Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010027.1 Corchorus capsularis cultivar CVL-1 contig10048, 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: 14610
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1569 original size:31 final size:31
Alignment explanation
Indices: 1534--1665 Score: 112
Period size: 31 Copynumber: 4.4 Consensus size: 31
1524 GCTAATTTTC
* *
1534 CAAATAAGGACCTAATGTTTGTCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
** * * *
1565 CAAATAAGGGTTTGATCTTT---AAATTTGGC-
1 CAAATAAGGGCCTAATGTTTGCCAAA-AT-GCT
*
1594 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
* *
1625 CAAATAAGGGCCTAA-ATTTACCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
*
1655 CAAGTAAGGGC
1 CAAATAAGGGC
1666 TCAATCTTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.04
29 16 0.20
30 27 0.34
31 31 0.39
32 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCT
Found at i:1651 original size:30 final size:31
Alignment explanation
Indices: 1594--1665 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 31
1584 TAAATTTGGC
* *
1594 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACATTTACCAAAATGCT
1625 CAAATAAGGGCCTAA-ATTTACCAAAATGCT
1 CAAATAAGGGCCTAACATTTACCAAAATGCT
*
1655 CAAGTAAGGGC
1 CAAATAAGGGC
1666 TCAATCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 23 0.61
31 15 0.39
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAAATAAGGGCCTAACATTTACCAAAATGCT
Found at i:1663 original size:90 final size:91
Alignment explanation
Indices: 1556--1723 Score: 241
Period size: 90 Copynumber: 1.9 Consensus size: 91
1546 TAATGTTTGT
* ** * *
1556 CAAAATGCTCAAATAAGGGTTTGATCTTTAAATTTGGCCAAATAAGGGCCTAACGTT-T-GCCAA
1 CAAAATGCTCAAATAAGGGCTCAATCTTTAAATTTGGCCAAATAAGGGCCTAACATTATCG-AAA
1619 AATGCTCAAATAAGGGCCTAAATTTAC
65 AATGCTCAAATAAGGGCCTAAATTTAC
* * *
1646 CAAAATGCTCAAGTAAGGGCTCAATCTTTTAATTTGGCCAAATAAGGGTCTAACATTATCGAAAA
1 CAAAATGCTCAAATAAGGGCTCAATCTTTAAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
1711 ATGCTCAAATAAG
66 ATGCTCAAATAAG
1724 AGTCTGGTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
90 50 0.74
91 17 0.25
92 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (91 bp):
CAAAATGCTCAAATAAGGGCTCAATCTTTAAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
ATGCTCAAATAAGGGCCTAAATTTAC
Found at i:1808 original size:31 final size:31
Alignment explanation
Indices: 1770--1870 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
1760 TGATGACATG
*
1770 CCCTTATTTGAGCATTTTCGATAATGTTAGA
1 CCCTTATTTGAGCATTTTCGATAAAGTTAGA
** **
1801 CCCTTATTTG-GTCAAATT--A-AAAGATCGGA
1 CCCTTATTTGAG-CATTTTCGATAAAG-TTAGA
* *
1830 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAAAGTTAGA
1861 CCCTTATTTG
1 CCCTTATTTG
1871 GCCAAATTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.06
29 18 0.34
30 2 0.04
31 27 0.51
32 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAAAGTTAGA
Found at i:1865 original size:60 final size:60
Alignment explanation
Indices: 1770--1930 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
1760 TGATGACATG
* * * **
1770 CCCTTATTTGAGCATTTTCGATAATGTTAGACCCTTATTTGGTCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAA
*
1830 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTTAAAGATCAAA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAA
** * *
1890 CCCTTATTTGAATATTTT-GACAAACATTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTCGA-TAACGTTAGGCCCTTATTTG
1931 AGCTATTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 2 0.02
60 88 0.98
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAA
Found at i:6410 original size:2 final size:2
Alignment explanation
Indices: 6403--6428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6393 AGTAATTCAA
6403 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6429 GGGATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11386 original size:135 final size:138
Alignment explanation
Indices: 11060--11387 Score: 502
Period size: 141 Copynumber: 2.4 Consensus size: 138
11050 TACAACTTTG
* * * * *
11060 ATTAGATAATGATCAATCAATTACAACTTTGATTGGCAAAATTAATTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
*
11125 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGAT
66 TTATTTTTTTGGTAACATAATTACTAATTG---TATTTATTTATGGTAATCTTTTTGGTAGCGAT
11190 TTTATGGTAAA
128 TTTATGGTAAA
*
11201 ATTATATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACGACATGTTCAATAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGA-AAAATTAACTAACGACATGTTCAATAA
* *
11265 TTTATTTTTTTGGTAACATAATTACTAATTG-ATTTATTTATGTTAAT-TTTTTTGTAGCGA-TT
65 TTTATTTTTTTGGTAACATAATTACTAATTGTATTTATTTATGGTAATCTTTTTGGTAGCGATTT
11327 TATGGTAAA
130 TATGGTAAA
*
11336 ATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
11388 TCACTAACTT
Statistics
Matches: 175, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
135 58 0.33
136 13 0.07
137 15 0.09
140 1 0.01
141 88 0.50
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (138 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
TTATTTTTTTGGTAACATAATTACTAATTGTATTTATTTATGGTAATCTTTTTGGTAGCGATTTT
ATGGTAAA
Found at i:11924 original size:138 final size:138
Alignment explanation
Indices: 11673--12064 Score: 450
Period size: 138 Copynumber: 2.8 Consensus size: 138
11663 TTTTTGGCAA
* * ** * * *
11673 TTAATTAACGACTAATTTGATTCCCTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTTCTA
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC-A---ATTTTTTTTGTA
*
11738 ACATAATTACTAATTGATTCATTTATTTAT-GACAAAATCAAATAATCATCAATCAATTATAACT
62 ACATAATTACTAATTGATTCATTTATTTATGGAAAAAAT-AAATAATCATCAATCAATTATAACT
11802 TTAATTGACAAAG
126 TTAATTGACAAAG
* * *
11815 TTGA-TCAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTGGTAATA
1 TTAACT-AACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGTAACA
* * *
11879 TAATTAGTAATTGAATT-ATTTATTTATGGAAAAAATAAATAATCATCCATCAATTATAACTTTG
65 TAATTACTAATTG-ATTCATTTATTTATGGAAAAAATAAATAATCATCAATCAATTATAACTTTA
**
11943 ATTGGTAAAG
129 ATTGACAAAG
* * * *
11953 TTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTTTTTTGTAA
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA--T-TTTTTTTGTAA
* * * *
12018 CATAA-TATTAATTGATTCATTTATTTGTGGCAAAATTAAATAATCAT
63 CATAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCAT
12065 TAGCTTTTGG
Statistics
Matches: 216, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
138 111 0.51
139 14 0.06
140 35 0.16
141 16 0.07
142 40 0.19
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (138 bp):
TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGTAACAT
AATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCATCAATCAATTATAACTTTAAT
TGACAAAG
Done.