Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023234.1 Corchorus olitorius cultivar O-4 contig23267, 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: 37741
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:7246 original size:50 final size:50
Alignment explanation
Indices: 7183--7288 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
7173 GATCAACTTC
7183 TTTGAATTATCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCA
1 TTTGAATTATCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCA
* * * * *
7233 TTTGAATTGTCTTCCAATTCTATCTTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAATTATCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCA
7283 TTTGAA
1 TTTGAA
7289 CTGTTGATCG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (50 bp):
TTTGAATTATCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCA
Found at i:8836 original size:22 final size:21
Alignment explanation
Indices: 8784--8837 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
8774 GCTTCTTGGA
8784 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
8805 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
8824 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
8838 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:9117 original size:50 final size:50
Alignment explanation
Indices: 9063--9181 Score: 193
Period size: 50 Copynumber: 2.4 Consensus size: 50
9053 TGGCTCGATC
* * *
9063 AACTGTCTTCCAATTCTATCTTAAAAGGACCGTCTTCTGTTTATCCTTTG
1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTG
*
9113 AACTGTCTTCCAATTCAATCTTGAAAGGACCGTCTTCCGCTTATCCTTTG
1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTG
*
9163 AATTGTCTTCCAATTCAAT
1 AACTGTCTTCCAATTCAAT
9182 TTTGAGAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (50 bp):
AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTG
Found at i:9549 original size:64 final size:64
Alignment explanation
Indices: 9398--9820 Score: 612
Period size: 64 Copynumber: 6.6 Consensus size: 64
9388 CCGGTGCATC
* * * *
9398 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAAACTATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACCATCTTCTAGTGTACT
* * * * * * *
9463 TTTTAACAAGATCGTCTCCCGATCAACTCCTGAAGACTCTTGAGAAACCATCTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
9527 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
* * * *
9591 TCTTGATAAGATCGTCTTCCGATCAACTTCTGAAGATTGTTGAGAAACCGTCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
* *
9655 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTTTTGAGAAACCATCTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
* * * * *
9719 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAGATTGTTGAAAAACCGTCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
* * *
9783 TCTTAACAAGATCGTCTTCCAATCATCTTCTGAAAATT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATT
9821 CTATCTAGCA
Statistics
Matches: 322, Mismatches: 36, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
64 284 0.88
65 38 0.12
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACT
Found at i:9952 original size:68 final size:68
Alignment explanation
Indices: 9791--9987 Score: 299
Period size: 68 Copynumber: 2.9 Consensus size: 68
9781 CTTCTTAACA
* * * * *
9791 AGATCGTCTTCCAATCATC-TTCTGAAAATTCTATCTAGCAAATCGTCTTTCGATGTATTCC-TT
1 AGATTGTCTTCCAATCAACATT-TGAAAATTCTTTCTAGCAAACCGTCTTTCGGTGTATTCCTTT
9854 AATG
65 AATG
*
9858 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTTCGGTGTACTCCTTTA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTTCGGTGTATTCCTTTA
9923 ATG
66 ATG
* *
9926 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTATTCCT
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTTCGGTGTATTCCT
9988 AAAATCCTCT
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
67 52 0.44
68 67 0.56
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (68 bp):
AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTTCGGTGTATTCCTTTA
ATG
Found at i:11815 original size:12 final size:12
Alignment explanation
Indices: 11798--11834 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
11788 CTTTTGGTTC
11798 ACTTTGATTTGA
1 ACTTTGATTTGA
*
11810 ACTTTGTTTTGA
1 ACTTTGATTTGA
11822 ACTTTGATTTGA
1 ACTTTGATTTGA
11834 A
1 A
11835 TTACTTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (12 bp):
ACTTTGATTTGA
Found at i:22172 original size:15 final size:15
Alignment explanation
Indices: 22152--22188 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
22142 TCGTCCACTG
22152 GAGGCTGAGAGATTT
1 GAGGCTGAGAGATTT
*
22167 GAGGCTGAGAGGTTT
1 GAGGCTGAGAGATTT
*
22182 GTGGCTG
1 GAGGCTG
22189 GGGTTGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.08, G:0.46, T:0.27
Consensus pattern (15 bp):
GAGGCTGAGAGATTT
Found at i:35267 original size:17 final size:17
Alignment explanation
Indices: 35241--35280 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
35231 AGACACACAC
*
35241 AAACTTGCAAGGACAGA
1 AAACTCGCAAGGACAGA
35258 AAACTCGCAAGGACAGA
1 AAACTCGCAAGGACAGA
35275 AAACTC
1 AAACTC
35281 TTTGACCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (17 bp):
AAACTCGCAAGGACAGA
Found at i:35624 original size:43 final size:43
Alignment explanation
Indices: 35558--35640 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
35548 AGGAATAGAC
* *
35558 GTTAGATGGGCCAGAAGTGGACCATGGCTT-TAAATCAATAAAA
1 GTTAAATGGGCCAAAAGTGGACCATGG-TTGTAAATCAATAAAA
* *
35601 GTTAAATGGGCTAAAAGTGGACCATGGTTGTAACTCAATA
1 GTTAAATGGGCCAAAAGTGGACCATGGTTGTAAATCAATA
35641 TAATCAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (43 bp):
GTTAAATGGGCCAAAAGTGGACCATGGTTGTAAATCAATAAAA
Done.