Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022921.1 Corchorus olitorius cultivar O-4 contig22954, 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: 41955
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7145 original size:9 final size:9
Alignment explanation
Indices: 7126--7159 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
7116 ATATAAATCT
7126 TATATTATAA
1 TATATT-TAA
7136 TATATTTAA
1 TATATTTAA
7145 TATATTTAA
1 TATATTTAA
7154 TTATAT
1 -TATAT
7160 ATATTACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 12 0.52
10 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATTTAA
Found at i:28195 original size:18 final size:17
Alignment explanation
Indices: 28167--28213 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
28157 TAGACAATTC
*
28167 TTTTTCCTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
*
28184 TTCTTTCTTTTTTGTTTT
1 TT-TTTCTTTTTTCTTTT
*
28202 TTTGTCTTTTTT
1 TTTTTCTTTTTT
28214 GGGTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTT
Found at i:28476 original size:32 final size:32
Alignment explanation
Indices: 28433--28499 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
28423 AAGGTGCGTT
*
28433 AACGCCACTATTTAGCGGCGTTTCTGAATATA
1 AACGCCACTATTTAGCGGCGTTTCTGAACATA
* * **
28465 AACGCCGCTATTTAGTGGTTTTTCTGAACATA
1 AACGCCACTATTTAGCGGCGTTTCTGAACATA
28497 AAC
1 AAC
28500 ACCCCTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (32 bp):
AACGCCACTATTTAGCGGCGTTTCTGAACATA
Found at i:28513 original size:32 final size:32
Alignment explanation
Indices: 28453--28515 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
28443 TTTAGCGGCG
* * * **
28453 TTTCTGAATATAAACGCCGCTATTTAGTGGTT
1 TTTCTGAACATAAACACCCCTAAATAGTGGTT
28485 TTTCTGAACATAAACACCCCTAAATAGTGGT
1 TTTCTGAACATAAACACCCCTAAATAGTGGT
28516 GTTTAGTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (32 bp):
TTTCTGAACATAAACACCCCTAAATAGTGGTT
Found at i:32619 original size:17 final size:17
Alignment explanation
Indices: 32597--32636 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
32587 TTTTCTTTCC
32597 ATATTACAAAATCTAAA
1 ATATTACAAAATCTAAA
32614 ATATTACAAAATCTAAA
1 ATATTACAAAATCTAAA
32631 ATATTA
1 ATATTA
32637 GTAATAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTACAAAATCTAAA
Found at i:32678 original size:15 final size:14
Alignment explanation
Indices: 32654--32696 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
32644 ACCTCTTATT
*
32654 ATTATAATTATTAA
1 ATTATTATTATTAA
*
32668 ACTTATTATTATTAT
1 A-TTATTATTATTAA
32683 ATTAATTATTATTA
1 ATT-ATTATTATTA
32697 GTGGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:32691 original size:18 final size:21
Alignment explanation
Indices: 32648--32696 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
32638 TAATAAACCT
32648 CTTATTATTATAATTATTAAA
1 CTTATTATTATAATTATTAAA
*
32669 CTTATTATTATTA-TATT-AA
1 CTTATTATTATAATTATTAAA
32688 -TTATTATTA
1 CTTATTATTA
32697 GTGGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 4 0.15
21 12 0.44
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
CTTATTATTATAATTATTAAA
Found at i:34228 original size:27 final size:27
Alignment explanation
Indices: 34192--34265 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
34182 TCCGGCATTT
*
34192 AAGGGCAAAACTGTAATTTAG-TCAACC
1 AAGGGTAAAACTGTAATTTAGCTCAA-C
* *
34219 AGGGGTAAAA-TGGTAATTTTAGCTGAAC
1 AAGGGTAAAACT-GTAA-TTTAGCTCAAC
*
34247 AAGGGTAAAACAGTAATTT
1 AAGGGTAAAACTGTAATTT
34266 TGACATCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
28 19 0.50
29 3 0.08
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.26
Consensus pattern (27 bp):
AAGGGTAAAACTGTAATTTAGCTCAAC
Done.