Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023333.1 Corchorus olitorius cultivar O-4 contig23366, 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: 12925
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4548 original size:28 final size:28
Alignment explanation
Indices: 4516--4593 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
4506 AGTGAACCTG
* *
4516 AAATGACCAAAATGCCCCTGAACGTGTA
1 AAATGACCAAAATGCCCCTAAACGTGAA
*
4544 AAATGACCAAAATGCCCCTAAATGTGAA
1 AAATGACCAAAATGCCCCTAAACGTGAA
4572 AAATGACCAAAATGCCCCTAAA
1 AAATGACCAAAATGCCCCTAAA
4594 GCCAATTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAAACGTGAA
Found at i:6242 original size:42 final size:43
Alignment explanation
Indices: 6160--6252 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 43
6150 ATTTGATAAG
*
6160 TTATCCATATCTCCATTGATATATGTCATACATCCTTCATGCA
1 TTATCCATATCTCCATTGATATATGTCATACATCCGTCATGCA
*
6203 TTGTCCATATCTCCA-T-ATATATGTTCATACATCCGTCATGCA
1 TTATCCATATCTCCATTGATATATG-TCATACATCCGTCATGCA
6245 TTATCCAT
1 TTATCCAT
6253 TCCTTTGTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 7 0.15
42 25 0.54
43 14 0.30
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.40
Consensus pattern (43 bp):
TTATCCATATCTCCATTGATATATGTCATACATCCGTCATGCA
Found at i:6264 original size:42 final size:42
Alignment explanation
Indices: 6160--6292 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
6150 ATTTGATAAG
*
6160 TTATCCATATCTCCATTGATATATG-TCATACATCCTTCATGCA
1 TTATCCATATCTCCA-T-ATATATGTTCATACATCCGTCATGCA
*
6203 TTGTCCATATCTCCATATATATGTTCATACATCCGTCATGCA
1 TTATCCATATCTCCATATATATGTTCATACATCCGTCATGCA
*** * ** *
6245 TTATCCAT-TCCTTTGTATATATGTTCATGCATAGGTCGTGCA
1 TTATCCATAT-CTCCATATATATGTTCATACATCCGTCATGCA
6287 TTATCC
1 TTATCC
6293 TTTCATTACT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 8 0.10
42 56 0.72
43 14 0.18
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.41
Consensus pattern (42 bp):
TTATCCATATCTCCATATATATGTTCATACATCCGTCATGCA
Found at i:7475 original size:15 final size:15
Alignment explanation
Indices: 7455--7505 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
7445 AAAGAGACGT
**
7455 TTTTCAAGAAAATTG
1 TTTTCAAGAAAAAAG
7470 TTTTCAAGAAAAAAG
1 TTTTCAAGAAAAAAG
**
7485 TTTTCAA-AAATGAG
1 TTTTCAAGAAAAAAG
7499 TTTTCAA
1 TTTTCAA
7506 AAGGTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (15 bp):
TTTTCAAGAAAAAAG
Found at i:8369 original size:21 final size:21
Alignment explanation
Indices: 8345--8415 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
8335 CTTAGGCAAT
**
8345 TCCAATGAGCTTTAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8366 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8387 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
8408 TCCAATGA
1 TCCAATGA
8416 TCTGCTAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:10713 original size:66 final size:66
Alignment explanation
Indices: 10628--11104 Score: 586
Period size: 67 Copynumber: 7.1 Consensus size: 66
10618 AGAGGATTTC
* *
10628 AGAAGTACA-CCGAAGACGGTTTGCTAGAAAGAATTTTCAAAGATGATTGGTAGACAATCTCATC
1 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGATGATTGGAAGACAATCTCATC
10692 A
66 A
*
10693 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATGGATTGGAAGACAATCTCAT
1 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGAT-GATTGGAAGACAATCTCAT
10758 CA
65 CA
* * * *
10760 AGAAGT-GATCGGAAGACAGTTTGCTAGAAAGAATTTGCAGAAGATGATTGGAAGACAATCTCGT
1 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAGATGATTGGAAGACAATCTCAT
10824 CA
65 CA
* ** * *
10826 AGAAGTACATAGGAAGACACTCTGCTAGAAAGAATTTTCGAAAGTTGATTGGAAGACAATCTCAT
1 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTC-AAAGATGATTGGAAGACAATCTCAT
*
10891 TA
65 CA
* * * *
10893 AGGAA-TACACCGGAAGACAGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTGA
1 A-GAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTC-AAAGATGATTGGAAGACAATCTCA
*
10957 TTAA
64 -TCA
* *
10961 AGAA-TACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGAGTAAACTGGAAGACAATCTCA
1 AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGA-T-GATTGGAAGACAATCTCA
*
11025 TTA
64 TCA
* * * *
11028 AGGAA-TATACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGAATTGGAAGACAATCTC
1 A-GAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAA-GATG-ATTGGAAGACAATCTC
*
11092 ATTA
63 ATCA
11096 AGAAGTACA
1 AGAAGTACA
11105 CTAGAAGATG
Statistics
Matches: 362, Mismatches: 37, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
65 9 0.02
66 93 0.26
67 176 0.49
68 83 0.23
69 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (66 bp):
AGAAGTACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGATGATTGGAAGACAATCTCATC
A
Found at i:10888 original size:200 final size:201
Alignment explanation
Indices: 10649--11105 Score: 602
Period size: 200 Copynumber: 2.3 Consensus size: 201
10639 GAAGACGGTT
* * * * *
10649 TGCTAGAAAGAATTTTCAAAGATGATTGGTAGACAATCTCATCAAGAAGTACATCGGAAGACGGT
1 TGCTAGAAAGAATTTTCAAAGTTGATTGGAAGACAATCTCATTAAGAAGTACACCGGAAGACAGT
* *
10714 TTGCTAGAAAGAATTTTCAAAAATGGATTGGAAGACAATCTCA-TCAAGAAGT-GATCGGAAGAC
66 TTGCTAGAAAGAATTTTCAAAAATGGATTGGAAGACAATCTCATTAAAGAA-TACATCGGAAGAC
* * * *
10777 AGTTTGCTAGAAAGAATTTGCAGAAGA-T-GATTGGAAGACAATCTCGTCAA-GAAGTACATAGG
130 AGTTTGCTAGAAAGAATTTGCA-AAGAGTAAACTGGAAGACAATCTCATCAAGGAA-TACACAGG
10839 AAGACACTC
193 AAGACACTC
10848 TGCTAGAAAGAATTTTCGAAAGTTGATTGGAAGACAATCTCATTAAGGAA-TACACCGGAAGACA
1 TGCTAGAAAGAATTTTC-AAAGTTGATTGGAAGACAATCTCATTAA-GAAGTACACCGGAAGACA
* * *
10912 GTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTGATTAAAGAATACATCGGAAGA
64 GTTTGCTAGAAAGAATTTTCAAAAATGGATTGGAAGACAATCTCATTAAAGAATACATCGGAAGA
* * * * *
10977 CGGTTTGCTAGAAAGAATTTTCAAAGAGTAAACTGGAAGACAATCTCATTAAGGAATATACCGGA
129 CAGTTTGCTAGAAAGAATTTGCAAAGAGTAAACTGGAAGACAATCTCATCAAGGAATACACAGGA
** *
11042 AGACGGTT
194 AGACACTC
*
11050 TGTTAGAAAGAATTTTCAAATGTTGAATTGGAAGACAATCTCATTAAGAAGTACAC
1 TGCTAGAAAGAATTTTCAAA-GTTG-ATTGGAAGACAATCTCATTAAGAAGTACAC
11106 TAGAAGATGG
Statistics
Matches: 225, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
199 17 0.08
200 84 0.37
201 43 0.19
202 52 0.23
203 29 0.13
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (201 bp):
TGCTAGAAAGAATTTTCAAAGTTGATTGGAAGACAATCTCATTAAGAAGTACACCGGAAGACAGT
TTGCTAGAAAGAATTTTCAAAAATGGATTGGAAGACAATCTCATTAAAGAATACATCGGAAGACA
GTTTGCTAGAAAGAATTTGCAAAGAGTAAACTGGAAGACAATCTCATCAAGGAATACACAGGAAG
ACACTC
Found at i:11193 original size:64 final size:64
Alignment explanation
Indices: 11124--11458 Score: 372
Period size: 64 Copynumber: 5.2 Consensus size: 64
11114 GGTTTCTCAG
* * *
11124 GATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAGGAATTTTCAGAAGTTGATCGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTCAGAAATTTTCAGAAGTTGATCGGAAGAC
* * * * * *
11188 GATCTTGTCAAGAACTACGCTAGAAGATAGCTTCTCAAAAATTTTCAGAAGTTGATTGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTCAGAAATTTTCAGAAGTTGATCGGAAGAC
* * * * * * *
11252 GATCTTGTTAAAAAGCACACCAAAAGATAGTTTCTC-GAAAAGGTTTCAGTAGTTTATCGGAAGA
1 GATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTCAG-AAA-TTTTCAGAAGTTGATCGGAAGA
11316 C
64 C
* * * * *
11317 GATCTTCTCAAGAAGTACACCAGAAGATGGTTTCTCA-AGAGTTTTCAGAAGTTGATTGGAAGAT
1 GATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTCAGA-AATTTTCAGAAGTTGATCGGAAGAC
* *
11381 GATCTTGTTCAA-AAGTACACCAGAAGATAGTTTCTC-GAAAAGGTTTCAGAAGATGATCGGAAG
1 GATCTTG-TCAAGAAGTACACCAGAAGATAGTTTCTCAG-AAA-TTTTCAGAAGTTGATCGGAAG
11444 AC
63 AC
*
11446 GATCTTGTTAAGA
1 GATCTTGTCAAGA
11459 GATGCACCGG
Statistics
Matches: 220, Mismatches: 42, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
64 138 0.63
65 82 0.37
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (64 bp):
GATCTTGTCAAGAAGTACACCAGAAGATAGTTTCTCAGAAATTTTCAGAAGTTGATCGGAAGAC
Found at i:11472 original size:129 final size:129
Alignment explanation
Indices: 11131--11458 Score: 453
Period size: 129 Copynumber: 2.5 Consensus size: 129
11121 CAGGATCTTA
* * *
11131 TCAAGAAGTACACCAGAAGATGGTTTCTC-AGGAA-TTTTCAGAAGTTGATCGGAAGACGATCTT
1 TCAA-AAGTACACCAGAAGATAGTTTCTCGA-AAAGGTTTCAGAAGTTGATCGGAAGACGATCTT
* *
11194 GTCAAGAACTACGCTAGAAGATAGCTTCTCAAAAATTTTCAGAAGTTGATTGGAAGACGATCTTG
64 GTCAAGAACTACACCAGAAGATAGCTTCTCAAAAATTTTCAGAAGTTGATTGGAAGACGATCTTG
11259 T
129 T
* * * * * *
11260 TAAAAAGCACACCAAAAGATAGTTTCTCGAAAAGGTTTCAGTAGTTTATCGGAAGACGATCTTCT
1 TCAAAAGTACACCAGAAGATAGTTTCTCGAAAAGGTTTCAGAAGTTGATCGGAAGACGATCTTGT
* * * * * *
11325 CAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATTGGAAGATGATCTTGT
66 CAAGAACTACACCAGAAGATAGCTTCTCAAAAATTTTCAGAAGTTGATTGGAAGACGATCTTGT
*
11389 TCAAAAGTACACCAGAAGATAGTTTCTCGAAAAGGTTTCAGAAGATGATCGGAAGACGATCTTGT
1 TCAAAAGTACACCAGAAGATAGTTTCTCGAAAAGGTTTCAGAAGTTGATCGGAAGACGATCTTGT
*
11454 TAAGA
66 CAAGA
11459 GATGCACCGG
Statistics
Matches: 172, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
128 23 0.13
129 149 0.87
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (129 bp):
TCAAAAGTACACCAGAAGATAGTTTCTCGAAAAGGTTTCAGAAGTTGATCGGAAGACGATCTTGT
CAAGAACTACACCAGAAGATAGCTTCTCAAAAATTTTCAGAAGTTGATTGGAAGACGATCTTGT
Found at i:11610 original size:25 final size:26
Alignment explanation
Indices: 11589--11637 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
11579 TAGAAATTGA
11589 TTGAAAGAC-AATCTCCTCAAATGTG
1 TTGAAAGACGAATCTCCTCAAATGTG
* * *
11614 TTGGAAGACGAATTTTCTCAAATG
1 TTGAAAGACGAATCTCCTCAAATG
11638 AAATTCCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (26 bp):
TTGAAAGACGAATCTCCTCAAATGTG
Found at i:11809 original size:51 final size:51
Alignment explanation
Indices: 11687--11964 Score: 381
Period size: 51 Copynumber: 5.5 Consensus size: 51
11677 TGATTTTCTC
* *
11687 AAGATTGAATTGGAAGACATTTCAAAGGATAAGCGGAAGACGGTCC--TTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTT
* * *
11736 AAGATGGAAATT-GAAGACAGTTCAAAGGATAAGGGGAAGACATTCCTTTTT
1 AAGATTG-AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTT
**
11787 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTT
11838 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-GATCCTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAG-TCCTTTTT
* *
11889 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-G-ACTCTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTT
* *
11938 AATATT-AGATTGGAAGACAATTCAAAG
1 AAGATTGA-ATTGGAAGACAGTTCAAAG
11965 AAGTTGATCC
Statistics
Matches: 208, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
48 1 0.00
49 64 0.31
50 9 0.04
51 134 0.64
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (51 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTT
Found at i:11962 original size:151 final size:149
Alignment explanation
Indices: 11687--11964 Score: 409
Period size: 151 Copynumber: 1.8 Consensus size: 149
11677 TGATTTTCTC
* *
11687 AAGATTGAATTGGAAGACATTTCAAAGGATAAGCGGAAGACGGTCCTTTAAGATGGAAATTGAAG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTAAGATGGAAATTGAAG
* * *
11752 ACAGTTCAAAGGATAAGGGGAAGACATTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGAT
66 ACAGTTCAAAGGATAAGCGGAAGACA-T-CTCTTTAAGATTGAATTGGAAGACAATTCAAAGGAT
11817 AAGCGGAAGATGGTCCTTTTT
129 AAGCGGAAGATGGTCCTTTTT
*
11838 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAGATTG-AATTGG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCC--TTTAAGATGGAAATT-G
*
11902 AAGACAGTTCAAAGGATAAGCGGAAGACGA-CTCTTTAATATT-AGATTGGAAGACAATTCAAAG
63 AAGACAGTTCAAAGGATAAGCGGAAGAC-ATCTCTTTAAGATTGA-ATTGGAAGACAATTCAAAG
11965 AAGTTGATCC
Statistics
Matches: 115, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
150 1 0.01
151 72 0.63
152 4 0.03
153 37 0.32
154 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (149 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTAAGATGGAAATTGAAG
ACAGTTCAAAGGATAAGCGGAAGACATCTCTTTAAGATTGAATTGGAAGACAATTCAAAGGATAA
GCGGAAGATGGTCCTTTTT
Found at i:12001 original size:102 final size:101
Alignment explanation
Indices: 11687--12011 Score: 326
Period size: 102 Copynumber: 3.2 Consensus size: 101
11677 TGATTTTCTC
* *
11687 AAGATTGAATTGGAAGACATTTCAAAGGATAAGCGGAAGA-CGGT-C-CTTTAAGATGGAAATT-
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATC-GTACTCTTTAAGATTG-AATTG
* ** * *
11748 GAAGACAGTTCAAAGGATAAGGGGAAGAC-ATTCCTTTTT
64 GAAGACAATTCAAAGGATAACCGGAAGACGA-TCC-TCTG
* * *
11787 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTTAAGATTGAATTGGA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATCGTACTCTTTAAGATTGAATTGGA
* * * *
11852 AGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTT
66 AGACAATTCAAAGGATAACCGGAAGACGATCC-TCTG
*
11889 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGA-CG-ACTCTTTAATATT-AGATTGG
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATCGTACTCTTTAAGATTGA-ATTGG
* *
11951 AAGACAATTCAAAGAAGTTGATCCGGAAGACGATACC-CTG
65 AAGACAATTCAAAG--GAT-AACCGGAAGACGAT-CCTCTG
* *
11991 AAGATGGAATTCGAAGACAGT
1 AAGATTGAATTGGAAGACAGT
12012 CTAAAGAAGT
Statistics
Matches: 198, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
99 1 0.01
100 69 0.35
101 6 0.03
102 107 0.54
103 13 0.07
104 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (101 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATCGTACTCTTTAAGATTGAATTGGA
AGACAATTCAAAGGATAACCGGAAGACGATCCTCTG
Done.