Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015048.1 Corchorus capsularis cultivar CVL-1 contig15069, 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: 25199
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4354 original size:12 final size:13
Alignment explanation
Indices: 4328--4365 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4318 ATAAATTATT
4328 ATAAAAAATAAAA
1 ATAAAAAATAAAA
*
4341 ATAAAAAAT-TAA
1 ATAAAAAATAAAA
*
4353 ATAAAAAAGAAAA
1 ATAAAAAATAAAA
4366 CCCCTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:8030 original size:12 final size:12
Alignment explanation
Indices: 8013--8042 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8003 ATGAATATAG
8013 TTCTTTGGGATT
1 TTCTTTGGGATT
*
8025 TTCTTTGTGATT
1 TTCTTTGGGATT
8037 TTCTTT
1 TTCTTT
8043 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.67
Consensus pattern (12 bp):
TTCTTTGGGATT
Found at i:12512 original size:146 final size:146
Alignment explanation
Indices: 12245--12528 Score: 451
Period size: 146 Copynumber: 1.9 Consensus size: 146
12235 AATTTTGTTT
* ** *
12245 TCATTCAACCATTAAATACAGCATTAAACTCCAATTGCAAGTTTGCTAAACTGTTTCTATTGAAA
1 TCATTCAACCAATAAATACAGCATTAAACTAAAATTGCAAGTTTGCTAAACTGCTTCTATTGAAA
* *
12310 AGGTAGGCCAATCATGGTGGTGACGTCAAAGATTCTTATAGATGCAGTATGCGCTAACTTGGCCT
66 AGGCAGGCCAATCATGGTGGTGACATCAAAGATTCTTATAGATGCAGTATGCGCTAACTTGGCCT
12375 TTAAGTGACGTCACCA
131 TTAAGTGACGTCACCA
* *
12391 TCATTCAACCAATAAATATAGCATTAAGCTAAAATTGCAAGTTTGCTAAACTGCTTCTATTGAAA
1 TCATTCAACCAATAAATACAGCATTAAACTAAAATTGCAAGTTTGCTAAACTGCTTCTATTGAAA
* * * *
12456 AGGCAGGCTAATGATGGTGGTGACATCAAAGCTTCTTATAGATGCAGTATGGGCTAACTTGGCCT
66 AGGCAGGCCAATCATGGTGGTGACATCAAAGATTCTTATAGATGCAGTATGCGCTAACTTGGCCT
*
12521 TTTAGTGA
131 TTAAGTGA
12529 ACGGCTTGTG
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
146 125 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (146 bp):
TCATTCAACCAATAAATACAGCATTAAACTAAAATTGCAAGTTTGCTAAACTGCTTCTATTGAAA
AGGCAGGCCAATCATGGTGGTGACATCAAAGATTCTTATAGATGCAGTATGCGCTAACTTGGCCT
TTAAGTGACGTCACCA
Found at i:14307 original size:13 final size:13
Alignment explanation
Indices: 14289--14357 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 13
14279 TCAATAATTA
14289 ATATATAAAATAT
1 ATATATAAAATAT
14302 ATATAT---ATAT
1 ATATATAAAATAT
14312 AT-T-T-AAATAT
1 ATATATAAAATAT
* *
14322 ATATTTTAAATAT
1 ATATATAAAATAT
*
14335 ATAGATAAAATAT
1 ATATATAAAATAT
*
14348 ATATTTAAAA
1 ATATATAAAA
14358 GACAATATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
8 1 0.02
9 1 0.02
10 12 0.26
11 1 0.02
12 1 0.02
13 30 0.65
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (13 bp):
ATATATAAAATAT
Found at i:14735 original size:3 final size:3
Alignment explanation
Indices: 14729--14761 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
14719 TCATTAAAAA
14729 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
14762 GAGGCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18415 original size:2 final size:2
Alignment explanation
Indices: 18408--18438 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18398 TTTATAGTAG
18408 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
18439 GCGAGAGAGA
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:22118 original size:31 final size:31
Alignment explanation
Indices: 22080--22144 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
22070 TTGGGTTATC
22080 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
22111 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
22142 AGT
1 AGT
22145 TTGTTCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Done.