Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014253.1 Corchorus capsularis cultivar CVL-1 contig14274, 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: 21752
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1824 original size:21 final size:21
Alignment explanation
Indices: 1800--1873 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1790 CTAGCCCTAG
*
1800 TTTCTTGTTCAAATTT-TAGCC
1 TTTCTTGCTCAAATTTAT-GCC
1821 TTTCTTGCTCAAATTTATGCC
1 TTTCTTGCTCAAATTTATGCC
* * *
1842 TTTCTTGCTCAGATCTCTGCC
1 TTTCTTGCTCAAATTTATGCC
1863 TTTCTTGCTCA
1 TTTCTTGCTCA
1874 CCTTTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.49
Consensus pattern (21 bp):
TTTCTTGCTCAAATTTATGCC
Found at i:4829 original size:18 final size:18
Alignment explanation
Indices: 4796--4833 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4786 TAGGCACTAA
*
4796 AAATTGACAAATTAAACAT
1 AAATTGACAAAGTAAA-AT
4815 AAATT-ACAAAGTAAAAT
1 AAATTGACAAAGTAAAAT
4832 AA
1 AA
4834 GTACTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATTGACAAAGTAAAAT
Found at i:9165 original size:56 final size:56
Alignment explanation
Indices: 9103--9210 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 56
9093 GATTTTTTAC
*
9103 AAACTTCCTTGGAAAATATGGGCTTCGGTTTGAAATGGAGACAGTGGATTATGACT
1 AAACTTCCTTGGAAAATATGGGCATCGGTTTGAAATGGAGACAGTGGATTATGACT
*
9159 AAACTTCCTTGGAAAATATGGTCATCGGTTTGAAATGGAGACAGTGGATTAT
1 AAACTTCCTTGGAAAATATGGGCATCGGTTTGAAATGGAGACAGTGGATTAT
9211 TACACGTGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (56 bp):
AAACTTCCTTGGAAAATATGGGCATCGGTTTGAAATGGAGACAGTGGATTATGACT
Found at i:13597 original size:29 final size:29
Alignment explanation
Indices: 13564--13622 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13554 ACCAGTTAAG
13564 TGGCCCGTTCTTTTCGGGTTTGTTCACAC
1 TGGCCCGTTCTTTTCGGGTTTGTTCACAC
*
13593 TGGCCCGTTCTTTTTGGGTTTGTTCACAC
1 TGGCCCGTTCTTTTCGGGTTTGTTCACAC
13622 T
1 T
13623 TAACCACACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.07, C:0.25, G:0.24, T:0.44
Consensus pattern (29 bp):
TGGCCCGTTCTTTTCGGGTTTGTTCACAC
Found at i:15488 original size:48 final size:48
Alignment explanation
Indices: 15436--15527 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
15426 AGTTCTTTTG
15436 CATCAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACATCTC
1 CATCAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACATCTC
15484 CATCAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACA
1 CATCAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACA
15528 AAGCAACAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (48 bp):
CATCAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACATCTC
Found at i:16965 original size:43 final size:41
Alignment explanation
Indices: 16824--17027 Score: 187
Period size: 41 Copynumber: 4.9 Consensus size: 41
16814 TTCTCTCTCC
* ** * *
16824 CCAAAGTCCCCAAGTACATTTATAAAACAGGGGCAACTCTCCTT
1 CCAAAGTCCTCAAACACATTTATAACACAGGGGC-A-TCT-ATT
* * *
16868 CTAAAGTCCTCAAACACATTTATAACATAGAGGCATCTATAT
1 CCAAAGTCCTCAAACACATTTATAACACAGGGGCATCTAT-T
* * *
16910 -CAAAATTCTCAAACACAATTATAACACAGGGGCACCTCTATT
1 CCAAAGTCCTCAAACACATTTATAACACAGGGGCA--TCTATT
* *
16952 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATA
1 CCAAAGTCCTCAAACACATTTATAACACAGGGGCATCTATT
* * *
16993 CTAAAGTCC-CTAAACACAATTATAACACAAGGGCA
1 CCAAAGTCCTC-AAACACATTTATAACACAGGGGCA
17028 ATTTCTATAT
Statistics
Matches: 132, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
40 1 0.01
41 63 0.48
42 5 0.04
43 36 0.27
44 27 0.20
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (41 bp):
CCAAAGTCCTCAAACACATTTATAACACAGGGGCATCTATT
Found at i:16968 original size:84 final size:85
Alignment explanation
Indices: 16843--17028 Score: 268
Period size: 84 Copynumber: 2.2 Consensus size: 85
16833 CCAAGTACAT
* * * *
16843 TTATAAAACAGGGGCAACTCTCCTTCTAAAGTCCTCAAACACATTTATAACATAGAGGCATCTAT
1 TTATAACACAGGGGCAACTCTCATTCCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTAT
* *
16908 ATCAAAATTCTC-AAACACAA
66 A-CAAAAGTCCCTAAACACAA
*
16928 TTATAACACAGGGGCACCTCT-ATTCCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTAT
1 TTATAACACAGGGGCAACTCTCATTCCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTAT
*
16992 ACTAAAGTCCCTAAACACAA
66 ACAAAAGTCCCTAAACACAA
*
17012 TTATAACACAAGGGCAA
1 TTATAACACAGGGGCAA
17029 TTTCTATATG
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
83 7 0.08
84 64 0.71
85 19 0.21
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (85 bp):
TTATAACACAGGGGCAACTCTCATTCCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTAT
ACAAAAGTCCCTAAACACAA
Done.