Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020641.1 Corchorus olitorius cultivar O-4 contig20674, 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: 11322
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:271 original size:40 final size:39
Alignment explanation
Indices: 186--1087 Score: 528
Period size: 40 Copynumber: 23.4 Consensus size: 39
176 CCTAAATCAG
* * * * *
186 GATCCTGAGTTGGATGCTGAAATCAACTGAT-AAGCCATT
1 GATCCTGAATAGGATTCTGAAATTAACTGATAAAG-CAAT
* * * *
225 GGTCCTGAATAGGATTTTTGAAATTGACTGATAAAGCAAG
1 GATCCTGAATAGGA-TTCTGAAATTAACTGATAAAGCAAT
* * *
265 GATCCTGAACAGGATTCTGAAATTGACTGATAAAGCAAG
1 GATCCTGAATAGGATTCTGAAATTAACTGATAAAGCAAT
* **
304 GATCCTGAATAGGATTCTGAAAAGTGTCTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTG-AAATTAAC-TGATAAAGCAAT
* * *
345 GATCCTGAGTAGGATTCTGAAATTAATTTGATAAAGCTAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
* *
385 GATCCTGAATAGGATTCTAAAATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
* * *
425 GATCCTGATTAGGATTGTG--ATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * *
463 GATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCTAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
503 GATCCTGAATAGGATTCTG-AA-T---T--T-----AAT
1 GATCCTGAATAGGATTCTGAAATTAACTGATAAAGCAAT
* * ** *
530 GATCCTGAGTAGGATTCTGAAATTGACCAATAAAGAAAT
1 GATCCTGAATAGGATTCTGAAATTAACTGATAAAGCAAT
* * **
569 GATCCTGAATAGGATTTTGAAAAGTGGCTCGATAAAGCAAT
1 GATCCTGAATAGGATTCTG-AAATTAACT-GATAAAGCAAT
*
610 GATCCT-AAGTAGGATTCTGAAATTAATTTGATAAAGCAAT
1 GATCCTGAA-TAGGATTCTGAAATTAA-CTGATAAAGCAAT
*
650 GATCATGAATAGGATTCT-AAA-T---T--T-----AAT
1 GATCCTGAATAGGATTCTGAAATTAACTGATAAAGCAAT
* * * *
677 GATCCTGAGTAGGATTTTGAAATTAATTTGATAAAGTAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * * * *
717 GATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * * *
757 GATCCTGAGCAGGGTT-TGAAAATTAATTTGATAAA-AAGAT
1 GATCCTGAATAGGATTCTG-AAATTAA-CTGATAAAGCA-AT
** * * *
797 GATCCTGAGCAAGATTC-GAAATTAATTTGATAAA-AAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * * *
835 GATCCTGAGCAGGATTTTGAAATTAATTTGATAAAACAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * *
875 GATCCTGAGCAGGGTT-TGAAATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * * *
914 GATCCTGAGCAGGGTT-TGAAATTAATTTGATAAA-AAGAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCA-AT
** * *
953 GATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
** * * *
993 GATCCTGAGCAGGGTT-TGAAATTAATTTGATAAA-AAGAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCA-AT
* ** * *
1032 GATTCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAAT
1 GATCCTGAATAGGATTCTGAAATTAA-CTGATAAAGCAAT
*
1072 GATCCTGAGTAGGATT
1 GATCCTGAATAGGATT
1088 GGTAAAAATA
Statistics
Matches: 740, Mismatches: 75, Indels: 95
0.81 0.08 0.10
Matches are distributed among these distances:
27 38 0.05
28 5 0.01
29 2 0.00
32 2 0.00
33 1 0.00
34 3 0.00
35 1 0.00
38 56 0.08
39 223 0.30
40 348 0.47
41 61 0.08
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (39 bp):
GATCCTGAATAGGATTCTGAAATTAACTGATAAAGCAAT
Found at i:481 original size:118 final size:118
Alignment explanation
Indices: 253--1079 Score: 747
Period size: 118 Copynumber: 7.2 Consensus size: 118
243 TGAAATTGAC
* * * * *
253 TGATAAAGCAAGGATCCTGAACAGGATTCTGAAATTGA-CTGATAAAGCAAGGATCCTGAATAGG
1 TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
* *
317 ATTCTGAA--AAGTGTCTTGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT
66 ATT-TGAATTAA---T-TTGATAAAGAAATGATCCTGAGCAGGATTCTGAAATTAATT
* * * *
373 TGATAAAGCTATGATCCTGAATAGGATTCTAAAATTAATTTGATAAAGCAATGATCCTGATTAGG
1 TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
*
438 ATTGTG-ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATT
66 ATT-TGAATTAATTTGATAAAGAAATGATCCTGAGCAGGATTCTGAAATTAATT
* *
491 TGATAAAGCTATGATCCTGAATAGGATTCTG-----AA-TT--T-----AATGATCCTGAGTAGG
1 TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
* *** ** * * ***
543 ATTCTGAAATTGA-CCAATAAAGAAATGATCCTGAATAGGATTTTGAAAAGTGGCT
66 ATT-TG-AATTAATTTGATAAAGAAATGATCCTGAGCAGGATTCTG-AAATTAATT
* * * *
598 CGATAAAGCAATGATCCT-AAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCATGAATAG
1 TGATAAAGCAATGATCCTGAA-CAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAG
* *
662 GATTCT--A--AA-TT--T-----AATGATCCTGAGTAGGATTTTGAAATTAATT
65 GATT-TGAATTAATTTGATAAAGAAATGATCCTGAGCAGGATTCTGAAATTAATT
* * * * * *
705 TGATAAAGTAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
* *
770 GTTTGAAAATTAATTTGATAAA-AAGATGATCCTGAGCAAGATTC-GAAATTAATT
66 ATTTG--AATTAATTTGATAAAGAA-ATGATCCTGAGCAGGATTCTGAAATTAATT
* * * * *
824 TGATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGG
1 TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
* * *
888 GTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTT-TGAAATTAATT
66 ATTTG-AATTAATTTGATAAAGAAATGATCCTGAGCAGGATTCTGAAATTAATT
* * * *
941 TGATAAA-AAGATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAG
1 TGATAAAGCA-ATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAG
* * *
1005 GGTTTGAAATTAATTTGATAAA-AAGATGATTCTGAGCAGGATTTTGAAATTAATT
65 GATTTG-AATTAATTTGATAAAGAA-ATGATCCTGAGCAGGATTCTGAAATTAATT
1060 TGATAAAGCAATGATCCTGA
1 TGATAAAGCAATGATCCTGA
1080 GTAGGATTGG
Statistics
Matches: 605, Mismatches: 61, Indels: 83
0.81 0.08 0.11
Matches are distributed among these distances:
105 20 0.03
106 28 0.05
107 95 0.16
108 22 0.04
110 2 0.00
112 6 0.01
113 7 0.01
115 3 0.00
117 53 0.09
118 222 0.37
119 47 0.08
120 70 0.12
121 28 0.05
122 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (118 bp):
TGATAAAGCAATGATCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
ATTTGAATTAATTTGATAAAGAAATGATCCTGAGCAGGATTCTGAAATTAATT
Found at i:710 original size:107 final size:108
Alignment explanation
Indices: 566--760 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 108
556 CCAATAAAGA
** *
566 AATGATCCTGAATAGGATTTTGAAAAGTGGCTCGATAAAGCAATGATCCTAAGTAGGATTCTGAA
1 AATGATCCTGAATAGGATTTTGAAAAGTAACTCGATAAAGCAATGATCCTAAGCAGGATTCTGAA
*
631 ATTAATTTGATAAAGCAATGATCATGAATAGGATTCTAAATTT
66 ATTAATTTGATAAAACAATGATCATGAATAGGATTCTAAATTT
* * * * * * * *
674 AATGATCCTGAGTAGGATTTTG-AAATTAATTTGATAAAGTAATGATCCTGAGCAGGGTTTTGAA
1 AATGATCCTGAATAGGATTTTGAAAAGTAACTCGATAAAGCAATGATCCTAAGCAGGATTCTGAA
738 ATTAATTTGATAAAACAATGATC
66 ATTAATTTGATAAAACAATGATC
761 CTGAGCAGGG
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
107 54 0.72
108 21 0.28
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (108 bp):
AATGATCCTGAATAGGATTTTGAAAAGTAACTCGATAAAGCAATGATCCTAAGCAGGATTCTGAA
ATTAATTTGATAAAACAATGATCATGAATAGGATTCTAAATTT
Found at i:854 original size:79 final size:78
Alignment explanation
Indices: 674--1080 Score: 622
Period size: 79 Copynumber: 5.2 Consensus size: 78
664 TTCTAAATTT
* * * *
674 AATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAGTA-ATGATCCTGAGCAGGGTTTTGAA
1 AATGATCCTGAGCAGG-GTTTGAAATTAATTTGATAAA-AAGATGATCCTGAGCA-GGATTTGAA
*
738 ATTAATTTGATAAAAC
63 ATTAATTTGATAAAGC
* *
754 AATGATCCTGAGCAGGGTTTGAAAATTAATTTGATAAAAAGATGATCCTGAGCAAGATTCGAAAT
1 AATGATCCTGAGCAGGGTTTG-AAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTTGAAAT
*
819 TAATTTGATAAA-A
65 TAATTTGATAAAGC
* *
832 AATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAACA-ATGATCCTGAGCAGGGTTTGAAA
1 AATGATCCTGAGCAGG-GTTTGAAATTAATTTGATAAAA-AGATGATCCTGAGCAGGATTTGAAA
896 TTAATTTGATAAAGC
64 TTAATTTGATAAAGC
911 AATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTTTGAAAT
1 AATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGA-TTTGAAAT
976 TAATTTGATAAAGC
65 TAATTTGATAAAGC
*
990 AATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAGATGATTCTGAGCAGGATTTTGAAAT
1 AATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGA-TTTGAAAT
1055 TAATTTGATAAAGC
65 TAATTTGATAAAGC
1069 AATGATCCTGAG
1 AATGATCCTGAG
1081 TAGGATTGGT
Statistics
Matches: 305, Mismatches: 15, Indels: 15
0.91 0.04 0.04
Matches are distributed among these distances:
77 1 0.00
78 102 0.33
79 158 0.52
80 44 0.14
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (78 bp):
AATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTTGAAATT
AATTTGATAAAGC
Found at i:1437 original size:145 final size:144
Alignment explanation
Indices: 1174--1624 Score: 722
Period size: 145 Copynumber: 3.1 Consensus size: 144
1164 ATATGGAATG
* * * * *
1174 CCCGGAGGACTTGTCAGAATTAATATCCAGAGGTTTCTGAAATTGTGCCCAGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
*
1239 GCAAACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAATACAGCTTTGATTAAAAACTTGA
66 GCAAACTCAACCTTGAGCAAGG-TTTGATTTTGAAACTTAAACACAGCTTTGATTAAAAACTTGA
1304 TGAAATGAAATGATA
130 TGAAATGAAATGATA
1319 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1384 GCAAACTCAACCTTGAGCAAGGCTTTGATTTTGAAACTTAAACACAGCTTTGATTAAAAACTTGA
66 GCAAACTCAACCTTGAGCAAGG-TTTGATTTTGAAACTTAAACACAGCTTTGATTAAAAACTTGA
*
1449 TGAAATGGAATGATA
130 TGAAATGAAATGATA
* *
1464 CTCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCTCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1529 GCAAACTCTGAATTGAGACCTTGAGCAAGGTTGTGATTTTGAAACTTAAACACAGCTTTGATTAA
66 GCAAACTC-------A-ACCTTGAGCAAGGTT-TGATTTTGAAACTTAAACACAGCTTTGATTAA
1594 AAACTTGATGAAATGAAATGATA
122 AAACTTGATGAAATGAAATGATA
1617 CCCGGAGG
1 CCCGGAGG
1625 TCTTACAAAT
Statistics
Matches: 285, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
145 208 0.73
152 3 0.01
153 74 0.26
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (144 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTGATTTTGAAACTTAAACACAGCTTTGATTAAAAACTTGAT
GAAATGAAATGATA
Found at i:2923 original size:6 final size:6
Alignment explanation
Indices: 2907--3009 Score: 165
Period size: 6 Copynumber: 17.2 Consensus size: 6
2897 TCTCACTTCT
*
2907 TTTTTCG TTTTCT- TTTTTG TTTTTG -TTTTG GTTTTG TTTTTG TTTTTG
1 TTTTT-G TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
2955 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
3003 TTTTTG T
1 TTTTTG T
3010 ATATTTATTG
Statistics
Matches: 92, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
5 6 0.07
6 81 0.88
7 4 0.04
8 1 0.01
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.82
Consensus pattern (6 bp):
TTTTTG
Done.