Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007948.1 Corchorus capsularis cultivar CVL-1 contig07969, 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: 4655
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:271 original size:45 final size:45
Alignment explanation
Indices: 222--307 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
212 AAGGAAAGCC
* * * *
222 TAAAATCCTAAAACTATTCAATAGTACAAACATCAAGAAATCATA
1 TAAAATCCAAAAAATATTCAATAGCAAAAACATCAAGAAATCATA
*
267 TAAAATCCAAAAAATATTCAATAGCAAAAACATTAAGAAAT
1 TAAAATCCAAAAAATATTCAATAGCAAAAACATCAAGAAAT
308 AATGTGATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (45 bp):
TAAAATCCAAAAAATATTCAATAGCAAAAACATCAAGAAATCATA
Found at i:656 original size:1 final size:1
Alignment explanation
Indices: 650--678 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
640 TGGGTTGAGG
650 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
679 GAAGAGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1753 original size:32 final size:32
Alignment explanation
Indices: 1717--1781 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1707 TCAATTACAT
* *
1717 AAACATGTTCATACAAACTTTATTACCAAAAA
1 AAACATGTTCATACAAACTTTAGTAACAAAAA
1749 AAACATGTTCATACAAACTTTAGTAACAAAAA
1 AAACATGTTCATACAAACTTTAGTAACAAAAA
1781 A
1 A
1782 TACCACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (32 bp):
AAACATGTTCATACAAACTTTAGTAACAAAAA
Found at i:3856 original size:19 final size:21
Alignment explanation
Indices: 3832--3877 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
3822 AAATTTCGAG
*
3832 AACCTTTTTAT-AATTTT-TT
1 AACCTTCTTATAAATTTTGTT
3851 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTAT-AAATTTTGTT
3873 AACCT
1 AACCT
3878 CCCTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (21 bp):
AACCTTCTTATAAATTTTGTT
Found at i:3877 original size:22 final size:22
Alignment explanation
Indices: 3818--3892 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
3808 AACCTGATAC
* ** *
3818 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGTTAACCTTCT
3840 TAT--AATTTT-TTAACCTTCT
1 TATGAAATTTTGTTAACCTTCT
* *
3859 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGTTAACCTTCT
*
3881 TAAGAAATTTTG
1 TATGAAATTTTG
3893 AAGACCTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 10 0.23
20 5 0.12
21 6 0.14
22 22 0.51
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTTCT
Found at i:4029 original size:21 final size:22
Alignment explanation
Indices: 3990--4030 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3980 TAACCAAAAA
*
3990 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCACTATGATT
*
4012 TTTTGAT-ACCTCATTATGA
1 TTTTGATAACCTCACTATGA
4031 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGATT
Found at i:4104 original size:22 final size:21
Alignment explanation
Indices: 3850--4104 Score: 109
Period size: 22 Copynumber: 12.0 Consensus size: 21
3840 TATAATTTTT
* *
3850 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCCTATGAAATTTTGA
*
3872 TAACCTCCCTAAGAAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
*
3894 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTC-CTATGAAATTTTGA
* *
3916 TAACTTCCCAAT-AAATTTTTGA
1 TAACCT-CCTATGAAA-TTTTGA
* * *
3938 TAACCAACACTATGAGA---CGA
1 TAACC-TC-CTATGAAATTTTGA
* * *
3958 TAACTTTCTTATGAAATCTTGA
1 TAAC-CTCCTATGAAATTTTGA
*
3980 TAA---CC-A-AAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
3996 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
* *
4018 T-ACCTCATTATGAAATTTTGT
1 TAACCTC-CTATGAAATTTTGA
*
4039 TAATCTTCCTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
* * *
4061 TCTACATACTATGAAATTTTGA
1 T-AACCTCCTATGAAATTTTGA
*
4083 TAACCCTCTTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
4105 AAACTAAACT
Statistics
Matches: 171, Mismatches: 38, Indels: 48
0.67 0.15 0.19
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
18 1 0.01
19 6 0.04
20 10 0.06
21 23 0.13
22 108 0.63
23 9 0.05
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Done.