Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018316.1 Corchorus olitorius cultivar O-4 contig18349, 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: 19097
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6465 original size:10 final size:10
Alignment explanation
Indices: 6450--6476 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6440 TAAAGAGAAT
6450 TATGTGAAGG
1 TATGTGAAGG
6460 TATGTGAAGG
1 TATGTGAAGG
6470 TATGTGA
1 TATGTGA
6477 TTTGTGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:7062 original size:19 final size:18
Alignment explanation
Indices: 7029--7064 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7019 TTGAAATAAT
7029 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
7047 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
7065 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:12119 original size:14 final size:15
Alignment explanation
Indices: 12100--12131 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
12090 AGCTTCCTAG
12100 AAAAACTCAAAA-AA
1 AAAAACTCAAAAGAA
12114 AAAAACTCAAAAGAA
1 AAAAACTCAAAAGAA
12129 AAA
1 AAA
12132 TTGTTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAACTCAAAAGAA
Found at i:12275 original size:29 final size:29
Alignment explanation
Indices: 12243--12304 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
12233 TTATGACGCA
12243 AAAACATTTTTTTTTCAAAAACGCAACAC
1 AAAACATTTTTTTTTCAAAAACGCAACAC
* *
12272 AAAACATTTTTTTTTCGAAAACGCAAGAC
1 AAAACATTTTTTTTTCAAAAACGCAACAC
12301 AAAA
1 AAAA
12305 AATTAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAACATTTTTTTTTCAAAAACGCAACAC
Found at i:14096 original size:22 final size:20
Alignment explanation
Indices: 14049--14097 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
14039 CTTGAAATAA
14049 TTCTTC-AATAATCTTCAAG
1 TTCTTCAAATAATCTTCAAG
*
14068 -TCTTCAAATTATCTTCAAATG
1 TTCTTCAAATAATCTTC-AA-G
14089 TTCTTCAAA
1 TTCTTCAAA
14098 CACGAACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 9 0.36
20 2 0.08
21 1 0.04
22 8 0.32
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
TTCTTCAAATAATCTTCAAG
Found at i:15168 original size:10 final size:10
Alignment explanation
Indices: 15153--15186 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
15143 TAAATCATAC
*
15153 ATACATACAT
1 ATACATATAT
15163 ATACATATAT
1 ATACATATAT
*
15173 ATATATATAT
1 ATACATATAT
15183 ATAC
1 ATAC
15187 CATTCCACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
ATACATATAT
Found at i:15595 original size:34 final size:34
Alignment explanation
Indices: 15534--15662 Score: 212
Period size: 34 Copynumber: 3.9 Consensus size: 34
15524 AGGGCTGTCC
15534 TCCAGTTATTATCAC-ACCCACTGGGCAGGGTCT
1 TCCAGTTATTATCACAACCCACTGGGCAGGGTCT
* *
15567 TCCAGTTATTATCTCAACTCACTGGGCAGGGTCT
1 TCCAGTTATTATCACAACCCACTGGGCAGGGTCT
15601 TCCAGTTATTATCACAACCCACTGGGCAGGGTCT
1 TCCAGTTATTATCACAACCCACTGGGCAGGGTCT
15635 TCCAGTTATTAT---AACCCACTGGGCAGGG
1 TCCAGTTATTATCACAACCCACTGGGCAGGG
15663 CTGATAAAAC
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
31 16 0.18
33 14 0.15
34 61 0.67
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (34 bp):
TCCAGTTATTATCACAACCCACTGGGCAGGGTCT
Found at i:16912 original size:2 final size:2
Alignment explanation
Indices: 16905--16939 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16895 GTTTCCAAAC
16905 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
16940 CTCTAGACGT
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:17118 original size:4 final size:4
Alignment explanation
Indices: 17109--17143 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
17099 ATGATATTAA
17109 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
17144 TGAATATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
ATTG
Found at i:17139 original size:81 final size:80
Alignment explanation
Indices: 17044--17204 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 80
17034 TATATATTAA
*
17044 ATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATT
1 ATTGATTGATTGA-TTGATATAATATCTTGATCCAATTAGAATCAATTAGTACT--AATGATATT
17107 AAATTGATTGATTGATTG
63 AAATTGATTGATTGATTG
*
17125 ATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
1 ATTGATTGATTGATTGATAT-AATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
17190 ATTGATTGATTGATT
65 ATTGATTGATTGATT
17205 TGAATATTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
80 4 0.05
81 40 0.53
83 31 0.41
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (80 bp):
ATTGATTGATTGATTGATATAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAA
TTGATTGATTGATTG
Found at i:17214 original size:81 final size:84
Alignment explanation
Indices: 17044--17215 Score: 280
Period size: 83 Copynumber: 2.1 Consensus size: 84
17034 TATATATTAA
*
17044 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT-AAATGATATTAA
*
17109 ATTGATTGATTGATTGATTG
65 ATTGATTGATTGATTGAATG
17129 ATTGATTGATTGATTTG-A-ATATCTTGATCCAATTAGAATCAATTAGTACT-AATGATATTAAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
17191 TTGATTGATTGATTTGAAT-
66 TTGATTGATTGA-TTGAATG
17210 ATTGAT
1 ATTGAT
17216 CAAATTAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
81 30 0.36
82 5 0.06
83 31 0.37
84 1 0.01
85 17 0.20
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (84 bp):
ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
TTGATTGATTGATTGAATG
Done.