Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010932.1 Corchorus olitorius cultivar O-4 contig10964, 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, 735
Length: 1226
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Found at i:317 original size:154 final size:154
Alignment explanation
Indices: 1--1226 Score: 1899
Period size: 154 Copynumber: 7.9 Consensus size: 154
* *
1 TTCTTT-CAGTTGTTTAGTGGCCAAACTATAATCATTTTGGTGAGATAAGTCCACTGTGAAGTTT
1 TTCTTTCCA-TTGTTTA-TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCGTTAGTGACGTTTTGAATCGT
64 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGT
* *
130 CTTCGATTTGGC-AACCTTCGATGCCT
129 CTTCGATTTGGCAAACC-TCAATGCTT
156 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* * * **
221 AGCTCATTCGGAACACTTGTTATTTTGTGCCTATCGAGGACCATTAGTTCCGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
286 TCGATTTGGCAAACCTCAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
* *
310 TTATTTCCATTGTTTATGGCCTAACTAT-ATCATTTTGGTGAGTATTAGTCCACTGTGAAGTTTG
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG-ATTAGTCCACTGTGAAGTTTT
374 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTC
65 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTC
* *
439 TTCGATTTGGC-AACCTTCGATGCCT
130 TTCGATTTGGCAAACC-TCAATGCTT
*
464 TTC-TTCCATTG-TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
527 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGCGAACCATTAGTGACGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
592 TCGATTTGGCAAACCTCAATGCTTT
131 TCGATTTGGCAAACCTCAATGC-TT
* * **
617 TTTTTTCCATTGTTTATGTCCTATTTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* * * * ** *
682 AGCTCAATTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
*
747 TCGATTTGGCAAACCTGAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
* *
771 TTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
*
836 AGCTCATTTGGAACACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
901 TCGATTTGGCAAACCTCAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
*
925 TTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
990 AGTTCATTTGGAACACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
1055 TCGATTTAGGCAAACCTCAATTGTCTT
131 TCGATTT-GGCAAACCTCAA-TG-CTT
* * * *
1082 TTCTTTCCTATTGTTTATGACCTAACTATAATCAGTTTGGTGAGTTTAGTCCACTGTGTAA-CTT
1 TTCTTTCC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTG-AAGTTT
* * * **
1146 TTAGGTCAGTTGGAACACGTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCG
64 TTAGCTCATTTGGAACAC-TTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCG
1211 TCTTCGATTTGGCAAA
128 TCTTCGATTTGGCAAA
Statistics
Matches: 988, Mismatches: 68, Indels: 27
0.91 0.06 0.02
Matches are distributed among these distances:
152 116 0.12
153 47 0.05
154 532 0.54
155 155 0.16
156 4 0.00
157 11 0.01
158 69 0.07
159 54 0.05
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (154 bp):
TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAATGCTT
Found at i:885 original size:461 final size:463
Alignment explanation
Indices: 1--1226 Score: 1979
Period size: 461 Copynumber: 2.6 Consensus size: 463
* *
1 TTCTTT-CAGTTGTTTAGTGGCCAAACTATAATCATTTTGGTGAGATAAGTCCACTGTGAAGTTT
1 TTCTTTCCA-TTGTTTA-TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCGTTAGTGACGTTTTGAATCGT
64 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGT
* * *
130 CTTCGATTTGGC-AACCTTCGATGC-CTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
129 CTTCGATTTGGCAAACC-TCAATGCTTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTT
193 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTCGGAACACTTGTTATTTTGTGCCTATCG
193 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCAATT-GGAACACTTGTTATTTTGTGCCTATCG
*
257 AGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTATTTCCATTG
257 AGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTATTTCCATTG
322 TTTATGGCCTAACTATATCATTTTGGTGAGTATTAGTCCACTGTGAAGTTTGTAGCTCATTTGGA
322 TTTATGGCCTAACTATATCATTTTGGTGAGTATTAGTCCACTGTGAAGTTTGTAGCTCATTTGGA
*
387 ACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-A
387 ACACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAA
*
451 ACCTTCGATGCCT
452 ACC-TCAATGCCT
*
464 TTC-TTCCATTG-TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
527 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGCGAACCATTAGTGACGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
* * **
592 TCGATTTGGCAAACCTCAATGCTTTTTTTTTCCATTGTTTATGTCCTATTTATAATCATTTTGGT
131 TCGATTTGGCAAACCTCAATGCTTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGT
657 GAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGTGCCTATCGAGGC
196 GAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGTGCCTATCGAGGC
* *
722 CCATTAGTTCCGTTTTGAATTGTCTTCGATTTGGCAAACCTGAATGCTTTTCA-TTCCATTGTTT
261 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-ATTTCCATTGTTT
* *
786 ATGGCCTAACTATAATCATTTTGGTGAG-ATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
325 ATGGCCTAACTAT-ATCATTTTGGTGAGTATTAGTCCACTGTGAAGTTTGTAGCTCATTTGGAAC
850 ACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
389 ACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAAC
*
915 CTCAATGCTT
454 CTCAATGCCT
*
925 TTCTTTCCTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
990 AGTTCATTTGGAACACTTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
*
1055 TCGATTTAGGCAAACCTCAATTG-TCTTTTCTTTCCTATTGTTTATGACCTAACTATAATCAGTT
131 TCGATTT-GGCAAACCTCAA-TGCT-TTTTCTTTCC-ATTGTTTATGACCTAACTATAATCATTT
* * * * *
1119 TGGTGAGTTTAGTCCACTGTGTAA-CTTTTAGGTCAGTTGGAACACGTTGTTATTTTGGGCCTAT
192 TGGTGAGATTAGTCCACTGTG-AAGTTTTTAGCTCAATTGGAACAC-TTGTTATTTTGTGCCTAT
*
1183 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
255 CGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
Statistics
Matches: 710, Mismatches: 38, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
460 124 0.17
461 281 0.40
462 34 0.05
463 124 0.17
464 13 0.02
465 11 0.02
466 62 0.09
467 61 0.09
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (463 bp):
TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAATGCTTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGT
GAGATTAGTCCACTGTGAAGTTTTTAGCTCAATTGGAACACTTGTTATTTTGTGCCTATCGAGGC
CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTATTTCCATTGTTTA
TGGCCTAACTATATCATTTTGGTGAGTATTAGTCCACTGTGAAGTTTGTAGCTCATTTGGAACAC
TTGTGATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCT
CAATGCCT
Done.