Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023709.1 Corchorus olitorius cultivar O-4 contig23742, 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: 10470
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:806 original size:27 final size:27
Alignment explanation
Indices: 768--862 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
758 AGTGAGCTTA
768 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
* *
795 AAATGACAAAAAT-ACCC-GAAACATGC
1 AAATGACTAAAATGCCCCTG-AACATGC
821 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
848 AAATGACTAAAATGC
1 AAATGACTAAAATGC
863 TCCTAAATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.02
26 22 0.36
27 37 0.61
28 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACATGC
Found at i:1291 original size:38 final size:39
Alignment explanation
Indices: 1244--1345 Score: 134
Period size: 38 Copynumber: 2.6 Consensus size: 39
1234 AAAACTGACG
* * * * *
1244 AAGCAATAATACTAAATCAGGATTGGAATTAGACTGATA
1 AAGCGATAATCCTAAATCAGGATTGGAATGAAAATGATA
* *
1283 AGGC-ATAATCCTAAACCAGGATTGGAATGAAAATGATA
1 AAGCGATAATCCTAAATCAGGATTGGAATGAAAATGATA
1321 AAGCGATAATCCTAAATCAGGATTG
1 AAGCGATAATCCTAAATCAGGATTG
1346 AAATAAAGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
38 32 0.59
39 22 0.41
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24
Consensus pattern (39 bp):
AAGCGATAATCCTAAATCAGGATTGGAATGAAAATGATA
Found at i:1354 original size:30 final size:30
Alignment explanation
Indices: 1318--2360 Score: 1261
Period size: 30 Copynumber: 34.4 Consensus size: 30
1308 AATGAAAATG
* * * * *
1318 ATAAAGCGATAATCCTAAATCAGGATTGAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
1348 ATAAAGCAATGATCCTAAACCAAGATCAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1378 ACT-AAGCAATGATCCT-AACTCAAGATTTAAA
1 A-TAAAGCAATGATCCTCAAC-CAGGA-TTAAA
* * *
1409 ATGAAG-AGGTGATCCTCAACCAGGATTAAG
1 ATAAAGCA-ATGATCCTCAACCAGGATTAAA
** * *
1439 ATGGAGCAAAGATCTTCAACCAGGATTTAAA
1 ATAAAGCAATGATCCTCAACCAGGA-TTAAA
*
1470 ATAAAACAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1500 ACAAAGCAACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1530 ATGAAGCAATGATCCTCAACCAGGATTAAAA
1 ATAAAGCAATGATCCTCAACCAGGATT-AAA
*
1561 ATAAAGCAATAATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
1591 ACAAAGCAACGTTCCTCAACCAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
1621 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * **
1651 ATAAAGCAATAATCCTAAAAAAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1681 ATAAAGCAACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1711 ATAAAACAATGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1741 ATAAAGCAAAGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1771 ATAAAGCAACGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1801 ACAAAGCAATAATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1831 ATAAAGCAACGATCCTCAACCATGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
1861 ATAAAGCAATAATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
1891 ACAAAGCAACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
1921 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
1951 ATAAAGCAACT-ATCCTCAACCAGGATTAAA
1 ATAAAGCAA-TGATCCTCAACCAGGATTAAA
*
1981 ATAAAGCAATGATCCTCAAACATGG-TTAAA
1 ATAAAGCAATGATCCTCAACCA-GGATTAAA
* *
2011 ATAAAGCAAGGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
2041 ATAAAGCAACGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
2071 ATAAAGCAATAATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
2101 ATAAAGCAACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
2131 ATAAAGTAACGATCCTCAACAAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
2161 ATAAAGCAAAGATCCTCAAACAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* **
2191 ATAAAGCAACGATCCTCAAATAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
2221 ATAAAGCAAAGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
2251 ATAAAACAACGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
2281 ACAAAGCAATGAAGCAAATATCCTC-ACCAGGATTTAA
1 ATAAAGCAAT---G-----ATCCTCAACCAGGATTAAA
* * **
2318 ATAAAGTAATGATCCTAAACCAGGATCGAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
2348 ATGAAGCAATGAT
1 ATAAAGCAATGAT
2361 GTAATGATCC
Statistics
Matches: 885, Mismatches: 106, Indels: 44
0.86 0.10 0.04
Matches are distributed among these distances:
29 11 0.01
30 769 0.87
31 76 0.09
32 3 0.00
33 1 0.00
34 1 0.00
37 18 0.02
38 6 0.01
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (30 bp):
ATAAAGCAATGATCCTCAACCAGGATTAAA
Found at i:2355 original size:67 final size:68
Alignment explanation
Indices: 2224--2359 Score: 159
Period size: 67 Copynumber: 2.0 Consensus size: 68
2214 GATTAAAATA
*
2224 AAGCAAAGATCCTCAAACAGGATTAAAATAAAACAACGATCCTCAAACAGGATTAAAACAAAGCA
1 AAGCAAAGATCCTCAAACAGGATTAAAATAAAACAACGATCCTCAAACAGGATCAAAACAAAGCA
2289 ATG
66 ATG
* * * ** * * **
2292 AAGCAAATATCCTC-ACCAGGATTTAAATAAAGTAATGATCCT-AAACCAGGATCGAAATGAAGC
1 AAGCAAAGATCCTCAAACAGGATTAAAATAAAACAACGATCCTCAAA-CAGGATCAAAACAAAGC
2355 AATG
65 AATG
2359 A
1 A
2360 TGTAATGATC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
66 3 0.05
67 41 0.72
68 13 0.23
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (68 bp):
AAGCAAAGATCCTCAAACAGGATTAAAATAAAACAACGATCCTCAAACAGGATCAAAACAAAGCA
ATG
Found at i:2489 original size:18 final size:19
Alignment explanation
Indices: 2466--2502 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2456 GAAATGAAAC
2466 CTTAAACAAGAA-TTTTGA
1 CTTAAACAAGAACTTTTGA
*
2484 CTTAAACATGAACTTTTGA
1 CTTAAACAAGAACTTTTGA
2503 AAAACTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (19 bp):
CTTAAACAAGAACTTTTGA
Found at i:2757 original size:69 final size:67
Alignment explanation
Indices: 2673--2963 Score: 341
Period size: 69 Copynumber: 4.2 Consensus size: 67
2663 CTCATTAAAC
* * * * *
2673 TTGGCTTATGGAAAAGCTTCAGTTG-TATGGATGGAACCAATGTTTAAACTGACTCGCATGGAAA
1 TTGGCTTGTGGAAAAGC-CCA-TTGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
2737 CGAGT
63 CGAGT
* * * * * *
2742 TTGACTTATGGAAAAGTCTATATGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAT
1 TTGGCTTGTGGAAAAGCCCAT-T-GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
2807 GAGT
64 GAGT
*
2811 TTGGCTTGTGGAAAAGCCCATATGGCTTGGATGGAACCAAGGCTTAAACTGACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCAT-T-GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
2876 CAGT
64 GAGT
* *
2880 TTGGCTTGTGGAAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAACTAACTCGTATGGAATC
1 TTGGCTTGTGGAAAAGCCCAT--TGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
2945 GAAT
64 GAGT
*
2949 TTGCCTTGTGGAAAA
1 TTGGCTTGTGGAAAA
2964 TTCTAAGTAT
Statistics
Matches: 194, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
67 1 0.01
68 2 0.01
69 189 0.97
70 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (67 bp):
TTGGCTTGTGGAAAAGCCCATTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGA
GT
Found at i:7617 original size:10 final size:10
Alignment explanation
Indices: 7602--7631 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
7592 AAAATATCCA
7602 ATTCCCGCTT
1 ATTCCCGCTT
7612 ATTCCCGCTT
1 ATTCCCGCTT
7622 ATTCCCGCTT
1 ATTCCCGCTT
7632 CTAGTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.40, G:0.10, T:0.40
Consensus pattern (10 bp):
ATTCCCGCTT
Found at i:8786 original size:35 final size:36
Alignment explanation
Indices: 8718--9094 Score: 345
Period size: 36 Copynumber: 10.6 Consensus size: 36
8708 TAATTTGCGG
*
8718 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
8754 TCCACTGTAATAAATTGAAG-AAAGA-CTGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATC-GCCCTGGA
* *
8789 TCAATTGAAATATACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
8825 TCAACTGAAATAAACTGAAGAAAAGATCGCTCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * *
8861 TCAGCTGAAGTAAAATGAAGAAACGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * * *
8897 TCAAACTAAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
8933 TCAACTGAAATGAATTGAA-TAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
8968 TCAAATCGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACT-GAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * ** * *
9005 TCAACTGAAATGATCTGAA-TAGGGA-CTACCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATC-GCCCTGGA
* * * *
9040 TCAACTTAAATAAACTGAA-TAAAGATCGTCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
9075 TCAACTGAAATGAACTGAAG
1 TCAACTGAAATAAACTGAAG
9095 CCTCTGAAAT
Statistics
Matches: 274, Mismatches: 58, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
34 2 0.01
35 108 0.39
36 131 0.48
37 33 0.12
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:8967 original size:107 final size:106
Alignment explanation
Indices: 8716--9094 Score: 350
Period size: 107 Copynumber: 3.5 Consensus size: 106
8706 ACTAATTTGC
* * * * *
8716 GGTCAACTGAAATAAACTGAAGAAAAGATCACCCTGGATCCACTGTAATAAATTGAAG-AAAGA-
1 GGTCAACTGAAATAAACTGAA-TAAAGATCGCCCTGGATCAACTGAAATAAAATGAAGAAAAGAT
* * * * * * ** * *
8779 CTGCCCTGGGTCAATTGAAATATACTGAAGAAAAGATCGCCCTG
65 C-ACCCTGGATCAACTAAAATAAACTGAA-TAGGGACCACCCTG
* * * * * *
8823 GATCAACTGAAATAAACTGAAGAAAAGATCGCTCTGGATCAGCTGAAGTAAAATGAAGAAACGAT
1 GGTCAACTGAAATAAACTGAA-TAAAGATCGCCCTGGATCAACTGAAATAAAATGAAGAAAAGAT
8888 CACCCTGGATCAAACTAAAATAAACTGAAATA-GGACCACCCTG
65 CACCCTGGATC-AACTAAAATAAACTG-AATAGGGACCACCCTG
* * * * *
8931 GGTCAACTGAAATGAATTGAATAAGGATCGCCCTGGATCAAATCGAAATAAACTGAAGAAAAGAT
1 GGTCAACTGAAATAAACTGAATAAAGATCGCCCTGGATCAACT-GAAATAAAATGAAGAAAAGAT
* * * * *
8996 CGCCCTGGATCAACTGAAATGATCTGAATAGGGACTACCCTG
65 CACCCTGGATCAACTAAAATAAACTGAATAGGGACCACCCTG
* * * * *
9038 GGTCAACTTAAATAAACTGAATAAAGATCGTCCTGGGTCAACTGAAATGAACTGAAG
1 GGTCAACTGAAATAAACTGAATAAAGATCGCCCTGGATCAACTGAAATAAAATGAAG
9095 CCTCTGAAAT
Statistics
Matches: 224, Mismatches: 42, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
106 17 0.08
107 125 0.56
108 66 0.29
109 14 0.06
110 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (106 bp):
GGTCAACTGAAATAAACTGAATAAAGATCGCCCTGGATCAACTGAAATAAAATGAAGAAAAGATC
ACCCTGGATCAACTAAAATAAACTGAATAGGGACCACCCTG
Found at i:8994 original size:144 final size:143
Alignment explanation
Indices: 8718--9094 Score: 397
Period size: 144 Copynumber: 2.6 Consensus size: 143
8708 TAATTTGCGG
* * ** * **
8718 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGATCCACTGTAATAAATTGAAGAAAGACTGC
1 TCAACTGAAATAAAATGAAGAAAAGATCACCCTGGATCAACTAAAATAAACTGAAGAAAGACCAC
* *
8783 CCTGGGTCAATTGAAATATACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA
66 CCTGGGTCAACTGAAATATACTGAAGAAAAGATCGCCCTGGATCAAATGAAATAAACTGAAGAAA
*
8848 AGATCGCTCTGGA
131 AGATCGCCCTGGA
* * * *
8861 TCAGCTGAAGTAAAATGAAGAAACGATCACCCTGGATCAAACTAAAATAAACTGAA-ATAGGACC
1 TCAACTGAAATAAAATGAAGAAAAGATCACCCTGGATC-AACTAAAATAAACTGAAGA-AAGACC
* * *
8925 ACCCTGGGTCAACTGAAATGA-ATTGAA-TAAGGATCGCCCTGGATCAAATCGAAATAAACTGAA
64 ACCCTGGGTCAACTGAAAT-ATACTGAAGAAAAGATCGCCCTGGATCAAAT-GAAATAAACTGAA
8988 GAAAAGATCGCCCTGGA
127 GAAAAGATCGCCCTGGA
* ** * ** * * * * *
9005 TCAACTGAAATGATCTGAA-TAGGGA-CTACCCTGGGTCAACTTAAATAAACTGAATAAAGATCG
1 TCAACTGAAATAAAATGAAGAAAAGATC-ACCCTGGATCAACTAAAATAAACTGAAGAAAGACCA
*
9068 TCCTGGGTCAACTGAAATGA-ACTGAAG
65 CCCTGGGTCAACTGAAAT-ATACTGAAG
9095 CCTCTGAAAT
Statistics
Matches: 195, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
142 45 0.23
143 67 0.34
144 82 0.42
145 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (143 bp):
TCAACTGAAATAAAATGAAGAAAAGATCACCCTGGATCAACTAAAATAAACTGAAGAAAGACCAC
CCTGGGTCAACTGAAATATACTGAAGAAAAGATCGCCCTGGATCAAATGAAATAAACTGAAGAAA
AGATCGCCCTGGA
Done.