Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013612.1 Kokia drynarioides strain JFW-HI SEQ_128640, 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: 24918
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:303 original size:21 final size:21
Alignment explanation
Indices: 274--313 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
264 AAAATTAATT
274 AAAACAAAAAATAA-AATATAC
1 AAAAC-AAAAATAATAATATAC
*
295 AAAATAAAAATAATAATAT
1 AAAACAAAAATAATAATAT
314 TTATAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAACAAAAATAATAATATAC
Found at i:641 original size:14 final size:13
Alignment explanation
Indices: 626--651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
616 ACAAATAAGA
626 AAAATTAATAAAG
1 AAAATTAATAAAG
639 AAAATTAATAAAG
1 AAAATTAATAAAG
652 GTTGTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATTAATAAAG
Found at i:8738 original size:42 final size:42
Alignment explanation
Indices: 8685--8788 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
8675 GGCACAGGTG
* * * *
8685 TTAACCTTTCATCCTTTTTACTTGGTGTATTTACT-GGTGTTT
1 TTAACCTTTCATCCCTTTTACTTGGGGTA-TCAATAGGTGTTT
**
8727 TTAACCTTTCATCCCTTACACTTGGGGTATCAATAGGTGTTT
1 TTAACCTTTCATCCCTTTTACTTGGGGTATCAATAGGTGTTT
*
8769 TTAACCCTTCATCCCTTTTA
1 TTAACCTTTCATCCCTTTTA
8789 GAAGGCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 3 0.06
42 49 0.94
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.47
Consensus pattern (42 bp):
TTAACCTTTCATCCCTTTTACTTGGGGTATCAATAGGTGTTT
Found at i:15005 original size:15 final size:15
Alignment explanation
Indices: 14985--15014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14975 TTTAATTAAT
*
14985 TATTATTTTGTATAA
1 TATTATTTTGCATAA
15000 TATTATTTTGCATAA
1 TATTATTTTGCATAA
15015 AATAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
TATTATTTTGCATAA
Found at i:15906 original size:5 final size:5
Alignment explanation
Indices: 15890--15923 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
15880 AGTTTTTTGG
*
15890 CCCGA GCCCGA CCCGA CTCGA CCCGA CCCGA CCC
1 CCCGA -CCCGA CCCGA CCCGA CCCGA CCCGA CCC
15924 AAATAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.59, G:0.21, T:0.03
Consensus pattern (5 bp):
CCCGA
Found at i:16027 original size:22 final size:20
Alignment explanation
Indices: 16002--16054 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
15992 TGATGTTGTG
16002 TTTTTATTGTTTTGGTGCTATT
1 TTTTTATTGTTTTGGTGC--TT
* *
16024 TTTTTACTATTTTGGTGCTT
1 TTTTTATTGTTTTGGTGCTT
16044 TTTTTATTGTT
1 TTTTTATTGTT
16055 ATTTCTGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (20 bp):
TTTTTATTGTTTTGGTGCTT
Found at i:16071 original size:24 final size:22
Alignment explanation
Indices: 16002--16095 Score: 89
Period size: 24 Copynumber: 4.1 Consensus size: 22
15992 TGATGTTGTG
* *
16002 TTTTTATTGTTTTGGTGCTATT
1 TTTTTATTATTTTGCTGCTATT
* * *
16024 TTTTTACTATTTTGGTGCTTTT
1 TTTTTATTATTTTGCTGCTATT
*
16046 TTTATTGTTATTTCTGCTGCTATT
1 TTT-TTATTATTT-TGCTGCTATT
*
16070 TTTCCTATTATTTTTGCTGCTATT
1 TTT-TTATTA-TTTTGCTGCTATT
16094 TT
1 TT
16096 GGTTGTTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
22 22 0.37
23 7 0.12
24 27 0.46
25 3 0.05
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.66
Consensus pattern (22 bp):
TTTTTATTATTTTGCTGCTATT
Found at i:16085 original size:48 final size:46
Alignment explanation
Indices: 16017--16106 Score: 108
Period size: 48 Copynumber: 1.9 Consensus size: 46
16007 ATTGTTTTGG
* * * *
16017 TGCTATTTTTTTACTATTTTGGTGCTTTTTTTATTGTTATTTCTGC
1 TGCTATTTTTCTACTATTTTGCTGCTATTTTGATTGTTATTTCTGC
* *
16063 TGCTATTTTTCCTATTATTTTTGCTGCTATTTTGGTTGTTATTT
1 TGCTATTTTT-CTACTA-TTTTGCTGCTATTTTGATTGTTATTT
16107 TGGTTGTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 10 0.28
47 4 0.11
48 22 0.61
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.64
Consensus pattern (46 bp):
TGCTATTTTTCTACTATTTTGCTGCTATTTTGATTGTTATTTCTGC
Found at i:16104 original size:24 final size:24
Alignment explanation
Indices: 16050--16107 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
16040 GCTTTTTTTA
* *
16050 TTGTTATTTCTGCTGCTATTTTTC
1 TTGTTATTTTTGCTGCTATTTTGC
* * *
16074 CTATTATTTTTGCTGCTATTTTGG
1 TTGTTATTTTTGCTGCTATTTTGC
16098 TTGTTATTTT
1 TTGTTATTTT
16108 GGTTGTTTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (24 bp):
TTGTTATTTTTGCTGCTATTTTGC
Found at i:16105 original size:12 final size:12
Alignment explanation
Indices: 16090--16114 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16080 TTTTTGCTGC
16090 TATTTTGGTTGT
1 TATTTTGGTTGT
16102 TATTTTGGTTGT
1 TATTTTGGTTGT
16114 T
1 T
16115 TGGATGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TATTTTGGTTGT
Found at i:18451 original size:19 final size:19
Alignment explanation
Indices: 18427--18488 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
18417 ACTTTAGCCG
18427 TTTATTTATTTATTTTTAT
1 TTTATTTATTTATTTTTAT
18446 TTTA-TTATTTTCATTTTTAGT
1 TTTATTTA-TTT-ATTTTTA-T
* *
18467 TTAATTT-TTCTATTTTAAT
1 TTTATTTATT-TATTTTTAT
18486 TTT
1 TTT
18489 TTCCCTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 15 0.43
21 5 0.14
22 2 0.06
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTATTTATTTTTAT
Found at i:18463 original size:20 final size:20
Alignment explanation
Indices: 18437--18488 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
18427 TTTATTTATT
*
18437 TATTTTTATTTTATTATTTTC
1 TATTTTTATTTTAAT-TTTTC
*
18458 -ATTTTTAGTTTAATTTTTC
1 TATTTTTATTTTAATTTTTC
*
18477 TATTTTAATTTT
1 TATTTTTATTTT
18489 TTCCCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTTATTTTAATTTTTC
Found at i:18485 original size:14 final size:13
Alignment explanation
Indices: 18430--18490 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
18420 TTAGCCGTTT
*
18430 ATTTATTTATTTTT
1 ATTT-TTTATTTTA
*
18444 ATTTTATTATTTTC
1 ATTTT-TTATTTTA
*
18458 A-TTTTTAGTTTA
1 ATTTTTTATTTTA
18470 ATTTTTCTATTTTA
1 ATTTTT-TATTTTA
18484 ATTTTTT
1 ATTTTTT
18491 CCCTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.17
13 9 0.22
14 24 0.60
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (13 bp):
ATTTTTTATTTTA
Found at i:23988 original size:10 final size:10
Alignment explanation
Indices: 23973--24031 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
23963 TGTTTTTTTA
23973 AAAAAAATTG
1 AAAAAAATTG
23983 AAAAAAAATT-
1 -AAAAAAATTG
*
23993 ACAAAAATTTG
1 A-AAAAAATTG
24004 AAAAAAAATTTG
1 -AAAAAAA-TTG
*
24016 -AAAAAATTC
1 AAAAAAATTG
24025 AAAAAAA
1 AAAAAAA
24032 ATTTAGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
9 3 0.08
10 19 0.47
11 14 0.35
12 4 0.10
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.20
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:23989 original size:12 final size:11
Alignment explanation
Indices: 23972--24034 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
23962 ATGTTTTTTT
23972 AAAAAAAATTG
1 AAAAAAAATTG
23983 AAAAAAAATT-
1 AAAAAAAATTG
* *
23993 ACAAAAATTTG
1 AAAAAAAATTG
24004 AAAAAAAATTTG
1 AAAAAAAA-TTG
*
24016 --AAAAAATTC
1 AAAAAAAATTG
24025 AAAAAAAATT
1 AAAAAAAATT
24035 TAGTATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.05
10 14 0.33
11 24 0.56
12 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:24035 original size:21 final size:21
Alignment explanation
Indices: 23974--24035 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
23964 GTTTTTTTAA
*
23974 AAAAAATTGAAAAAAAATTAC
1 AAAAAATTGAAAAAAAATTTC
* *
23995 AAAAATTTGAAAAAAAATTTG
1 AAAAAATTGAAAAAAAATTTC
*
24016 AAAAAATTCAAAAAAAATTT
1 AAAAAATTGAAAAAAAATTT
24036 AGTATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAAATTGAAAAAAAATTTC
Done.