Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004035.1 Corchorus capsularis cultivar CVL-1 contig04043, 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: 16652
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:2423 original size:10 final size:10
Alignment explanation
Indices: 2410--2435 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2400 AAATCTCGAT
2410 ATATCCGTAA
1 ATATCCGTAA
2420 ATATCCGTAA
1 ATATCCGTAA
2430 ATATCC
1 ATATCC
2436 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:6241 original size:186 final size:183
Alignment explanation
Indices: 5927--6492 Score: 750
Period size: 186 Copynumber: 3.0 Consensus size: 183
5917 TTTTTACATT
5927 ATATTATAAAAAACACTAATAGTAGGAAGTGTAATTACTAAAATACCCTCAAAATTTTTCCTAAC
1 ATATTATAAAAAACACTAATAGTAGGAAGTGTAATTACTAAAATA-CCTCAAAATTTTTCCTAAC
* *
5992 CGAATCACTATATTCAATTTGTTACTATTCAGCTTGGTTTTTTGGTCAATTCACTTTTGGTTTTT
65 CGAATCACTATATTC-ATTTGTTACTATTCAGCTTGGTTTTTTAGTCATTTCACTTTTGGTTTTT
** *
6057 TGTTATTTTCACAAATCTCTAAGGGTTTTTTTGACTTTCTAGTATTTTAAATTATA
129 T-TTATTTTCACAAATCTCTAAGGAATTTTTTGACTTTCTAGCATTTTAAATTATA
* * *
6113 ATATTATAAAAAAAACTAATAGTAAGAAGTGTAATTACTAAAATATCCACAAAATTTTTCCTAAC
1 ATATTATAAAAAACACTAATAGTAGGAAGTGTAATTACTAAAATA-CCTCAAAATTTTTCCTAAC
* *
6178 CGAATCACTACATTCATTTTGTTACTACTCAGCTTGGTTTTTTAGTCATTTCACTTTTGGTTTTT
65 CGAATCACTATATTCA-TTTGTTACTATTCAGCTTGGTTTTTTAGTCATTTCACTTTTGG-----
* * * *
6243 TTTTTTTTTTATTCTCACAAACCTCTAAGAGCATTTTTT-ATTTTCTAGCATTTTAAATTAT-
124 --TTTTTTTTATTTTCACAAATCTCTAAG-GAATTTTTTGACTTTCTAGCATTTTAAATTATA
** * * * **
6304 ATATTATATGAAACACCAATAGTAGGACGTGTAATTACTAAAATACCTTTAAGGTTTTTCCTAAC
1 ATATTATAAAAAACACTAATAGTAGGAAGTGTAATTACTAAAATACC-TCAAAATTTTTCCTAAC
6369 CGAATCACTATATTCATTTGTTACTATTC-GCTTGGTTTTTTAGTCATTTCACTTTTGG--TTTT
65 CGAATCACTATATTCATTTGTTACTATTCAGCTTGGTTTTTTAGTCATTTCACTTTTGGTTTTTT
6431 TT-TTTTCACAAATCTCTAAGGACA-TTTTTGACTTTCTAGCATTTTAAATTATA
130 TTATTTTCACAAATCTCTAAGGA-ATTTTTTGACTTTCTAGCATTTTAAATTATA
*
6484 ATATAATAA
1 ATATTATAA
6493 TATAACATAT
Statistics
Matches: 335, Mismatches: 32, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
178 6 0.02
179 38 0.11
180 13 0.04
185 1 0.00
186 115 0.34
189 29 0.09
190 14 0.04
191 67 0.20
192 39 0.12
193 13 0.04
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (183 bp):
ATATTATAAAAAACACTAATAGTAGGAAGTGTAATTACTAAAATACCTCAAAATTTTTCCTAACC
GAATCACTATATTCATTTGTTACTATTCAGCTTGGTTTTTTAGTCATTTCACTTTTGGTTTTTTT
TATTTTCACAAATCTCTAAGGAATTTTTTGACTTTCTAGCATTTTAAATTATA
Found at i:6883 original size:178 final size:179
Alignment explanation
Indices: 6560--7016 Score: 621
Period size: 178 Copynumber: 2.6 Consensus size: 179
6550 GCTTCAAATA
* * * * * * * *
6560 TCCGATCAAGTTGATTCAAGTGTCTATTAAAATGTTGTGT-CATGATCTAGAATTTTTATGAAGG
1 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTT-TTTCCATAATCTACAACTTTCATGAAGG
* * *
6624 ACTCGAAAACTAAATTTAATGTTTCAAGTATCAAAAAATACTTCCAAAAAATTAGTTGTTTCGGT
65 ACTCGAAAGCTAAATTTAATGTTTCAAGTATAAAAAAACACTTCCAAAAAATTAGTTGTTTCGGT
* * *
6689 TAACGGGAATGGACGGTCCACTTAATATTACTTAACTTTTGCTCCATATG
130 TAACGGGAAGGGACGGTCCACTTAATATTACATAACTTTTGCTCCAGATG
* * *
6739 TCTGATTAAGGTGATTCAAGTGTCTCTTAAAAGGTTTTTCCATTATCTACAACTTTCATGAAGGA
1 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTTTTTCCATAATCTACAACTTTCATGAAGGA
** *
6804 CTCGAAAGCT-AATTTAATGTTTCAAAAATAAAAAAACGCTTCCAAAAAATTAGTTGTTTCGGTT
66 CTCGAAAGCTAAATTTAATGTTTCAAGTATAAAAAAACACTTCCAAAAAATTAGTTGTTTCGGTT
* * *
6868 AATGGGAAGGGACGGTCTACTTAATATTACATAATTTTTGCTCCAGATG
131 AACGGGAAGGGACGGTCCACTTAATATTACATAACTTTTGCTCCAGATG
* * *
6917 TCCGATTGAGGTGATTCAAGTGTCTATTAAAAGTTTTTTCGATAATCTACAACTTTCATGAAGGA
1 TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTTTTTCCATAATCTACAACTTTCATGAAGGA
* * * *
6982 TTCGAAAGGTAAATTTGACGTTTCAAGTATAAAAA
66 CTCGAAAGCTAAATTTAATGTTTCAAGTATAAAAA
7017 GTGCTTCTGA
Statistics
Matches: 242, Mismatches: 34, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
178 161 0.67
179 81 0.33
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (179 bp):
TCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTTTTTCCATAATCTACAACTTTCATGAAGGA
CTCGAAAGCTAAATTTAATGTTTCAAGTATAAAAAAACACTTCCAAAAAATTAGTTGTTTCGGTT
AACGGGAAGGGACGGTCCACTTAATATTACATAACTTTTGCTCCAGATG
Found at i:14902 original size:18 final size:18
Alignment explanation
Indices: 14879--14913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14869 ACAATATTTA
14879 TAATAA-TTATTATTTTTT
1 TAATAATTTA-TATTTTTT
14897 TAATAATTTATATTTTT
1 TAATAATTTATATTTTT
14914 ATTTCTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATAATTTATATTTTTT
Found at i:15445 original size:14 final size:14
Alignment explanation
Indices: 15426--15454 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15416 TTGAGTGGTG
15426 CGGCACATTTAAGC
1 CGGCACATTTAAGC
15440 CGGCACATTTAAGC
1 CGGCACATTTAAGC
15454 C
1 C
15455 ACTTTTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (14 bp):
CGGCACATTTAAGC
Found at i:15858 original size:25 final size:26
Alignment explanation
Indices: 15826--15874 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
15816 ATTCTCTTGA
*
15826 ACAATTAAAGCCCAAGTT-TTTATAC
1 ACAATTAAAGCCCAAATTCTTTATAC
*
15851 ACAATTAAAGTCCAAATTCTTTAT
1 ACAATTAAAGCCCAAATTCTTTAT
15875 TAATGAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (26 bp):
ACAATTAAAGCCCAAATTCTTTATAC
Done.