Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018171.1 Corchorus olitorius cultivar O-4 contig18204, 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: 8362
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Found at i:2053 original size:20 final size:19
Alignment explanation
Indices: 2026--2384 Score: 128
Period size: 20 Copynumber: 17.7 Consensus size: 19
2016 CGCGGCATAT
2026 TCACATTGAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
2045 TCAACATTGAACTTGCCTTAA
1 TC-ACATTGAACTTTCC-CAA
*
2066 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
2086 TCGACATTGAACTTGCCTTGAT
1 TC-ACATTGAACTTTCC--CAA
***
2108 TCACATCCCACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* * *
2127 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
* * *
2149 TCACATTCAAATTTCCTAA
1 TCACATTGAACTTTCCCAA
* *
2168 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
* * *
2189 TTCACATTCAAATTTCCTAA
1 -TCACATTGAACTTTCCCAA
* *
2209 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
*
2230 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
2250 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
*
2272 TCACA--CAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
2289 TTCACATTGAACTTGCCTTCAT
1 -TCACATTGAACTTTCC--CAA
* * *
2311 TCATATTCAACTTTTCCAA
1 TCACATTGAACTTTCCCAA
* * *
2330 TTGACATTGAACTTGCCTTCAT
1 -TCACATTGAACTTTCC--CAA
* * *
2352 TCATATTCAACTTTCCAAA
1 TCACATTGAACTTTCCCAA
*
2371 TTGACATTGAACTT
1 -TCACATTGAACTT
2385 GCCTTCATTC
Statistics
Matches: 248, Mismatches: 69, Indels: 45
0.69 0.19 0.12
Matches are distributed among these distances:
17 1 0.00
18 5 0.02
19 16 0.06
20 114 0.46
21 101 0.41
22 11 0.04
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (19 bp):
TCACATTGAACTTTCCCAA
Found at i:2081 original size:41 final size:41
Alignment explanation
Indices: 2024--2399 Score: 535
Period size: 41 Copynumber: 9.2 Consensus size: 41
2014 TACGCGGCAT
*
2024 ATTCACATTGAACTTTCCCAA-TCAACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTA
*
2065 ATTCACATTCAACTTTCCCAA-TCGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTA
* * *
2106 ATTCACATCCCACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* *
2147 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* *
2188 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
*
2229 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
*
2270 ATTCACA--CAACTTTCCCAATTCACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* * * *
2309 ATTCATATTCAACTTTTCCAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* * * *
2350 ATTCATATTCAACTTTCCAAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
2391 ATTCACATT
1 ATTCACATT
2400 AGCCCTTAAT
Statistics
Matches: 312, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
39 37 0.12
41 273 0.88
42 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
Found at i:6603 original size:12 final size:12
Alignment explanation
Indices: 6586--6631 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
6576 GGGAGCTTTA
6586 AAACAAAAAAAC
1 AAACAAAAAAAC
6598 AAACAAAAAAAAC
1 AAAC-AAAAAAAC
6611 AAA-AACAAAAAC
1 AAACAA-AAAAAC
6623 AAAACAAAA
1 -AAACAAAA
6632 CAAAAGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 10 0.33
13 16 0.53
14 2 0.07
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACAAAAAAAC
Found at i:6609 original size:21 final size:22
Alignment explanation
Indices: 6585--6636 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
6575 AGGGAGCTTT
6585 AAAACAAAAA-AACAAACAAAA-
1 AAAACAAAAACAA-AAACAAAAC
6606 AAAACAAAAACAAAAACAAAAC
1 AAAACAAAAACAAAAACAAAAC
6628 AAAACAAAA
1 AAAACAAAA
6637 GGATGATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAACAAAAACAAAAACAAAAC
Found at i:6616 original size:6 final size:6
Alignment explanation
Indices: 6592--6636 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
6582 TTTAAAACAA
*
6592 AAAAAC AAACAAA AAAAAC AAAAAC AAAAAC -AAAAC -AAAAC AAAA
1 AAAAAC AAA-AAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
6637 GGATGATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.29
6 20 0.57
7 5 0.14
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:6620 original size:5 final size:5
Alignment explanation
Indices: 6585--6636 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
6575 AGGGAGCTTT
6585 AAAAC -AAA- AAAAC -AAAC AAAA- AAAAC AAAAAC AAAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC -AAAAC AAAAC AAAAC
6633 AAAA
1 AAAA
6637 GGATGATTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 14 0.33
5 17 0.40
6 11 0.26
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Done.