Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007559.1 Hibiscus syriacus cultivar Beakdansim tig00021370_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: 198499
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1784 original size:16 final size:17
Alignment explanation
Indices: 1763--1799 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1753 TGTAGGAGTC
1763 TTTTCTTTTCTT-TTG-T
1 TTTTC-TTTCTTGTTGCT
1779 TTTTCTTTCTTGTTGCT
1 TTTTCTTTCTTGTTGCT
1796 TTTT
1 TTTT
1800 TTGTAGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTGTTGCT
Found at i:2195 original size:33 final size:33
Alignment explanation
Indices: 2134--2201 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
2124 GTTGATGAAT
*
2134 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
2167 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
2200 GA
1 GA
2202 CGATTGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:10742 original size:33 final size:33
Alignment explanation
Indices: 10700--10768 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
10690 GTTGATGAAT
*
10700 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
10733 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
10766 GAA
1 GAA
10769 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:16004 original size:12 final size:13
Alignment explanation
Indices: 15987--16016 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15977 GTTGTAGGAG
15987 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
15999 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
16012 TCTTT
1 TCTTT
16017 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:16418 original size:33 final size:33
Alignment explanation
Indices: 16376--16444 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
16366 GTTGATGAAT
*
16376 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
16409 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
16442 GAA
1 GAA
16445 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:18705 original size:27 final size:27
Alignment explanation
Indices: 18656--18712 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
18646 GAAAATCAGA
*
18656 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
* *
18684 AAAGAAATT-CAGCATTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
18710 AAA
1 AAA
18713 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 11 0.42
28 9 0.35
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Found at i:19929 original size:24 final size:21
Alignment explanation
Indices: 19895--19937 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
19885 TCCACAAGAT
*
19895 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
19917 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
19938 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:23784 original size:19 final size:20
Alignment explanation
Indices: 23743--23793 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
23733 GAAACCCCTT
*
23743 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
23763 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
23782 TGAAGATACATG
1 TGAAAATACATG
23794 CTCTTAGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:24722 original size:30 final size:31
Alignment explanation
Indices: 24681--24740 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
24671 ACATGTTGCC
**
24681 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
24712 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
24741 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:29825 original size:35 final size:37
Alignment explanation
Indices: 29756--29825 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
29746 ATAAGATACA
* *
29756 ATATGTCCATCACCATTATCACGCCTATATCATCACC
1 ATATGTCCATCACCATTATCACGCCAATAACATCACC
29793 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGCCAATAACATCA
29826 TCCTTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
36 10 0.32
37 4 0.13
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.27
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCAATAACATCACC
Found at i:29840 original size:33 final size:33
Alignment explanation
Indices: 29761--29864 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
29751 ATACAATATG
* *
29761 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
29797 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
29830 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
29863 TC
1 TC
29865 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:34319 original size:33 final size:33
Alignment explanation
Indices: 34240--34343 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
34230 ATACAATCTG
* *
34240 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
34276 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
34309 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
34342 TC
1 TC
34344 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:38797 original size:33 final size:33
Alignment explanation
Indices: 38718--38821 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
38708 ATACAATCTG
* *
38718 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
38754 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
38787 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
38820 TC
1 TC
38822 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:39193 original size:36 final size:36
Alignment explanation
Indices: 39153--39254 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
39143 GATACAATCT
39153 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
39189 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
39225 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
39255 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:39197 original size:13 final size:11
Alignment explanation
Indices: 39156--39240 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
39146 ACAATCTGTC
39156 CATCACCATTAT
1 CATCACCA-TAT
*
39168 CA-CGCCTATAT
1 CATCACC-ATAT
39179 CATCACCATAGT
1 CATCACCATA-T
39191 CCATCACCATTAT
1 -CATCACCA-TAT
*
39204 CA-CGCCTATAT
1 CATCACC-ATAT
39215 CATCACCATATT
1 CATCACCATA-T
39227 CCATCACCATAT
1 -CATCACCATAT
39239 CA
1 CA
39241 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:39269 original size:33 final size:34
Alignment explanation
Indices: 39154--39270 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
39144 ATACAATCTG
* *
39154 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
39188 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
39226 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
39259 TCCATTACCATT
1 TCCATCACCATT
39271 TCATCTCCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:39288 original size:33 final size:33
Alignment explanation
Indices: 39154--39293 Score: 106
Period size: 36 Copynumber: 4.1 Consensus size: 33
39144 ATACAATCTG
* *
39154 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
39188 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
39226 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
39259 TCCATTACCATTTCATCTCCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
39292 TC
1 TC
39294 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:39601 original size:472 final size:472
Alignment explanation
Indices: 38717--40061 Score: 2608
Period size: 472 Copynumber: 2.9 Consensus size: 472
38707 GATACAATCT
38717 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
*
38782 ATCCTTCCATTACCATTTCATCACCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
66 ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
38847 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
131 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
38912 CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
196 CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
38977 TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
261 TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
39042 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
326 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
39107 GTTAGCCTCACATCAGGTTCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACG
391 GTTAGCCTCACATCAGGTTCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACG
39172 CCTATATCATCACCATA
456 CCTATATCATCACCATA
39189 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
39254 ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
66 ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
39319 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
131 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
39384 CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
196 CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
39449 TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
261 TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
39514 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
326 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
39579 GTTAGCCTCACATCAGGTTCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACG
391 GTTAGCCTCACATCAGGTTCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACG
39644 CCTATATCATCACCATA
456 CCTATATCATCACCATA
39661 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
39726 ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
66 ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
39791 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
131 ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
* *
39856 CTTTGATAATTATTCTATCCATTTCAAATTTTTCCATTTCTATTTAC---TTTTCATTTCTTAAT
196 CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
*
39918 TATCATATTACTTAATC-AATTCTTCTTCTTTTTGTGCAGATTACTTTCAATCCAAGGTGTAGCA
261 TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
*
39982 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTG
326 TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
*
40047 GTTAGCCTTACATCA
391 GTTAGCCTCACATCA
40062 AGAGGTAATC
Statistics
Matches: 867, Mismatches: 6, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
468 124 0.14
469 32 0.04
472 711 0.82
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (472 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCACCATATCACGCCAATAACATC
ATCCTTCCATTACCATTTCATCTCCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATC
ACCACCATTGGAGGCCGAAGTCAACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCAT
CTTTGATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTTTTCATTTCTTAAT
TATCATATTACTTAATCAAATTCTTCTTCTTTTTGTGCATATTACTTTCAATCCAAGGTGTAGCA
TTTGGTGTCTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATCATTGAAGAAGCCTG
GTTAGCCTCACATCAGGTTCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACG
CCTATATCATCACCATA
Found at i:39665 original size:36 final size:36
Alignment explanation
Indices: 39625--39726 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
39615 GATACAATCT
39625 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
39661 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
39697 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
39727 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:39669 original size:13 final size:11
Alignment explanation
Indices: 39628--39712 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
39618 ACAATCTGTC
39628 CATCACCATTAT
1 CATCACCA-TAT
*
39640 CA-CGCCTATAT
1 CATCACC-ATAT
39651 CATCACCATAGT
1 CATCACCATA-T
39663 CCATCACCATTAT
1 -CATCACCA-TAT
*
39676 CA-CGCCTATAT
1 CATCACC-ATAT
39687 CATCACCATATT
1 CATCACCATA-T
39699 CCATCACCATAT
1 -CATCACCATAT
39711 CA
1 CA
39713 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:39741 original size:33 final size:34
Alignment explanation
Indices: 39626--39742 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
39616 ATACAATCTG
* *
39626 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
39660 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
39698 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
39731 TCCATTACCATT
1 TCCATCACCATT
39743 TCATCTCCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:39760 original size:33 final size:33
Alignment explanation
Indices: 39626--39765 Score: 106
Period size: 36 Copynumber: 4.1 Consensus size: 33
39616 ATACAATCTG
* *
39626 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
39660 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
39698 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
39731 TCCATTACCATTTCATCTCCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
39764 TC
1 TC
39766 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:40145 original size:24 final size:24
Alignment explanation
Indices: 40105--40151 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40095 AAAGTGCTAC
40105 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
40130 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
40152 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:40207 original size:28 final size:27
Alignment explanation
Indices: 40174--40228 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
40164 ATTTGGAGTG
40174 CAAAAGAAAGAAAAGAAAA-GAAGAAAAT
1 CAAAAG-AA-AAAAGAAAAGGAAGAAAAT
*
40202 CAAAAGCAAAAAGAAAAGTGAAGAAAA
1 CAAAAGAAAAAAGAAAAG-GAAGAAAA
40229 GTTGCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
28 14 0.58
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (27 bp):
CAAAAGAAAAAAGAAAAGGAAGAAAAT
Found at i:40398 original size:23 final size:24
Alignment explanation
Indices: 40367--40415 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
40357 TTTCTTACTA
*
40367 TTTCATTTC-TTATTCTT-TCATCT
1 TTTCATTTCATTA-CCTTATCATCT
*
40390 TTTCTTTTCATTACCTTATCATCT
1 TTTCATTTCATTACCTTATCATCT
40414 TT
1 TT
40416 CTTAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTCATTACCTTATCATCT
Found at i:43272 original size:19 final size:20
Alignment explanation
Indices: 43231--43281 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
43221 GAAACCCCTT
*
43231 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
43251 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
43270 TGAAGATACATG
1 TGAAAATACATG
43282 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:44211 original size:30 final size:31
Alignment explanation
Indices: 44170--44229 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
44160 ACATGTTTCC
**
44170 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
44201 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
44230 TAAAGCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:45287 original size:36 final size:36
Alignment explanation
Indices: 45214--45318 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
45204 ATTTATAAGT
* * *
45214 TGGTGATAATATAGGCGTGAT-ATAGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
45249 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
45285 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
45319 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:47136 original size:13 final size:11
Alignment explanation
Indices: 47095--47179 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
47085 ACAATCTATC
47095 CATCACCATTAT
1 CATCACCA-TAT
*
47107 CA-CGCCTATAT
1 CATCACC-ATAT
47118 CATCACCATAGT
1 CATCACCATA-T
47130 CCATCACCATTAT
1 -CATCACCA-TAT
*
47143 CA-CGCCTATAT
1 CATCACC-ATAT
47154 CATCACCATATT
1 CATCACCATA-T
47166 CCATCACCATAT
1 -CATCACCATAT
47178 CA
1 CA
47180 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:47140 original size:36 final size:36
Alignment explanation
Indices: 47093--47196 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
47083 ATACAATCTA
47093 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
47129 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
47165 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
47197 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:51633 original size:13 final size:11
Alignment explanation
Indices: 51592--51676 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
51582 ACAATCTGTC
51592 CATCACCATTAT
1 CATCACCA-TAT
*
51604 CA-CGCCTATAT
1 CATCACC-ATAT
51615 CATCACCATAGT
1 CATCACCATA-T
51627 CCATCACCATTAT
1 -CATCACCA-TAT
*
51640 CA-CGCCTATAT
1 CATCACC-ATAT
51651 CATCACCATATT
1 CATCACCATA-T
51663 CCATCACCATAT
1 -CATCACCATAT
51675 CA
1 CA
51677 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:51636 original size:36 final size:36
Alignment explanation
Indices: 51589--51693 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
51579 GATACAATCT
51589 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
51625 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
51661 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
51694 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:53187 original size:432 final size:431
Alignment explanation
Indices: 52376--53236 Score: 1571
Period size: 432 Copynumber: 2.0 Consensus size: 431
52366 AAAATTGACC
* *
52376 TAGACCATATTTGTAGTTCTCTGTGTGGTGAAGATGATGGTGCAACTCTCCAACTGAAATGAAGT
1 TAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCCCCAACTGAAATGAAGT
*
52441 CTCTAGCTAGCTTAAAAGTCCAGCTCAAGTGAGCTATGAGCTCAGGGGTCAGCTAGCAACTTTTC
66 CTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCAGGGGTCAGCTAGCAACTTTTC
*
52506 ACCATTTGTTCTTCATGAACTTCCGAGTCATCCTATGTAAGATTTCCTAGCTTATTGACTCCAAT
131 ACCATTTGTTCTTCATGAACTCCCGAGTCATCCTATGTAAGATTTCCTAGCTTATTGACTCCAAT
52571 CTAGCTTTAAGTCAGCTCCCATGATGTGGCCGAACATGTACCTACAAAAGAAAACATTTATAAGC
196 CTAGCTTTAAGTCAGCTCCCATGATGTGGCCGAACATGTACCTACAAAAGAAAACATTTATAAGC
52636 TAAGTAATATAAGATATAAATATATGGTTCACAGATTATATTATATGTCAACATAAAACATATTA
261 TAAGTAATATAAGATATAAATATATGGTTCACAGATTATATTATATGTCAACATAAAACATATTA
52701 AATAATCTATTGTTTGGGGATGCATTTCTAAATGATTCAAAGGTTTTAATGCATTTGGTAGTAAG
326 AATAATCTATTGTTTGGGGATGCATTTCTAAATGATTCAAAGGTTTTAATGCATTTGGTAGTAAG
*
52766 AGCTTCCCTGAAAAGTTTGGCTCTTGATCGAGTTATTGGCT
391 AGCTTCCCTGAAAAGTTTGGCTCTTGATCAAGTTATTGGCT
*
52807 TAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCCCCAGCTGAAATGAAGT
1 TAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCCCCAACTGAAATGAAGT
*
52872 CTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAGCAACTTTTC
66 CTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCAGGGGTCAGCTAGCAACTTTTC
*
52937 ACCATTTGTTCTTCATGATA-TCCCGAGTCATCCTATGTAAGATTTCTTAGCTTATTGACTCCAA
131 ACCATTTGTTCTTCATGA-ACTCCCGAGTCATCCTATGTAAGATTTCCTAGCTTATTGACTCCAA
53001 TTCTAGCTTTAAGTCAGCTCCCATGATGTGGCCGAACATGTACCTACAAAAGAAAACATTTATAA
195 -TCTAGCTTTAAGTCAGCTCCCATGATGTGGCCGAACATGTACCTACAAAAGAAAACATTTATAA
* * *
53066 GCTATGTAATATAAGATATAAATATGTGGTTCATAGATTATATTATATGTCAACATAAAACATAT
259 GCTAAGTAATATAAGATATAAATATATGGTTCACAGATTATATTATATGTCAACATAAAACATAT
*
53131 TATATAATCTATTGTTTGGGGATGCATTTCTAAATGATTCAAAGGTTTTAATGCATTTGGTAGTA
324 TAAATAATCTATTGTTTGGGGATGCATTTCTAAATGATTCAAAGGTTTTAATGCATTTGGTAGTA
* *
53196 AGAGTTTCCTTGAAAAGTTTGGCTCTTGATCAAGTTATTGG
389 AGAGCTTCCCTGAAAAGTTTGGCTCTTGATCAAGTTATTGG
53237 TCCTTGTGGC
Statistics
Matches: 414, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
431 185 0.45
432 229 0.55
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (431 bp):
TAGACCATATTTGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCCCCAACTGAAATGAAGT
CTCTAGCTAGCTCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCAGGGGTCAGCTAGCAACTTTTC
ACCATTTGTTCTTCATGAACTCCCGAGTCATCCTATGTAAGATTTCCTAGCTTATTGACTCCAAT
CTAGCTTTAAGTCAGCTCCCATGATGTGGCCGAACATGTACCTACAAAAGAAAACATTTATAAGC
TAAGTAATATAAGATATAAATATATGGTTCACAGATTATATTATATGTCAACATAAAACATATTA
AATAATCTATTGTTTGGGGATGCATTTCTAAATGATTCAAAGGTTTTAATGCATTTGGTAGTAAG
AGCTTCCCTGAAAAGTTTGGCTCTTGATCAAGTTATTGGCT
Found at i:57650 original size:36 final size:36
Alignment explanation
Indices: 57573--57673 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
57563 ATTTATAAGT
* * *
57573 TGGTGATAATATAGGCGTGAT-ATAGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
* *
57608 TTGTGATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
*
57644 TGGTGATGATATAGGCATGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
57674 GGACAGATTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 19 0.33
36 39 0.67
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
Found at i:61941 original size:19 final size:19
Alignment explanation
Indices: 61917--61966 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
61907 GAAACCCCTT
* *
61917 TGAAAATATATGATTTTTA
1 TGAAAATACATGATTTTAA
61936 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
61955 TGAAGATACATG
1 TGAAAATACATG
61967 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:66114 original size:19 final size:20
Alignment explanation
Indices: 66073--66123 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
66063 GAAACCCCTT
*
66073 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
66093 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
66112 TGAAGATACATG
1 TGAAAATACATG
66124 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:67053 original size:30 final size:31
Alignment explanation
Indices: 67012--67071 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
67002 ACATATTTCC
**
67012 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
67043 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
67072 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:73011 original size:7 final size:7
Alignment explanation
Indices: 73001--73073 Score: 62
Period size: 7 Copynumber: 10.4 Consensus size: 7
72991 CTTTTTTGGC
73001 TTTGTTT
1 TTTGTTT
73008 TTTGTTT
1 TTTGTTT
73015 TTTGTTTT
1 TTTG-TTT
*
73023 TTTGCCTT
1 TTTG-TTT
73031 TTTGTTT
1 TTTGTTT
73038 TTT-TTT
1 TTTGTTT
***
73044 TGCCTTT
1 TTTGTTT
73051 TTT-TTGT
1 TTTGTT-T
73058 TTT-TTT
1 TTTGTTT
73064 TTTGTTT
1 TTTGTTT
73071 TTT
1 TTT
73074 TGAAAAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
6 10 0.18
7 32 0.58
8 13 0.24
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (7 bp):
TTTGTTT
Found at i:73036 original size:23 final size:22
Alignment explanation
Indices: 73006--73067 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 22
72996 TTGGCTTTGT
73006 TTTTTGTTTTTTGTTTTTTTGCC
1 TTTTTGTTTTTT-TTTTTTTGCC
73029 TTTTTG---TTTTTTTTTTGCC
1 TTTTTGTTTTTTTTTTTTTGCC
73048 TTTTT-TTTGTTTTTTTTTTG
1 TTTTTGTTT-TTTTTTTTTTG
73068 TTTTTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 15 0.43
20 3 0.09
22 11 0.31
23 6 0.17
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (22 bp):
TTTTTGTTTTTTTTTTTTTGCC
Found at i:73043 original size:11 final size:11
Alignment explanation
Indices: 73005--73074 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
72995 TTTGGCTTTG
73005 TTTTTTGTTTT
1 TTTTTTGTTTT
*
73016 TTGTTTT-TTTGC
1 TT-TTTTGTTT-T
*
73028 CTTTTTGTTTT
1 TTTTTTGTTTT
**
73039 TTTTTTGCCTT
1 TTTTTTGTTTT
73050 TTTTTTGTTTT
1 TTTTTTGTTTT
73061 TTTTTTGTTTT
1 TTTTTTGTTTT
73072 TTT
1 TTT
73075 GAAAAAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
11 40 0.83
12 8 0.17
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:73043 original size:19 final size:19
Alignment explanation
Indices: 73012--73063 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
73002 TTGTTTTTTG
73012 TTTTTTGTTTTTTTGCCTT
1 TTTTTTGTTTTTTTGCCTT
73031 TTTGTTT-TTTTTTTGCCTT
1 TTT-TTTGTTTTTTTGCCTT
73050 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
73064 TTTGTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTTTGTTTTTTTGCCTT
Found at i:76073 original size:19 final size:20
Alignment explanation
Indices: 76032--76082 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
76022 GAAACTCCTT
*
76032 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
76052 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
76071 TGAAGATACATG
1 TGAAAATACATG
76083 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:82271 original size:36 final size:36
Alignment explanation
Indices: 82224--82325 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
82214 GATACAATCT
82224 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
82260 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
82296 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
82326 TCCTTCCATT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 16 0.26
36 45 0.74
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:82286 original size:11 final size:11
Alignment explanation
Indices: 82227--82311 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
82217 ACAATCTGTC
82227 CATCACCATTAT
1 CATCACCA-TAT
*
82239 CA-CGCCTATAT
1 CATCACC-ATAT
82250 CATCACCATAGT
1 CATCACCATA-T
82262 CCATCACCATTAT
1 -CATCACCA-TAT
82275 CA-CACCTATAT
1 CATCACC-ATAT
82286 CATCACCATATT
1 CATCACCATA-T
82298 CCATCACCATAT
1 -CATCACCATAT
82310 CA
1 CA
82312 CGCCAATAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:82340 original size:33 final size:33
Alignment explanation
Indices: 82296--82364 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
82286 CATCACCATA
*
82296 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
82329 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
82362 TTC
1 TTC
82365 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:82998 original size:23 final size:24
Alignment explanation
Indices: 82967--83015 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
82957 TTTCTTACTA
*
82967 TTTCATTTC-TTATTCTT-TCATCT
1 TTTCATTTCATTA-CCTTATCATCT
*
82990 TTTCTTTTCATTACCTTATCATCT
1 TTTCATTTCATTACCTTATCATCT
83014 TT
1 TT
83016 CTTAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTCATTACCTTATCATCT
Found at i:87986 original size:36 final size:36
Alignment explanation
Indices: 87939--88040 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
87929 GATACAATCT
87939 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
87975 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
88011 TTCTATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
88041 TCCTTCCATT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:89221 original size:19 final size:20
Alignment explanation
Indices: 89180--89230 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
89170 GAAACCCCTT
*
89180 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
89200 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
89219 TGAAGATACATG
1 TGAAAATACATG
89231 CTCTTAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:93500 original size:19 final size:19
Alignment explanation
Indices: 93460--93501 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
93450 ATCCTTTCTT
*
93460 TATTTCATTTCATTCTTAA
1 TATTTCATTTCATTCATAA
93479 TATTTCATTTCATTACAT-A
1 TATTTCATTTCATT-CATAA
93498 TATT
1 TATT
93502 ATTATCCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTCATTTCATTCATAA
Found at i:104748 original size:36 final size:36
Alignment explanation
Indices: 104701--104805 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 36
104691 GATACAATCT
104701 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
*
104737 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
* * *
104773 TTCCATCACTA-TATC-TCGCCTATATTATCACCA
1 GTCCATCACCATTATCAT-GCCTATATCATCACCA
104806 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.34, G:0.05, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCATGCCTATATCATCACCATA
Found at i:104773 original size:11 final size:11
Alignment explanation
Indices: 104704--104805 Score: 57
Period size: 11 Copynumber: 8.7 Consensus size: 11
104694 ACAATCTGTC
104704 CATCACCATTAT
1 CATCACCA-TAT
*
104716 CATGC-CTATAT
1 CAT-CACCATAT
104727 CATCACCATAGT
1 CATCACCATA-T
104739 CCATCACCATTAT
1 -CATCACCA-TAT
*
104752 CA-CGCCTATAT
1 CATCACC-ATAT
104763 CATCACCATATT
1 CATCACCATA-T
*
104775 CCATCACTATAT
1 -CATCACCATAT
*
104787 C-TCGCCTATAT
1 CATCACC-ATAT
*
104798 TATCACCA
1 CATCACCA
104806 ACTTATAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 23
0.69 0.09 0.23
Matches are distributed among these distances:
10 4 0.06
11 27 0.39
12 18 0.26
13 19 0.27
14 2 0.03
ACGTcount: A:0.30, C:0.34, G:0.04, T:0.31
Consensus pattern (11 bp):
CATCACCATAT
Found at i:110452 original size:36 final size:36
Alignment explanation
Indices: 110405--110501 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
110395 GATACAATCT
*
110405 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACAATA
110441 GTCCATCACCATTATCACGCCTATATCATCACAATA
1 GTCCATCACCATTATCACGCCTATATCATCACAATA
*
110477 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
110502 TATAACCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 14 0.24
36 45 0.76
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACAATA
Found at i:121886 original size:33 final size:33
Alignment explanation
Indices: 121807--121910 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
121797 ATACAATCTG
* *
121807 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
121843 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
121876 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
121909 TC
1 TC
121911 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:126346 original size:33 final size:33
Alignment explanation
Indices: 126267--126370 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
126257 ATACAATCTG
* *
126267 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
126303 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
126336 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
126369 TC
1 TC
126371 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:131253 original size:13 final size:13
Alignment explanation
Indices: 131231--131260 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
131221 ACTAAACACC
131231 TTTC-ACATACCT
1 TTTCAACATACCT
131243 TTTCAACATACCT
1 TTTCAACATACCT
131256 TTTCA
1 TTTCA
131261 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:134048 original size:23 final size:24
Alignment explanation
Indices: 134010--134058 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
134000 TTTCTTTTTA
134010 TTCTTTTCGAGTGCTTTCAATTTC
1 TTCTTTTCGAGTGCTTTCAATTTC
* *
134034 TTCTTTT-GAGTGCTTTGATTTTC
1 TTCTTTTCGAGTGCTTTCAATTTC
134057 TT
1 TT
134059 TGCTGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (24 bp):
TTCTTTTCGAGTGCTTTCAATTTC
Found at i:142836 original size:26 final size:26
Alignment explanation
Indices: 142779--142837 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
142769 AGCAAAAAGA
*
142779 AAAATAGAAGAAAAGGCTCCTACATC
1 AAAATTGAAGAAAAGGCTCCTACATC
142805 AAAATTGAAGAAAAGGCTCCTACATC
1 AAAATTGAAGAAAAGGCTCCTACATC
142831 AAAATTG
1 AAAATTG
142838 GAGTGCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAATTGAAGAAAAGGCTCCTACATC
Found at i:147143 original size:19 final size:19
Alignment explanation
Indices: 147101--147140 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
147091 TATCCCATCC
*
147101 TTATTTCATTTCATTTTTA
1 TTATTTCATTTCATTCTTA
*
147120 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
147140 T
1 T
147141 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:150530 original size:13 final size:12
Alignment explanation
Indices: 150511--150596 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
150501 ATATAGGCGT
150511 GATATGGTGATG
1 GATATGGTGATG
150523 GAATATGGTGAT-
1 G-ATATGGTGATG
*
150535 GATATAGGCG-T-
1 GATAT-GGTGATG
150546 GATAATGGTGATG
1 GAT-ATGGTGATG
150559 GACTATGGTGAT-
1 GA-TATGGTGATG
*
150571 GATATAGGCG-T-
1 GATAT-GGTGATG
150582 GATAATGGTGATG
1 GAT-ATGGTGATG
150595 GA
1 GA
150597 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:150566 original size:36 final size:36
Alignment explanation
Indices: 150493--150597 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
150483 ATTTATAAGT
* *
150493 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
150528 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
150564 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
150598 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:154134 original size:31 final size:30
Alignment explanation
Indices: 154062--154138 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
154052 TTTCCTTGGC
154062 TTTCT-TTTTCTTTT-TGAATTTATTTTTT
1 TTTCTCTTTTCTTTTCTGAATTTATTTTTT
*
154090 TTTCTTTTCTTCTTTTCTGAATTT-TTCTTCTT
1 TTTCTCTT-TTCTTTTCTGAATTTATT-TT-TT
*
154122 TTTGTCTTTTCTTTTCT
1 TTTCTCTTTTCTTTTCT
154139 TTTTGCACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.12
29 2 0.05
30 9 0.21
31 18 0.43
32 8 0.19
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.75
Consensus pattern (30 bp):
TTTCTCTTTTCTTTTCTGAATTTATTTTTT
Found at i:154435 original size:21 final size:21
Alignment explanation
Indices: 154396--154435 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
154386 AAGGAAGATT
*
154396 AATGAAATGATAAAGATAATG
1 AATGAAATGATAAAAATAATG
154417 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
154436 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (21 bp):
AATGAAATGATAAAAATAATG
Found at i:154484 original size:22 final size:21
Alignment explanation
Indices: 154458--154498 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
154448 GCTACAGAAT
154458 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
154480 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
154499 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:164177 original size:35 final size:36
Alignment explanation
Indices: 164131--164230 Score: 141
Period size: 35 Copynumber: 2.8 Consensus size: 36
164121 CAATCTGTCG
*
164131 ATCACCATTATCATGCCTATATCATCACCATAGT-A
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
* * *
164166 ATCACCATTATCACGTCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
*
164202 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
164231 ACTTATAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 51 0.88
36 7 0.12
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCA
Found at i:164198 original size:11 final size:11
Alignment explanation
Indices: 164131--164213 Score: 55
Period size: 12 Copynumber: 7.1 Consensus size: 11
164121 CAATCTGTCG
164131 ATCACCATTATC
1 ATCACCA-TATC
*
164143 ATGC-CTATATC
1 AT-CACCATATC
*
164154 ATCACCATAGTA
1 ATCACCATA-TC
164166 ATCACCAT-T-
1 ATCACCATATC
164175 ATCACGTCTATATC
1 ATCAC--C-ATATC
164189 ATCACCATATTCC
1 ATCACCATA-T-C
164202 ATCACCATATC
1 ATCACCATATC
164213 A
1 A
164214 CGCCTATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
9 5 0.09
10 2 0.03
11 16 0.28
12 18 0.31
13 12 0.21
14 5 0.09
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (11 bp):
ATCACCATATC
Found at i:169273 original size:35 final size:36
Alignment explanation
Indices: 169227--169326 Score: 159
Period size: 35 Copynumber: 2.8 Consensus size: 36
169217 CAATATGTTC
169227 ATCACCATTATCACGCCTATATCATCACCATAGT-A
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
* *
169262 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
*
169298 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
169327 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 54 0.89
36 7 0.11
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCA
Found at i:169294 original size:11 final size:11
Alignment explanation
Indices: 169225--169309 Score: 66
Period size: 11 Copynumber: 7.3 Consensus size: 11
169215 TACAATATGT
169225 TCATCACCATTA
1 TCATCACCA-TA
*
169237 TCA-CGCCTATA
1 TCATCACC-ATA
169248 TCATCACCATA
1 TCATCACCATA
*
169259 GTAATCACCATTA
1 -TCATCACCA-TA
*
169272 TCA-CGCCTATA
1 TCATCACC-ATA
169283 TCATCACCATA
1 TCATCACCATA
169294 TTCCATCACCATA
1 -T-CATCACCATA
169307 TCA
1 TCA
169310 CGCCTATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
11 24 0.41
12 23 0.39
13 12 0.20
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:173851 original size:62 final size:62
Alignment explanation
Indices: 173749--173873 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
173739 CACAACCTTC
173749 TATCACCACAATCAATTTAAACGGCTTACTTGACTTGCTTGGTGGTGAGAATTATTGATGAG
1 TATCACCACAATCAATTTAAACGGCTTACTTGACTTGCTTGGTGGTGAGAATTATTGATGAG
*
173811 TATCGCCACAATCAATTTAAACGGCTTACTTGACTTGCTTGGTGGTGAGAATTATTGATGAG
1 TATCACCACAATCAATTTAAACGGCTTACTTGACTTGCTTGGTGGTGAGAATTATTGATGAG
173873 T
1 T
173874 GCTTCAACTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (62 bp):
TATCACCACAATCAATTTAAACGGCTTACTTGACTTGCTTGGTGGTGAGAATTATTGATGAG
Found at i:173924 original size:20 final size:21
Alignment explanation
Indices: 173885--173949 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 21
173875 CTTCAACTTC
***
173885 TTTTCTTTCTTTTCTTTGCTT
1 TTTTCTTTCTTTTGAGTGCTT
173906 TTTTC-TTCTTTTGAGTGCTGGAT
1 TTTTCTTTCTTTTGAGTGCT---T
173929 TTTTCTTTCTTTTGAGTGCTT
1 TTTTCTTTCTTTTGAGTGCTT
173950 CACTTTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 11 0.30
21 6 0.16
23 6 0.16
24 14 0.38
ACGTcount: A:0.05, C:0.15, G:0.14, T:0.66
Consensus pattern (21 bp):
TTTTCTTTCTTTTGAGTGCTT
Found at i:173956 original size:23 final size:24
Alignment explanation
Indices: 173907--173959 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
173897 TCTTTGCTTT
* *
173907 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
173930 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
173953 TTTCTTT
1 TTTCTTT
173960 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:176663 original size:19 final size:19
Alignment explanation
Indices: 176639--176677 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
176629 TATCCTTTCT
176639 TTATTTCATTTCATT-CTTA
1 TTATTT-ATTTCATTACTTA
*
176658 TTATTTTTTTCATTACTTA
1 TTATTTATTTCATTACTTA
176677 T
1 T
176678 ATTATTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTATTTCATTACTTA
Found at i:180631 original size:8 final size:8
Alignment explanation
Indices: 180618--180655 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
180608 GAATTTCTTT
180618 TTTTTTTC
1 TTTTTTTC
180626 TTTTTTTC
1 TTTTTTTC
180634 TTTTTTTTC
1 -TTTTTTTC
*
180643 TTTTTGTC
1 TTTTTTTC
180651 TTTTT
1 TTTTT
180656 CTTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:180637 original size:17 final size:17
Alignment explanation
Indices: 180617--180666 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
180607 TGAATTTCTT
180617 TTTTTTTTCTTTTTTTC
1 TTTTTTTTCTTTTTTTC
*
180634 TTTTTTTTCTTTTTGTC
1 TTTTTTTTCTTTTTTTC
*
180651 TTTTTCTTTATTTTTT
1 TTTTT-TTTCTTTTTT
180667 GAACTCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTTC
Found at i:183150 original size:2 final size:2
Alignment explanation
Indices: 183143--183179 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
183133 ATCACCAACT
183143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
183180 CCTCTACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:185093 original size:34 final size:34
Alignment explanation
Indices: 185050--185122 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
185040 TAAAGTCTGG
185050 GTCTTTGCTCTATATAGCATTGGTTCTTCTTTGA
1 GTCTTTGCTCTATATAGCATTGGTTCTTCTTTGA
185084 GTCTTTGCTCTATATAGCATTGGTTCTTCTTTGA
1 GTCTTTGCTCTATATAGCATTGGTTCTTCTTTGA
185118 GTCTT
1 GTCTT
185123 CTTTAAGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.51
Consensus pattern (34 bp):
GTCTTTGCTCTATATAGCATTGGTTCTTCTTTGA
Found at i:187518 original size:13 final size:13
Alignment explanation
Indices: 187495--187557 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
187485 AAGATACTAT
187495 ATATT-CATCACC
1 ATATTCCATCACC
187507 ATATTCCATCACC
1 ATATTCCATCACC
* *
187520 AT-TTTCAT-GCC
1 ATATTCCATCACC
**
187531 -TATAACATCACC
1 ATATTCCATCACC
*
187543 ATCTTCCATCACC
1 ATATTCCATCACC
187556 AT
1 AT
187558 TGCACGCCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 12 0.31
13 20 0.51
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATTCCATCACC
Found at i:187575 original size:35 final size:35
Alignment explanation
Indices: 187494--187645 Score: 223
Period size: 35 Copynumber: 4.3 Consensus size: 35
187484 TAAGATACTA
* *
187494 TATATTCATCACCATATTCCATCACCATTTTCATGCC
1 TATA-TCATCACCATCTTCCATCACCA-TTTCACGCC
* *
187531 TATAACATCACCATCTTCCATCACCATTGCACGCC
1 TATATCATCACCATCTTCCATCACCATTTCACGCC
*
187566 TATATCATCACCATCTTCTATCACCATTTCACGCC
1 TATATCATCACCATCTTCCATCACCATTTCACGCC
* *
187601 TATATCATAACCATCTTCTATCACCATTTCACGCC
1 TATATCATCACCATCTTCCATCACCATTTCACGCC
187636 TATATCATCA
1 TATATCATCA
187646 TGATGTGATC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
35 82 0.77
36 20 0.19
37 4 0.04
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.34
Consensus pattern (35 bp):
TATATCATCACCATCTTCCATCACCATTTCACGCC
Found at i:194193 original size:20 final size:20
Alignment explanation
Indices: 194168--194214 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
194158 TACTTATTTT
194168 AATTCATTTTGCAGCAATTC
1 AATTCATTTTGCAGCAATTC
194188 AATTCATTTTGCAGCAATTC
1 AATTCATTTTGCAGCAATTC
194208 AATTCAT
1 AATTCAT
194215 GTCTGTGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (20 bp):
AATTCATTTTGCAGCAATTC
Done.