Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006236.1 Corchorus capsularis cultivar CVL-1 contig06255, 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:0.23, C:0.19, G:0.19, T:0.40
Found at i:458 original size:154 final size:154
Alignment explanation
Indices: 1--463 Score: 656
Period size: 154 Copynumber: 3.1 Consensus size: 154
* *
1 AATTGTTTACGACCTAACTATAGTTATTTTGATGAGATTAGTCCATTGTGGAGTTTTTAGCTCAT
1 AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
* *
66 TCAGAACACTTGTTATTTCGGGCCTTTCGTGGCCCATTACTACTGTTTTGAATCGTCTTCGATTT
66 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCTTCGATTT
*
131 GGCAAACCACAAAGCTTTACTTTC
131 GGCAAACCACAAAGCTTTTCTTTC
* * * * * ** * *
155 CATAGTTTATGGCCTAACTATAATTATTTTGATGTGATTAGTCTTTTGTGAAGTTTCTATCTCAT
1 AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
*
220 TCAGAAAAC---TTA-TT-----CTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCTTCGATTT
66 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCTTCGATTT
*
276 AGCAAACCACAAAGCTTTTCTTTC
131 GGCAAACCACAAAGCTTTTCTTTC
300 AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
1 AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
* * * *
365 TTAGAACACTTGTTATTTCGGGCCTTTCGGGGCCAATTAGTGCTGTTTTGAATCGTCTTCAATTT
66 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCTTCGATTT
* * *
430 GGGAAACCAGAAAGCTTTTCTTTT
131 GGCAAACCACAAAGCTTTTCTTTC
454 AATTGTTTAC
1 AATTGTTTAC
464 ATTCAGAACA
Statistics
Matches: 266, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
145 125 0.47
148 3 0.01
149 2 0.01
150 2 0.01
151 3 0.01
154 131 0.49
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (154 bp):
AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCTTCGATTT
GGCAAACCACAAAGCTTTTCTTTC
Found at i:545 original size:101 final size:101
Alignment explanation
Indices: 362--553 Score: 312
Period size: 101 Copynumber: 1.9 Consensus size: 101
352 GTTTTTAGCT
* *
362 CATTTAGAACACTTGTTATTTCGGGCCTTTCGGGGCCAATTAGTGCTGTTTTGAATCGTCTTCAA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCAATTACTGCTGTTTTGAATCGTCTTCAA
* * *
427 TTTGGGAAACCAGAAAGCTTTTCTTTTAATTGTTTA
66 TTTGGCAAACCACAAAGCTTTACTTTTAATTGTTTA
* * *
463 CATTCAGAACACTTGTTATTTCGGGCCTTTCGTGGCCCATTACTGCTGTTTTGAATCGTCTTCGA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCAATTACTGCTGTTTTGAATCGTCTTCAA
528 TTTGGCAAACCACAAAGCTTTACTTT
66 TTTGGCAAACCACAAAGCTTTACTTT
554 CCATAGTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (101 bp):
CATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCAATTACTGCTGTTTTGAATCGTCTTCAA
TTTGGCAAACCACAAAGCTTTACTTTTAATTGTTTA
Found at i:993 original size:154 final size:154
Alignment explanation
Indices: 463--1280 Score: 1206
Period size: 154 Copynumber: 5.3 Consensus size: 154
453 TAATTGTTTA
* * * *
463 CATTCAGAACACTTGTTATTTCGGGCCTTTCGTGGCCCATTACTGCTGTTTTGAATCGTCTTCGA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
* * * * * *
528 TTTGGCAAACCACAAAGCTTTACTTTCCATAGTTTATGGCCTAAGTATAAAT-ATTTTGATGAGA
66 TTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTAT-AATCATTTTGGTGAGA
*** * **
592 TTAGTCTTTTGTGAAGTTTCTATCT
130 TTAGTCCACTGTGAAGTTTTTCGCT
* * * * *
617 CATTCAGAAAACTTATTCTTTCGGGCCTTTACGAGGCCCATTTAGTGCTGTTTTGAATCGTCTTC
1 CATTCAGAACACTTGTTATTTCGGGCCTTT-CGAGGCCC-GTTAGTGCTGTTTTGAATCGGCTTC
* *
682 GATTTGCCAAACCACAAAGCATTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAG
64 GATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAG
*
747 ATTAGTCCTACTGTTGAAGTTTTTAGCT
129 ATTAGTCC-ACTG-TGAAGTTTTTCGCT
* *
775 CATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
* * *
840 TTTGGGAAACCATAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTGAGAT
66 TTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGAT
905 TAGTCCACTGTGAAGTTTTTCGCT
131 TAGTCCACTGTGAAGTTTTTCGCT
* * *
929 CATTCAGAACACTTGTTATTTCGGGTCTTTCGGGGCCCGTTAGTGCTGTTTTGAATCGGATTCGA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
* *
994 TTTGGCAAACCACAAAGCTTTTCTTTTAATTGTTTACGACCTAACTATAATCATTTTGGTGAGAT
66 TTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGAT
1059 TAGTCCACTGTGAAGTTTTTCGCT
131 TAGTCCACTGTGAAGTTTTTCGCT
* *
1083 CATTCAGAACACTTGTAATTTCGGGTCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
* * *
1148 TTTGGGAAAGCACAAAGCTTTTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGAT
66 TTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGAT
1213 TAGTCCACTGTGAAGTTTTTCGCT
131 TAGTCCACTGTGAAGTTTTTCGCT
* * *
1237 CATTTAGAACACTTGTAATTTCGGGTCTTTCGAGGCCCGTTAGT
1 CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGT
Statistics
Matches: 613, Mismatches: 46, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
154 377 0.62
155 14 0.02
156 174 0.28
157 9 0.01
158 39 0.06
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (154 bp):
CATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCGTTAGTGCTGTTTTGAATCGGCTTCGA
TTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGAT
TAGTCCACTGTGAAGTTTTTCGCT
Done.