Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009609.1 Corchorus capsularis cultivar CVL-1 contig09630, 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: 12150
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3503 original size:26 final size:26
Alignment explanation
Indices: 3474--3527 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3464 AAATTTTAAT
3474 ATTTAAATT-TTATTTT-TTATTAAAAA
1 ATTT-AATTATTATTTTATT-TTAAAAA
3500 ATTTAATTATTATTTTATTTTAAAAA
1 ATTTAATTATTATTTTATTTTAAAAA
3526 AT
1 AT
3528 AAATATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 20 0.77
27 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTAATTATTATTTTATTTTAAAAA
Found at i:7171 original size:136 final size:136
Alignment explanation
Indices: 6927--7176 Score: 421
Period size: 136 Copynumber: 1.8 Consensus size: 136
6917 TGGAGAATAA
* *
6927 TTTGTAAAAGAGAGAGTGATCTGGTCTTGTCGTTACGATCAGTGTTGTCAGACTCGATCGGGTCA
1 TTTGTAAAAGAGAGAGTGATCTGGTCTTGTCGTTACGAGCAGTGTTGTCAAACTCGATCGGGTCA
*
6992 TCCGGTTAGTCTAGTCAACACTCGGTCAAAACCCAGTAGTTAGCCCGGATCGGGACCGACTGAAC
66 TCCGGTTAGCCTAGTCAACACTCGGTCAAAACCCAGTAGTTAGCCCGGATCGGGACCGACTGAAC
7057 CGGTTT
131 CGGTTT
* *
7063 TTTGTAAGAGAGAGAGTGATCTGGTCTTGTCGTTACGAGCAGTGTTGTCAAACTTGATCGGGTCA
1 TTTGTAAAAGAGAGAGTGATCTGGTCTTGTCGTTACGAGCAGTGTTGTCAAACTCGATCGGGTCA
* *
7128 -CTCGGTTAGCCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
66 TC-CGGTTAGCCTAGTCAACACTCGGTCAAAACCCAGTAGTTAGCCCGGA
7177 CCTAGTCAAC
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
135 1 0.01
136 105 0.99
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (136 bp):
TTTGTAAAAGAGAGAGTGATCTGGTCTTGTCGTTACGAGCAGTGTTGTCAAACTCGATCGGGTCA
TCCGGTTAGCCTAGTCAACACTCGGTCAAAACCCAGTAGTTAGCCCGGATCGGGACCGACTGAAC
CGGTTT
Found at i:7182 original size:40 final size:40
Alignment explanation
Indices: 7137--7217 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
7127 ACTCGGTTAG
7137 CCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
1 CCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
7177 CCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
1 CCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
7217 C
1 C
7218 TAGGACCGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (40 bp):
CCTAGTCAACACTCGGTCAAAATCCAGTGGTTAGCCCGGA
Found at i:8183 original size:70 final size:70
Alignment explanation
Indices: 8101--8330 Score: 255
Period size: 70 Copynumber: 3.2 Consensus size: 70
8091 TTGTTTAGGT
* * * *
8101 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTGTTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATATCTTTATAATT
8165 ATTTTA
65 ATTTTA
* * *
8171 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATACCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATA-TCTT-T-A-TA
*
8236 TTATATTTTACCA
62 AT-TATTTT---A
* * *
8249 TTTTACTATTTTACTCAACTAAAAAATCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
8314 TTATA
66 TTTTA
*
8319 TTTTACCATTTT
1 TTTTACTATTTT
8331 TACTATTTTA
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
70 57 0.42
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 51 0.38
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:8253 original size:78 final size:77
Alignment explanation
Indices: 8101--8340 Score: 307
Period size: 78 Copynumber: 3.2 Consensus size: 77
8091 TTGTTTAGGT
* * * * *
8101 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTGTTTAATTAAATATAATATCTT-T-A-TA
1 TTTTACTA-TTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATACCTTATAACTA
*
8162 AT-TATTTT---A
65 TTATATTTTACCA
* *
8171 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATACCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATA-CCTTATAACTA
8236 TTATATTTTACCA
65 TTATATTTTACCA
*
8249 TTTTACTATTTTACTCAACTAAAAAATCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATA-CCTTATAACTA
8314 TTATATTTTACCA
65 TTATATTTTACCA
8327 TTTTTACTATTTTA
1 -TTTTACTATTTTA
8341 ATTAAAAAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
70 45 0.30
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
78 75 0.50
79 13 0.09
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATCTAATACCTTATAACTAT
TATATTTTACCA
Found at i:8589 original size:60 final size:60
Alignment explanation
Indices: 8430--8590 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 60
8420 GCTAATTGCT
* * ****
8430 CAAATAAGGGCCTAACGTTTGACAAAATGCTCAAATAAGAGTTTGATCTATTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTATTAATTTGGC
* * *
8490 CAAATAAAGACCTAACGTTTACCAAAATGCTCAAATAAGGGCCCCATCT-TTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTATT-AATTTGGC
* *
8550 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
8591 TCTTACGCGT
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 2 0.02
60 84 0.98
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTATTAATTTGGC
Found at i:8655 original size:31 final size:30
Alignment explanation
Indices: 8617--8784 Score: 150
Period size: 31 Copynumber: 5.6 Consensus size: 30
8607 AATTGACACC
8617 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GATAACGTT
**
8648 AGGCCCTTATTTG-GCCAAATT-ATAA-GATT
1 AGGCCCTTATTTGAG-CATTTTGATAACG-TT
*
8677 GGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GATAACGTT
** * *
8708 AGGCCCTTATTTG-GCAAAATT-A-AAAGCTC
1 AGGCCCTTATTTGAGC-ATTTTGATAACG-TT
* *
8737 AGACCCTTATTTGAGCATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTGA-TAACGTT
8768 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
8785 ATTAGTCATT
Statistics
Matches: 109, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.04
29 39 0.36
30 7 0.06
31 55 0.50
32 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGATAACGTT
Found at i:8711 original size:60 final size:60
Alignment explanation
Indices: 8616--8785 Score: 252
Period size: 60 Copynumber: 2.8 Consensus size: 60
8606 AAATTGACAC
* *
8616 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTATAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGAT
** *
8676 TGGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGCT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGAT
* *
8736 CAGACCCTTATTTGAGCATTTT-GACAAACGTTAGGCCCTTATTTGAGCAA
1 CAGGCCCTTATTTGAGCATTTTCGA-TAACGTTAGGCCCTTATTTG-GCAA
8786 TTAGTCATTT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.02
60 93 0.94
61 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGAT
Done.