Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013967.1 Corchorus olitorius cultivar O-4 contig14000, 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: 45853
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:2028 original size:23 final size:23
Alignment explanation
Indices: 1998--2044 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1988 CCTATCTACA
1998 TTTATTTAGTAGTAGTTGTCTTG
1 TTTATTTAGTAGTAGTTGTCTTG
2021 TTTATTTAGTAGTAGTTGTCTTG
1 TTTATTTAGTAGTAGTTGTCTTG
2044 T
1 T
2045 GGAATTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.57
Consensus pattern (23 bp):
TTTATTTAGTAGTAGTTGTCTTG
Found at i:3220 original size:2 final size:2
Alignment explanation
Indices: 3213--3251 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3203 TATCATGTCC
3213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3252 CACACACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5837 original size:6 final size:6
Alignment explanation
Indices: 5826--5862 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
5816 AGGAGCTGGT
*
5826 AGGGAG AGGGAG AGGGAG AGGGAG AGCGAGG AGGGAG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGA-G AGGGAG
5863 CAACAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.32, C:0.03, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:6621 original size:42 final size:42
Alignment explanation
Indices: 6569--6649 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
6559 ATTTCTTTTT
6569 TTCTTCTAAATCAATTTCATTTTTTTTAATACAAACTCCTCC
1 TTCTTCTAAATCAATTTCATTTTTTTTAATACAAACTCCTCC
* *
6611 TTCTTTTAAATCGATTTCATTTTTTTTAATACAAACTCC
1 TTCTTCTAAATCAATTTCATTTTTTTTAATACAAACTCC
6650 AACTAGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.01, T:0.49
Consensus pattern (42 bp):
TTCTTCTAAATCAATTTCATTTTTTTTAATACAAACTCCTCC
Found at i:7579 original size:31 final size:31
Alignment explanation
Indices: 7541--7624 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
7531 GATGCTGAAA
* *
7541 AGCCATGTGGCATACCACGTCAGACGAAAAT
1 AGCCATGTGACATACCACATCAGACGAAAAT
*
7572 AGTCATGTGACATACCACATCAGACGAAAAT
1 AGCCATGTGACATACCACATCAGACGAAAAT
* *
7603 AGCCATGTAACATGCCACATCA
1 AGCCATGTGACATACCACATCA
7625 ACATAAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (31 bp):
AGCCATGTGACATACCACATCAGACGAAAAT
Found at i:7783 original size:29 final size:31
Alignment explanation
Indices: 7722--7792 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
7712 ACCATACCAG
*
7722 AGGGTGCAAAGTAGAACAAAAATAAAACATT
1 AGGGTGCAAAGTAGAACAAAAATAAAAAATT
*
7753 AGGGTGC-AAGT-GATC-AAAATAAAAAAGTT
1 AGGGTGCAAAGTAGAACAAAAATAAAAAA-TT
*
7782 A-GGTGAAAAGT
1 AGGGTGCAAAGT
7793 GTCAATCCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 14 0.40
29 10 0.29
30 4 0.11
31 7 0.20
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (31 bp):
AGGGTGCAAAGTAGAACAAAAATAAAAAATT
Found at i:8142 original size:74 final size:75
Alignment explanation
Indices: 8013--8154 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 75
8003 CATGGTAAAC
** * * * ** *
8013 TTTTACTGACGTGGTTTTTCCACGTCAGTACTCATGTAGGCCCCATTCTAGTATTTAGAGTCATG
1 TTTTACTGACGTGACTTTTCCACGTCAGCACTCATATAAGCCCCACCCTAGTATTTAGAATCATG
8078 TGGGGCATAT
66 TGGGGCATAT
*
8088 TTTTACT-ACGTGACTTTTCCACGTTAGCACTCATATAAGCCCCACCCTAGTATTTAGAATCATG
1 TTTTACTGACGTGACTTTTCCACGTCAGCACTCATATAAGCCCCACCCTAGTATTTAGAATCATG
8152 TGG
66 TGG
8155 ACCCATATGA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
74 51 0.88
75 7 0.12
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (75 bp):
TTTTACTGACGTGACTTTTCCACGTCAGCACTCATATAAGCCCCACCCTAGTATTTAGAATCATG
TGGGGCATAT
Found at i:11150 original size:18 final size:17
Alignment explanation
Indices: 11123--11157 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11113 ATGTTACATG
11123 TAATAATAATACTAAAAT
1 TAATAATAATA-TAAAAT
*
11141 TAATAGTAATATAAAAT
1 TAATAATAATATAAAAT
11158 AGTACGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
TAATAATAATATAAAAT
Found at i:11528 original size:2 final size:2
Alignment explanation
Indices: 11521--11553 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11511 TTGTTATTAC
*
11521 AT AT AT AT AT AT AT AT AT TT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11554 TGGCTGGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:24029 original size:16 final size:16
Alignment explanation
Indices: 24004--24036 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23994 GTGACCCTTT
24004 TTTATGTGTGGAATAC
1 TTTATGTGTGGAATAC
*
24020 TTTATTTGTGGAATAC
1 TTTATGTGTGGAATAC
24036 T
1 T
24037 CATGTGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (16 bp):
TTTATGTGTGGAATAC
Found at i:24135 original size:27 final size:27
Alignment explanation
Indices: 24095--24146 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
24085 GAGTACTCCG
24095 TATGTGTGTAGAATATTCATATGTGAA
1 TATGTGTGTAGAATATTCATATGTGAA
* *
24122 TATGTGTGTGGAATATTCGTATGTG
1 TATGTGTGTAGAATATTCATATGTG
24147 TGTAGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.42
Consensus pattern (27 bp):
TATGTGTGTAGAATATTCATATGTGAA
Found at i:24148 original size:21 final size:19
Alignment explanation
Indices: 24121--24169 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
24111 TCATATGTGA
24121 ATATGTGTGTGGAATATTC
1 ATATGTGTGTGGAATATTC
* *
24140 GTATGTGTGTAGAATATTC
1 ATATGTGTGTGGAATATTC
24159 ATATGTGTGTG
1 ATATGTGTGTG
24170 TGAGGTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.29, T:0.43
Consensus pattern (19 bp):
ATATGTGTGTGGAATATTC
Found at i:32686 original size:2 final size:2
Alignment explanation
Indices: 32679--32712 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32669 AATTTCTTCA
32679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32713 TTCAATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36277 original size:234 final size:234
Alignment explanation
Indices: 35868--36339 Score: 890
Period size: 234 Copynumber: 2.0 Consensus size: 234
35858 TCCCTTCTAG
* *
35868 CGAGAAGCCTTCAGGTTGATCTATATAAACATCCTCCTTAAGATCACCATTAAGAAAGGCTGTTT
1 CGAGAAGCCTTCAGGTTGATCCATATAAACATCCTCCTCAAGATCACCATTAAGAAAGGCTGTTT
35933 TCACATCCATTTGTTGCAACTCCAAATCATAATGAGCGAACAATGTCATAAAAATTCTTAAAGAG
66 TCACATCCATTTGTTGCAACTCCAAATCATAATGAGCGAACAATGTCATAAAAATTCTTAAAGAG
*
35998 TTTTTCTTTGAGACTGGTGAAAAAGTCTCATTGTAATCGACATCATCCTTTTGAGTATAGTCCTT
131 TTTTTCTTTGAGACTGGTGAAAAAGTCTCATTGCAATCGACATCATCCTTTTGAGTATAGTCCTT
*
36063 GGCAACGAGTCTAGCTTTATATCGTTCGATATTGCCATT
196 GGCAACGAGTCTAGCTTTATATCATTCGATATTGCCATT
*
36102 CGAGAAGCCTTCAGGTTGATCCATATAAACATCCTCCTCAAGATCACCATTAAGAAAGGTTGTTT
1 CGAGAAGCCTTCAGGTTGATCCATATAAACATCCTCCTCAAGATCACCATTAAGAAAGGCTGTTT
*
36167 TCACATCCATTTGTTGCAACTCCAAATCATAATGAGCGACCAATGTCATAAAAATTCTTAAAGAG
66 TCACATCCATTTGTTGCAACTCCAAATCATAATGAGCGAACAATGTCATAAAAATTCTTAAAGAG
36232 TTTTTCTTTGAGACTGGTGAAAAAGTCTCATTGCAATCGACATCATCCTTTTGAGTATAGTCCTT
131 TTTTTCTTTGAGACTGGTGAAAAAGTCTCATTGCAATCGACATCATCCTTTTGAGTATAGTCCTT
36297 GGCAACGAGTCTAGCTTTATATCATTCGATATTGCCATT
196 GGCAACGAGTCTAGCTTTATATCATTCGATATTGCCATT
36336 CGAG
1 CGAG
36340 TCACGTTTGG
Statistics
Matches: 232, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
234 232 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (234 bp):
CGAGAAGCCTTCAGGTTGATCCATATAAACATCCTCCTCAAGATCACCATTAAGAAAGGCTGTTT
TCACATCCATTTGTTGCAACTCCAAATCATAATGAGCGAACAATGTCATAAAAATTCTTAAAGAG
TTTTTCTTTGAGACTGGTGAAAAAGTCTCATTGCAATCGACATCATCCTTTTGAGTATAGTCCTT
GGCAACGAGTCTAGCTTTATATCATTCGATATTGCCATT
Found at i:39031 original size:19 final size:18
Alignment explanation
Indices: 39007--39042 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38997 TCTCAATCAA
*
39007 ATATACAAGATATCTTTGG
1 ATATACAA-ATATATTTGG
39026 ATATACAAATATATTTG
1 ATATACAAATATATTTG
39043 ACTAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (18 bp):
ATATACAAATATATTTGG
Found at i:39511 original size:2 final size:2
Alignment explanation
Indices: 39504--39546 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
39494 TTCGACCAGA
39504 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39544 AT A
1 AT A
39547 CATAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40949 original size:2 final size:2
Alignment explanation
Indices: 40942--41001 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
40932 CAATAAATAA
* * * * *
40942 AT AT AT AT AT AT AT AT AC AC AT AT AT AT AC AT AT AA AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40984 -T AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
41002 GTAGTATGCT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:41967 original size:3 final size:3
Alignment explanation
Indices: 41959--42061 Score: 154
Period size: 3 Copynumber: 34.3 Consensus size: 3
41949 CGAAAATACC
*
41959 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
42007 AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT -AT TAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
42052 ACT AAT AAT A
1 AAT AAT AAT A
42062 CTATTTTTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
2 2 0.02
3 88 0.95
4 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:44127 original size:5 final size:6
Alignment explanation
Indices: 44109--44133 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44099 AAAAAAAGTG
44109 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
44134 TCCAATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:45714 original size:14 final size:14
Alignment explanation
Indices: 45670--45706 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
45660 GCCACTAAAA
45670 ATAA-TATATAGTAT
1 ATAATTATATA-TAT
45684 AT-ATTATATATAT
1 ATAATTATATATAT
45697 ATAATTATAT
1 ATAATTATAT
45707 TCATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
ATAATTATATATAT
Done.