTT
1 TTTAATAGTA---TTTTTTTATCTT
*
1619 TTTAGTAGTATTTTTTTATC
1 TTTAATAGTATTTTTTTATC
1639 ATTAAAGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.18
22 11 0.29
25 20 0.53
ACGTcount: A:0.20, C:0.05, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTAATAGTATTTTTTTATCTT
Found at i:1607 original size:14 final size:13
Alignment explanation
Indices: 1588--1637 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1578 TCGATTTTTT
1588 TATTTTTTTAATAG
1 TATTTTTTT-ATAG
*
1602 TATTTTTTT-T-T
1 TATTTTTTTATAG
*
1613 TATCTTTTTAGTAG
1 TATTTTTTTA-TAG
1627 TATTTTTTTAT
1 TATTTTTTTAT
1638 CATTAAAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 2 0.07
14 18 0.62
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (13 bp):
TATTTTTTTATAG
Found at i:1610 original size:25 final size:25
Alignment explanation
Indices: 1582--1635 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1572 ATTTAATCGA
*
1582 TTTTTTTATTTTTTTAATAGTATTT
1 TTTTTTTATCTTTTTAATAGTATTT
*
1607 TTTTTTTATCTTTTTAGTAGTATTT
1 TTTTTTTATCTTTTTAATAGTATTT
1632 TTTT
1 TTTT
1636 ATCATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.76
Consensus pattern (25 bp):
TTTTTTTATCTTTTTAATAGTATTT
Done.