Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011500.1 Corchorus olitorius cultivar O-4 contig11533, 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, 883
Length: 1473
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Found at i:281 original size:154 final size:153
Alignment explanation
Indices: 1--483 Score: 830
Period size: 154 Copynumber: 3.2 Consensus size: 153
**
1 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTCGGCCTATCGGGGCCCATTAGTTCC
1 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCCCATTAGTGAC
66 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
65 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
131 TAATCATTTTGGTGAGATTAGTCC
130 TAATCATTTTGGTGAGATTAGTCC
*
155 ACTGTGAAGTGTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGTGAC
1 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG-GCCTATCGGGGCCCATTAGTGAC
*
220 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAA
65 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
*
285 TAATCATTTTTGTGAGATTAGTCC
130 TAATCATTTTGGTGAGATTAGTCC
* * *
309 ACTGTGAAGTTTTTAACTCAATTGGAACACTTGTTATTGTGGGCCTATC----CCCATTAGTGAC
1 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT-TTGGCCTATCGGGGCCCATTAGTGAC
*
370 GTTTTGAATCGTCTTCGATTTTGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
65 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
435 TAATCATTTTGGTGAGATTAGTCC
130 TAATCATTTTGGTGAGATTAGTCC
459 ACTGTGAAGTTTTTAGCTCATTTGG
1 ACTGTGAAGTTTTTAGCTCATTTGG
484 TGTACTTGTG
Statistics
Matches: 313, Mismatches: 14, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
150 121 0.39
153 1 0.00
154 189 0.60
155 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (153 bp):
ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCCATTAGTGACG
TTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
AATCATTTTGGTGAGATTAGTCC
Found at i:713 original size:21 final size:21
Alignment explanation
Indices: 687--775 Score: 135
Period size: 21 Copynumber: 4.2 Consensus size: 21
677 AGCTAGAAGT
687 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
708 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
729 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
750 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
771 TCATT
1 TCATT
776 AGAATTGCCT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 2 0.03
21 61 0.97
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.