Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012055.1 Corchorus olitorius cultivar O-4 contig12088, 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, 790
Length: 1318
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Found at i:385 original size:21 final size:21
Alignment explanation
Indices: 359--400 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
349 GCATCTTAGG
359 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
380 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
401 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:789 original size:154 final size:154
Alignment explanation
Indices: 509--1313 Score: 1265
Period size: 154 Copynumber: 5.2 Consensus size: 154
499 TTGGCGCATC
* *
509 AGTCCACTGTGAACTTTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * *
574 GTTCCGTTTTGAATCGTCCTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGCTTATGGCCT
66 GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
639 AACTATAATCATTTTGGTGAGATT
131 AACTATAATCATTTTGGTGAGATT
* *
663 AGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * *
728 GTTCCGTATTGAATCGTCTACGATTTGGCAAACCTCAATACTTTTCTTTCAATTGTTTATGGCCT
66 GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* *
793 AACTATAATCATTTTGTTTAGATT
131 AACTATAATCATTTTGGTGAGATT
* * * * *
817 AGTTCACTATGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGCCTATCGGAGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
*
882 GTTTCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
66 GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
947 AACTATAATCATTTTGGTGAGATT
131 AACTATAATCATTTTGGTGAGATT
* *
971 AGTCCACTGTGAAG-TTTTAGCTGATTTGGAATACTTGTTA-TTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * *
1034 GTTCCATTTTAAATCGTCTTCGATTTGGCAAACCTCAAAGCTGTTCTTTCCATTGTTTATGGCCT
66 GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
1099 AACTATAATCATTTTGGTGAGATT
131 AACTATAATCATTTTGGTGAGATT
* * *
1123 AGTCCACTGTGAAGTTTATAGCTCATTTGGAATACTTGTTATTTTGCGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
**
1188 GTGACGTTTTGAATCGTCTTCGATTTGGTCAAACCTACAATGCTTTTCTTTTCCTATTGTTTATT
66 GTTCCGTTTTGAATCGTCTTCGATTTGG-CAAACCT-CAATGCTTTTC-TTTCC-ATTGTTTA-T
1253 GGCCTAACTATAATCA-TTTGGTGAGATT
126 GGCCTAACTATAATCATTTTGGTGAGATT
1281 AGTCCACTGTGAAGTTTTTAGTCTCATTTGGAA
1 AGTCCACTGTGAAGTTTTTAG-CTCATTTGGAA
1314 AACTA
Statistics
Matches: 595, Mismatches: 48, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
152 120 0.20
153 47 0.08
154 339 0.57
155 7 0.01
156 9 0.02
157 5 0.01
158 40 0.07
159 28 0.05
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
AACTATAATCATTTTGGTGAGATT
Found at i:1186 original size:306 final size:308
Alignment explanation
Indices: 509--1313 Score: 1267
Period size: 306 Copynumber: 2.6 Consensus size: 308
499 TTGGCGCATC
* *
509 AGTCCACTGTGAACTTTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * * *
574 GTTCCGTTTTGAATCGTCCTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGCTTATGGCCT
66 GTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
*
639 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTA
131 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* * *
704 TTTTGGGCCTATCGGGGCTCATTAGTTCCGTATTGAATCGTCTACGATTTGGCAAACCTCAATAC
196 TTTTGGGCCTATCGGGGCCCATTAGTTCCATATTAAATCGTCTACGATTTGGCAAACCTCAATAC
* * *
769 TTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGTTTAGATT
261 TGTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
* * * * *
817 AGTTCACTATGAAGTTTTTAGCTTATTTTGAACACTTGTTATTTTGGGCCTATCGGAGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
*
882 GTTTCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
66 GTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
* *
947 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTGATTTGGAATACTTGTTA
131 AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
* *
1011 -TTTGGGCCTATCGGGGCCCATTAGTTCCATTTTAAATCGTCTTCGATTTGGCAAACCTCAA-AG
196 TTTTGGGCCTATCGGGGCCCATTAGTTCCATATTAAATCGTCTACGATTTGGCAAACCTCAATA-
*
1074 CTGTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
260 CTGTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
* * *
1123 AGTCCACTGTGAAGTTTATAGCTCATTTGGAATACTTGTTATTTTGCGCCTATCGGGGCCCATTA
1 AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
*
1188 GTGACGTTTTGAATCGTCTTCGATTTGGTCAAACCTACAATGCTTTTCTTTTCCTATTGTTTATT
66 GTTACGTTTTGAATCGTCTTCGATTTGG-CAAACCT-CAATGCTTTTC-TTTCC-ATTGTTTA-T
1253 GGCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGTCTCATTTGGAA
126 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAA
1314 AACTA
Statistics
Matches: 455, Mismatches: 34, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
305 1 0.00
306 184 0.40
307 30 0.07
308 168 0.37
309 5 0.01
310 34 0.07
311 23 0.05
312 10 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (308 bp):
AGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
GTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCT
AACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
TTTTGGGCCTATCGGGGCCCATTAGTTCCATATTAAATCGTCTACGATTTGGCAAACCTCAATAC
TGTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
Done.