Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010794.1 Kokia drynarioides strain JFW-HI SEQ_125761, 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: 53199
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:532 original size:6 final size:6
Alignment explanation
Indices: 468--535 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
458 TAATAGGGAT
* * * * **
468 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTCCAA TTTCAC TTTCTC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
515 TTTCAC TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
536 TGATCATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 42 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:866 original size:17 final size:18
Alignment explanation
Indices: 832--867 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
822 TAAATTACTA
832 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
850 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
867 T
1 T
868 AACTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:8321 original size:18 final size:18
Alignment explanation
Indices: 8298--8334 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8288 ACAATTCATA
8298 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
8316 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
8334 T
1 T
8335 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:12779 original size:59 final size:57
Alignment explanation
Indices: 12698--12810 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 57
12688 ATATTAATGT
*
12698 GATTATTTTAATATTAAATTAATATTTATGTTGTAGATAAATATTCTATTAATTTAATAA
1 GATTATTTTAATATTAAATTAATATTTAT-TT-T-GATAAATATTATATTAATTTAATAA
* * *
12758 GATT-TTTTAATTTTAATTTAATATTTATTTTGATAAGTATTATATTAATTTAA
1 GATTATTTTAATATTAAATTAATATTTATTTTGATAAATATTATATTAATTTAA
12811 AATTAAAGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 20 0.41
57 1 0.02
58 2 0.04
59 22 0.45
60 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (57 bp):
GATTATTTTAATATTAAATTAATATTTATTTTGATAAATATTATATTAATTTAATAA
Found at i:13174 original size:53 final size:53
Alignment explanation
Indices: 13094--13199 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
13084 AAATGGTGAT
13094 AGTTGGAATAATGTCACATATGTGGTAGGAGTCCAGAGGATAGGTATTTCATA
1 AGTTGGAATAATGTCACATATGTGGTAGGAGTCCAGAGGATAGGTATTTCATA
13147 AGTTGGAATAATGTCACATATGTGGTAGGAGTCCAGAGGATAGGTATTTCATA
1 AGTTGGAATAATGTCACATATGTGGTAGGAGTCCAGAGGATAGGTATTTCATA
13200 TTTTTTTGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.30
Consensus pattern (53 bp):
AGTTGGAATAATGTCACATATGTGGTAGGAGTCCAGAGGATAGGTATTTCATA
Found at i:13353 original size:32 final size:33
Alignment explanation
Indices: 13310--13376 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 33
13300 AGGGACCCAA
*
13310 GTGGGTGGTGGGACGGTGATGGTTTT-AGTCTT
1 GTGGGTGGTGGGACGGGGATGGTTTTGAGTCTT
* ** *
13342 GTGGGTTGTGGGGTGGGGATGGTTTTGAGTTTT
1 GTGGGTGGTGGGACGGGGATGGTTTTGAGTCTT
13375 GT
1 GT
13377 ACCTACAGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.07, C:0.03, G:0.49, T:0.40
Consensus pattern (33 bp):
GTGGGTGGTGGGACGGGGATGGTTTTGAGTCTT
Found at i:28470 original size:21 final size:20
Alignment explanation
Indices: 28426--28469 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
28416 AAAAAAACTC
*
28426 AAAATTCCTTTAAAATGTCA
1 AAAATTCATTTAAAATGTCA
28446 AAAAGTTCATTTAAAATG-CA
1 AAAA-TTCATTTAAAATGTCA
28466 AAAA
1 AAAA
28470 AAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAATTCATTTAAAATGTCA
Found at i:28482 original size:15 final size:15
Alignment explanation
Indices: 28464--28492 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28454 ATTTAAAATG
28464 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
28479 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
28493 TCTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:28483 original size:13 final size:13
Alignment explanation
Indices: 28467--28491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28457 TAAAATGCAA
28467 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
28480 AAAAAAAAAAAA
1 AAAAAAAAAAAA
28492 ATCTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:28483 original size:14 final size:14
Alignment explanation
Indices: 28466--28492 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28456 TTAAAATGCA
28466 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
28480 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
28493 TCTTTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:28988 original size:2 final size:2
Alignment explanation
Indices: 28981--29013 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28971 GAAACTCATG
28981 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
29014 AACTTGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38311 original size:16 final size:16
Alignment explanation
Indices: 38290--38321 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38280 CGAATATATT
*
38290 GTGACAATGTGACAAC
1 GTGACAATATGACAAC
38306 GTGACAATATGACAAC
1 GTGACAATATGACAAC
38322 AGTGTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (16 bp):
GTGACAATATGACAAC
Found at i:40448 original size:21 final size:21
Alignment explanation
Indices: 40423--40462 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40413 AAAAACAAAG
40423 TTAAAAGGCAAAACCATTAAA
1 TTAAAAGGCAAAACCATTAAA
*
40444 TTAAAAGGTAAAACCATTA
1 TTAAAAGGCAAAACCATTA
40463 CATTGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (21 bp):
TTAAAAGGCAAAACCATTAAA
Done.