Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022067.1 Corchorus olitorius cultivar O-4 contig22100, 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: 7011
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Found at i:156 original size:29 final size:29
Alignment explanation
Indices: 120--326 Score: 270
Period size: 29 Copynumber: 6.8 Consensus size: 29
110 TCTTCAAGGG
120 TTTCAATTTAGGGAAAGATCCCATCAAGT
1 TTTCAATTTAGGGAAAGATCCCATCAAGT
149 TTTCAATTTAGGGAAAGATCCCATCAAGT
1 TTTCAATTTAGGGAAAGATCCCATCAAGT
*
178 TTCCAATTTAGGGAAAGATCCCATCAAGT
1 TTTCAATTTAGGGAAAGATCCCATCAAGT
*
207 TTTCAAATTTAGGGAAAGATCCCATCAGTTTCTTCAAGAT
1 TTTC-AATTTAGGGAAAGATCCCATCA--------AG--T
247 TTTCAATTTAGGGAAAGATCCCATCAAGT
1 TTTCAATTTAGGGAAAGATCCCATCAAGT
* *
276 TTCCAATTTAGGAAAAGATCCCATCAAGT
1 TTTCAATTTAGGGAAAGATCCCATCAAGT
*
305 TTTCAATTTAGGGAAAGTTCCC
1 TTTCAATTTAGGGAAAGATCCC
327 GTCATTTTAA
Statistics
Matches: 158, Mismatches: 9, Indels: 22
0.84 0.05 0.12
Matches are distributed among these distances:
29 107 0.68
30 22 0.14
31 1 0.01
38 1 0.01
39 22 0.14
40 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (29 bp):
TTTCAATTTAGGGAAAGATCCCATCAAGT
Found at i:251 original size:127 final size:127
Alignment explanation
Indices: 76--326 Score: 439
Period size: 127 Copynumber: 2.0 Consensus size: 127
66 GGTTTTTTCA
* *
76 AAGTTTTCAAATTTAGGGAAAGATCTCATCAGTTTCTTCAAGGGTTTCAATTTAGGGAAAGATCC
1 AAGTTTTCAAATTTAGGGAAAGATCCCATCAGTTTCTTCAAGAGTTTCAATTTAGGGAAAGATCC
* *
141 CATCAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGGAAAGATCCCATC
66 CATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTTTCCAATTTAGGGAAAGATCCCATC
*
203 AAGTTTTCAAATTTAGGGAAAGATCCCATCAGTTTCTTCAAGATTTTCAATTTAGGGAAAGATCC
1 AAGTTTTCAAATTTAGGGAAAGATCCCATCAGTTTCTTCAAGAGTTTCAATTTAGGGAAAGATCC
* *
268 CATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTTTTCAATTTAGGGAAAGTTCCC
66 CATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTTTCCAATTTAGGGAAAGATCCC
327 GTCATTTTAA
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 117 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (127 bp):
AAGTTTTCAAATTTAGGGAAAGATCCCATCAGTTTCTTCAAGAGTTTCAATTTAGGGAAAGATCC
CATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTTTCCAATTTAGGGAAAGATCCCATC
Found at i:255 original size:39 final size:40
Alignment explanation
Indices: 201--278 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
191 AAAGATCCCA
201 TCAAGTTTTCAAATTTAGGGAAAGATCCCATC-AGTTTCT
1 TCAAGTTTTCAAATTTAGGGAAAGATCCCATCAAGTTTCT
240 TCAAGATTTTC-AATTTAGGGAAAGATCCCATCAAGTTTC
1 TCAAG-TTTTCAAATTTAGGGAAAGATCCCATCAAGTTTC
279 CAATTTAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (40 bp):
TCAAGTTTTCAAATTTAGGGAAAGATCCCATCAAGTTTCT
Found at i:350 original size:98 final size:97
Alignment explanation
Indices: 143--326 Score: 334
Period size: 98 Copynumber: 1.9 Consensus size: 97
133 AAAGATCCCA
*
143 TCAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGGAAAGATCCCATCAAGTT
1 TCAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTT
208 TTCAAATTTAGGGAAAGATCCCATCAGTTTCT
66 TTCAAATTTAGGGAAAGATCCCATCAGTTTCT
240 TCAAGATTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGT
1 TCAAG-TTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGT
*
305 TTTC-AATTTAGGGAAAGTTCCC
65 TTTCAAATTTAGGGAAAGATCCC
327 GTCATTTTAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
97 22 0.26
98 62 0.74
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (97 bp):
TCAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTCCAATTTAGGAAAAGATCCCATCAAGTT
TTCAAATTTAGGGAAAGATCCCATCAGTTTCT
Found at i:1028 original size:2 final size:2
Alignment explanation
Indices: 1021--1047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1011 TGTTTTGTTT
1021 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1048 GTTTTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4756 original size:20 final size:20
Alignment explanation
Indices: 4731--4768 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4721 TATTACTAGT
4731 TATATATATTCTTTCTTTGG
1 TATATATATTCTTTCTTTGG
* *
4751 TATATATTTTGTTTCTTT
1 TATATATATTCTTTCTTT
4769 ATTTCTGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (20 bp):
TATATATATTCTTTCTTTGG
Found at i:5738 original size:54 final size:54
Alignment explanation
Indices: 5639--5741 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
5629 GATGGGGGTC
*
5639 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGGA
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAGGA
* *
5693 ACTTGAGTTGAAAACCCGCAAAGGGCGGCTCAAGCGGAA-GTTGGAAAAG
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAG-GGAAGGATGGAAAAG
5742 ACATAGTCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 42 0.93
55 3 0.07
ACGTcount: A:0.37, C:0.16, G:0.34, T:0.14
Consensus pattern (54 bp):
ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGGGAAGGATGGAAAAGGAGGA
Done.