Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011747.1 Corchorus olitorius cultivar O-4 contig11780, 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: 1994
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:883 original size:154 final size:154
Alignment explanation
Indices: 8--1831 Score: 2522
Period size: 154 Copynumber: 11.9 Consensus size: 154
1 AAGCATC
* *
8 GAGGGTTGCCAAACTACGAACGTACGATTCAAAACGGTAACGTAATGGG-CCCGAAAGGCCTAAA
1 GAGGTTTGCCAAA-T-CGAA-GT-CGATTCAAAACGG-AAC-TAATGGGCCCCGAAAGGCCCAAA
*
72 ATAACGAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-TAATCTCACCAAAATGATTATAG
60 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAT-ATCTCACCAAAATGATTATAG
* * * *
136 ATAGGCCATAAACAATGGAACGAAAAGCATC
124 TTAGGCCATAAACAATGGAAAGAAAAGCTTT
* ** * * * * *
167 GAGGGTTGCCAAATCGAAGAAGATTTAAAACGGAAACTAAATGGTCCTCGATATGCCCAAAATAA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGG-AACT-AATGGGCCCCGAAAGGCCCAAAATAA
232 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-TAATCTCACCAAAATGATTATAGTTAG
64 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAT-ATCTCACCAAAATGATTATAGTTAG
* *
296 GCCATAAACAATGGAAACAAAAGCATT
128 GCCATAAACAATGGAAAGAAAAGCTTT
* ** *
323 GAGGTTTGCCAAATCGAAAGACGAATTACAAAACGTCACTAATGGGCCCCGATAGGCCC-AAAT-
1 GAGGTTTGCCAAATCG-AAGTCG-ATT-CAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATA
*
386 AC-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACA-ATCTTACCAAAATGATTATAGTTAG
63 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG
* * *
449 GCCTTACACAATGGAAAG-AAAGCATT
128 GCCATAAACAATGGAAAGAAAAGCTTT
* * *** * * *
475 GAAGTTTGCCAAATCGAAGACGATTC-AAACATCACTAATGGTCTCCGATAGGCCC-AAATAACA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* **
538 AGTGTTCCATATGAGCT--AAACTTCACAGTGGACATATCTCACC-AAATGATTATAGTTAGTTC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
* *
600 AT-AAGAATGG-AAG-AAAGTTTT
131 ATAAACAATGGAAAGAAAAGCTTT
* *
621 GAGGTTTGCCAAATCGAAGTCGATTC-AAACGGATCTAAT-GGCCCCGAAAGGCCC-AAATTACA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * * * *
683 ATTGTTCCAAAAGAGTTAAGAACTTCACAGTGGACATATATCACCAAAATGATTATAGTTAGGCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
748 ATAAACAATGGAAAGAAAAGCTTT
131 ATAAACAATGGAAAGAAAAGCTTT
* * *
772 GAGGTTTGCCAAATCGAAGTCGATTCAATATGGAACTAATGGGCCCCGAAAGGCCCAAAATAAGA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * *
837 AGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACATATCACACCAAAATGATTATAGTTAGTCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
*
902 ATAAACAATGGAAAGAAAAGTTTT
131 ATAAACAATGGAAAGAAAAGCTTT
** * *
926 GAGGTTTTTCAAATCGAAGTCGATTCAAAATGGAACTGATGGGCCCCGAAAGGCCCAAAAT-ACA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * *
990 ATTGTTCCAAAAGAGTTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
1055 ATAAACAATGGAAAGAAAAGCTTT
131 ATAAACAATGGAAAGAAAAGCTTT
* * *
1079 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAAGGGGCCCCGAAAGGCCCAAAATTACA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * * *
1144 ATTGTTCCAAAAGAGTTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGATAGGCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
1209 ATAAACAATGGAAAGAAAAGCTTT
131 ATAAACAATGGAAAGAAAAGCTTT
* * * *
1233 GAGGTTTGCCAAATCGAATTCGATTCAAAAC-GAATCTAATGGGCCTCGGAAGGCCCAAAATTAC
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAA-CTAATGGGCCCCGAAAGGCCCAAAATAAC
* * * *
1297 AATTGTTCCAAAAGAGTTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGATAGGC
65 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGC
1362 CATAAACAATGGAAAGAAAAGCTTT
130 CATAAACAATGGAAAGAAAAGCTTT
* * *
1387 GTGGTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAAGA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * *
1452 AGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACATATCACACCAAAATGATTATAGTTAGTCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
*
1517 ATAAACAATGGAAAGAGAAGCTTT
131 ATAAACAATGGAAAGAAAAGCTTT
* *
1541 GAGGTTTGCCAAATCGAAGTCGATTCCAAAC-GAATCTAATGGGCCCCGAAAGGCCCAAAATTAC
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAA-CTAATGGGCCCCGAAAGGCCCAAAATAAC
* * * *
1605 AATTGTTCCAAATGAGGTAAAAACTTAACAATGGACATATCTCACCAAAATGATTATAGTTAGGC
65 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGC
1670 CATAAACAATGGAAAGAAAAGCTTT
130 CATAAACAATGGAAAGAAAAGCTTT
* * *
1695 GAGGTTTGCCAAATCGAAGTCGATACAAAATGGAACTAATGGTCCCCGAAAGGCCCAAAATAACA
1 GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * *
1760 AGTGTTCCAAATGAGCTAAAAACATCACAGTGGACATATCTCACCAAAACGATTATTGTTAGGCC
66 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
1825 ATAAACA
131 ATAAACA
1832 TATCTCACCA
Statistics
Matches: 1505, Mismatches: 137, Indels: 51
0.89 0.08 0.03
Matches are distributed among these distances:
145 32 0.02
146 42 0.03
147 30 0.02
148 84 0.06
149 17 0.01
150 22 0.01
151 39 0.03
152 33 0.02
153 198 0.13
154 809 0.54
155 27 0.02
156 121 0.08
157 25 0.02
158 7 0.00
159 19 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
GAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCC
ATAAACAATGGAAAGAAAAGCTTT
Found at i:1833 original size:36 final size:36
Alignment explanation
Indices: 1793--1867 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
1783 ATCACAGTGG
*
1793 ACATATCTCACCAAAACGATTATTGTTAGGCCATAA
1 ACATATCTCACCAAAACGATTATTGTTAAGCCATAA
*
1829 ACATATCTCACCAAAATGATTATTGTTAAGCCATAA
1 ACATATCTCACCAAAACGATTATTGTTAAGCCATAA
1865 ACA
1 ACA
1868 ACTTAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (36 bp):
ACATATCTCACCAAAACGATTATTGTTAAGCCATAA
Found at i:1878 original size:190 final size:190
Alignment explanation
Indices: 1639--1994 Score: 579
Period size: 190 Copynumber: 1.9 Consensus size: 190
1629 TTAACAATGG
* *
1639 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
1 ACATATCTCACCAAAATGATTATAGTTAAGCCATAAACAATGGAAAGAAAAGATTTGAGGTTTGC
* * * *
1704 CAAATCGAAGTCGATACAAAATGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATACAAAACGGAACTAAGGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
1769 AATGAGCTAAAAACATCACAGTGGACATATCTCACCAAAACGATTATTGTTAGGCCATAA
131 AATGAGCTAAAAACATCACAGTGGACATATCTCACCAAAACGATTATTGTTAGGCCATAA
* *
1829 ACATATCTCACCAAAATGATTATTGTTAAGCCATAAACAACT-TAAAGAAAAGATTTGAGGTTTG
1 ACATATCTCACCAAAATGATTATAGTTAAGCCATAAACAA-TGGAAAGAAAAGATTTGAGGTTTG
* * * *
1893 CCAAATTGAAGACGATTCAAAGCGGAACTAAGGGGCCCCGAAAGGCCCAAAATAAGAAGTGTTCC
65 CCAAATCGAAGACGATACAAAACGGAACTAAGGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCC
*
1958 AAATGAGCTAAAAACTTCACAGTGGACATATCTCACC
130 AAATGAGCTAAAAACATCACAGTGGACATATCTCACC
Statistics
Matches: 152, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 151 0.99
191 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (190 bp):
ACATATCTCACCAAAATGATTATAGTTAAGCCATAAACAATGGAAAGAAAAGATTTGAGGTTTGC
CAAATCGAAGACGATACAAAACGGAACTAAGGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACATCACAGTGGACATATCTCACCAAAACGATTATTGTTAGGCCATAA
Done.