Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010788.1 Corchorus olitorius cultivar O-4 contig10820, 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: 5360
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Found at i:656 original size:20 final size:21
Alignment explanation
Indices: 614--656 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
604 TCCTTTGTTG
614 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
635 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
655 AT
1 AT
657 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:793 original size:21 final size:20
Alignment explanation
Indices: 769--862 Score: 125
Period size: 21 Copynumber: 4.5 Consensus size: 20
759 ATCTTAGGCA
*
769 TCTCCAATGATCTTGGAAACT
1 TCTCCAATGAGCTTGG-AACT
*
790 TCTCCAATGAACTTGGAACCT
1 TCTCCAATGAGCTTGGAA-CT
*
811 GCTCCAATGAGCTTGGAACT
1 TCTCCAATGAGCTTGGAACT
831 TGCTCCAATGAGCTTGGAACT
1 T-CTCCAATGAGCTTGGAACT
852 TGCTCCAATGA
1 T-CTCCAATGA
863 ACTTCTAGCA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.06
21 63 0.94
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
TCTCCAATGAGCTTGGAACT
Found at i:817 original size:42 final size:42
Alignment explanation
Indices: 770--862 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
760 TCTTAGGCAT
*
770 CTCCAATGATCTTGGAAACTT-CTCCAATGAACTTGGAACCTG
1 CTCCAATGAGCTTGG-AACTTGCTCCAATGAACTTGGAACCTG
* *
812 CTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTG
1 CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG
854 CTCCAATGA
1 CTCCAATGA
863 ACTTCTAGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 5 0.11
42 42 0.89
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (42 bp):
CTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTG
Found at i:4462 original size:154 final size:154
Alignment explanation
Indices: 4179--5356 Score: 1763
Period size: 154 Copynumber: 7.7 Consensus size: 154
4169 TGGCGCATCA
* * * *
4179 ACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGGAAATAAAAGCATTGAAGCTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * *
4244 CAATTCGAAGAAGATACAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
4309 AATTAGCTAAAAAGTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
*
4333 ACTAATCTCACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
*
4398 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
4463 AATGAGCTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
* * * * * *
4487 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAAGGAATGAAAATCATTAAGGTCTGA
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * * * * * *
4552 TAAATCGAATACGATTCAATACGTCACTAATGGACCCCAATAAGCCCAAAATAACAAGTATTCCG
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
4617 AATGAGCTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
*
4641 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * *
4706 TAAATCGAAGATGATTACAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT-ACAAGTGTTCC
66 CAAATCGAAGACGATT-CAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* * *
4770 TAATTGAACCAAAAA-TTCACAGTGG
130 -AAATGAGCTAAAAACTTCACAGTGG
*
4795 ACTAAT-TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * ** *
4859 CAAATCGAAGATGATTCAAAACGGAACTAATCGGGCCCCGATAGGACCTAAAATAACAAGTGTTC
66 CAAATCGAAGACGATTCAATACGTCACTAAT-GGGCCCCGATAGG-CCCAAAATAACAAGTGTTC
* *
4924 CAACTGAGCTAAAAAGTTCACAGTGG
129 CAAATGAGCTAAAAACTTCACAGTGG
*
4950 ACTAATCTCACCAAAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * *
5015 CAAATCGAAGACGATTCAATACGTCATTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCAA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
5080 AATGAACTAAAAACTTCAAAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
* * * * * *
5104 ACTAATCTAAACAAAATGATTATGGGTAGGCC--AAACAATGGAAACAAAAGCATTGAGGCTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* ** * *
5167 CAATTCGAAGAAAATTCAATACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTATTCCA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
5232 AATGAACTAAAAGCTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
5256 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
5321 CAAATCGAAGACGATTCAATACGTCACTAATGGGCC
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCC
5357 TTGA
Statistics
Matches: 923, Mismatches: 92, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
152 149 0.16
153 84 0.09
154 526 0.57
155 82 0.09
156 82 0.09
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGG
Done.