Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014096.1 Corchorus olitorius cultivar O-4 contig14129, 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: 6385
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:457 original size:30 final size:30
Alignment explanation
Indices: 421--807 Score: 555
Period size: 30 Copynumber: 12.9 Consensus size: 30
411 ATTCAATTCC
* *
421 AATCCTGATTT-AGGATTATTGCTTCATTTT
1 AATCCTG-TTTGAGGATCATTGCTTTATTTT
451 AATCCTGTTTGAGGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
481 AATCCTGTTTGTGGATCATTGCTTTATGTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
511 AATCCTGTTTGAGGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
541 AATCCTGTTTGAGGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * * *
571 AATCCTGGTTGAGGATGATGGCATTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * *
601 AATCCTGGTTGAGGATTATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
631 AATCCTGTTTGAGGATCATTGCTTTATGTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
661 AATCCTGTTTGAGGATCACTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
691 AATCCTGTTTGAGGAACATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * * *
721 AATCCTGGTTGAGGATCGTTCCTTTATTAT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
751 AATCCTGGTTT-AGGATCATTGCTTTATTTT
1 AATCCT-GTTTGAGGATCATTGCTTTATTTT
*
781 AATCCTGGTTT-AGGATCATTGTTTTAT
1 AATCCT-GTTTGAGGATCATTGCTTTAT
808 CAGTTAATTC
Statistics
Matches: 323, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
29 3 0.01
30 317 0.98
31 3 0.01
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (30 bp):
AATCCTGTTTGAGGATCATTGCTTTATTTT
Found at i:1721 original size:29 final size:28
Alignment explanation
Indices: 1657--1816 Score: 171
Period size: 29 Copynumber: 5.6 Consensus size: 28
1647 GGTCACCTAG
** * *
1657 GGGCATTTTGGTCATTTTTTATATTCAG
1 GGGCATTTTGGTCATTTTGCACATTCAA
1685 GGGCATTTTGGTCATTTCTGCACATTCAA
1 GGGCATTTTGGTCATTT-TGCACATTCAA
* * *
1714 CGGCATTTTGGTCATTTTTGCACACTCAG
1 GGGCATTTTGGTCA-TTTTGCACATTCAA
*
1743 GGGCATTTTGGTCATTTTTGGCATATTCAA
1 GGGCATTTTGGTCA-TTTT-GCACATTCAA
* *
1773 GGGTATTTTGGTCA-TTTGCACGTTC-A
1 GGGCATTTTGGTCATTTTGCACATTCAA
*
1799 GGGCATTTTGGTCCTTTT
1 GGGCATTTTGGTCATTTT
1817 TTTTTAAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
26 13 0.12
27 9 0.08
28 20 0.18
29 47 0.42
30 23 0.21
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATTCAA
Found at i:1756 original size:58 final size:59
Alignment explanation
Indices: 1658--1811 Score: 201
Period size: 57 Copynumber: 2.7 Consensus size: 59
1648 GTCACCTAGG
* *
1658 GGCATTTTGGTCATTTTT-TATATTCAGGGGCATTTTGGTCATTTCT-GCACATTCAAC
1 GGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTCATTTCTGGCACATTCAAC
* * * *
1715 GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGGCATATTCAAG
1 GGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTCATTTCTGGCACATTCAAC
* *
1774 GGTATTTTGGTCA--TTTGCACGTTCA-GGGCATTTTGGTC
1 GGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTC
1812 CTTTTTTTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
56 13 0.15
57 28 0.33
58 24 0.28
59 21 0.24
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (59 bp):
GGCATTTTGGTCATTTTTGCACATTCAGGGGCATTTTGGTCATTTCTGGCACATTCAAC
Found at i:1818 original size:86 final size:86
Alignment explanation
Indices: 1655--1817 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 86
1645 AGGGTCACCT
* *
1655 AGGGGCATTTTGGTCATTTTTTATATTCAGGGGCATTTTGGTCATTTCTGCACATTCAACGGCAT
1 AGGGGCATTTTGGTCATTTTTCATATTCAAGGGCATTTTGGTCATTTCTGCACATTCAACGGCAT
1720 TTTGGTCATTTTTGCACACTC
66 TTTGGTCATTTTTGCACACTC
* * *
1741 AGGGGCATTTTGGTCATTTTTGGCATATTCAAGGGTATTTTGGTCA-TT-TGCACGTTC-AGGGC
1 AGGGGCATTTTGGTCATTTTT--CATATTCAAGGGCATTTTGGTCATTTCTGCACATTCAACGGC
*
1803 ATTTTGGTCCTTTTT
64 ATTTTGGTCATTTTT
1818 TTTTAAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
85 18 0.26
86 29 0.42
87 2 0.03
88 20 0.29
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (86 bp):
AGGGGCATTTTGGTCATTTTTCATATTCAAGGGCATTTTGGTCATTTCTGCACATTCAACGGCAT
TTTGGTCATTTTTGCACACTC
Found at i:1820 original size:59 final size:58
Alignment explanation
Indices: 1658--1817 Score: 191
Period size: 58 Copynumber: 2.8 Consensus size: 58
1648 GTCACCTAGG
** * * * *
1658 GGCATTTTGGTCATTTTTTATATTCAGGGGCATTTTGGTCATTTCT-GCACATTCAAC
1 GGCATTTTGGTCATTTTGCACACTCAGGGGCATTTTGGTCATTTTTGGCATATTCAAC
*
1715 GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGGCATATTCAAG
1 GGCATTTTGGTCA-TTTTGCACACTCAGGGGCATTTTGGTCATTTTTGGCATATTCAAC
* ** *
1774 GGTATTTTGGTCA-TTTGCACGTTCA-GGGCATTTTGGTCCTTTTT
1 GGCATTTTGGTCATTTTGCACACTCAGGGGCATTTTGGTCATTTTT
1818 TTTTAAAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 18 0.20
57 23 0.26
58 28 0.31
59 21 0.23
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.44
Consensus pattern (58 bp):
GGCATTTTGGTCATTTTGCACACTCAGGGGCATTTTGGTCATTTTTGGCATATTCAAC
Found at i:5330 original size:65 final size:65
Alignment explanation
Indices: 5248--5374 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
5238 CGTTACGACA
5248 AACTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTGGAAAGTAAAATTG
1 AACTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTGGAAAGTAAAATTG
* * *
5313 AACTTAGATGTGAAAAATATGTAATTGACCCTTCGACCGGAAGGGTATTTTGGAAAGTAAAA
1 AACTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTGGAAAGTAAAA
5375 GAAAATACTA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (65 bp):
AACTTAAATGTGAAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTGGAAAGTAAAATTG
Done.