Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 109 of 131
Found at i:19401865 original size:10 final size:10
Alignment explanation
Indices: 19401826--19401865 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
19401816 ATATAAATAA
19401826 TATTATTATT
1 TATTATTATT
*
19401836 TATCATTATT
1 TATTATTATT
19401846 TATTATTTATT
1 TATTA-TTATT
*
19401857 AATTATTAT
1 TATTATTAT
19401866 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTATTATT
Found at i:19401901 original size:27 final size:26
Alignment explanation
Indices: 19401869--19401920 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
19401859 TTATTATATT
*
19401869 TATTAAAATATAAATATTATTTCTAAC
1 TATTAAAATATAAATA-TAATTCTAAC
19401896 TATTAAAATATAAATATAATTCTAA
1 TATTAAAATATAAATATAATTCTAA
19401921 TAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TATTAAAATATAAATATAATTCTAAC
Found at i:19404446 original size:26 final size:26
Alignment explanation
Indices: 19404397--19404462 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
19404387 TTAATATAAC
* *
19404397 TATTAAAATATA-AAAAATTATTTAT
1 TATTAAAATATATTAAAACTATTTAT
19404422 TATTAAAATATATTAAAACTATTTAT
1 TATTAAAATATATTAAAACTATTTAT
*
19404448 TATTAAAGT-TATTAA
1 TATTAAAATATATTAA
19404463 TATTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TATTAAAATATATTAAAACTATTTAT
Found at i:19404581 original size:23 final size:23
Alignment explanation
Indices: 19404555--19404715 Score: 141
Period size: 23 Copynumber: 6.7 Consensus size: 23
19404545 AGTATTCTTT
19404555 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
*
19404578 ATATTGTTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
*
19404601 ATATTATTTATTAATAATATTTGTTA
1 ATATTATTTATTAAT-ATA-TT-ATA
*
19404627 ATA-TATTATATTAATAGTA-TATT
1 ATATTATT-TATTAATA-TATTATA
*
19404650 AT-TTA-TTAATAATATATTATTTA
1 ATATTATTTATTAATATATTA--TA
*
19404673 TCACTATATATTTATTAATATAATATA
1 --A-TAT-TATTTATTAATATATTATA
*
19404700 ATATTATTTATAAATA
1 ATATTATTTATTAATA
19404716 AAATTATGCT
Statistics
Matches: 113, Mismatches: 10, Indels: 30
0.74 0.07 0.20
Matches are distributed among these distances:
20 2 0.02
21 9 0.08
22 1 0.01
23 53 0.47
24 7 0.06
25 9 0.08
26 15 0.13
27 3 0.03
28 2 0.02
29 12 0.11
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:19404594 original size:13 final size:13
Alignment explanation
Indices: 19404555--19404715 Score: 107
Period size: 13 Copynumber: 13.2 Consensus size: 13
19404545 AGTATTCTTT
19404555 ATATTATTTATTA
1 ATATTATTTATTA
19404568 ATA-TA-TTA-TA
1 ATATTATTTATTA
*
19404578 ATATTGTTTATTA
1 ATATTATTTATTA
19404591 ATA-TA-TTA-TA
1 ATATTATTTATTA
19404601 ATATTATTTATTA
1 ATATTATTTATTA
* *
19404614 ATAATATTTGTTA
1 ATATTATTTATTA
19404627 ATA-TATTATATTA
1 ATATTATT-TATTA
*
19404640 ATAGTA--TATT-
1 ATATTATTTATTA
* *
19404650 AT-TTATTAATAA
1 ATATTATTTATTA
*
19404662 TATATTATTTATCA
1 -ATATTATTTATTA
*
19404676 CTATATATTTATTA
1 ATAT-TATTTATTA
*
19404690 ATA-TA-ATA-TA
1 ATATTATTTATTA
*
19404700 ATATTATTTATAA
1 ATATTATTTATTA
19404713 ATA
1 ATA
19404716 AAATTATGCT
Statistics
Matches: 115, Mismatches: 16, Indels: 34
0.70 0.10 0.21
Matches are distributed among these distances:
9 2 0.02
10 17 0.15
11 19 0.17
12 17 0.15
13 40 0.35
14 20 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTATTTATTA
Found at i:19404651 original size:44 final size:40
Alignment explanation
Indices: 19404554--19404664 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 40
19404544 TAGTATTCTT
* * *
19404554 TATATTAT-TTATTAATATATT-ATAATA-TTGTTTATTAA
1 TATATTATAATATT-ATTTATTAATAATATTTGTTAATTAA
*
19404592 TATATTATAATATTATTTATTAATAATATTTGTTAATATAT
1 TATATTATAATATTATTTATTAATAATATTTGTTAAT-TAA
19404633 TATATTAATAGTATATTATTTATTAATAATAT
1 TATATT-ATA--ATATTATTTATTAATAATAT
19404665 ATTATTTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
38 14 0.23
39 10 0.16
40 7 0.11
41 8 0.13
42 3 0.05
44 20 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (40 bp):
TATATTATAATATTATTTATTAATAATATTTGTTAATTAA
Found at i:19404656 original size:18 final size:17
Alignment explanation
Indices: 19404554--19404715 Score: 91
Period size: 18 Copynumber: 9.0 Consensus size: 17
19404544 TAGTATTCTT
19404554 TATATTATTTATTAATA
1 TATATTATTTATTAATA
19404571 TATTATAATATTGTTTATTAATA
1 TA-TAT--TA---TTTATTAATA
* *
19404594 TATTATAATATTATTTAT-
1 TA-TATTAT-TTATTAATA
* *
19404612 TAATAATATTTGTT-A-A
1 T-ATATTATTTATTAATA
19404628 TATATTA--TATTAATA
1 TATATTATTTATTAATA
19404643 GTATATTATTTATTAATAA
1 -TATATTATTTATTAAT-A
* *
19404662 TATATTATTTATCACTA
1 TATATTATTTATTAATA
*
19404679 TATATTTATTAATATAATA
1 TATA-TTATTTAT-TAATA
*
19404698 TAATATTATTTATAAATA
1 T-ATATTATTTATTAATA
19404716 AAATTATGCT
Statistics
Matches: 113, Mismatches: 14, Indels: 35
0.70 0.09 0.22
Matches are distributed among these distances:
13 3 0.03
14 1 0.01
15 6 0.05
16 9 0.08
17 11 0.10
18 41 0.36
19 20 0.18
20 5 0.04
21 1 0.01
23 16 0.14
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTATTTATTAATA
Found at i:19404668 original size:34 final size:34
Alignment explanation
Indices: 19404625--19404705 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 34
19404615 TAATATTTGT
*
19404625 TAATATATTATATTAAT-AGTATATTATTTATTAA
1 TAATATATTATATTAATCACTATA-TATTTATTAA
19404659 TAATATATTAT-TT-ATCACTATATATTTATTAA
1 TAATATATTATATTAATCACTATATATTTATTAA
*
19404691 T-ATAATATAATATTA
1 TAAT-ATATTATATTA
19404706 TTTATAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 2 0.05
32 19 0.46
33 9 0.22
34 11 0.27
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (34 bp):
TAATATATTATATTAATCACTATATATTTATTAA
Found at i:19411176 original size:12 final size:12
Alignment explanation
Indices: 19411159--19411192 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19411149 AAGAAAGCCT
19411159 CACCTCCTCCTC
1 CACCTCCTCCTC
*
19411171 CACCTCCCCCTC
1 CACCTCCTCCTC
*
19411183 CCCCTCCTCC
1 CACCTCCTCC
19411193 ATTGCTTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.74, G:0.00, T:0.21
Consensus pattern (12 bp):
CACCTCCTCCTC
Found at i:19415877 original size:149 final size:149
Alignment explanation
Indices: 19415607--19415905 Score: 589
Period size: 149 Copynumber: 2.0 Consensus size: 149
19415597 TAAATATGCT
*
19415607 TAAAATTGTCGACTAAACCTAAGCAAAATACTCAAGAAATGAGCCTTAAACCTTCCATAAATGGT
1 TAAAATTGTCGACTAAACCTAAGCAAAATACTCAAGAAATGAGCCTTAAACCTTCCATAAATGGC
19415672 GATTGGTGAGGTAAGTCTTAGGATCAAGTTGAGCACATTTACAACTCCAGAACTTTCAAGGAGAA
66 GATTGGTGAGGTAAGTCTTAGGATCAAGTTGAGCACATTTACAACTCCAGAACTTTCAAGGAGAA
19415737 AAAACGAAAACCTAACAAA
131 AAAACGAAAACCTAACAAA
19415756 TAAAATTGTCGACTAAACCTAAGCAAAATACTCAAGAAATGAGCCTTAAACCTTCCATAAATGGC
1 TAAAATTGTCGACTAAACCTAAGCAAAATACTCAAGAAATGAGCCTTAAACCTTCCATAAATGGC
19415821 GATTGGTGAGGTAAGTCTTAGGATCAAGTTGAGCACATTTACAACTCCAGAACTTTCAAGGAGAA
66 GATTGGTGAGGTAAGTCTTAGGATCAAGTTGAGCACATTTACAACTCCAGAACTTTCAAGGAGAA
19415886 AAAACGAAAACCTAACAAA
131 AAAACGAAAACCTAACAAA
19415905 T
1 T
19415906 TATTCAGGTC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (149 bp):
TAAAATTGTCGACTAAACCTAAGCAAAATACTCAAGAAATGAGCCTTAAACCTTCCATAAATGGC
GATTGGTGAGGTAAGTCTTAGGATCAAGTTGAGCACATTTACAACTCCAGAACTTTCAAGGAGAA
AAAACGAAAACCTAACAAA
Found at i:19416683 original size:21 final size:20
Alignment explanation
Indices: 19416640--19416683 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19416630 TATAATGACA
* *
19416640 AAAAGCAGACACAAATCACC
1 AAAAGCACACACAAATCAAC
*
19416660 AAAAGCACACACAGATTCAAC
1 AAAAGCACACACA-AATCAAC
19416681 AAA
1 AAA
19416684 TGAAACATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.57, C:0.27, G:0.09, T:0.07
Consensus pattern (20 bp):
AAAAGCACACACAAATCAAC
Found at i:19419055 original size:59 final size:59
Alignment explanation
Indices: 19418992--19419110 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
19418982 TAGGAGTTAC
*
19418992 ATTAATTAATTAGGATAATTAATGGTTTTTGTATTTTTATGAAAAACTAAAATTTAAGT
1 ATTAATTAATTAGGATAATTAATGGTTTTTGTATTTTTATGAAAAAATAAAATTTAAGT
*
19419051 ATTAATTAATTAGGATAATTAATGGTTTTTGTATTTTTATGAAAAAATAAACTTTAAGT
1 ATTAATTAATTAGGATAATTAATGGTTTTTGTATTTTTATGAAAAAATAAAATTTAAGT
19419110 A
1 A
19419111 ATAAATGCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (59 bp):
ATTAATTAATTAGGATAATTAATGGTTTTTGTATTTTTATGAAAAAATAAAATTTAAGT
Found at i:19420032 original size:87 final size:87
Alignment explanation
Indices: 19419930--19420111 Score: 267
Period size: 87 Copynumber: 2.1 Consensus size: 87
19419920 TCTTTCTATT
*
19419930 AAAAAAAAGACAATATTTTTTTAATTGA-TTTCAAAAACTAAATTATTATGAATCCACTAACATT
1 AAAAAAAAGACAATATTCTTTTAATTGACTTT-AAAAACTAAATTATTATGAATCCACTAACATT
* *
19419994 ATATTAGAGGATGGAATTTGACA
65 ATATTAGAGGATGAAACTTGACA
* * * *
19420017 AAAAAAAAGAGAATATTCTTTTAATTTACTTTAAAAACTATATTATTATGAATCCATTAACATTA
1 AAAAAAAAGACAATATTCTTTTAATTGACTTTAAAAACTAAATTATTATGAATCCACTAACATTA
* *
19420082 TATTGGAGGATGAAACTTGAGA
66 TATTAGAGGATGAAACTTGACA
19420104 AAAAAAAA
1 AAAAAAAA
19420112 ATGATTGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 82 0.96
88 3 0.04
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (87 bp):
AAAAAAAAGACAATATTCTTTTAATTGACTTTAAAAACTAAATTATTATGAATCCACTAACATTA
TATTAGAGGATGAAACTTGACA
Found at i:19420873 original size:21 final size:21
Alignment explanation
Indices: 19420851--19420895 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
19420841 ATTCCACAAT
19420851 TAATATATTAAATTTTATTATTA
1 TAATA-ATT-AATTTTATTATTA
*
19420874 TAATAATTAATTTTATTTTTA
1 TAATAATTAATTTTATTATTA
19420895 T
1 T
19420896 TATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 3 0.14
23 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATAATTAATTTTATTATTA
Found at i:19420900 original size:18 final size:18
Alignment explanation
Indices: 19420856--19420913 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
19420846 ACAATTAATA
19420856 TATTAAATTTTATTATTATAAT
1 TATT-AATTTTATT-TT-T-AT
*
19420878 AATTAATTTTATTTTTAT
1 TATTAATTTTATTTTTAT
* *
19420896 TATTATTTTTAATTTTAT
1 TATTAATTTTATTTTTAT
19420914 CAGAATCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.53
19 1 0.03
20 2 0.06
21 9 0.28
22 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTAATTTTATTTTTAT
Found at i:19420913 original size:12 final size:12
Alignment explanation
Indices: 19420880--19420913 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
19420870 ATTATAATAA
19420880 TTAATTTTATTT
1 TTAATTTTATTT
19420892 TT-ATTATTATTT
1 TTAATT-TTATTT
19420904 TTAATTTTAT
1 TTAATTTTAT
19420914 CAGAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTAATTTTATTT
Found at i:19424854 original size:12 final size:12
Alignment explanation
Indices: 19424848--19424876 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19424838 CTAGGTTAGG
19424848 GTTTAGGGTTTA
1 GTTTAGGGTTTA
19424860 GTTTAGGGTTTA
1 GTTTAGGGTTTA
19424872 GTTTA
1 GTTTA
19424877 AGATTTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (12 bp):
GTTTAGGGTTTA
Found at i:19424855 original size:7 final size:7
Alignment explanation
Indices: 19424843--19424891 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
19424833 GGGGTCTAGG
19424843 TTAGGGT
1 TTAGGGT
19424850 TTAGGGT
1 TTAGGGT
19424857 TTA--GT
1 TTAGGGT
19424862 TTAGGGT
1 TTAGGGT
19424869 TTA--GT
1 TTAGGGT
* *
19424874 TTAAGAT
1 TTAGGGT
19424881 TTAGGGT
1 TTAGGGT
19424888 TTAG
1 TTAG
19424892 ATTTTAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
5 10 0.29
7 25 0.71
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:19424865 original size:19 final size:20
Alignment explanation
Indices: 19424843--19424891 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
19424833 GGGGTCTAGG
19424843 TTAGGGTTTAGGGTTT-AG-T
1 TTAGGGTTTA-GGTTTAAGAT
19424862 TTAGGGTTTA-GTTTAAGAT
1 TTAGGGTTTAGGTTTAAGAT
19424881 TTAGGGTTTAG
1 TTAGGGTTTAG
19424892 ATTTTAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 2 0.07
19 21 0.78
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (20 bp):
TTAGGGTTTAGGTTTAAGAT
Found at i:19424934 original size:14 final size:14
Alignment explanation
Indices: 19424915--19424954 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
19424905 ATGGGAATTG
19424915 AGGGTTTCAAGTTT
1 AGGGTTTCAAGTTT
19424929 AGGGTTTCAAGTTT
1 AGGGTTTCAAGTTT
*
19424943 GGGGTTTCAAGT
1 AGGGTTTCAAGT
19424955 GACATTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (14 bp):
AGGGTTTCAAGTTT
Found at i:19426908 original size:24 final size:24
Alignment explanation
Indices: 19426880--19426944 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
19426870 TTCAAAGTAC
**
19426880 AATCAGATTTTTCAATTCTTTAAA
1 AATCAGAAATTTCAATTCTTTAAA
*
19426904 AATCATAAATTTCAATTCTTTAAA
1 AATCAGAAATTTCAATTCTTTAAA
*
19426928 AATCATAAATTTCAATT
1 AATCAGAAATTTCAATT
19426945 TTAAACTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (24 bp):
AATCAGAAATTTCAATTCTTTAAA
Found at i:19427338 original size:22 final size:20
Alignment explanation
Indices: 19427303--19427354 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
19427293 ATCCGAAATT
19427303 AATAAAATA-TTTTTTTAAA
1 AATAAAATATTTTTTTTAAA
19427322 ATATAAAATATTATTTTTTAAA
1 A-ATAAAATATT-TTTTTTAAA
19427344 AAT-AAATATTT
1 AATAAAATATTT
19427355 AAATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 3 0.10
22 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAAAATATTTTTTTTAAA
Found at i:19427340 original size:23 final size:20
Alignment explanation
Indices: 19427313--19427353 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
19427303 AATAAAATAT
19427313 TTTTTTAAAATATAAAATATTA
1 TTTTTTAAAA-AT-AAATATTA
19427335 TTTTTTAAAAATAAATATT
1 TTTTTTAAAAATAAATATT
19427354 TAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTTAAAAATAAATATTA
Found at i:19427359 original size:8 final size:8
Alignment explanation
Indices: 19427345--19427380 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
19427335 TTTTTTAAAA
19427345 ATAAATAT
1 ATAAATAT
*
19427353 TTAAATAT
1 ATAAATAT
*
19427361 ATAAGTAT
1 ATAAATAT
19427369 ATAAATAT
1 ATAAATAT
19427377 ATAA
1 ATAA
19427381 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
ATAAATAT
Found at i:19427837 original size:21 final size:21
Alignment explanation
Indices: 19427798--19427838 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19427788 ATCTTTTGCT
* *
19427798 TTTGTAATTTTTCTTTTTTTG
1 TTTGTAATTTTTATCTTTTTG
*
19427819 TTTGTTATTTTTATCTTTTT
1 TTTGTAATTTTTATCTTTTT
19427839 AACTTTTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTGTAATTTTTATCTTTTTG
Found at i:19428059 original size:48 final size:49
Alignment explanation
Indices: 19427983--19428102 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 49
19427973 AAAAAGGCTA
*
19427983 TTATGAAATAGGCAATGAA-TTTAAAAAAAC-TATTTTGGATAA-AGCTC
1 TTATGAAATAGGTAATGAACTTTAAAAAAACTTATTTTGGA-AATAGCTC
* * *
19428030 TTATGAACATAGATAATGAACTTTAAAAAAACTTTTTTTGGAAATGGCTC
1 TTATGAA-ATAGGTAATGAACTTTAAAAAAACTTATTTTGGAAATAGCTC
*
19428080 TTATGAAAATAGGTAATAAACTT
1 TTATG-AAATAGGTAATGAACTT
19428103 AAATTTTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
47 7 0.11
48 10 0.16
49 13 0.21
50 30 0.48
51 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (49 bp):
TTATGAAATAGGTAATGAACTTTAAAAAAACTTATTTTGGAAATAGCTC
Found at i:19428105 original size:49 final size:49
Alignment explanation
Indices: 19427863--19428105 Score: 165
Period size: 49 Copynumber: 5.0 Consensus size: 49
19427853 TTTTTTTTGG
* * * ** *
19427863 AAAAACTATTTTTAGAAAAGGCTTTTATGAAAATAGGTAACAAACTTTA
1 AAAAACTTTTTTTGGAAAAGGCTCTTATGAAAATAGGTAATGAACTTAA
* ** * * * *** *
19427912 AAAATCTCATTTCGGGAATGGCTCTTATGAAAATATACAACGAA-TT--
1 AAAAACTTTTTTTGGAAAAGGCTCTTATGAAAATAGGTAATGAACTTAA
** * * * * *
19427958 TTAAAGTTTTTTATGAAAAAGGCTATTATG-AAATAGGCAATGAATTTAA
1 AAAAACTTTTTT-TGGAAAAGGCTCTTATGAAAATAGGTAATGAACTTAA
* * *
19428007 AAAAAC-TATTTTGGATAAA-GCTCTTATGAACATAGATAATGAACTTTAA
1 AAAAACTTTTTTTGGA-AAAGGCTCTTATGAAAATAGGTAATGAAC-TTAA
* *
19428056 AAAAACTTTTTTTGGAAATGGCTCTTATGAAAATAGGTAATAAACTTAA
1 AAAAACTTTTTTTGGAAAAGGCTCTTATGAAAATAGGTAATGAACTTAA
19428105 A
1 A
19428106 TTTTTTGAAA
Statistics
Matches: 144, Mismatches: 41, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
46 17 0.12
47 25 0.17
48 20 0.14
49 52 0.36
50 30 0.21
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (49 bp):
AAAAACTTTTTTTGGAAAAGGCTCTTATGAAAATAGGTAATGAACTTAA
Found at i:19428188 original size:31 final size:31
Alignment explanation
Indices: 19428153--19428219 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 31
19428143 TTTAAATATC
19428153 TCTTTTTGGTGTC-AGTTAATTCGAGCTTAAT
1 TCTTTTTGGT-TCAAGTTAATTCGAGCTTAAT
* *
19428184 TCTTTTTGGTTCTAGAGTTAGTTTGAGCTTAAT
1 TCTTTTTGGTTC-A-AGTTAATTCGAGCTTAAT
19428217 TCT
1 TCT
19428220 CATTGATGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 10 0.32
33 19 0.61
ACGTcount: A:0.18, C:0.12, G:0.19, T:0.51
Consensus pattern (31 bp):
TCTTTTTGGTTCAAGTTAATTCGAGCTTAAT
Found at i:19428636 original size:19 final size:16
Alignment explanation
Indices: 19428603--19428649 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
19428593 TTTGTTGTTG
19428603 TTTTTTTTTT-TAACT
1 TTTTTTTTTTATAACT
19428618 CTTTTTTTTTTAGTAAACT
1 -TTTTTTTTTTA-T-AACT
19428637 TTTCTTTTTTTAT
1 TTT-TTTTTTTAT
19428650 TTCTTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 10 0.37
18 5 0.19
19 12 0.44
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTTATAACT
Found at i:19428782 original size:23 final size:23
Alignment explanation
Indices: 19428752--19428795 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19428742 ATTTCTTTTT
19428752 CTTTTTTCTCTCCCTTTTTTTCC
1 CTTTTTTCTCTCCCTTTTTTTCC
* *
19428775 CTTTTTTCTCTTCTTTTTTTT
1 CTTTTTTCTCTCCCTTTTTTT
19428796 TTCTTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (23 bp):
CTTTTTTCTCTCCCTTTTTTTCC
Found at i:19428855 original size:36 final size:36
Alignment explanation
Indices: 19428785--19428865 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
19428775 CTTTTTTCTC
* *
19428785 TTCTTT-TTTTTTTCTTATTTGACAAAATTCTCTTT
1 TTCTTTCTTTTTTTCTTATTTAAAAAAATTCTCTTT
* *
19428820 TTCTTTCTTTTTTT-TTTTTTAAAAACAATTTTCTTT
1 TTCTTTCTTTTTTTCTTATTTAAAAA-AATTCTCTTT
*
19428856 TACTTTCTTT
1 TTCTTTCTTT
19428866 ACCTTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 14 0.36
36 25 0.64
ACGTcount: A:0.17, C:0.14, G:0.01, T:0.68
Consensus pattern (36 bp):
TTCTTTCTTTTTTTCTTATTTAAAAAAATTCTCTTT
Found at i:19429830 original size:11 final size:10
Alignment explanation
Indices: 19429814--19429883 Score: 61
Period size: 10 Copynumber: 6.5 Consensus size: 10
19429804 TCAACATTCA
*
19429814 TTTTTTCTTC
1 TTTTTTTTTC
19429824 TTTTTTTTT-
1 TTTTTTTTTC
19429833 TTTTGCTTCTTCCTC
1 TTTT--TT-TT--TC
19429848 TTTTTTTCTTC
1 TTTTTTT-TTC
*
19429859 TTTTTTTTCC
1 TTTTTTTTTC
19429869 TTTTTTTTTC
1 TTTTTTTTTC
19429879 TTTTT
1 TTTTT
19429884 CGAAACAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
9 4 0.08
10 24 0.48
11 11 0.22
12 3 0.06
13 3 0.06
14 1 0.02
15 4 0.08
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:19433548 original size:41 final size:41
Alignment explanation
Indices: 19433441--19433551 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 41
19433431 TGAATTTTAT
** ** * *
19433441 GCTATCTGTTTACTA-AAAAAGGCCATGTATACTTGTTTCAT
1 GCTATCTGTTTA-TACATGAAGGCCATGTGCACCTGTTTCAC
*
19433482 GCTATTTGTTTATACATGAAGGCCATGTGCACCTGTTTCAC
1 GCTATCTGTTTATACATGAAGGCCATGTGCACCTGTTTCAC
*
19433523 GCTATCTGTTTATGCATGCAA-GCCATGTG
1 GCTATCTGTTTATACATG-AAGGCCATGTG
19433552 TCTATTAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.03
41 55 0.93
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (41 bp):
GCTATCTGTTTATACATGAAGGCCATGTGCACCTGTTTCAC
Found at i:19441824 original size:15 final size:15
Alignment explanation
Indices: 19441784--19441831 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
19441774 ATTAAATTTG
* *
19441784 TATATATAT-TGTAA
1 TATATATATATATGA
19441798 TATAATATTATATATGA
1 TAT-ATA-TATATATGA
19441815 TATATATATATATGA
1 TATATATATATATGA
19441830 TA
1 TA
19441832 AAATATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 3 0.10
15 14 0.48
16 6 0.21
17 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TATATATATATATGA
Found at i:19443425 original size:10 final size:9
Alignment explanation
Indices: 19443403--19443432 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
19443393 AGCCCACTTC
19443403 TTTAAAAAT
1 TTTAAAAAT
19443412 TTTAAAATAT
1 TTTAAAA-AT
19443422 TTTAAAAAT
1 TTTAAAAAT
19443431 TT
1 TT
19443433 ATTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:19443425 original size:19 final size:20
Alignment explanation
Indices: 19443403--19443442 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19443393 AGCCCACTTC
19443403 TTTAAAAATTT-TAAAATAT
1 TTTAAAAATTTATAAAATAT
*
19443422 TTTAAAAATTTATTAAATAT
1 TTTAAAAATTTATAAAATAT
19443442 T
1 T
19443443 AAAGAGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAAAATTTATAAAATAT
Found at i:19444930 original size:19 final size:19
Alignment explanation
Indices: 19444906--19444956 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
19444896 ATTTATATAT
19444906 AAGATATAAAAAGCAATAC
1 AAGATATAAAAAGCAATAC
*
19444925 AAGATATAAAAAGTAATAC
1 AAGATATAAAAAGCAATAC
*
19444944 AAAATATAAAAAG
1 AAGATATAAAAAG
19444957 TGAAATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.18
Consensus pattern (19 bp):
AAGATATAAAAAGCAATAC
Found at i:19445077 original size:26 final size:27
Alignment explanation
Indices: 19445041--19445092 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
19445031 TAAATTTATG
* *
19445041 ATATTATATATTTAAAA-AATAAAAAA
1 ATATTAAATATTAAAAAGAATAAAAAA
19445067 ATATTAAATATTAAAAAGAATAAAAA
1 ATATTAAATATTAAAAAGAATAAAAA
19445093 TTGCAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
ATATTAAATATTAAAAAGAATAAAAAA
Found at i:19445332 original size:16 final size:15
Alignment explanation
Indices: 19445311--19445349 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
19445301 TAATACAAAC
19445311 AAAAAGAAAAAGGAAA
1 AAAAAGAAAAA-GAAA
* *
19445327 AAAAAGGAAAATAAA
1 AAAAAGAAAAAGAAA
19445342 AAAAAGAA
1 AAAAAGAA
19445350 TACCAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:19452747 original size:4 final size:4
Alignment explanation
Indices: 19452738--19452762 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19452728 TGTGCTAAGT
19452738 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
19452763 AACTATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:19456240 original size:84 final size:83
Alignment explanation
Indices: 19456099--19456268 Score: 313
Period size: 84 Copynumber: 2.0 Consensus size: 83
19456089 ACTTTAATCC
*
19456099 TTAATTATGTGAAATTATATTTGTAACATTTAATAAATATTATTAAGTTGTATTCATTAAATATT
1 TTAATTATGTCAAATTATATTTGTAACATTTAATAAATATTATTAAGTTGTATTCATTAAATATT
19456164 TTATTAACATATTTTTTCA
66 TTATTAACATATTTTTT-A
*
19456183 TTAATTATGTCAAATTATATTTGTAACGTTTAATAAATATTATTAAGTTGTATTCATTAAATATT
1 TTAATTATGTCAAATTATATTTGTAACATTTAATAAATATTATTAAGTTGTATTCATTAAATATT
19456248 TTATTAACATATTTTTTA
66 TTATTAACATATTTTTTA
19456266 TTA
1 TTA
19456269 TATTTTAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 4 0.05
84 80 0.95
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (83 bp):
TTAATTATGTCAAATTATATTTGTAACATTTAATAAATATTATTAAGTTGTATTCATTAAATATT
TTATTAACATATTTTTTA
Found at i:19456917 original size:19 final size:21
Alignment explanation
Indices: 19456889--19456928 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
19456879 AAAAATTTAT
*
19456889 TAAATTAAAT-AA-ATAAATA
1 TAAATAAAATGAATATAAATA
19456908 TAAATAAAATGAATATAAATA
1 TAAATAAAATGAATATAAATA
19456929 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAATAAAATGAATATAAATA
Found at i:19456922 original size:15 final size:15
Alignment explanation
Indices: 19456889--19456930 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19456879 AAAAATTTAT
19456889 TAAAT-TAAAT-AAA
1 TAAATATAAATAAAA
19456902 TAAATATAAATAAAA
1 TAAATATAAATAAAA
*
19456917 TGAATATAAATAAA
1 TAAATATAAATAAA
19456931 TTTTATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TAAATATAAATAAAA
Found at i:19461623 original size:19 final size:20
Alignment explanation
Indices: 19461590--19461630 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
19461580 TAACTTGTCA
19461590 TTGATCAAGTCAAATTCTAG
1 TTGATCAAGTCAAATTCTAG
19461610 TTGATCAA-TCAAATTCTAG
1 TTGATCAAGTCAAATTCTAG
19461629 TT
1 TT
19461631 ATTTTTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
TTGATCAAGTCAAATTCTAG
Found at i:19464831 original size:18 final size:17
Alignment explanation
Indices: 19464806--19464866 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
19464796 AATTGATTGA
* *
19464806 ATTAATTTATTATTTTT
1 ATTAATTTATTATATAT
*
19464823 ATTAGATTTTTTATATAT
1 ATTA-ATTTATTATATAT
* *
19464841 ATTATATTTAATATAAAT
1 ATTA-ATTTATTATATAT
19464859 ATATAATT
1 AT-TAATT
19464867 ATTTTTACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
17 4 0.11
18 29 0.83
19 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTAATTTATTATATAT
Found at i:19486112 original size:31 final size:31
Alignment explanation
Indices: 19486077--19486136 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
19486067 GAATTGTGAC
* * * *
19486077 AGATTTATAAATTGATTTTGTTTGTTATTAT
1 AGATTCATAAATTAATTATGTATGTTATTAT
19486108 AGATTCATAAATTAATTATGTATGTTATT
1 AGATTCATAAATTAATTATGTATGTTATT
19486137 TTGTTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (31 bp):
AGATTCATAAATTAATTATGTATGTTATTAT
Found at i:19488234 original size:3 final size:3
Alignment explanation
Indices: 19488221--19488265 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
19488211 GCTTGTTCTG
* *
19488221 ATT AAT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19488266 TTAAGTTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:19490217 original size:11 final size:12
Alignment explanation
Indices: 19490201--19490229 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
19490191 GAAAGACCTA
19490201 AACTCAGTC-TC
1 AACTCAGTCTTC
19490212 AACTCAGTCTTC
1 AACTCAGTCTTC
19490224 AACTCA
1 AACTCA
19490230 TCAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.28
Consensus pattern (12 bp):
AACTCAGTCTTC
Found at i:19490789 original size:160 final size:159
Alignment explanation
Indices: 19490422--19490789 Score: 400
Period size: 160 Copynumber: 2.3 Consensus size: 159
19490412 TGATTATTAC
* * * * * * *
19490422 ATACACTATAGTTTTCATTTTTCATAAATGTGATCTCATCTTAATACGCACAAAAAATTATCTAG
1 ATACACAATAATTTTCATATTTCACAAATGAGATCTCATCTTAATATGTACAAAAAATTATCTAG
** *** * *
19490487 TTAATACTGAATTTTGTACAATGTTTAGGCTTTCAATTATTACACTATCTATTTCATCAACATTC
66 TTAATACTGAATTTCCTACAATAACTAGGCTTTCAATTACTACACTATCTACTTCATCAACATTC
* * *
19490552 ATAATACACAACTAGAATTACAAAGTAAA
131 ATAATACACAACCAGAATCACAAAGCAAA
** * * *
19490581 ATACACAATAATTTTCACCTTTCACAAATGTA-ATCTTATCTGAATATGTACAAAATATTATCTA
1 ATACACAATAATTTTCATATTTCACAAATG-AGATCTCATCTTAATATGTACAAAAAATTATCTA
* * *
19490645 GTTCAATACTTAATTTCCTACAATAACTAGG-TGTTTAATTACTACACTATCTACTTCATTAACA
65 GTT-AATACTGAATTTCCTACAATAACTAGGCT-TTCAATTACTACACTATCTACTTCATCAAC-
* * * *
19490709 ATT-ATAATGCATAACCAGAATCATAATGCAAA
127 ATTCATAATACACAACCAGAATCACAAAGCAAA
* *
19490741 ATACGCAATAATTTTCATATTTCACAAATGAGATCTCATTTTAATATGT
1 ATACACAATAATTTTCATATTTCACAAATGAGATCTCATCTTAATATGT
19490790 TATAAAGATA
Statistics
Matches: 170, Mismatches: 34, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
159 57 0.34
160 110 0.65
161 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (159 bp):
ATACACAATAATTTTCATATTTCACAAATGAGATCTCATCTTAATATGTACAAAAAATTATCTAG
TTAATACTGAATTTCCTACAATAACTAGGCTTTCAATTACTACACTATCTACTTCATCAACATTC
ATAATACACAACCAGAATCACAAAGCAAA
Found at i:19490833 original size:102 final size:102
Alignment explanation
Indices: 19490699--19491175 Score: 485
Period size: 102 Copynumber: 4.7 Consensus size: 102
19490689 CACTATCTAC
* * * * * * *
19490699 TTCATTAACAATTATAATGCATAACCAGAATCATAATGCAAAATACGCAATAATTTTCATATTTC
1 TTCATCAACAATCATAATACACAACTAGAATCACAATGCAAAATACGCAATAATTTTCACATTTC
* * **
19490764 ACAAATGAGATCTCATTTTAATATGTTATAAAGATAG
66 ACAAATGTGATCTCATCTTAATATACTATAAAGATAG
* * * * * * *
19490801 TTCATCAACAATCATAGTACATAACCAGAATCAGAATGCAAAATATGCAATAGTTTCCACATTTC
1 TTCATCAACAATCATAATACACAACTAGAATCACAATGCAAAATACGCAATAATTTTCACATTTC
* * *
19490866 ACAAATGTGATCTCATCGTAATATGCTATTAA-ATAG
66 ACAAATGTGATCTCATCTTAATATACTATAAAGATAG
* ** * * * * * *
19490902 TTCATCAATAATCACCATACACAA-TTGTCATTACAATGCAAAATACACAATAATTTTAATATTT
1 TTCATCAACAATCATAATACACAACTAG-AATCACAATGCAAAATACGCAATAATTTTCACATTT
* * *
19490966 CATAAATGTGATCTCATCTGAATACACTATAAAGATAG
65 CACAAATGTGATCTCATCTTAATATACTATAAAGATAG
* * * **
19491004 TTCACCAACAATCATAATACACAACTATAATCACAATGCAAAATATGGGATAATTTTCACATTTC
1 TTCATCAACAATCATAATACACAACTAGAATCACAATGCAAAATACGCAATAATTTTCACATTTC
* *
19491069 ACAAATGTGATCTCAT-TACAATATACTATAAAGATAT
66 ACAAATGTGATCTCATCT-TAATATACTATAAAGATAG
* ** * * *
19491106 TTCAACAACAATCATAATACACAACTAGAATCACAGA-GCAAGTTACACAACAATTTTCACTTTT
1 TTCATCAACAATCATAATACACAACTAGAATCACA-ATGCAAAATACGCAATAATTTTCACATTT
19491170 CACAAA
65 CACAAA
19491176 GTTTTTGCAT
Statistics
Matches: 306, Mismatches: 64, Indels: 10
0.81 0.17 0.03
Matches are distributed among these distances:
100 1 0.00
101 78 0.25
102 225 0.74
103 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (102 bp):
TTCATCAACAATCATAATACACAACTAGAATCACAATGCAAAATACGCAATAATTTTCACATTTC
ACAAATGTGATCTCATCTTAATATACTATAAAGATAG
Found at i:19497419 original size:116 final size:118
Alignment explanation
Indices: 19497288--19497525 Score: 390
Period size: 117 Copynumber: 2.0 Consensus size: 118
19497278 TATAAACACA
* *
19497288 ATAATTTTTTTATTTCAATAATTATTATTAAATTCTAAAAAATATCAAATATAA-AAATTTTTTA
1 ATAATTTTTTTATTTCAATAATTATTATTAAATTCTAAAAAATATCAAATATAATAAAATTTTCA
19497352 AAACAAATATAAATCTTAATACACAGCAAACCCAAATTTAACATAAAATCAAC
66 AAACAAATATAAATCTTAATACACAGCAAACCCAAATTTAACATAAAATCAAC
*
19497405 ATAA-TTTTTTATTTCAATAATTATTATTAAATTTTAAAAAATATCAAATATAATAAAATTTTCA
1 ATAATTTTTTTATTTCAATAATTATTATTAAATTCTAAAAAATATCAAATATAATAAAATTTTCA
* * * * *
19497469 AAACAAATATAAATTTTAATACATATCAAACCTAAATTTATCATAAAATCAAC
66 AAACAAATATAAATCTTAATACACAGCAAACCCAAATTTAACATAAAATCAAC
19497522 ATAA
1 ATAA
19497526 ATCTTACATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
116 48 0.43
117 64 0.57
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (118 bp):
ATAATTTTTTTATTTCAATAATTATTATTAAATTCTAAAAAATATCAAATATAATAAAATTTTCA
AAACAAATATAAATCTTAATACACAGCAAACCCAAATTTAACATAAAATCAAC
Found at i:19498294 original size:38 final size:37
Alignment explanation
Indices: 19498247--19498318 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
19498237 ATTGATAATC
19498247 CATTCGTAATCAACCAATAATTACTGACAGAAAAATTT
1 CATTCGTAATCAACCAATAATTACTGAC-GAAAAATTT
* * ** *
19498285 CATTGGTAATTAGTCAGTAATTACTGACGAAAAA
1 CATTCGTAATCAACCAATAATTACTGACGAAAAA
19498319 ATTCCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 6 0.21
38 23 0.79
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (37 bp):
CATTCGTAATCAACCAATAATTACTGACGAAAAATTT
Found at i:19498486 original size:12 final size:13
Alignment explanation
Indices: 19498469--19498501 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19498459 AAATTAAAAT
*
19498469 TAAAAAAATGACA
1 TAAAAAAATCACA
19498482 TAAAAAAATCACA
1 TAAAAAAATCACA
19498495 TAAAAAA
1 TAAAAAA
19498502 GAGAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAAAAATCACA
Found at i:19498686 original size:18 final size:18
Alignment explanation
Indices: 19498665--19498700 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19498655 CTCTTTTCAC
19498665 TTTTTCTCTAATTTTTTA
1 TTTTTCTCTAATTTTTTA
* *
19498683 TTTTTCTTTATTTTTTTA
1 TTTTTCTCTAATTTTTTA
19498701 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTCTAATTTTTTA
Found at i:19499426 original size:3 final size:3
Alignment explanation
Indices: 19499418--19499442 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19499408 TTTTTATTTC
19499418 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19499443 GTTTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19499470 original size:11 final size:11
Alignment explanation
Indices: 19499407--19499488 Score: 58
Period size: 12 Copynumber: 6.9 Consensus size: 11
19499397 TGTATTTTAC
19499407 ATTTTTATTTCT
1 ATTTTTATTT-T
*
19499419 ATTATTATTATT
1 ATTTTTATT-TT
*
19499431 ATTATTATTATT
1 ATTTTTATT-TT
*
19499443 GTTTTTATATATT
1 ATTTTTAT-T-TT
*
19499456 -TTTTTCTTTT
1 ATTTTTATTTT
19499466 ATTTTTATTTT
1 ATTTTTATTTT
19499477 ATGTATTTATTT
1 AT-T-TTTATTT
19499489 ATTCATATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
10 2 0.03
11 12 0.20
12 34 0.57
13 12 0.20
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:19499650 original size:22 final size:21
Alignment explanation
Indices: 19499590--19499651 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
19499580 TTATCTGTTA
*
19499590 ATTTTTCTAATTTTTCTTATTT
1 ATTTTTTTAATTTTT-TTATTT
* *
19499612 ATTTTCATTAATATTTTTATTT
1 ATTTT-TTTAATTTTTTTATTT
*
19499634 GATTTTTTTTATTTTTTT
1 -ATTTTTTTAATTTTTTT
19499652 GATTCATCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTTTTAATTTTTTTATTT
Found at i:19499995 original size:19 final size:19
Alignment explanation
Indices: 19499967--19500010 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
19499957 TTCTGGAAAA
19499967 TTTT-GATGGACGTTGAAT
1 TTTTCGATGGACGTTGAAT
19499985 TTTTCGATGGACGTTGAAT
1 TTTTCGATGGACGTTGAAT
19500004 TTTTCGA
1 TTTTCGA
19500011 CGAAGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (19 bp):
TTTTCGATGGACGTTGAAT
Found at i:19500525 original size:11 final size:11
Alignment explanation
Indices: 19500511--19500571 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
19500501 TTATTTAATA
19500511 TTATTTTATCT
1 TTATTTTATCT
*
19500522 TTATTTTATTT
1 TTATTTTATCT
*
19500533 TTATTTT-TGT
1 TTATTTTATCT
*
19500543 TT-TACTTATCT
1 TTAT-TTTATCT
*
19500554 TTATTTTATTT
1 TTATTTTATCT
19500565 TTATTTT
1 TTATTTT
19500572 TTATTTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 6 0.15
11 33 0.80
12 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (11 bp):
TTATTTTATCT
Found at i:19500529 original size:5 final size:5
Alignment explanation
Indices: 19500500--19500608 Score: 75
Period size: 5 Copynumber: 21.6 Consensus size: 5
19500490 TTAGATTAGG
* * *
19500500 TTTAT TTAAT ATTAT TTTAT CTTTAT TTTATT TTTATT TTTGT TTTA-
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA-T TTTA-T TTTAT TTTAT
* * *
19500547 CTTAT CTTTAT TTTAT TTT-T ATT-T TTTATT TTTACT TTTAT TTTGT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTTAT
19500593 TTTA- -TTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
19500609 CTTTAAATAA
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
3 3 0.04
4 9 0.11
5 42 0.51
6 29 0.35
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:19500534 original size:6 final size:6
Alignment explanation
Indices: 19500514--19500608 Score: 72
Period size: 6 Copynumber: 15.5 Consensus size: 6
19500504 TTTAATATTA
* * *
19500514 TTTTAT CTTTA- TTTTAT TTTTAT TTTTGTT TTACTTAT CTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TT--TTAT TTTTAT TTTTAT
*
19500563 TTTTATT TTTTAT TTTTAC TTTTAT TTTGT-T TTATTA- TTTTAT TTT
1 TTTTA-T TTTTAT TTTTAT TTTTAT TTT-TAT TT-TTAT TTTTAT TTT
19500609 CTTTAAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
5 11 0.15
6 45 0.63
7 11 0.15
8 2 0.03
9 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:19510976 original size:19 final size:19
Alignment explanation
Indices: 19510952--19510994 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
19510942 ACTATGCTTG
19510952 AAAAAAATT-AAAAAATAA
1 AAAAAAATTAAAAAAATAA
19510970 AAAAAAATTAAAAAAATAA
1 AAAAAAATTAAAAAAATAA
19510989 AAAAAA
1 AAAAAA
19510995 GAAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAAATTAAAAAAATAA
Found at i:19510993 original size:8 final size:8
Alignment explanation
Indices: 19510952--19511009 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
19510942 ACTATGCTTG
19510952 AAAAAAATT
1 AAAAAAA-T
*
19510961 AAAAAATAA
1 AAAAAA-AT
19510970 AAAAAAATT
1 AAAAAAA-T
19510979 AAAAAAAT
1 AAAAAAAT
*
19510987 AAAAAAAAG
1 -AAAAAAAT
*
19510996 AAAAAAAG
1 AAAAAAAT
19511004 AAAAAA
1 AAAAAA
19511010 GTGAATGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 16 0.37
9 26 0.60
10 1 0.02
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:19510994 original size:9 final size:9
Alignment explanation
Indices: 19510952--19511002 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
19510942 ACTATGCTTG
19510952 AAAAAAAT-
1 AAAAAAATA
*
19510960 TAAAAAATAA
1 AAAAAAAT-A
*
19510970 AAAAAAATT
1 AAAAAAATA
19510979 AAAAAAATA
1 AAAAAAATA
*
19510988 AAAAAAAGA
1 AAAAAAATA
19510997 AAAAAA
1 AAAAAA
19511003 GAAAAAAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
8 7 0.19
9 22 0.61
10 7 0.19
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:19512105 original size:41 final size:41
Alignment explanation
Indices: 19512014--19512142 Score: 152
Period size: 41 Copynumber: 3.1 Consensus size: 41
19512004 GATTGTCAAA
* * * *
19512014 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAAAG
1 GAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
*
19512055 AAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
1 GAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
* * *
19512096 GAGTC-ATTTATGTTTTTCAAAGTCGTTGAGCATCTGCTTAGAG
1 GAG-CAATTTA--CTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
19512139 GAGC
1 GAGC
19512143 TTTGGTCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 43 0.57
42 2 0.03
43 31 0.41
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (41 bp):
GAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
Found at i:19512160 original size:1 final size:1
Alignment explanation
Indices: 19512150--19512204 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
19512140 AGCTTTGGTC
* * * * * *
19512150 AAAAACAAAAAAAAACAAAAAAAACAAAAAATAAAAAATAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19512205 TGAAAATGTC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:19512211 original size:15 final size:15
Alignment explanation
Indices: 19512158--19512202 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
19512148 TCAAAAACAA
* *
19512158 AAAAAAACAAAAAAA
1 AAAAAAATAAAAAAT
19512173 ACAAAAAATAAAAAAT
1 A-AAAAAATAAAAAAT
19512189 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
19512203 AATGAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.89, C:0.04, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:19512380 original size:6 final size:6
Alignment explanation
Indices: 19512352--19512440 Score: 56
Period size: 6 Copynumber: 14.7 Consensus size: 6
19512342 GTAAGTCTAT
* * * *
19512352 TTTTTT TTTTGTA TTTTACA TTTTTA -TTTTA TTTTTA TTTCTA TTATTA
1 TTTTTA TTTT-TA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * * *
19512401 TTATTG TTGTT- TTTATA TTTTTT TCTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA TTTT
19512441 ATGTATTTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
5 8 0.12
6 42 0.65
7 15 0.23
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:19512570 original size:21 final size:22
Alignment explanation
Indices: 19512541--19512584 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
19512531 TGTTATTTAA
19512541 TTTTAATTTATC-TATTAATTT
1 TTTTAATTTATCTTATTAATTT
* *
19512562 TTTTGATTTATCTTATTTATTT
1 TTTTAATTTATCTTATTAATTT
19512584 T
1 T
19512585 CATTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTAATTTATCTTATTAATTT
Found at i:19512590 original size:32 final size:32
Alignment explanation
Indices: 19512554--19512616 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
19512544 TAATTTATCT
*
19512554 ATTAATTTTTTTGATTT-ATCTTATTTATTTTC
1 ATTAATATTTTT-ATTTGATCTTATTTATTTTC
* *
19512586 ATTAATATTTTTATTTGATTTTTTTTATTTT
1 ATTAATATTTTTATTTGATCTTATTTATTTT
19512617 TTTAATTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (32 bp):
ATTAATATTTTTATTTGATCTTATTTATTTTC
Found at i:19512618 original size:22 final size:21
Alignment explanation
Indices: 19512541--19512620 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
19512531 TGTTATTTAA
* * *
19512541 TTTTAATTTATCTATTAATTT
1 TTTTAATTTTTTTATTTATTT
* *
19512562 TTTTGATTTATCTTATTTATTT
1 TTTTAATTT-TTTTATTTATTT
* *
19512584 TCATTAATATTTTTATTTGATTT
1 T-TTTAATTTTTTTATTT-ATTT
*
19512607 TTTTTATTTTTTTA
1 TTTTAATTTTTTTA
19512621 ATTCATCCGG
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 8 0.18
22 26 0.59
23 10 0.23
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTTAATTTTTTTATTTATTT
Found at i:19513037 original size:19 final size:19
Alignment explanation
Indices: 19513001--19513040 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19512991 CCAAGTTTGA
19513001 AGTTTTCGACCAACTTTCC
1 AGTTTTCGACCAACTTTCC
*
19513020 AGTTTTCG-GCAACATTTCC
1 AGTTTTCGACCAAC-TTTCC
19513039 AG
1 AG
19513041 AAACCGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (19 bp):
AGTTTTCGACCAACTTTCC
Found at i:19513499 original size:5 final size:5
Alignment explanation
Indices: 19513468--19513564 Score: 72
Period size: 5 Copynumber: 18.6 Consensus size: 5
19513458 TTAGATTAGG
* * * *
19513468 TTTAT TTAAT ATTCT TTTAT CTTTAT TTTATT TTTAT TTTTT TTCTACT
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA-T TTTAT TTTAT TT-TA-T
* *
19513517 TTTAT TTTTT TTTAT TTTCACT TTTAT TTTA- TTT-T GTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT-A-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
19513565 CTTTAAATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
4 5 0.07
5 45 0.62
6 15 0.21
7 7 0.10
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:19513502 original size:17 final size:16
Alignment explanation
Indices: 19513482--19513564 Score: 85
Period size: 17 Copynumber: 4.9 Consensus size: 16
19513472 TTTAATATTC
19513482 TTTTATCTTTATTTTAT
1 TTTTAT-TTTATTTTAT
* *
19513499 TTTTATTTTTTTTCTAC
1 TTTTATTTTATTT-TAT
*
19513516 TTTTATTTTTTTTTAT
1 TTTTATTTTATTTTAT
*
19513532 TTTCACTTTTATTTTATT
1 TTTTA-TTTTATTTTA-T
19513550 TTGTTATTTTATTTT
1 TT-TTATTTTATTTT
19513565 CTTTAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 12 0.21
17 30 0.54
18 12 0.21
19 2 0.04
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:19513507 original size:22 final size:22
Alignment explanation
Indices: 19513482--19513551 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
19513472 TTTAATATTC
19513482 TTTTATCTTTA-TTTTATTTTTA
1 TTTTAT-TTTACTTTTATTTTTA
*
19513504 TTTTTTTTCTACTTTTATTTTT-
1 TTTTATTT-TACTTTTATTTTTA
19513526 TTTTATTTTCACTTTTA-TTTTA
1 TTTTATTTT-ACTTTTATTTTTA
19513548 TTTT
1 TTTT
19513552 GTTATTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.17
22 25 0.60
23 10 0.24
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTATTTTACTTTTATTTTTA
Found at i:19513508 original size:7 final size:6
Alignment explanation
Indices: 19513482--19513564 Score: 61
Period size: 6 Copynumber: 14.5 Consensus size: 6
19513472 TTTAATATTC
* * *
19513482 TTTTAT CTTTA- TTTTAT TTTTAT TTTT-T TTCTAC TTTTA- TTTT-T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
19513526 TTTTAT TTTCAC TTTTA- TTTTAT TTTGT-T ATTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT -TTTTAT TTT
19513565 CTTTAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
5 21 0.34
6 35 0.57
7 5 0.08
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:19513519 original size:23 final size:23
Alignment explanation
Indices: 19513493--19513551 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 23
19513483 TTTATCTTTA
19513493 TTTTATTTTTATTTT-TTTTCTAC
1 TTTTATTTTTATTTTATTTTC-AC
19513516 TTTTATTTTT-TTTTATTTTCAC
1 TTTTATTTTTATTTTATTTTCAC
19513538 TTTTA-TTTTATTTT
1 TTTTATTTTTATTTT
19513552 GTTATTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.12
22 15 0.44
23 15 0.44
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTATTTTTATTTTATTTTCAC
Found at i:19513556 original size:13 final size:13
Alignment explanation
Indices: 19513540--19513564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19513530 ATTTTCACTT
19513540 TTATTTTATTTTG
1 TTATTTTATTTTG
19513553 TTATTTTATTTT
1 TTATTTTATTTT
19513565 CTTTAAATAA
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTG
Found at i:19514441 original size:21 final size:21
Alignment explanation
Indices: 19514399--19514447 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19514389 TGCAATTATA
* *
19514399 TATATATATATAACACTTAAT
1 TATATATATATAACAATAAAT
19514420 TATATA-ATATAACTAATAAAT
1 TATATATATATAAC-AATAAAT
*
19514441 TTTATAT
1 TATATAT
19514448 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATATATAACAATAAAT
Found at i:19516026 original size:2 final size:2
Alignment explanation
Indices: 19516021--19516065 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
19516011 TCATTAATCT
* *
19516021 TA TA TA AA TA TA TA -A AA T- TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19516060 TA TA TA
1 TA TA TA
19516066 CATGAATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19521444 original size:22 final size:20
Alignment explanation
Indices: 19521414--19521460 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
19521404 TTAATACTTT
19521414 AAATATTAA-ATATGATAAAATA
1 AAATATTAATAT-TG-TAAAA-A
*
19521436 AAATGTTAATATTGTAAAAA
1 AAATATTAATATTGTAAAAA
19521456 AAATA
1 AAATA
19521461 ATGATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 10 0.45
23 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATATTAATATTGTAAAAA
Found at i:19522949 original size:12 final size:12
Alignment explanation
Indices: 19522932--19522959 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19522922 TATCATAACC
19522932 TATTGGTCCAAT
1 TATTGGTCCAAT
19522944 TATTGGTCCAAT
1 TATTGGTCCAAT
19522956 TATT
1 TATT
19522960 CGATTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (12 bp):
TATTGGTCCAAT
Found at i:19523468 original size:3 final size:3
Alignment explanation
Indices: 19523460--19523490 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19523450 ATTTATTTAT
19523460 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19523491 GAACTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:19526652 original size:3 final size:3
Alignment explanation
Indices: 19526644--19526698 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
19526634 AAGCGACGTT
19526644 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19526692 TTA TTA T
1 TTA TTA T
19526699 GGTAAAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19528609 original size:17 final size:18
Alignment explanation
Indices: 19528582--19528616 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19528572 ATAATAAAAT
19528582 ATTTTATAAAATATTTAA
1 ATTTTATAAAATATTTAA
*
19528600 ATTTTA-AAAATTTTTAA
1 ATTTTATAAAATATTTAA
19528617 TATGATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATAAAATATTTAA
Found at i:19528710 original size:15 final size:14
Alignment explanation
Indices: 19528685--19528732 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 14
19528675 AGTACATATC
19528685 ATTATTTAAAATTA
1 ATTATTTAAAATTA
*
19528699 ATTATATTAAAAATTT
1 ATTAT-TT-AAAATTA
*
19528715 ATAATTTAAAGATTA
1 ATTATTTAAA-ATTA
19528730 ATT
1 ATT
19528733 TTAATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
16 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTATTTAAAATTA
Found at i:19529788 original size:24 final size:23
Alignment explanation
Indices: 19529761--19529810 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
19529751 TTTATATATA
19529761 ATTATTATTAAAATTTTAAATCAT
1 ATTATT-TTAAAATTTTAAATCAT
* * *
19529785 ATTATTTTATATTTTTTAATCAT
1 ATTATTTTAAAATTTTAAATCAT
19529808 ATT
1 ATT
19529811 TATAATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATTTTAAAATTTTAAATCAT
Found at i:19532124 original size:4 final size:4
Alignment explanation
Indices: 19532113--19532142 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
19532103 AAAAATTATC
19532113 AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
19532143 ATCATCCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:19536950 original size:141 final size:143
Alignment explanation
Indices: 19536667--19536943 Score: 303
Period size: 140 Copynumber: 2.0 Consensus size: 143
19536657 ACTGTTGAAC
* *
19536667 CTCAAAAAGGTGAAATTACAAAAATACTTTTTAGGAGCATTTTTATAATTTGGCCCTTTTTAGGT
1 CTCAAAAAGGTGAAATTACAAAAATACCTTTTAGGAGCATTTTTATAATTTAGCCCTTTTTAGGT
** * * *** * *
19536732 TGATTTTCCATGAAAAATTCCATATCATGTTTAAATAGTATTTTATGAATTTTGATGCATTAAAA
66 CAATTTTCCACGAAAAACTCCATATCATAACTAAATAGTATTTTATAAATTTTGATCCATTAAAA
* *
19536797 ATCTTGATTAAAT
131 ATCATGAATAAAT
* * * * *
19536810 CTCAAAGAGGTGAAATTAC-ACAATACCTTTTAGGCGTATTTTTATAATTTAG-CC-TTTTGGGC
1 CTCAAAAAGGTGAAATTACAAAAATACCTTTTAGGAGCATTTTTATAATTTAGCCCTTTTTAGG-
** * * *
19536872 TCAATTTTTGACGAAAAACTCTATATCATAACT-AATATTATTTTATAAATTTTGGTCCATT-AA
65 TCAATTTTCCACGAAAAACTCCATATCATAACTAAATAGTATTTTATAAATTTTGATCCATTAAA
19536935 AATCATGAA
130 AATCATGAA
19536944 AATAAATATT
Statistics
Matches: 110, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
139 9 0.08
140 30 0.27
141 25 0.23
142 28 0.25
143 18 0.16
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (143 bp):
CTCAAAAAGGTGAAATTACAAAAATACCTTTTAGGAGCATTTTTATAATTTAGCCCTTTTTAGGT
CAATTTTCCACGAAAAACTCCATATCATAACTAAATAGTATTTTATAAATTTTGATCCATTAAAA
ATCATGAATAAAT
Found at i:19537992 original size:12 final size:12
Alignment explanation
Indices: 19537977--19538046 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
19537967 ACCATACCCT
19537977 AAACCCTAAATC
1 AAACCCTAAATC
*
19537989 AAA-CCTAACCTC
1 AAACCCTAA-ATC
*
19538001 AAACCTTAAATC
1 AAACCCTAAATC
**
19538013 AAA-CCTAACCC
1 AAACCCTAAATC
19538024 TAAACCCTAAATC
1 -AAACCCTAAATC
*
19538037 AAACCATAAA
1 AAACCCTAAA
19538047 CCCTAAACAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 10 0.22
12 25 0.56
13 10 0.22
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (12 bp):
AAACCCTAAATC
Found at i:19538004 original size:24 final size:24
Alignment explanation
Indices: 19537972--19538054 Score: 123
Period size: 24 Copynumber: 3.4 Consensus size: 24
19537962 TCTAAACCAT
19537972 ACCCTAAACCCTAAATCAAACCTA
1 ACCCTAAACCCTAAATCAAACCTA
*
19537996 A-CCTCAAACCTTAAATCAAACCTA
1 ACCCT-AAACCCTAAATCAAACCTA
19538020 ACCCTAAACCCTAAATCAAACCATAA
1 ACCCTAAACCCTAAATCAAACC-T-A
19538046 ACCCTAAAC
1 ACCCTAAAC
19538055 ATAGCCTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 3 0.06
24 36 0.68
25 4 0.08
26 10 0.19
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (24 bp):
ACCCTAAACCCTAAATCAAACCTA
Found at i:19543385 original size:30 final size:31
Alignment explanation
Indices: 19543327--19543385 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
19543317 TCTCTTCCTC
* * *
19543327 TTTTGGCAGCTTTTTTCTTTTTTTCTTTTTT
1 TTTTGGCAGCTTTCTTCTTCTTTACTTTTTT
19543358 TTTTGGCAGC-TTCTTCTTCTTTACTTTT
1 TTTTGGCAGCTTTCTTCTTCTTTACTTTT
19543386 GGTAGCTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.05, C:0.17, G:0.10, T:0.68
Consensus pattern (31 bp):
TTTTGGCAGCTTTCTTCTTCTTTACTTTTTT
Found at i:19544145 original size:145 final size:145
Alignment explanation
Indices: 19543870--19544278 Score: 461
Period size: 145 Copynumber: 2.8 Consensus size: 145
19543860 GACTTTAAAA
* * * * *
19543870 CACCAAAAAATCATGAAGTATTATAAGATTATGA-CTTGAAAAGTTTCATGAAATTCT-AAGCTC
1 CACC-AAAAATCATGAAATATTATAAAAGTAGGATC-TGAAAAGTTTCATGAAATTTTGAA-CTC
* * * * *
19543933 AGAAAGGCTAAATTACAAAAATACCCTTATGAGGGTATTTTGATAATTTCACACTTTTAGGGGTA
63 GGAAAGGCTAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTCTAGGGATA
*
19543998 CTATTATAATT-TCAAAT
128 CTACTATAATTCTCAAAT
* * * *
19544015 GCATCAAAAATCATGAAATATTATAAAAGTAGGATCTGCAAAGTTTCATGAAATTTTGAAATTGG
1 -CACCAAAAATCATGAAATATTATAAAAGTAGGATCTGAAAAGTTTCATGAAATTTTGAACTCGG
* *
19544080 AAAGGCCAAATTACAAAAATACCCCTTA-AAGGGTATTTTGGTAATTTCACCCTTCCT-GGGATA
65 AAAGGCTAAATTACAAAAATA-CCCTTATAAGGGTATTTTGGTAATTTCACACTT-CTAGGGATA
* * * *
19544143 CTACTGTGATTCTGAACT
128 CTACTATAATTCTCAAAT
* * * * *
19544161 CACCAAAAACCATGAAATATTACAAAAGT-GAGATCTAAAAAGTTTCATGAAATTTTGAGCTCGA
1 CACCAAAAATCATGAAATATTATAAAAGTAG-GATCTGAAAAGTTTCATGAAATTTTGAACTCGG
* *
19544225 AAAGGCTAAATTACAAAAATACCCTTATAAGGGTATTTTTGTAATTTCATACTT
65 AAAGGCTAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTT
19544279 TTCGAAGGTA
Statistics
Matches: 222, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
144 7 0.03
145 198 0.89
146 17 0.08
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (145 bp):
CACCAAAAATCATGAAATATTATAAAAGTAGGATCTGAAAAGTTTCATGAAATTTTGAACTCGGA
AAGGCTAAATTACAAAAATACCCTTATAAGGGTATTTTGGTAATTTCACACTTCTAGGGATACTA
CTATAATTCTCAAAT
Found at i:19544367 original size:146 final size:142
Alignment explanation
Indices: 19543875--19544411 Score: 460
Period size: 145 Copynumber: 3.7 Consensus size: 142
19543865 TAAAACACCA
* * * * * * *
19543875 AAAAATCATGAAGTATTATAAGATTATGACTTGAAAAGTTTCATGAAATTCTAAGCTC-AGAAAG
1 AAAAATCATGAAATATTATAAAAGTAGGTC-TG-AAAGTTTCATGAAATTTTGAGCTCGA-AAAG
* * *
19543939 GCTAAATTACAAAAATA-CCCTTATGAGGGTA-TTTTGATAATTTCACACTTTTAGGGGTACTAT
63 GCTAAATTACAAAAATACCCCTTATAAGGGTATTTTTG-TAATTTCA-ACTTTT-CGGGTACTAC
* *
19544002 TATAATTTCAAATGCATC
125 TGTGATTTCAAATGCATC
** * *
19544020 AAAAATCATGAAATATTATAAAAGTAGGATCTGCAAAGTTTCATGAAATTTTGAAATTGGAAAGG
1 AAAAATCATGAAATATTATAAAAGTAGG-TCTG-AAAGTTTCATGAAATTTTGAGCTCGAAAAGG
* * * * *
19544085 CCAAATTACAAAAATACCCCTTA-AAGGGTATTTTGGTAATTTCACCCTTCCTGGGATACTACTG
64 CTAAATTACAAAAATACCCCTTATAAGGGTATTTTTGTAATTTCAACTTTTC-GGG-TACTACTG
* * *
19544149 TGATTCTGAACT-CACC
127 TGATT-TCAAATGCATC
* * * *
19544165 AAAAACCATGAAATATTACAAAAGTGAGATCTAAAAAGTTTCATGAAATTTTGAGCTCGAAAAGG
1 AAAAATCATGAAATATTATAAAAGT-AGGTCT-GAAAGTTTCATGAAATTTTGAGCTCGAAAAGG
**
19544230 CTAAATTACAAAAATA-CCCTTATAAGGGTATTTTTGTAATTTCATACTTTTCGAAGGTACCGCT
64 CTAAATTACAAAAATACCCCTTATAAGGGTATTTTTGTAATTTCA-ACTTTTCG--GGTACTACT
* *
19544294 GTGATTTTAAATGCATT
126 GTGATTTCAAATGCATC
* ** * ** * *
19544311 AAAAATTATGAAATATTATAGGATTAAGGTCTGAAAGGTTTCACAAAAATTTGAGCTC-ATGAAG
1 AAAAATCATGAAATATTATAAAAGT-AGGTCTGAAA-GTTTCATGAAATTTTGAGCTCGA-AAAG
*
19544375 G-TCAAATTATAAAAATACCCCCTTATAAGGGTATTTT
63 GCT-AAATTACAAAAATA-CCCCTTATAAGGGTATTTT
19544412 AATAATTTGG
Statistics
Matches: 315, Mismatches: 58, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
144 12 0.04
145 190 0.60
146 93 0.30
147 2 0.01
148 18 0.06
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (142 bp):
AAAAATCATGAAATATTATAAAAGTAGGTCTGAAAGTTTCATGAAATTTTGAGCTCGAAAAGGCT
AAATTACAAAAATACCCCTTATAAGGGTATTTTTGTAATTTCAACTTTTCGGGTACTACTGTGAT
TTCAAATGCATC
Found at i:19551313 original size:42 final size:43
Alignment explanation
Indices: 19551216--19551398 Score: 203
Period size: 42 Copynumber: 4.3 Consensus size: 43
19551206 TTTTGAAGTA
* **
19551216 AAATTTTAAAGTTGA-GTGCCTCTATTTAGAGGAGCCTTTTTTTC
1 AAATTTTAAAGTT-ATATGCCTCTATTTAGAGGAATC-TTTTTTC
*
19551260 AAAGTTTAAAGTTATATGCCTCTATTTAGAGGAATCTTTTTT-
1 AAATTTTAAAGTTATATGCCTCTATTTAGAGGAATCTTTTTTC
* * * * *
19551302 AAATTTTAAAGTTGTATACCTCTATCTAGATGAGTC-TTTTTC
1 AAATTTTAAAGTTATATGCCTCTATTTAGAGGAATCTTTTTTC
* * * *
19551344 AAATTTTAAAGTTATTTGTCTCAATTTAGAAGAA-CTTTTTTC
1 AAATTTTAAAGTTATATGCCTCTATTTAGAGGAATCTTTTTTC
19551386 AAATTTTAAAGTT
1 AAATTTTAAAGTT
19551399 GAAGGTTTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
41 6 0.05
42 75 0.64
43 7 0.06
44 30 0.25
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (43 bp):
AAATTTTAAAGTTATATGCCTCTATTTAGAGGAATCTTTTTTC
Found at i:19551373 original size:84 final size:85
Alignment explanation
Indices: 19551216--19551400 Score: 241
Period size: 84 Copynumber: 2.2 Consensus size: 85
19551206 TTTTGAAGTA
* * *
19551216 AAATTTTAAAGTTGAGTGCCTCTATTTAGAGGAGCCTTTTTTTCAAAGTTTAAAGTTATATGCCT
1 AAATTTTAAAGTTGAGTACCTCTATCTAGAGGAG-CTCTTTTTCAAAGTTTAAAGTTATATGCCT
* *
19551281 CTATTTAGAGGAATCTTTTTT-
65 CAATTTAGAAGAA-CTTTTTTC
* * * *
19551302 AAATTTTAAAGTTGTA-TACCTCTATCTAGATGAG-TCTTTTTCAAATTTTAAAGTTATTTGTCT
1 AAATTTTAAAGTTG-AGTACCTCTATCTAGAGGAGCTCTTTTTCAAAGTTTAAAGTTATATGCCT
19551365 CAATTTAGAAGAACTTTTTTC
65 CAATTTAGAAGAACTTTTTTC
19551386 AAATTTTAAAGTTGA
1 AAATTTTAAAGTTGA
19551401 AGGTTTTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
83 8 0.09
84 50 0.57
86 29 0.33
87 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (85 bp):
AAATTTTAAAGTTGAGTACCTCTATCTAGAGGAGCTCTTTTTCAAAGTTTAAAGTTATATGCCTC
AATTTAGAAGAACTTTTTTC
Found at i:19552693 original size:20 final size:20
Alignment explanation
Indices: 19552657--19552706 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
19552647 TTTTATTTTT
*
19552657 TATTTAAATTCTATTTTATG-
1 TATTTAAATTATATTTT-TGA
19552677 TATTTAAATTA-ATTTTTTGA
1 TATTTAAATTATA-TTTTTGA
*
19552697 TATATAAATT
1 TATTTAAATT
19552707 TTATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTTAAATTATATTTTTGA
Found at i:19556454 original size:22 final size:22
Alignment explanation
Indices: 19556428--19556471 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19556418 TGTATATTTA
* *
19556428 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
19556450 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
19556472 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:19560353 original size:22 final size:22
Alignment explanation
Indices: 19560328--19560371 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19560318 TGTATATTTA
19560328 TATTTGTAT-CTCTAGAATTAAG
1 TATTTGTATCCT-TAGAATTAAG
19560350 TATTTGTATCCTTAGAATTAAG
1 TATTTGTATCCTTAGAATTAAG
19560372 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCTTAGAATTAAG
Found at i:19565871 original size:70 final size:70
Alignment explanation
Indices: 19565751--19565892 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 70
19565741 ATATGATAGC
* * **
19565751 AGCTAGAGAACTCATTTTGTAAAGGGATAAAAAAAGGTCAACCATGACTATGTGATGGAATGGGG
1 AGCTAGAGAACTCATTTTGTAAAGGGATAAAAAAAGGTCAAACATGACTATATGACAGAATGGGG
*
19565816 TGCAA
66 AGCAA
* * *
19565821 AGCTAGAGAACTCATTTTGTTAAGTGAT-AAAAAATGTCAAACATGAACTATATGACAGAATGGG
1 AGCTAGAGAACTCATTTTGTAAAGGGATAAAAAAAGGTCAAACATG-ACTATATGACAGAATGGG
19565885 GAGCAA
65 GAGCAA
19565891 AG
1 AG
19565893 GATTTAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 15 0.24
70 48 0.76
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (70 bp):
AGCTAGAGAACTCATTTTGTAAAGGGATAAAAAAAGGTCAAACATGACTATATGACAGAATGGGG
AGCAA
Found at i:19570201 original size:25 final size:25
Alignment explanation
Indices: 19570173--19570221 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19570163 ATTACTGTGG
*
19570173 AAATCTGATTCTCCGATATTAGTGT
1 AAATCTGATTCTCCGACATTAGTGT
* *
19570198 AAATTTGATTCTCCTACATTAGTG
1 AAATCTGATTCTCCGACATTAGTG
19570222 CTTAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (25 bp):
AAATCTGATTCTCCGACATTAGTGT
Found at i:19574055 original size:25 final size:24
Alignment explanation
Indices: 19574015--19574072 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
19574005 GGAATGTAGA
* *
19574015 AATCTGATTTTGCTACATTAGTGC
1 AATCTGATTCTCCTACATTAGTGC
19574039 AGATCTGATTCTCCTACATTAGTGC
1 A-ATCTGATTCTCCTACATTAGTGC
*
19574064 AACCTGATT
1 AATCTGATT
19574073 TTCTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (24 bp):
AATCTGATTCTCCTACATTAGTGC
Found at i:19577210 original size:33 final size:33
Alignment explanation
Indices: 19577168--19577233 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
19577158 GGAGTAGATT
19577168 ATTTTAATACCTTTTCACTAGTGGCAAAGATGA
1 ATTTTAATACCTTTTCACTAGTGGCAAAGATGA
19577201 ATTTTAATACCTTTTCACTAGTGGCAAAGATGA
1 ATTTTAATACCTTTTCACTAGTGGCAAAGATGA
19577234 CATCGATTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
ATTTTAATACCTTTTCACTAGTGGCAAAGATGA
Found at i:19586612 original size:23 final size:23
Alignment explanation
Indices: 19586569--19586613 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19586559 TTTCGTTTTC
* *
19586569 TTTTTATTTTTGTTTTTCTCAAT
1 TTTTTATTTTTGTATTACTCAAT
19586592 TTTTTATTTTT-TAATTACTCAA
1 TTTTTATTTTTGT-ATTACTCAA
19586614 AATTGGGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTATTTTTGTATTACTCAAT
Found at i:19589416 original size:12 final size:13
Alignment explanation
Indices: 19589387--19589422 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
19589377 TATTTAATAA
*
19589387 AAATATATTTATT
1 AAATATATATATT
19589400 AAATATATATA-T
1 AAATATATATATT
19589412 AAATATATATA
1 AAATATATATA
19589423 AGATACGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATATATATATT
Found at i:19590671 original size:12 final size:12
Alignment explanation
Indices: 19590651--19590685 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
19590641 CACAACTCCA
*
19590651 ATTCAAATTTCT
1 ATTCTAATTTCT
19590663 ATTCTAATTTCT
1 ATTCTAATTTCT
19590675 ATTCTAATTTC
1 ATTCTAATTTC
19590686 ACTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTCTAATTTCT
Found at i:19591442 original size:34 final size:33
Alignment explanation
Indices: 19591404--19591468 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
19591394 TCAAAAATCT
*
19591404 ATTTTT-AAAAATTTATATAACTTATTAGAAATGG
1 ATTTTTGAAAAA-TTATAAAACTTATTA-AAATGG
*
19591438 ATTTTTGAAAAATTATAAAACTTTTTAAAAT
1 ATTTTTGAAAAATTATAAAACTTATTAAAAT
19591469 TCCATTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 19 0.68
35 5 0.18
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (33 bp):
ATTTTTGAAAAATTATAAAACTTATTAAAATGG
Found at i:19591529 original size:12 final size:11
Alignment explanation
Indices: 19591499--19591533 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
19591489 AGGTTTTAAG
19591499 AAAAA-TTATT
1 AAAAATTTATT
19591509 AAAAATTTATT
1 AAAAATTTATT
19591520 AAAAATTTTATT
1 AAAAA-TTTATT
19591532 AA
1 AA
19591534 TAAGTATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 10 0.43
12 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAAATTTATT
Found at i:19591849 original size:22 final size:21
Alignment explanation
Indices: 19591813--19591853 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
19591803 AGCCTTCTAA
19591813 ATACACCACAAAATTTTCTCT
1 ATACACCACAAAATTTTCTCT
*
19591834 ATACATCCCCAAAATTTTCT
1 ATACA-CCACAAAATTTTCT
19591854 TCCAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (21 bp):
ATACACCACAAAATTTTCTCT
Found at i:19598182 original size:11 final size:13
Alignment explanation
Indices: 19598154--19598203 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
19598144 TAAAAAATGA
19598154 TAAAATATAAAAC
1 TAAAATATAAAAC
19598167 TAAAATA-AAAAC
1 TAAAATATAAAAC
* *
19598179 AAAAGATATAAATC
1 TAAA-ATATAAAAC
*
19598193 TATAATATAAA
1 TAAAATATAAA
19598204 TTTTACAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 8 0.26
13 17 0.55
14 6 0.19
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (13 bp):
TAAAATATAAAAC
Found at i:19599501 original size:18 final size:17
Alignment explanation
Indices: 19599470--19599518 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
19599460 ATAACTAAGC
*
19599470 TTTTTTTATTTTTCTTACT
1 TTTTTTTA-GTTTCTT-CT
*
19599489 TTTTTTTAGTTTCTTTT
1 TTTTTTTAGTTTCTTCT
19599506 TATTTTTTAGTTT
1 T-TTTTTTAGTTT
19599519 ATAGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 17 0.63
19 8 0.30
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTTTAGTTTCTTCT
Found at i:19599528 original size:14 final size:14
Alignment explanation
Indices: 19599509--19599557 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
19599499 TTCTTTTTAT
* *
19599509 TTTTTAGTTTATAG
1 TTTTTAATTTATAA
*
19599523 TTTTTAATTTTTAA
1 TTTTTAATTTATAA
19599537 TTTTTAATTATATAA
1 TTTTTAATT-TATAA
*
19599552 ATTTTA
1 TTTTTA
19599558 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTTAATTTATAA
Found at i:19599540 original size:6 final size:7
Alignment explanation
Indices: 19599502--19599545 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
19599492 TTTTAGTTTC
*
19599502 TTTTTAT
1 TTTTTAA
*
19599509 TTTTTAG
1 TTTTTAA
* *
19599516 TTTATAG
1 TTTTTAA
19599523 TTTTTAA
1 TTTTTAA
19599530 TTTTTAA
1 TTTTTAA
19599537 TTTTTAA
1 TTTTTAA
19599544 TT
1 TT
19599546 ATATAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:19599556 original size:29 final size:28
Alignment explanation
Indices: 19599502--19599557 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
19599492 TTTTAGTTTC
* * **
19599502 TTTTTATTTTTTAGTTTATAGTTTTTAA
1 TTTTTAATTTTTAATTTATAAATTTTAA
19599530 TTTTTAATTTTTAATTATATAAATTTTA
1 TTTTTAATTTTTAATT-TATAAATTTTA
19599558 TGAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (28 bp):
TTTTTAATTTTTAATTTATAAATTTTAA
Found at i:19600254 original size:3 final size:3
Alignment explanation
Indices: 19600246--19600277 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19600236 TGCCCTAGAT
19600246 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19600278 GTATGTGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19613787 original size:18 final size:18
Alignment explanation
Indices: 19613764--19613798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19613754 GAATTTTTAA
19613764 TTTTATAAAATAAAATTT
1 TTTTATAAAATAAAATTT
* *
19613782 TTTTATTACATAAAATT
1 TTTTATAAAATAAAATT
19613799 AAAATTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTATAAAATAAAATTT
Found at i:19616178 original size:21 final size:21
Alignment explanation
Indices: 19616129--19616182 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
19616119 ATTAATTTTA
19616129 ATTAATTTA--AAAT-AAAAC
1 ATTAATTTATTAAATAAAAAC
19616147 -TT-ATATTATTAAATAAAAAC
1 ATTAAT-TTATTAAATAAAAAC
19616167 ATTAATTTATTAAATA
1 ATTAATTTATTAAATA
19616183 TATATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.07
17 5 0.17
19 4 0.13
20 5 0.17
21 12 0.40
22 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATTTATTAAATAAAAAC
Found at i:19624532 original size:21 final size:21
Alignment explanation
Indices: 19624506--19624549 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
19624496 GAATTATGTG
19624506 TAATAGATT-TTCAAGTTAATT
1 TAATAGATTCTT-AAGTTAATT
19624527 TAATAGATTCTTAAGTTAATT
1 TAATAGATTCTTAAGTTAATT
19624548 TA
1 TA
19624550 TTAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (21 bp):
TAATAGATTCTTAAGTTAATT
Found at i:19630881 original size:19 final size:19
Alignment explanation
Indices: 19630857--19630897 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
19630847 AAGTCGACTG
19630857 CCGTGATGAACGAAGCCTA
1 CCGTGATGAACGAAGCCTA
*
19630876 CCGTGATGAAGGAAGCCTA
1 CCGTGATGAACGAAGCCTA
19630895 CCG
1 CCG
19630898 GAACTAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.15
Consensus pattern (19 bp):
CCGTGATGAACGAAGCCTA
Found at i:19633386 original size:24 final size:27
Alignment explanation
Indices: 19633334--19633384 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19633324 TTGTTCTGTC
19633334 TAATAAAATGATATTTTATAATTAAAA
1 TAATAAAATGATATTTTATAATTAAAA
19633361 TAATAAAACT-AT-TTTTAT-ATTAAA
1 TAATAAAA-TGATATTTTATAATTAAA
19633385 TATTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 10 0.43
28 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TAATAAAATGATATTTTATAATTAAAA
Done.