Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018000.1 Corchorus olitorius cultivar O-4 contig18033, 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: 69618
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:5842 original size:22 final size:21
Alignment explanation
Indices: 5819--5869 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5809 ATAATTTCTA
*
5819 AAATCAGGGGTCAAATTGAAT
1 AAATCAGGGATCAAATTGAAT
* *
5840 AAAGCAGGGATCAAATTGCATT
1 AAATCAGGGATCAAATTG-AAT
5862 AAATCAGG
1 AAATCAGG
5870 AAATATACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (21 bp):
AAATCAGGGATCAAATTGAAT
Found at i:14412 original size:25 final size:26
Alignment explanation
Indices: 14377--14426 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
14367 AAAATTGAAA
14377 GAAGAAAGAAACAGAGGAC-TGAGAGG
1 GAAGAAAGAAACAGAGG-CTTGAGAGG
14403 GAAG-AAGAAACAGAGGCTTGAGAG
1 GAAGAAAGAAACAGAGGCTTGAGAG
14427 AAATGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 18 0.78
26 4 0.17
ACGTcount: A:0.48, C:0.08, G:0.38, T:0.06
Consensus pattern (26 bp):
GAAGAAAGAAACAGAGGCTTGAGAGG
Found at i:14434 original size:25 final size:25
Alignment explanation
Indices: 14382--14437 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
14372 TGAAAGAAGA
*
14382 AAGAAACAGAGGACTGAGAGGGAAG
1 AAGAAACAGAGGACTGAGAGGAAAG
14407 AAGAAACAGAGG-CTTGAGA-GAAATG
1 AAGAAACAGAGGAC-TGAGAGGAAA-G
14432 AAGAAA
1 AAGAAA
14438 AGGGCCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.52, C:0.07, G:0.34, T:0.07
Consensus pattern (25 bp):
AAGAAACAGAGGACTGAGAGGAAAG
Found at i:16163 original size:12 final size:12
Alignment explanation
Indices: 16146--16170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16136 TTTCTCTGTT
16146 ATTACCATATGA
1 ATTACCATATGA
16158 ATTACCATATGA
1 ATTACCATATGA
16170 A
1 A
16171 AATCTGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACCATATGA
Found at i:22197 original size:109 final size:109
Alignment explanation
Indices: 21979--22190 Score: 334
Period size: 109 Copynumber: 1.9 Consensus size: 109
21969 ACTTACGCAT
* * *
21979 TTAAGGTGCCTTGCATACTCATAATTTTTGTTCATGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCCTTGCATACTCATAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGACAC
*
22044 CGAACCCTGTGTGCTCCACTTCCCAAAAACAACGGAGTAATTTA
66 CGAACCCCGTGTGCTCCACTTCCCAAAAACAACGGAGTAATTTA
* ** *
22088 TTAAGATGCTTTGCATACTCATAATTTTGGTTTGTGACTGACGCGAAGGTTGATATTTGTGACAT
1 TTAAGATGCCTTGCATACTCATAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGACAC
* *
22153 CGAACCCCGTGTGGTCCACTTCCCAAAAACAGCGGAGT
66 CGAACCCCGTGTGCTCCACTTCCCAAAAACAACGGAGT
22191 GGTTTATAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 93 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (109 bp):
TTAAGATGCCTTGCATACTCATAATTTTGGTTCATGACTGACGCGAAGGTTGATATTTGTGACAC
CGAACCCCGTGTGCTCCACTTCCCAAAAACAACGGAGTAATTTA
Found at i:23257 original size:9 final size:9
Alignment explanation
Indices: 23221--23254 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
23211 ACTTGCGGTG
23221 CTTGTGGCT
1 CTTGTGGCT
*
23230 CTTGTGGCA
1 CTTGTGGCT
*
23239 CTTGTGGTT
1 CTTGTGGCT
23248 CTTGTGG
1 CTTGTGG
23255 TTCCTTCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.18, G:0.35, T:0.44
Consensus pattern (9 bp):
CTTGTGGCT
Found at i:24860 original size:74 final size:74
Alignment explanation
Indices: 24778--24921 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 74
24768 TCAAAAGGTG
* * * * * *
24778 AATCCCTGAGATTTTCTTCAAAAGGTAGAAACCATGGGGTTTCAAGATTGAAACCCCTGCTGTTC
1 AATCCCTGAAAATTTCTCCAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTC
24843 CAGAAAGCC
66 CAGAAAGCC
* * * *
24852 AATCCCTGAAAATTTGTCCAAAAGGCATAAACCTTGGGGTTTCAAAATTGAAACCTCTGCCGTTC
1 AATCCCTGAAAATTTCTCCAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTC
24917 CAGAA
66 CAGAA
24922 GGTCATTCCC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (74 bp):
AATCCCTGAAAATTTCTCCAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTC
CAGAAAGCC
Found at i:24932 original size:74 final size:75
Alignment explanation
Indices: 24796--24938 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 75
24786 AGATTTTCTT
* * *
24796 CAAAAGGTAGAAACCATGGGGTTTCAAGATTGAAACCCCTGCTGTTCCAGAAAGCCAATCCCT-G
1 CAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTCCAGAAAGCCAATCCCTGG
24860 AAAATTTGTC
66 AAAATTTGTC
* * * * * *
24870 CAAAAGGCATAAACCTTGGGGTTTCAAAATTGAAACCTCTGCCGTTCCAGAAGGTCATTCCCTGG
1 CAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTCCAGAAAGCCAATCCCTGG
24935 AAAA
66 AAAA
24939 AATCTCAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 54 0.92
75 5 0.08
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (75 bp):
CAAAAGGCAGAAACCATGGGGTTTCAAAATTGAAACCCCTGCCGTTCCAGAAAGCCAATCCCTGG
AAAATTTGTC
Found at i:26722 original size:27 final size:27
Alignment explanation
Indices: 26692--26770 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 27
26682 GCACTTAGGA
26692 CATTTAGGGGCATTTTGGTCATTTTTG
1 CATTTAGGGGCATTTTGGTCATTTTTG
26719 CATTCT-GGGGCATTTTGGTCATTTCCTTG
1 CATT-TAGGGGCATTTTGGTCATTT--TTG
26748 --TTTAGGGGCATTTTGGTCATTTT
1 CATTTAGGGGCATTTTGGTCATTTT
26771 AGGTTCATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 42 0.88
28 1 0.02
29 3 0.06
ACGTcount: A:0.13, C:0.14, G:0.25, T:0.48
Consensus pattern (27 bp):
CATTTAGGGGCATTTTGGTCATTTTTG
Found at i:38425 original size:129 final size:132
Alignment explanation
Indices: 38191--38464 Score: 405
Period size: 129 Copynumber: 2.1 Consensus size: 132
38181 TGATAGAAAT
* * *
38191 ACGCCGCCATATTAATATATGGAGGGATAGATTTTTTTTCCCCTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCTATATTAATATATGGAGAGAGAGATTTTTTTTCCCCTTTTTTTGGAGGGAAAAATTCC
*
38256 CTCCCTACTAAAACAACGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTGA-AAC
66 CTCCCTACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTT-ATAAC
38320 CAG
130 CAG
* *
38323 ATGCCGCTATTTTAATATATGGAGAGAGAGA-TTTTTTT-CCCTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCTATATTAATATATGGAGAGAGAGATTTTTTTTCCCCTTTTTTTGGAGGGAAAAATTCC
* ** * *
38386 CT-CCTCCTAAAACAAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTATCACC
66 CTCCCTACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTATAACC
38450 AG
131 AG
38452 ACGCCGCTA-ATTA
1 ACGCCGCTATATTA
38465 GCGGCGTTTT
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
128 4 0.03
129 64 0.50
130 27 0.21
131 7 0.05
132 26 0.20
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (132 bp):
ACGCCGCTATATTAATATATGGAGAGAGAGATTTTTTTTCCCCTTTTTTTGGAGGGAAAAATTCC
CTCCCTACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTATAACC
AG
Found at i:38694 original size:21 final size:21
Alignment explanation
Indices: 38668--38726 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
38658 CAACATCCTG
38668 GGGTTGCCCAGGCGTGGATAA
1 GGGTTGCCCAGGCGTGGATAA
38689 GGGTTGCCCAGGCGTGGATAA
1 GGGTTGCCCAGGCGTGGATAA
38710 GGGTTGCCCAGGCGTGG
1 GGGTTGCCCAGGCGTGG
38727 GCAAGTCCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.19
Consensus pattern (21 bp):
GGGTTGCCCAGGCGTGGATAA
Found at i:42612 original size:32 final size:32
Alignment explanation
Indices: 42576--42711 Score: 211
Period size: 32 Copynumber: 4.2 Consensus size: 32
42566 GTGTGTAAAG
42576 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
* *
42608 AAAACACCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
**
42640 AAAACGCCCTTATTTAGCGGCGTCTAGGGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
*
42672 AAAACGCCCTTATTTAGCGGCGTCT-TACGAAT
1 AAAACGCCCTTATTTAGCGGCGTCTATA-GAAC
42704 AAAACGCC
1 AAAACGCC
42712 GCTATATCTA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:48155 original size:21 final size:21
Alignment explanation
Indices: 48112--48155 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
48102 ATAATCGAAG
*** *
48112 TTGATCATCCATGTTTGTCGT
1 TTGATCATCCATGGAGGTAGT
48133 TTGATCATCCATGGAGGTAGT
1 TTGATCATCCATGGAGGTAGT
48154 TT
1 TT
48156 TCAGTCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (21 bp):
TTGATCATCCATGGAGGTAGT
Found at i:60605 original size:19 final size:18
Alignment explanation
Indices: 60581--60616 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
60571 TGATGATTTA
60581 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
60600 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
60617 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:67795 original size:19 final size:18
Alignment explanation
Indices: 67771--67806 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
67761 TGAAGATTTA
67771 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
67790 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
67807 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:68422 original size:12 final size:12
Alignment explanation
Indices: 68405--68429 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68395 TCTCTTCTAG
68405 TTCTAGTTTTTC
1 TTCTAGTTTTTC
68417 TTCTAGTTTTTC
1 TTCTAGTTTTTC
68429 T
1 T
68430 CACCATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (12 bp):
TTCTAGTTTTTC
Done.