Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011655.1 Corchorus olitorius cultivar O-4 contig11688, 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:0.22, C:0.20, G:0.19, T:0.39
Found at i:389 original size:151 final size:151
Alignment explanation
Indices: 114--508 Score: 620
Period size: 151 Copynumber: 2.6 Consensus size: 151
104 TGGCGCATCA
*
114 CTAACTATGATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCTAATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCT-ATTTGGAACACTTGT
* *
179 TATTTTGGGACTATCGGGGCCCATTAGTTCCGTTTGAATCGTCATCGATTTGGCAAACCTCAATG
65 TATTTTGGGCCTATCGGGGCCCATTAG-TCCGTTTGAATCGTCATCAATTTGGCAAACCTCAATG
244 CTTTTCATTCCATTG-TTATAGC
129 CTTTTCATTCCATTGTTTATAGC
*
266 CTAACTATAATCATTTCGGTGAGATTAGTACACTGTGAAG-TTTTAGCTAGTTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCTA-TTTGGAACACTTGT
330 TATTTTGGGCCTATCGGGGCCCATTAGTCCGTTTTGAATCGTCATCAATTTGGCAAACCTCAATG
65 TATTTTGGGCCTATCGGGGCCCATTAGTCCG-TTTGAATCGTCATCAATTTGGCAAACCTCAATG
* *
395 CTTTTCTTTCCATTGTTTATGGC
129 CTTTTCATTCCATTGTTTATAGC
* * *
418 CTAACTATAATCATTTTGGTCAGATTAGTCCACTGTCGAAGTTTTTAGCTCATTTGGAAGACTTG
1 CTAACTATAATCATTTTGGTGAGATTAGTACACTGT-GAAGTTTTTAGCT-ATTTGGAACACTTG
483 -TA-TTTGGGCCTATCGGGG-CCATTAGT
64 TTATTTTGGGCCTATCGGGGCCCATTAGT
509 TAGTTTCCAT
Statistics
Matches: 227, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
150 5 0.02
151 102 0.45
152 93 0.41
153 6 0.03
154 20 0.09
155 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (151 bp):
CTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCTATTTGGAACACTTGTT
ATTTTGGGCCTATCGGGGCCCATTAGTCCGTTTGAATCGTCATCAATTTGGCAAACCTCAATGCT
TTTCATTCCATTGTTTATAGC
Found at i:719 original size:264 final size:265
Alignment explanation
Indices: 251--775 Score: 821
Period size: 264 Copynumber: 2.0 Consensus size: 265
241 ATGCTTTTCA
251 TTCCATTGTTATAGCCTAACTATAATCATTTCGGTGAGATTAGTACACTGTGAAGTTTTAGCTAG
1 TTCCATTGTTATAGCCTAACTATAATCATTTCGGTGAGATTAGTACACTGTGAAGTTTTAGCTAG
* *
316 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTCCGTTTTGAATCGTCATCAATTT
66 TTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATAAGTCCGTTTTGAATCGTCATCAATTT
* * *
381 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAG
131 GGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTCGTCAGATTAG
*
446 TCCACTGTCGAAGTTTTTAGCTCATTTGGAAGACTTGTA-TTTGGGCC-TATCGGGG-CCATTAG
196 TCCACTGTCGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCGTATCGGGGCCCATTAG
508 TTAGT
261 TTAGT
* *
513 TTCCATTGTTTATAGCCTAACTATAATCATTT-GGTGAGATTAGTCCACTGTGAGGTTTTTA-CT
1 TTCCATTG-TTATAGCCTAACTATAATCATTTCGGTGAGATTAGTACACTGTGAAG-TTTTAGCT
* *
576 CA-TTTGGAACACTTG-TATTTTGGGCCTATCGAAGTCCCATAAGTTCCGTTTTGAATCGTCTTT
64 -AGTTTGGAACACTTGTTATTTTGGGCCTATCG-AGGCCCATAAG-TCCGTTTTGAATCGTC-AT
* **
639 CGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTCGTGT
125 CAATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTCGTCA
*
704 GATTAGTCCACTGTCGGAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCGTATCGGGGCC
190 GATTAGTCCACTGTCGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCGTATCGGGGCC
769 CATTAGT
255 CATTAGT
776 GTCGTTTTGA
Statistics
Matches: 240, Mismatches: 14, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
261 16 0.07
262 52 0.22
263 45 0.19
264 103 0.43
265 8 0.03
266 8 0.03
267 8 0.03
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (265 bp):
TTCCATTGTTATAGCCTAACTATAATCATTTCGGTGAGATTAGTACACTGTGAAGTTTTAGCTAG
TTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATAAGTCCGTTTTGAATCGTCATCAATTT
GGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTCGTCAGATTAG
TCCACTGTCGAAGTTTTTAGCTCATTTGGAACACTTGTATTTTGGGCCGTATCGGGGCCCATTAG
TTAGT
Found at i:1143 original size:153 final size:153
Alignment explanation
Indices: 512--1220 Score: 1038
Period size: 153 Copynumber: 4.6 Consensus size: 153
502 CATTAGTTAG
* * *
512 TTTCCATTGTTTATAGCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTGTGAGGTTTTTA-C
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
** * *
575 TCATTTGGAACACTTG-TATTTTGGGCCTATCGAAGTCCCATAAGT-TCCGTTTTGAATCGTCTT
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCG--GGGCCATTAGTGT-CGTTCTGAATCGTC-T
* *
638 TCGATTTGGCAAACCACAATGCTTTTC
127 TCGATTTGGGAAACCTCAATGCTTTTC
* * *
665 TTTCCATTGTTTATAGCCTAACTATAATCATTTTCGTGTGATTAGTCCACTGTCGGAGTTTTTAG
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGT-GAAGTTTTTAG
*
730 CTCATTTGGAACACTTG-TATTTTGGGCCGTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTT
65 CTCATTTGGAACACTTGTTATTTTGGGCC-TATCGGGG-CCATTAGTGTCGTTCTGAATCGTCTT
*
794 CGATTTGAGAAACCTCAATGCTTTTC
128 CGATTTGGGAAACCTCAATGCTTTTC
820 TTTCCATTGTTTATGGCCTAACTAT--T-ATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* *
882 TCATTTGGAACAATTGTTATTTTGGGCCTATCGGGGCTCATTAGTGTCGTTCTGAATCATCTTCG
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGC-CATTAGTGTCGTTCTGAATCGTCTTCG
947 ATTTGGGAAACCTCAATGCTTTTC
130 ATTTGGGAAACCTCAATGCTTTTC
* * *
971 TTTCCATTGTTTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * *
1036 TCATTTGGAACACTTGTTATTTTAGGCCTTTCGGGGCCATTAGTGACGTTCTGAATCGTCTTCGA
66 TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCATTAGTGTCGTTCTGAATCGTCTTCGA
*
1101 TTTGGGAACCCTCAATGCTTTTC
131 TTTGGGAAACCTCAATGCTTTTC
** * *
1124 TTTCCATTGTTTATGGCCTAACGCTTATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAAC
1 TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
*
1189 TCATTTGGAACACTTGTTATTTTGGGCGTATC
66 TCATTTGGAACACTTGTTATTTTGGGCCTATC
1221 AAGACC
Statistics
Matches: 509, Mismatches: 36, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
150 1 0.00
151 106 0.21
152 34 0.07
153 167 0.33
154 88 0.17
155 58 0.11
156 49 0.10
157 6 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (153 bp):
TTTCCATTGTTTATGGCCTAACTATAATCATTTTCGTGAGATTAGTCCACTGTGAAGTTTTTAGC
TCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCATTAGTGTCGTTCTGAATCGTCTTCGA
TTTGGGAAACCTCAATGCTTTTC
Done.