Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009789.1 Corchorus capsularis cultivar CVL-1 contig09810, 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: 32906
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34 ATGATGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4329 original size:32 final size:31
Alignment explanation
Indices: 4237--4335 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
4227 CGCACCAAGA
* * * **
4237 GGGCGGCAAACCATGGCTCATGCCACCCCAGG
1 GGGCGGCATACCGTGG-TCATGCCGCCCCCTG
*
4269 GGGCGGCATACCGTGGTCGTGCCGCCCCCTG
1 GGGCGGCATACCGTGGTCATGCCGCCCCCTG
*
4300 GGGCGGCATGCCGTGGTTCATGCCGCCCCCCTG
1 GGGCGGCATACCGTGG-TCATGCCG-CCCCCTG
4333 GGG
1 GGG
4336 TGGCGCCGTC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 26 0.46
32 21 0.37
33 10 0.18
ACGTcount: A:0.11, C:0.37, G:0.37, T:0.14
Consensus pattern (31 bp):
GGGCGGCATACCGTGGTCATGCCGCCCCCTG
Found at i:5301 original size:18 final size:19
Alignment explanation
Indices: 5278--5316 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5268 GTTACTACTC
*
5278 TTTTTTGAT-GGAGCAAAG
1 TTTTTTGATGGGAACAAAG
*
5296 TTTTTTGGTGGGAACAAAG
1 TTTTTTGATGGGAACAAAG
5315 TT
1 TT
5317 GTTTAGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (19 bp):
TTTTTTGATGGGAACAAAG
Found at i:13879 original size:25 final size:25
Alignment explanation
Indices: 13846--13894 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13836 GATTAGCTAT
13846 ATTACCGAAACGCTAATCTATGAGC
1 ATTACCGAAACGCTAATCTATGAGC
* *
13871 ATTATCGAAATGCTAATCTATGAG
1 ATTACCGAAACGCTAATCTATGAG
13895 ACAACAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (25 bp):
ATTACCGAAACGCTAATCTATGAGC
Found at i:19494 original size:13 final size:13
Alignment explanation
Indices: 19476--19501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19466 CAAGGGTTTG
19476 TGAGTATTATTTT
1 TGAGTATTATTTT
19489 TGAGTATTATTTT
1 TGAGTATTATTTT
19502 AACATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TGAGTATTATTTT
Found at i:21490 original size:1 final size:1
Alignment explanation
Indices: 21484--21515 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
21474 TCACTTGTAG
21484 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21516 ATCTTAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25856 original size:18 final size:19
Alignment explanation
Indices: 25809--25856 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
25799 GGAAATGAGA
25809 TCCTCTCTC-CTCTTCCAT
1 TCCTCTCTCTCTCTTCCAT
* *
25827 TCCTCCCT-TCTCTCTCGAT
1 TCCTCTCTCTCTCT-TCCAT
25846 TCCTCTCTCTC
1 TCCTCTCTCTC
25857 CCTTATCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.46
19 11 0.46
20 2 0.08
ACGTcount: A:0.04, C:0.50, G:0.02, T:0.44
Consensus pattern (19 bp):
TCCTCTCTCTCTCTTCCAT
Found at i:27643 original size:18 final size:18
Alignment explanation
Indices: 27620--27657 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27610 TTAACGATGA
*
27620 ACTAAACTGGATTAAACT
1 ACTAAACCGGATTAAACT
27638 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
27656 AC
1 AC
27658 CACAAAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:30563 original size:35 final size:35
Alignment explanation
Indices: 30490--30570 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
30480 ATATAGGGAG
** *
30490 TAATTAATAATAATTATTCCAAAAGTAATTATTAT
1 TAATTAATAATAATTATTCCAAAAAAAATTAATAT
*
30525 TAATTAAT-TTAATTATTCTTCAAAAAAAATTAAT-T
1 TAATTAATAATAATTATTC--CAAAAAAAATTAATAT
*
30560 TAATTATTAAT
1 TAATTAATAAT
30571 TTTGGCCCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
34 9 0.24
35 16 0.43
36 12 0.32
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (35 bp):
TAATTAATAATAATTATTCCAAAAAAAATTAATAT
Found at i:32367 original size:27 final size:27
Alignment explanation
Indices: 32309--32381 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
32299 TATCAGGGTT
**
32309 ATTCAGGGGCATTTTGGTCATCTGCGT
1 ATTCAGGGGCATTTTGGTCATCTGCAC
* *
32336 ATTCAGGGGCATTTTTGTCATTTGCAC
1 ATTCAGGGGCATTTTGGTCATCTGCAC
* * *
32363 CTTCAGGGGTATATTGGTC
1 ATTCAGGGGCATTTTGGTC
32382 TTCTCAAGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.38
Consensus pattern (27 bp):
ATTCAGGGGCATTTTGGTCATCTGCAC
Found at i:32857 original size:2 final size:2
Alignment explanation
Indices: 32850--32885 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32840 TGACTAATGG
32850 TA TA TA 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 TA TA TA
32886 CTATCATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.