Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010385.1 Kokia drynarioides strain JFW-HI SEQ_125262, 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: 8458
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2905 original size:27 final size:27
Alignment explanation
Indices: 2854--2914 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2844 CAATTTTCAA
*
2854 TTAATGATTATTTCCTTTGACCCTCCCT
1 TTAAT-ATTATTTCCTTCGACCCTCCCT
* * **
2882 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTATTTCCTTCGACCCTCCCT
2909 TTAATA
1 TTAATA
2915 GAATTCTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.51
Consensus pattern (27 bp):
TTAATATTATTTCCTTCGACCCTCCCT
Found at i:4227 original size:17 final size:17
Alignment explanation
Indices: 4205--4320 Score: 151
Period size: 17 Copynumber: 6.6 Consensus size: 17
4195 CATATTCCCT
4205 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4222 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
4240 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
4257 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
4275 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
4292 TTTAAACTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
4310 TTTAAAGTTTA
1 TTTAAA-TTTA
4321 AAATAAATAA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
17 43 0.51
18 39 0.46
19 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4242 original size:18 final size:17
Alignment explanation
Indices: 4205--4320 Score: 126
Period size: 18 Copynumber: 6.6 Consensus size: 17
4195 CATATTCCCT
*
4205 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTAAAA
*
4222 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-AAAA
*
4240 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTAAAA
4257 TTTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAAAA
*
4275 TTTAAATTTAATTT-AAG
1 TTTAAATTT-ATTTAAAA
* *
4292 TTTAAACTTATTTTCAAA
1 TTTAAATTTA-TTTAAAA
4310 TTTAAAGTTTA
1 TTTAAA-TTTA
4321 AAATAAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
16 1 0.01
17 38 0.45
18 41 0.49
19 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTAAAA
Found at i:4251 original size:35 final size:35
Alignment explanation
Indices: 4205--4320 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
4195 CATATTCCCT
* *
4205 TTTAAATTTATTTTAAATTTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
4240 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
* * * *
4275 TTTAAATTTAATTTAAGTTTAAACTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
4310 TTTAAAGTTTA
1 TTTAAA-TTTA
4321 AAATAAATAA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 70 0.95
36 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
Found at i:4295 original size:24 final size:24
Alignment explanation
Indices: 4251--4297 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4241 TTAAATTTAT
*
4251 TTTAAATTTAAATTTATTTTAAAA
1 TTTAAATTTAAATTTAGTTTAAAA
4275 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
4298 CTTATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAAATTTAAATTTAGTTTAAAA
Found at i:4984 original size:18 final size:19
Alignment explanation
Indices: 4950--4987 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4940 AAAACGTTTC
*
4950 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
4969 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
4987 A
1 A
4988 TTAATAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:5078 original size:12 final size:12
Alignment explanation
Indices: 5061--5100 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5051 AAATGTTTTG
5061 ATATTAATAATA
1 ATATTAATAATA
*
5073 ATATTATTAATA
1 ATATTAATAATA
5085 ATTATTAACTAATA
1 A-TATTAA-TAATA
5099 AT
1 AT
5101 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.50
13 6 0.25
14 6 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:6435 original size:59 final size:59
Alignment explanation
Indices: 6342--6837 Score: 606
Period size: 59 Copynumber: 8.4 Consensus size: 59
6332 TCCTTAAACT
* *
6342 TTCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAA-C
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
6400 TCTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCAGAA-C
1 T-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * *
6458 TCTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCTCATTTTTGACCTCGAACT
1 T-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
6518 TTCCAAAAATTTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * *
6577 TTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTGACCTCAAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * * * *
6636 TTCTAAAAA-TACCATTTTATCCTCAAACTCCCAAAAATCCTATTTTTGACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
6694 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * ** * * **
6753 TTTCGAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCTATTTTTTTTATTCCGAACC
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTGACCCCGAACC
* *
6814 TTCC-AAAACTACCATTTTGCCCCC
1 TTCCAAAAATTACCATTTTACCCCC
6838 CCGTGCATCC
Statistics
Matches: 383, Mismatches: 49, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
58 105 0.27
59 245 0.64
60 17 0.04
61 16 0.04
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:6552 original size:117 final size:118
Alignment explanation
Indices: 6346--6800 Score: 657
Period size: 117 Copynumber: 3.9 Consensus size: 118
6336 TAAACTTTCC
* * *
6346 AAAAATTACCATTTTATCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACTCTCCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACTTTCCAAAAAT
* *
6411 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCAGAA-CTCTCT
66 TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT-TCT
* *
6463 AAAAATTACCATTTTACCCCCAAACTTTCAAAAATCTCATTTTTGACCTCGAACTTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACTTTCCAAAAAT
*
6528 TTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
66 TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * * * *
6581 AAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTGACCTCAAACCTTCTAAAAA-
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACTTTCCAAAAAT
* * * *
6645 TACCATTTTATCCTCAAACTCCCAAAAATCCTATTTTTGACCCCGAACCTTCT
66 TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * *
6698 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTT-CGAAAA
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAA-CTTTCCAAAAA
* *
6762 TTACCATTTTACCCTTGAACTTCCAAAAATCCTATTTTT
65 TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT
6801 TTTATTCCGA
Statistics
Matches: 302, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
117 197 0.65
118 103 0.34
119 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (118 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACTTTCCAAAAAT
TACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
Found at i:6651 original size:176 final size:175
Alignment explanation
Indices: 6338--6800 Score: 652
Period size: 176 Copynumber: 2.6 Consensus size: 175
6328 GAGGTCCTTA
*
6338 AACTTTCCAAAAATTACCATTTTATCCC-CGAACTTCCAAAAATCTCATTTTTGACCCCGAA-CT
1 AACTTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*
6401 CTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCAGAACTCTCTAAA
65 -TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCAGAACTCTCTAAA
** *
6466 AATTACCATTTTACCCCCAAACTTTCAAAAAT-CTCATTTTTGACCTCG
128 AATTACCATTTTACCCCCAAACTCCCAAAAATCCT-ATTTTTGACCCCG
*
6514 AACTTTCCAAAAATTTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
*
6579 CTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTGACCTCA-AAC-CTTCTAA
66 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CATTTTTGA-C-CAGAACTC-TCTAA
* *
6642 AAA-TACCATTTTATCCTCAAACTCCCAAAAATCCTATTTTTGACCCCG
127 AAATTACCATTTTACCCCCAAACTCCCAAAAATCCTATTTTTGACCCCG
* * *
6690 AACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* **
6755 -TCGAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCTATTTTT
66 CT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCC-ATTTTT
6801 TTTATTCCGA
Statistics
Matches: 261, Mismatches: 17, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
175 6 0.02
176 237 0.91
177 16 0.06
178 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (175 bp):
AACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCATTTTTGACCAGAACTCTCTAAAAAT
TACCATTTTACCCCCAAACTCCCAAAAATCCTATTTTTGACCCCG
Done.