Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019655.1 Corchorus olitorius cultivar O-4 contig19688, 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: 31096
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1450 original size:34 final size:34
Alignment explanation
Indices: 1411--1478 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1401 TTGTTTGGTA
* *
1411 CTACTTTTTTAGTATTCAGTAACCATATTGAATT
1 CTACTTTTTTAGTATTCAATAACCACATTGAATT
* *
1445 CTACTTTTTTGGTATTCAATAACTACATTGAATT
1 CTACTTTTTTAGTATTCAATAACCACATTGAATT
1479 TTATCTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (34 bp):
CTACTTTTTTAGTATTCAATAACCACATTGAATT
Found at i:2553 original size:5 final size:5
Alignment explanation
Indices: 2539--2567 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2529 TTGAAAATTT
2539 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2568 TAGCAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:17519 original size:87 final size:87
Alignment explanation
Indices: 17371--17547 Score: 203
Period size: 87 Copynumber: 2.0 Consensus size: 87
17361 CGAGCGAGCC
* * * * *
17371 CTAGCTGCTGCTCTTTCCAGAGCTTTCAACCTATTAGCTTCTATGCGAGCGTGTTGCTCTTCTGT
1 CTAGCTGCAGCTCTCTCCAGAGCCTTCAACCTATTAGCTTCCATGCGAGCGTCTTGCTCTTCTGT
* * * *
17436 GATTTGGATTTCACTAGAGGAG
66 GATATGAACTTCACTAGAGCAG
* * * * *
17458 CTAGCTGCAGCTCTCTCCAGTGCCTTCAACTTGTTAGCTTCCATTCGAGC-TCTCTGTTCTTCTG
1 CTAGCTGCAGCTCTCTCCAGAGCCTTCAACCTATTAGCTTCCATGCGAGCGTCT-TGCTCTTCTG
*
17522 TTATATGAACTTCACTAGAGCAG
65 TGATATGAACTTCACTAGAGCAG
17545 CTA
1 CTA
17548 CTTCCATTGT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
86 2 0.03
87 72 0.97
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (87 bp):
CTAGCTGCAGCTCTCTCCAGAGCCTTCAACCTATTAGCTTCCATGCGAGCGTCTTGCTCTTCTGT
GATATGAACTTCACTAGAGCAG
Found at i:18160 original size:35 final size:35
Alignment explanation
Indices: 18114--18185 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
18104 TTTCATATTG
18114 AAGGACTAACTACAGCTTTGGTCAGACAAAACTAA
1 AAGGACTAACTACAGCTTTGGTCAGACAAAACTAA
18149 AAGGACTAACTACAGCTTTGGTCAGACAAAACTAA
1 AAGGACTAACTACAGCTTTGGTCAGACAAAACTAA
18184 AA
1 AA
18186 AGACAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (35 bp):
AAGGACTAACTACAGCTTTGGTCAGACAAAACTAA
Found at i:18854 original size:30 final size:30
Alignment explanation
Indices: 18818--18877 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
18808 TGCATTTCAT
18818 CAAAATGATCCCCCTCATAGTGGTTATTAG
1 CAAAATGATCCCCCTCATAGTGGTTATTAG
* *
18848 CAAAATGATTCCCCTCATTGTGGTTATTAG
1 CAAAATGATCCCCCTCATAGTGGTTATTAG
18878 TTTGTCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (30 bp):
CAAAATGATCCCCCTCATAGTGGTTATTAG
Found at i:24299 original size:74 final size:74
Alignment explanation
Indices: 24178--24328 Score: 266
Period size: 74 Copynumber: 2.0 Consensus size: 74
24168 GGTGGCAAAT
*
24178 TAACCTGAATTTGAGAAATTCGAGAGACAAATTATCTCGATTTTATGTTAGGGGGTAAACTGTAA
1 TAACCTGAATTTAAGAAATTCGAGAGACAAATTATCTCGATTTTATGTTAGGGGGTAAACTGTAA
24243 TTAACCTCA
66 TTAACCTCA
**
24252 TAACCTGAATTTAAGAAATTCGAGAGGTAAATTATCTCGATTTTATGTTAGGGGGTAAACTGTAA
1 TAACCTGAATTTAAGAAATTCGAGAGACAAATTATCTCGATTTTATGTTAGGGGGTAAACTGTAA
*
24317 TTAATCTCA
66 TTAACCTCA
24326 TAA
1 TAA
24329 TTCAAGGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (74 bp):
TAACCTGAATTTAAGAAATTCGAGAGACAAATTATCTCGATTTTATGTTAGGGGGTAAACTGTAA
TTAACCTCA
Found at i:30751 original size:21 final size:21
Alignment explanation
Indices: 30727--30793 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
30717 GTAACATAAA
30727 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
30748 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
30768 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
30790 TAAT
1 TAAT
30794 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Done.