Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008932.1 Kokia drynarioides strain JFW-HI SEQ_123623, 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: 411669
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:362476 original size:31 final size:31
Alignment explanation
Indices: 362435--362495 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
362425 AAAATGGTCT
* *
362435 TTAAATTATTC-AATAGTTTTCATTTAAGTCG
1 TTAAACTATTCGAA-AGTTTTCATTCAAGTCG
*
362466 TTAAACTATTCGAAAGTTTTTATTCAAGTC
1 TTAAACTATTCGAAAGTTTTCATTCAAGTC
362496 ATTGGGCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (31 bp):
TTAAACTATTCGAAAGTTTTCATTCAAGTCG
Found at i:364093 original size:2 final size:2
Alignment explanation
Indices: 364086--364121 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
364076 GTGAGTTGTT
364086 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
364122 TATATACACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:364855 original size:6 final size:6
Alignment explanation
Indices: 364844--364879 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
364834 CAGTTAAGAA
* *
364844 GGAACC GGAACC AGAACC AGAACC GGAACC GGAACC
1 GGAACC GGAACC GGAACC GGAACC GGAACC GGAACC
364880 AATGCCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.33, G:0.28, T:0.00
Consensus pattern (6 bp):
GGAACC
Found at i:364868 original size:18 final size:18
Alignment explanation
Indices: 364845--364880 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
364835 AGTTAAGAAG
364845 GAACCGGAACCAGAACCA
1 GAACCGGAACCAGAACCA
*
364863 GAACCGGAACCGGAACCA
1 GAACCGGAACCAGAACCA
364881 ATGCCTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.25, T:0.00
Consensus pattern (18 bp):
GAACCGGAACCAGAACCA
Found at i:366574 original size:57 final size:54
Alignment explanation
Indices: 366513--366622 Score: 157
Period size: 57 Copynumber: 2.0 Consensus size: 54
366503 TCACATCAGT
* * * *
366513 ATATTATCATGTAATTACATTAGTATATTCAAAAAATAAATGAATAGATCTAATAAG
1 ATATTACCATGTAATCACATCAGTATATT-AAAAAA-AAA-AAATAGATCTAATAAG
366570 ATATTACCATGTAATCACATCAGTATATTAAAAAAAAAAAATAGATCTAATAA
1 ATATTACCATGTAATCACATCAGTATATTAAAAAAAAAAAATAGATCTAATAA
366623 TTCATATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 14 0.29
55 3 0.06
56 6 0.12
57 26 0.53
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (54 bp):
ATATTACCATGTAATCACATCAGTATATTAAAAAAAAAAAATAGATCTAATAAG
Found at i:367847 original size:2 final size:2
Alignment explanation
Indices: 367840--367869 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
367830 AAATAAACAA
367840 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
367870 GTATTGAAGT
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:371834 original size:56 final size:55
Alignment explanation
Indices: 371767--371878 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 55
371757 AAATGGCGGG
*
371767 TAAAACAATTTTATGACTTTTTTAACTTTTAATTAATTATTTATTTTTTGTTTGGA
1 TAAAACAATTTTATGACTTTTTTAACTTTTAATTAATTATTTAATTTTTG-TTGGA
* * *
371823 TAAAACAATTTTATGATTTTTTTAATTTTTAATTATTTATTTAATTTTTGTTGGA
1 TAAAACAATTTTATGACTTTTTTAACTTTTAATTAATTATTTAATTTTTGTTGGA
371878 T
1 T
371879 CAATTTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 6 0.12
56 46 0.88
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (55 bp):
TAAAACAATTTTATGACTTTTTTAACTTTTAATTAATTATTTAATTTTTGTTGGA
Found at i:391859 original size:31 final size:31
Alignment explanation
Indices: 391823--391897 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
391813 CAGTCCAGTA
*
391823 ACTTAAATAAAAACGTTCAAATAGTTCAATG
1 ACTTAAATAAAAACGTTCAAACAGTTCAATG
* * * * *
391854 ACTTAAATGAAAACTTTCTAACAGTTTAGTG
1 ACTTAAATAAAAACGTTCAAACAGTTCAATG
*
391885 ACTTAAACAAAAA
1 ACTTAAATAAAAA
391898 TATTTTAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.29
Consensus pattern (31 bp):
ACTTAAATAAAAACGTTCAAACAGTTCAATG
Found at i:407918 original size:22 final size:20
Alignment explanation
Indices: 407878--407918 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
407868 TAGTATTTTT
407878 AATTTTTAATTTTTAAATTC
1 AATTTTTAATTTTTAAATTC
*
407898 AATTATTTATTTTGTTAAATT
1 AATT-TTTAATTT-TTAAATT
407919 TAGATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
AATTTTTAATTTTTAAATTC
Found at i:409312 original size:20 final size:20
Alignment explanation
Indices: 409268--409312 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
409258 AAACAGCAAT
409268 TTTCT-TTTCTCTTTCTTTC
1 TTTCTGTTTCTCTTTCTTTC
*
409287 TCTCTGTTTCTCTCTTC-TTC
1 TTTCTGTTTCTCT-TTCTTTC
409307 TTTCTG
1 TTTCTG
409313 GTGGAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 15 0.68
21 3 0.14
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTCTGTTTCTCTTTCTTTC
Done.