Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008962.1 Corchorus olitorius cultivar O-4 contig08989, 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, 930
Length: 1551
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Found at i:813 original size:154 final size:154
Alignment explanation
Indices: 1--1551 Score: 2338
Period size: 154 Copynumber: 10.1 Consensus size: 154
*
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAACACTTGTT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG-T
* * *
66 TATTTTGGGGCTATCGGGGACCATTAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCTCAAA
65 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AA
* *
131 T-CTTTTCGTTCCATTGTTTATGTCC
129 TGCTTTTCTTTCCATTGTTTATGGCC
*
156 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTTATTTGGAACACTTG-T
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
** *
220 ATTTTGTTCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
66 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
285 CTTTTCTTTCCATTGTTTATGGCC
131 CTTTTCTTTCCATTGTTTATGGCC
* *
309 TGACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
374 ATTTTGGGCCTATCGGAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCTAAT
66 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC-AAT
* * *
439 GCTTTTCTTTCCATCGTGTACGGCC
130 GCTTTTCTTTCCATTGTTTATGGCC
* *
464 TAACTATAATCATTTTGGTGAAGGTTAGTCCCACTGTGAAAGTTTTTAGGTCATTTGGAACACTT
1 TAACTATAATCATTTTGGTG-AGATTAGT-CCACTGTG-AAGTTTTTAGCTCATTTGGAACACTT
* * * *
529 GTTATTTTGGGCATATCGGGGGCCCATTAGTGTCGTTCTGAATCGTCTTCGATTTAG-AAACCT-
63 GTTATTTTGGGCCTATC-GGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTC
*
592 AATGC-TTTC-TTCCA-TG-TTATGGCG
127 AATGCTTTTCTTTCCATTGTTTATGGCC
* * * *
616 GACCTAGTAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGT
1 TAACTA-TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
** * * *
681 TATTTTTTGCCTATCGGGGTCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
65 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
746 GCTTTTCTTTCCATTGTTTATGGCC
130 GCTTTTCTTTCCATTGTTTATGGCC
771 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* * **
836 ATTTTGGGCCTATCTGGACCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
66 ATTTTGGGCCTATCGGGGCC-CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
*
901 GCTTTTCTTTCCATTGTTAATGGCC
130 GCTTTTCTTTCCATTGTTTATGGCC
*
926 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
991 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCAATG
66 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1056 CTTTTCTTTCCATTGTTTATGGCC
131 CTTTTCTTTCCATTGTTTATGGCC
* *
1080 TAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTGTT-GCTCATTCGGAACACTTGT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTGT
* * **
1144 TATTTTGGGCCTATCGAGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
65 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
* *
1209 ACTTTTCTTTCCATTGTTAATGGCC
130 GCTTTTCTTTCCATTGTTTATGGCC
* *
1234 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGTT-GCTCATTCGGAACCCTTGT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTGT
* * **
1298 TATTTTGGGCCTATCGAGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
65 TATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
1363 GCTTTTCTTTCCATTGTTTATGGCC
130 GCTTTTCTTTCCATTGTTTATGGCC
*
1388 TAACTATAATCATTTTAGG-GAGATTAGTCCACTGTGAAGTTTGTT-GCTCATTCGGAACACTTG
1 TAACTATAATCATTTT-GGTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTG
* * * *
1451 TTATTTTTGGCCTATCGGGGCTCCATTAGT-CCGTTTTCAATCGTCTTCGATTTGGCATACCTCA
64 TTATTTTGGGCCTATCGGGGC-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
1515 ATGCTTTTC-TTCCATTGTTTATGGCC
128 ATGCTTTTCTTTCCATTGTTTATGGCC
1541 TAACTATAATC
1 TAACTATAATC
Statistics
Matches: 1284, Mismatches: 94, Indels: 38
0.91 0.07 0.03
Matches are distributed among these distances:
149 34 0.03
150 44 0.03
151 12 0.01
152 23 0.02
153 185 0.14
154 609 0.47
155 277 0.22
156 12 0.01
157 8 0.01
158 46 0.04
159 34 0.03
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
CTTTTCTTTCCATTGTTTATGGCC
Found at i:1246 original size:617 final size:614
Alignment explanation
Indices: 1--1551 Score: 2356
Period size: 617 Copynumber: 2.5 Consensus size: 614
*
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATATGGAACACTTGTT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG-T
* *
66 TATTTTGGGGCTATCGGGGACCATTAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCTCAAA
65 TATTTTGGGCCTATCGGGG-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAA
* * *
131 TCTTTTCGTTCCATTGTTTATGTCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
129 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
* ** **
196 TTTTAGCTTATTTGGAACACTTG-TATTTTGTTCCTATCGAGGCC-CATTAGTGACGTTTTGAAT
194 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG-GGCCTCATTAGTTCCGTTTTGAAT
*
259 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTGACTATAATCATTT
258 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
324 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATCG
323 TGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATCG
* *
389 GAGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCTAATGCTTTTCTTTCCATC
388 GAGACCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCTAATGCTTTTCTTTCCATC
* *
454 GTGTACGGCCTAACTATAATCATTTTGGTGAAGGTTAGTCCCACTGTGAAAGTTTTTAGGTCATT
453 GTGTACGGCCTAACTATAATCATTTTGGTGAAGATTAGTCCCACTGTGAAAGTTTTTAGCTCATT
* *
519 TGGAACACTTGTTATTTTGGGCATATCGGGGGCCCATTAGTGTCGTTCTGAATCGTCTTCGATTT
518 CGGAACACTTGTTATTTTGGGCATATCGGAGGCCCATTAGTGTCGTTCTGAATCGTCTTCGATTT
* *
584 AGAAACCTAATGCTTTCTTCCATGTTATGGCG
583 AGAAACCTAATACTTTCTTCCATGTTATGGCC
* * * *
616 GACCTAGTAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGT
1 TAACTA-TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
** * *
681 TATTTTTTGCCTATCGGGGTCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
65 TATTTTGGGCCTATCGGGG-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAA
746 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
129 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
*
811 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCTGGACCTCATTAGTTCCGTTTTGAAT
194 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCTCATTAGTTCCGTTTTGAAT
*
876 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTAATGGCCTAACTATAATCATTT
258 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
941 TGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
323 TGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATCG
* * *
1006 GGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTC-AATGCTTTTCTTTCCATT
388 GAGACCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCTAATGCTTTTCTTTCCATC
* * *
1070 GTTTATGGCCTAACTATAATCATTTTGGTG-AGATTAGT-CCATTGTG-AAGTTTGTT-GCTCAT
453 GTGTACGGCCTAACTATAATCATTTTGGTGAAGATTAGTCCCACTGTGAAAGTTT-TTAGCTCAT
* * *
1131 TCGGAACACTTGTTATTTTGGGCCTATC-GAGGCTCATTAGT-TCCGTTTTGAATCGTCTTCGAT
517 TCGGAACACTTGTTATTTTGGGCATATCGGAGGCCCATTAGTGT-CGTTCTGAATCGTCTTCGAT
*
1194 TTGGCAAACCTCAATACTTTTCTTTCCATTGTTAATGGCC
581 TTAG-AAACCT-AATAC-TTTC-TTCCA-TGTT-ATGGCC
* *
1234 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGTT-GCTCATTCGGAACCCTTGT
1 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT-TTAGCTCATTTGGAACACTTGT
* ** *
1298 TATTTTGGGCCTATCGAGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
65 TATTTTGGGCCTATCGGGGC-CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAA
1363 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGG-GAGATTAGTCCACTGTGAAG
129 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT-GGTGAGATTAGTCCACTGTGAAG
* * * *
1427 TTTGTT-GCTCATTCGGAACACTTGTTATTTTTGGCCTATCGGGGCTCCATTAG-TCCGTTTTCA
193 TTT-TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCT-CATTAGTTCCGTTTTGA
*
1490 ATCGTCTTCGATTTGGCATACCTCAATGCTTTTC-TTCCATTGTTTATGGCCTAACTATAATC
256 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
Statistics
Matches: 856, Mismatches: 63, Indels: 34
0.90 0.07 0.04
Matches are distributed among these distances:
611 1 0.00
612 33 0.04
613 43 0.05
614 13 0.02
615 185 0.22
616 167 0.20
617 399 0.47
618 15 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (614 bp):
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
ATTTTGGGCCTATCGGGGCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCTCATTAGTTCCGTTTTGAATCGT
CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
TGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTCGTTATTTTGGGCCTATCGGAG
ACCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCTAATGCTTTTCTTTCCATCGTG
TACGGCCTAACTATAATCATTTTGGTGAAGATTAGTCCCACTGTGAAAGTTTTTAGCTCATTCGG
AACACTTGTTATTTTGGGCATATCGGAGGCCCATTAGTGTCGTTCTGAATCGTCTTCGATTTAGA
AACCTAATACTTTCTTCCATGTTATGGCC
Done.