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 66 of 147
Found at i:12423724 original size:182 final size:177
Alignment explanation
Indices: 12423247--12423849 Score: 837
Period size: 182 Copynumber: 3.3 Consensus size: 177
12423237 TTTTTTGTAG
* * *
12423247 GGAAGATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTCGATTTTC--AAAGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT--ATTTTCTTAAGGA
* *** *
12423310 AAATTGATACTTTCAAC-TTTTCCTCAAAA-ACCCTTTTTTTGAAAATTTATTTCTAAGGAAAAT
64 AAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTG-AAATTTATTTCTGAGGAAAAT
12423373 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGGAAAATTTATTTTTCTTTTAA
128 TGATACTTTCAACTTTTCCCCAAAAATA----TTTTTTGG-AAATTTA--TTTC---TAA
12423433 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTA--TTCTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTCTTAAGGAAA
*
12423495 ATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTT-AAATTTATTTCTGAGGAAAATTG
66 ATTGATACTTTCAACTTTTTCCTAAAAATAT-TTTTTTTTTGAAATTTATTTCTGAGGAAAATTG
12423559 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
130 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
12423607 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTTGGAAATTTA-TTTTC--TTAA
*
12423672 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTGAAATTTATTTTTGAGGAAA
61 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAA
*
12423737 ATTGATATTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
126 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
12423789 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGG-AATTTTTTATTCTTA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAA-ATATTTTTTTGGAAATTTATT-TTCTTA
12423850 TTTAAAGAAA
Statistics
Matches: 387, Mismatches: 13, Indels: 41
0.88 0.03 0.09
Matches are distributed among these distances:
174 38 0.10
177 19 0.05
179 10 0.03
180 13 0.03
181 20 0.05
182 145 0.37
183 26 0.07
184 61 0.16
185 15 0.04
186 40 0.10
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (177 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTCTTAAGGAAA
ATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAATTGA
TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:12423831 original size:117 final size:116
Alignment explanation
Indices: 12423247--12423836 Score: 724
Period size: 117 Copynumber: 4.9 Consensus size: 116
12423237 TTTTTTGTAG
* *
12423247 GGAAGATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTCGATTT-TCAAAGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT--ATTTCT-AAGGAA
* * *
12423311 AATTGATACTTTCAACTTTT-CCTCAAAAACCCT-TTTTTTGAAAATTTATTTCTAA
63 AATTGATACTTTCAACTTTTCCCT-AAAAA--ATATTTTTTGGAAATTTATTTTTAA
12423366 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGGAAAATTTATTTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTTGG-AAATTTA--TTTC---T
*
12423431 AAGGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTGGAAATTTATTCTTAA
57 AAGGAAAATTGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGGAAATTTATTTTTAA
* ** *
12423490 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTTAAATTTATTTCTGAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCC-CAAAA-ATATTTTTTTGGAAATTTATTTCTAAGGAAA
* *
12423555 ATTGATACTTTCAACTTTTCCC-CAAAAATATTTTTTGGAAATTTATTTCTAA
64 ATTGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGGAAATTTATTTTTAA
*
12423607 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTGGAAATTTA--TTTC---TAA
* * * *
12423672 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTTGAAATTTATTTTTGA
59 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA-A-TATTTTTTGGAAATTTATTTTTAA
*
12423732 GGAAAATTGATATTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAAT
12423796 TGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAA
66 TGATACTTTCAACTTTTCCCTAAAAA-ATA-TTTTTTGGAA
12423837 TTTTTTATTC
Statistics
Matches: 418, Mismatches: 27, Indels: 54
0.84 0.05 0.11
Matches are distributed among these distances:
115 3 0.01
116 5 0.01
117 143 0.34
119 38 0.09
120 8 0.02
121 1 0.00
122 59 0.14
123 21 0.05
124 47 0.11
125 61 0.15
126 28 0.07
127 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAAT
TGATACTTTCAACTTTTCCCTAAAAAATATTTTTTGGAAATTTATTTTTAA
Found at i:12423877 original size:10 final size:10
Alignment explanation
Indices: 12423862--12423894 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12423852 TAAAGAAAAT
12423862 AAAATAATAA
1 AAAATAATAA
12423872 AAAATAAT-A
1 AAAATAATAA
12423881 AAAATAAATAA
1 AAAAT-AATAA
12423892 AAA
1 AAA
12423895 GAATATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 11 0.52
11 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAA
Found at i:12423899 original size:19 final size:19
Alignment explanation
Indices: 12423862--12423899 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12423852 TAAAGAAAAT
*
12423862 AAAATAATAAAAAATAATA
1 AAAATAATAAAAAAGAATA
12423881 AAAATAA-ATAAAAAGAATA
1 AAAATAATA-AAAAAGAATA
12423900 TTACATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAATAAAAAAGAATA
Found at i:12423964 original size:22 final size:22
Alignment explanation
Indices: 12423939--12423980 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12423929 ATAAAATAAA
*
12423939 CAAATAAACAAAGAAAAAAATT
1 CAAAGAAACAAAGAAAAAAATT
*
12423961 CAAAGAAAGAAAGAAAAAAA
1 CAAAGAAACAAAGAAAAAAA
12423981 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (22 bp):
CAAAGAAACAAAGAAAAAAATT
Found at i:12424871 original size:17 final size:18
Alignment explanation
Indices: 12424849--12424882 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12424839 TAGATAAGTA
*
12424849 AAAATACAAAA-ATAAAT
1 AAAATAAAAAAGATAAAT
12424866 AAAATAAAAAAGATAAA
1 AAAATAAAAAAGATAAA
12424883 AAATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAAGATAAAT
Found at i:12424929 original size:16 final size:16
Alignment explanation
Indices: 12424910--12425014 Score: 60
Period size: 16 Copynumber: 6.6 Consensus size: 16
12424900 TATTAGTAAT
12424910 AATACATAAATAATAA
1 AATACATAAATAATAA
*
12424926 AATACACATAAATATTAA
1 AAT--ACATAAATAATAA
* *
12424944 CAAAAAATAAATAA-ATA
1 -AATACATAAATAATA-A
* * *
12424961 AATATATACAT-ATATT
1 AATACATAAATAATA-A
12424977 AATACAT-AATAAT--
1 AATACATAAATAATAA
*
12424990 AATA-ATAAATAATAC
1 AATACATAAATAATAA
12425005 AATACATAAA
1 AATACATAAA
12425015 ATACAAAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
12 2 0.03
13 10 0.14
15 7 0.10
16 27 0.39
17 9 0.13
18 12 0.17
19 2 0.03
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.28
Consensus pattern (16 bp):
AATACATAAATAATAA
Found at i:12424988 original size:35 final size:34
Alignment explanation
Indices: 12424878--12425005 Score: 95
Period size: 35 Copynumber: 3.6 Consensus size: 34
12424868 AATAAAAAAG
*
12424878 ATAAA-AAATATATATATATACATATTAGTAATAATA
1 ATAAATAAATA-A-ATATATACATA-TATTAATAATA
* * *
12424914 CATAAAT-AATAAA-ATACACATAAATATTAACAAAAA
1 -ATAAATAAATAAATATATACAT--ATATTAA-TAATA
12424950 ATAAATAAATAAATATATACATATATTAATACATA
1 ATAAATAAATAAATATATACATATATTAATA-ATA
12424985 AT-AATAATAATAAATA-ATACA
1 ATAAAT-A-AATAAATATATACA
12425006 ATACATAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
34 11 0.15
35 29 0.39
36 19 0.25
37 16 0.21
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (34 bp):
ATAAATAAATAAATATATACATATATTAATAATA
Found at i:12428287 original size:17 final size:17
Alignment explanation
Indices: 12428265--12428297 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12428255 GTTTGAAAAA
12428265 AAATTTTCCCTGGACAG
1 AAATTTTCCCTGGACAG
*
12428282 AAATTTTCCTTGGACA
1 AAATTTTCCCTGGACA
12428298 CTCAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (17 bp):
AAATTTTCCCTGGACAG
Found at i:12430505 original size:93 final size:93
Alignment explanation
Indices: 12430338--12430532 Score: 338
Period size: 93 Copynumber: 2.1 Consensus size: 93
12430328 GATACGTGTC
*
12430338 ATGT-TTTAATTGAACCTAAAAAGGTGTGGGCCATGAACCAAATGTTGCAATGTTTGAAATTTAT
1 ATGTATTTAATTGAACCTAAAAAGGTGCGGGCCATGAACCAAATGTTGCAATGTTTGAAATTTAT
* *
12430402 GCCTGCCGATCTTATCCCCATATGGAAT
66 GCCGGCCGATCTTATCCCCATATAGAAT
*
12430430 ATGTATTTAATTGAAGCTAAAAAGGTGCGGGCCATGAACCAAATGTTGCAATGTTTGAAATTTAT
1 ATGTATTTAATTGAACCTAAAAAGGTGCGGGCCATGAACCAAATGTTGCAATGTTTGAAATTTAT
*
12430495 GCCGGTCGATCTTATCCCCATATAGAAT
66 GCCGGCCGATCTTATCCCCATATAGAAT
12430523 ATGTATTTAA
1 ATGTATTTAA
12430533 GACGAAAACA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 4 0.04
93 93 0.96
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (93 bp):
ATGTATTTAATTGAACCTAAAAAGGTGCGGGCCATGAACCAAATGTTGCAATGTTTGAAATTTAT
GCCGGCCGATCTTATCCCCATATAGAAT
Found at i:12435322 original size:22 final size:22
Alignment explanation
Indices: 12435296--12435357 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
12435286 AGAAGGAAGT
12435296 TTTTTTGAAAAAATTTAGGGAA
1 TTTTTTGAAAAAATTTAGGGAA
* * *
12435318 -TTTTTGGAAAAATTT-GAGAT
1 TTTTTTGAAAAAATTTAGGGAA
*
12435338 TTTTTTGAAAAGAATCTAGG
1 TTTTTTGAAAA-AATTTAGG
12435358 AAATCTAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 4 0.13
23 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTTTTGAAAAAATTTAGGGAA
Found at i:12435771 original size:14 final size:15
Alignment explanation
Indices: 12435738--12435776 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
12435728 TTTAAAAATT
*
12435738 TTTTATTTGTTTTCTA
1 TTTTATTT-TGTTCTA
12435754 TTTTATTTTGTT-TA
1 TTTTATTTTGTTCTA
12435768 TTTTATTTT
1 TTTTATTTT
12435777 TATAATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 3 0.14
16 8 0.36
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTATTTTGTTCTA
Found at i:12438656 original size:21 final size:21
Alignment explanation
Indices: 12438630--12438675 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
12438620 AAGAAAAGTA
12438630 TGGTTAAAAATTTTAAATGTT
1 TGGTTAAAAATTTTAAATGTT
12438651 TGGTTAAAAATTTTAAATGTT
1 TGGTTAAAAATTTTAAATGTT
12438672 TGGT
1 TGGT
12438676 ATTACTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (21 bp):
TGGTTAAAAATTTTAAATGTT
Found at i:12441689 original size:30 final size:30
Alignment explanation
Indices: 12441629--12441689 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
12441619 TTTATATAAT
**
12441629 TTATTATTATTAAAAGGTTTATTTTTATTA
1 TTATTATTATTAAAAGGTTTATTTAAATTA
*
12441659 TTATTATTTTTAAAA-GTTTATCTTAAATTA
1 TTATTATTATTAAAAGGTTTAT-TTAAATTA
12441689 T
1 T
12441690 AAAAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (30 bp):
TTATTATTATTAAAAGGTTTATTTAAATTA
Found at i:12442787 original size:11 final size:11
Alignment explanation
Indices: 12442756--12442808 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
12442746 AAGAAAAAAG
12442756 AAAAATAG-AA
1 AAAAATAGTAA
12442766 AAAAA-AG-AA
1 AAAAATAGTAA
12442775 AAAAATAGTAA
1 AAAAATAGTAA
* *
12442786 AATAATAATAA
1 AAAAATAGTAA
*
12442797 TAAAATA-TAA
1 AAAAATAGTAA
12442807 AA
1 AA
12442809 TGATGTTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 9 0.25
10 11 0.31
11 16 0.44
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAATAGTAA
Found at i:12443026 original size:44 final size:43
Alignment explanation
Indices: 12442948--12443081 Score: 151
Period size: 44 Copynumber: 3.1 Consensus size: 43
12442938 TCAACAACAT
*
12442948 TTTTGAAAATTTAAAAGGCTCCTCTGAGCAAAGGCTAAATAAC
1 TTTTGAAAATTTAAAAGGCTCCTCTAAGCAAAGGCTAAATAAC
* * * * *
12442991 TTTTGAAAACTTAAAGAGACTCCTTTAAGCAAAGGCTCAATGAC
1 TTTTGAAAATTTAAA-AGGCTCCTCTAAGCAAAGGCTAAATAAC
* * * * *
12443035 TTTTAAAAATTTAAAAAGGCTTCTCTAAGCAGAGGCTTAACAAC
1 TTTTGAAAATTT-AAAAGGCTCCTCTAAGCAAAGGCTAAATAAC
12443079 TTT
1 TTT
12443082 AAAAATCTCA
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
43 14 0.19
44 57 0.77
45 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTTGAAAATTTAAAAGGCTCCTCTAAGCAAAGGCTAAATAAC
Found at i:12443110 original size:48 final size:49
Alignment explanation
Indices: 12443058--12443338 Score: 336
Period size: 49 Copynumber: 5.8 Consensus size: 49
12443048 AAAAGGCTTC
* *
12443058 TCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATC-TGAAAAAGCT-T
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCT
* * *
12443105 CTCTAAGCAGAGACTCAACGACTTTAAAAATCTCATCTTGGAAAAGCTCC
1 -TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCT
* *
12443155 TCTAAGCAAAAGCTCAACAACTTTAAAAATCT-ATCTTGGAAAAGCTCT
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCT
* * * **
12443203 TCTAAGTAGAGGATTAATGACTTTAAAAATCTCATCTTGGAAAAGCTCT
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCT
* * * **
12443252 TCTAAGTAGAGGATTAATGACTTTAAAAATCTCATCTTTGG-AAAGCTCT
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATC-TTGGAAAAGCTCT
* * *
12443301 TCTAAGTAAAGGCTCAACAACTTTAAAAATCTAATCTT
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTT
12443339 CTATTTTCGA
Statistics
Matches: 206, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
48 75 0.36
49 127 0.62
50 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (49 bp):
TCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCT
Found at i:12443177 original size:97 final size:97
Alignment explanation
Indices: 12443048--12443338 Score: 347
Period size: 97 Copynumber: 3.0 Consensus size: 97
12443038 TAAAAATTTA
*
12443048 AAAAGGCTTCTCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATC-TGAAAAAGCT-TCTCTAA
1 AAAA-GCTCCTCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATCTTG-AAAAGCTCT-TCTAA
*
12443111 GCAGAGACTCAACGACTTTAAAAATCTCATCTTGG
63 GTAGAGACTCAACGACTTTAAAAATCTCATCTTGG
* * *
12443146 AAAAGCTCCTCTAAGCAAAAGCTCAACAACTTTAAAAATCT-ATCTTGGAAAAGCTCTTCTAAGT
1 AAAAGCTCCTCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATCTT-GAAAAGCTCTTCTAAGT
* *
12443210 AGAGGA-TTAATGACTTTAAAAATCTCATCTTGG
65 AGA-GACTCAACGACTTTAAAAATCTCATCTTGG
* * * ** *
12443243 AAAAGCTCTTCTAAGTAGAGGATTAATGACTTTAAAAATCTCATCTTTGGAAAGCTCTTCTAAGT
1 AAAAGCTCCTCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATC-TTGAAAAGCTCTTCTAAGT
* * * *
12443308 AAAGGCTCAACAACTTTAAAAATCTAATCTT
65 AGAGACTCAACGACTTTAAAAATCTCATCTT
12443339 CTATTTTCGA
Statistics
Matches: 164, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
96 3 0.02
97 109 0.66
98 50 0.30
99 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (97 bp):
AAAAGCTCCTCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAGCTCTTCTAAGTA
GAGACTCAACGACTTTAAAAATCTCATCTTGG
Found at i:12443280 original size:146 final size:146
Alignment explanation
Indices: 12443058--12443338 Score: 399
Period size: 146 Copynumber: 1.9 Consensus size: 146
12443048 AAAAGGCTTC
*
12443058 TCTAAGCAGAGGCTTAACAACTTTAAAAATCTCATCTGAAAAAGCTTCTCTAAGCAGAGACTCAA
1 TCTAAGCAGAGGATTAACAACTTTAAAAATCTCATCTGAAAAAGCTTCTCTAAGCAGAGACTCAA
12443123 CGACTTTAAAAATCTCATC-TTGGAAAAGCTCCTCTAAGCAAAAGCTCAACAACTTTAAAAATCT
66 CGACTTTAAAAATCTCATCTTTGG-AAAGCTCCTCTAAGCAAAAGCTCAACAACTTTAAAAATCT
12443187 -ATCTTGGAAAAGCTCT
130 AATCTTGGAAAAGCTCT
* ** * *
12443203 TCTAAGTAGAGGATTAATGACTTTAAAAATCTCATCTTGGAAAAGC-TCTTCTAAGTAGAGGA-T
1 TCTAAGCAGAGGATTAACAACTTTAAAAATCTCATC-TGAAAAAGCTTC-TCTAAGCAGA-GACT
* * * * *
12443266 TAATGACTTTAAAAATCTCATCTTTGGAAAGCTCTTCTAAGTAAAGGCTCAACAACTTTAAAAAT
63 CAACGACTTTAAAAATCTCATCTTTGGAAAGCTCCTCTAAGCAAAAGCTCAACAACTTTAAAAAT
12443331 CTAATCTT
128 CTAATCTT
12443339 CTATTTTCGA
Statistics
Matches: 120, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
145 34 0.28
146 75 0.62
147 11 0.09
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (146 bp):
TCTAAGCAGAGGATTAACAACTTTAAAAATCTCATCTGAAAAAGCTTCTCTAAGCAGAGACTCAA
CGACTTTAAAAATCTCATCTTTGGAAAGCTCCTCTAAGCAAAAGCTCAACAACTTTAAAAATCTA
ATCTTGGAAAAGCTCT
Found at i:12454450 original size:15 final size:15
Alignment explanation
Indices: 12454408--12454450 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12454398 AAAATTTAGT
*
12454408 TTTCATTTATTATTG
1 TTTCATTTTTTATTG
* *
12454423 TTCCA-TATTTATTG
1 TTTCATTTTTTATTG
12454437 TTTCATTTTTTATT
1 TTTCATTTTTTATT
12454451 TAAGAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTCATTTTTTATTG
Found at i:12456268 original size:8 final size:8
Alignment explanation
Indices: 12456255--12456311 Score: 78
Period size: 8 Copynumber: 6.8 Consensus size: 8
12456245 AAGGAAAAAG
12456255 AAAATATA
1 AAAATATA
12456263 AAAATATA
1 AAAATATA
12456271 AAAATATAA
1 AAAATAT-A
12456280 AAAATATAAA
1 AAAATAT--A
12456290 AAAATATA
1 AAAATATA
12456298 AAAATATA
1 AAAATATA
*
12456306 ATAATA
1 AAAATA
12456312 ATAATAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
8 29 0.63
9 8 0.17
10 9 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATATA
Found at i:12456291 original size:10 final size:9
Alignment explanation
Indices: 12456255--12456330 Score: 77
Period size: 9 Copynumber: 8.2 Consensus size: 9
12456245 AAGGAAAAAG
12456255 AAAATAT-A
1 AAAATATAA
12456263 AAAATAT-A
1 AAAATATAA
12456271 AAAATATAA
1 AAAATATAA
12456280 AAAATATAA
1 AAAATATAA
12456289 AAAA-ATATA
1 AAAATATA-A
12456298 AAAATATAA
1 AAAATATAA
12456307 TAATAATAATAA
1 -AA-AAT-ATAA
*
12456319 TAAAATACAA
1 -AAAATATAA
12456329 AA
1 AA
12456331 TGGTGTTTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
8 18 0.30
9 22 0.36
10 8 0.13
11 6 0.10
12 7 0.11
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATATAA
Found at i:12456315 original size:17 final size:17
Alignment explanation
Indices: 12456255--12456320 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
12456245 AAGGAAAAAG
12456255 AAAAT-ATAAAAATATA
1 AAAATAATAAAAATATA
12456271 AAAAT-ATAAAAAATATA
1 AAAATAAT-AAAAATATA
*
12456288 AAAAAATATAAAAATATA
1 AAAATA-ATAAAAATATA
* *
12456306 ATAATAATAATAATA
1 AAAATAATAAAAATA
12456321 AAATACAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
16 7 0.16
17 21 0.49
18 13 0.30
19 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAATAAAAATATA
Found at i:12462793 original size:65 final size:65
Alignment explanation
Indices: 12462716--12462964 Score: 225
Period size: 65 Copynumber: 3.8 Consensus size: 65
12462706 TTGACTCGTG
* * * * *
12462716 GTTCAATACTGGTCACTCGTTTCAATCTCGACTTAGTCTAGATCATTTTATTTTTCAAACCTATA
1 GTTCAATCCTGGTCACTCATTTCGATCTCGACTCAGTCTAGATCATTTTATTTTTTAAACCTATA
* * * *
12462781 GTTCAATCCTGGTCACCCATTTTGATCTCAACTCAGTCTAGATCATTTTATTTTTTTAA-CTCAT
1 GTTCAATCCTGGTCACTCATTTCGATCTCGACTCAGTCTAGATCATTTTATTTTTTAAACCT-AT
*
12462845 G
65 A
* * ** * * * * ***
12462846 GTTCAATCTTAGTCACTTGTTTCGATCTTGACTCCA-TCGAAATCATTTTATTTTTTATACCCGC
1 GTTCAATCCTGGTCACTCATTTCGATCTCGACT-CAGTCTAGATCATTTTATTTTTTAAACCTAT
12462910 A
65 A
* * * *
12462911 GTTCAATCTTGGTCACTTATTTCGATCTCGGCTCAAT-TAAGATCATTTTATTTT
1 GTTCAATCCTGGTCACTCATTTCGATCTCGACTCAGTCT-AGATCATTTTATTTT
12462965 ATTGACTCAC
Statistics
Matches: 147, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
64 4 0.03
65 140 0.95
66 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (65 bp):
GTTCAATCCTGGTCACTCATTTCGATCTCGACTCAGTCTAGATCATTTTATTTTTTAAACCTATA
Found at i:12462914 original size:130 final size:129
Alignment explanation
Indices: 12462700--12463031 Score: 335
Period size: 130 Copynumber: 2.6 Consensus size: 129
12462690 AGTCCATATC
* * * * * * *
12462700 ATTTTTTTGACTCGTGGTTCAATACTGGTCACTCGTTTCAATCTCGACTTAGTCTAGATCATTTT
1 ATTTTTTTGACTCATGGTTCAAT-CTAGTCACTTGTTTCGATCTTGACTCAATCTAGATCATTTT
* * * * *
12462765 ATTTTTCAAACCTATAGTTCAATCCTGGTCACCCATTTTGATCTCAACTCAGTCT-AGATCATTT
65 ATTTTTTAAACCCACAGTTCAATCCTGGTCACCCATTTCGATCTCAACTCAAT-TAAGATCATTT
12462829 T
129 T
* * * *
12462830 ATTTTTTTAACTCATGGTTCAATCTTAGTCACTTGTTTCGATCTTGACTCCATCGAAATCATTTT
1 ATTTTTTTGACTCATGGTTCAATC-TAGTCACTTGTTTCGATCTTGACTCAATCTAGATCATTTT
* * * ** **
12462895 ATTTTTTATACCCGCAGTTCAATCTTGGTCACTTATTTCGATCTCGGCTCAATTAAGATCATTTT
65 ATTTTTTAAACCCACAGTTCAATCCTGGTCACCCATTTCGATCTCAACTCAATTAAGATCATTTT
* * * * * * *
12462960 ATTTTATTGACTCACGATTCAATCCTAATCACCTGTTTTGATC-TCAGCTCAATCTAGATCATTT
1 ATTTTTTTGACTCATGGTTCAAT-CTAGTCACTTGTTTCGATCTTGA-CTCAATCTAGATCATTT
12463024 TATTTTTT
64 TATTTTTT
12463032 GTTTCATAGT
Statistics
Matches: 164, Mismatches: 34, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
129 4 0.02
130 159 0.97
131 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.44
Consensus pattern (129 bp):
ATTTTTTTGACTCATGGTTCAATCTAGTCACTTGTTTCGATCTTGACTCAATCTAGATCATTTTA
TTTTTTAAACCCACAGTTCAATCCTGGTCACCCATTTCGATCTCAACTCAATTAAGATCATTTT
Found at i:12462981 original size:65 final size:64
Alignment explanation
Indices: 12462812--12463031 Score: 207
Period size: 65 Copynumber: 3.4 Consensus size: 64
12462802 TTGATCTCAA
* * * *
12462812 CTCAGTCT-AGATCATTTTATTTTTTTAACTCATGGTTCAATCTTAGTCACTTGTTTCGATCTTG
1 CTCAATCTAAGATCATTTTA-TTTTTT-ACTCACGATTCAATCTTAGTCACTTGTTTCGATCTCG
*
12462876 A
64 G
* * * * *
12462877 CTCCATCGAA-ATCATTTTATTTTTTA-TACCCGCAGTTCAATCTTGGTCACTTATTTCGATCTC
1 CTCAATCTAAGATCATTTTATTTTTTACT-CACG-A-TTCAATCTTAGTCACTTGTTTCGATCTC
12462940 GG
63 GG
* * * * *
12462942 CTCAAT-TAAGATCATTTTATTTTATTGACTCACGATTCAATCCTAATCACCTGTTTTGATCTCA
1 CTCAATCTAAGATCATTTTATTTT-TT-ACTCACGATTCAATCTTAGTCACTTGTTTCGATCTCG
12463006 G
64 G
12463007 CTCAATCT-AGATCATTTTATTTTTT
1 CTCAATCTAAGATCATTTTATTTTTT
12463032 GTTTCATAGT
Statistics
Matches: 126, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 10 0.08
65 102 0.81
66 5 0.04
67 4 0.03
68 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (64 bp):
CTCAATCTAAGATCATTTTATTTTTTACTCACGATTCAATCTTAGTCACTTGTTTCGATCTCGG
Found at i:12463344 original size:6 final size:7
Alignment explanation
Indices: 12463320--12463353 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
12463310 CCAATCGTTA
12463320 TTTTATT
1 TTTTATT
12463327 ATTATTATT
1 -TT-TTATT
12463336 TTTTATT
1 TTTTATT
12463343 TTTTATT
1 TTTTATT
12463350 TTTT
1 TTTT
12463354 TTCAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 16 0.64
8 4 0.16
9 5 0.20
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:12464236 original size:28 final size:28
Alignment explanation
Indices: 12464204--12464287 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
12464194 TTTTTTCATG
12464204 TTATTTTTCATTTATATTTATATTTATT
1 TTATTTTTCATTTATATTTATATTTATT
** *
12464232 TTATTTTTTCA-AAAT-TTTCTTATTTATT
1 TTA-TTTTTCATTTATATTT-ATATTTATT
* *
12464260 TTCTATTTCATTT-TATTTAT-TTTATT
1 TTATTTTTCATTTATATTTATATTTATT
12464286 TT
1 TT
12464288 TATAATTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
26 8 0.18
27 11 0.25
28 18 0.41
29 7 0.16
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATTTTTCATTTATATTTATATTTATT
Found at i:12464312 original size:16 final size:15
Alignment explanation
Indices: 12464270--12464312 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
12464260 TTCTATTTCA
*
12464270 TTTTATTTATTTTAT
1 TTTTATTTTTTTTAT
* *
12464285 TTTTATAATTTTCTAT
1 TTTTAT-TTTTTTTAT
12464301 TTTTATTTTTTT
1 TTTTATTTTTTT
12464313 AGATTCTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTTTAT
Found at i:12465356 original size:22 final size:22
Alignment explanation
Indices: 12465331--12465378 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
12465321 GTGGCGATAC
12465331 ATCATATCAATTAGGACATTAT
1 ATCATATCAATTAGGACATTAT
12465353 ATCATATCAATTAGGACATTAT
1 ATCATATCAATTAGGACATTAT
12465375 ATCA
1 ATCA
12465379 ATTCAGTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (22 bp):
ATCATATCAATTAGGACATTAT
Found at i:12465514 original size:19 final size:20
Alignment explanation
Indices: 12465479--12465516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12465469 TGGACACCTC
12465479 AAAAATTAAAAACAAATTTA
1 AAAAATTAAAAACAAATTTA
*
12465499 AAAAATTAGAAA-AAATTT
1 AAAAATTAAAAACAAATTT
12465517 TCACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAATTAAAAACAAATTTA
Found at i:12467620 original size:76 final size:76
Alignment explanation
Indices: 12467537--12467677 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 76
12467527 TCAAAGATTC
* *
12467537 TAAATAGTTGTATTGGGTACTAAAATAATAG-AAATCAATAAAAGTTATAATCGGATGTGAAAAG
1 TAAATAGTTGTATTGGATACTAAAATAATAGAAAAT-AATAAAAGTTATAATCGCATGTGAAAAG
12467601 CTTCTAAATCCG
65 CTTCTAAATCCG
* * * *
12467613 TAAATAGTTGTATTGGATATTAAAATAATAGAAAATAATAGAAGTTATAATTGCTTGTGAAAAGC
1 TAAATAGTTGTATTGGATACTAAAATAATAGAAAATAATAAAAGTTATAATCGCATGTGAAAAGC
12467678 ATGAATTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 54 0.93
77 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (76 bp):
TAAATAGTTGTATTGGATACTAAAATAATAGAAAATAATAAAAGTTATAATCGCATGTGAAAAGC
TTCTAAATCCG
Found at i:12467875 original size:25 final size:28
Alignment explanation
Indices: 12467831--12467886 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 28
12467821 GTAAACTAAA
*
12467831 ATTTGAAATTAAATCTTCTTTGCTC-AT
1 ATTTGAAATTAAATCCTCTTTGCTCAAT
*
12467858 ATTTG-AA-TAAATCCTCTTTGTTCAAT
1 ATTTGAAATTAAATCCTCTTTGCTCAAT
12467884 ATT
1 ATT
12467887 AAATTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 14 0.54
26 7 0.27
27 5 0.19
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTTGAAATTAAATCCTCTTTGCTCAAT
Found at i:12468372 original size:22 final size:23
Alignment explanation
Indices: 12468346--12468392 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12468336 ACCAACTCTC
*
12468346 TTTTCTCCCTTTTCT-CTTTATT
1 TTTTCTACCTTTTCTACTTTATT
* *
12468368 TTTTCTAGCTTTTCTACTTTCTT
1 TTTTCTACCTTTTCTACTTTATT
12468391 TT
1 TT
12468393 CTTGGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTCTACCTTTTCTACTTTATT
Found at i:12477506 original size:22 final size:22
Alignment explanation
Indices: 12477457--12477506 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12477447 TGATACGGTT
** *
12477457 TAAAT-TGACAAAAATAGTATA
1 TAAATATGACAAAAATAAAAAA
12477478 TAAATATGACAAAAATAAAAAA
1 TAAATATGACAAAAATAAAAAA
*
12477500 TATATAT
1 TAAATAT
12477507 TTAACGTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAATATGACAAAAATAAAAAA
Found at i:12479347 original size:21 final size:22
Alignment explanation
Indices: 12479322--12479384 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
12479312 TGATAAATAT
12479322 TTATTTT-AATAAATTAATTAA
1 TTATTTTAAATAAATTAATTAA
*
12479343 TTATTTTAAAATAAA-TAATTGA
1 TTATTTT-AAATAAATTAATTAA
*
12479365 TT-TTTTCAAT-AATATAATTA
1 TTATTTTAAATAAAT-TAATTA
12479385 TACAATATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 16 0.46
22 8 0.23
23 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTTTAAATAAATTAATTAA
Found at i:12479361 original size:18 final size:20
Alignment explanation
Indices: 12479314--12479368 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
12479304 TAATTAAATG
*
12479314 ATAAATATTTATTTTAATAA
1 ATAAATAATTATTTTAATAA
*
12479334 ATTAATTAATTATTTT-A-AA
1 A-TAAATAATTATTTTAATAA
12479353 ATAAATAATTGATTTT
1 ATAAATAATT-ATTTT
12479369 TTCAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 2 0.07
21 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAAATAATTATTTTAATAA
Found at i:12480808 original size:74 final size:75
Alignment explanation
Indices: 12480663--12480810 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 75
12480653 AAAAAATTCC
* * **
12480663 AAATCCATAAATAGTTGTATTGGGTACTAAAATAATAGAATTCAATGAAAGTTACAATTGCATGT
1 AAATCCATAAATAGTTGTATTGGGTACTAAAAT-ATAGAAATCAATAAAAGTTACAATTGCATCA
12480728 GAAAAGCATCT
65 GAAAAGCATCT
* *
12480739 AAATCCGTAAATAGTTGTATTGGGTACTAAAAT-TAGAAATCAATAAAAGTTATAATTGCATCAG
1 AAATCCATAAATAGTTGTATTGGGTACTAAAATATAGAAATCAATAAAAGTTACAATTGCATCAG
12480803 AAAAGCAT
66 AAAAGCAT
12480811 AAATTATTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 34 0.52
76 32 0.48
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (75 bp):
AAATCCATAAATAGTTGTATTGGGTACTAAAATATAGAAATCAATAAAAGTTACAATTGCATCAG
AAAAGCATCT
Found at i:12485024 original size:16 final size:16
Alignment explanation
Indices: 12485003--12485045 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
12484993 GATATGACTT
*
12485003 AATGATATGAAATAAA
1 AATGATATAAAATAAA
*
12485019 AATGATACAAAAAATAAA
1 AATGAT--ATAAAATAAA
12485037 AATGATATA
1 AATGATATA
12485046 GTTTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (16 bp):
AATGATATAAAATAAA
Found at i:12489290 original size:41 final size:41
Alignment explanation
Indices: 12489202--12489623 Score: 454
Period size: 41 Copynumber: 10.1 Consensus size: 41
12489192 AGTAAACAAA
* * * * *
12489202 GCTCCTCTAAACAAAGGCTCAACTACTTTGAGAAAA-ATAACT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGA-AAAATA-AAAT
**
12489244 GCTCCTCTAAATGGAGGCACCACAACTTTTG-AAAATAAAAT
1 GCTCCTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAAAT
* * * *
12489285 GCTCCTTTAAACAGAGACAGCACAACTTTGAAAAGTAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* * *
12489326 GTTCCTATAAATAGAGGCACCACAACTTTGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* * *
12489367 GCTCCTCTAAACAGAGGCACCATAATTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTG-AAAAATAAAAT
* * * *
12489409 GCTCATTTAAACAGAGGCATCACAACTTTAGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTT-GAAAAATAAAAT
* *
12489451 GCTCCTCTAAACAGAGGCACTACAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTG-AAAAATAAAAT
* * *
12489493 GTTCCTCTAAACAGAGGCATCACAACTTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAAC-TTTG-AAAAATAAAAT
* * *
12489536 GCTCCTCTAAACAAAGGTACTACAACTTT-AAAATATAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAA-ATAAAAT
* * *
12489577 GCTCCTCTAAACATAGGCACTACAACTTTGAAAAATAAAAG
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
12489618 GCTCCT
1 GCTCCT
12489624 TGACAATCAT
Statistics
Matches: 325, Mismatches: 46, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
40 8 0.02
41 143 0.44
42 132 0.41
43 42 0.13
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
Found at i:12489456 original size:84 final size:83
Alignment explanation
Indices: 12489202--12489623 Score: 474
Period size: 84 Copynumber: 5.1 Consensus size: 83
12489192 AGTAAACAAA
* * * * * **
12489202 GCTCCTCTAAACAAAGGCTCAACTACTTTGAGAAAAAT-AACTGCTCCTCTAAATGGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACAACTTTGA-AAAAATAAAATGCTCCTCTAAACAGAGGCACCA
12489266 CAACTTTTG-AAAATAAAAT
65 CAAC-TTTGAAAAATAAAAT
* * * * * * *
12489285 GCTCCTTTAAACAGAGACAGCACAACTTTG-AAAAGTAAAATGTTCCTATAAATAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAATGCTCCTCTAAACAGAGGCACCAC
12489349 AACTTTGAAAAATAAAAT
66 AACTTTGAAAAATAAAAT
* * * * * *
12489367 GCTCCTCTAAACAGAGGCACCATAATTTTGAAAAAATAAATTGCTCATTTAAACAGAGGCATCAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAATGCTCCTCTAAACAGAGGCACCAC
*
12489432 AACTTTAGAAAAATAAATT
66 AACTTT-GAAAAATAAAAT
* * * *
12489451 GCTCCTCTAAACAGAGGCACTACAACTTTGAAAAAATAAATTGTTCCTCTAAACAGAGGCATCAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAATGCTCCTCTAAACAGAGGCACCAC
*
12489516 AACTTTTGAAAAAATAAATT
66 AAC-TTTG-AAAAATAAAAT
* * * * * *
12489536 GCTCCTCTAAACAAAGGTACTACAACTTT-AAAATATAAAATGCTCCTCTAAACATAGGCACTAC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAATGCTCCTCTAAACAGAGGCACCAC
*
12489600 AACTTTGAAAAATAAAAG
66 AACTTTGAAAAATAAAAT
12489618 GCTCCT
1 GCTCCT
12489624 TGACAATCAT
Statistics
Matches: 292, Mismatches: 41, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
81 9 0.03
82 76 0.26
83 60 0.21
84 106 0.36
85 41 0.14
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAATAAAATGCTCCTCTAAACAGAGGCACCAC
AACTTTGAAAAATAAAAT
Found at i:12490009 original size:20 final size:21
Alignment explanation
Indices: 12489954--12489993 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12489944 GTTTCAAACC
*
12489954 TCAAATATTCTCATTTGAAAT
1 TCAAAAATTCTCATTTGAAAT
12489975 TCAAAAATTCTCATTTGAA
1 TCAAAAATTCTCATTTGAA
12489994 TTCGAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TCAAAAATTCTCATTTGAAAT
Found at i:12490058 original size:21 final size:22
Alignment explanation
Indices: 12490032--12490089 Score: 91
Period size: 21 Copynumber: 2.7 Consensus size: 22
12490022 GGTTTCACAC
*
12490032 CTCAAAAATTCTCATTTGA-AA
1 CTCAAAAATTCTCATTTAAGAA
*
12490053 TTCAAAAATTCTCATTTAAGAA
1 CTCAAAAATTCTCATTTAAGAA
12490075 CTCAAAAATTCTCAT
1 CTCAAAAATTCTCAT
12490090 CAAAAGATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
CTCAAAAATTCTCATTTAAGAA
Found at i:12491314 original size:7 final size:6
Alignment explanation
Indices: 12491300--12491383 Score: 70
Period size: 6 Copynumber: 13.8 Consensus size: 6
12491290 TTCTTTTCTC
*
12491300 TCTTTT TCATTTT TCTTTT CTCTTTT T-TTTT ATC-TTT T-TTTT CCTTTT
1 TCTTTT TC-TTTT TCTTTT -TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT
12491348 T-TTCTT TCTTTT TCTTTTT TCTTTT T-TTTT CTCTTT
1 TCTT-TT TCTTTT TC-TTTT TCTTTT TCTTTT -TCTTT
12491384 CACCCCATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
5 14 0.22
6 28 0.43
7 23 0.35
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:12491315 original size:22 final size:20
Alignment explanation
Indices: 12491289--12491383 Score: 90
Period size: 22 Copynumber: 4.7 Consensus size: 20
12491279 AATTTGAGTC
12491289 TTTCTTTTCTCTCTTTTTCATT
1 TTTCTTTTCTCT-TTTTTC-TT
12491311 TTTCTTTTCTCTTTTTT-TT
1 TTTCTTTTCTCTTTTTTCTT
* * *
12491330 TATCTTTTTTTTCCTTTTTT-TC
1 T-T-TCTTTTCT-CTTTTTTCTT
12491352 TTTCTTTT-TCTTTTTTCTT
1 TTTCTTTTCTCTTTTTTCTT
12491371 TTT-TTTTCTCTTT
1 TTTCTTTTCTCTTT
12491384 CACCCCATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
18 11 0.17
19 13 0.21
20 6 0.10
21 12 0.19
22 21 0.33
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTCTCTTTTTTCTT
Found at i:12491316 original size:13 final size:11
Alignment explanation
Indices: 12491302--12491383 Score: 76
Period size: 11 Copynumber: 6.8 Consensus size: 11
12491292 CTTTTCTCTC
12491302 TTTTTCATTTTT
1 TTTTTC-TTTTT
12491314 CTTTTCTCTTTTT
1 -TTTT-TCTTTTT
12491327 TTTTATC-TTTT
1 TTTT-TCTTTTT
*
12491338 TTTTCCTTTTT
1 TTTTTCTTTTT
12491349 TTCTTTCTTTTTCT
1 TT-TTTC-TTTT-T
12491363 TTTTTCTTTTT
1 TTTTTCTTTTT
12491374 TTTTCTCTTT
1 TTTT-TCTTT
12491384 CACCCCATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
10 1 0.02
11 19 0.32
12 18 0.30
13 17 0.28
14 5 0.08
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:12491337 original size:10 final size:9
Alignment explanation
Indices: 12491309--12491379 Score: 74
Period size: 9 Copynumber: 7.8 Consensus size: 9
12491299 CTCTTTTTCA
12491309 TTTTTCTTT
1 TTTTTCTTT
12491318 TCTCTTT-TTT
1 T-T-TTTCTTT
*
12491328 TTTATCTTT
1 TTTTTCTTT
*
12491337 TTTTTCCTT
1 TTTTTCTTT
12491346 TTTTTCTTT
1 TTTTTCTTT
12491355 CTTTTTCTTT
1 -TTTTTCTTT
*
12491365 TTTCT-TTT
1 TTTTTCTTT
12491373 TTTTTCT
1 TTTTTCT
12491380 CTTTCACCCC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
8 9 0.18
9 25 0.49
10 14 0.27
11 3 0.06
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:12491341 original size:35 final size:35
Alignment explanation
Indices: 12491289--12491376 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 35
12491279 AATTTGAGTC
* *
12491289 TTTCTTTTCTC-TCTTTTTCATTTTTCTT-TTCTCTT
1 TTTCTTTTATCTTTTTTTTCATTTTT-TTCTT-TCTT
*
12491324 TTT-TTTTATCTTTTTTTTCCTTTTTTTCTTTCTT
1 TTTCTTTTATCTTTTTTTTCATTTTTTTCTTTCTT
*
12491358 TTTCTTTTTTCTTTTTTTT
1 TTTCTTTTATCTTTTTTTT
12491377 TCTCTTTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 15 0.33
35 31 0.67
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTCTTTTATCTTTTTTTTCATTTTTTTCTTTCTT
Found at i:12491347 original size:18 final size:16
Alignment explanation
Indices: 12491289--12491376 Score: 79
Period size: 19 Copynumber: 5.2 Consensus size: 16
12491279 AATTTGAGTC
* *
12491289 TTTCTTTTCTC-TCTT
1 TTTCTTTTTTCTTTTT
*
12491304 TTTCATTTTTCTTTTCT
1 TTTCTTTTTTCTTTT-T
*
12491321 CTTTTTTTTTATCTTTTT
1 -TTTCTTTTT-TCTTTTT
12491339 TTTCCTTTTTTTCTTTCTT
1 TTT-C-TTTTTTCTTT-TT
12491358 TTTCTTTTTTCTTTTT
1 TTTCTTTTTTCTTTTT
12491374 TTT
1 TTT
12491377 TCTCTTTCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
15 9 0.15
16 7 0.12
17 14 0.23
18 14 0.23
19 16 0.27
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTT
Found at i:12491377 original size:36 final size:38
Alignment explanation
Indices: 12491309--12491383 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 38
12491299 CTCTTTTTCA
12491309 TTTTTCTTTTCTCTTTTTTTTTATCTTTTTTTTC-CTT
1 TTTTTCTTTTCTCTTTTTTTTTATCTTTTTTTTCTCTT
12491346 TTTTTC-TTTCT-TTTTCTTTTT-TCTTTTTTTTTCTCTT
1 TTTTTCTTTTCTCTTTT-TTTTTATC-TTTTTTTTCTCTT
12491383 T
1 T
12491384 CACCCCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
35 6 0.17
36 19 0.54
37 10 0.29
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (38 bp):
TTTTTCTTTTCTCTTTTTTTTTATCTTTTTTTTCTCTT
Found at i:12491468 original size:18 final size:18
Alignment explanation
Indices: 12491445--12491482 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12491435 GATTCTGTCA
12491445 TTTCATCATGAACATGCC
1 TTTCATCATGAACATGCC
12491463 TTTCATCATGAACATGCC
1 TTTCATCATGAACATGCC
12491481 TT
1 TT
12491483 AGCCCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (18 bp):
TTTCATCATGAACATGCC
Found at i:12491791 original size:13 final size:13
Alignment explanation
Indices: 12491773--12491802 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12491763 TTTTGTTTTG
*
12491773 CTTTTCTTTCTTT
1 CTTTTCTTTCTAT
12491786 CTTTTCTTTCTAT
1 CTTTTCTTTCTAT
12491799 CTTT
1 CTTT
12491803 GAGACCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTCTTTCTAT
Found at i:12492296 original size:19 final size:20
Alignment explanation
Indices: 12492272--12492322 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
12492262 GAAAACAAAT
12492272 GAAATCCTATTAC-ATAAAA
1 GAAATCCTATTACTATAAAA
*
12492291 GAAATCCTAACATTACTCTAAAA
1 GAAATCCT---ATTACTATAAAA
12492314 GAAATCCTA
1 GAAATCCTA
12492323 AAATGACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.30
20 1 0.04
22 5 0.19
23 13 0.48
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (20 bp):
GAAATCCTATTACTATAAAA
Found at i:12495051 original size:5 final size:5
Alignment explanation
Indices: 12495043--12495086 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
12495033 TAAAAATCCA
* *
12495043 AAAAT AAAAT GAAAAT AAAAC AAAA- AAAGT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12495087 CCAAAACAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.09
5 26 0.76
6 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:12498279 original size:144 final size:142
Alignment explanation
Indices: 12497864--12498279 Score: 464
Period size: 140 Copynumber: 2.9 Consensus size: 142
12497854 TATTAAAAAA
* * ** *
12497864 AAAAAAACCCTTAAAGGGCATTTTGATAATTTCACT-CTTTTTTGGTGCAATTAAGATTTTCAAT
1 AAAAATACCCTTAAAGGGCATTTTAATAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
* * * *** *
12497928 CCATCAAAATTTATGAAATAATATTTAAATATGATTAGGAGTTTTGTGAAAAATTAACCTC-AAA
66 GCATCAAAATTCATGAAATAATATTTAAATATGATT-GGATTTTTACAAAAAATCAACCTCAAAA
*
12497992 AAGGTTAAATTAC
130 AAGGCTAAATTAC
* * * * * *
12498005 AAAAATACCCATAAA-GGCATTTTAGTAATATCA-TCCTTTTGAGATACAATTAAGATTTTTAAT
1 AAAAATACCCTTAAAGGGCATTTTAATAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
* * * * * *
12498068 GGATCAAAATTCATGAAATAATATGTAAACATGATTGGAGTTTTTAACAAAAAAACCGACCTTAA
66 GCATCAAAATTCATGAAATAATATTTAAATATGATTGGA-TTTTT-AC-AAAAAATCAACCTCAA
12498133 AAAAGGCTAAATTAC
128 AAAAGGCTAAATTAC
* *
12498148 AAAAATA-CCTTAAAGGGCATTTAAATAATTTCACTCCTTTTAAGGTGCAATCAAGATTTTTAAT
1 AAAAATACCCTTAAAGGGCATTTTAATAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
* * *
12498212 GCATTAAAATTCATGGAATAATATTTAAATATGATTTGGGATTTTTCACAAAAAATCAACCCCAA
66 GCATCAAAATTCATGAAATAATATTTAAATATGA-TT-GGATTTTT-ACAAAAAATCAACCTCAA
12498277 AAA
128 AAA
12498280 TGCCAAATAA
Statistics
Matches: 224, Mismatches: 42, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
139 4 0.02
140 73 0.33
141 13 0.06
142 15 0.07
143 37 0.17
144 70 0.31
145 9 0.04
146 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (142 bp):
AAAAATACCCTTAAAGGGCATTTTAATAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
GCATCAAAATTCATGAAATAATATTTAAATATGATTGGATTTTTACAAAAAATCAACCTCAAAAA
AGGCTAAATTAC
Found at i:12498321 original size:144 final size:140
Alignment explanation
Indices: 12497865--12498322 Score: 420
Period size: 144 Copynumber: 3.2 Consensus size: 140
12497855 ATTAAAAAAA
* * * ** *
12497865 AAAAAACCCTTAAAGGGCATTTT-GATAATTTCACT-CTTTTTTGGTGCAATTAAGATTTTCAAT
1 AAAAATCCCATAAAAGGCATTTTAG-TAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
* * * *** *
12497928 CCATCAAAATTTATGAAATAATATTTAAATATGATTAGGAGTTTTGTGAAAAATTAACCTCAAAA
65 GCATCAAAATTCATGAAATAATATTTAAATATGATT-GGATTTTTACAAAAAATCAACCTCAAAA
*
12497993 AGGTTAAATTAC
129 AGGCTAAATTAC
* * * *
12498005 AAAAATACCCAT-AAAGGCATTTTAGTAATATCA-TCCTTTTGAGATACAATTAAGATTTTTAAT
1 AAAAAT-CCCATAAAAGGCATTTTAGTAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAAT
* * * * * *
12498068 GGATCAAAATTCATGAAATAATATGTAAACATGATTGGAGTTTTTAACAAAAAAACCGACCTTAA
65 GCATCAAAATTCATGAAATAATATTTAAATATGATTGGA-TTTTT-AC-AAAAAATCAACC-TCA
12498133 AAAAGGCTAAATTAC
126 AAAAGGCTAAATTAC
* * * * * *
12498148 AAAAATACCTTAAAGGGCATTTAAATAATTTCACTCCTTTTAAGGTGCAATCAAGATTTTTAATG
1 AAAAATCCCATAAAAGGCATTTTAGTAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAATG
* * *
12498213 CATTAAAATTCATGGAATAATATTTAAATATGATTTGGGATTTTTCACAAAAAATCAACCCCAAA
66 CATCAAAATTCATGAAATAATATTTAAATATGA-TT-GGATTTTT-ACAAAAAATCAACCTCAAA
* * * *
12498278 AATGCCAAATAAT
128 AAGGCTAAATTAC
* * * *
12498291 GAAAATCCCCCTAAAAGACATTTTTGTAATTT
1 AAAAAT-CCCATAAAAGGCATTTTAGTAATTT
12498323 TACCTTTCTT
Statistics
Matches: 251, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
139 4 0.02
140 80 0.32
141 5 0.02
142 11 0.04
143 56 0.22
144 83 0.33
145 9 0.04
146 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (140 bp):
AAAAATCCCATAAAAGGCATTTTAGTAATTTCACTCCTTTTAAGGTGCAATTAAGATTTTTAATG
CATCAAAATTCATGAAATAATATTTAAATATGATTGGATTTTTACAAAAAATCAACCTCAAAAAG
GCTAAATTAC
Found at i:12500354 original size:74 final size:70
Alignment explanation
Indices: 12500276--12500437 Score: 227
Period size: 74 Copynumber: 2.3 Consensus size: 70
12500266 TTAAATCCGC
* * *
12500276 AAATAGTTGTATTGGGTACTAAAATAATAGAAATCAATAAAAGTTATAATTGCATG-GGAAAGCA
1 AAATAATTGTATTAGGTACTAAAATAATAGAAATCAAT--AA---ATAATTGCATGTGAAAAGCA
12500340 TCTAATCCAT
61 TCTAATCCAT
* *
12500350 AAATAATTGTATTAGGTACTAAAATAATAGAAATTAATAAATAATTGCATGTGAAAAGCGTCTAA
1 AAATAATTGTATTAGGTACTAAAATAATAGAAATCAATAAATAATTGCATGTGAAAAGCATCTAA
12500415 TCCAT
66 TCCAT
12500420 AAATAATTGTATTAGGTA
1 AAATAATTGTATTAGGTA
12500438 TGAAAAGCAT
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
69 11 0.13
70 34 0.41
72 2 0.02
74 35 0.43
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (70 bp):
AAATAATTGTATTAGGTACTAAAATAATAGAAATCAATAAATAATTGCATGTGAAAAGCATCTAA
TCCAT
Found at i:12500442 original size:37 final size:37
Alignment explanation
Indices: 12500334--12500544 Score: 158
Period size: 37 Copynumber: 5.9 Consensus size: 37
12500324 ATTGCATGGG
12500334 AAAGCATCTAATCCATAAATAATTGTATTAGGTACT-A
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTA-TGA
** ** ** *
12500371 AAATAATAGAAATTAATAAATAATTGCA-T--G--TGA
1 AAAGCAT-CTAATCCATAAATAATTGTATTAGGTATGA
*
12500404 AAAGCGTCTAATCCATAAATAATTGTATTAGGTATGA
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTATGA
*
12500441 AAAGCATCTAATCCATAAATAATTGTATTAGGTA-CA
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTATGA
* * * ** *
12500477 AAAACAACAGAAATTAATAAATAATTGCA-T--G--TGA
1 AAAGCATC--TAATCCATAAATAATTGTATTAGGTATGA
*
12500511 AAAGCGTCTAATCCATAAATAATTGTATTAGGTA
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTA
12500545 CTAAAACAAT
Statistics
Matches: 128, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
32 31 0.24
33 7 0.05
34 6 0.05
35 4 0.03
36 7 0.05
37 43 0.34
38 30 0.23
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (37 bp):
AAAGCATCTAATCCATAAATAATTGTATTAGGTATGA
Found at i:12500520 original size:107 final size:107
Alignment explanation
Indices: 12500334--12500544 Score: 395
Period size: 107 Copynumber: 2.0 Consensus size: 107
12500324 ATTGCATGGG
* * *
12500334 AAAGCATCTAATCCATAAATAATTGTATTAGGTACTAAAATAATAGAAATTAATAAATAATTGCA
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTACAAAAACAACAGAAATTAATAAATAATTGCA
12500399 TGTGAAAAGCGTCTAATCCATAAATAATTGTATTAGGTATGA
66 TGTGAAAAGCGTCTAATCCATAAATAATTGTATTAGGTATGA
12500441 AAAGCATCTAATCCATAAATAATTGTATTAGGTACAAAAACAACAGAAATTAATAAATAATTGCA
1 AAAGCATCTAATCCATAAATAATTGTATTAGGTACAAAAACAACAGAAATTAATAAATAATTGCA
12500506 TGTGAAAAGCGTCTAATCCATAAATAATTGTATTAGGTA
66 TGTGAAAAGCGTCTAATCCATAAATAATTGTATTAGGTA
12500545 CTAAAACAAT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (107 bp):
AAAGCATCTAATCCATAAATAATTGTATTAGGTACAAAAACAACAGAAATTAATAAATAATTGCA
TGTGAAAAGCGTCTAATCCATAAATAATTGTATTAGGTATGA
Found at i:12500678 original size:5 final size:5
Alignment explanation
Indices: 12500668--12500706 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
12500658 TAGCTACGTT
*
12500668 TATAA TATAA TATAA TATAA TATAA TATAA TATAG TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
12500707 TTGTACTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12502166 original size:35 final size:35
Alignment explanation
Indices: 12502120--12502189 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
12502110 TGTATATGTC
*
12502120 AAGTCAGTTGTAGGTTTATGCCCAGAAAACATTTG
1 AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
* *
12502155 AAGTCAGTTGTATATTTATGCCCAGAAAATATTTG
1 AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
12502190 GTTTATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (35 bp):
AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
Found at i:12508754 original size:22 final size:19
Alignment explanation
Indices: 12508740--12508776 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12508730 ACTAACCCTA
12508740 ATTAACTATCAAACTAA-T
1 ATTAACTATCAAACTAACT
*
12508758 ATTAACTATCAAATTAACT
1 ATTAACTATCAAACTAACT
12508777 TACATAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAACTATCAAACTAACT
Found at i:12511988 original size:14 final size:14
Alignment explanation
Indices: 12511969--12511998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12511959 TTTGAACCCA
*
12511969 CGAACCTTAAACCT
1 CGAACCTCAAACCT
12511983 CGAACCTCAAACCT
1 CGAACCTCAAACCT
12511997 CG
1 CG
12511999 CTCTGATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (14 bp):
CGAACCTCAAACCT
Found at i:12513828 original size:14 final size:14
Alignment explanation
Indices: 12513809--12513838 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12513799 TTTGAACCCA
*
12513809 CGAACCTTAAACCT
1 CGAACCTCAAACCT
12513823 CGAACCTCAAACCT
1 CGAACCTCAAACCT
12513837 CG
1 CG
12513839 CTCTGATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (14 bp):
CGAACCTCAAACCT
Found at i:12517242 original size:9 final size:9
Alignment explanation
Indices: 12517228--12517268 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
12517218 TTAAAACGAA
12517228 AAATAAAAT
1 AAATAAAAT
12517237 AAAT--AAT
1 AAATAAAAT
12517244 -AATAATAAT
1 AAATAA-AAT
12517253 AAATAAAAT
1 AAATAAAAT
12517262 AAATAAA
1 AAATAAA
12517269 TAACAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 3 0.11
7 3 0.11
9 17 0.61
10 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:12520158 original size:15 final size:15
Alignment explanation
Indices: 12520138--12520175 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12520128 AATAAATGTT
*
12520138 AAAGAAAAAAAAGGA
1 AAAGAAAAAAAAGCA
*
12520153 AAAGAAAAGAAAGCA
1 AAAGAAAAAAAAGCA
12520168 AAA-AAAAA
1 AAAGAAAAA
12520176 TTAGAAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGCA
Found at i:12521305 original size:19 final size:20
Alignment explanation
Indices: 12521281--12521325 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
12521271 AGATATTTAA
12521281 ATTAGTTTAATT-TAATAAT
1 ATTAGTTTAATTATAATAAT
12521300 ATTAGTTTAATTAATAATAAT
1 ATTAGTTTAATT-ATAATAAT
12521321 ATTAG
1 ATTAG
12521326 GTAATCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTAGTTTAATTATAATAAT
Found at i:12522628 original size:17 final size:17
Alignment explanation
Indices: 12522577--12522629 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
12522567 ATATTGAAAC
*
12522577 AATTTTT-AAAATTTAA
1 AATTTTTAAAAATTCAA
* *
12522593 TA-TTTTAAAAACTTGAA
1 AATTTTTAAAAA-TTCAA
12522610 AATTTTTAAAAATTCAA
1 AATTTTTAAAAATTCAA
12522627 AAT
1 AAT
12522630 ATATTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.13
16 5 0.17
17 12 0.40
18 9 0.30
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATTTTTAAAAATTCAA
Found at i:12522636 original size:19 final size:19
Alignment explanation
Indices: 12522591--12522636 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
12522581 TTTAAAATTT
*
12522591 AATATTTTAAAAACTTGAA
1 AATATTTTAAAAACTTCAA
12522610 AAT-TTTTAAAAA-TTCAA
1 AATATTTTAAAAACTTCAA
12522627 AATATATTTA
1 AATAT-TTTA
12522637 TATTAGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AATATTTTAAAAACTTCAA
Found at i:12522684 original size:31 final size:31
Alignment explanation
Indices: 12522649--12522787 Score: 113
Period size: 31 Copynumber: 4.5 Consensus size: 31
12522639 TTAGAGAGAT
* *
12522649 TAAATTTCAAATTTTATGTAAATATAGAAAC
1 TAAATTTTAAATTTTATGTAAGTATAGAAAC
* ** * * *
12522680 TAAATTTTTAATTTCGTGTGAGTATA-AGGAT
1 TAAATTTTAAATTTTATGTAAGTATAGA-AAC
* *
12522711 TAAACTTTAAATTTTATATAAGTATAGAAAC
1 TAAATTTTAAATTTTATGTAAGTATAGAAAC
* * *
12522742 TAAATTTTAAA-TTT-CGTACGAGTATAGAGAT
1 TAAATTTTAAATTTTATGTA--AGTATAGAAAC
12522773 TAAATTTTAAATTTT
1 TAAATTTTAAATTTT
12522788 GTATAAATAC
Statistics
Matches: 82, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
29 2 0.02
30 4 0.05
31 72 0.88
32 4 0.05
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (31 bp):
TAAATTTTAAATTTTATGTAAGTATAGAAAC
Found at i:12522714 original size:62 final size:61
Alignment explanation
Indices: 12522643--12522805 Score: 211
Period size: 62 Copynumber: 2.6 Consensus size: 61
12522633 TTTATATTAG
* * **
12522643 AGAGATTAAATTTCAAATTTTATGTAAATATAGAAACTAAATTTTTAATTTCGTGTGAGTAT
1 AGAGATTAAATTT-AAATTTTATATAAATATAGAAACTAAATTTTAAATTTCGTACGAGTAT
*
12522705 A-AGGATTAAACTTTAAATTTTATATAAGTATAGAAACTAAATTTTAAATTTCGTACGAGTAT
1 AGA-GATTAAA-TTTAAATTTTATATAAATATAGAAACTAAATTTTAAATTTCGTACGAGTAT
* * *
12522767 AGAGATTAAATTTTAAATTTTGTATAAATACATAAACTA
1 AGAGATTAAA-TTTAAATTTTATATAAATATAGAAACTA
12522806 TTTATATAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
61 1 0.01
62 83 0.94
63 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.40
Consensus pattern (61 bp):
AGAGATTAAATTTAAATTTTATATAAATATAGAAACTAAATTTTAAATTTCGTACGAGTAT
Found at i:12528058 original size:22 final size:23
Alignment explanation
Indices: 12528021--12528071 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
12528011 AAGAAGAGTG
12528021 TGATATACATGTCAAGGTTAATC
1 TGATATACATGTCAAGGTTAATC
* *
12528044 TGATATA-TTGTCAAGGTTTATC
1 TGATATACATGTCAAGGTTAATC
12528066 T-ATATA
1 TGATATA
12528072 AGCGGTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (23 bp):
TGATATACATGTCAAGGTTAATC
Found at i:12532070 original size:21 final size:21
Alignment explanation
Indices: 12532046--12532113 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
12532036 TAATGGTCAT
12532046 TAAAATTATATCATAAGTTAC
1 TAAAATTATATCATAAGTTAC
*
12532067 T-AAATTA-ATAATAAAGTTTAC
1 TAAAATTATATCAT-AAG-TTAC
* *
12532088 TAAAATTTTATCA-AAGTTAT
1 TAAAATTATATCATAAGTTAC
12532108 TAAAAT
1 TAAAAT
12532114 CAAAATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.10
20 18 0.46
21 9 0.23
22 5 0.13
23 3 0.08
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATTATATCATAAGTTAC
Found at i:12532113 original size:20 final size:20
Alignment explanation
Indices: 12532021--12532113 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 20
12532011 GTATAAAAAA
* * *
12532021 TTATTAAAATTGTATTAATGG
1 TTATTAAAATTTTATCAA-AG
* *
12532042 TCATTAAAATTATATCATAAG
1 TTATTAAAATTTTATCA-AAG
* *
12532063 TTACT-AAATTAATAAT-AAAG
1 TTATTAAAATT--TTATCAAAG
*
12532083 TTTACTAAAATTTTATCAAAG
1 -TTATTAAAATTTTATCAAAG
12532104 TTATTAAAAT
1 TTATTAAAAT
12532114 CAAAATTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
20 20 0.36
21 28 0.50
22 8 0.14
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (20 bp):
TTATTAAAATTTTATCAAAG
Found at i:12532308 original size:18 final size:18
Alignment explanation
Indices: 12532268--12532307 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
12532258 TGTATGCGCC
12532268 AAAAATTAATATTAAAAT
1 AAAAATTAATATTAAAAT
12532286 AAAAATT-A-ATTAAAATT
1 AAAAATTAATATTAAAA-T
12532303 AAAAA
1 AAAAA
12532308 AATAACCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTAATATTAAAAT
Found at i:12545073 original size:33 final size:32
Alignment explanation
Indices: 12545031--12545097 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
12545021 AAGTTAGGAC
12545031 TAGGATAAGTCGACAACTGATAAGAAAAAAAGT
1 TAGGATAAGTCGACAACTGA-AAGAAAAAAAGT
* * * *
12545064 TAGGATAAGTTGATAGCTGAAGGAAAAAAAGT
1 TAGGATAAGTCGACAACTGAAAGAAAAAAAGT
12545096 TA
1 TA
12545098 TTAATATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.21
Consensus pattern (32 bp):
TAGGATAAGTCGACAACTGAAAGAAAAAAAGT
Found at i:12545163 original size:2 final size:2
Alignment explanation
Indices: 12545156--12545182 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12545146 AAACCCATCT
12545156 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12545183 TGTTTTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12550111 original size:32 final size:31
Alignment explanation
Indices: 12550042--12550111 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
12550032 AATTAAATAA
* *
12550042 AAAAATTTCGATTGAATTTAAATCAAATTAT
1 AAAAATATCGATTAAATTTAAATCAAATTAT
*
12550073 ATAAAATATCGATTTAAATTTAAATTAAACTT-T
1 A-AAAATATCGA-TTAAATTTAAATCAAA-TTAT
12550106 AAAAAT
1 AAAAAT
12550112 TTATAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 14 0.42
33 16 0.48
34 2 0.06
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
AAAAATATCGATTAAATTTAAATCAAATTAT
Found at i:12550457 original size:5 final size:5
Alignment explanation
Indices: 12550447--12550483 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
12550437 ATAAAACAAG
*
12550447 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT CTTGT TT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TT
12550484 AATAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.78
Consensus pattern (5 bp):
TTTGT
Found at i:12555183 original size:21 final size:22
Alignment explanation
Indices: 12555154--12555203 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12555144 TGTTTGATGT
12555154 ATAAAATTAT-AA-ACAAATAAA
1 ATAAAATTATGAATA-AAATAAA
*
12555175 ATAATATTATGAATAAAATAAA
1 ATAAAATTATGAATAAAATAAA
*
12555197 ATTAAAT
1 ATAAAAT
12555204 AATATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAAATTATGAATAAAATAAA
Found at i:12555285 original size:22 final size:22
Alignment explanation
Indices: 12555241--12555285 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12555231 ATAATTGAAA
* **
12555241 TAAAATAATTTTATTTTTTAAT
1 TAAAATAATTATATTTTAAAAT
*
12555263 TAAAATTATTATATTTTAAAAT
1 TAAAATAATTATATTTTAAAAT
12555285 T
1 T
12555286 TATACAACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAAATAATTATATTTTAAAAT
Found at i:12555436 original size:30 final size:30
Alignment explanation
Indices: 12555400--12555456 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12555390 TATTAAGAAC
12555400 ATGATTAATTTTTCATACAATCTTATCTAA
1 ATGATTAATTTTTCATACAATCTTATCTAA
* *
12555430 ATGATTAATTTTTCTTGCAATCTTATC
1 ATGATTAATTTTTCATACAATCTTATC
12555457 ATTTTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (30 bp):
ATGATTAATTTTTCATACAATCTTATCTAA
Found at i:12571144 original size:2 final size:2
Alignment explanation
Indices: 12571137--12571166 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12571127 TACAATGCGC
12571137 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
12571167 GCTTTGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12577291 original size:3 final size:3
Alignment explanation
Indices: 12577283--12577324 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
12577273 TAAATAAATT
12577283 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
12577325 TATTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12579372 original size:23 final size:22
Alignment explanation
Indices: 12579329--12579372 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
12579319 ATAATTAGAT
*
12579329 ATTTATCATAATAAATTTAAAC
1 ATTTATCATAATAAATATAAAC
*
12579351 ATTTATCATGCATAAATATAAA
1 ATTTATCAT-AATAAATATAAA
12579373 AAAAAATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTATCATAATAAATATAAAC
Found at i:12580586 original size:8 final size:8
Alignment explanation
Indices: 12580563--12580611 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
12580553 ATTAATTAAT
*
12580563 TATTTATT
1 TATTTATA
12580571 TATTTATA
1 TATTTATA
12580579 TATTTATA
1 TATTTATA
* *
12580587 TAATGATA
1 TATTTATA
* *
12580595 TTTTTAAA
1 TATTTATA
12580603 TATTTATA
1 TATTTATA
12580611 T
1 T
12580612 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:12580631 original size:21 final size:22
Alignment explanation
Indices: 12580601--12580652 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12580591 GATATTTTTA
12580601 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12580621 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12580643 AATATTTTAT
1 AATATTTTAT
12580653 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:12581217 original size:2 final size:2
Alignment explanation
Indices: 12581210--12581243 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12581200 CTCTGATAGA
12581210 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12581244 AGGGGAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12589736 original size:21 final size:23
Alignment explanation
Indices: 12589701--12589750 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
12589691 ATAATTATTG
*
12589701 TTAT-AACGTGTAAATTTAAAAA
1 TTATAAACGTGTAAATATAAAAA
12589723 TT-TAAACGT-TAAATATAAAAA
1 TTATAAACGTGTAAATATAAAAA
12589744 TTATAAA
1 TTATAAA
12589751 GTCGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (23 bp):
TTATAAACGTGTAAATATAAAAA
Found at i:12590938 original size:26 final size:26
Alignment explanation
Indices: 12590902--12590952 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12590892 CTAAATTTTT
* *
12590902 TTTTTTTGATTAATACCATTAAATTG
1 TTTTTTAGATTAACACCATTAAATTG
12590928 TTTTTTAGATTAACACCATTAAATT
1 TTTTTTAGATTAACACCATTAAATT
12590953 TTATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (26 bp):
TTTTTTAGATTAACACCATTAAATTG
Found at i:12595670 original size:115 final size:120
Alignment explanation
Indices: 12595447--12595676 Score: 371
Period size: 115 Copynumber: 1.9 Consensus size: 120
12595437 TCCAATTATC
*
12595447 GTAAAATTAATTAAAATTGCAAACTTTCTATTAATTTAAAAGGTAAAAAAAATACAAGAAAAAGA
1 GTAAAATTAATTAAAATTCCAAACTTTCTATTAATTTAAAAGG--AAAAAAATACAAGAAAAAGA
*
12595512 AACTCAATTCTGCAGAGCCAAATCAAAGCAATTTAACTGATTTTTCAAAAATTAATT
64 AACCCAATTCTGCAGAGCCAAATCAAAGCAATTTAACTGATTTTTCAAAAATTAATT
* *
12595569 GTAAAATTAATTGAAATTCCAAACTTTCTGTTAATTTAAAA-G-AAAAAATAC-AG-AAAA-AAA
1 GTAAAATTAATTAAAATTCCAAACTTTCTATTAATTTAAAAGGAAAAAAATACAAGAAAAAGAAA
12595629 CCCAATTCTGCAGAGCCAAATCAAAGCAATTTAACTGATTTTTCAAAA
66 CCCAATTCTGCAGAGCCAAATCAAAGCAATTTAACTGATTTTTCAAAA
12595677 TTTTAATCAA
Statistics
Matches: 104, Mismatches: 4, Indels: 7
0.90 0.03 0.06
Matches are distributed among these distances:
115 50 0.48
116 4 0.04
117 2 0.02
118 9 0.09
121 1 0.01
122 38 0.37
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (120 bp):
GTAAAATTAATTAAAATTCCAAACTTTCTATTAATTTAAAAGGAAAAAAATACAAGAAAAAGAAA
CCCAATTCTGCAGAGCCAAATCAAAGCAATTTAACTGATTTTTCAAAAATTAATT
Found at i:12595889 original size:70 final size:71
Alignment explanation
Indices: 12595774--12595916 Score: 252
Period size: 70 Copynumber: 2.0 Consensus size: 71
12595764 GATTTTCACA
*
12595774 CCAAAAAAATCTAAAAAAAAAAAAGAGAGGGAAAGAGAATTATAGTACGTACACAATATACACTT
1 CCAAAAAAATC-AAAAAAAAAAAAGAGAGGGAAAGAGAATTATAGTACATACACAATATACACTT
12595839 TGGTTGC
65 TGGTTGC
*
12595846 CCAAAAAAATC-CAAAAAAAAAAGAGAGGGAAAGAGAATTATAGTACATACACAATATACACTTT
1 CCAAAAAAATCAAAAAAAAAAAAGAGAGGGAAAGAGAATTATAGTACATACACAATATACACTTT
12595910 GGTTGC
66 GGTTGC
12595916 C
1 C
12595917 ATTGATGAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
70 58 0.84
72 11 0.16
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (71 bp):
CCAAAAAAATCAAAAAAAAAAAAGAGAGGGAAAGAGAATTATAGTACATACACAATATACACTTT
GGTTGC
Found at i:12596065 original size:21 final size:20
Alignment explanation
Indices: 12596039--12596082 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
12596029 AATTTAAAGC
* *
12596039 TTTTTTATTTAATTTCTAAAT
1 TTTTTTAATTAATTACT-AAT
12596060 TTTTTTAATTAATTACTAAT
1 TTTTTTAATTAATTACTAAT
12596080 TTT
1 TTT
12596083 ATGATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTAATTAATTACTAAT
Found at i:12596341 original size:21 final size:20
Alignment explanation
Indices: 12596248--12596348 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 20
12596238 TAGATTTAAT
*
12596248 AATTTAA-AAAATAATATAA
1 AATTTAATAAAATTATATAA
*
12596267 TAATATAATAGACAATTATATAAAA
1 -AATTTAATA-A-AATTATAT--AA
* * *
12596292 AATATAAAAATATATTATTTAA
1 AATTTAATAA-A-ATTATATAA
12596314 AATTTTAATAAAATTATATATA
1 AA-TTTAATAAAATTATATA-A
12596336 AATTTAATAAAAT
1 AATTTAATAAAAT
12596349 AAAAAATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.09
21 19 0.29
22 9 0.14
23 15 0.23
24 14 0.22
25 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
AATTTAATAAAATTATATAA
Found at i:12598114 original size:16 final size:17
Alignment explanation
Indices: 12598093--12598132 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
12598083 TATTCTTGAT
12598093 AATTAAAATTA-TAAAA
1 AATTAAAATTATTAAAA
*
12598109 AATT-AAATTATTATAA
1 AATTAAAATTATTAAAA
12598125 AATTAAAA
1 AATTAAAA
12598133 ATTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAAATTATTAAAA
Found at i:12603091 original size:614 final size:611
Alignment explanation
Indices: 12601927--12603154 Score: 2251
Period size: 614 Copynumber: 2.0 Consensus size: 611
12601917 ATAGATTGCC
12601927 AATATCTACTAAGAAATCATCATCAAGATCCAATGGCCCACCTTCTGCCCATAAACTCCATGCCT
1 AATATCTACTAAGAAATCATCATCAAGATCCAATGGCCCACCTTCTGCCCATAAACTCCATGCCT
* * *
12601992 GCGGCAAAATGAAATCCTTTTAGCATTTATTAGTTCAAGATAAGTAACAAAACTGTCGACGCTTA
66 GCAGCAAAATGAAACCCTTTTAGCATTTATTAGTTCAAGATAAGTAACAAAACTGTCAACGCTTA
12602057 CTTGTTCAATAAGGTTTCCGCTGTGATTTGGATGACAAAACCTTCTAGTTCTTCTTCCACTTATT
131 CTTGTTCAATAAGGTTTCCGCTGTGATTTGGATGACAAAACCTTCTAGTTCTTCTTCCACTTATT
*
12602122 ATCTCCAACAATAGTATACCAAAGCTGCAACATATGATTTAACTGAAAACAGCCCATCAATAGCA
196 ATCTCCAACAATAGTATACCAAAGCTGCAACATATGATTTAACTGAAAACAGACCATCAATAGCA
*
12602187 TATTCTGGTGCCACATAACCATTGCACGACAGTCTCAAAAATATGCATTTCTATGGGGATTTATA
261 TATTCTGGTGCCACATAACCATTGCACAACAGTCTCAAAAATATGCATTTCTATGGGGATTTATA
* *
12602252 TCAAATTATGTTGCATAAACACTTACTAAGTTCCAACCACTCTGTTTGTATTGGCTTCAGTCTGG
326 TCAAATTATGTTGCATAAACACTTACAAAGTTCCAAACACTCTGTTTGTATTGGCTTCAGTCTGG
12602317 TCTCCTCCAAAAGTTCTTGCCGTGCCAAAATCTGAAATTTCCGAGTTCATCTTGCTATCAAGCAG
391 TCTCCTCCAAAAGTTCTTGCCGTGCCAAAATCTGAAATTTCCGAGTTCATCTTGCTATCAAGCAG
*
12602382 AACATTACTAGCTTTTCGATCTCTATGAATACTGCTCAATCTGGAATCTAGATGAAGATAGAGTA
456 AACATTACTAGCTTTTCGATCTCTATGAATACTGCTCAATCTGAAATCTAGATGAAGATAGAGTA
*
12602447 GTCCCCTAGCAATCCCACAGATAATTTGGAAACGCTTGGACCAATTTAATACTTGGCGTCTTGTT
521 GTCCCCTAGCAATCCCACAGATAATTTGGAAACGCCTGGACCAATTTAATACTTGGCGTCTTGTT
12602512 TGATCTGCCAAGTATGCATTCATGCT
586 TGATCTGCCAAGTATGCATTCATGCT
**
12602538 AATATCTACTAAGAAATCATCATCAAGATCCAATGGCCCACCTTCTTTCCATAAACTCCATGCCT
1 AATATCTACTAAGAAATCATCATCAAGATCCAATGGCCCACCTTCTGCCCATAAACTCCATGCCT
12602603 GCAGCAAAATGAAACCCTTTTAGCATTTATTAGTTCAAGATAAGTAACAAAACTGTCAACGCTTA
66 GCAGCAAAATGAAACCCTTTTAGCATTTATTAGTTCAAGATAAGTAACAAAACTGTCAACGCTTA
*
12602668 CTTGTTCAATAAGGTTTCCGCTGTGATTTGGATGATAAAA-CTCTCTAGTTCTTCTTCCACTTAT
131 CTTGTTCAATAAGGTTTCCGCTGTGATTTGGATGACAAAACCT-TCTAGTTCTTCTTCCACTTAT
12602732 TATCTCCAACAATAGTATACCAAAGCTGCAAACATATGATTTAACTGAAAACAGACCATCAATAG
195 TATCTCCAACAATAGTATACCAAAGCTGC-AACATATGATTTAACTGAAAACAGACCATCAATAG
* *
12602797 CATATTCTGTTGCCATATAACCATTGCACAACAGTCTCAGAAAAATATGCATTTCTATGGGGATT
259 CATATTCTGGTGCCACATAACCATTGCACAACAGTCTC--AAAAATATGCATTTCTATGGGGATT
* *
12602862 TGTATCAAATTATGTTGCGTAAACACTTACAAAGTTCCAAACACTCTGTTTGTATTGGCTTCAGT
322 TATATCAAATTATGTTGCATAAACACTTACAAAGTTCCAAACACTCTGTTTGTATTGGCTTCAGT
12602927 CTGGTCTCCTCCAAAAGTTCTTGCCGTGCCAAAATCTGAAATTTCCGAGTTCATCTTGCTATCAA
387 CTGGTCTCCTCCAAAAGTTCTTGCCGTGCCAAAATCTGAAATTTCCGAGTTCATCTTGCTATCAA
*
12602992 GCAGAACATTACTAGCTTTTTGATCTCTATGAATACTGCTCAATCTGAAATCTAGATGAAGATAG
452 GCAGAACATTACTAGCTTTTCGATCTCTATGAATACTGCTCAATCTGAAATCTAGATGAAGATAG
*
12603057 AGTAGTCCCCTAGCAATCCCACAGATAATTTGGAAACGCCTGGACCAATTTAGTACTTGGCGTCT
517 AGTAGTCCCCTAGCAATCCCACAGATAATTTGGAAACGCCTGGACCAATTTAATACTTGGCGTCT
12603122 TGTTTGATCTGCCAAGTATGCATTCATGCT
582 TGTTTGATCTGCCAAGTATGCATTCATGCT
12603152 AAT
1 AAT
12603155 CCTGCATCTT
Statistics
Matches: 595, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
610 2 0.00
611 214 0.36
612 69 0.12
614 310 0.52
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (611 bp):
AATATCTACTAAGAAATCATCATCAAGATCCAATGGCCCACCTTCTGCCCATAAACTCCATGCCT
GCAGCAAAATGAAACCCTTTTAGCATTTATTAGTTCAAGATAAGTAACAAAACTGTCAACGCTTA
CTTGTTCAATAAGGTTTCCGCTGTGATTTGGATGACAAAACCTTCTAGTTCTTCTTCCACTTATT
ATCTCCAACAATAGTATACCAAAGCTGCAACATATGATTTAACTGAAAACAGACCATCAATAGCA
TATTCTGGTGCCACATAACCATTGCACAACAGTCTCAAAAATATGCATTTCTATGGGGATTTATA
TCAAATTATGTTGCATAAACACTTACAAAGTTCCAAACACTCTGTTTGTATTGGCTTCAGTCTGG
TCTCCTCCAAAAGTTCTTGCCGTGCCAAAATCTGAAATTTCCGAGTTCATCTTGCTATCAAGCAG
AACATTACTAGCTTTTCGATCTCTATGAATACTGCTCAATCTGAAATCTAGATGAAGATAGAGTA
GTCCCCTAGCAATCCCACAGATAATTTGGAAACGCCTGGACCAATTTAATACTTGGCGTCTTGTT
TGATCTGCCAAGTATGCATTCATGCT
Found at i:12606055 original size:20 final size:21
Alignment explanation
Indices: 12606030--12606068 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
12606020 TCGAATATTC
12606030 AGATCATTCAC-TTTTCTTTA
1 AGATCATTCACATTTTCTTTA
12606050 AGATCATTCACATTTTCTT
1 AGATCATTCACATTTTCTT
12606069 CAAGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (21 bp):
AGATCATTCACATTTTCTTTA
Found at i:12626981 original size:21 final size:23
Alignment explanation
Indices: 12626957--12627011 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
12626947 TATATTATAT
12626957 TTAATTTATATTTTAA-A-AAAA
1 TTAATTTATATTTTAACATAAAA
12626978 TTAA--TATCATTTTAACATAAAA
1 TTAATTTAT-ATTTTAACATAAAA
12627000 TT-ATTTA-ATTTT
1 TTAATTTATATTTT
12627012 TTTAAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 3 0.10
20 7 0.24
21 11 0.38
22 6 0.21
23 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATTTATATTTTAACATAAAA
Found at i:12629856 original size:15 final size:15
Alignment explanation
Indices: 12629833--12629880 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12629823 CAACACAAAA
12629833 TAATATAATATTATT
1 TAATATAATATTATT
* *
12629848 TAATTTAATCTTATTT
1 TAATATAATATTA-TT
*
12629864 ATAATATAATCTTATT
1 -TAATATAATATTATT
12629880 T
1 T
12629881 TATCTTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 12 0.43
16 4 0.14
17 12 0.43
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATATAATATTATT
Found at i:12629873 original size:17 final size:17
Alignment explanation
Indices: 12629832--12629880 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
12629822 ACAACACAAA
*
12629832 ATAATATAATATTA-TT
1 ATAATATAATCTTATTT
*
12629848 -TAATTTAATCTTATTT
1 ATAATATAATCTTATTT
12629864 ATAATATAATCTTATTT
1 ATAATATAATCTTATTT
12629881 TATCTTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 15 0.54
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATATAATCTTATTT
Found at i:12630480 original size:67 final size:67
Alignment explanation
Indices: 12630372--12630505 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
12630362 CTTTATCTGT
*
12630372 GAAATTTCAATATTTTAATTATAAAGATGGGAAAAATATTGGAATGTCATGGTTACAATGCAATT
1 GAAATTTCAATATTTTAATCATAAAGATGGGAAAAATATTGGAATGTCATGGTTACAATGCAATT
12630437 CA
66 CA
*
12630439 GAAATTTCAATATTTTAATCATAAAGATGGGAAAAATATTGGAATGTCATGGTTACAATGCACTT
1 GAAATTTCAATATTTTAATCATAAAGATGGGAAAAATATTGGAATGTCATGGTTACAATGCAATT
12630504 CA
66 CA
12630506 TTCAAGATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (67 bp):
GAAATTTCAATATTTTAATCATAAAGATGGGAAAAATATTGGAATGTCATGGTTACAATGCAATT
CA
Found at i:12632909 original size:23 final size:23
Alignment explanation
Indices: 12632861--12632912 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12632851 ATGACTCATT
* * * *
12632861 AAATAGGATGATATTTTTAGATA
1 AAATAAGATGATATTTTAAAAAA
12632884 AAATAAGATGATATTTTAAAAAA
1 AAATAAGATGATATTTTAAAAAA
12632907 AAATAA
1 AAATAA
12632913 TTTTAGAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
AAATAAGATGATATTTTAAAAAA
Found at i:12636054 original size:3 final size:3
Alignment explanation
Indices: 12636037--12636079 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
12636027 TTAAAAATAA
*
12636037 ATT ATT AGT ATTT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12636080 AAAATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12643963 original size:9 final size:9
Alignment explanation
Indices: 12643951--12643985 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
12643941 TATTTTTTCT
12643951 TAAAATATA
1 TAAAATATA
12643960 TAAAATATA
1 TAAAATATA
12643969 TTAATAATATA
1 -TAA-AATATA
12643980 TAAAAT
1 TAAAAT
12643986 TTTTTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.50
10 6 0.25
11 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAAATATA
Found at i:12660443 original size:2 final size:2
Alignment explanation
Indices: 12660438--12660465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12660428 ATATATATAG
12660438 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12660466 TGTCATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12663688 original size:27 final size:27
Alignment explanation
Indices: 12663665--12663719 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12663655 CATACATGCA
12663665 TATACATAAAGAGAGGTGCAACATAAT
1 TATACATAAAGAGAGGTGCAACATAAT
* *
12663692 TATACATAAAGAGAGGTGCGATATAAT
1 TATACATAAAGAGAGGTGCAACATAAT
12663719 T
1 T
12663720 TATAACGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (27 bp):
TATACATAAAGAGAGGTGCAACATAAT
Found at i:12664525 original size:33 final size:33
Alignment explanation
Indices: 12664464--12664528 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
12664454 CCTTTGTTCT
* *
12664464 TGATACATTTGAGGTGAAAGATATATTTGAGGG
1 TGATACATTTGAGATGAAAGATACATTTGAGGG
*
12664497 TGATACATTTGTGAT-AAACGATACATTTGAGG
1 TGATACATTTGAGATGAAA-GATACATTTGAGG
12664529 AGATGAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (33 bp):
TGATACATTTGAGATGAAAGATACATTTGAGGG
Found at i:12664908 original size:6 final size:6
Alignment explanation
Indices: 12664897--12664970 Score: 76
Period size: 6 Copynumber: 12.3 Consensus size: 6
12664887 CCAAAATTAA
* * * * *
12664897 CACCAT CACCAT CACTAT CACTAT CATCAT CACTAT CACCAT CATCAT
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT
* * *
12664945 CACTAT CACCAT CATCAT CATCAT CA
1 CACCAT CACCAT CACCAT CACCAT CA
12664971 TCTGGACTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (6 bp):
CACCAT
Found at i:12664927 original size:3 final size:3
Alignment explanation
Indices: 12664919--12664972 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
12664909 CACTATCACT
* *
12664919 ATC ATC ATC A-C TATC ACC ATC ATC ATC A-C TATC ACC ATC ATC ATC
1 ATC ATC ATC ATC -ATC ATC ATC ATC ATC ATC -ATC ATC ATC ATC ATC
12664964 ATC ATC ATC
1 ATC ATC ATC
12664973 TGGACTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:12664970 original size:18 final size:18
Alignment explanation
Indices: 12664897--12664964 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
12664887 CCAAAATTAA
*
12664897 CACCATCACCATCACTAT
1 CACCATCATCATCACTAT
*
12664915 CACTATCATCATCACTAT
1 CACCATCATCATCACTAT
12664933 CACCATCATCATCACTAT
1 CACCATCATCATCACTAT
12664951 CACCATCATCATCA
1 CACCATCATCATCA
12664965 TCATCATCTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (18 bp):
CACCATCATCATCACTAT
Found at i:12670414 original size:104 final size:105
Alignment explanation
Indices: 12670249--12670503 Score: 309
Period size: 104 Copynumber: 2.4 Consensus size: 105
12670239 AAAAATTTGG
** * * * * *
12670249 GAAAGTAAAAATAGAAGATTTAATGAGATTTTGGTACACAAAGGCTACGTTTCTTACATAAAAAA
1 GAAAGTAAAAGGAAAAGATTTGATGAGATTTTAGTACACAAAGACTACATTTCTTACATAAAAAA
* * *
12670314 GGTAGTCTTTGTAGTTTTTTGGTTA-AAAAAAATTCTTAA
66 GGTAGTCTATGTAGTTTTTTGCTTATAAAAAAATTATTAA
* * *
12670353 -AAATGTAAAAGGAAAAGATTTGATAAGATTTTAGTGCACAAAGATTACATTTCTTACATAAAAA
1 GAAA-GTAAAAGGAAAAGATTTGATGAGATTTTAGTACACAAAGACTACATTTCTTACATAAAAA
**
12670417 AGGTAGTCTATGTAGTTTTTTGCTTATAAAAATGTTATTAA
65 AGGTAGTCTATGTAGTTTTTTGCTTATAAAAAAATTATTAA
* * *
12670458 GAAAGTAAAAGGAAAATATTTGGTGAGATTTT-GATACACAATGACT
1 GAAAGTAAAAGGAAAAGATTTGATGAGATTTTAG-TACACAAAGACT
12670504 GCTTTTTTTG
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
103 3 0.02
104 75 0.60
105 45 0.36
106 3 0.02
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (105 bp):
GAAAGTAAAAGGAAAAGATTTGATGAGATTTTAGTACACAAAGACTACATTTCTTACATAAAAAA
GGTAGTCTATGTAGTTTTTTGCTTATAAAAAAATTATTAA
Found at i:12670498 original size:105 final size:104
Alignment explanation
Indices: 12670263--12670589 Score: 308
Period size: 104 Copynumber: 3.2 Consensus size: 104
12670253 GTAAAAATAG
* * * * *
12670263 AAGATTTAATGAGATTTTGGTACACAAAGGCTACGTTTCTTACATAAAAAAGGTAGTCTTTGTAG
1 AAGATTTGATGAGATTTTGATACACAAAGACTACATTTCTTACATAAAAAAGGTAGTCTATGTAG
* *
12670328 TTTTTTGGTTAAAAAAAATTCTTAAAAATGTAAAAGGAA
66 TTTTTTGCTTAAAAAAAATTATTAAAAATGTAAAAGGAA
* * *
12670367 AAGATTTGATAAGATTTT-AGTGCACAAAGATTACATTTCTTACATAAAAAAGGTAGTCTATGTA
1 AAGATTTGATGAGATTTTGA-TACACAAAGACTACATTTCTTACATAAAAAAGGTAGTCTATGTA
**
12670431 GTTTTTTGCTTATAAAAATGTTATTAAGAAA-GTAAAAGGAA
65 GTTTTTTGCTTA-AAAAAAATTATTAA-AAATGTAAAAGGAA
* * * * * * * * *
12670472 AATATTTGGTGAGATTTTGATACACAATGACTGCTTTTTTTGCAT-AAGAAGGTAGT-TTTGTA-
1 AAGATTTGATGAGATTTTGATACACAAAGACTACATTTCTTACATAAAAAAGGTAGTCTATGTAG
* * * * *
12670534 ATTTTTGTTGTAAAAAAGAATTCTTGAAAAA-CTAAAA-GAT
66 TTTTTTGCT-TAAAAAA-AATTATT-AAAAATGTAAAAGGAA
*
12670574 AAGATTTGGTGAGATT
1 AAGATTTGATGAGATT
12670590 CATTAACTTC
Statistics
Matches: 184, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
102 29 0.16
103 19 0.10
104 78 0.42
105 54 0.29
106 4 0.02
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (104 bp):
AAGATTTGATGAGATTTTGATACACAAAGACTACATTTCTTACATAAAAAAGGTAGTCTATGTAG
TTTTTTGCTTAAAAAAAATTATTAAAAATGTAAAAGGAA
Found at i:12671030 original size:9 final size:9
Alignment explanation
Indices: 12671005--12671038 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12670995 CTCCATTTGT
*
12671005 TATTAATAG
1 TATTAATAA
12671014 TA-TAATAA
1 TATTAATAA
12671022 TATTAATAA
1 TATTAATAA
12671031 TATTAATA
1 TATTAATA
12671039 TAATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TATTAATAA
Found at i:12671044 original size:23 final size:23
Alignment explanation
Indices: 12671014--12671132 Score: 68
Period size: 23 Copynumber: 5.1 Consensus size: 23
12671004 TTATTAATAG
12671014 TATAATAATATTAATAATATTAA
1 TATAATAATATTAATAATATTAA
* * *
12671037 TATAATAATTTTATTATTTATTAA
1 TATAATAATATTAATA-ATATTAA
* * *
12671061 TATTATGTTATATT-AT-TTATTAA
1 TA-TA-ATAATATTAATAATATTAA
* *
12671084 TATTATATTATTTATATAATA--AA
1 TATAATAATA-TTA-ATAATATTAA
*
12671107 TATAATAATATTTATTAATA-TAA
1 TATAATAATA-TTAATAATATTAA
12671130 TAT
1 TAT
12671133 TTATATAATA
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
21 3 0.04
22 8 0.11
23 42 0.58
24 10 0.14
25 5 0.07
26 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
TATAATAATATTAATAATATTAA
Found at i:12671098 original size:41 final size:41
Alignment explanation
Indices: 12671014--12671163 Score: 143
Period size: 41 Copynumber: 3.7 Consensus size: 41
12671004 TTATTAATAG
* *
12671014 TATAAT-AATATTAATAATATTAATATAATAATTTTATTATTTA
1 TATAATAAATA-TAATAATATTTAT-TAAT-ATTATATTATTTA
* * * *
12671057 T-TAATATTATGTTATATTATTTATTAATATTATATTATTTA
1 TATAATA-AATATAATAATATTTATTAATATTATATTATTTA
12671098 TATAATAAATATAATAATATTTATTAATA-TA-A-TATTTA
1 TATAATAAATATAATAATATTTATTAATATTATATTATTTA
* *
12671136 TATAATAAA-ATTATTAT-TTTATTAATAT
1 TATAATAAATATAATAATATTTATTAATAT
12671164 AATAATTTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
36 10 0.11
37 6 0.07
38 15 0.16
39 1 0.01
40 2 0.02
41 31 0.34
42 13 0.14
43 11 0.12
44 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (41 bp):
TATAATAAATATAATAATATTTATTAATATTATATTATTTA
Found at i:12671143 original size:38 final size:37
Alignment explanation
Indices: 12671074--12671167 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 37
12671064 TATGTTATAT
12671074 TATTTATTAATATTATATTATTTATATAATAAATATAATAA
1 TATTTATTAATA-TA-A-TATTTATATAATAAA-ATAATAA
* *
12671115 TATTTATTAATATAATATTTATATAATAAAATTATTA
1 TATTTATTAATATAATATTTATATAATAAAATAATAA
12671152 T-TTTATTAATATAATA
1 TATTTATTAATATAATA
12671168 ATTTTAGCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
36 15 0.29
37 6 0.12
38 15 0.29
39 1 0.02
40 2 0.04
41 12 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATTTATTAATATAATATTTATATAATAAAATAATAA
Found at i:12671167 original size:41 final size:39
Alignment explanation
Indices: 12671070--12671167 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 39
12671060 ATATTATGTT
*
12671070 ATATTA-TTTATTAATAT--TATATTATTTATATAATAA
1 ATATTATTTTATTAATATAATATAATATTTATATAATAA
* ** *
12671106 ATATAATAATATTTAT-TAATATAATATTTATATAATAAA
1 ATATTATTTTATTAATATAATATAATATTTATATAAT-AA
12671145 ATTATTATTTTATTAATATAATA
1 A-TATTATTTTATTAATATAATA
12671168 ATTTTAGCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
36 6 0.13
37 6 0.13
38 16 0.34
39 3 0.06
40 11 0.23
41 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
ATATTATTTTATTAATATAATATAATATTTATATAATAA
Found at i:12679905 original size:14 final size:14
Alignment explanation
Indices: 12679868--12679905 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
12679858 AAATATTTGT
12679868 TTTTATTTTTAAAAA
1 TTTTA-TTTTAAAAA
12679883 TCTTT-TTTTAAAAA
1 T-TTTATTTTAAAAA
12679897 TTTTATTTT
1 TTTTATTTT
12679906 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 14 0.67
15 1 0.05
16 3 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATTTTAAAAA
Found at i:12683176 original size:24 final size:24
Alignment explanation
Indices: 12683149--12683199 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
12683139 CTATTTGGAC
*
12683149 TTAGTGTTTTACTTGTTGGGCTTG
1 TTAGTGTTTTACTAGTTGGGCTTG
12683173 TTAGTGTTTTACTAGTTGGGCTTG
1 TTAGTGTTTTACTAGTTGGGCTTG
12683197 TTA
1 TTA
12683200 CTTTATTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.27, T:0.53
Consensus pattern (24 bp):
TTAGTGTTTTACTAGTTGGGCTTG
Found at i:12687093 original size:61 final size:60
Alignment explanation
Indices: 12686965--12687380 Score: 508
Period size: 60 Copynumber: 6.9 Consensus size: 60
12686955 TTGTGTAGGA
* *
12686965 AAAATTGATACTTTCAACTTTTTCCCAAAAATA--TTTTTTGGAAA-TTT-ATTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
*
12687022 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAATTTTGATTTCCAAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
*** *
12687083 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTCAAAAATTTTGGTTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
* * *
12687143 AAAATTGATATTTTCAACTTTTCCTCAAAAATATTTTTTTTCGAAACTTT-ATTCTT-AAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTGAAATTTTGATT-TTCAAGG
* ** * * **
12687203 AAAATTGATACTTTTAACTTTTCCCCAAAAACCTTTTTTTTTTAAA-TTT-ATTTTTAAAA
1 AAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
12687262 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTTTG-AAATTTTGATTTTCAAGG
* *
12687325 AAAATTGATACTTTCAGCTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTT
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTTGAAATTTTGATTTT
12687381 TTATTTAAAG
Statistics
Matches: 312, Mismatches: 31, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
56 6 0.02
57 26 0.08
58 5 0.02
59 44 0.14
60 108 0.35
61 72 0.23
62 12 0.04
63 39 0.12
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
Done.