Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015873.1 Corchorus capsularis cultivar CVL-1 contig15894, 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: 45464
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:97 original size:2 final size:2
Alignment explanation
Indices: 90--121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
80 CTACAGTTTA
90 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
122 GATGTTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14113 original size:36 final size:36
Alignment explanation
Indices: 14068--14149 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 36
14058 TTAGGTTCAA
*
14068 TATAAAACAGTGCTTTG-GATATACCTGTTCATCTGAC
1 TATACAACAG-GCTTTGAG-TATACCTGTTCATCTGAC
* *
14105 -CTACAACA-GCTTTTATGTATACCTGTTCATCTGAC
1 TATACAACAGGCTTTGA-GTATACCTGTTCATCTGAC
14140 TATACAACAG
1 TATACAACAG
14150 ATTTTAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
34 5 0.14
35 18 0.49
36 14 0.38
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (36 bp):
TATACAACAGGCTTTGAGTATACCTGTTCATCTGAC
Found at i:14126 original size:35 final size:36
Alignment explanation
Indices: 14087--14155 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
14077 GTGCTTTGGA
* *
14087 TATACCTGTTCATCTGAC-CTACAACAGCTTTTATG
1 TATACCTGTTCATCTGACTATACAACAGATTTTATG
14122 TATACCTGTTCATCTGACTATACAACAGATTTTA
1 TATACCTGTTCATCTGACTATACAACAGATTTTA
14156 AGTAGTCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 18 0.58
36 13 0.42
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (36 bp):
TATACCTGTTCATCTGACTATACAACAGATTTTATG
Found at i:28797 original size:14 final size:14
Alignment explanation
Indices: 28778--28805 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28768 ACTACATACA
28778 ACCTTTTATAAATG
1 ACCTTTTATAAATG
28792 ACCTTTTATAAATG
1 ACCTTTTATAAATG
28806 GTACCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
ACCTTTTATAAATG
Found at i:29273 original size:21 final size:19
Alignment explanation
Indices: 29249--29288 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
29239 CCTAAGCTGC
29249 AAAGGAAGACAAACAGACAAA
1 AAAGGAAGA-AAACA-ACAAA
*
29270 AAAGGGAGAAAACAACAAA
1 AAAGGAAGAAAACAACAAA
29289 GAAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.68, C:0.12, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAGGAAGAAAACAACAAA
Found at i:39456 original size:31 final size:31
Alignment explanation
Indices: 39418--39478 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
39408 ATACCAAATC
39418 ATGACTGAGAAGAACTTAATCCATCACTCTT
1 ATGACTGAGAAGAACTTAATCCATCACTCTT
39449 ATGACTGAGAAGAACTTAATCCATCACTCT
1 ATGACTGAGAAGAACTTAATCCATCACTCT
39479 GATAGCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (31 bp):
ATGACTGAGAAGAACTTAATCCATCACTCTT
Found at i:43021 original size:93 final size:91
Alignment explanation
Indices: 42862--43059 Score: 242
Period size: 93 Copynumber: 2.2 Consensus size: 91
42852 ACAAATGTAG
* *
42862 CTCGAACCTTAT-TTTCAGATTCTGATTCAATCAAGTTGTTGTTGCTACCCATTTGTAGAAAATG
1 CTCGAACCTTATCTTTCAGAATCTGATTCAATCAAGTTGTTGTTGCCACCCATTTGTAGAAAATG
*
42926 GGATGTCCAATATTGCTGCTCTTCT-GAGT
66 GGATG-CCAA-A-TGCTGCTCTTCTGGA-C
* * * *
42955 CTCGAACCTTATCTTTC-GAATCTGATTTAATCAAGTTGTTTTTGCCACCCGTTTGT-GCAGAAT
1 CTCGAACCTTATCTTTCAGAATCTGATTCAATCAAGTTGTTGTTGCCACCCATTTGTAG-AAAAT
*
43018 GGGATGCCCAATGCTGCTCTTCTGGAC
65 GGGATGCCAAATGCTGCTCTTCTGGAC
*
43045 CTCGAATCTTATCTT
1 CTCGAACCTTATCTT
43060 CCAGTCCCAT
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
90 26 0.28
91 3 0.03
92 4 0.04
93 56 0.60
94 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (91 bp):
CTCGAACCTTATCTTTCAGAATCTGATTCAATCAAGTTGTTGTTGCCACCCATTTGTAGAAAATG
GGATGCCAAATGCTGCTCTTCTGGAC
Found at i:45443 original size:22 final size:22
Alignment explanation
Indices: 45392--45443 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
45382 TTTTTGAGAT
* *
45392 AATAAAATATTGAATTTATTTA
1 AATAAAATAGTGAATTTATGTA
*
45414 AATGAAAATAGTGATTTTA-GTA
1 AAT-AAAATAGTGAATTTATGTA
45436 GAATAAAA
1 -AATAAAA
45444 CTGTATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
AATAAAATAGTGAATTTATGTA
Done.