Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012025.1 Corchorus olitorius cultivar O-4 contig12058, 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: 35784
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2468 original size:52 final size:52
Alignment explanation
Indices: 2406--2508 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
2396 AAAGCATGGA
*
2406 TATAGCAAATGAAATAATATATTTTTCCTATTATAATCTAGCCAATTTTTGC
1 TATAGCAAATGAAATAATATATTTTTCCTATTATAACCTAGCCAATTTTTGC
* * *
2458 TATAGCAAATGAAATAATATATTTTTTCTATTATAACCTTGTCAATTTTTG
1 TATAGCAAATGAAATAATATATTTTTCCTATTATAACCTAGCCAATTTTTG
2509 TTTTCTCTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.45
Consensus pattern (52 bp):
TATAGCAAATGAAATAATATATTTTTCCTATTATAACCTAGCCAATTTTTGC
Found at i:3831 original size:31 final size:31
Alignment explanation
Indices: 3796--3867 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3786 AGGTTAATTA
** * *
3796 AGTCCCTAACGTTACAAAATGGGCTCAAATC
1 AGTCCCTAAAATTACAAAATCGACTCAAATC
*
3827 AGTCCCTAAAATTGCAAAATCGACTCAAATC
1 AGTCCCTAAAATTACAAAATCGACTCAAATC
*
3858 AATCCCTAAA
1 AGTCCCTAAA
3868 GTCAATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (31 bp):
AGTCCCTAAAATTACAAAATCGACTCAAATC
Found at i:4472 original size:31 final size:31
Alignment explanation
Indices: 4437--4515 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
4427 ACCGTTTCTA
* *
4437 TTTAGCCTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGACTCAAATTGGTCAACTTCTGAAAGG
4468 TTTAGACTCAAATTGAG-CAACTTCTGAAAGG
1 TTTAGACTCAAATTG-GTCAACTTCTGAAAGG
*
4499 TTTAGACTCAAGTTGGT
1 TTTAGACTCAAATTGGT
4516 GGCTAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 41 0.95
32 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTCTGAAAGG
Found at i:5763 original size:17 final size:17
Alignment explanation
Indices: 5741--5776 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5731 ATCAATCATC
*
5741 TATTATAAGACAATGGT
1 TATTATAAAACAATGGT
5758 TATTATAAAACAATGGT
1 TATTATAAAACAATGGT
5775 TA
1 TA
5777 AATGAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (17 bp):
TATTATAAAACAATGGT
Found at i:8882 original size:50 final size:50
Alignment explanation
Indices: 8821--8916 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
8811 TACAAACATG
*
8821 CAAAATCGTGAAGTTCAAGTTTTAGGTTTTGAAGAAATTTTTTTTTTTTT
1 CAAAATCGTGAAGTTCAAGTTTTAGGTTTTGAAGAAAGTTTTTTTTTTTT
8871 CAAAATCGTGAAGTTCAAGTTTTAGGTTTTGAAGAAAGTTTTTTTT
1 CAAAATCGTGAAGTTCAAGTTTTAGGTTTTGAAGAAAGTTTTTTTT
8917 GCCTAGCCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (50 bp):
CAAAATCGTGAAGTTCAAGTTTTAGGTTTTGAAGAAAGTTTTTTTTTTTT
Found at i:9243 original size:22 final size:21
Alignment explanation
Indices: 9218--9274 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
9208 AACCACACTG
**
9218 TGAAAATTTGATAAACTCGTTA
1 TGAAAATTTGATAAACT-AATA
* *
9240 TG-AAATTTCAATAACCTAATA
1 TGAAAATTT-GATAAACTAATA
9261 TGAAAATTTGATAA
1 TGAAAATTTGATAA
9275 CCACACTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (21 bp):
TGAAAATTTGATAAACTAATA
Found at i:9286 original size:22 final size:22
Alignment explanation
Indices: 9198--9398 Score: 139
Period size: 22 Copynumber: 9.2 Consensus size: 22
9188 GCTAACGTAG
* *
9198 AAATATTGTTAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* * **
9221 AAATTTGATAAACTCGTTATG-
1 AAATTTGATAACCACACTATGA
*
9242 AAATTTCAATAACCTA-A-TATGA
1 AAATTT-GATAACC-ACACTATGA
*
9264 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACACTATGA
*
9286 AATTTTGATAACCACACTATGA
1 AAATTTGATAACCACACTATGA
* * *
9308 AATTTTGATAATCACACAAT-A
1 AAATTTGATAACCACACTATGA
* * *
9329 AAA-TTGGTAACCGCATTATGA
1 AAATTTGATAACCACACTATGA
9350 AAATTTTGATAACCACA-TCATG-
1 AAA-TTTGATAACCACACT-ATGA
*
9372 AAATTTCGATAACCTTC-CTATGA
1 AAATTT-GATAACC-ACACTATGA
9395 AAAT
1 AAAT
9399 GAAACTATGA
Statistics
Matches: 140, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
20 12 0.09
21 27 0.19
22 78 0.56
23 23 0.16
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:9287 original size:43 final size:44
Alignment explanation
Indices: 9207--9398 Score: 126
Period size: 43 Copynumber: 4.4 Consensus size: 44
9197 GAAATATTGT
* * * ** *
9207 TAACCACACTGTGAAAATTTGATAAACTCGTTATGAAATTTCAA
1 TAACCACACTATGAAAATTTGATAACCACACTGTGAAATTTCAA
**
9251 TAACCTA-A-TATGAAAATTTGATAACCACACTGTGAAATTTTGA
1 TAACC-ACACTATGAAAATTTGATAACCACACTGTGAAATTTCAA
* * ** * **
9294 TAACCACACTATGAAATTTTGATAATCACACAAT-AAAATT-GG
1 TAACCACACTATGAAAATTTGATAACCACACTGTGAAATTTCAA
* * * *
9336 TAACCGCATTATGAAAATTTTGATAACCACA-TCATGAAATTTCGA
1 TAACCACACTATGAAAA-TTTGATAACCACACT-GTGAAATTTCAA
*
9381 TAACCTTC-CTATGAAAAT
1 TAACC-ACACTATGAAAAT
9399 GAAACTATGA
Statistics
Matches: 117, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
42 16 0.14
43 52 0.44
44 33 0.28
45 15 0.13
46 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (44 bp):
TAACCACACTATGAAAATTTGATAACCACACTGTGAAATTTCAA
Found at i:9311 original size:65 final size:63
Alignment explanation
Indices: 9198--9386 Score: 177
Period size: 65 Copynumber: 2.9 Consensus size: 63
9188 GCTAACGTAG
* * * * * *
9198 AAATATTGTTAACCACACTGTGAAAATTTGATAAACTCGTTATGAAATTTCAATAACCTA-ATAT
1 AAAT-TTGATAACCACACTGTGAAATTTTGATAACCAC-ATATGAAATTTCGATAACCTACA-AT
9262 GA
63 -A
*
9264 AAATTTGATAACCACACTGTGAAATTTTGATAACCACACTATGAAATTTTGATAATCAC-ACAAT
1 AAATTTGATAACCACACTGTGAAATTTTGATAACCACA-TATGAAATTTCGATAA-C-CTACAAT
9328 A
63 A
* * * *
9329 AAA-TTGGTAACCGCATTATGAAAATTTTGATAACCACATCATGAAATTTCGATAACCT
1 AAATTTGATAACCACACTGTG-AAATTTTGATAACCACAT-ATGAAATTTCGATAACCT
9387 TCCTATGAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
63 1 0.01
64 15 0.14
65 78 0.75
66 8 0.08
67 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (63 bp):
AAATTTGATAACCACACTGTGAAATTTTGATAACCACATATGAAATTTCGATAACCTACAATA
Found at i:9333 original size:87 final size:87
Alignment explanation
Indices: 9197--9398 Score: 187
Period size: 87 Copynumber: 2.3 Consensus size: 87
9187 TGCTAACGTA
* * * * *** * *
9197 GAAATATTGTTAACCACACTGTGAAAATTTGATAAACTCGTTATGAAATTTCAATAACC-TAATA
1 GAAATTTTGATAACCACACTATGAAAATTTGATAAACACACAAT-AAAATT-AATAACCGCAATA
*
9261 TGAAAA-TTTGATAACCACA-CTGT
64 TGAAAATTTTGATAACCACATC-AT
* * ** *
9284 GAAATTTTGATAACCACACTATGAAATTTTGATAATCACACAATAAAATTGGTAACCGCATTATG
1 GAAATTTTGATAACCACACTATGAAAATTTGATAAACACACAATAAAATTAATAACCGCAATATG
9349 AAAATTTTGATAACCACATCAT
66 AAAATTTTGATAACCACATCAT
* *
9371 GAAATTTCGATAACCTTC-CTATGAAAAT
1 GAAATTTTGATAACC-ACACTATGAAAAT
9399 GAAACTATGA
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
85 5 0.05
86 14 0.15
87 72 0.77
88 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (87 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAAACACACAATAAAATTAATAACCGCAATATG
AAAATTTTGATAACCACATCAT
Found at i:25055 original size:50 final size:50
Alignment explanation
Indices: 24976--25076 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
24966 TCTCTAATAT
* *
24976 CGAAATTCAGAGAGAATGCATCAATCAGTTGAGTCAAATGCTCGGTGCAA
1 CGAAATTCAGAGAGAATGCATCAACCAGTTGAGTCAAATGCTCGATGCAA
*
25026 CGAAATTTAGAGA-ACATGCATCAACCAGTTGAGTCAAATGCTCGATGCAA
1 CGAAATTCAGAGAGA-ATGCATCAACCAGTTGAGTCAAATGCTCGATGCAA
25076 C
1 C
25077 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (50 bp):
CGAAATTCAGAGAGAATGCATCAACCAGTTGAGTCAAATGCTCGATGCAA
Found at i:28399 original size:21 final size:21
Alignment explanation
Indices: 28375--28441 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
28365 AATTCTCTGT
28375 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
28396 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
28417 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
28438 AAAT
1 AAAT
28442 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:28611 original size:56 final size:57
Alignment explanation
Indices: 28508--28622 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 57
28498 TTTATTTTGT
*** *
28508 AGAATAATTAAGTAGAGATATGAGGGATATTTTTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGAGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
28565 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGAGGGATAGGATTTATTATAACATTTATTGTGTGAA
28621 AG
1 AG
28623 GAAACAGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 33 0.62
57 20 0.38
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATATGAGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:35499 original size:51 final size:50
Alignment explanation
Indices: 35398--35500 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
35388 GTTCTTCATA
** *
35398 TTTTTCTTGTTTAGATCTTGTCTCAGGACATTCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT
* * *
35448 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT
35499 TT
1 TT
35501 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.09
51 40 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTATTAGTGT
Done.