Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010749.1 Corchorus olitorius cultivar O-4 contig10781, 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: 2016
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Found at i:448 original size:154 final size:154
Alignment explanation
Indices: 4--2012 Score: 3196
Period size: 154 Copynumber: 13.0 Consensus size: 154
1 AAG
* * * * *
4 CCTCAATGCTTTTGTTTCCATTGTTTATAGCCTACCTATAATCATTTTGTTTAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* ** * * ** *
69 TTGAGGTTTTTAGCTCATTTTGAACACTTG-TATTTTGGGCCTATCGGGG-TCATTAGTTCCGTT
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
132 TTGAATTCGTCTTCGATTTGGCAAA
131 TTGAA-TCGTCTTCGATTTGGCAAA
*
157 CCTCAATGCTTTTCTTGCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTAGTCCAC
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TTAGTCCAC
* *
222 TGTTAACTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
65 TGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
*
287 ATTGAATCGTCTTCGATTTGGCAAG
130 ATTGAATCGTCTTCGATTTGGCAAA
*
312 CCTCAATGCTTTTGTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* *
377 GTGAACTTTTTAGCTAATTTTGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
* * *
442 TTGAATCTTCTTCGAATTGGCAAG
131 TTGAATCGTCTTCGATTTGGCAAA
* * * * *
466 CCTCAATGC-TTTCGTTTCCATTGTTTATGGCCTACCTATAATCACTTTGTTTAGATTAGTCCAT
1 CCTCAATGCTTTTC-TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
* * * *
530 TGTGTAGTTATTAGCTCATTTGGGACACTTGTTATTTTTGGGCCTATCGGGGCCCATTAGTGACG
65 TGTGAACTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGGGCCTATCGGGGCCCATTAGTGACG
595 TATTGAATCGTCTTCGATTTGGCAAA
129 TATTGAATCGTCTTCGATTTGGCAAA
621 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * * * ** *
686 GTAAACTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTATAGAGGCCCATTAGTTCCGTT
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
751 TTGAATCGTCTTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
* *
775 CCTCAATGCTTTTCTCTCCATTGTTTCTGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * *
840 GTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
* * *
905 TTGAATCTTCTTCGAATTGGCAAG
131 TTGAATCGTCTTCGATTTGGCAAA
* * * * *
929 CCTCAATGCTTTTGTTTCCATTGTTTATGGCCTACCTATAATCATTTTGTTTAGATTAGTCCATT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
*
994 GTGAACTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
1059 TTGAATCGTCTTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
* *
1083 CCTCAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACA
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * * ** *
1148 GTGAACTTTATAGCTCAGTTGGAACACTGGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
*
1213 TTAAATCGTCTTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
*
1237 CCTCAATGCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* *
1302 GTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
* *
1367 TTGATTCGTATTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
* *
1391 CCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* *
1456 GTGAACTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
* * *
1521 TTGAATCTTCTTCGAATTGGCAAG
131 TTGAATCGTCTTCGATTTGGCAAA
* * * * *
1545 CCTCAATGCTTTTGTTTCCATTGTTTATGGCCTACCTATAATCATTTTGTTTAGATTAGTCCATT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * *
1610 GTGAACTTTTTAGCTCATTTGGAATACTTGTTATTTTGGTCCTATCGGGGCCAATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
*
1675 TTGAATCATCTTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
1699 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1764 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
1829 TTGAATCGTCTTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
1853 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
1 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
*
1918 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
66 GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
*
1983 TTGAATCGTATTCGATTTGGCAAA
131 TTGAATCGTCTTCGATTTGGCAAA
2007 CCTCAA
1 CCTCAA
2013 GGCT
Statistics
Matches: 1698, Mismatches: 152, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
153 52 0.03
154 1402 0.83
155 225 0.13
156 19 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
GTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
TTGAATCGTCTTCGATTTGGCAAA
Done.