Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023662.1 Corchorus olitorius cultivar O-4 contig23695, 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: 7356
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:63 original size:30 final size:30
Alignment explanation
Indices: 1--1362 Score: 1633
Period size: 30 Copynumber: 45.1 Consensus size: 30
* *
1 GCAACGATCCTCAAACAAGATTAAACATAAA
1 GCAATGATCCTCAAACAGGATTAAA-ATAAA
*
32 ACAATGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
62 ACAATGATCCTCAAACAGGTTTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * * * * *
92 GTAACGATCCTCGACCAGGATTAAAATGAC
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
122 GCAATGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
152 GCAATAATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
182 GCAATGATCCTCAAACAGGATTAAAACAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* **
212 GCAATGATCCTCAAATACAATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * * *
242 GTACTGATCCTCAAACAGGATTAAAATGAT
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
272 GCGAAT-ATCCTCCACCAGGATTAAAATAAA
1 GC-AATGATCCTCAAACAGGATTAAAATAAA
* ** * *
302 GCAACGATCCTTGACCATGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
** * *
332 GCAACAATCCTCAACCACGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
362 GCAATGATCCTCAACCAGGATTAAAATAAAA
1 GCAATGATCCTCAAACAGGATTAAAAT-AAA
* *
393 GCAATGATCCTTAACCAGGATTAAAATGAAA
1 GCAATGATCCTCAAACAGGATTAAAAT-AAA
* * * *
424 GCGATGATCCTTAACCAGGATTAAAAACAAA
1 GCAATGATCCTCAAACAGGATT-AAAATAAA
* *
455 GCAATAATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
485 GCAATGATCCTCAAACAAGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
515 GCAACGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
545 GCAAAGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
575 GCAATGATCCTCAAACAAGATTAAACATAAA
1 GCAATGATCCTCAAACAGGATTAAA-ATAAA
*
606 GCAATGATCCTCAAACAGGATCAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
636 ACAATGATCCTCAAACAGGATTTAAAATAAA
1 GCAATGATCCTCAAACAGGA-TTAAAATAAA
* *
667 GCAATGATCCTCAACCAGGATTAAAACAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
697 GCAACGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
727 GCAAAGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* **
757 GCAAAGATCCTCAAACAGGATTAAAATGGA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* ** *
787 GTAACAATCCTCAACCAGGATTAAAAT-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
816 -C---GATCCTCAACCAGGATTAAAAGAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * * * * *
842 GTAACGATCCTCAACCAGAATTAAAATGAC
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
872 GCAATGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
902 GCAATGATCCTCAAACAGGATTAAAACAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
932 GCAATGATCCTCAAATAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * * *
962 GTAATGATCCTCAAACAGGAATAAAATGAT
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * *
992 GCGAAT-ATCCTCCACCAAGATTAAAATAAA
1 GC-AATGATCCTCAAACAGGATTAAAATAAA
** * *
1022 GCAGCGATCCTCGACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
** *
1052 GCAACAATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
1082 GTAATGATCCTCAACCAGGATTAAAATAAAA
1 GCAATGATCCTCAAACAGGATTAAAAT-AAA
* * *
1113 GCAATGATCCTTAACCAGGATTAAAAGGAAAGCGA
1 GCAATGATCCTCAAACAGGATTAAAA--TAA---A
* *
1148 TGATCAATAATCCTCAAACAGGATTAAAATGAA
1 -G--CAATGATCCTCAAACAGGATTAAAATAAA
*
1181 GCAATGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
1211 GCAATGATCCTCAAACAGGATTAACATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
1241 GCAATGACCCTCAAACAGGATTAACATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
1271 GCAATGATCCT-AAACCAGGATTAACATAAA
1 GCAATGATCCTCAAA-CAGGATTAAAATAAA
*
1301 GCAATGATCCTCAAACAGGATTAACATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
1331 GCAATGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
1361 GC
1 GC
1363 TGACAAAGTA
Statistics
Matches: 1167, Mismatches: 140, Indels: 49
0.86 0.10 0.04
Matches are distributed among these distances:
25 20 0.02
26 2 0.00
29 7 0.01
30 919 0.79
31 186 0.16
32 7 0.01
33 1 0.00
35 1 0.00
36 2 0.00
38 22 0.02
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.20
Consensus pattern (30 bp):
GCAATGATCCTCAAACAGGATTAAAATAAA
Found at i:1170 original size:38 final size:37
Alignment explanation
Indices: 1114--1189 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1104 AAAATAAAAG
* * * *
1114 CAATGATCCTTAACCAGGATTAAAAGGAAAGCGATGAT
1 CAATAATCCTCAAACAGGATTAAAAGG-AAGCAATGAT
*
1152 CAATAATCCTCAAACAGGATTAAAATGAAGCAATGAT
1 CAATAATCCTCAAACAGGATTAAAAGGAAGCAATGAT
1189 C
1 C
1190 CTCAACCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 10 0.30
38 23 0.70
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (37 bp):
CAATAATCCTCAAACAGGATTAAAAGGAAGCAATGAT
Found at i:1733 original size:36 final size:36
Alignment explanation
Indices: 1624--2144 Score: 551
Period size: 36 Copynumber: 14.9 Consensus size: 36
1614 CATTTTGCAG
* * *
1624 TCAATTGAACTAAACT-ACAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGA-AGAAAAGATCGCCCTGGA
* * * *
1660 T-ATACTGAACTAAATTG-AGGAAAGATCGCCCTCGA
1 TCA-ACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
1695 TCAAATGAAATAAACTGAAGAAAAGATTGCCCCGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
1731 TCAATTGAAATAAACTGAAGAAAAGATCGCCTTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
1767 T---C-------AACTGAAGAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
1793 TCAATTGAAATAAACTGTAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
1829 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
1865 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGAA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
1901 TTAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
1937 TCAACTGAAATAAACTGAAG-AAACACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
1972 TCAACTGAAATAAGCTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
2007 TCAACT-AAATAAACTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
2041 TCAATTGCAATAAATTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
2077 TCAATTGAAATAAACTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
2112 TCAACT-AAAGTGAATTGAAG-AAAGACCGCCCTG
1 TCAACTGAAA-TAAACTGAAGAAAAGATCGCCCTG
2145 TGTCGGCTGA
Statistics
Matches: 418, Mismatches: 50, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.06
34 35 0.08
35 129 0.31
36 231 0.55
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:1772 original size:26 final size:26
Alignment explanation
Indices: 1743--1801 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
1733 AATTGAAATA
*
1743 AACTGAAGAAAAGATCGCCTTGGATC
1 AACTGAAGAAAAGATCGCCCTGGATC
*
1769 AACTGAAGAAAGGATCGCCCTGGATC
1 AACTGAAGAAAAGATCGCCCTGGATC
*
1795 AATTGAA
1 AACTGAA
1802 ATAAACTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (26 bp):
AACTGAAGAAAAGATCGCCCTGGATC
Found at i:2067 original size:140 final size:140
Alignment explanation
Indices: 1769--2201 Score: 564
Period size: 140 Copynumber: 3.1 Consensus size: 140
1759 GCCTTGGATC
* * * *
1769 AACTGAAGAAAGGATCGCCCTGGATCAATTGAAATAAACTGTAGAAAAGATCGCCCTGGATCAAC
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
* * * *
1834 TGAAATAAACTGAAGAAAAGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAAGATCGCCCTG
65 TGAAAT-AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG-AAAGACCGCCCTG
** *
1899 AATTAATTGAAATA
127 GGTCAATTGAAATA
* *
1913 AACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAACACCGCCCTGGGTCAACT
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACT
1978 GAAATAAGCTGAAGAAAGACCGCCCTGGGTCAACT-AAATAAACTGAAGAAAGACCGCCCTGGGT
66 GAAATAA-CTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGT
*
2042 CAATTGCAATA
130 CAATTGAAATA
*
2053 AATTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACT
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACT
* * ** * * * *
2118 -AAAGTGAATTGAAGAAAGACCGCCCTGTGTCGGCTGAAATAGACTGAATAAAGACCGTCTTGGG
66 GAAA-T-AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
*
2182 TCAATTGAAATG
129 TCAATTGAAATA
*
2194 AACCGAAG
1 AACTGAAG
2202 CATCTGAAAT
Statistics
Matches: 256, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
139 3 0.01
140 108 0.42
141 55 0.21
142 20 0.08
143 29 0.11
144 41 0.16
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (140 bp):
AACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACT
GAAATAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTC
AATTGAAATA
Found at i:2171 original size:35 final size:35
Alignment explanation
Indices: 1769--2201 Score: 465
Period size: 36 Copynumber: 12.2 Consensus size: 35
1759 GCCTTGGATC
* * *
1769 AACTGAAGAAAGGATCGCCCTGGATCAATTGAAATA
1 AACTGAAGAAA-GACCGCCCTGGGTCAACTGAAATA
* * *
1805 AACTGTAGAAAAGATCGCCCTGGATCAACTGAAATA
1 AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATA
* * *
1841 AACTGAAGAAAAGATCGCCCTAGATCAACTGAAATA
1 AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATA
* ** * *
1877 AACTGAAGAAAAGATCGCCCTGAATTAATTGAAATA
1 AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATA
* *
1913 AACTGAAGAAAAGATCGCCCTGGATCAACTGAAATA
1 AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATA
*
1949 AACTGAAGAAACACCGCCCTGGGTCAACTGAAATA
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
*
1984 AGCTGAAGAAAGACCGCCCTGGGTCAACT-AAATA
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
* *
2018 AACTGAAGAAAGACCGCCCTGGGTCAATTGCAATA
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
* * * *
2053 AATTGAAGAAAAGATCGCCCTGGATCAATTGAAATA
1 AACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATA
*
2089 AACTGAAGAAAGACCGCCCTGGGTCAACT-AAAGTG
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAA-TA
* * **
2124 AATTGAAGAAAGACCGCCCTGTGTCGGCTGAAATA
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
* * * * * *
2159 GACTGAATAAAGACCGTCTTGGGTCAATTGAAATG
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
*
2194 AACCGAAG
1 AACTGAAG
2202 CATCTGAAAT
Statistics
Matches: 346, Mismatches: 46, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
34 35 0.10
35 137 0.40
36 171 0.49
37 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (35 bp):
AACTGAAGAAAGACCGCCCTGGGTCAACTGAAATA
Done.