Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008499.1 Corchorus capsularis cultivar CVL-1 contig08520, 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: 10698
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:6601 original size:75 final size:75
Alignment explanation
Indices: 6449--6674 Score: 337
Period size: 75 Copynumber: 3.0 Consensus size: 75
6439 TTATCTAGAC
* *
6449 TGTGAGCAAAGGAATGATGGGTTTTAATCAAAACAAGTTTC-AAATCAGTTTCAATCAAAGCAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAACAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
6513 GGTTTCGAGG
66 GGTTTCGAGG
* * *
6523 TGTGGGCAAAAGAATGATGAGTTTTAATCAAAACAGGTTTCAAAATCAGTTTCAATCAAAGAAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAACAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
6588 GGTTTCGAGG
66 GGTTTCGAGG
* * * * *
6598 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTAAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAACAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
* *
6663 GATTTCAAGG
66 GGTTTCGAGG
6673 TG
1 TG
6675 ATTGAATCCA
Statistics
Matches: 137, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 37 0.27
75 100 0.73
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (75 bp):
TGTGAGCAAAAGAATGATGAGTTTTAATCAAAACAAGTTTCAAAATCAGTTTCAATCAAAGCAAT
GGTTTCGAGG
Found at i:8770 original size:26 final size:26
Alignment explanation
Indices: 8741--8825 Score: 61
Period size: 26 Copynumber: 3.3 Consensus size: 26
8731 ATAAGATTGC
8741 ATTCCATTTGTAAGTCCAATATCAAA
1 ATTCCATTTGTAAGTCCAATATCAAA
* * ***
8767 ATTCGATTT-TCAAGAT--AAGAT-TGC
1 ATTCCATTTGT-AAG-TCCAATATCAAA
*
8791 ATTCCATTTGTAAGACCAATATCAAA
1 ATTCCATTTGTAAGTCCAATATCAAA
*
8817 ATTCGATTT
1 ATTCCATTT
8826 TCAAGATAAG
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
24 11 0.27
25 10 0.24
26 19 0.46
27 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (26 bp):
ATTCCATTTGTAAGTCCAATATCAAA
Found at i:8789 original size:50 final size:50
Alignment explanation
Indices: 8731--8879 Score: 244
Period size: 50 Copynumber: 3.0 Consensus size: 50
8721 AAGTTTTATA
8731 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
*
8781 ATAAGATTGCATTCCATTTGTAAGACCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
* * * * *
8831 ATAAGATTGCATTCCATTTGTGAGTCCAAGATTAAAATTTGCTTTTCAA
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAA
8880 AGGGCATTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
Found at i:8799 original size:24 final size:24
Alignment explanation
Indices: 8767--8849 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
8757 CAATATCAAA
*
8767 ATTCGATTTTCAAGATAAGATTGC
1 ATTCCATTTTCAAGATAAGATTGC
* * ***
8791 ATTCCATTTGT-AAGACCAATATCAAA
1 ATTCCATTT-TCAAGA-TAAGAT-TGC
*
8817 ATTCGATTTTCAAGATAAGATTGC
1 ATTCCATTTTCAAGATAAGATTGC
8841 ATTCCATTT
1 ATTCCATTT
8850 GTGAGTCCAA
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
24 20 0.48
25 10 0.24
26 12 0.29
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (24 bp):
ATTCCATTTTCAAGATAAGATTGC
Found at i:8996 original size:24 final size:22
Alignment explanation
Indices: 8952--8997 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8942 TAAATGAGTT
* *
8952 TTTCCAAAGAGTTCATGACATG
1 TTTCAAAAGAGTTCATCACATG
8974 TTTCAAAAGAGTTTCAATCACATG
1 TTTCAAAAGAG-TTC-ATCACATG
8998 ATTTTTACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (22 bp):
TTTCAAAAGAGTTCATCACATG
Found at i:9591 original size:69 final size:69
Alignment explanation
Indices: 9342--9768 Score: 524
Period size: 70 Copynumber: 6.2 Consensus size: 69
9332 AATGCTTCGA
* * * * * * *
9342 CTTTTCCATAAGTCAAACTCATTTCCGTACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
9407 AGGGG
65 AGGGG
* * **
9412 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
9477 AGGGG
65 AGGGG
* *
9482 CTTTTCCAGAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
9547 ACGG
66 GGGG
* * * *
9551 CTTTTGCACAAGCCAAACTCGTTTCTATACGAGTCAGTTCAAGCTTTGATTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
9616 GGGG
66 GGGG
* *
9620 CTTTTCCACAAGCCAAACTCGTTTTCACACGAGTCAAGTT--AGCCTTGGTTCCATCCAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTC-AGTTCAAGCCTTGGTTCCATCCAAGCAGC
*
9683 AAGGG
65 AGGGG
* * * * * *
9688 TTTTTCCACTAGCCGAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--AGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
9749 GGGG
66 GGGG
*
9753 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
9769 GTTCATTTCC
Statistics
Matches: 311, Mismatches: 44, Indels: 9
0.85 0.12 0.02
Matches are distributed among these distances:
65 19 0.06
67 5 0.02
68 69 0.22
69 95 0.31
70 123 0.40
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:10080 original size:11 final size:11
Alignment explanation
Indices: 10066--10098 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10056 GAAATGAATG
10066 AATGATGAAAA
1 AATGATGAAAA
10077 AATGATGAAAA
1 AATGATGAAAA
*
10088 AAGGA-GAAAA
1 AATGATGAAAA
10098 A
1 A
10099 GAATAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (11 bp):
AATGATGAAAA
Done.