Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3762312 original size:30 final size:30
Alignment explanation
Indices: 3762254--3762353 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
3762244 CATCTTCTAT
* *
3762254 AACCTAAATCCAAACCTGAACCCTAACCCAA
1 AACC-AAACCCAAACCTGAACCCAAACCCAA
* * *
3762285 ACCCAAACCCGAACCCGAACCCAAACCCAA
1 AACCAAACCCAAACCTGAACCCAAACCCAA
* * *
3762315 AATCAAACCCAAACATGAACCCGAACCCAA
1 AACCAAACCCAAACCTGAACCCAAACCCAA
*
3762345 ATCCAAACC
1 AACCAAACC
3762354 AAAATCCAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
30 53 0.95
31 3 0.05
ACGTcount: A:0.46, C:0.42, G:0.05, T:0.07
Consensus pattern (30 bp):
AACCAAACCCAAACCTGAACCCAAACCCAA
Found at i:3762322 original size:36 final size:36
Alignment explanation
Indices: 3762282--3762351 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3762272 AACCCTAACC
*
3762282 CAAACCCAAACCCGAACCCGAACCCAAACCCAAAAT
1 CAAACCCAAACACGAACCCGAACCCAAACCCAAAAT
* *
3762318 CAAACCCAAACATGAACCCGAACCCAAATCCAAA
1 CAAACCCAAACACGAACCCGAACCCAAACCCAAA
3762352 CCAAAATCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.49, C:0.41, G:0.06, T:0.04
Consensus pattern (36 bp):
CAAACCCAAACACGAACCCGAACCCAAACCCAAAAT
Found at i:3762364 original size:36 final size:36
Alignment explanation
Indices: 3762272--3762356 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
3762262 TCCAAACCTG
* * **
3762272 AACCCTAACCCAAACCCAAACCCGAACCCGAACCCA
1 AACCCAAAACCAAACCCAAACATGAACCCGAACCCA
*
3762308 AACCCAAAATCAAACCCAAACATGAACCCGAACCCA
1 AACCCAAAACCAAACCCAAACATGAACCCGAACCCA
*
3762344 AATCC-AAACCAAA
1 AACCCAAAACCAAA
3762357 ATCCAAACTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.48, C:0.42, G:0.05, T:0.05
Consensus pattern (36 bp):
AACCCAAAACCAAACCCAAACATGAACCCGAACCCA
Found at i:3762818 original size:97 final size:98
Alignment explanation
Indices: 3762695--3762876 Score: 240
Period size: 97 Copynumber: 1.9 Consensus size: 98
3762685 AATTTTTTAA
* *
3762695 TTGTATAGCTGTTGGTTGTTCATTGGGAATGGTTGTATAGGGTCGTTAGTTGCC-TTGTTAGCAG
1 TTGTATAGCTGTTGGTTGCTCATTGGGAATGGTTGTATAAGGTCGTTAGTTGCCTTTGTTAGCAG
* *
3762759 TTAGTGTTTATTTGTTTCCTTTGTAGTCCTTGT
66 CTAGTATTTATTTGTTTCCTTTGTAGTCCTTGT
* * * * * * * *
3762792 TTGTGTAGTTGTTGGTTGCTCATTGGGATTGGTTGTATAAGGTTGTTTGTTTCCTTTGTTTGTAG
1 TTGTATAGCTGTTGGTTGCTCATTGGGAATGGTTGTATAAGGTCGTTAGTTGCCTTTGTTAGCAG
*
3762857 CTAGTATTTCTTTGTTTCCT
66 CTAGTATTTATTTGTTTCCT
3762877 CTTATAACAC
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
97 46 0.65
98 25 0.35
ACGTcount: A:0.12, C:0.10, G:0.27, T:0.51
Consensus pattern (98 bp):
TTGTATAGCTGTTGGTTGCTCATTGGGAATGGTTGTATAAGGTCGTTAGTTGCCTTTGTTAGCAG
CTAGTATTTATTTGTTTCCTTTGTAGTCCTTGT
Found at i:3763614 original size:24 final size:24
Alignment explanation
Indices: 3763571--3763650 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 24
3763561 CACCGAAGTT
* *
3763571 CCACATAG-ATTT-TCCAGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* *
3763593 CCGCGTAGAATTTGTCTCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
3763617 CCACATAGAA-TTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
3763640 CCACGTAGAAT
1 CCACGTAGAAT
3763651 GCTCGACTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
22 6 0.13
23 25 0.53
24 16 0.34
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.21
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:3769566 original size:20 final size:20
Alignment explanation
Indices: 3769541--3769589 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3769531 AACCTGATAG
3769541 CATCATCAACATAGTGCATT
1 CATCATCAACATAGTGCATT
3769561 CATCATCAACATAGTGCATT
1 CATCATCAACATAGTGCATT
3769581 CATCATCAA
1 CATCATCAA
3769590 ATTCCATCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.29
Consensus pattern (20 bp):
CATCATCAACATAGTGCATT
Found at i:3772009 original size:21 final size:21
Alignment explanation
Indices: 3771979--3772018 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3771969 TAACGCAGGA
*
3771979 AGTATCGATACTTATAGATAT
1 AGTATCGATACTAATAGATAT
*
3772000 AGTATTGATACTAATAGAT
1 AGTATCGATACTAATAGAT
3772019 TCTGAGCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTAATAGATAT
Found at i:3772701 original size:27 final size:27
Alignment explanation
Indices: 3772649--3772709 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
3772639 TGTTTCATAG
**
3772649 AACATATTCACTTAGCATGTATTCACAT
1 AACAT-TTCACTTAGCACATATTCACAT
3772677 AACATTTCACTTAGCACAT-TGTCACAT
1 AACATTTCACTTAGCACATAT-TCACAT
*
3772704 AGCATT
1 AACATT
3772710 ATCAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 23 0.79
28 5 0.17
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.34
Consensus pattern (27 bp):
AACATTTCACTTAGCACATATTCACAT
Found at i:3774802 original size:45 final size:46
Alignment explanation
Indices: 3774738--3774833 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
3774728 CCACTAAGTG
* * *
3774738 TGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAAGTGTATCGA
1 TGCATAAAATGCAATCGATGTTTTGAATAAAACCTAAGTGCATCGA
* * *
3774783 TGCATAAAATGCAATCGATGTTTTTATTAAAACCTGAGTGCATCGA
1 TGCATAAAATGCAATCGATGTTTTGAATAAAACCTAAGTGCATCGA
3774829 TGCAT
1 TGCAT
3774834 GGAGAGTGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 25 0.57
46 19 0.43
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (46 bp):
TGCATAAAATGCAATCGATGTTTTGAATAAAACCTAAGTGCATCGA
Found at i:3775547 original size:16 final size:16
Alignment explanation
Indices: 3775526--3775556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3775516 CAAAACACTA
*
3775526 ATCCAAACATTCAATC
1 ATCCAAACAATCAATC
3775542 ATCCAAACAATCAAT
1 ATCCAAACAATCAAT
3775557 GCCCTATATA
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:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (16 bp):
ATCCAAACAATCAATC
Found at i:3775937 original size:21 final size:23
Alignment explanation
Indices: 3775881--3775962 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
3775871 GCATGGCTTT
*
3775881 GTGCATCGATGTACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
3775904 GTGCATCGGTGCATATTCAA-GA
1 GTGCATCGATGCACATTCAAGGA
* *
3775926 -TGTATCGATGCACATACAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
3775948 GATGCATCTATGCAC
1 G-TGCATCGATGCAC
3775963 TGTTCAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 13 0.28
22 4 0.09
23 18 0.39
24 11 0.24
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:3781539 original size:62 final size:60
Alignment explanation
Indices: 3781429--3781552 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 60
3781419 TATCCACACT
3781429 AAGGATTTTCTAACAAATCACTAATTTGTTCTTCTTTTGAGGCCAAAGAGATAAACTTAC
1 AAGGATTTTCTAACAAATCACTAATTTGTTCTTCTTTTGAGGCCAAAGAGATAAACTTAC
3781489 AAGGATTTTCTAACAAATTCACTAATTTGTTCTTTCTTTTGAGGCCAAAGAGATAAACTTAC
1 AAGGATTTTCTAACAAA-TCACTAATTTGTTC-TTCTTTTGAGGCCAAAGAGATAAACTTAC
3781551 AA
1 AA
3781553 CTCCCTCAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 17 0.27
61 14 0.23
62 31 0.50
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (60 bp):
AAGGATTTTCTAACAAATCACTAATTTGTTCTTCTTTTGAGGCCAAAGAGATAAACTTAC
Found at i:3782017 original size:66 final size:66
Alignment explanation
Indices: 3781911--3782040 Score: 260
Period size: 66 Copynumber: 2.0 Consensus size: 66
3781901 GTCAATAGAG
3781911 CCGTTTAAGTGTGAAAACAAATAATAAAATCAGTTGGGAGTGCATCGATGCATACACAAGGTGCA
1 CCGTTTAAGTGTGAAAACAAATAATAAAATCAGTTGGGAGTGCATCGATGCATACACAAGGTGCA
3781976 T
66 T
3781977 CCGTTTAAGTGTGAAAACAAATAATAAAATCAGTTGGGAGTGCATCGATGCATACACAAGGTGC
1 CCGTTTAAGTGTGAAAACAAATAATAAAATCAGTTGGGAGTGCATCGATGCATACACAAGGTGC
3782041 TCGTGCATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (66 bp):
CCGTTTAAGTGTGAAAACAAATAATAAAATCAGTTGGGAGTGCATCGATGCATACACAAGGTGCA
T
Found at i:3782182 original size:64 final size:65
Alignment explanation
Indices: 3782114--3782264 Score: 180
Period size: 65 Copynumber: 2.3 Consensus size: 65
3782104 CCACTAAGTG
* * * *
3782114 TGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAAGTGTATCGATGCATGGTA-TGTAAATCG
1 TGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG-AGAGTAAATCG
3782177 A
65 A
* * * * **
3782178 TGCATAAAATGCAATCGATATTTTCATTAAAACCTCAGTGCATCGATGCATGGAGAGTGCATCGA
1 TGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGGAGAGTAAATCGA
*
3782243 TGCATAAACTGCATTCGATGTT
1 TGCATAAAATGCATTCGATGTT
3782265 CAATTTATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 25 0.35
65 47 0.65
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (65 bp):
TGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGGAGAGTAAATCGA
Found at i:3782326 original size:20 final size:20
Alignment explanation
Indices: 3782275--3782345 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
3782265 CAATTTATTC
*
3782275 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGTATGG
3782295 ATT-GTGCATCGATGTATGG
1 ATTGGTGCATCGATGTATGG
*
3782314 ATTGGTACATCGATGTATGG
1 ATTGGTGCATCGATGTATGG
3782334 ATTGGTGCATCG
1 ATTGGTGCATCG
3782346 GTGCATTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGTATGG
Found at i:3787465 original size:45 final size:44
Alignment explanation
Indices: 3787409--3787603 Score: 210
Period size: 45 Copynumber: 4.3 Consensus size: 44
3787399 TAAATTGTTC
* * *
3787409 ATCTAACCGAGATTGTTCATGTTATGTTCATCTCTTTAACCATAA
1 ATCTAAACGAGACTGTTCATGTTATGTT-ATCTCTCTAACCATAA
*
3787454 ATCTAAACGAGACTGTTCATGTTATGATTACCTCTCTAACCATAA
1 ATCTAAACGAGACTGTTCATGTTATG-TTATCTCTCTAACCATAA
*
3787499 ATCTAAACGAGACTGTTCATGTTATGTTTATCTCTCTAACCCTAA
1 ATCTAAACGAGACTGTTCATGTTATG-TTATCTCTCTAACCATAA
** ** * * * *
3787544 ATCTAATTGAGACACTTCATCTTTTGTTCATATTCTCTAACCCTAA
1 ATCTAAACGAGACTGTTCATGTTATGTT-AT-CTCTCTAACCATAA
* *
3787590 ATCTTATCGAGACT
1 ATCTAAACGAGACT
3787604 CATCATCTCA
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 2 0.02
45 102 0.78
46 26 0.20
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (44 bp):
ATCTAAACGAGACTGTTCATGTTATGTTATCTCTCTAACCATAA
Found at i:3791250 original size:73 final size:75
Alignment explanation
Indices: 3791163--3791320 Score: 198
Period size: 73 Copynumber: 2.1 Consensus size: 75
3791153 GTACCTCTAA
* * * * *
3791163 AGGGGTATCGGTACCCATAGGGCATTTTGTTTTTCTCGGAGCCAAAAATT-GCATA-GGGTATC-
1 AGGGGTATCAGTACCCATAGGGCAATCTATTTTTCTCAGAGCC-AAAATTAGCATAGGGGTATCG
3791225 GATACA-CTATG
65 GA-ACACCTATG
* *
3791236 AGGGGTATCAGTACCCTTTGGGCAATCTATTTTTCTCAGAGCCAAAATTAGCATAGGGGTATCGG
1 AGGGGTATCAGTACCCATAGGGCAATCTATTTTTCTCAGAGCCAAAATTAGCATAGGGGTATCGG
3791301 AACACCCTATG
66 AACA-CCTATG
3791312 AGGGGTATC
1 AGGGGTATC
3791321 GATAACTCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
72 6 0.08
73 41 0.56
74 10 0.14
75 2 0.03
76 14 0.19
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (75 bp):
AGGGGTATCAGTACCCATAGGGCAATCTATTTTTCTCAGAGCCAAAATTAGCATAGGGGTATCGG
AACACCTATG
Found at i:3791641 original size:13 final size:13
Alignment explanation
Indices: 3791623--3791656 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3791613 TAAGATTTTC
*
3791623 TTTGAAAATCATT
1 TTTGAAAATCAAT
3791636 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3791648 TTTGAAAAT
1 TTTGAAAAT
3791657 TACTCTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3794034 original size:21 final size:21
Alignment explanation
Indices: 3793945--3794039 Score: 88
Period size: 20 Copynumber: 4.6 Consensus size: 21
3793935 ACCCTTATAG
** *
3793945 GGGTATCGATACACATTCAAAGG
1 GGGTATCGATAC-C-TAGAAAGT
* *
3793968 GGGTATCGATACATTG-AAG-
1 GGGTATCGATACCTAGAAAGT
3793987 GGGTATCGATACCTAGAAAGT
1 GGGTATCGATACCTAGAAAGT
* *
3794008 -GGTATCGATACCTATAGAGT
1 GGGTATCGATACCTAGAAAGT
3794028 GGGTATCGATAC
1 GGGTATCGATAC
3794040 TGGTGCACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.22
20 24 0.38
21 13 0.21
23 12 0.19
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACCTAGAAAGT
Found at i:3798865 original size:20 final size:20
Alignment explanation
Indices: 3798840--3798882 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3798830 TGAAGTATCT
3798840 CATTCTATTCTTCCAATAAG
1 CATTCTATTCTTCCAATAAG
3798860 CATTCTATTCTTCCAATAAG
1 CATTCTATTCTTCCAATAAG
3798880 CAT
1 CAT
3798883 AATTAGCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (20 bp):
CATTCTATTCTTCCAATAAG
Found at i:3799861 original size:73 final size:74
Alignment explanation
Indices: 3799703--3799887 Score: 241
Period size: 74 Copynumber: 2.5 Consensus size: 74
3799693 GTTAAATGAC
* * * * *
3799703 TAGGGGTATCGATACCTCTA-AAGGGGTATCGGTACCCATAGGTCATTTTGTTTTTCTCGGAGCC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGGTACCCATAGGGCAATCTGTTTTTCTCGGAGCC
3799767 AAAAATTGCA
65 AAAAATTGCA
* *
3799777 TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCTTTGGGCAATCTG-TTTTCTCGGAGCC-
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATAGGGCAATCTGTTTTTCTCGGAGCCA
3799840 AAAATTAGCA
66 AAAATT-GCA
*
3799850 TAGGGGTATCGGTATACCCTATGAGGGGTATCAGTACC
1 TAGGGGTATCGG--TACCCTATGAGGGGTATCGGTACC
3799888 TCCCTATTTA
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
72 6 0.06
73 31 0.31
74 39 0.39
75 23 0.23
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (74 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATAGGGCAATCTGTTTTTCTCGGAGCCA
AAAATTGCA
Found at i:3801362 original size:16 final size:16
Alignment explanation
Indices: 3801341--3801387 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
3801331 TCCTCTCTCT
3801341 TCCTTTTTATTTTCCC
1 TCCTTTTTATTTTCCC
3801357 TCCTTTTTATTTTCCC
1 TCCTTTTTATTTTCCC
3801373 TCCTTTTTATTTTCC
1 TCCTTTTTATTTTCC
3801388 AACACATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (16 bp):
TCCTTTTTATTTTCCC
Found at i:3806756 original size:26 final size:26
Alignment explanation
Indices: 3806720--3806794 Score: 114
Period size: 26 Copynumber: 2.9 Consensus size: 26
3806710 TTGATTTCAC
* * *
3806720 CCCCTAGAATTTTATAAATTCGTCCT
1 CCCCTAAAATTTTAGAAATTCATCCT
*
3806746 CCTCTAAAATTTTAGAAATTCATCCT
1 CCCCTAAAATTTTAGAAATTCATCCT
3806772 CCCCTAAAATTTTAGAAATTCAT
1 CCCCTAAAATTTTAGAAATTCAT
3806795 TGCCTAACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.37
Consensus pattern (26 bp):
CCCCTAAAATTTTAGAAATTCATCCT
Found at i:3808723 original size:17 final size:17
Alignment explanation
Indices: 3808696--3808730 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3808686 AAAGAAATAA
3808696 AACTTTCAAATAATATTT
1 AACTTTCAAATAAT-TTT
3808714 AACTTT-AAATAATTTT
1 AACTTTCAAATAATTTT
3808730 A
1 A
3808731 CATTGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 7 0.41
18 6 0.35
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (17 bp):
AACTTTCAAATAATTTT
Found at i:3808811 original size:28 final size:28
Alignment explanation
Indices: 3808752--3808815 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
3808742 AAAACAAAAT
* **
3808752 AAATTTAATATTTTTATAATTTTAAATT
1 AAATTTATTATTTTTATAATTTTAAACA
3808780 AAATTTATTATTTTTAT-ATTTTCAAACA
1 AAATTTATTATTTTTATAATTTT-AAACA
3808808 AAATTTAT
1 AAATTTAT
3808816 GAAAGAAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATTTATTATTTTTATAATTTTAAACA
Found at i:3811949 original size:29 final size:29
Alignment explanation
Indices: 3811907--3811963 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3811897 AATGTTGGCC
3811907 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
3811936 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
3811964 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.35, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:3812125 original size:33 final size:33
Alignment explanation
Indices: 3812084--3812151 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3812074 GCGACCTACC
*
3812084 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
3812117 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
3812150 CT
1 CT
3812152 TGTTCGGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.09, C:0.40, G:0.25, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:3812140 original size:10 final size:10
Alignment explanation
Indices: 3812088--3812218 Score: 55
Period size: 10 Copynumber: 12.1 Consensus size: 10
3812078 CCTACCCTCG
*
3812088 CTCGGTTGCC
1 CTCGGATGCC
*
3812098 CTCGGATTCC
1 CTCGGATGCC
*
3812108 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
3812120 GCTCGGTTGCC
1 -CTCGGATGCC
3812131 CTCGGATGCC
1 CTCGGATGCC
* *
3812141 CTCGCATAGCTTG
1 CTCGGAT-GC--C
*
3812154 TTCGGATGGCC
1 CTCGGAT-GCC
*
3812165 TCGGTCGGATGGC
1 -C--TCGGATGCC
*
3812178 CTCGGATGGC
1 CTCGGATGCC
*
3812188 CTCGGATGCT
1 CTCGGATGCC
* *
3812198 TTCGGATGGC
1 CTCGGATGCC
*
3812208 CTCGAATGCC
1 CTCGGATGCC
3812218 C
1 C
3812219 AGCGTGTTGG
Statistics
Matches: 89, Mismatches: 23, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
10 61 0.69
11 4 0.04
12 4 0.04
13 14 0.16
14 6 0.07
ACGTcount: A:0.10, C:0.34, G:0.31, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:3812167 original size:33 final size:33
Alignment explanation
Indices: 3812084--3812168 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
3812074 GCGACCTACC
* *
3812084 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
*
3812117 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* * *
3812150 CTTGTTCGGATGGCCTCGG
1 CTCGCTCGGATGCCCTCGG
3812169 TCGGATGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.36, G:0.28, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:3812174 original size:14 final size:14
Alignment explanation
Indices: 3812155--3812182 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3812145 CATAGCTTGT
3812155 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
3812169 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
3812183 ATGGCCTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:3812194 original size:20 final size:20
Alignment explanation
Indices: 3812169--3812216 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3812159 ATGGCCTCGG
3812169 TCGGATGGC-CTCGGATGGCC
1 TCGGAT-GCTCTCGGATGGCC
*
3812189 TCGGATGCTTTCGGATGGCC
1 TCGGATGCTCTCGGATGGCC
*
3812209 TCGAATGC
1 TCGGATGC
3812217 CCAGCGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.12, C:0.27, G:0.35, T:0.25
Consensus pattern (20 bp):
TCGGATGCTCTCGGATGGCC
Found at i:3816268 original size:99 final size:99
Alignment explanation
Indices: 3816116--3816328 Score: 426
Period size: 99 Copynumber: 2.2 Consensus size: 99
3816106 GACAAAAGGA
3816116 TATATATATATATATATATATGGGATATGATTTTGTTACACTATGTAAAACTCTTTTAGTTTTAC
1 TATATATATATATATATATATGGGATATGATTTTGTTACACTATGTAAAACTCTTTTAGTTTTAC
3816181 ATAGATTTTATATTGTATAAGTTGATCCTAACCC
66 ATAGATTTTATATTGTATAAGTTGATCCTAACCC
3816215 TATATATATATATATATATATGGGATATGATTTTGTTACACTATGTAAAACTCTTTTAGTTTTAC
1 TATATATATATATATATATATGGGATATGATTTTGTTACACTATGTAAAACTCTTTTAGTTTTAC
3816280 ATAGATTTTATATTGTATAAGTTGATCCTAACCC
66 ATAGATTTTATATTGTATAAGTTGATCCTAACCC
3816314 TATATATATATATAT
1 TATATATATATATAT
3816329 TGATCAGACA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 114 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (99 bp):
TATATATATATATATATATATGGGATATGATTTTGTTACACTATGTAAAACTCTTTTAGTTTTAC
ATAGATTTTATATTGTATAAGTTGATCCTAACCC
Found at i:3820292 original size:34 final size:32
Alignment explanation
Indices: 3820230--3820300 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 32
3820220 ACCTTACAAC
* *
3820230 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
3820262 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
3820296 TCCCT
1 TCCCT
3820301 TTTACAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:3820692 original size:20 final size:20
Alignment explanation
Indices: 3820662--3820746 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
3820652 TTGGTGTATG
*
3820662 GATGCATAGCAGGATGCATC
1 GATGCACAGCAGGATGCATC
*
3820682 GATGTACAGCAGGATGCATC
1 GATGCACAGCAGGATGCATC
**
3820702 GATGCACATTAGGATGCATC
1 GATGCACAGCAGGATGCATC
*
3820722 GATGCACAGTAGGATGCATC
1 GATGCACAGCAGGATGCATC
3820742 GATGC
1 GATGC
3820747 CCTAATTGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (20 bp):
GATGCACAGCAGGATGCATC
Found at i:3820840 original size:21 final size:21
Alignment explanation
Indices: 3820814--3820867 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3820804 GTGGCAGGTG
3820814 CATGGATGCACTGCAGGGGTA
1 CATGGATGCACTGCAGGGGTA
* *
3820835 CATGGATGCACTGTAGGGGTG
1 CATGGATGCACTGCAGGGGTA
3820856 CATGGATGCACT
1 CATGGATGCACT
3820868 TTGACATCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGGTA
Found at i:3824559 original size:16 final size:16
Alignment explanation
Indices: 3824538--3824571 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3824528 CGTATCGCCA
*
3824538 ACAAAATTTACTATTC
1 ACAAAATTCACTATTC
3824554 ACAAAATTCACTATTC
1 ACAAAATTCACTATTC
3824570 AC
1 AC
3824572 GTGAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (16 bp):
ACAAAATTCACTATTC
Found at i:3825123 original size:18 final size:18
Alignment explanation
Indices: 3825091--3825125 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3825081 CCGGTTCTTC
*
3825091 CGACCGGTCGGACCAGTT
1 CGACCGGTCGAACCAGTT
*
3825109 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
3825126 GAACCGGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (18 bp):
CGACCGGTCGAACCAGTT
Found at i:3828499 original size:29 final size:28
Alignment explanation
Indices: 3828466--3828536 Score: 124
Period size: 29 Copynumber: 2.5 Consensus size: 28
3828456 AACAAAATCC
3828466 AAACAGTGACTAAAATGAATAAACATTAA
1 AAACAGTGACTAAAATGAATAAACA-TAA
3828495 AAACAGTGACTAAAATGAATAAACATAA
1 AAACAGTGACTAAAATGAATAAACATAA
*
3828523 AAAAAGTGACTAAA
1 AAACAGTGACTAAA
3828537 TTCAAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 16 0.39
29 25 0.61
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.18
Consensus pattern (28 bp):
AAACAGTGACTAAAATGAATAAACATAA
Found at i:3828553 original size:28 final size:30
Alignment explanation
Indices: 3828466--3828553 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 30
3828456 AACAAAATCC
*
3828466 AAACAGTGACTAAAATGAATAAACAT-TAA
1 AAACAGTGACTAAAATCAATAAACATATAA
*
3828495 AAACAGTGACTAAAATGAATAAACATA-AA
1 AAACAGTGACTAAAATCAATAAACATATAA
*
3828524 AAA-AGTGACTAAATTCAA-AAA-ATAATAA
1 AAACAGTGACTAAAATCAATAAACAT-ATAA
3828552 AA
1 AA
3828554 TTAATACACA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.04
27 4 0.07
28 17 0.31
29 31 0.57
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (30 bp):
AAACAGTGACTAAAATCAATAAACATATAA
Found at i:3830267 original size:138 final size:139
Alignment explanation
Indices: 3829879--3830413 Score: 745
Period size: 139 Copynumber: 3.8 Consensus size: 139
3829869 ACGATGATGT
* * * * * *
3829879 TGATCCAACTCCTTATGCGATAGAAACAAGCTAAGGTTGAAA-AAGTTCTTCTCATTATAAAACT
1 TGATTCAACTCCATATGCGAT-GAATCGAGCTAAGG-TCAAACAAGCTCTTCTCATTAT-AAACT
* * *
3829943 TCGTCTCCCTT-ATCGAATGAGTTCTTCTCATTATGAACTCTCCAATGGAAATGATGATCCCTCG
63 TCTTCT-CCTTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCG
* * *
3830007 AGTGAAGTATTAC
127 AGTGAGGTGTTGC
* * * *
3830020 TGATTCAACTCCATATGTGACGAATAGAGCTAAGGAT-AAACAAGCTCTTCTCATTATGAACTTC
1 TGATTCAACTCCATATGCGATGAATCGAGCTAAGG-TCAAACAAGCTCTTCTCATTATAAACTTC
* * *
3830084 TTCTCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTTGATCCCTCTAGT
65 TTCTCCTTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGT
3830149 GAGGTGTTGC
130 GAGGTGTTGC
* * *
3830159 TGATTCAACTCCATATGCGATGAATCGAGCTAAGGTCGAA-TAGCTCTTCTCATTATGAACTTCT
1 TGATTCAACTCCATATGCGATGAATCGAGCTAAGGTCAAACAAGCTCTTCTCATTATAAACTTCT
*
3830223 TCTCCTTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATACCTCGAGTG
66 TCTCCTTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTG
3830288 AGGTGTTGC
131 AGGTGTTGC
*
3830297 TGATTCAACTCCATATACGATGAATCGAGCTAAGGTCAAACAAGCTCTTCTCATTATAAACTTCT
1 TGATTCAACTCCATATGCGATGAATCGAGCTAAGGTCAAACAAGCTCTTCTCATTATAAACTTCT
* * *
3830362 TCTCCTTCATCGGGATGAGTTCTTCTAATTATGAACTCTCCATTTGAAATGT
66 TCTCCTTCATC-GAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
3830414 GTATTGGTTC
Statistics
Matches: 354, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
138 136 0.38
139 137 0.39
140 64 0.18
141 17 0.05
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (139 bp):
TGATTCAACTCCATATGCGATGAATCGAGCTAAGGTCAAACAAGCTCTTCTCATTATAAACTTCT
TCTCCTTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTG
AGGTGTTGC
Found at i:3831448 original size:42 final size:41
Alignment explanation
Indices: 3831348--3831448 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
3831338 ATGGATGGCT
* *
3831348 CGAAGGACTTATCATCTTGCTCGAATGACTTATAGATGACC
1 CGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGACC
* * *
3831389 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTA-ATGCCC
1 CGAAGGACTT-ATCATCATGCTCGAAAGACTTA-TAGATGACC
3831431 CAGAA-GACTTATTCATCA
1 C-GAAGGACTTA-TCATCA
3831449 AGAAACCCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
41 10 0.20
42 34 0.69
43 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGACC
Found at i:3831449 original size:274 final size:274
Alignment explanation
Indices: 3830939--3831476 Score: 758
Period size: 274 Copynumber: 2.0 Consensus size: 274
3830929 AGTTGTCATC
** * *
3830939 AAGGAACCCCTAAAAATTAGGCCTAGCTTCCTTTAAAAATTATTTGGAGATAATCGTCAAGAAAC
1 AAGGAACCCCTAAAAATTAGGCCTAAATTCCTTTAAAAACTATTTGGAGATAATCATCAAGAAAC
* * * * * * * * *
3831004 CCTTGAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCGTGCCCGAAGGTCTTATTGA
66 CCCTGAAAATCAAGCTTAATTTCTAAAAACTCATTTGAAAACATCCTGCCCAAAGGCCATATGGA
* *
3831069 TGGTCCGAATGACTTATCATCTTGCTCAAAAGACTTATAGATGGCCCAAAAGATTTAAGCACCAC
131 TGGTCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCAAAAGATTTAAGCACCAC
* *
3831134 GCTCGAAAGACTTACTGATATCCAGAATGACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
196 GCTCGAAAGACTTACTAATACCCAGAATGACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
3831199 GTTTTTTAGCTGTT
261 GTTTTTTAGCTGTT
** * *
3831213 AAGGAA-CCCTAAAAATTAGGTTTAAATTCTTTTTAAAAACTCTTTGGAGATAATCATCAAGAAA
1 AAGGAACCCCTAAAAATTAGGCCTAAATTC-CTTTAAAAACTATTTGGAGATAATCATCAAGAAA
*
3831277 CCCCTGAAAATCAAGCTTAATTTCTAAAAACTTATTTGAAAACATCCTGCCCAAAGGCCATATGG
65 CCCCTGAAAATCAAGCTTAATTTCTAAAAACTCATTTGAAAACATCCTGCCCAAAGGCCATATGG
* * * * *
3831342 ATGG-CTCGAAGGACTTATCATCTTGCTCGAATGACTTATAGATGACCCGAAGGATTTAAGCATC
130 ATGGTC-CGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCAAAAGATTTAAGCACC
* * *
3831406 ATGCTCGAAAGACTTACTAATGCCCCAGAA-GACTTATTCATCAAGAAACCCTTGAAAATCAAGC
194 ACGCTCGAAAGACTTACTAAT-ACCCAGAATGACTTACTCATCAAGAAACCCTTGAAAATCAAGC
3831470 TTAGTTT
258 TTAGTTT
3831477 CTTAAAATAT
Statistics
Matches: 231, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
273 20 0.09
274 205 0.89
275 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (274 bp):
AAGGAACCCCTAAAAATTAGGCCTAAATTCCTTTAAAAACTATTTGGAGATAATCATCAAGAAAC
CCCTGAAAATCAAGCTTAATTTCTAAAAACTCATTTGAAAACATCCTGCCCAAAGGCCATATGGA
TGGTCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCAAAAGATTTAAGCACCAC
GCTCGAAAGACTTACTAATACCCAGAATGACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
GTTTTTTAGCTGTT
Found at i:3831660 original size:107 final size:107
Alignment explanation
Indices: 3831501--3831799 Score: 323
Period size: 107 Copynumber: 2.8 Consensus size: 107
3831491 TTTTTCAGTT
* * *
3831501 ATCATCAAGAAACTCCTAAAATTAGGTTTAGTTTCTTTAAAAATGCATTTGAAAATAACATGAAA
1 ATCATCAAGAAACTCCTAAAATTAGGCTTAGTTTCTTT-AAAATTCATTTGAAAATAACAAGAAA
* * * *
3831566 CCCCTGAAAATTAGGCTGAATTTCTTTGAAA-ATTCATTTGAAA
65 CCCCTGAAAATCAGACTGAATTTATTTGAAAGATT-ATTTAAAA
* * * * * *
3831609 A-CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCAGTTGAAAACATCAAGAAA
1 ATCATCAAGAAACTCCT-AAAATTAGGCTTAGTTTCTTTAAAATTCATTTGAAAATAACAAGAAA
* * *
3831673 CCCCTGAAAATCAGACTTAGTTTATTTGAAAGGTTATTTAAAA
65 CCCCTGAAAATCAGACTGAATTTATTTGAAAGATTATTTAAAA
* * * **
3831716 ATCATCAAGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATTGTCAAGA
1 ATCATCAAGAAACTCCT-AAAATTAGGCTTAGTTTCTTTAAAA-TTCATTTGAAAA-TAACAAGA
**
3831781 AACTTCTGAAAATCAGACT
63 AACCCCTGAAAATCAGACT
3831800 TAGTTTCCAA
Statistics
Matches: 158, Mismatches: 28, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
107 68 0.43
108 57 0.36
109 10 0.06
110 23 0.15
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (107 bp):
ATCATCAAGAAACTCCTAAAATTAGGCTTAGTTTCTTTAAAATTCATTTGAAAATAACAAGAAAC
CCCTGAAAATCAGACTGAATTTATTTGAAAGATTATTTAAAA
Found at i:3831674 original size:53 final size:54
Alignment explanation
Indices: 3831503--3831806 Score: 290
Period size: 55 Copynumber: 5.6 Consensus size: 54
3831493 TTTCAGTTAT
* * *
3831503 CATCAAGAAACTCCT-AAAATTAGGTTTAGTTTCTTTAAAAATGCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAAA
* * * * * *
3831556 TAACATGAAACCCCTGAAAATTAGGCTGAATTTCTTTGAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAAA
* * * *
3831610 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-CAAATTCAGTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAAA
* * * ** *
3831663 CATCAAGAAACCCCTGAAAATCAGACTTAGTTTATTTGAAAGGTT-ATTTAAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTT-AAAAATTCATTTGAAAA
** * **
3831717 TCATCAAGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAGCTCATTTGAAAA
1 -CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAAA
** ** * *
3831772 TTGTCAAGAAACTTCTGAAAATCAGACTTAGTTTC
1 -CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTC
3831807 CAAAAAAAAA
Statistics
Matches: 208, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
53 57 0.27
54 75 0.36
55 76 0.37
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (54 bp):
CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAAA
Found at i:3831806 original size:55 final size:53
Alignment explanation
Indices: 3831503--3831806 Score: 288
Period size: 54 Copynumber: 5.6 Consensus size: 53
3831493 TTTCAGTTAT
* ** *
3831503 CATCAAGAAACTCCT-AAAATTAGGTTTAGTTTCTTTAAAAATGCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTT-AAAATTCATTTGAAAA
* * * * * *
3831556 TAACATGAAACCCCTGAAAATTAGGCTGAATTTCTTTGAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTT-AAAATTCATTTGAAAA
* * * * *
3831610 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCAGTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTTAAAATTCATTTGAAAA
* * * *
3831663 CATCAAGAAACCCCTGAAAATCAGACTTAGTTTATTTGAAAGGTT-ATTTAAAAA
1 CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTT-AAA-ATTCATTTGAAAA
** *
3831717 TCATCAAGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAGCTCATTTGAAAA
1 -CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTTAAAA-TTCATTTGAAAA
** ** *
3831772 TTGTCAAGAAACTTCTGAAAATCAGACTTAGTTTC
1 -CATCAAGAAACCCCTGAAAATTAGACTTAGTTTC
3831807 CAAAAAAAAA
Statistics
Matches: 208, Mismatches: 37, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
53 57 0.27
54 76 0.37
55 75 0.36
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (53 bp):
CATCAAGAAACCCCTGAAAATTAGACTTAGTTTCTTTAAAATTCATTTGAAAA
Found at i:3833031 original size:19 final size:19
Alignment explanation
Indices: 3833007--3833054 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3832997 TTGAACAGTA
3833007 GGGGGAATCGATACCCCTG
1 GGGGGAATCGATACCCCTG
3833026 GGGGGAATCGATACCCCTG
1 GGGGGAATCGATACCCCTG
3833045 GGGGGAATCG
1 GGGGGAATCG
3833055 GTTCCCTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.42, T:0.15
Consensus pattern (19 bp):
GGGGGAATCGATACCCCTG
Found at i:3835688 original size:22 final size:23
Alignment explanation
Indices: 3835661--3835722 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3835651 CGATTTCCCT
3835661 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCATTCAA
*
3835684 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCATTCAA
* *
3835706 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
3835723 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCATTCAA
Found at i:3842619 original size:28 final size:28
Alignment explanation
Indices: 3842581--3842652 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
3842571 AGGATTCCTT
* *
3842581 GGGAAGGTAATGTGTTTCAGGTTAGTTTG
1 GGGAA-GTAATGTGTTTCAGGTCAATTTG
** *
3842610 GGGAAGTAATACGTTTTAGGTCAATTTG
1 GGGAAGTAATGTGTTTCAGGTCAATTTG
* *
3842638 GGGAGGCAATGTGTT
1 GGGAAGTAATGTGTT
3842653 CCGGGTTGGC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.24, C:0.06, G:0.36, T:0.35
Consensus pattern (28 bp):
GGGAAGTAATGTGTTTCAGGTCAATTTG
Found at i:3843325 original size:8 final size:8
Alignment explanation
Indices: 3843312--3843393 Score: 60
Period size: 9 Copynumber: 9.9 Consensus size: 8
3843302 TATTTTCTTC
3843312 TTTCTTTT
1 TTTCTTTT
3843320 TTTCTTTT
1 TTTCTTTT
3843328 TTTCCTTTT
1 TTT-CTTTT
*
3843337 CTTCTGTTT
1 TTTCT-TTT
*
3843346 TCTCTTTCT
1 TTTCTTT-T
*
3843355 TTT-TTTC
1 TTTCTTTT
*
3843362 TTT-TTTC
1 TTTCTTTT
3843369 TTTCTCTTT
1 TTTCT-TTT
3843378 TTTCTGTTT
1 TTTCT-TTT
*
3843387 TTACTTT
1 TTTCTTT
3843394 CCTTTTGTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
7 10 0.16
8 21 0.34
9 30 0.49
ACGTcount: A:0.01, C:0.18, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTCTTTT
Found at i:3843376 original size:21 final size:21
Alignment explanation
Indices: 3843304--3843399 Score: 80
Period size: 21 Copynumber: 4.7 Consensus size: 21
3843294 GATATGTCTA
*
3843304 TTTTCTTCTTTCTTTTTTTC--
1 TTTTCTT-TCTCTTTTTTTCTT
* *
3843324 TTTT-TTTC-CTTTTCTTCTG
1 TTTTCTTTCTCTTTTTTTCTT
3843343 TTTTCTCTT-TCTTTTTTTCTT
1 TTTTCT-TTCTCTTTTTTTCTT
3843364 TTTTCTTTCTC-TTTTTTCTGT
1 TTTTCTTTCTCTTTTTTTCT-T
3843385 TTTTACTTTC-CTTTT
1 TTTT-CTTTCTCTTTT
3843400 GTGTGTGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
17 8 0.13
18 1 0.02
19 6 0.10
20 15 0.24
21 25 0.40
22 8 0.13
ACGTcount: A:0.01, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTTTCTCTTTTTTTCTT
Found at i:3843387 original size:7 final size:7
Alignment explanation
Indices: 3843304--3843393 Score: 67
Period size: 8 Copynumber: 12.1 Consensus size: 7
3843294 GATATGTCTA
3843304 TTTTCTT
1 TTTTCTT
*
3843311 CTTTCTTT
1 TTTTC-TT
3843319 TTTTCTTT
1 TTTTC-TT
3843327 TTTTCCTT
1 TTTT-CTT
*
3843335 TTCTTCTG
1 TT-TTCTT
3843343 TTTTC-T
1 TTTTCTT
*
3843349 CTTTCTTT
1 TTTTC-TT
3843357 TTTTCTT
1 TTTTCTT
3843364 TTTTC-T
1 TTTTCTT
*
3843370 TTCTCTT
1 TTTTCTT
3843377 TTTTCTGT
1 TTTTCT-T
3843385 TTTTACTT
1 TTTT-CTT
3843393 T
1 T
3843394 CCTTTTGTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
6 9 0.13
7 20 0.30
8 33 0.49
9 5 0.07
ACGTcount: A:0.01, C:0.19, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:3843410 original size:22 final size:22
Alignment explanation
Indices: 3843339--3843410 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
3843329 TTCCTTTTCT
*
3843339 TCTGTTTTCT-CTTTCT-TTTTT
1 TCTGTTTT-TACTTTCTCTTTTG
*
3843360 TCT-TTTTT-CTTTCTCTTTTT
1 TCTGTTTTTACTTTCTCTTTTG
3843380 TCTGTTTTTACTTTC-CTTTTG
1 TCTGTTTTTACTTTCTCTTTTG
*
3843401 TGTGTGTTTT
1 TCTGT-TTTT
3843411 TTTCTATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.16
20 12 0.27
21 17 0.38
22 9 0.20
ACGTcount: A:0.01, C:0.17, G:0.08, T:0.74
Consensus pattern (22 bp):
TCTGTTTTTACTTTCTCTTTTG
Found at i:3849697 original size:18 final size:19
Alignment explanation
Indices: 3849674--3849710 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3849664 CCAGTAATCC
3849674 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
3849692 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
3849711 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:3856840 original size:14 final size:14
Alignment explanation
Indices: 3856823--3856855 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3856813 ATTTCTATGT
*
3856823 AGGGAATTATTTGC
1 AGGGAATTATTTAC
3856837 AGGGAATTATTTAC
1 AGGGAATTATTTAC
3856851 AGGGA
1 AGGGA
3856856 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:3870618 original size:16 final size:16
Alignment explanation
Indices: 3870597--3870628 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3870587 ACTATTCATA
*
3870597 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
3870613 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
3870629 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:3885240 original size:10 final size:10
Alignment explanation
Indices: 3885215--3885252 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3885205 TGCTTGAAGA
*
3885215 AGAAATAAAAG
1 AGAAA-AAATG
3885226 AGAAAAAATG
1 AGAAAAAATG
3885236 AG-AAAAATG
1 AGAAAAAATG
3885245 AGAAAAAA
1 AGAAAAAA
3885253 GAAAAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 11 0.44
11 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (10 bp):
AGAAAAAATG
Found at i:3885241 original size:8 final size:9
Alignment explanation
Indices: 3885229--3885344 Score: 58
Period size: 8 Copynumber: 13.6 Consensus size: 9
3885219 ATAAAAGAGA
3885229 AAAAATGAG
1 AAAAATGAG
3885238 AAAAATGAG
1 AAAAATGAG
3885247 AAAAA--AG
1 AAAAATGAG
3885254 AAAAATGATGG
1 AAAAATGA--G
*
3885265 AAAAA--AT
1 AAAAATGAG
3885272 AAAAA-GA-
1 AAAAATGAG
3885279 AAAAATG-G
1 AAAAATGAG
**
3885287 AAAAGGGAAG
1 AAAAATG-AG
3885297 AAAAA--ATG
1 AAAAATGA-G
*
3885305 AAAAATGAAAA
1 AAAAATG--AG
3885316 AAAAATGA-
1 AAAAATGAG
3885324 AAAAA-GAG
1 AAAAATGAG
3885332 AAAAATGA-
1 AAAAATGAG
3885340 AAAAA
1 AAAAA
3885345 AAAGAAATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 33
0.69 0.04 0.27
Matches are distributed among these distances:
7 20 0.23
8 28 0.33
9 19 0.22
10 5 0.06
11 13 0.15
12 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (9 bp):
AAAAATGAG
Found at i:3885345 original size:18 final size:18
Alignment explanation
Indices: 3885228--3885351 Score: 64
Period size: 18 Copynumber: 6.7 Consensus size: 18
3885218 AATAAAAGAG
*
3885228 AAAAAATGAGAAAAATGA
1 AAAAAAAGAGAAAAATGA
*
3885246 GAAAAAAGA-AAAATGATGGAA
1 AAAAAAAGAGAAAA--AT-G-A
*
3885267 AAAATAAAAAGAAAAAATGGA
1 AAAA-AAAGAG-AAAAAT-GA
**
3885288 AAAGGGAAGA-AAAAATGA
1 AAA-AAAAGAGAAAAATGA
3885306 AAAATGAAA-A-AAAAATG-
1 AAAA--AAAGAGAAAAATGA
3885323 -AAAAAAGAGAAAAATGA
1 AAAAAAAGAGAAAAATGA
3885340 AAAAAAA-AGAAA
1 AAAAAAAGAGAAA
3885352 TAAAAGGAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 10 0.12
17 9 0.11
18 26 0.31
19 10 0.12
20 1 0.01
21 11 0.13
22 8 0.10
24 4 0.05
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAAAAAGAGAAAAATGA
Found at i:3885345 original size:19 final size:18
Alignment explanation
Indices: 3885267--3885351 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
3885257 AATGATGGAA
3885267 AAAATAAAAAGAAAAAATGG
1 AAAA-AAAAAGAAAAAAT-G
***
3885287 AAAAGGGAAGAAAAAATG
1 AAAAAAAAAGAAAAAATG
*
3885305 AAAAATGAAA-AAAAAATG
1 AAAAA-AAAAGAAAAAATG
*
3885323 -AAAAAAGAG-AAAAATG
1 AAAAAAAAAGAAAAAATG
3885339 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
3885352 TAAAAGGAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
16 9 0.17
17 12 0.23
18 15 0.28
19 13 0.25
20 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAATG
Found at i:3885346 original size:26 final size:26
Alignment explanation
Indices: 3885221--3885351 Score: 96
Period size: 26 Copynumber: 5.0 Consensus size: 26
3885211 AAGAAGAAAT
*
3885221 AAAAGAGAAAAAATG-AGAAAAATGAGA
1 AAAAGAG-AAAAATGAAAAAAAATGA-A
*
3885248 AAAA-AGAAAAATGATGGAAAAAAT--A
1 AAAAGAGAAAAATGA--AAAAAAATGAA
**
3885273 AAAAGA-AAAAATGGAAAAGGGAA-GAA
1 AAAAGAGAAAAAT-GAAAA-AAAATGAA
*
3885299 AAAA-TGAAAAATGAAAAAAAAATGAA
1 AAAAGAGAAAAATG-AAAAAAAATGAA
*
3885325 AAAAGAGAAAAATGAAAAAAAAAGAA
1 AAAAGAGAAAAATGAAAAAAAATGAA
3885351 A
1 A
3885352 TAAAAGGAGG
Statistics
Matches: 82, Mismatches: 10, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
24 2 0.02
25 23 0.28
26 39 0.48
27 12 0.15
28 6 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAAGAGAAAAATGAAAAAAAATGAA
Found at i:3894904 original size:29 final size:29
Alignment explanation
Indices: 3894870--3894928 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3894860 CCTAAATTAA
*
3894870 TTTGATGTCATTGCTTACGTCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3894899 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3894928 T
1 T
3894929 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:3899573 original size:29 final size:29
Alignment explanation
Indices: 3899539--3899597 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3899529 CCTAAATTAA
3899539 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGTTTACATCAATTTAGT
*
3899568 TTTGATGTCATTGTTTACGTCAATTTAGT
1 TTTGATGTCATTGTTTACATCAATTTAGT
3899597 T
1 T
3899598 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTGTTTACATCAATTTAGT
Found at i:3915817 original size:21 final size:22
Alignment explanation
Indices: 3915771--3915818 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3915761 CTAGCACTCC
*
3915771 AAAAGAAGAAAACAAAAAGAAT
1 AAAAGAAGAAAACAAAAAGAAG
*
3915793 AAAA-AAGAAAATAAAATA-AAG
1 AAAAGAAGAAAACAAAA-AGAAG
3915814 AAAAG
1 AAAAG
3915819 TTGAAAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (22 bp):
AAAAGAAGAAAACAAAAAGAAG
Found at i:3925877 original size:112 final size:112
Alignment explanation
Indices: 3925675--3925896 Score: 417
Period size: 112 Copynumber: 2.0 Consensus size: 112
3925665 TAAACTATGC
*
3925675 TAGTATTTTTTATTTTTAGTCCGATCAACTTTGGTCATCAATTTAAAAATTAAGGGGAAATGTTT
1 TAGTATTTTTTATTTTTAGGCCGATCAACTTTGGTCATCAATTTAAAAATTAAGGGGAAATGTTT
3925740 CTTAACATTATCGATTCGTTTGGTTTAAGTCCCTAATATTATCAGCA
66 CTTAACATTATCGATTCGTTTGGTTTAAGTCCCTAATATTATCAGCA
* *
3925787 TAGTCTTTTTTATTTTTAGGCTGATCAACTTTGGTCATCAATTTAAAAATTAAGGGGAAATGTTT
1 TAGTATTTTTTATTTTTAGGCCGATCAACTTTGGTCATCAATTTAAAAATTAAGGGGAAATGTTT
3925852 CTTAACATTATCGATTCGTTTGGTTTAAGTCCCTAATATTATCAG
66 CTTAACATTATCGATTCGTTTGGTTTAAGTCCCTAATATTATCAG
3925897 TCCATTCAAT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (112 bp):
TAGTATTTTTTATTTTTAGGCCGATCAACTTTGGTCATCAATTTAAAAATTAAGGGGAAATGTTT
CTTAACATTATCGATTCGTTTGGTTTAAGTCCCTAATATTATCAGCA
Found at i:3925997 original size:3 final size:3
Alignment explanation
Indices: 3925989--3926058 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
3925979 AAATTCAAAA
3925989 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
3926037 CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT C
3926059 AAAAGTCTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:3926747 original size:19 final size:18
Alignment explanation
Indices: 3926723--3926784 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
3926713 AAAATCGAAA
3926723 TCGGTTTTTTCGGTTCGGT
1 TCGGTTTTTTC-GTTCGGT
*
3926742 TCGGTTTTTT--TAACGGT
1 TCGGTTTTTTCGT-TCGGT
*
3926759 TCGGATTTTTCGATTCGGT
1 TCGGTTTTTTCG-TTCGGT
3926778 TCGGTTT
1 TCGGTTT
3926785 ATAGGTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.27, T:0.52
Consensus pattern (18 bp):
TCGGTTTTTTCGTTCGGT
Found at i:3930119 original size:407 final size:408
Alignment explanation
Indices: 3929360--3930172 Score: 1331
Period size: 407 Copynumber: 2.0 Consensus size: 408
3929350 TCAAATTCTC
*
3929360 ACTTGAACTGATCTGATTAACTTTTATCTCTTTAATCTTCTGAAGGTCATAAGTGAAGAAGAATT
1 ACTTGAACTGATCTGATTAACTTTTATCTCTTTAAGCTTCTGAAGGTCATAAGTGAAGAAGAATT
* *
3929425 TAGGTACAATGTGTTTTGTTCTATTACCTTTGATATGCCCACTCTTGAGTTGTTCAATGCATGCT
66 TAGGTACAATGTGTTTTGTTCCATTACCATTGATATGCCCACTCTTGAGTTGTTCAATGCATGCT
* * * *
3929490 ATATTATCTTCAAACAAGACACTAAAAAAACTTCTTTTCCATATGATAAACCATAATTATTCCGT
131 ATATTATCTTAAAAAAAGACACT-AAAAAACTTCTTTTCCAGATGATAAACCACAATTATTCCGT
*
3929555 ATATGCTGAATCATAGATCTTAGTCATACACATTCACGACTAGCTTCATGGATTGCTAAGATTTT
195 ATATGCTGAATCATAGATCTTAGCCATACACATTCACGACTAGCTTCATGGATTGCTAAGATTTT
* * * *
3929620 TGTATGATTAGAAGAAGTTGCTACAATCATTTGCTTCATGGAGCACCAAGAGATTGTTGTACCAC
260 TGCATGATTAGAAGAAGTTGATACAAGCATTTGCTTCATGGAGCACCAAGAGATTATTGTACCAC
* * * *
3929685 CATATGTAAAAACATATCCAGTCTATGATTTACCATTATAAGGATATGACGTAAATATTGCATAT
325 CATATATAAAAAAATATCCAATCTATGATTTACCATTATAAGGATATGACATAAATATTGCATAT
3929750 GCAAAACCAATTAACTCTT
390 GCAAAACCAATTAACTCTT
* *
3929769 ACTTGAACTGATCTGGTTAACTTTTATCTCTTTAAGCTTCTGAAGGTCATGAGTGAAGAAGAATT
1 ACTTGAACTGATCTGATTAACTTTTATCTCTTTAAGCTTCTGAAGGTCATAAGTGAAGAAGAATT
*
3929834 TAGGTACAATGTGTTTTGTTCCATTACCATTGATGTGCCCACTCTTGAGTTGTTCAATGCATGCT
66 TAGGTACAATGTGTTTTGTTCCATTACCATTGATATGCCCACTCTTGAGTTGTTCAATGCATGCT
* * ** *
3929899 ATATTGTCTTAAAAAAAGACAGT-AGGAACTTCTTTTCTAGATGATAAACCACAATTATTCCGTA
131 ATATTATCTTAAAAAAAGACACTAAAAAACTTCTTTTCCAGATGATAAACCACAATTATTCCGTA
*
3929963 TATGCTGAATCATAGATTTTAGCCATACACATTCACGACTAGCTTCATGGATTGCTAAGATTTTT
196 TATGCTGAATCATAGATCTTAGCCATACACATTCACGACTAGCTTCATGGATTGCTAAGATTTTT
* * *
3930028 GCATGATTAGAAGAAGTTGATGCAAGCGTTTGCTTCATGGAGCGCCAAGAGATTATTGTACCACC
261 GCATGATTAGAAGAAGTTGATACAAGCATTTGCTTCATGGAGCACCAAGAGATTATTGTACCACC
* * *
3930093 ATATATAAAAAAATATCCAATCTATGATTTACCATTATGAGGATCTGACATAAATATTGTATATG
326 ATATATAAAAAAATATCCAATCTATGATTTACCATTATAAGGATATGACATAAATATTGCATATG
3930158 CAAAACCAATTAACT
391 CAAAACCAATTAACT
3930173 TTGTTTTGGA
Statistics
Matches: 373, Mismatches: 31, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
407 230 0.62
409 143 0.38
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (408 bp):
ACTTGAACTGATCTGATTAACTTTTATCTCTTTAAGCTTCTGAAGGTCATAAGTGAAGAAGAATT
TAGGTACAATGTGTTTTGTTCCATTACCATTGATATGCCCACTCTTGAGTTGTTCAATGCATGCT
ATATTATCTTAAAAAAAGACACTAAAAAACTTCTTTTCCAGATGATAAACCACAATTATTCCGTA
TATGCTGAATCATAGATCTTAGCCATACACATTCACGACTAGCTTCATGGATTGCTAAGATTTTT
GCATGATTAGAAGAAGTTGATACAAGCATTTGCTTCATGGAGCACCAAGAGATTATTGTACCACC
ATATATAAAAAAATATCCAATCTATGATTTACCATTATAAGGATATGACATAAATATTGCATATG
CAAAACCAATTAACTCTT
Found at i:3933102 original size:24 final size:24
Alignment explanation
Indices: 3933075--3933120 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3933065 AGATATATAA
* *
3933075 TTTTTATATTTGT-AGTTATGTAT
1 TTTTTTTATTTCTAAGTTATGTAT
*
3933098 TTTTTTTCTTTCTAAGTTATGTA
1 TTTTTTTATTTCTAAGTTATGTA
3933121 AAAATGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTTTATTTCTAAGTTATGTAT
Found at i:3933299 original size:20 final size:20
Alignment explanation
Indices: 3933260--3933304 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3933250 TTTTTTTTAA
*
3933260 TAAATTTTTATCTATGAAAT
1 TAAATTTTTATCTATAAAAT
* *
3933280 TAAATTTTTATTTTTAAAAT
1 TAAATTTTTATCTATAAAAT
*
3933300 AAAAT
1 TAAAT
3933305 ATTAAAAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TAAATTTTTATCTATAAAAT
Found at i:3939891 original size:30 final size:29
Alignment explanation
Indices: 3939855--3939925 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
3939845 TATTATATTC
3939855 TATTTAATTTTTGTTAGTATTTTATTTAAT
1 TATTTAATTTTT-TTAGTATTTTATTTAAT
3939885 TATTTAATTTTTTTAGTATTTTATTTAAT
1 TATTTAATTTTTTTAGTATTTTATTTAAT
*
3939914 TATTTTATTTTT
1 TATTTAATTTTT
3939926 CTTTTGTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.70
Consensus pattern (29 bp):
TATTTAATTTTTTTAGTATTTTATTTAAT
Found at i:3939919 original size:13 final size:13
Alignment explanation
Indices: 3939872--3939923 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3939862 TTTTTGTTAG
3939872 TATTTTATTTAAT
1 TATTTTATTTAAT
* * *
3939885 TATTTAATTTTTTTAG
1 TA-TT--TTATTTAAT
3939901 TATTTTATTTAAT
1 TATTTTATTTAAT
3939914 TATTTTATTT
1 TATTTTATTT
3939924 TTCTTTTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 18 0.60
14 2 0.07
15 2 0.07
16 8 0.27
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:3942016 original size:15 final size:15
Alignment explanation
Indices: 3941996--3942024 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3941986 GGACCCCTAT
3941996 ATCCCGAAGGACTAC
1 ATCCCGAAGGACTAC
3942011 ATCCCGAAGGACTA
1 ATCCCGAAGGACTA
3942025 TTATACCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (15 bp):
ATCCCGAAGGACTAC
Found at i:3942173 original size:23 final size:26
Alignment explanation
Indices: 3942136--3942188 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
3942126 TTCTCTTGTG
3942136 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
3942160 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
3942185 ATCA
1 ATCA
3942189 CATGAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:3942607 original size:64 final size:63
Alignment explanation
Indices: 3942495--3942720 Score: 215
Period size: 64 Copynumber: 3.5 Consensus size: 63
3942485 TAATGAAGGT
* * ** ** * * *
3942495 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTTGATGTATTATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTATTATTAATGGG
* *
3942559 ATGCATCGATGCACTCCTTATGCATCGAAT-CACCAATTGCATTCGATGTTTCATTATAAATGGG
1 ATGCATCGATGCACTACTTATGCATCG-ATGCACCAATTGCATTCGATGTTT-ATTATTAATGGG
** **
3942623 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTATTA--TTAATGGG
** *
3942686 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
3942721 TTCAAACAAT
Statistics
Matches: 134, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
62 3 0.02
63 6 0.04
64 124 0.93
65 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTATTATTAATGGG
Found at i:3948706 original size:23 final size:26
Alignment explanation
Indices: 3948669--3948737 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
3948659 TTCTCTTGTG
3948669 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
3948693 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
3948718 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
3948738 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:3948719 original size:12 final size:12
Alignment explanation
Indices: 3948702--3948737 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3948692 TATCATGTTC
3948702 TCATATCACATG
1 TCATATCACATG
*
3948714 TCATATCACATA
1 TCATATCACATG
3948726 TCATATCACATG
1 TCATATCACATG
3948738 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:3949125 original size:64 final size:64
Alignment explanation
Indices: 3949046--3949266 Score: 241
Period size: 64 Copynumber: 3.5 Consensus size: 64
3949036 TAATGAAGGT
* * * **
3949046 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGT-TTCATTATTAATGGG
** **
3949110 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGG
* ** * **
3949174 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATG-TTTCATTATTAATGGG
**
3949237 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3949267 ACACCTTCAA
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGG
Found at i:3959865 original size:15 final size:16
Alignment explanation
Indices: 3959837--3959866 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3959827 CGAACAGTTT
3959837 ATGTATACAAGTGTAC
1 ATGTATACAAGTGTAC
3959853 ATGTATA-AAGTGTA
1 ATGTATACAAGTGTA
3959867 TATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (16 bp):
ATGTATACAAGTGTAC
Found at i:3965906 original size:17 final size:17
Alignment explanation
Indices: 3965884--3965922 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3965874 AGTCGAGCTA
*
3965884 GAAGAGGCAGTTAGGAG
1 GAAGAGGCAGTAAGGAG
*
3965901 GAAGAGGCAGTAAGGCG
1 GAAGAGGCAGTAAGGAG
3965918 GAAGA
1 GAAGA
3965923 AGATTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.46, T:0.08
Consensus pattern (17 bp):
GAAGAGGCAGTAAGGAG
Found at i:3980205 original size:24 final size:25
Alignment explanation
Indices: 3980154--3980225 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 25
3980144 TAATCTTATA
*
3980154 TGGCACTACGGTGC--ATTTCTACG
1 TGGCACTACGGTGCAAATTTATACG
* *
3980177 AGGCACTTCGGTGCAAATTT-TACG
1 TGGCACTACGGTGCAAATTTATACG
**
3980201 TGGCACTAAAGTGCAAATTTATACG
1 TGGCACTACGGTGCAAATTTATACG
3980226 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 12 0.30
24 20 0.50
25 8 0.20
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
TGGCACTACGGTGCAAATTTATACG
Found at i:3980990 original size:12 final size:12
Alignment explanation
Indices: 3980973--3981004 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3980963 GAAATTTTTC
3980973 ACTGTTCACAGT
1 ACTGTTCACAGT
*
3980985 ACTGTTCACGGT
1 ACTGTTCACAGT
3980997 ACTGTTCA
1 ACTGTTCA
3981005 TACCGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (12 bp):
ACTGTTCACAGT
Found at i:3982875 original size:18 final size:18
Alignment explanation
Indices: 3982854--3982901 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3982844 TGTTTTAATA
*
3982854 TTATTATTATT-ATATTAT
1 TTATTATTATTAATA-AAT
3982872 TTATTATTATTAATAAAT
1 TTATTATTATTAATAAAT
*
3982890 TTAATATTATTA
1 TTATTATTATTA
3982902 CAAACAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTATTAATAAAT
Found at i:3982877 original size:15 final size:15
Alignment explanation
Indices: 3982827--3982881 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
3982817 TTTCATTTAT
* *
3982827 TTTATTACTATATTT
1 TTTATTATTATATTA
*
3982842 TTTGTT-TTAATATTA
1 TTTATTATT-ATATTA
3982857 -TTATTATTATATTA
1 TTTATTATTATATTA
3982871 TTTATTATTAT
1 TTTATTATTAT
3982882 TAATAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTATTATTATATTA
Found at i:3982897 original size:21 final size:21
Alignment explanation
Indices: 3982847--3982901 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3982837 TATTTTTTGT
* *
3982847 TTTAATATTATTATTATTATA
1 TTTAATATTATTATTAATAAA
*
3982868 -TTATTTATTATTATTAATAAA
1 TTTA-ATATTATTATTAATAAA
3982889 TTTAATATTATTA
1 TTTAATATTATTA
3982902 CAAACAGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATATTATTATTAATAAA
Done.