Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007083.1 Hibiscus syriacus cultivar Beakdansim tig00018481_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: 59778
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:89 original size:19 final size:19
Alignment explanation
Indices: 65--103 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55 TACAGAAATG
65 CACCATTAGGAGCAAATTC
1 CACCATTAGGAGCAAATTC
84 CACCATTAGGAGCAAATTC
1 CACCATTAGGAGCAAATTC
103 C
1 C
104 CTTCCCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (19 bp):
CACCATTAGGAGCAAATTC
Found at i:1719 original size:2 final size:2
Alignment explanation
Indices: 1712--1757 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1702 CCTTTTTCAA
1712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1754 AT AT
1 AT AT
1758 TTAATTTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1921 original size:13 final size:14
Alignment explanation
Indices: 1903--1933 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1893 TTTTTAAAAT
1903 AAAATATTTTT-TA
1 AAAATATTTTTCTA
1916 AAAATATTTTTCTA
1 AAAATATTTTTCTA
1930 AAAA
1 AAAA
1934 ATCTAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATATTTTTCTA
Found at i:6293 original size:14 final size:14
Alignment explanation
Indices: 6274--6314 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
6264 AAAAACATGA
6274 TTTCTGATTACTAG
1 TTTCTGATTACTAG
* *
6288 TTTCTGATTTCTGG
1 TTTCTGATTACTAG
6302 TTTCTGA-TACTAG
1 TTTCTGATTACTAG
6315 GTATAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (14 bp):
TTTCTGATTACTAG
Found at i:9151 original size:20 final size:20
Alignment explanation
Indices: 9115--9152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9105 ATCCTATTCT
**
9115 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
9135 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
9153 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:9269 original size:20 final size:20
Alignment explanation
Indices: 9192--9262 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
9182 AGGCTATTCC
9192 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
9212 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
9232 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
9252 CTGGTAATCTT
1 CTGGTAATCTT
9263 ACATTCCGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:9417 original size:20 final size:20
Alignment explanation
Indices: 9380--9417 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9370 TTTTAATAAA
*
9380 AAAATATATTAAATTTTTTT
1 AAAATATATTAAAATTTTTT
9400 AAAATATA-TAATAATTTT
1 AAAATATATTAA-AATTTT
9418 ATAATTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATATTAAAATTTTTT
Found at i:16817 original size:33 final size:33
Alignment explanation
Indices: 16750--16836 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
16740 CCTGATGTTT
* * *
16750 ACTTTTTGTTTCATTTCAG--CACCCTTCGTTA
1 ACTTTTTGTTTCATTTTAGTACCCCCGTCGTTA
*
16781 ACTTTTTGTTTCGTTTTAGTACCCCCGTCGTTA
1 ACTTTTTGTTTCATTTTAGTACCCCCGTCGTTA
*
16814 ACTTTTGGTTTCATTTTAGTACC
1 ACTTTTTGTTTCATTTTAGTACC
16837 TAAATTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
31 17 0.35
33 31 0.65
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (33 bp):
ACTTTTTGTTTCATTTTAGTACCCCCGTCGTTA
Found at i:18141 original size:2 final size:2
Alignment explanation
Indices: 18134--18189 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
18124 ATCTAAAATA
18134 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18175 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
18190 ATTATGTGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20364 original size:60 final size:59
Alignment explanation
Indices: 20242--20401 Score: 146
Period size: 60 Copynumber: 2.7 Consensus size: 59
20232 TTTTAATCTG
* * * *
20242 GTCCTTAAACTTTTAAATATTTTAATTTCAT-CCTCAAACTATAACTCTCATTCTCAATTA
1 GTCCTTAAACTTTT-GATTTTTTAATTTCATCCCT-AAATTATAACTCTCATTCTCAAATA
* *
20302 GTCCTTAAACTTTTGATTGTTTTAGTTTCATCCCTAAATTATGAC-CATCATTC-CAAAATA
1 GTCCTTAAACTTTTGATT-TTTTAATTTCATCCCTAAATTATAACTC-TCATTCTC-AAATA
** * **
20362 GTCCCCAAGCTTTTGAATTTTCCAATTTCATCCCTAAATT
1 GTCCTTAAACTTTTG-ATTTTTTAATTTCATCCCTAAATT
20402 CATCCAAATA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
59 4 0.05
60 73 0.88
61 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (59 bp):
GTCCTTAAACTTTTGATTTTTTAATTTCATCCCTAAATTATAACTCTCATTCTCAAATA
Found at i:24714 original size:3 final size:3
Alignment explanation
Indices: 24708--24762 Score: 92
Period size: 3 Copynumber: 17.7 Consensus size: 3
24698 AAAAAAAAAG
24708 GAA GAA GAA GGAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GAA GAA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA
24755 GAA GAA GA
1 GAA GAA GA
24763 GGAGGAGGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24742 original size:25 final size:25
Alignment explanation
Indices: 24708--24775 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
24698 AAAAAAAAAG
24708 GAAGAAGAAGGAAGAAGAAGAAGAA
1 GAAGAAGAAGGAAGAAGAAGAAGAA
24733 GAAGAAGAAGGAAGAAGAAGAAGAA
1 GAAGAAGAAGGAAGAAGAAGAAGAA
* *
24758 GAAG-AGGAGGAGGAAGAA
1 GAAGAAGAAGGAAGAAGAA
24776 ACTAAGAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 12 0.29
25 29 0.71
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (25 bp):
GAAGAAGAAGGAAGAAGAAGAAGAA
Found at i:25773 original size:17 final size:17
Alignment explanation
Indices: 25744--25776 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25734 AAGAAAAGAA
25744 AAAGAAAATAATAAAAG
1 AAAGAAAATAATAAAAG
25761 AAAGTAAAA-AATAAAA
1 AAAG-AAAATAATAAAA
25777 AAAAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAGAAAATAATAAAAG
Found at i:25773 original size:20 final size:19
Alignment explanation
Indices: 25748--25789 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25738 AAAGAAAAAG
* *
25748 AAAATAATAAAAGAAAGTAA
1 AAAATAA-AAAAAAAACTAA
25768 AAAATAAAAAAAAAACTAA
1 AAAATAAAAAAAAAACTAA
25787 AAA
1 AAA
25790 TCAGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAAAAAACTAA
Found at i:27590 original size:2 final size:2
Alignment explanation
Indices: 27583--27618 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27573 TTATAAAACA
27583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27619 GAAAAGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29172 original size:68 final size:67
Alignment explanation
Indices: 29098--29258 Score: 192
Period size: 61 Copynumber: 2.5 Consensus size: 67
29088 CCCTAAACTT
*
29098 AAACCCCAAAATATAAACCTTAAATTATAAACTCT-AAACCTAAAACCCTTATCTCAAATACTAA
1 AAACCCCAAAATATAAACC-TAAATTATAAACTCTAAAACCT-AAACCCTAATCTCAAATACTAA
29162 ACCC
64 ACCC
* * * *
29166 AAACCCCAAATTATAAA-C---A--ATAAATTCTAAAATCTAAACCCTAATCTCAAATCCTAAAC
1 AAACCCCAAAATATAAACCTAAATTATAAACTCTAAAACCTAAACCCTAATCTCAAATACTAAAC
29225 CC
66 CC
*
29227 AAACCCCAAACTATAAATCCTAAATTATAAAC
1 AAACCCCAAAATATAAA-CCTAAATTATAAAC
29259 ATAAAATCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
61 48 0.62
62 5 0.06
63 2 0.03
66 1 0.01
67 1 0.01
68 21 0.27
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (67 bp):
AAACCCCAAAATATAAACCTAAATTATAAACTCTAAAACCTAAACCCTAATCTCAAATACTAAAC
CC
Found at i:29224 original size:20 final size:19
Alignment explanation
Indices: 29140--29226 Score: 57
Period size: 20 Copynumber: 4.3 Consensus size: 19
29130 TCTAAACCTA
*
29140 AAACCCTTATCTCAAATACT
1 AAACCCTAATCTCAAAT-CT
* * * *
29160 AAACCCAAACCCCAAATTAT
1 AAACCCTAATCTCAAA-TCT
** *
29180 AAACAATAAATTCTAAAATCT
1 AAACCCT-AA-TCTCAAATCT
29201 AAACCCTAATCTCAAATCCT
1 AAACCCTAATCTCAAAT-CT
29221 AAACCC
1 AAACCC
29227 AAACCCCAAA
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
19 7 0.15
20 27 0.56
21 10 0.21
22 4 0.08
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (19 bp):
AAACCCTAATCTCAAATCT
Found at i:29273 original size:61 final size:60
Alignment explanation
Indices: 29132--29284 Score: 166
Period size: 61 Copynumber: 2.5 Consensus size: 60
29122 TTATAAACTC
* * * * *
29132 TAAACCTAAAACCCTTATCTCAAATACTAAACCCAAACCCCAAATTATAAACAATAAATTC
1 TAAAACTAAAA-CCTAATCTCAAATCCTAAACCCAAACCCCAAACTATAAACAATAAATTA
* *
29193 TAAAATCTAAACCCTAATCTCAAATCCTAAACCCAAACCCCAAACTATAAATC-CTAAATTA
1 TAAAA-CTAAAACCTAATCTCAAATCCTAAACCCAAACCCCAAACTATAAA-CAATAAATTA
* *
29254 T-AAACATAAAATCTAAATCTTAAATCCTAAA
1 TAAAAC-TAAAACCT-AATCTCAAATCCTAAA
29285 TCTTAAACCC
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
59 1 0.01
60 9 0.12
61 62 0.79
62 6 0.08
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (60 bp):
TAAAACTAAAACCTAATCTCAAATCCTAAACCCAAACCCCAAACTATAAACAATAAATTA
Found at i:29277 original size:14 final size:15
Alignment explanation
Indices: 29260--29291 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29250 ATTATAAACA
29260 TAAAAT-CTAAATCT
1 TAAAATCCTAAATCT
29274 T-AAATCCTAAATCT
1 TAAAATCCTAAATCT
29288 TAAA
1 TAAA
29292 CCCAACCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.25
14 10 0.62
15 2 0.12
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATCCTAAATCT
Found at i:29511 original size:57 final size:57
Alignment explanation
Indices: 29449--29557 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
29439 TCTCTCTCTC
* * *
29449 TATATATATATCGAAAACTATTTAAATTAGAAAGCAAACATACTAAAAGTTTATATA
1 TATATATAAATAGAAAACTATTTAAATTAGAAAGCAAACACACTAAAAGTTTATATA
*
29506 TATATATAAATAGAAAGCTATTTAAATTAGAAAGCAAACACACTAAAAGTTT
1 TATATATAAATAGAAAACTATTTAAATTAGAAAGCAAACACACTAAAAGTTT
29558 TGTAACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.31
Consensus pattern (57 bp):
TATATATAAATAGAAAACTATTTAAATTAGAAAGCAAACACACTAAAAGTTTATATA
Found at i:32806 original size:16 final size:16
Alignment explanation
Indices: 32777--32812 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
32767 AAATTATTTG
32777 AAAT-TATTAAATATT
1 AAATATATTAAATATT
*
32792 AAATATATTATATATT
1 AAATATATTAAATATT
32808 AAATA
1 AAATA
32813 CATTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATTAAATATT
Found at i:34055 original size:51 final size:51
Alignment explanation
Indices: 33972--34089 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
33962 TAGAATCTCT
* * * *
33972 GATGAAATTCAATTCCATCAAATGAGGGAAAGTAAATTCCATTCAAAAATG
1 GATGAAATTCAATTCTATCAAACGAGGAAAAGTAAATTCCATCCAAAAATG
*
34023 GATTG-AATTCAATTCTATTAAACGAGGAAAAGTAAATTCCATCCAAAAATG
1 GA-TGAAATTCAATTCTATCAAACGAGGAAAAGTAAATTCCATCCAAAAATG
34074 GATGAAATTCAATTCT
1 GATGAAATTCAATTCT
34090 CTTGTTGGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 2 0.03
51 56 0.93
52 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (51 bp):
GATGAAATTCAATTCTATCAAACGAGGAAAAGTAAATTCCATCCAAAAATG
Found at i:34480 original size:32 final size:34
Alignment explanation
Indices: 34408--34490 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 34
34398 TTTATTTTGT
*
34408 TCGGGTCGGGTTTTTTTAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAGTGTGATATTC-GAT--AG
34445 TCGGGTC-GGTTTTTTTAAGTGTGATATTC-AT-G
1 TCGGGTCGGGTTTTTTT-AGTGTGATATTCGATAG
34477 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
34491 AGGGTGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
32 6 0.14
33 2 0.05
34 5 0.12
35 1 0.02
36 9 0.21
37 19 0.45
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (34 bp):
TCGGGTCGGGTTTTTTTAGTGTGATATTCGATAG
Found at i:34686 original size:27 final size:28
Alignment explanation
Indices: 34656--34717 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
34646 TTTGTTCGGG
*
34656 TCGGGTCGGGTTTTTT-AAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAAGTATGATAT
34683 TCGGGTCGGGTTTTTTAAAGTATGATAT
1 TCGGGTCGGGTTTTTTAAAGTATGATAT
34711 TCGGGTC
1 TCGGGTC
34718 AGGTCGGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.16, C:0.10, G:0.32, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTAAAGTATGATAT
Found at i:35321 original size:16 final size:17
Alignment explanation
Indices: 35295--35341 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
35285 ATATGAAATT
*
35295 AGATTTCAATTCC-TAC
1 AGATTCCAATTCCTTAC
*
35311 AGATTCTAATTCCTTTAC
1 AGATTCCAATTCC-TTAC
35329 AGATTCCAATTCC
1 AGATTCCAATTCC
35342 CTCATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (17 bp):
AGATTCCAATTCCTTAC
Found at i:37078 original size:84 final size:82
Alignment explanation
Indices: 36977--37202 Score: 247
Period size: 84 Copynumber: 2.7 Consensus size: 82
36967 GCGTTTCTTA
* *
36977 AACAAACGTCGCTATAGAGTAGTACTTTAGCGGTGTTTTTATACAAACACCGTAATAGGGATCGT
1 AACAAACGTCG-TATAGAGTAGTACTTTAGCAGTGTTTTTATACAAACGCCGTAATAGGGATCGT
* *
37042 TTATAGTGGCGTTTTTTTC
65 TCATAGTGGCG-TTTTTCC
* * ** * * *
37061 AACAAACGCCGTGATAGATTAGTACTTTAGCAGTGTTTTTATACAAACGTTGCAATAGGGTTTGT
1 AACAAACGTCGT-ATAGAGTAGTACTTTAGCAGTGTTTTTATACAAACGCCGTAATAGGGATCGT
37126 TCATAGTGGCGTTTTTCC
65 TCATAGTGGCGTTTTTCC
* * * * * * *
37144 AACAAATGTCGCAATAAAG-AGTAATTTAGTAGCGTTTTTATACAAATGCCGTAATAGGG
1 AACAAACGTCG-TATAGAGTAGTACTTTAGCAGTGTTTTTATACAAACGCCGTAATAGGG
37203 TTCTTTAGCG
Statistics
Matches: 117, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
82 33 0.28
83 20 0.17
84 64 0.55
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (82 bp):
AACAAACGTCGTATAGAGTAGTACTTTAGCAGTGTTTTTATACAAACGCCGTAATAGGGATCGTT
CATAGTGGCGTTTTTCC
Found at i:37109 original size:41 final size:39
Alignment explanation
Indices: 36957--37109 Score: 112
Period size: 41 Copynumber: 3.7 Consensus size: 39
36947 CACAAAACGA
* *
36957 TACTTTAGCGGCGTTTCTTAAACAAACGTCGCTATAGAGTAG
1 TACTTTAGCGGCGTTT-TTATACAAACGCCG-TATAGA-TAG
* * *
36999 TACTTTAGCGGTGTTTTTATACAAACACCGTAATAGGGATCG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGT-ATA--GATAG
* *
37041 T--TTATAGTGGCGTTTTTTTCAACAAACGCCGTGATAGATTAG
1 TACTT-TAGCGGCGTTTTTAT--ACAAACGCCGT-ATAGA-TAG
* *
37083 TACTTTAGCAGTGTTTTTATACAAACG
1 TACTTTAGCGGCGTTTTTATACAAACG
37110 TTGCAATAGG
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
40 3 0.03
41 35 0.40
42 21 0.24
43 26 0.30
44 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (39 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGTATAGATAG
Found at i:37428 original size:41 final size:40
Alignment explanation
Indices: 37333--37454 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 40
37323 ACACCATAAT
* *
37333 AAATCAGTGAATTAGC-AGCGTTTTTAAATACAAACGTCAC-A
1 AAATCAGTGCATTAGCGA-CGTTTTTAAA-A-AAACGTCGCAA
*
37374 AAAT-AGTAACATTAGCGACGTTTTTAAAAAAACGTCGCAA
1 AAATCAGT-GCATTAGCGACGTTTTTAAAAAAACGTCGCAA
* * * *
37414 GAAATCAGTGCATTAGTGGCGTTTTTAAACAAACGCCGCAA
1 -AAATCAGTGCATTAGCGACGTTTTTAAAAAAACGTCGCAA
37455 TAAGTTTTGG
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
39 8 0.12
40 5 0.07
41 51 0.75
42 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (40 bp):
AAATCAGTGCATTAGCGACGTTTTTAAAAAAACGTCGCAA
Found at i:38775 original size:13 final size:13
Alignment explanation
Indices: 38757--38781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38747 TTCCAATGGC
38757 AGGATCATGCTAA
1 AGGATCATGCTAA
38770 AGGATCATGCTA
1 AGGATCATGCTA
38782 TATTACATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (13 bp):
AGGATCATGCTAA
Found at i:42804 original size:43 final size:42
Alignment explanation
Indices: 42732--42909 Score: 142
Period size: 43 Copynumber: 4.1 Consensus size: 42
42722 CGTTTTCGAT
* * * * **
42732 AAAAACGCCGCTAAATC-TCAACGCTTATTGCAGCGCTTGTTTG
1 AAAAACGCCGCTAAA-CAACAACACCTATTGC-GCGTTTGTAAG
* **
42775 AAAAACGCCGCTAAACAACAACACCTATTGCGACGTTTATGGG
1 AAAAACGCCGCTAAACAACAACACCTATTGCG-CGTTTGTAAG
*
42818 AAAAACGCCGCTAAACAACGACACCTATTGCGGCGTTTGTAAG
1 AAAAACGCCGCTAAACAACAACACCTATTGC-GCGTTTGTAAG
** * * * * **
42861 CCAAACGCCGCTAAATAGCAATACCTACTGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAACAACAACACCTATTGC-GCGTTTGTAAG
42904 AAAAAC
1 AAAAAC
42910 AACAACACCT
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
42 2 0.02
43 107 0.97
44 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (42 bp):
AAAAACGCCGCTAAACAACAACACCTATTGCGCGTTTGTAAG
Found at i:42922 original size:76 final size:76
Alignment explanation
Indices: 42830--42974 Score: 227
Period size: 76 Copynumber: 1.9 Consensus size: 76
42820 AAACGCCGCT
* * * * *
42830 AAACAACGACACCTATTGCGGCGTTTGTAAGCCAAACGCCGCTAAATAGCAATACCTACTGCGGC
1 AAACAACAACACCTATTGCGGCATTTGTAAGACAAACGCCGCTAAATAGCAAAACCTACTACGGC
42895 GTTTGTGGGAA
66 GTTTGTGGGAA
* *
42906 AAACAACAACACCTATTGCGGCATTTTTAAGACAAACGCCGCTAAATAGCAAAACCTATTACGGC
1 AAACAACAACACCTATTGCGGCATTTGTAAGACAAACGCCGCTAAATAGCAAAACCTACTACGGC
42971 GTTT
66 GTTT
42975 TTTCAACAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (76 bp):
AAACAACAACACCTATTGCGGCATTTGTAAGACAAACGCCGCTAAATAGCAAAACCTACTACGGC
GTTTGTGGGAA
Found at i:42984 original size:43 final size:44
Alignment explanation
Indices: 42937--43035 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 44
42927 CATTTTTAAG
42937 ACAAACGCCGCTAAATAGCAAAACCTATTACGGCGTTTTT-TCA
1 ACAAACGCCGCTAAATAGCAAAACCTATTACGGCGTTTTTCTCA
* * * *** * *
42980 ACAAACGTCGCTATATATCGTCACCTATTGCGGCGTTTTTCGTTA
1 ACAAACGCCGCTAAATAGCAAAACCTATTACGGCGTTTTTC-TCA
43025 ACAAACGCCGC
1 ACAAACGCCGC
43036 GAACTTTAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 33 0.73
45 12 0.27
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
ACAAACGCCGCTAAATAGCAAAACCTATTACGGCGTTTTTCTCA
Found at i:46576 original size:20 final size:20
Alignment explanation
Indices: 46553--46604 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
46543 ATCGCGATCC
46553 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
46573 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
46593 CCAAAATCGCAA
1 CCAGAATCGCAA
46605 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:46621 original size:21 final size:20
Alignment explanation
Indices: 46594--46692 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
46584 AATCAGTTTC
46594 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
46615 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
46636 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
46656 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
46677 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
46693 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:46721 original size:20 final size:20
Alignment explanation
Indices: 46659--46852 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
46649 CGATTTTCCA
* ** *
46659 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
46679 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
46699 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
46719 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
46739 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
46759 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
46779 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
46799 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
46819 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
46840 AAATCGCAACGCG
1 AAATCGCAACGCG
46853 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:46743 original size:60 final size:60
Alignment explanation
Indices: 46659--46852 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
46649 CGATTTTCCA
* ** * *
46659 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
46719 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
46779 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
46840 AAATCGCAACGCG
1 AAATCGCAACGCG
46853 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:47273 original size:33 final size:33
Alignment explanation
Indices: 47234--47304 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
47224 TTCACTTAGA
*
47234 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
47267 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
47300 TTTCA
1 TTTCA
47305 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:47444 original size:14 final size:14
Alignment explanation
Indices: 47425--47479 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
47415 AGAATGACTG
47425 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
47439 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
47458 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
47472 TCGCAACG
1 TCGCAACG
47480 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:47492 original size:33 final size:33
Alignment explanation
Indices: 47425--47495 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
47415 AGAATGACTG
***
47425 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
47458 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
47491 TCGCA
1 TCGCA
47496 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:47513 original size:19 final size:19
Alignment explanation
Indices: 47491--47588 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
47481 GAAACCAAAA
*
47491 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47510 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
47524 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47543 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
47557 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
47576 TCGCGTTGCGATT
1 TCGCGTTGCGATT
47589 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47532 original size:14 final size:14
Alignment explanation
Indices: 47513--47602 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
47503 TTTCATTTCG
47513 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
47527 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
47546 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
47560 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
47577 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
47593 CGTTGCGATT
1 CGTTGCGATT
47603 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:47538 original size:33 final size:33
Alignment explanation
Indices: 47496--47610 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
47486 CAAAATCGCA
47496 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
47529 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
47562 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
47595 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
47611 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:49538 original size:185 final size:186
Alignment explanation
Indices: 49309--49688 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
49299 TAGATTGCTT
49309 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49374 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
49439 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
49494 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49559 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
49624 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
49680 AGTAAATTT
1 AGTAAATTT
49689 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:49623 original size:93 final size:93
Alignment explanation
Indices: 49309--49688 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
49299 TAGATTGCTT
49309 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49374 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49402 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49466 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49494 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49559 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49587 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49652 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49680 AGTAAATTT
1 AGTAAATTT
49689 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:49772 original size:19 final size:19
Alignment explanation
Indices: 49732--49860 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
49722 TAGTTTACTT
* *
49732 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
49752 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
49771 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
49790 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
49804 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
49823 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
49837 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
49856 TCGCA
1 TCGCA
49861 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:49811 original size:33 final size:32
Alignment explanation
Indices: 49768--49860 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
49758 CGCGAAACCA
**
49768 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
49800 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
49833 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
49861 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:49858 original size:52 final size:52
Alignment explanation
Indices: 49732--49860 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
49722 TAGTTTACTT
**
49732 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
49784 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
49837 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
49861 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:49878 original size:19 final size:19
Alignment explanation
Indices: 49856--49990 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
49846 GAAACCAAAA
*
49856 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
49875 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
49891 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
49908 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
49924 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
49941 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
49960 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
49980 TCGTGTTGCGA
1 TCGCGTTGCGA
49991 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:49897 original size:14 final size:14
Alignment explanation
Indices: 49878--49934 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
49868 TTTCATTTCG
49878 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
49892 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
49909 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
49925 CGTTGCGATT
1 CGTTGCGATT
49935 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:49903 original size:33 final size:33
Alignment explanation
Indices: 49861--49953 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
49851 CAAAATCGCA
*
49861 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
49894 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
49927 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
49954 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:51846 original size:38 final size:38
Alignment explanation
Indices: 51803--51875 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
51793 AATTGATTGT
*
51803 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
51841 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
51876 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:51862 original size:19 final size:19
Alignment explanation
Indices: 51798--51862 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
51788 AGTTTAATTG
*
51798 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
51817 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
51835 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
51855 ATTGATTT
1 ATTGATTT
51863 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:51876 original size:14 final size:14
Alignment explanation
Indices: 51857--51892 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
51847 ATTGTTTAAT
51857 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
51871 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
51885 TGATTTGT
1 TGATTTGT
51893 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:52015 original size:19 final size:19
Alignment explanation
Indices: 51999--52100 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
51989 AAAAATGACT
51999 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52018 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
52037 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
52051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52070 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
52090 ATCGCAATGCG
1 ATCGCAATGCG
52101 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:52153 original size:19 final size:19
Alignment explanation
Indices: 52129--52435 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
52119 GATTATCTCG
52129 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52148 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52167 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
52181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52200 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
52219 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
52238 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
52257 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
52272 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52290 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
52309 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
52323 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52342 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
52361 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
52375 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
52395 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
52409 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
52428 TTGCGATT
1 TTGCGATT
52436 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 28 0.11
18 5 0.02
19 139 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:52204 original size:71 final size:71
Alignment explanation
Indices: 52129--52368 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
52119 GATTATCTCG
52129 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
52194 TTCGCA
66 TTCGCA
* *
52200 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
52263 TT-ATGTCG-G
61 TTCATTTCGCA
*
52272 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
52336 TTCGCA
66 TTCGCA
52342 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
52369 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:52288 original size:142 final size:136
Alignment explanation
Indices: 52097--52435 Score: 504
Period size: 142 Copynumber: 2.4 Consensus size: 136
52087 AAAATCGCAA
52097 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
52161 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
52226 TTTCATTTCGTAT
128 -TTC-TCTCG--T
52239 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
52303 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
52368 TCTCTCGT
129 TCTCTCGT
* * *
52376 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
52436 GTATTTTCCG
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 34 0.18
139 4 0.02
140 3 0.02
142 118 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
TCTCGT
Found at i:52374 original size:52 final size:52
Alignment explanation
Indices: 52129--52407 Score: 354
Period size: 52 Copynumber: 5.2 Consensus size: 52
52119 GATTATCTCG
*
52129 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
52181 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
52238 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
52290 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
52342 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
52395 TTGCGATTTTCAT
1 TTGCGATTTTCAT
52408 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 152 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:54751 original size:13 final size:13
Alignment explanation
Indices: 54733--54757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54723 TCTTCGGGAC
54733 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
54746 TTTTTCTTCTTC
1 TTTTTCTTCTTC
54758 AGGATTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:54963 original size:24 final size:24
Alignment explanation
Indices: 54929--54975 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54919 CTGAAACATC
54929 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
54953 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
54976 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:55675 original size:20 final size:20
Alignment explanation
Indices: 55647--56012 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
55637 AAATTTCAGT
* * * *
55647 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
55667 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
55687 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
55707 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
55727 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55747 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
55767 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
55787 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55807 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55827 GTTGCGATTTACGGAT-CAC
1 GTTGCGATTTACGGATACGC
55846 GTTGCG-TTTACGGATA-GC
1 GTTGCGATTTACGGATACGC
55864 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55884 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
55904 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
55924 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
55944 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
55964 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
55984 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
56004 GTTGCGATT
1 GTTGCGATT
56013 ATGGAAAATC
Statistics
Matches: 305, Mismatches: 30, Indels: 22
0.85 0.08 0.06
Matches are distributed among these distances:
18 16 0.05
19 23 0.08
20 261 0.86
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:57082 original size:30 final size:29
Alignment explanation
Indices: 57046--57103 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
57036 AGTGTTAGCC
57046 GTAGGTCGCCATGC-CTTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC--TCCGGGCGACCTT
57076 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
57104 AGCCTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.44
30 14 0.52
31 1 0.04
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:57191 original size:23 final size:23
Alignment explanation
Indices: 57161--57209 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
57151 GCGACCTACC
57161 CTCGCTCGGCTGCCCTTGCATAG
1 CTCGCTCGGCTGCCCTTGCATAG
57184 CTCGCTCGGCTGCCCTTGCATAG
1 CTCGCTCGGCTGCCCTTGCATAG
57207 CTC
1 CTC
57210 ATTCGGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.08, C:0.41, G:0.24, T:0.27
Consensus pattern (23 bp):
CTCGCTCGGCTGCCCTTGCATAG
Found at i:57215 original size:23 final size:23
Alignment explanation
Indices: 57165--57215 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
57155 CCTACCCTCG
*
57165 CTCGGCTGCCCTTGCATAGCTCG
1 CTCGGCTGCCCTTGCATAGCTCA
57188 CTCGGCTGCCCTTGCATAGCTCA
1 CTCGGCTGCCCTTGCATAGCTCA
*
57211 TTCGG
1 CTCGG
57216 ATGGCCTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.37, G:0.25, T:0.27
Consensus pattern (23 bp):
CTCGGCTGCCCTTGCATAGCTCA
Found at i:57240 original size:24 final size:24
Alignment explanation
Indices: 57212--57266 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
57202 CATAGCTCAT
57212 TCGGATGGCCTCGGTCAGAT-GCTC
1 TCGGATGGCCTCGGTCAGATGGC-C
* *
57236 TCGGATAGCCTCGGTCGGATGGCC
1 TCGGATGGCCTCGGTCAGATGGCC
57260 TCGGATG
1 TCGGATG
57267 CCCAGCGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (24 bp):
TCGGATGGCCTCGGTCAGATGGCC
Found at i:57253 original size:14 final size:14
Alignment explanation
Indices: 57212--57263 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
57202 CATAGCTCAT
57212 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
*
57226 TCAGAT-G-CTC--
1 TCGGATGGCCTCGG
*
57236 TCGGATAGCCTCGG
1 TCGGATGGCCTCGG
57250 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
57264 ATGCCCAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 1 0.03
12 6 0.19
13 1 0.03
14 18 0.58
ACGTcount: A:0.12, C:0.29, G:0.37, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:57343 original size:29 final size:29
Alignment explanation
Indices: 57306--57420 Score: 187
Period size: 29 Copynumber: 4.0 Consensus size: 29
57296 GCTATCTCTT
* * *
57306 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
57335 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
*
57364 GTAGGTCGCCCGGAAGGCATGACGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
57393 GTAGGTCG-CCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
57421 CGGCCAACAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 19 0.23
29 62 0.77
ACGTcount: A:0.23, C:0.27, G:0.37, T:0.14
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGGCATGGCGACCTA
Found at i:58139 original size:21 final size:24
Alignment explanation
Indices: 58114--58157 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
58104 TATAAAATTG
58114 AAAAT-AT-AAATTTT-TTTTAAT
1 AAAATGATAAAATTTTATTTTAAT
*
58135 AAAATGGTAAAATTTTATTTTAA
1 AAAATGATAAAATTTTATTTTAA
58158 CTCCGGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 1 0.05
23 7 0.37
24 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
AAAATGATAAAATTTTATTTTAAT
Found at i:58155 original size:28 final size:28
Alignment explanation
Indices: 58089--58147 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
58079 TCATAAAGTT
* *
58089 TATATAATTTTTTTTTATAAAATTGAAAA
1 TATA-AATTTTTTTTAATAAAATGGAAAA
58118 TATAAATTTTTTTTAATAAAATGGTAAAA
1 TATAAATTTTTTTTAATAAAATGG-AAAA
58147 T
1 T
58148 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (28 bp):
TATAAATTTTTTTTAATAAAATGGAAAA
Found at i:58768 original size:31 final size:31
Alignment explanation
Indices: 58733--58804 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
58723 TATAACGTAA
* *
58733 AAAAAATAAATATAATAATGTAT-TAAAATAT
1 AAAAAATAAACATAA-AATGTATATAAAATAG
* *
58764 AAAAAATAAACATCAGATGTATATAAAATAG
1 AAAAAATAAACATAAAATGTATATAAAATAG
*
58795 AAATAATAAA
1 AAAAAATAAA
58805 AAAAAGTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (31 bp):
AAAAAATAAACATAAAATGTATATAAAATAG
Done.