Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013178.1 Corchorus olitorius cultivar O-4 contig13211, 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: 52114
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6588 original size:11 final size:11
Alignment explanation
Indices: 6572--6597 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6562 GTTTTAGATC
6572 TTTTCTTCTAG
1 TTTTCTTCTAG
6583 TTTTCTTCTAG
1 TTTTCTTCTAG
6594 TTTT
1 TTTT
6598 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:7932 original size:70 final size:70
Alignment explanation
Indices: 7842--7989 Score: 244
Period size: 70 Copynumber: 2.1 Consensus size: 70
7832 TGATTGCTTT
*
7842 GGCTTTTCCACAAGCCAAACTCGTTTCCATACG-AGCCAGTTCAAGCTTTGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAAG-CAGGTCAAGCTTTGGTTCCATCCAAGCA
7906 ATCAAG
65 ATCAAG
* *
7912 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAAGCAGGTCAAGCTTTGGTTCCATCCGAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAAGCAGGTCAAGCTTTGGTTCCATCCAAGCAA
*
7977 TCAGG
66 TCAAG
7982 GGCTTTTC
1 GGCTTTTC
7990 GATAAGTCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 71 0.97
71 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (70 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAAGCAGGTCAAGCTTTGGTTCCATCCAAGCAA
TCAAG
Found at i:12267 original size:51 final size:51
Alignment explanation
Indices: 12195--12467 Score: 331
Period size: 51 Copynumber: 5.5 Consensus size: 51
12185 TCAAAAACAA
*
12195 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTATCAAT
1 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTACCAAT
*
12246 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTATCAAT
1 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTACCAAT
* * *
12297 TTGTCCTTCTCCATCGGAAGGTGTTGTACAAAGTTGTCTA-CTTTTACCAAT
1 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTC-AGCATTTACCAAT
* *
12348 TTGCTCTTCTTCATCGGAAGGTG-T-T-----G-T-TC-GCATTTACCAAT
1 TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTACCAAT
* *
12389 TTGCCCTTC-CTCATCGGAAGGTGTTGTCCAAGGTTGTCTA-CTTTTACCAAT
1 TTGCCCTTCTC-CATCGGAAGGTGTTGTCCAAAGTTGTC-AGCATTTACCAAT
12440 TTGCCCTTC-CTCATCGGAAGGTGTTGTC
1 TTGCCCTTCTC-CATCGGAAGGTGTTGTC
12468 GGCATTTACC
Statistics
Matches: 197, Mismatches: 11, Indels: 28
0.83 0.05 0.12
Matches are distributed among these distances:
41 30 0.15
42 3 0.02
43 2 0.01
44 1 0.01
48 1 0.01
49 2 0.01
50 3 0.02
51 154 0.78
52 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (51 bp):
TTGCCCTTCTCCATCGGAAGGTGTTGTCCAAAGTTGTCAGCATTTACCAAT
Found at i:12386 original size:41 final size:41
Alignment explanation
Indices: 12339--12917 Score: 555
Period size: 41 Copynumber: 13.9 Consensus size: 41
12329 GTTGTCTACT
* *
12339 TTTACCAATTTGCTCTTCTTCATCGGAAGGTGTTGTTC-GCA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCA
12380 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCCAAGGTTGTCTA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGT-C-A----G-C-A
*
12429 CTTTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCGGCA
1 --TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* *
12472 TTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGT-TGCCA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAG-CA
* ** ** *
12513 TTGT-CCAGTTTGCTGTTCCTCATTAGAAGGTGTTGTCAGCT
1 TT-TACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* * * *
12554 TTTGCCAATTTGCCCTTTCTCATCGGGAGGTGTTGT-TGCTA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGC-A
* *
12595 TTGT-CCAGTTTGCTCTTCCTCATCGGAAGGTGTTGTCAGCA
1 TT-TACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* *
12636 TTTACCAATTTGCCCATCCTCATCAGAAGGTGTTGTCAGCA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
12677 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* * * * * * *
12718 TTTACCAATATGCCCTTTCTCATTGGGAGGTGTAGT-TGCC
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* * * *
12758 TTTGTCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTCAACA
1 TTT-ACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* * *
12800 TTTCCCAATTTGCCCTTCCTCATCAGAAGGTGTTGTTTA--A
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCA
* * * * *
12840 GTTCACCAGTTTGCCCATCCTCATCGGAAGGTGTTGCCTGCA
1 -TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
* * *
12882 TTT-CTCAGTTTGCCCTCCCTCATCGGGAGGTGTTGT
1 TTTAC-CAATTTGCCCTTCCTCATCGGAAGGTGTTGT
12918 TCCTATTCCT
Statistics
Matches: 443, Mismatches: 69, Indels: 52
0.79 0.12 0.09
Matches are distributed among these distances:
40 13 0.03
41 375 0.85
42 12 0.03
43 1 0.00
44 1 0.00
45 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 36 0.08
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCA
Found at i:12716 original size:164 final size:164
Alignment explanation
Indices: 12339--12924 Score: 655
Period size: 164 Copynumber: 3.5 Consensus size: 164
12329 GTTGTCTACT
* *
12339 TTTACCAATTTGCTCTTCTTCATCGGAAGGTGTTGTTC-GCATTTACCAATTTGCCCTTCCTCAT
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCATTTACCAATTTGCCCTTCCTCAT
* * * * *
12403 CGGAAGGTGTTGTCCAAGGTTGTCTACTTTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTC
65 CGGGAGGTG-T-T-----GTTGCCTA-TTGT-CCAGTTTGCTCTTCCTCATCGGAAGGTGTTGTC
* * * *
12468 GGCATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCA
121 AGCATTTACCAATTTGCCCTTCCTCATCAGAAGGTGTTGTAG-CA
* ** ** * * *
12513 TTGT-CCAGTTTGCTGTTCCTCATTAGAAGGTGTTGTCAGCTTTTGCCAATTTGCCCTTTCTCAT
1 TT-TACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCAT
12577 CGGGAGGTGTTGTTG-CTATTGTCCAGTTTGCTCTTCCTCATCGGAAGGTGTTGTCAGCATTTAC
65 CGGGAGGTGTTGTTGCCTATTGTCCAGTTTGCTCTTCCTCATCGGAAGGTGTTGTCAGCATTTAC
*
12641 CAATTTGCCCATCCTCATCAGAAGGTGTTGTCAGCA
130 CAATTTGCCCTTCCTCATCAGAAGGTGTTGT-AGCA
* * *
12677 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATATGCCCTTTCTCATT
1 TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCATC
* * *
12742 GGGAGGTGTAGTTGCCT-TTGTCCAGTTTG-TCCTTCCTCATCGGAAGGTGTTGTCAACATTTCC
66 GGGAGGTGTTGTTGCCTATTGTCCAGTTTGCT-CTTCCTCATCGGAAGGTGTTGTCAGCATTTAC
***
12805 CAATTTGCCCTTCCTCATCAGAAGGTGTTGTTTAA
130 CAATTTGCCCTTCCTCATCAGAAGGTGTTGTAGCA
* * * * * * *
12840 GTTCACCAGTTTGCCCATCCTCATCGGAAGGTGTTGCCTGCATTT-CTCAGTTTGCCCTCCCTCA
1 -TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTAC-CAATTTGCCCTTCCTCA
12904 TCGGGAGGTGTTGTT-CCTATT
64 TCGGGAGGTGTTGTTGCCTATT
12925 CCTGTTATGT
Statistics
Matches: 359, Mismatches: 44, Indels: 28
0.83 0.10 0.06
Matches are distributed among these distances:
163 7 0.02
164 275 0.77
165 6 0.02
166 3 0.01
167 4 0.01
172 1 0.00
173 3 0.01
174 59 0.16
175 1 0.00
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (164 bp):
TTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTACCAATTTGCCCTTCCTCATC
GGGAGGTGTTGTTGCCTATTGTCCAGTTTGCTCTTCCTCATCGGAAGGTGTTGTCAGCATTTACC
AATTTGCCCTTCCTCATCAGAAGGTGTTGTAGCA
Found at i:17675 original size:19 final size:18
Alignment explanation
Indices: 17642--17677 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17632 TGGAAATAAT
17642 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
17660 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
17678 TAAGTCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:21317 original size:26 final size:26
Alignment explanation
Indices: 21281--21334 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
21271 GATGGTACTG
21281 TAAAAATTGAATTTTTCTAAATAAAA
1 TAAAAATTGAATTTTTCTAAATAAAA
21307 TAAAAATTGAATTTTTCTAAATAAAA
1 TAAAAATTGAATTTTTCTAAATAAAA
21333 TA
1 TA
21335 TTTTAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (26 bp):
TAAAAATTGAATTTTTCTAAATAAAA
Found at i:30653 original size:26 final size:26
Alignment explanation
Indices: 30624--30675 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
30614 CTAATAACTC
*
30624 CTCGCTCAACTGGATTTATAGAGAAT
1 CTCGCTCAACTAGATTTATAGAGAAT
30650 CTCGCTCAACTAGATTTATAGAGAAT
1 CTCGCTCAACTAGATTTATAGAGAAT
30676 TTGAGATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (26 bp):
CTCGCTCAACTAGATTTATAGAGAAT
Found at i:36414 original size:20 final size:20
Alignment explanation
Indices: 36389--36429 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
36379 TTGGAGAATA
36389 GTAGTCCACCTCCATGACTT
1 GTAGTCCACCTCCATGACTT
*
36409 GTAGTCCACCTCCTTGACTT
1 GTAGTCCACCTCCATGACTT
36429 G
1 G
36430 CAACATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.32
Consensus pattern (20 bp):
GTAGTCCACCTCCATGACTT
Found at i:36930 original size:49 final size:50
Alignment explanation
Indices: 36695--36929 Score: 368
Period size: 50 Copynumber: 4.7 Consensus size: 50
36685 TCCACAATTA
* *
36695 CGAAAGACTTTCCC-AATTAATCAAGAAATTCTACATATAGATTTAGTGT
1 CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
*
36744 CGAAAGACTTACCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
1 CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
*
36794 CAAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
1 CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
* * * *
36844 CAAAACACTTTCCCAAATCAATCAAGAAATTCTACATGT-AATTCTAGTAT
1 CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATT-TAGTGT
36894 CGAAAGAC-TTCCCAAATCAATCAAGAAATTCTACAT
1 CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACAT
36930 GAGACTTTCC
Statistics
Matches: 174, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
49 45 0.26
50 129 0.74
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (50 bp):
CGAAAGACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGT
Found at i:36942 original size:34 final size:33
Alignment explanation
Indices: 36898--36963 Score: 123
Period size: 34 Copynumber: 2.0 Consensus size: 33
36888 TAGTATCGAA
36898 AGACTTCCCAAATCAATCAAGAAATTCTACATG
1 AGACTTCCCAAATCAATCAAGAAATTCTACATG
36931 AGACTTTCCCAAATCAATCAAGAAATTCTACAT
1 AGAC-TTCCCAAATCAATCAAGAAATTCTACAT
36964 ATAAATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (33 bp):
AGACTTCCCAAATCAATCAAGAAATTCTACATG
Found at i:36951 original size:83 final size:84
Alignment explanation
Indices: 36850--37010 Score: 272
Period size: 83 Copynumber: 1.9 Consensus size: 84
36840 GTGTCAAAAC
* *
36850 ACTTTCCCAAATCAATCAAGAAATTCTACATGT-AATTCTAGTATCGAAAGAC-TTCCCAAATCA
1 ACTTTCCCAAATCAATCAAGAAATTCTACATATAAATT-TAGTACCGAAAGACTTTCCCAAATCA
36913 ATCAAGAAATTCTACATGAG
65 ATCAAGAAATTCTACATGAG
*
36933 ACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTGCCGAAAGACTTTCCCAAATCAA
1 ACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTACCGAAAGACTTTCCCAAATCAA
36998 TCAAGAAATTCTA
66 TCAAGAAATTCTA
37011 AATATAGATA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 44 0.60
84 29 0.40
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.28
Consensus pattern (84 bp):
ACTTTCCCAAATCAATCAAGAAATTCTACATATAAATTTAGTACCGAAAGACTTTCCCAAATCAA
TCAAGAAATTCTACATGAG
Found at i:37098 original size:18 final size:18
Alignment explanation
Indices: 37077--37141 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 18
37067 TGCAACCAAT
*
37077 CCAATCCACCCTCCACAT
1 CCAATCCACCCTCCACAG
37095 CCAATCCAACCCACCCTCCACAG
1 CCAAT-----CCACCCTCCACAG
*
37118 CCAATCCAGCCTCCACAG
1 CCAATCCACCCTCCACAG
37136 CCAATC
1 CCAATC
37142 GTGTCGACCG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 23 0.57
23 17 0.43
ACGTcount: A:0.29, C:0.54, G:0.05, T:0.12
Consensus pattern (18 bp):
CCAATCCACCCTCCACAG
Found at i:37099 original size:23 final size:23
Alignment explanation
Indices: 37072--37125 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
37062 ACAAATGCAA
* *
37072 CCAATCCAATCCACCCTCCACAT
1 CCAATCCAACCCACCCTCCACAG
37095 CCAATCCAACCCACCCTCCACAG
1 CCAATCCAACCCACCCTCCACAG
37118 CCAATCCA
1 CCAATCCA
37126 GCCTCCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.54, G:0.02, T:0.13
Consensus pattern (23 bp):
CCAATCCAACCCACCCTCCACAG
Found at i:39985 original size:22 final size:22
Alignment explanation
Indices: 39959--40112 Score: 195
Period size: 22 Copynumber: 7.1 Consensus size: 22
39949 TTACTCTAAT
39959 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* **
39981 CTTCTGATTACTCTTTCATTGG
1 CTTCTGATTACTCTTTCTTTTA
* * *
40003 CTTTTGATTATTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
**
40025 C-TCTGATTACTCTTTCTTTGG
1 CTTCTGATTACTCTTTCTTTTA
* *
40046 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
40068 C-TCTGATTACTCTTTCTATTA
1 CTTCTGATTACTCTTTCTTTTA
40089 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
40111 CT
1 CT
40113 GCTTAGCTTG
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
21 34 0.31
22 74 0.69
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:40037 original size:65 final size:65
Alignment explanation
Indices: 39959--40112 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 65
39949 TTACTCTAAT
* * * * *
39959 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCATTGGCTTTTGATTATTCTTCCTTTT
1 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTCCATTGAC-TCTGATTACTCTTCCTATT
40024 A
65 A
** * * * *
40025 C-TCTGATTACTCTTTCTTTGGCTTTTGATTACTCTTCCTTTTACTCTGATTACTCTTTCTATTA
1 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTCCATTGACTCTGATTACTCTTCCTATTA
40089 CTTCTGATTACTCTTTCTTTTACT
1 CTTCTGATTACTCTTTCTTTTACT
40113 GCTTAGCTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
64 17 0.23
65 56 0.76
66 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (65 bp):
CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTCCATTGACTCTGATTACTCTTCCTATTA
Found at i:40039 original size:43 final size:43
Alignment explanation
Indices: 39963--40112 Score: 221
Period size: 43 Copynumber: 3.5 Consensus size: 43
39953 TCTAATCTTC
*
39963 TGATTACTCTTTCTTTTACTTCTGATTACTCTTTCATTGGCTTT
1 TGATTACTCTTCCTTTTAC-TCTGATTACTCTTTCATTGGCTTT
* *
40007 TGATTATTCTTCCTTTTACTCTGATTACTCTTTCTTTGGCTTT
1 TGATTACTCTTCCTTTTACTCTGATTACTCTTTCATTGGCTTT
* *
40050 TGATTACTCTTCCTTTTACTCTGATTACTCTTTCTATT-ACTTC
1 TGATTACTCTTCCTTTTACTCTGATTACTCTTTC-ATTGGCTTT
*
40093 TGATTACTCTTTCTTTTACT
1 TGATTACTCTTCCTTTTACT
40113 GCTTAGCTTG
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
43 78 0.80
44 19 0.20
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.57
Consensus pattern (43 bp):
TGATTACTCTTCCTTTTACTCTGATTACTCTTTCATTGGCTTT
Found at i:40176 original size:47 final size:47
Alignment explanation
Indices: 40103--40850 Score: 694
Period size: 47 Copynumber: 15.5 Consensus size: 47
40093 TGATTACTCT
** * * *
40103 TTCTTTTACTGCTTAGCTTGATTACCCAGAATCAAACTGTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* * * *
40150 TTCTCTTGCTCTTTAGTTTAATTACCCTA-AATTAAACTCTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCC-AGAATTAAACTGTTTTCTTC
* * *
40197 CTCTTTTACTTTTTAGTTTAATTACCCAAAATTAAACTAGCCTCTGTGTACTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT-G--T-T-T-T-CTTC
* * *
40251 TTCTTTTACTCTTTAGTTTGATTACCAAGAATTAAACTGTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* * * ** *
40298 TTCTCTTGCTCTTTAGTTTAATTACCCTTAATTAAACTCTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* ****
40345 TTCTCTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
****
40392 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
**
40439 TTCTTTTACT-TCTTAGTTTAATTACCCAGAATTAAACTAACCTCTGTTTAGTTC
1 TTCTTTTACTAT-TTAGTTTAATTACCCAGAATT--A--AA---CTGTTTTCTTC
* *
40493 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATCTCTGTTTACTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATT--A--AA---CTGTTTTCTTC
* * * *
40547 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACAT-ATCTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAAC-TGTTTTCTTC
* ****
40594 TTCTTTTACTATTTAGTTTAATTACCCATAATTAAACTAACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* ****
40641 TTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* * ****
40688 TTCTTTTACTATTTAGTTTAATTACCCATAATTAAATTAACCTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* *
40735 TTCTTTTACTTTTTAGTTTAATTACCCAGAATT-AACTGTTTTCTTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* * * *
40781 TTCTCTTACTTTTTAGTTTAATTACCCAAAATTAAACCGTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
* *
40828 TTCTCTTACTTTTTAGTTTAATT
1 TTCTTTTACTATTTAGTTTAATT
40851 GCTCTGATTT
Statistics
Matches: 610, Mismatches: 70, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
46 41 0.07
47 427 0.70
48 3 0.00
49 2 0.00
50 4 0.01
51 4 0.01
52 2 0.00
53 2 0.00
54 124 0.20
55 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (47 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTC
Found at i:40630 original size:296 final size:296
Alignment explanation
Indices: 40198--40769 Score: 939
Period size: 296 Copynumber: 1.9 Consensus size: 296
40188 CTTTTCTTCC
* *
40198 TCTTTTACTTTTTAGTTTAATTACCCAAAATTAAACTAGCCTCTGTGTACTTCTTCTTTTACTCT
1 TCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAACCTCTGTGTACTTCTTCTTTTACTCT
* * * * * *
40263 TTAGTTTGATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCTTA
66 TTAGTTTAATTACCAAGAATTAAACTGATCTCTTCTTCTCTTACTATTTAGTTTAATTACCCATA
****
40328 ATTAAACTCTTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCT
131 ATTAAACTAACATCTTCTTCTCTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCT
40393 TCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTCTTAGTTT
196 TCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTCTTAGTTT
40458 AATTACCCAGAATTAAACTAACCTCTGTTTAGTTCT
261 AATTACCCAGAATTAAACTAACCTCTGTTTAGTTCT
* * *
40494 TCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATCTCTGTTTACTTCTTCTTTTACTCT
1 TCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAACCTCTGTGTACTTCTTCTTTTACTCT
*
40559 TTAGTTTAATTACCAAGAATTAAACAT-ATCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAT
66 TTAGTTTAATTACCAAGAATTAAAC-TGATCTCTTCTTCTCTTACTATTTAGTTTAATTACCCAT
* *
40623 AATTAAACTAACATCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACATCTTC
130 AATTAAACTAACATCTTCTTCTCTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTC
* * *
40688 TTCTTTTACTATTTAGTTTAATTACCCATAATTAAATTAACCTCTTCTTCTTTTACTTTTTAGTT
195 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTCTTAGTT
40753 TAATTACCCAGAATTAA
260 TAATTACCCAGAATTAA
40770 CTGTTTTCTT
Statistics
Matches: 254, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
296 253 1.00
297 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (296 bp):
TCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAACCTCTGTGTACTTCTTCTTTTACTCT
TTAGTTTAATTACCAAGAATTAAACTGATCTCTTCTTCTCTTACTATTTAGTTTAATTACCCATA
ATTAAACTAACATCTTCTTCTCTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCT
TCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTCTTAGTTT
AATTACCCAGAATTAAACTAACCTCTGTTTAGTTCT
Found at i:43258 original size:21 final size:21
Alignment explanation
Indices: 43232--43271 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43222 TAGTGCCATA
43232 TTTAATCTGGGTAACTACGTG
1 TTTAATCTGGGTAACTACGTG
*
43253 TTTAATTTGGGTAACTACG
1 TTTAATCTGGGTAACTACG
43272 AACCCACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (21 bp):
TTTAATCTGGGTAACTACGTG
Found at i:43318 original size:14 final size:14
Alignment explanation
Indices: 43301--43327 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43291 ATCCAAAATT
43301 CTAAATTACTAATA
1 CTAAATTACTAATA
43315 CTAAATTACTAAT
1 CTAAATTACTAAT
43328 TTATGAAAAA
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
CTAAATTACTAATA
Found at i:44529 original size:47 final size:47
Alignment explanation
Indices: 44460--44549 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
44450 GGGACTACAA
*
44460 AGGAGAAGACCTCACCCCTCGCTGCAGCTTCTTCGGAGCACTTCCAG
1 AGGAGAAGACCTCACCCCTCGCTCCAGCTTCTTCGGAGCACTTCCAG
*
44507 AGGAGAAGACC-CTGCCCCTCGCTCCAGCTTCTTCGGAGCACTT
1 AGGAGAAGACCTC-ACCCCTCGCTCCAGCTTCTTCGGAGCACTT
44550 TTGCGTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.20, C:0.37, G:0.23, T:0.20
Consensus pattern (47 bp):
AGGAGAAGACCTCACCCCTCGCTCCAGCTTCTTCGGAGCACTTCCAG
Found at i:45126 original size:45 final size:45
Alignment explanation
Indices: 45072--45168 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
45062 AGTGCATTAC
* *
45072 CTAA-ATTCTACTCCTCCATATTTAGGGAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCCATATCTAGAGAATTCATCAAAATAAAG
* * * *
45116 CTAATATTCTACTCCTCCGTCTCTATATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCCATATCTAGAGAATTCATCAAAATAAAG
45161 CTAATATT
1 CTAATATT
45169 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (45 bp):
CTAATATTCTACTCCTCCATATCTAGAGAATTCATCAAAATAAAG
Found at i:45849 original size:13 final size:13
Alignment explanation
Indices: 45831--45856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45821 AATTAAAAGC
45831 TATTTTGTATTTT
1 TATTTTGTATTTT
45844 TATTTTGTATTTT
1 TATTTTGTATTTT
45857 ATGTTAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TATTTTGTATTTT
Found at i:47972 original size:2 final size:2
Alignment explanation
Indices: 47965--47994 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47955 TGCTTTACAC
47965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47995 CAATTGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48146 original size:13 final size:13
Alignment explanation
Indices: 48128--48152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48118 GACTTCAAAT
48128 TACAGGTAAAAAA
1 TACAGGTAAAAAA
48141 TACAGGTAAAAA
1 TACAGGTAAAAA
48153 GGATTGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
TACAGGTAAAAAA
Done.