Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021707.1 Corchorus olitorius cultivar O-4 contig21740, 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: 29390
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:52 original size:2 final size:2
Alignment explanation
Indices: 45--69 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35 TAAATTTTAA
45 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 A
70 AAAACTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:266 original size:21 final size:23
Alignment explanation
Indices: 241--287 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
231 AAACTAATAA
241 TAAAG-TTTGAATCCCTCTA-AT
1 TAAAGATTTGAATCCCTCTATAT
*
262 TAAAGATTTTTAATCCCTCTATAT
1 TAAAGA-TTTGAATCCCTCTATAT
286 TA
1 TA
288 TTATTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAAGATTTGAATCCCTCTATAT
Found at i:8745 original size:3 final size:3
Alignment explanation
Indices: 8732--8781 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
8722 TTTGGATTGA
*
8732 ATT ATTT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT -TT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
8777 ATT AT
1 ATT AT
8782 CTATCTATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:15015 original size:18 final size:17
Alignment explanation
Indices: 14988--15021 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
14978 GAGGGCATGG
14988 CTTTCTTTCTCCAGTTT
1 CTTTCTTTCTCCAGTTT
*
15005 CTTTGCTTTCTGCAGTT
1 CTTT-CTTTCTCCAGTT
15022 GGCTTCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.06, C:0.26, G:0.12, T:0.56
Consensus pattern (17 bp):
CTTTCTTTCTCCAGTTT
Found at i:19626 original size:33 final size:33
Alignment explanation
Indices: 19580--19717 Score: 106
Period size: 32 Copynumber: 4.2 Consensus size: 33
19570 CCCAACTGGT
19580 GCGGCACAGCCATGGGC-ATGCCGCACCAGTTGG
1 GCGGCACAGCCAT-GGCTATGCCGCACCAGTTGG
*
19613 GCGGCAC-GTCCATGGCTGTGCCGCACCAGTTGG
1 GCGGCACAG-CCATGGCTATGCCGCACCAGTTGG
* ** * * * *
19646 GCGGCACCGCTGTGGCGA-GCCACACCAGCTGT
1 GCGGCACAGCCATGGCTATGCCGCACCAGTTGG
* * * *
19678 GCGGCTTC-GCCGTGGC-GTGCCGCACCAGCTGG
1 GCGGC-ACAGCCATGGCTATGCCGCACCAGTTGG
19710 GCGGCACA
1 GCGGCACA
19718 ACCAATTTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.01
32 44 0.52
33 39 0.46
34 1 0.01
ACGTcount: A:0.14, C:0.36, G:0.37, T:0.14
Consensus pattern (33 bp):
GCGGCACAGCCATGGCTATGCCGCACCAGTTGG
Found at i:19981 original size:18 final size:18
Alignment explanation
Indices: 19955--19998 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19945 ATTTAATTAA
*
19955 AATTAATTATTCTTGA-TT
1 AATTTATTATT-TTGACTT
19973 AATTTATTATTTTGACTT
1 AATTTATTATTTTGACTT
*
19991 AGTTTATT
1 AATTTATT
19999 TACTATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (18 bp):
AATTTATTATTTTGACTT
Found at i:20467 original size:29 final size:29
Alignment explanation
Indices: 20435--20491 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
20425 TAGGGTAAAA
* *
20435 TTGATTTATGAATTAATTTTATAAATTAT
1 TTGAGTTATGAATTAATATTATAAATTAT
* * *
20464 TTGAGTTATTATTTGATATTATAAATTA
1 TTGAGTTATGAATTAATATTATAAATTA
20492 AAATGAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (29 bp):
TTGAGTTATGAATTAATATTATAAATTAT
Found at i:22806 original size:76 final size:76
Alignment explanation
Indices: 22669--22820 Score: 168
Period size: 76 Copynumber: 2.0 Consensus size: 76
22659 ACAAGGACCC
* *
22669 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCATG-
1 CGACTCCACCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCA-GA
22733 TGGGCAGTGTCA
65 TGGGCAGTGTCA
* * * **
22745 CGACTCCAGCTAGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTAGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
22807 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
22821 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
75 5 0.08
76 53 0.83
77 6 0.09
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:23793 original size:26 final size:26
Alignment explanation
Indices: 23751--23800 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
23741 ATGATTTAGG
*
23751 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
* *
23777 GGTTACTAACGCTCTTTTTTTTTT
1 GGTTACTAACGCCCTTTTTCTTTT
23801 TTTTTCAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Found at i:23871 original size:3 final size:3
Alignment explanation
Indices: 23863--23897 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
23853 GTTACTAACC
* *
23863 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23898 TTTTCAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:23898 original size:12 final size:12
Alignment explanation
Indices: 23863--23900 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
23853 GTTACTAACC
*
23863 TTATTATTATTA
1 TTATTATTATTT
23875 TTATTATTATTT
1 TTATTATTATTT
*
23887 TTATTTTTATTT
1 TTATTATTATTT
23899 TT
1 TT
23901 TCAAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:25984 original size:21 final size:22
Alignment explanation
Indices: 25948--25988 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25938 AGTTTCTGAT
*
25948 TCGACCTCCTTGAAGGTTGACG
1 TCGACCTCCATGAAGGTTGACG
25970 TCGACC-CCATGAAGGTTGA
1 TCGACCTCCATGAAGGTTGA
25989 AACAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
TCGACCTCCATGAAGGTTGACG
Done.