Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000887.1 Hibiscus syriacus cultivar Beakdansim tig00001732_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 662576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:382977 original size:142 final size:141
Alignment explanation
Indices: 382714--383048 Score: 367
Period size: 142 Copynumber: 2.3 Consensus size: 141
382704 GCCGCAATCT
* *
382714 AAATTCTGTTCGTTCCCATGCATAGAATCAGTAGA--GATGAAATCTATGTCCGTGATGTAACCG
1 AAATTCTG-TCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATGTAACCG
* * * * * *
382777 CTTCTAAGTTCTGTCCACTCCTATGCATAGTATTAGTAGAGTGATAAATAAATATATGTCTC-TA
65 CTTCTAAATTCTGCCCACTCCCATGCATAGTATCAGTAGAGTGAT--AGAAATATATGTC-CGCA
* **
382841 A-TCTTTCTGCATTCC
127 AGGC-AACTGCATTCC
* * *
382856 ACATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGAT-TCAGCT
1 AAATTCTGT-CATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATGT-AACC
** *
382920 GCATTCTAAATTCTGCCCGTTCCCATGCATAGTATCAGTAGAGTGAT-GAAATCTATGTCCGCAA
64 GC-TTCTAAATTCTGCCCACTCCCATGCATAGTATCAGTAGAGTGATAGAAATATATGTCCGCAA
*
382984 GGCAACTGCATTCT
128 GGCAACTGCATTCC
*
382998 AAATTCTGATCATTCCCATGCATAGAATCAGTAGCGTGATGAATATCTATG
1 AAATTCTG-TCATTCCCATGCATAGAATCAGTAGAGTGATGAA-ATCTATG
383049 TCCTGAATCT
Statistics
Matches: 164, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
141 2 0.01
142 90 0.55
143 10 0.06
144 24 0.15
145 38 0.23
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (141 bp):
AAATTCTGTCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATGTAACCGC
TTCTAAATTCTGCCCACTCCCATGCATAGTATCAGTAGAGTGATAGAAATATATGTCCGCAAGGC
AACTGCATTCC
Found at i:385409 original size:17 final size:17
Alignment explanation
Indices: 385384--385417 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
385374 CCGGTTTTGG
*
385384 TTTTAAAAAAATTGGTT
1 TTTTAAAAAAATCGGTT
*
385401 TTTTTAAAAAATCGGTT
1 TTTTAAAAAAATCGGTT
385418 ATAAAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAAATCGGTT
Found at i:386178 original size:33 final size:33
Alignment explanation
Indices: 386131--386229 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
386121 AACTCAACAT
* * *
386131 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
386164 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
386197 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
386229 A
1 A
386230 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:386248 original size:21 final size:21
Alignment explanation
Indices: 386224--386265 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
386214 ACTTCAAGTT
386224 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
386245 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
386266 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:388674 original size:19 final size:20
Alignment explanation
Indices: 388645--388683 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
388635 GTTAAAATAA
*
388645 CCGGTTTAAAAAAATCCGAT
1 CCGGTTTAAAAAAAACCGAT
388665 CCGG-TTAAAAAAAACCGAT
1 CCGGTTTAAAAAAAACCGAT
388684 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
CCGGTTTAAAAAAAACCGAT
Found at i:388900 original size:7 final size:7
Alignment explanation
Indices: 388888--388914 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
388878 TCCAACCCTA
388888 GAACTTT
1 GAACTTT
388895 GAACTTT
1 GAACTTT
388902 GAACTTT
1 GAACTTT
388909 GAACTT
1 GAACTT
388915 AACTGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
GAACTTT
Found at i:391125 original size:32 final size:32
Alignment explanation
Indices: 391040--391127 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
391030 ATGTGTTTAA
* *
391040 AGGATTTCTCAGCGTCTTCTTCACATTGGGGG
1 AGGATGTCTCGGCGTCTTCTTCACATTGGGGG
*
391072 TAGGATTTCTCGGCGTCTTCTTCACATTGGAGGG
1 -AGGATGTCTCGGCGTCTTCTTCACATTGG-GGG
* *
391106 -GGATGTCTTGGCGTATTCTTCA
1 AGGATGTCTCGGCGTCTTCTTCA
391128 GCCCACATGC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 19 0.38
33 28 0.56
34 3 0.06
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.36
Consensus pattern (32 bp):
AGGATGTCTCGGCGTCTTCTTCACATTGGGGG
Found at i:391248 original size:33 final size:33
Alignment explanation
Indices: 391211--391273 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
391201 TTCAATTACG
391211 GAAGCAAAGAGAGTGAGAGGATATCGATCATAA
1 GAAGCAAAGAGAGTGAGAGGATATCGATCATAA
391244 GAAGCAAAGAGAGTGAGAGGATATCGATCA
1 GAAGCAAAGAGAGTGAGAGGATATCGATCA
391274 GCGTCGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.32, T:0.14
Consensus pattern (33 bp):
GAAGCAAAGAGAGTGAGAGGATATCGATCATAA
Found at i:391436 original size:32 final size:31
Alignment explanation
Indices: 391399--391463 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
391389 AATTTTGTGA
*
391399 TTATATATTGTTACATACTTTGAAATAATGAT
1 TTATATATTGTTACATAATTTGAAATAA-GAT
*
391431 TTATATGTTGTTACATAATTTGAAATAAGAT
1 TTATATATTGTTACATAATTTGAAATAAGAT
391462 TT
1 TT
391464 GGACCACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.48
Consensus pattern (31 bp):
TTATATATTGTTACATAATTTGAAATAAGAT
Found at i:394053 original size:15 final size:15
Alignment explanation
Indices: 394021--394062 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
394011 TTTACTACTA
*
394021 AATAATTATT--AGT
1 AATAATTATTAAATT
394034 AATAATTATTAAATT
1 AATAATTATTAAATT
*
394049 AATAATTAGTAAAT
1 AATAATTATTAAAT
394063 CATTATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 10 0.40
15 15 0.60
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
AATAATTATTAAATT
Found at i:394159 original size:25 final size:26
Alignment explanation
Indices: 394104--394162 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
394094 TTTAATTAGT
394104 AATCATTACTAAATCATTAAATATCA
1 AATCATTACTAAATCATTAAATATCA
**
394130 AATCATTACTAAATCATT-TGTATCA
1 AATCATTACTAAATCATTAAATATCA
394155 AATCATTA
1 AATCATTA
394163 AATTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (26 bp):
AATCATTACTAAATCATTAAATATCA
Found at i:394229 original size:10 final size:10
Alignment explanation
Indices: 394214--394264 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
394204 GATGAAATCA
394214 TTACTAAATT
1 TTACTAAATT
394224 TTACTAAATT
1 TTACTAAATT
*
394234 ATTACT-AATCA
1 -TTACTAAAT-T
*
394245 TTATTAAATT
1 TTACTAAATT
394255 TTACTAAATT
1 TTACTAAATT
394265 ATTAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (10 bp):
TTACTAAATT
Found at i:394237 original size:21 final size:21
Alignment explanation
Indices: 394208--394280 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
394198 AATAATGATG
* *
394208 AAATCATTACTAAATTTTACT
1 AAATTATTACTAAATTTTAAT
* *
394229 AAATTATTACT-AATCATTATT
1 AAATTATTACTAAAT-TTTAAT
394250 AAATT-TTACTAAATTATTAAT
1 AAATTATTACTAAATT-TTAAT
394271 AATATTATTA
1 AA-ATTATTA
394281 GTATCATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.19
21 28 0.67
22 3 0.07
23 3 0.07
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTATTACTAAATTTTAAT
Found at i:394247 original size:31 final size:31
Alignment explanation
Indices: 394209--394277 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
394199 ATAATGATGA
*
394209 AATCATTACTAAATTTTACTAAATTATTACT
1 AATCATTACTAAATTTTACTAAATTATTAAT
*
394240 AATCATTATTAAATTTTACTAAATTATTAAT
1 AATCATTACTAAATTTTACTAAATTATTAAT
394271 AAT-ATTA
1 AATCATTA
394278 TTAGTATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (31 bp):
AATCATTACTAAATTTTACTAAATTATTAAT
Found at i:394279 original size:12 final size:13
Alignment explanation
Indices: 394262--394305 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
394252 ATTTTACTAA
394262 ATTATTAATAAT-
1 ATTATTAATAATC
*
394274 ATTATTAGT-ATC
1 ATTATTAATAATC
*
394286 ATTATTACTAATC
1 ATTATTAATAATC
394299 ATTATTA
1 ATTATTA
394306 GTATCAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 16 0.57
13 10 0.36
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (13 bp):
ATTATTAATAATC
Found at i:394308 original size:25 final size:24
Alignment explanation
Indices: 394262--394311 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
394252 ATTTTACTAA
394262 ATTATTAATAATATTATTAGTATC
1 ATTATTAATAATATTATTAGTATC
*
394286 ATTATTACTAATCATTATTAGTATC
1 ATTATTAATAAT-ATTATTAGTATC
394311 A
1 A
394312 ATCTACTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTATTAATAATATTATTAGTATC
Found at i:397035 original size:56 final size:53
Alignment explanation
Indices: 396975--397079 Score: 140
Period size: 53 Copynumber: 1.9 Consensus size: 53
396965 GCTCATAAGC
396975 TTATTTTTACCAA-ATACTTATCATTTAAATTCCATAAGCTCATAAGCTTATTATTA
1 TTATTTTT-CCAATATACTTATCA-TT--ATTCCATAAGCTCATAAGCTTATTATTA
* * *
397031 TTATTTTTTCAATATACTTGTCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTCCAATATACTTATCATTATTCCATAAGCTCATAAGCTTATT
397080 TGCATGGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 23 0.51
55 5 0.11
56 17 0.38
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (53 bp):
TTATTTTTCCAATATACTTATCATTATTCCATAAGCTCATAAGCTTATTATTA
Found at i:399510 original size:15 final size:15
Alignment explanation
Indices: 399490--399520 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
399480 ATTCTCCCTC
399490 CTTAAGAAAATTCGT
1 CTTAAGAAAATTCGT
399505 CTTAAGAAAATTCGT
1 CTTAAGAAAATTCGT
399520 C
1 C
399521 CTCGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (15 bp):
CTTAAGAAAATTCGT
Found at i:405881 original size:19 final size:19
Alignment explanation
Indices: 405833--405889 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
405823 GCGATTTTGA
*
405833 AAAATGTGTTACGATAGTT
1 AAAATGTGTTGCGATAGTT
405852 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
405871 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGATAGTT
405890 TGAAAAACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:405918 original size:22 final size:19
Alignment explanation
Indices: 405833--405918 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
405823 GCGATTTTGA
* *
405833 AAAATGTGTTACGATAGTT
1 AAAATGTGTTGCGATAGTG
*
405852 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
405871 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
405892 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
405915 AAAA
1 AAAA
405919 ATCCAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
19 34 0.60
21 1 0.02
22 8 0.14
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:408969 original size:53 final size:53
Alignment explanation
Indices: 408873--409026 Score: 175
Period size: 53 Copynumber: 2.9 Consensus size: 53
408863 TTCAAATGAT
* *
408873 GGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAATAATCTTCTAAAAAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAATAATCTTCTAAAAAC
* **** *
408927 GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTAAAAAC
* * * *
408980 GGGTTCACTCCCTCTTGCTTCAGGGGGTAAAACTCGAACAATCTTCT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCT
409027 GGTGTGATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
53 61 0.71
54 16 0.19
55 9 0.10
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTAAAAAC
Found at i:409479 original size:42 final size:42
Alignment explanation
Indices: 409399--409607 Score: 145
Period size: 42 Copynumber: 5.1 Consensus size: 42
409389 CCCGAGAAGG
*
409399 CTTA-AAATGGCCCGAAGGACTTATCATC-TCA--CTCGAAAGA
1 CTTACAAATGACCCGAAGGA-TT-TCATCATCATGCTCGAAAGA
409439 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
* ** * * * *
409481 CTTAC---TGA--TGAATTTACTTCA-CTACTCTTCGGT-G-AAGG
1 CTTACAAATGACCCGAA-GGATTTCATC-A-TCAT-GCTCGAAAGA
* * *
409519 CTTACAAATTATCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
** * *
409561 CTTACTGATGGCCCGAAGGATTTCATCATCATGCTCAAAAGA
1 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
409603 CTTAC
1 CTTAC
409608 TGATGACACT
Statistics
Matches: 129, Mismatches: 24, Indels: 30
0.70 0.13 0.16
Matches are distributed among these distances:
37 4 0.03
38 14 0.11
39 12 0.09
40 13 0.10
41 20 0.16
42 62 0.48
43 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
CTTACAAATGACCCGAAGGATTTCATCATCATGCTCGAAAGA
Found at i:409608 original size:42 final size:42
Alignment explanation
Indices: 409531--409612 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
409521 TACAAATTAT
*
409531 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
*
409573 CCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATG
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATG
409613 ACACTTACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
Found at i:410037 original size:211 final size:214
Alignment explanation
Indices: 409650--410087 Score: 731
Period size: 210 Copynumber: 2.1 Consensus size: 214
409640 CTCTTCGGTG
* * *
409650 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
1 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
409715 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
409780 ATCGTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTA-CGATGGCCTGAAGG
131 ATCGTTTTCATTTTCAAAATCTTTTGAAAACATCTTACCCGAAGGTTTTATCGATGGCCCGAAGG
409844 ACTTATCATC-T-GCTCTA
196 ACTTATCATCTTGGCTCTA
*
409861 AAGGCTTACAGATGACCCGAAGGATTTAAGC-TCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
*
409925 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* * *
409990 ATCATTTTTTATTTTCAAAATCTTTTGAAAACATCTTACCCGAAGGTTTTATGGATGGCCCGAAG
131 ATC-GTTTTCATTTTCAAAATCTTTTGAAAACATCTTACCCGAAGGTTTTATCGATGGCCCGAAG
410055 GACTTATCATCTTGGCTCTA
195 GACTTATCATCTTGGCTCTA
410075 AAGGCTTACAGAT
1 AAGGCTTACAGAT
410088 TACTGATGGC
Statistics
Matches: 211, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
210 97 0.46
211 72 0.34
212 22 0.10
213 1 0.00
214 19 0.09
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCGTTTTCATTTTCAAAATCTTTTGAAAACATCTTACCCGAAGGTTTTATCGATGGCCCGAAGG
ACTTATCATCTTGGCTCTA
Found at i:411281 original size:184 final size:183
Alignment explanation
Indices: 410972--411339 Score: 645
Period size: 184 Copynumber: 2.0 Consensus size: 183
410962 GGCTCATTCT
*
410972 CAATATCTTGTGCTGAATCTTGTCATCCCAACATGATCTGGGTTTCTGGTCATGCCCTAAGTGGG
1 CAATATCTTCTGCTGAATCTTGTCATCCCAACAT-ATCTGGGTTTCTGGTCATGCCCTAAGTGGG
411037 TACTCTTGGATCTCTTTGTGCCCAAATCATAACTTGAATGTTCTCATTCGTGTCACTACATAGTA
65 TACTCTTGGATCTCTTTGTGCCCAAATCATAACTTGAATGTTCTCATTCGTGTCACTACATAGTA
411102 GTGTTGTCAGTAGTTTTGAAGGCATCTCTTCACATTGTCA-AACACTTAAGTGCC
130 GTGTTGTCAGTAG-TTTGAAGGCATCTCTTCACATTGTCATAACACTTAAGTGCC
411156 CAATATCTTCTGATCTGAATC-TGTCATCCCAACAT-TCTGGGTTTCTGGTCATGCCCTAAAGTG
1 CAATATCTTCTG--CTGAATCTTGTCATCCCAACATATCTGGGTTTCTGGTCATGCCCT-AAGTG
411219 GGTACTCTTGGATCTCTTTGTGCCCAAATCATAACTTGAATGTTCTCATTC-TCGTCACTACATA
63 GGTACTCTTGGATCTCTTTGTGCCCAAATCATAACTTGAATGTTCTCATTCGT-GTCACTACATA
411283 GTAGTGTTGTCAGTAGTTTGAAGGCATCTCTTCACATTGTCATAACACTTAAGTGCC
127 GTAGTGTTGTCAGTAGTTTGAAGGCATCTCTTCACATTGTCATAACACTTAAGTGCC
411340 TAATTTTTCT
Statistics
Matches: 178, Mismatches: 1, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
183 49 0.28
184 108 0.61
185 14 0.08
186 7 0.04
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (183 bp):
CAATATCTTCTGCTGAATCTTGTCATCCCAACATATCTGGGTTTCTGGTCATGCCCTAAGTGGGT
ACTCTTGGATCTCTTTGTGCCCAAATCATAACTTGAATGTTCTCATTCGTGTCACTACATAGTAG
TGTTGTCAGTAGTTTGAAGGCATCTCTTCACATTGTCATAACACTTAAGTGCC
Found at i:412425 original size:105 final size:107
Alignment explanation
Indices: 412227--412442 Score: 393
Period size: 105 Copynumber: 2.0 Consensus size: 107
412217 CATACACCAA
*
412227 ATTGCCAGGTACCCGATCAAGGTCCTGGTTTGAATATAATCTATTCATAAAGCCAGGGCTTCGAG
1 ATTGCCAGGTACCCGATCAAGGTCATGGTTTGAATATAATCTATTCATAAAGCCAGGGCTTCGAG
412292 TTTCCTTTATAACCAATTGCTTTAGCAGAATAGCCC-GCTTT
66 TTTCCTTTATAACCAATTGCTTTAGCAGAATAGCCCAGCTTT
412333 ATTGCCAGGTACCCGATCAAGGTCATGGTTTG-A-ATAATCTATTCATAAAGCCAGGGCTTTCGA
1 ATTGCCAGGTACCCGATCAAGGTCATGGTTTGAATATAATCTATTCATAAAGCCAGGGC-TTCGA
412396 GTTTCCTTTATAACCAATTGCTTTAGCAGAATAGCCCAGCTTT
65 GTTTCCTTTATAACCAATTGCTTTAGCAGAATAGCCCAGCTTT
412439 ATTG
1 ATTG
412443 TATATATATA
Statistics
Matches: 107, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
104 24 0.22
105 43 0.40
106 40 0.37
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (107 bp):
ATTGCCAGGTACCCGATCAAGGTCATGGTTTGAATATAATCTATTCATAAAGCCAGGGCTTCGAG
TTTCCTTTATAACCAATTGCTTTAGCAGAATAGCCCAGCTTT
Found at i:416474 original size:6 final size:6
Alignment explanation
Indices: 416465--416496 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
416455 TGCTAATAAG
*
416465 AATGCA AATGCA AATGCA AATGCA CATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AA
416497 AGGTGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (6 bp):
AATGCA
Found at i:424328 original size:13 final size:13
Alignment explanation
Indices: 424310--424353 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
424300 ATACGTATGA
424310 ACAGTAACCTGCT
1 ACAGTAACCTGCT
*
424323 ACAGT-ACCGTG-A
1 ACAGTAACC-TGCT
424335 ACAGTAACCTGCT
1 ACAGTAACCTGCT
424348 ACAGTA
1 ACAGTA
424354 CCAAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (13 bp):
ACAGTAACCTGCT
Found at i:424341 original size:25 final size:25
Alignment explanation
Indices: 424307--424355 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
424297 AAAATACGTA
424307 TGAACAGTAACCTGCTACAGTACCG
1 TGAACAGTAACCTGCTACAGTACCG
424332 TGAACAGTAACCTGCTACAGTACC
1 TGAACAGTAACCTGCTACAGTACC
424356 AAAATGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (25 bp):
TGAACAGTAACCTGCTACAGTACCG
Found at i:424417 original size:21 final size:22
Alignment explanation
Indices: 424384--424428 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
424374 TTTTACAAAT
424384 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
424406 AGGGAA-CGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
424427 AG
1 AG
424429 TACTGCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAATCGATTCCCCTGCTAC
Found at i:425967 original size:19 final size:19
Alignment explanation
Indices: 425918--425959 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
425908 CACGTTTGGA
425918 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
425938 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
425957 AGA
1 AGA
425960 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:429466 original size:17 final size:17
Alignment explanation
Indices: 429444--429485 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
429434 GATCATCCTC
429444 CATTATTCCATTGTTGT
1 CATTATTCCATTGTTGT
*
429461 CATTATTTCATTGTTGT
1 CATTATTCCATTGTTGT
*
429478 CCTTATTC
1 CATTATTC
429486 TTTGAGGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.55
Consensus pattern (17 bp):
CATTATTCCATTGTTGT
Found at i:429719 original size:22 final size:22
Alignment explanation
Indices: 429693--429736 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
429683 CCTCCAAACT
429693 CAACATCTTCAAAATATTGTTA
1 CAACATCTTCAAAATATTGTTA
429715 CAACATCTTCAAAATATTGTTA
1 CAACATCTTCAAAATATTGTTA
429737 TAGATCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (22 bp):
CAACATCTTCAAAATATTGTTA
Found at i:431106 original size:63 final size:61
Alignment explanation
Indices: 431028--431206 Score: 175
Period size: 64 Copynumber: 2.8 Consensus size: 61
431018 GAATTAAATT
*
431028 GAACATCAAATGCATTCCG-TGCATCGATGCACACCATGCACCGATGCACTGAGGAT-TTTATAA
1 GAACATCGAATGCATT--GATGCATCGATGCACACCATGCACCGATGCACTG-GGATATTT-TAA
* * * *
431091 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGTATCGATGCACTTGGGCTATTTTGA
1 GAACATCGAATGCA-TTGATGCATCGATGCA-CA-CCATGCACCGATGCAC-TGGGATATTTTAA
* *
431156 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCA-TTGATGCATCGATGCACAC-CA-TGCACCGATGCACT
431207 AAGGTTCCAA
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
62 2 0.02
63 28 0.29
64 44 0.45
65 19 0.19
66 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (61 bp):
GAACATCGAATGCATTGATGCATCGATGCACACCATGCACCGATGCACTGGGATATTTTAA
Found at i:431186 original size:17 final size:19
Alignment explanation
Indices: 431158--431206 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
431148 TATTTTGAAA
431158 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
431176 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
431195 CACCGATGCACT
1 CATCGATGCACT
431207 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:439331 original size:20 final size:22
Alignment explanation
Indices: 439293--439343 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
439283 ATTTAACAAA
439293 AAGGGGGAGAAATGTTTTTA-T
1 AAGGGGGAGAAATGTTTTTAGT
439314 AAGGGGGA-AAACTG-TTTTAGT
1 AAGGGGGAGAAA-TGTTTTTAGT
439335 AAGGGGGAG
1 AAGGGGGAG
439344 TAATCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.33, C:0.02, G:0.39, T:0.25
Consensus pattern (22 bp):
AAGGGGGAGAAATGTTTTTAGT
Found at i:439748 original size:17 final size:17
Alignment explanation
Indices: 439735--439767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
439725 CGAATGCATT
439735 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
439752 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
439768 TGAGGATTTT
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:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:439797 original size:63 final size:64
Alignment explanation
Indices: 439720--439861 Score: 191
Period size: 63 Copynumber: 2.2 Consensus size: 64
439710 AATTAAATTG
*
439720 AACATCGAATGCATTCCATGCATCGATGCA-CA-CCATGCACCGATGCACTGAGGAT-TTTATAA
1 AACATCGAATGCATTCCATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTT-T-A
439782 A
64 A
** * * *
439783 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTCCATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTAA
439847 AACATCGAATGCATT
1 AACATCGAATGCATT
439862 TGATGCACTC
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
63 28 0.40
64 18 0.26
65 21 0.30
66 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (64 bp):
AACATCGAATGCATTCCATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTAA
Found at i:441483 original size:17 final size:17
Alignment explanation
Indices: 441461--441496 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
441451 TACAATATCT
441461 GAAATATCCTTGAATAA
1 GAAATATCCTTGAATAA
441478 GAAATATCCTTGAATAA
1 GAAATATCCTTGAATAA
441495 GA
1 GA
441497 TTACCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (17 bp):
GAAATATCCTTGAATAA
Found at i:441918 original size:2 final size:2
Alignment explanation
Indices: 441913--441964 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
441903 CGAATAATTA
441913 AT AT AT AT AT 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 AT AT AT AT AT
441955 AT AT AT AT AT
1 AT AT AT AT AT
441965 TCAAAATCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444395 original size:21 final size:21
Alignment explanation
Indices: 444348--444395 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
444338 GGCTGTTCTC
*
444348 AATTTT-TTTTATATTTATAA
1 AATTTTATTTCATATTTATAA
*
444368 AACTTTATTTCATCATTTA-AA
1 AATTTTATTTCAT-ATTTATAA
444389 AATTTTA
1 AATTTTA
444396 AAAATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTATTTCATATTTATAA
Found at i:445166 original size:34 final size:31
Alignment explanation
Indices: 445086--445174 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
445076 GTTAGTATTT
* * *
445086 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
445118 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
445152 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
445175 GAGTTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:447005 original size:21 final size:21
Alignment explanation
Indices: 446945--447017 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
446935 TATGCCATCT
* *
446945 CCGCAGGGTTACATTCCGAGC
1 CCGCAAGGTTACATTCCTAGC
446966 CCGCAAGGTTACATTCCTAGC
1 CCGCAAGGTTACATTCCTAGC
* *
446987 CCGCCAGGTTACATGCCTAGC
1 CCGCAAGGTTACATTCCTAGC
* *
447008 TCGCAGGGTT
1 CCGCAAGGTT
447018 TTATACCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (21 bp):
CCGCAAGGTTACATTCCTAGC
Found at i:447589 original size:34 final size:34
Alignment explanation
Indices: 447539--447636 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
447529 AAATGTTTTT
*
447539 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
447573 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
447607 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
447637 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:452780 original size:7 final size:7
Alignment explanation
Indices: 452768--452795 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
452758 GTAAATAAAT
452768 TTAAAAA
1 TTAAAAA
452775 TTAAAAA
1 TTAAAAA
452782 TTAAAAA
1 TTAAAAA
452789 TTAAAAA
1 TTAAAAA
452796 AATGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:453078 original size:12 final size:12
Alignment explanation
Indices: 453061--453091 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
453051 ACAGTAATAC
453061 AAGAAGAAGATG
1 AAGAAGAAGATG
453073 AAGAAGAAGATG
1 AAGAAGAAGATG
453085 AAGAAGA
1 AAGAAGA
453092 GGATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.06
Consensus pattern (12 bp):
AAGAAGAAGATG
Found at i:464030 original size:22 final size:22
Alignment explanation
Indices: 464002--464046 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
463992 ACTCCGACTC
464002 AAGTTATGTTCTCTCAATGAGA
1 AAGTTATGTTCTCTCAATGAGA
464024 AAGTTATGTTCTCTCAATGAGA
1 AAGTTATGTTCTCTCAATGAGA
464046 A
1 A
464047 TCGAACCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (22 bp):
AAGTTATGTTCTCTCAATGAGA
Found at i:464528 original size:17 final size:16
Alignment explanation
Indices: 464506--464537 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
464496 AGACTTTTAT
464506 TTCTCTTCATCTTCTTA
1 TTCTCTTCAT-TTCTTA
464523 TTCTCTTCATTTCTT
1 TTCTCTTCATTTCTT
464538 CTTCCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCTCTTCATTTCTTA
Found at i:474308 original size:20 final size:21
Alignment explanation
Indices: 474272--474318 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
474262 AAAAACATGG
* *
474272 AAAAATGGAAAACAAAGCAAC
1 AAAAATGGAAAACAAAGAAAA
474293 AAAAATGTG-AAA-AAAGAAAA
1 AAAAATG-GAAAACAAAGAAAA
474313 AAAAAT
1 AAAAAT
474319 CAAATGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 12 0.52
21 10 0.43
22 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.13, T:0.09
Consensus pattern (21 bp):
AAAAATGGAAAACAAAGAAAA
Found at i:481254 original size:19 final size:19
Alignment explanation
Indices: 481230--481272 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
481220 AAGTGTGTTC
*
481230 ACAAGAAGTCGAATGTGCT
1 ACAAGAAGTCGAATGTACT
*
481249 ACAAGAAGTTGAATGTACT
1 ACAAGAAGTCGAATGTACT
481268 ACAAG
1 ACAAG
481273 TCGATCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (19 bp):
ACAAGAAGTCGAATGTACT
Found at i:484384 original size:15 final size:16
Alignment explanation
Indices: 484355--484410 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
484345 TATTTTTTTA
484355 TAGA-TTTTAAGTTTCT
1 TAGATTTTTAA-TTTCT
484371 TA-ATTTTTAATTTCT
1 TAGATTTTTAATTTCT
484386 TAGATTTTTAATTTCT
1 TAGATTTTTAATTTCT
484402 TAGATTTTT
1 TAGATTTTT
484411 TTAATCTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.21
16 30 0.79
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (16 bp):
TAGATTTTTAATTTCT
Found at i:484589 original size:2 final size:2
Alignment explanation
Indices: 484582--484634 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
484572 TTGATTAAAC
484582 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
484624 TA TA TA TA TA T
1 TA TA TA TA TA T
484635 GCCAATTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:485631 original size:16 final size:16
Alignment explanation
Indices: 485610--485640 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
485600 TAATATTGAA
485610 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
485626 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
485641 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:486668 original size:20 final size:21
Alignment explanation
Indices: 486643--486683 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
486633 TATAGCTTCC
486643 TAAAAT-CCTAAAAATAAAAT
1 TAAAATACCTAAAAATAAAAT
* *
486663 TAAAATAGCTAAAGATAAAAT
1 TAAAATACCTAAAAATAAAAT
486684 CTTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (21 bp):
TAAAATACCTAAAAATAAAAT
Found at i:489751 original size:35 final size:33
Alignment explanation
Indices: 489712--489795 Score: 123
Period size: 35 Copynumber: 2.5 Consensus size: 33
489702 CGAGGGTTTG
* *
489712 GTGTTTCAAGAGAAACATTTTCAAATGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAA-G-GTTTTTT
489747 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
*
489780 GTATTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
489796 TGTATTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 21 0.46
34 1 0.02
35 24 0.52
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
Found at i:489787 original size:33 final size:35
Alignment explanation
Indices: 489715--489795 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 35
489705 GGGTTTGGTG
* * *
489715 TTTCAAGAGAAACATTTTCAAATGTTTTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAATGTGTTTTTTGTA
489750 TTTCAAGAGAAACAATTTCAAA-G-GTTTTTTGTA
1 TTTCAAGAGAAACAATTTCAAATGTGTTTTTTGTA
489783 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
489796 TGTATTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 21 0.49
34 1 0.02
35 21 0.49
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41
Consensus pattern (35 bp):
TTTCAAGAGAAACAATTTCAAATGTGTTTTTTGTA
Found at i:489862 original size:36 final size:36
Alignment explanation
Indices: 489813--489881 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
489803 AAAGATTGAA
*
489813 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
489849 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
489882 ACTTCCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:489895 original size:34 final size:35
Alignment explanation
Indices: 489822--489911 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 35
489812 AGTTTCAAGG
** * *
489822 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
489858 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
* *
489892 GAAACTATCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
489912 GAGATTTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
34 24 0.50
36 24 0.50
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:490027 original size:36 final size:36
Alignment explanation
Indices: 489980--490062 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
489970 AAGTTTACGC
* * * **
489980 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
* *
490016 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
*
490052 TTCAATGGAAA
1 TTCAAGGGAAA
490063 TGTTTTCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:490175 original size:65 final size:65
Alignment explanation
Indices: 490013--490176 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
490003 AGACAAAATT
* * * *
490013 TGTTTCAAGGGAAACTATCTC-ATGAGTGACAAAATTCATTTCAATGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTATCTCAAT-AGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTT
490077 A
65 A
* * ** *
490078 TGTTTCAAAAGAAACTGTCTCAAGGGACACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTATCTCAATAGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTA
490143 TGTTTCAAGAGAAACTATCTCAATAGAGACAAAA
1 TGTTTCAAGAGAAACTATCTCAATAGAGACAAAA
490177 CTTAGTTCCA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 83 0.99
66 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTATCTCAATAGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTA
Found at i:490224 original size:102 final size:102
Alignment explanation
Indices: 490083--490278 Score: 261
Period size: 102 Copynumber: 1.9 Consensus size: 102
490073 GTTTATGTTT
* * * *
490083 CAAAAGAAACTGTCTCAAGGGACACAAAATTCATCTCAAGGGAAA-TGTTTTCAATG-TTTATGT
1 CAAAAGAAAATGTCTCAAGGGACACAAAATTCATCTCAAGGGAAACAG-ATTCAAAGATTT-TGT
*
490146 TTCAAGAGAAACTATCTCAATAGAGACAAAACTTAGTTC
64 TTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTC
* * ** *
490185 CAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTT
1 CAAAAGAAAATGTCTCAAGGGACACAAAATTCATCTCAAGGGAAACAGATTCAAAGATTTTGTTT
*
490250 CAAGAGAAACTATCTCAAGGGAGACAAAA
66 CAAGAGAAACTATCTCAAGAGAGACAAAA
490279 TTCATTTCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
102 77 0.95
103 4 0.05
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (102 bp):
CAAAAGAAAATGTCTCAAGGGACACAAAATTCATCTCAAGGGAAACAGATTCAAAGATTTTGTTT
CAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTC
Found at i:490279 original size:167 final size:167
Alignment explanation
Indices: 489949--490593 Score: 884
Period size: 167 Copynumber: 3.9 Consensus size: 167
489939 AAAGATTTTG
* * * * * *
489949 TTTCAAAGGAAACTGTTTTCAAAGTTTACGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * ** * * * * * * ** * * * *
490013 TGTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCATTTCAATGGAAA-TGTTTTCAATG-TT
65 AGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATT
* * *
490076 TATGTTTCAAAAGAAACTGTCTCAAGGGACACAAAATTCA
129 T-TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCA
* *
490116 TCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAATAGAGACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
490181 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
66 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
490246 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCA
131 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCA
490283 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
490348 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
66 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
*
490413 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCA
131 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCA
* * * *
490450 TTTCAAGGGAAAT-TTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAAATTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
* * * * * *
490514 GTTCCAAAAGAACATGTCTCAAGGGAGACGAAATTAGTTTCAATGAAAACAGATTTAAATATTTT
66 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
*
490579 GTTTCAAGGGAAACT
131 GTTTCAAGAGAAACT
490594 TGGAAACTGT
Statistics
Matches: 434, Mismatches: 41, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
166 163 0.38
167 267 0.62
168 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCA
Found at i:490293 original size:65 final size:65
Alignment explanation
Indices: 490197--490343 Score: 199
Period size: 65 Copynumber: 2.3 Consensus size: 65
490187 AAAGAAAATG
* **
490197 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAAC
1 TCTCAAGGGAGACAAAATTCATTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAAC
490260 TA
64 TA
* * *
490262 TCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGGGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
*
490327 TCTCAAGAGAGACAAAA
1 TCTCAAGGGAGACAAAA
490344 CTTAGTTCCA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 4 0.05
65 69 0.95
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (65 bp):
TCTCAAGGGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:490360 original size:102 final size:102
Alignment explanation
Indices: 490254--490445 Score: 280
Period size: 102 Copynumber: 1.9 Consensus size: 102
490244 TTGTTTCAAG
* * * *
490254 AGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAA-TGTTTTCAATG-TTTATGTTTCA
1 AGAAAATATCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCA
490317 AGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
64 AGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
* * **
490356 AGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAAATATCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
490421 AGAAACTATCTCAAGAGAGACAAAA
66 AGAAACTATCTCAAGAGAGACAAAA
490446 TTCATTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 76 0.95
103 4 0.05
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (102 bp):
AGAAAATATCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
AGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:490511 original size:65 final size:65
Alignment explanation
Indices: 490356--490509 Score: 186
Period size: 64 Copynumber: 2.4 Consensus size: 65
490346 TAGTTCCAAA
* **
490356 AGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAAATGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
* * * *** *
490421 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TTTTTCAATG-TTTATGTTTCAA
1 AGAAAATGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTT-TGTTTCAA
490484 G
65 G
*
490485 AGAAATTGTCTCAAGGGAGACAAAA
1 AGAAAATGTCTCAAGGGAGACAAAA
490510 ATTAGTTCCA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
63 3 0.04
64 37 0.49
65 35 0.47
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (65 bp):
AGAAAATGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
Found at i:490926 original size:106 final size:105
Alignment explanation
Indices: 490741--491063 Score: 466
Period size: 106 Copynumber: 3.0 Consensus size: 105
490731 TGTATTGTTC
* * * * **
490741 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGACTCTGGAACTAAGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTG-CTCTGAAATTGGGAAATTATTTGTTGACA
* * * * * *
490806 GCCAGCCATCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGTCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
* *
490847 CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTAGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATT-GCTCTGAAATTGGGAAATTATTTGTTGACA
490912 ACCAGTCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGTCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
*
490953 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATT-GCTCTGAAATTGGGAAATTATTTGTTGACA
* *
491018 ACAAGTCGTCCCTTTGTTGTGGAGTTGAACTTGTGTTGTCT
65 ACCAGTCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
491059 CGAGT
1 CGAGT
491064 GGCACGATAT
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
106 195 0.99
107 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGCTCTGAAATTGGGAAATTATTTGTTGACAA
CCAGTCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:491697 original size:32 final size:32
Alignment explanation
Indices: 491661--491752 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
491651 CCCAAAGATG
* *
491661 CCCCAATATTCGATGTTGAATCTCAAAAAATA
1 CCCCAACATTTGATGTTGAATCTCAAAAAATA
* * *
491693 CCCCAACATTTGATGTTAAATCTAAAAAAATG
1 CCCCAACATTTGATGTTGAATCTCAAAAAATA
*
491725 CTCCAACATTTGATGTTGAATCTTCAAA
1 CCCCAACATTTGATGTTGAATC-TCAAA
491753 GATGCCCTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 47 0.92
33 4 0.08
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (32 bp):
CCCCAACATTTGATGTTGAATCTCAAAAAATA
Found at i:492289 original size:25 final size:25
Alignment explanation
Indices: 492252--492311 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
492242 TCGGATTGTG
*
492252 CGAT-GCCTTATCAAGGAATTCATA
1 CGATCGCCTCATCAAGGAATTCATA
* *
492276 CGATCGCCTCATCAAGGAATTCGTG
1 CGATCGCCTCATCAAGGAATTCATA
492301 CGATCGCCTCA
1 CGATCGCCTCA
492312 GCTGCCCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (25 bp):
CGATCGCCTCATCAAGGAATTCATA
Found at i:492800 original size:69 final size:69
Alignment explanation
Indices: 492689--492826 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
492679 TGTCTCTCTC
*
492689 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
492754 TCAT
66 TCAT
* * *
492758 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
492823 TCAT
66 TCAT
492827 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:497961 original size:35 final size:35
Alignment explanation
Indices: 497911--497998 Score: 149
Period size: 35 Copynumber: 2.5 Consensus size: 35
497901 GGGTTCCTAA
* *
497911 AAAATAAAAAATAAAAATTAGCACAAATAAATATTC
1 AAAAT-AAAAATAAAAAATAACACAAATAAATATTC
497947 AAAATAAAAATAAAAAATAACACAAATAAATATTC
1 AAAATAAAAATAAAAAATAACACAAATAAATATTC
497982 AAAATAAAAATAAAAAA
1 AAAATAAAAATAAAAAA
497999 CCAAATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 45 0.90
36 5 0.10
ACGTcount: A:0.73, C:0.07, G:0.01, T:0.19
Consensus pattern (35 bp):
AAAATAAAAATAAAAAATAACACAAATAAATATTC
Found at i:497998 original size:13 final size:13
Alignment explanation
Indices: 497910--497997 Score: 52
Period size: 13 Copynumber: 6.4 Consensus size: 13
497900 CGGGTTCCTA
497910 AAAAATAAAAAAT
1 AAAAATAAAAAAT
*
497923 AAAAATTAGCACAAAT
1 AAAAA-TA--AAAAAT
* **
497939 AAATATTCAAAAT
1 AAAAATAAAAAAT
497952 AAAAATAAAAAAT
1 AAAAATAAAAAAT
* *
497965 AACACAAATAAATATT
1 -A-A-AAATAAAAAAT
*
497981 CAAAAT-AAAAAT
1 AAAAATAAAAAAT
497993 AAAAA
1 AAAAA
497998 ACCAAATAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
12 8 0.15
13 23 0.42
14 4 0.07
15 2 0.04
16 18 0.33
ACGTcount: A:0.73, C:0.07, G:0.01, T:0.19
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:503469 original size:31 final size:31
Alignment explanation
Indices: 503431--503524 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
503421 CCCGAAGGAC
*
503431 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
503462 CAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
503493 CAGTCCATATGTCCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
503524 C
1 C
503525 CCTCGACCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:504287 original size:64 final size:62
Alignment explanation
Indices: 504179--504399 Score: 264
Period size: 64 Copynumber: 3.5 Consensus size: 62
504169 TAATGAAGGT
* * * ** *
504179 ATGCATCGATGCACTACTGATGTATCGGTGCATAAAATGTATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTT-TATTATTA-TGGG
*
504243 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTTT-ATTATT-ATGGG
***
504307 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTATTTATT-TTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATG--TTTATTATTATGGG
**
504370 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
504400 ACACCTTCAA
Statistics
Matches: 139, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
63 4 0.03
64 128 0.92
65 4 0.03
66 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTTTATTATTATGGG
Found at i:507413 original size:31 final size:31
Alignment explanation
Indices: 507365--507489 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
507355 CCCGAAGGAC
*
507365 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
507396 CATTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
507427 CAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
507458 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
507489 C
1 C
507490 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:508253 original size:64 final size:64
Alignment explanation
Indices: 508145--508429 Score: 405
Period size: 64 Copynumber: 4.5 Consensus size: 64
508135 TAATGAAGGT
* * ** * * *
508145 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAATGGG
508209 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
*
508273 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
* **
508337 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAATGGG
**
508400 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
508430 ACACCTTCAA
Statistics
Matches: 204, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
63 3 0.01
64 196 0.96
65 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:517658 original size:51 final size:51
Alignment explanation
Indices: 517599--517703 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
517589 TAATTTAAAT
517599 TTAATTTAATATTTTTTCTATTCAATCAAGAGAAAAACAAGTGTCACCACC
1 TTAATTTAATATTTTTTCTATTCAATCAAGAGAAAAACAAGTGTCACCACC
* *
517650 TTAATTTAATATTTTTTTTATTCAATCAAGAGAAAAACACGTGTCACCACC
1 TTAATTTAATATTTTTTCTATTCAATCAAGAGAAAAACAAGTGTCACCACC
517701 TTA
1 TTA
517704 TTGATAGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (51 bp):
TTAATTTAATATTTTTTCTATTCAATCAAGAGAAAAACAAGTGTCACCACC
Found at i:518550 original size:25 final size:25
Alignment explanation
Indices: 518520--518569 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
518510 AATATTAAGG
*
518520 ACTAAATGTATAAACATACTAATTC
1 ACTAAATGTATAAACATACCAATTC
518545 ACTAAATGTATAAACATACCAATTC
1 ACTAAATGTATAAACATACCAATTC
518570 TTCTAACTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (25 bp):
ACTAAATGTATAAACATACCAATTC
Found at i:519419 original size:2 final size:2
Alignment explanation
Indices: 519412--519438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
519402 TTACAGCCGA
519412 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
519439 CACACACAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527806 original size:18 final size:17
Alignment explanation
Indices: 527775--527847 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 17
527765 TGAATTCTAA
* *
527775 ATATTTTCAGTTATCAG
1 ATATTTACAATTATCAG
527792 ATGATTTACAATTATCAG
1 AT-ATTTACAATTATCAG
* * * *
527810 ATAATTACAAATATAAT
1 ATATTTACAATTATCAG
*
527827 ATATTTTACACTTATCAG
1 ATA-TTTACAATTATCAG
527845 ATA
1 ATA
527848 CAAATTAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
17 16 0.37
18 27 0.63
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (17 bp):
ATATTTACAATTATCAG
Found at i:533210 original size:77 final size:79
Alignment explanation
Indices: 533080--533233 Score: 231
Period size: 77 Copynumber: 2.0 Consensus size: 79
533070 ATATAGAAGG
*
533080 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATGGATATTTAATTTGAAATAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACGCTTTTAATGGATATTTAATTTGAAATAATTA
*
533145 AATAAGAGTTTATA
66 AATAAGAATTTATA
* * * * *
533159 TAAACATT-AAAGAGTGTAATTCGGATTATAAGGC-TTTAATGGATATTTAATTTGAATTAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACGCTTTTAATGGATATTTAATTTGAAATAATTA
533222 AATAAGAATTTA
66 AATAAGAATTTA
533234 ATTAATTCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 39 0.57
78 21 0.31
79 8 0.12
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.38
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACGCTTTTAATGGATATTTAATTTGAAATAATTA
AATAAGAATTTATA
Found at i:535053 original size:31 final size:31
Alignment explanation
Indices: 535017--535093 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
535007 AAAGAAATTA
*
535017 AAAGTTTAGTGGTATAGATGATATATCACCT
1 AAAGTTTAGTGGTATAAATGATATATCACCT
* * *
535048 AAAGTTTAGTGATATAAATGATATGTCATCT
1 AAAGTTTAGTGGTATAAATGATATATCACCT
*
535079 AAAGTTTAATGGTAT
1 AAAGTTTAGTGGTAT
535094 CCATTATAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (31 bp):
AAAGTTTAGTGGTATAAATGATATATCACCT
Found at i:538093 original size:39 final size:38
Alignment explanation
Indices: 538031--538145 Score: 131
Period size: 39 Copynumber: 3.0 Consensus size: 38
538021 TACTTAATTT
*
538031 CCAAGAAAATAAATTCAACGATTTGTTTTCTTTTACAAA
1 CCAAGAAAATAAATCCAACGATTT-TTTTCTTTTACAAA
* *
538070 CCAAGAAAATAAATCCAATGATTTATTTTCATTTACAAA
1 CCAAGAAAATAAATCCAACGATTT-TTTTCTTTTACAAA
** * * * *
538109 ATAGGAAAATAAATCTAACGATTTATTCCTTTTACAA
1 CCAAGAAAATAAATCCAACGATTTTTTTCTTTTACAA
538146 CTCAGAATCA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
38 10 0.16
39 54 0.84
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (38 bp):
CCAAGAAAATAAATCCAACGATTTTTTTCTTTTACAAA
Found at i:538244 original size:135 final size:136
Alignment explanation
Indices: 538032--538380 Score: 413
Period size: 137 Copynumber: 2.6 Consensus size: 136
538022 ACTTAATTTC
* * * *
538032 CAAGAAAATAAATTCAACGATTTGTTTTCTTTTACAAACCA-AGAAAATAAATCCAATGATTTAT
1 CAAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAGA-AAAATAAATCTAA-GATTTAT
* * * *
538096 TTTCATTTACAAAATAGGAAAATAAATCTAACGATTTA-TTC-CTTTTAC-AACTCAGAATCATA
64 TTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCTCTTTTACAAAC-CAGAATAATA
538158 TAAGATTAT
128 TAAGATTAT
* * *
538167 CAAGAAAATAAATTCAACAAGTTATTTCCTTTTCCAAAACAGAAAAATAAATCTAGCAGA-TTAT
1 CAAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAGAAAAATAAATCTA--AGATTTAT
* * * *
538231 TTCCTTTTACAAAATAGGAAAATAAATCCAATGATTTATTTCTTTTTTACAAACCATAATAATTT
64 TTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCTCTTTTACAAACCAGAATAATAT
*
538296 AAGATTCT
129 AAGATTAT
* * * *
538304 CATGAAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGTAAAATAAAT-TCAATAATTTAT
1 CAAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAGAAAAATAAATCT-AA-GATTTAT
538368 TTCCTTTTACAAA
64 TTCCTTTTACAAA
538381 CCAGAATTAT
Statistics
Matches: 182, Mismatches: 23, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
135 85 0.47
136 8 0.04
137 86 0.47
138 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (136 bp):
CAAGAAAATAAATTCAACAATTTATTTTCTTTTACAAAACAGAAAAATAAATCTAAGATTTATTT
CCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCTCTTTTACAAACCAGAATAATATAA
GATTAT
Found at i:538270 original size:39 final size:37
Alignment explanation
Indices: 538170--538283 Score: 104
Period size: 39 Copynumber: 2.9 Consensus size: 37
538160 AGATTATCAA
*
538170 GAAAATAAATTCAACAAG-TTATTTCCTTTTCCAAAACAG
1 GAAAATAAA-TC--CAAGATTATTTCCTTTTACAAAACAG
* * *
538209 AAAAATAAATCTAGCAGATTATTTCCTTTTACAAAATAG
1 GAAAATAAATCCA--AGATTATTTCCTTTTACAAAACAG
*
538248 GAAAATAAATCCAATGATTTATTTCTTTTTTACAAA
1 GAAAATAAATCCAA-GA-TTATTTC-CTTTTACAAA
538284 CCATAATAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
36 1 0.02
37 1 0.02
38 6 0.10
39 45 0.73
40 9 0.15
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (37 bp):
GAAAATAAATCCAAGATTATTTCCTTTTACAAAACAG
Found at i:538503 original size:39 final size:39
Alignment explanation
Indices: 538459--538633 Score: 244
Period size: 39 Copynumber: 4.5 Consensus size: 39
538449 GATTTGTTTT
* *
538459 GATTTATTTCCTTTTACAAAATAGGAAACTAAATTTAAC
1 GATTTATTTCCTTTTACAAAATAGGAAAATAAATTCAAC
* *
538498 GATTTATTTCCTTTTATAAAATAGGAAAATAAATTCACC
1 GATTTATTTCCTTTTACAAAATAGGAAAATAAATTCAAC
* * *
538537 TATTTATTTCCTTCTACAAAATAGGAAAGA-AAATCCAAC
1 GATTTATTTCCTTTTACAAAATAGGAAA-ATAAATTCAAC
* *
538576 GATTTATTTCCTTTTACAAAATAGGAAAATAAGTTCACC
1 GATTTATTTCCTTTTACAAAATAGGAAAATAAATTCAAC
*
538615 GATTTATTTCATTTTACAA
1 GATTTATTTCCTTTTACAA
538634 TCATAATCAT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.01
39 117 0.98
40 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (39 bp):
GATTTATTTCCTTTTACAAAATAGGAAAATAAATTCAAC
Found at i:538514 original size:49 final size:49
Alignment explanation
Indices: 538415--538514 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
538405 AAAACAATTA
* * **
538415 ATTTTCTTTTACAAAATAGGAAAATAAATCCAACGATTTGTTTTGATTT
1 ATTTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCATTT
* ** *
538464 ATTTCCTTTTACAAAATAGGAAACTAAATTTAACGATTTATTTCCTTTT
1 ATTTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCATTT
538513 AT
1 AT
538515 AAAATAGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (49 bp):
ATTTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCATTT
Found at i:538544 original size:78 final size:78
Alignment explanation
Indices: 538459--538633 Score: 269
Period size: 78 Copynumber: 2.2 Consensus size: 78
538449 GATTTGTTTT
* ** *
538459 GATTTATTTCCTTTTACAAAATAGGAAACTAAATTTAACGATTTATTTCCTTTTATAAAATAGGA
1 GATTTATTTCCTTTTACAAAATAGGAAACAAAATCCAACGATTTATTTCCTTTTACAAAATAGGA
538524 AAATAAATTCACC
66 AAATAAATTCACC
* * *
538537 TATTTATTTCCTTCTACAAAATAGGAAAGAAAATCCAACGATTTATTTCCTTTTACAAAATAGGA
1 GATTTATTTCCTTTTACAAAATAGGAAACAAAATCCAACGATTTATTTCCTTTTACAAAATAGGA
*
538602 AAATAAGTTCACC
66 AAATAAATTCACC
*
538615 GATTTATTTCATTTTACAA
1 GATTTATTTCCTTTTACAA
538634 TCATAATCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 86 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (78 bp):
GATTTATTTCCTTTTACAAAATAGGAAACAAAATCCAACGATTTATTTCCTTTTACAAAATAGGA
AAATAAATTCACC
Found at i:538997 original size:45 final size:43
Alignment explanation
Indices: 538928--539086 Score: 192
Period size: 45 Copynumber: 3.5 Consensus size: 43
538918 GGAATTAATC
* * *
538928 TTTTAATTTTACCAACCCAATAATCACAAGGAACTAATCCTTTGA
1 TTTT-ATTTTAGCAA-CTAATAATCAAAAGGAACTAATCCTTTGA
* *
538973 TTTTAGTTTTCGTAATCTAATAATCAAAAGGAACTAATCCTTTGA
1 TTTTA-TTTTAGCAA-CTAATAATCAAAAGGAACTAATCCTTTGA
*
539018 TTTTTATTTTGGCAACTCAATAATCAAAAGGAACTAATCCTTTGA
1 -TTTTATTTTAGCAACT-AATAATCAAAAGGAACTAATCCTTTGA
539063 TTTTACTTTTAGCAACCTAATAAT
1 TTTTA-TTTTAGCAA-CTAATAAT
539087 TACAAGCATT
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
44 8 0.08
45 85 0.85
46 7 0.07
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (43 bp):
TTTTATTTTAGCAACTAATAATCAAAAGGAACTAATCCTTTGA
Found at i:539490 original size:14 final size:14
Alignment explanation
Indices: 539469--539508 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
539459 AAAAAGGGCA
*
539469 AATCACCATGCGCT
1 AATCACCATGCACT
*
539483 AGTCACCATGCACT
1 AATCACCATGCACT
539497 AATCACCATGCA
1 AATCACCATGCA
539509 TTTGTGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (14 bp):
AATCACCATGCACT
Found at i:545139 original size:15 final size:15
Alignment explanation
Indices: 545119--545208 Score: 53
Period size: 15 Copynumber: 5.9 Consensus size: 15
545109 AAATAAGTAA
545119 ATGAATAAATATAAT
1 ATGAATAAATATAAT
*
545134 ATGAATAATAATATTATT
1 ATGAAT-A-AATA-TAAT
*
545152 AT-AATAATATATAAC
1 ATGAATAA-ATATAAT
*
545167 AT-CAT-AATATAAT
1 ATGAATAAATATAAT
*
545180 ATATAATAATATATAAT
1 AT-GAATAA-ATATAAT
*
545197 ATGTA-AAATATA
1 ATGAATAAATATA
545209 CTATCTAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.14
14 6 0.10
15 17 0.29
16 7 0.12
17 16 0.27
18 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (15 bp):
ATGAATAAATATAAT
Found at i:545196 original size:37 final size:37
Alignment explanation
Indices: 545125--545241 Score: 100
Period size: 37 Copynumber: 3.1 Consensus size: 37
545115 GTAAATGAAT
545125 AAATATA-ATATGAATA-ATAATATTATTATAATAATATATA
1 AAATATACATAT-AATATATAATA--A-TAT-ATAATATATA
* *
545165 ACATCATA-ATATAATATATAATAATATATAATATGTA
1 AAAT-ATACATATAATATATAATAATATATAATATATA
*
545202 AAATATACTATCTAAT-TAGTAAT-ATATATAATATATA
1 AAATATAC-ATATAATATA-TAATAATATATAATATATA
545239 AAA
1 AAA
545242 CATATTATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
36 3 0.04
37 30 0.45
38 13 0.19
39 1 0.01
40 7 0.10
41 13 0.19
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (37 bp):
AAATATACATATAATATATAATAATATATAATATATA
Found at i:545208 original size:44 final size:44
Alignment explanation
Indices: 545126--545239 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
545116 TAAATGAATA
* *
545126 AATATAATATGAATAATAATAT-TATTATAATAATATATAAC-ATCAT
1 AATATAATAT--ATAATAATATATAATATAATAAAATAT-ACTATC-T
*
545172 AATATAATATATAATAATATATAATAT-GTAAAATATACTATCT
1 AATATAATATATAATAATATATAATATAATAAAATATACTATCT
545215 AATTAGTAATATAT-ATAATATATAA
1 AA-TA-TAATATATAATAATATATAA
545240 AACATATTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
43 5 0.08
44 33 0.54
45 13 0.21
46 10 0.16
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (44 bp):
AATATAATATATAATAATATATAATATAATAAAATATACTATCT
Found at i:552296 original size:6 final size:6
Alignment explanation
Indices: 552277--552309 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
552267 TGTCTCAGAA
*
552277 AGGAAG AGGTAG AGGAAG AGGAAG AGGAAG AGG
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGG
552310 CAGAAGTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (6 bp):
AGGAAG
Found at i:556727 original size:22 final size:21
Alignment explanation
Indices: 556676--556727 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
556666 ACCGATACCT
*
556676 AGTATCGATA-CCTAGGAAGG
1 AGTATCGGTACCCTAGGAAGG
* *
556696 -GTATCAGTACCCTAGAGTAGG
1 AGTATCGGTACCCTAG-GAAGG
556717 AGTATCGGTAC
1 AGTATCGGTAC
556728 TGTGCTTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.28
20 5 0.20
21 4 0.16
22 9 0.36
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (21 bp):
AGTATCGGTACCCTAGGAAGG
Found at i:557333 original size:30 final size:30
Alignment explanation
Indices: 557297--557357 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
557287 CGTCGAGGGT
*
557297 TACCTATGTCCTTCAGG-ATATATGGACAGG
1 TACCTATGTCCTTC-GGAACATATGGACAGG
* *
557327 TACCTATGTTCTTCGGAACATATGGATAGG
1 TACCTATGTCCTTCGGAACATATGGACAGG
557357 T
1 T
557358 TATTCGGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
TACCTATGTCCTTCGGAACATATGGACAGG
Found at i:558950 original size:20 final size:22
Alignment explanation
Indices: 558905--558962 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
558895 GCATGGGTAG
558905 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
558929 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
558949 TGTATCGATGCACT
1 TGCATCGATGCACT
558963 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:559292 original size:13 final size:13
Alignment explanation
Indices: 559274--559314 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
559264 GATATGTTAC
559274 ATATGTGTTAATG
1 ATATGTGTTAATG
*
559287 ATATGTGTGAAT-
1 ATATGTGTTAATG
559299 ATATGT-TTATATG
1 ATATGTGTTA-ATG
559312 ATA
1 ATA
559315 CAGGTTCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (13 bp):
ATATGTGTTAATG
Found at i:559819 original size:23 final size:23
Alignment explanation
Indices: 559782--559832 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
559772 TCCTTCGGGA
* *
559782 CATAGTGGTCCTTCGA-AACATTT
1 CATAGTAGTCATTCGACAA-ATTT
559805 CATAGTAGTCATTCGACAAATTT
1 CATAGTAGTCATTCGACAAATTT
559828 CATAG
1 CATAG
559833 CCCCTAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (23 bp):
CATAGTAGTCATTCGACAAATTT
Found at i:562335 original size:23 final size:22
Alignment explanation
Indices: 562292--562335 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
562282 AAGGCCAGAG
*
562292 GAAAATACAGAATCGAATGAGA
1 GAAAATACAGAATAGAATGAGA
*
562314 GAAAATACATGAATAGATTGAG
1 GAAAATACA-GAATAGAATGAG
562336 GTTACTAGTT
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:0.52, C:0.07, G:0.23, T:0.18
Consensus pattern (22 bp):
GAAAATACAGAATAGAATGAGA
Found at i:563583 original size:13 final size:13
Alignment explanation
Indices: 563565--563605 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
563555 AATATGTTAC
563565 ATATGTGTTAATG
1 ATATGTGTTAATG
*
563578 ATATGTGTGAAT-
1 ATATGTGTTAATG
563590 ATATGT-TTATATG
1 ATATGTGTTA-ATG
563603 ATA
1 ATA
563606 CAGGTTCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (13 bp):
ATATGTGTTAATG
Found at i:566858 original size:53 final size:53
Alignment explanation
Indices: 566778--566888 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
566768 ACTAATGTAA
*
566778 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTACACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATACACACATAGTGC
* *
566831 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATACACACATAGTGC
566884 CGAAA
1 CGAAA
566889 GTACACAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATACACACATAGTGC
Found at i:568141 original size:11 final size:10
Alignment explanation
Indices: 568108--568141 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
568098 ATGGCCTAAG
*
568108 TTTCATGAAA
1 TTTCATGTAA
568118 TTTCATGTAA
1 TTTCATGTAA
568128 TTTCATGTTAA
1 TTTCATG-TAA
568139 TTT
1 TTT
568142 AACCTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TTTCATGTAA
Found at i:573334 original size:53 final size:53
Alignment explanation
Indices: 573270--573380 Score: 177
Period size: 53 Copynumber: 2.1 Consensus size: 53
573260 ATTAATGTAA
* * *
573270 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGGTGCACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATACACACATAGTGC
* *
573323 TGAAATGGTAATTCACAAACTCGTTATGAATAACATGGATACACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATACACACATAGTGC
573376 CGAAA
1 CGAAA
573381 GTACACAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATACACACATAGTGC
Found at i:575941 original size:9 final size:9
Alignment explanation
Indices: 575922--576216 Score: 61
Period size: 9 Copynumber: 31.6 Consensus size: 9
575912 TAAATACATA
575922 AATATATAAT
1 AATA-ATAAT
575932 AATAATAAT
1 AATAATAAT
575941 AAT-ATAAT
1 AATAATAAT
*
575949 ATATAA-CAT
1 A-ATAATAAT
*
575958 CATAAT-AT
1 AATAATAAT
575966 AATATATAAT
1 AATA-ATAAT
*
575976 -ATATGTAAT
1 AATA-ATAAT
* *
575985 ATATACTACT
1 A-ATAATAAT
*
575995 -ATTATATAT
1 AATAATA-AT
*
576004 AAT-ATACT
1 AATAATAAT
576012 ATATAAT-AT
1 A-ATAATAAT
576021 AATATATAAT
1 AATA-ATAAT
*
576031 AGTATATAAT
1 AATA-ATAAT
576041 ATATAA-AAT
1 A-ATAATAAT
*
576050 -ATACTATAT
1 AATAATA-AT
576059 AATAAGTAAT
1 AATAA-TAAT
576069 -ATATATAAT
1 AATA-ATAAT
*
576078 -ATACT-AT
1 AATAATAAT
576085 AAT-ATATAT
1 AATAATA-AT
576094 ATATAAT-AT
1 A-ATAATAAT
576103 ATATAA-AAT
1 A-ATAATAAT
576112 -ATATATATAT
1 AATA-ATA-AT
*
576122 AATACTATAT
1 AATAATA-AT
*
576132 AATACTATAT
1 AATAATA-AT
*
576142 AAATAATATAG
1 -AATAATA-AT
576153 AAT-ATAAT
1 AATAATAAT
576161 ATATATATAAT
1 A-ATA-ATAAT
576172 -ATATATAAT
1 AATA-ATAAT
*
576181 ATATGATATAT
1 A-ATAATA-AT
576192 AAT-ATATAT
1 AATAATA-AT
576201 AATATATAAT
1 AATA-ATAAT
576211 ATATAA
1 A-ATAA
576217 AACATATTAT
Statistics
Matches: 224, Mismatches: 22, Indels: 78
0.69 0.07 0.24
Matches are distributed among these distances:
7 9 0.04
8 31 0.14
9 84 0.38
10 64 0.29
11 36 0.16
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (9 bp):
AATAATAAT
Found at i:575942 original size:32 final size:34
Alignment explanation
Indices: 575930--576029 Score: 76
Period size: 39 Copynumber: 2.7 Consensus size: 34
575920 TAAATATATA
*
575930 ATAATAATAATAATATAATATATAACATCATAAT
1 ATAATAATAATAATATAATACATAACATCATAAT
* * *
575964 ATAATATATAATATATGTAATATATACTACTATTAT-AT
1 ATAATA-ATAATA-ATATAATACATA--AC-ATCATAAT
*
576002 ATAATATACTATATAATATAATATATAA
1 ATAATA-A-TA-ATAATATAATACATAA
576030 TAGTATATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
34 6 0.11
35 6 0.11
36 11 0.20
37 1 0.02
38 12 0.21
39 17 0.30
40 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (34 bp):
ATAATAATAATAATATAATACATAACATCATAAT
Found at i:575954 original size:7 final size:7
Alignment explanation
Indices: 575922--576232 Score: 222
Period size: 7 Copynumber: 43.6 Consensus size: 7
575912 TAAATACATA
575922 AATATAT
1 AATATAT
575929 AATAATAAT
1 AAT-AT-AT
575938 AATAATAT
1 AAT-ATAT
575946 AATATAT
1 AATATAT
*
575953 AACATCAT
1 AATAT-AT
575961 -A-ATAT
1 AATATAT
575966 AATATAT
1 AATATAT
575973 AATATATGT
1 AATATA--T
575982 AATATAT
1 AATATAT
*
575989 ACTACTAT
1 AATA-TAT
*
575997 TATATAT
1 AATATAT
576004 AATATACT
1 AATATA-T
576012 ATATAATAT
1 A-AT-ATAT
576021 AATATAT
1 AATATAT
576028 AATAGTATAT
1 -A-A-TATAT
576038 AATATAT
1 AATATAT
*
576045 AAAATAT
1 AATATAT
*
576052 ACTATAT
1 AATATAT
576059 AATA-AGT
1 AATATA-T
576066 AATATAT
1 AATATAT
576073 -ATA-AT
1 AATATAT
576078 -ATACTAT
1 AATA-TAT
576085 AATATAT
1 AATATAT
576092 -ATATAT
1 AATATAT
576098 AATATAT
1 AATATAT
576105 -ATA-A-
1 AATATAT
576109 AATATAT
1 AATATAT
576116 -ATATAT
1 AATATAT
576122 AATACTAT
1 AATA-TAT
576130 -ATA-AT
1 AATATAT
*
576135 ACTATAT
1 AATATAT
576142 AAATAATAT
1 -AAT-ATAT
576151 AGA-ATAT
1 A-ATATAT
576158 AATATAT
1 AATATAT
576165 -ATATA-
1 AATATAT
576170 ATATATAT
1 A-ATATAT
576178 AATATAT
1 AATATAT
*
576185 GATATAT
1 AATATAT
576192 AATATATAT
1 -A-ATATAT
576201 AATATAT
1 AATATAT
576208 AATATAT
1 AATATAT
* *
576215 AAAACAT
1 AATATAT
*
576222 ATTATAT
1 AATATAT
576229 AATA
1 AATA
576233 AAGTATACCG
Statistics
Matches: 249, Mismatches: 19, Indels: 72
0.73 0.06 0.21
Matches are distributed among these distances:
5 13 0.05
6 31 0.12
7 133 0.53
8 32 0.13
9 32 0.13
10 8 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:576229 original size:2 final size:2
Alignment explanation
Indices: 575923--576215 Score: 188
Period size: 2 Copynumber: 158.5 Consensus size: 2
575913 AAATACATAA
*
575923 AT AT AT A- AT A- AT A- AT A- AT A- AT AT A- AT AT AT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
575958 CAT A- AT AT A- AT AT AT A- AT AT AT GT A- AT AT AT ACT ACT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT
575997 -T AT AT AT A- AT AT ACT AT AT A- AT AT A- AT AT AT A- AT AGT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
576036 AT A- AT AT AT A- AA AT AT ACT AT AT A- AT A- AGT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
*
576075 A- AT AT ACT AT A- AT AT AT AT AT AT A- AT AT AT AT A- AA AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
576114 AT AT AT AT A- AT ACT AT AT A- AT ACT AT AT AA AT A- AT AT AG A-
1 AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
576154 AT AT A- AT AT AT AT AT A- AT AT AT AT A- AT AT AT GAT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
576193 AT AT AT AT A- AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
576216 AAACATATTA
Statistics
Matches: 238, Mismatches: 8, Indels: 90
0.71 0.02 0.27
Matches are distributed among these distances:
1 35 0.15
2 181 0.76
3 22 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:578856 original size:12 final size:12
Alignment explanation
Indices: 578839--578875 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
578829 GAACAAGTTT
578839 ATGTTTGTGTTC
1 ATGTTTGTGTTC
578851 ATGTTTGTGTTC
1 ATGTTTGTGTTC
*
578863 -GGTTTGTGTTC
1 ATGTTTGTGTTC
578874 AT
1 AT
578876 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.57
Consensus pattern (12 bp):
ATGTTTGTGTTC
Found at i:578964 original size:23 final size:23
Alignment explanation
Indices: 578933--579006 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
578923 TGTTCGTGTT
* *
578933 TGTTTATTTATTGTTCATGAATA
1 TGTTCATTTATTGTTCATGAATG
* **
578956 TGTTCATTTAGTGTTTGTGAATG
1 TGTTCATTTATTGTTCATGAATG
*
578979 TGTTCATTTATATGTTCACGAATG
1 TGTTCATTTAT-TGTTCATGAATG
579003 TGTT
1 TGTT
579007 AATTAGAGCT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 28 0.68
24 13 0.32
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.53
Consensus pattern (23 bp):
TGTTCATTTATTGTTCATGAATG
Found at i:579361 original size:42 final size:42
Alignment explanation
Indices: 579310--579451 Score: 223
Period size: 42 Copynumber: 3.4 Consensus size: 42
579300 ATAAACAAGT
579310 AAATAAATAACATCATAACACCATTAAGTCTCAATAAGTCTA
1 AAATAAATAACATCATAACACCATTAAGTCTCAATAAGTCTA
*
579352 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
1 AAATAAATAACATCATAACACCATTAAGTCTCAATAAGTCTA
* * *
579394 AAATAAATAACATCATAACACTAATAAGCCTCAATAAGTCT-
1 AAATAAATAACATCATAACACCATTAAGTCTCAATAAGTCTA
579435 AAATAAAATCAACATCA
1 AAAT-AAAT-AACATCA
579452 ATAATATTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.04
42 82 0.88
43 7 0.08
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (42 bp):
AAATAAATAACATCATAACACCATTAAGTCTCAATAAGTCTA
Found at i:581227 original size:65 final size:65
Alignment explanation
Indices: 581090--581219 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
581080 ACAAATGATT
581090 CACAAACAGTTCACCGAACGTTATGTTCATTTACACCCCCTACAAATAGTTATCAAATAATTATA
1 CACAAACAGTTCACCGAACGTTATGTTCATTTACACCCCCTACAAATAGTTATCAAATAATTATA
*
581155 CACAAACAGTTCACCGAACGTTCTGTTCATTTACACCCCCTACAAATAGTTATCAAATAATTATA
1 CACAAACAGTTCACCGAACGTTATGTTCATTTACACCCCCTACAAATAGTTATCAAATAATTATA
581220 TTAAAACATA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (65 bp):
CACAAACAGTTCACCGAACGTTATGTTCATTTACACCCCCTACAAATAGTTATCAAATAATTATA
Found at i:581593 original size:21 final size:22
Alignment explanation
Indices: 581569--581617 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
581559 ACATTAACTA
*
581569 TCACAATA-CTTACATGACATT
1 TCACAATAGCTTACATGACAAT
581590 TCACAA-AGCTTACATGACAAT
1 TCACAATAGCTTACATGACAAT
*
581611 ACACAAT
1 TCACAAT
581618 TTTGATGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (22 bp):
TCACAATAGCTTACATGACAAT
Found at i:582515 original size:28 final size:29
Alignment explanation
Indices: 582484--582541 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
582474 TAGTATTTAC
582484 AGACTGATTTTTTTTAT-AAAAAAAGCTA
1 AGACTGATTTTTTTTATAAAAAAAAGCTA
582512 AGACTGATTTTTTTTATAAAAAAAAGCTA
1 AGACTGATTTTTTTTATAAAAAAAAGCTA
582541 A
1 A
582542 AAGTGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (29 bp):
AGACTGATTTTTTTTATAAAAAAAAGCTA
Found at i:600260 original size:17 final size:17
Alignment explanation
Indices: 600238--600276 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
600228 GAAAAATGAA
600238 AAGAGTGACTAAACTTG
1 AAGAGTGACTAAACTTG
600255 AAGAGTGACTAAACTTG
1 AAGAGTGACTAAACTTG
600272 AAGAG
1 AAGAG
600277 GGGCTCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (17 bp):
AAGAGTGACTAAACTTG
Found at i:601001 original size:23 final size:23
Alignment explanation
Indices: 600975--601033 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
600965 GGATTAAAGG
* * *
600975 TGTTCGCGAACGTTAAATGAACA
1 TGTTCGCAAACATTAAACGAACA
*
600998 TGTTCGCAAACATTAAACGCACA
1 TGTTCGCAAACATTAAACGAACA
601021 TGTTCGCAAACAT
1 TGTTCGCAAACAT
601034 CAAGCGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (23 bp):
TGTTCGCAAACATTAAACGAACA
Found at i:601050 original size:23 final size:23
Alignment explanation
Indices: 600993--601050 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
600983 AACGTTAAAT
* *
600993 GAACATGTTCGCAAACATTAAAC
1 GAACATGATCGCAAACATCAAAC
* * *
601016 GCACATGTTCGCAAACATCAAGC
1 GAACATGATCGCAAACATCAAAC
*
601039 GAATATGATCGC
1 GAACATGATCGC
601051 GAACGCTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (23 bp):
GAACATGATCGCAAACATCAAAC
Found at i:603227 original size:20 final size:21
Alignment explanation
Indices: 603202--603294 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
603192 TTTTCCCAAT
*
603202 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
603222 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
603243 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
603263 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
603284 TCGCAATGCGA
1 TCGCAATGCGA
603295 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:603247 original size:41 final size:41
Alignment explanation
Indices: 603202--603294 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
603192 TTTTCCCAAT
603202 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
603243 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
603284 TCGCAATGCGA
1 TCGCAATGCGA
603295 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:603307 original size:41 final size:41
Alignment explanation
Indices: 603221--603355 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
603211 GAATAAGTAA
** *
603221 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
603262 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
603303 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
603344 TTCGCAACGCGA
1 ATCGCAACGCGA
603356 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:603308 original size:20 final size:20
Alignment explanation
Indices: 603283--603376 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
603273 AATTGGGAAA
*
603283 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
603303 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
603324 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
603344 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
603364 TTCGCAACGCGAT
1 ATCGCAACGCGAT
603377 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Done.