Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013970.1 Corchorus olitorius cultivar O-4 contig14003, 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: 65054
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:68 original size:22 final size:23
Alignment explanation
Indices: 28--76 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
18 TTTTTTTATT
**
28 ATTTAAAAAAATTGATTTTCAGA
1 ATTTAAAAAAAAAGATTTTCAGA
*
51 ATTTAAAAAAAAAG-TTTTGAGA
1 ATTTAAAAAAAAAGATTTTCAGA
73 ATTT
1 ATTT
77 TGAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (23 bp):
ATTTAAAAAAAAAGATTTTCAGA
Found at i:2582 original size:12 final size:13
Alignment explanation
Indices: 2565--2594 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2555 GTTTTCTTTA
2565 ATTTTCTTGATT-
1 ATTTTCTTGATTG
2577 ATTTTCTTGATTG
1 ATTTTCTTGATTG
2590 ATTTT
1 ATTTT
2595 AATTACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:20527 original size:16 final size:15
Alignment explanation
Indices: 20489--20530 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
20479 ACAGAGGTTG
20489 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
20504 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
20519 ACTAGAAAACAA
1 AC-AGAAAACAA
20531 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:22657 original size:9 final size:9
Alignment explanation
Indices: 22633--22667 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
22623 ACCTTTTTTT
22633 AAGAACACCTC
1 AAGAACA-C-C
22644 AAGAACACC
1 AAGAACACC
22653 AAGAACACC
1 AAGAACACC
22662 AAGAAC
1 AAGAAC
22668 GAACCCAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 16 0.67
10 1 0.04
11 7 0.29
ACGTcount: A:0.54, C:0.31, G:0.11, T:0.03
Consensus pattern (9 bp):
AAGAACACC
Found at i:28975 original size:27 final size:27
Alignment explanation
Indices: 28934--29024 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
28924 TTTACTTCTT
* **
28934 ATTTTGGTCACTTGCATGTCCAGGGGA
1 ATTTTGGTCATTTGCACATCCAGGGGA
*
28961 ATTTTGGTCATTTGCACATCCAGGGGC
1 ATTTTGGTCATTTGCACATCCAGGGGA
* * *
28988 ATTTTGGTCATTTGCGCATCTAGGGGC
1 ATTTTGGTCATTTGCACATCCAGGGGA
29015 ATTTTGGTCA
1 ATTTTGGTCA
29025 CTTCAAGTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (27 bp):
ATTTTGGTCATTTGCACATCCAGGGGA
Found at i:37385 original size:13 final size:13
Alignment explanation
Indices: 37367--37391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37357 TTAGATTTAG
37367 TTTCTAGTTTTTT
1 TTTCTAGTTTTTT
37380 TTTCTAGTTTTT
1 TTTCTAGTTTTT
37392 AGGCAAAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTCTAGTTTTTT
Found at i:38454 original size:29 final size:30
Alignment explanation
Indices: 38350--38452 Score: 181
Period size: 30 Copynumber: 3.4 Consensus size: 30
38340 TTTGGCGCCG
38350 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
38380 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
*
38410 TTGCCGGGGAAGGG-AACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
38439 TTGCCAGGGGAAGG
1 TTGCC-GGGGAAGG
38453 AAAATACACT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 19 0.27
30 52 0.73
ACGTcount: A:0.17, C:0.14, G:0.36, T:0.34
Consensus pattern (30 bp):
TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
Found at i:39649 original size:15 final size:14
Alignment explanation
Indices: 39629--39658 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
39619 ATCTTTTTAA
39629 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
39644 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
39658 T
1 T
39659 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:41336 original size:19 final size:18
Alignment explanation
Indices: 41312--41347 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41302 TGAAGACTTA
41312 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
41331 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
41348 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:45558 original size:13 final size:14
Alignment explanation
Indices: 45529--45558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45519 CCATTTTTTG
45529 AAAAAAAATTTGAA
1 AAAAAAAATTTGAA
*
45543 AAAAAAAATTTCAA
1 AAAAAAAATTTGAA
45557 AA
1 AA
45559 TTTCAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:45874 original size:18 final size:18
Alignment explanation
Indices: 45853--45888 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45843 GGGTAATTAC
*
45853 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
45871 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
45889 GATAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:46763 original size:19 final size:18
Alignment explanation
Indices: 46739--46774 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
46729 TGAAGACTTA
46739 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
46758 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
46775 ATTATCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:55065 original size:50 final size:50
Alignment explanation
Indices: 55011--55156 Score: 222
Period size: 50 Copynumber: 2.9 Consensus size: 50
55001 AGAAGAGTTT
55011 ATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAAGAGTGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAAGAGTGA
* * * * *
55061 ATTGGAAGACGGTTCAAAGGATAAGCGGAAGACGGTTCTTTTAAGATTTA
1 ATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAAGAGTGA
*
55111 ATTGGGAGACAGTTCAAAGGATAAGC-AGAAGACGGTCCTTTTAAGA
1 ATTGGAAGACAGTTCAAAGGATAAGCGA-AAGACGGTCCTTTTAAGA
55157 ATATATCGGA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (50 bp):
ATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAAGAGTGA
Found at i:55459 original size:27 final size:27
Alignment explanation
Indices: 55428--55517 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
55418 TTTACTTCTT
* *
55428 ATTTTGGTCACTTGCATGTCCAAGGGC
1 ATTTTGGTCATTTGCATGTCCAGGGGC
55455 ATTTTGGTCATTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTGCATGTCCAGGGGC
* *
55482 ATTTTGGTCATTTGCGTATCCAGGGGC
1 ATTTTGGTCATTTGCATGTCCAGGGGC
55509 ATTTTGGTC
1 ATTTTGGTC
55518 CCTTCAAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTGCATGTCCAGGGGC
Done.