Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009820.1 Corchorus capsularis cultivar CVL-1 contig09841, 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: 6156
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1677 original size:62 final size:61
Alignment explanation
Indices: 1526--1652 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
1516 CTTTCTCAAA
* * * * * *
1526 TCTTCAATTCTCA-ACCTCAAACAGGTCTTTCTCAATTTCAACGTCGACCATACACTGGTCT
1 TCTTCAATT-TCAGACCTCAAACAGGTCTTTCTTAAATTCAAAGCCGACCACACACGGGTCT
*
1587 TCTTCAATTTCAGATCTCAAACAGGTCTTTCTTAACATTCAAAGCCGACCACACACGGGTCT
1 TCTTCAATTTCAGACCTCAAACAGGTCTTTCTTAA-ATTCAAAGCCGACCACACACGGGTCT
1649 TCTT
1 TCTT
1653 AAGTTTCTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
60 3 0.05
61 29 0.51
62 25 0.44
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (61 bp):
TCTTCAATTTCAGACCTCAAACAGGTCTTTCTTAAATTCAAAGCCGACCACACACGGGTCT
Found at i:2218 original size:2 final size:2
Alignment explanation
Indices: 2213--2249 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2203 CATGTGTGTC
2213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2250 CGATGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3482 original size:49 final size:48
Alignment explanation
Indices: 3440--3816 Score: 596
Period size: 49 Copynumber: 7.7 Consensus size: 48
3430 AAATAAGCAA
*
3440 CTTCCGTCCGGGAAGGG-AGTTTTAGGAAAATAACAGGTAAAATCAAATGC
1 CTTCCGTCCGGGAAGGGCA-TTTT-GGGAAATAACAGGTAAAATC-AATGC
3490 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
* *
3539 CTTGCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATAC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
3588 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
* *
3637 CTTGCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATAC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
*
3686 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATAC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
3735 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGC
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATC-AATGC
*
3784 CTTCCGTCCGGGAAGGGCATTTCGGGAAA-AACA
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACA
3817 AAATTTGAGT
Statistics
Matches: 316, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
48 4 0.01
49 290 0.92
50 21 0.07
51 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (48 bp):
CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAATGC
Found at i:3656 original size:147 final size:147
Alignment explanation
Indices: 3440--3816 Score: 677
Period size: 147 Copynumber: 2.6 Consensus size: 147
3430 AAATAAGCAA
*
3440 CTTCCGTCCGGGAAGGG-AGTTTTAGGAAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAA
1 CTTCCGTCCGGGAAGGGCA-TTTT-GGGAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAA
* *
3504 GGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTGCGTCCGGGAAGGGCATTTTGGGAAAT
64 GGGCATTTTGGGAAATAACAGGTAAAATCAAATACCTTCCGTCCGGGAAGGGCATTTTGGGAAAT
3569 AACAGGTAAAATCAAATAC
129 AACAGGTAAAATCAAATAC
*
3588 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTGCGTCCGGGAAGG
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAAGG
3653 GCATTTTGGGAAATAACAGGTAAAATCAAATACCTTCCGTCCGGGAAGGGCATTTTGGGAAATAA
66 GCATTTTGGGAAATAACAGGTAAAATCAAATACCTTCCGTCCGGGAAGGGCATTTTGGGAAATAA
3718 CAGGTAAAATCAAATAC
131 CAGGTAAAATCAAATAC
3735 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAAGG
1 CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAAGG
*
3800 GCATTTCGGGAAA-AACA
66 GCATTTTGGGAAATAACA
3817 AAATTTGAGT
Statistics
Matches: 222, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
146 4 0.02
147 196 0.88
148 21 0.09
149 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (147 bp):
CTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGGTAAAATCAAATGCCTTCCGTCCGGGAAGG
GCATTTTGGGAAATAACAGGTAAAATCAAATACCTTCCGTCCGGGAAGGGCATTTTGGGAAATAA
CAGGTAAAATCAAATAC
Found at i:5236 original size:18 final size:18
Alignment explanation
Indices: 5213--5278 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
5203 CTGCGATAAC
*
5213 ACTATGAACTCTTAAGGA
1 ACTATGAACCCTTAAGGA
5231 ACTATGAACCCTTAA-GA
1 ACTATGAACCCTTAAGGA
* *
5248 AGCTATGAACCCTAAAGAA
1 A-CTATGAACCCTTAAGGA
5267 ACTATGAACCCT
1 ACTATGAACCCT
5279 CAAGTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 3 0.07
18 38 0.88
19 2 0.05
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (18 bp):
ACTATGAACCCTTAAGGA
Done.