Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 153 of 199
Found at i:45770492 original size:41 final size:40
Alignment explanation
Indices: 45770379--45770513 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 40
45770369 ACCAGTTTGG
* * * *
45770379 CACCCAGTGCCTCATTGGA-TAATTCGAAGTAATAACTTGA
1 CACCCAGTGCCTCATCGAATTAA-TCGAAGTAGTAAATTGA
* * *
45770419 CACCCAG-GTCTCATCG-GTTAAATCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATT-AATCGAAGTAGTAAATTGA
45770455 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAAT-CGAAGTAGTAAATTGA
* * *
45770496 CATCTAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
45770514 CTCGAAGTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
36 14 0.19
37 11 0.15
38 5 0.07
39 12 0.16
40 9 0.12
41 24 0.32
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATTAATCGAAGTAGTAAATTGA
Found at i:45771107 original size:42 final size:42
Alignment explanation
Indices: 45770989--45771234 Score: 258
Period size: 42 Copynumber: 5.7 Consensus size: 42
45770979 GCGTCGCTAA
* * * * * * *
45770989 CTTTAGCGGCACTTTTCCCACAAACGCCTCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTT-ACACAAACGCCGCTATAGATCAAGAC
* *
45771032 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 CTTTAGCGGCGCTTTT-ACACAAACGCCGCTATAGATCAAGAC
45771075 CTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGAC
* * *
45771117 CTTTAGCGGTGCTTTTACACAAACGCCGTTATAGATCAAGAT
1 CTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGAC
* ** * *
45771159 CTTTAGCGGCGTTTTTTTTTATAAACGCCGCTATAGATCATGAC
1 CTTTAGCGGCG--CTTTTACACAAACGCCGCTATAGATCAAGAC
* * * *
45771203 TTTTAGCGACGCTTTTTTCACAAACACCGCTA
1 CTTTAGCGGCGC-TTTTACACAAACGCCGCTA
45771235 AAAGTGCCAT
Statistics
Matches: 175, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 73 0.42
43 69 0.39
44 33 0.19
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTACACAAACGCCGCTATAGATCAAGAC
Found at i:45775814 original size:21 final size:21
Alignment explanation
Indices: 45775790--45775830 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45775780 AACCCTAAAT
45775790 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTCTTAACCCCTAAC
*
45775811 CCCTAACTCTTAATCCCTAA
1 CCCTAACTCTTAACCCCTAA
45775831 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTCTTAACCCCTAAC
Found at i:45776068 original size:24 final size:25
Alignment explanation
Indices: 45776028--45776074 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
45776018 TATATGAAAT
*
45776028 TATTTAATATATAAATTAAAAAAAA
1 TATTTAATAAATAAATTAAAAAAAA
45776053 TATTTAA-AAATAAATTAAAAAA
1 TATTTAATAAATAAATTAAAAAA
45776075 TAATTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TATTTAATAAATAAATTAAAAAAAA
Found at i:45776168 original size:23 final size:23
Alignment explanation
Indices: 45776141--45776190 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
45776131 CCTAACTCTT
45776141 AACCCCATAA-CATCTAA-CCCCTA
1 AACCCC-TAACCA-CTAACCCCCTA
45776164 AACCCCTAACCACTAACCCCCTA
1 AACCCCTAACCACTAACCCCCTA
45776187 AACC
1 AACC
45776191 TTAAATCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.14
Consensus pattern (23 bp):
AACCCCTAACCACTAACCCCCTA
Found at i:45776172 original size:15 final size:15
Alignment explanation
Indices: 45776154--45776187 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45776144 CCCATAACAT
*
45776154 CTAACCCCTAAACCC
1 CTAACCACTAAACCC
*
45776169 CTAACCACTAACCCC
1 CTAACCACTAAACCC
45776184 CTAA
1 CTAA
45776188 ACCTTAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (15 bp):
CTAACCACTAAACCC
Found at i:45776173 original size:22 final size:22
Alignment explanation
Indices: 45776141--45776211 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
45776131 CCTAACTCTT
45776141 AACCCCATAACATCTAACCCCTA
1 AACCCC-TAACATCTAACCCCTA
45776164 AACCCCTAACCA-CTAACCCCCTA
1 AACCCCTAA-CATCTAA-CCCCTA
* *
45776187 AA-CCTTAA-ATCTCAACCCTTA
1 AACCCCTAACATCT-AACCCCTA
45776208 AACC
1 AACC
45776212 ACAATCCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.02
21 9 0.22
22 15 0.37
23 16 0.39
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACATCTAACCCCTA
Found at i:45776239 original size:15 final size:15
Alignment explanation
Indices: 45776203--45776243 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
45776193 AAATCTCAAC
*
45776203 CCTTAAA-CCACAAT
1 CCTTAAATCCATAAT
*
45776217 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
45776231 CCTTAAATCCATA
1 CCTTAAATCCATA
45776244 CTCCCTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:45776252 original size:15 final size:15
Alignment explanation
Indices: 45776214--45776252 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
45776204 CTTAAACCAC
45776214 AATCCCT-AATCCAT
1 AATCCCTAAATCCAT
*
45776228 AATCCTTAAATCCAT
1 AATCCCTAAATCCAT
*
45776243 ACTCCCTAAA
1 AATCCCTAAA
45776253 CCTTAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (15 bp):
AATCCCTAAATCCAT
Found at i:45776256 original size:22 final size:22
Alignment explanation
Indices: 45776182--45776259 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
45776172 ACCACTAACC
45776182 CCCTAAACCTTAAATCTCA-AC-
1 CCCTAAACCTTAAATC-CATACT
* * *
45776203 CCTTAAACC--ACAATCCCTAAT
1 CCCTAAACCTTA-AATCCATACT
* *
45776224 CCATAATCCTTAAATCCATACT
1 CCCTAAACCTTAAATCCATACT
45776246 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
45776260 ACAGTAACTC
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.05
20 5 0.12
21 15 0.35
22 20 0.47
23 1 0.02
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (22 bp):
CCCTAAACCTTAAATCCATACT
Found at i:45776537 original size:41 final size:41
Alignment explanation
Indices: 45776477--45776592 Score: 173
Period size: 41 Copynumber: 2.8 Consensus size: 41
45776467 TAAAATGTTT
45776477 TTAGCGGCGCTTTAT-CAAAAACGCCGCTAAAGCCCCTAC-CA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCCCC-ACGCA
*
45776518 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCACGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCACGCA
* *
45776559 TTAGCGGCGCTTTTCGAAAATCGCCGCTAAAGCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
45776593 ACGAAATGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
40 3 0.04
41 66 0.96
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCACGCA
Found at i:45776672 original size:39 final size:39
Alignment explanation
Indices: 45776628--45776704 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
45776618 TGGGCTTAGG
* * *
45776628 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTTA
45776668 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCT
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCT
45776705 CAATCTTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTTA
Found at i:45776678 original size:40 final size:39
Alignment explanation
Indices: 45776628--45776781 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 39
45776618 TGGGCTTAGG
*
45776628 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTTTT-AAAAACGCCGCTAATGCTTA
* * *
45776668 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTAAAAACGCCGCTAATGCT-TA
* * * ** *
45776708 TCTTTAGTGGCG-ATTTCCATAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTTTA-AAAACGCCGCTAATGCTT-A
* **
45776748 TTTTTACCGGCGTTTTTTGTCCAAACGCCGCTAA
1 TTTTTAGCGGCGTTTTTT-TAAAAACGCCGCTAA
45776782 AAGTGCCGCT
Statistics
Matches: 87, Mismatches: 22, Indels: 9
0.74 0.19 0.08
Matches are distributed among these distances:
39 21 0.24
40 52 0.60
41 14 0.16
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTTTAAAAACGCCGCTAATGCTTA
Found at i:45776903 original size:5 final size:5
Alignment explanation
Indices: 45776893--45776921 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
45776883 TATTTTTTAT
45776893 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
45776922 TATGCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:45781536 original size:28 final size:29
Alignment explanation
Indices: 45781464--45781536 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
45781454 TATAAAGGCT
* **
45781464 TATTCTTATAAATTTTAAAAAAATTGGTC
1 TATTTTTATAAATTTTAAAAAAATTGACC
45781493 TATTTTTATAATATTTTAAAAAAATTGACC
1 TATTTTTATAA-ATTTTAAAAAAATTGACC
45781523 T-TTTTTGA-AAATTT
1 TATTTTT-ATAAATTT
45781537 AGTCTGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.10
29 17 0.44
30 18 0.46
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (29 bp):
TATTTTTATAAATTTTAAAAAAATTGACC
Found at i:45787033 original size:29 final size:28
Alignment explanation
Indices: 45786990--45787045 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
45786980 CTGTCTTCTC
45786990 CCCCAAACGTTTTTCCCCTCTGCTGGTT
1 CCCCAAACGTTTTTCCCCTCTGCTGGTT
*
45787018 CCCCAAATGTTCTTTCCCCTCTGCTGGT
1 CCCCAAACGTT-TTTCCCCTCTGCTGGT
45787046 GAAATTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.11, C:0.39, G:0.14, T:0.36
Consensus pattern (28 bp):
CCCCAAACGTTTTTCCCCTCTGCTGGTT
Found at i:45787520 original size:15 final size:15
Alignment explanation
Indices: 45787477--45787520 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
45787467 ATGTTTTGTT
45787477 TCTTTCATTTACCTG
1 TCTTTCATTTACCTG
* *
45787492 TC-TT-GTTTAACTG
1 TCTTTCATTTACCTG
45787505 TCTTTCATTTACCTG
1 TCTTTCATTTACCTG
45787520 T
1 T
45787521 TCTTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.55
Consensus pattern (15 bp):
TCTTTCATTTACCTG
Found at i:45790349 original size:18 final size:18
Alignment explanation
Indices: 45790325--45790390 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
45790315 AGAATATGAG
*
45790325 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
* *
45790343 GAATGATGTTTACATTTC
1 AAATGATGTTCACATTTC
*
45790361 AAATGATGTTCACATGTC
1 AAATGATGTTCACATTTC
45790379 AAATGATGTTCA
1 AAATGATGTTCA
45790391 AATTGATGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:45790967 original size:67 final size:67
Alignment explanation
Indices: 45790842--45790980 Score: 178
Period size: 67 Copynumber: 2.1 Consensus size: 67
45790832 TAGTTATTTA
* * * *
45790842 TGTTT-GGTTTTCGGATATTGAATTTATGTTCTATTTATTTATGTGTAATGTAGCTTTATTAATA
1 TGTTTAGGTTTTCGGATATTGAATTTATGTTCTATTAATTTATCTGAAATGTAGCTTTATCAATA
45790906 GT
66 GT
*
45790908 TGTTTAGGTCTTT-GGATATTGAATTTATGTTCTACTTAATTTATACT-AAAT-TAGTTTTATCA
1 TGTTTAGGT-TTTCGGATATTGAATTTATGTTCTA-TTAATTTAT-CTGAAATGTAGCTTTATCA
45790970 ATAGT
63 ATAGT
45790975 TGTTTA
1 TGTTTA
45790981 AATATGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
66 5 0.08
67 44 0.69
68 14 0.22
69 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (67 bp):
TGTTTAGGTTTTCGGATATTGAATTTATGTTCTATTAATTTATCTGAAATGTAGCTTTATCAATA
GT
Found at i:45792981 original size:13 final size:13
Alignment explanation
Indices: 45792963--45792987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45792953 ACACTCAAAT
45792963 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
45792976 TTCTCAAAAGCA
1 TTCTCAAAAGCA
45792988 AGAAAGAACT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:45796892 original size:5 final size:5
Alignment explanation
Indices: 45796882--45796907 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45796872 TGAGAAAAGG
45796882 GTGCA GTGCA GTGCA GTGCA GTGCA G
1 GTGCA GTGCA GTGCA GTGCA GTGCA G
45796908 GTTTCTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (5 bp):
GTGCA
Found at i:45802635 original size:972 final size:971
Alignment explanation
Indices: 45797435--45802805 Score: 8736
Period size: 971 Copynumber: 5.5 Consensus size: 971
45797425 ATGAAGCTTA
* * * *
45797435 AATATGAACCGTTAAATAGACATGAAAGCTACCAACAAAAAAATAATTACATTAACCATCAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
* * ** *
45797500 AATTTAGACTCAAATCAAATTCTTAAACTTGAAATCCAACACCAATCAAATTTTAAGTAATGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
*
45797565 GTTATTTACTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
* * * *
45797630 TTTATTAGAATGTTAGACAATCGGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
* * * *
45797695 GGACACGTGCCAGCGTGACAAACCATCTGAGAAATAATCGTAACCAATCATTTGGCTCTACTAGA
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
* *
45797760 ACGCCTTGGTGACTGTCTCTCCCAGATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGAGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
* ** * * * *
45797825 TTGGACTGCATGCGTCTTCTTGAAAGAGTTAAACCTCCCGCTTCTAGAGATAATCCACTTGCTTG
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
* * * *
45797890 GCAAACATCCTTGCTAGCCACAAGTTTTGAACATA-CCGTTGTTGGAAAAAATGTATTTTATAGG
456 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTA-CGG
* * *
45797954 AACTTTGAGGCATAATCTCAATAGGTAAAGGTGA-AGAGTTGAATCATAAAACTATGTTTTCATA
520 AACTTTGAGGCATATTCTCAATAGGTAAAGGT-ACAGAGTTGAATCATAAAATTATGGTTTCATA
* * * * *
45798018 TTCTACTCCATAAGACCTTTATAACGGTATATCATATGCTCAAAATGGCTGA-CTGATGAATGAG
584 TTCTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGC-GATGAATGAG
* * * *
45798082 AAATTGATGCTCAAAGTAAGCTACTTGGAAATATTTGTTGAGGAAAAGAAAAGCTTAAATCTCAC
648 AAATTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCAC
* * * * * *
45798147 ATTGGTTAAATACCAAGTGTGAGATGTGTTTCTATATGTGAATCCTTTTGAAAAATGATTGAATG
713 ATTGGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATG
* * * *
45798212 ACTAAGTTTGGAACCTTGCCT-TGCGCACA-GGGGTGCAAGTCCAAACTCGT-T-AGGGTTGGGG
778 ACTAAGTTTGGAACCTTACCTCT-TGCATAGGGGGTGCAAGTCCAAA-TC-TATCGGGGTTGGGG
** * * * * * *
45798273 TGCACCCGCACTACGT-CTGCAACGCGAAAAATATTTGGAATGTTTAAACTGGTCATGCTCAAAA
840 TGCACTTGTACGACGTGC-GCAACGCG--AAATGTTTAGAATGTTCAAACTAGTCATGC-C----
* * * * * *
45798337 TGGGCTTGTAGATATTTTAGCCCAACACTAAAAAATGGGCTCC---TTTTTTTTCAACATTTCGG
897 ----C------A-A----A----AATACGAAAAAGTAGGCTCCTTATTTTTTTTCGATATTTCGG
*
45798399 TGATAGAAAAAAACAT-TTTTGTTCGTTG
943 TGATAGAAAAAATCATCTTTTGTTCGTTG
* * * *
45798427 AATATGGACCGTGAAAGAAACATGAAAGCTACCAACAAAAAAATGATTACATTAAACATCAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
* * * *
45798492 AATATAGACTCGAATCAAATTCTTAAACCCAAAATCCAACACCAATCAGATTTTAAGTAACGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
45798557 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
*
45798622 TTTATTAAAAGGTTAGATAATCAAACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
* * * * *
45798687 GGACACGTGCTAGCGTGATAAGCCATCTGAGAAATAACCGTAACCAATCATTCGGCTCTCCTCGA
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
*
45798752 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCTGTTTGACCCTCTATCTCAGCAAGGGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
* * *
45798817 TTGGACTGCATGCGTTTTCTTGAAAGACCTAAACCTCCCTCTTTTAGAGACAATCTACCTGCTTG
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
* * *
45798882 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCATTGTTAGAAAAATTACATTTTACGGA
456 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
45798947 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
521 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
* *
45799012 CTACTCCATGAGACCTTTAGAACGGTATATTATATGCTAAAAATGGTTTAGCGATGAATGAGAAA
586 CTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
*
45799077 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTCAGATCTCACATT
651 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCACATT
* *
45799142 GGTTAAACACCAAGTGTGATATGTGTTTATATATGGGAACCCTCTTGAAAGATAATTGAATGACT
716 GGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
*
45799207 AAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCAGGGTTGGGGTGCACT
781 AAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCACT
**
45799272 TGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATTTGAAAA
846 TGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATACGAAAA
*
45799337 AGTAGGCTCCTTATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATTTTTTGTTCGTTG
911 AGTAGGCTCCTTATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTCGTTG
*
45799398 AATATGAACCGTGAAATAAACATGAAAGCTACTAACAAAAAAATAATTACATTAAACATAAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
45799463 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
*
45799528 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATTAATATGTA
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
45799593 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
*
45799658 GGACACGTGCCAGCATGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
* * *
45799723 ACGCCTTGGTGATTGTCTCTCCTATATTCTTACTCTCCGTTTGACCCTCTATCTTAGCAAGGGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
* *
45799788 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCTCTCTTTTAGAGACAATCTACCTGCTTG
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
* *
45799853 GCAAGCATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTACATTTTACGGA
456 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
* * *
45799918 AATTTGAGGCATATTCTCAACAGGTGAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
521 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
*
45799983 ATACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
586 CTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
*
45800048 TTGATACTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCACATT
651 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCACATT
*
45800113 GGTTAAATACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
716 GGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
*
45800178 AAGTTTGGAACCTTACCTCTTGCATAGAGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCACT
781 AAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCACT
* * * *
45800243 TGTACAACGTGGGCAACGCGAAATGTTCAAAATGTTCAAACTAGTCATGCCCAAAAATACGAAAA
846 TGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATACGAAAA
*
45800308 AGTAGGCT-CTTAATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTTGTTG
911 AGTAGGCTCCTT-ATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTCGTTG
45800369 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
*
45800434 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAAGTTTTAAGTAACGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
* *
45800499 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATTAATATGTT
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
* *
45800564 TTTGTTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTGCAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
* *
45800629 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTTGACTCTACTCGA
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
* * * *
45800694 ACGCCTTGGTGACTGTCGCTCCCGTATTCTTACTCTCCATTTGACCCTCTATCTTAGCAAGGGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
45800759 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
*
45800824 GCAAACATTCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
456 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
*
45800889 ACTTTAAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
521 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
*
45800954 CTACTCCATGAGACCTTTACAACGGTATATTATATGCTAAAAATGGTTTAGCGATGAATGAGAAA
586 CTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
*
45801019 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAAGAAAAGCTTAGATCCCACAT
651 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGG-AAAAGAAAAGCTTAGATCTCACAT
45801084 TGGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGAC
715 TGGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGAC
45801149 TAAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCAC
780 TAAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCAC
45801214 TTGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATACGAAA
845 TTGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATACGAAA
*
45801279 AAGTAGGCTCCTTATTTTTTTTTCGATATTTCGGTGATAGAAAAAATCATTTTTTGTTCGTTG
910 AAGTAGGCTCCTTA-TTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTCGTTG
*
45801342 AATATGAACCGTGAAATAAACATGAAAGCTACTAACAAAAAAATAATTACATTAAACATAAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
45801407 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
* *
45801472 GTTATCTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATTAATATGTA
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
* *
45801537 TTTATTAAAAGGTTAGATAATTAGACAAAAAATAAATCGTAAATTATTATACTTCCACTACAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
* *
45801602 GGACACGTGCTAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGG
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
45801667 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
* *
45801732 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATTTATCTGCTTG
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
*
45801797 GCAAACATCCTTGCTATCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
456 GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
45801862 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
521 ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
*
45801927 ATACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
586 CTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
* *
45801992 TTGATGCTTAAAGTAAGCTAGTAGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCCCACATT
651 TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCACATT
45802057 GGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
716 GGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
45802122 AAGTTTGGAACCTTACCTCTTGCATAGCGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCA-
781 AAGTTTGGAACCTTACCTCTTGCATAG-GGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCAC
* * *
45802186 TTGTACGACGTGGGCAACGCGAAATGTTCAAAATGGTTCAAACTAGTCATGCCCAAAAATACGAA
845 TTGTACGACGTGCGCAACGCGAAATGTTTAGAAT-GTTCAAACTAGTCATGCCCAAAAATACGAA
* *
45802251 AAAGTAGGCTCCTTATTTTTTTTCGATATTTCGGTGCTAGAAAAAATCATCTTTTGTTTGTTG
909 AAAGTAGGCTCCTTATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTCGTTG
*
45802314 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATTAATTA
1 AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
* * *
45802379 AATTTAGACTCGAATTAAATTCTTAAACTTGAAATCCAACACCAATCAGGTTTTAAGTAATGCAA
66 AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
* *
45802444 GTTATTTATTTCTGCAATAATAACCATTGAATAACATTAATAACACTCGATCTGATCAATATGTA
131 GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
* *
45802509 TTTATTAAAAGGTTAGATAATCAGAAAAAAAATAAACCGTAAATTATTATACTTCCAGTACAGGT
196 TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
* * * *
45802574 GGACATGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGAAACCAATCCTTTGACTCTACTCGA
261 GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
* * * *
45802639 ACGCCTTGGTGGCTGTCTCTCCCAGATTCTTACTCTTCGTTTGACCCTCTATCTCAGCAAGAGAC
326 ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
* * *
45802704 TTGGACTGCATGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTCTAGAGACAATCCACCTGCTTA
391 TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTT-
45802769 GGCAAACATCCTTGCTAGCCACAAGCTTTGAACATAC
455 GGCAAACATCCTTGCTAGCCACAAGCTTTGAACATAC
45802806 TTGTAAGTCT
Statistics
Matches: 4133, Mismatches: 227, Indels: 57
0.94 0.05 0.01
Matches are distributed among these distances:
967 14 0.00
970 35 0.01
971 1597 0.39
972 841 0.20
973 832 0.20
975 1 0.00
976 1 0.00
982 1 0.00
990 1 0.00
991 28 0.01
992 713 0.17
993 68 0.02
994 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (971 bp):
AATATGAACCGTGAAATAAACATGAAAGCTACCAACAAAAAAATAATTACATTAAACATAAATTA
AATTTAGACTCGAATCAAATTCTTAAACTCGAAATCCAACACCAATCAGGTTTTAAGTAACGCAA
GTTATTTATTTCTGCAATAATAACCATTGAATAGCATTAATAACACTCGATTTGATCAATATGTA
TTTATTAAAAGGTTAGATAATCAGACAAAAAATAAACCGTAAATTATTATACTTCCACTACAGGT
GGACACGTGCCAGCGTGACAAGCCATCTGAGAAATAATCGTAACCAATCCTTCGGCTCTACTCGA
ACGCCTTGGTGACTGTCTCTCCCATATTCTTACTCTCCGTTTGACCCTCTATCTCAGCAAGGGAC
TTGGACTGCACGCGTCTTCTTGAAAGACCTAAACCTCCCGCTTTTAGAGACAATCTACCTGCTTG
GCAAACATCCTTGCTAGCCACAAGCTTTGAACATACCCGTTGTTGGAAAAATTGCATTTTACGGA
ACTTTGAGGCATATTCTCAATAGGTAAAGGTACAGAGTTGAATCATAAAATTATGGTTTCATATT
CTACTCCATGAGACCTTTACAACGGTATATTATATGCTCAAAATGGTTTAGCGATGAATGAGAAA
TTGATGCTTAAAGTAAGCTAGTTGAAAATATTTGTTGAGGAAAAGAAAAGCTTAGATCTCACATT
GGTTAAACACCAAGTGTGAGATGTGTTTATATATGGGAACCCTCTTGAAAAATAATTGAATGACT
AAGTTTGGAACCTTACCTCTTGCATAGGGGGTGCAAGTCCAAATCTATCGGGGTTGGGGTGCACT
TGTACGACGTGCGCAACGCGAAATGTTTAGAATGTTCAAACTAGTCATGCCCAAAAATACGAAAA
AGTAGGCTCCTTATTTTTTTTCGATATTTCGGTGATAGAAAAAATCATCTTTTGTTCGTTG
Found at i:45805011 original size:7 final size:7
Alignment explanation
Indices: 45804999--45805028 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
45804989 TCTCTTCAAT
45804999 CTGCATG
1 CTGCATG
45805006 CTGCATG
1 CTGCATG
45805013 CTGCATG
1 CTGCATG
45805020 CTGCATG
1 CTGCATG
45805027 CT
1 CT
45805029 TAGGTCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.27, T:0.30
Consensus pattern (7 bp):
CTGCATG
Found at i:45805053 original size:5 final size:6
Alignment explanation
Indices: 45805039--45805063 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45805029 TAGGTCTTCC
45805039 TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT T
45805064 CCTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:45806496 original size:20 final size:23
Alignment explanation
Indices: 45806444--45806496 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
45806434 ATGTAACTTT
45806444 AAAAAAAATAAAGATGATTTTAAA
1 AAAAAAAATAAAGA-GATTTTAAA
45806468 AAAATAAAATAAA-A-ATTTTAAA
1 AAAA-AAAATAAAGAGATTTTAAA
45806490 AAAAAAA
1 AAAAAAA
45806497 GTGTATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
24 5 0.18
25 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAAAAAAATAAAGAGATTTTAAA
Found at i:45815053 original size:12 final size:13
Alignment explanation
Indices: 45815029--45815053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45815019 CCAAAAGTGC
45815029 TTTGTATTTTTTT
1 TTTGTATTTTTTT
45815042 TTTGTATTTTTT
1 TTTGTATTTTTT
45815054 GAGCTACAAA
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTGTATTTTTTT
Found at i:45816204 original size:9 final size:10
Alignment explanation
Indices: 45816187--45816237 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
45816177 TCATGATAAA
45816187 ATAAAAAAAT
1 ATAAAAAAAT
*
45816197 -TCAAAAAAT
1 ATAAAAAAAT
45816206 ATAAAAAAAT
1 ATAAAAAAAT
*
45816216 AATAATAGAAAT
1 -ATAA-AAAAAT
*
45816228 ATAAATAAAT
1 ATAAAAAAAT
45816238 TATTTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.24
10 13 0.38
11 8 0.24
12 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:45826125 original size:31 final size:31
Alignment explanation
Indices: 45826087--45826152 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
45826077 TTAAGAGTAT
* *
45826087 AAAATTCACAATTAGCATCGGATAATCATCC
1 AAAATTCACAATTAACATCGAATAATCATCC
* * *
45826118 AAAATTCACGATTAACATTGAATAATCATTC
1 AAAATTCACAATTAACATCGAATAATCATCC
45826149 AAAA
1 AAAA
45826153 GCGCGTTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (31 bp):
AAAATTCACAATTAACATCGAATAATCATCC
Found at i:45826281 original size:18 final size:19
Alignment explanation
Indices: 45826240--45826282 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
45826230 GTATATTAAC
45826240 ATATATGTTATTAAAAACT
1 ATATATGTTATTAAAAACT
* *
45826259 A-ATATTTTATTATAAA-T
1 ATATATGTTATTAAAAACT
45826276 ATATATG
1 ATATATG
45826283 AAAAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.85
19 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
ATATATGTTATTAAAAACT
Found at i:45827843 original size:15 final size:16
Alignment explanation
Indices: 45827823--45827855 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
45827813 GAATGGCTCA
*
45827823 TTAATTACT-TAAAGT
1 TTAATTAATATAAAGT
45827838 TTAATTAATATAAAGT
1 TTAATTAATATAAAGT
45827854 TT
1 TT
45827856 CGTAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
TTAATTAATATAAAGT
Found at i:45828966 original size:37 final size:37
Alignment explanation
Indices: 45828901--45829010 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
45828891 TACGTATGAT
* *
45828901 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
45828936 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
45828973 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
45829010 C
1 C
45829011 GAAGCTATCA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:45836902 original size:43 final size:43
Alignment explanation
Indices: 45836854--45836942 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
45836844 TACTATGCTA
45836854 TTAAAGTCAATTTTCATTTCAGTTACATGTCGTTAATTCAATG
1 TTAAAGTCAATTTTCATTTCAGTTACATGTCGTTAATTCAATG
45836897 TTAAAGTCAATTTTCATTTCAGTTACATGTCGTTAATTCAATG
1 TTAAAGTCAATTTTCATTTCAGTTACATGTCGTTAATTCAATG
45836940 TTA
1 TTA
45836943 TTGTACATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (43 bp):
TTAAAGTCAATTTTCATTTCAGTTACATGTCGTTAATTCAATG
Found at i:45837252 original size:18 final size:18
Alignment explanation
Indices: 45837231--45837266 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45837221 TTTACAAGAA
*
45837231 AAAATAATTTTATTTTTT
1 AAAATAATTTAATTTTTT
*
45837249 AAAATTATTTAATTTTTT
1 AAAATAATTTAATTTTTT
45837267 TCATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAAATAATTTAATTTTTT
Found at i:45854295 original size:31 final size:27
Alignment explanation
Indices: 45854251--45854334 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 27
45854241 AATCTCAAAA
45854251 TAATACATT-AACTTTGATTTAGTGTGCAATT
1 TAATAC-TTGAACTTTGATTT-G-GTG-AA-T
45854282 TAATACTTGAACTTTGATTTGGTGAAT
1 TAATACTTGAACTTTGATTTGGTGAAT
*
45854309 TATATACATGTAACTTTGATTATGGT
1 TA-ATACTTG-AACTTTGATT-TGGT
45854335 TCAAATGCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
27 3 0.06
28 8 0.17
29 13 0.27
30 7 0.15
31 17 0.35
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (27 bp):
TAATACTTGAACTTTGATTTGGTGAAT
Found at i:45858544 original size:26 final size:25
Alignment explanation
Indices: 45858481--45858547 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
45858471 TTCAAATATG
*
45858481 ATTAAACTTAATCACTTTAATATTAA
1 ATTAAACTTAAT-ATTTTAATATTAA
* *
45858507 ATTTAA-TCTAATATTTATAATATTAT
1 ATTAAACT-TAATATTT-TAATATTAA
45858533 ATTAAACTTAATATT
1 ATTAAACTTAATATT
45858548 AAATCTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 4 0.12
26 29 0.85
27 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTAAACTTAATATTTTAATATTAA
Found at i:45859776 original size:17 final size:18
Alignment explanation
Indices: 45859754--45859787 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
45859744 AAAACTCTCA
45859754 AAAATAAACC-TTATTTT
1 AAAATAAACCTTTATTTT
45859771 AAAATAAACCTTTATTT
1 AAAATAAACCTTTATTT
45859788 AAAGTCAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAAACCTTTATTTT
Found at i:45867159 original size:13 final size:14
Alignment explanation
Indices: 45867141--45867181 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
45867131 TCCATTTCAA
45867141 ATACAGATA-ACAG
1 ATACAGATATACAG
45867154 ATACAGATATACAG
1 ATACAGATATACAG
*
45867168 AT-CAAATATACAG
1 ATACAGATATACAG
45867181 A
1 A
45867182 ATCTTACCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (14 bp):
ATACAGATATACAG
Found at i:45867760 original size:5 final size:5
Alignment explanation
Indices: 45867750--45867775 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45867740 CTCGAAAATT
45867750 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
45867776 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:45881703 original size:18 final size:17
Alignment explanation
Indices: 45881669--45881763 Score: 63
Period size: 17 Copynumber: 5.6 Consensus size: 17
45881659 ATTTTAATAG
45881669 ATTTAATATTAAATTAA
1 ATTTAATATTAAATTAA
*
45881686 ATTTAATACTTAACTT-A
1 ATTTAATA-TTAAATTAA
* **
45881703 A--TAGTATTTTATT-A
1 ATTTAATATTAAATTAA
* *
45881717 ATTTAATATTAAAGTGATT
1 ATTTAATATTAAA-TTA-A
*
45881736 ATCTTAATATTAAATTTA
1 AT-TTAATATTAAATTAA
45881754 ATTTAATATT
1 ATTTAATATT
45881764 TATCTTGTAG
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
14 6 0.10
15 4 0.07
16 7 0.12
17 19 0.33
18 8 0.14
19 3 0.05
20 11 0.19
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAATATTAAATTAA
Found at i:45881812 original size:62 final size:58
Alignment explanation
Indices: 45881739--45881854 Score: 160
Period size: 58 Copynumber: 1.9 Consensus size: 58
45881729 AGTGATTATC
* * *
45881739 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAAT-TTTAT-AT-T-GATAAATATTATATTAATTTAATAAGAT
*
45881801 TTAATATTAAATTTAATCTAATTTTATATTGATTAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATTTTATATTGATAAATATTATATTAATTTAATA
45881855 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 22 0.44
59 1 0.02
60 1 0.02
61 5 0.10
62 21 0.42
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (58 bp):
TTAATATTAAATTTAATCTAATTTTATATTGATAAATATTATATTAATTTAATAAGAT
Found at i:45881842 original size:15 final size:15
Alignment explanation
Indices: 45881819--45881867 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
45881809 AAATTTAATC
*
45881819 TAATTTTATATTGAT
1 TAATATTATATTGAT
*
45881834 TAATATTATATTAATT
1 TAATATTATATTGA-T
* *
45881850 TAATATTAAAGTGAT
1 TAATATTATATTGAT
45881865 TAA
1 TAA
45881868 GTTTAATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
TAATATTATATTGAT
Found at i:45881848 original size:11 final size:11
Alignment explanation
Indices: 45881784--45881858 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
45881774 ATAAATATTC
45881784 TATTAATTTAA
1 TATTAATTTAA
45881795 TA--AGATTTAA
1 TATTA-ATTTAA
45881805 TATTAAATTTAA
1 TATT-AATTTAA
*
45881817 T-CTAATTTTATA
1 TATTAA-TTTA-A
45881829 TTGATTAATATT-A
1 -T-ATTAAT-TTAA
45881842 TATTAATTTAA
1 TATTAATTTAA
45881853 TATTAA
1 TATTAA
45881859 AGTGATTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 22
0.68 0.03 0.29
Matches are distributed among these distances:
9 1 0.02
10 12 0.24
11 20 0.39
12 9 0.18
13 3 0.06
14 1 0.02
15 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:45889410 original size:43 final size:43
Alignment explanation
Indices: 45889344--45889513 Score: 208
Period size: 43 Copynumber: 4.0 Consensus size: 43
45889334 ATAGGATTTC
45889344 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
45889387 CGACT-TGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
*
45889430 C-ATATTTGATT-CGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* *
45889471 CGATATGTGATTACATGTAAGACAACGTCTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
45889514 TGTACGAGTC
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 28 0.26
42 16 0.15
43 60 0.55
44 5 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:45889501 original size:84 final size:84
Alignment explanation
Indices: 45889356--45889513 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
45889346 ATATGTGTTA
* * * *
45889356 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACAACGTCTGGGA
45889421 CATTGGCATCATATTTGAT
66 CATTGGCATCATATTTGAT
45889440 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACAACGTCTG
1 TCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACAACGTCTG
*
45889502 GGACGTTGGCAT
63 GGACATTGGCAT
45889514 TGTACGAGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.95
85 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACAACGTCTGGGA
CATTGGCATCATATTTGAT
Found at i:45894625 original size:71 final size:72
Alignment explanation
Indices: 45894462--45894625 Score: 190
Period size: 71 Copynumber: 2.3 Consensus size: 72
45894452 TTTGATGCAA
* ** *** *
45894462 CTCACTCAAGCTGTCGAGAA-TCTACAACTTATGTTGGATCTTAGTCATTGCTAAATAATGATTT
1 CTCACTCAAGCTGTCGAGAATTCTACAACTTATGTTGGATCTCAACCACCACTAAATAATGATTC
*
45894526 AATGCTT
66 AATGATT
* * *
45894533 CTCATTCAAGCTGTTGAGAATTC-GCAACTTATGTTGGATCTCAACCACCACTAAATAATGATTC
1 CTCACTCAAGCTGTCGAGAATTCTACAACTTATGTTGGATCTCAACCACCACTAAATAATGATTC
*
45894597 GAT-ATT
66 AATGATT
45894603 GCTCACTCAAGCTGTCGAGAATT
1 -CTCACTCAAGCTGTCGAGAATT
45894626 TGAAAGATTA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
70 2 0.03
71 73 0.95
72 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (72 bp):
CTCACTCAAGCTGTCGAGAATTCTACAACTTATGTTGGATCTCAACCACCACTAAATAATGATTC
AATGATT
Found at i:45896037 original size:28 final size:26
Alignment explanation
Indices: 45896005--45896072 Score: 95
Period size: 25 Copynumber: 2.6 Consensus size: 26
45895995 TTGTGGAAAA
*
45896005 TTTCTTTCTTGTGATTTTTAGAAATAGT
1 TTTC-TTCTTGT-ATTTTTAGAAAAAGT
45896033 TTTCTTCTT-TATTTTTAGAAAAAGT
1 TTTCTTCTTGTATTTTTAGAAAAAGT
45896058 TTTCTTCTTG-ATTTT
1 TTTCTTCTTGTATTTT
45896073 CTTGAAGGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 28 0.74
26 1 0.03
27 5 0.13
28 4 0.11
ACGTcount: A:0.21, C:0.09, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTGTATTTTTAGAAAAAGT
Found at i:45896046 original size:25 final size:25
Alignment explanation
Indices: 45896016--45896072 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
45896006 TTCTTTCTTG
*
45896016 TGATTTTTAGAAATAGTTTTCTTCT
1 TGATTTTTAGAAAAAGTTTTCTTCT
*
45896041 TTATTTTTAGAAAAAGTTTTCTTCT
1 TGATTTTTAGAAAAAGTTTTCTTCT
45896066 TGATTTT
1 TGATTTT
45896073 CTTGAAGGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.58
Consensus pattern (25 bp):
TGATTTTTAGAAAAAGTTTTCTTCT
Found at i:45896299 original size:7 final size:7
Alignment explanation
Indices: 45896268--45896297 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
45896258 TTTTTTTTCT
45896268 TTATTTA
1 TTATTTA
45896275 TTATTTA
1 TTATTTA
45896282 TTATTTA
1 TTATTTA
*
45896289 TTCTTTA
1 TTATTTA
45896296 TT
1 TT
45896298 CTCAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:45896661 original size:19 final size:19
Alignment explanation
Indices: 45896637--45896690 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
45896627 CTATTTCCCC
45896637 AAAAAATTGAAAAAAAA-AT
1 AAAAAATT-AAAAAAAAGAT
45896656 AAAAAATTAAAAAAAAGAT
1 AAAAAATTAAAAAAAAGAT
*
45896675 AAAAAAATAAAAAAAA
1 AAAAAATTAAAAAAAA
45896691 TTGTGGGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 8 0.24
19 25 0.76
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (19 bp):
AAAAAATTAAAAAAAAGAT
Found at i:45897678 original size:17 final size:18
Alignment explanation
Indices: 45897648--45897682 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
45897638 CATTTTAATA
45897648 TTAAATTAAGTATTAAAT
1 TTAAATTAAGTATTAAAT
*
45897666 TTAATTTAA-TATTAAAT
1 TTAAATTAAGTATTAAAT
45897683 CTATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTAAATTAAGTATTAAAT
Found at i:45900794 original size:47 final size:47
Alignment explanation
Indices: 45900719--45900812 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
45900709 AACGCTAGAC
* *
45900719 CACCTCCACATGTATTAATCAAATCCTAAATTATCTTTTAGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
* * *
45900766 CACCTCCATATGCATTAATCAAGCCCTAAATTATCTTTTGGAAGGGG
1 CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
45900813 AATCGAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (47 bp):
CACCTCCACATGCATTAATCAAACCCTAAATTATCTTTTAGAAGGGG
Found at i:45909307 original size:31 final size:31
Alignment explanation
Indices: 45909224--45909307 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
45909214 ATTAAATTAT
* **
45909224 CCCGGGTTGCCCGACAACGATAATTCACCAC
1 CCCGGGTTGCCCGACAACGATGACCCACCAC
* *
45909255 CCCGGGTTGCTCGACAACGATGACCCGCCAC
1 CCCGGGTTGCCCGACAACGATGACCCACCAC
45909286 CCCGGGTTGCCCGACAACGATG
1 CCCGGGTTGCCCGACAACGATG
45909308 GCTTACTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.14
Consensus pattern (31 bp):
CCCGGGTTGCCCGACAACGATGACCCACCAC
Found at i:45909541 original size:35 final size:35
Alignment explanation
Indices: 45909458--45909621 Score: 193
Period size: 35 Copynumber: 4.6 Consensus size: 35
45909448 TAACACAATG
* *
45909458 ACATGCTTAACATGCGAATCAAAATTAGAAATAATG
1 ACATGCTTAACATGCGAATCAAAATCAG-AATAATA
* * *
45909494 GCATGCTTAACATGCGAGTCAAAATCAGATTAATA
1 ACATGCTTAACATGCGAATCAAAATCAGAATAATA
** *
45909529 ACATGCTTAACATGCGAGCCAAAATCAGATTAATA
1 ACATGCTTAACATGCGAATCAAAATCAGAATAATA
* * *
45909564 GCATGCTTAACACGCGAATCAAAATATCAGAATATTA
1 ACATGCTTAACATGCGAATC-AAA-ATCAGAATAATA
*
45909601 ACATGTTTAACATGCGAATCA
1 ACATGCTTAACATGCGAATCA
45909622 TAACATCAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
35 54 0.49
36 29 0.26
37 27 0.25
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (35 bp):
ACATGCTTAACATGCGAATCAAAATCAGAATAATA
Found at i:45911959 original size:36 final size:36
Alignment explanation
Indices: 45911919--45911994 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
45911909 ATATCGATAT
* * *
45911919 TCCAATTGAAACACACCATATGCTCATAAGAGCTAG
1 TCCAACTGAAACACACCAAATGCTCATAAGAGCCAG
45911955 TCCAACTGAAACACACCAAATGCTCATAAGAGCCAG
1 TCCAACTGAAACACACCAAATGCTCATAAGAGCCAG
45911991 TCCA
1 TCCA
45911995 CCCAATAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.18
Consensus pattern (36 bp):
TCCAACTGAAACACACCAAATGCTCATAAGAGCCAG
Found at i:45913395 original size:62 final size:61
Alignment explanation
Indices: 45913324--45913448 Score: 196
Period size: 61 Copynumber: 2.0 Consensus size: 61
45913314 ACCACTATTC
* * * *
45913324 TGTCACCACTAAAAATCAGGTTGTTATAAGGGGACAAAGGTATGGAAATGGGATAATGTGAG
1 TGTCACCACTAAAAATCAGGTTGTTACAA-GGGACAAAGGCATGAAAATGGGATAATGGGAG
*
45913386 TGTCACCACTAAAAATCGGGTTGTTACAAGGGACAAAGGCATGAAAATGGGATAATGGGAG
1 TGTCACCACTAAAAATCAGGTTGTTACAAGGGACAAAGGCATGAAAATGGGATAATGGGAG
45913447 TG
1 TG
45913449 AAAATGGGAG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
61 31 0.53
62 27 0.47
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (61 bp):
TGTCACCACTAAAAATCAGGTTGTTACAAGGGACAAAGGCATGAAAATGGGATAATGGGAG
Found at i:45917338 original size:16 final size:16
Alignment explanation
Indices: 45917313--45917343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45917303 AAAAGAAAAC
45917313 ACAAAGAGTTGTATTG
1 ACAAAGAGTTGTATTG
*
45917329 ACAAATAGTTGTATT
1 ACAAAGAGTTGTATT
45917344 AAATCAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
ACAAAGAGTTGTATTG
Found at i:45917908 original size:21 final size:22
Alignment explanation
Indices: 45917869--45917909 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
45917859 CAGTCAAATG
*
45917869 ATATCTCCACCCATAAATGCCT
1 ATATCTCCACCCAAAAATGCCT
*
45917891 ATATC-CCATCCAAAAATGC
1 ATATCTCCACCCAAAAATGC
45917910 ATTGTAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.34, G:0.05, T:0.24
Consensus pattern (22 bp):
ATATCTCCACCCAAAAATGCCT
Found at i:45918436 original size:3 final size:3
Alignment explanation
Indices: 45918421--45918486 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
45918411 CATGGCATTG
*
45918421 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
45918469 TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
45918487 AAGGGAGAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:45922841 original size:20 final size:19
Alignment explanation
Indices: 45922813--45922882 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
45922803 TTAAAATTAC
*
45922813 AAAAATTATTAAAAATCAAT
1 AAAATTTATTAAAAAT-AAT
45922833 AAAATTTA-T-AAAAT-A-
1 AAAATTTATTAAAAATAAT
* * *
45922848 AAAATTTCTTTAAAATATT
1 AAAATTTATTAAAAATAAT
45922867 AAAAATTTATTAAAAA
1 -AAAATTTATTAAAAA
45922883 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.17
16 2 0.05
17 5 0.12
18 5 0.12
19 1 0.03
20 20 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTTATTAAAAATAAT
Found at i:45923189 original size:20 final size:21
Alignment explanation
Indices: 45923138--45923182 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
45923128 AAAAAAAAAT
45923138 TATAAC-ATTTAAAATTTTTC
1 TATAACTATTTAAAATTTTTC
* *
45923158 TATAACTTTTTAATATTTTT-
1 TATAACTATTTAAAATTTTTC
45923178 TATAA
1 TATAA
45923183 TAATTTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TATAACTATTTAAAATTTTTC
Found at i:45923933 original size:16 final size:17
Alignment explanation
Indices: 45923912--45923954 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
45923902 TCTTTCGTAC
45923912 ATTTGTTTATTGA-TAA
1 ATTTGTTTATTGAGTAA
45923928 ATTTGTTTATTGAGTTAA
1 ATTTGTTTATTGAG-TAA
*
45923946 ATTTTTTTA
1 ATTTGTTTA
45923955 GATAATTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (17 bp):
ATTTGTTTATTGAGTAA
Found at i:45925456 original size:26 final size:26
Alignment explanation
Indices: 45925426--45925495 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
45925416 ATGCATATTT
45925426 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
45925452 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
45925481 AATTATTTAATATTT
1 AATTATTT-ATATTT
45925496 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 7 0.19
29 18 0.49
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:45925465 original size:16 final size:16
Alignment explanation
Indices: 45925444--45925493 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
45925434 ATATTTAGTC
45925444 ATATAATAAATTATTA
1 ATATAATAAATTATTA
45925460 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
45925473 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
45925490 ATAT
1 ATAT
45925494 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:45925469 original size:29 final size:30
Alignment explanation
Indices: 45925436--45925493 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
45925426 AATTATTTAT
45925436 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
45925465 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
45925494 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:45925583 original size:15 final size:15
Alignment explanation
Indices: 45925563--45925619 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
45925553 ATTCAATATT
45925563 AATATTTTAATAATA
1 AATATTTTAATAATA
* *
45925578 AATATTTATTACAATTATG
1 AATA-TT-TT--AATAATA
*
45925597 AATATATTAATAATA
1 AATATTTTAATAATA
45925612 AATATTTT
1 AATATTTT
45925620 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 9 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:45935009 original size:19 final size:19
Alignment explanation
Indices: 45934985--45935025 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
45934975 TAGTCGTTAC
45934985 CTTAGCAGGATCTCTCAAT
1 CTTAGCAGGATCTCTCAAT
*
45935004 CTTAGCAGGATCTCTCCAT
1 CTTAGCAGGATCTCTCAAT
45935023 CTT
1 CTT
45935026 CTACTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (19 bp):
CTTAGCAGGATCTCTCAAT
Found at i:45935614 original size:23 final size:21
Alignment explanation
Indices: 45935584--45935627 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
45935574 TATATTCTTT
*
45935584 GTTATATTCTATCCTTATGTTA
1 GTTATATTATATCCTT-TGTTA
*
45935606 GTTAGTATTATATTCTTTGTTA
1 GTTA-TATTATATCCTTTGTTA
45935628 ATTTTAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
GTTATATTATATCCTTTGTTA
Found at i:45936072 original size:30 final size:30
Alignment explanation
Indices: 45936037--45936098 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
45936027 TATTTTATTG
45936037 TTAATTTTGTTATTATTTTAAAGAAATTTA
1 TTAATTTTGTTATTATTTTAAAGAAATTTA
* *
45936067 TTAATTTTGTTATTATTTTAGAGACATTTA
1 TTAATTTTGTTATTATTTTAAAGAAATTTA
45936097 TT
1 TT
45936099 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGAAATTTA
Found at i:45946340 original size:71 final size:72
Alignment explanation
Indices: 45946202--45946343 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 72
45946192 CGCCGCAAAA
** * * *
45946202 TATCTTAACCAAAACGCATCGTTTCGGTCTTGATGTATCCTAAAATTAGTGGCGCTTACGGGGAA
1 TATCTTAACCAAAACGCAGAGTTTCGGTCTTGAGGTATCCTAAAATTAGTGCCGCTTACGGGAAA
45946267 ACGCCGT
66 ACGCCGT
** * * *
45946274 TATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATGTTAGAATTAGTGCCGTTTATGGGAAA
1 TATCTTAACCAAAACGCAGAGTTTCGGTCTTGAGGTATCCTAAAATTAGTGCCGCTTACGGGAAA
45946338 ACGCCG
66 ACGCCG
45946344 CAAAAGGACA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
71 38 0.63
72 22 0.37
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (72 bp):
TATCTTAACCAAAACGCAGAGTTTCGGTCTTGAGGTATCCTAAAATTAGTGCCGCTTACGGGAAA
ACGCCGT
Found at i:45946418 original size:185 final size:184
Alignment explanation
Indices: 45946092--45946455 Score: 527
Period size: 185 Copynumber: 2.0 Consensus size: 184
45946082 CCGCAAAATC
* * *
45946092 TCTTAACCAAAACGCAGCGTTTTCGTCTTGATGTATACTAGAATTAGTGGCGATTATGGGAAAAC
1 TCTTAACCAAAACGCAGAGTTTTCGTCTTGAGGTATACTAGAATTAGTGCCGATTATGGGAAAAC
* * *
45946157 GCCGCTAAATCGTATTAGCGGCGTTTTCCGATAAGCGCCGCAAAATATCTTAACCAAAACGCATC
66 GCCGCAAAAACGTATTAGCGGCGTTTTCCGATAAGCGCCGCAAAATATCTGAACCAAAACGCATC
*
45946222 GTTTCGGTCTTGATGTATCCTAAAATTAGTGGCGCTTACGGGGAAACGCCGTTA
131 GTTTCGGTCTTGATGTATACTAAAATTAGTGGCGCTTACGGGGAAACGCCGTTA
* ** *
45946276 TCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATGTTAGAATTAGTGCCGTTTATGGGAAAAC
1 TCTTAACCAAAACGCAGAGTTTTCGTCTTGAGGTATACTAGAATTAGTGCCGATTATGGGAAAAC
**
45946340 GCCGCAAAAGGACAGTATTAGCGGCGCTTTTTGGA-AA-CGCCGCAAAATATCTGAACCAAAACG
66 GCCGCAAAA--AC-GTATTAGCGGCG-TTTTCCGATAAGCGCCGCAAAATATCTGAACCAAAACG
* * *
45946403 CATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGTGAAACGC
127 CATCGTTTCGGTCTTGATGTATACTAAAATTAGTGGCGCTTACGGGGAAACGC
45946456 TACTAAAAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
183 47 0.29
184 18 0.11
185 75 0.47
186 14 0.09
187 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (184 bp):
TCTTAACCAAAACGCAGAGTTTTCGTCTTGAGGTATACTAGAATTAGTGCCGATTATGGGAAAAC
GCCGCAAAAACGTATTAGCGGCGTTTTCCGATAAGCGCCGCAAAATATCTGAACCAAAACGCATC
GTTTCGGTCTTGATGTATACTAAAATTAGTGGCGCTTACGGGGAAACGCCGTTA
Found at i:45946454 original size:114 final size:113
Alignment explanation
Indices: 45946274--45946786 Score: 588
Period size: 114 Copynumber: 4.5 Consensus size: 113
45946264 GAAACGCCGT
* ** * * *
45946274 TATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATGTTAGAATTAGTGCCGTTTATGGGAAA
1 TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGG-AA
* * *
45946338 ACGCCGCAAAAGGACAGTATTAGCGGCGCTTTTTGGAAACGCCGCAAAA
65 ACGCCGCAAAAGAATAGTATTAGCGGCGCTTTGTGGAAACGCCGCAAAA
* **
45946387 TATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGTGAA
1 TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGG-GAA
** * * * * *
45946452 ACGCTACTAAAA-ATTTAGTATTAGCGGCGATTCGTGGCTAGCGCCGCAAAA
65 ACGCCGC-AAAAGA-ATAGTATTAGCGGCGCTTTGTGG-AAACGCCGCAAAA
* *
45946503 TATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATA-TAAAATTAGTGGCGCTTACGGGAAA
1 TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAA
* * * **
45946567 CCGCCGCGAAAGAATGGTAATAGCGGCGCTTTGTGAGAAGTGCCGCAAAA
66 -CGCCGCAAAAGAATAGTATTAGCGGCGCTTTGTG-GAAACGCCGCAAAA
*
45946617 TATCTTAACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAA
1 TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAA
** * * *
45946682 CGCCGTTAAAGCATAGTATTAGCGGTGCTTTGCT-AAAAGCGCCGCAAAA
66 CGCCGCAAAAGAATAGTATTAGCGGCGCTTTG-TGGAAA-CGCCGCAAAA
* *
45946731 TATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTAT-GTAAGAATTAGTGGCGCTT
1 TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACT-AGAATTAGTGGCGCTT
45946787 TTTGTAAGCG
Statistics
Matches: 341, Mismatches: 47, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
112 1 0.00
113 51 0.15
114 167 0.49
115 74 0.22
116 48 0.14
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (113 bp):
TATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAA
CGCCGCAAAAGAATAGTATTAGCGGCGCTTTGTGGAAACGCCGCAAAA
Found at i:45946676 original size:230 final size:224
Alignment explanation
Indices: 45946274--45946786 Score: 679
Period size: 230 Copynumber: 2.2 Consensus size: 224
45946264 GAAACGCCGT
* * * * *
45946274 TATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATGTTAGAATTAGTGCCGTTTATGGGAAAA
1 TATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTAT-ATAAAATTAGTGGCGCTTACGGGAAAA
* * *
45946339 CGCCGCAAAAGGACAGTATTAGCGGCGCTTTTTGGAAACGCCGCAAAATATCTGAACCAAAACGC
65 CGCCGCAAAAGAACAGTAATAGCGGCGCTTTGTGGAAACGCCGCAAAATATCTGAACCAAAACGC
* **
45946404 ATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGTGAAACGCTAC-TAAAAATTT
130 ATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGG-GAAACGC--CGTAAAAACAT
45946468 AGTATTAGCGGCGATTCGTGGCT-AGCGCCGCAAAA
192 AGTATTAGCGGCGATT--T-GCTAAGCGCCGCAAAA
* * *
45946503 TATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATATAAAATTAGTGGCGCTTACGGGAAAC
1 TATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATAAAATTAGTGGCGCTTACGGGAAAA
* ** ** *
45946568 CGCCGCGAAAGAATGGTAATAGCGGCGCTTTGTGAGAAGTGCCGCAAAATATCTTAACCAAAACG
65 CGCCGCAAAAGAACAGTAATAGCGGCGCTTTGTG-GAAACGCCGCAAAATATCTGAACCAAAACG
* *
45946633 CATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAACGCCGTTAAAGCATAG
129 CATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAACGCCGTAAAAACATAG
* *
45946698 TATTAGCGGTGCTTTGCTAAAAGCGCCGCAAAA
194 TATTAGCGGCGATTTGCT--AAGCGCCGCAAAA
*
45946731 TATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATGTAAGAATTAGTGGCGCTT
1 TATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATAA-AATTAGTGGCGCTT
45946787 TTTGTAAGCG
Statistics
Matches: 250, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
225 3 0.01
226 1 0.00
227 19 0.08
228 65 0.26
229 76 0.30
230 86 0.34
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (224 bp):
TATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATAAAATTAGTGGCGCTTACGGGAAAAC
GCCGCAAAAGAACAGTAATAGCGGCGCTTTGTGGAAACGCCGCAAAATATCTGAACCAAAACGCA
TAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAACGCCGTAAAAACATAGTA
TTAGCGGCGATTTGCTAAGCGCCGCAAAA
Found at i:45946859 original size:75 final size:74
Alignment explanation
Indices: 45946718--45946861 Score: 193
Period size: 74 Copynumber: 1.9 Consensus size: 74
45946708 GCTTTGCTAA
* *
45946718 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATGTAAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTGAACCAAAACGCAGAGTTTGGTCTTGAGGTATCTAAGAATTAGTGGC
45946783 GCTTTTTGT
66 GCTTTTTGT
* * * *
45946792 AAGCGCCGCAAAATATCTGAACGAAAACGCA-ACGTTTTGGTCTTGATGTATACT-TGATTTAGT
1 AAGCGCCGCAAAATATCTGAACCAAAACGCAGA-G-TTTGGTCTTGAGGTAT-CTAAGAATTAGT
45946855 GGCGCTT
63 GGCGCTT
45946862 ACGATGAAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 1 0.02
74 30 0.49
75 29 0.48
76 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (74 bp):
AAGCGCCGCAAAATATCTGAACCAAAACGCAGAGTTTGGTCTTGAGGTATCTAAGAATTAGTGGC
GCTTTTTGT
Found at i:45946935 original size:189 final size:189
Alignment explanation
Indices: 45946608--45946976 Score: 512
Period size: 188 Copynumber: 2.0 Consensus size: 189
45946598 TGTGAGAAGT
*
45946608 GCCGCAAAATATCTTAACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCT
1 GCCGCAAAATATCTGAACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCT
* * * *
45946673 TACGGGAAACGCCGTTAAAGCATAGTATTAGCGGTGCTTTGCTAAAAGCGCCGCAAAATATCTTA
66 TACGGGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGCTAAAAGCGCCGCAAAATACCTTA
* *
45946738 ACCAAAACGCAGAG-TTTGGTCTTGAGGTAT-GTAAGAATTAGTGGCGCTTTTTGTAAGC
131 AACAAAACGCAGAGTTTTGGTCTTGAGGTATACTAA-AATTAGTGGCGCTTTTTGTAAGC
* * *
45946796 GCCGCAAAATATCTGAACGAAAACGCA-ACGTTTTGGTCTTGATGTATACTTGATTTAGTGGCGC
1 GCCGCAAAATATCTGAACCAAAACGCATA-GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
* *** *
45946860 TTACGATGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTG-TGGCTATCGCCGCAAAATACC
65 TTACG-GGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGCT-AAAAGCGCCGCAAAATACC
* **
45946924 TTAAACAAAACGCAGCGTTTTGGTCTTGATTTATACTAAAATTAGTGGCGCTT
128 TTAAACAAAACGCAGAGTTTTGGTCTTGAGGTATACTAAAATTAGTGGCGCTT
45946977 AGAGGAAACC
Statistics
Matches: 158, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
187 1 0.01
188 64 0.41
189 62 0.39
190 28 0.18
191 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (189 bp):
GCCGCAAAATATCTGAACCAAAACGCATAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCT
TACGGGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGCTAAAAGCGCCGCAAAATACCTTA
AACAAAACGCAGAGTTTTGGTCTTGAGGTATACTAAAATTAGTGGCGCTTTTTGTAAGC
Found at i:45947320 original size:7 final size:7
Alignment explanation
Indices: 45947310--45947379 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
45947300 AGAGTTTTGA
45947310 GTTTAGG
1 GTTTAGG
*
45947317 GTTTATG
1 GTTTAGG
* *
45947324 ATGTA-G
1 GTTTAGG
*
45947330 GTTTTGG
1 GTTTAGG
45947337 TGTTTAGG
1 -GTTTAGG
*
45947345 GTTTAAG
1 GTTTAGG
*
45947352 GTTTAAG
1 GTTTAGG
45947359 GTTTAGG
1 GTTTAGG
*
45947366 GTTTGGG
1 GTTTAGG
45947373 GTTTAGG
1 GTTTAGG
45947380 CTGCTTTAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 3 0.06
7 41 0.82
8 6 0.12
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:45947349 original size:35 final size:35
Alignment explanation
Indices: 45947310--45947379 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
45947300 AGAGTTTTGA
* * * *
45947310 GTTTAGGGTTTATGATGTAGGTTTTGGTGTTTAGG
1 GTTTAAGGTTTAAGATGTAGGGTTTGGGGTTTAGG
* *
45947345 GTTTAAGGTTTAAGGTTTAGGGTTTGGGGTTTAGG
1 GTTTAAGGTTTAAGATGTAGGGTTTGGGGTTTAGG
45947380 CTGCTTTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (35 bp):
GTTTAAGGTTTAAGATGTAGGGTTTGGGGTTTAGG
Found at i:45949243 original size:15 final size:15
Alignment explanation
Indices: 45949223--45949253 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
45949213 TTCTTATATT
45949223 GCATTAAGTTGTTTC
1 GCATTAAGTTGTTTC
45949238 GCATTAAGTTGTTTC
1 GCATTAAGTTGTTTC
45949253 G
1 G
45949254 ATTGGTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (15 bp):
GCATTAAGTTGTTTC
Found at i:45949619 original size:12 final size:13
Alignment explanation
Indices: 45949580--45949616 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
45949570 GCTGTTTTTC
*
45949580 TTTAACATATATT
1 TTTAATATATATT
45949593 TTTAATATATATT
1 TTTAATATATATT
45949606 TTTAAGTATAT
1 TTTAA-TATAT
45949617 TTTACATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (13 bp):
TTTAATATATATT
Found at i:45949679 original size:13 final size:13
Alignment explanation
Indices: 45949663--45949752 Score: 74
Period size: 13 Copynumber: 6.8 Consensus size: 13
45949653 TTACTAAAAT
*
45949663 TTACTTTAATATA
1 TTACTTAAATATA
* *
45949676 TTACTTGAATATG
1 TTACTTAAATATA
*
45949689 TTACTTAAATAAA
1 TTACTTAAATATA
*
45949702 TTACTTAAATACA
1 TTACTTAAATATA
*
45949715 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
45949729 TTGGTTAAATTTA
1 TTACTTAAATATA
45949742 TTACTTAAATA
1 TTACTTAAATA
45949753 AATCAGTACC
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
12 3 0.05
13 48 0.81
14 5 0.08
15 3 0.05
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:45950529 original size:9 final size:9
Alignment explanation
Indices: 45950504--45951087 Score: 251
Period size: 9 Copynumber: 66.7 Consensus size: 9
45950494 CTTATATATA
45950504 AACTTACAT
1 AACTTACAT
45950513 AA--TACAT
1 AACTTACAT
45950520 AACTTACAT
1 AACTTACAT
*
45950529 AACTTATAT
1 AACTTACAT
*
45950538 AGAACTTATAT
1 --AACTTACAT
*
45950549 AACAACTTGCAT
1 ---AACTTACAT
45950561 AACTTACAT
1 AACTTACAT
*
45950570 AA-TAACATAAT
1 AACTTAC---AT
*
45950581 AACGTACAT
1 AACTTACAT
*
45950590 -AC-TATAT
1 AACTTACAT
* * *
45950597 AGCCTACGT
1 AACTTACAT
* *
45950606 AAATTGCAT
1 AACTTACAT
*
45950615 AACTCACAT
1 AACTTACAT
*
45950624 AA--TACAC
1 AACTTACAT
45950631 AACTTACAT
1 AACTTACAT
* *
45950640 AACTAAAAT
1 AACTTACAT
45950649 AACTTACAT
1 AACTTACAT
45950658 AA--TACAT
1 AACTTACAT
45950665 AACTTACATT
1 AACTTACA-T
*
45950675 AATATTATACAT
1 -A-ACT-TACAT
45950687 AACTTACAT
1 AACTTACAT
45950696 AACTTA-ATT
1 AACTTACA-T
*
45950705 AATACTAAACAT
1 -A-ACT-TACAT
*
45950717 AACTTGTCA-
1 AACTT-ACAT
*
45950726 GACTTACAT
1 AACTTACAT
45950735 AACTTACAT
1 AACTTACAT
*
45950744 AA--TACAC
1 AACTTACAT
*
45950751 AACTTACAC
1 AACTTACAT
*
45950760 AACTTACAC
1 AACTTACAT
45950769 AACTTACAT
1 AACTTACAT
45950778 AACTTA-ATT
1 AACTTACA-T
45950787 AA-TTA-AT
1 AACTTACAT
*
45950794 -ACTAAACAT
1 AACT-TACAT
*
45950803 AACTTGTCA-
1 AACTT-ACAT
*
45950812 GACTTACAT
1 AACTTACAT
45950821 AACTTACAT
1 AACTTACAT
*
45950830 AA--TACAC
1 AACTTACAT
*
45950837 AACTTACAC
1 AACTTACAT
45950846 AACTTACAT
1 AACTTACAT
45950855 AACTTA-ATT
1 AACTTACA-T
45950864 AA-TTA-AT
1 AACTTACAT
*
45950871 -ACTAAACAT
1 AACT-TACAT
*
45950880 AACTTGTCA-
1 AACTT-ACAT
*
45950889 GACTTACAT
1 AACTTACAT
45950898 AACTTACAT
1 AACTTACAT
*
45950907 AA--TACAC
1 AACTTACAT
*
45950914 AACTTACAC
1 AACTTACAT
45950923 AACTTACAT
1 AACTTACAT
45950932 AACTTACAT
1 AACTTACAT
*
45950941 AA--TACAC
1 AACTTACAT
* *
45950948 AATTTACAC
1 AACTTACAT
45950957 AACTTACAT
1 AACTTACAT
45950966 AACTTACAT
1 AACTTACAT
*
45950975 AA--TACAC
1 AACTTACAT
*
45950982 AACTTATAT
1 AACTTACAT
* *
45950991 AACTTAAAA
1 AACTTACAT
45951000 AACTTACAT
1 AACTTACAT
*
45951009 AA--TACAC
1 AACTTACAT
*
45951016 AACTTATATAT
1 AAC-T-TACAT
*
45951027 AACTTTCAT
1 AACTTACAT
45951036 AACTTAC-T
1 AACTTACAT
*
45951044 TA--TA-AT
1 AACTTACAT
45951050 AACTTACAT
1 AACTTACAT
*
45951059 AACGTAC-T
1 AACTTACAT
*
45951067 TA--TA-AT
1 AACTTACAT
45951073 AACTTACAT
1 AACTTACAT
45951082 AACTTA
1 AACTTA
45951088 TTAATATTTA
Statistics
Matches: 439, Mismatches: 74, Indels: 124
0.69 0.12 0.19
Matches are distributed among these distances:
6 10 0.02
7 63 0.14
8 33 0.08
9 268 0.61
10 20 0.05
11 25 0.06
12 15 0.03
13 5 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:45950583 original size:32 final size:31
Alignment explanation
Indices: 45950509--45950583 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
45950499 ATATAAACTT
* *
45950509 ACATAATACATAACTTACATAACTTATATAGA
1 ACATAATA-ACAACTTACATAACTTACATAGA
* * *
45950541 ACTTATATAACAACTTGCATAACTTACATAATA
1 ACATA-ATAACAACTTACATAACTTACAT-AGA
45950574 ACATAATAAC
1 ACATAATAAC
45950584 GTACATACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (31 bp):
ACATAATAACAACTTACATAACTTACATAGA
Found at i:45950654 original size:18 final size:16
Alignment explanation
Indices: 45950613--45950678 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
45950603 CGTAAATTGC
* *
45950613 ATAACTCACATAATAC
1 ATAACTTACATAATAA
*
45950629 ACAACTTACATAACTAAA
1 ATAACTTACATAA-T-AA
*
45950647 ATAACTTACATAATAC
1 ATAACTTACATAATAA
45950663 ATAACTTACATTAATA
1 ATAACTTACA-TAATA
45950679 TTATACATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 22 0.52
17 7 0.17
18 13 0.31
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAACTTACATAATAA
Found at i:45950731 original size:30 final size:31
Alignment explanation
Indices: 45950660--45950721 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
45950650 ACTTACATAA
* *
45950660 TACATAACTTACATTAATATTATACATAACT
1 TACATAACTTACATTAATACTAAACATAACT
45950691 TACATAACTTA-ATTAATACTAAACATAACT
1 TACATAACTTACATTAATACTAAACATAACT
45950721 T
1 T
45950722 GTCAGACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (31 bp):
TACATAACTTACATTAATACTAAACATAACT
Found at i:45950731 original size:77 final size:76
Alignment explanation
Indices: 45950650--45950934 Score: 307
Period size: 77 Copynumber: 3.6 Consensus size: 76
45950640 AACTAAAATA
* *
45950650 ACTTACATAA-TACATAACTTACATTAATATTATACATAACTTACATAAC-TTAATTAATACTAA
1 ACTTACATAACTACATAA-TTACATTAA-ACT-TACACAACTTACATAACATTAATTAATACTAA
45950713 ACATAACTTGTCAG
63 ACATAACTTGTCAG
*
45950727 ACTTACATAACTTACATAATACACAACTTACACAACTTACACAACTTACATAACTTAATTAATTA
1 ACTTACATAAC-TACATAAT-TAC-A-TT--A-AACTTACACAACTTACATAAC---ATTAATTA
45950792 ATACTAAACATAACTTGTCAG
56 ATACTAAACATAACTTGTCAG
*
45950813 ACTTACATAACTTACATAA-TACA--CAACTTACACAACTTACATAACTTAATTAATTAATACTA
1 ACTTACATAAC-TACATAATTACATTAAACTTACACAACTTACATAAC---ATTAATTAATACTA
45950875 AACATAACTTGTCAG
62 AACATAACTTGTCAG
*
45950890 ACTTACATAACTTACATAA-TACA--CAACTTACACAACTTACATAAC
1 ACTTACATAAC-TACATAATTACATTAAACTTACACAACTTACATAAC
45950935 TTACATAATA
Statistics
Matches: 191, Mismatches: 5, Indels: 24
0.87 0.02 0.11
Matches are distributed among these distances:
77 108 0.57
78 1 0.01
79 9 0.05
80 1 0.01
81 2 0.01
82 16 0.08
83 4 0.02
84 3 0.02
86 47 0.25
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (76 bp):
ACTTACATAACTACATAATTACATTAAACTTACACAACTTACATAACATTAATTAATACTAAACA
TAACTTGTCAG
Found at i:45950742 original size:86 final size:82
Alignment explanation
Indices: 45950647--45950942 Score: 449
Period size: 86 Copynumber: 3.6 Consensus size: 82
45950637 CATAACTAAA
* * *
45950647 ATAACTTACATAATACATAACTTACATTAATATTATACATAACTTACATAACTTAATTAATACTA
1 ATAACTTACATAATACACAACTTACA--CA-ACT-TACATAACTTACATAACTTAATTAATACTA
45950712 AACATAACTTGTCAGACTTAC
62 AACATAACTTGTCAGACTTAC
*
45950733 ATAACTTACATAATACACAACTTACACAACTTACACAACTTACATAACTTAATTAATTAATACTA
1 ATAACTTACATAATACACAACTTACACAACTTACATAACTTACATAAC----TTAATTAATACTA
45950798 AACATAACTTGTCAGACTTAC
62 AACATAACTTGTCAGACTTAC
45950819 ATAACTTACATAATACACAACTTACACAACTTACATAAC-T---TAA-TTAATTAATACTAAACA
1 ATAACTTACATAATACACAACTTACACAACTTACATAACTTACATAACTTAATTAATACTAAACA
45950879 TAACTTGTCAGACTTAC
66 TAACTTGTCAGACTTAC
45950896 ATAACTTACATAATACACAACTTACACAACTTACATAACTTACATAA
1 ATAACTTACATAATACACAACTTACACAACTTACATAACTTACATAA
45950943 TACACAATTT
Statistics
Matches: 197, Mismatches: 5, Indels: 21
0.88 0.02 0.09
Matches are distributed among these distances:
77 73 0.37
78 1 0.01
81 3 0.02
82 19 0.10
83 2 0.01
84 1 0.01
85 1 0.01
86 97 0.49
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (82 bp):
ATAACTTACATAATACACAACTTACACAACTTACATAACTTACATAACTTAATTAATACTAAACA
TAACTTGTCAGACTTAC
Found at i:45950807 original size:34 final size:34
Alignment explanation
Indices: 45950769--45950884 Score: 90
Period size: 38 Copynumber: 3.1 Consensus size: 34
45950759 CAACTTACAC
45950769 AACTTACATAACTTAATTAATTAATACTAAACAT
1 AACTTACATAACTTAATTAATTAATACTAAACAT
* * * * *
45950803 AACTTGTCAGACTTACATAACTTACA-TAATACACAACTTACAC
1 AAC-T-T-ACA-TAACTTAA-TTA-ATTAATAC-TAA---ACAT
45950846 AACTTACATAACTTAATTAATTAATACTAAACAT
1 AACTTACATAACTTAATTAATTAATACTAAACAT
45950880 AACTT
1 AACTT
45950885 GTCAGACTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 22
0.66 0.11 0.24
Matches are distributed among these distances:
34 11 0.18
35 1 0.02
36 1 0.02
37 5 0.08
38 15 0.25
39 15 0.25
40 5 0.08
41 1 0.02
42 1 0.02
43 6 0.10
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (34 bp):
AACTTACATAACTTAATTAATTAATACTAAACAT
Found at i:45950843 original size:25 final size:25
Alignment explanation
Indices: 45950813--45951087 Score: 130
Period size: 25 Copynumber: 11.6 Consensus size: 25
45950803 AACTTGTCAG
*
45950813 ACTTACATAACTTACATAATACACA
1 ACTTACATAACTTACATAATACATA
* *
45950838 ACTTACACAACTTACAT-A-ACTTA
1 ACTTACATAACTTACATAATACATA
45950861 A-TTA-ATTAA--TAC-TAA-ACATA
1 ACTTACA-TAACTTACATAATACATA
* *
45950881 ACTTGTCA-GACTTACATAACTTACATA
1 ACTT-ACATAACTTACATAA--TACATA
* *
45950908 A--TACACAACTTACACAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
* *
45950933 ACTTACATAA--TACACAATTTACACA
1 ACTTACATAACTTACATAA--TACATA
*
45950958 ACTTACATAACTTACATAATACACA
1 ACTTACATAACTTACATAATACATA
* * *
45950983 ACTTATATAACTTAAAAAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
*
45951010 A--TACACAACTT--AT-AT--ATA
1 ACTTACATAACTTACATAATACATA
* *
45951028 ACTTTCATAACTTAC-TTATA-ATA
1 ACTTACATAACTTACATAATACATA
* *
45951051 ACTTACATAACGTAC-TTATA-ATA
1 ACTTACATAACTTACATAATACATA
45951074 ACTTACATAACTTA
1 ACTTACATAACTTA
45951088 TTAATATTTA
Statistics
Matches: 200, Mismatches: 26, Indels: 50
0.72 0.09 0.18
Matches are distributed among these distances:
18 4 0.02
19 1 0.00
20 18 0.09
21 5 0.03
22 8 0.04
23 46 0.23
24 6 0.03
25 88 0.44
27 24 0.12
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACATA
Found at i:45950935 original size:77 final size:77
Alignment explanation
Indices: 45950755--45950937 Score: 366
Period size: 77 Copynumber: 2.4 Consensus size: 77
45950745 ATACACAACT
45950755 TACACAACTTACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACA
1 TACACAACTTACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACA
45950820 TAACTTACATAA
66 TAACTTACATAA
45950832 TACACAACTTACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACA
1 TACACAACTTACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACA
45950897 TAACTTACATAA
66 TAACTTACATAA
45950909 TACACAACTTACACAACTTACATAACTTA
1 TACACAACTTACACAACTTACATAACTTA
45950938 CATAATACAC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 106 1.00
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (77 bp):
TACACAACTTACACAACTTACATAACTTAATTAATTAATACTAAACATAACTTGTCAGACTTACA
TAACTTACATAA
Found at i:45950971 original size:77 final size:77
Alignment explanation
Indices: 45950755--45951011 Score: 286
Period size: 77 Copynumber: 3.5 Consensus size: 77
45950745 ATACACAACT
* ** *
45950755 TACACAACTTACACAACTTACATAACTTA-ATTAATTAATACTAAACATAACTTGTCAGACTTAC
1 TACACAACTTACACAACTTACATAACTTACA-TAATTAATAATTTACACAACTTGTCAGACTTAC
45950819 ATAACTTACATAA
65 ATAACTTACATAA
* ** *
45950832 TACACAACTTACACAACTTACATAACTTA-ATTAATTAATACTAAACATAACTTGTCAGACTTAC
1 TACACAACTTACACAACTTACATAACTTACA-TAATTAATAATTTACACAACTTGTCAGACTTAC
45950896 ATAACTTACATAA
65 ATAACTTACATAA
*
45950909 TACACAACTTACACAACTTACATAACTTACATAA-TACACAATTT--AC-A-----CA-ACTTAC
1 TACACAACTTACACAACTTACATAACTTACATAATTA-ATAATTTACACAACTTGTCAGACTTAC
45950964 ATAACTTACATAA
65 ATAACTTACATAA
* * * *
45950977 TACACAACTTATATAACTTAAAAAACTTACATAAT
1 TACACAACTTACACAACTTACATAACTTACATAAT
45951012 ACACAACTTA
Statistics
Matches: 168, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
68 49 0.29
69 2 0.01
74 1 0.01
75 1 0.01
76 2 0.01
77 112 0.67
78 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (77 bp):
TACACAACTTACACAACTTACATAACTTACATAATTAATAATTTACACAACTTGTCAGACTTACA
TAACTTACATAA
Found at i:45951025 original size:34 final size:34
Alignment explanation
Indices: 45950890--45951021 Score: 219
Period size: 34 Copynumber: 3.9 Consensus size: 34
45950880 AACTTGTCAG
45950890 ACTTACATAACTTACATAATACACAACTTACACA
1 ACTTACATAACTTACATAATACACAACTTACACA
*
45950924 ACTTACATAACTTACATAATACACAATTTACACA
1 ACTTACATAACTTACATAATACACAACTTACACA
* *
45950958 ACTTACATAACTTACATAATACACAACTTATATA
1 ACTTACATAACTTACATAATACACAACTTACACA
* *
45950992 ACTTAAAAAACTTACATAATACACAACTTA
1 ACTTACATAACTTACATAATACACAACTTA
45951022 TATATAACTT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 92 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (34 bp):
ACTTACATAACTTACATAATACACAACTTACACA
Found at i:45951059 original size:23 final size:23
Alignment explanation
Indices: 45951017--45951087 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 23
45951007 ATAATACACA
*
45951017 ACTTATATATAACTTTCATAACTT
1 ACTTATA-ATAACTTACATAACTT
*
45951041 ACTTATAATAACTTACATAACGT
1 ACTTATAATAACTTACATAACTT
45951064 ACTTATAATAACTTACATAACTT
1 ACTTATAATAACTTACATAACTT
45951087 A
1 A
45951088 TTAATATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 37 0.84
24 7 0.16
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.39
Consensus pattern (23 bp):
ACTTATAATAACTTACATAACTT
Found at i:45955017 original size:13 final size:13
Alignment explanation
Indices: 45954967--45955017 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
45954957 TTTGGCAATA
45954967 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* * *
45954980 CTGTGGAAAATTG
1 CTTTTGAAAAGTG
45954993 CTTTT-AAGAAGTG
1 CTTTTGAA-AAGTG
*
45955006 TTTTTGAAAAGT
1 CTTTTGAAAAGT
45955018 TTGGTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:45961529 original size:2 final size:2
Alignment explanation
Indices: 45961522--45961557 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45961512 TTTTTAAAAG
45961522 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
45961558 AAAATTTATA
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):
TA
Found at i:45961635 original size:24 final size:22
Alignment explanation
Indices: 45961603--45961647 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45961593 AGAATCTTTT
45961603 TATAATTTTATTGATTTTTTAAAA
1 TATAATTTTA-T-ATTTTTTAAAA
*
45961627 TATATTTTTATATTTTTTAAA
1 TATAATTTTATATTTTTTAAA
45961648 TTTAGAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 1 0.05
24 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATAATTTTATATTTTTTAAAA
Found at i:45965487 original size:7 final size:7
Alignment explanation
Indices: 45965475--45965505 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
45965465 TTGGATGGCT
45965475 ATTGGTG
1 ATTGGTG
*
45965482 ATTGGTA
1 ATTGGTG
45965489 ATTGGTG
1 ATTGGTG
45965496 ATTGGTG
1 ATTGGTG
45965503 ATT
1 ATT
45965506 TTCATGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
ATTGGTG
Found at i:45967859 original size:19 final size:18
Alignment explanation
Indices: 45967792--45967859 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
45967782 AAAATTGTAT
*
45967792 TTTTAAAAAAAATTATAAA
1 TTTTAAAAAAATTTA-AAA
*
45967811 TTTTAAAAAAATCTAAAAAA
1 TTTTAAAAAAAT-T-TAAAA
*
45967831 TATATAAAAAAATTTAAAA
1 T-TTTAAAAAAATTTAAAA
*
45967850 TTTTATAAAA
1 TTTTAAAAAA
45967860 TAATAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 7 0.17
19 16 0.40
20 6 0.15
21 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTAAAAAAATTTAAAA
Found at i:45976462 original size:2 final size:2
Alignment explanation
Indices: 45976455--45976480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45976445 TTATTATTAT
45976455 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
45976481 CTCTCCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45976977 original size:16 final size:16
Alignment explanation
Indices: 45976956--45976991 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
45976946 GTGGAAGTTA
45976956 AAAAGAAAGTT-GAGCT
1 AAAAG-AAGTTAGAGCT
45976972 AAAAGAAGTTAGAGCT
1 AAAAGAAGTTAGAGCT
45976988 AAAA
1 AAAA
45976992 TAGATAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (16 bp):
AAAAGAAGTTAGAGCT
Found at i:45985394 original size:23 final size:23
Alignment explanation
Indices: 45985368--45985463 Score: 174
Period size: 23 Copynumber: 4.2 Consensus size: 23
45985358 AGTGCCACAT
45985368 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
45985391 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
45985414 TGATATGTAGCCAAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
45985437 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
45985460 TGAT
1 TGAT
45985464 CAATAACACT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:45985715 original size:18 final size:17
Alignment explanation
Indices: 45985689--45985727 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
45985679 ATTTTTCTTC
45985689 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
45985706 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
45985724 CACA
1 CACA
45985728 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:45988591 original size:17 final size:15
Alignment explanation
Indices: 45988547--45988584 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
45988537 GATACACGGC
45988547 TGTGTCACCTGGCCG
1 TGTGTCACCTGGCCG
45988562 TGTGTCACCTGGCCG
1 TGTGTCACCTGGCCG
45988577 TGTGTCAC
1 TGTGTCAC
45988585 ACATGGCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.29
Consensus pattern (15 bp):
TGTGTCACCTGGCCG
Found at i:45991543 original size:44 final size:43
Alignment explanation
Indices: 45991440--45991566 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 43
45991430 AAAGCTCATA
* * *
45991440 CAATGCCAACGTCCCAGATGTGGTCTTACATGTAATTACATAT
1 CAATGCCAACGTCCCAGATGTGGTCTTACACGTAATCACAAAT
* *
45991483 CGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACAAAT
1 CAATGCCAAC-GTCCCAGA-TGTGGTCTTACACGT-AATCACAAAT
45991527 CAATGCCAACGTCCCAGATGTGGTCTTACACGATAA-CACA
1 CAATGCCAACGTCCCAGATGTGGTCTTACACG-TAATCACA
45991567 CAACAGAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 30 0.42
44 36 0.51
45 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGATGTGGTCTTACACGTAATCACAAAT
Found at i:45999299 original size:2 final size:2
Alignment explanation
Indices: 45999292--45999347 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
45999282 NNNNNTAATA
45999292 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
45999334 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
45999348 GATAGTGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46006542 original size:22 final size:23
Alignment explanation
Indices: 46006517--46006564 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
46006507 AAGAGTTATA
*
46006517 AAAAATTCTAATAA-ATAACAAC
1 AAAAATACTAATAATATAACAAC
*
46006539 -AAAATAGTAATAATATAACAAC
1 AAAAATACTAATAATATAACAAC
46006561 AAAA
1 AAAA
46006565 TAACAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 11 0.50
22 8 0.36
23 3 0.14
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAAATACTAATAATATAACAAC
Found at i:46006565 original size:22 final size:21
Alignment explanation
Indices: 46006525--46006566 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
46006515 TAAAAAATTC
46006525 TAATAAATAACAACAAAATAG
1 TAATAAATAACAACAAAATAG
46006546 TAATAATATAACAACAAAATA
1 TAATAA-ATAACAACAAAATA
46006567 ACAATGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (21 bp):
TAATAAATAACAACAAAATAG
Found at i:46018630 original size:24 final size:24
Alignment explanation
Indices: 46018603--46018656 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
46018593 AAAAAAATTT
46018603 CGGCCCGGGTCCTAGGCCTAGCCC
1 CGGCCCGGGTCCTAGGCCTAGCCC
*
46018627 CGGCCTGGGTCCTAGGCCTAGCCC
1 CGGCCCGGGTCCTAGGCCTAGCCC
46018651 CGGCCC
1 CGGCCC
46018657 AGCCCGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.07, C:0.46, G:0.33, T:0.13
Consensus pattern (24 bp):
CGGCCCGGGTCCTAGGCCTAGCCC
Found at i:46028434 original size:19 final size:19
Alignment explanation
Indices: 46028412--46028463 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
46028402 AAATTACAAA
46028412 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTTT
*
46028431 AAAAATTTAAAATAATTTTT
1 AAAAA-TCAAAATAATTTTT
*
46028451 AAAATTCAAAATA
1 AAAAATCAAAATA
46028464 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATCAAAATAATTTTT
Found at i:46028439 original size:8 final size:8
Alignment explanation
Indices: 46028428--46028506 Score: 50
Period size: 8 Copynumber: 9.0 Consensus size: 8
46028418 CAAAATAATT
46028428 TTTAAAAA
1 TTTAAAAA
46028436 TTTAAAATAA
1 TTT-AAA-AA
*
46028446 TTTTTAAAA
1 -TTTAAAAA
*
46028455 TTCAAAATA
1 TTTAAAA-A
46028464 TTAATAAAAA
1 TT--TAAAAA
* *
46028474 TTTCAAAT
1 TTTAAAAA
*
46028482 TTTAAAAT
1 TTTAAAAA
46028490 TTTAAAAA
1 TTTAAAAA
46028498 TTATAAAAA
1 TT-TAAAAA
46028507 ATATATAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
8 28 0.50
9 14 0.25
10 7 0.12
11 7 0.12
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (8 bp):
TTTAAAAA
Found at i:46028442 original size:20 final size:20
Alignment explanation
Indices: 46028419--46028481 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
46028409 AAAAAAAATC
46028419 AAAATAATTTTTAAAAATTT
1 AAAATAATTTTTAAAAATTT
*
46028439 AAAATAATTTTT-AAAATTC
1 AAAATAATTTTTAAAAATTT
**
46028458 AAAAT-ATTAATAAAAATTT
1 AAAATAATTTTTAAAAATTT
*
46028477 CAAAT
1 AAAAT
46028482 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.11
19 21 0.57
20 12 0.32
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATTTTTAAAAATTT
Found at i:46028475 original size:19 final size:19
Alignment explanation
Indices: 46028411--46028463 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
46028401 AAAATTACAA
*
46028411 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAA-TTTT
*
46028431 AAAAATTTAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
46028450 TAAAATTCAAAATA
1 AAAAATTCAAAATA
46028464 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:46030102 original size:20 final size:20
Alignment explanation
Indices: 46030074--46030111 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46030064 ACGAATCTGG
46030074 ATAAAAATTGATG-TAATGGA
1 ATAAAAATT-ATGATAATGGA
*
46030094 ATAACAATTATGATAATG
1 ATAAAAATTATGATAATG
46030112 TAAATGAAAA
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:0.03, G:0.16, T:0.32
Consensus pattern (20 bp):
ATAAAAATTATGATAATGGA
Found at i:46030576 original size:3 final size:3
Alignment explanation
Indices: 46030568--46030625 Score: 80
Period size: 3 Copynumber: 18.3 Consensus size: 3
46030558 TAAATGGGTA
*
46030568 AAT AAT AAT AAT GAT AAGGT AAGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT AAT AAT AAT AAT
46030616 AAT AAT AAT A
1 AAT AAT AAT A
46030626 CAACTATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 44 0.86
4 4 0.08
5 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46033214 original size:72 final size:73
Alignment explanation
Indices: 46033097--46033292 Score: 223
Period size: 72 Copynumber: 2.7 Consensus size: 73
46033087 TTAATGATCT
* * * * * *
46033097 ATGGCTTGAGATCCAATACATGTTTTTGATTATTTGAAGCTTGTGTGAACAACATCGAATCATTC
1 ATGGCTTGAGATCCAACACGTGTTTTGGATTCTCTAAAGCTTGTGTGAACAACATCGAATCATTC
*
46033162 TTT-ATCG
66 TTTAATAG
** *
46033169 ATGGCTTGAGATCCAACACGTGTTTTGGATTCTCTAAAGCTTGTGTGAGTAACATTGAATCATTC
1 ATGGCTTGAGATCCAACACGTGTTTTGGATTCTCTAAAGCTTGTGTGAACAACATCGAATCATTC
*
46033234 TTTACCAATAT
66 TTT---AATAG
* * **
46033245 ATAGCTTGAGATCCAGCACGTGTTACGGATTCTCTAAAGCTTGTGTGA
1 ATGGCTTGAGATCCAACACGTGTTTTGGATTCTCTAAAGCTTGTGTGA
46033293 GCATCGTCGA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
72 59 0.56
76 46 0.44
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (73 bp):
ATGGCTTGAGATCCAACACGTGTTTTGGATTCTCTAAAGCTTGTGTGAACAACATCGAATCATTC
TTTAATAG
Found at i:46037311 original size:31 final size:31
Alignment explanation
Indices: 46037248--46037311 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
46037238 TTTTTTTCTT
* *
46037248 TTTTTTTCTATTTCAACTGTTTCTTTTCAAA
1 TTTTTTTCTATTTCAACTATTTCTTTTAAAA
*
46037279 TTTTTTTCTATTTCACCTATATT-TTTTAAAA
1 TTTTTTTCTATTTCAACTAT-TTCTTTTAAAA
46037310 TT
1 TT
46037312 CCCATCGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTTTTCTATTTCAACTATTTCTTTTAAAA
Found at i:46042441 original size:13 final size:13
Alignment explanation
Indices: 46042423--46042447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46042413 CATACTCTCA
46042423 ATTTTTAATATTC
1 ATTTTTAATATTC
46042436 ATTTTTAATATT
1 ATTTTTAATATT
46042448 TTAGGATTAT
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTAATATTC
Found at i:46042473 original size:17 final size:17
Alignment explanation
Indices: 46042453--46042494 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
46042443 ATATTTTAGG
*
46042453 ATTATTTATGTTTTACA
1 ATTATTTAGGTTTTACA
*
46042470 ATTACTTAGGTTTTACA
1 ATTATTTAGGTTTTACA
46042487 ATTATTTA
1 ATTATTTA
46042495 AGCATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (17 bp):
ATTATTTAGGTTTTACA
Found at i:46044432 original size:24 final size:24
Alignment explanation
Indices: 46044405--46044452 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
46044395 TCCACAGCAT
46044405 TTACTGGATGACCATCCAAGCTAC
1 TTACTGGATGACCATCCAAGCTAC
*
46044429 TTACTGGATGACTATCCAAGCTAC
1 TTACTGGATGACCATCCAAGCTAC
46044453 CCTAGTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (24 bp):
TTACTGGATGACCATCCAAGCTAC
Found at i:46051402 original size:2 final size:2
Alignment explanation
Indices: 46051395--46051434 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
46051385 TTATAAAACT
46051395 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
46051435 AAACATAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46051812 original size:3 final size:3
Alignment explanation
Indices: 46051798--46051842 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
46051788 ATATGTAGGT
*
46051798 ATA ATA AGA ATA ATA ATA TATA AT- ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
46051842 A
1 A
46051843 CAACAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:46051855 original size:26 final size:26
Alignment explanation
Indices: 46051798--46051861 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
46051788 ATATGTAGGT
* * *
46051798 ATAATAAGAATAATAATATATAATATA
1 ATAATAA-AATAATAATATACAACAAA
46051825 ATAATAAAATAATAATA-ACAACAAA
1 ATAATAAAATAATAATATACAACAAA
46051850 ATTAATAAAATA
1 A-TAATAAAATA
46051862 GACTAAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.18
26 20 0.61
27 7 0.21
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAATAAAATAATAATATACAACAAA
Done.