Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023010.1 Corchorus olitorius cultivar O-4 contig23043, 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: 38788
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:49 original size:2 final size:2
Alignment explanation
Indices: 37--67 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
27 TTGTTGGGAG
37 GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
68 CAAGAGACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:391 original size:6 final size:6
Alignment explanation
Indices: 382--420 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
372 TAGGTTTTAG
382 TTTT-T TTTT-T TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
421 AAAGACAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:5246 original size:25 final size:25
Alignment explanation
Indices: 5210--5259 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
5200 TGTTAGTTTG
* *
5210 TAGAGACTGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTACTCAAA
5235 TAGAGACCGAGCGAGAGTACTCAAA
1 TAGAGACCGAGCGAGAGTACTCAAA
5260 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTACTCAAA
Found at i:7990 original size:2 final size:2
Alignment explanation
Indices: 7983--8017 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7973 GCAACAATTA
7983 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 A
8018 GTAAGTACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8474 original size:42 final size:43
Alignment explanation
Indices: 8427--8514 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 43
8417 TGCATTACTT
* *
8427 AAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
8469 AAATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
8514 A
1 A
8515 TATTAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 8 0.20
45 33 0.80
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:12352 original size:14 final size:14
Alignment explanation
Indices: 12333--12363 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12323 TTTAACTCAA
12333 TTACTTAAATTTTG
1 TTACTTAAATTTTG
12347 TTACTTAAATTTTG
1 TTACTTAAATTTTG
12361 TTA
1 TTA
12364 TGTTGCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (14 bp):
TTACTTAAATTTTG
Found at i:16955 original size:5 final size:5
Alignment explanation
Indices: 16945--16983 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
16935 TATATAGTAG
16945 TAAGA TAAGA TAAGA TAAGA TATAGTA GTAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TA-AG-A -TAAGA TAAGA T
16984 TACAAGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 23 0.74
6 3 0.10
7 3 0.10
8 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (5 bp):
TAAGA
Found at i:20873 original size:19 final size:19
Alignment explanation
Indices: 20851--20888 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20841 AGTTCCATCG
20851 ATGTGGGT-TTTGTCCAATT
1 ATGTGGGTGTTTGT-CAATT
*
20870 ATGTTGGTGTTTGTCAATT
1 ATGTGGGTGTTTGTCAATT
20889 TATCAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.08, G:0.26, T:0.50
Consensus pattern (19 bp):
ATGTGGGTGTTTGTCAATT
Found at i:23408 original size:13 final size:13
Alignment explanation
Indices: 23390--23415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23380 TAACATTTGT
23390 CTTTGTTTTACAG
1 CTTTGTTTTACAG
23403 CTTTGTTTTACAG
1 CTTTGTTTTACAG
23416 TCCATATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTTGTTTTACAG
Found at i:25352 original size:40 final size:41
Alignment explanation
Indices: 25299--25385 Score: 131
Period size: 40 Copynumber: 2.1 Consensus size: 41
25289 TGATTTCATT
* *
25299 CAATTTCGTCCCTGATTTAGAATTTTAGTT-CTATTTAATG
1 CAATTTAGCCCCTGATTTAGAATTTTAGTTACTATTTAATG
* *
25339 CAATTTAGCCCCTGATTTAGGATTTTAGTTACTATTTAATT
1 CAATTTAGCCCCTGATTTAGAATTTTAGTTACTATTTAATG
25380 CAATTT
1 CAATTT
25386 GGTCCCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 27 0.64
41 15 0.36
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.47
Consensus pattern (41 bp):
CAATTTAGCCCCTGATTTAGAATTTTAGTTACTATTTAATG
Found at i:32779 original size:22 final size:22
Alignment explanation
Indices: 32754--32833 Score: 108
Period size: 22 Copynumber: 3.6 Consensus size: 22
32744 TATTCTTATG
*
32754 AAAATTTTGATAACCACCCTAT
1 AAAATTTTGATAACTACCCTAT
*
32776 AAAATTTTGATAATTACCCTAT
1 AAAATTTTGATAACTACCCTAT
*
32798 AAAATTATGATAAACTA-CCTAT
1 AAAATTTTGAT-AACTACCCTAT
*
32820 AAAACTTTGATAAC
1 AAAATTTTGATAAC
32834 GTGATTATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 3 0.06
22 44 0.86
23 4 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAATTTTGATAACTACCCTAT
Done.