Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014057.1 Kokia drynarioides strain JFW-HI SEQ_129088, 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: 21291
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:206 original size:21 final size:21
Alignment explanation
Indices: 170--229 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
160 TTCGACTTCC
170 CTATTTTCTATTTATTTTAATT
1 CTATTTTCT-TTTATTTTAATT
192 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTA-TTTTAATT
*
214 CT-GTTTCTTTTATTTT
1 CTATTTTCTTTTATTTT
230 TCCTTAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 19 0.53
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.72
Consensus pattern (21 bp):
CTATTTTCTTTTATTTTAATT
Found at i:230 original size:22 final size:22
Alignment explanation
Indices: 174--230 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
164 ACTTCCCTAT
*
174 TTTCTATTTA-TTTTAATTCTAT
1 TTTCT-TTTATTTTTAATTCTAG
196 TTTCTTTTATTTTTAATTCT-G
1 TTTCTTTTATTTTTAATTCTAG
217 TTTCTTTTATTTTT
1 TTTCTTTTATTTTT
231 CCTTAGATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTCTTTTATTTTTAATTCTAG
Found at i:3384 original size:21 final size:20
Alignment explanation
Indices: 3346--3384 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3336 ATGATTCTTG
*
3346 TTTGCTAAGTTAATTTTGAT
1 TTTGCTAAGTTAAATTTGAT
*
3366 TTTGCTATGATTAAATTTG
1 TTTGCTAAG-TTAAATTTG
3385 TCTCCACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTGCTAAGTTAAATTTGAT
Found at i:6640 original size:24 final size:24
Alignment explanation
Indices: 6607--6657 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
6597 AGAAATAATA
* *
6607 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
6631 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
6655 TTT
1 TTT
6658 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:10173 original size:29 final size:27
Alignment explanation
Indices: 10141--10497 Score: 261
Period size: 29 Copynumber: 12.2 Consensus size: 27
10131 TAAACTGTCA
10141 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAA-TACCATTTTACCC-CGAACTTCC
*
10170 AAAAAT-CTCATTTTTGACCACGAACCTTCC
1 AAAAATAC-CA-TTTT-ACCCCGAA-CTTCC
10200 AAAAATTACCATTTTACCCCCGAA-TTACC
1 AAAAA-TACCATTTTA-CCCCGAACTT-CC
*
10229 AAAAAT-CTCATTTTGACCCTGAACTTTCC
1 AAAAATAC-CATTTT-ACCCCGAAC-TTCC
*
10258 AAAACTACCATTTTACCCCTGAACTTCC
1 AAAAATACCATTTTACCCC-GAACTTCC
*
10286 AAAAAATCCCATTTTAACCCCGAACCTTCC
1 -AAAAATACCATTTT-ACCCCGAA-CTTCC
*
10316 AAAAATTACCATTTTACCCCCAAACTTCC
1 AAAAA-TACCATTTTA-CCCCGAACTTCC
*
10345 AAAAATCCCATTTTTGACCCCGAACCTTCC
1 AAAAATACCA-TTTT-ACCCCGAA-CTTCC
* *
10375 TAAAATTACCATTTTACCCCTAGACTTCC
1 -AAAAATACCATTTTACCCCGA-ACTTCC
* ** *
10404 AAAAATCCCATTTTTGACCTTGAACCTTCTA
1 AAAAATACCA-TTTT-ACCCCGAA-CTTC-C
*
10435 AAAAATACCATTTTACCCCCGAACATCC
1 AAAAATACCATTTTA-CCCCGAACTTCC
* * * *
10463 TAAAATCCCATATTTGACCTCGAGACATCC
1 AAAAATACCAT-TTT-ACCCCGA-ACTTCC
10493 AAAAA
1 AAAAA
10498 ATTACTATTT
Statistics
Matches: 267, Mismatches: 29, Indels: 63
0.74 0.08 0.18
Matches are distributed among these distances:
27 2 0.01
28 47 0.18
29 108 0.40
30 89 0.33
31 20 0.07
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.29
Consensus pattern (27 bp):
AAAAATACCATTTTACCCCGAACTTCC
Found at i:10232 original size:59 final size:58
Alignment explanation
Indices: 10141--10578 Score: 444
Period size: 59 Copynumber: 7.4 Consensus size: 58
10131 TAAACTGTCA
* * *
10141 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAACCTTCC
1 AAAAATTACCATTTTACCCCCGAA-TTCCAAAAATCCCATTTTTGACCTCGAACCTTCC
* *
10200 AAAAATTACCATTTTACCCCCGAATTACCAAAAATCTCA-TTTTGACC-CTGAACTTTCC
1 AAAAATTACCATTTTACCCCCGAATT-CCAAAAATCCCATTTTTGACCTC-GAACCTTCC
* * * *
10258 -AAAACTACCATTTTACCCCTGAACTTCCAAAAAATCCCA-TTTTAACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCCCGAA-TTCC-AAAAATCCCATTTTTGACCTCGAACCTTCC
* *
10316 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCCCGAA-TTCCAAAAATCCCATTTTTGACCTCGAACCTTCC
* * * * *
10375 TAAAATTACCATTTTACCCCTAGACTTCCAAAAATCCCATTTTTGACCTTGAACCTTCT
1 AAAAATTACCATTTTACCCC-CGAATTCCAAAAATCCCATTTTTGACCTCGAACCTTCC
* * * * *
10434 AAAAAATACCATTTTACCCCCGAACATCCTAAAATCCCATATTTGACCTCGAGA-CATCC
1 AAAAATTACCATTTTACCCCCGAA-TTCCAAAAATCCCATTTTTGACCTCGA-ACCTTCC
* * * *
10493 AAAAAATTACTATTTTACTCCC-AGATGTCCAAAAA-CTCCGTTTTTCGACCTCGAAAC-TCTC
1 -AAAAATTACCATTTTACCCCCGA-AT-TCCAAAAATC-CCATTTTT-GACCTCGAACCTTC-C
10554 -AAAATTACCATTTTTACCCCCGAAT
1 AAAAATTACCA-TTTTACCCCCGAAT
10579 GTTTCAAATT
Statistics
Matches: 323, Mismatches: 37, Indels: 37
0.81 0.09 0.09
Matches are distributed among these distances:
57 24 0.07
58 56 0.17
59 184 0.57
60 48 0.15
61 11 0.03
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.29
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCGAATTCCAAAAATCCCATTTTTGACCTCGAACCTTCC
Found at i:12833 original size:43 final size:43
Alignment explanation
Indices: 12784--13041 Score: 286
Period size: 43 Copynumber: 6.0 Consensus size: 43
12774 ACGTTATTAT
* ** * *
12784 AGAACATGGTCTTTAACGAAGCTTTTTCCACAAACGCCCCTAT
1 AGAACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
* * * *
12827 AGAACATGGTCTTTAGCGGCGCTTATCCCACAAACGTCGTTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
** * *
12870 AGAACATGGTCTTTAATGGCGCTTTTACCACAAACGTCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
* * * *
12913 AGACCATGTTCTTTAGCGGCGCTTTTACCATAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
* ** *
12956 AGACCATCATCTTTAGCGGCTC-TTTTCACACAAACG-CGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTTC-CACAAACGCCGCTAA
*
12998 AGACCATGGTCTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTT-CCACAAACGCCGCTAA
13042 CATTAACAGA
Statistics
Matches: 183, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
42 29 0.16
43 147 0.80
44 7 0.04
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAA
Found at i:13030 original size:129 final size:129
Alignment explanation
Indices: 12804--13041 Score: 316
Period size: 129 Copynumber: 1.8 Consensus size: 129
12794 CTTTAACGAA
* * ** * *
12804 GCTTTTTCCACAAACGCCCCTATAGAACATGGTCTTTAGCGGCGCTTATCCCACAAACGTCGTTA
1 GCTTTTACCACAAACGCCCCTAAAGAACATCATCTTTAGCGGCGCTTATCACACAAACGTCGCTA
* *
12869 AAGAACATGGTCTTTAATGGCGCTTTTACCACAAACGTCGCTAAAGACCATGTTCTTTAGCGGC
66 AAGAACATGGTCTTTAACGGCGCTTTTACCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
* * * * *
12933 GCTTTTACCATAAACGCCGCTAAAGACCATCATCTTTAGCGGCTCTTTTCACACAAACG-CGCTA
1 GCTTTTACCACAAACGCCCCTAAAGAACATCATCTTTAGCGGCGCTTATCACACAAACGTCGCTA
* * *
12997 AAGACCATGGTCTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAA
66 AAGAACATGGTCTTTAACGGCGC-TTTTACCACAAACGCCGCTAA
13042 CATTAACAGA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
128 24 0.26
129 68 0.74
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (129 bp):
GCTTTTACCACAAACGCCCCTAAAGAACATCATCTTTAGCGGCGCTTATCACACAAACGTCGCTA
AAGAACATGGTCTTTAACGGCGCTTTTACCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
Found at i:14290 original size:30 final size:30
Alignment explanation
Indices: 14246--14313 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
14236 TTAAAAAGCG
* * *
14246 TAAAAT-TATTAAAAATGATGTA-ATCTTAT
1 TAAAATATTTTAAAAAT-ATGAATATATTAT
14275 TAAAATATTTTAAAAATATGAATATATTAT
1 TAAAATATTTTAAAAATATGAATATATTAT
14305 TAAAATATT
1 TAAAATATT
14314 ATGAAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (30 bp):
TAAAATATTTTAAAAATATGAATATATTAT
Found at i:14312 original size:11 final size:11
Alignment explanation
Indices: 14271--14320 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
14261 TGATGTAATC
14271 TTATTAAAATA
1 TTATTAAAATA
14282 TT-TTAAAA-A
1 TTATTAAAATA
* *
14291 -TATGAATATA
1 TTATTAAAATA
14301 TTATTAAAATA
1 TTATTAAAATA
*
14312 TTATGAAAA
1 TTATTAAAA
14321 GTTTATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
8 1 0.03
9 5 0.16
10 7 0.23
11 18 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:21262 original size:2 final size:2
Alignment explanation
Indices: 21255--21291 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21245 AGTTAAGAAT
21255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.