Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012736.1 Corchorus olitorius cultivar O-4 contig12769, 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: 2956
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Found at i:1275 original size:154 final size:154
Alignment explanation
Indices: 990--2956 Score: 2867
Period size: 154 Copynumber: 12.8 Consensus size: 154
980 AGGATTGGAC
* * ** * *
990 TTTTTAGCTCATTTGAAACACTTGTTATTTTGGGTCTATCGGGGCCCATTAGTTCCATTTTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* * ** * *
1055 CGTATCCGATTCAGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATCAATT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
1120 TGGTGAGATTAGTCCACTGTGAAG
131 TGGTGAGATTAGTCCACTGTGAAG
* * *
1144 TTTTAAGCTCATTTGGAATACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* * * *
1209 CGTCTTCGATTTGGTAAACTTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATCAATT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
* *
1274 TGGTGAGATTAGTCCACTCTGAAC
131 TGGTGAGATTAGTCCACTGTGAAG
** *
1298 TTTGAAGCTCATTTGGAATACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* *
1362 CGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
1427 TGGTGAGATTAGTCCACTGTGAAC
131 TGGTGAGATTAGTCCACTGTGAAG
* * * *
1451 CTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGCGCCCATTAGT-TCTGTTTTGAA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGAC-GTATTGAA
** *
1515 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAACGTTTATGGCCAAACTATAATCATT
65 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* *
1580 TTGGTGAGATTAGTCCACTGTAAAC
130 TTGGTGAGATTAGTCCACTGTGAAG
1605 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* * * *
1670 CGTCTACGATTTGGCAAACCACAATACTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
* * * * *
1735 TGTTTAGATTAGTTCACTATAAAG
131 TGGTGAGATTAGTCCACTGTGAAG
** *
1759 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
***
1824 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATCTTCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
1889 CGGTGAGATTAGTCCACTGTGAAG
131 TGGTGAGATTAGTCCACTGTGAAG
* *
1913 TTTTTAGCACATTTGGAACACTTGTTATTTTGGGCCTATCGTGGG-CCATTAGTGACGTATGGAA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG-GGGCCCATTAGTGACGTATTGAA
* * ** * * *
1977 TCGTCTTCGATTCGGCAAACCTCCATGCTTTTCTTTAAATTGTTTAGGGCCTAACGATAATTATT
65 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
*
2042 TTGGTGAGATTAGTCCACTGTGAAC
130 TTGGTGAGATTAGTCCACTGTGAAG
* *
2067 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG-GTCTGTTTTGAA
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGAC-GTATTGAA
* * * * *
2131 TCGTCTTGGATTTTTGCAAACCTCAATGCTTTTCTTACCATTATTTATGGTCTAACTATAATCAT
65 TCGTCTTCGA-TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
*
2196 TTTGGTGAGATTAGTCCACTGTGAAC
129 TTTGGTGAGATTAGTCCACTGTGAAG
* * * *
2222 TTTTTCAGATCATTAGGAAAACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGGA
1 TTTTT-AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
2287 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
65 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* *
2352 TTGGTGAGATTAGTCCACTCTGAAA
130 TTGGTGAGATTAGTCCACTGTGAAG
* *
2377 TTTATAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTATTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
2442 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
2507 TGGTGAGATTAGTCCACTGTGAAA
131 TGGTGAGATTAGTCCACTGTGAAG
* * *
2531 TTTATAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTCTTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* *
2596 TGTTTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTGTTTATGGCCTAACTATAATCATTT
66 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
*
2660 TGGTGAGATTTGTCCACTGTGAAG
131 TGGTGAGATTAGTCCACTGTGAAG
* *
2684 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAAT
1 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
* * * *
2749 CGTCTTCGATTTGG-AAACCTTCGATGCCTTTCTTTCAATTGTTTATGGCATAACTATAATCATT
66 CGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
2813 TTGGTGAGATTAGTCCACTGTGAAAG
130 TTGGTGAGATTAGTCCACTGTG-AAG
* * * **
2839 -TTTTAGTCTAATTTGGAACACTTGTTATTTTGTCGTCCGT-TC-GGGTCCATTAGTTCCGT-TT
1 TTTTTAG-CTCATTTGGAACACTTGTTATTTTG--GGCC-TATCGGGGCCCATTAGTGACGTATT
* *
2900 CGAATCGTCTTCGATTTGGCAAACCTCGATGC-TTTCTTTCAATTGTTTATGGCCTAA
62 -GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
Statistics
Matches: 1649, Mismatches: 146, Indels: 35
0.90 0.08 0.02
Matches are distributed among these distances:
152 5 0.00
153 285 0.17
154 1039 0.63
155 209 0.13
156 98 0.06
157 12 0.01
158 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAT
CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTT
TGGTGAGATTAGTCCACTGTGAAG
Done.