Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011691.1 Corchorus olitorius cultivar O-4 contig11724, 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, 792
Length: 1320
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Found at i:556 original size:154 final size:154
Alignment explanation
Indices: 1--1313 Score: 1951
Period size: 154 Copynumber: 8.5 Consensus size: 154
* * * *
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCTGGGCCCATTAGTGATGTTTTGAATCGTTTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
* * * * *
66 GATTTGGCAAACCTCAAAGCTTTTGTTT-AAGGTGTTTATGGCCTAACTATAATCATTTTGATGA
66 GATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGA
* *
130 GATTAGTCCACTGTGCAGTTCTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
* *
155 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
* *
220 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAATTTGGTGTA
66 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG-A
*
285 GATTAGTCCACTGTGAAGTTCTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
* * * *
310 CTCATTTGGATCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
*
375 GATTTGGCAAACCTCAATGCTTTTCTTTCCCATTGTTTATGGACTAACTATAATCATTTTGGTGA
66 GATTTGGCAAACCTCAAAGCTTTTCTTT-CCATTGTTTATGGACTAACTATAATCATTTTGGTGA
440 GATTAGTCCACTGTGAAGTTTTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
*
465 CTCATTTGGAACACTTGTTATTTT-GGCCTATCAGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
529 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATT-TTTAATGGACTAACTATAATCATTTTGGTGA
66 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT-ATGGACTAACTATAATCATTTTGGTGA
*
593 GATTAGTCCACTGCGAAGTTTTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
* * *
618 CT-ATTTTGGAACACTTGTTATTTTTGGCCTATCAGTGCCCATTAGTGACGTTTTGAATCGTCTT
1 CTCA-TTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTT
*** * * *** * *
682 CGATTTTATAAACCTCAAAGTTTTTTTTTATGTTGTTTATGGCCTAACTATAATCATTTTGATGA
65 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGA
*
747 GATTAATCCACTGTGAAGTTTTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
* * * *
772 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACATTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
* * *
837 GATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTACCTATAATCATTTTGGTGAG
66 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAG
*
902 ATTAGTCCACTGTGAAGGTTTTAG
131 ATTAGTCCACTGTGAAGTTTTTAG
926 CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGTACG-TTTGAATCGTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGT-TACGTTTTGAATCGTCTT
* *
989 CGATTTGGCAAACCTCAATGCTTTTC-TTCCATTGGTTTATGGACTAACTATAATCATTTTGGTC
65 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATT-GTTTATGGACTAACTATAATCATTTTGGTG
1053 AGATTAGTCCACTGTGAAGTTTTTAG
129 AGATTAGTCCACTGTGAAGTTTTTAG
* * * *
1079 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTTCCGTTTCGAATCGTCTTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
* * * *
1144 GATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATCGCCTAACTATAATCATTTTGGTGAG
66 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAG
*
1209 ATTAGTCCACTATGAAGTTTTTAG
131 ATTAGTCCACTGTGAAGTTTTTAG
* *
1233 CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GAGGCCCATTTG-TCCGTTTTGAATCGTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAG-GGCCCATTAGTTACGTTTTGAATCGTCTT
* *
1296 CGATTTGTCAAATCTCAA
65 CGATTTGGCAAACCTCAA
1314 TGCTCTT
Statistics
Matches: 1064, Mismatches: 81, Indels: 29
0.91 0.07 0.02
Matches are distributed among these distances:
152 11 0.01
153 249 0.23
154 598 0.56
155 173 0.16
156 33 0.03
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTACGTTTTGAATCGTCTTC
GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAG
Found at i:1015 original size:461 final size:462
Alignment explanation
Indices: 1--1317 Score: 2051
Period size: 461 Copynumber: 2.9 Consensus size: 462
* * *
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCTGGGCCCATTAGTG-ATGTTTTGAATCGTTTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGTACGTTTTGAATCGTCTT
* * * * *
65 CGATTTGGCAAACCTCAAAGCTTTTGTTT-AAGGTGTTTATGGCCTAACTATAATCATTTTGATG
66 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCA--TTTTTATGGACTAACTATAATCATTTTGGTG
* * *
129 AGATTAGTCCACTGTGCAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
129 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-AGGCC
194 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT
193 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT
* * *
259 GGCCTAACTATAATCAATTTGGTGTAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGATCAC
258 GGCCTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
*
324 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCT
322 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCT
389 CAATGCTTTTCTTTCCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
387 CAATGCTTTTCTTTCCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
*
454 GAAGTTTTTAG
452 GAAGGTTTTAG
*
465 CTCATTTGGAACACTTGTTATTTT-GGCCTATCAGGGCCCATTAGT-TCCGTTTTGAATCGTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGTACGTTTTGAATCGTCTT
528 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTTTTAATGGACTAACTATAATCATTTTGGTGA
66 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTTTT-ATGGACTAACTATAATCATTTTGGTGA
* *
593 GATTAGTCCACTGCGAAGTTTTTAGCT-ATTTTGGAACACTTGTTATTTTTGGCCTATCAGTGCC
130 GATTAGTCCACTGTGAAGTTTTTAGCTCA-TTTGGAACACTTGTTATTTTGGGCCTATCAG-GCC
** *** * * ***
657 CATTAGTGACGTTTTGAATCGTCTTCGATTTTATAAACCTCAAAGTTTTTTTTTATGTTGTTTAT
193 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT
* *
722 GGCCTAACTATAATCATTTTGATGAGATTAATCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
258 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
*
787 TGTTATTTTGGGCCTATCGGGGACCATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCTC
323 TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCTC
*
852 AATGCTTTTCTTT-CCATTGTTTATGGACTACCTATAATCATTTTGGTGAGATTAGTCCACTGTG
388 AATGCTTTTCTTTCCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTG
916 AAGGTTTTAG
453 AAGGTTTTAG
926 CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGTACG-TTTGAATCGTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGTACGTTTTGAATCGTCTT
* *
989 CGATTTGGCAAACCTCAATGCTTTTC-TTCCATTGGTTTATGGACTAACTATAATCATTTTGGTC
66 CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATT--TTTATGGACTAACTATAATCATTTTGGTG
1053 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGCC
129 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-AGGCC
* * * *
1118 CATTAGTTCCGTTTCGAATCGTCTTTGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTAT
193 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT
* *
1183 CGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACT
258 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
* * * * * *
1248 TGTTATTTTGGGCCTATCGAGGCCCATTTGT-CCGTTTTGAATCGTCTTCGATTTGTCAAATCTC
323 TGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCTC
1312 AATGCT
388 AATGCT
1318 CTT
Statistics
Matches: 779, Mismatches: 63, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
460 42 0.05
461 356 0.46
462 137 0.18
463 219 0.28
464 25 0.03
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (462 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTGTACGTTTTGAATCGTCTT
CGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTTTTATGGACTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGCCCAT
TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCTCAAT
GCTTTTCTTTCCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
GTTTTAG
Found at i:1315 original size:307 final size:307
Alignment explanation
Indices: 1--1317 Score: 1993
Period size: 307 Copynumber: 4.3 Consensus size: 307
* *
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCTGGGCCCATTAGTGATGTTTTGAATCGTTTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGTCTTC
* * * ** *
66 GATTTGGCAAACCTCAAAGCTTTTGTT-TAAGGTGTTTATGGCCTAACTATAATCATTTTGATGA
65 GATTTGGCAAACCTCAATGCTTTTCTTCCATTG-GTTTATGGACTAACTATAATCATTTTGATGA
* * *
130 GATTAGTCCACTGTGCAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
129 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCC
195 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATG
194 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATG
* * *
260 GCCTAACTATAATCAATTTGGTGTAGATTAGTCCACTGTGAAGTTCTTAG
259 GACTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTGAAGTTTTTAG
* *
310 CTCATTTGGATCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGTCTTC
*
375 GATTTGGCAAACCTCAATGCTTTTCTTTCCCATT-GTTTATGGACTAACTATAATCATTTTGGTG
65 GATTTGGCAAACCTCAATGCTTTTC-TT-CCATTGGTTTATGGACTAACTATAATCATTTTGATG
439 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCAGGGCC
128 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCC
503 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATT-TTTAA
193 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTT-A
*
567 TGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGCGAAGTTTTTAG
257 TGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* *
618 CT-ATTTTGGAACACTTGTTATTTTTGGCCTATCAGTGCCCATTAGTGACGTTTTGAATCGTCTT
1 CTCA-TTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGTCTT
*** * * ** * *
682 CGATTTTATAAACCTCAAAG-TTTTTTTTTATGTTGTTTATGGCCTAACTATAATCATTTTGATG
64 CGATTTGGCAAACCTCAATGCTTTTCTTCCAT-TGGTTTATGGACTAACTATAATCATTTTGATG
* * *
746 AGATTAATCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC
128 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCC
** * * *
811 CATTAGTGACATTTTGAATCGTCTTCGATTTGCCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
193 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT
* *
876 GGACTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAG
258 GGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
926 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGTACG-TTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTG-ACGTTTTGAATCGTCTTC
* *
990 GATTTGGCAAACCTCAATGCTTTTCTTCCATTGGTTTATGGACTAACTATAATCATTTTGGTCAG
65 GATTTGGCAAACCTCAATGCTTTTCTTCCATTGGTTTATGGACTAACTATAATCATTTTGATGAG
*
1055 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGCCCA
130 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCA
* * * * *
1120 TTAGTTCCGTTTCGAATCGTCTTTGATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATCG
195 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGG
* *
1185 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAG
260 ACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* *
1233 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTTGT-CCGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCG-GGCCCATTAGTGACGTTTTGAATCGTCTTC
* *
1297 GATTTGTCAAATCTCAATGCT
65 GATTTGGCAAACCTCAATGCT
1318 CTT
Statistics
Matches: 917, Mismatches: 77, Indels: 30
0.90 0.08 0.03
Matches are distributed among these distances:
305 2 0.00
306 5 0.01
307 382 0.42
308 266 0.29
309 183 0.20
310 78 0.09
312 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (307 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGACGTTTTGAATCGTCTTCG
ATTTGGCAAACCTCAATGCTTTTCTTCCATTGGTTTATGGACTAACTATAATCATTTTGATGAGA
TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCAT
TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGA
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
Done.