Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001686.1 Kokia drynarioides strain JFW-HI SEQ_113361, 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: 6136
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1746 original size:97 final size:98
Alignment explanation
Indices: 1615--1797 Score: 235
Period size: 97 Copynumber: 1.9 Consensus size: 98
1605 GGATGTTTGG
* * * *
1615 TTATCTCGATTTAAAGAAAAAATCGCACCTAGTAAGTTTAGGTACAAATTTCCAGAA-TCAGAGA
1 TTATCTCGATTTAAAGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTCCAAAACTC-GAAA
*
1679 TAAAAAAACATTGCCTTGATTTAAGGATATTCAA
65 TAAAAAAACATTGCATTGATTTAAGGATATTCAA
* * ** *
1713 TTATTTCGATTTGAAG-AAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTCGAAAT
1 TTATCTCGATTTAAAGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTCCAAAACTCGAAAT
* *
1777 AAAAGAATATTGCATTGATTT
66 AAAAAAACATTGCATTGATTT
1798 TAAAGTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
97 56 0.78
98 16 0.22
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (98 bp):
TTATCTCGATTTAAAGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTCCAAAACTCGAAAT
AAAAAAACATTGCATTGATTTAAGGATATTCAA
Found at i:2162 original size:59 final size:58
Alignment explanation
Indices: 2114--2424 Score: 183
Period size: 58 Copynumber: 5.3 Consensus size: 58
2104 TAGACATCCT
* * *
2114 GGGGTAAAATGGTAATTTTGGAA-AAAAATCGGGATCAAAAATAGAATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTT--AAGAAAAATAGGGATCAAAAATAGAA-TTTTAGAAGTCTA
* * * *
2174 GGGGTAAAATGGTAATTTTAAGAAAAATAGGGGTCAAAAATGGAA-TATAGGAAGT-TC
1 GGGGTAAAATGGTAATTTTAAGAAAAATAGGGATCAAAAATAGAATTTTA-GAAGTCTA
** ** * * * *
2231 GAGGGTAAAAACGTAATTTTTTGGAAAATAGGG-TTAAAAATGGAATTTTTAGAAGT-TT
1 G-GGGTAAAATGGTAATTTTAAGAAAAATAGGGATCAAAAATAGAA-TTTTAGAAGTCTA
** * * * *
2289 GAGGGTAAAATGGTAATTTTGGGAAAAA-AAGG-TCTAAAATGGAATTTTAGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTAAGAAAAATAGGGATCAAAAATAGAATTTTA-GAAGTCTA
** * * * * *
2347 GGGGTGAAAAT-GTAATTTTTGGAAAAATCGAGG-TTAAAAATTGAATTTTGGAAAGTTTAA
1 GGGGT-AAAATGGTAATTTTAAGAAAAATAG-GGATCAAAAATAGAATTTTAG-AAGTCT-A
*
2407 GGGTTAAAAT-GTAATTTT
1 GGGGTAAAATGGTAATTTT
2425 TGGAAAGTTC
Statistics
Matches: 208, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
56 5 0.02
57 52 0.25
58 70 0.34
59 57 0.27
60 24 0.12
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTAAGAAAAATAGGGATCAAAAATAGAATTTTAGAAGTCTA
Found at i:2259 original size:58 final size:58
Alignment explanation
Indices: 2138--2487 Score: 272
Period size: 59 Copynumber: 6.0 Consensus size: 58
2128 ATTTTGGAAA
* * * * * *
2138 AAAATCGGGATCAAAAATAGAATTTTTGGAAGTTT-AGGGGT-AAAATGGTAATTTTAAGA
1 AAAATAGGGGTCAAAAATGGAATTTTAGGAAGTTTGA-GGGTAAAAAT-GTAATTTT-TGG
* * *
2197 AAAATAGGGGTCAAAAATGGAA-TATAGGAAGTTCGAGGGTAAAAACGTAATTTTTTGG
1 AAAATAGGGGTCAAAAATGGAATTTTAGGAAGTTTGAGGGTAAAAATGTAA-TTTTTGG
* *
2255 AAAATA-GGGTTAAAAATGGAATTTTTA-GAAGTTTGAGGGT-AAAATGGTAATTTTGGG
1 AAAATAGGGGTCAAAAATGGAA-TTTTAGGAAGTTTGAGGGTAAAAAT-GTAATTTTTGG
** * *
2312 AAAA-AAAGGTCTAAAATGGAATTTTAGGAAGTTT-AGGGGTGAAAATGTAATTTTTGG
1 AAAATAGGGGTCAAAAATGGAATTTTAGGAAGTTTGA-GGGTAAAAATGTAATTTTTGG
* * * * * *
2369 AAAAATCGAGGTTAAAAATTGAATTTT-GGAAAGTTTAAGGGTTAAAATGTAATTTTTGG
1 -AAAATAGGGGTCAAAAATGGAATTTTAGG-AAGTTTGAGGGTAAAAATGTAATTTTTGG
* * ** * *
2428 AAAGTTCGGGGTCAAAAATATAATTTT-GGATAAGTTTGA-GGTCAAAATATAATTTTTGG
1 AAA-ATAGGGGTCAAAAATGGAATTTTAGG--AAGTTTGAGGGTAAAAATGTAATTTTTGG
2487 A
1 A
2488 CAGTTTAAGG
Statistics
Matches: 242, Mismatches: 33, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
56 7 0.03
57 61 0.25
58 54 0.22
59 112 0.46
60 8 0.03
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (58 bp):
AAAATAGGGGTCAAAAATGGAATTTTAGGAAGTTTGAGGGTAAAAATGTAATTTTTGG
Found at i:2295 original size:116 final size:115
Alignment explanation
Indices: 2150--2424 Score: 319
Period size: 116 Copynumber: 2.4 Consensus size: 115
2140 AATCGGGATC
*
2150 AAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTAAGAAAAATAGGGGTCAAAAAT
1 AAAAATAGAATTTTTGGAAGTTTA-GGGTAAAATGGTAATTTTAAGAAAAA-A-AGGTCAAAAAT
2215 GGAA-TATAGGAAGTTCGA-GGGTAAAAACGTAATTTTTTGG-AAAATAG-GGTT
63 GGAATTATAGGAAGTT-GAGGGGTAAAAACGTAA-TTTTTGGAAAAATAGAGGTT
* * ** *
2266 AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAATGGTAATTTTGGGAAAAAAAGGTCTAAAATGG
1 AAAAATAGAATTTTTGGAAGTTT-AGGGTAAAATGGTAATTTTAAGAAAAAAAGGTCAAAAATGG
* * * * *
2331 AATTTTAGGAAGTTTAGGGGTGAAAATGTAATTTTTGGAAAAATCGAGGTT
65 AATTATAGGAAGTTGAGGGGTAAAAACGTAATTTTTGGAAAAATAGAGGTT
*
2382 AAAAATTGAA-TTTTGGAAAGTTTAAGGGTTAAAAT-GTAATTTT
1 AAAAATAGAATTTTTGG-AAGTTT-AGGG-TAAAATGGTAATTTT
2425 TGGAAAGTTC
Statistics
Matches: 138, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
114 21 0.15
115 34 0.25
116 76 0.55
117 7 0.05
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (115 bp):
AAAAATAGAATTTTTGGAAGTTTAGGGTAAAATGGTAATTTTAAGAAAAAAAGGTCAAAAATGGA
ATTATAGGAAGTTGAGGGGTAAAAACGTAATTTTTGGAAAAATAGAGGTT
Found at i:2385 original size:29 final size:31
Alignment explanation
Indices: 2353--2430 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
2343 TTTAGGGGTG
*
2353 AAAATGTAATTTTTGGAAAAATCGA-GGTTA
1 AAAATGTAATTTTTGGAAAAATCAAGGGTTA
** *
2383 AAAAT-TGAA-TTTTGGAAAGTTTAAGGGTT-
1 AAAATGT-AATTTTTGGAAAAATCAAGGGTTA
2412 AAAATGTAATTTTTGGAAA
1 AAAATGTAATTTTTGGAAA
2431 GTTCGGGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (31 bp):
AAAATGTAATTTTTGGAAAAATCAAGGGTTA
Found at i:2425 original size:59 final size:59
Alignment explanation
Indices: 2065--2487 Score: 270
Period size: 59 Copynumber: 7.2 Consensus size: 59
2055 AGGCAAATTG
** * * * *
2065 GTAATTTTTGGAAAGTTCGAGGTTAAAAAATTGAAATTTTAGACA-TCCTG-GGG-TAAAAT
1 GTAATTTTTGGAAAAATCGAGGTT-AAAAA-TGGAATTTTGGAAAGT-TTGAGGGTTAAAAT
* * *
2124 GGTAA-TTTTGGAAAAAAATCG-GGATCAAAAATAGAATTTTTGG-AAGTTT-AGGGGTAAAAT
1 -GTAATTTTTGG--AAAAATCGAGG-TTAAAAATGGAA-TTTTGGAAAGTTTGAGGGTTAAAAT
** * * * * * * * *
2184 GGTAATTTTAAGAAAAATAGGGGTCAAAAATGGAATATAGG-AAGTTCGAGGGTAAAAAC
1 -GTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTTAAAAT
* *
2243 GTAATTTTTTGG-AAAATAG-GGTTAAAAATGGAATTTT-TAGAAGTTTGAGGG-TAAAAT
1 GTAA-TTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGA-AAGTTTGAGGGTTAAAAT
* * *
2300 GGTAATTTTGGGAAAAA--AAGGTCT-AAAATGGAATTTTAGG-AAGTTT-AGGGGTGAAAAT
1 -GTAATTTTTGGAAAAATCGAGGT-TAAAAATGGAATTTT-GGAAAGTTTGA-GGGTTAAAAT
* *
2358 GTAATTTTTGGAAAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTTAAGGGTTAAAAT
1 GTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTTAAAAT
** * * ** *
2417 GTAATTTTTGGAAAGTTCGGGGTCAAAAATATAATTTTGGATAAGTTTGA-GGTCAAAAT
1 GTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGA-AAGTTTGAGGGTTAAAAT
*
2476 ATAATTTTTGGA
1 GTAATTTTTGGA
2488 CAGTTTAAGG
Statistics
Matches: 292, Mismatches: 44, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
56 1 0.00
57 65 0.22
58 47 0.16
59 130 0.45
60 38 0.13
61 11 0.04
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (59 bp):
GTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTTAAAAT
Found at i:2430 original size:116 final size:113
Alignment explanation
Indices: 2114--2430 Score: 315
Period size: 116 Copynumber: 2.7 Consensus size: 113
2104 TAGACATCCT
*
2114 GGGGTAAAATGGTAA-TTTTGGAAAAAAATCGGGATCAAAAATAGAATTTTTGG-AAGTTTAGGG
1 GGGGTAAAAT-GTAATTTTTGG--AAAAATCGGG-TTAAAAATAGAA-TTTTGGAAAGTTTA-GG
* * *
2177 GTAAAATGGTAATTTTAAGAAAAATAGGGGTCAAAAATGGAATATAGGAAGTTC
60 GTAAAATGGTAATTTTAGGAAAAATAGAGGTCAAAAATGGAATATAGGAAGTTA
* * * *
2231 GAGGGTAAAAACGTAATTTTTTGG-AAAATAGGGTTAAAAATGGAATTTT-TAGAAGTTTGAGGG
1 G-GGGT-AAAATGTAA-TTTTTGGAAAAATCGGGTTAAAAATAGAATTTTGGA-AAGTTT-AGGG
* * *
2294 TAAAATGGTAATTTTGGGAAAAA-A-AGGTCTAAAATGGAATTTTAGGAAGTTTA
61 TAAAATGGTAATTTTAGGAAAAATAGAGGTCAAAAATGGAA-TATAGGAAG-TTA
*
2347 GGGGTGAAAATGTAATTTTTGGAAAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTTAAGGGTT
1 GGGGT-AAAATGTAATTTTTGGAAAAATCG-GGTTAAAAATAGAATTTTGGAAAGTTT-AGGG-T
*
2412 AAAAT-GTAATTTTTGGAAA
62 AAAATGGTAATTTTAGGAAA
2431 GTTCGGGGTC
Statistics
Matches: 169, Mismatches: 18, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
114 20 0.12
115 31 0.18
116 83 0.49
117 17 0.10
118 8 0.05
119 4 0.02
120 6 0.04
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31
Consensus pattern (113 bp):
GGGGTAAAATGTAATTTTTGGAAAAATCGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGTAAAA
TGGTAATTTTAGGAAAAATAGAGGTCAAAAATGGAATATAGGAAGTTA
Found at i:2439 original size:29 final size:29
Alignment explanation
Indices: 2158--2492 Score: 122
Period size: 29 Copynumber: 11.5 Consensus size: 29
2148 TCAAAAATAG
2158 AATTTTTGG-AAGTTTAGGGG-TAAAATGGT
1 AATTTTTGGAAAG-TTAGGGGTTAAAAT-GT
** ** * *
2187 AATTTTAAGAAAAATAGGGGTCAAAAATGG
1 AATTTTTGGAAAGTTAGGGGT-TAAAATGT
* * * * *
2217 AA-TATAGG-AAGTTCGAGGGTAAAAACGT
1 AATTTTTGGAAAGTTAG-GGGTTAAAATGT
* *
2245 AATTTTTTGGAAA-ATA-GGGTTAAAAATGG
1 AA-TTTTTGGAAAGTTAGGGGTT-AAAATGT
* *
2274 AATTTTTAG-AAGTTTGAGGG-TAAAATGGT
1 AATTTTTGGAAAGTTAG-GGGTTAAAAT-GT
* * ** *
2303 AATTTTGGGAAA--AAAAGGTCTAAAATGG
1 AATTTTTGGAAAGTTAGGGGT-TAAAATGT
* *
2331 AATTTTAGG-AAGTTTAGGGGTGAAAATGT
1 AATTTTTGGAAAG-TTAGGGGTTAAAATGT
** * *
2360 AATTTTTGGAAAAATCGAGGTTAAAAAT-T
1 AATTTTTGGAAAGTTAGGGGTT-AAAATGT
*
2389 GAA-TTTTGGAAAGTTTAAGGGTTAAAATGT
1 -AATTTTTGGAAAG-TTAGGGGTTAAAATGT
* * *
2419 AATTTTTGGAAAGTTCGGGGTCAAAAATAT
1 AATTTTTGGAAAGTTAGGGGT-TAAAATGT
* * * *
2449 AA-TTTTGGATAAGTTTGAGGTCAAAATAT
1 AATTTTTGGA-AAGTTAGGGGTTAAAATGT
*
2478 AATTTTTGGACAGTT
1 AATTTTTGGAAAGTT
2493 TAAGGACCTT
Statistics
Matches: 223, Mismatches: 56, Indels: 54
0.67 0.17 0.16
Matches are distributed among these distances:
27 6 0.03
28 37 0.17
29 105 0.47
30 68 0.30
31 7 0.03
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAAGTTAGGGGTTAAAATGT
Found at i:3297 original size:14 final size:15
Alignment explanation
Indices: 3278--3308 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3268 GCACATCTCT
3278 TTATTTTTTC-TTTA
1 TTATTTTTTCATTTA
3292 TTATTTTTTCATTTA
1 TTATTTTTTCATTTA
3307 TT
1 TT
3309 TAAAAACCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTTTCATTTA
Found at i:5050 original size:23 final size:22
Alignment explanation
Indices: 5018--5097 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
5008 GCTGGGGAAA
*
5018 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
5040 CCAGTAGGCACACAC-GTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
5062 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
5085 CAGTAGGCACACA
1 CAGTAGGCACACA
5098 AAGTACGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 12 0.24
22 10 0.20
23 28 0.56
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:5053 original size:21 final size:20
Alignment explanation
Indices: 5027--5097 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 20
5017 ACAGTAAGCA
5027 CACACAGTGCAATCCAGTAGG
1 CACACAGTGCAAT-CAGTAGG
5048 CACACACGTGCAATCAGTAGGCG
1 CACACA-GTGCAATCAGTA-G-G
* *
5071 CACATAGCGCAAATCAGTAGG
1 CACACAGTGC-AATCAGTAGG
5092 CACACA
1 CACACA
5098 AAGTACGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 17 0.40
22 12 0.28
23 14 0.33
ACGTcount: A:0.35, C:0.30, G:0.23, T:0.13
Consensus pattern (20 bp):
CACACAGTGCAATCAGTAGG
Found at i:5111 original size:23 final size:23
Alignment explanation
Indices: 5085--5138 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5075 TAGCGCAAAT
*
5085 CAGTAGGCACACAAAGTAC-GAAA
1 CAGTAAGCACACAAAGTACTG-AA
* *
5108 CAGTAAGCGCACATAGTACTGAA
1 CAGTAAGCACACAAAGTACTGAA
5131 CAGTAAGC
1 CAGTAAGC
5139 GCGCTAGCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTACTGAA
Done.