Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006667.1 Hibiscus syriacus cultivar Beakdansim tig00016512_pilon, 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: 123713
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2301 original size:41 final size:41
Alignment explanation
Indices: 2244--2322 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2234 CGTTCTATCG
* *
2244 GATTATAAAAACTTTTAAATTGAAGGTTATTGTATTTAGGA
1 GATTAGAAAAACTTTTAAATTAAAGGTTATTGTATTTAGGA
2285 GATTAGAAAAACTTTTAAATTAAAGGTTATTGTATTTA
1 GATTAGAAAAACTTTTAAATTAAAGGTTATTGTATTTA
2323 TTTTAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.42
Consensus pattern (41 bp):
GATTAGAAAAACTTTTAAATTAAAGGTTATTGTATTTAGGA
Found at i:4269 original size:15 final size:15
Alignment explanation
Indices: 4249--4278 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4239 ACAATAGAGA
4249 AGCATTAAAACTCGG
1 AGCATTAAAACTCGG
4264 AGCATTAAAACTCGG
1 AGCATTAAAACTCGG
4279 TTGTTTCTCT
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:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
AGCATTAAAACTCGG
Found at i:4814 original size:18 final size:18
Alignment explanation
Indices: 4791--4828 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4781 TAATTATTTT
4791 TCAGGTTCCATATCTTTC
1 TCAGGTTCCATATCTTTC
4809 TCAGGTTCCATATCTTTC
1 TCAGGTTCCATATCTTTC
4827 TC
1 TC
4829 GATATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.45
Consensus pattern (18 bp):
TCAGGTTCCATATCTTTC
Found at i:12006 original size:22 final size:23
Alignment explanation
Indices: 11965--12008 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11955 ACCCTGCATT
**
11965 TTGCATATGCATTTTTATTTTTC
1 TTGCATATGCATTTAAATTTTTC
11988 TTGCA-ATGCATTTAAATTTTT
1 TTGCATATGCATTTAAATTTTT
12009 TGCACCGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (23 bp):
TTGCATATGCATTTAAATTTTTC
Found at i:12011 original size:20 final size:22
Alignment explanation
Indices: 11963--12012 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
11953 ACACCCTGCA
* *
11963 TTTTGCATATGCATTTTTATTT
1 TTTTGCATATGCATTTTAAATT
11985 TTCTTGCA-ATGCA-TTTAAATT
1 TT-TTGCATATGCATTTTAAATT
12006 TTTTGCA
1 TTTTGCA
12013 CCGTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 5 0.20
21 8 0.32
22 7 0.28
23 5 0.20
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTGCATATGCATTTTAAATT
Found at i:15194 original size:16 final size:16
Alignment explanation
Indices: 15173--15210 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
15163 GGCATTAAAA
15173 AGAGTCGGGAAATAAG
1 AGAGTCGGGAAATAAG
15189 AGAGTCGGGAAATAAG
1 AGAGTCGGGAAATAAG
*
15205 AAAGTC
1 AGAGTC
15211 AAGATTGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.34, T:0.13
Consensus pattern (16 bp):
AGAGTCGGGAAATAAG
Found at i:19179 original size:16 final size:17
Alignment explanation
Indices: 19149--19181 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19139 TTGTTTGAAT
19149 AAAAAATGAAAAAAATG
1 AAAAAATGAAAAAAATG
*
19166 AAAAAA-GAATAAAATG
1 AAAAAATGAAAAAAATG
19182 GGGGTCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAAAATGAAAAAAATG
Found at i:19430 original size:16 final size:16
Alignment explanation
Indices: 19409--19443 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
19399 CAGGAGAGAA
19409 ATTGAATGCACATGAG
1 ATTGAATGCACATGAG
19425 ATTGAATGCACATGAG
1 ATTGAATGCACATGAG
19441 ATT
1 ATT
19444 CAATACTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (16 bp):
ATTGAATGCACATGAG
Found at i:20593 original size:36 final size:37
Alignment explanation
Indices: 20454--20614 Score: 198
Period size: 37 Copynumber: 4.4 Consensus size: 37
20444 CTGACCTTCA
* * * *
20454 AAGCAAATCAATATTAAGCCTTCACGAAAAAGTAGTG
1 AAGCAAATCAATCTTAAGCCTTCAAGGAAGAGTAGTG
* * * * *
20491 AAACAAATCATTCTTAATCCTTCACGAAAGAGTAGTG
1 AAGCAAATCAATCTTAAGCCTTCAAGGAAGAGTAGTG
* *
20528 AAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGTG
1 AAGCAAATCAATCTTAAGCCTTCAAGGAAGAGTAGTG
* *
20565 AAGAAAATCAATCTT-AGCCTTTAAGGAAGAGTAGTG
1 AAGCAAATCAATCTTAAGCCTTCAAGGAAGAGTAGTG
20601 AAGCAAATCAATCT
1 AAGCAAATCAATCT
20615 CGAGTCTGAT
Statistics
Matches: 109, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 32 0.29
37 77 0.71
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (37 bp):
AAGCAAATCAATCTTAAGCCTTCAAGGAAGAGTAGTG
Found at i:26316 original size:35 final size:35
Alignment explanation
Indices: 26256--26351 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 35
26246 GTCCTACTAG
* *
26256 GATTCAAACTCTCAAAAATATGATAGAATTCTGCTAT
1 GATTC-AACTC-CTAAAATAGGATAGAATTCTGCTAT
*
26293 GATTCAACTCCTAAAATAGGATAGAATTTTGCTAT
1 GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
* *
26328 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTCAACTCCTAAA-ATAGGAT
26352 CCACAAGCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 23 0.44
36 17 0.33
37 12 0.23
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (35 bp):
GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
Found at i:27031 original size:16 final size:16
Alignment explanation
Indices: 27010--27043 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27000 CATGTATTTA
27010 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
27026 TATTATTTTACTTTAT
1 TATTATATTACATTAT
27042 TA
1 TA
27044 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:31829 original size:9 final size:8
Alignment explanation
Indices: 31802--31871 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 8
31792 AGATCCAATC
*
31802 AAGAACAA
1 AAGAAGAA
31810 AA-AAGAA
1 AAGAAGAA
31817 AAGAAGCAA
1 AAGAAG-AA
31826 AAGAAGAAA
1 AAGAAG-AA
*
31835 AAAAAGAA
1 AAGAAGAA
31843 AA-AAGAA
1 AAGAAGAA
*
31850 AA-AA-AC
1 AAGAAGAA
*
31856 AAGAACAA
1 AAGAAGAA
31864 AA-AAGAA
1 AAGAAGAA
31871 A
1 A
31872 GAACAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
6 3 0.06
7 22 0.42
8 12 0.23
9 15 0.29
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:31841 original size:21 final size:20
Alignment explanation
Indices: 31810--31871 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 20
31800 TCAAGAACAA
31810 AAAAGAAAAGAAGCAAAAGAAG
1 AAAA-AAAAGAA-CAAAAGAAG
31832 AAAAAAAAGAA-AAAAGAA-
1 AAAAAAAAGAACAAAAGAAG
*
31850 AAAAACAAGAACAAAA-AAG
1 AAAAAAAAGAACAAAAGAAG
31869 AAA
1 AAA
31872 GAACAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 12 0.32
19 14 0.38
21 7 0.19
22 4 0.11
ACGTcount: A:0.81, C:0.05, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAACAAAAGAAG
Found at i:31880 original size:14 final size:14
Alignment explanation
Indices: 31802--31880 Score: 78
Period size: 14 Copynumber: 5.8 Consensus size: 14
31792 AGATCCAATC
31802 AAGAACAAAAAAGAA
1 AAGAACAAAAAAG-A
31817 AAGAAGC--AAAAG-
1 AAGAA-CAAAAAAGA
31829 AAGAA-AAAAAAGA
1 AAGAACAAAAAAGA
* *
31842 AAAAAGAAAAAA-A
1 AAGAACAAAAAAGA
31855 CAAGAACAAAAAAGA
1 -AAGAACAAAAAAGA
31870 AAGAACAAAAA
1 AAGAACAAAAA
31881 TAAAAAAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.19
13 5 0.09
14 32 0.59
15 6 0.11
16 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGAACAAAAAAGA
Found at i:31880 original size:27 final size:28
Alignment explanation
Indices: 31801--31880 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 28
31791 AAGATCCAAT
31801 CAAGAACAAAAAAGAAAAGAAGC--AAAA
1 CAAGAACAAAAAAG-AAAGAAGCAAAAAA
* * *
31828 GAAGAA-AAAAAAGAAAAAAGAAAAAAA
1 CAAGAACAAAAAAGAAAGAAGCAAAAAA
31855 CAAGAACAAAAAAGAAAGAA-CAAAAA
1 CAAGAACAAAAAAGAAAGAAGCAAAAA
31881 TAAAAAAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 6 0.14
26 7 0.16
27 19 0.43
28 12 0.27
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (28 bp):
CAAGAACAAAAAAGAAAGAAGCAAAAAA
Found at i:32525 original size:22 final size:22
Alignment explanation
Indices: 32497--32547 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
32487 CCCCATCAAT
32497 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
32519 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
32541 CCTTTGA
1 CCTTTGA
32548 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:33456 original size:36 final size:37
Alignment explanation
Indices: 33409--33513 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
33399 GTGCTCACCA
33409 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
*
33445 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
* * *
33482 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
33514 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 34 0.53
37 30 0.47
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
Found at i:33603 original size:102 final size:102
Alignment explanation
Indices: 33427--33884 Score: 754
Period size: 102 Copynumber: 4.5 Consensus size: 102
33417 CTTGAGACAG
** * * * * *
33427 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
33492 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
33529 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCACCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
*
33594 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
33631 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
33696 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
33733 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAAATTTGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
*
33798 TGAGACAGTTTCTCTTAAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
33835 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
33885 TAAACATTGA
Statistics
Matches: 331, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 331 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:33698 original size:37 final size:37
Alignment explanation
Indices: 33631--33717 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
33621 ATTGGAAACA
** * *
33631 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
33667 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
33704 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
33718 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:33874 original size:65 final size:65
Alignment explanation
Indices: 33785--33949 Score: 289
Period size: 65 Copynumber: 2.6 Consensus size: 65
33775 TCGAAACAAA
*
33785 AATTT-GTCTC-CATTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AATTTCGTCTCTC-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
33848 G
65 G
*
33849 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
33914 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
33950 AAATTTTGTC
Statistics
Matches: 96, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
64 5 0.05
65 90 0.94
66 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:33885 original size:167 final size:169
Alignment explanation
Indices: 33667--33981 Score: 517
Period size: 167 Copynumber: 1.9 Consensus size: 169
33657 CTTGAGATAG
*
33667 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
33732 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAAATTTGTCTCCA
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAAATTTGTCTCCA
33797 TTGAGACAG-TTTCTCTTAAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTAAAACATAAACATTGAAAACA
** * *
33835 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * * *
33899 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAAATTTGTCTCCA
33964 TTGAGACAGTTTTCTCTT
131 TTGAGACAGTTTTCTCTT
33982 GAAGCGTCAT
Statistics
Matches: 135, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
167 115 0.85
168 20 0.15
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAAATTTGTCTCCA
TTGAGACAGTTTTCTCTTAAAACATAAACATTGAAAACA
Found at i:34127 original size:37 final size:37
Alignment explanation
Indices: 34057--34128 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
34047 TGGAACTAAG
* * **
34057 TTTTATCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
34094 TTTTATCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAA
34129 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (37 bp):
TTTTATCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:34836 original size:203 final size:204
Alignment explanation
Indices: 34487--35446 Score: 1045
Period size: 203 Copynumber: 4.6 Consensus size: 204
34477 GTCAATTTCG
* *
34487 ACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* *
34552 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACC
66 GGTTGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * * *
34617 CAAGGCAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTT-GGAG
131 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTTCGGAG
34681 CCAATCTCA
196 CCAATCTCA
34690 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * **
34755 -GTATGTCAACAATAATTTCCCAGTTTTAGGGCCAATTTCAACTTCACAATGAAGGATATTGGAC
66 GGT-TGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
** * * * *
34819 CCAAGACAGGACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAA-TTTCGGA
130 CCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTTCGGA
34883 GCCAATCTCA
195 GCCAATCTCA
* **
34893 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGTGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * * * * * *
34958 GGTTGTCAACAAATAATTTCCTAATTCCAGCGCCGATTTCAACTCCAC-GACGGAGGATATCGTG
66 GGTTGTCAAC-AATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG
* * * ** *
35022 CTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTT
127 -GACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAA-TTT
* * * *
35087 TCAGTTTCATCCGCGATTTCA
190 TC-G---GA-GC-CAATCTCA
* * *
35108 ACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
1 ACTTCACAG-CGAAGGATAT--TG-AACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * * * *
35172 GACTGGTTGTCAACAA-ACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATAT
62 GGCTGGTTGTCAACAATA-A-TTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* * * * * * *
35236 TGGACTCGAGACAATACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGATTTC
125 TGGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATT-
* * *
35300 GTTCAGAGTCAATTTCA
189 -TTCGGAGCCAATCTCA
* * * *
35317 ACTTCACAGCGAAGGATATT-AGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGC
1 ACTTCACAGCGAAGGATATTGA-ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
** * * * * *
35381 TGACTGTCAACAAACAATTTCCCGGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGA
65 TGGTTGTCAAC-AATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
35446 C
129 C
35447 TCGGAACAAT
Statistics
Matches: 649, Mismatches: 79, Indels: 55
0.83 0.10 0.07
Matches are distributed among these distances:
202 5 0.01
203 258 0.40
204 40 0.06
206 89 0.14
207 52 0.08
208 1 0.00
209 26 0.04
210 2 0.00
211 1 0.00
213 3 0.00
214 5 0.01
215 74 0.11
216 3 0.00
217 5 0.01
218 84 0.13
219 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (204 bp):
ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
GGTTGTCAACAATAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTTCGGAG
CCAATCTCA
Found at i:35288 original size:106 final size:105
Alignment explanation
Indices: 34474--35449 Score: 904
Period size: 109 Copynumber: 9.4 Consensus size: 105
34464 GGTTTTAGCT
* * *
34474 AGAGTCAATTTCGACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
34539 CGAAGGGACGGCTGGTTGTCAAC-AATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTC
* * * * * * * *
34579 AGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACCCAAGGCAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* ** *
34644 CGAAGGGGCGGCTGACTGTCGACAAACAA---T---TTT-
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
* * *
34677 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
34742 CGAAGGGACGGCT-GTATGTCAAC-AATAATTTCCCAGTTTT
66 CGAAGGGACGGCTGGT-TGTCAACAAACAATTT-TCAATTTC
* ** * * ** * *
34782 AGGGCCAATTTCAACTTCACAATGAAGGATATTGGACCCAAGACAGGACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* ** * *
34847 CGAAGGGGCGGCTGACTGT---C-GACAA---GCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
* * *
34880 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
34945 TGAAGGGACGGCTGGTTGTCAACAAATAATTTCCTAATTCC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTC
* * * * * *
34986 AGCGCCGATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTC
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTC
* *
35050 ACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTC
62 ACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTC
** * * * *
35095 A-TCCGCGATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTT
1 AGAGC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTT
* *
35158 CACAACGAAGGGACGACTGGTTGTCAACAAACATTTTTCAAATTTC
61 CACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTC
* *
35204 AGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAATACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
35269 CGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC--GTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
* * * * *
35304 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* ** * ** *
35369 CGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTC
* *
35410 AGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
35450 GAACAATATT
Statistics
Matches: 714, Mismatches: 123, Indels: 67
0.79 0.14 0.07
Matches are distributed among these distances:
97 4 0.01
98 147 0.21
99 3 0.00
100 82 0.11
101 3 0.00
102 8 0.01
103 6 0.01
104 4 0.01
105 147 0.21
106 121 0.17
107 2 0.00
108 8 0.01
109 173 0.24
110 6 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
Found at i:35969 original size:35 final size:35
Alignment explanation
Indices: 35914--36009 Score: 120
Period size: 35 Copynumber: 2.6 Consensus size: 35
35904 GTCCTACTAG
*
35914 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAT
1 GATTC-AACTC-CTAAAATAGGATAGAATTCTGCTAT
*
35951 GATTCAACTCCTAAAATAGGATAGAATTTTGCTAT
1 GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
* *
35986 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTCAACTCCTAAA-ATAGGAT
36010 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 24 0.45
36 17 0.32
37 12 0.23
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
Found at i:36436 original size:11 final size:11
Alignment explanation
Indices: 36416--36501 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
36406 TTAATTATTT
*
36416 TTATTCTAATA
1 TTATTTTAATA
*
36427 TTATTTTAATG
1 TTATTTTAATA
36438 TT-TTTTAA-A
1 TTATTTTAATA
36447 GTTATTATATATATA
1 -TTATT-T-TA-ATA
36462 TATATTTATAATTA
1 T-TATTT-TAA-TA
*
36476 TTATATTTATTA
1 TTAT-TTTAATA
*
36488 TTATTTTACTA
1 TTATTTTAATA
36499 TTA
1 TTA
36502 ACGTATATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.13
11 22 0.36
12 7 0.11
13 8 0.13
14 11 0.18
15 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:36480 original size:15 final size:15
Alignment explanation
Indices: 36462--36492 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36452 TATATATATA
36462 TATATTTATAATTAT
1 TATATTTATAATTAT
*
36477 TATATTTATTATTAT
1 TATATTTATAATTAT
36492 T
1 T
36493 TTACTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTATAATTAT
Found at i:36688 original size:16 final size:16
Alignment explanation
Indices: 36667--36700 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36657 CATGTATTTA
36667 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
36683 TATTATTTTACTTTAT
1 TATTATATTACATTAT
36699 TA
1 TA
36701 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:47409 original size:109 final size:109
Alignment explanation
Indices: 47218--47423 Score: 331
Period size: 109 Copynumber: 1.9 Consensus size: 109
47208 TAAGAATAGA
* * **
47218 TTCTATAGTCTATGCTTTGGGGAACAGAATGAGGTTCCTAATGTTTTTCTTAGCTGGGCCATTTA
1 TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
* *
47283 TATTAGTCAAAACCGGCACATAGAATCTATCAAAATATATTCAT
66 TATTAATCAAAAACGGCACATAGAATCTATCAAAATATATTCAT
* * *
47327 TTCTATAGTCTTTGCTTTGGGGAACATAACGGGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
1 TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
47392 TATTAATCAAAAACGGCACATAGAATCTATCA
66 TATTAATCAAAAACGGCACATAGAATCTATCA
47424 TACAAAATCA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 88 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (109 bp):
TTCTATAGTCTATGCTTTGGGGAACAGAACGAGGTTCCAAATGTTTTTCTTAGCTAAGCCATTTA
TATTAATCAAAAACGGCACATAGAATCTATCAAAATATATTCAT
Found at i:56621 original size:32 final size:31
Alignment explanation
Indices: 56585--56660 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
56575 GGGGCCACGT
*
56585 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
56617 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
56648 AGCCTACCTAAGA
1 GGCCTACCTAAGA
56661 GTCACATAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:61832 original size:32 final size:31
Alignment explanation
Indices: 61796--61871 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
61786 GGGGCCACGT
* *
61796 GGCCTACCTAAGAACACATCTTAGGGTCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
61828 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
61859 AGCCTACCTAAGA
1 GGCCTACCTAAGA
61872 GTCACATAAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:75338 original size:303 final size:301
Alignment explanation
Indices: 74783--75365 Score: 880
Period size: 303 Copynumber: 1.9 Consensus size: 301
74773 CATCGATGAG
* **
74783 GGGTAACCCGATCCGATCTGGAGTGTCACATTAGAGTCACCGGAGCAACCCACTGTAAAAATAGC
1 GGGTAACCCGATCCGATCTGGAGAGTCACATTAGAGTCACCGGAGCAACCCACCATAAAAATAGC
*
74848 GGAAAATTTAAAACTTTTATTAAAACATGTAAATTATAAAATGATTTATCAGTACGAAGAAATAA
66 GGAAAATTTAAAACTTTTATCAAAACATGTAAATTATAAAATGATTTATCAGTACGAAGAAATAA
* *
74913 AACATATTTTCAGACTCGTATATAAAACAAAATACAATTACATGCCCCCCAATCACATGTACCAT
131 AACAGATTTTCAGACTCGTACATAAAACAAAATACAATTACATGCCCCCCAATCACATGTACCAT
*
74978 ACTCTGCAAACAACGCCGGAAGAACTCCCTTACTGAAGTCGATAGCTGTACTGGTACAATTCTTT
196 ACTCTGCAAACAACGCCGGAAGAACTCCCTTACTGAAGTCGATAGCTGCACTGGTACAATTCTTT
*
75043 TAACCTGCAATGTTGAGTAATTGTAACCTCCTGACCGATGC
261 TAACCTGAAATGTTGAGTAATTGTAACCTCCTGACCGATGC
* * * *
75084 GGGTAACCTGATCTGATCTGG-GAAGTCACATTAGGGTCACCGGAGCGACCCACCATAAAAATAG
1 GGGTAACCCGATCCGATCTGGAG-AGTCACATTAGAGTCACCGGAGCAACCCACCATAAAAATAG
* * * *
75148 CGGAAAATTTAAAACTTTTTATCAGAACATGTAAACTTATAAAATGATTTATCAGTATGTATAAA
65 CGGAAAATTTAAAAC-TTTTATCAAAACATGTAAA-TTATAAAATGATTTATCAGTACGAAGAAA
* * * *
75213 TAAAACAGATTTTCAGACTTGTACATAAAACAAAATTCAATTACATGCCCCCTAATCACATGTAT
128 TAAAACAGATTTTCAGACTCGTACATAAAACAAAATACAATTACATGCCCCCCAATCACATGTAC
* * * * * * * *
75278 CATTCTCTGGAAATAACGCCGGAAGAATTCCTTTACTGATGTCGATAGTTGCATTGGTACAATTC
193 CATACTCTGCAAACAACGCCGGAAGAACTCCCTTACTGAAGTCGATAGCTGCACTGGTACAATTC
75343 TTTTAACCTGAAATGTTGAGTAA
258 TTTTAACCTGAAATGTTGAGTAA
75366 AATAGTGAGC
Statistics
Matches: 251, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
300 1 0.00
301 70 0.28
302 17 0.07
303 163 0.65
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (301 bp):
GGGTAACCCGATCCGATCTGGAGAGTCACATTAGAGTCACCGGAGCAACCCACCATAAAAATAGC
GGAAAATTTAAAACTTTTATCAAAACATGTAAATTATAAAATGATTTATCAGTACGAAGAAATAA
AACAGATTTTCAGACTCGTACATAAAACAAAATACAATTACATGCCCCCCAATCACATGTACCAT
ACTCTGCAAACAACGCCGGAAGAACTCCCTTACTGAAGTCGATAGCTGCACTGGTACAATTCTTT
TAACCTGAAATGTTGAGTAATTGTAACCTCCTGACCGATGC
Found at i:75873 original size:24 final size:25
Alignment explanation
Indices: 75846--75928 Score: 118
Period size: 24 Copynumber: 3.4 Consensus size: 25
75836 ATTATAACAT
*
75846 AATCCAGTTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCAGATCAA
75870 AATCCAGGTCAAGTATTCA-ATCAA
1 AATCCAGGTCAAGTATTCAGATCAA
* *
75894 AATTCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTATTCAGATCAA
75918 AATCCAGGTCA
1 AATCCAGGTCA
75929 GATATATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
24 50 0.94
25 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (25 bp):
AATCCAGGTCAAGTATTCAGATCAA
Found at i:77094 original size:18 final size:18
Alignment explanation
Indices: 77073--77107 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
77063 TTTCTTTCGG
*
77073 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
77091 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
77108 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:78431 original size:18 final size:18
Alignment explanation
Indices: 78410--78448 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
78400 GTCAACGCCA
78410 GTCAACGGGTCGGGTAGG
1 GTCAACGGGTCGGGTAGG
*
78428 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTAGG
78446 GTC
1 GTC
78449 GGGTTGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
GTCAACGGGTCGGGTAGG
Found at i:81754 original size:44 final size:44
Alignment explanation
Indices: 81648--81999 Score: 528
Period size: 44 Copynumber: 8.0 Consensus size: 44
81638 AAAAGAGCCT
*
81648 GGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACCT-
1 GGGGAAACTGTAAGGCTTACCCTTGCACACA-ACAAAGGGACCTG
* *
81691 GGGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGGACATG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* *
81735 GGGGAAACTGTAAGGCTTACCCTTGCACATAGCAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
*
81779 AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
*
81823 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAAC-AAAGGGACCTG
* * *
81868 GGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACATG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* * *
81912 AGGGAAACTGTAAAGCTTACCCTTGCATACAACAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* * *
81956 GGGGAAACTGTAAGGCTTACTCTTGCACACAGCAAAGGAACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
82000 CTGTAATGGT
Statistics
Matches: 280, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 1 0.00
43 38 0.14
44 197 0.70
45 44 0.16
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (44 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
Found at i:81902 original size:133 final size:132
Alignment explanation
Indices: 81625--81999 Score: 576
Period size: 133 Copynumber: 2.8 Consensus size: 132
81615 AAGGTGTTAT
* * * * *
81625 CCTTGTACATAGCAAAAGAGCCTG-GGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAA
1 CCTTGCACACAGCAAAGGAACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACA-ACAAAGGGA
* * *
81688 CCT-GGGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGGACATGGGGGAAACTGTAAGGCT
65 CCTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCT
81752 TAC
130 TAC
* *
81755 CCTTGCACATAGCAAAGGGACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
1 CCTTGCACACAGCAAAGGAACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
81820 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTGGGGGAAACTGTAAGGCT
66 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAAACTGTAAGGCT
81885 TAC
130 TAC
* * *
81888 CCTTGCACACAGCAAAGGAACATGAGGGAAACTGTAAAGCTTACCCTTGCATACAACAAAGGGAC
1 CCTTGCACACAGCAAAGGAACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
* *
81953 CTGGGGGAAACTGTAAGGCTTACTCTTGCACACAGCAAAGGAACCTG
66 CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
82000 CTGTAATGGT
Statistics
Matches: 226, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
130 21 0.09
131 39 0.17
132 41 0.18
133 125 0.55
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.17
Consensus pattern (132 bp):
CCTTGCACACAGCAAAGGAACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
CTGGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAAACTGTAAGGCTT
AC
Found at i:92236 original size:38 final size:38
Alignment explanation
Indices: 92194--92279 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
92184 GCACAAGTTA
* *
92194 AAAAATAAATTAAGACAATATAATTAA-ACACAT-T-ATT
1 AAAAATAAATTAAAAAAATA-AATTAAGACA-ATATAATT
92231 GAAAAA-ATAATTAAAAAAATAAATTAAGACAATATAATT
1 -AAAAATA-AATTAAAAAAATAAATTAAGACAATATAATT
92270 AAAAATAAAT
1 AAAAATAAAT
92280 AAATTACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
37 9 0.22
38 28 0.68
39 4 0.10
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (38 bp):
AAAAATAAATTAAAAAAATAAATTAAGACAATATAATT
Found at i:92906 original size:21 final size:22
Alignment explanation
Indices: 92876--92916 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
92866 GTTAAAATTG
*
92876 AATTTGAAT-ATTTTATTATAT
1 AATTTAAATAATTTTATTATAT
*
92897 AATTTAAATAATTTTTTTAT
1 AATTTAAATAATTTTATTAT
92917 TTTAATTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AATTTAAATAATTTTATTATAT
Found at i:93527 original size:22 final size:23
Alignment explanation
Indices: 93484--93528 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
93474 AAGTATCAGG
*
93484 TCCAAAAAAAAAAAACTGAAGCA
1 TCCAAAAAAAAAAAACTCAAGCA
*
93507 TCCAAAAAAAATAAA-TCAAGCA
1 TCCAAAAAAAAAAAACTCAAGCA
93529 GTAAACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.64, C:0.18, G:0.07, T:0.11
Consensus pattern (23 bp):
TCCAAAAAAAAAAAACTCAAGCA
Found at i:95893 original size:28 final size:27
Alignment explanation
Indices: 95861--95917 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
95851 TGTAAAAATA
**
95861 AATAAATAATTTTAATATAAAATGTATT
1 AATAAATAATCATAATATAAAATGT-TT
* *
95889 AATAAATCATCATAATATTAAATGTTT
1 AATAAATAATCATAATATAAAATGTTT
95916 AA
1 AA
95918 ATTAATTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (27 bp):
AATAAATAATCATAATATAAAATGTTT
Found at i:98922 original size:20 final size:20
Alignment explanation
Indices: 98890--98938 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
98880 CGGGAAGTCA
98890 GGTCGGG-CAAACCGGATCG
1 GGTCGGGTCAAACCGGATCG
*
98909 GGTCGGGTCAAACCGGGTCG
1 GGTCGGGTCAAACCGGATCG
98929 GGTCGGGTCA
1 GGTCGGGTCA
98939 TATCAGGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.14
Consensus pattern (20 bp):
GGTCGGGTCAAACCGGATCG
Found at i:102114 original size:30 final size:32
Alignment explanation
Indices: 102044--102115 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
102034 GGCCTGCGAA
* *
102044 CCTACCCAAGATAATTCTCGGGGCCACAAAGG
1 CCTACCCAAGATAAATCTCAGGGCCACAAAGG
* *
102076 CTTACCCAAGA-AAATCTTAGGGCCACAAA-G
1 CCTACCCAAGATAAATCTCAGGGCCACAAAGG
102106 CCTACCCAAG
1 CCTACCCAAG
102116 GGTCGCCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 10 0.29
31 15 0.43
32 10 0.29
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (32 bp):
CCTACCCAAGATAAATCTCAGGGCCACAAAGG
Found at i:103832 original size:72 final size:72
Alignment explanation
Indices: 103714--103862 Score: 190
Period size: 72 Copynumber: 2.1 Consensus size: 72
103704 CCATTTCAAA
* * * ** ** *
103714 TTTGAAAGGTTTCCCATAGTCACGGGGATTGACCCTTTGAGATTGTTGTTGGTCAAGGTCAACGC
1 TTTGAAAGGCTTCCCACAGTCACGGGGATTGAACCTTCAAGATTGTTGTTGCCCAAGCTCAACGC
103779 TTCTAGT
66 TTCTAGT
* * * *
103786 TTTGAAAGGCTTCCCACAGTCATGGGGATTTAACCTTCAAGGTTGTTGTTGCCCAAGCTCAACGT
1 TTTGAAAGGCTTCCCACAGTCACGGGGATTGAACCTTCAAGATTGTTGTTGCCCAAGCTCAACGC
103851 TTCTAGT
66 TTCTAGT
103858 TTTGA
1 TTTGA
103863 CAAATTGCCA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (72 bp):
TTTGAAAGGCTTCCCACAGTCACGGGGATTGAACCTTCAAGATTGTTGTTGCCCAAGCTCAACGC
TTCTAGT
Found at i:110012 original size:9 final size:9
Alignment explanation
Indices: 109985--110032 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
109975 GGAGCTGCAA
*
109985 AATAAAATT
1 AATAATATT
*
109994 AAATAGTATT
1 -AATAATATT
110004 AATAATATT
1 AATAATATT
110013 AATAATA-T
1 AATAATATT
*
110021 AATAATAAT
1 AATAATATT
110030 AAT
1 AAT
110033 TATTATATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.24
9 19 0.56
10 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
AATAATATT
Found at i:110267 original size:37 final size:37
Alignment explanation
Indices: 110208--110360 Score: 245
Period size: 37 Copynumber: 4.2 Consensus size: 37
110198 ATCAGACTCG
* * *
110208 AGATTGATTTGCTTCACCACTCTTCGATGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
110245 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
110282 AAATGGA-TCGCTTCACTACCCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
110318 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
110355 AGATGG
1 AGATGG
110361 CCCGAAGGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
36 33 0.31
37 73 0.69
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (37 bp):
AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
Found at i:110337 original size:73 final size:73
Alignment explanation
Indices: 110218--110360 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 73
110208 AGATTGATTT
*
110218 GCTTCACCACTCTTCGATGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GCTTCACCACCCTTCGATGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
110283 AATGGATC
66 AATGGATC
* *
110291 GCTTCACTACCCTTCGGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GCTTCACCACCCTTCGATGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
*
110356 GATGG
66 AATGG
110361 CCCGAAGGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (73 bp):
GCTTCACCACCCTTCGATGAAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
AATGGATC
Found at i:110400 original size:41 final size:42
Alignment explanation
Indices: 110351--110478 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 42
110341 TCGGTGAAGG
* * *
110351 CTTA-AGATGGCCCGAAGGACTT-ATCATCTTACTCAAAACA
1 CTTATAGATGACCCGAAGGATTTAATCATCATACTCAAAACA
* * * * *
110391 CTTATAGATGACCCAAATGATTTAATCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAATCATCATACTCAAAACA
* * *
110433 CTTACT-GATGTCCCGAAGGATTTCATCATCATGCTCGAAAA-A
1 CTTA-TAGATGACCCGAAGGATTTAATCATCATACTC-AAAACA
110475 CTTA
1 CTTA
110479 CTGATGGATT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.06
41 14 0.20
42 49 0.69
43 4 0.06
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAATCATCATACTCAAAACA
Found at i:110436 original size:42 final size:42
Alignment explanation
Indices: 110397--110484 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
110387 AACACTTATA
* *
110397 GATGACCCAAATGATTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCCAAAGGATTTAATCATCATGCTCGAAAAACTTACT
* * *
110439 GATGTCCCGAAGGATTTCATCATCATGCTCGAAAAACTTACT
1 GATGACCCAAAGGATTTAATCATCATGCTCGAAAAACTTACT
110481 GATG
1 GATG
110485 GATTTGCTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
GATGACCCAAAGGATTTAATCATCATGCTCGAAAAACTTACT
Found at i:110586 original size:161 final size:162
Alignment explanation
Indices: 110319--110613 Score: 425
Period size: 161 Copynumber: 1.8 Consensus size: 162
110309 GAAGGCTTAA
* * *
110319 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTTATCATCTTACT
1 GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAGGACTTATCATCTTACT
* * * *
110384 CAAAACACTTATAGATGACCCAAATGATTTAATCATCATGCTCGAAAGACTTACTGATGTCCCGA
66 CAAAACACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGA
110449 AGGATTTCATCATCATGCTCGAAAAACTTACT
131 AGGATTTCATCATCATGCTCGAAAAACTTACT
* * *
110481 GATGGATTTGCTTCACTACTCTTCCGTGAA-G-TTACAAATTATCCGAAGGACTTATCATCTTGC
1 GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTA-AAATGACCCGAAGGACTTATCATCTTAC
* * * *
110544 TCTAAAA-GCTTACAGATGACCCGAAGGATTTAAGCGTCATGCTCGAAAGACTTATTGATGGCCC
65 TC-AAAACACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC
110608 GAAGGA
129 GAAGGA
110614 CTTATAAATT
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
160 3 0.03
161 81 0.69
162 33 0.28
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (162 bp):
GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAATGACCCGAAGGACTTATCATCTTACT
CAAAACACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGA
AGGATTTCATCATCATGCTCGAAAAACTTACT
Found at i:110814 original size:42 final size:41
Alignment explanation
Indices: 110733--110833 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
110723 AGGTCTTATG
* * * *
110733 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* * *
110774 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
110816 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
110834 TAAATTGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:111281 original size:213 final size:215
Alignment explanation
Indices: 110523--111420 Score: 1523
Period size: 215 Copynumber: 4.2 Consensus size: 215
110513 TACAAATTAT
* *
110523 CCGAAGGACTTATCATCTTGCTCTAAAAGCTTACAGATGACCCGAAGGATTTAAGCGTCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
*
110588 GAAAGACTTATTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
* *
110653 TTCAAAAATTTCATCTTCTTAAAACATCATTTTTTTCATTTTCAAATTCATGTGAAACCATCCTA
131 TTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTTCATTTTCAAATTCATGTGAAAACATCCTA
110718 CCCGAAGGTCTTATGGATGGC
195 CCCGAAGGTCTTATGGATGGC
110739 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
* *
110804 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCGTTCTTAGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
* *
110869 TTCAAAAATTTCATCTTCTTAAAACATCATTTTTTCATTTTCAATTTCATGTGAAAACATCCTAC
131 TTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTAC
110934 CCGAAGGTCTTATGGATGGC
196 CCGAAGGTCTTATGGATGGC
*
110954 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
* * * *
111019 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATTGCATTTTTCGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
*
111084 TTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATTTTCAAATTCATGTGAAAACATCATAC
131 TTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTAC
* *
111148 CCGAAGGTTTTACGGATGGC
196 CCGAAGGTCTTATGGATGGC
* * *
111168 TCGAAGTACTTATCATCTTGCTCAAAAGGCTTA-AGATGACCCGAAGGATTTAAGCATCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
* *
111232 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCTCATTCTTAGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
*
111297 TTAAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATTTTCAAATTCATGTGAAAACATCCTAC
131 TTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTAC
*
111361 CCGAAGGTCTTATGTATGGC
196 CCGAAGGTCTTATGGATGGC
* * *
111381 TCGAAGGACTTATCATCTTGCCCTAAAGGCATACAGATGA
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGA
111421 GTTTGCTTCA
Statistics
Matches: 643, Mismatches: 38, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
213 197 0.31
214 87 0.14
215 205 0.32
216 154 0.24
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (215 bp):
CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGCATTCTTAGTT
TTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTAC
CCGAAGGTCTTATGGATGGC
Found at i:111485 original size:36 final size:36
Alignment explanation
Indices: 111406--111816 Score: 493
Period size: 36 Copynumber: 11.3 Consensus size: 36
111396 TCTTGCCCTA
* *
111406 AAGGCATACAGATGAGTTTGCTTCACTAC-CTCTGGTG
1 AAGGCTTA-AGATG-GTTTGCTTCACTACTCTCCGGTG
* * * *
111443 AAGGCTTAAGATTGTTTGCTTCACCACTATTCGGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
* * * * *
111479 AAGGCTTAAGATGAATTTGCTTCACCACTTTTCAGTG
1 AAGGCTTAAGATG-GTTTGCTTCACTACTCTCCGGTG
* * *
111516 AAGACTTAAGATGGATTTGCTTCACTACTCTTCAGTG
1 AAGGCTTAAGATGG-TTTGCTTCACTACTCTCCGGTG
* * *
111553 AAGGCTTAAAAAGGATTT-CTTCACTACTCTCCAGTG
1 AAGGCTTAAGATGG-TTTGCTTCACTACTCTCCGGTG
*
111589 AAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
*
111625 AAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
** * * *
111661 AAGGCTTAAGATTATTTACTTCACTACTATCCAGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
*
111697 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGGG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
*
111733 AAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
** * *
111769 AAGGCTTAAGATTATTTACTTCACTACTCTCCAGTG
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
111805 AAGGCTTAAGAT
1 AAGGCTTAAGAT
111817 TGACTTGCCC
Statistics
Matches: 329, Mismatches: 41, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
35 16 0.05
36 239 0.73
37 74 0.22
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (36 bp):
AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
Found at i:111683 original size:108 final size:108
Alignment explanation
Indices: 111406--111816 Score: 547
Period size: 108 Copynumber: 3.8 Consensus size: 108
111396 TCTTGCCCTA
* * * * *
111406 AAGGCATACAGATGAGTTTGCTTCACTAC-CTCTGGTGAAGGCTTAAGATTGTTTGCTTCACCAC
1 AAGGCTTA-AGATG-GTTTGCTTCACTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTAC
* * * * * * *
111470 TATTCGGTGAAGGCTTAAGATGAATTTGCTTCACCACTTTTCAGTG
64 TATCCAGTGAAGGCTTAAGATG-GTTTGCTTCACTACTCTCCGGTG
* * * * **
111516 AAGACTTAAGATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAAAAGGATTT-CTTCACTAC
1 AAGGCTTAAGATGG-TTTGCTTCACTACTCTCCGGTGAAGGCTT-AAGATTATTTACTTCACTAC
* *
111580 TCTCCAGTGAAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTG
64 TATCCAGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
*
111625 AAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTACTA
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTACTA
*
111690 TCCAGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGGG
66 TCCAGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
* *
111733 AAGGCTTAAGATGGTTTGCTTCAGTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTACTC
1 AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTACTA
111798 TCCAGTGAAGGCTTAAGAT
66 TCCAGTGAAGGCTTAAGAT
111817 TGACTTGCCC
Statistics
Matches: 267, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
107 7 0.03
108 161 0.60
109 48 0.18
110 45 0.17
111 6 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (108 bp):
AAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTAAGATTATTTACTTCACTACTA
TCCAGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTCCGGTG
Found at i:118074 original size:21 final size:21
Alignment explanation
Indices: 118050--118104 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
118040 AATGCAAAGT
118050 GGTCTTCATGTCTTTATGAAG
1 GGTCTTCATGTCTTTATGAAG
*
118071 GGTCTTCATGTCTTTATGAAT
1 GGTCTTCATGTCTTTATGAAG
118092 GGTCTTCATGTCT
1 GGTCTTCATGTCT
118105 CCCGGTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATGAAG
Found at i:120458 original size:25 final size:26
Alignment explanation
Indices: 120410--120458 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
120400 TCTAACACAA
** *
120410 AAATTATAAACATATATTTTTTAATT
1 AAATTATAAACATATACATATTAATT
120436 AAATTATAAA-ATATACATATTAA
1 AAATTATAAACATATACATATTAA
120459 CATATATTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATTATAAACATATACATATTAATT
Found at i:120608 original size:21 final size:21
Alignment explanation
Indices: 120570--120609 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
120560 AAATTTAAAT
* * *
120570 AATCGTAAAATTAGACATACA
1 AATCGAAAAATAAAACATACA
120591 AATCGAAAAATAAAACATA
1 AATCGAAAAATAAAACATA
120610 TACTTAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.20
Consensus pattern (21 bp):
AATCGAAAAATAAAACATACA
Found at i:121938 original size:9 final size:9
Alignment explanation
Indices: 121921--121958 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
121911 AATAAAAATA
*
121921 AATATTATT
1 AATAATATT
121930 AATAATATT
1 AATAATATT
121939 AATAATA-T
1 AATAATATT
*
121947 AATAATAAT
1 AATAATATT
121956 AAT
1 AAT
121959 TATTATATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATAATATT
Done.