Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013227.1 Corchorus capsularis cultivar CVL-1 contig13248, 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: 20456
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1154 original size:2 final size:2
Alignment explanation
Indices: 1147--1179 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1137 ATGTGCATTC
*
1147 AT AT AT AT AT AT GT 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 AT A
1180 ATAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2501 original size:23 final size:24
Alignment explanation
Indices: 2471--2520 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
2461 GCACAAAGTG
*
2471 ATACTAATATTCTTTCTC-TTTAC
1 ATACTAATATTCTCTCTCTTTTAC
2494 ATACTAATATTCTCTCTCTTTTAC
1 ATACTAATATTCTCTCTCTTTTAC
2518 ATA
1 ATA
2521 TATAATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (24 bp):
ATACTAATATTCTCTCTCTTTTAC
Found at i:3392 original size:13 final size:12
Alignment explanation
Indices: 3371--3404 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3361 CTTGGAATTC
* *
3371 AAAATAAAAATG
1 AAAAAAAAAAGG
3383 AAAAAAAAAAGG
1 AAAAAAAAAAGG
3395 AAAAAAAAAA
1 AAAAAAAAAA
3405 AGAGAGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:9256 original size:15 final size:15
Alignment explanation
Indices: 9234--9280 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9224 GTTATGAACT
9234 TATTTTATTATATTA
1 TATTTTATTATATTA
* * *
9249 TTTTTTATGATAACTA
1 TATTTTATTAT-ATTA
9265 -ATTTTATTATATTA
1 TATTTTATTATATTA
9279 TA
1 TA
9281 ATTGCATCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTTATTATATTA
Found at i:18077 original size:3 final size:3
Alignment explanation
Indices: 18069--18095 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18059 TTAGTATATA
18069 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
18096 TGTTTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19959 original size:31 final size:31
Alignment explanation
Indices: 19924--19988 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
19914 TTGGGTTATC
*
19924 AGTCTCCAGACCTTTCGATCTTGGATGTTTG
1 AGTCTCCAGACCTTTAGATCTTGGATGTTTG
*
19955 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGACCTTTAGATCTTGGATGTTTG
19986 AGT
1 AGT
19989 TAGTTCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
AGTCTCCAGACCTTTAGATCTTGGATGTTTG
Found at i:20145 original size:21 final size:21
Alignment explanation
Indices: 20092--20148 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
20082 TTCTTTGTGG
* * * *
20092 TTTTTGGATCAATCGGGGAGG
1 TTTTCGGATCACTCAGGGAGA
20113 TTTTCGGATCACTCAGGGAGA
1 TTTTCGGATCACTCAGGGAGA
20134 TTTTCGGATCACTCA
1 TTTTCGGATCACTCA
20149 CCTTTCTGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (21 bp):
TTTTCGGATCACTCAGGGAGA
Found at i:20368 original size:21 final size:21
Alignment explanation
Indices: 20326--20369 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20316 TGAACTATGT
* * *
20326 AATTTCATTTTCATGAATAAA
1 AATTACATTTTCATAAAAAAA
*
20347 AATTACATTTTCTTAAAAAAA
1 AATTACATTTTCATAAAAAAA
20368 AA
1 AA
20370 AACAAGAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTACATTTTCATAAAAAAA
Done.