Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010997.1 Corchorus capsularis cultivar CVL-1 contig11018, 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: 21611
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:3581 original size:33 final size:33
Alignment explanation
Indices: 3514--3650 Score: 118
Period size: 33 Copynumber: 4.2 Consensus size: 33
3504 GGATCATATA
* * **
3514 GCCGGTTGTGGCCGGGCATGGCCGA-GTCATGTG
1 GCCGGGTGTGGCCGGGCATCGCC-ATGTCGCGTG
* *
3547 GCCGGGTGTGGCCGGGCATGGCCATGTTGCGTG
1 GCCGGGTGTGGCCGGGCATCGCCATGTCGCGTG
* * *
3580 GCC-AGTGATGGCCGGGCATCTCCATGTCGCATG
1 GCCGGGTG-TGGCCGGGCATCGCCATGTCGCGTG
* * *
3613 GCC-GGTGTTGCGCGGGCATCTCCAAGTCGCGTG
1 GCCGGGTGTGGC-CGGGCATCGCCATGTCGCGTG
3646 GCCGG
1 GCCGG
3651 TCACTTATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
32 7 0.08
33 79 0.91
34 1 0.01
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.20
Consensus pattern (33 bp):
GCCGGGTGTGGCCGGGCATCGCCATGTCGCGTG
Found at i:9015 original size:5 final size:5
Alignment explanation
Indices: 9000--9030 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
8990 TCTGGTCGAA
9000 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
9031 ATTTTTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:9025 original size:15 final size:14
Alignment explanation
Indices: 9000--9036 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
8990 TCTGGTCGAA
9000 ATTTTTTTTATTTT
1 ATTTTTTTTATTTT
9014 ATTTTATTTTATTTT
1 ATTTT-TTTTATTTT
9029 ATATTTTT
1 AT-TTTTT
9037 CGATATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTATTTT
Found at i:10082 original size:33 final size:33
Alignment explanation
Indices: 10032--10132 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
10022 AGCTAAAGGA
* *
10032 TCATATGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCATGTGGCCGGGTGTGGCCGGGCATGGCC-ATG
*
10065 TCATGTGGCCGGGTGTGGTCGGGCATGGCCATG
1 TCATGTGGCCGGGTGTGGCCGGGCATGGCCATG
* * **
10098 TCACGTGGCC-AGTGATGGCCGGGCATCTCCATG
1 TCATGTGGCCGGGTG-TGGCCGGGCATGGCCATG
10131 TC
1 TC
10133 GCATGGCCGG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 4 0.07
33 54 0.93
ACGTcount: A:0.12, C:0.26, G:0.40, T:0.23
Consensus pattern (33 bp):
TCATGTGGCCGGGTGTGGCCGGGCATGGCCATG
Found at i:10140 original size:33 final size:33
Alignment explanation
Indices: 10084--10173 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
10074 CGGGTGTGGT
** *
10084 CGGGCATGGCCATGTCACGTGGCCAGTGATGGC-
1 CGGGCATCTCCATGTCGCGTGGCCAGTG-TGGCG
* * *
10117 CGGGCATCTCCATGTCGCATGGCCGGTGTTGCG
1 CGGGCATCTCCATGTCGCGTGGCCAGTGTGGCG
*
10150 CGGGCATCTCCAAGTCGCGTGGCC
1 CGGGCATCTCCATGTCGCGTGGCC
10174 GGTCACTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 3 0.06
33 45 0.94
ACGTcount: A:0.12, C:0.31, G:0.37, T:0.20
Consensus pattern (33 bp):
CGGGCATCTCCATGTCGCGTGGCCAGTGTGGCG
Found at i:13993 original size:23 final size:22
Alignment explanation
Indices: 13939--13993 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
13929 GGATGAAAGG
13939 TTACTTATTTTTTTATAGCATTA
1 TTACTT-TTTTTTTATAGCATTA
**
13962 TTA-TGTTTTTTTTATAAGTTTTA
1 TTACT-TTTTTTTTAT-AGCATTA
13985 TTACTTTTT
1 TTACTTTTT
13994 CAGTAACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 10 0.37
23 16 0.59
24 1 0.04
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.67
Consensus pattern (22 bp):
TTACTTTTTTTTTATAGCATTA
Found at i:15411 original size:16 final size:16
Alignment explanation
Indices: 15390--15448 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
15380 AGTCAACGTT
*
15390 CCGAACCCGAAATTAC
1 CCGAACCCGAAAATAC
15406 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
15422 CCGAACCTGAGACA-AC
1 CCGAACCCGA-AAATAC
15438 CCGAACCCGAA
1 CCGAACCCGAA
15449 CCCGACCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 1 0.03
16 35 0.92
17 2 0.05
ACGTcount: A:0.39, C:0.39, G:0.15, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:16194 original size:38 final size:38
Alignment explanation
Indices: 16143--16217 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
16133 TAAAAAAAAG
16143 TTTGGATCGGACTCTAAATATCGAAAGTGAACCCGAAA
1 TTTGGATCGGACTCTAAATATCGAAAGTGAACCCGAAA
16181 TTTGGATCGGACTCTAAATATCGAAAGTGAACCCGAA
1 TTTGGATCGGACTCTAAATATCGAAAGTGAACCCGAA
16218 CCTGATCCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (38 bp):
TTTGGATCGGACTCTAAATATCGAAAGTGAACCCGAAA
Found at i:16235 original size:23 final size:23
Alignment explanation
Indices: 16209--16263 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
16199 TATCGAAAGT
*
16209 GAACCCGAACCTGATCCGAACCC
1 GAACCCGAACCCGATCCGAACCC
* *
16232 GAACCCGATCCCGATCCGAGCCC
1 GAACCCGAACCCGATCCGAACCC
16255 GAACCCGAA
1 GAACCCGAA
16264 AATACCCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.44, G:0.20, T:0.07
Consensus pattern (23 bp):
GAACCCGAACCCGATCCGAACCC
Found at i:16262 original size:17 final size:17
Alignment explanation
Indices: 16209--16242 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16199 TATCGAAAGT
*
16209 GAACCCGAACCTGATCC
1 GAACCCGAACCCGATCC
16226 GAACCCGAACCCGATCC
1 GAACCCGAACCCGATCC
16243 CGATCCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.44, G:0.18, T:0.09
Consensus pattern (17 bp):
GAACCCGAACCCGATCC
Found at i:16273 original size:16 final size:16
Alignment explanation
Indices: 16252--16323 Score: 119
Period size: 16 Copynumber: 4.6 Consensus size: 16
16242 CCGATCCGAG
16252 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
16268 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
16284 TCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
16300 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
16315 CCCGAACCC
1 CCCGAACCC
16324 AAACCCGCCC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 13 0.25
16 40 0.75
ACGTcount: A:0.39, C:0.40, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:16279 original size:6 final size:6
Alignment explanation
Indices: 16209--16263 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
16199 TATCGAAAGT
* * * * *
16209 GAACCC GAACCT G-ATCC GAACCC GAACCC GATCCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
16255 GAACCC GAA
1 GAACCC GAA
16264 AATACCCGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
5 6 0.16
6 31 0.84
ACGTcount: A:0.29, C:0.44, G:0.20, T:0.07
Consensus pattern (6 bp):
GAACCC
Found at i:17247 original size:15 final size:15
Alignment explanation
Indices: 17227--17274 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
17217 GCGCCGGTGG
17227 CTTAGGCTCATCTTT
1 CTTAGGCTCATCTTT
* *
17242 CTTAGGCTCCTCCTT
1 CTTAGGCTCATCTTT
* **
17257 CTTGGGCGGATCTTT
1 CTTAGGCTCATCTTT
17272 CTT
1 CTT
17275 TTCTTCCTTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.08, C:0.29, G:0.19, T:0.44
Consensus pattern (15 bp):
CTTAGGCTCATCTTT
Found at i:19252 original size:2 final size:2
Alignment explanation
Indices: 19245--19274 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19235 TCTTATCTTC
19245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19275 ATAAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19537 original size:101 final size:101
Alignment explanation
Indices: 19418--19619 Score: 350
Period size: 101 Copynumber: 2.0 Consensus size: 101
19408 GATTGGAGGA
19418 ATCTAATTTTATGTGGGAATATCATTCCCATCACTTTATCACTCAAGTGGGAAAGTAGTGGAAAT
1 ATCTAATTTTATGTGGGAATATCATTCCCATCACTTTATCACTCAAGTGGGAAAGTAGTGGAAAT
* *
19483 AACATTCCCATCTAAAATGGTGGGAAAGTTCACTTT
66 AACATTCCAATCTAAAAGGGTGGGAAAGTTCACTTT
* *
19519 ATCTAATTTTATGTGGGAATGTCATTCCCATCACTTTATCACTCAAGTGGGAAAGTAGTGGGAAT
1 ATCTAATTTTATGTGGGAATATCATTCCCATCACTTTATCACTCAAGTGGGAAAGTAGTGGAAAT
* *
19584 AACATTTCAATCTAAAAGGGTGGGAAAGTTCTCTTT
66 AACATTCCAATCTAAAAGGGTGGGAAAGTTCACTTT
19620 CCCAGGAAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (101 bp):
ATCTAATTTTATGTGGGAATATCATTCCCATCACTTTATCACTCAAGTGGGAAAGTAGTGGAAAT
AACATTCCAATCTAAAAGGGTGGGAAAGTTCACTTT
Done.