Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011673.1 Corchorus olitorius cultivar O-4 contig11706, 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, 711
Length: 1186
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1186 Score: 1918
Period size: 154 Copynumber: 7.7 Consensus size: 154
* * **
1 TTAGCTCATTTAGATCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* * * *
66 CTTCGATTTGGCAAACCTCAATGGTTTTGTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
131 TGAGATTAGTCCACTGTGAAGTTT
131 TGAGATTAGTCCACTGTGAAGTTT
* *
155 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGTCATTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* *
220 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTTCATTGTTTATGGCCTAACAATAATCATTTTGT
66 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
285 TGAGATTAGTCCACTGTGAAGTTT
131 TGAGATTAGTCCACTGTGAAGTTT
**
309 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
*
374 CTTCGATTTGGC-AACCGGTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 CTTTGATTTGGCAAACC--TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
*
438 GATGAGATTAGTCCACTGTGAAGTTT
129 GTTGAGATTAGTCCACTGTGAAGTTT
*
464 TTAGCTCATTTGGAATACTTGTTATTTTGACCCTATCGGGGCCCATTAGT-AGCCTTTTGAATCG
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGA-CCTTTTGAATCG
528 CCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
65 CCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
593 TTGAGATTAGTCCACTGTGAAGTTT
130 TTGAGATTAGTCCACTGTGAAGTTT
* * * *
618 TTAGCTCATTTGGAATACTTGTTATTATGACCCTATCGGGGCCCATTAGTGGCTTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
683 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
66 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
*
748 TCAGATTAGTCCACTCGTGAAG-TT
131 TGAGATTAGTCCACT-GTGAAGTTT
* *
772 TTAGCTCATTTGG-ACACTTGTTATTTTGTAGCCTATCGGGGACCATTAGTGACCTTTTGAATCG
1 TTAGCTCATTTGGAACACTTGTTATTTTG-ACCCTATCGGGGCCCATTAGTGACCTTTTGAATCG
* *
836 CCTTTGATTTGTCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCATTTTG
65 CCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
901 TTGAGATTAGTCCACTGTGAAG-TT
130 TTGAGATTAGTCCACTGTGAAGTTT
* ** *
925 TTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTATTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* * * * *
990 CTTCGATTTGGCAACCCTAAATACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
1055 TGAGATTAGTCCACTGTGAAGTTT
131 TGAGATTAGTCCACTGTGAAGTTT
* * *
1079 TTAGCTCATTTGGAATACTTGTTATTTTGACCCTATCGGGGCCCATTAGT-TCCGTTTTGAACCG
1 TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACC-TTTTGAATCG
*
1143 CC-TTGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATG
65 CCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
Statistics
Matches: 962, Mismatches: 60, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
153 189 0.20
154 623 0.65
155 146 0.15
156 4 0.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (154 bp):
TTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
TGAGATTAGTCCACTGTGAAGTTT
Found at i:869 original size:308 final size:307
Alignment explanation
Indices: 1--1186 Score: 1986
Period size: 309 Copynumber: 3.9 Consensus size: 307
* *
1 TTAGCTCATTTAGATCACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* *
66 CTTCGATTTGGCAAACCTCAATGGTTTTGTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGG
* * *
196 CCCATTAGTGTCATTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTTCATTGTTT
196 CCCATTAGT-ACCTTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
261 ATGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
260 ATGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
309 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
374 CTTCGATTTGGC-AACCGGTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
66 CTTCGATTTGGCAAACC--TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* *
438 GATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGACCCTATCGG
129 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGG
503 GGCCCATTAGTAGCCTTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
194 GGCCCATTAGTA-CCTTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
*
568 TTATGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
258 TTATGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
* * ** * *
618 TTAGCTCATTTGGAATACTTGTTATTATGACCCTATCGGGGCCCATTAGTGGCTTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* *
683 CTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGT
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
748 TCAGATTAGTCCACTCGTGAAG-TTTTAGCTCATTTGG-ACACTTGTTATTTTGTAGCCTATCGG
131 TGAGATTAGTCCACT-GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG-ACCCTATCGG
* *
811 GGACCATTAGTGACCTTTTGAATCGCCTTTGATTTGTCAAACCTCAATGCTTTTCTTTCCATTGT
194 GGCCCATTAGT-ACCTTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
876 TTATGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAG-TT
258 TTATGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
* *
925 TTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTATTGACCTTTTGAATCGC
1 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
* * *
990 CTTCGATTTGGCAACCCTAAATACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
66 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
*
1055 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGACCCTATCGGGG
131 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGG
* * *
1120 CCCATTAGTTCCGTTTTGAACCGCC-TTGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTT
196 CCCATTAGTACC-TTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
1184 ATG
260 ATG
Statistics
Matches: 823, Mismatches: 45, Indels: 22
0.92 0.05 0.02
Matches are distributed among these distances:
306 48 0.06
307 196 0.24
308 281 0.34
309 294 0.36
310 4 0.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (307 bp):
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACCTTTTGAATCGC
CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGACCCTATCGGGG
CCCATTAGTACCTTTTGAATCGCCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
TGGCCTAACAATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTT
Done.