Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007988.1 Corchorus capsularis cultivar CVL-1 contig08009, 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: 23089
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1466 original size:42 final size:42
Alignment explanation
Indices: 1417--1507 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
1407 GCCAAGACTG
*
1417 CCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCATCGCCTA
1 CCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCACCGCCTA
*
1459 CCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCACCGCCTG
1 CCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCACCGCCTA
1501 CCCGGCC
1 CCCGGCC
1508 ATGCTCGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.14, C:0.53, G:0.23, T:0.10
Consensus pattern (42 bp):
CCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCACCGCCTA
Found at i:1704 original size:23 final size:23
Alignment explanation
Indices: 1678--1734 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1668 ACCGCGTCAT
* *
1678 GCCCGGCCATGTCCGCGCCTTCA
1 GCCCGGCCATGTCCGCACCTCCA
1701 GCCCGGCCATGTCCGCACCTCCA
1 GCCCGGCCATGTCCGCACCTCCA
1724 GCCCGGCCATG
1 GCCCGGCCATG
1735 CCCGACCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.11, C:0.49, G:0.26, T:0.14
Consensus pattern (23 bp):
GCCCGGCCATGTCCGCACCTCCA
Found at i:4922 original size:13 final size:13
Alignment explanation
Indices: 4904--4938 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4894 ATAATTATTG
4904 TTTGCTTTATTAA
1 TTTGCTTTATTAA
4917 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
4930 TCTGCTTTA
1 TTTGCTTTA
4939 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:4964 original size:28 final size:24
Alignment explanation
Indices: 4932--4990 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
4922 TTTATTAATC
4932 TGCTTTAGATTTAGATTTAGATTTGCTT
1 TGCTTTAGATTTAG-TTTA-A-TTG-TT
**
4960 TGCTTTATTTTTAGTTTAATTGTT
1 TGCTTTAGATTTAGTTTAATTGTT
4984 TGCTTTA
1 TGCTTTA
4991 TAATTGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 3 0.10
26 1 0.03
27 4 0.14
28 12 0.41
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (24 bp):
TGCTTTAGATTTAGTTTAATTGTT
Found at i:14509 original size:10 final size:9
Alignment explanation
Indices: 14482--14511 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
14472 ATATGAAAAA
14482 TTCAAAATT
1 TTCAAAATT
14491 TTCAAAATT
1 TTCAAAATT
14500 TTCGAAAATT
1 TTC-AAAATT
14510 TT
1 TT
14512 TCATGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (9 bp):
TTCAAAATT
Found at i:14970 original size:22 final size:21
Alignment explanation
Indices: 14928--14982 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
14918 AGGTGACCGA
*
14928 TGGTGGCATGGTGATGGCCGG
1 TGGTGGCACGGTGATGGCCGG
*
14949 TGGTTGCACGGTGATTGGCCGG
1 TGGTGGCACGGTGA-TGGCCGG
14971 TGGTGGCACGGT
1 TGGTGGCACGGT
14983 TGTGGCTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.09, C:0.16, G:0.49, T:0.25
Consensus pattern (21 bp):
TGGTGGCACGGTGATGGCCGG
Found at i:17476 original size:23 final size:23
Alignment explanation
Indices: 17450--17504 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
17440 TTTATAACGC
* *
17450 AAACCCTAATTTTTTTTTTCGAA
1 AAACCCAAATTTTTTTTTTAGAA
*
17473 AAACGCAAATTTTTTTTTTAGAA
1 AAACCCAAATTTTTTTTTTAGAA
*
17496 AAACGCAAA
1 AAACCCAAA
17505 AAGAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (23 bp):
AAACCCAAATTTTTTTTTTAGAA
Found at i:17485 original size:22 final size:23
Alignment explanation
Indices: 17457--17504 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
17447 CGCAAACCCT
*
17457 AATTTTTTTTTTCGAAAAACGCA
1 AATTTTTTTTTTAGAAAAACGCA
17480 AATTTTTTTTTTAGAAAAACGCA
1 AATTTTTTTTTTAGAAAAACGCA
17503 AA
1 AA
17505 AAGAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (23 bp):
AATTTTTTTTTTAGAAAAACGCA
Done.