Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011649.1 Corchorus olitorius cultivar O-4 contig11682, 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: 2259
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Found at i:533 original size:154 final size:154
Alignment explanation
Indices: 15--2248 Score: 3045
Period size: 154 Copynumber: 14.5 Consensus size: 154
5 GATCCGTTTA
* *
15 AATCGACTTCGATTTAGCAAACCTCAAAAGCTTTTCTTTCCATTGTTTATCGCCTAACTATAATC
1 AATCGACTTCGATTTGGCAAACCTC-AAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
* * *
80 ATTTTGGTAAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAATTGTAATTTTGGGCCT
65 ATTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
145 TTCGGGGCCCATTAG-ATCCGTTTTG
130 TTCGGGGCCCATTAGTA-CCGTTTTG
* * * **
170 ATTCGACTTCGATTTAGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* *
235 -TTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAATTGTAATTTTGGGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
299 TCGGGGCCCATTAG-ATCCGTTTTG
131 TCGGGGCCCATTAGTA-CCGTTTTG
* * *
323 ATTCGACTTCGATTTAGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * * *
388 TTTTGCTAAGAT-TAGTCCGCTGTGAAATTTTTAGCTGATTTGGAACACTTGTTATTTTGGGCCT
66 TTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* *
452 TTCCGGGCTCATTAGTACCGTTTTG
130 TTCGGGGCCCATTAGTACCGTTTTG
*
477 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
542 TTTTGTTGAGATATGTCCACTGTGAAGTTTTTAGCTCGTTTGGAACACTTGTTATTTTGGGCCTC
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
607 TCGGGGCCCATTAG-ATCCGTTTTG
131 TCGGGGCCCATTAGTA-CCGTTTTG
* * **
631 AATCGACTTCGATTTAGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
696 TTTTGGTGAGATATGTCCACTGTGAAGTTATTAGCTCATTTAGAACACTTGTTATTTTGGGCTTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
*
761 TCGGGGCCCATTAGTTCCGTTTTG
131 TCGGGGCCCATTAGTACCGTTTTG
* * * * *
785 AATAGATTTCGATTTGGAAAACCTAAAAGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * *
850 TTTT-TTAGAGATATGTCCACTGTGAAATTTTTAGCTCATTTGGAACAGTTGTAATTTTGGGCCT
66 TTTTGGT-GAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
914 TTCGGGGCCCATTAGTACCGTTTTG
130 TTCGGGGCCCATTAGTACCGTTTTG
* *
939 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATGGCATAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* *
1004 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCGTTTGGAACACTAGTTATTTTGGGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
*
1069 TCGGGGCCCATTAG-ATCCGTTTTA
131 TCGGGGCCCATTAGTA-CCGTTTTG
* * *
1093 AATCGACTTCGATTTAGCAAACCTCAAAGTTTTTCTTTCCATTGTTTATGGCCTCACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
1158 TTTTGGTAAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAATTGTAATTTTGGGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
1223 TCGGGGCCCCATTAG-ATCCGTTTTTG
131 TCGGGG-CCCATTAGTA-CCG-TTTTG
**
1249 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGAACTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
*
1314 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTAGGGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
* *
1379 TCGGGGCGCATTAGTTCCGTTTTG
131 TCGGGGCCCATTAGTACCGTTTTG
* *
1403 AATAGACTTCGATTTGGCAAACCTAAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * *
1468 TTTTGGTGAGAT-TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTCGTTATTCTAGGACT
66 TTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* ** * * *
1532 ATCAAGGACCATTAGTTCCATTTTG
130 TTCGGGGCCCATTAGTACCGTTTTG
* * * * * * *
1557 AATCGTCTTCGATTTGGCAACCCTCAATGCTATCCGTTCCATCGTTTATGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * * * * *
1622 TTTTGGTCAGAT-TAGTCCACTGTGAA-TTTTTGGTTCACTAGGAACACTTTTTATTTTGGCCCT
66 TTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* *
1685 ATCGCGGCCCATTAGTGA-CGTTTTG
130 TTCGGGGCCCATTAGT-ACCGTTTTG
* *
1710 AATC-ATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
1 AATCGA-CTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
* * * *
1774 ATTTTGGTGAGGT-TAGTCCACTGTGAAGTATTTAGCTCAATTGGAACACTTGTTATTATGGGCC
65 ATTTTGGTGAGATAT-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
* * * * *
1838 TATCGGGGACCACTAATTCCGTTTTG
129 TTTCGGGGCCCATTAGTACCGTTTTG
* *
1864 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTCTAGGGCCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * *
1929 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAACTCTTTTGGAACAATTGTAATTTTGGGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
* *
1994 TCTGGGCCCATTAG-ATTCGTTTTG
131 TCGGGGCCCATTAGTA-CCGTTTTG
* * * * * *
2018 AATCGACTTTGATTTGGCAAACCTCAAAGCCTTTCTTTCAATTGTTCAAGGGCTAACTATAATCA
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * * *
2083 TTTTGGTGTGATATGTCCACTGTGAAGTTTTTAACTCTTTTGGAATAATTG-TA-----GGCCTT
66 TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
* *
2142 TCGGGGCCCATTAGTGA-CATATTG
131 TCGGGGCCCATTAGT-ACCGTTTTG
** * *
2166 AATCCTCTTAGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACCTATAAGC
1 AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAA-CTATAATC
2231 ATTTTGGTGAGATATGTC
65 ATTTTGGTGAGATATGTC
2249 AAAAGTGTAA
Statistics
Matches: 1859, Mismatches: 197, Indels: 52
0.88 0.09 0.02
Matches are distributed among these distances:
148 72 0.04
149 24 0.01
150 1 0.00
153 285 0.15
154 1294 0.70
155 52 0.03
156 131 0.07
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (154 bp):
AATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
TTTTGGTGAGATATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTT
TCGGGGCCCATTAGTACCGTTTTG
Done.