Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011741.1 Corchorus olitorius cultivar O-4 contig11774, 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: 2949
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Found at i:282 original size:154 final size:153
Alignment explanation
Indices: 9--2946 Score: 4174
Period size: 154 Copynumber: 19.1 Consensus size: 153
1 ATTAGTTC
* * * * *
9 CGTTTTGAATCGTCTTCGATTTTGCCAACCCTGAATGC-TTTC-TTCCAATGTTCT-CGGACCTA
1 CGTTTTGAATCGTCTTCGA-TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT-TATGGA-CTA
*
71 ACTATAATCTATTTTGGT-ACGATTAGTCAACT-TGAAGTTTTTAGCTCATTTGGAACACTTGTT
63 ACTATAATC-ATTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
134 ATTTTGGGCCTTTCGGGGCCCGATTAGTT
126 ATTTTGGGCCTATCGGGGCCC-ATTAGTA
* * *
163 CTGTTTTGAATCGTCTTCGATTTGGCAGACCTCAAAGCTTTTCTTTCCACT-TTTATGGACTAAC
1 C-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
227 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
292 TGGGCCTATCGCGGACCC-TTAGTGA
130 TGGGCCTATCG-GGGCCCATTAGT-A
* * *
317 CGTTTTGAATCGTTTTCGATTTGACAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
*
382 ATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* *
447 GGACCTATCGGTGCCCATTAGTGA
131 GGGCCTATCGGGGCCCATTAGT-A
* * * * *
471 CGTTTTGAATCGTCTTCGATTTGGCAAATCTCAAAGCTTTTCTTT-AAGTTTTTTATGGCCTAAC
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGACTAAC
* * * *
535 TATAATCATTTTGGTGAGATTAGTCCACCGTGAAGTTTTTAGCTCAATTAGAACAGTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
600 TGGACCTATCGGGGCCCATTAGTTC
130 TGGGCCTATCGGGGCCCATTAG-TA
* * *
625 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTATTTATGTACTAACC
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* * *
690 GTAATCATTTTGGTGAGATTAGACCACTGTGATGTTTTTAGCTCATTTGGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
755 GGGCCTAT-GTGGGCCCATTAGTGA
131 GGGCCTATCG-GGGCCCATTAGT-A
* * * *
779 CGTTTTGAATCGTTTTCGATTTGGCAAACCTCAAAGCTTTTCTTT-AAGTTGTTTATGGCCTAAC
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGACTAAC
* *
843 TATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
908 TGGGCCTATCGGGGCCCATTAGTT
130 TGGGCCTATCGGGGCCCATTAGTA
* * *
932 CTGTTTTGTATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 C-GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
* *
997 TATAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGATCACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1062 TGGGCCTATCGGGGCCCATTAGTGA
130 TGGGCCTATCGGGGCCCATTAGT-A
*
1087 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* * * *
1152 ATAATC-TATTTGGTGACATTAGTCCATTGTGAAGTTCTTAGCTCATTTGGATCACTTGTTATTT
66 ATAATCAT-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1216 TGGGCCTATCGGGGCCCATTAGTGA
130 TGGGCCTATCGGGGCCCATTAGT-A
*
1241 CATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
1306 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* *
1371 GGGCCTATTGGGGCCCCATTAGTTC
131 GGGCCTATCGGGG-CCCATTAG-TA
*
1396 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
*
1461 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCATCTGGAACACTTGTTATTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACACTTGTTATTT
* * *
1526 TAGGCCTAGTCGGGGCCTATTAGTTTC
130 TGGGCCTA-TCGGGGCCCATTAG--TA
* * * *
1553 CGTTTTGAATCGTCTTCGGTTTTTAGGAAAACCTACAAAGTCTTTTC-TTCCTATTTTTTATGGA
1 CGTTTTGAATCGTCTTC-G-ATTT-GGCAAACCT-CAATG-CTTTTCTTTCC-ATTGTTTATGGA
* *
1617 CTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTCTTAGCTCATTTGGAACACTTGT
60 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
1682 TATTTTGGACCTATCGGGGCCTATTAGTA
125 TATTTTGGGCCTATCGGGGCCCATTAGTA
* * *
1711 CCGTTTTGAATCGTCTTCGATTTGGAAAACCTCAAAGCTTTTCTTTCCATTTTTTATGGACTAAC
1 -CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
* * * *
1776 TATAATCATTTTGGTAAGATTAGTACACTGTGAAGTTCTTAGCTCATTTGGATCACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1841 TGGGCCTATCGGGGCCCATTAGTGA
130 TGGGCCTATCGGGGCCCATTAGT-A
* * *
1866 CATTTTTAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCATTGTTTATGGACTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* *
1931 AAAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTTATTTGGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
1996 GGGCCTATCGGGGCCCATTAGTGA
131 GGGCCTATCGGGGCCCATTAGT-A
* * *
2020 CGTTTTGAATCGTCTTCGATTTGGCTAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACC
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* * * *
2085 ATAATCAATTTGGTGAGATTAGTACACTGTGAAGTTCTTAGCTCATTTGGATCACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* *
2150 GGGCCTAGTCGGGGCCCGATTAAATC
131 GGGCCTA-TCGGGGCCC-ATT-AGTA
* * * *
2176 CGTTTTAAAGTCGTCTTCGATTTGGCAAACCTAAACGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CGTTTTGAA-TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
* *
2241 TATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
2306 TGGGCCTATCGGGGCCTATTAGTTC
130 TGGGCCTATCGGGGCCCATTAG-TA
* * * *
2331 CGTTTTGAATTGTCTTCGATTTGGAAAACCTCAAAGCTTTTCTTTCCATTTTTTATGGACTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* * * *
2396 ATAATCATTTTGGTGAGATTAGTACACTGGGAAGTTCTTAGCTCATTTGGATCACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
2461 GGGCCTATCGGGGCCCATTAGTGA
131 GGGCCTATCGGGGCCCATTAGT-A
* * * * *
2485 CATTTTGAATAGTCTTCGATTTGGCAAACCTAAATGCTTTTCTTTCCATTGTTAAT-GACAAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
* * *
2549 AAAATCATTTTGGTGAGATTAGTCCACTGTGAAGTGTTTAGCTCATTTCGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
*
2614 GGACCTATCGGGGCCCATTAGTGA
131 GGGCCTATCGGGGCCCATTAGT-A
*
2638 CGTTTTGAATCGTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CGTTTTGAATCG-TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAAC
*
2703 TATAATCAATTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * *
2767 TGGGCCTATAGGGGCCCCTTAGTTC
130 TGGGCCTATCGGGGCCCATTAG-TA
* * *
2792 CGTTTTGATTCCTCTTCGATTTGGCAACCCTCAATGC-TTTC-TTCCA-TG-TTAT-G-CGTAAC
1 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGAC-TAAC
* *
2851 TATAATCATTTT-GTGGGATTAGTCCACTGTGAAGTATTTAGCTCATTTGGAACTACTTG-TATT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATT
* * *
2914 TTGGGCCTATAGGGGCCCCTTAGTC
129 TTGGGCCTATCGGGGCCCATTAGTA
2939 CGTTTTGA
1 CGTTTTGA
2947 TTC
Statistics
Matches: 2541, Mismatches: 195, Indels: 103
0.90 0.07 0.04
Matches are distributed among these distances:
147 32 0.01
148 60 0.02
149 9 0.00
150 2 0.00
151 5 0.00
152 4 0.00
153 200 0.08
154 1645 0.65
155 214 0.08
156 78 0.03
157 150 0.06
158 3 0.00
159 20 0.01
160 22 0.01
161 42 0.02
162 55 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (153 bp):
CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACT
ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
GGGCCTATCGGGGCCCATTAGTA
Done.