Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010506.1 Corchorus capsularis cultivar CVL-1 contig10527, 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: 30459
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:227 original size:35 final size:35
Alignment explanation
Indices: 188--256 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
178 TGACAGGGTA
188 TTGGTTTTTGGGACTCCTTTGTGAGAGCTTTTGTT
1 TTGGTTTTTGGGACTCCTTTGTGAGAGCTTTTGTT
223 TTGGTTTTTGGGACTCCTTTGTGAGAGCTTTTGT
1 TTGGTTTTTGGGACTCCTTTGTGAGAGCTTTTGT
257 ATTGTCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.09, C:0.12, G:0.29, T:0.51
Consensus pattern (35 bp):
TTGGTTTTTGGGACTCCTTTGTGAGAGCTTTTGTT
Found at i:1315 original size:2 final size:2
Alignment explanation
Indices: 1310--1340 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1300 TTTCTTTTTT
1310 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1341 GTTAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21759 original size:310 final size:310
Alignment explanation
Indices: 21197--21817 Score: 1242
Period size: 310 Copynumber: 2.0 Consensus size: 310
21187 AAGCTATTCT
21197 TGTGAACTTGGATTTCTCCCAAAGACTTGGAAGGTATGGAAAATGTTTGGAAATTTAAGATTACC
1 TGTGAACTTGGATTTCTCCCAAAGACTTGGAAGGTATGGAAAATGTTTGGAAATTTAAGATTACC
21262 CCCAATTTGGATTGTGGGTGTTTTTGATTCAGTCTAGAAGGTTGAAGAAGGAAACCTCAACCGAA
66 CCCAATTTGGATTGTGGGTGTTTTTGATTCAGTCTAGAAGGTTGAAGAAGGAAACCTCAACCGAA
21327 AAAGAGTACGTAGACTAAAACCCATTAGATTACTTGGATTGGAAGTTGTATAGAGAGATTCTTTA
131 AAAGAGTACGTAGACTAAAACCCATTAGATTACTTGGATTGGAAGTTGTATAGAGAGATTCTTTA
21392 ACTGTCGTTTGCTAGTATTTTCTTCTCCTTTGAAAAATGAAAATACTACATTTGAGTCATCAATA
196 ACTGTCGTTTGCTAGTATTTTCTTCTCCTTTGAAAAATGAAAATACTACATTTGAGTCATCAATA
21457 GTGGCTTACAAAAAGTCAACAATCTCATAATTAATCTACATTTTCTTTCA
261 GTGGCTTACAAAAAGTCAACAATCTCATAATTAATCTACATTTTCTTTCA
21507 TGTGAACTTGGATTTCTCCCAAAGACTTGGAAGGTATGGAAAATGTTTGGAAATTTAAGATTACC
1 TGTGAACTTGGATTTCTCCCAAAGACTTGGAAGGTATGGAAAATGTTTGGAAATTTAAGATTACC
21572 CCCAATTTGGATTGTGGGTGTTTTTGATTCAGTCTAGAAGGTTGAAGAAGGAAACCTCAACCGAA
66 CCCAATTTGGATTGTGGGTGTTTTTGATTCAGTCTAGAAGGTTGAAGAAGGAAACCTCAACCGAA
21637 AAAGAGTACGTAGACTAAAACCCATTAGATTACTTGGATTGGAAGTTGTATAGAGAGATTCTTTA
131 AAAGAGTACGTAGACTAAAACCCATTAGATTACTTGGATTGGAAGTTGTATAGAGAGATTCTTTA
21702 ACTGTCGTTTGCTAGTATTTTCTTCTCCTTTGAAAAATGAAAATACTACATTTGAGTCATCAATA
196 ACTGTCGTTTGCTAGTATTTTCTTCTCCTTTGAAAAATGAAAATACTACATTTGAGTCATCAATA
21767 GTGGCTTACAAAAAGTCAACAATCTCATAATTAATCTACATTTTCTTTCA
261 GTGGCTTACAAAAAGTCAACAATCTCATAATTAATCTACATTTTCTTTCA
21817 T
1 T
21818 AATCATATAT
Statistics
Matches: 311, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
310 311 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (310 bp):
TGTGAACTTGGATTTCTCCCAAAGACTTGGAAGGTATGGAAAATGTTTGGAAATTTAAGATTACC
CCCAATTTGGATTGTGGGTGTTTTTGATTCAGTCTAGAAGGTTGAAGAAGGAAACCTCAACCGAA
AAAGAGTACGTAGACTAAAACCCATTAGATTACTTGGATTGGAAGTTGTATAGAGAGATTCTTTA
ACTGTCGTTTGCTAGTATTTTCTTCTCCTTTGAAAAATGAAAATACTACATTTGAGTCATCAATA
GTGGCTTACAAAAAGTCAACAATCTCATAATTAATCTACATTTTCTTTCA
Found at i:25263 original size:13 final size:13
Alignment explanation
Indices: 25245--25269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25235 AAGAAGATTA
25245 AAGCTTAGTCAAT
1 AAGCTTAGTCAAT
25258 AAGCTTAGTCAA
1 AAGCTTAGTCAA
25270 AACTCGAAAG
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AAGCTTAGTCAAT
Found at i:27228 original size:151 final size:149
Alignment explanation
Indices: 27032--27508 Score: 650
Period size: 151 Copynumber: 3.2 Consensus size: 149
27022 TTGCAAATAT
* * *
27032 TTGGAATTTCTACTCTGAATAAGTTACATTTGTTAGTTTGAAAGATCGTAGGCTATCCTATTATT
1 TTGGAATTTCTACTCTGGATAA-TTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTA-T
* * * * * * * *
27097 TGCTTGCTCAATACCTTGTTCCAACGGATAAAAATTCGTTAATTCATGCTTAGTCTTAGTTTGAA
64 TGCTTGCTCAACAGCTTGTTCCAATGTATAAAAGTTCGTTAATTCATGCATAGTTTTAGTTTCAA
* *
27162 AGATTATTGGCCAATCTGTTA
129 AGATTATAGGCTAATCTGTTA
*
27183 TTGGAATTTCTACTCTGGATAATCTACATTTGTTAGTTTGGAAGATCATAGGCTAACCTATGTA-
1 TTGGAATTTCTACTCTGGATAAT-TACATTTGTTAGTTTGAAAGATCATAGGCTAACCTAT-TAT
* * * *
27247 TGCTTGCTAAACAGCTTGTTCCAATGTATAAAAGTTTGTCAATTCATGCATAGTTTTAGTTCCAA
64 TGCTTGCTCAACAGCTTGTTCCAATGTATAAAAGTTCGTTAATTCATGCATAGTTTTAGTTTCAA
* *
27312 AGATCATAGGCTAATATGTTA
129 AGATTATAGGCTAATCTGTTA
*
27333 TTGGAATTTCTACTCTGGATAATTTACATTTGTTAGTTTGAAAGATTATAGGCTAACCTATTATA
1 TTGGAATTTCTACTCTGGATAA-TTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTAT-
* * * *
27398 TGCTTGCTCAACAGCTCGTTCCAATGTTTGAAAGTTCGTTAATTCATGCCTAGTTTTAGTTTCAA
64 TGCTTGCTCAACAGCTTGTTCCAATGTATAAAAGTTCGTTAATTCATGCATAGTTTTAGTTTCAA
* *
27463 AGATTATAGGCTAATCTATAA
129 AGATTATAGGCTAATCTGTTA
27484 TTGGAATTTCTACTCTGGATAATTA
1 TTGGAATTTCTACTCTGGATAATTA
27509 TATTCCTTAC
Statistics
Matches: 287, Mismatches: 34, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
149 2 0.01
150 131 0.46
151 152 0.53
152 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (149 bp):
TTGGAATTTCTACTCTGGATAATTACATTTGTTAGTTTGAAAGATCATAGGCTAACCTATTATTG
CTTGCTCAACAGCTTGTTCCAATGTATAAAAGTTCGTTAATTCATGCATAGTTTTAGTTTCAAAG
ATTATAGGCTAATCTGTTA
Done.