Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011201.1 Corchorus olitorius cultivar O-4 contig11234, 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: 1909
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Found at i:287 original size:154 final size:154
Alignment explanation
Indices: 1--1328 Score: 1806
Period size: 154 Copynumber: 8.7 Consensus size: 154
* * * * **
1 AGCTCATTTCGAATACTTGTTATTTTG-GACCTATT-AGGGCCCTTTAGTTTTGTTTTGAATCGT
1 AGCTCATTTGGAACACTTGTTATTTTGTG-CCT-TTCGGGGCCCATTAGTTACGTTTTGAATCGT
* * *
64 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCTATTGTTTATGGCCTAACTATAATCATTTTAG
64 CTTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG
*
129 TGAGATTAGTCCACTGTGAAGTTGTT
129 TGAGATTAGTCCACTGTGAAGTTTTT
* * * * *
155 AGCTCATTTCGAACACTTGTTATTTCGTGCCATTCGGGGCCCATTAGTTCCGTTTTAAATCGTCT
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
* *
220 TCGATTTGGCAATCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTAAAATCATTTT-GTT
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG-T
* ** ** *
284 GAGATTTGGGCTTTGTGAAGCTTTT
130 GAGATTAGTCCACTGTGAAGTTTTT
* * *
309 AGTTCATTTGGAACACTTATTATTTTG-GTCCTTTCGGGGCCCATTAGTGACGTTTTGAATCGTC
1 AGCTCATTTGGAACACTTGTTATTTTGTG-CCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTC
* * * * * * *
373 TTCGATTTGACAAACCTCAATGCTTTTGTTTCCATCGTTTATGGCATAACTATAATCATTTTGGT
65 TTCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* *
438 GAGATTAGTCCACTATGAAGGTTTT
130 GAGATTAGTCCACTGTGAAGTTTTT
* *
463 AGCTCATCTGGAACACTTGTTATTGTGTGCCTTTCGGGGCCC---A-TTA------G--T--TC-
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
*
513 -CGATTTGGCAACCCTCGATGCTTTTCTTTCCATTATTTATGGCCTAACTATAATCATTTTAGTG
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTG
577 AGATTAGTCCACTGTGAAGTTTTT
131 AGATTAGTCCACTGTGAAGTTTTT
* *
601 AGCTCATTTGGAACACTTG-TATTTTGTGCCTTTCGGGGCCCATTAGTTCCGTTTTAAATCGTCT
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
* *
665 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTGTATCGCCTAACTATAATCATTTT-GCT
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAG-T
729 GAGATTAGTCCACTGTGAAGTTTTT
130 GAGATTAGTCCACTGTGAAGTTTTT
* * * * *
754 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCTATTAGTGACGTTTTGAATCGTCT
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
* * * *
819 TCGATTAGGCAAACCTCAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTG
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTG
*
884 AGATTAGTCTACTGTGAAGTTTTT
131 AGATTAGTCCACTGTGAAGTTTTT
* ** **
908 AGCTCATTTGGAACACTTGTTATTTTG-GACCTATCAAGGCCC-TATAGTTTTGTTTTGAATCGT
1 AGCTCATTTGGAACACTTGTTATTTTGTG-CCTTTCGGGGCCCAT-TAGTTACGTTTTGAATCGT
* *
971 CTTCGATTTGGCAAACCCTCGATGCGTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTA
64 CTTCGATTTGGC-AACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTA
1036 GTGAGATTAGTCCACTGTGAAGTTTTT
128 GTGAGATTAGTCCACTGTGAAGTTTTT
* *
1063 AGCTCATTTGGAAAAATTGTTA-TTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
* * * *
1127 TCGATTTGGTAACCCTCGATACTTTTCTTTCCATTGTTTATGGCCTAACTATAATAACTTTAGTG
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTG
1192 AGATTAGTCCACTGTGAAGTTTTT
131 AGATTAGTCCACTGTGAAGTTTTT
*
1216 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
1 AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
*
1281 TCGATTTGGCAACCCTCGATGCTTTCCTTTCCATTGTTTATGGCCTAA
66 TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAA
1329 TTGATGCGCT
Statistics
Matches: 1036, Mismatches: 107, Indels: 62
0.86 0.09 0.05
Matches are distributed among these distances:
137 21 0.02
138 96 0.09
140 3 0.00
141 2 0.00
142 1 0.00
144 1 0.00
149 1 0.00
150 2 0.00
151 3 0.00
152 1 0.00
153 202 0.19
154 603 0.58
155 100 0.10
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
AGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTACGTTTTGAATCGTCT
TCGATTTGGCAACCCTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGTG
AGATTAGTCCACTGTGAAGTTTTT
Done.