Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011399.1 Corchorus olitorius cultivar O-4 contig11432, 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: 1813
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Found at i:301 original size:11 final size:11
Alignment explanation
Indices: 261--294 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
251 AGGAGTAGGG
261 TCCTTCCTAGC
1 TCCTTCCTAGC
272 TCCTTCCTAGC
1 TCCTTCCTAGC
283 TCCTTCCTAGC
1 TCCTTCCTAGC
294 T
1 T
295 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:1509 original size:153 final size:153
Alignment explanation
Indices: 715--1813 Score: 1733
Period size: 154 Copynumber: 7.2 Consensus size: 153
705 ACTAGTCCAC
* * *
715 TTTGAAACGTGTTCGATTTGGCAACCCTCAATGCTTTTCATTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* * *
780 ATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGTTCATTTGGAACACTTGTTATTTTAGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTTTGGG
*
845 CATATCGGGGCCCATTAGTTCCGT
130 CCTATCGGGGCCCATTAGTTCCGT
*
869 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATA
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* *
934 ATCATTTTGGTGAGATTAGTCCACAGTG--TTTTTAGCTCATTTGGAACACTTGTTATTTT-GGC
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
* *
996 CTATCGAGGACCATTAGTTCCGT
131 CTATCGGGGCCCATTAGTTCCGT
** * * * * *
1019 TTTGAAAAGTGTTCGATTTGGCAACCCTCAATGCTTTCCTTTCCAATATTTAGGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
1084 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTATAGCTCATTTGGAACACTTGTTATTTTCGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT-TAGCTCATTTGGAACACTTGTTATTTTGGG
*
1149 CCTATCGGGGCCCATTAGTTACGT
130 CCTATCGGGGCCCATTAGTTCCGT
*
1173 TTTTAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
** * *
1238 ATCATTTTGGTGATTTTGGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTTTGGG
*
1303 CCTTTCGGGGCCCATTAGTTCCGT
130 CCTATCGGGGCCCATTAGTTCCGT
*
1327 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
1392 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCACTTGGAACACTTGTTATTTTGGGC
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
* * *
1457 ATATCGAGGACCATTAGTTCCGT
131 CTATCGGGGCCCATTAGTTCCGT
1480 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCC-TATGTTTATGGCCTAACTAT
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT-TGTTTATGGCCTAACTAT
* *
1544 AATCATTTTGGTAAGATTAGTCCACTTTGAAGTCTTTAGCTCATTTGGAACACTTGTTACTTTTG
65 AATCATTTTGGTGAGATTAGTCCACTGTGAAGT-TTTAGCTCATTTGGAACACTTGTTA-TTTTG
1609 GGCCTATCGGGGCCCATTAGTTCCG-
128 GGCCTATCGGGGCCCATTAGTTCCGT
1634 -TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAACTAT
1 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCT-AACTAT
**
1698 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCAAATTTGGAACACTTGTTATTTTGGG
65 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* *
1763 CCTATCGAGGACCATTAGTTCCGT
130 CCTATCGGGGCCCATTAGTTCCGT
* *
1787 TTTGAAACGTGTTCGATTTGGCAACCC
1 TTTGAATCGTCTTCGATTTGGCAACCC
Statistics
Matches: 869, Mismatches: 64, Indels: 24
0.91 0.07 0.03
Matches are distributed among these distances:
150 107 0.12
151 29 0.03
152 32 0.04
153 248 0.29
154 423 0.49
155 30 0.03
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (153 bp):
TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
CTATCGGGGCCCATTAGTTCCGT
Found at i:1512 original size:307 final size:307
Alignment explanation
Indices: 715--1813 Score: 1744
Period size: 307 Copynumber: 3.6 Consensus size: 307
705 ACTAGTCCAC
* *
715 TTTGAAACGTGTTCGATTTGGCAACCCTCAATGCTTTTCATTCCATTGTTTATGGCCTAACTATA
1 TTTGAAACGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* * *
780 ATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGTTCATTTGGAACACTTGTTATTTTAGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* *
845 CATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTT
130 CATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTT
* *
910 TCCATTGTTTATGGCCTAACCATAATCATTTTGGTGAGATTAGTCCACAGT---GTTTTTAGCTC
195 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* *
972 ATTTGGAACACTTGTTATTTT-GGCCTATCGAGGACCATTAGTTCCGT
260 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGT
* * * * * *
1019 TTTGAAAAGTGTTCGATTTGGCAACCCTCAATGCTTTCCTTTCCAATATTTAGGGCCTAACTATA
1 TTTGAAACGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
1084 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTATAGCTCATTTGGAACACTTGTTATTTTCGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT-TAGCTCATTTGGAACACTTGTTATTTTGGG
* * * * *
1149 CCTATCGGGGCCCATTAGTTACGTTTTTAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTT
130 CATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTT
** *
1214 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATTTTGGTCCACTGTGAAGTTTTTAGCTC
195 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* *
1279 ATTTGGAACACTTTTTATTTTGGGCCTTTCGGGGCCCATTAGTTCCGT
260 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGT
* *
1327 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAAACGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
1392 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCACTTGGAACACTTGTTATTTTGGGC
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
1457 ATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
131 ATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
* * *
1522 CC-TATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTCTTTAGCTC
196 CCAT-TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
1586 ATTTGGAACACTTGTTACTTTTGGGCCTATCGGGGCCCATTAGTTCCG-
260 ATTTGGAACACTTGTTA-TTTTGGGCCTATCGGGGCCCATTAGTTCCGT
*
1634 -TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAACTAT
1 TTTGAAACGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCT-AACTAT
**
1698 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCAAATTTGGAACACTTGTTATTTTGGG
65 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* * *
1763 CCTATCGAGGACCATTAGTTCCGTTTTGAAACGTGTTCGATTTGGCAACCC
130 CATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCC
Statistics
Matches: 736, Mismatches: 51, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
303 3 0.00
304 225 0.31
306 57 0.08
307 308 0.42
308 143 0.19
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (307 bp):
TTTGAAACGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
ATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTT
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGT
Done.