Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001265.1 Corchorus olitorius cultivar O-4 contig01265, 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, 718
Length: 1197
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Found at i:384 original size:154 final size:154
Alignment explanation
Indices: 1--684 Score: 1104
Period size: 153 Copynumber: 4.5 Consensus size: 154
* * *
1 TTATGGCCTAACTATAATCATTTTAGTTAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * * *
66 CAATTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAAC
66 CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
*
131 CCTCAATGCTTTTC-GTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
* *
154 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTTGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * * *
219 CACTTGTTATTTTGGGCTTATCGGGGCCTATTAGTGACGTTTTGAATCGTCTTCTATTTGGCAAC
66 CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
*
284 CCTTAATGCTTTTCTTTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
*
308 TTATGGTCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * *
373 AACTTTTTATTTTGGGCCT-TCAGGGCCCATTAGT-TCTGTTTTGAATCGTCTTCGATTTGGCAA
66 CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAA
436 CCCTCAATGCTTTTCTTTCCATTGT
130 CCCTCAATGCTTTTCTTTCCATTGT
* * *
461 TTATGGCCTAACTATAATCATTTTAGTTAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
526 CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTGGGCAAC
66 CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
591 CCTCAATGCTTTTCTTTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
* * *
615 TTATGGCCTAACCATAATCATTTTGGTGAGATTAGTGCACTGAGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
680 CACTT
66 CACTT
685 TACACTTGTT
Statistics
Matches: 490, Mismatches: 37, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
152 1 0.00
153 273 0.56
154 215 0.44
155 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
CACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
CCTCAATGCTTTTCTTTCCATTGT
Found at i:562 original size:307 final size:307
Alignment explanation
Indices: 1--685 Score: 1097
Period size: 307 Copynumber: 2.2 Consensus size: 307
* * *
1 TTATGGCCTAACTATAATCATTTTAGTTAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* *
66 CAA-TTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAA
66 -AACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAA
*
130 CCCTCAATGCTTTTCGTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
130 CCCTCAATGCTTTTCGTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACT
* * * * *
195 ATGAAGTTTTTTGCTCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCTATTAGTGACGTT
195 ATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTT
* * *
260 TTGAATCGTCTTCTATTTGGCAACCCTTAATGCTTTTCTTTCCATTGT
260 TTGAATCGTCTTCGATTGGGCAACCCTCAATGCTTTTCTTTCCATTGT
*
308 TTATGGTCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * *
373 AACTTTTTATTTTGGGCCT-TCAGGGCCCATTAGT-TCTGTTTTGAATCGTCTTCGATTTGGCAA
66 AACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTGAC-GTTTTGAATCGTCTTCAATTTGACAA
* *
436 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTTAGATTAGTCCAC
130 CCCTCAATGCTTTTC-GTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCAC
*
501 TGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGT
194 TATGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGT
566 TTTGAATCGTCTTCGATTGGGCAACCCTCAATGCTTTTCTTTCCATTGT
259 TTTGAATCGTCTTCGATTGGGCAACCCTCAATGCTTTTCTTTCCATTGT
* * *
615 TTATGGCCTAACCATAATCATTTTGGTGAGATTAGTGCACTGAGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
680 CACTTT
66 AACTTT
686 ACACTTGTTA
Statistics
Matches: 349, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
305 1 0.00
306 55 0.16
307 293 0.84
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (307 bp):
TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
AACTTTTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGACAAC
CCTCAATGCTTTTCGTCCATTGTTTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTA
TGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGACGTTT
TGAATCGTCTTCGATTGGGCAACCCTCAATGCTTTTCTTTCCATTGT
Done.