Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015355.1 Kokia drynarioides strain JFW-HI SEQ_130402, 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: 322319
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 56 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:306634 original size:32 final size:33
Alignment explanation
Indices: 306593--306655 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
306583 TCCTAAAAAG
306593 ACTGTTTCTTCTTTTAAAAATAATTG-AAGTTT
1 ACTGTTTCTTCTTTTAAAAATAATTGTAAGTTT
306625 ACTGTTTCTTCTTTTAAAAATAATTGTAAGT
1 ACTGTTTCTTCTTTTAAAAATAATTGTAAGT
306656 AAACTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (33 bp):
ACTGTTTCTTCTTTTAAAAATAATTGTAAGTTT
Found at i:311455 original size:6 final size:6
Alignment explanation
Indices: 311434--311472 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
311424 TTTAATTTAT
*
311434 TTTAAA TTT-GA TTTAAA TTTAAA TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
311473 CTTCAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:311456 original size:17 final size:17
Alignment explanation
Indices: 311424--311472 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
311414 CTGGACCCTT
*
311424 TTTAATTT-ATTTTAAA
1 TTTAATTTAAATTTAAA
*
311440 TTTGATTTAAATTTAAA
1 TTTAATTTAAATTTAAA
311457 TTTAATTTAAATTTAA
1 TTTAATTTAAATTTAA
311473 CTTCAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAATTTAAATTTAAA
Found at i:311463 original size:11 final size:12
Alignment explanation
Indices: 311434--311472 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
311424 TTTAATTTAT
*
311434 TTTAAATTT-GA
1 TTTAAATTTAAA
311445 TTTAAATTTAAA
1 TTTAAATTTAAA
311457 TTT-AATTTAAA
1 TTTAAATTTAAA
311468 TTTAA
1 TTTAA
311473 CTTCAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:312408 original size:20 final size:20
Alignment explanation
Indices: 312379--312417 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
312369 GAAATCAAAT
312379 AAAACGTTTTAAAAAAGGGG
1 AAAACGTTTTAAAAAAGGGG
*
312399 AAAACTTTTTAAAAAAGGG
1 AAAACGTTTTAAAAAAGGG
312418 TTTGGAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (20 bp):
AAAACGTTTTAAAAAAGGGG
Found at i:313378 original size:59 final size:59
Alignment explanation
Indices: 313219--313775 Score: 744
Period size: 59 Copynumber: 9.5 Consensus size: 59
313209 GAAGGTCCCT
** * * *
313219 AAACTATCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCA-TTTTAGCCTCG
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
313278 AAACTTCCAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
313336 AAACCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTA-TTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
*
313394 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* ** *
313453 AAACCTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * ** * * *
313512 AAACCTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
313571 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
313630 AAAC-TCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
** * * * * *
313688 AAACTTTAAAAAATTACCATTTTACCCCCAAACTCCCATAAATCCCTTTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
313747 AAACTTCCCAAAAATTACCATTTCTACCC
1 AAACTT-CCAAAAATTACCATTT-TACCC
313776 TCGGATGTCC
Statistics
Matches: 444, Mismatches: 48, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
57 25 0.06
58 147 0.33
59 253 0.57
60 14 0.03
61 5 0.01
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:313478 original size:117 final size:115
Alignment explanation
Indices: 313225--313775 Score: 719
Period size: 117 Copynumber: 4.7 Consensus size: 115
313215 CCCTAAACTA
* *
313225 TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTAGCCTCGAAACTTCCAAAA
1 TCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTAACCTCAAAACTTCCAAAA
313290 ATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACC
65 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA-CCCAAAACC
* * * *
313341 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTGACCCCAAAACTTCCAAAA
1 TCCAAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTAACCTCAAAACTTCCAAAA
313406 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCAAAACC
65 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACC-CAAAACC
* *
313458 TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAAACCTCTAAA
1 TCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCA-TTTTAACCTCAAAACTTCCAAA
** * * *
313523 AATTACCATTTTACCCCTAAACTTCCAAAAATCCTATTTTTGACCCTAAAACT
64 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC-AAAACC
* * * *
313576 TCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCGAAAC-TCCTAA
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCA-TTTTAACCTCAAAACTTCCAAA
* * *
313640 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCGAAACT
64 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-AACCCAAAACC
** * * * * *
313693 TTAAAAAATTACCATTTTACCCCCAAACTCCCATAAATCCCTTTTTTGACCCCAAAACTTCCCAA
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCC-ATTTTAACCTCAAAACTT-CCAA
313758 AAATTACCATTTCTACCC
63 AAATTACCATTT-TACCC
313776 TCGGATGTCC
Statistics
Matches: 384, Mismatches: 39, Indels: 20
0.87 0.09 0.05
Matches are distributed among these distances:
116 67 0.17
117 175 0.46
118 118 0.31
119 19 0.05
120 5 0.01
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.29
Consensus pattern (115 bp):
TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATCCCATTTTAACCTCAAAACTTCCAAAAA
TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCAAAACC
Found at i:317147 original size:12 final size:12
Alignment explanation
Indices: 317130--317163 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
317120 GTCCGTCAAC
317130 ATCAAGATAAAA
1 ATCAAGATAAAA
* *
317142 ATCAAGATCAAG
1 ATCAAGATAAAA
317154 ATCAAGATAA
1 ATCAAGATAA
317164 GGTTTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (12 bp):
ATCAAGATAAAA
Found at i:318049 original size:12 final size:13
Alignment explanation
Indices: 318032--318061 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
318022 ATAATATTTA
318032 TATTTTAAAA-AT
1 TATTTTAAAATAT
318044 TATTTTAAAATAT
1 TATTTTAAAATAT
318057 TATTT
1 TATTT
318062 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTAAAATAT
Found at i:319752 original size:27 final size:28
Alignment explanation
Indices: 319707--319767 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
319697 AAATGAGACT
319707 TTTTGGATACCCGGAGGT-AAATGGTAA
1 TTTTGGATACCCGGAGGTAAAATGGTAA
* * *
319734 TTTTGGATTCTCGGGGGTAAAATGGTAA
1 TTTTGGATACCCGGAGGTAAAATGGTAA
319762 TTTTGG
1 TTTTGG
319768 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.25, C:0.08, G:0.31, T:0.36
Consensus pattern (28 bp):
TTTTGGATACCCGGAGGTAAAATGGTAA
Found at i:319870 original size:28 final size:28
Alignment explanation
Indices: 319782--319880 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 28
319772 ATTTGGGGTT
* *
319782 TAAAATGGAA-TTTTAGACATCCGAGGG
1 TAAAACGGAATTTTTAGACATTCGAGGG
* * *
319809 TAAAACGGTAATTTTTAAAAAATTC--GGA
1 TAAAACGG-AATTTTT-AGACATTCGAGGG
*
319837 TAAAAACGGAATTTTTGGACATTCGAGGG
1 T-AAAACGGAATTTTTAGACATTCGAGGG
* *
319866 TAAAATGTAATTTTT
1 TAAAACGGAATTTTT
319881 GGAAGTTTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
27 12 0.22
28 24 0.44
29 14 0.25
30 5 0.09
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (28 bp):
TAAAACGGAATTTTTAGACATTCGAGGG
Found at i:319894 original size:28 final size:30
Alignment explanation
Indices: 319837--319915 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 30
319827 AAAATTCGGA
*
319837 TAAAAACGGAATTTTTGGACATTCGAGGG-
1 TAAAAATGGAATTTTTGGACATTCGAGGGT
*
319866 T-AAAATGTAATTTTTGGA-AGTTTCG-GGGT
1 TAAAAATGGAATTTTTGGACA--TTCGAGGGT
*
319895 TAAAAATGGGATTTTTGGACA
1 TAAAAATGGAATTTTTGGACA
319916 ATTTAGGGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 18 0.44
29 6 0.15
30 15 0.37
31 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGGACATTCGAGGGT
Found at i:319914 original size:58 final size:58
Alignment explanation
Indices: 319748--319915 Score: 164
Period size: 58 Copynumber: 2.9 Consensus size: 58
319738 GGATTCTCGG
* * * *
319748 GGGTAAAATGGTAATTTTGGGAAAATTT-GGGGTTTAAAAT-GGAATTTTAGACATCCGA
1 GGGTAAAAT-GTAATTTTTGG-AAATTTCGGGGTTAAAAATGGGATTTTTGGACATCCGA
* ** * * * * *
319806 GGGTAAAACGGTAATTTTTAAAAAATTC--GGATAAAAACGGAATTTTTGGACATTCGA
1 GGGTAAAA-TGTAATTTTTGGAAATTTCGGGGTTAAAAATGGGATTTTTGGACATCCGA
*
319863 GGGTAAAATGTAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGACA
1 GGGTAAAATGTAATTTTTGGAAATTTCGGGGTTAAAAATGGGATTTTTGGACA
319916 ATTTAGGGAC
Statistics
Matches: 85, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
56 21 0.25
57 27 0.32
58 37 0.44
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGAAATTTCGGGGTTAAAAATGGGATTTTTGGACATCCGA
Done.