Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022612.1 Corchorus olitorius cultivar O-4 contig22645, 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: 44868
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1797 original size:42 final size:43
Alignment explanation
Indices: 1746--1839 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
1736 AGTACATTAC
**
1746 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
*
1787 CTAATATTCTACTCCTCCATTTCTAAATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAAATAATTCATCAAAATAAAG
1832 CTAATATT
1 CTAATATT
1840 AATGTTGCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
Found at i:3766 original size:42 final size:42
Alignment explanation
Indices: 3687--3767 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
3677 AGTTTAGCTC
*
3687 TTTTCAAAGTGGGAAAGATCCCATCAAGTCTTAAAAGTTCTT
1 TTTTCAAAGTGGGAAAGATCCCATCAAGTCTCAAAAGTTCTT
* *
3729 TTTTCAAATTGGGAAAGATCCCATCAAGTCTCCAAAGTT
1 TTTTCAAAGTGGGAAAGATCCCATCAAGTCTCAAAAGTT
3768 TTTAATTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (42 bp):
TTTTCAAAGTGGGAAAGATCCCATCAAGTCTCAAAAGTTCTT
Found at i:3781 original size:38 final size:38
Alignment explanation
Indices: 3697--3913 Score: 136
Period size: 42 Copynumber: 5.4 Consensus size: 38
3687 TTTTCAAAGT
* *
3697 GGGAAAGATCCCATCAAGTCTTAAAAGTTCTTTTTTCAAATT-
1 GGGAAAGATCCCATCAAGTCTTCAAAG----TTTTT-AATTTA
*
3739 GGGAAAGATCCCATCAAGTCTCCAAAGTTTTTAATTTA
1 GGGAAAGATCCCATCAAGTCTTCAAAGTTTTTAATTTA
* * * *
3777 GGGAAAGATCTCATCATGT-TATCAAAGTTGTCAATTTA
1 GGGAAAGATCCCATCAAGTCT-TCAAAGTTTTTAATTTA
*** * *
3815 GGGAAAGATCTTTTCAAGTGGTTTTCAAAAGTTTTCAATTTA
1 GGGAAAGATCCCATCAA---GTCTTC-AAAGTTTTTAATTTA
* * * *
3857 GGGATAGATCCCATCCAATTTTTTTCAAAGATTTT-A-TTA
1 GGGAAAGATCCCAT-CAA--GTCTTCAAAGTTTTTAATTTA
3896 GGGGAAAGATCCCATCAA
1 -GGGAAAGATCCCATCAA
3914 AGCTTTAAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
37 5 0.03
38 50 0.34
39 6 0.04
40 14 0.10
41 11 0.08
42 56 0.39
43 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (38 bp):
GGGAAAGATCCCATCAAGTCTTCAAAGTTTTTAATTTA
Found at i:3859 original size:42 final size:38
Alignment explanation
Indices: 3729--3871 Score: 128
Period size: 38 Copynumber: 3.7 Consensus size: 38
3719 AAAAGTTCTT
* * * *
3729 TTTTCAAATT-GGGAAAGATCCCATCAAGTCT-CCAAAG
1 TTTTCAATTTAGGGAAAGATCTCATCATGT-TATCAAAG
*
3766 TTTTTAATTTAGGGAAAGATCTCATCATGTTATCAAAG
1 TTTTCAATTTAGGGAAAGATCTCATCATGTTATCAAAG
* ** *
3804 TTGTCAATTTAGGGAAAGATCTTTTCAAGTGGTTTTCAAAAG
1 TTTTCAATTTAGGGAAAGATCTCATC-A-T-GTTATC-AAAG
* *
3846 TTTTCAATTTAGGGATAGATCCCATC
1 TTTTCAATTTAGGGAAAGATCTCATC
3872 CAATTTTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 9 0.11
38 44 0.52
39 1 0.01
40 1 0.01
41 5 0.06
42 25 0.29
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (38 bp):
TTTTCAATTTAGGGAAAGATCTCATCATGTTATCAAAG
Found at i:15818 original size:68 final size:68
Alignment explanation
Indices: 15709--15847 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
15699 AAATCCAAAC
*
15709 ATTGTTATGATACGATGGCATTCTTTCTGATCTATCTTTGACTTGTATACTAATCCATATGGCCG
1 ATTGTTATGATACGATGGCATTCTTTCTGATCTATCTTTGACTTGTATACTAATCCATATAGCCG
15774 TTT
66 TTT
15777 ATTGTTATGATACGATGGCATTCTTTCTGATCTATCTTTGACTTGTATACTAATCCATATAGCCG
1 ATTGTTATGATACGATGGCATTCTTTCTGATCTATCTTTGACTTGTATACTAATCCATATAGCCG
15842 TTT
66 TTT
15845 ATT
1 ATT
15848 CTATTGTAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (68 bp):
ATTGTTATGATACGATGGCATTCTTTCTGATCTATCTTTGACTTGTATACTAATCCATATAGCCG
TTT
Found at i:16546 original size:2 final size:2
Alignment explanation
Indices: 16539--16567 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16529 CTCAGTCTTT
16539 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16568 ATACATCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26762 original size:3 final size:3
Alignment explanation
Indices: 26742--26864 Score: 203
Period size: 3 Copynumber: 40.7 Consensus size: 3
26732 ATATATACTC
* *
26742 TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26790 TAA T-A TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
26835 TATA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
26865 TATACTAAAT
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.02
3 105 0.93
4 6 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28232 original size:49 final size:47
Alignment explanation
Indices: 28127--28261 Score: 164
Period size: 49 Copynumber: 2.8 Consensus size: 47
28117 GAGCGTGGCA
* * * * *
28127 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAATGAAAATTAAATG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGG
28174 ATCAATTTTGTCTTAAAAATTGAGAAAAATGTGCAAGGAAAAATAAAGG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAA-GTGCAAGGAAAAATAAAGG
* * *
28223 TTCAGTTTTGTAGTAAAAATTGAGAAAAAGTGC-AGGAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGGAAA
28262 TGTAAAAGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
47 18 0.23
48 18 0.23
49 41 0.53
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGG
Found at i:32966 original size:11 final size:11
Alignment explanation
Indices: 32950--32987 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
32940 GAAGATGAAG
32950 AAGAAAATAGA
1 AAGAAAATAGA
*
32961 AAGAAAA-AGG
1 AAGAAAATAGA
32971 AAG-AAATAGA
1 AAGAAAATAGA
32981 AAGAAAA
1 AAGAAAA
32988 AAATAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.13
10 10 0.43
11 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (11 bp):
AAGAAAATAGA
Found at i:32989 original size:21 final size:21
Alignment explanation
Indices: 32949--32988 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
32939 AGAAGATGAA
32949 GAAGAAAATAGAAAGAAAAAG
1 GAAGAAAATAGAAAGAAAAAG
32970 GAAG-AAATAGAAAGAAAAA
1 GAAGAAAATAGAAAGAAAAA
32989 AATAATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (21 bp):
GAAGAAAATAGAAAGAAAAAG
Found at i:33271 original size:15 final size:15
Alignment explanation
Indices: 33251--33280 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33241 AGGGGACAAT
33251 GGAGCTATTTAGCCA
1 GGAGCTATTTAGCCA
33266 GGAGCTATTTAGCCA
1 GGAGCTATTTAGCCA
33281 TATAGAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
GGAGCTATTTAGCCA
Found at i:35009 original size:25 final size:24
Alignment explanation
Indices: 34958--35014 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
34948 GTCAGTCTTG
*
34958 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
34981 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
35006 AATTTATTT
1 AATTTATTT
35015 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:42603 original size:34 final size:34
Alignment explanation
Indices: 42565--42631 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42555 GCGTTTCTGA
42565 TCTAAAAAAAAAATATAT-ATTTTCTGCATTTTTT
1 TCTAAAAAAAAAATATATGATTTT-TGCATTTTTT
* *
42599 TCTAAAAAAAAAATATTTGATTTTTGCGTTTTT
1 TCTAAAAAAAAAATATATGATTTTTGCATTTTT
42632 AATTTTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 25 0.83
35 5 0.17
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (34 bp):
TCTAAAAAAAAAATATATGATTTTTGCATTTTTT
Done.