Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011564.1 Corchorus olitorius cultivar O-4 contig11597, 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: 3270
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Found at i:642 original size:21 final size:21
Alignment explanation
Indices: 618--665 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
608 TCCCGTGTCA
*
618 CAATGAGCTTAGATCCTT-CTC
1 CAATGAGCTTAGA-ACTTGCTC
*
639 CAATGAGCTTGGAACTTGCTC
1 CAATGAGCTTAGAACTTGCTC
660 CAATGA
1 CAATGA
666 TCTCCTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (21 bp):
CAATGAGCTTAGAACTTGCTC
Found at i:725 original size:40 final size:40
Alignment explanation
Indices: 670--748 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
660 CAATGATCTC
670 CTAGCATCTTCAAGACCATGATGAGT-CTGTGGCGCATCAG
1 CTAGCATCTTCAAGACCATGATGAGTCCT-TGGCGCATCAG
710 CTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
1 CTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
749 ATCAGGTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCAG
Found at i:1036 original size:154 final size:154
Alignment explanation
Indices: 756--1814 Score: 1800
Period size: 154 Copynumber: 6.9 Consensus size: 154
746 TCAATCAGGT
*
756 CATAAACATTGGAAAGTAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * *
821 GGGCCCCGATAGGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAAC
66 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAAT
885 CTCACCAAAATGATTATAGTTAGGC
130 CTCACCAAAATGATTATAGTTAGGC
910 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
975 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1040 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* * * * **
1064 CATAAACAATGGAAAGAAAAGCAATGAGGGTTGCGAAATCGAAGATGATTCAAAACGTCACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
1129 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1194 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* * **
1218 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * * *
1283 GGGCCCCGATAGGCCCAAAAGT-ACAAGTGTTCCAAATGAGCTAAATACTTCACAGTAGACTAAT
66 GGTCCTCGATATGCCCAAAA-TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
1347 CTCACCAAAATGATTATAGTTAAGT
130 CTCACCAAAATGATTATAGTTAGGC
*
1372 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACCATTCAAAACGGAACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1437 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1502 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
*
1526 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACCATTCAAAACGGAACTAAT
1 CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
1591 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
66 GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
1656 TCACCAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
*
1680 CATAAACAATGGAAAG-AAAGCATATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
1 CATAAACATTGGAAAGAAAAGC--ATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
*
1744 ATGGTCCTCGATATGCCCATAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
64 ATGGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1809 TCTCAC
129 TCTCAC
1815 TGATACGAAT
Statistics
Matches: 863, Mismatches: 37, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
153 6 0.01
154 726 0.84
155 131 0.15
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
GGTCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGC
Found at i:2640 original size:21 final size:21
Alignment explanation
Indices: 2616--2665 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2606 CTTAGGCAAT
2616 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
** *
2637 TCCAATGATTTTGGAACCTTC
1 TCCAATGAGCTTGAAACCTTC
2658 TCCAATGA
1 TCCAATGA
2666 ACTTCTAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:3052 original size:154 final size:153
Alignment explanation
Indices: 2772--3270 Score: 795
Period size: 154 Copynumber: 3.2 Consensus size: 153
2762 TGGCGCATCA
* **
2772 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG-AGCACGATTGAAAACGGAACTA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG-ACGATTCAAAACGTCACTA
* *
2836 ATTGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAA
65 A-TGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAA
2901 TCTCACCAAATTGATTATAGTTAGG
129 TCTCACCAAATTGATTATAGTTAGG
*
2926 CCATAGACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
2991 TGGTTCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAAT
66 TGG-CCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAAT
*
3056 CTCACCAAATTGATTATAGTAAGG
130 CTCACCAAATTGATTATAGTTAGG
* *
3080 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAATGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
3145 TGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGAACTAAT
66 T-GGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAAT
* *
3210 CTCATCAAAATGATTATAGTTAGG
130 CTCACCAAATTGATTATAGTTAGG
* * *
3234 CCATAAACAACT-TAAAGAATAGCTTTGAGGTTTGCCA
1 CCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCA
Statistics
Matches: 321, Mismatches: 20, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
153 3 0.01
154 313 0.98
155 5 0.02
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (153 bp):
CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
TGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATC
TCACCAAATTGATTATAGTTAGG
Done.