Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013880.1 Kokia drynarioides strain JFW-HI SEQ_128908, 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: 11311
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1145 original size:21 final size:20
Alignment explanation
Indices: 1094--1147 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1084 CCTGTACTAG
1094 TTTTACCGATACAAGTATAA
1 TTTTACCGATACAAGTATAA
* *
1114 TTTCTATCGATACATGTCATGAA
1 TTT-TACCGATACAAGT-AT-AA
1137 -TTTACCGATAC
1 TTTTACCGATAC
1148 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.11
21 19 0.68
22 4 0.14
23 2 0.07
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TTTTACCGATACAAGTATAA
Found at i:1910 original size:51 final size:51
Alignment explanation
Indices: 1805--2021 Score: 274
Period size: 51 Copynumber: 4.2 Consensus size: 51
1795 GATAACATAA
* ** * * ** *
1805 AGTCATCGGACCCTTGTTCCATATAGGAATCCATAAACTCCCGATGACACTT
1 AGTCATCGGACCATTAATCCATAAAGG-ATTCATTCACTCACGATGACACTT
* * * *
1857 AGTCATCGAATCC-TTAATCCATAAAGGATTTATTTACTTACGATGACACTT
1 AGTCATCGGA-CCATTAATCCATAAAGGATTCATTCACTCACGATGACACTT
*
1908 AGTCATCGGACCATTAATCCATAAAGGATTCATTCACTCACAATGACACTT
1 AGTCATCGGACCATTAATCCATAAAGGATTCATTCACTCACGATGACACTT
1959 AGTCATCGGACCATTAATCCATAAAGGATTCATTCACTCACGATGACACTT
1 AGTCATCGGACCATTAATCCATAAAGGATTCATTCACTCACGATGACACTT
* *
2010 AGTTATTGGACC
1 AGTCATCGGACC
2022 CTTTCGTTTA
Statistics
Matches: 145, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
50 2 0.01
51 121 0.83
52 20 0.14
53 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (51 bp):
AGTCATCGGACCATTAATCCATAAAGGATTCATTCACTCACGATGACACTT
Found at i:4834 original size:192 final size:192
Alignment explanation
Indices: 4507--4885 Score: 659
Period size: 192 Copynumber: 2.0 Consensus size: 192
4497 CTCGTACACT
* * * *
4507 CCATTCTGCTATGAAGTGTAGATATTGATGAGCTGGTGTTGGATTCTATCTTCTTCATAATAGCT
1 CCATTCTGCTATGAACTGTAGATATGGATGAGCTGGTGTTGGATTCTAGCTTCTTCACAATAGCT
*
4572 TTGGAATTTCTATAAGGTGTACTCGATTCCATTGTCAGACCTGATCTTCTTCAGTTTTATATCAG
66 TTGGAATTTCTATAAGGTGTACTCAATTCCATTGTCAGACCTGATCTTCTTCAGTTTTATATCAG
*
4637 TTTGGTTTTCAACATCTACTTGAAATTTTCGAAAAACTTATGTGACATAAGTTTTTTTTTTA
131 TTTGGTTTTCAACATCTACTTGAAATTTTCGAAAAACTTATATGACATAAGTTTTTTTTTTA
4699 CCATTCTGCTATGAACTGTAGATATGGATGAGCTGGTGTTGGATTCTAGCTTCTTCACAATAGCT
1 CCATTCTGCTATGAACTGTAGATATGGATGAGCTGGTGTTGGATTCTAGCTTCTTCACAATAGCT
* * *
4764 TTGGAATTTCTATGAGGTGTACTCAATTCCATTGTTAGACCTGATCTTCTTCAGTTTTATATTAG
66 TTGGAATTTCTATAAGGTGTACTCAATTCCATTGTCAGACCTGATCTTCTTCAGTTTTATATCAG
* *
4829 TTTGGTTTTCAACATCTACTTGAAATTTTCGAAAAACTTCTATGACATCAGTTTTTT
131 TTTGGTTTTCAACATCTACTTGAAATTTTCGAAAAACTTATATGACATAAGTTTTTT
4886 GTTTCAAAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
192 176 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (192 bp):
CCATTCTGCTATGAACTGTAGATATGGATGAGCTGGTGTTGGATTCTAGCTTCTTCACAATAGCT
TTGGAATTTCTATAAGGTGTACTCAATTCCATTGTCAGACCTGATCTTCTTCAGTTTTATATCAG
TTTGGTTTTCAACATCTACTTGAAATTTTCGAAAAACTTATATGACATAAGTTTTTTTTTTA
Found at i:8653 original size:21 final size:21
Alignment explanation
Indices: 8627--8669 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
8617 ATAAACAATA
8627 TAATGATTTT-ATCTTTTAATT
1 TAATGATTTTGA-CTTTTAATT
8648 TAATGATTTTGACTTTTAATT
1 TAATGATTTTGACTTTTAATT
8669 T
1 T
8670 TAGAAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
TAATGATTTTGACTTTTAATT
Done.