Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022331.1 Corchorus olitorius cultivar O-4 contig22364, 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: 23214
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:10367 original size:2 final size:2
Alignment explanation
Indices: 10360--10390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10350 AACCAGGTCA
10360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10391 CTTATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12807 original size:27 final size:27
Alignment explanation
Indices: 12769--12821 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12759 AAGTGAAGTG
* *
12769 AGAATTGCACTCCCTGGTTTGTTTTTT
1 AGAATTGCACTCACTGGTTTGATTTTT
* *
12796 AGAATTGTACTCACTGTTTTGATTTT
1 AGAATTGCACTCACTGGTTTGATTTT
12822 AATAAATGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (27 bp):
AGAATTGCACTCACTGGTTTGATTTTT
Found at i:14332 original size:21 final size:21
Alignment explanation
Indices: 14308--14376 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
14298 CCTTGTCAAG
14308 TTTCTCTTTTTTCTTTTTTCA-
1 TTTCT-TTTTTTCTTTTTTCAC
* *
14329 TTTCATTTTCTTCCTTTTTCAC
1 TTTC-TTTTTTTCTTTTTTCAC
14351 TTT-TTTTTTTCTTTTTTC-C
1 TTTCTTTTTTTCTTTTTTCAC
14370 TTT-TTTT
1 TTTCTTTT
14377 CTCACTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.19
20 13 0.31
21 17 0.40
22 4 0.10
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTTTTCTTTTTTCAC
Found at i:14357 original size:20 final size:19
Alignment explanation
Indices: 14334--14378 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
14324 TTTCATTTCA
14334 TTTTCTTCCTTTTTCACTTT
1 TTTTCTTCCTTTTTC-CTTT
* *
14354 TTTTTTTCTTTTTTCCTTT
1 TTTTCTTCCTTTTTCCTTT
14373 TTTTCT
1 TTTTCT
14379 CACTTCTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTTCCTTTTTCCTTT
Found at i:17081 original size:23 final size:21
Alignment explanation
Indices: 17041--17082 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
17031 AACAGTTAAA
*
17041 GAAAATTAAGAAAGCAATTAC
1 GAAAATTAAGAAAACAATTAC
17062 GAAAATTAAAGGAAAACAATT
1 GAAAATT-AA-GAAAACAATT
17083 TATCAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (21 bp):
GAAAATTAAGAAAACAATTAC
Found at i:18868 original size:15 final size:15
Alignment explanation
Indices: 18848--18877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18838 CATCATTCTC
18848 AAGTAGCCATAATCA
1 AAGTAGCCATAATCA
*
18863 AAGTAGCCTTAATCA
1 AAGTAGCCATAATCA
18878 CTTACAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (15 bp):
AAGTAGCCATAATCA
Found at i:22379 original size:34 final size:32
Alignment explanation
Indices: 22320--22420 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 32
22310 GCTATGATCA
**
22320 ACCAAAACA-AATTTGTTTTCATCACAATTAAC
1 ACCAAAACAGAATTTG-TTTCATCACAAACAAC
22352 ATCCAAAACAGAATTTGTTTCATTCACAAACAAC
1 A-CCAAAACAGAATTTGTTTCA-TCACAAACAAC
*
22386 ACCTAAAACAG-ATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGAATTT-GTTTCATCACAAACAAC
22419 AC
1 AC
22421 TTAAATTAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
32 1 0.02
33 32 0.52
34 28 0.46
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.26
Consensus pattern (32 bp):
ACCAAAACAGAATTTGTTTCATCACAAACAAC
Found at i:22415 original size:33 final size:33
Alignment explanation
Indices: 22338--22486 Score: 124
Period size: 33 Copynumber: 4.5 Consensus size: 33
22328 AAATTTGTTT
** *
22338 TCATCACAATTAACATCC-AAAACAGAATTT-GTT
1 TCATCACAAACAACA-CCTAAAACAG-ATTTAGTG
22371 TCATTCACAAACAACACCTAAAACAGATTTAGTG
1 TCA-TCACAAACAACACCTAAAACAGATTTAGTG
* ** * *
22405 TCATCACAAACAACACTTAAATTAGGTTTAGTA
1 TCATCACAAACAACACCTAAAACAGATTTAGTG
* * *
22438 TCATCACTAACAACATCTAAAACGGATTTCA-TG
1 TCATCACAAACAACACCTAAAACAGATTT-AGTG
**
22471 TCATTGCAAACAACAC
1 TCATCACAAACAACAC
22487 TCAAATCAGG
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
33 69 0.75
34 23 0.25
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (33 bp):
TCATCACAAACAACACCTAAAACAGATTTAGTG
Found at i:22466 original size:66 final size:66
Alignment explanation
Indices: 22375--22498 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
22365 TTTGTTTCAT
* *
22375 TCACAAACAACACCTAAAACAGATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAGTAT
1 TCACAAACAACACCTAAAACAGATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAGTAT
22439 CA
65 CA
* * * **
22441 TCACTAACAACATCTAAAACGGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
1 TCACAAACAACACCTAAAACAGATTTCATGTCATCACAAACAACACTCAAATCAGGTT
22499 CAGAATTACT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (66 bp):
TCACAAACAACACCTAAAACAGATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGTATC
A
Done.