Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013824.1 Kokia drynarioides strain JFW-HI SEQ_128852, 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: 47749
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:54 original size:6 final size:6
Alignment explanation
Indices: 11--75 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
1 TTTTATTTAT
* * *
11 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTT-AA TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
59 TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
76 GGGAGTATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
5 10 0.22
6 27 0.59
7 9 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:58 original size:17 final size:17
Alignment explanation
Indices: 13--75 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
3 TTATTTATTT
*
13 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAACTT-AAAA
* **
32 TAATTTTAAACTTAATT
1 TAAATTTAAACTTAAAA
*
49 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
66 TAAATTTAAA
1 TAAATTTAAA
76 GGGAGTATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
17 25 0.69
18 8 0.22
19 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:13128 original size:23 final size:23
Alignment explanation
Indices: 13084--13129 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13074 TGCTAGTATA
*
13084 TTAAAATTTTGACGTGTTTTTTT
1 TTAAAATTTTGACGTGTATTTTT
*
13107 TTAAAATATTTTAC-TGTATTTTT
1 TTAAAAT-TTTGACGTGTATTTTT
13130 ATAATCTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (23 bp):
TTAAAATTTTGACGTGTATTTTT
Found at i:15800 original size:123 final size:123
Alignment explanation
Indices: 15566--15813 Score: 372
Period size: 123 Copynumber: 2.0 Consensus size: 123
15556 TATCATGTTG
* ** * *
15566 AACCTAGTCAGAATTTTGGGTTTATATGAAGAATGCATAGTTTAGAATAGCTTTTTTTCATGCTA
1 AACCTAGTCAGAATTTTGGGTTTATATGAAGAATGAATAACTTAGAAAAGCTTTCTTTCATGCTA
* *
15631 TAAGCTATCCTGGATATTTGTTTGGTTGATTTAAAGTTATCCAAGGGTTTCAAAGGAA
66 TAAGCTATCCTGCATATTTGTTTGATTGATTTAAAGTTATCCAAGGGTTTCAAAGGAA
*
15689 AACCTAGTTAGAATTTTGGG-TTATATGAAGAATGAATAACTTAGAAAAGCTTTCTTTCATGCTA
1 AACCTAGTCAGAATTTTGGGTTTATATGAAGAATGAATAACTTAGAAAAGCTTTCTTTCATGCTA
* * * *
15753 TAAGCTATCCTGCCTTTTTTGTTTGATTGATTTAAAGTTATCTAAGGGTTTCGAAGGAA
66 TAAGCTATCCTG-CATATTTGTTTGATTGATTTAAAGTTATCCAAGGGTTTCAAAGGAA
15812 AA
1 AA
15814 AATATTCGAG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
122 51 0.46
123 61 0.54
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (123 bp):
AACCTAGTCAGAATTTTGGGTTTATATGAAGAATGAATAACTTAGAAAAGCTTTCTTTCATGCTA
TAAGCTATCCTGCATATTTGTTTGATTGATTTAAAGTTATCCAAGGGTTTCAAAGGAA
Found at i:20516 original size:31 final size:31
Alignment explanation
Indices: 20482--20543 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
20472 TTTGGTTTAA
*
20482 TTTTTCGAGGAAATCATTGTTATTATTATTAT
1 TTTTTCGAAG-AATCATTGTTATTATTATTAT
* *
20514 TTTTTTGAAGTATCATTGTTATTATTATTA
1 TTTTTCGAAGAATCATTGTTATTATTATTA
20544 ATGTTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.56
Consensus pattern (31 bp):
TTTTTCGAAGAATCATTGTTATTATTATTAT
Found at i:39174 original size:34 final size:34
Alignment explanation
Indices: 39126--39208 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
39116 GCATACATGC
* *
39126 ATACCTACATACATACATATCTACACATGTGCAT
1 ATACATACATACATACATACCTACACATGTGCAT
*
39160 ATACATACATACATACATACCTACATATGTGCAT
1 ATACATACATACATACATACCTACACATGTGCAT
* *
39194 ATACATGCATGCATA
1 ATACATACATACATA
39209 TGTGTGAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (34 bp):
ATACATACATACATACATACCTACACATGTGCAT
Found at i:41235 original size:17 final size:17
Alignment explanation
Indices: 41213--41246 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41203 GTGTTAACCT
41213 GCATAAAAATTTATTTA
1 GCATAAAAATTTATTTA
41230 GCATAAAAATTTATTTA
1 GCATAAAAATTTATTTA
41247 ATCTTAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
GCATAAAAATTTATTTA
Found at i:41780 original size:18 final size:19
Alignment explanation
Indices: 41754--41792 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
41744 TTAAACAATG
41754 AAATCAAAT-TTAAATATCA
1 AAATCAAATATTAAA-ATCA
41773 AAAT-AAATATTAAAATCA
1 AAATCAAATATTAAAATCA
41791 AA
1 AA
41793 CTCGCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATCAAATATTAAAATCA
Found at i:47653 original size:41 final size:41
Alignment explanation
Indices: 47608--47687 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
47598 ATTAAAAATC
* *
47608 TTTTTACCACATCAATTGAAAAA-GCTTTCAATTGAAATTTTT
1 TTTTTA-CAAATCAATT-AAAAATGCTTTCAAGTGAAATTTTT
*
47650 TTTTTACAAATCCATTAAAAATGCTTTCAAGTGAAATT
1 TTTTTACAAATCAATTAAAAATGCTTTCAAGTGAAATT
47688 CGTTATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 5 0.15
41 23 0.68
42 6 0.18
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (41 bp):
TTTTTACAAATCAATTAAAAATGCTTTCAAGTGAAATTTTT
Done.