Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004540.1 Hibiscus syriacus cultivar Beakdansim tig00010050_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: 429677
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:9014 original size:16 final size:15
Alignment explanation
Indices: 8977--9016 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
8967 AAAATTATAT
*
8977 AAAAAGTAAAACTTA
1 AAAAAATAAAACTTA
*
8992 ACAAAATAAAACTTA
1 AAAAAATAAAACTTA
9007 AAACAAATAA
1 AAA-AAATAA
9017 TATAGATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAAATAAAACTTA
Found at i:17337 original size:32 final size:32
Alignment explanation
Indices: 17301--17459 Score: 165
Period size: 32 Copynumber: 5.0 Consensus size: 32
17291 AATATATTGA
* * *
17301 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* *
17333 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* * * * * * * *
17365 GGCTTTAGAGTCTACTTAAGGAAATGCCCTGG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* * *
17397 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
*
17429 GGCCTAAGAGCTTACCTAAGGAAGTACCTTA
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTA
17460 AGGCTTCAGA
Statistics
Matches: 98, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (32 bp):
GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
Found at i:17449 original size:96 final size:96
Alignment explanation
Indices: 17301--17502 Score: 368
Period size: 96 Copynumber: 2.1 Consensus size: 96
17291 AATATATTGA
17301 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
1 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
* *
17366 GCTTTAGAGTCTACTTAAGGAAATGCCCTGG
66 GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
17397 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
1 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
*
17462 GCTTCAGAGTCTACTCAAGGAAATGCCTTGG
66 GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
*
17493 GGCCTCAGAG
1 GGCCTGAGAG
17503 TTTGCCCAAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 102 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (96 bp):
GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
Found at i:17513 original size:32 final size:32
Alignment explanation
Indices: 17301--17502 Score: 143
Period size: 32 Copynumber: 6.3 Consensus size: 32
17291 AATATATTGA
* * *
17301 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
17333 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * ** * * *
17365 GGCTTTAGAGTCTACTTAAGGAAATGCCCTGG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * *
17397 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
17429 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
17461 GGCTTCAGAGTCTACTCAAGGAAATGCCTTGG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
17493 GGCCTCAGAG
1 GGCCTCAGAG
17503 TTTGCCCAAG
Statistics
Matches: 129, Mismatches: 41, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 129 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (32 bp):
GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
Found at i:18625 original size:28 final size:28
Alignment explanation
Indices: 18594--18660 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
18584 ATAGGGATTG
18594 GGGGTATTTTAGGTCATTTTACACTTCA
1 GGGGTATTTTAGGTCATTTTACACTTCA
*
18622 GGGGTATTTT-GGTCATTTTACAGTTCA
1 GGGGTATTTTAGGTCATTTTACACTTCA
*
18649 AGGGTATTTTAG
1 GGGGTATTTTAG
18661 TCTTTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 25 0.69
28 11 0.31
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.43
Consensus pattern (28 bp):
GGGGTATTTTAGGTCATTTTACACTTCA
Found at i:21983 original size:16 final size:16
Alignment explanation
Indices: 21944--21986 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
21934 GTGTATAATT
* *
21944 ATAATAATTT-AAGTG
1 ATAATAATTTAAAATA
21959 ATAATTAATTTAAAATA
1 ATAA-TAATTTAAAATA
21976 ATAATAATTTA
1 ATAATAATTTA
21987 TTCTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
ATAATAATTTAAAATA
Found at i:22031 original size:7 final size:7
Alignment explanation
Indices: 22019--22043 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22009 AACATAATAT
22019 TTATAAA
1 TTATAAA
22026 TTATAAA
1 TTATAAA
22033 TTATAAA
1 TTATAAA
22040 TTAT
1 TTAT
22044 TATATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTATAAA
Found at i:22423 original size:11 final size:11
Alignment explanation
Indices: 22404--22441 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22394 AAGAAAAGAA
*
22404 AATTCTTTTTG
1 AATTGTTTTTG
22415 AATTGTTTTTG
1 AATTGTTTTTG
*
22426 AGTTG-TTTTG
1 AATTGTTTTTG
22436 AATTGT
1 AATTGT
22442 GTTTAACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (11 bp):
AATTGTTTTTG
Found at i:22901 original size:43 final size:43
Alignment explanation
Indices: 22848--23186 Score: 396
Period size: 43 Copynumber: 7.9 Consensus size: 43
22838 AAGGCACAAT
* *
22848 AGGTCAAGATCTATAGTGGCGTTTTTGGAACAAACGCCGTAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
22891 AGGTCGAGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
22934 AGGTCAACATCTATAGCGGCGTTTTTGTAACAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * * *
22977 AGGTCAACATATATAGCGGCATTTTTGTAACACACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
23020 AGGTC-AGATCTATAGCGGCATTTTTGGAATAAACGCCGTAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * *
23062 AGGTCGATATATATAGCGGCGTTTTTGGAATAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
** * * *
23105 A-GTTGATATCTATAGCGGCGTTTTCGGGAAAAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTT-TGGAACAAACGCCGCAAA
* * * *
23148 ATGAC-AGATCTATAGAGGCGTTTTTGGATTCAAACGCCG
1 AGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCG
23187 TTAGTTACCT
Statistics
Matches: 262, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
42 60 0.23
43 201 0.77
44 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
Found at i:23074 original size:85 final size:86
Alignment explanation
Indices: 22848--23186 Score: 396
Period size: 85 Copynumber: 4.0 Consensus size: 86
22838 AAGGCACAAT
* * * * *
22848 AGGTCAAGATCTATAGTGGCGTTTTTGGAACAAACGCCGTAAAAGGTCGAGATCTATAGTGGCGT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGACATATATAGCGGCGT
22913 TTTTGGAACAAACGCCGCAAA
66 TTTTGGAACAAACGCCGCAAA
* * * *
22934 AGGTCAACATCTATAGCGGCGTTTTTGTAACAAACGCCGCAAAAGGTCAACATATATAGCGGCAT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGACATATATAGCGGCGT
* *
22999 TTTTGTAACACACGCCGCAAA
66 TTTTGGAACAAACGCCGCAAA
* * * *
23020 AGGTC-AGATCTATAGCGGCATTTTTGGAATAAACGCCGTAAAAGGTCGATATATATAGCGGCGT
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGACATATATAGCGGCGT
*
23084 TTTTGGAATAAACGCCGCAAA
66 TTTTGGAACAAACGCCGCAAA
** * * * * * * * *
23105 A-GTTGATATCTATAGCGGCGTTTTCGGGAAAAAACGCCGCAAAATGAC-AGATCTATAGAGGCG
1 AGGTCAAGATCTATAGCGGCGTTTT-TGGAACAAACGCCGCAAAAGGTCGACATATATAGCGGCG
*
23168 TTTTTGGATTCAAACGCCG
65 TTTTTGGA-ACAAACGCCG
23187 TTAGTTACCT
Statistics
Matches: 215, Mismatches: 35, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.01
85 107 0.50
86 106 0.49
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (86 bp):
AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGACATATATAGCGGCGT
TTTTGGAACAAACGCCGCAAA
Found at i:26597 original size:43 final size:41
Alignment explanation
Indices: 26550--26851 Score: 238
Period size: 41 Copynumber: 7.4 Consensus size: 41
26540 TTTTAAACAC
*
26550 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-TAAAATAT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT---ATAA
* *
26593 AAACGCCACTAAAATACAAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
26634 AAACGCCATTAGAGTATGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
26675 AAACGCCACTAAAGTACTACTCTATTGCAGCGTTTGT-TGAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AA
* * * * * * *
26716 AAACGCCACTATAG-ATGAATCTATTGTGGCGTTTTTATAT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * * * *
26756 AAACGCTGCTAAAGTACTACTCTGTCA-CGACGTTTGT-TAAA
1 AAACGCCACTAAAGTACGAGTCTAT-AGCGGCGTTTGTAT-AA
** * ** *
26797 AAACGCCACTACTG-ATGAACCTATTGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
26837 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
26852 TACCATTTTG
Statistics
Matches: 201, Mismatches: 49, Indels: 20
0.74 0.18 0.07
Matches are distributed among these distances:
40 57 0.28
41 110 0.55
43 33 0.16
44 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:26711 original size:82 final size:81
Alignment explanation
Indices: 26550--26851 Score: 279
Period size: 81 Copynumber: 3.7 Consensus size: 81
26540 TTTTAAACAC
* * * * * *
26550 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-TAAAATATAAACGCCACTAAAATACAAGT
1 AAACGCCACTAAAG-ATGAATCTATAGCGGCGTTTGT---ATAAAAACGCCACTAAAGTACTACT
* *
26614 CTATAGCGGCGTTTG-TATAA
62 CTATTGCAGCGTTTGTTA-AA
* * *
26634 AAACGCCATTAGAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTA
1 AAACGCCACTAAAG-ATGAATCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTA
*
26699 TTGCAGCGTTTGTTGAA
65 TTGCAGCGTTTGTTAAA
* * * * * ** *
26716 AAACGCCACTATAGATGAATCTATTGTGGCGTTTTTATATAAACGCTGCTAAAGTACTACTCT-G
1 AAACGCCACTAAAGATGAATCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTAT
26780 T-CACGACGTTTGTTAAA
66 TGCA-G-CGTTTGTTAAA
** * * *
26797 AAACGCCACTACTGATGAACCTATTGCGGCGTTTGTATAAAAACGCCGCTAAAGT
1 AAACGCCACTAAAGATGAATCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
26852 TACCATTTTG
Statistics
Matches: 186, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
79 2 0.01
80 2 0.01
81 100 0.54
82 48 0.26
83 1 0.01
84 32 0.17
85 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (81 bp):
AAACGCCACTAAAGATGAATCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTAT
TGCAGCGTTTGTTAAA
Found at i:26769 original size:81 final size:80
Alignment explanation
Indices: 26593--26851 Score: 281
Period size: 81 Copynumber: 3.2 Consensus size: 80
26583 TTTAAAATAT
* * * * * * * *
26593 AAACGCCACTAAAATACAAGTCTATAGCGGCGTTTGTATAAAAACGCCATTAGAGTATGAGTCTA
1 AAACGCCACTAAAGTACTACTCTATTGCAGCGTTTGT-TAAAAACGCCACTATAG-ATGAATCTA
*
26658 TAGCGGCGTTTGTATAA
64 TTGCGGCGTTTGTATAA
26675 AAACGCCACTAAAGTACTACTCTATTGCAGCGTTTGTTGAAAAACGCCACTATAGATGAATCTAT
1 AAACGCCACTAAAGTACTACTCTATTGCAGCGTTTGTT-AAAAACGCCACTATAGATGAATCTAT
* * *
26740 TGTGGCGTTTTTATAT
65 TGCGGCGTTTGTATAA
** * *
26756 AAACGCTGCTAAAGTACTACTCT-GT-CACGACGTTTGTTAAAAAACGCCACTACT-GATGAACC
1 AAACGCCACTAAAGTACTACTCTATTGCA-G-CGTTTGTT-AAAAACGCCACTA-TAGATGAATC
26818 TATTGCGGCGTTTGTATAA
62 TATTGCGGCGTTTGTATAA
*
26837 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
26852 TACCATTTTG
Statistics
Matches: 152, Mismatches: 21, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
79 2 0.01
80 2 0.01
81 101 0.66
82 47 0.31
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (80 bp):
AAACGCCACTAAAGTACTACTCTATTGCAGCGTTTGTTAAAAACGCCACTATAGATGAATCTATT
GCGGCGTTTGTATAA
Found at i:28854 original size:26 final size:29
Alignment explanation
Indices: 28817--28876 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
28807 ATGTTAGAAA
28817 AAAAAAATAAATC-AAAT-AATAA-AAAAG
1 AAAAAAATAAATCAAAATGAA-AACAAAAG
28844 AAAAAAA-AAATCAAAATGAAAACAAAAG
1 AAAAAAATAAATCAAAATGAAAACAAAAG
28872 AAAAA
1 AAAAA
28877 GGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.17
27 13 0.43
28 12 0.40
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (29 bp):
AAAAAAATAAATCAAAATGAAAACAAAAG
Found at i:28883 original size:18 final size:18
Alignment explanation
Indices: 28861--28902 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28851 AAATCAAAAT
*
28861 GAAAACAAAAGAAA-AAG
1 GAAAAAAAAAGAAATAAG
**
28878 GAAAAAAAATTAAATAAG
1 GAAAAAAAAAGAAATAAG
28896 GAAAAAA
1 GAAAAAA
28903 TAATAAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (18 bp):
GAAAAAAAAAGAAATAAG
Found at i:30195 original size:11 final size:10
Alignment explanation
Indices: 30179--30228 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
30169 GACCCTGCAC
30179 AAAAATAAAT
1 AAAAATAAAT
30189 GAAAAATAAAT
1 -AAAAATAAAT
30200 AAATTAA-AAAT
1 AAA--AATAAAT
30211 AAAAATAAAT
1 AAAAATAAAT
*
30221 AATAATAA
1 AAAAATAA
30229 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
9 2 0.06
10 14 0.40
11 17 0.49
12 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:30201 original size:15 final size:15
Alignment explanation
Indices: 30181--30213 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30171 CCCTGCACAA
30181 AAATAAATGAAAAAT
1 AAATAAATGAAAAAT
*
30196 AAATAAATTAAAAAT
1 AAATAAATGAAAAAT
30211 AAA
1 AAA
30214 AATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAATGAAAAAT
Found at i:30274 original size:26 final size:27
Alignment explanation
Indices: 30228--30278 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
30218 AATAATAATA
30228 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
30256 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
30279 TGTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:30284 original size:36 final size:36
Alignment explanation
Indices: 30240--30431 Score: 154
Period size: 39 Copynumber: 5.1 Consensus size: 36
30230 ATATATATAT
*
30240 AAACGTTTTCAAAAACATATAATATATAAATTTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
* * * *
30276 AAATGTTTTTTTAAAAAAACTATATATTATATATATTTTCA
1 AAACG---TTTT-CAAAAAC-ATATATTATATAAATTTTTA
* * *
30317 AAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 AAA-CG-TTTTCAAAAA-CATATATTATATAAAT-TTTT-A
* ** *
30358 TAACGTTTTCAAAAGTATATATTATATATA-TTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
*
30393 AAACGTTTTCAAAAACTATATATTATAT-AATTTTCA
1 AAACGTTTTCAAAAAC-ATATATTATATAAATTTTTA
30429 AAA
1 AAA
30432 AATATTTTCA
Statistics
Matches: 125, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
35 15 0.12
36 26 0.21
38 14 0.11
39 31 0.25
40 15 0.12
41 23 0.18
42 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAACGTTTTCAAAAACATATATTATATAAATTTTTA
Found at i:30307 original size:41 final size:39
Alignment explanation
Indices: 30245--30431 Score: 156
Period size: 41 Copynumber: 4.9 Consensus size: 39
30235 TATATAAACG
* * *
30245 TTTTCAAAAAC-ATATAATATATAAATTTTTAAAATGTT
1 TTTTTAAAAACTATATATTATATAAATTTTTAAAATGGT
* *
30283 TTTTTAAAAAAACTATATATTATATATATTTTCAAAATGGT
1 TTTTT--AAAAACTATATATTATATAAATTTTTAAAATGGT
* * *
30324 TTTTTAAAAATTATATATTATATAAATGTTTTCATAA-CG-
1 TTTTTAAAAACTATATATTATATAAAT-TTTT-AAAATGGT
* * * *
30363 -TTTTCAAAAGTATATATTATATATA-TTTTAAAA-CG-
1 TTTTTAAAAACTATATATTATATAAATTTTTAAAATGGT
* *
30398 TTTTCAAAAACTATATATTATAT-AATTTTCAAAA
1 TTTTTAAAAACTATATATTATATAAATTTTTAAAA
30432 AATATTTTCA
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
35 6 0.05
36 30 0.24
38 26 0.21
39 20 0.16
40 10 0.08
41 31 0.25
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (39 bp):
TTTTTAAAAACTATATATTATATAAATTTTTAAAATGGT
Found at i:30412 original size:25 final size:25
Alignment explanation
Indices: 30381--30481 Score: 75
Period size: 25 Copynumber: 3.9 Consensus size: 25
30371 AGTATATATT
*
30381 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTATAAAA-GTTTTCAAAA
*
30407 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATTATAAAAGTTTTCAAAA
*
30432 A-ATAT-TT-TCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAA--GTTTTCAAAA
30457 ATTATATATTATATAAATGTTTTCA
1 A-TATATATTATA-AAA-GTTTTCA
30482 TAACGTTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
21 1 0.02
22 5 0.08
23 4 0.07
25 19 0.32
26 1 0.02
27 16 0.27
28 9 0.15
29 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATATATTATAAAAGTTTTCAAAA
Found at i:30481 original size:124 final size:125
Alignment explanation
Indices: 30308--30568 Score: 481
Period size: 124 Copynumber: 2.1 Consensus size: 125
30298 TATATTATAT
30308 ATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAG
1 ATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAG
30373 TATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTC-AAAA
30433 ATATTTTCAAAATGG-TTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAG
1 ATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAG
*
30497 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATGTATTATATAATTTTCAAAA
66 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
*
30557 ATATTTTAAAAA
1 ATATTTTCAAAA
30569 CTATATAATA
Statistics
Matches: 133, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
124 83 0.62
125 50 0.38
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (125 bp):
ATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAG
TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
Found at i:30557 original size:37 final size:37
Alignment explanation
Indices: 30433--30632 Score: 194
Period size: 37 Copynumber: 5.4 Consensus size: 37
30423 TTTTCAAAAA
** *
30433 ATATTTTCAAAATGGTTTTTAAAAATTATATATTATAT
1 ATATTTTCAAAAACG-TTTTAAAAACTATATATTATAT
* * * *
30471 AAATGTTTTC-ATAACGTTTTCAAAAGTATATATTATAT
1 --ATATTTTCAAAAACGTTTTAAAAACTATATATTATAT
*
30509 ATATTTT-AAAAACGTTTTCAAAAACTATGTATTATAT
1 ATATTTTCAAAAACGTTTT-AAAAACTATATATTATAT
** * *
30546 A-ATTTTCAAAAATATTTTAAAAACTATATAATATAC
1 ATATTTTCAAAAACGTTTTAAAAACTATATATTATAT
*
30582 ATATTTTCAAAAATGTTTT--AAACTATATATTATAT
1 ATATTTTCAAAAACGTTTTAAAAACTATATATTATAT
30617 ATGTATTTTCAAAAAC
1 A--TATTTTCAAAAAC
30633 AATTTGCAAA
Statistics
Matches: 134, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
35 15 0.11
36 36 0.27
37 53 0.40
38 20 0.15
39 3 0.02
40 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATTTTCAAAAACGTTTTAAAAACTATATATTATAT
Found at i:30644 original size:74 final size:71
Alignment explanation
Indices: 30492--30654 Score: 175
Period size: 74 Copynumber: 2.2 Consensus size: 71
30482 TAACGTTTTC
* * * *
30492 AAAAGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATGTATTATATAATTTTCAAAA
1 AAAACTATATAATATACATATTTTAAAAACGTTTT--AAAACTATATATTATATAATTTTCAAAA
* *
30557 ATATTTTA
64 ACAATTTA
*
30565 AAAACTATATAATATACATATTTTCAAAAATGTTTT-AAACTATATATTATATATGTATTTTCAA
1 AAAACTATATAATATACATATTTT-AAAAACGTTTTAAAACTATATATTATATA---ATTTTCAA
*
30629 AAACAATTTG
62 AAACAATTTA
* *
30639 CAAACTGTATAATATA
1 AAAACTATATAATATA
30655 TATGTGTATA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
71 16 0.21
73 21 0.28
74 39 0.51
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (71 bp):
AAAACTATATAATATACATATTTTAAAAACGTTTTAAAACTATATATTATATAATTTTCAAAAAC
AATTTA
Found at i:30654 original size:37 final size:35
Alignment explanation
Indices: 30492--30657 Score: 111
Period size: 37 Copynumber: 4.5 Consensus size: 35
30482 TAACGTTTTC
* * **
30492 AAAAGTATATATTATATATATTTT-AAAAACGTTTT
1 AAAACTATATAATATATATATTTTCAAAAA-AATTT
* * *
30527 CAAAAACTATGTATTATATA-ATTTTCAAAAATATTTT
1 --AAAACTATATAATATATATATTTTCAAAAA-AATTT
* **
30564 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATATATATTTTCAAAAAAATTT
* *
30600 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATATATATTTTCAAAAA-AATTT
* *
30638 GCAAACTGTATAATATATAT
1 -AAAACTATATAATATATAT
30658 GTGTATATAT
Statistics
Matches: 106, Mismatches: 17, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
35 10 0.09
36 24 0.23
37 60 0.57
38 3 0.03
39 9 0.08
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (35 bp):
AAAACTATATAATATATATATTTTCAAAAAAATTT
Found at i:31773 original size:329 final size:330
Alignment explanation
Indices: 31247--31840 Score: 1037
Period size: 329 Copynumber: 1.8 Consensus size: 330
31237 AAGTTGAATA
*
31247 TAATCGACCTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
31312 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTAGGAGCTGAGCGGAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
* **
31377 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAG
31442 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
196 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
31507 GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
261 GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
31572 GAGTG
326 GAGTG
* * *
31577 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
31642 CCTAGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAG
66 CCTAGGAGCTGAGCGGAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
* * *
31706 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAG
*
31771 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
196 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
31836 GTCTT
261 GTCTT
31841 GGTGGCAGGT
Statistics
Matches: 248, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
329 157 0.63
330 91 0.37
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (330 bp):
TAATCGAACTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTAGGAGCTGAGCGGAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAG
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
GAGTG
Found at i:31780 original size:164 final size:165
Alignment explanation
Indices: 31247--31840 Score: 1037
Period size: 165 Copynumber: 3.6 Consensus size: 165
31237 AAGTTGAATA
* * *
31247 TAATCGACCTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
31312 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
31377 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
31412 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
31477 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
31542 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
31577 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
31642 CCTAGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * *
31706 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*** *
31741 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
31806 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
31841 GGTGGCAGGT
Statistics
Matches: 409, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
164 152 0.37
165 257 0.63
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:35253 original size:19 final size:19
Alignment explanation
Indices: 35229--35274 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
35219 AGTTAATGTG
35229 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
35248 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
35267 AATGCAAA
1 AATGCAAA
35275 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:38387 original size:16 final size:16
Alignment explanation
Indices: 38339--38388 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
38329 GACCCTGCAC
38339 AAAAATAAATGAAAAAT
1 AAAAATAAAT-AAAAAT
* *
38356 -AAATTAATTAAAAAT
1 AAAAATAAATAAAAAT
*
38371 AAAAATAAATAATAAT
1 AAAAATAAATAAAAAT
38387 AA
1 AA
38389 TATATATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:38389 original size:26 final size:25
Alignment explanation
Indices: 38339--38389 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
38329 GACCCTGCAC
*
38339 AAAAATAAATGAAAAATAAATTAATT
1 AAAAATAAA-GAAAAATAAAATAATT
38365 AAAAATAAA-AATAAATAATAATAAT
1 AAAAATAAAGAA-AAATAA-AATAAT
38390 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.09
25 6 0.27
26 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAATAAAGAAAAATAAAATAATT
Found at i:38468 original size:41 final size:40
Alignment explanation
Indices: 38405--38592 Score: 146
Period size: 41 Copynumber: 4.9 Consensus size: 40
38395 TATATAAACG
* * *
38405 TTTTCAAAAAAC-ATATAATATATAAATTTTTAAAATGTT
1 TTTTTAAAAAACTATATATTATATAAATTTTTAAAATGGT
* *
38444 TTTTTAAAAAAACTATATATTATATATATTTTCAAAATGGT
1 TTTTT-AAAAAACTATATATTATATAAATTTTTAAAATGGT
* * *
38485 TTTTT-AAAAATTATATATTATATAAATGTTTTCATAA-CG-
1 TTTTTAAAAAACTATATATTATATAAAT-TTTT-AAAATGGT
* * * *
38524 -TTTT-CAAAAGTATATATTATATATA-TTTTAAAA-CG-
1 TTTTTAAAAAACTATATATTATATAAATTTTTAAAATGGT
* *
38559 -TTTTCAAAAACTATATATTATAT-AATTTTCAAAA
1 TTTTTAAAAAACTATATATTATATAAATTTTTAAAA
38593 AATATATTTT
Statistics
Matches: 125, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
35 10 0.08
36 27 0.22
38 22 0.18
39 24 0.19
40 11 0.09
41 31 0.25
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (40 bp):
TTTTTAAAAAACTATATATTATATAAATTTTTAAAATGGT
Found at i:38577 original size:27 final size:25
Alignment explanation
Indices: 38542--38642 Score: 89
Period size: 27 Copynumber: 3.9 Consensus size: 25
38532 AGTATATATT
*
38542 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTATAAAA-GTTTTCAAAA
*
38568 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATTATAAAAGTTTTCAAAA
* *
38593 A-ATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAA--GTTTTCAAAA
*
38620 ATTATATATTATAAATGTTTTCA
1 A-TATATATTATAAAAGTTTTCA
38643 TAACGTTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
23 8 0.13
24 3 0.05
25 10 0.17
26 7 0.12
27 21 0.35
28 3 0.05
29 8 0.13
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATATATTATAAAAGTTTTCAAAA
Found at i:38581 original size:36 final size:37
Alignment explanation
Indices: 38400--38793 Score: 223
Period size: 36 Copynumber: 10.1 Consensus size: 37
38390 ATATATATAT
* * *
38400 AAACGTTTTCAAAAAAC-ATATAATATATAAATTTTTA
1 AAACGTTTTC-AAAAACTATATATTATATATATTTTAA
* *
38437 AAATGTTTTTTTAAAAAAACTATATATTATATATATTTTCAA
1 AAACG---TTTT-CAAAAACTATATATTATATATATTTT-AA
** * * * *
38479 AATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 AAACG-TTTTCAAAAACTATATATTATAT--ATATTTTAA
* *
38519 TAACGTTTTC-AAAAGTATATATTATATATATTTT-A
1 AAACGTTTTCAAAAACTATATATTATATATATTTTAA
38554 AAACGTTTTCAAAAACTATATATTATATA-ATTTTCAAAAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT----AA
* * * * *
38594 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATAAATGTTTTCA
1 A-A-A----C------GTTTTCAAAAACTATATATTATATATATTTTAA
* *
38643 TAACGTTTTC-AAAAGTATATATTATATATATTTTAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTAA
38679 AAACGTTTTCAAAAACTATATATTATATA-ATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT-AA
** * *
38716 AAATATTTT-AAAAACTATATAATATACATATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT-AA
*
38753 AAATGTTTT---AAACTATATATTATATATGTATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATA--TATTTT-AA
38790 AAAC
1 AAAC
38794 AATTTGTAAA
Statistics
Matches: 285, Mismatches: 40, Indels: 64
0.73 0.10 0.16
Matches are distributed among these distances:
35 30 0.11
36 76 0.27
37 63 0.22
38 16 0.06
39 21 0.07
40 20 0.07
41 23 0.08
42 5 0.02
43 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
52 22 0.08
53 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACGTTTTCAAAAACTATATATTATATATATTTTAA
Found at i:38603 original size:15 final size:16
Alignment explanation
Indices: 38578--38607 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38568 ACTATATATT
38578 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
38594 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
38608 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:38650 original size:124 final size:128
Alignment explanation
Indices: 38467--38718 Score: 476
Period size: 124 Copynumber: 2.0 Consensus size: 128
38457 TATATATTAT
38467 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
38532 AGTATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
38594 ATATATTTTCAAAATGG-TTTTTAAAAATTATATA-T-TATAAATGTTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
38656 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
38719 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
124 48 0.39
125 42 0.34
126 17 0.14
127 17 0.14
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (128 bp):
ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:38693 original size:73 final size:74
Alignment explanation
Indices: 38594--38818 Score: 219
Period size: 74 Copynumber: 3.1 Consensus size: 74
38584 TTTTCAAAAA
** * * * * *
38594 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATAAATGTTTTC-ATAACGTTTTCAAAAG
1 ATATATTTTCAAAAACG-TTTTAAAAACTATATATTATAAATGTTTTCAAAAACATTTTAAAAAC
*
38658 TATATATTAT
65 TATATAATAT
*
38668 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTATATAA--TTTTCAAAAATATTTTAAAAA
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTATA-AATGTTTTCAAAAACATTTTAAAAA
38730 CTATATAATAT
64 CTATATAATAT
* * * * **
38741 ACATATTTTCAAAAATGTTTT--AAACTATATATTATATATGTATTTTCAAAAACAATTTGTAAA
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTATAAATG--TTTTCAAAAACATTTTAAAAA
*
38804 CTGTATAATAT
64 CTATATAATAT
38815 ATAT
1 ATAT
38819 GTGTATATAT
Statistics
Matches: 125, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
70 1 0.01
71 15 0.12
72 9 0.07
73 49 0.39
74 51 0.41
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTATAAATGTTTTCAAAAACATTTTAAAAACT
ATATAATAT
Found at i:38699 original size:37 final size:37
Alignment explanation
Indices: 38594--38793 Score: 212
Period size: 37 Copynumber: 5.4 Consensus size: 37
38584 TTTTCAAAAA
** *
38594 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTAT
1 ATATATTTTCAAAAACG-TTTTAAAAACTATATATTAT
* * * * *
38632 AAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
38668 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTAT
** *
38705 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
* *
38741 ACATATTTTCAAAAATGTTTT--AAACTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
38776 ATATGTATTTTCAAAAAC
1 ATA--TATTTTCAAAAAC
38794 AATTTGTAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
35 15 0.11
36 56 0.41
37 57 0.42
38 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
Found at i:38816 original size:39 final size:37
Alignment explanation
Indices: 38691--38820 Score: 126
Period size: 37 Copynumber: 3.5 Consensus size: 37
38681 ACGTTTTCAA
* *
38691 AAACTATAT-AT-TATAT-AATTTTCAAAAATATTTT
1 AAACTATATAATATATATGTATTTTCAAAAAAATTTT
* **
38725 AAAAACTATATAATATACA--TATTTTCAAAAATGTTTT
1 --AAACTATATAATATATATGTATTTTCAAAAAAATTTT
*
38762 AAACTATATATTATATATGTATTTTCAAAAACAATTTGT
1 AAACTATATAATATATATGTATTTTCAAAAA-AATTT-T
*
38801 AAACTGTATAATATATATGT
1 AAACTATATAATATATATGT
38821 GTATATATGT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
35 15 0.19
36 9 0.11
37 30 0.38
38 6 0.08
39 19 0.24
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
AAACTATATAATATATATGTATTTTCAAAAAAATTTT
Found at i:38979 original size:18 final size:18
Alignment explanation
Indices: 38948--38997 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
38938 ATAGAATATG
*
38948 TGATTTTTTCTTTAAAATT
1 TGATTTTAT-TTTAAAATT
*
38967 TGATTTTATTTTAAAGTT
1 TGATTTTATTTTAAAATT
38985 TAGATTATTATTT
1 T-GATT-TTATTT
38998 GATAAATAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (18 bp):
TGATTTTATTTTAAAATT
Found at i:39580 original size:93 final size:92
Alignment explanation
Indices: 39422--39606 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 92
39412 TGAGGGTAAG
* **
39422 AGTTAGAACCGTATGAGAGAGTGTGTTAGAGTTATCTAATGTTGTATGGTTCGAACATTACACTT
1 AGTTAGAACCGTATGAGAGAGTGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACTT
39487 CTCTTTTATCTGATGTTGTATGATCTA
66 CTCTTTTATCTGATGTTGTATGATCTA
* *
39514 AGTTAGCACCGTATGAGAGAGTCGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTGCACT
1 AGTTAGAACCGTATGAGAGAGT-GTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACT
*
39579 TCTCTTTTATCTGATGTTGTGTGATCTA
65 TCTCTTTTATCTGATGTTGTATGATCTA
39607 GGCATCCATA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 21 0.24
93 65 0.76
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (92 bp):
AGTTAGAACCGTATGAGAGAGTGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACTT
CTCTTTTATCTGATGTTGTATGATCTA
Found at i:45183 original size:3 final size:3
Alignment explanation
Indices: 45175--45227 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
45165 GAGAAGATGA
*
45175 AAG AAG AAG AA- ATG AAG AAG AAG AAG AAG AA- AATG AAG AA- AATG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AA-G
45219 AAG -AG AAG A
1 AAG AAG AAG A
45228 GAAATATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 7 0.17
3 31 0.74
4 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (3 bp):
AAG
Found at i:45225 original size:26 final size:28
Alignment explanation
Indices: 45164--45236 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
45154 ATAACTACTT
* *
45164 AGAGAAGATGAAAGAAGAAGAAATGAAGA
1 AGAGAAGAAGAAAGATGAAGAAA-GAAGA
*
45193 AGAAGAAGAAGAAA-ATGAAGAAA-ATGA
1 AG-AGAAGAAGAAAGATGAAGAAAGAAGA
*
45220 AGAGAAG-AGAAATATGA
1 AGAGAAGAAGAAAGATGA
45237 TGAGATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.13
26 9 0.23
27 5 0.13
29 10 0.26
30 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (28 bp):
AGAGAAGAAGAAAGATGAAGAAAGAAGA
Found at i:45670 original size:3 final size:3
Alignment explanation
Indices: 45662--45700 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
45652 ATAAAAGTGA
45662 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
45701 ATAGGAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45685 original size:19 final size:19
Alignment explanation
Indices: 45661--45703 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
45651 CATAAAAGTG
45661 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
45680 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
45699 AAATA
1 AAATA
45704 GGAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:45703 original size:16 final size:16
Alignment explanation
Indices: 45665--45697 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45655 AAAGTGAAAT
45665 AATAATAATAATAATA
1 AATAATAATAATAATA
45681 AATAATAATAATAATA
1 AATAATAATAATAATA
45697 A
1 A
45698 TAAATAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:45709 original size:19 final size:19
Alignment explanation
Indices: 45661--45716 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
45651 CATAAAAGTG
*
45661 AAATAATAATAATAATAAT
1 AAATAAGAATAATAATAAT
*
45680 AAATAATAATAATAATAAT
1 AAATAAGAATAATAATAAT
* *
45699 AAATAGGAATAAAAATAA
1 AAATAAGAATAATAATAA
45717 GTATAATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAATAAGAATAATAATAAT
Found at i:47822 original size:21 final size:21
Alignment explanation
Indices: 47796--47835 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
47786 TGCTGGACTG
47796 GGTCTTACAAGGTCAAGAAAA
1 GGTCTTACAAGGTCAAGAAAA
47817 GGTCTTACAAGGTCAAGAA
1 GGTCTTACAAGGTCAAGAA
47836 GATCAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCTTACAAGGTCAAGAAAA
Found at i:49112 original size:16 final size:16
Alignment explanation
Indices: 49091--49122 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49081 TATCTTTATA
49091 AAATGAAAATATATTT
1 AAATGAAAATATATTT
*
49107 AAATGAAAGTATATTT
1 AAATGAAAATATATTT
49123 GATTTATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
AAATGAAAATATATTT
Found at i:49622 original size:20 final size:20
Alignment explanation
Indices: 49590--49642 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
49580 TCATACTAAT
*
49590 ATTTTTGTA-ATTTTTT-TGG
1 ATTTTTTTATATTTTTTCT-G
*
49609 ATTTTTTTCTATTTTTTCTG
1 ATTTTTTTATATTTTTTCTG
49629 ATTTTTTTATATTT
1 ATTTTTTTATATTT
49643 GTAAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.24
20 21 0.72
21 1 0.03
ACGTcount: A:0.15, C:0.04, G:0.08, T:0.74
Consensus pattern (20 bp):
ATTTTTTTATATTTTTTCTG
Found at i:55735 original size:17 final size:19
Alignment explanation
Indices: 55710--55748 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
55700 ATATCTGTAT
55710 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
55728 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
55747 TA
1 TA
55749 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:57087 original size:12 final size:12
Alignment explanation
Indices: 57070--57101 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
57060 CTCATTCAGT
57070 TCGTACTCCCGC
1 TCGTACTCCCGC
57082 TCGTACTCCCGC
1 TCGTACTCCCGC
57094 TCGTACTC
1 TCGTACTC
57102 AGAGTACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.47, G:0.16, T:0.28
Consensus pattern (12 bp):
TCGTACTCCCGC
Found at i:60649 original size:19 final size:19
Alignment explanation
Indices: 60591--60651 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
60581 TCGGTTTTTG
* *
60591 ACCGGTTTGACCGGTCAAA
1 ACCGGGTTGACCGGTCAGA
* *
60610 ACCAGGTTGACCGGTCTGA
1 ACCGGGTTGACCGGTCAGA
*
60629 ACCGGGTTGACCGGTCCGA
1 ACCGGGTTGACCGGTCAGA
60648 ACCG
1 ACCG
60652 ACCTGACCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.21, C:0.30, G:0.31, T:0.18
Consensus pattern (19 bp):
ACCGGGTTGACCGGTCAGA
Found at i:60658 original size:19 final size:19
Alignment explanation
Indices: 60617--60659 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
60607 AAAACCAGGT
* ***
60617 TGACCGGTCTGAACCGGGT
1 TGACCGGTCCGAACCGACC
60636 TGACCGGTCCGAACCGACC
1 TGACCGGTCCGAACCGACC
60655 TGACC
1 TGACC
60660 CGTTGACCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (19 bp):
TGACCGGTCCGAACCGACC
Found at i:61603 original size:14 final size:14
Alignment explanation
Indices: 61580--61609 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61570 AATTACTATC
*
61580 ATTGGGGGAATATT
1 ATTGGAGGAATATT
61594 ATTGGAGGAATATT
1 ATTGGAGGAATATT
61608 AT
1 AT
61610 CTGCAGGCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (14 bp):
ATTGGAGGAATATT
Found at i:69851 original size:30 final size:30
Alignment explanation
Indices: 69815--69873 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
69805 ACAAATGAGT
69815 TAATTTCAAATTTTTATAAATGAGACATTA
1 TAATTTCAAATTTTTATAAATGAGACATTA
*
69845 TAATTTCAAATTTTTATAAATGAGTCATT
1 TAATTTCAAATTTTTATAAATGAGACATT
69874 CAGTTAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TAATTTCAAATTTTTATAAATGAGACATTA
Found at i:70897 original size:14 final size:14
Alignment explanation
Indices: 70878--70905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
70868 CGAACGCTCA
70878 CCCCTAGACAAGAT
1 CCCCTAGACAAGAT
70892 CCCCTAGACAAGAT
1 CCCCTAGACAAGAT
70906 TGGTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCCCTAGACAAGAT
Found at i:79132 original size:2 final size:2
Alignment explanation
Indices: 79125--79181 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
79115 TCTAATCGAA
79125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
79166 -T AT AT AT AT CAT AT AT
1 AT AT AT AT AT -AT AT AT
79182 GTGTATTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:80619 original size:33 final size:32
Alignment explanation
Indices: 80582--80659 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
80572 TCCCTGATTT
*
80582 TATTTTTTATTTACTTTA-TATTGTATATGTATA
1 TATTTTTTATTTACTTTATTATT-TAT-TCTATA
*
80615 TATTTTTATTTTTACTTTATTTATTTATTCTATA
1 TATTTTT-TATTTACTTTA-TTATTTATTCTATA
80649 T-TTTTTTATTT
1 TATTTTTTATTT
80660 TTCCCTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 4 0.10
33 12 0.31
34 16 0.41
35 3 0.08
36 4 0.10
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (32 bp):
TATTTTTTATTTACTTTATTATTTATTCTATA
Found at i:80682 original size:36 final size:34
Alignment explanation
Indices: 80611--80683 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
80601 ATTGTATATG
*
80611 TATATATTTTTATTTTTACTTTATTTATTTATTC
1 TATATATTTTTATTTTTACTTTATTTATCTATTC
* *
80645 TATATTTTTTTATTTTTCCCTTTTATTTTATCT-TTC
1 TATATATTTTTATTTTT-AC-TTTA-TTTATCTATTC
80681 TAT
1 TAT
80684 CTTCATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 16 0.48
35 1 0.03
36 10 0.30
37 6 0.18
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (34 bp):
TATATATTTTTATTTTTACTTTATTTATCTATTC
Found at i:81662 original size:20 final size:18
Alignment explanation
Indices: 81629--81674 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
81619 TGTTGTTTTC
81629 TTTTTTTTCTTTCATTTA
1 TTTTTTTTCTTTCATTTA
81647 TTTTTCTTTACTTTCATTACTA
1 TTTTT-TTT-CTTTCATT--TA
81669 TTTTTT
1 TTTTTT
81675 CCTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 3 0.12
20 8 0.33
21 1 0.04
22 7 0.29
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTCTTTCATTTA
Found at i:83001 original size:22 final size:22
Alignment explanation
Indices: 82969--83021 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
82959 AATAATGATC
* *
82969 TGAAGCAGAGGGTAGGGGAACT
1 TGAAGCTGAGGGTAAGGGAACT
82991 TGAAGCTGAGGGTAAGGGAACT
1 TGAAGCTGAGGGTAAGGGAACT
83013 TGAAGCTGA
1 TGAAGCTGA
83022 ACGCTATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.09, G:0.42, T:0.17
Consensus pattern (22 bp):
TGAAGCTGAGGGTAAGGGAACT
Found at i:89993 original size:23 final size:21
Alignment explanation
Indices: 89950--89995 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
89940 ATCCTAAATT
89950 AGAAAAAAAAAGAAAGAAAAA
1 AGAAAAAAAAAGAAAGAAAAA
*
89971 AGAACAAAAGAAAGAAGATAAAAA
1 AGAA-AAAA-AAAGAA-AGAAAAA
89995 A
1 A
89996 AAGGTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 4 0.19
23 6 0.29
24 7 0.33
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAAAGAAAGAAAAA
Found at i:91853 original size:2 final size:2
Alignment explanation
Indices: 91840--91899 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
91830 TCTAATCGAA
* *
91840 AT AT AC AT AT AT AT TT AT AT -T 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
91881 AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT -AT AT AT
91900 GTGTATTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93331 original size:4 final size:4
Alignment explanation
Indices: 93272--93360 Score: 51
Period size: 4 Copynumber: 21.5 Consensus size: 4
93262 TTTCCATGAT
* * *
93272 TTTA TTT- TTTA TTTA CTTTA TATTA TATA TGTA TATA -TT- TTTA TTTTCA
1 TTTA TTTA TTTA TTTA -TTTA T-TTA TTTA TTTA TTTA TTTA TTTA -TTT-A
*
93321 CTTTA TTTA TTTA TTTT TTCTA TATTA TTTA TTT- TTTA TT
1 -TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TT
93361 CCTTTTTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
3 9 0.13
4 37 0.54
5 17 0.25
6 5 0.07
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:93350 original size:18 final size:18
Alignment explanation
Indices: 93305--93357 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
93295 TATATATGTA
**
93305 TATATT-TTTATTTTCAC
1 TATATTATTTATTTTTTC
*
93322 TTTATTTATTTATTTTTTC
1 TATA-TTATTTATTTTTTC
93341 TATATTATTTATTTTTT
1 TATATTATTTATTTTTT
93358 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 15 0.50
19 12 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TATATTATTTATTTTTTC
Found at i:93374 original size:26 final size:25
Alignment explanation
Indices: 93272--93374 Score: 75
Period size: 26 Copynumber: 3.9 Consensus size: 25
93262 TTTCCATGAT
* *
93272 TTTATTT-TTTATTTACTTTATATTA
1 TTTATTTATTTTTTTATTTTAT-TTA
* *
93297 TATATGTATATATTTTTATTTTCACTTTA
1 TTTAT-T-TATTTTTTTATTTT-A-TTTA
*
93326 TTTATTTATTTTTTCTATATTATTTA
1 TTTATTTATTTTTT-TATTTTATTTA
93352 TTT-TTTATTCCTTTTTATTTTAT
1 TTTATTTATT--TTTTTATTTTAT
93375 CTTTCTATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
25 10 0.16
26 15 0.24
27 13 0.21
28 15 0.24
29 8 0.13
30 1 0.02
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (25 bp):
TTTATTTATTTTTTTATTTTATTTA
Found at i:93436 original size:20 final size:21
Alignment explanation
Indices: 93392--93436 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
93382 TCTTCATGTT
*
93392 ATTTTCTTTATTTCTATTGTC
1 ATTTTCTCTATTTCTATTGTC
*
93413 -TTTTCTCTATTT-TATTTTC
1 ATTTTCTCTATTTCTATTGTC
93432 ATTTT
1 ATTTT
93437 TTCCTCTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTCTCTATTTCTATTGTC
Found at i:93944 original size:19 final size:19
Alignment explanation
Indices: 93890--93945 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
93880 ATTATATATG
* **
93890 TATATATTTTTATTTTCAC
1 TATATTTTTTTATTTTTTC
* *
93909 TTTATTTATTTATTTTTTC
1 TATATTTTTTTATTTTTTC
93928 TATATTTTTTTATTTTTT
1 TATATTTTTTTATTTTTT
93946 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TATATTTTTTTATTTTTTC
Found at i:94024 original size:20 final size:21
Alignment explanation
Indices: 93980--94024 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
93970 TCTTCATGTT
*
93980 ATTTTCTTTATTTATATTGTC
1 ATTTTCTCTATTTATATTGTC
*
94001 -TTTTCTCTATTT-TATTTTC
1 ATTTTCTCTATTTATATTGTC
94020 ATTTT
1 ATTTT
94025 TTCTCTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTCTCTATTTATATTGTC
Found at i:94320 original size:587 final size:587
Alignment explanation
Indices: 93193--94364 Score: 2123
Period size: 587 Copynumber: 2.0 Consensus size: 587
93183 ATTATATTTT
93193 ATTATTATTATATATATATATATATACTATTAATATTTTATTTATACGCCTATTATTATATTAAT
1 ATTATTATTATATATATATATATATACTATTAATATTTTATTTATACGCCTATTATTATATTAAT
93258 TGTTTTTCCATGATTTTATTTTTTATTTACTTTATATTATATATGTATATATTTTTATTTTCACT
66 TGTTTTTCCATGATTTTATTTTTTATTTACTTTATATTATATATGTATATATTTTTATTTTCACT
93323 TTATTTATTTATTTTTTCTATATTATTTATTTTTTATTCCTTTTTATTTTATCTTTCTATCTTCA
131 TTATTTATTTATTTTTTCTATATTATTTATTTTTTATTCCTTTTTATTTTATCTTTCTATCTTCA
*
93388 TGTTATTTTCTTTATTTCTATTGTCTTTTCTCTATTTTATTTTCATTTTTTCCTCTCTAACACGT
196 TGTTATTTTCTTTATTTATATTGTCTTTTCTCTATTTTATTTTCATTTTTTCCTCTCTAACACGT
* *
93453 TTCTAAACTTGTTTAAGGATGATTTCAAATCAATCTAAGGTAAGAAATTCATATCATTATTTTAC
261 TTCTAAAATTGTTTAAGGATGATTTCAAATCAATCTAAGGTAAAAAATTCATATCATTATTTTAC
*
93518 CTTTTAATTTTAACTTTCAATTTTCTTAATTAAAGACAACTGAAAATTACGCAGTACCGAAAGAG
326 CTTTTAATTTTAACTTTCAATTTTCTTAATTAAAGACAAATGAAAATTACGCAGTACCGAAAGAG
* *
93583 CAGTTTAAGGGTGCAAACCCTTCCTTGACTGTAACTGACTCCTGAATCCGACATATCTTTGGTAA
391 CAGTTTAAGGGTGCAAACCCTTCCTTGACTGTAACTGACTCCTGAATCCGACACATATTTGGTAA
* *
93648 GGCGCAGTTCAGGAAAGAAATAAGGTATCCGATCAACCCATTTTTCATAAAATAAATTATCGGTG
456 GGCACAATTCAGGAAAGAAATAAGGTATCCGATCAACCCATTTTTCATAAAATAAATTATCGGTG
* * *
93713 ATGACTTCTAAGCATTTAATCCATGTCGAAGCCCAATTCCGGGCCCGCCCGAAAGAATGTTCTGA
521 ACGACTTCTAAGCATTTAATCCATGTCGAAGACCAATTACGGGCCCGCCCGAAAGAATGTTCTGA
93778 TA
586 TA
93780 ATTA-TATTATATTATATATATATATACTATTAATATTTTATTTATACGCCTATTATTATATTAA
1 ATTATTATTATA-TATATATATATATACTATTAATATTTTATTTATACGCCTATTATTATATTAA
93844 TTGTTTTTCCATGATTTTATTTTTTATTTACTTTATATTATATATGTATATATTTTTATTTTCAC
65 TTGTTTTTCCATGATTTTATTTTTTATTTACTTTATATTATATATGTATATATTTTTATTTTCAC
*
93909 TTTATTTATTTATTTTTTCTATATTTTTTTATTTTTTATTCCTTTTTATTTTATCTTTCTATCTT
130 TTTATTTATTTATTTTTTCTATA-TTATTTATTTTTTATTCCTTTTTATTTTATCTTTCTATCTT
93974 CATGTTATTTTCTTTATTTATATTGTCTTTTCTCTATTTTATTTTCATTTTTT-CTCTCTAACAC
194 CATGTTATTTTCTTTATTTATATTGTCTTTTCTCTATTTTATTTTCATTTTTTCCTCTCTAACAC
*
94038 GTTTCTAAAATTGTTTAAGGATGATTTCAAATCAATCTAAGGTAAAAAATTCATATCGTTATTTT
259 GTTTCTAAAATTGTTTAAGGATGATTTCAAATCAATCTAAGGTAAAAAATTCATATCATTATTTT
*
94103 ACCTTTTAATTTTAACTTTCAATTTTCTTAATTAAAGACAAATGAAAATTATGCAGTACCGAAAG
324 ACCTTTTAATTTTAACTTTCAATTTTCTTAATTAAAGACAAATGAAAATTACGCAGTACCGAAAG
*
94168 GGCAGTTTAAGGGTGCAAACCCTTCCTTGACTGTAACTGACTCCTGAATCCGACACATATTTGGT
389 AGCAGTTTAAGGGTGCAAACCCTTCCTTGACTGTAACTGACTCCTGAATCCGACACATATTTGGT
* *
94233 AAGGCACAATTCAGGTAAGAAATAAGGTATCCGATCAACCCATTTTTCATAAAATAAATTATTGG
454 AAGGCACAATTCAGGAAAGAAATAAGGTATCCGATCAACCCATTTTTCATAAAATAAATTATCGG
* * * *
94298 TGACGACTTCTAAGCGTTTAATCCATGTCGAAGACTAATTATGGGCCCGCCCGAAAGACTGTTCT
519 TGACGACTTCTAAGCATTTAATCCATGTCGAAGACCAATTACGGGCCCGCCCGAAAGAATGTTCT
94363 GA
584 GA
94365 CATATATTAT
Statistics
Matches: 562, Mismatches: 21, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
586 7 0.01
587 463 0.82
588 92 0.16
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (587 bp):
ATTATTATTATATATATATATATATACTATTAATATTTTATTTATACGCCTATTATTATATTAAT
TGTTTTTCCATGATTTTATTTTTTATTTACTTTATATTATATATGTATATATTTTTATTTTCACT
TTATTTATTTATTTTTTCTATATTATTTATTTTTTATTCCTTTTTATTTTATCTTTCTATCTTCA
TGTTATTTTCTTTATTTATATTGTCTTTTCTCTATTTTATTTTCATTTTTTCCTCTCTAACACGT
TTCTAAAATTGTTTAAGGATGATTTCAAATCAATCTAAGGTAAAAAATTCATATCATTATTTTAC
CTTTTAATTTTAACTTTCAATTTTCTTAATTAAAGACAAATGAAAATTACGCAGTACCGAAAGAG
CAGTTTAAGGGTGCAAACCCTTCCTTGACTGTAACTGACTCCTGAATCCGACACATATTTGGTAA
GGCACAATTCAGGAAAGAAATAAGGTATCCGATCAACCCATTTTTCATAAAATAAATTATCGGTG
ACGACTTCTAAGCATTTAATCCATGTCGAAGACCAATTACGGGCCCGCCCGAAAGAATGTTCTGA
TA
Found at i:115011 original size:12 final size:13
Alignment explanation
Indices: 114994--115022 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
114984 TTAATTGCGA
114994 AAAATTAAAA-TT
1 AAAATTAAAATTT
115006 AAAATTAAAATTT
1 AAAATTAAAATTT
115019 AAAA
1 AAAA
115023 AACTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:115136 original size:3 final size:3
Alignment explanation
Indices: 115128--115170 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
115118 AAAGAACAAA
115128 AAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
115171 ATCAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:115142 original size:9 final size:8
Alignment explanation
Indices: 115126--115200 Score: 68
Period size: 9 Copynumber: 9.4 Consensus size: 8
115116 TCAAAGAACA
115126 AAAATAAT
1 AAAATAAT
115134 AATAATAAT
1 AA-AATAAT
115143 AATAATAAAT
1 AA-AAT-AAT
115153 AAAATAAT
1 AAAATAAT
115161 AAAATAAT
1 AAAATAAT
*
115169 -AAATCA-
1 AAAATAAT
*
115175 AAAAGAA-
1 AAAATAAT
115182 AAAA-AAT
1 AAAATAAT
115189 AAAATAAAT
1 AAAAT-AAT
115198 AAA
1 AAA
115201 TAAGTCAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
6 2 0.03
7 17 0.29
8 13 0.22
9 21 0.36
10 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:115184 original size:20 final size:20
Alignment explanation
Indices: 115127--115177 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 20
115117 CAAAGAACAA
115127 AAATAATAATAATAATAATAAT
1 AAATAA-AATAATAA-AATAAT
115149 AAATAAAATAATAAAATAAT
1 AAATAAAATAATAAAATAAT
115169 AAATCAAAA
1 AAAT-AAAA
115178 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.36
21 12 0.43
22 6 0.21
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAAATAATAAAATAAT
Found at i:115198 original size:32 final size:31
Alignment explanation
Indices: 115091--115218 Score: 99
Period size: 32 Copynumber: 4.2 Consensus size: 31
115081 AATGTTAGAT
*
115091 AAAAAATAAATAAATATTAAA-CAGATCAAAGAA
1 AAAAAATAAATAAATAATAAATCA-A--AAAGAA
* * *
115124 CAAAAAT-AAT-AATAAT-AAT-AATAATAA
1 AAAAAATAAATAAATAATAAATCAAAAAGAA
*
115151 ATAAAAT-AATAAAATAATAAATCAAAAAGAA
1 AAAAAATAAAT-AAATAATAAATCAAAAAGAA
*
115182 AAAAAATAAAATAAATAAATAAGTC-AAAAGAA
1 AAAAAAT-AAATAAAT-AATAAATCAAAAAGAA
115214 AAAAA
1 AAAAA
115219 GAATTGAATA
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
27 12 0.16
29 7 0.09
30 6 0.08
31 17 0.22
32 19 0.25
33 16 0.21
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (31 bp):
AAAAAATAAATAAATAATAAATCAAAAAGAA
Found at i:117229 original size:84 final size:84
Alignment explanation
Indices: 116930--118068 Score: 1562
Period size: 84 Copynumber: 13.5 Consensus size: 84
116920 AAATTTGACA
* * * * * * *
116930 TGCCCTTGAGCTAAATGGAATCGAACTCGAAGGTC-TTTATTGACAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * * *
116994 AGTTATACTGCAAAATTAATA
66 AGCTATGCTGC-AAA-TGATG
* *
117015 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGATCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117080 AGCTATGCTACAAATTTGATG
66 AGCTATGCTGCAAA--TGATG
* * * *
117101 TGCCTTTGAGCTGAGTGTAATCGAAATCGAAGTTCTTTTATTGGCAGATAACCCTTCTAGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117166 AGATATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* *
117185 TGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117250 AGCTATGCTACAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * * *
117269 TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTATTTTGTTAGCAGATAACCCATCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
117334 AGTTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
117353 TGCCTTTTAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117418 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* *
117437 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTTCCTTA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
117502 AGTTATGCTAG-AAATTATG
66 AGCTATGCT-GCAAATGATG
* * * *
117521 TGCCTTTGAGCTAAGTGTAATCGAAGTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTTCATTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117586 AGCTATGCTGCAATTGATG
66 AGCTATGCTGCAAATGATG
* * * *
117605 TGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTAGTTGGCAGATAGCCCTTCTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
117670 AGCTATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* *
117689 TGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTTTTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
117754 AGTTATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
117773 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTATGATGGCAGATAACCCTTCTTGCTTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * *
117838 AGCTATACTACAATTGATG
66 AGCTATGCTGCAAATGATG
* * * * * * *
117857 TGCCTTTAAGCTAAGTGTAATCGAACTCAAAGGTATTTTGTTGGCATATAACCCTTTTTTGTCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCC-TTCTTGCCTT
* *
117922 GAGTTATGCTGCAAATTATG
65 GAGCTATGCTGCAAATGATG
* * *
117942 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * *
118007 AGTTATACAGCAAATGATG
66 AGCTATGCTGCAAATGATG
*
118026 CGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
118069 AAGGTGCTTT
Statistics
Matches: 938, Mismatches: 111, Indels: 11
0.88 0.10 0.01
Matches are distributed among these distances:
83 1 0.00
84 723 0.77
85 104 0.11
86 110 0.12
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (84 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
AGCTATGCTGCAAATGATG
Found at i:119696 original size:23 final size:23
Alignment explanation
Indices: 119631--119688 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
119621 CACCACTGCT
*
119631 CGTATAAA-TGCACCGAAGTGCCA
1 CGTA-AAATTGCATCGAAGTGCCA
* *
119654 CGTAGAATTGCATCGAAGTGCCC
1 CGTAAAATTGCATCGAAGTGCCA
119677 CGTAAAATTGCA
1 CGTAAAATTGCA
119689 CTGTAGTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (23 bp):
CGTAAAATTGCATCGAAGTGCCA
Found at i:120410 original size:63 final size:65
Alignment explanation
Indices: 120341--120502 Score: 199
Period size: 63 Copynumber: 2.6 Consensus size: 65
120331 ATCCCTTGAC
* * *
120341 GGGTGCATCGATGCACTATC-TATGCATCGGTACA-TAAATCCCATTCGATGTTTGTA-TTTAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAA
120403 G
65 G
* * ** *
120404 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
*
120468 GAGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATGTGCATCGATACAC
120503 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 46 0.53
64 39 0.45
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:125269 original size:21 final size:21
Alignment explanation
Indices: 125227--125269 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
125217 TTTTTGGGCT
* * *
125227 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
125248 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
125269 A
1 A
125270 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:126009 original size:149 final size:150
Alignment explanation
Indices: 125815--126130 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
125805 GGGTAGAGGG
* *
125815 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
125879 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
125944 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
* *
125964 TCTATGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
126029 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
126094 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
126114 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
126131 TGCATTTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
149 51 0.32
150 107 0.68
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:126142 original size:23 final size:23
Alignment explanation
Indices: 126098--126142 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
126088 ATCATTATAT
*
126098 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
126121 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
126143 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:132233 original size:21 final size:21
Alignment explanation
Indices: 132191--132233 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
132181 TTTTTGGGCT
* * *
132191 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
132212 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
132233 A
1 A
132234 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:132326 original size:13 final size:12
Alignment explanation
Indices: 132301--132333 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
132291 TTCCCCCATG
132301 AGAAA-AAAAAA
1 AGAAAGAAAAAA
132312 AGAAAGAAAAGAA
1 AGAAAGAAAA-AA
132325 AGAAAGAAA
1 AGAAAGAAA
132334 GACTAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:132332 original size:17 final size:15
Alignment explanation
Indices: 132301--132335 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
132291 TTCCCCCATG
132301 AGAAAAAAAAAAGAA
1 AGAAAAAAAAAAGAA
132316 AGAAAAGAAAGAAAGAA
1 AGAAAA-AAA-AAAGAA
132333 AGA
1 AGA
132336 CTAAGCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 3 0.17
17 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAGAA
Found at i:133053 original size:152 final size:149
Alignment explanation
Indices: 132780--133097 Score: 530
Period size: 152 Copynumber: 2.1 Consensus size: 149
132770 GGGTAGAGGG
* *
132780 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
132845 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
132910 TATGACACTACGGTGCAAT
131 TATGACACTACGGTGCAAT
*
132929 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACA
1 TCTACGCGGTCCTTCGGG--ACATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACA
132994 CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCA
63 CATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCA
* *
133059 TTATATGGCACTATGGTGCAAT
128 TTATATGACACTACGGTGCAAT
133081 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
133098 TGCATTTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
149 18 0.11
151 34 0.22
152 106 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGACACTACGGTGCAAT
Found at i:133109 original size:23 final size:23
Alignment explanation
Indices: 133065--133109 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
133055 ATCATTATAT
*
133065 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTATACGC
*
133088 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
133110 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGC
Found at i:135260 original size:3 final size:3
Alignment explanation
Indices: 135252--135285 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
135242 GCGAGGCAAT
135252 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
135286 CAAGAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:135525 original size:23 final size:23
Alignment explanation
Indices: 135507--135567 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
135497 CTCGTATAAA
135507 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
135530 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
135553 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
135568 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:140350 original size:23 final size:24
Alignment explanation
Indices: 140276--140369 Score: 106
Period size: 23 Copynumber: 4.0 Consensus size: 24
140266 CACCACAGCT
* *
140276 CGTATAAATTGCACTGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
140300 CGTAGAAATTGTC-CCGAAG-GACCG
1 CGTAGAAATTG-CACCGAAGTG-CCA
140324 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
140347 CGTAG-AATTGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
140370 TATAAGATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
22 3 0.05
23 30 0.50
24 26 0.43
25 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:141440 original size:35 final size:36
Alignment explanation
Indices: 141394--141464 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
141384 TTCATTTAGG
141394 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
*
141429 GGGGAATCGATACCTCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
141465 CCTGCACAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.20, C:0.30, G:0.32, T:0.18
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:142553 original size:3 final size:3
Alignment explanation
Indices: 142545--142603 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
142535 CCAAGAACAA
*
142545 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
142591 ACT AA- AAT AAT AA
1 AAT AAT AAT AAT AA
142604 ATCATAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 5 0.10
3 44 0.90
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:142610 original size:7 final size:7
Alignment explanation
Indices: 142548--142611 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 7
142538 AGAACAAAAT
142548 AATAAT-
1 AATAATA
142554 AATAAT-
1 AATAATA
142560 AATAAT-
1 AATAATA
142566 AATAAT-
1 AATAATA
142572 AATAATA
1 AATAATA
142579 AATTAATAA
1 AA-TAAT-A
*
142588 AATACTAA
1 AATAAT-A
142596 AATAATA
1 AATAATA
*
142603 AATCATA
1 AATAATA
142610 AA
1 AA
142612 GGAAAAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
6 24 0.46
7 11 0.21
8 14 0.27
9 3 0.06
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:144746 original size:20 final size:20
Alignment explanation
Indices: 144721--144772 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
144711 AAGTTGTCCT
144721 GAAGGACCTATGTATATCCC
1 GAAGGACCTATGTATATCCC
* * * *
144741 GAAGGATCTCTGTATGTCTC
1 GAAGGACCTATGTATATCCC
*
144761 GAAAGACCTATG
1 GAAGGACCTATG
144773 AACCCTCGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (20 bp):
GAAGGACCTATGTATATCCC
Found at i:148461 original size:13 final size:13
Alignment explanation
Indices: 148443--148468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
148433 GCCAGTAAGA
148443 CTAGTATTTGATG
1 CTAGTATTTGATG
148456 CTAGTATTTGATG
1 CTAGTATTTGATG
148469 TTGTATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
CTAGTATTTGATG
Found at i:151288 original size:31 final size:31
Alignment explanation
Indices: 151234--151315 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
151224 TTTTTGCCAT
* **
151234 TTATTACACTAAATTTTGGTTTTCATTTCAA
1 TTATAACACTAAATTTTAATTTTCATTTCAA
* * *
151265 TTATAACACTAAATTTTAATTTTCGTTTTAG
1 TTATAACACTAAATTTTAATTTTCATTTCAA
* *
151296 TTATACCACTGAATTATTAA
1 TTATAACACTAAATT-TTAA
151316 ATCATTAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATAACACTAAATTTTAATTTTCATTTCAA
Found at i:152408 original size:21 final size:21
Alignment explanation
Indices: 152379--152492 Score: 117
Period size: 21 Copynumber: 5.5 Consensus size: 21
152369 TTCCAGATTT
* *
152379 GCAACGCGAACTTCGACAATC
1 GCAATGCGAACTTCGACTATC
*
152400 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
*
152421 GCAATGCGAACTT-GTA-AATC
1 GCAATGCGAACTTCG-ACTATC
* *
152441 GCAATGTGATA-GTCGACTATC
1 GCAATGCGA-ACTTCGACTATC
*
152462 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
*
152483 GCAATACGAA
1 GCAATGCGAA
152493 TATGTAAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 15 0.19
21 62 0.81
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
GCAATGCGAACTTCGACTATC
Found at i:152441 original size:41 final size:41
Alignment explanation
Indices: 152379--152487 Score: 123
Period size: 41 Copynumber: 2.6 Consensus size: 41
152369 TTCCAGATTT
* * *
152379 GCAACGCGAACTTCGACAATCGCAATGCGA-ACTTGGACTATC
1 GCAATGCGAACTT-GACAATCGCAATGCGATA-GTCGACTATC
*
152421 GCAATGCGAACTTGTA-AATCGCAATGTGATAGTCGACTATC
1 GCAATGCGAACTTG-ACAATCGCAATGCGATAGTCGACTATC
*
152462 GCAATGCGAACTTGGACTATCGCAAT
1 GCAATGCGAACTT-GACAATCGCAAT
152488 ACGAATATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 35 0.60
42 23 0.40
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
GCAATGCGAACTTGACAATCGCAATGCGATAGTCGACTATC
Found at i:152532 original size:62 final size:62
Alignment explanation
Indices: 152391--152518 Score: 204
Period size: 62 Copynumber: 2.1 Consensus size: 62
152381 AACGCGAACT
* * **
152391 TCGACAATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGTAAATCGCAATGTGATAG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGTAAATCGCAATACGATAG
152453 TCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAA-TATGTAAATCGCAATACGATAG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACT-TGTAAATCGCAATACGATAG
152515 TCGA
1 TCGA
152519 AGTTCGCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 1 0.02
62 60 0.98
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (62 bp):
TCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGTAAATCGCAATACGATAG
Found at i:152533 original size:21 final size:21
Alignment explanation
Indices: 152509--152614 Score: 144
Period size: 21 Copynumber: 5.1 Consensus size: 21
152499 AATCGCAATA
152509 CGATAGTCGAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
152530 CGATAGTCGAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
152551 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCATTG
** * *
152572 CGATTTTCCAAATTCG--TTG
1 CGATAGTCGAAGTTCGCATTG
*
152591 CGCTAGTCGAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
152612 CGA
1 CGA
152615 ATCTGGAAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
19 14 0.19
21 58 0.81
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCATTG
Found at i:153317 original size:2 final size:2
Alignment explanation
Indices: 153310--153392 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
153300 AAATGATCTA
153310 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
153352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
153393 AGAGAGAGAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:154363 original size:22 final size:21
Alignment explanation
Indices: 154322--154361 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
154312 TATTGACTTT
154322 TGACCATTATAATTGCATATCC
1 TGACCATTAT-ATTGCATATCC
154344 TGACCATTAT-TTGCATAT
1 TGACCATTATATTGCATAT
154362 ATTATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
TGACCATTATATTGCATATCC
Found at i:160326 original size:27 final size:27
Alignment explanation
Indices: 160296--160349 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
160286 CTTGTATATT
* *
160296 CTGAAATGGTTTTACATTCTCTTTCAA
1 CTGAAATGGTTGTACATTCTCATTCAA
*
160323 CTGAAATTGTTGTACATTCTCATTCAA
1 CTGAAATGGTTGTACATTCTCATTCAA
160350 ATTCACAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (27 bp):
CTGAAATGGTTGTACATTCTCATTCAA
Found at i:164008 original size:16 final size:16
Alignment explanation
Indices: 163982--164032 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
163972 GTGAAGCATC
163982 CAGACTTGTGTAGAAAA
1 CAGA-TTGTGTAGAAAA
163999 CAGATTGTGTAGAAAA
1 CAGATTGTGTAGAAAA
*
164015 CAGA--CTGTAGAAAA
1 CAGATTGTGTAGAAAA
164029 CAGA
1 CAGA
164033 CAAGTCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 13 0.39
16 16 0.48
17 4 0.12
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (16 bp):
CAGATTGTGTAGAAAA
Found at i:164025 original size:14 final size:14
Alignment explanation
Indices: 163990--164033 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
163980 TCCAGACTTG
*
163990 TGTAGAAAACAGATTG
1 TGTAGAAAACAGA--C
164006 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
164020 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
164034 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:166331 original size:51 final size:51
Alignment explanation
Indices: 166255--166355 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
166245 TAAGGAAAGG
166255 ATAGGCTGTAAAGAAATATCGGTTTGAAC-AGCTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGC-TGAAATTCCTTGTAACTA
166306 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACT
166356 CTCCCCCTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 46 0.94
52 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACTA
Found at i:167778 original size:14 final size:15
Alignment explanation
Indices: 167743--167786 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
167733 CCTGATACCA
167743 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
167759 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
167773 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
167787 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:170801 original size:24 final size:24
Alignment explanation
Indices: 170771--170827 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
170761 GAAGTATCTG
170771 GGTCAACAAACTCAGTTACA-CGCT
1 GGTCAACAAACTCAGTTACAGC-CT
* *
170795 GGTCAACAAGCTCATTTACAGCCT
1 GGTCAACAAACTCAGTTACAGCCT
*
170819 GGCCAACAA
1 GGTCAACAA
170828 CCTTCACAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (24 bp):
GGTCAACAAACTCAGTTACAGCCT
Found at i:170979 original size:22 final size:22
Alignment explanation
Indices: 170949--171002 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
170939 AGATATTCAG
*
170949 TTGTGGAAATGTTAACTCTGCT
1 TTGTGGAAATGCTAACTCTGCT
*
170971 TTGTAGAAATGCTAACTCTGCT
1 TTGTGGAAATGCTAACTCTGCT
170993 TTGTGGAAAT
1 TTGTGGAAAT
171003 CCAGTATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (22 bp):
TTGTGGAAATGCTAACTCTGCT
Found at i:173127 original size:19 final size:19
Alignment explanation
Indices: 173103--173146 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
173093 CGCCCCGCAT
* *
173103 CCGCCCGTCCCATATTCGC
1 CCGCCCGCCCCATATCCGC
173122 CCGCCCGCCCCATATCCGC
1 CCGCCCGCCCCATATCCGC
173141 CCGCCC
1 CCGCCC
173147 AGCTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.61, G:0.16, T:0.14
Consensus pattern (19 bp):
CCGCCCGCCCCATATCCGC
Found at i:180489 original size:2 final size:2
Alignment explanation
Indices: 180482--180542 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
180472 ACAGTTAAAT
180482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
180524 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
180543 TGAAATGTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:181797 original size:26 final size:26
Alignment explanation
Indices: 181761--181821 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
181751 ATTATATTAA
181761 TGGTGCTCAGCAGTTCTCAGCGTTAG
1 TGGTGCTCAGCAGTTCTCAGCGTTAG
181787 TGGTGCTCAGCAGTTCTCAGCGTTAG
1 TGGTGCTCAGCAGTTCTCAGCGTTAG
*
181813 TGATGCTCA
1 TGGTGCTCA
181822 ACGGTGCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.31
Consensus pattern (26 bp):
TGGTGCTCAGCAGTTCTCAGCGTTAG
Found at i:183543 original size:21 final size:21
Alignment explanation
Indices: 183519--183569 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
183509 ATAAAATTAT
* *
183519 TTTGAATGATGATTTTGTTAA
1 TTTGAATGATAATTGTGTTAA
*
183540 TTTGAATGATAATTGTGTTGA
1 TTTGAATGATAATTGTGTTAA
183561 TTTGAATGA
1 TTTGAATGA
183570 CATTATGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (21 bp):
TTTGAATGATAATTGTGTTAA
Found at i:192054 original size:12 final size:12
Alignment explanation
Indices: 192037--192061 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
192027 GATTTCTCTG
192037 ATGCAGAGATCA
1 ATGCAGAGATCA
192049 ATGCAGAGATCA
1 ATGCAGAGATCA
192061 A
1 A
192062 GGAAGCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
ATGCAGAGATCA
Found at i:195241 original size:46 final size:46
Alignment explanation
Indices: 195165--195253 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
195155 AGCAAAAGAG
* * * *
195165 TAATAGTTTAGAGACTTATTTTTACCAAAAAATTGTTTAGGTACTA
1 TAATAGTTTAGAGACTTAGTTTGACAAAAAAATAGTTTAGGTACTA
*
195211 TAATAGTTTA-AGGATTTAGTTTGACAAAAAAATAGTTTAGGTA
1 TAATAGTTTAGA-GACTTAGTTTGACAAAAAAATAGTTTAGGTA
195254 ATTAAAGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 1 0.03
46 36 0.97
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (46 bp):
TAATAGTTTAGAGACTTAGTTTGACAAAAAAATAGTTTAGGTACTA
Found at i:197880 original size:31 final size:31
Alignment explanation
Indices: 197837--198084 Score: 408
Period size: 31 Copynumber: 8.0 Consensus size: 31
197827 TGAGGTTTAT
*
197837 CTAT-TTCATTCGGGACATATGGACAGTTTAC
1 CTATGTTC-TTCGGGACATATGGACAGATTAC
* * *
197868 CTATGTTTTTCGGGACATAAGGACAGTTTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
197899 CTATGTTCTTCGGGACATATGGACAGATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
*
197930 CTATGTTCTTCGGGACATATGGATAGATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
197961 CTATGTTCTTCGGGACATATGGACAGATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
* *
197992 CTATGTTCTTCGAGACATATGAACAGATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
198023 CTATGTTCTTCGGGACATATGGACAGATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
*
198054 CTATGTTCTTCGGGACATATGGACAAATTAC
1 CTATGTTCTTCGGGACATATGGACAGATTAC
198085 TATATGAGCT
Statistics
Matches: 204, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
31 202 0.99
32 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (31 bp):
CTATGTTCTTCGGGACATATGGACAGATTAC
Found at i:199809 original size:18 final size:19
Alignment explanation
Indices: 199783--199840 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
199773 TCGAGGGATA
199783 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* * *
199802 AT-AGTGGTTCTTTGGAAC
1 ATCAGTGGTCCTTCGGGAC
199820 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
199840 A
1 A
199841 AATATTCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 13 0.42
19 5 0.16
20 13 0.42
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:199829 original size:20 final size:20
Alignment explanation
Indices: 199782--199841 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
199772 TTCGAGGGAT
*
199782 AATCAGTGGTCCTTCGGGAC
1 AATCAGTGGTCCTTCGGAAC
* *
199802 -AT-AGTGGTTCTTTGGAAC
1 AATCAGTGGTCCTTCGGAAC
*
199820 AATCAGTGGTCCTTCGGGAC
1 AATCAGTGGTCCTTCGGAAC
199840 AA
1 AA
199842 ATATTCAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 15 0.47
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
AATCAGTGGTCCTTCGGAAC
Found at i:206570 original size:18 final size:18
Alignment explanation
Indices: 206547--206619 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
206537 AGGGATAATC
*
206547 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
* * *
206565 AGTGGTTATTCAGAACAAT
1 AGTGGTCATTCGGGAC-AT
*
206584 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCATTCGGGACAT
*
206603 AGTAGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
206620 AATATTCAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 27 0.63
19 4 0.09
20 12 0.28
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:216339 original size:29 final size:29
Alignment explanation
Indices: 216306--216390 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
216296 AAGTAAAATT
*
216306 ATTAATTAATAACTAAATACATGTTAATA
1 ATTAATTAATAATTAAATACATGTTAATA
216335 ATTAATTAATAATTAAATACATGTTAATA
1 ATTAATTAATAATTAAATACATGTTAATA
*
216364 ATTAATTAATAATTAAATACATATTAA
1 ATTAATTAATAATTAAATACATGTTAA
216391 AAATATTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTAATTAATAATTAAATACATGTTAATA
Found at i:216390 original size:18 final size:18
Alignment explanation
Indices: 216308--216382 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 18
216298 GTAAAATTAT
*
216308 TAATTAATAACTAAATACA
1 TAATTAATAATTAAATA-A
* *
216327 T-GTTAATAATTAATTAA
1 TAATTAATAATTAAATAA
*
216344 TAATTAAATACATGTTAATAA
1 TAATT-AATA-AT-TAAATAA
216365 TTAATTAATAATTAAATA
1 -TAATTAATAATTAAATA
216383 CATATTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
17 2 0.05
18 14 0.32
19 10 0.23
20 4 0.09
21 9 0.20
22 5 0.11
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (18 bp):
TAATTAATAATTAAATAA
Done.