Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009775.1 Kokia drynarioides strain JFW-HI SEQ_124496, 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: 47368
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:2645 original size:15 final size:16
Alignment explanation
Indices: 2603--2645 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2593 CAGAATTAAA
2603 TTAATAATTTTATCATT
1 TTAAT-ATTTTATCATT
*
2620 TTAATAGTTTAT-ATT
1 TTAATATTTTATCATT
*
2635 TTATTATTTTA
1 TTAATATTTTA
2646 AAGGGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 6 0.26
17 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAATATTTTATCATT
Found at i:3768 original size:20 final size:21
Alignment explanation
Indices: 3745--3791 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
3735 TCTGACACTC
* *
3745 TTCTTTT-AATGTCTTGTTTT
1 TTCTTTTAAATGCCTTGATTT
3765 TTCTTTTACAATGCCTTGATTT
1 TTCTTTTA-AATGCCTTGATTT
3787 TTCTT
1 TTCTT
3792 CTGGCACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.64
Consensus pattern (21 bp):
TTCTTTTAAATGCCTTGATTT
Found at i:5982 original size:15 final size:15
Alignment explanation
Indices: 5964--5995 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5954 ATCCTAAAAA
*
5964 TTCTATTTCTATTTT
1 TTCTAGTTCTATTTT
5979 TTCTAGTTCTATTTT
1 TTCTAGTTCTATTTT
5994 TT
1 TT
5996 AGGGTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (15 bp):
TTCTAGTTCTATTTT
Found at i:8089 original size:30 final size:30
Alignment explanation
Indices: 8041--8101 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
8031 GTGTCCATAT
* *
8041 TTTAAAATTTGATATTTTATATATTTTTTC
1 TTTAAAATATGATATTTTATATATTTATTC
*
8071 TTTAGAAATATGAT-TTTTATTTATTTATTC
1 TTTA-AAATATGATATTTTATATATTTATTC
8101 T
1 T
8102 ATCATTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTAAAATATGATATTTTATATATTTATTC
Found at i:12233 original size:12 final size:12
Alignment explanation
Indices: 12212--12303 Score: 51
Period size: 12 Copynumber: 7.3 Consensus size: 12
12202 ATAACATCCA
12212 AACAACAAAAAT
1 AACAACAAAAAT
* *
12224 AACAATAAAAAC
1 AACAACAAAAAT
* *
12236 AGCAA-ATAATATT
1 AACAACA-AA-AAT
*
12249 AAAAACAACAAAAAT
1 AACAAC-A-AA-AAT
* *
12264 AGCAACAAAAAC
1 AACAACAAAAAT
12276 AACAACAAAAAT
1 AACAACAAAAAT
* *
12288 AACAGCAAAAAC
1 AACAACAAAAAT
12300 AACA
1 AACA
12304 CGAAAACAGC
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
11 1 0.02
12 42 0.71
13 6 0.10
14 1 0.02
15 9 0.15
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:12235 original size:21 final size:21
Alignment explanation
Indices: 12198--12303 Score: 85
Period size: 21 Copynumber: 5.0 Consensus size: 21
12188 AAATGCATAA
**
12198 AAAAATAAC-ATCCAAACAAC
1 AAAAATAACAATAAAAACAAC
*
12218 AAAAATAACAATAAAAACAGC
1 AAAAATAACAATAAAAACAAC
* *
12239 --AAATAATATTAAAAACAAC
1 AAAAATAACAATAAAAACAAC
12258 AAAAATAGCAACAA-AAACAACAAC
1 AAAAAT---AACAATAAA-AACAAC
**
12282 AAAAATAACAGCAAAAACAAC
1 AAAAATAACAATAAAAACAAC
12303 A
1 A
12304 CGAAAACAGC
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
19 16 0.23
20 9 0.13
21 23 0.33
22 3 0.04
23 3 0.04
24 15 0.22
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.09
Consensus pattern (21 bp):
AAAAATAACAATAAAAACAAC
Found at i:12244 original size:19 final size:19
Alignment explanation
Indices: 12215--12280 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
12205 ACATCCAAAC
12215 AACAA-AAATAACAATAAA
1 AACAACAAATAACAATAAA
* * *
12233 AACAGCAAATAATATTAAA
1 AACAACAAATAACAATAAA
* *
12252 AACAACAAAAATAGCAACAAA
1 AACAAC--AAATAACAATAAA
12273 AACAACAA
1 AACAACAA
12281 CAAAAATAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
21 15 0.41
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.11
Consensus pattern (19 bp):
AACAACAAATAACAATAAA
Found at i:12284 original size:24 final size:24
Alignment explanation
Indices: 12252--12321 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
12242 TAATATTAAA
12252 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
12276 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
12300 AAC-ACGAAAACAGCAATCAAAA
1 AACAACAAAAATAGCAA-CAAAA
12322 CAGTAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.23
24 30 0.77
ACGTcount: A:0.69, C:0.21, G:0.06, T:0.04
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:12376 original size:9 final size:9
Alignment explanation
Indices: 12339--12377 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12329 AAAACACACC
12339 AAAACAATA
1 AAAACAATA
12348 AAAA-AATA
1 AAAACAATA
*
12356 AAAACAACA
1 AAAACAATA
*
12365 AAAACAGTA
1 AAAACAATA
12374 AAAA
1 AAAA
12378 AACAGCACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.79, C:0.10, G:0.03, T:0.08
Consensus pattern (9 bp):
AAAACAATA
Found at i:12377 original size:27 final size:27
Alignment explanation
Indices: 12328--12379 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
12318 AAAACAGTAA
*
12328 AAAAACACACCAAAACAATAAAAAAAT
1 AAAAACACACAAAAACAATAAAAAAAT
*
12355 AAAAACA-ACAAAAACAGTAAAAAAA
1 AAAAACACACAAAAACAATAAAAAAA
12380 CAGCACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.77, C:0.15, G:0.02, T:0.06
Consensus pattern (27 bp):
AAAAACACACAAAAACAATAAAAAAAT
Found at i:12902 original size:29 final size:30
Alignment explanation
Indices: 12870--12951 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
12860 AATTTATTTT
*
12870 AAATTAAAATTGAATAATAAAGTTC-A-ATA
1 AAATTAAAATT-AATAATAAAATTCTATATA
* *
12899 AAATAAAAATAAATCAATAAAATTCTATATA
1 AAATTAAAATTAAT-AATAAAATTCTATATA
12930 AAATTTAAAATATAATAATAAA
1 AAA-TTAAAAT-TAATAATAAA
12952 TTTATCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.07
29 18 0.42
30 1 0.02
31 6 0.14
32 12 0.28
33 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATTAAAATTAATAATAAAATTCTATATA
Found at i:24410 original size:2 final size:2
Alignment explanation
Indices: 24403--24439 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24393 GTTTTTAAAG
24403 CT CT 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 CT CT C
24440 ATACATACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:26015 original size:24 final size:23
Alignment explanation
Indices: 25968--26017 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
25958 TAAAGTAGGT
*
25968 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATTA
25991 TATATTATGATTTTTACTAAT-TTA
1 TATA-TATGATTTTT-CTAATATTA
26015 TAT
1 TAT
26018 TTTAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATTA
Found at i:26096 original size:58 final size:57
Alignment explanation
Indices: 26002--26145 Score: 182
Period size: 58 Copynumber: 2.5 Consensus size: 57
25992 ATATTATGAT
* * * *
26002 TTTTACTAATTTATATTTTAATAATAATTATATTAAAAATGTTAA-TAAATTATATATTA
1 TTTTATTAAATTATA-TTTAATAATAATTAGATT-AAAAT-ATAATTAAATTATATATTA
* * *
26061 TTTTATTAAATTATATTTAATAATTATTAGGTTAAAATATAATTAAATTATTTATTA
1 TTTTATTAAATTATATTTAATAATAATTAGATTAAAATATAATTAAATTATATATTA
26118 TTTTCATTAAATTATATTTAATAATAAT
1 TTTT-ATTAAATTATATTTAATAATAAT
26146 CTTAATAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
56 3 0.04
57 22 0.29
58 37 0.49
59 13 0.17
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (57 bp):
TTTTATTAAATTATATTTAATAATAATTAGATTAAAATATAATTAAATTATATATTA
Found at i:29862 original size:21 final size:21
Alignment explanation
Indices: 29817--29863 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29807 GATTCCAGGT
*
29817 GGAGGTGGAGAACGGGGAAGT
1 GGAGGTGGAGAACGGGGAAGG
* * *
29838 GGAGGTGGAGCAGGGGGAGGG
1 GGAGGTGGAGAACGGGGAAGG
29859 GGAGG
1 GGAGG
29864 GGAAGGGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.04, G:0.66, T:0.06
Consensus pattern (21 bp):
GGAGGTGGAGAACGGGGAAGG
Found at i:37923 original size:26 final size:26
Alignment explanation
Indices: 37875--37925 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
37865 GCTGATCCAG
*
37875 TTCAAATTTAATTTAAATAATAAAAT
1 TTCAAATTTAACTTAAATAATAAAAT
*
37901 TTCAAATTTAAACTT-AATTATAAAA
1 TTCAAATTT-AACTTAAATAATAAAA
37926 ATATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (26 bp):
TTCAAATTTAACTTAAATAATAAAAT
Found at i:41632 original size:15 final size:17
Alignment explanation
Indices: 41608--41643 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
41598 TCTTTAATTT
41608 TTTTTAAAAAATAT-AA
1 TTTTTAAAAAATATAAA
41624 TTTTT-AAAAATATAAA
1 TTTTTAAAAAATATAAA
41640 TTTT
1 TTTT
41644 GAAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTAAAAAATATAAA
Found at i:41671 original size:18 final size:19
Alignment explanation
Indices: 41634--41670 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41624 TTTTTAAAAA
*
41634 TATAAAT-TTTGAAATTTT
1 TATAAATATTTCAAATTTT
41652 TATAAATATTTCAAATTTT
1 TATAAATATTTCAAATTTT
41671 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAAATATTTCAAATTTT
Found at i:44026 original size:2 final size:2
Alignment explanation
Indices: 43971--44007 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43961 AGTATATGTA
43971 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
44008 ATACACGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.