Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014948.1 Corchorus olitorius cultivar O-4 contig14981, 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: 2196
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Found at i:285 original size:154 final size:155
Alignment explanation
Indices: 1--2196 Score: 1760
Period size: 154 Copynumber: 13.7 Consensus size: 155
* * * *
1 CGAAGACGATTCAAAACGTTACTAATGGTCCCCGATTGCCCCAAAATAACAAGTGTTCCATATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * *
66 GCAAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
131 GAAAGGCATCGAAGG-TTGCCAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
* * * *
155 CGAAGACGATTCCAAACGTCACTAATGGGCCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
*
220 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * **
285 GAAAAGCATTG-CGGTTTGAAAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
* *
309 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGACCCAAAATAACAAGTGTTCCATATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * * * *
374 GCTAAAAACTTCACAGTGTACTAATCTTACTAAAATGATTTTAGTTAGGCCATAAACAATAGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
439 GAAAAGCATCGAAGG-TTGCCAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
* * *
463 CGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGGCCCGAAATAACGAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
*
528 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* **
593 GAAAAGCATTG-AGGTTTGAAAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
617 CGAAGACGATTCAAAACGTCACTAAT-GTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
681 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAGTTATAGTTAGGCCATAAACAATGGAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA-TTATAGTTAGGCCATAAACAATGGAA
*
746 AGAAAGGCATCGAAGG-TTGCCAAAT
130 AGAAAAGCATCGAAGGTTTGCCAAAT
* * **
771 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCGAAAATAACAAGGGCCCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
** *
836 GCTAAAAACTTCACAGTGGA-TAAATCTCACCAAAATGATTATAGTTAGATCATAAACTATGGAA
66 GCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* *
900 AGAAAAGCAT-TAAGGTTTTCCAAAT
130 AGAAAAGCATCGAAGGTTTGCCAAAT
* * * **** * *
925 CGAAGACGATTCAGACTCATC-TCACCAAAATGATTATAG-TCAGGCCATAAACAATGGAAAGAA
1 CGAAGACGATTCA-A---AACGTCA-C-TAATGGTCCCCGAT-AGGCC--CAA-AAT----A-AC
* ** * * ****
988 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACTGAACTAATGGGTCTCCGGT-AGGCCC
51 AAG---T---G-TT-CCAAAT-G-AG-C---TAAAAACTTCAC-AGT-GGACTAATCTCA---CC
* ** * * * * *** * * *
1052 AAAATAACAAGT-GTTCCAAATGAGCTAAAAACTTCACTGTGGACA-AATCTCACCAAAATGATT
97 AAAATGATTA-TAGTT----A-G-GCCATAAA---CA--ATGGAAAGAAAAGCATC-GAA-GGTT
** **
1115 ATAG-TTAGG
148 -T-GCCAAAT
* * * ** * * * ** *
1124 CCATAAACAATGGAAAGAAAAG-CATTGA-GGTTTCCCAAATCGA-AGACGATTCAAAACGTCAC
1 CGA-AGACGAT--TCA-AAACGTCACTAATGG--TCCC----CGATAG--G-CCCAAAA--TAAC
* * ** ** * ** * * * *
1186 TAAGGGTCCCCGAT-AGGCCCAAAA--TAACAAGTGTTCCAA-ATGAGCTAAAA--ACTTCACAC
51 -AAGTGTTCCAAATGA-GCTAAAAACTTCAC-AGTGGACTAATCTCA-CCAAAATGA-TT---A-
* * ** ** ** * * * *** **
1245 TGGACTAATCTCACCAA-AAT-GATTATAGTTAGGCCTTACACAATGGAAAGAAAAGCAT
107 TAG-TTAGGC-CATAAACAATGGA--A-AGAAAAG-CAT-C-GAA-GGTTTGCCAA--AT
* * * * * * * * * ** ** *
1303 TGAAGTTTGCCAAATCGAAGACGAT-TCAAAAGCTGAGCTAATGGGCCCCGAAAGGCCCAAAATA
1 CGAA----GACGATTC-AAAACG-TCACTAATGGT-CCCCGATAGGCCC----------AAAATA
**
1367 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAG
49 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* * *
1432 GACATAAACAATGGAAAAAAAAAGCATTG-AGGTTTGCCAAAT
114 GCCATAAACAATGG-AAAGAAAAGCATCGAAGGTTTGCCAAAT
* **
1474 CGAAGACGATTCAAAACGTCACTAATGGTTCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
1539 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1604 GAAAGGCATCGAAGG-TTGCCAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
* * * *
1628 CGAAGACGATTCAGAACATCACTAATGGTCTCCGATTGGCCCAAAATAACAAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * * *
1693 GCTAAAAACTTTACAGTGGACAAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGAAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
1758 GAAAAGCATTG-AGGTTTGCCAAAC
131 GAAAAGCATCGAAGGTTTGCCAAAT
* *
1782 CGAAGACGATTCAAAACGTCACTAATGGTTCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
*
1847 GCTACAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1912 GAAAGGCATCGAAGG-TTGCCAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
*
1936 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAAGCCC-AAAT-ACAAGTG-TCCAAATGA
1 CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
* *
1998 GCTAAAAACCTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAA
66 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
2063 GAAAGGCATCGAAGG-TTGCCAAAT
131 GAAAAGCATCGAAGGTTTGCCAAAT
* *
2087 CGAAGACGAGTTCAAAACGTCACTAATGGTCTCCGATAGGCCCAAAATAACGAGTGTTCCAAATG
1 CGAAGACGA-TTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
2152 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAG
65 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
Statistics
Matches: 1629, Mismatches: 281, Indels: 263
0.75 0.13 0.12
Matches are distributed among these distances:
151 104 0.06
152 38 0.02
153 93 0.06
154 890 0.55
155 215 0.13
157 3 0.00
158 4 0.00
159 11 0.01
161 2 0.00
162 3 0.00
165 11 0.01
166 11 0.01
167 9 0.01
171 5 0.00
172 2 0.00
173 7 0.00
174 1 0.00
175 9 0.01
176 3 0.00
177 7 0.00
178 18 0.01
179 10 0.01
180 12 0.01
181 15 0.01
182 28 0.02
183 25 0.02
184 9 0.01
185 22 0.01
186 1 0.00
188 2 0.00
189 2 0.00
190 1 0.00
191 8 0.00
192 1 0.00
193 1 0.00
194 1 0.00
195 4 0.00
196 6 0.00
197 3 0.00
198 5 0.00
199 10 0.01
200 5 0.00
201 4 0.00
202 6 0.00
203 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (155 bp):
CGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCATCGAAGGTTTGCCAAAT
Found at i:1000 original size:84 final size:84
Alignment explanation
Indices: 859--1021 Score: 272
Period size: 84 Copynumber: 1.9 Consensus size: 84
849 CAGTGGATAA
* * * *
859 ATCTCACCAAAATGATTATAGTTAGATCATAAACTATGGAAAGAAAAGCATTAAGGTTTTCCAAA
1 ATCTCACCAAAATGATTATAGTCAGACCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCCAAA
924 TCGAAGACGATTCAGACTC
66 TCGAAGACGATTCAGACTC
* *
943 ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTCAGACCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCCAAA
1008 TCGAAGACGATTCA
66 TCGAAGACGATTCA
1022 AAACTGAACT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (84 bp):
ATCTCACCAAAATGATTATAGTCAGACCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCCAAA
TCGAAGACGATTCAGACTC
Found at i:1131 original size:239 final size:239
Alignment explanation
Indices: 699--1176 Score: 746
Period size: 239 Copynumber: 2.0 Consensus size: 239
689 CTTCACAGTG
* *
699 GACTAATCTCACCAAAATGAGTTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGGTT
1 GACTAATCTCACCAAAATGAGTTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTT
* *
764 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCGAAAATAACAAGGGCCC
66 GCCAAATCGAAGACGATTCAAAACGTAACTAATGGTCCCCGATAGGCCCAAAATAACAAGGGCCC
* * *
829 CAAATGAGCTAAAAACTTCACAGTGGATAAATCTCACCAAAATGATTATAGTTAGATCATAAACT
131 CAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGACCATAAACA
*
894 ATGGAAAGAAAAGCATTAAGGTTTTCCAAATCGAAGACGATTCA
196 ATGGAAAGAAAAGCATTAAGGTTTCCCAAATCGAAGACGATTCA
* *
938 GACTCATCTCACCAAAATGA-TTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTT
1 GACTAATCTCACCAAAATGAGTTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATCGAAGG-T
* * *
1001 TGCCAAATCGAAGACGATTCAAAAC-TGAACTAATGGGTCTCCGGTAGGCCCAAAATAACAAGTG
65 TGCCAAATCGAAGACGATTCAAAACGT-AACTAAT-GGTCCCCGATAGGCCCAAAATAACAAGGG
** * *
1065 TTCCAAATGAGCTAAAAACTTCACTGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAA
128 CCCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGACCATAA
*
1130 ACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCA
193 ACAATGGAAAGAAAAGCATTAAGGTTTCCCAAATCGAAGACGATTCA
1177 AAACGTCACT
Statistics
Matches: 218, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
237 4 0.02
238 67 0.31
239 147 0.67
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (239 bp):
GACTAATCTCACCAAAATGAGTTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTT
GCCAAATCGAAGACGATTCAAAACGTAACTAATGGTCCCCGATAGGCCCAAAATAACAAGGGCCC
CAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGACCATAAACA
ATGGAAAGAAAAGCATTAAGGTTTCCCAAATCGAAGACGATTCA
Found at i:1499 original size:155 final size:154
Alignment explanation
Indices: 938--2196 Score: 1915
Period size: 154 Copynumber: 8.2 Consensus size: 154
928 AGACGATTCA
* *
938 GACTCATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
* * *
1003 CCAAATCGAAGACGATTCAAAAC-TGAACTAATGGGTCTCCGGTAGGCCCAAAATAACAAGTGTT
66 CCAAATCGAAGACGATTCAAAACGT-CACTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTT
*
1067 CCAAATGAGCTAAAAACTTCACTGTG
129 CCAAATGAGCTAAAAACTTCACAGTG
* *
1093 GACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
1158 CCAAATCGAAGACGATTCAAAACGTCACTAA-GGGTCCCCGATAGGCCCAAAATAACAAGTGTTC
66 CCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTTC
*
1222 CAAATGAGCTAAAAACTTCACACTG
130 CAAATGAGCTAAAAACTTCACAGTG
* * *
1247 GACTAATCTCACCAAAATGATTATAGTTAGGCCTTACACAATGGAAAGAAAAGCATTGAAGTTTG
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
* *
1312 CCAAATCGAAGACGATTCAAAA-GCTGAGCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTT
66 CCAAATCGAAGACGATTCAAAACG-TCA-CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
1376 CCAAATGAGCTAAAAACTTCACAGTG
129 CCAAATGAGCTAAAAACTTCACAGTG
** * *
1402 GACTAATCTCACCAAAATGATTATAAATAGGACATAAACAATGGAAAAAAAAAGCATTGAGGTTT
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGTTT
** **
1467 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGTTCCTAATAGGCCCAAAATAACAAGTGTTC
65 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
1532 CAAATGAGCTAAAAACTTCACAGTG
130 CAAATGAGCTAAAAACTTCACAGTG
* *
1557 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGG-TT
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTT
* * * * *
1621 GCCAAATCGAAGACGATTCAGAACATCACTAATGGTCTCCGATTGGCCCAAAATAACAAGTGTTC
65 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
*
1686 CAAATGAGCTAAAAACTTTACAGTG
130 CAAATGAGCTAAAAACTTCACAGTG
* * *
1711 GACAAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTG
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
* ** *
1776 CCAAACCGAAGACGATTCAAAACGTCACTAATGGTTCGCGATAGGCCCAAAATAACAAGTGTTCC
66 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
*
1841 AAATGAGCTACAAACTTCACAGTG
131 AAATGAGCTAAAAACTTCACAGTG
* *
1865 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGG-TT
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTT
* *
1929 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAAGCCC-AAAT-ACAAGTG-TC
65 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
*
1991 CAAATGAGCTAAAAACCTCACAGTG
130 CAAATGAGCTAAAAACTTCACAGTG
* * *
2016 GACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAGGCATCGAAGG-TT
1 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTT
* * *
2080 GCCAAATCGAAGACGAGTTCAAAACGTCACTAATGGTCTCCGATAGGCCCAAAATAACGAGTGTT
65 GCCAAATCGAAGACGA-TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
2145 CCAAATGAGCTAAAAACTTCACAGTG
129 CCAAATGAGCTAAAAACTTCACAGTG
*
2171 GACTAATCTCACCAAAATTATTATAG
1 GACTAATCTCACCAAAATGATTATAG
Statistics
Matches: 1016, Mismatches: 75, Indels: 26
0.91 0.07 0.02
Matches are distributed among these distances:
151 104 0.10
152 38 0.04
153 12 0.01
154 475 0.47
155 339 0.33
156 47 0.05
157 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
AAATGAGCTAAAAACTTCACAGTG
Done.