Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014757.1 Corchorus capsularis cultivar CVL-1 contig14778, 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: 23163
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1512 original size:42 final size:42
Alignment explanation
Indices: 1465--1549 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
1455 CAATCAATTC
1465 CTATAATTCGAGCTTCAATAACCAACACTCAGTGGCAAAAAG
1 CTATAATTCGAGCTTCAATAACCAACACTCAGTGGCAAAAAG
*
1507 CTATAATTCGAGCTTCAATAACCAACACTGAGTGGCAAAAAG
1 CTATAATTCGAGCTTCAATAACCAACACTCAGTGGCAAAAAG
1549 C
1 C
1550 ATGGATTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (42 bp):
CTATAATTCGAGCTTCAATAACCAACACTCAGTGGCAAAAAG
Found at i:8328 original size:156 final size:156
Alignment explanation
Indices: 8044--8455 Score: 553
Period size: 156 Copynumber: 2.6 Consensus size: 156
8034 TGTAGACCAT
* * * * * ** *
8044 CTTGGCTAAGTTTCATCTCAAACGGACTTA-AGATGAAAAACTTATACACGTTTTTCAGATAAGA
1 CTTGGCCAAATTTCATCTCAATCGGACTTAGA-ATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * *
8108 ACAGTTTGGGGTA-TGAAACCAACTTCACTATGAAAGGGAGTTTGGTTTAACTTGGAATTTTTTC
65 ACAGTTTGGGG-AGTGAAACCAAGTTCACTATGAAAGGGAGTTCGGTTTAACTTAGAATTTTTTC
*
8172 CATAGTTTTGTGGAGATAATCTAAGTCC
129 CATAGTTTTATGGAGATAATCTAAGTCC
* * * *
8200 CTTGGCCAAATTTCAGCTCAATTGGACTTAGAATGAAGAACTTATGCATGTTTTTAATTTAAGGA
1 CTTGGCCAAATTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
* * *
8265 CAGTTTGGGGAGAGAAACCAAGTTCACTAT-CAAGGAGAGTTCGGTTTTACTTAGAATTTTTTCC
66 CAGTTTGGGGAGTGAAACCAAGTTCACTATGAAAGG-GAGTTCGGTTTAACTTAGAATTTTTTCC
8329 ATAGTTTTATGGAGATAATCTAAGTCC
130 ATAGTTTTATGGAGATAATCTAAGTCC
*
8356 CTTGG-CAAAGTTTCATCTCAATCAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGG
1 CTTGGCCAAA-TTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * *
8420 ACAGTTTGGGGTGTGAAACCTAGTTCACCATGAAAG
65 ACAGTTTGGGGAGTGAAACCAAGTTCACTATGAAAG
8456 AGGTTCAAAC
Statistics
Matches: 222, Mismatches: 29, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
155 9 0.04
156 209 0.94
157 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (156 bp):
CTTGGCCAAATTTCATCTCAATCGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
CAGTTTGGGGAGTGAAACCAAGTTCACTATGAAAGGGAGTTCGGTTTAACTTAGAATTTTTTCCA
TAGTTTTATGGAGATAATCTAAGTCC
Found at i:21797 original size:156 final size:156
Alignment explanation
Indices: 21513--21926 Score: 514
Period size: 156 Copynumber: 2.7 Consensus size: 156
21503 TGTAGACCAT
* * ** * * **
21513 CTTGGCTAAGTTTCATCTCAAACAAACTTA-AGATGAAAAACTTATAC-TCGTTTTTCAGATAAG
1 CTTGGCAAAGTTTCAGCTCAATTAGACTTAGA-ATGAAAAACTTATGCAT-GTTTTTCATTTAAG
* * * * * ** * *
21576 GACAGTTTGGGGTGTGAAACCAACTTCACTGTGAAAGG-GAGTTCGGTTTTACTTAGAATTTTTT
64 GACAATTTGGGGAGAGAAACCTAGTTCACCAT-CAAGGAGAGTTCGGTTTTACTTAGAATATTTT
* *
21640 CCATAGTTTTTTGGTGATAATCTAAGTCC
128 CCATAGTTTTATGGAGATAATCTAAGTCC
* *
21669 CTTGGCCAAA-TTTCAGCTCAATTGGACTTAGAATGAAAAGCTTATGCATGTTTTTCATTTAAGG
1 CTTGG-CAAAGTTTCAGCTCAATTAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGG
21733 ACAATTTGGGGAGAGAAACC-ATGTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATATTTTC
65 ACAATTTGGGGAGAGAAACCTA-GTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATATTTTC
21797 CATAGTTTTATGGAGATAATCTAAGTCC
129 CATAGTTTTATGGAGATAATCTAAGTCC
*
21825 CTTGGCAAAGTTTCATCTCAATTAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
1 CTTGGCAAAGTTTCAGCTCAATTAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
* * * *
21890 CAGTTTGGGGTGTGAAACCTAGTTCACCATGAAGGAG
66 CAATTTGGGGAGAGAAACCTAGTTCACCATCAAGGAG
21927 GGCTCGAACC
Statistics
Matches: 224, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
155 9 0.04
156 209 0.93
157 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (156 bp):
CTTGGCAAAGTTTCAGCTCAATTAGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
CAATTTGGGGAGAGAAACCTAGTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATATTTTCCA
TAGTTTTATGGAGATAATCTAAGTCC
Found at i:22271 original size:28 final size:28
Alignment explanation
Indices: 22231--22298 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
22221 GCCGTGTGAC
* *
22231 ATATCGGAAGGAAGATTTTCCGCCTGAT
1 ATATCAGAGGGAAGATTTTCCGCCTGAT
22259 ATATCAGAGGGAAGATTTTCCGCCTGAT
1 ATATCAGAGGGAAGATTTTCCGCCTGAT
*
22287 ATACCAGAGGGA
1 ATATCAGAGGGA
22299 GACGTCCTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (28 bp):
ATATCAGAGGGAAGATTTTCCGCCTGAT
Done.