Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003051.1 Kokia drynarioides strain JFW-HI SEQ_115579, 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: 44880
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:3107 original size:30 final size:30
Alignment explanation
Indices: 3073--3140 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
3063 CTGCAATCTC
3073 TATTAGAAGACTGAAGTAAGTATCACGGTT
1 TATTAGAAGACTGAAGTAAGTATCACGGTT
*
3103 TATTAGAAGGCTGAAGTAAGTATCACGGTT
1 TATTAGAAGACTGAAGTAAGTATCACGGTT
3133 TATTAGAA
1 TATTAGAA
3141 TTTGATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.31
Consensus pattern (30 bp):
TATTAGAAGACTGAAGTAAGTATCACGGTT
Found at i:9322 original size:24 final size:27
Alignment explanation
Indices: 9288--9352 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
9278 TTGCAGAAAC
9288 TAAATCAAATTAATTT-TTTT-T-TTAT
1 TAAAT-AAATTAATTTATTTTATATTAT
9313 TAAATAAATTAATTTAGTTTTATATTAT
1 TAAATAAATTAATTTA-TTTTATATTAT
*
9341 TAAAAAAATTAA
1 TAAATAAATTAA
9353 ATAAAACTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 10 0.29
25 5 0.14
26 4 0.11
27 1 0.03
28 15 0.43
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TAAATAAATTAATTTATTTTATATTAT
Found at i:9333 original size:25 final size:25
Alignment explanation
Indices: 9288--9339 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
9278 TTGCAGAAAC
* *
9288 TAAATCAAATTAATTTTTTTTTTAT
1 TAAATCAAATTAATTTGTTTTATAT
9313 TAAAT-AAATTAATTTAGTTTTATAT
1 TAAATCAAATTAATTT-GTTTTATAT
9338 TA
1 TA
9340 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TAAATCAAATTAATTTGTTTTATAT
Found at i:18003 original size:16 final size:17
Alignment explanation
Indices: 17982--18014 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17972 AATATTTCTG
17982 TAACA-TATTTTTTTTA
1 TAACACTATTTTTTTTA
17998 TAACATCTATTTTTTTT
1 TAACA-CTATTTTTTTT
18015 TAAGCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (17 bp):
TAACACTATTTTTTTTA
Found at i:26554 original size:2 final size:2
Alignment explanation
Indices: 26549--26578 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26539 AAAAAAGTAA
26549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26579 TGCTTTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29464 original size:23 final size:23
Alignment explanation
Indices: 29438--29525 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 23
29428 TTTTATCTTA
29438 TTTTGATGTTTTGGATTCTGGGT
1 TTTTGATGTTTTGGATTCTGGGT
* * * * *
29461 TTTTGGTATTTTAGTCTAATTCTTGAT
1 TTTTGATGTTTT-G---GATTCTGGGT
* *
29488 CTTTAGATGTTTTGGTTTCTGGGT
1 -TTTTGATGTTTTGGATTCTGGGT
*
29512 TTTTGTTGTTTTGG
1 TTTTGATGTTTTGG
29526 TCAAAAGATG
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
23 22 0.48
24 7 0.15
27 8 0.17
28 9 0.20
ACGTcount: A:0.10, C:0.06, G:0.25, T:0.59
Consensus pattern (23 bp):
TTTTGATGTTTTGGATTCTGGGT
Found at i:31241 original size:14 final size:14
Alignment explanation
Indices: 31224--31270 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
31214 ATCTTGAACT
31224 TTGAATCCAAAATC
1 TTGAATCCAAAATC
31238 TTGAATCTCAAAAT-
1 TTGAATC-CAAAATC
* **
31252 TTAAATCTTAAATC
1 TTGAATCCAAAATC
31266 TTGAA
1 TTGAA
31271 CTCTAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 17 0.63
15 6 0.22
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (14 bp):
TTGAATCCAAAATC
Found at i:39549 original size:33 final size:33
Alignment explanation
Indices: 39498--39570 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
39488 AAGGTTGAAA
39498 ATATTAAGATAAATTTATTTATTAAAACAT-ATT
1 ATATTAAGATAAATTTATTTATTAAAA-ATAATT
* *
39531 ATATTTAGAATAAA-TTATTTTTTAAAAATAATT
1 ATATTAAG-ATAAATTTATTTATTAAAAATAATT
39564 AT-TTAAG
1 ATATTAAG
39571 TTATTATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 6 0.17
33 24 0.69
34 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (33 bp):
ATATTAAGATAAATTTATTTATTAAAAATAATT
Found at i:39750 original size:16 final size:15
Alignment explanation
Indices: 39729--39773 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
39719 TTTTTAATAT
39729 AAATTTAATATTTATA
1 AAATTTAATATTTA-A
39745 AAATTTAATA-TTAA
1 AAATTTAATATTTAA
*
39759 AAATTTAACATTTAA
1 AAATTTAATATTTAA
39774 TTGAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.37
15 7 0.26
16 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTAATATTTAA
Found at i:40769 original size:62 final size:62
Alignment explanation
Indices: 40672--40796 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
40662 TTCCAAAGTG
40672 TGGAAATTCAATAAAAGGATATGCTAAATGGTAATTTTGCTTTTCTGTATGATTAGATCATA
1 TGGAAATTCAATAAAAGGATATGCTAAATGGTAATTTTGCTTTTCTGTATGATTAGATCATA
40734 TGGAAATTCAATAAAAGGATATGCTAAATGGTAATTTTGCTTTTCTGTATGATTAGATCATA
1 TGGAAATTCAATAAAAGGATATGCTAAATGGTAATTTTGCTTTTCTGTATGATTAGATCATA
40796 T
1 T
40797 AGTAACTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (62 bp):
TGGAAATTCAATAAAAGGATATGCTAAATGGTAATTTTGCTTTTCTGTATGATTAGATCATA
Found at i:44180 original size:29 final size:29
Alignment explanation
Indices: 44135--44356 Score: 252
Period size: 29 Copynumber: 7.5 Consensus size: 29
44125 CAAAATGGTA
*
44135 ATTTTTGGAAGTTTCGGGGATAAAAATGAT
1 ATTTTTGGAAGTTTCGGGG-TAAAAATGAG
44165 ATTTTTGGAAG-TTCGGGGGTAAAAAT-AGG
1 ATTTTTGGAAGTTTC-GGGGTAAAAATGA-G
* *
44194 ATTTTTGGAAGTTTCGGGATCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGAG
* * * *
44224 ATTTTCGAAAGTTTAGGAGTAAAAATGAG
1 ATTTTTGGAAGTTTCGGGGTAAAAATGAG
44253 ATTTTTGGAAG-TTCGAGGGTAAAAATGAG
1 ATTTTTGGAAGTTTCG-GGGTAAAAATGAG
* *
44282 ATTTTTGGAAGTTTTGGGGTCAAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT--AAAAATGAG
* *
44313 ATTTTTGGAAGTTTAGGGGTAAAAATGTG
1 ATTTTTGGAAGTTTCGGGGTAAAAATGAG
44342 ATTTTTGGATAGTTT
1 ATTTTTGGA-AGTTT
44357 AGGGACCTTC
Statistics
Matches: 165, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.02
29 86 0.52
30 48 0.29
31 27 0.16
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
ATTTTTGGAAGTTTCGGGGTAAAAATGAG
Found at i:44200 original size:59 final size:57
Alignment explanation
Indices: 44126--44360 Score: 265
Period size: 59 Copynumber: 3.9 Consensus size: 57
44116 ACCCGGAGGC
* **
44126 AAAATGGTAATTTTTGGAAGTTTCGGGGATAAAAATGATATTTTTGGAAGTTCGGGGGTA
1 AAAATGG--ATTTTTGGAAGTTTCGGGG-TAAAAATGAGATTTTTGGAAGTTTAGGGGTA
* * * * *
44186 AAAATAGGATTTTTGGAAGTTTCGGGATCAAAAATGGGATTTTCGAAAGTTTAGGAGTA
1 AAAAT-GGATTTTTGGAAGTTTCGGGGT-AAAAATGAGATTTTTGGAAGTTTAGGGGTA
*
44245 AAAATGAGATTTTTGGAAG-TTCGAGGGTAAAAATGAGATTTTTGGAAGTTTTGGGGTCAA
1 AAAATG-GATTTTTGGAAGTTTCG-GGGTAAAAATGAGATTTTTGGAAGTTTAGGGGT--A
* *
44305 AAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGATAGTTTAGGG
1 AAAAT-GGATTTTTGGAAGTTTCGGGGTAAAAATGAGATTTTTGGA-AGTTTAGGG
44361 ACCTTCAGGA
Statistics
Matches: 149, Mismatches: 17, Indels: 17
0.81 0.09 0.09
Matches are distributed among these distances:
58 30 0.20
59 61 0.41
60 44 0.30
61 14 0.09
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (57 bp):
AAAATGGATTTTTGGAAGTTTCGGGGTAAAAATGAGATTTTTGGAAGTTTAGGGGTA
Found at i:44259 original size:88 final size:89
Alignment explanation
Indices: 44155--44355 Score: 298
Period size: 88 Copynumber: 2.3 Consensus size: 89
44145 GTTTCGGGGA
* *
44155 TAAAAATGATATTTTTGGAAGTTCGGGGGTAAAAAT-AGGATTTTTGGAAGTTTCGGGATC-AAA
1 TAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGA-GATTTTTGGAAGTTTCGGGATCAAAA
44218 AATGGGATTTTCGAAAGTTTAGGAG
65 AATGGGATTTTCGAAAGTTTAGGAG
* *
44243 TAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTTGGGGTCAAAAA
1 TAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTCGGGATCAAAAA
* * *
44308 ATGGGATTTTTGGAAGTTTAGGGG
66 ATGGGATTTTCGAAAGTTTAGGAG
*
44332 TAAAAATGTGATTTTTGGATAGTT
1 TAAAAATGAGATTTTTGGA-AGTT
44356 TAGGGACCTT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
88 54 0.53
89 44 0.43
90 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (89 bp):
TAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTCGGGATCAAAAA
ATGGGATTTTCGAAAGTTTAGGAG
Done.