Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007617.1 Corchorus capsularis cultivar CVL-1 contig07638, 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: 35969
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:565 original size:19 final size:18
Alignment explanation
Indices: 532--567 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
522 TTGAAATAAT
532 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
550 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
568 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11413 original size:17 final size:18
Alignment explanation
Indices: 11372--11418 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
11362 GACGGCCCTG
11372 TCCTCTCTTCTCCACTCCC
1 TCCTCT-TTCTCCACTCCC
* *
11391 TTCTCTTTCTCGACTCCC
1 TCCTCTTTCTCCACTCCC
*
11409 -CCTCTCTCTC
1 TCCTCTTTCTC
11419 TCTCAACGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.04, C:0.53, G:0.02, T:0.40
Consensus pattern (18 bp):
TCCTCTTTCTCCACTCCC
Found at i:11414 original size:19 final size:18
Alignment explanation
Indices: 11373--11420 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
11363 ACGGCCCTGT
11373 CCTCTC-TTCTCCACTCC
1 CCTCTCTTTCTCCACTCC
* *
11390 CTTCTCTTTCTCGACTCCC
1 CCTCTCTTTCTCCACT-CC
*
11409 CCTCTCTCTCTC
1 CCTCTCTTTCTC
11421 TCAACGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 12 0.48
ACGTcount: A:0.04, C:0.54, G:0.02, T:0.40
Consensus pattern (18 bp):
CCTCTCTTTCTCCACTCC
Found at i:13172 original size:24 final size:25
Alignment explanation
Indices: 13145--13201 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
13135 TTACAAAAAC
*
13145 CTTGTTTTTA-TTAATCAAACTGCT
1 CTTGTTTTTAGGTAATCAAACTGCT
* *
13169 CTTGATTTTTTAGGTCATCAAATTGCT
1 CTTG--TTTTTAGGTAATCAAACTGCT
13196 CTTGTT
1 CTTGTT
13202 CTTCCTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 4 0.15
25 2 0.07
26 6 0.22
27 15 0.56
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (25 bp):
CTTGTTTTTAGGTAATCAAACTGCT
Found at i:14676 original size:2 final size:2
Alignment explanation
Indices: 14669--14711 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
14659 TATTTGGATT
* *
14669 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14711 T
1 T
14712 TCTCCTCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19994 original size:35 final size:35
Alignment explanation
Indices: 19948--20018 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
19938 CACTGTCAGT
19948 GGAGTTTAGCATACTACACAAGCGGGTCCTGAAGA
1 GGAGTTTAGCATACTACACAAGCGGGTCCTGAAGA
19983 GGAGTTTAGCATACTACACAAGCGGGTCCTGAAGA
1 GGAGTTTAGCATACTACACAAGCGGGTCCTGAAGA
20018 G
1 G
20019 TGACACGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.20
Consensus pattern (35 bp):
GGAGTTTAGCATACTACACAAGCGGGTCCTGAAGA
Found at i:25778 original size:24 final size:24
Alignment explanation
Indices: 25744--25816 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
25734 AAGTGTGATT
* * *
25744 GTGCTGCCATGACTGCTTCTTCCG
1 GTGCTGACATGACTGTTTCTTCCA
*
25768 GTGCTGACATGACTGTTTCTGCCA
1 GTGCTGACATGACTGTTTCTTCCA
*
25792 GTGCTGACATGACTATTTCTTCCA
1 GTGCTGACATGACTGTTTCTTCCA
25816 G
1 G
25817 ATGAGTCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.34
Consensus pattern (24 bp):
GTGCTGACATGACTGTTTCTTCCA
Found at i:31106 original size:1 final size:1
Alignment explanation
Indices: 31100--31126 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31090 AGTTGACGAC
31100 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
31127 GAGTTAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35607 original size:21 final size:21
Alignment explanation
Indices: 35581--35624 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35571 ATTTACTGGA
35581 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
35602 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
35623 TT
1 TT
35625 AACGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:35946 original size:32 final size:33
Alignment explanation
Indices: 35870--35958 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
35860 CAACCACGGC
*
35870 GCAGGCCGCCCCACTGGGGTGGCTTCACCATGA
1 GCAGGCCGCCCCACTGGGGCGGCTTCACCATGA
** * *
35903 AAAGGCCGCCCCATTGGGGCGGCTT-AGCCA-GG
1 GCAGGCCGCCCCACTGGGGCGGCTTCA-CCATGA
**
35935 GCAGGCCGCCCCGGTGGGGCGGCT
1 GCAGGCCGCCCCACTGGGGCGGCT
35959 CGGCTCTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
32 22 0.48
33 24 0.52
ACGTcount: A:0.13, C:0.35, G:0.39, T:0.12
Consensus pattern (33 bp):
GCAGGCCGCCCCACTGGGGCGGCTTCACCATGA
Done.