Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 115 of 144
Found at i:26687648 original size:28 final size:28
Alignment explanation
Indices: 26687616--26687676 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
26687606 AGCTAGCTAG
*
26687616 GCAAAGATGATTAGAGAGCTCGCACAAA
1 GCAAAGATGAATAGAGAGCTCGCACAAA
* * * *
26687644 GCAAA-CTTAATAGTGAGCTCGCATAAA
1 GCAAAGATGAATAGAGAGCTCGCACAAA
26687671 GCAAAG
1 GCAAAG
26687677 CTAAAACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (28 bp):
GCAAAGATGAATAGAGAGCTCGCACAAA
Found at i:26688456 original size:25 final size:25
Alignment explanation
Indices: 26688428--26688477 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
26688418 CGCACTTTGA
* *
26688428 CTTGCAAACCCTATTCGTAACTTAC
1 CTTGAAAACCCTATTCGCAACTTAC
*
26688453 CTTGAAAACTCTATTCGCAACTTAC
1 CTTGAAAACCCTATTCGCAACTTAC
26688478 TTGGCGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (25 bp):
CTTGAAAACCCTATTCGCAACTTAC
Found at i:26690378 original size:23 final size:22
Alignment explanation
Indices: 26690330--26690379 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
26690320 TAAAACAAAT
* *
26690330 TATGTATTTAAAAAGAATTAAA
1 TATGTATGTAAAAAGAAATAAA
*
26690352 -ATGTCATGTAAAAATAAATAAA
1 TATGT-ATGTAAAAAGAAATAAA
26690374 TATGTA
1 TATGTA
26690380 CATAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (22 bp):
TATGTATGTAAAAAGAAATAAA
Found at i:26690691 original size:19 final size:19
Alignment explanation
Indices: 26690652--26690693 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
26690642 ACAAAGATAT
26690652 AAATAGCATAAAAAATAAA
1 AAATAGCATAAAAAATAAA
26690671 AAATA-CATAAAATAAATAAA
1 AAATAGCAT-AAA-AAATAAA
26690691 AAA
1 AAA
26690694 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 8 0.38
20 10 0.48
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATAGCATAAAAAATAAA
Found at i:26693580 original size:40 final size:40
Alignment explanation
Indices: 26693544--26693624 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
26693534 AAACTGTAGG
* * *
26693544 CGTTACAACATTGTTATTGTACTAGTCGTGATACTGTGAA
1 CGTTACAACATTGTAACTATACTAGTCGTGATACTGTGAA
* *
26693584 TGTTGCAACATTGTAACTATACTAGTCGTGATACTGTGAA
1 CGTTACAACATTGTAACTATACTAGTCGTGATACTGTGAA
26693624 C
1 C
26693625 TTTGTATGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (40 bp):
CGTTACAACATTGTAACTATACTAGTCGTGATACTGTGAA
Found at i:26698930 original size:46 final size:46
Alignment explanation
Indices: 26698863--26698960 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 46
26698853 CAATATAATG
*
26698863 GTTTTGCCTTTTAACCTAATGAGTAAACATTTATTAAAACGACATA
1 GTTTTGCCTTTTAACCTAATGAATAAACATTTATTAAAACGACATA
26698909 GTTTTGCCTTTTAACCTAATGAATAAACATTTATTAAAACGACATA
1 GTTTTGCCTTTTAACCTAATGAATAAACATTTATTAAAACGACATA
*
26698955 ATTTTG
1 GTTTTG
26698961 AATTAATGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (46 bp):
GTTTTGCCTTTTAACCTAATGAATAAACATTTATTAAAACGACATA
Found at i:26700160 original size:29 final size:26
Alignment explanation
Indices: 26700128--26700184 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
26700118 TTTTAGTCCT
26700128 AATTTGTTTGAATTAAAAAAATAAAATCA
1 AATTT-TTTGAA-T-AAAAAATAAAATCA
*
26700157 AA--TTTTGTATAAAAAATAAAATCA
1 AATTTTTTGAATAAAAAATAAAATCA
26700181 AATT
1 AATT
26700185 AATTACAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
24 16 0.64
25 1 0.04
26 5 0.20
27 1 0.04
29 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (26 bp):
AATTTTTTGAATAAAAAATAAAATCA
Found at i:26700551 original size:209 final size:209
Alignment explanation
Indices: 26700191--26700609 Score: 838
Period size: 209 Copynumber: 2.0 Consensus size: 209
26700181 AATTAATTAC
26700191 AGTACTAAACAATTTCTGTTAAATTTGAATAAGTGATGTTTTATTATTCAAAGTCCTGAAAAAAC
1 AGTACTAAACAATTTCTGTTAAATTTGAATAAGTGATGTTTTATTATTCAAAGTCCTGAAAAAAC
26700256 AAGAGTATTAAAATTTAAAAAATATAAAGAGTAAAGGGACTGAAGACGGAATTAGACCAGAGAAA
66 AAGAGTATTAAAATTTAAAAAATATAAAGAGTAAAGGGACTGAAGACGGAATTAGACCAGAGAAA
26700321 AAATTGATAAAAAAATATCTAAAAAACATGGGACTGAATGCATAATTAAGCCAAAAGTATTTGTT
131 AAATTGATAAAAAAATATCTAAAAAACATGGGACTGAATGCATAATTAAGCCAAAAGTATTTGTT
26700386 TAGAGTGGGATTTG
196 TAGAGTGGGATTTG
26700400 AGTACTAAACAATTTCTGTTAAATTTGAATAAGTGATGTTTTATTATTCAAAGTCCTGAAAAAAC
1 AGTACTAAACAATTTCTGTTAAATTTGAATAAGTGATGTTTTATTATTCAAAGTCCTGAAAAAAC
26700465 AAGAGTATTAAAATTTAAAAAATATAAAGAGTAAAGGGACTGAAGACGGAATTAGACCAGAGAAA
66 AAGAGTATTAAAATTTAAAAAATATAAAGAGTAAAGGGACTGAAGACGGAATTAGACCAGAGAAA
26700530 AAATTGATAAAAAAATATCTAAAAAACATGGGACTGAATGCATAATTAAGCCAAAAGTATTTGTT
131 AAATTGATAAAAAAATATCTAAAAAACATGGGACTGAATGCATAATTAAGCCAAAAGTATTTGTT
26700595 TAGAGTGGGATTTG
196 TAGAGTGGGATTTG
26700609 A
1 A
26700610 ACCCACGCCC
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 210 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (209 bp):
AGTACTAAACAATTTCTGTTAAATTTGAATAAGTGATGTTTTATTATTCAAAGTCCTGAAAAAAC
AAGAGTATTAAAATTTAAAAAATATAAAGAGTAAAGGGACTGAAGACGGAATTAGACCAGAGAAA
AAATTGATAAAAAAATATCTAAAAAACATGGGACTGAATGCATAATTAAGCCAAAAGTATTTGTT
TAGAGTGGGATTTG
Found at i:26702827 original size:8 final size:8
Alignment explanation
Indices: 26702805--26702862 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
26702795 CAAAATGATT
26702805 ATTTTATAA
1 ATTTT-TAA
*
26702814 AATTTTAA
1 ATTTTTAA
*
26702822 ATTTTTTA
1 ATTTTTAA
*
26702830 ATTTTCAA
1 ATTTTTAA
*
26702838 AATTTTAA
1 ATTTTTAA
*
26702846 ATTTTTTA
1 ATTTTTAA
*
26702854 TTTTTTAA
1 ATTTTTAA
26702862 A
1 A
26702863 AATATATAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
8 33 0.89
9 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:26702833 original size:25 final size:23
Alignment explanation
Indices: 26702803--26702877 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
26702793 TCCAAAATGA
26702803 TTATTTTATAAAATTTTAAATTTT
1 TTATTTT-TAAAATTTTAAATTTT
*
26702827 TTAATTTTCAAAATTTTAAATTTT
1 TT-ATTTTTAAAATTTTAAATTTT
* *
26702851 TTATTTTTTAAAAATATATAATTTT
1 TTA-TTTTTAAAATTTTA-AATTTT
26702876 TT
1 TT
26702878 TAAAATTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 1 0.02
24 30 0.68
25 13 0.30
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTTTAAAATTTTAAATTTT
Found at i:26702891 original size:18 final size:19
Alignment explanation
Indices: 26702854--26702893 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
26702844 AAATTTTTTA
*
26702854 TTTTTTAAAAATATATAAT
1 TTTTTTAAAAATACATAAT
*
26702873 TTTTTTAAAATTACA-AAT
1 TTTTTTAAAAATACATAAT
26702891 TTT
1 TTT
26702894 AGAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTTAAAAATACATAAT
Found at i:26706384 original size:2 final size:2
Alignment explanation
Indices: 26706377--26706407 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26706367 ATTAAGAGGG
26706377 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
26706408 CTTGAGTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:26717138 original size:16 final size:16
Alignment explanation
Indices: 26717089--26717138 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
26717079 ATTAATTTTT
26717089 AAAATT-AAAAAAATA
1 AAAATTAAAAAAAATA
*
26717104 AAATTATTAAAAAATATA
1 AAA--ATTAAAAAAAATA
26717122 AAAATTAAAAAAAATA
1 AAAATTAAAAAAAATA
26717138 A
1 A
26717139 CTTTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 13 0.43
17 3 0.10
18 11 0.37
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATTAAAAAAAATA
Found at i:26719212 original size:21 final size:21
Alignment explanation
Indices: 26719182--26719260 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 21
26719172 TAATATATTA
26719182 ATAATA-TAAAAAATTAAAAT
1 ATAATATTAAAAAATTAAAAT
*
26719202 ATAATTTTAAAAGTAATATAAAAT
1 ATAATATTAAAA--AAT-TAAAAT
* *
26719226 ATTATATTAATAATATTAAAAGT
1 ATAATATTAA-AAAATTAAAA-T
26719249 AATAATA-TAAAA
1 -ATAATATTAAAA
26719261 GTAATAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.11
21 5 0.11
22 7 0.15
23 9 0.19
24 19 0.40
25 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATAATATTAAAAAATTAAAAT
Found at i:26719232 original size:53 final size:50
Alignment explanation
Indices: 26719160--26719307 Score: 183
Period size: 50 Copynumber: 2.9 Consensus size: 50
26719150 AAATGTCTCG
* * ***
26719160 AATAATATAAAATAATATATTAATAATATAAAAAATTAA-AATATAATTTT
1 AATAATATAAAATATTATATTAATAATAT-AAAAAGTAATAATATAAAAGT
*
26719210 AAAAGTAATATAAAATATTATATTAATAATATTAAAAGTAATAATATAAAAGT
1 --AA-TAATATAAAATATTATATTAATAATATAAAAAGTAATAATATAAAAGT
*
26719263 AATAATATAAAATATTATATTAATAATATTAAAAGTAATAA-ATAA
1 AATAATATAAAATATTATATTAATAATATAAAAAGTAATAATATAA
26719308 GTATTTAATA
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
49 4 0.05
50 39 0.44
51 2 0.02
52 9 0.10
53 34 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (50 bp):
AATAATATAAAATATTATATTAATAATATAAAAAGTAATAATATAAAAGT
Found at i:26719235 original size:24 final size:24
Alignment explanation
Indices: 26719196--26719285 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 24
26719186 TATAAAAAAT
* *
26719196 TAAAATATAATTTTAAAAGTAATA
1 TAAAATATTATATTAAAAGTAATA
26719220 TAAAATATTATATT--AA-TAATA
1 TAAAATATTATATTAAAAGTAATA
*
26719241 TTAAAAGTAATA-ATATAAAAGTAATAATA
1 -TAAAA-TATTATAT-TAAAAG---TAATA
26719270 TAAAATATTATATTAA
1 TAAAATATTATATTAA
26719286 TAATATTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
21 5 0.10
22 9 0.17
23 5 0.10
24 12 0.23
25 2 0.04
27 7 0.13
28 7 0.13
29 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
TAAAATATTATATTAAAAGTAATA
Found at i:26719242 original size:14 final size:13
Alignment explanation
Indices: 26719217--26719293 Score: 58
Period size: 14 Copynumber: 6.1 Consensus size: 13
26719207 TTTAAAAGTA
26719217 ATATAA-AATATT
1 ATATAATAATATT
26719229 ATATTAATAATATT
1 ATA-TAATAATATT
*
26719243 A-A-AAGTAATAAT
1 ATATAA-TAATATT
*
26719255 ATAAAAGTAATA--
1 ATATAA-TAATATT
26719267 ATATAA-AATATT
1 ATATAATAATATT
26719279 ATATTAATAATATT
1 ATA-TAATAATATT
26719293 A
1 A
26719294 AAAGTAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
10 4 0.07
11 2 0.04
12 18 0.33
13 8 0.15
14 22 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATAATAATATT
Found at i:26719245 original size:33 final size:32
Alignment explanation
Indices: 26719183--26719272 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
26719173 AATATATTAA
*
26719183 TAATATAAAAAATTAAAATATAATTTTAAAAG
1 TAATATAAAAAATTAAAATATAATATTAAAAG
* * *
26719215 TAATATAAAATATTATATTAATAATATTAAAAG
1 TAATATAAAAAATTAAAAT-ATAATATTAAAAG
* *
26719248 TAATAATATAAAAGTAATAATATAA
1 TAAT-ATAAAAAATTAA-AATATAA
26719273 AATATTATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 16 0.35
33 16 0.35
34 12 0.26
35 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
TAATATAAAAAATTAAAATATAATATTAAAAG
Found at i:26719253 original size:15 final size:14
Alignment explanation
Indices: 26719233--26719274 Score: 75
Period size: 14 Copynumber: 2.9 Consensus size: 14
26719223 AATATTATAT
26719233 TAATAATATTAAAAG
1 TAATAATA-TAAAAG
26719248 TAATAATATAAAAG
1 TAATAATATAAAAG
26719262 TAATAATATAAAA
1 TAATAATATAAAA
26719275 TATTATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (14 bp):
TAATAATATAAAAG
Found at i:26719276 original size:21 final size:22
Alignment explanation
Indices: 26719252--26719296 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
26719242 TAAAAGTAAT
26719252 AATATAAAAGTAATAATA-TAA
1 AATATAAAAGTAATAATATTAA
* * *
26719273 AATATTATATTAATAATATTAA
1 AATATAAAAGTAATAATATTAA
26719295 AA
1 AA
26719297 GTAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATATAAAAGTAATAATATTAA
Found at i:26719319 original size:36 final size:36
Alignment explanation
Indices: 26719160--26719324 Score: 104
Period size: 36 Copynumber: 4.7 Consensus size: 36
26719150 AAATGTCTCG
*
26719160 AATAATATAAAATAATATA-TTAATAATAT--AA--
1 AATAATATAAAATATTATATTTAATAATATAAAAGT
*
26719191 AA-AAT-TAAAATATAAT-TTTAAAAGTAATATAAAA-T
1 AATAATATAAAATATTATATTT--AA-TAATATAAAAGT
* * **
26719226 -ATTATATTAATAATATTAAAAGTAATAATATAAAAGT
1 AATAATA-TAA-AATATTATATTTAATAATATAAAAGT
26719263 AATAATATAAAATATTATA-TTAATAATATTAAAAGT
1 AATAATATAAAATATTATATTTAATAATA-TAAAAGT
*
26719299 AATAA-AT-AAGTATTTAATATTTAATA
1 AATAATATAAAATA-TT-ATATTTAATA
26719325 TTTTACTAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 30
0.72 0.08 0.21
Matches are distributed among these distances:
29 11 0.10
30 3 0.03
31 4 0.04
32 6 0.06
34 7 0.07
35 14 0.13
36 33 0.31
37 15 0.14
38 11 0.10
39 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (36 bp):
AATAATATAAAATATTATATTTAATAATATAAAAGT
Found at i:26719363 original size:28 final size:29
Alignment explanation
Indices: 26719309--26719365 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
26719299 AATAAATAAG
* *
26719309 TATTTAATATTTAATATTTTACTAATTTA
1 TATTCAATATTTAATATTTTACGAATTTA
26719338 TATTCAATATTT-ATATTTTACGAATTTA
1 TATTCAATATTTAATATTTTACGAATTTA
26719366 CGAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (29 bp):
TATTCAATATTTAATATTTTACGAATTTA
Found at i:26721266 original size:27 final size:27
Alignment explanation
Indices: 26721224--26721281 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
26721214 AATCGTATCA
*
26721224 TCCAGGGTGTTCAGGTGATGGATACGT
1 TCCAGGGTGTTCAGGTGATGGATACAT
26721251 TCCAGGGTGGTT-AGGTGATGGATACAT
1 TCCAGGGT-GTTCAGGTGATGGATACAT
26721278 TCCA
1 TCCA
26721282 TCATGGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (27 bp):
TCCAGGGTGTTCAGGTGATGGATACAT
Found at i:26721288 original size:27 final size:27
Alignment explanation
Indices: 26721236--26721288 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
26721226 CAGGGTGTTC
* **
26721236 AGGTGATGGATACGTTCCAGGGTGGTT
1 AGGTGATGGATACATTCCAGCATGGTT
*
26721263 AGGTGATGGATACATTCCATCATGGT
1 AGGTGATGGATACATTCCAGCATGGT
26721289 CAGGCGATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (27 bp):
AGGTGATGGATACATTCCAGCATGGTT
Found at i:26721440 original size:27 final size:27
Alignment explanation
Indices: 26721385--26721440 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
26721375 CCCAAACCAC
* *
26721385 TGTAGTACTCTACTCCTTTCAGCCTAT
1 TGTAGTACTCTACTCCTCTCAGCCCAT
26721412 TGTAGTACTCTACTCCTCCTC-GCCCAT
1 TGTAGTACTCTACTCCT-CTCAGCCCAT
26721439 TG
1 TG
26721441 CCATCGCCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.16, C:0.34, G:0.12, T:0.38
Consensus pattern (27 bp):
TGTAGTACTCTACTCCTCTCAGCCCAT
Found at i:26721874 original size:28 final size:28
Alignment explanation
Indices: 26721782--26721874 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
26721772 TTAAAGTCTT
** *
26721782 AAACCTTAAAATCAAAACCCTAACCT-A
1 AAACCTTAAAATTTAAACCCTAAACTCA
* * *
26721809 AACCCTTAAAATCTTAAACACTAAAATCA
1 AAACCTTAAAAT-TTAAACCCTAAACTCA
* ** *
26721838 TAATTTTAAACTTTAAACCCTAAACTCA
1 AAACCTTAAAATTTAAACCCTAAACTCA
26721866 AAACCTTAA
1 AAACCTTAA
26721875 CCCTAAACAC
Statistics
Matches: 48, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
27 11 0.23
28 29 0.60
29 8 0.17
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (28 bp):
AAACCTTAAAATTTAAACCCTAAACTCA
Found at i:26721979 original size:18 final size:17
Alignment explanation
Indices: 26721956--26722003 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
26721946 TCAAATCCAA
26721956 ATAAATATGATATTATT
1 ATAAATATGATATTATT
26721973 GATAAAT-T-A-ATTA--
1 -ATAAATATGATATTATT
26721986 ATAAATATGATATTATT
1 ATAAATATGATATTATT
26722003 A
1 A
26722004 GAACCCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 1 0.04
15 8 0.32
16 1 0.04
17 2 0.08
18 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATAAATATGATATTATT
Found at i:26722100 original size:28 final size:28
Alignment explanation
Indices: 26722066--26722121 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
26722056 AATGTTTTAA
*
26722066 TTAAATTCAATT-TTAAACATAATTAATT
1 TTAAATTC-ATTCATAAACATAATTAATT
*
26722094 TTAAATTCATTCATAAACTTAATTAATT
1 TTAAATTCATTCATAAACATAATTAATT
26722122 CCAAGTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAAATTCATTCATAAACATAATTAATT
Found at i:26724590 original size:122 final size:122
Alignment explanation
Indices: 26724429--26724650 Score: 315
Period size: 122 Copynumber: 1.8 Consensus size: 122
26724419 ATTTGAATTT
* ** *
26724429 AAGATTTTAAAGGTAAATTGGTAAAATATCAATTATTAAGGGAATAAAAAAGGGGCAATTAAAG-
1 AAGATTTTAAAAGTAAATTGGTAAAATATCAATTATTAAGGGAATAAAAAA-AAGAAATTAAAGA
* * *
26724493 GGTTTAAAAGATGTG-GACTAAGAAGGGAAGCCACGTAACTATGTCAATTTAAATTTAA
65 GATTTAAAAGATATGAG-CTAAGAAGGGAAACCACGTAACTATGTCAATTTAAATTTAA
* *
26724551 AAGATTTTAAAAGTAAATTGGTAAAATAT-ATATTATTAAGGGTATAAAAAAAAGAAATTGAAGA
1 AAGATTTTAAAAGTAAATTGGTAAAATATCA-ATTATTAAGGGAATAAAAAAAAGAAATTAAAGA
26724615 GATTTAAAAGATATGAGCTAAGAAGGGAAACCACGT
65 GATTTAAAAGATATGAGCTAAGAAGGGAAACCACGT
26724651 GTGTGTGTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
121 9 0.10
122 78 0.89
123 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (122 bp):
AAGATTTTAAAAGTAAATTGGTAAAATATCAATTATTAAGGGAATAAAAAAAAGAAATTAAAGAG
ATTTAAAAGATATGAGCTAAGAAGGGAAACCACGTAACTATGTCAATTTAAATTTAA
Found at i:26726056 original size:26 final size:26
Alignment explanation
Indices: 26726022--26726082 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
26726012 GTGGAGCTTG
* *
26726022 TTGATGTGGACGTGATGATATGGCAA
1 TTGACGTGGACGTGATGACATGGCAA
* *
26726048 TTGACGTGGACGTGCTGACATGGCAG
1 TTGACGTGGACGTGATGACATGGCAA
*
26726074 CTGACGTGG
1 TTGACGTGG
26726083 CAGCTTAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (26 bp):
TTGACGTGGACGTGATGACATGGCAA
Found at i:26728316 original size:27 final size:27
Alignment explanation
Indices: 26728242--26728316 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
26728232 AAATTGGGGT
* * *
26728242 TTGGTGCCGTCTGTCAGGTAGATATCA
1 TTGGTGCCGTCTGTCAAGTAGACACCA
* * * * * *
26728269 TCGGTACTGCCTATCATGTAGACACCA
1 TTGGTGCCGTCTGTCAAGTAGACACCA
26728296 TTGGTGCCGTCTGTCAAGTAG
1 TTGGTGCCGTCTGTCAAGTAG
26728317 GCATCATCCT
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (27 bp):
TTGGTGCCGTCTGTCAAGTAGACACCA
Found at i:26728407 original size:9 final size:9
Alignment explanation
Indices: 26728377--26728406 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
26728367 ACCAGTCTTT
26728377 TTTTAATTA
1 TTTTAATTA
26728386 TTTTAATTA
1 TTTTAATTA
26728395 TTTTAA-TA
1 TTTTAATTA
26728403 TTTT
1 TTTT
26728407 TTAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTAATTA
Found at i:26728408 original size:19 final size:18
Alignment explanation
Indices: 26728377--26728415 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
26728367 ACCAGTCTTT
*
26728377 TTTTAATTATTTTAATTA
1 TTTTAATTATTTTAAATA
*
26728395 TTTTAATATTTTTTAAATA
1 TTTTAAT-TATTTTAAATA
26728414 TT
1 TT
26728416 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATTATTTTAAATA
Found at i:26732340 original size:18 final size:19
Alignment explanation
Indices: 26732297--26732341 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
26732287 AGCCCAATTC
*
26732297 AAAATTTAATTAATAAAAT
1 AAAATTTTATTAATAAAAT
*
26732316 AAAATTTTATTAA-AATAT
1 AAAATTTTATTAATAAAAT
*
26732334 TAAATTTT
1 AAAATTTT
26732342 TAATAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTTTATTAATAAAAT
Found at i:26732496 original size:8 final size:8
Alignment explanation
Indices: 26732483--26732507 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
26732473 ATTACATACC
26732483 AAAGTAGT
1 AAAGTAGT
26732491 AAAGTAGT
1 AAAGTAGT
26732499 AAAGTAGT
1 AAAGTAGT
26732507 A
1 A
26732508 CATTAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AAAGTAGT
Found at i:26741723 original size:59 final size:60
Alignment explanation
Indices: 26741646--26741762 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
26741636 TGGACCTTCG
* *
26741646 GGGGCAAAATGGTAATTTTT-GTGAAATCGA-AGCTAAAAATGGAATTTTGGAAAGTTTGA
1 GGGGCAAAATGGTAATTTTTGGTGAAATCGAGA-CTAAAAATGAAATTTTAGAAAGTTTGA
* * *
26741705 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGAAATTTTAGAAAGTTT
1 GGGGCAAAATGGTAATTTTTGGTGAAATCGAGACTAAAAATGAAATTTTAGAAAGTTT
26741763 AAATGTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 19 0.37
60 31 0.61
61 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (60 bp):
GGGGCAAAATGGTAATTTTTGGTGAAATCGAGACTAAAAATGAAATTTTAGAAAGTTTGA
Found at i:26741772 original size:21 final size:22
Alignment explanation
Indices: 26741742--26741784 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
26741732 TCGGGATTAA
*
26741742 AAATGAAATTTT-AGAAAGTTT
1 AAATGAAATTTTCAAAAAGTTT
*
26741763 AAATGTAATTTTCAAAAAGTTT
1 AAATGAAATTTTCAAAAAGTTT
26741785 TGAGGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (22 bp):
AAATGAAATTTTCAAAAAGTTT
Found at i:26741814 original size:30 final size:28
Alignment explanation
Indices: 26741778--26741864 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 28
26741768 TAATTTTCAA
* *
26741778 AAAGTTTTGAGGTCAAAATATATTTTTTG
1 AAAGTTTTG-GGTTAAAATATATTTTTAG
26741807 AAGAGTTTTGGGGTTAAAATATAATTTTTAG
1 AA-AGTTTT-GGGTTAAAATAT-ATTTTTAG
*
26741838 AAAGTTTTTGGGTTAAAATATAGTTTT
1 AAAG-TTTTGGGTTAAAATATATTTTT
26741865 GGACTGTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 7 0.14
30 30 0.59
31 14 0.27
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (28 bp):
AAAGTTTTGGGTTAAAATATATTTTTAG
Found at i:26743830 original size:6 final size:6
Alignment explanation
Indices: 26743821--26743924 Score: 87
Period size: 6 Copynumber: 18.0 Consensus size: 6
26743811 TTAATATCAT
* *
26743821 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
26743868 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
26743913 TTTAAA CTTAAA
1 TTTAAA TTTAAA
26743925 AAATCAAAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 51 0.65
7 1 0.01
8 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:26743830 original size:17 final size:17
Alignment explanation
Indices: 26743805--26743924 Score: 124
Period size: 17 Copynumber: 7.3 Consensus size: 17
26743795 TTTCTATTTA
* * *
26743805 TTAATTTTAATATCATT
1 TTAAATTTAATATAAAT
26743822 TTAAATTTAAT-TAAAT
1 TTAAATTTAATATAAAT
*
26743838 TTAAATTTAAAATAAAT
1 TTAAATTTAATATAAAT
26743855 TTAAA--TAA-ATAAAT
1 TTAAATTTAATATAAAT
*
26743869 TTAAATTTAAGATAAAT
1 TTAAATTTAATATAAAT
26743886 TTAAATTTAA-ATAAAAT
1 TTAAATTTAATAT-AAAT
* * *
26743903 TTAAAATTAATTTAAAC
1 TTAAATTTAATATAAAT
26743920 TTAAA
1 TTAAA
26743925 AAATCAAAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 11 0.12
15 3 0.03
16 18 0.20
17 57 0.63
18 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TTAAATTTAATATAAAT
Found at i:26743844 original size:11 final size:11
Alignment explanation
Indices: 26743821--26743924 Score: 77
Period size: 11 Copynumber: 9.0 Consensus size: 11
26743811 TTAATATCAT
*
26743821 TTTAAATTTAA
1 TTTAAATTAAA
26743832 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
26743843 TTTAAAATAAA
1 TTTAAATTAAA
26743854 TTTAAATAAATAAA
1 TTTAAAT---TAAA
*
26743868 TTTAAATTTAA
1 TTTAAATTAAA
**
26743879 GATAAATTTAAA
1 TTTAAA-TTAAA
*
26743891 TTTAAATAAAA
1 TTTAAATTAAA
26743902 TTTAAAATT-AA
1 TTT-AAATTAAA
26743913 TTTAAACTTAAA
1 TTTAAA-TTAAA
26743925 AAATCAAAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.11
11 35 0.48
12 19 0.26
14 11 0.15
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:26744491 original size:92 final size:91
Alignment explanation
Indices: 26744189--26744725 Score: 655
Period size: 92 Copynumber: 5.9 Consensus size: 91
26744179 CGAGGTTTCG
* ** *
26744189 TCTTGCTCTTACTTCAATTTCAGAGAGG--AATGATTTGATATCCAGCTCTACTTCAATTTCAAG
1 TCTTGCTCTTACTTCAATTTCAGAG-GGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAG
26744252 AGGATAGGAAAAATGATGTTGGTGCTTCA
65 AGGATAGG--AAATGATGTTGGTGCTTCA
* * * *
26744281 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGTTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
* * *
26744346 AGATAGGAAAAGATGTCGGTGCTTCA
66 GGATAGGAAATGATGTTGGTGCTTCA
* * * *
26744372 TCTTACTCTTACTTCAATTTCGGAGGGACAAAGGCTTGATACCCAGCTCTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
* *
26744437 AGATAGGAAAATGATGTTAGTGCTTCA
66 GGATAGG-AAATGATGTTGGTGCTTCA
* *
26744464 TCTTGCTTTTGCTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
* * ** *
26744529 GGATAAGAAATGATATTTTTGCTTTA
66 GGATAGGAAATGATGTTGGTGCTTCA
* * * * * **
26744555 TCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCATTTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
* * *
26744620 GGATAGGAAATGATATTTGATGCTTTA
66 GGATAGGAAATGAT-GTTGGTGCTTCA
* * * * * *
26744647 TCTAGCTCTTACTTCAATTTCAGAGAGATAAAGGCTTGCTATCCAACTTTACTTCAATTTCACGA
1 TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
26744712 GGATAGGAAATGAT
66 GGATAGGAAATGAT
26744726 CTTACTCTTA
Statistics
Matches: 393, Mismatches: 48, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
91 169 0.43
92 187 0.48
93 37 0.09
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (91 bp):
TCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGA
GGATAGGAAATGATGTTGGTGCTTCA
Found at i:26744509 original size:183 final size:182
Alignment explanation
Indices: 26744189--26744953 Score: 692
Period size: 183 Copynumber: 4.4 Consensus size: 182
26744179 CGAGGTTTCG
* * *
26744189 TCTTGCTCTTACTTCAATTTCAGAGAGG-AATGATTTGATATCCAGCTCTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAG-GGAAAAGACTTGATATCCAGCTCTACTTCAATTTCAAGA
* * * *
26744253 GGATAGGAAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTCAGAGGGACGAAGGTTT
65 GGATAGG-AAAATGATGTTAGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTT
* * *
26744318 GTTATCCAGCTTTACTTCAATTTCAAGAAGATAGGAAAAGATGTCGGTGCTTCA
129 GATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATATCGGTGCTTCA
* * *
26744372 TCTTACTCTTACTTCAATTTCGGAGGGACAAAGGCTTGATACCCAGCTCTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGA-AAAGACTTGATATCCAGCTCTACTTCAATTTCAAGA
* * *
26744437 AGATAGGAAAATGATGTTAGTGCTTCATCTTGCTTTTGCTTCAATTTCAGAGGGACAAAGGCTTG
65 GGATAGGAAAATGATGTTAGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTG
* * *** *
26744502 ATATCCAGCTTTACTTCAATTTCAAGAGGATAAGAAATGATATTTTTGCTTTA
130 ATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATATCGGTGCTTCA
* * ** *
26744555 TC-TAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCATTTTTACTTCAATTTCAAG
1 TCTTA-CTCTTACTTCAATTTCAGAGGGA-AAAGACTTGATATCCAGCTCTACTTCAATTTCAAG
* * * * * *
26744619 AGGATAGG-AAATGATATTTGATGCTTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGGCT
64 AGGATAGGAAAATGATGTTAG-TGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCT
* * *
26744683 TGCTATCCAACTTTACTTCAATTTCACGAGGATAGG---A-A-A----TG----A
128 TGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATATCGGTGCTTCA
* * * *
26744725 TCTTACTCTTACTTCAATTTCAGA-GAAAAAGACTTCATATTCAGCTTTACTTCAATTTCAAGAG
1 TCTTACTCTTACTTCAATTTCAGAGGGAAAAGACTTGATATCCAGCTCTACTTCAATTTCAAGAG
* ** *
26744789 GAAAGG---A--A----A-TG----ATCTTGCTCTTACTTCAATTTCAGA--GATGAAGACTTGA
66 GATAGGAAAATGATGTTAGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGA
26744838 TATCCAGCTTTACTTCAATTTCAAGAGGATAGG---A-A-A----TG----A
131 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATATCGGTGCTTCA
* * * *
26744877 TCTTGCTCTTACTTCAATTTCAGA--GATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGA-AAAGACTTGATATCCAGCTCTACTTCAATTTCAAGA
26744940 GGATAGG-AAATGAT
65 GGATAGGAAAATGAT
26744954 CTTGCTCTTA
Statistics
Matches: 504, Mismatches: 67, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
151 1 0.00
152 108 0.21
154 25 0.05
156 1 0.00
158 2 0.00
164 1 0.00
166 1 0.00
168 37 0.07
169 1 0.00
170 22 0.04
171 2 0.00
174 2 0.00
178 1 0.00
179 1 0.00
182 14 0.03
183 247 0.49
184 38 0.08
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (182 bp):
TCTTACTCTTACTTCAATTTCAGAGGGAAAAGACTTGATATCCAGCTCTACTTCAATTTCAAGAG
GATAGGAAAATGATGTTAGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGGGACAAAGGCTTGA
TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATATCGGTGCTTCA
Found at i:26744784 original size:76 final size:76
Alignment explanation
Indices: 26744646--26745407 Score: 1008
Period size: 76 Copynumber: 10.1 Consensus size: 76
26744636 TTGATGCTTT
* * * * * *
26744646 ATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGGCTTGCTATCCAACTTTACTTCAATTTCACG
1 ATCTTGCTCTTACTTCAATTTC--AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAG
26744711 AGGATAGGAAATG
64 AGGATAGGAAATG
* * * ** * * *
26744724 ATCTTACTCTTACTTCAATTTCAGAGAAAAAGACTTCATATTCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
*
26744789 GAAAGGAAATG
66 GATAGGAAATG
* * * * *
26744800 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
26744865 GATAGGAAATG
66 GATAGGAAATG
* * * *
26744876 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
26744941 GATAGGAAATG
66 GATAGGAAATG
26744952 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
*
26745016 GATAGAAAATG
66 GATAGGAAATG
* * *
26745027 ATGTTGCTCTTACTTCAATTTC--------AGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
26745084 GATAGGAAATG
66 GATAGGAAATG
* *
26745095 A-CGTTGCTCTTAC-TCTATTTTAGAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAA
1 ATC-TTGCTCTTACTTC-AATTT-CAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAA
*
26745158 GCGGATAGGAAATG
63 GAGGATAGGAAATG
* *
26745172 ATGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
* *
26745237 GACAGGGAATG
66 GATAGGAAATG
* *
26745248 ACCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
*
26745313 GATAGGGAATG
66 GATAGGAAATG
* *
26745324 A-CTTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCAAGA
1 ATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
* *
26745388 AGATAGGGAATG
65 GGATAGGAAATG
26745400 ATCTTGCT
1 ATCTTGCT
26745408 GCGGTTTGAT
Statistics
Matches: 624, Mismatches: 44, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
67 13 0.02
68 46 0.07
75 51 0.08
76 433 0.69
77 59 0.09
78 22 0.04
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:26745376 original size:38 final size:39
Alignment explanation
Indices: 26745118--26745392 Score: 168
Period size: 38 Copynumber: 7.2 Consensus size: 39
26745108 TCTATTTTAG
26745118 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
* * * *
26745157 AGCGGATAGGAA-ATGATG-T-TGC-TCT-TACTTCAATTTC-
1 AG-AGATA--AAGACG-TGTTATCCAACTCTACTTCAATTTCA
*
26745194 AGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCA
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
* ** * **
26745233 AGAGGACAGGGA-ATG--A-CCTTGCTCTTACTTCAATTTC-
1 AGA-GATAAAGACGTGTTATCC-AACTC-TACTTCAATTTCA
*
26745270 AGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCA
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
** * * * *
26745309 AGAGGATAGGGA-ATGACTT-TGC-TCT-TACTTCAATTT-T
1 AGA-GATAAAGACGTG--TTATCCAACTCTACTTCAATTTCA
*
26745346 AGAGATAAAGACGTGTTATCCAACTCTACTTCAGTTTCA
1 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
26745385 AGAAGATA
1 AG-AGATA
26745393 GGGAATGATC
Statistics
Matches: 172, Mismatches: 37, Indels: 53
0.66 0.14 0.20
Matches are distributed among these distances:
34 4 0.02
35 5 0.03
36 21 0.12
37 20 0.12
38 65 0.38
39 22 0.13
40 26 0.15
41 5 0.03
42 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (39 bp):
AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCA
Found at i:26757400 original size:30 final size:30
Alignment explanation
Indices: 26757364--26757459 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
26757354 CTTCGGGGGC
26757364 AAAATGGTAATTTTTGTGAAATCGAGGCTA
1 AAAATGGTAATTTTTGTGAAATCGAGGCTA
* *
26757394 AAAATGG-AA-TTTTG-GAAAGTTTGAGGGGT-
1 AAAATGGTAATTTTTGTGAAA--TCGA-GGCTA
* *
26757423 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGAGGCTA
26757454 AAAATG
1 AAAATG
26757460 AAATTTTGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
27 4 0.08
28 5 0.09
29 12 0.23
30 15 0.28
31 12 0.23
32 1 0.02
33 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTTGTGAAATCGAGGCTA
Found at i:26757436 original size:59 final size:60
Alignment explanation
Indices: 26757359--26757475 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
26757349 TGGACCTTCG
*
26757359 GGGGCAAAATGGTAATTTTT-GTGAAATCGAGGCTAAAAATGGAATTTTGGAAAGTTTGA
1 GGGGCAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATGAAATTTTGGAAAGTTTGA
* * *
26757418 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTT
1 GGGGCAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATGAAATTTTGGAAAGTTT
26757476 AAATGTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 19 0.36
60 34 0.64
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (60 bp):
GGGGCAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATGAAATTTTGGAAAGTTTGA
Found at i:26757540 original size:30 final size:30
Alignment explanation
Indices: 26757506--26757577 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
26757496 ATTTGGGTCG
** * *
26757506 AAATATAATTTTTGAAGAGTTTTAGGGTAA
1 AAATATAATTTTCAAAAAGTTTTAAGGTAA
*
26757536 AAATATAATTTTCAAAAAGTTTTAAGGTTA
1 AAATATAATTTTCAAAAAGTTTTAAGGTAA
26757566 AAATATAATTTT
1 AAATATAATTTT
26757578 GGACTGTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (30 bp):
AAATATAATTTTCAAAAAGTTTTAAGGTAA
Found at i:26759540 original size:6 final size:6
Alignment explanation
Indices: 26759541--26759633 Score: 79
Period size: 6 Copynumber: 15.8 Consensus size: 6
26759531 TTAAACTTAA
* *
26759541 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT AAATAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
* * *
26759590 -TAAAT TTAAAT TTAAA- TAAAAT TTAAAA TT-AAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
26759634 AAATCAAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 1 0.01
5 15 0.21
6 48 0.69
7 1 0.01
8 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:26759548 original size:17 final size:16
Alignment explanation
Indices: 26759530--26759621 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
26759520 TTAATATCAT
* *
26759530 TTTAAACTTAATTAAA
1 TTTAAATTTAAATAAA
26759546 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
26759563 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
26759577 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
26759594 TTTAAATTTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
26759611 TTTAAAATTAA
1 TTTAAATTTAA
26759622 TTTAAACTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 13 0.19
17 41 0.60
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:26759553 original size:11 final size:11
Alignment explanation
Indices: 26759541--26759633 Score: 71
Period size: 11 Copynumber: 7.9 Consensus size: 11
26759531 TTAAACTTAA
26759541 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
26759553 TTAAAATAAAT
1 TTAAATTAAAT
26759564 TTAAATAAATAAAT
1 TTAAAT---TAAAT
* *
26759578 TTAAATTTAAG
1 TTAAATTAAAT
*
26759589 ATAAATTTAAAT
1 TTAAA-TTAAAT
*
26759601 TTAAATAAAAT
1 TTAAATTAAAT
26759612 TTAAAATT-AAT
1 TT-AAATTAAAT
26759623 TTAAACTTAAA
1 TTAAA-TTAAA
26759634 AAATCAAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 3 0.05
11 31 0.48
12 19 0.30
14 11 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:26764826 original size:2 final size:2
Alignment explanation
Indices: 26764819--26764867 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
26764809 ATAATCATTT
26764819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26764861 TA TA TA T
1 TA TA TA T
26764868 TAATTATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26767392 original size:12 final size:12
Alignment explanation
Indices: 26767377--26767514 Score: 70
Period size: 12 Copynumber: 11.3 Consensus size: 12
26767367 GTTATTTTCG
*
26767377 TGTTGTTTTTGC
1 TGTTGTTTTTGT
*
26767389 TGTTATTTTTGT
1 TGTTGTTTTTGT
26767401 TGCTT-TTTTTGT
1 TG-TTGTTTTTGT
*
26767413 TGTTTTTAATGTTGTT
1 TGTTGTT--T-TTG-T
*
26767429 TATTGTTATTT-T
1 TGTTGTT-TTTGT
26767441 TGTTGCTTTTT-T
1 TGTTG-TTTTTGT
**
26767453 TGTTGTTTTTAA
1 TGTTGTTTTTGT
**
26767465 TGTTG--TTTAC
1 TGTTGTTTTTGT
* *
26767475 TGTTATTTTTGC
1 TGTTGTTTTTGT
*
26767487 TGTTGTTTTGGT
1 TGTTGTTTTTGT
*
26767499 TGTTATTTTTGT
1 TGTTGTTTTTGT
26767511 TGTT
1 TGTT
26767515 TGAATGTTAT
Statistics
Matches: 102, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.08
11 7 0.07
12 69 0.68
13 4 0.04
14 3 0.03
15 5 0.05
16 6 0.06
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:26767443 original size:43 final size:43
Alignment explanation
Indices: 26767389--26767528 Score: 194
Period size: 43 Copynumber: 3.2 Consensus size: 43
26767379 TTGTTTTTGC
*
26767389 TGTTATTTTTGTTGCTTTTTTTGTTGTTTTTAATGTTGTTTAT
1 TGTTATTTTTGTTGCTTTTTTTGTTGTTTTTAATGTTGTTTAA
*
26767432 TGTTATTTTTGTTGCTTTTTTTGTTGTTTTTAATGTTGTTTAC
1 TGTTATTTTTGTTGCTTTTTTTGTTGTTTTTAATGTTGTTTAA
* * *
26767475 TGTTATTTTTGCTG-TTGTTTTGGTTGTTATTT-TTGTTGTTTGAA
1 TGTTATTTTTGTTGCTT-TTTTTGTTGTT-TTTAATGTTGTTT-AA
26767519 TGTTATTTTT
1 TGTTATTTTT
26767529 TATGCGTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
42 2 0.02
43 73 0.82
44 14 0.16
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (43 bp):
TGTTATTTTTGTTGCTTTTTTTGTTGTTTTTAATGTTGTTTAA
Found at i:26767444 original size:31 final size:31
Alignment explanation
Indices: 26767356--26767515 Score: 108
Period size: 33 Copynumber: 4.8 Consensus size: 31
26767346 GCTTTTTTTA
*
26767356 TTGTTTTACTTGTTATTTTCGTGTTGTTTTTGCTG
1 TTGTTTTA-TTGTTATTTT--TGTTGTTTTT-ATG
* *
26767391 TTATTTTTGTTGCTT-TTTTTGTTGTTTTTAATG
1 TT-GTTTTATTG-TTATTTTTGTTGTTTTT-ATG
*
26767424 TTG-TTTATTGTTATTTTTGTTGCTTTTTTTG
1 TTGTTTTATTGTTATTTTTGTTG-TTTTTATG
* * * * *
26767455 TTGTTTTTAATGTTGTTTACTGTTATTTTTGCTG
1 TTG-TTTTATTGTTATTT-TTGTTGTTTTT-ATG
*
26767489 TTGTTTTGGTTGTTATTTTTGTTGTTT
1 TTGTTTT-ATTGTTATTTTTGTTGTTT
26767516 GAATGTTATT
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
30 2 0.02
31 20 0.20
32 5 0.05
33 41 0.41
34 16 0.16
35 9 0.09
36 6 0.06
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.70
Consensus pattern (31 bp):
TTGTTTTATTGTTATTTTTGTTGTTTTTATG
Found at i:26767478 original size:22 final size:22
Alignment explanation
Indices: 26767409--26767528 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
26767399 GTTGCTTTTT
*
26767409 TTGTTGTTTTTAATGTTGTTTA
1 TTGTTATTTTTAATGTTGTTTA
**
26767431 TTGTTATTTTTGTTGCTT-TTT-
1 TTGTTATTTTTAATG-TTGTTTA
*
26767452 TTGTTGTTTTTAATGTTGTTTA
1 TTGTTATTTTTAATGTTGTTTA
* ** *
26767474 CTGTTATTTTTGCTGTTGTTTTGG
1 TTGTTATTTTTAATGTTG-TTT-A
26767498 TTGTTA-TTTT--TGTTGTTTGA
1 TTGTTATTTTTAATGTTGTTT-A
*
26767518 ATGTTATTTTT
1 TTGTTATTTTT
26767529 TATGCGTTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
20 11 0.14
21 24 0.31
22 29 0.37
23 9 0.12
24 5 0.06
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (22 bp):
TTGTTATTTTTAATGTTGTTTA
Found at i:26767508 original size:55 final size:54
Alignment explanation
Indices: 26767356--26767515 Score: 173
Period size: 55 Copynumber: 2.9 Consensus size: 54
26767346 GCTTTTTTTA
* * *
26767356 TTGTTTTACTTGTTATTTTCGTGTTGTTTTTGCTGTTATTTTTGTTGCTTTTTTTG
1 TTGTTTTAC-TGTTATTTTTGTGTTGTTTTTGTTGTTATTTTTGTTG-TTTTTATG
* * * *
26767412 TTGTTTTTAATGTTGTTTAT-TGTTATTTTTGTTGCTT-TTTTTGTTGTTTTTAATG
1 TTG-TTTTACTGTTATTTTTGTGTTGTTTTTGTTG-TTATTTTTGTTGTTTTT-ATG
*
26767467 TTG-TTTACTGTTATTTTTGCTGTTGTTTTGGTTGTTATTTTTGTTGTTT
1 TTGTTTTACTGTTATTTTTG-TGTTGTTTTTGTTGTTATTTTTGTTGTTT
26767516 GAATGTTATT
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
53 12 0.14
54 7 0.08
55 50 0.58
56 12 0.14
57 5 0.06
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.70
Consensus pattern (54 bp):
TTGTTTTACTGTTATTTTTGTGTTGTTTTTGTTGTTATTTTTGTTGTTTTTATG
Found at i:26771417 original size:6 final size:6
Alignment explanation
Indices: 26771397--26771494 Score: 89
Period size: 6 Copynumber: 17.0 Consensus size: 6
26771387 ACCGGACCCT
* * * *
26771397 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
26771443 -TTAAT TTTAAA TTTAAA TTT-GA TTTAAA TTTAAA TTT-AT TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
26771489 TTTAAA
1 TTTAAA
26771495 AAAAAAATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
5 19 0.26
6 49 0.68
7 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:26771422 original size:17 final size:17
Alignment explanation
Indices: 26771397--26771494 Score: 99
Period size: 17 Copynumber: 5.4 Consensus size: 17
26771387 ACCGGACCCT
26771397 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
26771414 TTTAGATTTATTTTAAATTTGAA
1 TTTAAATTTATTTT--A----AA
*
26771437 TTTAAATTAATTTTAAA
1 TTTAAATTTATTTTAAA
26771454 TTTAAATTTGA-TTTAAA
1 TTTAAATTT-ATTTTAAA
26771471 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
26771489 TTTAAA
1 TTTAAA
26771495 AAAAAAATTG
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
16 1 0.01
17 41 0.60
18 10 0.15
19 1 0.01
21 1 0.01
23 14 0.21
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:26771438 original size:23 final size:23
Alignment explanation
Indices: 26771408--26771480 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
26771398 TTAAATTTAT
26771408 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAGATTTATTTTAAA
* * *
26771431 TTTGAATTTAAATTAATTTTAAA
1 TTTAAATTTAGATTTATTTTAAA
*
26771454 TTTAAATTT-GATTTAAATTTAAA
1 TTTAAATTTAGATTT-ATTTTAAA
26771477 TTTA
1 TTTA
26771481 TTTTCAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.07
23 39 0.93
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAGATTTATTTTAAA
Found at i:26772351 original size:17 final size:15
Alignment explanation
Indices: 26772315--26772353 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
26772305 TTAATGATAA
26772315 TAATAATAATTTTAT
1 TAATAATAATTTTAT
*
26772330 TAATAATAGTATTTAT
1 TAATAATAAT-TTTAT
26772346 TAAATAAT
1 T-AATAAT
26772354 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 6 0.29
17 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
TAATAATAATTTTAT
Found at i:26773576 original size:58 final size:58
Alignment explanation
Indices: 26773458--26773595 Score: 154
Period size: 58 Copynumber: 2.4 Consensus size: 58
26773448 CTCGAACTTC
* * * * *
26773458 TCTAAAATTCCATTTTTGACCCCAAAACTTACAAAAATTACCATTTTATCCTCGAGTG
1 TCTAAAATTTCATTTTTAACCCCAAAACTTACAAAAATTACCATTTCACCCTCGAATG
* * * *
26773516 TCTAAAAATTTCA-TTTTAACCCCAAAGCTTTCAAAAATTATCGTTTCACCCAT-GAATG
1 TCT-AAAATTTCATTTTTAACCCCAAAACTTACAAAAATTACCATTTCACCC-TCGAATG
*
26773574 TCTAAAATGTCATTTTTAACCC
1 TCTAAAATTTCATTTTTAACCC
26773596 TAAATTTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 8 0.12
58 50 0.75
59 9 0.13
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.36
Consensus pattern (58 bp):
TCTAAAATTTCATTTTTAACCCCAAAACTTACAAAAATTACCATTTCACCCTCGAATG
Found at i:26775637 original size:13 final size:13
Alignment explanation
Indices: 26775619--26775643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26775609 AACAAAAATT
26775619 AAATTAAATTTTC
1 AAATTAAATTTTC
26775632 AAATTAAATTTT
1 AAATTAAATTTT
26775644 AATTTAAAAG
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTAAATTTTC
Found at i:26777298 original size:24 final size:25
Alignment explanation
Indices: 26777251--26777299 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
26777241 TTTTTTCTCT
*
26777251 AAAATTGAAACCTTTATTCGTTTTA
1 AAAATTGAAACCTTCATTCGTTTTA
* *
26777276 AAAATTGAGATCTTCATTC-TTTTA
1 AAAATTGAAACCTTCATTCGTTTTA
26777300 TTGTTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (25 bp):
AAAATTGAAACCTTCATTCGTTTTA
Found at i:26788866 original size:49 final size:48
Alignment explanation
Indices: 26788790--26789258 Score: 355
Period size: 49 Copynumber: 9.6 Consensus size: 48
26788780 ACAAGTTTGG
* * * *
26788790 AGGGAAAGGTTTAAGTCGCAACAGTGAACCTTGTACCTCAAAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGCATGA
* * * * * * * * *
26788839 AAGGAAAGATTTAAGCCGTAACGGTGAATCTAGTACCACGAAGATATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCGAAG-CATGA
* * * * *
26788888 AGCGAAAGGTTTAAGTCGCAACGACGAACCCTGTACCTCAAAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGCATGA
* * * * * * ** * *
26788937 AGGGAAAGATTTAAGCCGTACCGGTGAATCTAGTACGACGAAGATATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCGAAG-CATGA
* * * *
26788986 AGGGAAAGGTTTAAATCGCAACGACAAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGCATGA
* * * * * * * *
26789035 AGGGAAATATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCGAAG-CATGA
* *
26789084 AGGGAAAGGTTTAAGTCGCAACGGCGAACCCTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGCATGA
* * * *
26789133 AGGGAAAGATTTAAGCCGCAACGGCGAA-TTTAGTACCACGAAGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTT-GTACCTCGAAG-CATGA
* * * * *
26789182 AGGGAAAGGTCTAAGTCGTAACGGCGAACCTTGCACCTCGGGAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGCATGA
* * *
26789231 AGGGAAGGATTTAAGCCGCAATGGCGAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA
26789259 TCCAATACCA
Statistics
Matches: 313, Mismatches: 97, Indels: 20
0.73 0.23 0.05
Matches are distributed among these distances:
48 15 0.05
49 282 0.90
50 16 0.05
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGCATGA
Found at i:26789285 original size:98 final size:98
Alignment explanation
Indices: 26788790--26789277 Score: 697
Period size: 98 Copynumber: 5.0 Consensus size: 98
26788780 ACAAGTTTGG
* * * *
26788790 AGGGAAAGGTTTAAGTCGCAACAGTGAACCTTGTACCTCAAAAGCATGAAAGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
26788855 CGTAACGGTGAATCTAGTACCACGAAGATATAA
66 CGTAACGGTGAATCTAGTACCACGAAGATATAA
* * * *
26788888 AGCGAAAGGTTTAAGTCGCAACGACGAACCCTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* *
26788953 CGTACCGGTGAATCTAGTACGACGAAGATATAA
66 CGTAACGGTGAATCTAGTACCACGAAGATATAA
* * * * *
26788986 AGGGAAAGGTTTAAATCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAATATTTAAGT
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
26789051 CGTAACGGTGAATCTAGTACCACGAAGATATAA
66 CGTAACGGTGAATCTAGTACCACGAAGATATAA
*
26789084 AGGGAAAGGTTTAAGTCGCAACGGCGAACCCTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * *
26789149 CGCAACGGCGAATTTAGTACCACGAAGATATGA
66 CGTAACGGTGAATCTAGTACCACGAAGATATAA
* * * * * *
26789182 AGGGAAAGGTCTAAGTCGTAACGGCGAACCTTGCACCTCGGGAGCATGAAGGGAAGGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * * *
26789247 CGCAATGGCGAATCCAATACCACGAAGATAT
66 CGTAACGGTGAATCTAGTACCACGAAGATAT
26789278 GGAGGGAAGG
Statistics
Matches: 352, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 352 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGTAACGGTGAATCTAGTACCACGAAGATATAA
Found at i:26789788 original size:9 final size:10
Alignment explanation
Indices: 26789763--26789787 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26789753 AACCAAGCCT
26789763 AAAAAATAAA
1 AAAAAATAAA
26789773 AAAAAATAAA
1 AAAAAATAAA
26789783 AAAAA
1 AAAAA
26789788 TCAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:26793987 original size:2 final size:2
Alignment explanation
Indices: 26793980--26794011 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26793970 TATAACTTCA
26793980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26794012 GAAAGTAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26796159 original size:2 final size:2
Alignment explanation
Indices: 26796152--26796179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26796142 GTAATTTTAG
26796152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26796180 GATCTGAACG
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26815415 original size:22 final size:23
Alignment explanation
Indices: 26815390--26815432 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
26815380 TCATTATTAA
*
26815390 ATTTCACAAAT-AAAAATAAACT
1 ATTTAACAAATCAAAAATAAACT
*
26815412 ATTTAACAAATCTAAAATAAA
1 ATTTAACAAATCAAAAATAAA
26815433 AAATATCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (23 bp):
ATTTAACAAATCAAAAATAAACT
Found at i:26825044 original size:47 final size:47
Alignment explanation
Indices: 26824975--26825070 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
26824965 AATATATTTA
26824975 ATATTTAAATTAATCAAGTTTGAACTAAAAATCTTGGTTATTACACT
1 ATATTTAAATTAATCAAGTTTGAACTAAAAATCTTGGTTATTACACT
26825022 ATATTTAAATTAATCAAGTTTGAACTAAAAATCTTGGTTATTACACT
1 ATATTTAAATTAATCAAGTTTGAACTAAAAATCTTGGTTATTACACT
26825069 AT
1 AT
26825071 TATTGACTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (47 bp):
ATATTTAAATTAATCAAGTTTGAACTAAAAATCTTGGTTATTACACT
Found at i:26826362 original size:26 final size:26
Alignment explanation
Indices: 26826323--26826400 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
26826313 TTTTTATTTT
* *
26826323 TAAAAATTATAAAATACATTCAATAAA
1 TAAAAA-TAAAAAATATATTCAATAAA
* *
26826350 TAAAAATAAAAAAATATTTTCAATAAT
1 TAAAAAT-AAAAAATATATTCAATAAA
* *
26826377 TAAATATAAAAAATATATTTAATA
1 TAAAAATAAAAAATATATTCAATA
26826401 TAAACAACCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 16 0.37
27 27 0.63
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAAATAAAAAATATATTCAATAAA
Found at i:26826403 original size:28 final size:25
Alignment explanation
Indices: 26826346--26826403 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
26826336 ATACATTCAA
26826346 TAAATAA--AAATAAAAAAATATTT
1 TAAATAATTAAATAAAAAAATATTT
*
26826369 TCAATAATTAAATATAAAAAATATATT
1 TAAATAATTAAATA-AAAAAATAT-TT
26826396 TAATATAA
1 TAA-ATAA
26826404 ACAACCGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
25 5 0.18
26 9 0.32
27 4 0.14
28 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAATAATTAAATAAAAAAATATTT
Found at i:26833661 original size:3 final size:3
Alignment explanation
Indices: 26833653--26833682 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26833643 GAAACAAGGT
26833653 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
26833683 GGGATTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:26843880 original size:39 final size:39
Alignment explanation
Indices: 26843825--26843974 Score: 185
Period size: 39 Copynumber: 3.8 Consensus size: 39
26843815 CTTAGTTGCA
* *
26843825 CAGTGTTTACAGTGTCACCGTTAATTCAAT-ATGATATTG
1 CAGTGTTTACAGTGTCACTGCTAATTCAATAATG-TATTG
* * *
26843864 TAGTGTTTACAGTGTCACTGCCAATTTAATAATGTATTG
1 CAGTGTTTACAGTGTCACTGCTAATTCAATAATGTATTG
* * *
26843903 CAGTGTTTCCAGTGTCACTGCTAGTTCAGTAATGTATTG
1 CAGTGTTTACAGTGTCACTGCTAATTCAATAATGTATTG
* * *
26843942 CAGTGTTTCCAGTGTCACTGCCAGTTCAATAAT
1 CAGTGTTTACAGTGTCACTGCTAATTCAATAAT
26843975 TCGAGAACTT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
39 94 0.97
40 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (39 bp):
CAGTGTTTACAGTGTCACTGCTAATTCAATAATGTATTG
Found at i:26847225 original size:23 final size:23
Alignment explanation
Indices: 26847199--26847243 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
26847189 AACTAATTAA
26847199 TAAATT-TATAAAAATATAAAATC
1 TAAATTATATAAAAAT-TAAAATC
26847222 TAAATTATATAAAAATTAAAAT
1 TAAATTATATAAAAATTAAAAT
26847244 ATAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATTATATAAAAATTAAAATC
Found at i:26847241 original size:16 final size:15
Alignment explanation
Indices: 26847207--26847262 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
26847197 AATAAATTTA
*
26847207 TAAAAATAT-AAAAT
1 TAAATATATAAAAAT
26847221 CTAAATTATATAAAAAT
1 -TAAA-TATATAAAAAT
*
26847238 TAAA-ATATAAGAAT
1 TAAATATATAAAAAT
26847252 TAAATAT-TAAA
1 TAAATATATAAA
26847263 TTTAAGCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 16 0.46
15 6 0.17
16 8 0.23
17 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
TAAATATATAAAAAT
Found at i:26847268 original size:20 final size:21
Alignment explanation
Indices: 26847232--26847282 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
26847222 TAAATTATAT
26847232 AAAAATTAAAATATAAGAATT-
1 AAAAATT-AAATATAAGAATTC
* * *
26847253 AAATATTAAATTTAAGCATTC
1 AAAAATTAAATATAAGAATTC
26847274 AAAAATTAA
1 AAAAATTAA
26847283 TTATTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATTAAATATAAGAATTC
Found at i:26856463 original size:27 final size:27
Alignment explanation
Indices: 26856428--26856490 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
26856418 CCATACGAGC
26856428 CCAGAATCAGAATAACGCTTTTTTGAG
1 CCAGAATCAGAATAACGCTTTTTTGAG
*
26856455 CCAGAATCAGAATAATGCTTTTTTGAG
1 CCAGAATCAGAATAACGCTTTTTTGAG
26856482 CCAGAATCA
1 CCAGAATCA
26856491 TATTACTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (27 bp):
CCAGAATCAGAATAACGCTTTTTTGAG
Found at i:26857844 original size:22 final size:20
Alignment explanation
Indices: 26857798--26857838 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
26857788 TCACTTACAC
26857798 AAAATTTTAATTCAATAATT
1 AAAATTTTAATTCAATAATT
26857818 AAAATTCTTCAATTCAA-AATT
1 AAAATT-TT-AATTCAATAATT
26857839 CCAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTTAATTCAATAATT
Found at i:26865358 original size:2 final size:2
Alignment explanation
Indices: 26865347--26865432 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
26865337 ATATTATTAT
26865347 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26865388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26865429 TA TA
1 TA TA
26865433 AAAGAATAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:26867459 original size:43 final size:43
Alignment explanation
Indices: 26867395--26867564 Score: 205
Period size: 43 Copynumber: 4.0 Consensus size: 43
26867385 TAATATTGTC
* *
26867395 GGCGTTTGTGGGAAAAACGCCGCTAAAGAACATGTTCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGT
*
26867438 GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGT
* * * * * * *
26867481 GGCGTTTGTTGGAAAAGCGCCGTTGAAGATCACGTTCTTTAAT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGT
** * * *
26867524 GATGTTTGTTGGAAAAGCACCACTAAAGACCATGTTCTATA
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATA
26867565 ACGGTGATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 109 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGT
Found at i:26872215 original size:20 final size:20
Alignment explanation
Indices: 26872189--26872234 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
26872179 AAAATTTATA
26872189 AAAAAAAATTTTGAA-GCTCTT
1 AAAAAAAA-TTT-AAGGCTCTT
*
26872210 AAAAAAAATTTAAGGCTTTT
1 AAAAAAAATTTAAGGCTCTT
26872230 AAAAA
1 AAAAA
26872235 TTGATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 13 0.57
21 8 0.35
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAAAAAATTTAAGGCTCTT
Found at i:26876949 original size:6 final size:7
Alignment explanation
Indices: 26876901--26876961 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
26876891 AACCCCAAAT
26876901 CCTTAAA
1 CCTTAAA
*
26876908 CATTAAA
1 CCTTAAA
*
26876915 CCCTAAA
1 CCTTAAA
**
26876922 CCCCAAA
1 CCTTAAA
26876929 TCCTTAAA
1 -CCTTAAA
*
26876937 TCTTAAA
1 CCTTAAA
26876944 -CTTAAA
1 CCTTAAA
26876950 CC-TAAA
1 CCTTAAA
26876956 CCTTAA
1 CCTTAA
26876962 TACCCCAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 12 0.27
7 27 0.61
8 5 0.11
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
CCTTAAA
Found at i:26880497 original size:3 final size:3
Alignment explanation
Indices: 26880489--26880513 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
26880479 TCGTATTTTT
26880489 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
26880514 TGATTTGATA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:26883472 original size:29 final size:29
Alignment explanation
Indices: 26883411--26883472 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
26883401 CAAATTCATA
*
26883411 AATTGAGAGCTGAATTGAATGTCGTTTTT
1 AATTGAGAGCTGAATTGAATGTCGTTTTG
* *
26883440 AATTGAGAGCTTAATTGAAT-TGGTTATTG
1 AATTGAGAGCTGAATTGAATGTCGTT-TTG
26883469 AATT
1 AATT
26883473 ATCTTTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
AATTGAGAGCTGAATTGAATGTCGTTTTG
Found at i:26884481 original size:11 final size:11
Alignment explanation
Indices: 26884465--26884504 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
26884455 TATTTTCTCA
26884465 TAAAAATAATT
1 TAAAAATAATT
26884476 TAAAAATAA--
1 TAAAAATAATT
*
26884485 TAAAAATATTT
1 TAAAAATAATT
26884496 TAAAAATAA
1 TAAAAATAA
26884505 AAAACTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATAATT
Found at i:26884503 original size:17 final size:20
Alignment explanation
Indices: 26884464--26884508 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
26884454 ATATTTTCTC
26884464 ATAAAAATAATTTAAAAATA
1 ATAAAAATAATTTAAAAATA
*
26884484 ATAAAAATATTTTAAAAATA
1 ATAAAAATAATTTAAAAATA
26884504 A-AAAA
1 ATAAAA
26884509 CTATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAATAATTTAAAAATA
Found at i:26884600 original size:36 final size:37
Alignment explanation
Indices: 26884535--26884617 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 37
26884525 AAACTAAAAT
26884535 TATTA-AAACATATATTAAAATTGATATAAATTTATAAA
1 TATTATAAACATATA-TAAAATTGATATAAA-TTATAAA
*
26884573 TATTATAAACATATA-AAAATCT-A-ATAAATTATAAT
1 TATTATAAACATATATAAAAT-TGATATAAATTATAAA
26884608 TAATTATAAA
1 T-ATTATAAA
26884618 ATCAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
35 7 0.17
36 13 0.32
37 6 0.15
38 6 0.15
39 9 0.22
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (37 bp):
TATTATAAACATATATAAAATTGATATAAATTATAAA
Found at i:26890774 original size:13 final size:13
Alignment explanation
Indices: 26890756--26890780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26890746 TTGATTTACT
26890756 ATTTTTTTATATA
1 ATTTTTTTATATA
26890769 ATTTTTTTATAT
1 ATTTTTTTATAT
26890781 TTCTCAAAGT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTATATA
Found at i:26906735 original size:18 final size:19
Alignment explanation
Indices: 26906709--26906744 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
26906699 TAATAATAAA
*
26906709 TATAGATTT-TAAAATTTT
1 TATAAATTTATAAAATTTT
26906727 TATAAATTTATAAAATTT
1 TATAAATTTATAAAATTT
26906745 AATGAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TATAAATTTATAAAATTTT
Found at i:26916087 original size:2 final size:2
Alignment explanation
Indices: 26916080--26916104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26916070 ACATACATAA
26916080 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
26916105 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:26920987 original size:42 final size:42
Alignment explanation
Indices: 26920940--26921023 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
26920930 ACATTGAACC
26920940 TAAAAT-TAAAACAAATTTTAAATTTAAATTTACTTTAAATTT
1 TAAAATGTAAAACAAATTTTAAATTTAAATTTA-TTTAAATTT
** * * *
26920982 TAAAATGTCCAATACATTTTAAATTTAAGTTTATTTAAATTT
1 TAAAATGTAAAACAAATTTTAAATTTAAATTTATTTAAATTT
26921024 AAAGGCCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 15 0.42
43 21 0.58
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (42 bp):
TAAAATGTAAAACAAATTTTAAATTTAAATTTATTTAAATTT
Found at i:26922840 original size:29 final size:29
Alignment explanation
Indices: 26922778--26923158 Score: 300
Period size: 29 Copynumber: 13.2 Consensus size: 29
26922768 TAAAATTTCT
*
26922778 AAAAATTGCA-TTTTGCCC-CAAACTTCC
1 AAAAATTGCATTTTTACCCTCAAACTTCC
* * *
26922805 AAAAATTGCATTTTTGCTCTCGAACTTCC
1 AAAAATTGCATTTTTACCCTCAAACTTCC
*
26922834 AAAAATTACATTTTTACCCTCAAACTTCC
1 AAAAATTGCATTTTTACCCTCAAACTTCC
* * * *
26922863 AACAATTGCATTTTTAACCCCCAAAATTTTC
1 AAAAATTGCATTTTT-ACCCTC-AAACTTCC
**
26922894 AAAAATCACATTTTTACCCTCAAACTTCC
1 AAAAATTGCATTTTTACCCTCAAACTTCC
*
26922923 AAAAAATGTCA-TTTTATCCCT-AAACTTCC
1 AAAAATTG-CATTTTTA-CCCTCAAACTTCC
* * *
26922952 AAAAATTACATTTTGA-CCTCGAACTTTCC
1 AAAAATTGCATTTTTACCCTCAAAC-TTCC
**
26922981 AAAAATT--ATGTTTTACCC-CAAAGATCC
1 AAAAATTGCAT-TTTTACCCTCAAACTTCC
* * *
26923008 AAAAATTACCA-TTTTACCCTCGAACTTTC
1 AAAAATT-GCATTTTTACCCTCAAACTTCC
* * *
26923037 AAAATTTACAATTTTGACCC-CAAACTTCC
1 AAAAATTGC-ATTTTTACCCTCAAACTTCC
* *
26923066 AAAAATTACATTTTTACCCTCAAACTTCTT
1 AAAAATTGCATTTTTACCCTCAAACTTC-C
**
26923096 AAAAATTATATTTTTATCCCT-AAACTTCC
1 AAAAATTGCATTTTTA-CCCTCAAACTTCC
* * * *
26923125 AAAAATTACCA-TTGTACCCTCGAATTTCC
1 AAAAATT-GCATTTTTACCCTCAAACTTCC
26923154 AAAAA
1 AAAAA
26923159 ATCACACTTT
Statistics
Matches: 285, Mismatches: 47, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
27 25 0.09
28 41 0.14
29 150 0.53
30 47 0.16
31 22 0.08
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTGCATTTTTACCCTCAAACTTCC
Found at i:26922870 original size:58 final size:57
Alignment explanation
Indices: 26922778--26923158 Score: 346
Period size: 58 Copynumber: 6.6 Consensus size: 57
26922768 TAAAATTTCT
* * * * *
26922778 AAAAATTGCA-TTTTGCCC-CAAACTTCCAAAAATTGCATTTTTGCTCTCGAACTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCCAAAAATTGCATTTTTAC-CCCAAACTTCC
* * *
26922834 AAAAATTACATTTTTACCCTCAAACTTCCAACAATTGCATTTTTAACCCCCAAAATTTTC
1 AAAAATTACATTTTTACCCTCAAACTTCCAAAAATTGCATTTTT-A-CCCC-AAACTTCC
* * *
26922894 AAAAATCACATTTTTACCCTCAAACTTCCAAAAAATGTCA-TTTTATCCCTAAACTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCCAAAAATTG-CATTTTTA-CCCCAAACTTCC
* * **
26922952 AAAAATTACATTTTGA-CCTCGAACTTTCCAAAAATT--ATGTTTTACCCCAAAGATCC
1 AAAAATTACATTTTTACCCTCAAAC-TTCCAAAAATTGCAT-TTTTACCCCAAACTTCC
* * * * *
26923008 AAAAATTACCA-TTTTACCCTCGAACTTTCAAAATTTACAATTTTGACCCCAAACTTCC
1 AAAAATTA-CATTTTTACCCTCAAACTTCCAAAAATTGC-ATTTTTACCCCAAACTTCC
* ** *
26923066 AAAAATTACATTTTTACCCTCAAACTTCTTAAAAATTATATTTTTATCCCTAAACTTCC
1 AAAAATTACATTTTTACCCTCAAACTTC-CAAAAATTGCATTTTTA-CCCCAAACTTCC
* * *
26923125 AAAAATTACCA-TTGTACCCTCGAATTTCCAAAAA
1 AAAAATTA-CATTTTTACCCTCAAACTTCCAAAAA
26923159 ATCACACTTT
Statistics
Matches: 268, Mismatches: 39, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
55 1 0.00
56 39 0.15
57 31 0.12
58 101 0.38
59 48 0.18
60 46 0.17
61 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCTCAAACTTCCAAAAATTGCATTTTTACCCCAAACTTCC
Found at i:26923672 original size:99 final size:99
Alignment explanation
Indices: 26923545--26923724 Score: 254
Period size: 99 Copynumber: 1.8 Consensus size: 99
26923535 AATCGAGGTA
* * * *
26923545 ATATTCCTTTATTTCGAGTTTTGAAAATTCATGCCTTAACTTACT-AGCCGCGATTTTTCTTCAA
1 ATATTCCTTTACTTCGAGTTTTGAAAATTCATGCCTTAACTTACTAAG-CGCAACTTTTCTTAAA
26923609 ACCGAGATAATCGAATACCCTTAAATCGAGGCAAT
65 ACCGAGATAATCGAATACCCTTAAATCGAGGCAAT
* * **
26923644 ATATTCCTTTACTTCGGGTTTTGGAAATTTGTGCCTTAACTTACTAAGCGCAACTTTTCTTAAAA
1 ATATTCCTTTACTTCGAGTTTTGAAAATTCATGCCTTAACTTACTAAGCGCAACTTTTCTTAAAA
* *
26923709 CCGGGATAATTGAATA
66 CCGAGATAATCGAATA
26923725 TCTTTTTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
99 68 0.97
100 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (99 bp):
ATATTCCTTTACTTCGAGTTTTGAAAATTCATGCCTTAACTTACTAAGCGCAACTTTTCTTAAAA
CCGAGATAATCGAATACCCTTAAATCGAGGCAAT
Found at i:26924304 original size:21 final size:21
Alignment explanation
Indices: 26924263--26924305 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
26924253 TATAATAGCA
* *
26924263 AAACAACATCAAAATGACAAC
1 AAACAACAACAAAAAGACAAC
26924284 AAACAACAACAACAAAG-CAAC
1 AAACAACAACAA-AAAGACAAC
26924305 A
1 A
26924306 GTGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.65, C:0.26, G:0.05, T:0.05
Consensus pattern (21 bp):
AAACAACAACAAAAAGACAAC
Found at i:26924863 original size:17 final size:17
Alignment explanation
Indices: 26924838--26924896 Score: 109
Period size: 17 Copynumber: 3.5 Consensus size: 17
26924828 CTCATTCTCT
*
26924838 CAATATGCATAACTGTC
1 CAATCTGCATAACTGTC
26924855 CAATCTGCATAACTGTC
1 CAATCTGCATAACTGTC
26924872 CAATCTGCATAACTGTC
1 CAATCTGCATAACTGTC
26924889 CAATCTGC
1 CAATCTGC
26924897 CGCTCCCTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CAATCTGCATAACTGTC
Found at i:26927182 original size:24 final size:25
Alignment explanation
Indices: 26927131--26927184 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
26927121 GTTCAGATGT
*
26927131 AAATAAAAATTTATTATTATTTTGAA
1 AAATAAAAATTTA-TATTATGTTGAA
*
26927157 AAATAAAAATATTA-ATTATGTTAAA
1 AAATAAAAAT-TTATATTATGTTGAA
26927182 AAA
1 AAA
26927185 AAGTAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 10 0.40
27 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
AAATAAAAATTTATATTATGTTGAA
Found at i:26936208 original size:23 final size:22
Alignment explanation
Indices: 26936182--26936226 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
26936172 AACAAATAAT
26936182 TCAAAATTATAAAAATCA-AAAAA
1 TCAAAATTA-AAAAA-CATAAAAA
26936205 TCAAAATTAAAAAACATAAAAA
1 TCAAAATTAAAAAACATAAAAA
26936227 GTTCATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.48
23 9 0.43
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (22 bp):
TCAAAATTAAAAAACATAAAAA
Found at i:26937033 original size:30 final size:30
Alignment explanation
Indices: 26936997--26937094 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
26936987 TTTTAGTCCC
26936997 TGTACTTACAATTAGATCCATTTTGGTACT
1 TGTACTTACAATTAGATCCATTTTGGTACT
* **** * *
26937027 TTTACTTTTTGTTTAG-TTCACTTTGGTACT
1 TGTAC-TTACAATTAGATCCATTTTGGTACT
* *
26937057 TGAACTTCACAATTAGATCCATTTTGGTATT
1 TGTACTT-ACAATTAGATCCATTTTGGTACT
*
26937088 TGAACTT
1 TGTACTT
26937095 GGATTTCGTT
Statistics
Matches: 49, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
29 2 0.04
30 23 0.47
31 24 0.49
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (30 bp):
TGTACTTACAATTAGATCCATTTTGGTACT
Found at i:26943519 original size:3 final size:3
Alignment explanation
Indices: 26943511--26943550 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
26943501 CCAACAGTTC
* *
26943511 TCT TCT TCT TCT TCC TCT TCT CCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
26943551 TCCCAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:26947208 original size:35 final size:35
Alignment explanation
Indices: 26947164--26947233 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
26947154 ATAAAGATTT
26947164 ATAAATGAATCAAATGTTGTAAATATTTTGTTAAG
1 ATAAATGAATCAAATGTTGTAAATATTTTGTTAAG
26947199 ATAAATGAATCAAATGTTGTAAATATTTTGTTAAG
1 ATAAATGAATCAAATGTTGTAAATATTTTGTTAAG
26947234 GGTATCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (35 bp):
ATAAATGAATCAAATGTTGTAAATATTTTGTTAAG
Found at i:26947254 original size:8 final size:8
Alignment explanation
Indices: 26947241--26947271 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
26947231 AAGGGTATCT
26947241 TTTATTGA
1 TTTATTGA
26947249 TTTATTGA
1 TTTATTGA
26947257 TTTATTGA
1 TTTATTGA
26947265 TTTATTG
1 TTTATTG
26947272 GTCAAAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (8 bp):
TTTATTGA
Found at i:26952958 original size:23 final size:23
Alignment explanation
Indices: 26952900--26952952 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
26952890 TCTCATGTTG
*
26952900 TTAATATCCACCAAAGTTTGCAT
1 TTAATATCCACCAAAATTTGCAT
26952923 TTAATATCCACCAAAATTTGCAT
1 TTAATATCCACCAAAATTTGCAT
26952946 TTAATAT
1 TTAATAT
26952953 TTACCATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TTAATATCCACCAAAATTTGCAT
Found at i:26964246 original size:23 final size:24
Alignment explanation
Indices: 26964198--26964246 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
26964188 ATAAAAAAAA
*
26964198 ATTTAATTTCAAAATATCATTTTT
1 ATTTAATTCCAAAATATCATTTTT
*
26964222 ATTTAATTCCAATATAT-ATTTTT
1 ATTTAATTCCAAAATATCATTTTT
26964245 AT
1 AT
26964247 ATTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAATTCCAAAATATCATTTTT
Found at i:26966035 original size:12 final size:12
Alignment explanation
Indices: 26966018--26966059 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
26966008 TAACTTAAAC
26966018 GAACATGTTCAT
1 GAACATGTTCAT
* *
26966030 GAACAT-ATAATT
1 GAACATGTTCA-T
26966042 GAACATGTTCAT
1 GAACATGTTCAT
26966054 GAACAT
1 GAACAT
26966060 AAACAAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (12 bp):
GAACATGTTCAT
Found at i:26968420 original size:3 final size:3
Alignment explanation
Indices: 26968412--26968443 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
26968402 TAATGCATCC
*
26968412 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
26968444 GTTTGTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:26971942 original size:19 final size:19
Alignment explanation
Indices: 26971918--26971968 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
26971908 CTCTGAAGAA
26971918 TTTACAAATTTTAATTTTG
1 TTTACAAATTTTAATTTTG
* *
26971937 TTTAC-AATATTCAATTTTT
1 TTTACAAAT-TTTAATTTTG
26971956 TTTA-AAATTTTAA
1 TTTACAAATTTTAA
26971969 AAGAGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTACAAATTTTAATTTTG
Found at i:26973998 original size:2 final size:2
Alignment explanation
Indices: 26973982--26974014 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
26973972 TACTTTTTCC
*
26973982 CT CT CG CT C- CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
26974015 TTGAGCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:26978960 original size:23 final size:23
Alignment explanation
Indices: 26978907--26978964 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
26978897 CTGACATAGC
** *
26978907 ATCCAGTCAGCAGCTTTTAGAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
26978930 ATCCAGTCAGCAGCTTCCAAAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
* *
26978953 GTCTAGTCAGCA
1 ATCCAGTCAGCA
26978965 AGGATGGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCCAAAAG
Found at i:26985481 original size:23 final size:24
Alignment explanation
Indices: 26985455--26985504 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
26985445 ATGCTTCGTC
26985455 ATTAATTTATTTC-AGTTATTTAT
1 ATTAATTTATTTCTAGTTATTTAT
* * *
26985478 ATTATTTTATTTCTATTTATTTTT
1 ATTAATTTATTTCTAGTTATTTAT
26985502 ATT
1 ATT
26985505 TTTGGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTAATTTATTTCTAGTTATTTAT
Found at i:26985507 original size:6 final size:6
Alignment explanation
Indices: 26985493--26985550 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
26985483 TTTATTTCTA
* * * *
26985493 TTTATT TTTATTT TTGGTATT TTAATT TTTATT TATAAT ATTATT TTTATT
1 TTTATT TTTA-TT TT--TATT TTTATT TTTATT TTTATT TTTATT TTTATT
26985544 TTTATT T
1 TTTATT T
26985551 CAGACTCGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 31 0.76
7 4 0.10
8 4 0.10
9 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:26989115 original size:23 final size:23
Alignment explanation
Indices: 26989034--26989102 Score: 129
Period size: 23 Copynumber: 3.0 Consensus size: 23
26989024 TCTGACGTGG
26989034 CATCCAGTCAGCAGCTTCTAGAA
1 CATCCAGTCAGCAGCTTCTAGAA
26989057 CATCCAGTCAGCAGCTTCTAGAA
1 CATCCAGTCAGCAGCTTCTAGAA
*
26989080 CATCCAGTCAGCAGCTTCCAGAA
1 CATCCAGTCAGCAGCTTCTAGAA
26989103 GGTCTAGTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.20
Consensus pattern (23 bp):
CATCCAGTCAGCAGCTTCTAGAA
Found at i:26995802 original size:12 final size:12
Alignment explanation
Indices: 26995769--26995871 Score: 99
Period size: 12 Copynumber: 8.9 Consensus size: 12
26995759 GTTTTTATTG
26995769 TTTTTG-TGTTA
1 TTTTTGTTGTTA
* *
26995780 CTTTTGCTGTTA
1 TTTTTGTTGTTA
*
26995792 TTTTTGTTGTTG
1 TTTTTGTTGTTA
*
26995804 TTTTTGTTGCTA
1 TTTTTGTTGTTA
*
26995816 TTTTT-AT-TT-
1 TTTTTGTTGTTA
*
26995825 TTTTTGTTATTA
1 TTTTTGTTGTTA
*
26995837 TTTTTGTTGCTGA
1 TTTTTGTTG-TTA
26995850 -TTTTGTTGTTA
1 TTTTTGTTGTTA
26995861 TTTTTGTTGTT
1 TTTTTGTTGTT
26995872 TGGGTGTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 10 0.14
12 55 0.74
13 2 0.03
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.72
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:26995811 original size:21 final size:21
Alignment explanation
Indices: 26995710--26995871 Score: 78
Period size: 24 Copynumber: 7.2 Consensus size: 21
26995700 AAAAATTATA
* *
26995710 TTGTTGTTTTTTGCTATTTCTAG
1 TTGTTG-TTTTTGTTATTT-TTG
* *
26995733 -TGTGTGTTTTTGCTATTTTGG
1 TTGT-TGTTTTTGTTATTTTTG
* * *
26995754 TTGCTGTTTTTATTGTTTTTG
1 TTGTTGTTTTTGTTATTTTTG
*
26995775 -TGTTACTTTTGCTGTTATTTTTG
1 TTGTT-GTTTT--TGTTATTTTTG
*
26995798 TTGTTGTTTTTGTTGCTATTTTTA
1 TTGTTGTTTTTG-T--TATTTTTG
* *
26995822 TT-TTTTTTGTTATTATTTTTG
1 TTGTTGTTT-TTGTTATTTTTG
*
26995843 TTGCTGATTTTGTTGTTATTTTTG
1 TTGTTG--TTT-TTGTTATTTTTG
26995867 TTGTT
1 TTGTT
26995872 TGGGTGTTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 25
0.71 0.13 0.17
Matches are distributed among these distances:
20 3 0.03
21 30 0.28
22 19 0.18
23 21 0.20
24 34 0.32
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (21 bp):
TTGTTGTTTTTGTTATTTTTG
Found at i:26995857 original size:57 final size:56
Alignment explanation
Indices: 26995746--26995869 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 56
26995736 GTGTTTTTGC
* * * *
26995746 TATTTTGGTTGCTGTTTTTATTGTTTTTGTGTTACTTTTGCTGTTATTTTTGTTGT
1 TATTTTTGTTGCTATTTTTATTGTTTTTGTATTACTTTTGCTGTGATTTTTGTTGT
* * * *
26995802 TGTTTTTGTTGCTATTTTTATTTTTTTTGTTATTATTTTTGTTGCTGA-TTTTGTTGT
1 TATTTTTGTTGCTATTTTTATTGTTTTTG-TATTACTTTTGCTG-TGATTTTTGTTGT
26995859 TATTTTTGTTG
1 TATTTTTGTTG
26995870 TTTGGGTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 25 0.44
57 30 0.53
58 2 0.04
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (56 bp):
TATTTTTGTTGCTATTTTTATTGTTTTTGTATTACTTTTGCTGTGATTTTTGTTGT
Found at i:26995886 original size:45 final size:43
Alignment explanation
Indices: 26995781--26995886 Score: 106
Period size: 45 Copynumber: 2.4 Consensus size: 43
26995771 TTTGTGTTAC
* * *
26995781 TTTTGCTGTTA-TTTTTGTTGTTGTTTTTGTTGCTATTTTTAT
1 TTTTGGTGTTATTTTTTGTTGCTGATTTTGTTGCTATTTTTAT
** * *
26995823 TTTTTTTGTTATTATTTTTGTTGCTGATTTTGTTGTTATTTTTGT
1 TTTTGGTGTTA-T-TTTTTGTTGCTGATTTTGTTGCTATTTTTAT
26995868 TGTTTGGGTGTTATTTTTT
1 T-TTT-GGTGTTATTTTTT
26995887 CATGCGTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
42 9 0.18
45 33 0.65
46 4 0.08
47 5 0.10
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.72
Consensus pattern (43 bp):
TTTTGGTGTTATTTTTTGTTGCTGATTTTGTTGCTATTTTTAT
Found at i:26998930 original size:2 final size:2
Alignment explanation
Indices: 26998925--26998963 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26998915 CTTCTTCTAT
*
26998925 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
26998964 AAATTCTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:27000405 original size:26 final size:26
Alignment explanation
Indices: 27000362--27000413 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
27000352 GCTTATAAAA
27000362 TTAATATAAAAATATATTGAATATAAT
1 TTAATATAAAAATATATTGAAT-TAAT
*
27000389 TTAAT-TAAAAA-AGTATTTAATTAAT
1 TTAATATAAAAATA-TATTGAATTAAT
27000414 ATTTAGAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 13 0.57
27 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
TTAATATAAAAATATATTGAATTAAT
Done.