Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009295.1 Corchorus capsularis cultivar CVL-1 contig09316, 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: 27177
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3834 original size:69 final size:69
Alignment explanation
Indices: 3718--3862 Score: 247
Period size: 69 Copynumber: 2.1 Consensus size: 69
3708 TTACATCTAT
*
3718 AACATATATTAAAGTTGGAAAGGAAATTACCCTTCTGTCCAGCTATAAGATGCA-CAACATTCAC
1 AACAAATATTAAAGTTGGAAAGGAAATTACCCTTCTGTCCAGCTATAAGATGCATC-ACATTCAC
*
3782 CCAAG
65 CCAAA
*
3787 AACAAATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAGCTATAAGATGCATCACATTCACC
1 AACAAATATTAAAGTTGGAAAGGAAATTACCCTTCTGTCCAGCTATAAGATGCATCACATTCACC
3852 CAAA
66 CAAA
3856 AACAAAT
1 AACAAAT
3863 TGTCAGAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
69 71 0.99
70 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (69 bp):
AACAAATATTAAAGTTGGAAAGGAAATTACCCTTCTGTCCAGCTATAAGATGCATCACATTCACC
CAAA
Found at i:5257 original size:120 final size:120
Alignment explanation
Indices: 5044--5280 Score: 465
Period size: 120 Copynumber: 2.0 Consensus size: 120
5034 GGTTTTAATT
5044 TCACAACTTACGACAAATAATCATTATTTATAGAAGCTAACTAAGTTTTAAAAAAACACCAACTA
1 TCACAACTTACGACAAATAATCATTATTTATAGAAGCTAACTAAGTTTTAAAAAAACACCAACTA
5109 AATATTTTACTTATAACATTTTTATACTTTCGATGTTCATAGCCTATACAAATAA
66 AATATTTTACTTATAACATTTTTATACTTTCGATGTTCATAGCCTATACAAATAA
*
5164 TCACAACTTACGACAAATAATCATTATTTATAGAAGCTAACTAAGTTTTAAAAAAACACTAACTA
1 TCACAACTTACGACAAATAATCATTATTTATAGAAGCTAACTAAGTTTTAAAAAAACACCAACTA
5229 AATATTTTACTTATAACATTTTTATACTTTCGATGTTCATAGCCTATACAAA
66 AATATTTTACTTATAACATTTTTATACTTTCGATGTTCATAGCCTATACAAA
5281 AGCTATGAAA
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (120 bp):
TCACAACTTACGACAAATAATCATTATTTATAGAAGCTAACTAAGTTTTAAAAAAACACCAACTA
AATATTTTACTTATAACATTTTTATACTTTCGATGTTCATAGCCTATACAAATAA
Found at i:6396 original size:121 final size:122
Alignment explanation
Indices: 6260--6518 Score: 319
Period size: 123 Copynumber: 2.1 Consensus size: 122
6250 TATTTTGTAG
** * * * * *
6260 CGACACCTCCGGAGCCTCCTATTGATACGGGTAGGACACTCTTTCA-CTTTTTTTT-T-AACTAC
1 CGACACCTTTGGAGCCTCCCATCGATACCGGTAGGACAATCTTTCATCTTTTTTTTCTAAAATAC
*
6322 AATTTCATCCAAATTTTATGCAATTTAAACATATATATACTTATATTTTGTAGGGACAT
66 AATTTCATCCAAATGTTATGCAATTTAAAC--ATATATACTTATATTTTGTAGGGACAT
* * * * *
6381 GGACA-CTTGTGGAGCCTCCCATCGATACCGGTATGATAATTTTTCATTTTTTTTTTCTAAAAAT
1 CGACACCTT-TGGAGCCTCCCATCGATACCGGTAGGACAATCTTTCATCTTTTTTTTCT-AAAAT
**
6445 ATGATTTCATCCAAATGTTATGCAATTTAAACATATATACTTATATTTTGTAGGGACAT
64 ACAATTTCATCCAAATGTTATGCAATTTAAACATATATACTTATATTTTGTAGGGACAT
6504 CGACACCTTTGGAGC
1 CGACACCTTTGGAGC
6519 GTCTTAATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
120 2 0.02
121 33 0.28
122 8 0.07
123 38 0.33
124 3 0.03
125 32 0.28
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (122 bp):
CGACACCTTTGGAGCCTCCCATCGATACCGGTAGGACAATCTTTCATCTTTTTTTTCTAAAATAC
AATTTCATCCAAATGTTATGCAATTTAAACATATATACTTATATTTTGTAGGGACAT
Found at i:6929 original size:21 final size:21
Alignment explanation
Indices: 6896--6935 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6886 TACTTGTAGA
*
6896 TGATAATAATGAGGAGGCATG
1 TGATAATAATGAGAAGGCATG
**
6917 TGATAATGTTGAGAAGGCA
1 TGATAATAATGAGAAGGCA
6936 AATGAGAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.25
Consensus pattern (21 bp):
TGATAATAATGAGAAGGCATG
Found at i:8622 original size:87 final size:86
Alignment explanation
Indices: 8477--8649 Score: 283
Period size: 87 Copynumber: 2.0 Consensus size: 86
8467 ATGAATATTT
* * *
8477 TCAGTGGACTAAACAGTGAAAGGTGAATTTTTTTATGCAGTATCCTTGTGTGAACATGATTGCTC
1 TCAGTGGACTAAACAATGAAAAGTGAATTCTTTTATGCAGTATCCTTGTGTGAACATGATTGCTC
8542 ATATTTTCAATGCACCAGTGG
66 ATATTTTCAATGCACCAGTGG
**
8563 TCAGTGGACTAAACAATGAAAAGTGAATTGCTTTTATGCAGTATTGTTGTGTGAACATGATTGCT
1 TCAGTGGACTAAACAATGAAAAGTGAATT-CTTTTATGCAGTATCCTTGTGTGAACATGATTGCT
*
8628 CATATTTTCAATGCACTAGTGG
65 CATATTTTCAATGCACCAGTGG
8650 GAGAAAAAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 27 0.34
87 53 0.66
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (86 bp):
TCAGTGGACTAAACAATGAAAAGTGAATTCTTTTATGCAGTATCCTTGTGTGAACATGATTGCTC
ATATTTTCAATGCACCAGTGG
Found at i:14498 original size:115 final size:115
Alignment explanation
Indices: 14296--14519 Score: 403
Period size: 115 Copynumber: 1.9 Consensus size: 115
14286 GTCTTTTCTC
* *
14296 GCTTGCCGGATTACTAAGAAGCCCCTCAATCAGTTTTCTGCACTTCCTTTTCTCCCTGCCCTTTT
1 GCTTGCCGGATTACTAAGAAGCCCCTCAATCAGTATTCTGCACTTCCTTTTCTCCCTGCCATTTT
14361 TGGTAATTGACTGTTTGGCCACTTAAAAGCGTTTTCTCTTTCTTTTGGGG
66 TGGTAATTGACTGTTTGGCCACTTAAAAGCGTTTTCTCTTTCTTTTGGGG
* *
14411 GCTTGCCGGATTACTAAGAAGCCCCTCAATCAGTATTCTGCACTTCTTTTTCTCCCTTCCATTTT
1 GCTTGCCGGATTACTAAGAAGCCCCTCAATCAGTATTCTGCACTTCCTTTTCTCCCTGCCATTTT
*
14476 TGGTAATTGACTGTTTGGCCACTTGAAAGCGTTTTCTCTTTCTT
66 TGGTAATTGACTGTTTGGCCACTTAAAAGCGTTTTCTCTTTCTT
14520 CTGGACATAA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 104 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.41
Consensus pattern (115 bp):
GCTTGCCGGATTACTAAGAAGCCCCTCAATCAGTATTCTGCACTTCCTTTTCTCCCTGCCATTTT
TGGTAATTGACTGTTTGGCCACTTAAAAGCGTTTTCTCTTTCTTTTGGGG
Found at i:17742 original size:33 final size:33
Alignment explanation
Indices: 17679--17742 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17669 TTCTGACGAC
* *
17679 ATTTATAAATATTTAAAAGGGGTTTGTATTAGT
1 ATTTATAAATATTTAAAAGAGGTTTATATTAGT
*
17712 ATTTTTAAAT-TTTAAAAGAGGTATTATATTA
1 ATTTATAAATATTTAAAAGAGGT-TTATATTA
17743 AGAGTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (33 bp):
ATTTATAAATATTTAAAAGAGGTTTATATTAGT
Found at i:17854 original size:30 final size:30
Alignment explanation
Indices: 17820--17876 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17810 TTGATGAAAT
17820 AAGTCAACTA-TGTATTTACAGCAGGATTCA
1 AAGTCAAC-AGTGTATTTACAGCAGGATTCA
* *
17850 AAGTCAACAGTTTGTTTACAGCAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
17877 CCAAGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATTCA
Found at i:17917 original size:21 final size:21
Alignment explanation
Indices: 17893--17943 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
17883 TTGAAGCCGA
17893 AAATCATGTTGA-CGTGTCCGC
1 AAATCATGTT-ACCGTGTCCGC
17914 AAATCATGTTACCGTGTCCGC
1 AAATCATGTTACCGTGTCCGC
17935 AAATCATGT
1 AAATCATGT
17944 AGATTGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
AAATCATGTTACCGTGTCCGC
Found at i:18629 original size:22 final size:24
Alignment explanation
Indices: 18573--18629 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
18563 AATTTTGAAA
*
18573 ATGCTGTGACAAATCCTTTTATTTT
1 ATGCTTTGA-AAATCCTTTTATTTT
*
18598 AT--TTTTAAAAT-CTTTTATTTT
1 ATGCTTTGAAAATCCTTTTATTTT
18619 -TGCTTTGAAAA
1 ATGCTTTGAAAA
18630 CTTCCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.04
21 10 0.37
22 11 0.41
23 3 0.11
25 2 0.07
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
ATGCTTTGAAAATCCTTTTATTTT
Found at i:22424 original size:27 final size:27
Alignment explanation
Indices: 22394--22469 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
22384 GTGAACTTAG
** *
22394 AATGACCAAAATGCCCCTGAATGTGCA
1 AATGACCAAAATGCCCCTGAACATGAA
*
22421 AATGACCAAAATGTCCCTGAACATGAA
1 AATGACCAAAATGCCCCTGAACATGAA
22448 AATGACCAAAATGCCCCTGAAC
1 AATGACCAAAATGCCCCTGAAC
22470 GACCCTAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGAACATGAA
Found at i:27085 original size:30 final size:30
Alignment explanation
Indices: 27051--27107 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
27041 GTGATGAAAT
*
27051 AAGTCAACTGTGTATTTACAGCAGGATTCA
1 AAGTCAACAGTGTATTTACAGCAGGATTCA
* *
27081 AAGTCAACAGTTTGTTTACAGCAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
27108 CCAAGATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATTCA
Found at i:27148 original size:21 final size:21
Alignment explanation
Indices: 27124--27174 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
27114 TTGAAGCCGA
27124 AAATCATGTTGA-CGTGTCCGC
1 AAATCATGTT-ACCGTGTCCGC
27145 AAATCATGTTACCGTGTCCGC
1 AAATCATGTTACCGTGTCCGC
27166 AAATCATGT
1 AAATCATGT
27175 AGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
AAATCATGTTACCGTGTCCGC
Done.