Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006607.1 Corchorus capsularis cultivar CVL-1 contig06628, 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, 768
Length: 1280
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Found at i:800 original size:428 final size:427
Alignment explanation
Indices: 1--1269 Score: 2270
Period size: 428 Copynumber: 3.0 Consensus size: 427
*
1 GTTTGTGTGTAGCGCTGTCTAACAAGCTCATCTCATTCCGACACACGACTTTTGAGTACTCGTTG
1 GTTTGTGTGTAGCGCTGTCTAACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTTG
*
66 CGCGAAAAAGCGCATCCAGAAAGAGTTTTTGCTAAGAACTATGAATAGCACAAAAACGCGCAATG
66 CGCGAAAAAGCGCATCCAGAAAGAG-TTTTGCTAAGAACTATGAATAGCACAAAAACGCGCAAAG
131 TTGAGGCTTTGGACTTCGTGAAAGCTTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGCAAT
130 TTGAGGCTTTGGACTTCGTGAAAGCTTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGCAAT
196 TCGACGCACGACATTTGAGTACTCGTTGCGCAAAAAAAGCATCTGGAATGAGCCTTTCGCTAAAA
195 TCGACGCACGACATTTGAGTACTCGTTGCGCAAAAAAAGCATCTGGAATGAGCCTTTCGCTAAAA
* * *
261 ATGATGTTTTGCATACAACCGCTCAAAGTTGAGGTTTTGGGCATCTAGGGAAGCTTTGTTGCTGA
260 ATGATGTTTTGCATACAACCGCTCAAAGTTGAGGTTTTGGGCATCTAGGAAAGCTTTGTTTCTGC
* *
326 ACAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCTCTAAGAACGATGTGTTGCATACAAA
325 ACAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCACTAAGAACGAAGTGTTGCATACAAA
391 CTCGCAAAGTTGATGCTTTGGACTTCGAGGAGAGCTTT
390 CTCGCAAAGTTGATGCTTTGGACTTCGAGGAGAGCTTT
429 GTTTGTGTGTAGCGCTGTCTAACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTTG
1 GTTTGTGTGTAGCGCTGTCTAACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTTG
*
494 CGCGAAAAAGCGCATCCAGTAAAGAGTTTTGCTAAGAACTATGAATAGCACAACAACGCGCAAAG
66 CGCGAAAAAGCGCATCCAG-AAAGAGTTTTGCTAAGAACTATGAATAGCACAAAAACGCGCAAAG
* *
559 TTGAGTCTTTGGACTTCGTGAAAGCTTTGTTTGTGCACAGTGCTGTCCAACAATCTCATCGCAAT
130 TTGAGGCTTTGGACTTCGTGAAAGCTTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGCAAT
**
624 TCGACGCACGACATTTGAGTACTCGTTGCGCAAAAAAAGTTTCTGGAATGAGCCTTTCGCTAAAA
195 TCGACGCACGACATTTGAGTACTCGTTGCGCAAAAAAAGCATCTGGAATGAGCCTTTCGCTAAAA
* * *
689 ATGATGTTTTGCATACAACCGCTCAAAGTTGAGATTTTTGGCATCTAGGAAAGCTTTGTTTTTGC
260 ATGATGTTTTGCATACAACCGCTCAAAGTTGAGGTTTTGGGCATCTAGGAAAGCTTTGTTTCTGC
754 ACAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCACTAAGAACGAAGTGTTGCATACAAA
325 ACAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCACTAAGAACGAAGTGTTGCATACAAA
819 CTCGCAAAGTTGATGCTTTGGACTTCGAGGAGAGCTTT
390 CTCGCAAAGTTGATGCTTTGGACTTCGAGGAGAGCTTT
**
857 GTTTGTGCATAGCGCTGT-TGAACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTT
1 GTTTGTGTGTAGCGCTGTCT-AACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTT
921 GCGCGAAAAAGCGCATCCAGAAAGAGTTTTGCTAAGAACTATGAATAGTCACAAAAACGCGCAAA
65 GCGCGAAAAAGCGCATCCAGAAAGAGTTTTGCTAAGAACTATGAATAG-CACAAAAACGCGCAAA
986 GTTGAGGCTTTGGACTTTCGTGAAAGCTTTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGC
129 GTTGAGGCTTTGGAC-TTCGTGAAAGC-TTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGC
1051 AATTCGACGCACGACATTTGAGTACTCGTTGCGACAAAAAAAGCATCTGGAATGAGCCTTTCGAC
192 AATTCGACGCACGACATTTGAGTACTCGTTGCG-CAAAAAAAGCATCTGGAATGAGCCTTTCG-C
*
1116 TAAAAATGATGTTTTGCATACAACCGCTCAAAGTTGTAGGTTTTGGGCTTCTAGGAAAGCTTTGT
255 TAAAAATGATGTTTTGCATACAACCGCTCAAAGTTG-AGGTTTTGGGCATCTAGGAAAGCTTTGT
*
1181 TTCTGCACAGGGCTGTCCAAAAAGTTCATCTCACTACGACAAACCACTAAGAACGAAGTGTTGCA
319 TTCTGCACAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCACTAAGAACGAAGTGTTGCA
*
1246 TACAAACTCGCAAAGTTCATGCTT
384 TACAAACTCGCAAAGTTGATGCTT
1270 ATGCTTTAGA
Statistics
Matches: 805, Mismatches: 28, Indels: 11
0.95 0.03 0.01
Matches are distributed among these distances:
427 29 0.04
428 515 0.64
429 17 0.02
430 69 0.09
431 27 0.03
432 37 0.05
433 111 0.14
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (427 bp):
GTTTGTGTGTAGCGCTGTCTAACAAGCTCATCTCATTCCGACACACGACTTTTGAGCACTCGTTG
CGCGAAAAAGCGCATCCAGAAAGAGTTTTGCTAAGAACTATGAATAGCACAAAAACGCGCAAAGT
TGAGGCTTTGGACTTCGTGAAAGCTTTGTTTGTGCACAGGGCTGTCCAACAATCTCATCGCAATT
CGACGCACGACATTTGAGTACTCGTTGCGCAAAAAAAGCATCTGGAATGAGCCTTTCGCTAAAAA
TGATGTTTTGCATACAACCGCTCAAAGTTGAGGTTTTGGGCATCTAGGAAAGCTTTGTTTCTGCA
CAGGGCTGTCCAAAAAGTTCATCTCACTCCGACAAACCACTAAGAACGAAGTGTTGCATACAAAC
TCGCAAAGTTGATGCTTTGGACTTCGAGGAGAGCTTT
Done.