Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 65 of 147
Found at i:12282371 original size:85 final size:85
Alignment explanation
Indices: 12282227--12282539 Score: 509
Period size: 85 Copynumber: 3.7 Consensus size: 85
12282217 TTTAGAATGA
* * *
12282227 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAATCTGACATTATTATCCTATT
1 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAGTCCGACATTGTTATCCTATT
12282292 TTTTTAGAATTGATTGATAT
66 TTTTTAGAATTGATTGATAT
* *
12282312 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATATGTCCCACATTGTTATCCTATT
1 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAGTCCGACATTGTTATCCTATT
*
12282377 TCTTTAGAATTGATTGATAT
66 TTTTTAGAATTGATTGATAT
* *
12282397 TTTGAAAATTTTATTCAAGATGCAATTAAGCTAAACTTGAATAAGTGCGACATTGTTATCCTATT
1 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAGTCCGACATTGTTATCCTATT
* *
12282462 TTTCTAGAATTGATTGATTT
66 TTTTTAGAATTGATTGATAT
* * *
12282482 TTTGAAAATTTTATTTTAGATGCAATTAAGCTAAACTTGAATAAGTCTGAAATTGTTA
1 TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAGTCCGACATTGTTA
12282540 AAAATATTAA
Statistics
Matches: 210, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 210 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (85 bp):
TTTGAAAATTTTATTCTAGATGCAATTAAGCTAAACTTGAATAAGTCCGACATTGTTATCCTATT
TTTTTAGAATTGATTGATAT
Found at i:12283951 original size:5 final size:5
Alignment explanation
Indices: 12283941--12283977 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
12283931 AGAATGTGAG
12283941 GATAT GATAT GATAT GATAT GATAT -ATAT -ATAT -ATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
12283978 ATCTAAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (5 bp):
GATAT
Found at i:12284122 original size:63 final size:63
Alignment explanation
Indices: 12284042--12284167 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
12284032 GGATAAAAAT
* *
12284042 AAACGATATCTTGCAACTTAGATGTAGGTTTTCACAAATAAAATTTTAACATAATAGTGGGGC
1 AAACAATATCTTACAACTTAGATGTAGGTTTTCACAAATAAAATTTTAACATAATAGTGGGGC
12284105 AAACAATATCTTACAACTTAGATGTAGGTTTTCACAAATAAAATTTTAACATAATAGTGGGGC
1 AAACAATATCTTACAACTTAGATGTAGGTTTTCACAAATAAAATTTTAACATAATAGTGGGGC
12284168 CAAGACAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (63 bp):
AAACAATATCTTACAACTTAGATGTAGGTTTTCACAAATAAAATTTTAACATAATAGTGGGGC
Found at i:12289415 original size:12 final size:12
Alignment explanation
Indices: 12289398--12289432 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12289388 ACTTAGAAAC
12289398 ACCATTCAACAA
1 ACCATTCAACAA
*
12289410 ACCATTCAACCA
1 ACCATTCAACAA
12289422 ACCATTCAACA
1 ACCATTCAACA
12289433 TACGATTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (12 bp):
ACCATTCAACAA
Found at i:12289538 original size:79 final size:79
Alignment explanation
Indices: 12289421--12289663 Score: 301
Period size: 79 Copynumber: 3.1 Consensus size: 79
12289411 CCATTCAACC
* * *
12289421 AACCATTCAACATACGATTCAGCCCCCCAATATCATACAAAATCATTTAGCAAAATAATATCAGA
1 AACCATTCAGCATACGATTCAGCCCCCCAATATCATACAATACCATTTAGCAAAA-AATATCAGA
*
12289486 CAACAAGGTTCAGCA
65 CAACAAGGTTTAGCA
* * * * * * *
12289501 AACCATTCAGCATATGATTTAG-CCCCCAATATCATACAATAGCA-TTCGACAATACAATACCAT
1 AACCATTCAGCATACGATTCAGCCCCCCAATATCATACAATACCATTTAG-CAA-AAAATATCAG
* *
12289564 ACAATAAGATTTAGCA
64 ACAACAAGGTTTAGCA
* * *
12289580 AACCATTCAGCATACGATTCAGCCCCCCAATATCATATAATACCATTCAGCAAAAAAAATCAGAC
1 AACCATTCAGCATACGATTCAGCCCCCCAATATCATACAATACCATTTAGCAAAAAATATCAGAC
12289645 AACAAGGTTTAGCA
66 AACAAGGTTTAGCA
12289659 AACCA
1 AACCA
12289664 CAATATTTAA
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
78 3 0.02
79 87 0.64
80 43 0.32
81 2 0.01
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (79 bp):
AACCATTCAGCATACGATTCAGCCCCCCAATATCATACAATACCATTTAGCAAAAAATATCAGAC
AACAAGGTTTAGCA
Found at i:12295339 original size:21 final size:21
Alignment explanation
Indices: 12295315--12295377 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
12295305 GTTCTCGTTA
*
12295315 TTTGGAAGATGTTGCAATGAG
1 TTTGGAAGATGTTGAAATGAG
12295336 TTTGGAAGATGTTGAAATGAG
1 TTTGGAAGATGTTGAAATGAG
*
12295357 TTTGAAAGATGTTGAAATGAG
1 TTTGGAAGATGTTGAAATGAG
12295378 ATTTAATAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.33
Consensus pattern (21 bp):
TTTGGAAGATGTTGAAATGAG
Found at i:12299747 original size:134 final size:133
Alignment explanation
Indices: 12299573--12300001 Score: 466
Period size: 134 Copynumber: 3.2 Consensus size: 133
12299563 CAAATGCTAT
* * * * * * *
12299573 CAAAGCAACGTCATTTTTCT-AAAAAAAAATCACTAAATTAGTGACGTCTCAAAGATATAAATAC
1 CAAAACAACGACATTTTTCTCATAAAAACATCACTAAATTAGCGACGTCTCAAAGATACAAATGC
* * *
12299637 CGTTAATATAGAGACATTTTTAGATACAAACGCCTCTAAAGTAGTGACAGTTTAAGTTACAAACG
66 CGTTAATATAGAGACATTTTCAGATACAAATGCCTCTAAAGTAGTGAC-GTTTCAGTTACAAACG
12299702 TCAC
130 TCAC
* * * * *
12299706 TAAAACAATGACGTTTTTCTCATAAAAACATCACTAAATTAGCGACGTCTCAAATATACAAACGC
1 CAAAACAACGACATTTTTCTCATAAAAACATCACTAAATTAGCGACGTCTCAAAGATACAAATGC
* * * * * * ** *
12299771 TGCTAATATAGAGACGTTTTCATATATAAATGCCTCTAAAGTAATGGTGGTTTCAGTTACAAATG
66 CGTTAATATAGAGACATTTTCAGATACAAATGCCTCTAAAGTAGT-GACGTTTCAGTTACAAACG
12299836 TCAC
130 TCAC
* * * ** *
12299840 CAAAGCAACGCCATTTTTCTCATAAAAACGTCACTAAATTAGCGGTGTCTGAAAGATACAAATGC
1 CAAAACAACGACATTTTTCTCATAAAAACATCACTAAATTAGCGACGTCTCAAAGATACAAATGC
* * * *
12299905 CGTTAATATAAAGGCATTTTCAGATACAAATGCCTCTAAAGGAGTGACGTTTTCAGTTACAAATG
66 CGTTAATATAGAGACATTTTCAGATACAAATGCCTCTAAAGTAGTGACG-TTTCAGTTACAAACG
*
12299970 CCAC
130 TCAC
* * *
12299974 CAAAGCAAC-ATTATTTTTTTCATAAAAA
1 CAAAACAACGA-CATTTTTCTCATAAAAA
12300002 TGCAACTAAT
Statistics
Matches: 242, Mismatches: 50, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
133 17 0.07
134 224 0.93
135 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (133 bp):
CAAAACAACGACATTTTTCTCATAAAAACATCACTAAATTAGCGACGTCTCAAAGATACAAATGC
CGTTAATATAGAGACATTTTCAGATACAAATGCCTCTAAAGTAGTGACGTTTCAGTTACAAACGT
CAC
Found at i:12301496 original size:2 final size:2
Alignment explanation
Indices: 12301489--12301522 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12301479 TGGAATTTTC
12301489 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12301523 TTATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12301529 original size:2 final size:2
Alignment explanation
Indices: 12301524--12301563 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12301514 TCTCTCTCTT
12301524 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
12301564 AGTTCCTAAT
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:12302213 original size:15 final size:16
Alignment explanation
Indices: 12302193--12302226 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12302183 ATCACCAGAA
12302193 ATATAAGTTTT-ATTG
1 ATATAAGTTTTCATTG
*
12302208 ATATAATTTTTCATTG
1 ATATAAGTTTTCATTG
12302224 ATA
1 ATA
12302227 AAAACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (16 bp):
ATATAAGTTTTCATTG
Found at i:12302723 original size:11 final size:11
Alignment explanation
Indices: 12302703--12302746 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
12302693 ATACATTATC
12302703 AAACATCCATA
1 AAACATCCATA
*
12302714 AAATATCCAT-
1 AAACATCCATA
12302724 -AACATCCATA
1 AAACATCCATA
12302734 AAACAT-CATA
1 AAACATCCATA
12302744 AAA
1 AAA
12302747 TATCAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 7 0.24
11 14 0.48
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (11 bp):
AAACATCCATA
Found at i:12302759 original size:15 final size:15
Alignment explanation
Indices: 12302739--12302768 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12302729 CCATAAAACA
*
12302739 TCATAAAATATCAAT
1 TCATAAAACATCAAT
12302754 TCATAAAACATCAAT
1 TCATAAAACATCAAT
12302769 AGCATCCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATAAAACATCAAT
Found at i:12303312 original size:17 final size:17
Alignment explanation
Indices: 12303290--12303335 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
12303280 CACTAAAATA
*
12303290 TCACAATTTCAAACAAT
1 TCACAACTTCAAACAAT
12303307 TCACAACTTCAAACAAT
1 TCACAACTTCAAACAAT
*
12303324 TTACAACTTCAA
1 TCACAACTTCAA
12303336 GCATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (17 bp):
TCACAACTTCAAACAAT
Found at i:12304856 original size:18 final size:18
Alignment explanation
Indices: 12304833--12304872 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12304823 TTGTATCTGG
12304833 GGTGAACTTGACCAGTAT
1 GGTGAACTTGACCAGTAT
* *
12304851 GGTGAAGTTGACCCGTAT
1 GGTGAACTTGACCAGTAT
12304869 GGTG
1 GGTG
12304873 GATCATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.28
Consensus pattern (18 bp):
GGTGAACTTGACCAGTAT
Found at i:12305238 original size:3 final size:3
Alignment explanation
Indices: 12305230--12305288 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
12305220 CTCATGTGTT
* * *
12305230 TCA TCA TCA TCA TCA TCA TTA TCA TCA TCGG T-A TCA TCA TCA TTA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA
*
12305275 TCA TCA TCT TCA TC
1 TCA TCA TCA TCA TC
12305289 TTTTTTTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:12310045 original size:59 final size:59
Alignment explanation
Indices: 12309964--12310123 Score: 173
Period size: 59 Copynumber: 2.7 Consensus size: 59
12309954 CCAATAAATG
* *
12309964 TTAACAAATAT-GTAGCCAAAACCTAAACAAATTTCAA-AAA-ACATAAAACCAACAAAAAC
1 TTAACAAAT-TGGTAACCAAAACCCAAACAAATTTCAACAAATA-AT-AAACCAACAAAAAC
* * * * *
12310023 TTAACAAATTGGTAACCGAAACCCAAATAAATTTTAACAAATAATTAACTAACAAAAAC
1 TTAACAAATTGGTAACCAAAACCCAAACAAATTTCAACAAATAATAAACCAACAAAAAC
* * *
12310082 TCAATACATTGGTAACCAAAACCCAAACAAATTTCTAACAAA
1 TTAACAAATTGGTAACCAAAACCCAAACAAATTTC-AACAAA
12310124 AAATTGAACC
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 71 0.85
60 11 0.13
61 1 0.01
ACGTcount: A:0.55, C:0.20, G:0.04, T:0.21
Consensus pattern (59 bp):
TTAACAAATTGGTAACCAAAACCCAAACAAATTTCAACAAATAATAAACCAACAAAAAC
Found at i:12313565 original size:61 final size:60
Alignment explanation
Indices: 12313367--12313637 Score: 317
Period size: 61 Copynumber: 4.6 Consensus size: 60
12313357 TGCTTTTATA
*
12313367 CAAGGAAAATTGATACTTTCAACTTTTT-CTTAAAATACTTTTTAGAA-A-TTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATACTTTTTAGAACACTTTTATTTT
* * * *
12313424 TAAGGAAAATTGATACTTTC-ACCTTTTCCTCAAAATACTTTTT--AACAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATACTTTTTAGAACACTTTTATTTT
*
12313481 CAAGGAAAAATTGATACTTTCAACTTTTTCCTCAAAAATATTTTTTAGAACACTTTTATTTT
1 CAAGG-AAAATTGATACTTTCAACTTTTTCCT-AAAAATACTTTTTAGAACACTTTTATTTT
* * * * *
12313543 CAA-GACAAATTGATACTTTCAAC-TTTCCCTAAAAATATTTTTTTAAAAAAACTTTTACTTT
1 CAAGGA-AAATTGATACTTTCAACTTTTTCCTAAAAATA-CTTTTT-AGAACACTTTTATTTT
* *
12313604 CGAGGAAAATTGATATTTTCAACTTTTTCC-AAAA
1 CAAGGAAAATTGATACTTTCAACTTTTTCCTAAAA
12313638 TGCTTTTGGT
Statistics
Matches: 186, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
55 2 0.01
56 7 0.04
57 46 0.25
58 15 0.08
59 16 0.09
60 24 0.13
61 53 0.28
62 23 0.12
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (60 bp):
CAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATACTTTTTAGAACACTTTTATTTT
Found at i:12313822 original size:37 final size:38
Alignment explanation
Indices: 12313781--12313852 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
12313771 TTTTTTTAAA
*
12313781 AAAATAAA-CACAT-AAATGAAAAA-AATATAAAAAAAAG
1 AAAATAAACCA-ATAAAATAAAAAATAAT-TAAAAAAAAG
12313818 AAAATAAACCAATAAAATAAAAAATAATTAAAAAA
1 AAAATAAACCAATAAAATAAAAAATAATTAAAAAA
12313853 TACAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
37 10 0.32
38 18 0.58
39 3 0.10
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (38 bp):
AAAATAAACCAATAAAATAAAAAATAATTAAAAAAAAG
Found at i:12314707 original size:3 final size:3
Alignment explanation
Indices: 12314690--12314808 Score: 68
Period size: 3 Copynumber: 38.3 Consensus size: 3
12314680 CAAAAAAAAG
* * *
12314690 ATA AAA ATA AAA ATA ATA GATAA ATA ATA A-A AT- ATA TTA ATA GATA
1 ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA -ATA
* *
12314736 ACTA A-A A-A ATA ATA ATA ATA GATAA ATA A-A AAA ATA TTA ATA GATAA
1 A-TA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA -AT-A
*
12314783 ATA ATA ATA ATA ATGA AAA ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA A
12314809 AATTAAAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
2 10 0.11
3 59 0.64
4 20 0.22
5 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:12314746 original size:28 final size:24
Alignment explanation
Indices: 12314692--12314796 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
12314682 AAAAAAAGAT
*
12314692 AAAAATAAAAATAATAGATAAATA
1 AAAAATAATAATAATAGATAAATA
* *
12314716 ATAAAAT-ATATTAATAGATAACTA
1 A-AAAATAATAATAATAGATAAATA
12314740 AAAAATAATAATAATAGATAAAT-
1 AAAAATAATAATAATAGATAAATA
*
12314763 AAAAA-AATATTAATAGATAAAT-
1 AAAAATAATAATAATAGATAAATA
*
12314785 AATAATAATAAT
1 AAAAATAATAAT
12314797 GAAAAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
22 20 0.29
23 15 0.21
24 30 0.43
25 5 0.07
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAATAATAATAATAGATAAATA
Found at i:12314753 original size:48 final size:44
Alignment explanation
Indices: 12314688--12314811 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 44
12314678 ATCAAAAAAA
*
12314688 AGAT-AAAAATAAAAATAATAGATAAATAATAAAATATATTAAT
1 AGATAAAAAATAATAATAATAGATAAATAATAAAATATATTAAT
12314731 AGATAACTAAAAAATAATAATAATAGATAAATAA-AAAA-ATATTAAT
1 AG---A-TAAAAAATAATAATAATAGATAAATAATAAAATATATTAAT
* *
12314777 AGATAAATAATAATAATAAT-GAAAAATAATAAAAT
1 AGATAAAAAATAATAATAATAGATAAATAATAAAAT
12314812 TAAAAATTAA
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
41 8 0.11
42 20 0.28
43 3 0.04
46 11 0.15
47 5 0.07
48 24 0.34
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.27
Consensus pattern (44 bp):
AGATAAAAAATAATAATAATAGATAAATAATAAAATATATTAAT
Found at i:12314895 original size:19 final size:20
Alignment explanation
Indices: 12314863--12314900 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12314853 TATATTACCC
12314863 ATTTGGACCAGGA-CAATTA
1 ATTTGGACCAGGACCAATTA
* *
12314882 ATTTGGGCCTGGACCAATT
1 ATTTGGACCAGGACCAATT
12314901 TGGGTGTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
ATTTGGACCAGGACCAATTA
Found at i:12315138 original size:42 final size:42
Alignment explanation
Indices: 12315091--12315405 Score: 237
Period size: 42 Copynumber: 7.4 Consensus size: 42
12315081 AATAAACAAA
* *
12315091 GCTCCTCTAAGTAGAGGCTCAACAACTTTTAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCTCAACAACTTTTAGAAAATAAATT
* * *
12315133 GCTCCTCTAAATAGAGGCTCAACAATTTTTGGAAAGTAAATT
1 GCTCCTCTAAATAGAGGCTCAACAACTTTTAGAAAATAAATT
* * * *
12315175 GCTCCTCTAAACAGAGGCTCAATAACTTTTGGAAAGTAAATT
1 GCTCCTCTAAATAGAGGCTCAACAACTTTTAGAAAATAAATT
* * * * * ** * **
12315217 GTTCTTCTAAACAGATGTTCAATGAC-TTTGGAAAAATAAACAAA
1 GCTCCTCTAAATAGAGGCTCAACAACTTTTAG-AAAAT-AA-ATT
* *
12315261 GCTCCTCTAAATAGAGGCTCAACGACTTTT--AAAATAAATAAA
1 GCTCCTCTAAATAGAGGCTCAACAACTTTTAGAAAATAAAT--T
* * *
12315303 GCTCCTCTAAACAGA-G-ACAACAGAACTTTTGAGAAAATAAATA
1 GCTCCTCTAAATAGAGGCTCAAC--AACTTTT-AGAAAATAAATT
* * * * *
12315346 GCTCTTCTAAATAAAGGCAACAA-AACTTTGAGAAAATAAATG
1 GCTCCTCTAAATAGAGGC-TCAACAACTTTTAGAAAATAAATT
*
12315388 GCTCATCTAAATAGAGGC
1 GCTCCTCTAAATAGAGGC
12315406 AATAGAACTT
Statistics
Matches: 226, Mismatches: 33, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
40 5 0.02
41 8 0.04
42 154 0.68
43 21 0.09
44 22 0.10
45 12 0.05
46 4 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (42 bp):
GCTCCTCTAAATAGAGGCTCAACAACTTTTAGAAAATAAATT
Found at i:12315406 original size:42 final size:41
Alignment explanation
Indices: 12315296--12315418 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 41
12315286 CTTTTAAAAT
* * *
12315296 AAATAAA-GCTCCTCTAAACAGAGACAACAGAACTTTTGAGA
1 AAATAAATGCTCATCTAAATAGAGGCAACAGAAC-TTTGAGA
* * *
12315337 AAATAAATAGCTCTTCTAAATAAAGGCAACAAAACTTTGAGA
1 AAATAAAT-GCTCATCTAAATAGAGGCAACAGAACTTTGAGA
*
12315379 AAATAAATGGCTCATCTAAATAGAGGCAATAGAACTTTGA
1 AAATAAAT-GCTCATCTAAATAGAGGCAACAGAACTTTGA
12315419 AGGTAAATTG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 7 0.10
42 42 0.60
43 21 0.30
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (41 bp):
AAATAAATGCTCATCTAAATAGAGGCAACAGAACTTTGAGA
Found at i:12324565 original size:3 final size:3
Alignment explanation
Indices: 12324552--12324587 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
12324542 TATTCTATAG
12324552 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12324588 TTTCTTCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12325487 original size:24 final size:24
Alignment explanation
Indices: 12325442--12325496 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
12325432 CCTTTTCCTT
* * *
12325442 TTTA-TTTTATTTTTTGATTTTTA
1 TTTATTTTTATATTTTAAGTTTTA
*
12325465 TTTATTTTTATATTTTAAGTTTTG
1 TTTATTTTTATATTTTAAGTTTTA
12325489 TTT-TTTTT
1 TTTATTTTT
12325497 CAATTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTATTTTTATATTTTAAGTTTTA
Found at i:12325516 original size:25 final size:26
Alignment explanation
Indices: 12325484--12325532 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12325474 ATATTTTAAG
12325484 TTTTGTTTT-TTTT-CAATTTTTTCT
1 TTTTGTTTTATTTTACAATTTTTTCT
*
12325508 TTTTCGTTTTATTTTACTATTTTTT
1 TTTT-GTTTTATTTTACAATTTTTT
12325533 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 5 0.24
26 4 0.19
27 8 0.38
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTTGTTTTATTTTACAATTTTTTCT
Found at i:12325686 original size:36 final size:38
Alignment explanation
Indices: 12325607--12325689 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
12325597 AAACGTAAAA
12325607 AAAAAAAAAAAACACAAAAAAATCTTTTCAAATAAGTTTTC
1 AAAAAAAAAAAACACAAAAAAATCTTTT---ATAAGTTTTC
* *
12325648 AAAATAAAAAAACA-AAAAAGATCTTTT-TAAGTTTTC
1 AAAAAAAAAAAACACAAAAAAATCTTTTATAAGTTTTC
12325684 AAAAAA
1 AAAAAA
12325690 TATTTTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 14 0.36
40 12 0.31
41 13 0.33
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (38 bp):
AAAAAAAAAAAACACAAAAAAATCTTTTATAAGTTTTC
Found at i:12326532 original size:46 final size:46
Alignment explanation
Indices: 12326480--12326573 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
12326470 TAAATTTGAG
*
12326480 ATTTTTTATTTCTTTTC-ATTGCTTACACTTGCTTAATTATTTATTT
1 ATTTTTTACTT-TTTTCTATTGCTTACACTTGCTTAATTATTTATTT
*
12326526 ATTTTTTACTTTTTTCTATTGCTTATACTTGCTTAATTATTTATTT
1 ATTTTTTACTTTTTTCTATTGCTTACACTTGCTTAATTATTTATTT
12326572 AT
1 AT
12326574 CATATATACA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 5 0.11
46 40 0.89
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (46 bp):
ATTTTTTACTTTTTTCTATTGCTTACACTTGCTTAATTATTTATTT
Found at i:12329600 original size:5 final size:5
Alignment explanation
Indices: 12329590--12329634 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
12329580 GGTATGCAAA
* *
12329590 AAAAG AAAAG AAAA- AAAAT AAAA- AAAAT AAAA- AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
12329635 CAAAGAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 12 0.32
5 25 0.68
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:12329613 original size:10 final size:9
Alignment explanation
Indices: 12329590--12329630 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
12329580 GGTATGCAAA
*
12329590 AAAAGAAAAG
1 AAAA-AAAAT
12329600 AAAAAAAAT
1 AAAAAAAAT
12329609 AAAAAAAAT
1 AAAAAAAAT
*
12329618 AAAAAAAAG
1 AAAAAAAAT
12329627 AAAA
1 AAAA
12329631 GAAACAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 25 0.86
10 4 0.14
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:12331752 original size:3 final size:3
Alignment explanation
Indices: 12331714--12331849 Score: 156
Period size: 3 Copynumber: 46.7 Consensus size: 3
12331704 GGACTTTGTT
* * * *
12331714 TTA TTA TTT TTG TTA -TA TTA CTA -TA TTG TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * *
12331758 TTA CTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
12331805 -TA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12331850 TTCTTTCTTC
Statistics
Matches: 113, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
2 10 0.09
3 101 0.89
4 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12331752 original size:32 final size:32
Alignment explanation
Indices: 12331714--12331849 Score: 181
Period size: 32 Copynumber: 4.2 Consensus size: 32
12331704 GGACTTTGTT
* * *
12331714 TTATTATTTTTGTTAT-ATTACTA-TATTGTATA
1 TTATTATTATTATTATCATTA-TATTATTAT-TA
12331746 TTATTATTATTATTA-CTATTATATTATTATTA
1 TTATTATTATTATTATC-ATTATATTATTATTA
12331778 TTATTATTATTATTATCATTATCATTA-TATTA
1 TTATTATTATTATTATCATTAT-ATTATTATTA
12331810 TTATTATTATTATTATCATTATATTATTATTA
1 TTATTATTATTATTATCATTATATTATTATTA
12331842 TTATTATT
1 TTATTATT
12331850 TTCTTTCTTC
Statistics
Matches: 95, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.04
32 77 0.81
33 14 0.15
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (32 bp):
TTATTATTATTATTATCATTATATTATTATTA
Found at i:12331836 original size:26 final size:27
Alignment explanation
Indices: 12331748--12331849 Score: 156
Period size: 26 Copynumber: 3.9 Consensus size: 27
12331738 ATTGTATATT
* *
12331748 ATTATTATTATTACTATTA-TATTATT
1 ATTATTATTATTATTATTATTATTATC
*
12331774 ATTATTATTATTATTATTATCATTATC
1 ATTATTATTATTATTATTATTATTATC
12331801 ATTA-TATTATTATTATTATTATTATC
1 ATTATTATTATTATTATTATTATTATC
12331827 ATTA-TATTATTATTATTATTATT
1 ATTATTATTATTATTATTATTATT
12331850 TTCTTTCTTC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 62 0.87
27 9 0.13
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTATTATTATTATTATTATTATTATC
Found at i:12332310 original size:19 final size:18
Alignment explanation
Indices: 12332282--12332325 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12332272 ATTTTCTAAA
*
12332282 GAAATATGGGAATTTTGGG
1 GAAATTTGGG-ATTTTGGG
* *
12332301 GAAATTTGGGTTTTTTGG
1 GAAATTTGGGATTTTGGG
12332319 GAAATTT
1 GAAATTT
12332326 TTGGGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (18 bp):
GAAATTTGGGATTTTGGG
Found at i:12332320 original size:18 final size:18
Alignment explanation
Indices: 12332294--12332353 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
12332284 AATATGGGAA
*
12332294 TTTTGGGGAAATTTGGGT
1 TTTTTGGGAAATTTGGGT
12332312 TTTTTGGGAAATTTTTGGGT
1 TTTTTGGGAAA--TTTGGGT
***
12332332 TTTTTGGGCTTTTTGGGT
1 TTTTTGGGAAATTTGGGT
12332350 TTTT
1 TTTT
12332354 GGGCTTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 21 0.58
20 15 0.42
ACGTcount: A:0.10, C:0.02, G:0.32, T:0.57
Consensus pattern (18 bp):
TTTTTGGGAAATTTGGGT
Found at i:12332335 original size:9 final size:9
Alignment explanation
Indices: 12332323--12332365 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
12332313 TTTTGGGAAA
*
12332323 TTTTTGGGT
1 TTTTTGGGC
12332332 TTTTTGGGC
1 TTTTTGGGC
12332341 TTTTTGGG-
1 TTTTTGGGC
12332349 TTTTTGGGC
1 TTTTTGGGC
12332358 TTTTTGGG
1 TTTTTGGG
12332366 ATGAACATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.00, C:0.05, G:0.35, T:0.60
Consensus pattern (9 bp):
TTTTTGGGC
Found at i:12332352 original size:17 final size:18
Alignment explanation
Indices: 12332305--12332365 Score: 88
Period size: 17 Copynumber: 3.3 Consensus size: 18
12332295 TTTGGGGAAA
*
12332305 TTTGGGTTTTTTGGGAAATT
1 TTTGGGTTTTTTGGG--CTT
12332325 TTTGGGTTTTTTGGGCTT
1 TTTGGGTTTTTTGGGCTT
12332343 TTTGGG-TTTTTGGGCTT
1 TTTGGGTTTTTTGGGCTT
12332360 TTTGGG
1 TTTGGG
12332366 ATGAACATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 17 0.43
18 8 0.20
20 15 0.38
ACGTcount: A:0.05, C:0.03, G:0.34, T:0.57
Consensus pattern (18 bp):
TTTGGGTTTTTTGGGCTT
Found at i:12332785 original size:17 final size:15
Alignment explanation
Indices: 12332743--12332808 Score: 53
Period size: 17 Copynumber: 4.1 Consensus size: 15
12332733 TCCCTTTTCC
*
12332743 TTTTTATTTTTATTGAT
1 TTTTTATTTTAATT--T
12332760 TTTTATATTTTAAGTTT
1 TTTT-TATTTTAA-TTT
12332777 TGTTTTATTTTCAATTT
1 T-TTTTATTTT-AATTT
*
12332794 TTTTCATTTT-ATTT
1 TTTTTATTTTAATTT
12332808 T
1 T
12332809 ACTGGTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
14 5 0.12
16 8 0.19
17 16 0.37
18 12 0.28
19 2 0.05
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTAATTT
Found at i:12339170 original size:28 final size:25
Alignment explanation
Indices: 12339102--12339174 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
12339092 AAAAATCTTT
*
12339102 GAATTTTGAATGAGAATATTTAAGA
1 GAATTTTGAATGAGAATCTTTAAGA
* * *
12339127 -AGTTTTAAATAAGAATCTTTAAATGA
1 GAATTTTGAATGAGAATCTTT-AA-GA
12339153 GAATCTTTGAATGAGAATCTTT
1 GAAT-TTTGAATGAGAATCTTT
12339175 GTCTTTGAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 16 0.43
25 2 0.05
26 2 0.05
27 2 0.05
28 15 0.41
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.38
Consensus pattern (25 bp):
GAATTTTGAATGAGAATCTTTAAGA
Found at i:12339175 original size:14 final size:14
Alignment explanation
Indices: 12339102--12339175 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
12339092 AAAAATCTTT
12339102 GAAT-TTTGAATGA
1 GAATCTTTGAATGA
*
12339115 GAATATTT-AA-GA
1 GAATCTTTGAATGA
* * *
12339127 -AGT-TTTAAATAA
1 GAATCTTTGAATGA
*
12339139 GAATCTTTAAATGA
1 GAATCTTTGAATGA
12339153 GAATCTTTGAATGA
1 GAATCTTTGAATGA
12339167 GAATCTTTG
1 GAATCTTTG
12339176 TCTTTGAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
10 3 0.06
11 4 0.08
12 3 0.06
13 8 0.16
14 33 0.65
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (14 bp):
GAATCTTTGAATGA
Found at i:12339339 original size:23 final size:22
Alignment explanation
Indices: 12339271--12339340 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
12339261 TCACCAAAAG
*
12339271 TTTTTGAATGAGAAGCTTTGAA
1 TTTTTGAATGAGAACCTTTGAA
* * * * *
12339293 ATTTTGGATGTGAACCTCTAAA
1 TTTTTGAATGAGAACCTTTGAA
*
12339315 TTTTTCGAATGGGAACCTTTGAA
1 TTTTT-GAATGAGAACCTTTGAA
12339338 TTT
1 TTT
12339341 AGATTTTATC
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTTTGAATGAGAACCTTTGAA
Found at i:12339521 original size:33 final size:33
Alignment explanation
Indices: 12339461--12339531 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
12339451 AATTGACATT
* * ** * *
12339461 TGCATAGCATGCATTGCATTTTTGAATGTTTAG
1 TGCATAGCAGGCATTCCATTTAAGAATGTCTAA
*
12339494 TGCATAGTAGGCATTCCATTTAAGAATGTCTAA
1 TGCATAGCAGGCATTCCATTTAAGAATGTCTAA
12339527 TGCAT
1 TGCAT
12339532 GAGTTTAGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (33 bp):
TGCATAGCAGGCATTCCATTTAAGAATGTCTAA
Found at i:12340080 original size:4 final size:4
Alignment explanation
Indices: 12340073--12340119 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
12340063 TATTTTATAT
* * *
12340073 TTTA TTTA TTTA TTTA TTTA TCTA TTTA CTTA TTTA TTTA GTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
12340120 TTAGGTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:12341327 original size:12 final size:13
Alignment explanation
Indices: 12341303--12341327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12341293 AAAATAAAAA
12341303 AATAAAAATTTTT
1 AATAAAAATTTTT
12341316 AATAAAAATTTT
1 AATAAAAATTTT
12341328 GGAATTAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAAAAATTTTT
Found at i:12343140 original size:46 final size:46
Alignment explanation
Indices: 12343073--12343168 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
12343063 TTGGGTCAAA
12343073 TTAGAAATATCTTTTAATTTTTAAAATTTTCACCATTTAGGCCAAT
1 TTAGAAATATCTTTTAATTTTTAAAATTTTCACCATTTAGGCCAAT
* * * * *
12343119 TTAGAAATATCTTTTAATTTTTAAATTTTTTACTATTTGGGCCTAT
1 TTAGAAATATCTTTTAATTTTTAAAATTTTCACCATTTAGGCCAAT
12343165 TTAG
1 TTAG
12343169 TATTTTGCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (46 bp):
TTAGAAATATCTTTTAATTTTTAAAATTTTCACCATTTAGGCCAAT
Found at i:12343874 original size:9 final size:9
Alignment explanation
Indices: 12343853--12343885 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
12343843 AAAAGAACTT
12343853 ATAAAAT-A
1 ATAAAATAA
12343861 ATAAAATAA
1 ATAAAATAA
12343870 ATAAAATAAA
1 ATAAAAT-AA
12343880 ATAAAA
1 ATAAAA
12343886 AATACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.30
9 8 0.35
10 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAATAA
Found at i:12348607 original size:11 final size:11
Alignment explanation
Indices: 12348591--12348635 Score: 72
Period size: 11 Copynumber: 3.9 Consensus size: 11
12348581 TTGTCCTACA
12348591 ATCAACATATC
1 ATCAACATATC
12348602 ATCAACATATAC
1 ATCAACATAT-C
12348614 AATCAACATATC
1 -ATCAACATATC
12348626 ATCAACATAT
1 ATCAACATAT
12348636 AATAATAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.62
12 2 0.06
13 10 0.31
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCAACATATC
Found at i:12348614 original size:24 final size:24
Alignment explanation
Indices: 12348587--12348636 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
12348577 CATCTTGTCC
12348587 TACAATCAACATATCATCAACATA
1 TACAATCAACATATCATCAACATA
12348611 TACAATCAACATATCATCAACATA
1 TACAATCAACATATCATCAACATA
12348635 TA
1 TA
12348637 ATAATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (24 bp):
TACAATCAACATATCATCAACATA
Found at i:12354495 original size:15 final size:14
Alignment explanation
Indices: 12354470--12354499 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12354460 AGATGATTAT
12354470 TTATTTTTATTTTA
1 TTATTTTTATTTTA
12354484 TTATTTTATATTTTA
1 TTATTTT-TATTTTA
12354499 T
1 T
12354500 ATGTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:12354831 original size:9 final size:9
Alignment explanation
Indices: 12354817--12354850 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12354807 GAGAGCAAAA
12354817 TTTTAAATT
1 TTTTAAATT
12354826 TTTTAAATT
1 TTTTAAATT
* *
12354835 CTTGAAATT
1 TTTTAAATT
12354844 TTTTAAA
1 TTTTAAA
12354851 ATAAAATAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTAAATT
Found at i:12355602 original size:58 final size:57
Alignment explanation
Indices: 12355504--12355621 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 57
12355494 ATGTCACCTC
* *
12355504 TTAAGATAAAGATAACAATATGAATTAATTGTTCCTAATTCATACATTATTCTTATTT
1 TTAAAATAAAGATAACAATATGAATTAACTGTT-CTAATTCATACATTATTCTTATTT
** * *
12355562 TTAAAATAAAGATAACTGTATGAATTAACTGCTT-TGAATTCATTCATTATTTTTATTT
1 TTAAAATAAAGATAACAATATGAATTAACTG-TTCT-AATTCATACATTATTCTTATTT
12355620 TT
1 TT
12355622 CTACACATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.02
58 49 0.94
59 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (57 bp):
TTAAAATAAAGATAACAATATGAATTAACTGTTCTAATTCATACATTATTCTTATTT
Found at i:12356155 original size:21 final size:20
Alignment explanation
Indices: 12356130--12356168 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12356120 AAAGAAGTAT
*
12356130 TTTTTTTCTTTCCTGAGGTC
1 TTTTTTTATTTCCTGAGGTC
12356150 TTTTTTTATTTCCTGAGGT
1 TTTTTTTATTTCCTGAGGT
12356169 ATGTGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (20 bp):
TTTTTTTATTTCCTGAGGTC
Found at i:12359993 original size:13 final size:13
Alignment explanation
Indices: 12359977--12360021 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12359967 ACATATCTAA
12359977 TTTTATTATTTAC
1 TTTTATTATTTAC
* *
12359990 TTTTAATATATTAG
1 TTTTATTAT-TTAC
*
12360004 TTTTATTATTTTC
1 TTTTATTATTTAC
12360017 TTTTA
1 TTTTA
12360022 ATAAACAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTATTATTTAC
Found at i:12360165 original size:14 final size:13
Alignment explanation
Indices: 12360141--12360182 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
12360131 AAGATGATTA
12360141 TTTAT-TTTTATT
1 TTTATATTTTATT
12360153 TTTATTATTTTATAT
1 TTTA-TATTTTAT-T
*
12360168 TTTATATGTTATT
1 TTTATATTTTATT
12360181 TT
1 TT
12360183 GTGGTGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 13 0.50
15 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATATTTTATT
Found at i:12360179 original size:22 final size:19
Alignment explanation
Indices: 12360137--12360180 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
12360127 GTTAAAGATG
*
12360137 ATTATTTATTTTTATTTTT
1 ATTATTTATTTTTATTGTT
12360156 ATTATTTTATATTTTATATGTT
1 ATTA-TTTAT-TTTTAT-TGTT
12360178 ATT
1 ATT
12360181 TTGTGGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 6 0.29
22 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTATTTATTTTTATTGTT
Found at i:12360523 original size:10 final size:9
Alignment explanation
Indices: 12360490--12360522 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12360480 CAATGGGGGC
12360490 AAAATTTT-
1 AAAATTTTA
12360498 -AAATTTTA
1 AAAATTTTA
12360506 AAAATTTTA
1 AAAATTTTA
12360515 AAAATTTT
1 AAAATTTT
12360523 TTATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AAAATTTTA
Found at i:12360784 original size:93 final size:96
Alignment explanation
Indices: 12360650--12360834 Score: 259
Period size: 93 Copynumber: 2.0 Consensus size: 96
12360640 CTAATATTAG
* **
12360650 ATTTTTAATTTTAATGGTCAAATTCAATTAATGGTAGTCT-AAAGTGACAAGTACATTATTT-TT
1 ATTTTTAATTTTAATGGTCAAATTCAATTAATGGTAGTCTAAAAGTGACAAGCACATTATTTAGA
* *
12360713 AAAAAATGTTCATCCTTTTGGATTTTTTTGA
66 AAAAAATGTTCAACCTCTTGGATTTTTTTGA
* * ** *
12360744 ATTTTTAA-TTTATTGGTCAAATTCAATTCATGGTAGTCTAAAAGTGATGAGCGCATTATTTAGA
1 ATTTTTAATTTTAATGGTCAAATTCAATTAATGGTAGTCTAAAAGTGACAAGCACATTATTTAGA
12360808 AAAAAATGTTCAACCTCTTGGATTTTT
66 AAAAAATGTTCAACCTCTTGGATTTTT
12360835 AATTCTAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 29 0.37
94 25 0.32
95 25 0.32
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (96 bp):
ATTTTTAATTTTAATGGTCAAATTCAATTAATGGTAGTCTAAAAGTGACAAGCACATTATTTAGA
AAAAAATGTTCAACCTCTTGGATTTTTTTGA
Found at i:12361039 original size:87 final size:86
Alignment explanation
Indices: 12360740--12361064 Score: 458
Period size: 86 Copynumber: 3.8 Consensus size: 86
12360730 TTGGATTTTT
* * * *
12360740 TTGAATTTTTAATT-TATTGG-TCAAATTCAATTCATGGTAGTCTAAAAGTGATGAGCGCATTAT
1 TTGAATTTTTAATTCTAATGGCT-AAATTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTAT
12360803 TTAGAAAAAAATGTTCAACCTC
65 TTAGAAAAAAATGTTCAACCTC
* * *
12360825 TTGGATTTTTAATTCTAATGGCTAATTTCAATTCATGATAGTCTAAAACTGACGAGTGCATTATT
1 TTGAATTTTTAATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTATT
*
12360890 AAGAAAAAAATGTTCAACCTC
66 TAGAAAAAAATGTTCAACCTC
* *
12360911 TTGGAA-TTTTAATTCTACTGGCTAATTTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTAT
1 TT-GAATTTTTAATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTAT
*
12360975 TTAGAAAAAAAATGTTTAACCTC
65 TTAG-AAAAAAATGTTCAACCTC
* * * * *
12360998 TTGAATTTTTAATTCTAATTGTTAAATTCAATTTATGATAGTCTAAAAGTGACAAGTGTATTATT
1 TTGAATTTTTAATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTATT
12361063 TA
66 TA
12361065 ATGATAGTCT
Statistics
Matches: 215, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
85 13 0.06
86 126 0.59
87 76 0.35
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (86 bp):
TTGAATTTTTAATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTATT
TAGAAAAAAATGTTCAACCTC
Found at i:12361069 original size:33 final size:33
Alignment explanation
Indices: 12361028--12361097 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
12361018 GTTAAATTCA
*
12361028 ATTT-ATGATAGTCTAAAAGTGACAAGTGTATT
1 ATTTAATGATAGTCTAAAAGTGACAAGTGCATT
**
12361060 ATTTAATGATAGTCTAAAAGTGATGAGTGCATT
1 ATTTAATGATAGTCTAAAAGTGACAAGTGCATT
12361093 ATTTA
1 ATTTA
12361098 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (33 bp):
ATTTAATGATAGTCTAAAAGTGACAAGTGCATT
Found at i:12361159 original size:120 final size:120
Alignment explanation
Indices: 12360945--12361184 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 120
12360935 ATTTCAATTC
*
12360945 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTTAACCTCTTGAATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGAATTTTTAA
* * * *
12361010 TTCTAATTGTTAAATTCAATTTATGATAGTCTAAAAGTGACAAGTGTATTATTTA
66 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACAAGTGCATTATTTA
* *
12361065 ATGATAGTCTAAAAGTGATGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGAATTTTTAA
*
12361130 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTA
66 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACAAGTGCATTATTTA
12361185 GAAAAAAATG
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (120 bp):
ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGAATTTTTAA
TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACAAGTGCATTATTTA
Found at i:12361214 original size:206 final size:206
Alignment explanation
Indices: 12360859--12361270 Score: 673
Period size: 206 Copynumber: 2.0 Consensus size: 206
12360849 ATTTCAATTC
12360859 ATGATAGTCTAAAACTGACGAGTGCATTATTAAGAAAAAAATGTTCAACCTCTTGGAATTTTAAT
1 ATGATAGTCTAAAACTGACGAGTGCATTATTAAGAAAAAAATGTTCAACCTCTTGGAATTTTAAT
* * *
12360924 TCTACTGGCTAATTTCAATTCATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATG
66 TCTAATGGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATG
* * *
12360989 TTTAACCTCTTGAATTTTTAATTCTAATTGTTAAATTCAATTTATGATAGTCTAAAAGTGACAAG
131 TTCAACCTCTTGAATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACAAG
*
12361054 TGTATTATTTA
196 TGCATTATTTA
* * * *
12361065 ATGATAGTCTAAAAGTGATGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
1 ATGATAGTCTAAAACTGACGAGTGCATTATTAAG-AAAAAAATGTTCAACCTCTTGGAATTTTAA
*
12361130 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAG-AAAAAAAT
65 TTCTAATGGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAAT
* * *
12361194 GTTCGACCTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACGA
130 GTTCAACCTCTTGAATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACAA
12361259 GTGCATTATTTA
195 GTGCATTATTTA
12361271 GAAAAAAAAT
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
206 109 0.57
207 81 0.43
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (206 bp):
ATGATAGTCTAAAACTGACGAGTGCATTATTAAGAAAAAAATGTTCAACCTCTTGGAATTTTAAT
TCTAATGGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATG
TTCAACCTCTTGAATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACAAG
TGCATTATTTA
Found at i:12361223 original size:86 final size:86
Alignment explanation
Indices: 12361065--12361734 Score: 925
Period size: 86 Copynumber: 7.7 Consensus size: 86
12361055 GTATTATTTA
*
12361065 ATGATAGTCTAAAAGTGATGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAG-AAAAAAATGTTCAACCTCTTGGATTTTTAA
*
12361130 TTCTAATTGCTAAATTCAATTC
65 TTCTAATGGCTAAATTCAATTC
* *
12361152 ATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCGACCTCTTGGATTTTTAAT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
*
12361217 TCTAATTGCTAAATTCAATTC
66 TCTAATGGCTAAATTCAATTC
12361238 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTTCTTGGATTT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAG-AAAAAAATGTTCAA-C-C--TCTTGGATTT
12361303 TTAATTCTAATGGCTAAATTCAATTC
61 TTAATTCTAATGGCTAAATTCAATTC
* *
12361329 ATGGTAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTAGATTTTTAAT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
*
12361394 TCTAATGGCCAAATTCAATTC
66 TCTAATGGCTAAATTCAATTC
* * * * *
12361415 ATAATAGTCTAAAAGTTACGAATGCATTATTTAGAAAAAAATATTCAAACTCTTGGATTTTTAAT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
* *
12361480 TCTAATTGTTAAATTCAATTC
66 TCTAATGGCTAAATTCAATTC
* **
12361501 ATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAAAAAATTCAACCTCTTGGATTTTTAAT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
* **
12361566 TATAACAGCTAAATTCAATTC
66 TCTAATGGCTAAATTCAATTC
* * * * *
12361587 ATGATAGTATAAAAGTGACTTA-TACTTTATTTTGAAAAAAAAATGTTCAACCTCTTGGATTTTT
1 ATGATAGTCTAAAAGTGAC-GAGTGCATTA-TTT-AGAAAAAAATGTTCAACCTCTTGGATTTTT
* * *
12361651 AATTATAAAGGCTAAATTCAATTT
63 AATTCTAATGGCTAAATTCAATTC
* * * *
12361675 ATGATAGTATAAAAGTGACGTA-TACTTTATTTAG-AAAAAATGTTCAACCTC-TAGATTTTT
1 ATGATAGTCTAAAAGTGACG-AGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTT
12361735 TTGAAGTTAA
Statistics
Matches: 533, Mismatches: 41, Indels: 21
0.90 0.07 0.04
Matches are distributed among these distances:
84 8 0.02
85 17 0.03
86 295 0.55
87 52 0.10
88 77 0.14
89 2 0.00
90 14 0.03
91 68 0.13
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (86 bp):
ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
TCTAATGGCTAAATTCAATTC
Found at i:12361357 original size:177 final size:173
Alignment explanation
Indices: 12361065--12361734 Score: 945
Period size: 177 Copynumber: 3.9 Consensus size: 173
12361055 GTATTATTTA
*
12361065 ATGATAGTCTAAAAGTGATGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
* * *
12361130 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATG
66 TTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAAAATG
* * *
12361195 TTCGACCTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTC
131 TTCAACCTCTTAGATTTTTAATTCTAATAGCTAAATTCAATTC
12361238 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTTCTTGGATTT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAA-C-C--TCTTGGATTT
* *
12361303 TTAATTCTAATGGCTAAATTCAATTCATGGTAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAA
62 TTAATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAA
* *
12361368 AATGTTCAACCTCTTAGATTTTTAATTCTAATGGCCAAATTCAATTC
127 AATGTTCAACCTCTTAGATTTTTAATTCTAATAGCTAAATTCAATTC
* * * * *
12361415 ATAATAGTCTAAAAGTTACGAATGCATTATTTAG-AAAAAAATATTCAAACTCTTGGATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
* * **
12361479 TTCTAATTGTTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAAAAAA
66 TTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAAAATG
* * *
12361544 TTCAACCTCTTGGATTTTTAATTATAACAGCTAAATTCAATTC
131 TTCAACCTCTTAGATTTTTAATTCTAATAGCTAAATTCAATTC
* * * * *
12361587 ATGATAGTATAAAAGTGACTTA-TACTTTATTTTGAAAAAAAAATGTTCAACCTCTTGGATTTTT
1 ATGATAGTCTAAAAGTGAC-GAGTGCATTATTTAG-AAAAAAAATGTTCAACCTCTTGGATTTTT
* * * * *
12361651 AATTATAAAGGCTAAATTCAATTTATGATAGTATAAAAGTGACGTA-TACTTTATTTAG-AAAAA
64 AATTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACG-AGTACATTATTTAGAAAAAA
12361714 ATGTTCAACCTC-TAGATTTTT
128 ATGTTCAACCTCTTAGATTTTT
12361735 TTGAAGTTAA
Statistics
Matches: 446, Mismatches: 43, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
172 144 0.32
173 64 0.14
174 77 0.17
175 2 0.00
176 13 0.03
177 146 0.33
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (173 bp):
ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
TTCTAATGGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGTACATTATTTAGAAAAAAATG
TTCAACCTCTTAGATTTTTAATTCTAATAGCTAAATTCAATTC
Found at i:12361537 original size:263 final size:258
Alignment explanation
Indices: 12361065--12361714 Score: 942
Period size: 263 Copynumber: 2.5 Consensus size: 258
12361055 GTATTATTTA
*
12361065 ATGATAGTCTAAAAGTGATGAGTGCATTATTTAGAAAAAAAATGTTCAACCTCTTGGATTTTTAA
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAG-AAAAAAATGTTCAACCTCTTGGATTTTTAA
* * * *
12361130 TTCTAATTGCTAAATTCAATTCATCATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATG
65 TTCTAATGGCTAAATTCAATTCATAATAGTCTAAAAGTGACGAATGCATTATTTAGAAAAAAATA
* *
12361195 TTCGACCTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAG
130 TTCAAACTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAG
* * * **
12361260 TGCATTATTTAGAAAAAAAATGTTCAACCTCTTTCTTGGATTTTTAATTCTAATGGCTAAATTCA
195 TACATTATTTAGAAAAAAAA-ATTCAA-C-C--TCTTGGATTTTTAATTATAACAGCTAAATTCA
12361325 ATTC
255 ATTC
* *
12361329 ATGGTAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTAGATTTTTAAT
1 ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
* *
12361394 TCTAATGGCCAAATTCAATTCATAATAGTCTAAAAGTTACGAATGCATTATTTAGAAAAAAATAT
66 TCTAATGGCTAAATTCAATTCATAATAGTCTAAAAGTGACGAATGCATTATTTAGAAAAAAATAT
*
12361459 TCAAACTCTTGGATTTTTAATTCTAATTGTTAAATTCAATTCATGATAGTCTAAAAGTGACGAGT
131 TCAAACTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGT
12361524 ACATTATTTAGAAAAAAAAATTCAACCTCTTGGATTTTTAATTATAACAGCTAAATTCAATTC
196 ACATTATTTAGAAAAAAAAATTCAACCTCTTGGATTTTTAATTATAACAGCTAAATTCAATTC
* * * * *
12361587 ATGATAGTATAAAAGTGACTTA-TACTTTATTTTGAAAAAAAAATGTTCAACCTCTTGGATTTTT
1 ATGATAGTCTAAAAGTGAC-GAGTGCATTA-TTT-AGAAAAAAATGTTCAACCTCTTGGATTTTT
* * * * * * * *
12361651 AATTATAAAGGCTAAATTCAATTTATGATAGTATAAAAGTGACGTATACTTTATTTAGAAAAAA
63 AATTCTAATGGCTAAATTCAATTCATAATAGTCTAAAAGTGACGAATGCATTATTTAGAAAAAA
12361715 TGTTCAACCT
Statistics
Matches: 349, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
258 55 0.16
259 4 0.01
260 83 0.24
261 1 0.00
262 5 0.01
263 169 0.48
264 32 0.09
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (258 bp):
ATGATAGTCTAAAAGTGACGAGTGCATTATTTAGAAAAAAATGTTCAACCTCTTGGATTTTTAAT
TCTAATGGCTAAATTCAATTCATAATAGTCTAAAAGTGACGAATGCATTATTTAGAAAAAAATAT
TCAAACTCTTGGATTTTTAATTCTAATTGCTAAATTCAATTCATGATAGTCTAAAAGTGACGAGT
ACATTATTTAGAAAAAAAAATTCAACCTCTTGGATTTTTAATTATAACAGCTAAATTCAATTC
Found at i:12363501 original size:16 final size:15
Alignment explanation
Indices: 12363465--12363519 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
12363455 CCATTTTTTG
12363465 TTTTTTTTTT-GTAT
1 TTTTTTTTTTAGTAT
*
12363479 TTATTTTATTTAGTATT
1 TT-TTTTTTTTAGTA-T
12363496 TTTTTTCTTCTTAGTAT
1 TTTTTT-TT-TTAGTAT
12363513 TTTTTTT
1 TTTTTTT
12363520 CATGATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 8 0.24
17 11 0.32
18 6 0.18
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTTAGTAT
Found at i:12366203 original size:24 final size:23
Alignment explanation
Indices: 12366148--12366201 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
12366138 TTTTCTTTTG
12366148 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
12366171 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
12366197 TATTT
1 TATTT
12366202 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:12366260 original size:3 final size:3
Alignment explanation
Indices: 12366252--12366280 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12366242 AGTTATATAT
12366252 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12366281 TTTGTAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12367228 original size:12 final size:12
Alignment explanation
Indices: 12367213--12367245 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12367203 TTTTTTTTTT
12367213 TTTTTTTTTGAA
1 TTTTTTTTTGAA
12367225 TTTTTTTTTGAA
1 TTTTTTTTTGAA
12367237 TTTTTTTTT
1 TTTTTTTTT
12367246 ATTTGACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:12367261 original size:28 final size:28
Alignment explanation
Indices: 12367209--12367263 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
12367199 GGTTTTTTTT
* **
12367209 TTTTTTTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTTATTTGAATTTGATTTTGAA
*
12367237 TTTTTTTTTATTTGACTTTGATTTTGA
1 TTTTTTTTTATTTGAATTTGATTTTGA
12367264 TCTTGATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTATTTGAATTTGATTTTGAA
Found at i:12367699 original size:151 final size:152
Alignment explanation
Indices: 12367273--12367722 Score: 812
Period size: 153 Copynumber: 3.0 Consensus size: 152
12367263 ATCTTGATTT
* *
12367273 TTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
12367338 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
12367403 TTTCCAATAATTAATTGGATGA
131 TTTCCAATAATTAATTGGATGA
*
12367425 TTTTGTATTTTTTTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
1 TTTTGT-TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
12367490 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATA
65 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATA
12367555 A-TTCCAATAATTAATTGGATGA
130 ATTTCCAATAATTAATTGGATGA
*
12367577 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
* *
12367642 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
* *
12367707 TTTCCAACAACTAATT
131 TTTCCAATAATTAATT
12367723 ACTTGGTAAA
Statistics
Matches: 287, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
151 120 0.42
152 45 0.16
153 122 0.43
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (152 bp):
TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:12371441 original size:28 final size:28
Alignment explanation
Indices: 12371373--12371441 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
12371363 ACAATGGATG
** *
12371373 AAAAATGAGAAAAAAAGAAGATGATGAA
1 AAAAATGAGAAAAAAAGAAGAAAAAGAA
* *
12371401 AAAAAAGA-AAAAAATAGAAGAAAAAGGA
1 AAAAATGAGAAAAAA-AGAAGAAAAAGAA
12371429 AAAAATGAGAAAA
1 AAAAATGAGAAAA
12371442 TGAAAAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 6 0.18
28 23 0.70
29 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (28 bp):
AAAAATGAGAAAAAAAGAAGAAAAAGAA
Found at i:12371446 original size:16 final size:16
Alignment explanation
Indices: 12371403--12371454 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
12371393 ATGATGAAAA
*
12371403 AAAAGAAAAAAATAGAAG
1 AAAAGGAAAAAA-AG-AG
*
12371421 AAAAAGGAAAAAATGAG
1 -AAAAGGAAAAAAAGAG
*
12371438 AAAATGAAAAAAAGAG
1 AAAAGGAAAAAAAGAG
12371454 A
1 A
12371455 TTCAAATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 15 0.52
17 2 0.07
18 1 0.03
19 11 0.38
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (16 bp):
AAAAGGAAAAAAAGAG
Found at i:12372768 original size:41 final size:41
Alignment explanation
Indices: 12372685--12373280 Score: 932
Period size: 41 Copynumber: 14.5 Consensus size: 41
12372675 AAAGTTCCGT
*
12372685 TGCCTCTGTTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGTGG
12372727 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
12372768 TACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
12372809 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
12372850 TGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
12372891 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
* *
12372932 TGCCTCTGTTGAGAGGAGCAATTTAATTTCCAAAGTTCCGT--
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGG
*
12372973 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
12373014 TGCCTCTGTTGAGAGGAGCAATTTAATTTTCAAAGTTCCGT--
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGG
* *
12373055 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTT-CAAAGTCGTGG
*
12373097 TACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
12373138 TGCCTCTGTTGAAGAGGAGCAATTTACTTTCCAAAGTCGTGG
1 TGCCTCTGTTG-AGAGGAGCAATTTACTTTTCAAAGTCGTGG
12373180 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
* *
12373221 TACCTCTGTTGAGAGGAGCAATTTAC-TTTCAAAAGTCGTTG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTC-AAAGTCGTGG
* * *
12373262 AGTCTCTGTTTAGAGGAGC
1 TGCCTCTGTTGAGAGGAGC
12373281 TTCGGCAAAA
Statistics
Matches: 515, Mismatches: 28, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.01
40 8 0.02
41 400 0.78
42 98 0.19
43 6 0.01
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
Found at i:12373293 original size:1 final size:1
Alignment explanation
Indices: 12373287--12373403 Score: 72
Period size: 1 Copynumber: 117.0 Consensus size: 1
12373277 GAGCTTCGGC
* * * ** ** **
12373287 AAAAAAAAAAAAACAAAAAAAAACAAAAAAATAAAAAAAAATCAAAAAAAAAATCAAAAAAATCA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * ** *
12373352 GAAAAAATCAAAAAAATAAAAAACAAAATAAAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12373404 TGTTGAGTTG
Statistics
Matches: 85, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 85 1.00
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.08
Consensus pattern (1 bp):
A
Found at i:12373306 original size:10 final size:10
Alignment explanation
Indices: 12373287--12373397 Score: 95
Period size: 10 Copynumber: 11.1 Consensus size: 10
12373277 GAGCTTCGGC
12373287 AAAA-AAAAA
1 AAAACAAAAA
12373296 AAAACAAAAA
1 AAAACAAAAA
12373306 AAAACAAAAA
1 AAAACAAAAA
*
12373316 AATA-AAAAA
1 AAAACAAAAA
*
12373325 AAATCAAAAA
1 AAAACAAAAA
12373335 AAAA-ATCAAAA
1 AAAACA--AAAA
* *
12373346 AAATCAGAAA
1 AAAACAAAAA
*
12373356 AAATCAAAAA
1 AAAACAAAAA
*
12373366 AATAA-AAAAC
1 AA-AACAAAAA
*
12373376 AAAATAAAAA
1 AAAACAAAAA
12373386 AAAATCAAAAA
1 AAAA-CAAAAA
12373397 A
1 A
12373398 TAAAAATGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
9 14 0.17
10 54 0.65
11 14 0.17
12 1 0.01
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.07
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:12373326 original size:31 final size:30
Alignment explanation
Indices: 12373288--12373403 Score: 108
Period size: 31 Copynumber: 3.7 Consensus size: 30
12373278 AGCTTCGGCA
12373288 AAAAAAAAAAAACAAAAAAAAACAAAAAAAT
1 AAAAAAAAAAAA-AAAAAAAAACAAAAAAAT
* *
12373319 AAAAAAAAATCAAAAAAAAAATCAAAAAAAT
1 AAAAAAAAA-AAAAAAAAAAAACAAAAAAAT
* *
12373350 CAGAAAAAATCAAAAAAATAAAAAACAAAATAA-
1 -A-AAAAAA--AAAAAAAAAAAAAACAAAAAAAT
** *
12373383 AAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
12373404 TGTTGAGTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
29 10 0.14
31 32 0.46
32 4 0.06
33 6 0.09
34 16 0.23
35 2 0.03
ACGTcount: A:0.84, C:0.07, G:0.01, T:0.08
Consensus pattern (30 bp):
AAAAAAAAAAAAAAAAAAAAACAAAAAAAT
Found at i:12373347 original size:50 final size:50
Alignment explanation
Indices: 12373292--12373397 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
12373282 TCGGCAAAAA
12373292 AAAAAAAACAAAAAAAAACAAAAAAAT-AAAAA-AAAATCAAAAAAAAAATC
1 AAAAAAAACAAAAAAAAACAAAAAAATAAAAAACAAAAT--AAAAAAAAATC
* * *
12373342 AAAAAAATCAGAAAAAATCAAAAAAATAAAAAACAAAATAAAAAAAAATC
1 AAAAAAAACAAAAAAAAACAAAAAAATAAAAAACAAAATAAAAAAAAATC
12373392 AAAAAA
1 AAAAAA
12373398 TAAAAATGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 41 0.80
51 5 0.10
52 5 0.10
ACGTcount: A:0.84, C:0.08, G:0.01, T:0.08
Consensus pattern (50 bp):
AAAAAAAACAAAAAAAAACAAAAAAATAAAAAACAAAATAAAAAAAAATC
Found at i:12373628 original size:24 final size:23
Alignment explanation
Indices: 12373573--12373626 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
12373563 TTTTCTTTTG
12373573 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
12373596 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
12373622 TATTT
1 TATTT
12373627 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:12373685 original size:3 final size:3
Alignment explanation
Indices: 12373677--12373705 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12373667 AGTTATATAT
12373677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12373706 TTTGTAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12374269 original size:20 final size:20
Alignment explanation
Indices: 12374246--12374288 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
12374236 TGCCCAGTTT
*
12374246 CCGACGAAGAATCCCAGAAA
1 CCGACAAAGAATCCCAGAAA
12374266 CCGACAAAGAATCCCAGAAA
1 CCGACAAAGAATCCCAGAAA
12374286 CCG
1 CCG
12374289 GTGAATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.33, G:0.19, T:0.05
Consensus pattern (20 bp):
CCGACAAAGAATCCCAGAAA
Found at i:12374612 original size:14 final size:15
Alignment explanation
Indices: 12374593--12374634 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
12374583 CCGAGCCGAG
12374593 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
12374607 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
12374620 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
12374634 C
1 C
12374635 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:12374625 original size:13 final size:14
Alignment explanation
Indices: 12374593--12374629 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
12374583 CCGAGCCGAG
12374593 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
12374607 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
12374619 TCCGAGCCGTT
1 -CCGAGCCGTT
12374630 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:12374716 original size:15 final size:15
Alignment explanation
Indices: 12374683--12374726 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12374673 GCTCCAGGTT
***
12374683 TTTTTTTTTTTTTTT
1 TTTTTTTTTTTTGAA
12374698 TTTTTTTTTTTTGAA
1 TTTTTTTTTTTTGAA
*
12374713 TTTTTTTTATTTGA
1 TTTTTTTTTTTTGA
12374727 CTTTGATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTGAA
Found at i:12374720 original size:1 final size:1
Alignment explanation
Indices: 12374681--12374709 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
12374671 CCGCTCCAGG
12374681 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12374710 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12375188 original size:152 final size:152
Alignment explanation
Indices: 12374748--12375198 Score: 812
Period size: 153 Copynumber: 3.0 Consensus size: 152
12374738 ATCTTGATTT
* *
12374748 TTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
12374813 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
12374878 TTTCCAATAATTAATTGGATGA
131 TTTCCAATAATTAATTGGATGA
*
12374900 TTTTGTATTTTTTTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
1 TTTTGT-TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
12374965 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATA
65 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATA
*
12375030 AATTCCAATAATTAATTGGATGA
130 ATTTCCAATAATTAATTGGATGA
*
12375053 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
* *
12375118 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
* *
12375183 TTTCCAACAACTAATT
131 TTTCCAATAATTAATT
12375199 ACTTGGTAAA
Statistics
Matches: 287, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
152 138 0.48
153 149 0.52
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (152 bp):
TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:12376199 original size:107 final size:106
Alignment explanation
Indices: 12375998--12376199 Score: 235
Period size: 107 Copynumber: 1.9 Consensus size: 106
12375988 CTTACAAGTG
* *
12375998 TTAATTCCAAATTTATAACGAAACAACAAATGCCCACAAATATTTTAAATTTATGACTCAAATAT
1 TTAATTCCAAATTTATAACGAAACAACAAATGCCCACAAATAATTCAAATTTATGACTCAAATAT
** ** *
12376063 TGCATTTCTATTCATAGAAATGCAGTAATTGCAAGACAGATA
66 TG-ATTTCTATGAATAGAAACACAATAATTGCAAGACAGATA
* * * * * * *
12376105 TTAATTGCAAATTTATGACTAAATAACAGATGCCCACAAATAATTCAAATTTATGACTTAGATAC
1 TTAATTCCAAATTTATAACGAAACAACAAATGCCCACAAATAATTCAAATTTATGACTCAAATA-
*
12376170 CTTG-TTTTTATGAATAGAAACACAATAATT
65 -TTGATTTCTATGAATAGAAACACAATAATT
12376200 ACAAAATATA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
107 75 0.96
109 3 0.04
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (106 bp):
TTAATTCCAAATTTATAACGAAACAACAAATGCCCACAAATAATTCAAATTTATGACTCAAATAT
TGATTTCTATGAATAGAAACACAATAATTGCAAGACAGATA
Found at i:12377225 original size:18 final size:19
Alignment explanation
Indices: 12377202--12377237 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12377192 TGACATAATG
12377202 ACAAAAA-ATAAAAATGAA
1 ACAAAAAGATAAAAATGAA
12377220 ACAAAAAGATAAAAATGA
1 ACAAAAAGATAAAAATGA
12377238 TATGGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.11
Consensus pattern (19 bp):
ACAAAAAGATAAAAATGAA
Found at i:12378828 original size:19 final size:20
Alignment explanation
Indices: 12378806--12378843 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12378796 TCTCAATTCA
*
12378806 TATTTTCTCTCTA-AAAATT
1 TATTATCTCTCTATAAAATT
*
12378825 TATTATGTCTCTATAAAAT
1 TATTATCTCTCTATAAAAT
12378844 CAAACCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTATCTCTCTATAAAATT
Found at i:12378897 original size:19 final size:19
Alignment explanation
Indices: 12378873--12378909 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12378863 ACGGTTTAGC
12378873 TTGATTTGATTTTAGAGAA
1 TTGATTTGATTTTAGAGAA
*
12378892 TTGATTTGGTTTTAGAGA
1 TTGATTTGATTTTAGAGA
12378910 GAGAGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (19 bp):
TTGATTTGATTTTAGAGAA
Found at i:12379720 original size:13 final size:13
Alignment explanation
Indices: 12379702--12379727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12379692 GTTTGGTTTT
12379702 GTTGGAGAGAGAA
1 GTTGGAGAGAGAA
12379715 GTTGGAGAGAGAA
1 GTTGGAGAGAGAA
12379728 ATGATTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.46, T:0.15
Consensus pattern (13 bp):
GTTGGAGAGAGAA
Found at i:12379761 original size:21 final size:21
Alignment explanation
Indices: 12379737--12379779 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12379727 AATGATTTGG
12379737 TTTTAGAGAGAGAGAATGAAT
1 TTTTAGAGAGAGAGAATGAAT
* * *
12379758 TTTTAGAGTGAGTGTATGAAT
1 TTTTAGAGAGAGAGAATGAAT
12379779 T
1 T
12379780 CAGATGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.37
Consensus pattern (21 bp):
TTTTAGAGAGAGAGAATGAAT
Found at i:12380083 original size:21 final size:21
Alignment explanation
Indices: 12380044--12380083 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12380034 TTTTTTTTTG
*
12380044 TTTGAGATGAAAAATTAAAAT
1 TTTGAGATGAAAAACTAAAAT
* *
12380065 TTTGAGCTGAAAAGCTAAA
1 TTTGAGATGAAAAACTAAA
12380084 TTATTTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (21 bp):
TTTGAGATGAAAAACTAAAAT
Found at i:12388178 original size:29 final size:29
Alignment explanation
Indices: 12388138--12388195 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
12388128 ACAGTTGCCA
*
12388138 GGGTTATTAGAATAAGCTTGGCAGAAGAG
1 GGGTTAGTAGAATAAGCTTGGCAGAAGAG
12388167 GGGTTAGTAGAATAAGCTTGGCAGAAGAG
1 GGGTTAGTAGAATAAGCTTGGCAGAAGAG
12388196 TCCAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.36, T:0.22
Consensus pattern (29 bp):
GGGTTAGTAGAATAAGCTTGGCAGAAGAG
Found at i:12392509 original size:5 final size:5
Alignment explanation
Indices: 12392499--12392525 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12392489 TAATCATGTT
12392499 TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TA
12392526 ATTAAGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12394652 original size:23 final size:23
Alignment explanation
Indices: 12394583--12394656 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 23
12394573 TTTATGAAGG
*
12394583 AGATTAACATTATTTGTTAAACT
1 AGATTAACATTGTTTGTTAAACT
*
12394606 AGATTTTAA-ACTCGTGCTTCGTTAAACT
1 AGA--TTAACA-T--TG-TTTGTTAAACT
12394634 AGATTAACATTGTTTGTTAAACT
1 AGATTAACATTGTTTGTTAAACT
12394657 CAACGTGTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
23 13 0.32
24 3 0.07
25 5 0.12
26 5 0.12
27 2 0.05
28 13 0.32
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
AGATTAACATTGTTTGTTAAACT
Found at i:12395575 original size:5 final size:5
Alignment explanation
Indices: 12395565--12395603 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
12395555 TACTTCCGTC
12395565 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
12395604 CTAATTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12401940 original size:9 final size:9
Alignment explanation
Indices: 12401928--12401973 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
12401918 TTTTTTTCTT
*
12401928 TTTTTTGTA
1 TTTTATGTA
12401937 TTTTATGTA
1 TTTTATGTA
12401946 TTTTAT-TA
1 TTTTATGTA
12401954 TTATTAT-TA
1 TT-TTATGTA
12401963 TTATTATGTA
1 TT-TTATGTA
12401973 T
1 T
12401974 ATCTTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 4 0.12
9 27 0.79
10 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (9 bp):
TTTTATGTA
Found at i:12402686 original size:20 final size:20
Alignment explanation
Indices: 12402651--12402705 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
12402641 CCGGTGAACC
12402651 TCCGACGAAATTTCCAG-AT
1 TCCGACGAAATTTCCAGAAT
*
12402670 TCCGACGACATTTTCCAGAAT
1 TCCGACGA-AATTTCCAGAAT
*
12402691 T-CGACGAAAATTCCA
1 TCCGACGAAATTTCCA
12402706 CCGGTGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 14 0.45
20 14 0.45
21 3 0.10
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (20 bp):
TCCGACGAAATTTCCAGAAT
Found at i:12403062 original size:17 final size:17
Alignment explanation
Indices: 12403027--12403161 Score: 57
Period size: 17 Copynumber: 7.5 Consensus size: 17
12403017 TTTTTTTTCA
12403027 TTCATTTGTTTATTTTATT
1 TTCATTT-TTTA-TTTATT
12403046 TTCATTTTTTATTTA-T
1 TTCATTTTTTATTTATT
** *
12403062 TAGATTATGTTTATTTAATA
1 TTCATT-T-TTTATTT-ATT
*
12403082 TTC-TTTTTATCTTTATT
1 TTCATTTTT-TATTTATT
12403099 TT-ATTTTTGT-TTTACTT
1 TTCATTTTT-TATTTA-TT
12403116 TTC-TTTATTT-TTTATTT
1 TTCATTT-TTTATTTA-TT
*
12403133 TTCTTTATTTTTATTTATT
1 TTC-AT-TTTTTATTTATT
12403152 ATTCTATTTT
1 -TTC-ATTTT
12403162 CTTTAAATAA
Statistics
Matches: 92, Mismatches: 10, Indels: 28
0.71 0.08 0.22
Matches are distributed among these distances:
16 9 0.10
17 34 0.37
18 18 0.20
19 19 0.21
20 12 0.13
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTCATTTTTTATTTATT
Found at i:12403102 original size:11 final size:11
Alignment explanation
Indices: 12403086--12403143 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
12403076 TTAATATTCT
12403086 TTTTATCTTTA
1 TTTTATCTTTA
* *
12403097 TTTTATTTTTG
1 TTTTATCTTTA
12403108 TTTTA-CTTT-
1 TTTTATCTTTA
*
12403117 TCTTTATTTTTTA
1 T-TTTA-TCTTTA
12403130 TTTT-TCTTTA
1 TTTTATCTTTA
12403140 TTTT
1 TTTT
12403144 TATTTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
9 1 0.03
10 16 0.42
11 14 0.37
12 6 0.16
13 1 0.03
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATCTTTA
Found at i:12403127 original size:10 final size:10
Alignment explanation
Indices: 12403098--12403156 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
12403088 TTATCTTTAT
*
12403098 TTTATTTTTGT
1 TTTATTTTT-C
*
12403109 TTTACTTTTC
1 TTTATTTTTC
12403119 TTTA--TTT-
1 TTTATTTTTC
12403126 TTTATTTTTC
1 TTTATTTTTC
*
12403136 TTTATTTTTA
1 TTTATTTTTC
*
12403146 TTTATTATTC
1 TTTATTTTTC
12403156 T
1 T
12403157 ATTTTCTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
7 4 0.10
8 3 0.08
9 3 0.08
10 22 0.55
11 8 0.20
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:12403127 original size:27 final size:26
Alignment explanation
Indices: 12403091--12403166 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
12403081 ATTCTTTTTA
*
12403091 TCTTTA-TTTTATTTTTGTTTTACTTT
1 TCTTTATTTTTATTTTT-CTTTACTTT
*
12403117 TCTTTATTTTTTATTTTTCTTTATTTT
1 TCTTTA-TTTTTATTTTTCTTTACTTT
*
12403144 TATTTATTATTCTA-TTTTCTTTA
1 TCTTTATT-TT-TATTTTTCTTTA
12403167 AATAAAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 8 0.19
27 23 0.53
28 12 0.28
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.76
Consensus pattern (26 bp):
TCTTTATTTTTATTTTTCTTTACTTT
Found at i:12403271 original size:60 final size:60
Alignment explanation
Indices: 12403171--12403531 Score: 446
Period size: 60 Copynumber: 6.0 Consensus size: 60
12403161 TCTTTAAATA
* *
12403171 AAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATCAAAATTTCC---AAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
*
12403234 AAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTT-
1 AAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
* * * *
12403293 AGAAAT-AAATTTTCAAAAAAAGGGATTTTGAGA-AAAAGTTGAAAGTATCAATTTTCCTTG
1 A-AAATCAAAATTTCCAAAAAA-GTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
*
12403353 AAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTT-
1 AAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
* * * *
12403412 AGAAAT-AAATTTTCAAAAAAAGGGATTTTGAGA-AAAAGTTGAAAGTATCAATTTTCCTTG
1 A-AAATCAAAATTTCCAAAAAA-GTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
* * * *
12403472 AAAATCAAAGTTTCCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAATCAAAATTTCC---AAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCC
12403532 CTACACAAGA
Statistics
Matches: 260, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
59 95 0.37
60 114 0.44
62 6 0.02
63 45 0.17
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (60 bp):
AAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:12403338 original size:119 final size:119
Alignment explanation
Indices: 12403207--12403529 Score: 583
Period size: 119 Copynumber: 2.7 Consensus size: 119
12403197 ATTTTTAGGG
12403207 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAG
12403272 TTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAAAAAGGGATTTTGAGA
66 TTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAAAAAGGGATTTTGAGA
12403326 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAG
12403391 TTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAAAAAGGGATTTTGAGA
66 TTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAAAAAGGGATTTTGAGA
* * * *
12403445 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAAAAAATATTTTTGGGGAA
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCC---AAAAAAGTATTTTTAGAGAA
12403510 AAGTTGAAAGTATCAATTTT
63 AAGTTGAAAGTATCAATTTT
12403530 CCCTACACAA
Statistics
Matches: 197, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
119 160 0.81
122 37 0.19
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (119 bp):
AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAAAAAAGTATTTTTAGAGAAAAG
TTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAAAAAGGGATTTTGAGA
Found at i:12408177 original size:23 final size:24
Alignment explanation
Indices: 12408129--12408177 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
12408119 TTAGTAAATC
* *
12408129 ATTTAGCATACGATTCAACATACA
1 ATTTAGCATACCAATCAACATACA
*
12408153 ATTTAGCATACCAAT-ATCATACA
1 ATTTAGCATACCAATCAACATACA
12408176 AT
1 AT
12408178 ACCATTTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (24 bp):
ATTTAGCATACCAATCAACATACA
Found at i:12408188 original size:28 final size:26
Alignment explanation
Indices: 12408128--12408206 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 26
12408118 TTTAGTAAAT
*
12408128 CATTTAGCATACGAT-TCAAC-ATAC
1 CATTTAGCATACAATATCAACAATAC
*
12408152 AATTTAGCATACCAATATCATACAATAC
1 CATTTAGCATA-CAATATCA-ACAATAC
*
12408180 CATTTAGCAAAACAATATCACACAATA
1 CATTTAGC-ATACAATATCA-ACAATA
12408207 AGGTTTAGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 10 0.22
25 3 0.07
26 3 0.07
27 2 0.04
28 25 0.56
29 2 0.04
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.27
Consensus pattern (26 bp):
CATTTAGCATACAATATCAACAATAC
Found at i:12408213 original size:28 final size:28
Alignment explanation
Indices: 12408153--12408218 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
12408143 TCAACATACA
* * * *
12408153 ATTTAGCATACCAATATCATACAATACC
1 ATTTAGCAAAACAATATCACACAATAAC
*
12408181 ATTTAGCAAAACAATATCACACAATAAG
1 ATTTAGCAAAACAATATCACACAATAAC
*
12408209 GTTTAGCAAA
1 ATTTAGCAAA
12408219 CCATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.26
Consensus pattern (28 bp):
ATTTAGCAAAACAATATCACACAATAAC
Found at i:12409430 original size:187 final size:188
Alignment explanation
Indices: 12408704--12409830 Score: 1103
Period size: 191 Copynumber: 6.0 Consensus size: 188
12408694 ATTTTGAACA
* * *
12408704 AAAATTATTAAAGGCATTT-TTAGTAAAAAACCAT--CTTCAATAATTATGTACAAAAATTAAAA
1 AAAATTATTGAAGGCATTTGTT-CTAAAAAA--ATGCCTTCAATAACTATGTACAAAAATTAAAA
* * * *
12408766 GG-AATTA-GTGAAGGCATTTTTCTAAAATAAATGCCTTCACTAACCGTCTTGAAATATGAGTAG
63 GGAAATTATGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTA-
** * *
12408829 TAG-AATATTAAAGGCATTTTTCACTAGAAAACACCTTTAATAATCTC-AAAAATTTTAAGACG
127 TAGTAATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATC-CAAAAAATTTTAAGA-G
* * * ** *
12408891 -AAACTA-TGAAAGCATTTGTTCTTAAAAAATGCCTTCAAT-ACTTACATACAAATATTAGAAA-
1 AAAATTATTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATAAC-TATGTACAAAAATTA-AAAG
* * * * *
12408952 G-AATTA-GTAAAAGCATTTATTCTAGAAAAAATGCCTTTAGTAACCATCTTAAAATTTGAGTAT
64 GAAATTATGTGAAGGCATTT-TTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTAT
* * * * * * *
12409015 AGTAATATTGAAGGCGTTTTTCACTGGAAGACGCCTTTAATAATTCAAAAAATTTTAAAAG
128 AGTAATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATCCAAAAAATTTTAAGAG
* ***
12409076 AAAATTATTGAAGGCGTTTGTTCT-AAAAAATGGCCTTCAATAACTATGTATGTAAATTAAAAGG
1 AAAATTATTGAAGGCATTTGTTCTAAAAAAAT-GCCTTCAATAACTATGTACAAAAATTAAAAGG
* * * ** * *
12409140 AATTTATGTGTGAAGGTATTTTTTTAGAATAAATGCCTTCACTAACTGTATAAAAATTTGAGTAG
65 AAATTA--TGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTA-
* * * * *
12409205 T-TTAATATTGAAGGTGTTTTGCACTAGAACACACCTTTAATAATCCCAAAAATTTTAAGAG
127 TAGTAATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATCCAAAAAATTTTAAGAG
*
12409266 AAAATTATTGAAGGCATTTGTTCTCAAAAAAATACCTTCAATAA-TAATGTACAAAAATTAAAA-
1 AAAATTATTGAAGGCATTTGTTCT-AAAAAAATGCCTTCAATAACT-ATGTACAAAAATTAAAAG
** * * *
12409329 GAAATTA-GTGAAGGTGTTTATTATAGAA-AAATACCTTCACTAACCATCTTAAAATTTGAGTAC
64 GAAATTATGTGAAGGCATTT-TTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTAT
* * * *
12409392 AGTAATATTAAAGGTATTTTTCACTGGAAAACACCTTTAATAATCCTAAAACTTTTAAGAG
128 AGTAATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATCCAAAAAATTTTAAGAG
* * ***
12409453 GAAATTATTGAAGGCATTTGTTCTAAAAAAAATGTCTTCAATAACTATGTATGTAAATTAAAAGG
1 AAAATTATTGAAGGCATTTGTTCT-AAAAAAATGCCTTCAATAACTATGTACAAAAATTAAAAGG
* *
12409518 AATTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATATTAAAATTTGAGTAG
65 AAATTA--TGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTA-
* * * *
12409583 T-GGAATATTAAAGGTGTTTTGCACT-GAAAGACACCTTTTATAATTCTAAAAATTTTTTAA-AG
127 TAGTAATATTAAAGGTGTTTTGCACTGGAAA-ACACCTTTAATAA-TCCAAAAA-ATTTTAAGAG
* * * * * * ***
12409645 GAAATTGTTGTAGTCATTTGTTCTAAAAAGATGCCTTTAATAACTATGTATGTAAATTAAAAGGA
1 AAAATTATTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATAACTATGTACAAAAATTAAAAGGA
* * * * * *
12409710 ATTTATGTGTGAAGGCATTTTTTTAGAACAAACGCCTTCACTAACAATCTTAAAATTTAAGTAGT
66 AATTA--TGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTA-T
* *
12409775 AG-AATATTGAAGGTGTTTTGCACTGGAAGACACCTTTAATAATCTCAAAAAATTTT
128 AGTAATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATC-CAAAAAATTTT
12409831 TAAAATGAAA
Statistics
Matches: 789, Mismatches: 115, Indels: 69
0.81 0.12 0.07
Matches are distributed among these distances:
183 2 0.00
184 1 0.00
185 55 0.07
186 109 0.14
187 179 0.23
188 20 0.03
190 133 0.17
191 244 0.31
192 40 0.05
193 6 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (188 bp):
AAAATTATTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATAACTATGTACAAAAATTAAAAGGA
AATTATGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATCTTAAAATTTGAGTATAGT
AATATTAAAGGTGTTTTGCACTGGAAAACACCTTTAATAATCCAAAAAATTTTAAGAG
Found at i:12409558 original size:378 final size:374
Alignment explanation
Indices: 12408705--12409850 Score: 1326
Period size: 378 Copynumber: 3.0 Consensus size: 374
12408695 TTTTGAACAA
* * *** * ***
12408705 AAATTATTAAAGGCATTT-TTAGTAAAAAACCATCTTCAATAATTATGTACAAAAATTAAAAGGA
1 AAATTATTGAAGGCATTTGTT-CTAAAAAATGGTCTTCAATAACTATGTATGTAAATTAAAAGGA
* * * *
12408769 A-TTA---GTGAAGGCATTTTTCTAAAATAAATGCCTTCACTAACCGTCTTGAAATATGAGTAGT
65 ATTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCGTATTAAAATTTGAGTAGT
** * * *
12408830 AGAATATTAAAGGCATTTTTCACTAGAAAACACCTTTAATAATCTCAAAAATTTTAAGACGAAAC
130 AGAATATTAAAGGTGTTTTGCACTAGAAAACACCTTTAATAATCCCAAAAATTTTAAGA-GAAAT
* * * ** *
12408895 TA-TGAAAGCATTTGTTCTTAAAAAATGCCTTCAATACTTACATACAAATATTAGAAAG-AATTA
194 TATTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATA-ATATGTACAAAAATTA-AAAGAAATTA
* * * * *
12408958 GTAAAAGCATTTATTCTAGAAAAAATGCCTTTAGTAACCATCTTAAAATTTGAGTATAGTAATAT
257 GTGAAGGCATTTATTATAG-AAAAATGCCTTCACTAACCATCTTAAAATTTGAGTATAGTAATAT
* * * *
12409023 TGAAGGCGTTTTTCACTGGAAGACGCCTTTAATAATTCAAAAAATTTTAAAAGA
321 TGAAGGTGTTTTTCACTGGAAGACACCTTTAATAATCCAAAAAATTTTAAAAGG
* *
12409077 AAATTATTGAAGGCGTTTGTTCTAAAAAATGGCCTTCAATAACTATGTATGTAAATTAAAAGGAA
1 AAATTATTGAAGGCATTTGTTCTAAAAAATGGTCTTCAATAACTATGTATGTAAATTAAAAGGAA
* * * * *
12409142 TTTATGTGTGAAGGTATTTTTTTAGAATAAATGCCTTCACTAACTGTATAAAAATTTGAGTAGTT
66 TTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCGTATTAAAATTTGAGTAGTA
* * *
12409207 TAATATTGAAGGTGTTTTGCACTAGAACACACCTTTAATAATCCCAAAAATTTTAAGAGAAAATT
131 GAATATTAAAGGTGTTTTGCACTAGAAAACACCTTTAATAATCCCAAAAATTTTAAGAG-AAATT
*
12409272 ATTGAAGGCATTTGTTCTCAAAAAAATACCTTCAATAATAATGTACAAAAATTAAAAGAAATTAG
195 ATTGAAGGCATTTGTTCT-AAAAAAATGCCTTCAATAAT-ATGTACAAAAATTAAAAGAAATTAG
** * * *
12409337 TGAAGGTGTTTATTATAGAAAAATACCTTCACTAACCATCTTAAAATTTGAGTACAGTAATATTA
258 TGAAGGCATTTATTATAGAAAAATGCCTTCACTAACCATCTTAAAATTTGAGTATAGTAATATTG
* * * * *
12409402 AAGGTATTTTTCACTGGAAAACACCTTTAATAATCCTAAAACTTTTAAGAGG
323 AAGGTGTTTTTCACTGGAAGACACCTTTAATAATCCAAAAAATTTTAAAAGG
12409454 AAATTATTGAAGGCATTTGTTCTAAAAAAAAT-GTCTTCAATAACTATGTATGTAAATTAAAAGG
1 AAATTATTGAAGGCATTTGTTCT--AAAAAATGGTCTTCAATAACTATGTATGTAAATTAAAAGG
*
12409518 AATTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCATATTAAAATTTGAGTAG
64 AATTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCGTATTAAAATTTGAGTAG
* * * *
12409583 TGGAATATTAAAGGTGTTTTGCACT-GAAAGACACCTTTTATAATTCTAAAAATTTTTTAA-AGG
129 TAGAATATTAAAGGTGTTTTGCACTAGAAA-ACACCTTTAATAATCCCAAAAA--TTTTAAGA-G
* * * * * ***
12409646 AAATTGTTGTAGTCATTTGTTCTAAAAAGATGCCTTTAATAACTATGTATGTAAATTAAAAGGAA
190 AAATTATTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATAA-TATGTACAAAAATTAAAA-GAA
* * * * *
12409711 TTTATGTGTGAAGGCATTT-TTTTAGAACAAACGCCTTCACTAACAATCTTAAAATTTAAGTAGT
253 ATTA---GTGAAGGCATTTATTATAGAA-AAATGCCTTCACTAACCATCTTAAAATTTGAGTA-T
* *
12409775 AG-AATATTGAAGGTGTTTTGCACTGGAAGACACCTTTAATAATCTCAAAAAATTTTTAAAATG
313 AGTAATATTGAAGGTGTTTTTCACTGGAAGACACCTTTAATAATC-CAAAAAA-TTTTAAAAGG
*
12409838 AAATTATTAAAGG
1 AAATTATTGAAGG
12409851 TGTTTTTAGT
Statistics
Matches: 654, Mismatches: 95, Indels: 38
0.83 0.12 0.05
Matches are distributed among these distances:
372 51 0.08
373 5 0.01
375 1 0.00
376 105 0.16
377 130 0.20
378 208 0.32
379 35 0.05
380 7 0.01
381 7 0.01
382 78 0.12
383 7 0.01
384 20 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (374 bp):
AAATTATTGAAGGCATTTGTTCTAAAAAATGGTCTTCAATAACTATGTATGTAAATTAAAAGGAA
TTTATGTGTGAAGGCATTTTTCTAGAATAAATGCCTTCACTAACCGTATTAAAATTTGAGTAGTA
GAATATTAAAGGTGTTTTGCACTAGAAAACACCTTTAATAATCCCAAAAATTTTAAGAGAAATTA
TTGAAGGCATTTGTTCTAAAAAAATGCCTTCAATAATATGTACAAAAATTAAAAGAAATTAGTGA
AGGCATTTATTATAGAAAAATGCCTTCACTAACCATCTTAAAATTTGAGTATAGTAATATTGAAG
GTGTTTTTCACTGGAAGACACCTTTAATAATCCAAAAAATTTTAAAAGG
Found at i:12416897 original size:21 final size:21
Alignment explanation
Indices: 12416872--12416930 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
12416862 AAAAAGAGAA
12416872 CAAGAGCATGCCAAAATTGAG
1 CAAGAGCATGCCAAAATTGAG
* * * * *
12416893 GAAGAACATGCTAGAATAGAG
1 CAAGAGCATGCCAAAATTGAG
*
12416914 CAAGAGTATG-CAAAATT
1 CAAGAGCATGCCAAAATT
12416931 TCAACAATTG
Statistics
Matches: 27, Mismatches: 11, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.17
Consensus pattern (21 bp):
CAAGAGCATGCCAAAATTGAG
Found at i:12417649 original size:34 final size:34
Alignment explanation
Indices: 12417611--12417677 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
12417601 GACATTTTTT
* *
12417611 AGATACAAATGCTATTAATATAGCAGCGTTTTCA
1 AGATACAAATGCCACTAATATAGCAGCGTTTTCA
* * *
12417645 AGATATAAATGCCGCTAATATAGCGGCGTTTTC
1 AGATACAAATGCCACTAATATAGCAGCGTTTTC
12417678 CATATATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (34 bp):
AGATACAAATGCCACTAATATAGCAGCGTTTTCA
Found at i:12417685 original size:34 final size:34
Alignment explanation
Indices: 12417626--12417710 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
12417616 CAAATGCTAT
**
12417626 TAATATAGCAGCGTTTTCAAGATATAAATGCCGC
1 TAATATAGCAGCGTTTTCAAGATATAAACACCGC
* * * *
12417660 TAATATAGCGGCGTTTTCCATATATAAACACCGT
1 TAATATAGCAGCGTTTTCAAGATATAAACACCGC
* *
12417694 TAATATAGTAGCATTTT
1 TAATATAGCAGCGTTTT
12417711 TCAGATACAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (34 bp):
TAATATAGCAGCGTTTTCAAGATATAAACACCGC
Found at i:12419098 original size:22 final size:22
Alignment explanation
Indices: 12419065--12419115 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12419055 TATTTATTTC
*
12419065 AATA-AATTAATTATTTTATAAT
1 AATATAATGAATT-TTTTATAAT
*
12419087 AA-ATAATGAATTTTTTTTAAT
1 AATATAATGAATTTTTTATAAT
12419108 AATATAAT
1 AATATAAT
12419116 TATGCAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATAATGAATTTTTTATAAT
Found at i:12420408 original size:22 final size:25
Alignment explanation
Indices: 12420357--12420408 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
12420347 TAATTGCTTG
*
12420357 CTAAAAAAATAGAATCAAAGAGATT
1 CTAAAAAAATAAAATCAAAGAGATT
*
12420382 ATAAAAAAA-AAAATC-AA-AGATT
1 CTAAAAAAATAAAATCAAAGAGATT
12420404 CTAAA
1 CTAAA
12420409 TCCGTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 5 0.21
25 8 0.33
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (25 bp):
CTAAAAAAATAAAATCAAAGAGATT
Found at i:12420565 original size:5 final size:5
Alignment explanation
Indices: 12420555--12420581 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12420545 TAGCTATGTT
12420555 TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TA
12420582 ATTGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12421939 original size:20 final size:20
Alignment explanation
Indices: 12421914--12421956 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12421904 TAATAAATTC
12421914 ATTGGTGAGTTTTTATCTAT
1 ATTGGTGAGTTTTTATCTAT
12421934 ATTGGTGAGTTTTTATCTAT
1 ATTGGTGAGTTTTTATCTAT
12421954 ATT
1 ATT
12421957 ATAAATGGAC
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:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (20 bp):
ATTGGTGAGTTTTTATCTAT
Found at i:12423347 original size:60 final size:59
Alignment explanation
Indices: 12423247--12423836 Score: 696
Period size: 57 Copynumber: 9.8 Consensus size: 59
12423237 TTTTTTGTAG
* *
12423247 GGAAGATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTCGATTTTC-AA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTGGAAATTT--ATTTTCTAA
* * ** *
12423307 AGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TTTTTTTTTGGAAATTTATTTTCTAA
12423366 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGGAAAATTTATTTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCC-AAAA-A-TTTTTTTTTGG-AAATTTA-TTTTC---T
12423431 AA
58 AA
* * *
12423433 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-TATTTTTTGGAAATTTATTCT-TAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTGGAAATTTATTTTCTAA
* ** *
12423490 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTTAAATTTA-TTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-T-TTTTTTTGGAAATTTATTTTCTAA
*
12423550 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGGAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTGGAAATTTATTTTCTAA
*
12423607 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-CAAAA-ATTTTTTTTTGGAAATTTA-TTTTC---TAA
** * *
12423672 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTGAAATTTATTTT-TGA
1 GGAAAATTGATACTTTCAAC-TTTTCCCCAAAA-ATTTTTTTTTGGAAATTTATTTTCTAA
* *
12423732 GGAAAATTGATATTTTCAACTTTTCCCCAAAAA-TATTTTTTGGAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTGGAAATTTATTTTCTAA
*
12423789 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-T-TTTTTTTGGAA
12423837 TTTTTTATTC
Statistics
Matches: 464, Mismatches: 39, Indels: 54
0.83 0.07 0.10
Matches are distributed among these distances:
56 3 0.01
57 130 0.28
58 10 0.02
59 44 0.09
60 128 0.28
61 26 0.06
62 18 0.04
63 9 0.02
64 8 0.02
65 48 0.10
66 10 0.02
67 30 0.06
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTGGAAATTTATTTTCTAA
Found at i:12423422 original size:20 final size:22
Alignment explanation
Indices: 12423399--12423440 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12423389 TCCCCAAAAA
*
12423399 TATTTTT-TTTT-TGGAAAATT
1 TATTTTTCTTTTAAGGAAAATT
12423419 TATTTTTCTTTTAAGGAAAATT
1 TATTTTTCTTTTAAGGAAAATT
12423441 GATACTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (22 bp):
TATTTTTCTTTTAAGGAAAATT
Found at i:12423523 original size:27 final size:27
Alignment explanation
Indices: 12423435--12423523 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
12423425 TCTTTTAAGG
12423435 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * * *
12423462 AAAA-T-ATTTTTTGGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
12423490 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
12423519 AAAAT
1 AAAAT
12423524 ATATTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Done.