Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018977.1 Corchorus olitorius cultivar O-4 contig19010, 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: 65712
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:961 original size:11 final size:11
Alignment explanation
Indices: 943--985 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
933 ATCTGGTTTC
943 GCCGTGTCCAT
1 GCCGTGTCCAT
*
954 GTCGTGTCCAT
1 GCCGTGTCCAT
*
965 GCCGTGTCCCT
1 GCCGTGTCCAT
*
976 CCCGTGTCCA
1 GCCGTGTCCA
986 CCACCTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.07, C:0.40, G:0.26, T:0.28
Consensus pattern (11 bp):
GCCGTGTCCAT
Found at i:1281 original size:59 final size:59
Alignment explanation
Indices: 1189--1306 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
1179 TAGAGTGAGT
1189 TTATCTGACGCATAGGAAGTCAACTTGAACTTAAAATGTTCGCTGAAATTACCCAGAGA
1 TTATCTGACGCATAGGAAGTCAACTTGAACTTAAAATGTTCGCTGAAATTACCCAGAGA
1248 TTATCTGACGCATAGGAAGTCAACTTGAACTTAAAATGTTCGCTGAAATTACCCAGAGA
1 TTATCTGACGCATAGGAAGTCAACTTGAACTTAAAATGTTCGCTGAAATTACCCAGAGA
1307 CGATTTTAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (59 bp):
TTATCTGACGCATAGGAAGTCAACTTGAACTTAAAATGTTCGCTGAAATTACCCAGAGA
Found at i:12757 original size:15 final size:14
Alignment explanation
Indices: 12738--12764 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12728 AGTGAGATTT
12738 TTTTTTTTAATCAA
1 TTTTTTTTAATCAA
12752 TTTTTTTTAATCA
1 TTTTTTTTAATCA
12765 CCATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTTTAATCAA
Found at i:21932 original size:128 final size:128
Alignment explanation
Indices: 21704--22088 Score: 734
Period size: 128 Copynumber: 3.0 Consensus size: 128
21694 ACCTGTTTGA
* *
21704 GCATTTCATTTGCAAAGCCATTTTATTCCAACAATGAAAAATCACTAAGCTTCCCAACGCATTTT
1 GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
*
21769 GAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
66 TAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
21832 GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
1 GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
21897 TAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
66 TAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
21960 GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
1 GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
*
22025 TAAAAAACCAAAAAGTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
66 TAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
22088 G
1 G
22089 AAGTGTTACA
Statistics
Matches: 253, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 253 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (128 bp):
GCATTTCATTTGCAAAGCCATTTTATTCCAATAATGAAAAATTACTAAGCTTCCCAACGCATTTT
TAAAAAACCAAAAATTTCACATGGTTAACAAGACAGTTCTAATGTTTTCAGAGATGATAATAG
Found at i:34096 original size:105 final size:103
Alignment explanation
Indices: 33985--34182 Score: 299
Period size: 105 Copynumber: 1.9 Consensus size: 103
33975 TTGATTAAAT
* * * *
33985 TTTTATAGTTTTACTCAGCTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAGTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTACTTTTATTTAATTAAATATAATATCCTTAT-A--A
34050 CTATTTTATTTTTACCATTTTACT-ATTTTAATGAAAATAC
63 CTATTTTATTTTTACCATTTTACTAATTTTAATGAAAATAC
* *
34090 TTTTATAGTTTTATTCAACTAAAAACTCTACTTTTATTTAATTAAATATAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTACTTTTATTTAATTAAATATAATATCCTTATAACTA
*
34155 TTTTATTTTTATCATTTTACTAATTTTA
66 TTTTATTTTTACCATTTTACTAATTTTA
34183 TTAAAAAACT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 23 0.27
103 6 0.07
104 1 0.01
105 55 0.65
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (103 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTACTTTTATTTAATTAAATATAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTTAATGAAAATAC
Found at i:34167 original size:23 final size:23
Alignment explanation
Indices: 34141--34184 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
34131 TTAAATATAA
*
34141 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
34164 TATCATTTTACTAATTTTATT
1 TATCATTATACTAATTTTATT
34185 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:39867 original size:42 final size:42
Alignment explanation
Indices: 39812--39894 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
39802 TAAATTCTAG
* *
39812 TACTCTATCTCTAGGTAATTCATCAAAATAAAGCTAATATTT
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTT
* *
39854 TACTCCATTTCTAGATAATTCATCAAAATAAAGGTAATATT
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
39895 AATTGTTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (42 bp):
TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTT
Found at i:41213 original size:24 final size:22
Alignment explanation
Indices: 41158--41214 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
41148 AAAAATTGTT
**
41158 TATCATTAGTTTGAATCTGTAC
1 TATCATTAGTTTGAATCTAAAC
41180 -A-CATTAGTTTGAATCCTAAAC
1 TATCATTAGTTTGAAT-CTAAAC
41201 ATATCATTAGTTTG
1 -TATCATTAGTTTG
41215 TGTACAGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 13 0.45
21 5 0.17
23 1 0.03
24 10 0.34
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (22 bp):
TATCATTAGTTTGAATCTAAAC
Found at i:44360 original size:12 final size:12
Alignment explanation
Indices: 44300--44377 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
44290 TAGTAATATT
44300 TATAATTAAATA
1 TATAATTAAATA
*
44312 TATATTTTAAATA
1 TATA-ATTAAATA
44325 TAT-A--AAATA
1 TATAATTAAATA
44334 -AT-ATTAGATATA
1 TATAATTA-A-ATA
44346 TATAATTAAATA
1 TATAATTAAATA
44358 TATAA-TAATATA
1 TATAATTAA-ATA
44370 TATAATTA
1 TATAATTA
44378 TTAAACAGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
8 3 0.05
9 5 0.09
10 1 0.02
11 4 0.07
12 23 0.42
13 15 0.27
14 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (12 bp):
TATAATTAAATA
Found at i:44831 original size:1 final size:1
Alignment explanation
Indices: 44825--44849 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
44815 CTATAATTCA
44825 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
44850 AAACTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:50394 original size:4 final size:4
Alignment explanation
Indices: 50385--50523 Score: 269
Period size: 4 Copynumber: 34.8 Consensus size: 4
50375 ACAAAGGAGT
50385 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50433 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50481 TATG TATG TATG TATG TATG TATG TATG TATG TATG TGTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
50524 ATAAATACCA
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 133 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:52099 original size:36 final size:37
Alignment explanation
Indices: 52035--52104 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
52025 TTTTAATTTT
* *
52035 AAATATATTATATATATGCTATAAATTAAAAATCTGA
1 AAATATATTAAATATATGATATAAATTAAAAATCTGA
*
52072 AAATATA-TAAATATAT-ATATAACATTAATAATC
1 AAATATATTAAATATATGATATAA-ATTAAAAATC
52105 AAAAAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 5 0.17
36 17 0.59
37 7 0.24
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (37 bp):
AAATATATTAAATATATGATATAAATTAAAAATCTGA
Found at i:59399 original size:15 final size:16
Alignment explanation
Indices: 59379--59416 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
59369 AGGTTGACAG
59379 AAAACAATTAAAC-AA
1 AAAACAATTAAACTAA
*
59394 AAAACAATTAAACTAG
1 AAAACAATTAAACTAA
59410 AAAACAA
1 AAAACAA
59417 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACTAA
Found at i:62029 original size:26 final size:26
Alignment explanation
Indices: 61993--62046 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
61983 TTCTGAAAAA
61993 ATTATGGCATATTTAGAACTTGATGC
1 ATTATGGCATATTTAGAACTTGATGC
*
62019 ATTATGGCATATTTAGATCTTGATGC
1 ATTATGGCATATTTAGAACTTGATGC
62045 AT
1 AT
62047 GCAGACTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (26 bp):
ATTATGGCATATTTAGAACTTGATGC
Found at i:62251 original size:14 final size:15
Alignment explanation
Indices: 62232--62261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62222 CAATTAAAGC
62232 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
62246 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
62261 A
1 A
62262 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Done.