Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016636.1 Corchorus olitorius cultivar O-4 contig16669, 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: 31024
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:862 original size:31 final size:30
Alignment explanation
Indices: 700--867 Score: 96
Period size: 31 Copynumber: 5.6 Consensus size: 30
690 TTAGGCTAAT
*
700 TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * * * **
731 TGTTCAAATAAGGACTCGATCTTT--TAATT
1 TGCTCAAATAAGGGC-CTAACTTTGCCAAAA
* *
760 TGAC-CAAATAAGGGCTTAACATTTGCCAAAG
1 TG-CTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * **
791 TGCTCAAATAAGGGCCCGATCTTT--TAATT
1 TGCTCAAATAAGGG-CCTAACTTTGCCAAAA
820 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGCCAAAA
851 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
868 GGCATCAAAA
Statistics
Matches: 98, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
28 6 0.06
29 33 0.34
30 5 0.05
31 48 0.49
32 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:864 original size:60 final size:60
Alignment explanation
Indices: 704--866 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
694 GCTAATTGCT
* * * *
704 CAAATAAGGGTCTAACGTTTGCCAAAATGTTCAAATAAGGACTCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * * *
764 CAAATAAGGGCTTAACATTTGCCAAAGTGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
824 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
867 TGGCATCAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:941 original size:31 final size:29
Alignment explanation
Indices: 906--1044 Score: 129
Period size: 31 Copynumber: 4.6 Consensus size: 29
896 AACTGATGCC
906 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT--CAAACGTT
** * *
937 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCAAACG-TT
*
966 GGGCCCTTATTTGAGCATTTTCAATAACGTT
1 AGGCCCTTATTTGAGCATTTTC-A-AACGTT
*
997 AGGCCCTTATTTAAGCATTTTGTCAAACGTT
1 AGGCCCTTATTTGAGCA-TTT-TCAAACGTT
*
1028 AAGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
1045 ATTAGCCAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.05
29 17 0.20
30 2 0.02
31 55 0.63
32 7 0.08
33 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTCAAACGTT
Found at i:13049 original size:66 final size:66
Alignment explanation
Indices: 12956--13528 Score: 671
Period size: 66 Copynumber: 8.7 Consensus size: 66
12946 AGACCATTCT
* * * * * *
12956 GGCAGCTCCTGTCCAAACAAAC-GTTGCTTCTGGCGCTTATTAGCAGCATATA-G-CCATGACCC
1 GGCAGCTCCTTTCCAAGC-ATCGGTTGCTTCTGGCGCATATCAGCACCATATATGCCCA--ACCC
*
13018 TTGT
63 TTGC
* * * *
13022 GGCAGCTCTTTTCCAAGCAT-GGATTGCTTCTGGCATC-TATCAGCACCAAAAATGCCCAACCCT
1 GGCAGCTCCTTTCCAAGCATCGG-TTGCTTCTGGC-GCATATCAGCACCATATATGCCCAACCCT
13085 TGC
64 TGC
* * * *
13088 GGCAGTTCCTTTCCAAACATCGGTTGCTTCTGG-GACATATCAGCACCATATATGCTCAATCCTT
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCG-CATATCAGCACCATATATGCCCAACCCTT
*
13152 GA
65 GC
* * * *
13154 GGCAGCTCCTTTCCAAGCATAGGTTGCTTCTGGCATC-TATCAGCAGCATATATGCCCAATCCTT
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGC-GCATATCAGCACCATATATGCCCAACCCTT
*
13218 GT
65 GC
* * *
13220 GGCAGCTCCTTTCCAAGCATCAGTTGCTTC-GGGGACATATCAGCACCATATTTGCCCAACCCTT
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCG-CATATCAGCACCATATATGCCCAACCCTT
*
13284 GT
65 GC
*
13286 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCGCCTATCAGCACCATATATGCCCAACCCTTG
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCGCATATCAGCACCATATATGCCCAACCCTTG
13351 C
66 C
* * * *
13352 GGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGTG-ACATATTAGCACCAAATATGCCCAACCCTT
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTG-GCGCATATCAGCACCATATATGCCCAACCCTT
13416 GC
65 GC
* *
13418 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGG-GACATATTAGCACCAAATATGCCCAACCCTT
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCG-CATATCAGCACCATATATGCCCAACCCTT
13482 GC
65 GC
* * *
13484 GGCAGCTCCTTTCCAAGCATAGGTTGCTTCTGGCACCTATCAGCA
1 GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCGCATATCAGCA
13529 GCAGCAGCTC
Statistics
Matches: 442, Mismatches: 49, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
65 7 0.02
66 423 0.96
67 9 0.02
68 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.27
Consensus pattern (66 bp):
GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCGCATATCAGCACCATATATGCCCAACCCTTG
C
Found at i:13193 original size:132 final size:132
Alignment explanation
Indices: 13014--13528 Score: 748
Period size: 132 Copynumber: 3.9 Consensus size: 132
13004 TATAGCCATG
* *
13014 ACCCTTGTGGCAGCTCTTTTCCAAGCAT-GGATTGCTTCTGGCATCTATCAGCACCAAAAATGCC
1 ACCCTTGTGGCAGCTCCTTTCCAAGCATCGG-TTGCTTCTGGCATCTATCAGCACCAAATATGCC
* * *
13078 CAACCCTTGCGGCAGTTCCTTTCCAAACATCGGTTGCTTCTGGGACATATCAGCACCATATATGC
65 CAACCCTTGCGGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGGGACATATCAGCACCATATATGC
*
13143 TCA
130 CCA
* * * * *
13146 ATCCTTGAGGCAGCTCCTTTCCAAGCATAGGTTGCTTCTGGCATCTATCAGCAGCATATATGCCC
1 ACCCTTGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCATCTATCAGCACCAAATATGCCC
* * * *
13211 AATCCTTGTGGCAGCTCCTTTCCAAGCATCAGTTGCTTCGGGGACATATCAGCACCATATTTGCC
66 AACCCTTGCGGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGGGACATATCAGCACCATATATGCC
13276 CA
131 CA
** *
13278 ACCCTTGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCGCCTATCAGCACCATATATGCCC
1 ACCCTTGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCATCTATCAGCACCAAATATGCCC
* * *
13343 AACCCTTGCGGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGTGACATATTAGCACCAAATATGCC
66 AACCCTTGCGGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGGGACATATCAGCACCATATATGCC
13408 CA
131 CA
* * *
13410 ACCCTTGCGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGA-CATATTAGCACCAAATATGCC
1 ACCCTTGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCATC-TATCAGCACCAAATATGCC
* *
13474 CAACCCTTGCGGCAGCTCCTTTCCAAGCAT-AGGTTGCTTCTGGCACCTATCAGCA
65 CAACCCTTGCGGCAGCTCCTTTCCAAGCATCA-GTTGCTTCTGGGACATATCAGCA
13529 GCAGCAGCTC
Statistics
Matches: 344, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.01
132 340 0.99
133 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (132 bp):
ACCCTTGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCATCTATCAGCACCAAATATGCCC
AACCCTTGCGGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGGGACATATCAGCACCATATATGCC
CA
Found at i:13298 original size:198 final size:197
Alignment explanation
Indices: 12956--13528 Score: 764
Period size: 198 Copynumber: 2.9 Consensus size: 197
12946 AGACCATTCT
* * * * *
12956 GGCAGCTCCTGTCCAAACAAACGTTGCTTCTGGCGCTTATTAGCAGCATATA-G-CCATGACCCT
1 GGCAGCTCCTTTCCAAGCATA-GTTGCTTCTGGCACATATTAGCAGCATATATGCCCA--ACCCT
* * *
13019 TGTGGCAGCTCTTTTCCAAGCAT-GGATTGCTTCTGGCATC-TATCAGCACCAAAAATGCCCAAC
63 TGTGGCAGCTCCTTTCCAAGCATCGG-TTGCTTCTGGGA-CATATCAGCACCAAATATGCCCAAC
* * * *
13082 CCTTGCGGCAGTTCCTTTCCAAACATCGGTTGCTTCTGGGACATATCAGCACCATATATGCTCAA
126 CCTTGCGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACCTATCAGCACCATATATGCCCAA
*
13147 TCCTTGA
191 CCCTTGA
* *
13154 GGCAGCTCCTTTCCAAGCATAGGTTGCTTCTGGCATC-TATCAGCAGCATATATGCCCAATCCTT
1 GGCAGCTCCTTTCCAAGCATA-GTTGCTTCTGGCA-CATATTAGCAGCATATATGCCCAACCCTT
* * * *
13218 GTGGCAGCTCCTTTCCAAGCATCAGTTGCTTCGGGGACATATCAGCACCATATTTGCCCAACCCT
64 GTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACATATCAGCACCAAATATGCCCAACCCT
*
13283 TGTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGCG-CCTATCAGCACCATATATGCCCAACC
129 TGCGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGG-GACCTATCAGCACCATATATGCCCAACC
*
13347 CTTGC
193 CTTGA
* *
13352 GGCAGCTCCTTTCCAAGCATCAGTTGCTTCTGTG-ACATATTAGCACCAAATATGCCCAACCCTT
1 GGCAGCTCCTTTCCAAGCAT-AGTTGCTTCTG-GCACATATTAGCAGCATATATGCCCAACCCTT
* *
13416 GCGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACATATTAGCACCAAATATGCCCAACCCT
64 GTGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACATATCAGCACCAAATATGCCCAACCCT
* *
13481 TGCGGCAGCTCCTTTCCAAGCATAGGTTGCTTCTGGCACCTATCAGCA
129 TGCGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACCTATCAGCA
13529 GCAGCAGCTC
Statistics
Matches: 331, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
197 2 0.01
198 320 0.97
199 6 0.02
200 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.27
Consensus pattern (197 bp):
GGCAGCTCCTTTCCAAGCATAGTTGCTTCTGGCACATATTAGCAGCATATATGCCCAACCCTTGT
GGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACATATCAGCACCAAATATGCCCAACCCTTG
CGGCAGCTCCTTTCCAAGCATCGGTTGCTTCTGGGACCTATCAGCACCATATATGCCCAACCCTT
GA
Found at i:18095 original size:54 final size:53
Alignment explanation
Indices: 18014--18119 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 53
18004 AATAATAAAT
**
18014 TTATCAGCCTTTTGTTTGCAGAAACACATCCCTAAATCAATGTCCCAATTCCC
1 TTATCAGCCTTTTGTTTGCAGAAACACATCCCTAAATCAACATCCCAATTCCC
*
18067 TTATCAGCCTTTTTGTTTGCAGAAACACATCCCTGAATCAACATCCCAATTCC
1 TTATCAGCC-TTTTGTTTGCAGAAACACATCCCTAAATCAACATCCCAATTCC
18120 ACAAATACTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 9 0.18
54 40 0.82
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (53 bp):
TTATCAGCCTTTTGTTTGCAGAAACACATCCCTAAATCAACATCCCAATTCCC
Found at i:25909 original size:13 final size:13
Alignment explanation
Indices: 25891--25915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25881 AATACTCCCA
25891 TATATATATATAG
1 TATATATATATAG
25904 TATATATATATA
1 TATATATATATA
25916 TTCTGTAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATATATATATAG
Done.