Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011089.1 Corchorus olitorius cultivar O-4 contig11122, 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, 1000
Length: 1832
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Found at i:519 original size:153 final size:153
Alignment explanation
Indices: 1--1832 Score: 2654
Period size: 153 Copynumber: 11.9 Consensus size: 153
* * * * *
1 GGGGCCGACTTAGTTTCGTTTTGTAATCGTCATCGATTTGGCCAACCCTCGATGTCTTTTTGTTT
1 GGGGCCCA-TTAGTTCCGTTTTG-AATCGTCTTCGATTTGG-CAACCCTCAATG-C-TTTTCTTT
66 CCATTTGTTTATGGCCTAACTAATAATCTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
61 CCA-TTGTTTATGGCCTAACT-ATAATC-ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
*
131 TCATTTGGAACACTTGTTATTTTAGGCCTTTC
123 TCATTTGGAACACTTGTTATTTT-GGCCTATC
* *
163 GGGG-CCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* * *** *
227 GTTTATGGCCTAACTATAATCATTTTGCTAAGATTAGTCTTTTGTGAAGTTTATAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
292 AACACTTGTTATTTTGGGCCTATC
131 AACACTTGTTATTTT-GGCCTATC
* * * * *
316 GGGACCCATTAGTGT-TGTTCTGAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTTCCAT
1 GGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT
* *
380 TGTTTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-TCATTTA
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
*
444 GAACACTTGTTATTTTGTGCCAATC
130 GAACACTTGTTATTTTG-GCCTATC
** ** * * * *
469 AAGGCCCATTAGTGACGTTATAAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* * *
534 GTTTATGGCCTAACTATAATCATTTTAGTAAGATTAGTCTACTGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
599 AACACTTGTTATTTTGGGCCTATC
131 AACACTTGTTATTTT-GGCCTATC
* * * * *
623 GGGGCCCATTAGTGT-CGCTATGAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTT-CTT
1 GGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT
* *
686 TGTTTATGGCCTAACTATAATCATTTTCGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
751 GAACACTTGTTATTTTGCGCCTATC
130 GAACACTTGTTATTTTG-GCCTATC
* * * *
776 TGGGCCCATTAGTGT-CGTTATGAATCGTCTT-AATTTGG-AAACCTCAATGCTTTTCTTTCCAT
1 GGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT
*
838 TGTTTATGGCCTAACTATAATCATTTTGGTGATATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
65 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
* *
903 TAACACTTTTTATTTTGGCCTATC
130 GAACACTTGTTATTTTGGCCTATC
* * * * *
927 GGGGCCCATTAGTTTCGTTTTGAATCATCTTCGATCTGGCAATCCTCAATGCTTTTCTTTCCGTT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
*
992 GTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
1057 AACACTTGTTA-TTTGGACCTATC
131 AACACTTGTTATTTTGG-CCTATC
1080 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
*
1145 -TTTGATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTATGCTCATTT
66 GTTT-ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA-GCTCATTT
1209 GGAACACTTGTTATTTTGGGCCTATC
129 GGAACACTTGTTATTTT-GGCCTATC
*
1235 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC-TTTCTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* * * *
1299 GTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCGACTGTGATGTTTTAAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1364 AACACTTGTTATTTTAGGCCTTTC
131 AACACTTGTTATTTT-GGCCTATC
* * *
1388 GGGG-CCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAACCCTCGATGCTTTTGTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
*
1452 GTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1517 AACACTTGTTATTTTAGGCCTTTC
131 AACACTTGTTATTTT-GGCCTATC
*
1541 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
1606 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
66 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1671 AACACTTGTTATTTTAGGCCTTTC
131 AACACTTGTTATTTT-GGCCTATC
* * *
1695 -GGG-CCATTAG-TCCG-TTTGAATCGTATTCGATTTGGCAACCCTCGATGCTTTTGGTTTCCAT
1 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTT-CTTTCCAT
* ***
1756 TGTTTGATGGCCTAACTATAATCATTTTGGTGAGATTGGTCTTTTGTGAAG-TTTTAGCTCATTT
65 TGTTT-ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
1820 GGAACACTTGTTA
129 GGAACACTTGTTA
Statistics
Matches: 1549, Mismatches: 99, Indels: 55
0.91 0.06 0.03
Matches are distributed among these distances:
150 38 0.02
151 95 0.06
152 194 0.13
153 667 0.43
154 414 0.27
155 82 0.05
156 12 0.01
157 1 0.00
158 12 0.01
159 15 0.01
160 13 0.01
161 2 0.00
162 4 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (153 bp):
GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
AACACTTGTTATTTTGGCCTATC
Found at i:649 original size:307 final size:306
Alignment explanation
Indices: 1--1832 Score: 2670
Period size: 307 Copynumber: 6.0 Consensus size: 306
* * * *
1 GGGGCCGACTTAGTTTCGTTTTGTAATCGTCATCGATTTGGCCAACCCTCGATGTCTTTTTGTTT
1 GGGGCCCA-TTAG-TTCGTTTTG-AATCGTCTTCGATTTGG-CAACCCTCAATG-C-TTTTCTTT
66 CCATTTGTTTATGGCCTAACTAATAATCTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
60 CCA-TTGTTTATGGCCTAACT-ATAATC-ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* *
131 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCATTAGTTCCGTTTTGAATCGTATTCGA
122 TCATTTGGAACACTTGTTATTTTAGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTATTCGA
* * *
196 TTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTAAGAT
187 TTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
*** *
261 TAGTCTTTTGTGAAGTTTATAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
252 TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
* * * * *
316 GGGACCCATTAGTGTTGTTCTGAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTTCCATT
1 GGGGCCCATTAGT-TCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* *
381 GTTTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-TCATTTAG
65 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
* * ** * * * *
445 AACACTTGTTATTTT-GTGCCAATCAAGGCCCATTAGTGACGTTATAAATCGTCTTCGATTTGGG
130 AACACTTGTTATTTTAG-GCCTATC-GGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGC
* * * *
509 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTAAGATTAGTCT
193 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
574 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
258 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
* * * * *
623 GGGGCCCATTAGTGTCGCTATGAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTT-CTTT
1 GGGGCCCATTAGT-TCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* *
687 GTTTATGGCCTAACTATAATCATTTTCGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
65 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
* * *
752 AACACTTGTTATTTT-GCGCCTATCTGGGCCCATTAGTGT-CGTTATGAATCGTCTT-AATTTGG
130 AACACTTGTTATTTTAG-GCCTATC-GGGCCCATTAGT-TCCGTTTTGAATCGTATTCGATTTGG
* *
814 -AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATATTAGTC
192 CAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
* *
878 CACTGTGAAGTTTTTAGCTCATTTGTAACACTTTTTATTTT-GGCCTATC
257 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
* * * *
927 GGGGCCCATTAGTTTCGTTTTGAATCATCTTCGATCTGGCAATCCTCAATGCTTTTCTTTCCGTT
1 GGGGCCCATTAG-TTCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
*
992 GTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
65 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1057 AACACTTGTTA-TTT-GGACCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
130 AACACTTGTTATTTTAGG-CCTATC-GGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGC
1120 AACCCTCAATGCTTTTCTTTCCATT-TTTGATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
193 AACCCTCAATGCTTTTCTTTCCATTGTTT-ATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
*
1184 CACTATGAAGTTTTTATGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
257 CACTGTGAAGTTTTTA-GCTCATTTGGAACACTTGTTATTTTGGGCCTATC
*
1235 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGC-TTTCTTTCCATT
1 GGGGCCCATTAGTT-CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
* * * *
1299 GTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCGACTGTGATGTTTTAAGCTCATTTGG
65 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
* *
1364 AACACTTGTTATTTTAGGCCTTTCGGGGCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAA
130 AACACTTGTTATTTTAGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAA
* * *
1429 CCCTCGATGCTTTTGTTTCCATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCAC
195 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
* *
1494 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGGCCTTTC
260 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
*
1541 GGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATT
1 GGGGCCCATTAGTT-CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATT
1606 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
65 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
*
1671 AACACTTGTTATTTTAGGCCTTTCGGG-CCATTAG-TCCG-TTTGAATCGTATTCGATTTGGCAA
130 AACACTTGTTATTTTAGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAA
* * * *
1733 CCCTCGATGCTTTTGGTTTCCATTGTTTGATGGCCTAACTATAATCATTTTGGTGAGATTGGTCT
195 CCCTCAATGCTTTT-CTTTCCATTGTTT-ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
**
1798 TTTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTA
258 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
Statistics
Matches: 1400, Mismatches: 96, Indels: 52
0.90 0.06 0.03
Matches are distributed among these distances:
303 2 0.00
304 135 0.10
305 229 0.16
306 293 0.21
307 600 0.43
308 70 0.05
309 18 0.01
310 10 0.01
311 1 0.00
312 9 0.01
313 17 0.01
314 10 0.01
315 6 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (306 bp):
GGGGCCCATTAGTTCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTG
TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
ACACTTGTTATTTTAGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAAC
CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
Done.