Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 94 of 325
Found at i:27559264 original size:46 final size:48
Alignment explanation
Indices: 27559063--27559287 Score: 191
Period size: 46 Copynumber: 4.8 Consensus size: 48
27559053 AGGGTATAAT
* * *
27559063 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCTAAAT-TGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTACATCTAAG
* * * * * *
27559112 GCCGACGCCATGTCCCAAACATAGTCTTACACTAGCTCTCACATATAGG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-ACATCTAAG
* * *
27559161 TGCCGATGCCATGTCCCAGACATGGTCTTTCACT-G-AC-ACATCT-CG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTAAG
*
27559206 TAGCTGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCAAG
1 --GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCT-AAG
*
27559254 GCCGATG-CATGTCCCAGACAT-GTCTTACATTGGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC
27559288 ACACAAATAA
Statistics
Matches: 145, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
44 9 0.06
45 16 0.11
46 49 0.34
47 3 0.02
48 5 0.03
49 34 0.23
50 29 0.20
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTAAG
Found at i:27561118 original size:23 final size:23
Alignment explanation
Indices: 27561092--27561166 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
27561082 TGATTTTTAA
*
27561092 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
* *
27561115 ATTTACAATTATTTAGTGATTAT
1 ATTTAGAATTATTTAGTGATAAT
*
27561138 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
27561161 ATTTAG
1 ATTTAG
27561167 GAAAAATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:27561119 original size:13 final size:13
Alignment explanation
Indices: 27561101--27561166 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
27561091 AATTTTGAAT
27561101 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
27561114 TATTTA--CA-AT
1 TATTTAGTGATAA
*
27561124 TATTTAGTGATTA
1 TATTTAGTGATAA
27561137 TATTTAG-GAT--
1 TATTTAGTGATAA
27561147 TATTTAGTGATAA
1 TATTTAGTGATAA
27561160 TATTTAG
1 TATTTAG
27561167 GAAAAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
12 4 0.10
13 20 0.48
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:27566576 original size:105 final size:102
Alignment explanation
Indices: 27566397--27566593 Score: 263
Period size: 105 Copynumber: 1.9 Consensus size: 102
27566387 ATTGACGAAC
* * * * *
27566397 AAGACCATGGTTGGACCATGGCAAAGTGTTAAATGTAAGACCATAACTGGGCTATGGCATTTTAG
1 AAGACCATAGTTGGACCATGGCAAAATGTTAAATGTAAGACCATAACTGGGCTATGACATCTGAG
27566462 TGAAAAGACCATAACTAGGTTATGGCATCGTGAACGT
66 TGAAAAGACCATAACTAGGTTATGGCATCGTGAACGT
*
27566499 AAGACCATAGTTGGACCATGGCAATATATGTATAAGA-GTAAGACCATAGCTGGGCTATGACATC
1 AAGACCATAGTTGGACCATGGCAA-A-ATGT-TAA-ATGTAAGACCATAACTGGGCTATGACAT-
* *
27566563 CTGA-TGATAAGACCATAACTGGGTTATGGCA
61 CTGAGTGAAAAGACCATAACTAGGTTATGGCA
27566594 CTACGAGTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
102 23 0.28
103 1 0.01
104 3 0.04
105 52 0.63
106 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (102 bp):
AAGACCATAGTTGGACCATGGCAAAATGTTAAATGTAAGACCATAACTGGGCTATGACATCTGAG
TGAAAAGACCATAACTAGGTTATGGCATCGTGAACGT
Found at i:27566607 original size:33 final size:32
Alignment explanation
Indices: 27566536--27566611 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
27566526 ATGTATAAGA
* *
27566536 GTAAGACCATAGCTGGGCTATGACATCCTGAT
1 GTAAGACCATAACTGGGCTATGACATACTGAT
* *
27566568 GATAAGACCATAACTGGGTTATGGCACTAC-GAGT
1 G-TAAGACCATAACTGGGCTATGACA-TACTGA-T
27566602 GTAAGACCAT
1 GTAAGACCAT
27566612 GGCAAGGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.03
33 32 0.86
34 4 0.11
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGACATACTGAT
Found at i:27566623 original size:105 final size:104
Alignment explanation
Indices: 27566431--27566640 Score: 237
Period size: 105 Copynumber: 2.0 Consensus size: 104
27566421 AGTGTTAAAT
* * *
27566431 GTAAGACCATAACTGGGCTATGGCATTTTAGTGAAAAGACCATAACTAGGTTATGGCATCGTGAA
1 GTAAGACCATAACTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGTTATGGCATCG-GAA
** *
27566496 CGTAAGACCATAGTTGGACCATGGCAATATATGTATAAGA
65 CGTAAGACCATAGAAGGACCATGGCAATATACGTATAAGA
* * *
27566536 GTAAGACCATAGCTGGGCTATGACATCCTGA-TGATAAGACCATAACTGGGTTATGGCACTAC-G
1 GTAAGACCATAACTGGGCTATGACAT-CTGAGTGAAAAGACCATAACTAGGTTATGGCA-T-CGG
** * *
27566599 AGTGTAAGACCATGGCAAGG-CCATGGCAATATACGTGTAAGA
63 AACGTAAGACCATAG-AAGGACCATGGCAATATACGTATAAGA
27566641 CCATAGTTGG
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
105 82 0.93
106 5 0.06
107 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (104 bp):
GTAAGACCATAACTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGTTATGGCATCGGAAC
GTAAGACCATAGAAGGACCATGGCAATATACGTATAAGA
Found at i:27568847 original size:6 final size:6
Alignment explanation
Indices: 27568836--27568898 Score: 56
Period size: 6 Copynumber: 9.7 Consensus size: 6
27568826 TACGTTTGAA
27568836 AAAAAT AAAAAT AAAAAT AAAAATT AAACAA- AAAAAT AATAATAT ATATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAA-T AAA-AAT AAAAAT AA-AA-AT A-A-AAAT
*
27568889 ATAAAT AAAA
1 AAAAAT AAAA
27568899 GTATATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 2 0.04
6 29 0.59
7 6 0.12
8 8 0.16
9 4 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:27572951 original size:16 final size:17
Alignment explanation
Indices: 27572930--27572965 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
27572920 CGATAAACTG
27572930 AAAAAA-TAAATATTGA
1 AAAAAATTAAATATTGA
27572946 AAAAAATTAAATATTGA
1 AAAAAATTAAATATTGA
27572963 AAA
1 AAA
27572966 GTTAAGTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAAAATTAAATATTGA
Found at i:27572970 original size:15 final size:16
Alignment explanation
Indices: 27572928--27572965 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
27572918 TTCGATAAAC
27572928 TGAAAAAA-TAAATAT
1 TGAAAAAATTAAATAT
27572943 TGAAAAAAATTAAATAT
1 TG-AAAAAATTAAATAT
27572960 TGAAAA
1 TGAAAA
27572966 GTTAAGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (16 bp):
TGAAAAAATTAAATAT
Found at i:27573381 original size:20 final size:22
Alignment explanation
Indices: 27573356--27573395 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27573346 ACCGATGTTT
27573356 AATTTAATT-AT-TTTTTATAC
1 AATTTAATTAATATTTTTATAC
27573376 AATTTAATTAATATTTTTAT
1 AATTTAATTAATATTTTTAT
27573396 TGCAGAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTAATTAATATTTTTATAC
Found at i:27573858 original size:18 final size:19
Alignment explanation
Indices: 27573835--27573872 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
27573825 ACTAAATTAA
27573835 AAAATA-AAAAATTATATT
1 AAAATAGAAAAATTATATT
27573853 AAAATAGAAAAATTATATT
1 AAAATAGAAAAATTATATT
27573872 A
1 A
27573873 CAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATAGAAAAATTATATT
Found at i:27574246 original size:28 final size:24
Alignment explanation
Indices: 27574199--27574249 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 24
27574189 ATAAAAGGTA
27574199 TTTTTTACTTTTTTTTTAAATTAG
1 TTTTTTACTTTTTTTTTAAATTAG
27574223 TTTTTTATCTTATTTATTATTAAATTA
1 TTTTTTA-CTT-TTT-TT-TTAAATTA
27574250 ATAAAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 3 0.13
27 2 0.09
28 8 0.35
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTTACTTTTTTTTTAAATTAG
Found at i:27574331 original size:21 final size:22
Alignment explanation
Indices: 27574297--27574337 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27574287 TTAAAACTCT
27574297 CCCAAAGAGCGCG-TGCATTAA
1 CCCAAAGAGCGCGTTGCATTAA
* *
27574318 CCCAAAGGGTGCGTTGCATT
1 CCCAAAGAGCGCGTTGCATT
27574338 TCCTTATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
CCCAAAGAGCGCGTTGCATTAA
Found at i:27578230 original size:12 final size:12
Alignment explanation
Indices: 27578213--27578238 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27578203 TAATTTAAGG
27578213 TTTTAGTGGCAT
1 TTTTAGTGGCAT
27578225 TTTTAGTGGCAT
1 TTTTAGTGGCAT
27578237 TT
1 TT
27578239 GGATGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (12 bp):
TTTTAGTGGCAT
Found at i:27578398 original size:40 final size:41
Alignment explanation
Indices: 27578282--27578404 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
27578272 GGCGCTAACG
* * * *
27578282 GAAAAACACCATAATAGGTAAAGCAGTAGCTGCGTTTATGA
1 GAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTTTATGA
*
27578323 GAAAAACACCACAAAAGGTCAAGCAATAGCGGCGTTTATGA
1 GAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTTTATGA
** * *
27578364 GAAAAATGCCGCAAAAGGT-AAGCAATAGCGGCGTTTTTGA
1 GAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTTTATGA
27578404 G
1 G
27578405 CAAAGTATCA
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 21 0.29
41 52 0.71
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (41 bp):
GAAAAACACCACAAAAGGTAAAGCAATAGCGGCGTTTATGA
Found at i:27578632 original size:25 final size:25
Alignment explanation
Indices: 27578577--27578659 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 25
27578567 ACAATTTGTT
** *
27578577 GCATCGTCGTCGACTGTCCCTTCTGCT
1 GCATCGTCGTCGACACT-CC-TCTGCC
27578604 GCATCGTCGTCGACACTCCTCTGCC
1 GCATCGTCGTCGACACTCCTCTGCC
* *
27578629 GCATTGCCGTCGACACTCCTCTGCC
1 GCATCGTCGTCGACACTCCTCTGCC
*
27578654 ACATCG
1 GCATCG
27578660 CCATGTAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
25 32 0.65
26 2 0.04
27 15 0.31
ACGTcount: A:0.12, C:0.41, G:0.20, T:0.27
Consensus pattern (25 bp):
GCATCGTCGTCGACACTCCTCTGCC
Found at i:27580389 original size:49 final size:49
Alignment explanation
Indices: 27580317--27580504 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
27580307 TGAGGTCACG
* *
27580317 TGTGTAGTACTAAGTGCAGGCTACGACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * * * *
27580366 TGTGTGGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCGCA
*
27580417 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
27580466 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
27580505 GCTTAGGCTA
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 75 0.65
50 2 0.02
51 39 0.34
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:27580485 original size:100 final size:100
Alignment explanation
Indices: 27580312--27580499 Score: 340
Period size: 100 Copynumber: 1.9 Consensus size: 100
27580302 TATTGTGAGG
* *
27580312 TCACGTGTGTAGTACTAAGTGCAGGCTACGACGTGTACCGGATAATTGGTCGCATGTGTGGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACGACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
27580377 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
* *
27580412 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACGACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
27580477 AAGTGCAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCGTACC
27580500 AGATAGCTTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACGACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:27583322 original size:15 final size:16
Alignment explanation
Indices: 27583299--27583346 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
27583289 TAGTATCGTA
27583299 TCTTGGGTTTCTTTAT
1 TCTTGGGTTTCTTTAT
27583315 TC-TGGGTTT-TTCTA-
1 TCTTGGGTTTCTT-TAT
*
27583329 TCTTGGATTTCTTTAT
1 TCTTGGGTTTCTTTAT
27583345 TC
1 TC
27583347 AGTTTTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.15
15 17 0.63
16 6 0.22
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (16 bp):
TCTTGGGTTTCTTTAT
Found at i:27584861 original size:20 final size:20
Alignment explanation
Indices: 27584838--27584882 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
27584828 TGTCCATGAT
27584838 TTAAATATAAAAATTTTCTA
1 TTAAATATAAAAATTTTCTA
27584858 TTAAATATAAAAATTTTCTA
1 TTAAATATAAAAATTTTCTA
27584878 TTAAA
1 TTAAA
27584883 ATTCATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATATAAAAATTTTCTA
Found at i:27584945 original size:19 final size:19
Alignment explanation
Indices: 27584900--27584946 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
27584890 ATCAAATTAA
*
27584900 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
27584919 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
27584938 AATAAAAAT
1 AATAAAAAT
27584947 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:27588073 original size:26 final size:26
Alignment explanation
Indices: 27588035--27588140 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
27588025 TGATACAAAT
*
27588035 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27588061 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
27588087 TGATAATGGATTAGGTAAA--TTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27588111 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27588137 TGAT
1 TGAT
27588141 GGAAATTTTG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
24 22 0.30
26 51 0.70
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27588123 original size:50 final size:51
Alignment explanation
Indices: 27588035--27588140 Score: 171
Period size: 50 Copynumber: 2.1 Consensus size: 51
27588025 TGATACAAAT
*
27588035 TGATAATGAGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGAGTTAGGTAAA-GTTCCATGATAATGGGTTAGGTAAATGTTCCA
27588087 TGATAATG-GATTAGGTAAA-TTCCATGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGAG-TTAGGTAAAGTTCCATGATAATGGGTTAGGTAAATGTTCCA
27588137 TGAT
1 TGAT
27588141 GGAAATTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
50 34 0.65
51 1 0.02
52 17 0.33
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (51 bp):
TGATAATGAGTTAGGTAAAGTTCCATGATAATGGGTTAGGTAAATGTTCCA
Found at i:27595021 original size:26 final size:26
Alignment explanation
Indices: 27594980--27595086 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
27594970 TGATACAAAT
27594980 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
27595005 TGATAATGGGTTAGGTAAATTTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
27595031 TGATAATGGGTTAGGTAAATATTCAA
1 TGATAATGGGTTAGGTAAATGTTCCA
27595057 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
27595083 TGAT
1 TGAT
27595087 GGAAATTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 7 0.09
26 67 0.91
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27595546 original size:26 final size:26
Alignment explanation
Indices: 27595485--27595592 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
27595475 TGGTACAAAT
*
27595485 TGATAAT-AGTTAGGTAAATG-TTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
27595509 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
27595535 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
27595561 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
27595587 TGATAA
1 TGATAA
27595593 GAATTTCATG
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
24 7 0.09
25 12 0.15
26 59 0.76
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:27597257 original size:27 final size:26
Alignment explanation
Indices: 27597205--27597292 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
27597195 TGGAGGAAGC
* * *
27597205 GTTCTGGTGGCTATACCATATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
27597232 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
27597259 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
27597286 GTTCTGG
1 GTTCTGG
27597293 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.09
27 32 0.59
28 17 0.31
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:27602420 original size:40 final size:39
Alignment explanation
Indices: 27602375--27602504 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
27602365 CGGAATACAA
27602375 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
27602415 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
27602455 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
27602495 CCGGATATAA
1 CCGGATATAA
27602505 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:27610484 original size:40 final size:39
Alignment explanation
Indices: 27610439--27610568 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
27610429 CGGAATACAA
27610439 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
27610479 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
27610519 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
27610559 CCGGATATAA
1 CCGGATATAA
27610569 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:27612606 original size:26 final size:26
Alignment explanation
Indices: 27612577--27612686 Score: 150
Period size: 26 Copynumber: 4.2 Consensus size: 26
27612567 TGGTACAAAT
*
27612577 TGATAATATGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
* * *
27612603 TGATAATAGATTAGGTAAATGCTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
27612629 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
27612655 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
27612681 TGATAA
1 TGATAA
27612687 GAATTTCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
26 74 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:27615885 original size:14 final size:14
Alignment explanation
Indices: 27615866--27615895 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27615856 AAATCAAAGG
27615866 GATGGAGATTTAGA
1 GATGGAGATTTAGA
27615880 GATGGAGATTTAGA
1 GATGGAGATTTAGA
27615894 GA
1 GA
27615896 ACCAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GATGGAGATTTAGA
Found at i:27617649 original size:41 final size:41
Alignment explanation
Indices: 27617552--27617728 Score: 220
Period size: 41 Copynumber: 4.4 Consensus size: 41
27617542 ATTATATGAC
* * *
27617552 TTTTAG-TGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGG
1 TTTTAGCTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
27617592 TTTTAGC-GGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCTGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
*
27617633 TTTTAGCT-GCGTTTTACCAAAAGCGCCACTAATGCTCTGT
1 TTTTAGCTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * * *
27617673 TTTTAG-TGGCGTTTTAACAAAAAGTGCCGCTATTGCTCTAT
1 TTTTAGCTGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGT
*
27617714 TTTTAGC-GGTGTTTT
1 TTTTAGCTGGCGTTTT
27617729 TGGTAAAACG
Statistics
Matches: 121, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
39 1 0.01
40 50 0.41
41 70 0.58
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTTAGCTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
Found at i:27617750 original size:81 final size:81
Alignment explanation
Indices: 27617552--27617728 Score: 230
Period size: 81 Copynumber: 2.2 Consensus size: 81
27617542 ATTATATGAC
* * * * *
27617552 TTTTAGTGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGTTTTAGCGGCGTTTTACCAAAAGCG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTACAAAAAGCG
*
27617617 CCGCTAATGCTCTGGT
66 CCGCTAATGCTCTGAT
* * * *
27617633 TTTTAGCTGCGTTTTACCAAAAGCGCCACTAATGCTCTGTTTTTAGTGGCGTTTTAACAAAAAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTT-ACAAAAAGC
*
27617698 GCCGCTATTGCTCT-AT
65 GCCGCTAATGCTCTGAT
*
27617714 TTTTAGCGGTGTTTT
1 TTTTAGCGGCGTTTT
27617729 TGGTAAAACG
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 62 0.76
82 20 0.24
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTACAAAAAGCG
CCGCTAATGCTCTGAT
Found at i:27619274 original size:6 final size:6
Alignment explanation
Indices: 27619223--27619293 Score: 54
Period size: 6 Copynumber: 11.0 Consensus size: 6
27619213 TTATAGTAAT
* *
27619223 AAAGAA AAA-AA GAAAGAAA AAAGCAA AACGAA ACAAAAA GAAAGAA AAAGAA
1 AAAGAA AAAGAA -AAAG-AA AAAG-AA AAAGAA A-AAGAA -AAAGAA AAAGAA
*
27619275 AAAGAG AAAGAA AGAAGAA
1 AAAGAA AAAGAA A-AAGAA
27619294 CCCACAGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
5 2 0.04
6 26 0.50
7 21 0.40
8 3 0.06
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:27619283 original size:28 final size:28
Alignment explanation
Indices: 27619229--27619293 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
27619219 TAATAAAGAA
* *
27619229 AAAAAGAAAGAAAAAAGCAAAACGAAAC
1 AAAAAGAAAGAAAAAAGAAAAAAGAAAC
*
27619257 AAAAAGAAAG-AAAAAGAAAAAGAGAAAG
1 AAAAAGAAAGAAAAAAGAAAAA-AGAAAC
27619285 AAAGAAGAA
1 AAA-AAGAA
27619294 CCCACAGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 17 0.53
29 5 0.16
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAAGAAAAAAGAAAC
Found at i:27619657 original size:19 final size:20
Alignment explanation
Indices: 27619633--27619673 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
27619623 GAGTTTAGGC
*
27619633 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
27619652 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
27619672 AA
1 AA
27619674 TTGCGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:27621246 original size:35 final size:35
Alignment explanation
Indices: 27621205--27621278 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
27621195 TCAATTATAT
27621205 GTTTTTAAAAAGGCTATTTTAGTTCAATTGATTGA
1 GTTTTTAAAAAGGCTATTTTAGTTCAATTGATTGA
27621240 GTTTTTAAAAAGGCTATTTTAGTTCAATTGATTGA
1 GTTTTTAAAAAGGCTATTTTAGTTCAATTGATTGA
27621275 GTTT
1 GTTT
27621279 CGATATTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.47
Consensus pattern (35 bp):
GTTTTTAAAAAGGCTATTTTAGTTCAATTGATTGA
Found at i:27621353 original size:106 final size:106
Alignment explanation
Indices: 27621151--27621351 Score: 242
Period size: 107 Copynumber: 1.9 Consensus size: 106
27621141 AAAAAGTTAA
* * * *
27621151 TTTAGTTCAATTTATTGAATTTTGATATTAAGTGATCCGTTTATTCAATTATATGTTTTTAAAAA
1 TTTAGTTCAATTGATTGAATTTCGATATTAAGTAAACCGTTTATTCAATTATATGTTTTTAAAAA
* ** *
27621216 GGCTATTTTAGTTCAATTGATTGAGTTTTTAAAAAGGCTAT
66 GACTAAATTAATTCAATTGATTGAGTTTTTAAAAAGGCTAT
* * *
27621257 TTTAGTTCAATTGATTGAGTTTCGATATTAAGTAAAACCGTTTATTCAAGTTATATG-TTTTGAG
1 TTTAGTTCAATTGATTGAATTTCGATATTAAGT-AAACCGTTTATTCAA-TTATATGTTTTTAAA
* ** *
27621321 AAGATTAAATTAATTTGATTTATTGAGTTTT
64 AAGACTAAATTAATTCAATTGATTGAGTTTT
27621352 AATATTAAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
106 30 0.38
107 41 0.53
108 7 0.09
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (106 bp):
TTTAGTTCAATTGATTGAATTTCGATATTAAGTAAACCGTTTATTCAATTATATGTTTTTAAAAA
GACTAAATTAATTCAATTGATTGAGTTTTTAAAAAGGCTAT
Found at i:27623898 original size:24 final size:25
Alignment explanation
Indices: 27623871--27623918 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
27623861 CAATCAGAAA
*
27623871 TAGATACAGAT-TCAGTTTCAGATT
1 TAGATACAGATATCAGATTCAGATT
27623895 TAGATACAGATATCAGATTCAGAT
1 TAGATACAGATATCAGATTCAGAT
27623919 ATGCCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (25 bp):
TAGATACAGATATCAGATTCAGATT
Found at i:27627150 original size:26 final size:26
Alignment explanation
Indices: 27627120--27627172 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
27627110 GTTGCATTTG
27627120 TTTTAATTATATATTTCGTTTCTAAC
1 TTTTAATTATATATTTCGTTTCTAAC
27627146 TTTTAATTATATATTTCGTTTCTAAC
1 TTTTAATTATATATTTCGTTTCTAAC
27627172 T
1 T
27627173 CTTTGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTAATTATATATTTCGTTTCTAAC
Found at i:27627582 original size:66 final size:66
Alignment explanation
Indices: 27627467--27627604 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
27627457 GCAAATTGCT
* * * * * *
27627467 CAACTTAAAGCGGAGGTAGCATCGAGAGAAGTAGAGGCTCAAAGGAAATATAATGAACTCCAACT
1 CAACTTAAAGCGGAGGGAGCAGCAAGAGAAGCAGAGGCTCAAAGAAAATATAACGAACTCCAACT
27627532 A
66 A
* * *
27627533 CAACTTAAAGCGGAGGGAGCAGCAAGAGAAGCAGAGG-T-AGCAAGAAAATATGACGAACTCTAG
1 CAACTTAAAGCGGAGGGAGCAGCAAGAGAAGCAGAGGCTCA--AAGAAAATATAACGAACTCCAA
27627596 CTA
64 CTA
27627599 CAACTT
1 CAACTT
27627605 CAGAATATGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
64 1 0.02
65 1 0.02
66 59 0.97
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.15
Consensus pattern (66 bp):
CAACTTAAAGCGGAGGGAGCAGCAAGAGAAGCAGAGGCTCAAAGAAAATATAACGAACTCCAACT
A
Found at i:27627961 original size:43 final size:43
Alignment explanation
Indices: 27627914--27628055 Score: 124
Period size: 43 Copynumber: 3.2 Consensus size: 43
27627904 AGAACATGAG
*
27627914 CTTTAGCAGCGTTTGTGGGAGAAGCACCGCTAAAGGTCATATT
1 CTTTAGCAGCGTTTGTGGGAGAAGCACCGCTAAAGGTCATGTT
* * * *
27627957 CTTTAGCAACGTTTGTGTTAGTGGGAGAAGCGCCACTAAATGTCATGTT
1 CTTTAGC-A-G--CGT-TT-GTGGGAGAAGCACCGCTAAAGGTCATGTT
* * * *
27628006 CTTTAGCGGCATTTGTGGCA-ATTGCACCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGGGAGA-AGCACCGCTAAAGGTCATGTT
*
27628049 CTATAGC
1 CTTTAGC
27628056 GGCATTTTTG
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
42 1 0.01
43 35 0.45
44 3 0.04
45 2 0.03
47 3 0.04
48 2 0.03
49 32 0.41
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
CTTTAGCAGCGTTTGTGGGAGAAGCACCGCTAAAGGTCATGTT
Found at i:27628021 original size:49 final size:49
Alignment explanation
Indices: 27627928--27628022 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
27627918 AGCAGCGTTT
* *
27627928 GTGGGAGAAGCACCGCTAAAGGTCATATTCTTTAGCAACGTTTGTGTTA
1 GTGGGAGAAGCACCACTAAAGGTCATATTCTTTAGCAACATTTGTGTTA
* * * **
27627977 GTGGGAGAAGCGCCACTAAATGTCATGTTCTTTAGCGGCATTTGTG
1 GTGGGAGAAGCACCACTAAAGGTCATATTCTTTAGCAACATTTGTG
27628023 GCAATTGCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
GTGGGAGAAGCACCACTAAAGGTCATATTCTTTAGCAACATTTGTGTTA
Found at i:27630632 original size:31 final size:32
Alignment explanation
Indices: 27630581--27630640 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
27630571 TCCTTTAATT
27630581 TTCAATCGTGTTAAAATTTTAGAAATTTTAGC
1 TTCAATCGTGTTAAAATTTTAGAAATTTTAGC
27630613 TTCAATCGTGTT-AAATTTTAGAAATTTT
1 TTCAATCGTGTTAAAATTTTAGAAATTTT
27630641 TTAATTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (32 bp):
TTCAATCGTGTTAAAATTTTAGAAATTTTAGC
Found at i:27634668 original size:23 final size:23
Alignment explanation
Indices: 27634637--27634709 Score: 89
Period size: 22 Copynumber: 3.2 Consensus size: 23
27634627 GAATTGAAAT
27634637 TTAACTTAAATCTATTTAGAACAC
1 TTAA-TTAAATCTATTTAGAACAC
27634661 TTAATT-AATCATATTATA-AACA-
1 TTAATTAAATC-TATT-TAGAACAC
*
27634683 TGAATTAAATCTATTTAGAACAC
1 TTAATTAAATCTATTTAGAACAC
27634706 TTAA
1 TTAA
27634710 GTAACCGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 2 0.05
22 17 0.40
23 17 0.40
24 6 0.14
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAATTAAATCTATTTAGAACAC
Found at i:27639290 original size:26 final size:26
Alignment explanation
Indices: 27639251--27639332 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 26
27639241 TGAAATGCCC
27639251 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACTCATT
*
27639277 ATCATGGAATATTTACCTAA-TCCATT
1 ATCATGGAACATTTACCTAACT-CATT
*
27639303 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACTCATT
27639329 ATCA
1 ATCA
27639333 ATTTGTACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACTCATT
Found at i:27646286 original size:26 final size:26
Alignment explanation
Indices: 27646250--27646357 Score: 146
Period size: 26 Copynumber: 4.2 Consensus size: 26
27646240 TGAAATGCCC
27646250 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
** *
27646276 ATCATAAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* * *
27646302 ATCATGGAATATTTACCTAATCTATT
1 ATCATGGAACATTTACCTAAACCATT
27646328 ATCATGGAACATTTACCT-AACACATT
1 ATCATGGAACATTTACCTAAAC-CATT
27646354 ATCA
1 ATCA
27646358 ATTTGTACCA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
25 2 0.03
26 68 0.97
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:27646329 original size:52 final size:52
Alignment explanation
Indices: 27646250--27646357 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
27646240 TGAAATGCCC
*
27646250 ATCATGGAACATTTACCTAAACCATTATCATAAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATAAAACATTTACCTAACACATT
* * * **
27646302 ATCATGGAATATTTACCTAATCTATTATCATGGAACATTTACCTAACACATT
1 ATCATGGAACATTTACCTAAACCATTATCATAAAACATTTACCTAACACATT
27646354 ATCA
1 ATCA
27646358 ATTTGTACCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATAAAACATTTACCTAACACATT
Found at i:27648514 original size:21 final size:21
Alignment explanation
Indices: 27648452--27648520 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
27648442 GATTTTATAT
27648452 TTTTTTTAATTATATGTAATA
1 TTTTTTTAATTATATGTAATA
* * * *
27648473 ---TTATAATTTAGATTTTATA
1 TTTTTTTAA-TTATATGTAATA
27648492 TTTTTTTAATTATATGTAATA
1 TTTTTTTAATTATATGTAATA
27648513 TTTTTTTA
1 TTTTTTTA
27648521 TATGTACTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 5 0.14
19 9 0.25
21 17 0.47
22 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATTATATGTAATA
Found at i:27649979 original size:21 final size:21
Alignment explanation
Indices: 27649955--27649996 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27649945 TGAAAGGTAT
*
27649955 GGTCAGGTTCGATTTCAAGGA
1 GGTCAGGTTCAATTTCAAGGA
27649976 GGTCAGGTTCAATTTCAAGGA
1 GGTCAGGTTCAATTTCAAGGA
27649997 TCTTTTGTTA
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:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (21 bp):
GGTCAGGTTCAATTTCAAGGA
Found at i:27650632 original size:43 final size:43
Alignment explanation
Indices: 27650559--27650689 Score: 181
Period size: 43 Copynumber: 3.0 Consensus size: 43
27650549 TCTGTTAATG
* *
27650559 TTAGCGGCACTTTTCCCACAAATGCTGCTAAAGAACATGATCT
1 TTAGCGGCACTTTTACCACAAACGCTGCTAAAGAACATGATCT
* * *
27650602 TTAGTGGCACTTTTACCACAAACGCCGCTAAAGAACATGATTT
1 TTAGCGGCACTTTTACCACAAACGCTGCTAAAGAACATGATCT
* * * *
27650645 TTAGCAGCGCTTTTACTACAGACGCTGCTAAAGAACATGATCT
1 TTAGCGGCACTTTTACCACAAACGCTGCTAAAGAACATGATCT
27650688 TT
1 TT
27650690 TGCAGCGATT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
TTAGCGGCACTTTTACCACAAACGCTGCTAAAGAACATGATCT
Found at i:27652256 original size:40 final size:41
Alignment explanation
Indices: 27652194--27652289 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
27652184 ATAAAAATAC
27652194 TTATTATATTATTA-TTATTGTATTCTTTA-T-CATA-TCATAT
1 TTATTATATT-TTATTTATTGTATT-TTTACTACATACT-ATAT
27652234 TTCATTATATTTTATTTA-TGTATTTTTACTACATACTATAT
1 TT-ATTATATTTTATTTATTGTATTTTTACTACATACTATAT
*
27652275 TTATTATATATTATT
1 TTATTATATTTTATT
27652290 CCTTATAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
39 4 0.08
40 24 0.48
41 21 0.42
42 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (41 bp):
TTATTATATTTTATTTATTGTATTTTTACTACATACTATAT
Found at i:27652356 original size:8 final size:9
Alignment explanation
Indices: 27652310--27652387 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
27652300 TCTATCTTTC
*
27652310 TTATATATA
1 TTATTTATA
27652319 TTATATTATA
1 TTAT-TTATA
*
27652329 TAGATTT-TA
1 T-TATTTATA
*
27652338 TTATATATA
1 TTATTTATA
27652347 TT-TTTATA
1 TTATTTATA
27652355 TTATTTATTA
1 TTATTTA-TA
*
27652365 TAGGATTTATA
1 T--TATTTATA
27652376 TTATTATATA
1 TTATT-TATA
27652386 TT
1 TT
27652388 TTATTTGTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
8 10 0.19
9 18 0.33
10 16 0.30
11 5 0.09
12 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (9 bp):
TTATTTATA
Found at i:27652361 original size:24 final size:28
Alignment explanation
Indices: 27652310--27652408 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
27652300 TCTATCTTTC
27652310 TTATATATATTATATTATATAGATTTTA
1 TTATATATATTATATTATATAGATTTTA
*
27652338 TTATATATATT-T-TTATAT-TA-TTTA
1 TTATATATATTATATTATATAGATTTTA
* *
27652362 TTATAGGAT-TTATATTATTATATATTTTA
1 TTATA-TATATTATATTA-TATAGATTTTA
* *
27652391 TT-TGTAAATTATATTATA
1 TTATATATATTATATTATA
27652409 CACTCTATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
24 11 0.19
25 4 0.07
26 9 0.15
27 7 0.12
28 22 0.37
29 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (28 bp):
TTATATATATTATATTATATAGATTTTA
Found at i:27652393 original size:21 final size:21
Alignment explanation
Indices: 27652310--27652393 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
27652300 TCTATCTTTC
27652310 TTATATATATTATAT-TA-TAT
1 TTATAT-TATTATATATATTAT
** *
27652330 AGATTTTATTATATATATT-T
1 TTATATTATTATATATATTAT
**
27652350 TTATATTATT-TATTATAGGAT
1 TTATATTATTATA-TATATTAT
*
27652371 TTATATTATTATATATTTTAT
1 TTATATTATTATATATATTAT
27652392 TT
1 TT
27652394 GTAAATTATA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
19 10 0.21
20 17 0.35
21 19 0.40
22 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTATATTATTATATATATTAT
Found at i:27660590 original size:29 final size:29
Alignment explanation
Indices: 27660557--27660621 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
27660547 GTGACGAGAT
27660557 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
27660586 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
27660615 CGGCACT
1 TGGCACT
27660622 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:27668620 original size:29 final size:29
Alignment explanation
Indices: 27668587--27668651 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
27668577 GTGACGAGAT
27668587 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
27668616 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
27668645 CGGCACT
1 TGGCACT
27668652 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:27670194 original size:40 final size:40
Alignment explanation
Indices: 27670150--27670231 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
27670140 GGGGTGTTAC
27670150 ATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT
1 ATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT
27670190 ATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT
1 ATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT
27670230 AT
1 AT
27670232 CATTCAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
ATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT
Found at i:27678125 original size:40 final size:40
Alignment explanation
Indices: 27678045--27678225 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
27678035 ACCCAAGTTT
* * * *
27678045 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
27678084 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
27678124 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
27678164 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
27678204 CTTCGGGTCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
27678226 CATTCAAATG
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.08
40 119 0.92
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:27683001 original size:40 final size:40
Alignment explanation
Indices: 27682950--27683194 Score: 361
Period size: 40 Copynumber: 6.1 Consensus size: 40
27682940 GGATGATAAT
*
27682950 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
*
27682989 TTCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-A
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
* *
27683029 TTCCGGGCTAAGTCCCGAAGGCATTTGTTCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
*
27683070 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
* *
27683110 TCCGGGCTAAGTCCCGAAGACATTTGTGCGAACT-ACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTATA
* *
27683150 TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
27683190 TCCGG
1 TCCGG
27683195 TTAAAGCCTG
Statistics
Matches: 192, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 2 0.01
40 187 0.97
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
Found at i:27691089 original size:40 final size:40
Alignment explanation
Indices: 27691034--27691275 Score: 357
Period size: 40 Copynumber: 6.1 Consensus size: 40
27691024 CGGATGATAA
*
27691034 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
*
27691074 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
*
27691114 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
*
27691154 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
* *
27691194 CGGGCTAAGTCCCGAA-GCATTTGTGCAAACT-ACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTATATC
* *
27691233 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
27691273 CGG
1 CGG
27691276 TTAAAGCCCG
Statistics
Matches: 190, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
39 36 0.19
40 153 0.81
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
Found at i:27697157 original size:18 final size:18
Alignment explanation
Indices: 27697136--27697195 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
27697126 AATCGGTTAA
*
27697136 TCAGTAATATTCATTTAT
1 TCAGTAATAGTCATTTAT
*
27697154 TCAGT-ATCAGTCGTTTAT
1 TCAGTAAT-AGTCATTTAT
* * *
27697172 TCTGTAACAGTCAATTAT
1 TCAGTAATAGTCATTTAT
27697190 TCAGTA
1 TCAGTA
27697196 GCAGATAGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.91
19 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (18 bp):
TCAGTAATAGTCATTTAT
Found at i:27697335 original size:6 final size:6
Alignment explanation
Indices: 27697326--27697369 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
27697316 CACCGTAAGG
27697326 GTAACA GTAACA GTAACA GTAACA GTAACA GTAA-A TGTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA -GTAACA GT
27697370 GGCGGTACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.03
6 34 0.94
7 1 0.03
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
GTAACA
Found at i:27698537 original size:21 final size:21
Alignment explanation
Indices: 27698499--27698539 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27698489 TTTTTTATTT
27698499 TAATTACTTTATAATATTATA
1 TAATTACTTTATAATATTATA
*
27698520 TAATATACTTTA-ATTATTAT
1 TAAT-TACTTTATAATATTAT
27698540 TTTTTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATTACTTTATAATATTATA
Found at i:27701604 original size:40 final size:40
Alignment explanation
Indices: 27701550--27701672 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 40
27701540 CATACCAGAT
*
27701550 AGAAGCTCATAAGAGCTAATCCAACTGAAACACGCTAGAC
1 AGAAGCTCATAAGAGCTAATCCAAATGAAACACGCTAGAC
* * *
27701590 AGATGGTCATAAGAGCTAAT-CAAATCGAAACACGCTAAAC
1 AGAAGCTCATAAGAGCTAATCCAAAT-GAAACACGCTAGAC
*
27701630 AGAAGCTCATAAGAGCTAATCCAATTGAAACACG-TCAGAC
1 AGAAGCTCATAAGAGCTAATCCAAATGAAACACGCT-AGAC
27701670 AGA
1 AGA
27701673 GAGTATAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 5 0.07
40 63 0.88
41 4 0.06
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (40 bp):
AGAAGCTCATAAGAGCTAATCCAAATGAAACACGCTAGAC
Found at i:27701926 original size:26 final size:26
Alignment explanation
Indices: 27701897--27701949 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
27701887 TTGTACCATG
27701897 TTAATCTACTCAACAATTCATATTGC
1 TTAATCTACTCAACAATTCATATTGC
27701923 TTAATCTACTCAACAATTCATATTGC
1 TTAATCTACTCAACAATTCATATTGC
27701949 T
1 T
27701950 GTTAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (26 bp):
TTAATCTACTCAACAATTCATATTGC
Found at i:27705679 original size:40 final size:40
Alignment explanation
Indices: 27705619--27705774 Score: 176
Period size: 40 Copynumber: 4.0 Consensus size: 40
27705609 ACCGAACACA
* *
27705619 CCAGATAGAA-TTCATAAGAGCTAATCCAATTGAAACATG
1 CCAGATAGAAGCTCATAAGAGCTAATCCAATCGAAACATG
27705658 CCAGATAGAAGCTCATAAGAGCTAATCCAATCGAAACATG
1 CCAGATAGAAGCTCATAAGAGCTAATCCAATCGAAACATG
* * * * * *
27705698 CCAGACAGAACCTCATAAGAGCTAATAC-AGCCAAA-ATTT
1 CCAGATAGAAGCTCATAAGAGCTAATCCAATCGAAACA-TG
* *
27705737 CTAGAGAGAAGCTCATAAGAGCTAATCCAA-CAGAAACA
1 CCAGATAGAAGCTCATAAGAGCTAATCCAATC-GAAACA
27705775 CGCTAGACAG
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 41 0.41
40 56 0.57
41 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (40 bp):
CCAGATAGAAGCTCATAAGAGCTAATCCAATCGAAACATG
Found at i:27712442 original size:40 final size:40
Alignment explanation
Indices: 27712383--27712590 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 40
27712373 CAATTGAATG
* * * *
27712383 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
27712423 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27712463 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27712503 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27712543 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
27712583 ATATCCGG
1 ATATCCGG
27712591 TTGTATTCCG
Statistics
Matches: 144, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 144 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:27712521 original size:80 final size:80
Alignment explanation
Indices: 27712385--27712590 Score: 252
Period size: 80 Copynumber: 2.6 Consensus size: 80
27712375 ATTGAATGAT
* * ** * * *
27712385 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
27712450 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
27712465 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
27712530 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
27712545 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
27712591 TTGTATTCCG
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 107 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:27720452 original size:40 final size:40
Alignment explanation
Indices: 27720393--27720600 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 40
27720383 CAATTGAATG
* * * *
27720393 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
27720433 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27720473 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27720513 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27720553 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
27720593 ATATCCGG
1 ATATCCGG
27720601 TTGTATTCCG
Statistics
Matches: 144, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 144 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:27720531 original size:80 final size:80
Alignment explanation
Indices: 27720395--27720600 Score: 252
Period size: 80 Copynumber: 2.6 Consensus size: 80
27720385 ATTGAATGAT
* * ** * * *
27720395 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
27720460 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
27720475 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
27720540 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
27720555 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
27720601 TTGTATTCCG
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 107 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:27725839 original size:38 final size:38
Alignment explanation
Indices: 27725768--27725911 Score: 166
Period size: 38 Copynumber: 3.7 Consensus size: 38
27725758 ATTTGATATG
* *
27725768 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGG-AATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGTAA-TA
*
27725808 TATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * *
27725846 TATCCGGATTAAATCCCGCAGGCTTCGTACGGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
27725884 TATCCGGGTTAAATCCTAGCAGGCTTCG
1 TATCCGGGTTAAATCC-CGCAGGCTTCG
27725912 GCCGGTGATG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
37 1 0.01
38 66 0.72
39 17 0.18
40 8 0.09
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:27726091 original size:43 final size:43
Alignment explanation
Indices: 27725898--27726078 Score: 292
Period size: 43 Copynumber: 4.2 Consensus size: 43
27725888 CGGGTTAAAT
27725898 CCTAGCAGGCTTCG-GCCGGTGATGTGTATTCGGGCCTTCGTG
1 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
27725940 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
1 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
* * **
27725983 CCTAGCAGGCTTCGTGCTGGTGAAGTGTATTCGGGTTTTCGTG
1 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
* * *
27726026 CCTAGCAGGCTTTGTGCTGGTGACGTGTATTCGGGCCTTCGTG
1 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
27726069 CCTAGCAGGC
1 CCTAGCAGGC
27726079 GTAATGCCGG
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
42 14 0.11
43 116 0.89
ACGTcount: A:0.10, C:0.24, G:0.35, T:0.30
Consensus pattern (43 bp):
CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
Found at i:27726475 original size:45 final size:45
Alignment explanation
Indices: 27726408--27726516 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
27726398 TTGATTTGAT
* * * *
27726408 TATTCGGCCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGAT-A
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAATGA
** *
27726452 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCTGGTGAAATGA
1 -TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAATGA
27726498 TA-TCGGGCC-TCGAGCCTAG
1 TATTCGGGCCTTCGAGCCTAG
27726517 TAGGCGAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 10 0.18
44 7 0.12
45 38 0.68
46 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAATGA
Found at i:27731594 original size:38 final size:36
Alignment explanation
Indices: 27731560--27731662 Score: 136
Period size: 38 Copynumber: 2.8 Consensus size: 36
27731550 GCAGGCTATA
27731560 TGTTGG-AATTATATCCGGGTTAAATCCCGTAGGCTT
1 TGTTGGTAA-TATATCCGGGTTAAATCCCGTAGGCTT
*
27731596 CGTGCTGGTAATATATCCGGGTTAAATCCCGTAGGCTT
1 --TGTTGGTAATATATCCGGGTTAAATCCCGTAGGCTT
*
27731634 CGTACTGGTAATATATCCGGGTTAAATCC
1 TGT--TGGTAATATATCCGGGTTAAATCC
27731663 TAGCAGGCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
36 1 0.02
38 56 0.95
39 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (36 bp):
TGTTGGTAATATATCCGGGTTAAATCCCGTAGGCTT
Found at i:27731722 original size:43 final size:43
Alignment explanation
Indices: 27731661--27731769 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
27731651 CGGGTTAAAT
** * *
27731661 CCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTG
1 CCTAGCAGGCTTAATGCCGGTGACGTGTATTCGCGCCTTCGTG
* *
27731704 CCTAGTAGGCTTTATGCCGGTGACGTGTATTCGCGCCTTCGTG
1 CCTAGCAGGCTTAATGCCGGTGACGTGTATTCGCGCCTTCGTG
*
27731747 CCTAGCAGGCGTAATGCCGGTGA
1 CCTAGCAGGCTTAATGCCGGTGA
27731770 AATGATATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.13, C:0.26, G:0.33, T:0.28
Consensus pattern (43 bp):
CCTAGCAGGCTTAATGCCGGTGACGTGTATTCGCGCCTTCGTG
Found at i:27732198 original size:43 final size:45
Alignment explanation
Indices: 27732086--27732199 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
27732076 TTAATTTGAT
* * ** * *
27732086 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGATGAAATAC
27732131 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGATGAAATGA-
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGATGAAAT-AC
27732176 TA-TCGGGCC-TCGAGCCTAGCAGGC
1 TATTCGGGCCTTCGAGCCTAGCAGGC
27732200 GAATTGCCGG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 15 0.24
44 7 0.11
45 39 0.63
46 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (45 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGATGAAATAC
Found at i:27737758 original size:148 final size:148
Alignment explanation
Indices: 27737490--27737779 Score: 517
Period size: 148 Copynumber: 2.0 Consensus size: 148
27737480 TAGATAAACC
*
27737490 TAATTGCTTTTCTACTTCAGCAGGAAACTCTCAAAATTTATCAAAGGTTTGTTTTTGTGGTGCAT
1 TAATTGCTTTTCTACTTCAGCACGAAACTCTCAAAATTTATCAAAGGTTTGTTTTTGTGGTGCAT
* *
27737555 TAGATGAACATATCCATATCGAGAATAGTCCTCGATGAAAGTCACATAATAATCATAACCTCTTC
66 TAGATAAACATATCCATATCGAGAATAGTCATCGATGAAAGTCACATAATAATCATAACCTCTTC
27737620 GGGCACTGATGCTCATAA
131 GGGCACTGATGCTCATAA
27737638 TAATTGCTTTTCTACTTCAGCACGAAACTCTCAAAATTTATCAAAGGTTTGTTTTTGTGGTGCAT
1 TAATTGCTTTTCTACTTCAGCACGAAACTCTCAAAATTTATCAAAGGTTTGTTTTTGTGGTGCAT
* * * *
27737703 TAGATAAACATGTCCATATCGAGAATATTCATTGATGAAAGTCACATAATAATCATAACCTTTTC
66 TAGATAAACATATCCATATCGAGAATAGTCATCGATGAAAGTCACATAATAATCATAACCTCTTC
27737768 GGGCACTGATGC
131 GGGCACTGATGC
27737780 ACATGAGACC
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 135 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (148 bp):
TAATTGCTTTTCTACTTCAGCACGAAACTCTCAAAATTTATCAAAGGTTTGTTTTTGTGGTGCAT
TAGATAAACATATCCATATCGAGAATAGTCATCGATGAAAGTCACATAATAATCATAACCTCTTC
GGGCACTGATGCTCATAA
Found at i:27748286 original size:46 final size:46
Alignment explanation
Indices: 27748236--27748411 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
27748226 TGGTTGAGCA
27748236 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27748282 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
27748327 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
27748375 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27748412 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 65 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27748392 original size:93 final size:93
Alignment explanation
Indices: 27748233--27748403 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
27748223 GGATGGTTGA
* *
27748233 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27748298 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
27748326 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27748391 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
27748404 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27752334 original size:54 final size:54
Alignment explanation
Indices: 27752128--27752334 Score: 163
Period size: 54 Copynumber: 3.9 Consensus size: 54
27752118 TTTCCTTTTT
* * * *
27752128 AAACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCC-T-TA
1 AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATGTA
* * * * * *
27752180 TGAACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGAT-TTTGCCTTATCGT-
1 -AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCC--AT-GTA
** ** * * * *
27752236 -AGTTTATGAATGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCATGTA
1 AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATGTA
* *
27752289 AAACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
27752335 AAACCTAATG
Statistics
Matches: 115, Mismatches: 31, Indels: 15
0.71 0.19 0.09
Matches are distributed among these distances:
52 7 0.06
53 37 0.32
54 64 0.56
55 6 0.05
57 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (54 bp):
AAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATGTA
Found at i:27754776 original size:40 final size:40
Alignment explanation
Indices: 27754721--27754884 Score: 195
Period size: 40 Copynumber: 4.1 Consensus size: 40
27754711 TGAATGATAC
* *
27754721 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
27754761 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
27754801 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
27754841 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
27754881 CCGG
1 CCGG
27754885 TTAAATTCCG
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.97
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:27762834 original size:40 final size:40
Alignment explanation
Indices: 27762776--27762939 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 40
27762766 TGAATGATAC
* * * *
27762776 CCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
* * *
27762816 CTGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGATTATAT
* ** *
27762856 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
* * * ** *
27762896 CCGGGTTAAGACCCGAAGGCAATTGTACTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
27762936 CCGG
1 CCGG
27762940 TTAAATTCCG
Statistics
Matches: 99, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 96 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
Found at i:27762933 original size:80 final size:80
Alignment explanation
Indices: 27762776--27762939 Score: 186
Period size: 80 Copynumber: 2.0 Consensus size: 80
27762766 TGAATGATAC
* * * ** * *
27762776 CCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTATATCTGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
* *
27762841 TGCGAGTTGTTATAT
66 TACGAGTGGTTATAT
* * *
27762856 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGC-ATTC
**
27762920 GTACTTGTGGTTATAT
65 GTACGAGTGGTTATAT
27762936 CCGG
1 CCGG
27762940 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
80 66 0.96
81 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
TACGAGTGGTTATAT
Found at i:27771170 original size:17 final size:17
Alignment explanation
Indices: 27771148--27771186 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
27771138 ATTTTATCAT
27771148 TTATCATTTATTGGGTA
1 TTATCATTTATTGGGTA
*
27771165 TTATCATTTATTGGGTT
1 TTATCATTTATTGGGTA
27771182 TTATC
1 TTATC
27771187 GGATATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (17 bp):
TTATCATTTATTGGGTA
Found at i:27774141 original size:15 final size:15
Alignment explanation
Indices: 27774121--27774152 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27774111 TAACATGCAT
27774121 ATTAGCCAACGGTAC
1 ATTAGCCAACGGTAC
27774136 ATTAGCCAACGGTAC
1 ATTAGCCAACGGTAC
27774151 AT
1 AT
27774153 CGATCAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (15 bp):
ATTAGCCAACGGTAC
Found at i:27780984 original size:40 final size:40
Alignment explanation
Indices: 27780947--27781136 Score: 237
Period size: 40 Copynumber: 4.7 Consensus size: 40
27780937 GCTACTCGTT
*
27780947 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
27780987 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
27781027 CAAATGCCTTC-AGATCTTAGTCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAACTCGCA
* *
27781067 CAAATGCCTTCGGGACTTAGCCCGG-AACTAGTCACTAGCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACT--CGCA
27781109 -AAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
27781137 CATCCAAATA
Statistics
Matches: 132, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.02
40 96 0.73
41 29 0.22
42 5 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:27785407 original size:41 final size:42
Alignment explanation
Indices: 27785345--27785472 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
27785335 TAGGGTTAGT
*
27785345 TGAGATTACGTGTAAGACCATATTTGGGATATGGCA-TGATA
1 TGAGATTACGTGTAAGACCATATTTGGGATATGCCATTGATA
* * ** *
27785386 TGAGATTTCGTGTAAGGCCATAGCTGGGCTATTGCCATTGATA
1 TGAGATTACGTGTAAGACCATATTTGGGATA-TGCCATTGATA
* ** * * *
27785429 TGATATCCCATGTAAGACCATATTTGGGATATGTCATTGGTA
1 TGAGATTACGTGTAAGACCATATTTGGGATATGCCATTGATA
27785471 TG
1 TG
27785473 GTACTATGTG
Statistics
Matches: 69, Mismatches: 16, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
41 26 0.38
42 15 0.22
43 28 0.41
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATTTGGGATATGCCATTGATA
Found at i:27785551 original size:20 final size:20
Alignment explanation
Indices: 27785523--27785569 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
27785513 CCAAGTGGTT
27785523 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
27785543 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
27785563 TAAGTTG
1 TAAGTTG
27785570 CAAATTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:27792045 original size:50 final size:50
Alignment explanation
Indices: 27791926--27792221 Score: 283
Period size: 50 Copynumber: 5.9 Consensus size: 50
27791916 ATTGTGAGAA
* * * *** *
27791926 CACATGTGTAGTACTATGTGTAGGCTACTATGTATTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG--TTAGGT
* *
27791978 CACGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * * * * * *
27792028 CACATGTGCAGTACTAAGTGCAGGCTATTATGCGTACCCGACAACTTCA-AT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA-TAGTT-AGGT
** * * *
27792079 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
** * * * *
27792129 CATGTGTGTAGTACCAAGTGCAGGCTACTACGTGTACTAGATTGTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
27792178 CACATGTGTAGTACTAAGTGCAGGCTACTATGCT-TACCAGATAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATG-TGTACCAGATAG
27792222 CTTTGGTTAC
Statistics
Matches: 202, Mismatches: 38, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
49 40 0.20
50 87 0.43
51 37 0.18
52 38 0.19
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
Found at i:27792184 original size:101 final size:100
Alignment explanation
Indices: 27791981--27792221 Score: 256
Period size: 101 Copynumber: 2.4 Consensus size: 100
27791971 TTTAGGTCAC
* * *
27791981 GTGTGTAGTACTAAGTGTAGGCTACTATGTGTACCAGATAGTTAGGTCACATGTGCAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGCAGTACCAAG
* * *
27792046 TGCAGGCTATTATGCGTACCCGACAACTTCAATCA
66 TGCAGGCTACTACGCGTACCAGACAACTTCAATCA
* * ** *
27792081 TGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACCAA
1 -GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGCAGTACCAA
* * ****
27792146 GTGCAGGCTACTACGTGTACTAGATTGTTGGTC-A-CA
65 GTGCAGGCTACTACGCGTACCAGACAACT--TCAATCA
*
27792182 -TGTGTAGTACTAAGTGCAGGCTACTATGCT-TACCAGATAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACG-TGTACCAGATAG
27792222 CTTTGGTTAC
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
99 35 0.30
100 1 0.01
101 78 0.67
102 1 0.01
103 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (100 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGCAGTACCAAG
TGCAGGCTACTACGCGTACCAGACAACTTCAATCA
Found at i:27795083 original size:21 final size:20
Alignment explanation
Indices: 27795059--27795098 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27795049 TAATAGAGGC
*
27795059 ACACATCCATGTGAAGCAAGG
1 ACACAGCCATGTGAA-CAAGG
*
27795080 ACACAGCCGTGTGAACAAG
1 ACACAGCCATGTGAACAAG
27795099 CCGTGTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (20 bp):
ACACAGCCATGTGAACAAGG
Found at i:27795751 original size:17 final size:17
Alignment explanation
Indices: 27795726--27795758 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
27795716 AGGCTAAAAA
27795726 GAAAGAACAAATAAAGAG
1 GAAAGAAC-AATAAAGAG
27795744 GAAA-AACAATAAAGA
1 GAAAGAACAATAAAGA
27795759 AAGAAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.70, C:0.06, G:0.18, T:0.06
Consensus pattern (17 bp):
GAAAGAACAATAAAGAG
Found at i:27795803 original size:18 final size:18
Alignment explanation
Indices: 27795780--27795824 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
27795770 TCTAGTTAAA
27795780 GAAAAATAAAATAAAAAT
1 GAAAAATAAAATAAAAAT
* *
27795798 GAAAAATGAGAATCAAAAT
1 GAAAAAT-AAAATAAAAAT
27795817 -AAAAATAA
1 GAAAAATAA
27795825 CCTTTTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (18 bp):
GAAAAATAAAATAAAAAT
Found at i:27797389 original size:16 final size:17
Alignment explanation
Indices: 27797360--27797395 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
27797350 GAGAGATTTC
27797360 AAGAAAAAGCAAGAAGA
1 AAGAAAAAGCAAGAAGA
27797377 AAGAAAAAG-AAGAAGA
1 AAGAAAAAGCAAGAAGA
27797393 AAG
1 AAG
27797396 CCTCCAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGCAAGAAGA
Found at i:27799349 original size:56 final size:54
Alignment explanation
Indices: 27799275--27799380 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 54
27799265 ACCCTTTTAC
* *
27799275 TTTTCCCCAAAAAATTTACTTCCCCCAAGCCCCCAAAACTTTTTTTTCCTTTAAAT
1 TTTTCCCCAAAAAATTTACTTCCCCCAAACCCCC-AAA-TTTTTTTCCCTTTAAAT
* ** *
27799331 TTTTTCCCAAAACTTTTACTTCCTCCAAACCCCCAAATTTTTTTCCCTTT
1 TTTTCCCCAAAAAATTTACTTCCCCCAAACCCCCAAATTTTTTTCCCTTT
27799381 GCTTTACCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 12 0.27
55 3 0.07
56 29 0.66
ACGTcount: A:0.25, C:0.33, G:0.01, T:0.41
Consensus pattern (54 bp):
TTTTCCCCAAAAAATTTACTTCCCCCAAACCCCCAAATTTTTTTCCCTTTAAAT
Found at i:27806984 original size:20 final size:20
Alignment explanation
Indices: 27806959--27806999 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27806949 AGGGGCACAC
27806959 GCCCGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
*
27806979 GCCCGTGTGGCTTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
27806999 G
1 G
27807000 GCCATGGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGGACAT
Found at i:27808870 original size:14 final size:14
Alignment explanation
Indices: 27808834--27808872 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27808824 GTTTTTATTC
*
27808834 TTTCTTTTA-TTTC
1 TTTCTTTTATTTTA
27808847 TTTCTTTTATTTTA
1 TTTCTTTTATTTTA
*
27808861 TTTGTTTTATTT
1 TTTCTTTTATTT
27808873 AATTACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTCTTTTATTTTA
Found at i:27808910 original size:13 final size:13
Alignment explanation
Indices: 27808886--27808910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27808876 TACTTTATTA
27808886 TATTATATTATAT
1 TATTATATTATAT
27808899 TATTATATTATA
1 TATTATATTATA
27808911 CTTTAATCAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:27810162 original size:48 final size:47
Alignment explanation
Indices: 27809793--27810209 Score: 235
Period size: 46 Copynumber: 8.8 Consensus size: 47
27809783 CATAGGGTAT
* *
27809793 AATGCCGATGCCATATCCCAAACATGGTCTTACACT-GACTCATC-CATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTC-TCTC-TC
* * **
27809841 AA-GTCGATGCCATGTCCC-GAACATGGTCTTACACT-GACTATCAAAATC
1 AATGCCGATGCCATGTCCCAG-ACATGGTCTTACACTAG-CTCTC--TCTC
* * * * *
27809889 GAGGCCAATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--C-TCTC
* * * * * *
27809939 CATACTGATGCCATGTCCCAGACATGGTCTTATACTCA-CAC-CT-TT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCTCTC
* * *
27809984 ATACGTGTCGATGCCATGTCCCAGACATGGTCTTACACTAACAC-CTCTC
1 A-A--TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCTCTC
* * *
27810033 -GTAGCCGATG-CATGTCCCAGACAT-GTCTTATACTGGCT-TACATCTC
1 AAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-C-TCTC
* * *
27810079 GAGGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC-TCTC
* *
27810125 AATGCCGATGCCATGTGCCAGACATGGTCTTACACTAG-T-TTTCAT-
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCTC-TC
*
27810170 AATGTGGTCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 AA--T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
27810210 ACACAAATAA
Statistics
Matches: 296, Mismatches: 45, Indels: 57
0.74 0.11 0.14
Matches are distributed among these distances:
44 10 0.03
45 21 0.07
46 73 0.25
47 63 0.21
48 58 0.20
49 33 0.11
50 36 0.12
51 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCTCTC
Found at i:27810185 original size:94 final size:95
Alignment explanation
Indices: 27809796--27810209 Score: 340
Period size: 94 Copynumber: 4.4 Consensus size: 95
27809786 AGGGTATAAT
* *
27809796 GCCGATGCCATATCCCAAACATGGTCTTACACT-GACTCATC-CATCAA-GTCGATGCCATGTCC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAG-CTC-TCTC-TCAATGCCGATGCCATGTCC
* *
27809858 C-GAACATGGTCTTACACT-GACTATCAAAATCGAG
63 CAG-ACATGGTCTTACACTAG-CTTTC-ATATCGAG
* * * * *
27809892 GCCAATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCCATACTGATGCCATGTCC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCT--C-TCTCAATGCCGATGCCATGTCC
* * *
27809957 CAGACATGGTCTTATACTCACACCTTT-ATA-CG-T
63 CAGACATGGTCTTACACT---AGCTTTCATATCGAG
* * * * *
27809990 GTCGATGCCATGTCCCAGACATGGTCTTACACTAACAC-CTCTC-GTAGCCGATG-CATGTCCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCTCTCAAT-GCCGATGCCATGTCCCA
* * * *
27810052 GACAT-GTCTTATACTGGCTTACATCTCGAG
65 GACATGGTCTTACACTAGCTTTCATATCGAG
*
27810082 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTGCCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTC-TCTCAATGCCGATGCCATGTCCCA
* *
27810145 GACATGGTCTTACACTAGTTTTCATAAT-GTG
65 GACATGGTCTTACACTAGCTTTCAT-ATCGAG
* *
27810176 GTCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGC
27810210 ACACAAATAA
Statistics
Matches: 257, Mismatches: 40, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
89 3 0.01
90 15 0.06
91 16 0.06
92 27 0.11
93 29 0.11
94 57 0.22
95 3 0.01
96 34 0.13
97 2 0.01
98 36 0.14
99 29 0.11
100 3 0.01
102 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (95 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCTCTCAATGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTTTCATATCGAG
Found at i:27810901 original size:13 final size:13
Alignment explanation
Indices: 27810883--27810907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27810873 TTAAAAGTAT
27810883 AAAAATCATCAAG
1 AAAAATCATCAAG
27810896 AAAAATCATCAA
1 AAAAATCATCAA
27810908 AATCACTTAC
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:27819095 original size:19 final size:19
Alignment explanation
Indices: 27819071--27819107 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27819061 GAGGAAGCGT
27819071 TCTGGTAGCCTCACCACAA
1 TCTGGTAGCCTCACCACAA
* *
27819090 TCTGGTGGCCTCGCCACA
1 TCTGGTAGCCTCACCACA
27819108 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.22
Consensus pattern (19 bp):
TCTGGTAGCCTCACCACAA
Found at i:27819114 original size:2 final size:2
Alignment explanation
Indices: 27819107--27819132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27819097 GCCTCGCCAC
27819107 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
27819133 GTTCTGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27829018 original size:5 final size:5
Alignment explanation
Indices: 27829008--27829032 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27828998 TAAATAATAA
27829008 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
27829033 GCAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:27837778 original size:43 final size:44
Alignment explanation
Indices: 27837725--27837814 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
27837715 GTAGGCCAAA
*
27837725 TAATATTAAAATAACCTACATTAATGAGAGTTTAAGTAGG-AAAC
1 TAATATTAAAATAACCTACACTAATGAGAGTTTAAGT-GGTAAAC
* *
27837769 TAAT-TTAAAATAACCTGCACTAATTAGAGTTTAAGTGGTAAAC
1 TAATATTAAAATAACCTACACTAATGAGAGTTTAAGTGGTAAAC
27837812 TAA
1 TAA
27837815 AAACAAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 2 0.05
43 36 0.86
44 4 0.10
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATGAGAGTTTAAGTGGTAAAC
Found at i:27846082 original size:34 final size:34
Alignment explanation
Indices: 27846017--27846116 Score: 154
Period size: 34 Copynumber: 3.1 Consensus size: 34
27846007 ATTGGGACTC
*
27846017 TTAGATTAGAGTTACATG--TCTC--CATGTTTT
1 TTAGATTAGAGTTACTTGTCTCTCAACATGTTTT
27846047 TTAGATTAGAGTTACTTGTCTCTCAACATGTTTT
1 TTAGATTAGAGTTACTTGTCTCTCAACATGTTTT
*
27846081 TTAGATTAGAATTACTTGTCTCTCAACATGTTTT
1 TTAGATTAGAGTTACTTGTCTCTCAACATGTTTT
27846115 TT
1 TT
27846117 CTTTGTTTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
30 17 0.27
32 4 0.06
34 43 0.67
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (34 bp):
TTAGATTAGAGTTACTTGTCTCTCAACATGTTTT
Found at i:27846716 original size:14 final size:14
Alignment explanation
Indices: 27846697--27846726 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27846687 TTTTTCTATT
*
27846697 AAAAAATAAAATTA
1 AAAAAATAAAAATA
27846711 AAAAAATAAAAATA
1 AAAAAATAAAAATA
27846725 AA
1 AA
27846727 TTAGTCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:27848704 original size:21 final size:21
Alignment explanation
Indices: 27848663--27848701 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27848653 AATTCAATTT
27848663 TTTTATTTAATTTATAATTAA
1 TTTTATTTAATTTATAATTAA
*
27848684 TTTTATTT-TTTTATAATT
1 TTTTATTTAATTTATAATT
27848702 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTAATTTATAATTAA
Found at i:27852925 original size:31 final size:31
Alignment explanation
Indices: 27852889--27852993 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
27852879 TAATCACATT
27852889 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATATTATCTAGATA
** * *
27852920 AATATTAAATTAAATTTAATA-TATC-ATATT
1 AATATTAAATT-AATAAAATATTATCTAGATA
* *
27852950 AATATTAATTTAATAAAATATTATTTAGATA
1 AATATTAAATTAATAAAATATTATCTAGATA
*
27852981 AGTATTAAATTAA
1 AATATTAAATTAA
27852994 ATTTAATATC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 7 0.12
30 16 0.27
31 29 0.49
32 7 0.12
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (31 bp):
AATATTAAATTAATAAAATATTATCTAGATA
Found at i:27852957 original size:61 final size:61
Alignment explanation
Indices: 27852881--27853015 Score: 225
Period size: 61 Copynumber: 2.2 Consensus size: 61
27852871 ATTAGATTTA
*
27852881 ATCACATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATAT
1 ATCATATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATAT
* * *
27852942 ATCATATTAATATTAATTTAATAAAATATTATTTAGATAAGTATTAAATTAAATTTAATAT
1 ATCATATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATAT
*
27853003 CTCATATTAATAT
1 ATCATATTAATAT
27853016 CTAGATAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (61 bp):
ATCATATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATAT
Found at i:27859039 original size:22 final size:22
Alignment explanation
Indices: 27859013--27859069 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
27859003 GTCTTAGGGT
*
27859013 CACACGGGTGTGTCCCTCGAAC
1 CACACGGGCGTGTCCCTCGAAC
**
27859035 CACACGGGCGTGTCCCTCGGGC
1 CACACGGGCGTGTCCCTCGAAC
27859057 CACACGGGCGTGT
1 CACACGGGCGTGT
27859070 GAGCCTAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.14, C:0.37, G:0.33, T:0.16
Consensus pattern (22 bp):
CACACGGGCGTGTCCCTCGAAC
Found at i:27867933 original size:2 final size:2
Alignment explanation
Indices: 27867926--27867952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27867916 TCAATGGATA
27867926 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
27867953 AGACATGAGA
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:27871114 original size:48 final size:48
Alignment explanation
Indices: 27871060--27871336 Score: 382
Period size: 48 Copynumber: 5.8 Consensus size: 48
27871050 ACCGTGCTAA
* * *
27871060 ATGTGCCTGTGTAAGACCATGTTTGGGACATGACATC-GACGATGGTAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAG-CGATGATAT
*
27871108 ATGTGCCTGTGTAAAACCATGTCTGGGACATGGCATCAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* *
27871156 ATGTGCCTATGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
*
27871204 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGTGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* *
27871252 GTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGAT-A-AT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
** *
27871298 ATGTGGATTCATGTAAGACCATGTC-GAGGACATGGCATC
1 ATGT-GCCT-GTGTAAGACCATGTCTG-GGACATGGCATC
27871337 GGTGACGGTA
Statistics
Matches: 207, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
46 5 0.02
47 3 0.01
48 198 0.96
49 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
Found at i:27871349 original size:48 final size:48
Alignment explanation
Indices: 27871069--27871381 Score: 291
Period size: 48 Copynumber: 6.5 Consensus size: 48
27871059 AATGTGCCTG
* * ** *
27871069 TGTAAGACCATGTTTGGGACATGACATC-GACGATGGTATATGT-GCCT-G
1 TGTAAGACCATGTCTGGGACATGGCATCAG-CGAT-G-ATATGTGGATTCA
* * **
27871117 TGTAAAACCATGTCTGGGACATGGCATCAGCGATGATATATGTGCCT-A
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTG-GATTCA
* * ** *
27871165 TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCT-G
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTG-GATTCA
* *
27871213 TGTAAGACCATGTCTGGGACATGGCATCAGTGATGATATGT-G-TGCCA
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGGAT-TCA
*
27871260 GTGTAAGACCATGTCTGGGACATGGCATCAGCGATAATATGTGGATTCA
1 -TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGGATTCA
* * * *
27871309 TGTAAGACCATGTC-GAGGACATGGCATCGGTGACGGTATGTGGATTCA
1 TGTAAGACCATGTCTG-GGACATGGCATCAGCGATGATATGTGGATTCA
* *
27871357 TGCAAGACCATGTCGGGGACATGGC
1 TGTAAGACCATGTCTGGGACATGGC
27871382 TTGGTACTTT
Statistics
Matches: 232, Mismatches: 23, Indels: 20
0.84 0.08 0.07
Matches are distributed among these distances:
46 6 0.03
47 2 0.01
48 218 0.94
49 5 0.02
50 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGGATTCA
Found at i:27871349 original size:96 final size:93
Alignment explanation
Indices: 27871069--27871381 Score: 362
Period size: 96 Copynumber: 3.3 Consensus size: 93
27871059 AATGTGCCTG
* * * *
27871069 TGTAAGACCATGTTTGGGACATGACATCGACGATGGTATATGTGCCTGTGTAAAACCATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCG-CGAT-GAATATGTGCCTGTGTAAGACCATGTCTGG
* *
27871134 GACATGGCATCAGCGATGATATATGTGCCTA
64 GACATGGCATCAGTGATGATATGTGTGCC-A
27871165 TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCTGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATC-GCGATGA-ATATGTGCCTGTGTAAGACCATGTCTGG
27871230 GACATGGCATCAGTGATGATATGTGTGCCA
64 GACATGGCATCAGTGATGATATGTGTGCCA
** *
27871260 GTGTAAGACCATGTCTGGGACATGGCATCAGCGAT-AATATGTGGATTCATGTAAGACCATGTC-
1 -TGTAAGACCATGTCTGGGACATGGCATC-GCGATGAATATGT-GCCT-GTGTAAGACCATGTCT
* * * *
27871323 GAGGACATGGCATCGGTGACGGTATGTG-GATTCA
62 G-GGACATGGCATCAGTGATGATATGTGTG--CCA
* *
27871357 TGCAAGACCATGTCGGGGACATGGC
1 TGTAAGACCATGTCTGGGACATGGC
27871382 TTGGTACTTT
Statistics
Matches: 193, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
94 6 0.03
95 7 0.04
96 177 0.92
97 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (93 bp):
TGTAAGACCATGTCTGGGACATGGCATCGCGATGAATATGTGCCTGTGTAAGACCATGTCTGGGA
CATGGCATCAGTGATGATATGTGTGCCA
Found at i:27871364 original size:144 final size:144
Alignment explanation
Indices: 27871072--27871381 Score: 378
Period size: 144 Copynumber: 2.2 Consensus size: 144
27871062 GTGCCTGTGT
* * * *
27871072 AAGACCATGTTTGGGACATGACATCGACGATGGTATATGTGCCTGTGTAAAACCATGTCTGGGAC
1 AAGACCATGTCTGGGACATGGCATCGACGATGATATATGTGCCAGTGTAAAACCATGTCTGGGAC
* *
27871137 ATGGCATCAGCGATGATATATGTGCCTATGTAAGACCATGTCTGGGACATGGCATCGGCGATGAT
66 ATGGCATCAGCGATGATATATGTGACTATGTAAGACCATGTCTGGGACATGGCATCGGCGACGAT
* * *
27871202 ATATGTGCCTGTGT
131 ATATGTGACTATGC
* * *
27871216 AAGACCATGTCTGGGACATGGCATC-AGTGATGATATGTGTGCCAGTGTAAGACCATGTCTGGGA
1 AAGACCATGTCTGGGACATGGCATCGA-CGATGATATATGTGCCAGTGTAAAACCATGTCTGGGA
* *
27871280 CATGGCATCAGCGAT-A-ATATGTGGATTCATGTAAGACCATGTC-GAGGACATGGCATCGGTGA
65 CATGGCATCAGCGATGATATATGT-GACT-ATGTAAGACCATGTCTG-GGACATGGCATCGGCGA
* * *
27871342 CGGTATGTG-GATTCATGC
127 CGATATATGTGACT-ATGC
*
27871360 AAGACCATGTCGGGGACATGGC
1 AAGACCATGTCTGGGACATGGC
27871382 TTGGTACTTT
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
142 6 0.04
143 7 0.05
144 130 0.91
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (144 bp):
AAGACCATGTCTGGGACATGGCATCGACGATGATATATGTGCCAGTGTAAAACCATGTCTGGGAC
ATGGCATCAGCGATGATATATGTGACTATGTAAGACCATGTCTGGGACATGGCATCGGCGACGAT
ATATGTGACTATGC
Found at i:27872818 original size:93 final size:93
Alignment explanation
Indices: 27872706--27872877 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
27872696 GCCCATAAGT
* *
27872706 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27872771 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
27872799 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27872864 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
27872878 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:27872873 original size:46 final size:46
Alignment explanation
Indices: 27872698--27872873 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
27872688 TGTAACCCGC
* * *
27872698 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
27872744 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
27872794 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
27872837 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
27872874 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:27875297 original size:29 final size:29
Alignment explanation
Indices: 27875258--27875345 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
27875248 CAAAGATAAC
*
27875258 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
27875287 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
27875316 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
27875346 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:27875316 original size:15 final size:15
Alignment explanation
Indices: 27875258--27875336 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
27875248 CAAAGATAAC
*
27875258 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
27875272 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
27875287 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
27875301 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
27875316 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
27875331 AAGAAA
1 AAGAAA
27875337 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Done.