Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013529.1 Corchorus olitorius cultivar O-4 contig13562, 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: 62431
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5246 original size:14 final size:14
Alignment explanation
Indices: 5227--5258 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5217 CCTGTTGGTC
5227 TTCAGAGTAGTGAG
1 TTCAGAGTAGTGAG
5241 TTCAGAGTAGTGAG
1 TTCAGAGTAGTGAG
5255 TTCA
1 TTCA
5259 CCCTCCACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (14 bp):
TTCAGAGTAGTGAG
Found at i:5792 original size:13 final size:13
Alignment explanation
Indices: 5774--5798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5764 TTTTTACCAC
5774 CTTAAAATTATTG
1 CTTAAAATTATTG
5787 CTTAAAATTATT
1 CTTAAAATTATT
5799 TTTTGGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:9240 original size:51 final size:50
Alignment explanation
Indices: 9139--9240 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
9129 GTTCTTCATA
* **
9139 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
9189 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
9240 T
1 T
9241 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:16155 original size:10 final size:10
Alignment explanation
Indices: 16136--16165 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16126 GAAATATCCA
16136 ATTCCCGCTT
1 ATTCCCGCTT
*
16146 ATTCCTGCTT
1 ATTCCCGCTT
16156 ATTCCCGCTT
1 ATTCCCGCTT
16166 CTAGTCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.10, T:0.43
Consensus pattern (10 bp):
ATTCCCGCTT
Found at i:34030 original size:19 final size:17
Alignment explanation
Indices: 34006--34040 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
33996 TGAAGATTTA
34006 TTGAAGACAATTTGAAGAT
1 TTGAAGAC--TTTGAAGAT
34025 TTGAAGACTTTGAAGA
1 TTGAAGACTTTGAAGA
34041 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (17 bp):
TTGAAGACTTTGAAGAT
Found at i:34671 original size:19 final size:18
Alignment explanation
Indices: 34633--34671 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
34623 ATTCACATAA
* *
34633 TTCTCTCTAGATTTATTT
1 TTCTCTCTAGATCTAGTT
34651 TTCTCTTCTAGATCTAGTT
1 TTCTC-TCTAGATCTAGTT
34670 TT
1 TT
34672 TAGGCAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.15, C:0.18, G:0.08, T:0.59
Consensus pattern (18 bp):
TTCTCTCTAGATCTAGTT
Found at i:49651 original size:46 final size:45
Alignment explanation
Indices: 49585--49674 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 45
49575 ACTTAACGGC
49585 GTGTGGGTATACTCACTTAGTCTAACCTGAAAAAGTATTAAATTT
1 GTGTGGGTATACTCACTTAGTCTAACCTGAAAAAGTATTAAATTT
*
49630 GTGTGGGGTATACTCACTTAGTCTAATCTGAAAAAGTATTAAATT
1 GTGT-GGGTATACTCACTTAGTCTAACCTGAAAAAGTATTAAATT
49675 GGTCCATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.09
46 39 0.91
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (45 bp):
GTGTGGGTATACTCACTTAGTCTAACCTGAAAAAGTATTAAATTT
Found at i:56157 original size:25 final size:25
Alignment explanation
Indices: 56123--56172 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
56113 GAAATCATTA
*
56123 CCACCTAGGTGTGGGTTTTATATTG
1 CCACCTAGGTGTGGGCTTTATATTG
*
56148 CCACGTAGGTGTGGGCTTTATATTG
1 CCACCTAGGTGTGGGCTTTATATTG
56173 AACCATGGGG
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:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (25 bp):
CCACCTAGGTGTGGGCTTTATATTG
Found at i:57855 original size:19 final size:19
Alignment explanation
Indices: 57833--57883 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
57823 AGGCTGAAAT
57833 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
57852 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
57871 TAATT-ATTATTAA
1 TAATTAATTATTAA
57884 GAATCTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:57887 original size:16 final size:16
Alignment explanation
Indices: 57837--57887 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
57827 TGAAATTAAT
*
57837 TAATTATTAATTAAATAA
1 TAATTATT-ATT-AAGAA
*
57855 TAATTATT-TTATTGAA
1 TAATTATTATTA-AGAA
57871 TAATTATTATTAAGAA
1 TAATTATTATTAAGAA
57887 T
1 T
57888 CTTATGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 3 0.11
18 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
TAATTATTATTAAGAA
Found at i:58698 original size:29 final size:29
Alignment explanation
Indices: 58656--58749 Score: 152
Period size: 29 Copynumber: 3.1 Consensus size: 29
58646 TTAATTAATT
58656 ATTTGAAGAGCTAAATATGACTAAGTATG
1 ATTTGAAGAGCTAAATATGACTAAGTATG
58685 ATTTGAAGAGCTAAATATGACTAAGTATG
1 ATTTGAAGAGCTAAATATGACTAAGTATG
58714 ATTAATTTGAAGAGCTAAATATGACTAAGTATG
1 ----ATTTGAAGAGCTAAATATGACTAAGTATG
58747 ATT
1 ATT
58750 AATTTCGTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
29 32 0.52
33 29 0.48
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
ATTTGAAGAGCTAAATATGACTAAGTATG
Found at i:58727 original size:33 final size:33
Alignment explanation
Indices: 58656--58754 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
58646 TTAATTAATT
58656 ATTTGAAGAGCTAAATATGACTAAGTATG----
1 ATTTGAAGAGCTAAATATGACTAAGTATGATTA
58685 ATTTGAAGAGCTAAATATGACTAAGTATGATTA
1 ATTTGAAGAGCTAAATATGACTAAGTATGATTA
58718 ATTTGAAGAGCTAAATATGACTAAGTATGATTA
1 ATTTGAAGAGCTAAATATGACTAAGTATGATTA
58751 ATTT
1 ATTT
58755 CGTGGCCTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.44
33 37 0.56
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.34
Consensus pattern (33 bp):
ATTTGAAGAGCTAAATATGACTAAGTATGATTA
Done.