Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018098.1 Corchorus olitorius cultivar O-4 contig18131, 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: 43472
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:14276 original size:8 final size:8
Alignment explanation
Indices: 14262--14340 Score: 86
Period size: 8 Copynumber: 9.4 Consensus size: 8
14252 AAGTTATACA
14262 AGTAATTT
1 AGTAATTT
*
14270 TGTAATTT
1 AGTAATTT
14278 AGTAATTT
1 AGTAATTT
14286 AGTAAATTT
1 AGT-AATTT
14295 AGTAATTT
1 AGTAATTT
*
14303 TGTAATTT
1 AGTAATTT
*
14311 TGTAATTAT
1 AGTAATT-T
*
14320 CAATAAATTT
1 -AGT-AATTT
14330 AGTAATTT
1 AGTAATTT
14338 AGT
1 AGT
14341 TAGCATTCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
8 44 0.72
9 11 0.18
10 2 0.03
11 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (8 bp):
AGTAATTT
Found at i:14299 original size:25 final size:24
Alignment explanation
Indices: 14262--14340 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 24
14252 AAGTTATACA
*
14262 AGTAATTTTGTAATTTAGTAATTT
1 AGTAATTTAGTAATTTAGTAATTT
*
14286 AGTAAATTTAGTAATTTTGTAATTT
1 AGT-AATTTAGTAATTTAGTAATTT
* *
14311 TGTAATTATCAATAAATTTAGTAATTT
1 AGTAATT-T-AGT-AATTTAGTAATTT
14338 AGT
1 AGT
14341 TAGCATTCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 7 0.16
25 22 0.49
26 2 0.04
27 14 0.31
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (24 bp):
AGTAATTTAGTAATTTAGTAATTT
Found at i:14304 original size:33 final size:35
Alignment explanation
Indices: 14262--14337 Score: 120
Period size: 33 Copynumber: 2.2 Consensus size: 35
14252 AAGTTATACA
*
14262 AGTAATTTTGTAATTTAGTAATT-T-AGTAAATTT
1 AGTAATTTTGTAATTTAGTAATTATCAATAAATTT
*
14295 AGTAATTTTGTAATTTTGTAATTATCAATAAATTT
1 AGTAATTTTGTAATTTAGTAATTATCAATAAATTT
14330 AGTAATTT
1 AGTAATTT
14338 AGTTAGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 22 0.56
34 1 0.03
35 16 0.41
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (35 bp):
AGTAATTTTGTAATTTAGTAATTATCAATAAATTT
Found at i:16353 original size:41 final size:41
Alignment explanation
Indices: 16291--16579 Score: 320
Period size: 41 Copynumber: 6.9 Consensus size: 41
16281 ATATAGAAAT
* *
16291 TGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAGTATG-GA
1 TGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGTATGAGA
16332 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG-A-GAGAA
1 TGCCCCTGTGTTATAAATGTGTTTG-GGACTTTAGTATGAG-A
16373 TTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT-GATAT-AGA
1 -TGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAG-TATGAGA
* * * *
16415 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGG
1 TGCCCCTGTGTTATAAATGTGTTTG-GGACTTTAGTAT-GAGA
16458 TGCCCCCTGTGTTATAAATGTGTTTGGGGACTTTAGTATG-GA
1 TG-CCCCTGTGTTATAAATGTGTTT-GGGACTTTAGTATGAGA
* * *
16500 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGAA
1 TGCCCCTGTGTTATAAATGTGTTTG-GGACTTTAGTATGAG-A
*
16543 TTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTAGT
1 -TGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGT
16580 TATTGGGTAA
Statistics
Matches: 214, Mismatches: 15, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 97 0.45
42 37 0.17
43 10 0.05
44 62 0.29
45 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.39
Consensus pattern (41 bp):
TGCCCCTGTGTTATAAATGTGTTTGGGACTTTAGTATGAGA
Found at i:16427 original size:83 final size:84
Alignment explanation
Indices: 16288--16579 Score: 453
Period size: 85 Copynumber: 3.5 Consensus size: 84
16278 GCCATATAGA
* * * *
16288 AATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAGTATGGATGCCCCTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGGATGCCTCTGTGTTATAAATGTG
16353 TTTGAGGACTTTAG-AGAG
66 TTTGAGGACTTTAGAAGAG
*
16371 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT-GATATAGATGCCTCTGTGTTATAAATGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTAG-TATGGATGCCTCTGTGTTATAAATGT
* *
16435 GTTTGAGGACTTTGGAATAG
65 GTTTGAGGACTTTAGAAGAG
**
16455 AGGTGCCCCCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGGATGCCTCTGTGTTATAAATGT
1 AATTG-CCCCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGGATGCCTCTGTGTTATAAATGT
16520 GTTTGAGGACTTTAGAAAGAG
65 GTTTGAGGACTTTAG-AAGAG
*
16541 AATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTAGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTAGT
16580 TATTGGGTAA
Statistics
Matches: 189, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
82 1 0.01
83 71 0.38
84 6 0.03
85 103 0.54
86 8 0.04
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (84 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTAGTATGGATGCCTCTGTGTTATAAATGTG
TTTGAGGACTTTAGAAGAG
Found at i:17766 original size:37 final size:37
Alignment explanation
Indices: 17725--17799 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
17715 TGAAACATAA
* *
17725 AAATTCTCTTTTGAACCCTTCATGAAACTCGTAGATC
1 AAATTCACTTTCGAACCCTTCATGAAACTCGTAGATC
**** *
17762 AAATTCACTTTCGGGTTCTTCATGAAAGTCGTAGATC
1 AAATTCACTTTCGAACCCTTCATGAAACTCGTAGATC
17799 A
1 A
17800 TACAGTAACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (37 bp):
AAATTCACTTTCGAACCCTTCATGAAACTCGTAGATC
Found at i:21202 original size:51 final size:53
Alignment explanation
Indices: 21142--21262 Score: 147
Period size: 53 Copynumber: 2.3 Consensus size: 53
21132 TTGGCTGCAT
* * *
21142 AAAGGTATAATGGTGCGAATT-AAGTCAT-CCAAGCATTCCTCTTACATAGTG
1 AAAGGTATAATGGTGCAAATTGAAGACATACCAAGCATTCCTATTACATAGTG
** * *
21193 AAAGGTATAATGGTGCAAATTGAAGACATATGATGCATTCCTATTACATAGTT
1 AAAGGTATAATGGTGCAAATTGAAGACATACCAAGCATTCCTATTACATAGTG
* *
21246 AAAGGTGTAATGATGCA
1 AAAGGTATAATGGTGCA
21263 TTCCTATTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 20 0.34
52 6 0.10
53 33 0.56
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (53 bp):
AAAGGTATAATGGTGCAAATTGAAGACATACCAAGCATTCCTATTACATAGTG
Found at i:22445 original size:53 final size:53
Alignment explanation
Indices: 22370--22541 Score: 285
Period size: 53 Copynumber: 3.2 Consensus size: 53
22360 AAAGGTATAA
* *
22370 TAATGGTGCAAATTAAATTCATACTATGCATTCCTATTACATAGTGAAAGGTG
1 TAATGGTGCAAATTGAAGTCATACTATGCATTCCTATTACATAGTGAAAGGTG
*
22423 TAATGGTGCAAATTGAAGTCATACTATGCATTCCTATTACACAGTGAAAGGTG
1 TAATGGTGCAAATTGAAGTCATACTATGCATTCCTATTACATAGTGAAAGGTG
22476 TAATGGTGCAAATTGAAGTCATA-TGATGCATTCCTATTACATAGAT-AAAGGTG
1 TAATGGTGCAAATTGAAGTCATACT-ATGCATTCCTATTACATAG-TGAAAGGTG
22529 TAATGGTGCAAAT
1 TAATGGTGCAAAT
22542 AATTTCACGA
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
52 1 0.01
53 111 0.98
54 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (53 bp):
TAATGGTGCAAATTGAAGTCATACTATGCATTCCTATTACATAGTGAAAGGTG
Found at i:25196 original size:2 final size:2
Alignment explanation
Indices: 25189--25235 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
25179 ATATGTATTT
*
25189 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA T- TA CA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
25229 TA TA TA T
1 TA TA TA T
25236 CAGATTTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 34 0.87
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.