Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012686.1 Kokia drynarioides strain JFW-HI SEQ_127697, 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: 29900
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4097 original size:21 final size:20
Alignment explanation
Indices: 4073--4136 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
4063 GACTTAAAAA
4073 TTAATTTTCAAAAATATAATT
1 TTAATTTTCAAAAAT-TAATT
*
4094 TTAATTTT-AATTAATTTAATT
1 TTAATTTTCAA--AAATTAATT
*
4115 TTACTTTATC-AAAATTAATT
1 TTAATTT-TCAAAAATTAATT
4135 TT
1 TT
4137 CGCAAAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 12 0.33
21 19 0.53
22 5 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTTTCAAAAATTAATT
Found at i:12993 original size:5 final size:5
Alignment explanation
Indices: 12983--13009 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12973 AAGAAGTGAT
12983 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
13010 AATCAACCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:16157 original size:21 final size:21
Alignment explanation
Indices: 16112--16155 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16102 GTGAAACATG
16112 TTTT-TTTTTTATTTTTTTCA
1 TTTTCTTTTTTATTTTTTTCA
*
16132 ATTTCTTTTTTATTTTTTT-A
1 TTTTCTTTTTTATTTTTTTCA
16152 TTTT
1 TTTT
16156 TCATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTTTTTTATTTTTTTCA
Found at i:21961 original size:23 final size:23
Alignment explanation
Indices: 21933--21996 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
21923 ATGATCTTAA
*
21933 GATTTTGA-GTTTTAGGGTTTAT
1 GATTTTTAGGTTTTAGGGTTTAT
*
21955 GATTTTTATGG-TTTATGGTTTAT
1 GATTTTTA-GGTTTTAGGGTTTAT
21978 GATTTTTAAGGTTTTAGGG
1 GATTTTT-AGGTTTTAGGG
21997 ATAAGGCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 7 0.20
23 20 0.57
24 8 0.23
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.55
Consensus pattern (23 bp):
GATTTTTAGGTTTTAGGGTTTAT
Found at i:21991 original size:16 final size:16
Alignment explanation
Indices: 21911--21971 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
21901 TTTCGTGGAT
21911 TTTTTAGGGTTTATGA
1 TTTTTAGGGTTTATGA
* * *
21927 -TCTTAAGATTT-TGA
1 TTTTTAGGGTTTATGA
*
21941 GTTTTAGGGTTTATGA
1 TTTTTAGGGTTTATGA
*
21957 TTTTTATGGTTTATG
1 TTTTTAGGGTTTATG
21972 GTTTATGATT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.09
15 16 0.46
16 16 0.46
ACGTcount: A:0.20, C:0.02, G:0.23, T:0.56
Consensus pattern (16 bp):
TTTTTAGGGTTTATGA
Found at i:22120 original size:7 final size:7
Alignment explanation
Indices: 22086--22165 Score: 61
Period size: 7 Copynumber: 10.7 Consensus size: 7
22076 TTTTATAGTA
22086 TTTAGGTT
1 TTTAGG-T
22094 TTTAAGGT
1 TTT-AGGT
22102 TTTAAGGGT
1 TTT-A-GGT
22111 TTTAGGT
1 TTTAGGT
*
22118 TTTAAGAT
1 TTT-AGGT
*
22126 TTAAGGT
1 TTTAGGT
*
22133 TTAAGGT
1 TTTAGGT
*
22140 TTAAGGT
1 TTTAGGT
*
22147 TTAAGGT
1 TTTAGGT
*
22154 TTAAGGT
1 TTTAGGT
22161 TTTAG
1 TTTAG
22166 TGATATATGG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
7 41 0.63
8 15 0.23
9 9 0.14
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (7 bp):
TTTAGGT
Found at i:22135 original size:14 final size:14
Alignment explanation
Indices: 22094--22162 Score: 93
Period size: 14 Copynumber: 4.7 Consensus size: 14
22084 TATTTAGGTT
22094 TTTAAGGTTTTAAGGG
1 TTTAAGG-TTTAA-GG
* *
22110 TTTTAGGTTTTAAGA
1 TTTAAGG-TTTAAGG
22125 TTTAAGGTTTAAGG
1 TTTAAGGTTTAAGG
22139 TTTAAGGTTTAAGG
1 TTTAAGGTTTAAGG
22153 TTTAAGGTTT
1 TTTAAGGTTT
22163 TAGTGATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 30 0.61
15 7 0.14
16 12 0.24
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (14 bp):
TTTAAGGTTTAAGG
Found at i:22142 original size:21 final size:21
Alignment explanation
Indices: 22102--22162 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
22092 TTTTTAAGGT
*
22102 TTTAAGGGTTTTAGGTTTTAAGA
1 TTTAA-GGTTTAAGG-TTTAAGA
*
22125 TTTAAGGTTTAAGGTTTAAGG
1 TTTAAGGTTTAAGGTTTAAGA
22146 TTTAAGGTTTAAGGTTT
1 TTTAAGGTTTAAGGTTT
22163 TAGTGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 23 0.64
22 8 0.22
23 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTAAGGTTTAAGA
Found at i:22273 original size:14 final size:14
Alignment explanation
Indices: 22244--22299 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
22234 CTTAAGTTGA
*
22244 CCTAAACCATAAAC
1 CCTAAACCTTAAAC
*
22258 CCTAAACCTTACAC
1 CCTAAACCTTAAAC
*
22272 CCGAAA-CTTAAAAC
1 CCTAAACCTT-AAAC
*
22286 CTTAAACCTTAAAC
1 CCTAAACCTTAAAC
22300 ATAAACATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 3 0.09
14 28 0.82
15 3 0.09
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:22299 original size:21 final size:21
Alignment explanation
Indices: 22261--22304 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
22251 CATAAACCCT
* *
22261 AAACCTTACACCCGAAACTTA
1 AAACCTTAAACCCGAAACATA
**
22282 AAACCTTAAACCTTAAACATA
1 AAACCTTAAACCCGAAACATA
22303 AA
1 AA
22305 CATAATTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACCTTAAACCCGAAACATA
Found at i:22747 original size:27 final size:27
Alignment explanation
Indices: 22716--22773 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
22706 TTTTGGCTTA
* * *
22716 ACCAACTCATATTATAT-TCATGGTCTG
1 ACCAACCCATATGATATCT-ATCGTCTG
22743 ACCAACCCATATGATATCTATCGTCTG
1 ACCAACCCATATGATATCTATCGTCTG
22770 ACCA
1 ACCA
22774 CCCCGAAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (27 bp):
ACCAACCCATATGATATCTATCGTCTG
Found at i:23658 original size:13 final size:13
Alignment explanation
Indices: 23640--23669 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
23630 CTAATATTAG
23640 CCGAGAAAGGCAT
1 CCGAGAAAGGCAT
23653 CCGAGAAAGGCAT
1 CCGAGAAAGGCAT
23666 CCGA
1 CCGA
23670 TACAGGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.30, T:0.07
Consensus pattern (13 bp):
CCGAGAAAGGCAT
Found at i:24122 original size:20 final size:21
Alignment explanation
Indices: 24089--24127 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24079 TTACAAAATT
*
24089 AAAAATAATTAATTTTATTGA
1 AAAAATAATCAATTTTATTGA
24110 AAAAATAA-CAATTTTATT
1 AAAAATAATCAATTTTATT
24128 TATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAAATAATCAATTTTATTGA
Found at i:24435 original size:18 final size:18
Alignment explanation
Indices: 24399--24437 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24389 AAAGTAAATC
*
24399 AAAAACAAAAAAATTTAT
1 AAAAACAAAAAAATATAT
24417 AAAAACATAAAAAA-ATAT
1 AAAAACA-AAAAAATATAT
24435 AAA
1 AAA
24438 CACTACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAACAAAAAAATATAT
Found at i:24583 original size:26 final size:28
Alignment explanation
Indices: 24524--24584 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
24514 ATCCACTATA
*
24524 AACAAACACACTTAACTAATATTATTTT
1 AACAAACACACTTAACTAATATTATATT
*
24552 AAACAACCACACTTAACTAATATT-TATT
1 -AACAAACACACTTAACTAATATTATATT
24580 -ACAAA
1 AACAAA
24585 GTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
28 3 0.10
29 22 0.76
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
AACAAACACACTTAACTAATATTATATT
Found at i:25355 original size:4 final size:4
Alignment explanation
Indices: 25346--25411 Score: 82
Period size: 4 Copynumber: 16.2 Consensus size: 4
25336 AAATAAACGG
*
25346 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA G-AA GAAGA GGAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA
25396 G-AA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
25412 GTAATATGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
3 6 0.11
4 41 0.73
5 6 0.11
6 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:25370 original size:21 final size:20
Alignment explanation
Indices: 25346--25411 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
25336 AAATAAACGG
25346 GAAAGAAAGAAAGAAAAGAAA
1 GAAAGAAAG-AAGAAAAGAAA
*
25367 GAAAGAAAGGAAGAAGAAG-AG
1 GAAAGAAA-GAAGAA-AAGAAA
25388 GAAAGAAAGAAG-AAAGAAA
1 GAAAGAAAGAAGAAAAGAAA
25407 GAAAG
1 GAAAG
25412 GTAATATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.08
19 7 0.17
20 4 0.10
21 22 0.55
22 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAGAAAAGAAA
Found at i:28691 original size:14 final size:14
Alignment explanation
Indices: 28674--28720 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
28664 CAAGTCTAGT
*
28674 GTTTATGATTTAGG
1 GTTTATAATTTAGG
*
28688 GTTT-TAAGTCTAGG
1 GTTTATAA-TTTAGG
28702 GTTTATAATTTAGG
1 GTTTATAATTTAGG
*
28716 TTTTA
1 GTTTA
28721 GGGTTTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 22 0.81
15 3 0.11
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.51
Consensus pattern (14 bp):
GTTTATAATTTAGG
Found at i:28707 original size:28 final size:28
Alignment explanation
Indices: 28640--28720 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
28630 CTTTAATCAA
* * * *
28640 TCTAGTGTTTACGGTTTAGAGTTTCAAG
1 TCTAGTGTTTATGATTTAGGGTTTTAAG
28668 TCTAGTGTTTATGATTTAGGGTTTTAAG
1 TCTAGTGTTTATGATTTAGGGTTTTAAG
* *
28696 TCTAGGGTTTATAATTTA-GGTTTTA
1 TCTAGTGTTTATGATTTAGGGTTTTA
28721 GGGTTTAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 7 0.15
28 40 0.85
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TCTAGTGTTTATGATTTAGGGTTTTAAG
Found at i:29063 original size:45 final size:45
Alignment explanation
Indices: 28985--29121 Score: 168
Period size: 45 Copynumber: 3.0 Consensus size: 45
28975 GAGAGTAATA
* * * * **
28985 GAGTATCGTGGTGGCTAGTCAAACTCAACCTGATATCCTT-CCTTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGCC-TT
* * *
29030 GAGTATTGCGGTGGCTCGTTAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGCCTT
*
29075 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGCCTT
29120 GA
1 GA
29122 TGAGCTATGC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 79 0.99
46 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGCCTT
Done.