Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012820.1 Corchorus capsularis cultivar CVL-1 contig12841, 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: 34742
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1055 original size:2 final size:2
Alignment explanation
Indices: 1044--1085 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1034 ATAATATGTA
1044 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1085 A
1 A
1086 CTAGATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7563 original size:2 final size:2
Alignment explanation
Indices: 7556--7585 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7546 CTGACAGAAA
7556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7586 GTAAACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13653 original size:273 final size:274
Alignment explanation
Indices: 13144--13694 Score: 833
Period size: 273 Copynumber: 2.0 Consensus size: 274
13134 CTAGGGCTGT
*
13144 GATGGACTAGGAGATGTTGGAGGCTTCAAATCTGGATACTGTAACCATAGAGAAACGAGAAGACA
1 GATGGACTAGGAGATGTTGGAGGCTTCAAATCTGGATACTGTAACCATAGAGAAACAAGAAGACA
*
13209 TGTTAGCATTTTCCTGAGTATATACACAATAAGAAGGCAAGATCATGAGGAAGTAATGGAGTAAT
66 TGTTAGCATTTTCCCGAGTATATACACAATAAGAAGGCAAGATCATGAGGAAGTAATGGAGTAAT
* * *
13274 GGAAGTGACATTACAGAAGTATATGGTGAAAGTGGACTTGGACCAGAGTCTGCCTTGGCTTCTAT
131 GAAAGGGACATTACAGAAGTATATGGTGAAAGTGGACTTGAACCAGAGTCTGCCTTGGCTTCTAT
*
13339 TTTGGGTACTGAATTGATTCGAGGAGGGGGTTCTGCTGCTGCTTCTACTTT-GAGCTCTGCTTT-
196 TTTGGGTACTGAAGTGATTCGAGGAGGGGGTTCTGCTGCTGCTTCTACTTTAG-GCTCTGCTTTG
13402 AGCCTCTGAAGGTGCA
260 A-CCTCTGAAGGTGCA
* * *
13418 GATGGAGTAGGAGATGTTGGAGGCTTCAAATCTGGATACTGTAACCATTA-AGAAATAAGGAGA-
1 GATGGACTAGGAGATGTTGGAGGCTTCAAATCTGGATACTGTAACCA-TAGAGAAACAAGAAGAC
* * * *
13481 ATGTTAGCATTTTCCCGATTATATACACAGTAAGAAGGCAATG-TTATGAGGAAGTAATGGGGTA
65 ATGTTAGCATTTTCCCGAGTATATACACAATAAGAAGGCAA-GATCATGAGGAAGTAATGGAGTA
* *
13545 ATGAAAGGGTCATTACAGAAGTATATGGTGAAAGTGGTCTTGAAATTCCAGAGTCTGCCTTGGCT
129 ATGAAAGGGACATTACAGAAGTATATGGTGAAAGTGGACTTG-AA--CCAGAGTCTGCCTTGGCT
* * * *
13610 TCTGTTTTGGGTGCTGAAGTGATTTGAGGAGGGGGTTCTGCTGCTGCTTCTACTTTAGGCTCTGG
191 TCTATTTTGGGTACTGAAGTGATTCGAGGAGGGGGTTCTGCTGCTGCTTCTACTTTAGGCTCTGC
13675 TTTGACCTCTGAAGGTGCA
256 TTTGACCTCTGAAGGTGCA
13694 G
1 G
13695 GAAGAGCCTT
Statistics
Matches: 251, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
273 95 0.38
274 58 0.23
275 2 0.01
276 94 0.37
277 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (274 bp):
GATGGACTAGGAGATGTTGGAGGCTTCAAATCTGGATACTGTAACCATAGAGAAACAAGAAGACA
TGTTAGCATTTTCCCGAGTATATACACAATAAGAAGGCAAGATCATGAGGAAGTAATGGAGTAAT
GAAAGGGACATTACAGAAGTATATGGTGAAAGTGGACTTGAACCAGAGTCTGCCTTGGCTTCTAT
TTTGGGTACTGAAGTGATTCGAGGAGGGGGTTCTGCTGCTGCTTCTACTTTAGGCTCTGCTTTGA
CCTCTGAAGGTGCA
Found at i:21490 original size:12 final size:12
Alignment explanation
Indices: 21462--21517 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
21452 ATGACCAGGG
21462 TGATGAAGATGA
1 TGATGAAGATGA
*
21474 AGATGAAGACT-A
1 TGATGAAGA-TGA
*
21486 TGATGATGAATGGA
1 TGATGAAG-AT-GA
21500 GTGATGAAGATGA
1 -TGATGAAGATGA
21513 TGATG
1 TGATG
21518 CACCACCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
12 21 0.60
13 4 0.11
14 3 0.09
15 7 0.20
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (12 bp):
TGATGAAGATGA
Found at i:32922 original size:17 final size:18
Alignment explanation
Indices: 32886--32923 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
32876 GTACCAACTT
* *
32886 TATTTATTTTTTACTATA
1 TATTAATTTGTTACTATA
32904 TATTAATTTGTTA-TATA
1 TATTAATTTGTTACTATA
32921 TAT
1 TAT
32924 ATATATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTAATTTGTTACTATA
Done.