Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 88 of 161
Found at i:27935820 original size:150 final size:150
Alignment explanation
Indices: 27935549--27935848 Score: 501
Period size: 150 Copynumber: 2.0 Consensus size: 150
27935539 TGCAGTGGAG
* * * *
27935549 CAGACTAAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACCTTGGGTCTT
1 CAGACTAAAGAAACTAATCCTATCTCCCTAAAGTTGCAGCGAAGCGGATTAAAACCATGGATCTT
27935614 ATCTCTCTGAAATTACAGTAGAGCAGATCGCATCAAATTCATCTTTAAGTTGCAGCAGACCAAGC
66 ATCTCTCTGAAATTACAGTAGAGCAGATCGCATCAAATTCATCTTTAAGTTGCAGCAGACCAAGC
27935679 CGAAACTACCAATCCTATCT
131 CGAAACTACCAATCCTATCT
* * * * * **
27935699 CAGACTAAATAAACTAATCCTATCTCCCTAAAGTTGTAGCGGAGTGGATTAGAATGATGGATCTT
1 CAGACTAAAGAAACTAATCCTATCTCCCTAAAGTTGCAGCGAAGCGGATTAAAACCATGGATCTT
27935764 ATCTCTCTGAAATTACAGTAGAGCAGATCGCATCAAATTCATCTTTAAGTTGCAGCAGACCAAGC
66 ATCTCTCTGAAATTACAGTAGAGCAGATCGCATCAAATTCATCTTTAAGTTGCAGCAGACCAAGC
27935829 CGAAACTACCAATCCTATCT
131 CGAAACTACCAATCCTATCT
27935849 TTCCGGCGTT
Statistics
Matches: 139, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 139 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (150 bp):
CAGACTAAAGAAACTAATCCTATCTCCCTAAAGTTGCAGCGAAGCGGATTAAAACCATGGATCTT
ATCTCTCTGAAATTACAGTAGAGCAGATCGCATCAAATTCATCTTTAAGTTGCAGCAGACCAAGC
CGAAACTACCAATCCTATCT
Found at i:27936104 original size:19 final size:19
Alignment explanation
Indices: 27936080--27936133 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
27936070 AATCTTCGAG
27936080 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
27936099 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
27936118 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
27936134 AGTTATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:27952346 original size:28 final size:28
Alignment explanation
Indices: 27952314--27952412 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
27952304 ATAGTAAGTC
*
27952314 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
27952342 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
27952370 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
27952399 CGCACACTTAGTGC
1 CGCACACTTAGTGC
27952413 AAATCTCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:27965034 original size:79 final size:81
Alignment explanation
Indices: 27964898--27965082 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
27964888 TTGAATGATG
*
27964898 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
27964962 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
27964977 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
27965039 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
27965057 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27965083 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:27965096 original size:40 final size:40
Alignment explanation
Indices: 27964899--27965082 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
27964889 TGAATGATGT
* * * *
27964899 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
27964939 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
27964979 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27965017 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27965058 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27965083 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:27965104 original size:79 final size:79
Alignment explanation
Indices: 27964951--27965115 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
27964941 GGACTAAGAT
* **
27964951 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
27965016 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
27965030 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
27965093 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
27965109 CCGAAGG
1 CCGAAGG
27965116 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:27969823 original size:21 final size:21
Alignment explanation
Indices: 27969797--27969854 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
27969787 TAGAATTTAA
27969797 TTCCACACGGGTGTGTT-ACTC
1 TTCCACACGGGTGTGTTAAC-C
* *
27969818 TTCCACACAGGCGTGTTAACC
1 TTCCACACGGGTGTGTTAACC
*
27969839 TTCCACACGAGTGTGT
1 TTCCACACGGGTGTGT
27969855 GCCCTGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
TTCCACACGGGTGTGTTAACC
Found at i:27971119 original size:23 final size:23
Alignment explanation
Indices: 27971052--27971155 Score: 88
Period size: 23 Copynumber: 4.4 Consensus size: 23
27971042 TGGCTCATTG
** *
27971052 GAGCTTACCATTTCAGCTC-GTA
1 GAGCTTACTGTTTCAGCTCAATA
* *
27971074 TGAGCTTACT-ATTCAGCTTAATA
1 -GAGCTTACTGTTTCAGCTCAATA
27971097 GAGCTTACTGTTTCAGCTCAATA
1 GAGCTTACTGTTTCAGCTCAATA
*
27971120 GAGCATACTGTTCATCAGCT-AATGAA
1 GAGCTTACTGTT--TCAGCTCAAT--A
27971146 GAGCTTACTG
1 GAGCTTACTG
27971156 ATCATGGCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
22 16 0.24
23 32 0.48
24 3 0.04
25 6 0.09
26 10 0.15
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (23 bp):
GAGCTTACTGTTTCAGCTCAATA
Found at i:27972234 original size:65 final size:65
Alignment explanation
Indices: 27972130--27972266 Score: 229
Period size: 65 Copynumber: 2.1 Consensus size: 65
27972120 CAGTATGCTC
* * *
27972130 CACACGGCCTCATACATAGGCGTTTGACCGGTCGTGTGGTACAAGTCAGTATACCCCCTAAATGG
1 CACACGGCCTCATACACAGGCATGTGACCGGTCGTGTGGTACAAGTCAGTATACCCCCTAAATGG
* *
27972195 CACACGGCCTCATACACAGGCATGTGACCGGTCGTGTGGTACAAGTTAGTATACTCCCTAAATGG
1 CACACGGCCTCATACACAGGCATGTGACCGGTCGTGTGGTACAAGTCAGTATACCCCCTAAATGG
27972260 CACACGG
1 CACACGG
27972267 GCGTGTGACA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.22
Consensus pattern (65 bp):
CACACGGCCTCATACACAGGCATGTGACCGGTCGTGTGGTACAAGTCAGTATACCCCCTAAATGG
Found at i:27975392 original size:56 final size:56
Alignment explanation
Indices: 27975306--27975425 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
27975296 ACAAGGGATG
27975306 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
27975362 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
27975418 ATGGGCAA
1 ATGGGCAA
27975426 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:27976982 original size:47 final size:48
Alignment explanation
Indices: 27976928--27977506 Score: 791
Period size: 49 Copynumber: 12.1 Consensus size: 48
27976918 TATTTGAATA
27976928 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27976975 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977024 AATGTGAAAGTG-TATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977071 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATCTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
27977120 AATGTGAAAGTG-TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977167 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGTCAATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
27977216 AATGTGAACA-TG-TGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977263 AATGTGAACA-TG-TGTATGTGTGATAAGG-CTGAATGGCCAATGTGATG
1 AATGTGAA-AGTGATATATATGTGATAAGGCCT-AATGGCCAATGTGATG
* * *
27977310 AATGTGAACA-TG-CATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977357 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977406 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
27977455 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCAATGTGATG
27977504 AAT
1 AAT
27977507 ACAGGCTTTA
Statistics
Matches: 496, Mismatches: 24, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
46 2 0.00
47 227 0.46
48 1 0.00
49 265 0.53
50 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (48 bp):
AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCAATGTGATG
Found at i:27977036 original size:96 final size:96
Alignment explanation
Indices: 27976928--27977506 Score: 873
Period size: 96 Copynumber: 6.0 Consensus size: 96
27976918 TATTTGAATA
*
27976928 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
27976993 TATGTGATAACGCCTAATGGCCGATGTGATG
66 TATGTGATAACGCCTAATGGCCGATGTGATG
* * *
27977024 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* *
27977089 TATGTGATAAGGCCTAATGGCCGATCTGATG
66 TATGTGATAACGCCTAATGGCCGATGTGATG
27977120 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* * * *
27977185 TATGTGATAAGGCCGAATGGTCAATGTGATG
66 TATGTGATAACGCCTAATGGCCGATGTGATG
* * *
27977216 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--TG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATA
* * *
27977277 TATGTGTGATAA-GGCTGAATGGCCAATGTGATG
64 TATATGTGATAACGCCT-AATGGCCGATGTGATG
* *
27977310 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
27977374 ATATGTGATAACGCCTAATGGCCGATGTGATG
65 ATATGTGATAACGCCTAATGGCCGATGTGATG
* * *
27977406 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
27977471 TATATGTGATAACGCCTAATGGCCGATGTGATG
64 TATATGTGATAACGCCTAATGGCCGATGTGATG
27977504 AAT
1 AAT
27977507 ACAGGCTTTA
Statistics
Matches: 442, Mismatches: 31, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
93 3 0.01
94 80 0.18
95 1 0.00
96 271 0.61
97 5 0.01
98 82 0.19
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAACGCCTAATGGCCGATGTGATG
Found at i:27977258 original size:38 final size:39
Alignment explanation
Indices: 27977216--27977307 Score: 96
Period size: 47 Copynumber: 2.2 Consensus size: 39
27977206 CAATGTGATG
27977216 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGA
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCC------A
*
27977261 TGAATGTGAACATGTGTATGTGTGATAAGGCTGAATGGCC-
1 --AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
27977301 AATGTGA
1 AATGTGA
27977308 TGAATGTGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
38 7 0.16
47 37 0.84
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (39 bp):
AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
Found at i:27984380 original size:46 final size:46
Alignment explanation
Indices: 27984330--27984505 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
27984320 TGGTTGAGCA
27984330 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27984376 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
27984421 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27984469 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27984506 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
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:27984486 original size:93 final size:93
Alignment explanation
Indices: 27984327--27984498 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
27984317 GGATGGTTGA
* *
27984327 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27984392 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27984420 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27984485 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
27984499 CTTATGGGCG
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:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27992697 original size:49 final size:49
Alignment explanation
Indices: 27992625--27992899 Score: 514
Period size: 49 Copynumber: 5.6 Consensus size: 49
27992615 TATTTGAATT
* * * *
27992625 AATGTGAAAGTGTATATACATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
27992674 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
27992723 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
27992772 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
27992821 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
27992870 AATGTGAAAGTGTATATATATGTGATAGGG
1 AATGTGAAAGTGTATATATATGTGATAGGG
27992900 TATATATGTG
Statistics
Matches: 222, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 222 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATG
Found at i:27992894 original size:18 final size:18
Alignment explanation
Indices: 27992871--27992906 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27992861 GATGTGATGA
*
27992871 ATGTGAAAGTGTATATAT
1 ATGTGAAAGGGTATATAT
*
27992889 ATGTGATAGGGTATATAT
1 ATGTGAAAGGGTATATAT
27992907 GTGACAGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (18 bp):
ATGTGAAAGGGTATATAT
Found at i:27992905 original size:16 final size:16
Alignment explanation
Indices: 27992884--27992915 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27992874 TGAAAGTGTA
*
27992884 TATATATGTGATAGGG
1 TATATATGTGACAGGG
27992900 TATATATGTGACAGGG
1 TATATATGTGACAGGG
27992916 CCGAGTGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (16 bp):
TATATATGTGACAGGG
Found at i:27992933 original size:65 final size:63
Alignment explanation
Indices: 27992835--27992959 Score: 178
Period size: 65 Copynumber: 2.0 Consensus size: 63
27992825 TGAAAGTGTA
* * * *
27992835 TATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGG
1 TATATATGTGACAGGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAGGG
* *
27992900 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATA
1 TATATATGTGACAGGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATA
27992960 AGTCCCGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 8 0.15
64 1 0.02
65 45 0.83
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (63 bp):
TATATATGTGACAGGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAGGG
Found at i:27993136 original size:37 final size:37
Alignment explanation
Indices: 27993084--27993156 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
27993074 GCTCTAAAGA
* * *
27993084 CCCGATGACTACGTGTGGGGATTTTGTCCGGGTAAGG
1 CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGG
*
27993121 CCCGATAACTTCGTGTGGAGATTATGTCCGGGTAAG
1 CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAG
27993157 ACTTCGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.27
Consensus pattern (37 bp):
CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGG
Found at i:27995021 original size:40 final size:40
Alignment explanation
Indices: 27994976--27995285 Score: 426
Period size: 40 Copynumber: 7.8 Consensus size: 40
27994966 GAGAATTGAG
*
27994976 AGTGATGTATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
27995016 AGTGATGTATCCGGACCAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
27995056 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTTGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
27995096 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
27995136 AGTGATGTATCCGGGCTAAGTGT-CGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGT-TCCGAAGAGCATTCGTGCT
27995176 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* *** *
27995216 AGTGATATATCCGTG-CTAAACCCCGAAGAGCATTTGTGCT
1 AGTGATGTATCCG-GACTAAGTTCCGAAGAGCATTCGTGCT
* * * * * *
27995256 GGTGTTATATCCGGGCTAGGTCCCGAAGAG
1 AGTGATGTATCCGGACTAAGTTCCGAAGAG
27995286 TAATCATGCT
Statistics
Matches: 245, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
39 2 0.01
40 242 0.99
41 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:28004893 original size:25 final size:25
Alignment explanation
Indices: 28004865--28004933 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
28004855 CAGTGAATGG
* *
28004865 GTATGCTCACTCAAGCTGTAGATCT
1 GTATGCTCACTCGAGCTGTAGATCA
* * *
28004890 GTATGCTCTCTTGAGTTGTAGATCA
1 GTATGCTCACTCGAGCTGTAGATCA
* *
28004915 CTATGCTCACACGAGCTGT
1 GTATGCTCACTCGAGCTGT
28004934 GGGTCAAAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (25 bp):
GTATGCTCACTCGAGCTGTAGATCA
Found at i:28006645 original size:47 final size:47
Alignment explanation
Indices: 28006567--28006964 Score: 643
Period size: 47 Copynumber: 8.5 Consensus size: 47
28006557 CCCTTCGGGA
* * * * * * *
28006567 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28006614 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28006661 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28006708 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28006755 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
28006802 CTTATCACACATATACACTTTCACATTCATCACATCGGATATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28006849 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28006896 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28006943 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
28006965 TTGGCTGAAT
Statistics
Matches: 332, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 332 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28016343 original size:44 final size:43
Alignment explanation
Indices: 28016295--28016378 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 43
28016285 AACTTCTTGA
* *
28016295 ACCGCTCCCATGCCTGATATAAAGATTCTTCATCAAGTTTTTG
1 ACCGCTCACATGCCTCATATAAAGATTCTTCATCAAGTTTTTG
28016338 NACCGCTCACATGCCTCATATAAAGATTCTTCATCAAGTTT
1 -ACCGCTCACATGCCTCATATAAAGATTCTTCATCAAGTTT
28016379 CTGAAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.33
Consensus pattern (43 bp):
ACCGCTCACATGCCTCATATAAAGATTCTTCATCAAGTTTTTG
Found at i:28018772 original size:27 final size:27
Alignment explanation
Indices: 28018742--28018796 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
28018732 TATTATAAAA
28018742 TTAA-TTAAAATTAAATATTTTAATAAT
1 TTAAGTTAAAATTAAATATTTT-ATAAT
* * *
28018769 TTAAGTTCAATTTAATTATTTTATAAT
1 TTAAGTTAAAATTAAATATTTTATAAT
28018796 T
1 T
28018797 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TTAAGTTAAAATTAAATATTTTATAAT
Found at i:28019627 original size:12 final size:12
Alignment explanation
Indices: 28019610--28019634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28019600 ATTTGGGAAG
28019610 TATAAGGAAAAT
1 TATAAGGAAAAT
28019622 TATAAGGAAAAT
1 TATAAGGAAAAT
28019634 T
1 T
28019635 CACCAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TATAAGGAAAAT
Found at i:28025520 original size:40 final size:40
Alignment explanation
Indices: 28025472--28025618 Score: 258
Period size: 40 Copynumber: 3.7 Consensus size: 40
28025462 GCAAACACAT
* *
28025472 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28025512 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28025552 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28025592 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
28025619 ATCCAATGCT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:28035751 original size:20 final size:20
Alignment explanation
Indices: 28035726--28035841 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
28035716 CGTCTGTGCA
28035726 GTGCCTCTGTTTGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
**
28035746 GTGCCTCTAATTGCACATTT-
1 GTGCCTCTGTTTGCAC-TTTG
* * *
28035766 GTACCTCTTTTTGCACTTCG
1 GTGCCTCTGTTTGCACTTTG
* * *
28035786 ATGCCTCTGATTACACATTT-
1 GTGCCTCTGTTTGCAC-TTTG
* * *
28035806 GTGCCTCTGTCTACACTTCG
1 GTGCCTCTGTTTGCACTTTG
28035826 GTGCCTCTGTTATGCA
1 GTGCCTCTGTT-TGCA
28035842 TATTTGATGC
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.05
20 61 0.84
21 8 0.11
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.41
Consensus pattern (20 bp):
GTGCCTCTGTTTGCACTTTG
Found at i:28035834 original size:40 final size:40
Alignment explanation
Indices: 28035726--28035834 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
28035716 CGTCTGTGCA
* * *
28035726 GTGCCTCTGTTTGCACTTTGGTGCCTCTAATTGCACATTT
1 GTGCCTCTGTTTGCACTTCGGTGCCTCTGATTACACATTT
* * *
28035766 GTACCTCTTTTTGCACTTCGATGCCTCTGATTACACATTT
1 GTGCCTCTGTTTGCACTTCGGTGCCTCTGATTACACATTT
* *
28035806 GTGCCTCTGTCTACACTTCGGTGCCTCTG
1 GTGCCTCTGTTTGCACTTCGGTGCCTCTG
28035835 TTATGCATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (40 bp):
GTGCCTCTGTTTGCACTTCGGTGCCTCTGATTACACATTT
Found at i:28037098 original size:11 final size:11
Alignment explanation
Indices: 28037080--28037109 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28037070 CGCATAGGCT
28037080 GCATGTTTTTG
1 GCATGTTTTTG
*
28037091 GTATGTTTTTG
1 GCATGTTTTTG
28037102 GCATGTTT
1 GCATGTTT
28037110 AGATGTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.27, T:0.57
Consensus pattern (11 bp):
GCATGTTTTTG
Found at i:28051653 original size:18 final size:18
Alignment explanation
Indices: 28051630--28051672 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28051620 AAAGAAAATG
28051630 AAGAAA-AGAAAATTGAAA
1 AAGAAATAG-AAATTGAAA
* *
28051648 AAGAAATTGAGATTGAAA
1 AAGAAATAGAAATTGAAA
28051666 AAGAAAT
1 AAGAAAT
28051673 TGAACAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (18 bp):
AAGAAATAGAAATTGAAA
Found at i:28051654 original size:12 final size:12
Alignment explanation
Indices: 28051617--28051711 Score: 58
Period size: 13 Copynumber: 7.8 Consensus size: 12
28051607 AAAAGTGAGA
*
28051617 GAAAAAGAAAAT
1 GAAAAAGAAATT
28051629 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
28051644 GAAAAAGAAATT
1 GAAAAAGAAATT
28051656 G----AG--ATT
1 GAAAAAGAAATT
28051662 GAAAAAGAAATT
1 GAAAAAGAAATT
*
28051674 GAACAAGAGAAACTC
1 GAA-AA-AGAAA-TT
*
28051689 GAAACAGAAATT
1 GAAAAAGAAATT
28051701 GAAGAAAGAAA
1 GAA-AAAGAAA
28051712 AGAAAATGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 25
0.68 0.05 0.26
Matches are distributed among these distances:
6 4 0.06
8 2 0.03
10 2 0.03
12 17 0.26
13 19 0.29
14 12 0.18
15 9 0.14
ACGTcount: A:0.63, C:0.04, G:0.20, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:28051668 original size:45 final size:46
Alignment explanation
Indices: 28051616--28051720 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
28051606 AAAAAGTGAG
* * *
28051616 AGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAATTG-AGAT
1 AGAAAAAGAAAATGAACAAAAGAAAATCGAAAAAGAAATTGAAGAA
* * * * *
28051661 TGAAAAAGAAATTGAACAAGAGAAACTCGAAACAGAAATTGAAGAA
1 AGAAAAAGAAAATGAACAAAAGAAAATCGAAAAAGAAATTGAAGAA
28051707 AG-AAAAGAAAATGA
1 AGAAAAAGAAAATGA
28051721 GTTAGAAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
45 45 0.92
46 4 0.08
ACGTcount: A:0.64, C:0.04, G:0.20, T:0.12
Consensus pattern (46 bp):
AGAAAAAGAAAATGAACAAAAGAAAATCGAAAAAGAAATTGAAGAA
Found at i:28051673 original size:18 final size:18
Alignment explanation
Indices: 28051641--28051675 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28051631 AGAAAAGAAA
28051641 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
28051659 ATTGAAAAAGAAATTGA
1 ATTGAAAAAGAAATTGA
28051676 ACAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:28061347 original size:21 final size:20
Alignment explanation
Indices: 28061322--28061361 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28061312 CGCTGTAGCG
28061322 ACATCAAAGGGCTGTGTCACA
1 ACATCAAA-GGCTGTGTCACA
* *
28061343 ACATCGAAGGCTGTTTCAC
1 ACATCAAAGGCTGTGTCAC
28061362 TCTAGGGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
ACATCAAAGGCTGTGTCACA
Found at i:28071975 original size:18 final size:18
Alignment explanation
Indices: 28071954--28071988 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28071944 TGAGAAAATT
28071954 AAGATTATTGAGGAGACC
1 AAGATTATTGAGGAGACC
28071972 AAGATTATTGAGGAGAC
1 AAGATTATTGAGGAGAC
28071989 TAAGCACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.23
Consensus pattern (18 bp):
AAGATTATTGAGGAGACC
Found at i:28083096 original size:54 final size:55
Alignment explanation
Indices: 28083029--28083136 Score: 155
Period size: 56 Copynumber: 2.0 Consensus size: 55
28083019 ATGTCATGAC
* *
28083029 ATTAAGGGAATGAGA-TCTCATGTAAGACCATGTCTGGGACATGGCATTAGCATT
1 ATTAAGGGAATGAGAGTCTCACGTAAGACCATGTCTGGGACATAGCATTAGCATT
** *
28083083 ATTAAGGTTATGAGAGGTCTCACGTAAGACCATGTCTGGGACATAGCGTTAGCA
1 ATTAAGGGAATGAGA-GTCTCACGTAAGACCATGTCTGGGACATAGCATTAGCA
28083137 CCGAGATGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 13 0.28
56 34 0.72
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (55 bp):
ATTAAGGGAATGAGAGTCTCACGTAAGACCATGTCTGGGACATAGCATTAGCATT
Found at i:28083513 original size:20 final size:20
Alignment explanation
Indices: 28083488--28083536 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28083478 TGAATTATTT
* *
28083488 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAA
*
28083508 AAGTAAGAAAGTAAGTAAAA
1 AAGTAAGCAAGTAAGTAAAA
28083528 AAG-AAGCAA
1 AAGTAAGCAA
28083537 AGACCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAA
Found at i:28087320 original size:72 final size:72
Alignment explanation
Indices: 28087234--28087383 Score: 255
Period size: 72 Copynumber: 2.1 Consensus size: 72
28087224 ATCAAATTGT
* *
28087234 AATTTTTTATAATTTAACAATCAAAGTGTAAACTTATTAATAATTAAATGACTATAAGTATAATT
1 AATTTTTTATAATTTAACAATCAAAGTGTAAACTTATTAATAATTAAATGACCACAAGTATAATT
28087299 TACCCAA
66 TACCCAA
* * *
28087306 ATTTTTTTATAATTTAACAATTAAAGTGTAACCTTATTAATAATTAAATGACCACAAGTATAATT
1 AATTTTTTATAATTTAACAATCAAAGTGTAAACTTATTAATAATTAAATGACCACAAGTATAATT
28087371 TACCCAA
66 TACCCAA
28087378 AATTTT
1 AATTTT
28087384 AAACACATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (72 bp):
AATTTTTTATAATTTAACAATCAAAGTGTAAACTTATTAATAATTAAATGACCACAAGTATAATT
TACCCAA
Found at i:28099533 original size:166 final size:167
Alignment explanation
Indices: 28099239--28099568 Score: 590
Period size: 166 Copynumber: 2.0 Consensus size: 167
28099229 AATAGGGTCA
* *
28099239 AAAAAAATTTTATGTTCTCCGGACAAACACAAGTACCTGGATATTGTGGACTAAGGCAGAATTCT
1 AAAAAAATTTTACGTTCTCCGGACAAACACAAGTACCTGGATATAGTGGACTAAGGCAGAATTCT
*
28099304 CATCACTTGTATTAAGGCCTTCCTTACTGTAGCAGTAATTCATGCCTTTTCCAAGTTTAACTACT
66 CATCACTTGGATTAAGGCCTTCCTTACTGTAGCAGTAATTCATGCCTTTTCCAAGTTTAACTACT
28099369 CTATTTCTTAGAATCTAGGATGGAAACAGCGGTTCAC
131 CTATTTCTTAGAATCTAGGATGGAAACAGCGGTTCAC
* *
28099406 AAAAAAA-TTTACGTTCTCTGGACAAACACAATTACCTGGATATAGTGGACTAAGGCAGAATTCT
1 AAAAAAATTTTACGTTCTCCGGACAAACACAAGTACCTGGATATAGTGGACTAAGGCAGAATTCT
*
28099470 CATCACTTGGATTGAGGCCTTCCTTACTGTAGCAGTAATTCATGCCTTTTCCAAGTTTAACTACT
66 CATCACTTGGATTAAGGCCTTCCTTACTGTAGCAGTAATTCATGCCTTTTCCAAGTTTAACTACT
*
28099535 CTATTTCTTAGAATCTGGGATGGAAACAGCGGTT
131 CTATTTCTTAGAATCTAGGATGGAAACAGCGGTT
28099569 GGCATATAGG
Statistics
Matches: 156, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
166 149 0.96
167 7 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (167 bp):
AAAAAAATTTTACGTTCTCCGGACAAACACAAGTACCTGGATATAGTGGACTAAGGCAGAATTCT
CATCACTTGGATTAAGGCCTTCCTTACTGTAGCAGTAATTCATGCCTTTTCCAAGTTTAACTACT
CTATTTCTTAGAATCTAGGATGGAAACAGCGGTTCAC
Found at i:28101922 original size:23 final size:24
Alignment explanation
Indices: 28101890--28101935 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
28101880 TTTTCATTAG
* *
28101890 TATATTTTCTTTTCTT-ATTTTCA
1 TATATATTCTTCTCTTCATTTTCA
28101913 TATATATTCTTCTCTTCATTTTC
1 TATATATTCTTCTCTTCATTTTC
28101936 GATAACACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (24 bp):
TATATATTCTTCTCTTCATTTTCA
Found at i:28107213 original size:53 final size:53
Alignment explanation
Indices: 28107130--28107241 Score: 188
Period size: 53 Copynumber: 2.1 Consensus size: 53
28107120 AGTTACTTCC
*
28107130 AAAAGATGTCAATTTTTTCTTTCTGTAATCCCATTTAGTTGTAGTGTATTTGT
1 AAAAGATGTCAATTTTTTCTTTCTGCAATCCCATTTAGTTGTAGTGTATTTGT
* * *
28107183 ATAAGATGTCAGTTTTTTCTTTCTGCAATCCCATTTAGTTGTGGTGTATTTGT
1 AAAAGATGTCAATTTTTTCTTTCTGCAATCCCATTTAGTTGTAGTGTATTTGT
28107236 AAAAGA
1 AAAAGA
28107242 ACTTTGATGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (53 bp):
AAAAGATGTCAATTTTTTCTTTCTGCAATCCCATTTAGTTGTAGTGTATTTGT
Found at i:28108967 original size:19 final size:18
Alignment explanation
Indices: 28108939--28108978 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
28108929 TGAACAAAAC
*
28108939 TTATCTACCTAAATAAGAT
1 TTATCGACCTAAATAA-AT
28108958 TTATCGACCTAAATAAAT
1 TTATCGACCTAAATAAAT
28108976 TTA
1 TTA
28108979 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (18 bp):
TTATCGACCTAAATAAAT
Found at i:28121086 original size:24 final size:23
Alignment explanation
Indices: 28121045--28121091 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
28121035 CTAAATACTA
28121045 TTAAAAAAATAGAAAATACAAATT
1 TTAAAAAAATAGAAAATA-AAATT
* *
28121069 TTAAAAAAATATATAATAAAATT
1 TTAAAAAAATAGAAAATAAAATT
28121092 ATATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAAAAATAGAAAATAAAATT
Found at i:28122255 original size:14 final size:15
Alignment explanation
Indices: 28122228--28122260 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28122218 ACAATTTTTG
*
28122228 AATAATAATTTATCA
1 AATAATAATATATCA
28122243 AATAATAA-ATATCA
1 AATAATAATATATCA
28122257 AATA
1 AATA
28122261 TTTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAATATATCA
Found at i:28123426 original size:28 final size:27
Alignment explanation
Indices: 28123381--28123461 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
28123371 CAAATTTGTA
* *
28123381 AAGGGAAAAAGTGCAAAATCTAAAAAAT
1 AAGGG-AAAACTGTAAAATCTAAAAAAT
* * *
28123409 AAGGGAAATATTTTAAAATCTGAAAAAT
1 AAGGGAAA-ACTGTAAAATCTAAAAAAT
*
28123437 ATGGGAAAACTGTAAAATCTAAAAA
1 AAGGGAAAACTGTAAAATCTAAAAA
28123462 CTAGGGGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 17 0.39
28 27 0.61
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.21
Consensus pattern (27 bp):
AAGGGAAAACTGTAAAATCTAAAAAAT
Found at i:28124791 original size:51 final size:51
Alignment explanation
Indices: 28124731--28125065 Score: 312
Period size: 51 Copynumber: 6.6 Consensus size: 51
28124721 GATGAACACG
* * *
28124731 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGTCACA
* * * * * *
28124782 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-CACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTG-GTCACA
* * * * *
28124833 TGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTA-TGGTTACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTGGTCACA
* * * * *
28124884 TGTGTGGTACTAAGTGAAGGCTACTATG-GATACCGGA-AAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTG-TACC-GATAA-ATATTGGTCACA
* *
28124935 TATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGTCACA
* * * *
28124985 TGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ATTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGTCACA
28125034 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
28125066 TCGAATGATA
Statistics
Matches: 230, Mismatches: 41, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
49 39 0.17
50 49 0.21
51 138 0.60
52 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGTCACA
Found at i:28124903 original size:102 final size:101
Alignment explanation
Indices: 28124727--28125068 Score: 412
Period size: 102 Copynumber: 3.4 Consensus size: 101
28124717 TATCGATGAA
* *
28124727 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
28124791 CTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCGAGAAG-TTTGAG
* * * *
28124829 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTGGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
28124894 TAAGTGAAGGCTACTATG-GATACCG-GAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTG-TACCGAG-AAG-TTTGAG
* * * *
28124930 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACATGTGTAGT
1 -CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT
* * * * * *
28124993 ACTATGTGAAGGCTACTACGTGAACTGTA-AA-ATTGAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AGAAGTTTGAG
28125030 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
28125069 AATGATAAAA
Statistics
Matches: 208, Mismatches: 22, Indels: 22
0.83 0.09 0.09
Matches are distributed among these distances:
99 36 0.17
100 2 0.01
101 43 0.21
102 126 0.61
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAAGTTTGAG
Found at i:28126105 original size:366 final size:366
Alignment explanation
Indices: 28125430--28126129 Score: 1170
Period size: 366 Copynumber: 1.9 Consensus size: 366
28125420 TAAATTTTAT
*
28125430 TGAGACAGGGTTGGATTGATTTCGAAATCCCCTGTTCCAAATTTGGAAAATCACCAAAAATTTAA
1 TGAGACAGGGTTGGATTGATTTCGAAATCCCCTGTTCCAAATTTGAAAAATCACCAAAAATTT-A
* * *
28125495 AAAAAAATAATTATGGCTTAAAATTTACATTCTTTAATTCCTTAATGAGTCTATTTTTAAGAGAA
65 AAAAAAATAATTATGGCTTAAAATTTACATTATTGAATTCATTAATGAGTCTATTTTTAAGAGAA
28125560 AGAAATGAGAACATTGTCTGAATTTTTTACAAAGAGTTAAATAAATTTTAGTATGGAGAGGTCAG
130 AGAAATGAGAACATTGTCTGAATTTTTTACAAAGAGTTAAATAAATTTTAGTATGGAGAGGTCAG
** *
28125625 AACTGTCAGGCAGTGAAACAGGGGAAGGTTTAAAGAATAAACTGTACTAATTGGCTGAATCAAAA
195 AACTGTCAGGCAGTGAAACAGGGGAAGGTTTAAAGAATAAACTGTACTAATTGGAAGAACCAAAA
* * * * *
28125690 ATTCGTAAAATTTTATGGTGGAAAGGTATATGAGTCTAGTTTCAGGGAAAATTTACGGATCTTAA
260 ATTCGTAAAAATTTATGGTGAAAAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATCTAAA
28125755 TTTGGAGTTCCGTAGCTCTAGATAAAAATAATTTAGTGACTG
325 TTTGGAGTTCCGTAGCTCTAGATAAAAATAATTTAGTGACTG
*
28125797 TGAGACAGGGTTGGTTTGATTTCGAAATCCCCTGTTCCAAATTTGAAAAATCACCAAAAATTGT-
1 TGAGACAGGGTTGGATTGATTTCGAAATCCCCTGTTCCAAATTTGAAAAATCACCAAAAATT-TA
*
28125861 AAAAAAATAATTATGGCTTGAAATTTACATTATTGAATTCATTAATGAGTCTATTTTTAAGAGAA
65 AAAAAAATAATTATGGCTTAAAATTTACATTATTGAATTCATTAATGAGTCTATTTTTAAGAGAA
*
28125926 AGAAATGAGAACATTGTTTGAATTTTTTACAAAGAGTTAAATAAATTTTAGTATGGAGAGGTCAG
130 AGAAATGAGAACATTGTCTGAATTTTTTACAAAGAGTTAAATAAATTTTAGTATGGAGAGGTCAG
*
28125991 AACTGTCAGGCAGTGAAATAGGGGAAGGTTTAAAGAATAAACTGTACTAATTGGAAGAACCAAAA
195 AACTGTCAGGCAGTGAAACAGGGGAAGGTTTAAAGAATAAACTGTACTAATTGGAAGAACCAAAA
* * * *
28126056 ATTCTTAAAAATTTATGGT-AAACATATATATGAGTCTCGTTTTAGGGAAAATTTACAGATCTAA
260 ATTCGTAAAAATTTATGGTGAAA-AGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATCTAA
*
28126120 ATTTTGAGTT
324 ATTTGGAGTT
28126130 TTTTAGCTCG
Statistics
Matches: 310, Mismatches: 21, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
365 2 0.01
366 247 0.80
367 60 0.19
368 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (366 bp):
TGAGACAGGGTTGGATTGATTTCGAAATCCCCTGTTCCAAATTTGAAAAATCACCAAAAATTTAA
AAAAAATAATTATGGCTTAAAATTTACATTATTGAATTCATTAATGAGTCTATTTTTAAGAGAAA
GAAATGAGAACATTGTCTGAATTTTTTACAAAGAGTTAAATAAATTTTAGTATGGAGAGGTCAGA
ACTGTCAGGCAGTGAAACAGGGGAAGGTTTAAAGAATAAACTGTACTAATTGGAAGAACCAAAAA
TTCGTAAAAATTTATGGTGAAAAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATCTAAAT
TTGGAGTTCCGTAGCTCTAGATAAAAATAATTTAGTGACTG
Found at i:28126883 original size:370 final size:370
Alignment explanation
Indices: 28126202--28126915 Score: 1428
Period size: 370 Copynumber: 1.9 Consensus size: 370
28126192 AGTGAATGAT
28126202 GCAGAAAAACAGTTTGCTGGAAATTGAATAAATGATAGATTTATGTGTGATAGAAATTTTATTAT
1 GCAGAAAAACAGTTTGCTGGAAATTGAATAAATGATAGATTTATGTGTGATAGAAATTTTATTAT
28126267 ATATGATATTATTCTAGAAATTTATTTATCGATTACATACATACTTTCTAAGCTATAATCTTACT
66 ATATGATATTATTCTAGAAATTTATTTATCGATTACATACATACTTTCTAAGCTATAATCTTACT
28126332 CCTCTTTATTTTTATTTTGTTTTATAGTGATATTAATCAGCTCGGGAATTGGACGGAGTCAGGAC
131 CCTCTTTATTTTTATTTTGTTTTATAGTGATATTAATCAGCTCGGGAATTGGACGGAGTCAGGAC
28126397 ATCATCCTCACTATCATCATCATCTTTTGGGTATTTTGCAACCAGTACTTTTGAAAAATGGCATG
196 ATCATCCTCACTATCATCATCATCTTTTGGGTATTTTGCAACCAGTACTTTTGAAAAATGGCATG
28126462 TATAGATGACTTTATGTAATGTGGTATAAATATGTATATATATAGTATTTTTCGGTTAAATATGT
261 TATAGATGACTTTATGTAATGTGGTATAAATATGTATATATATAGTATTTTTCGGTTAAATATGT
28126527 TGGAGTTTATTAATGGATAGATAAAAATAATTTAGTGACTGTGAC
326 TGGAGTTTATTAATGGATAGATAAAAATAATTTAGTGACTGTGAC
28126572 GCAGAAAAACAGTTTGCTGGAAATTGAATAAATGATAGATTTATGTGTGATAGAAATTTTATTAT
1 GCAGAAAAACAGTTTGCTGGAAATTGAATAAATGATAGATTTATGTGTGATAGAAATTTTATTAT
28126637 ATATGATATTATTCTAGAAATTTATTTATCGATTACATACATACTTTCTAAGCTATAATCTTACT
66 ATATGATATTATTCTAGAAATTTATTTATCGATTACATACATACTTTCTAAGCTATAATCTTACT
28126702 CCTCTTTATTTTTATTTTGTTTTATAGTGATATTAATCAGCTCGGGAATTGGACGGAGTCAGGAC
131 CCTCTTTATTTTTATTTTGTTTTATAGTGATATTAATCAGCTCGGGAATTGGACGGAGTCAGGAC
28126767 ATCATCCTCACTATCATCATCATCTTTTGGGTATTTTGCAACCAGTACTTTTGAAAAATGGCATG
196 ATCATCCTCACTATCATCATCATCTTTTGGGTATTTTGCAACCAGTACTTTTGAAAAATGGCATG
28126832 TATAGATGACTTTATGTAATGTGGTATAAATATGTATATATATAGTATTTTTCGGTTAAATATGT
261 TATAGATGACTTTATGTAATGTGGTATAAATATGTATATATATAGTATTTTTCGGTTAAATATGT
28126897 TGGAGTTTATTAATGGATA
326 TGGAGTTTATTAATGGATA
28126916 ATTTATGTCT
Statistics
Matches: 344, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
370 344 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (370 bp):
GCAGAAAAACAGTTTGCTGGAAATTGAATAAATGATAGATTTATGTGTGATAGAAATTTTATTAT
ATATGATATTATTCTAGAAATTTATTTATCGATTACATACATACTTTCTAAGCTATAATCTTACT
CCTCTTTATTTTTATTTTGTTTTATAGTGATATTAATCAGCTCGGGAATTGGACGGAGTCAGGAC
ATCATCCTCACTATCATCATCATCTTTTGGGTATTTTGCAACCAGTACTTTTGAAAAATGGCATG
TATAGATGACTTTATGTAATGTGGTATAAATATGTATATATATAGTATTTTTCGGTTAAATATGT
TGGAGTTTATTAATGGATAGATAAAAATAATTTAGTGACTGTGAC
Found at i:28128270 original size:32 final size:32
Alignment explanation
Indices: 28128201--28128277 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
28128191 TTGTATAGAG
*
28128201 TTTAATTGATTTTATAAATTATTTTACAATAG
1 TTTAATTGATTTTATAAATTATTTTACAATAA
* *
28128233 CTTAATTGATATTTCT-AATTATTTTACGAA-AA
1 TTTAATTGAT-TTTATAAATTATTTTAC-AATAA
*
28128265 TTTAATTTATTTT
1 TTTAATTGATTTT
28128278 TTATTTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 3 0.08
32 29 0.76
33 6 0.16
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (32 bp):
TTTAATTGATTTTATAAATTATTTTACAATAA
Found at i:28128344 original size:11 final size:11
Alignment explanation
Indices: 28128306--28128358 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
28128296 TTTAAATATT
*
28128306 AAAAAA-TATT
1 AAAAAATTATA
28128316 AAAAAATTAT-
1 AAAAAATTATA
*
28128326 -AGAAATTATA
1 AAAAAATTATA
28128336 AAAAAATTATA
1 AAAAAATTATA
*
28128347 GAAAAA-TATA
1 AAAAAATTATA
28128357 AA
1 AA
28128359 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.22
10 11 0.31
11 17 0.47
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:28129961 original size:24 final size:24
Alignment explanation
Indices: 28129916--28129961 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28129906 TCATATTGAG
* * *
28129916 ATTAATTTTCTATTTTTCATTTTC
1 ATTAAATTTCAATTTTACATTTTC
*
28129940 ATTAAATTTCAATTTTAGATTT
1 ATTAAATTTCAATTTTACATTT
28129962 AATTTTTGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTAAATTTCAATTTTACATTTTC
Found at i:28131610 original size:15 final size:15
Alignment explanation
Indices: 28131575--28131621 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
28131565 AAAGTATTTT
*
28131575 AAAAATATTTTTAAA
1 AAAAATTTTTTTAAA
28131590 ATAAAATTTTTTTAAA
1 A-AAAATTTTTTTAAA
* *
28131606 AAAAAGTATTTTAAA
1 AAAAATTTTTTTAAA
28131621 A
1 A
28131622 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAAATTTTTTTAAA
Found at i:28131621 original size:11 final size:11
Alignment explanation
Indices: 28131607--28131643 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
28131597 TTTTTTAAAA
28131607 AAAAGTATTTT
1 AAAAGTATTTT
28131618 AAAAGTATTTT
1 AAAAGTATTTT
*
28131629 AAAAATATTTT
1 AAAAGTATTTT
28131640 AAAA
1 AAAA
28131644 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:28131649 original size:43 final size:45
Alignment explanation
Indices: 28131542--28131653 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 45
28131532 AATAAACACC
*
28131542 AAAAAAATTTTAAAAAAATAAAAAAAGTATTTTAAAAATATTTTTA
1 AAAAAAATTTTAAAAATA-AAAAAAAGTATTTTAAAAATATTTTTA
** *
28131588 AAATAAAATTTT---TTTAAAAAAAAGTATTTTAAAAGTA-TTTT-
1 AAA-AAAATTTTAAAAATAAAAAAAAGTATTTTAAAAATATTTTTA
*
28131629 AAAAATATTTTAAAAATAAAAAAAA
1 AAAAAAATTTTAAAAATAAAAAAAA
28131654 TAAAAATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
40 7 0.13
41 3 0.05
42 4 0.07
43 29 0.53
44 1 0.02
46 3 0.05
47 8 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (45 bp):
AAAAAAATTTTAAAAATAAAAAAAAGTATTTTAAAAATATTTTTA
Found at i:28132701 original size:198 final size:197
Alignment explanation
Indices: 28132341--28132699 Score: 479
Period size: 197 Copynumber: 1.8 Consensus size: 197
28132331 CACGTTTATA
* * * * *
28132341 TCAACATTTTGATCATAATAAAGTATTTAGGCTAACAATGACATCTAAGAGTTGAGGTACCAAAT
1 TCAACATTTTAATCAGAATAAAGTATTTAGACTAACAATGACATATAAAAGTTGAGGTACCAAAT
* * *
28132406 TATGTCAAAAATTAAAGCATAAAGACTGAATTTCAAATTTGAGCATAATATAGGAACCAAAACTA
66 TATGTAAAAAATTAAAGCATAAAAACTAAATTTCAAATTTGAGCATAATATAGGAACCAAAACTA
* * * *
28132471 AAATTTGACCATTTTTATATAATCTCAAAAAAGAAGTGAAAATGTTGTATATTTAGACACACGCA
131 AAATTGGACCATTATTATAAAATCTAAAAAAAGAAGTGAAAATGTTGTATATTTAGACACACGCA
28132536 TG
196 TG
* * *
28132538 TCAACATTTTAATCAGAATGAAGTATTTAGACTAA-ATTTGCCAATATAAAAGTTGAGGTACCAA
1 TCAACATTTTAATCAGAATAAAGTATTTAGACTAACA-ATGAC-ATATAAAAGTTGAGGTACCAA
* * * * * * *
28132602 ATTATGTAAAAAATTAAAGTATAAAAATTAAATTTGAAATTTGAGCA-ATTATAGGGACTAAAAT
64 ATTATGTAAAAAATTAAAGCATAAAAACTAAATTTCAAATTTGAGCATAATATAGGAACCAAAAC
*
28132666 TGAAATTGGACCATTATTATAAAATCTAAAAAAA
129 TAAAATTGGACCATTATTATAAAATCTAAAAAAA
28132700 AGTCTTTGTT
Statistics
Matches: 137, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
196 1 0.01
197 76 0.55
198 60 0.44
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (197 bp):
TCAACATTTTAATCAGAATAAAGTATTTAGACTAACAATGACATATAAAAGTTGAGGTACCAAAT
TATGTAAAAAATTAAAGCATAAAAACTAAATTTCAAATTTGAGCATAATATAGGAACCAAAACTA
AAATTGGACCATTATTATAAAATCTAAAAAAAGAAGTGAAAATGTTGTATATTTAGACACACGCA
TG
Found at i:28132853 original size:164 final size:163
Alignment explanation
Indices: 28132578--28133211 Score: 637
Period size: 164 Copynumber: 3.9 Consensus size: 163
28132568 ACTAAATTTG
28132578 CCAATATAAAAGTTGAGGTACCAAATTATGTAAAAAATTAAAGTATAAAAATTAAATTTGAAATT
1 CCAA-ATAAAAGTTGAGGTACCAAATTATGTAAAAAATTAAAGTAT-AAAATTAAATTTGAAATT
* * *
28132643 TGAGCA-ATTATAGGGACTAAAATTGAAATTGGACCATTATTATAAAATCTAAAAAAAAG-TCTT
64 TGAGCATATTATAGAGACTAAAATTGAAATTGGACCATTCTTATAAAATCTAAAAAAAAGAGCTT
*
28132706 TGTTTTATTATTTGGACAAATATAAAAAAGGAATGT
129 TGTTTCATTATTTGGACAAAT-TAAAAAAGGAATGT
* *
28132742 CCAAATAAAAGTTGTGGTACCAAATTATGTAAAAAAATTAAAGTATAAAATTAAATCTGAAATTT
1 CCAAATAAAAGTTGAGGTACCAAATTATGT-AAAAAATTAAAGTATAAAATTAAATTTGAAATTT
28132807 GAGCATATTATAGAGACTAAAATTGAAATTGGACCATTCTTATAAAATCTAAAAAAAGAGAGCTT
65 GAGCATATTATAGAGACTAAAATTGAAATTGGACCATTCTTATAAAATCTAAAAAAA-AGAGCTT
* * *
28132872 TCTTTCATTATTTGGACAAGTTTCATAAAAGGAATG-
129 TGTTTCATTATTTGGACAA-ATT-AAAAAAGGAATGT
* * * * *
28132908 CC---------TT-A-G-A-C-ATTTAT-T--TATATTAAAGTACAAAAATTAAATTTAAAATTT
1 CCAAATAAAAGTTGAGGTACCAAATTATGTAAAAAATTAAAGTA-TAAAATTAAATTTGAAATTT
* * * *
28132956 GAGCATGTTATAGGGATTAAAATTGAAATTGGACCATTTTTATAAAATCTCAAAAAAAGAAGAAG
65 GAGCATATTATAGAGACTAAAATTGAAATTGGACCATTCTTATAAAATCT------AA-AA-AA-
* *
28133021 AAGAAAAAGCTTTGTTTCATTATTTGGACAAACTTCATAAAGGAATGT
121 AAG----AGCTTTGTTTCATTATTTGGACAAA-TTAAAAAAGGAATGT
* * *
28133069 CCAAATAAAAGTTAAGGTACCAAATTATGT-AAAAATTAAAGTATAAAATTAAATTTGAAATCTA
1 CCAAATAAAAGTTGAGGTACCAAATTATGTAAAAAATTAAAGTATAAAATTAAATTTGAAATTTG
* * * *
28133133 AGCATATTATA-AGGACTAAAACTAAAATTGGACCGTTCTTATAAAATCAAAAAAGAGAAGAAGC
66 AGCATATTATAGA-GACTAAAATTGAAATTGGACCATTCTTATAAAATCTAAAAA-A-AAG-AGC
28133197 TTTGTTTCATTATTT
127 TTTGTTTCATTATTT
28133212 ATATAGATGT
Statistics
Matches: 390, Mismatches: 40, Indels: 78
0.77 0.08 0.15
Matches are distributed among these distances:
148 10 0.03
149 63 0.16
151 1 0.00
152 5 0.01
153 1 0.00
154 1 0.00
155 3 0.01
156 2 0.01
157 6 0.02
158 1 0.00
160 9 0.02
161 27 0.07
163 48 0.12
164 68 0.17
165 2 0.01
166 42 0.11
167 12 0.03
168 1 0.00
169 7 0.02
170 4 0.01
171 1 0.00
172 1 0.00
173 1 0.00
174 1 0.00
175 5 0.01
176 58 0.15
177 10 0.03
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (163 bp):
CCAAATAAAAGTTGAGGTACCAAATTATGTAAAAAATTAAAGTATAAAATTAAATTTGAAATTTG
AGCATATTATAGAGACTAAAATTGAAATTGGACCATTCTTATAAAATCTAAAAAAAAGAGCTTTG
TTTCATTATTTGGACAAATTAAAAAAGGAATGT
Found at i:28135003 original size:35 final size:35
Alignment explanation
Indices: 28134954--28135452 Score: 385
Period size: 35 Copynumber: 14.1 Consensus size: 35
28134944 ATGGCTAATA
* * * *
28134954 AATGAATTACCAGTGTTGTGGTGGGATATTAATTG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
*
28134989 AGTGAAGTATCAGTGTTGTGGTGGGATGTTAAATGAATGAAG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTT--A--AAT---G
* *
28135031 AATGAAGTATCAGTGTTGTGGTAGGATATTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * * * *
28135066 AATTAATTAACGGTGTTGTGGTGAGATGTTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
** ** *
28135101 AATGAAGTATTGGTGTTGTGGCAGAATGTTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
** * *
28135136 AATGAAGAAGTATTGGTGTTATGATGGGATGTTAAATG
1 AAT---GAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * * * * *
28135174 AAAGTAGTA--A-CGTTGTGGCGGGATATTAATTG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * *
28135206 AATGAGGTATC-GATGTTGTGATAGGATGTTAAATG
1 AATGAAGTATCAG-TGTTGTGGTGGGATGTTAAATG
* ** * * * *
28135241 AATGTAGTAAAAATGTTGTAGTGGGATATTAATTG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * *
28135276 AATGAAGTATCGGTATTGTGGTAGGATGTTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * *
28135311 AATAAAGTATCGGTGTTGTGGTGGGATATTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * *
28135346 AATAAAGTAACAATGTTGTGGTGGGATGTTAAATG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * *
28135381 AATGAAGTATCAGTGTTGTGGCGAGATGTTAATTG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
* * * * *
28135416 AAAGAAGTATCAATGTTGTGGCGGAATGTTAATTG
1 AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
28135451 AA
1 AA
28135453 AAAGGATTGG
Statistics
Matches: 365, Mismatches: 84, Indels: 30
0.76 0.18 0.06
Matches are distributed among these distances:
32 22 0.06
35 279 0.76
37 1 0.00
38 32 0.09
39 2 0.01
40 1 0.00
42 28 0.08
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (35 bp):
AATGAAGTATCAGTGTTGTGGTGGGATGTTAAATG
Found at i:28149804 original size:21 final size:20
Alignment explanation
Indices: 28149780--28149830 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
28149770 GTGTTGTGGC
28149780 TGCATCTGATTCTGGTGTAGA
1 TGCATCTGATT-TGGTGTAGA
* *
28149801 TGCATCTAGCTTTGTTGTAGA
1 TGCATCT-GATTTGGTGTAGA
28149822 TGCATCTGA
1 TGCATCTGA
28149831 CCGTGTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (20 bp):
TGCATCTGATTTGGTGTAGA
Found at i:28149837 original size:21 final size:21
Alignment explanation
Indices: 28149795--28149838 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28149785 CTGATTCTGG
**
28149795 TGTAGATGCATCTAGCTTTGT
1 TGTAGATGCATCTAGCCGTGT
28149816 TGTAGATGCATCT-GACCGTGT
1 TGTAGATGCATCTAG-CCGTGT
28149837 TG
1 TG
28149839 ATTGTAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (21 bp):
TGTAGATGCATCTAGCCGTGT
Found at i:28152531 original size:22 final size:22
Alignment explanation
Indices: 28152503--28152545 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28152493 TACATATGAG
*
28152503 CCCTGTTATATTTTCATGCGAA
1 CCCTGTTATAATTTCATGCGAA
* *
28152525 CCCTGTTGTAATTTGATGCGA
1 CCCTGTTATAATTTCATGCGA
28152546 GCTCTGAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
CCCTGTTATAATTTCATGCGAA
Found at i:28156459 original size:27 final size:27
Alignment explanation
Indices: 28156424--28156479 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
28156414 TTTTTTCAAA
28156424 TTTTTTATTTTTATAGCTAAAACTAAT
1 TTTTTTATTTTTATAGCTAAAACTAAT
*
28156451 TTTTTTATTTTTATAGCTAAATCTAAT
1 TTTTTTATTTTTATAGCTAAAACTAAT
28156478 TT
1 TT
28156480 AAATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTTTATTTTTATAGCTAAAACTAAT
Found at i:28156591 original size:12 final size:12
Alignment explanation
Indices: 28156576--28156601 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28156566 TAAAATTATT
28156576 TTGAATAAAAAA
1 TTGAATAAAAAA
28156588 TTGAATAAAAAA
1 TTGAATAAAAAA
28156600 TT
1 TT
28156602 AACTTTAATG
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
TTGAATAAAAAA
Found at i:28158455 original size:228 final size:228
Alignment explanation
Indices: 28158029--28159134 Score: 1089
Period size: 228 Copynumber: 4.9 Consensus size: 228
28158019 GATTCAATAG
* * * * * * * * *
28158029 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * * *
28158094 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
66 CATTGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * * * *
28158159 TATTTGCTGGCAAA-CAACTTGAGGATGGCCGCACGC-TAGCCGACTACAACATTCAGAAA-GAA
131 TATTTGCTGG-AAAGCAACTTGAAGATGGTCGCAC-CTTAGCCGATTACAATATCCA-AAAGGAG
* *
28158221 TCCACCCTTCACTTGGTTCTTCGACTTCGTGGCGGC
193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * *
28158257 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * *
28158322 AATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGATCAGCAGAGGCTTA
66 CATTGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
* * * *
28158387 TCTTTGCTGGAAAGCAGCTTGAAGATGGTCGCACCTTAGCTGATTACAATATCCAAAAAGAGTCC
131 TATTTGCTGGAAAGCAACTTGAAGATGGTCGCACCTTAGCCGATTACAATATCCAAAAGGAGTCC
* * * *
28158452 ACCCTCCACCTGGTACTTCGTCTTCGAGGTGGC
196 ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * * * * *
28158485 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTCGAGAGTTCGGATAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * * *
28158550 CATTGACAATGTGAAA-GCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAA-GATT
66 CATTGACAATGT-AAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * ** * * *
28158613 GATTTTTGCTGGAAAACAACTTGAAGATGGAAGAACTCTT-GCCGATTATAATATCCAGAAGGAG
130 -ATATTTGCTGGAAAGCAACTTGAAGATGGTCGCAC-CTTAGCCGATTACAATATCCAAAAGGAG
* * * * * * *
28158677 TCTACTCTCCATTTGGTTCTCCGCCTTCGGGGTGGT
193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
* * * * * * * *
28158713 ATGCAGATCTTTGTAAAGACTCTTACCGGAAAGACCATCACTTTGGAGGTTGAAAGTTCCGATAC
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
* * *
28158778 CATTGACAATGTGAAGGCAAAGATCCAAGACAAGG-AGGGTATCCCCCCAGACCAGCAAAGGCTC
66 CATTGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG-ATCCCACCAGACCAGCAAAGGCTT
* * * * * * * * *
28158842 ATCTTTGCTGGCAAGCAGCTCGAAGATGGTAGGACATTGGCCGACTACAATATCCAAAAGGAGTC
130 ATATTTGCTGGAAAGCAACTTGAAGATGGTCGCACCTTAGCCGATTACAATATCCAAAAGGAGTC
* * * * * * *
28158907 TACCCTTCATTTGGTGT-TGCGGCTGCGTGGTGGG
195 CACCCTCCACTTGGT-TCTTCGACTTCGTGGTGGC
* * * * *
28158941 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCT-TGGAGGTTGAAAGTTCAGACA
* * *
28159005 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
65 CCATTGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * * * * *
28159070 ATATTTGCTGGCAAGCAACTTGAAGATGG-CAGGACATTGGCTGATTATAATATCCAAAAGGAGT
130 ATATTTGCTGGAAAGCAACTTGAAGATGGTC-GCACCTTAGCCGATTACAATATCCAAAAGGAGT
28159134 C
194 C
28159135 TACTCTGCAT
Statistics
Matches: 740, Mismatches: 124, Indels: 28
0.83 0.14 0.03
Matches are distributed among these distances:
227 18 0.02
228 709 0.96
229 13 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (228 bp):
ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
CATTGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
TATTTGCTGGAAAGCAACTTGAAGATGGTCGCACCTTAGCCGATTACAATATCCAAAAGGAGTCC
ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC
Found at i:28158893 original size:456 final size:455
Alignment explanation
Indices: 28158029--28159168 Score: 1273
Period size: 456 Copynumber: 2.5 Consensus size: 455
28158019 GATTCAATAG
* * * * * *
28158029 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTCGAGAGTTCAGACAC
* * * * * * * *
28158094 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
66 CATTGACAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCA-AAGATTA
* * * * * * * * * * *
28158159 TATTTGCTGGCAAACAACTTGAGGATGGCCGCACGCTAGCCGACTACAACATTCAGAAAGAATCC
130 TATTTGCTGGCAAACAACTTGAAGATGGCAGAACTCTAGCCGATTATAATATCCAGAAGGAGTCT
* * * * * * * * *
28158224 ACCCTTCACTTGGTTCTTCGACTTCGTGGCGGCATGCAAATCTTTGTCAAGACTCTCACTGGAAA
195 ACTCTCCATTTGGTTCTTCGCCTTCGCGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA
* * *
28158289 GACAATTACCTTGGAGGTTGAAAGCTCTGACACAATTGATAATGTAAAGGCAAAGATCCAAGACA
260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATTGACAATGTAAAGGCAAAGATCCAAGACA
* * * * *
28158354 AGGAAGGGATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTCGC
325 AGGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGC
* * * * *
28158419 ACCTTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTGGTACTT-CGTCTTCGAGGTG
390 ACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTGGT-CTTGCGGCTGCGAGGTG
28158483 GC
454 GC
* * * * *
28158485 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTCGAGAGTTCGGATAC
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTCGAGAGTTCAGACAC
* * * * * *
28158550 CATTGACAATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAAGATTGA
66 CATTGACAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATT-A
* * * *
28158615 TTTTTGCTGGAAAACAACTTGAAGATGGAAGAACTCTTGCCGATTATAATATCCAGAAGGAGTCT
130 TATTTGCTGGCAAACAACTTGAAGATGGCAGAACTCTAGCCGATTATAATATCCAGAAGGAGTCT
* * * *
28158680 ACTCTCCATTTGGTTCTCCGCCTTCGGGGTGGTATGCAGATCTTTGTAAAGACTCTTACCGGAAA
195 ACTCTCCATTTGGTTCTTCGCCTTCGCGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA
* * * * * *
28158745 GACCATCACTTTGGAGGTTGAAAGTTCCGATACCATTGACAATGTGAAGGCAAAGATCCAAGACA
260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATTGACAATGTAAAGGCAAAGATCCAAGACA
* *
28158810 AGG-AGGGTATCCCCCCAGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTCGAAGATGGTAG
325 AGGAAGGG-ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAG
* * * * * ** * *
28158874 GACATTGGCCGACTACAATATCCAAAAGGAGTCTACCCTTCATTTGGTGTTGCGGCTGCGTGGTG
389 CACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTGGTCTTGCGGCTGCGAGGTG
*
28158939 GG
454 GC
* * * * * *
28158941 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCT-TAGAGGTCGAGAGTTCAGACA
* * *
28159005 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
65 CCATTGACAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAA-GATT
* * * * *
28159070 ATATTTGCTGGCAAGCAACTTGAAGATGGCAGGACAT-TGGCTGATTATAATATCCAAAAGGAGT
129 ATATTTGCTGGCAAACAACTTGAAGATGGCAGAAC-TCTAGCCGATTATAATATCCAGAAGGAGT
* *
28159134 CTACTCTGCATCTT-GTCCTTCGCCTTCGCGGTGGT
193 CTACTCTCCAT-TTGGTTCTTCGCCTTCGCGGTGGT
28159169 TTCTAGGTAA
Statistics
Matches: 564, Mismatches: 113, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
455 12 0.02
456 547 0.97
457 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (455 bp):
ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTCGAGAGTTCAGACAC
CATTGACAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATTAT
ATTTGCTGGCAAACAACTTGAAGATGGCAGAACTCTAGCCGATTATAATATCCAGAAGGAGTCTA
CTCTCCATTTGGTTCTTCGCCTTCGCGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAG
ACAATCACCTTGGAGGTTGAAAGCTCCGACACAATTGACAATGTAAAGGCAAAGATCCAAGACAA
GGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCA
CATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTGGTCTTGCGGCTGCGAGGTGGC
Found at i:28166934 original size:25 final size:25
Alignment explanation
Indices: 28166906--28166980 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
28166896 AATCACAATT
28166906 TGGTATAAAAATTCAATAATTTGAA
1 TGGTATAAAAATTCAATAATTTGAA
** ** *
28166931 TGGT-GGATGATTAAACTAA-TT---
1 TGGTATAAAAATTCAA-TAATTTGAA
28166952 TGGTATAAAAATTCAATAATTTGAA
1 TGGTATAAAAATTCAATAATTTGAA
28166977 TGGT
1 TGGT
28166981 GGATGATTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
24 8 0.24
25 11 0.32
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (25 bp):
TGGTATAAAAATTCAATAATTTGAA
Found at i:28166952 original size:46 final size:46
Alignment explanation
Indices: 28166902--28166995 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
28166892 TTTAAATCAC
28166902 AATTTGGTATAAAAATTCAATAATTTGAATGGTGGATGATTAAACT
1 AATTTGGTATAAAAATTCAATAATTTGAATGGTGGATGATTAAACT
28166948 AATTTGGTATAAAAATTCAATAATTTGAATGGTGGATGATTAAACT
1 AATTTGGTATAAAAATTCAATAATTTGAATGGTGGATGATTAAACT
28166994 AA
1 AA
28166996 CTTATTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (46 bp):
AATTTGGTATAAAAATTCAATAATTTGAATGGTGGATGATTAAACT
Found at i:28171806 original size:40 final size:40
Alignment explanation
Indices: 28171762--28171866 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
28171752 GTGATGTCAG
*
28171762 GGACATCAAAGTGCATT-CAGAGGCACAATTGTGCAAACAA
1 GGACACCAAAGTG-ATTACAGAGGCACAATTGTGCAAACAA
* * * * *
28171802 GGACACCAAAGTGTTTATAGGGGCACAGTTGTGCAAACAG
1 GGACACCAAAGTGATTACAGAGGCACAATTGTGCAAACAA
* *
28171842 GGACACCGAAGTGTTTACAG-GGCAC
1 GGACACCAAAGTGATTACAGAGGCAC
28171867 CGAGGAGCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 7 0.12
40 49 0.88
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (40 bp):
GGACACCAAAGTGATTACAGAGGCACAATTGTGCAAACAA
Found at i:28176003 original size:62 final size:59
Alignment explanation
Indices: 28175900--28176093 Score: 185
Period size: 62 Copynumber: 3.1 Consensus size: 59
28175890 TCACTTTAAG
* *
28175900 ATTAAATTAATATAATACTTATTAAGACAAATATTAGATTAAATTTAATATTAAATCTT
1 ATTAAATTAATAGAATACTTATTAAGACAAATATTAAATTAAATTTAATATTAAATCTT
* *
28175959 ATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTGTGATAATCA
1 ATTAAATTAATAGAATACTTAT-T--AAGACAAATATTAAATTAAATTTAATA-T-T-A-AAT--
28176024 CTTTAAT
57 C--T--T
* * * *
28176031 ATTAAATTAATAAAATAC-TATTAAGATAGATATTAAATTAAATTAAATATTAAATC-T
1 ATTAAATTAATAGAATACTTATTAAGACAAATATTAAATTAAATTTAATATTAAATCTT
28176088 ATTAAA
1 ATTAAA
28176094 ATATTATTAT
Statistics
Matches: 114, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
57 7 0.06
59 20 0.18
60 1 0.01
62 26 0.23
63 1 0.01
64 4 0.04
65 2 0.02
66 4 0.04
67 1 0.01
68 26 0.23
70 2 0.02
71 3 0.03
72 17 0.15
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (59 bp):
ATTAAATTAATAGAATACTTATTAAGACAAATATTAAATTAAATTTAATATTAAATCTT
Found at i:28177256 original size:34 final size:34
Alignment explanation
Indices: 28177203--28177270 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
28177193 GCACAGTTGA
* * *
28177203 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGACCTAAGCCCATCTCAGTA-CAGTG
*
28177238 ACAGT-TTGGACCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGACCTAAGCCCATCTCAGTACAGTG
28177271 TCAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGACCTAAGCCCATCTCAGTACAGTG
Found at i:28178149 original size:12 final size:12
Alignment explanation
Indices: 28178132--28178156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28178122 AAATAAACTC
28178132 ATTAAGGATTTA
1 ATTAAGGATTTA
28178144 ATTAAGGATTTA
1 ATTAAGGATTTA
28178156 A
1 A
28178157 ACGTATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTAAGGATTTA
Found at i:28185714 original size:26 final size:26
Alignment explanation
Indices: 28185685--28185746 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
28185675 TACCTACAAT
*
28185685 AGTTTTAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
28185711 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
28185737 AGTTTCAGAA
1 AGTTTCAGAA
28185747 CACTTACAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:28193080 original size:466 final size:464
Alignment explanation
Indices: 28192206--28194045 Score: 2720
Period size: 466 Copynumber: 4.0 Consensus size: 464
28192196 GCTCAAATCC
28192206 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
1 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
*
28192271 CAAAAATTCTTACCATGCAAGAGAGATTCTATCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
* *
28192336 CCCCTTTTTCACTTCCTTTGTTCCCCCTCCTTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
131 CCCCTTTTTCACTCCCTTTGTTCCCCCTCATTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
28192401 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
196 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
** * *
28192466 CAACTCATCCACTTGTTTCTCTCATCATTTTCTCTTCTCTTCCAATAGCCACCACTATTTTCACA
261 CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACT-TTTTCACA
* *
28192531 ATTTAGTCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACC
325 TTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACC
* * * *
28192596 GTCACTCCTCTTTCACCCTTTTCTTGCCATTTATGCACCACCGATTGACCTCTACTTTGCCGATG
390 GTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGATTGACCTCTACTTTGCCG-TG
28192661 TCGTCTCACCG
454 TCGTCTCACCG
* ** * * *
28192672 CCTCTCTTATTATTTTTATTTTTAATTTTGGCATTAAAAGCTTAGTCAAACCCCTCATTGCCACC
1 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
* *
28192737 AAAAAATTCTTACCATGCCAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
* * * *
28192802 CCCCCTTTTCACTCCCTTCT-TATCCCCTTCATTTCATTTTCTTTCCAATGTCTCACTCCTTGCA
131 CCCCTTTTTCACTCCCTT-TGT-TCCCCCTCATTTCCTTTTCTTTCCCATGTCTCACTCCTTGCA
* * *
28192866 ATTTTTTCCCTTCACCCATTGACTTTTGCCATCCCATGCACCCAGACAAAATAAAATTTTTGTGT
194 ATTTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTT
* *
28192931 CTCTTCTCATCCACTTTTTTCTCTTATTATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCAC
259 CTCTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCAC
*
28192996 ATTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCTATACACCAC
324 ATTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCAC
* * *
28193061 TGTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTCCA-TTGTCGCCG
389 CGTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGATTGACCTCTACTT-T-GCCG
28193125 TTGTCGTCTCACCG
452 -TGTCGTCTCACCG
* *
28193139 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCTGCC
1 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
* *
28193204 CAAAAATTCTTACCATGCCAGATAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
* *
28193269 CCCCTTTTTCACTCCCTTTGTTCCCACTCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAA-
131 CCCCTTTTTCACTCCCTTTGTTCCCCCTCATTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
* * * * *
28193333 TTTTTCCCTTCACCTATTGAACTTTGCCGTCTCATGCACCTAGACAAAATAAAAGTTTTGTTTCT
196 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
* *
28193398 CTTCTCATCCACTTTTTTTCTCTCATCATTTTCCCTTCTC-TTCTAATAGCCACTACTTTTTCAC
261 CTTCTCATCCAC-TTTTTTCTCTCATCATTTTCTCTTCTCTTTC-AATAGCCACCACTTTTTCAC
* * *
28193462 ATTTTACCCATCTTATCACCACCTTCAACCACCATT--------AAATCACCACCCATACACTAC
324 ATTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCAC
* * * *
28193519 CGTCACTCCCCTCTCACCCTCTTCTTGCCATCTTTGCACCACCTATTGGCCTCTACTGTTGCTGT
389 CGTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGATTGACCTCTACT-TTGCCGT
* *
28193584 CGTCATCTCGCCG
453 -GTCGTCTCACCG
* * * *
28193597 CCTCTC---TTA---TTATTTTTAATGTCAGCTTTGAAAGCTTGGTCAAACCTCTCCTTACCGCC
1 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
*
28193656 CAAAAATTCTTACCATGCAAAAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
*
28193721 CCCCTTTTTCACTCCCTTTGTTCCCCCTCCTTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
131 CCCCTTTTTCACTCCCTTTGTTCCCCCTCATTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
* *
28193786 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATACACCTAGAC-AAA-ACAA-TTTT-TTTCT
196 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
* * * *
28193847 CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTATCTTTCAATAACCACCAGTTTTTCAAAT
261 CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCACAT
* * * *
28193912 TTTAGCCATCTTATCACCACCTTCGACCATCATTACAACACCAAATCACCACCCATACAGCACCA
326 TTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACCG
* * * *
28193977 TCACTCCCCTTTCACCCTTTTCTTGCCATTTTTGCACCACCGCTTAACCTCTAC--TGCCGTCGT
391 TCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGATTGACCTCTACTTTGCCGT-GT
28194040 CGTCTC
455 CGTCTC
28194046 GCGGCCTTTA
Statistics
Matches: 1241, Mismatches: 113, Indels: 53
0.88 0.08 0.04
Matches are distributed among these distances:
448 74 0.06
449 20 0.02
450 4 0.00
451 3 0.00
452 170 0.14
453 53 0.04
455 3 0.00
456 67 0.05
457 1 0.00
458 87 0.07
459 2 0.00
460 1 0.00
465 74 0.06
466 372 0.30
467 310 0.25
ACGTcount: A:0.20, C:0.34, G:0.07, T:0.39
Consensus pattern (464 bp):
CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
CCCCTTTTTCACTCCCTTTGTTCCCCCTCATTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCACAT
TTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACCG
TCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGATTGACCTCTACTTTGCCGTGTC
GTCTCACCG
Found at i:28194461 original size:20 final size:20
Alignment explanation
Indices: 28194438--28194516 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
28194428 AATGAAGTTT
*
28194438 AAATGATTTTAACCAAGTCA
1 AAATGATTTCAACCAAGTCA
* *
28194458 AAATGACTTCAACCAAGTTA
1 AAATGATTTCAACCAAGTCA
* *
28194478 AAATCATTTTAA-CACA-TCA
1 AAATGATTTCAACCA-AGTCA
* *
28194497 AAATTATTTCAAACAAGTCA
1 AAATGATTTCAACCAAGTCA
28194517 GAATTGCTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (20 bp):
AAATGATTTCAACCAAGTCA
Found at i:28194498 original size:39 final size:40
Alignment explanation
Indices: 28194432--28194514 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
28194422 TTTAAAAATG
* * *
28194432 AAGTTTAAATGATTTTAACCAAGTCAAAATGACTTCAACC
1 AAGTTAAAATCATTTTAACCAAGTCAAAATGACTTCAAAC
* *
28194472 AAGTTAAAATCATTTTAA-CACA-TCAAAATTATTTCAAAC
1 AAGTTAAAATCATTTTAACCA-AGTCAAAATGACTTCAAAC
28194511 AAGT
1 AAGT
28194515 CAGAATTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.54
40 17 0.46
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
AAGTTAAAATCATTTTAACCAAGTCAAAATGACTTCAAAC
Found at i:28202831 original size:20 final size:20
Alignment explanation
Indices: 28202802--28202886 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
28202792 AAGTTAAGTT
*
28202802 AAAATTATTTTAACCAAGAC
1 AAAATGATTTTAACCAAGAC
* **
28202822 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACCAAGAC
* *
28202842 AAAATCATTTT-AGCACA-AC
1 AAAATGATTTTAACCA-AGAC
* *
28202861 AAAATGATTTTCAAACAAGTC
1 AAAATGATTTT-AACCAAGAC
28202882 AAAAT
1 AAAAT
28202887 TTCTCCAGTC
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
19 13 0.27
20 27 0.55
21 9 0.18
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGAC
Found at i:28202841 original size:40 final size:40
Alignment explanation
Indices: 28202797--28202887 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
28202787 TTTTAAAGTT
*
28202797 AAGTTAAAATTATTTTAACCA-AGACAAAATGA-TTTCAACC
1 AAGTTAAAATTATTTT-ACCACA-ACAAAATGATTTTCAAAC
* *
28202837 AAGTTAAAATCATTTTAGCACAACAAAATGATTTTCAAAC
1 AAGTTAAAATTATTTTACCACAACAAAATGATTTTCAAAC
*
28202877 AAGTCAAAATT
1 AAGTTAAAATT
28202888 TCTCCAGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 12 0.27
40 32 0.73
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (40 bp):
AAGTTAAAATTATTTTACCACAACAAAATGATTTTCAAAC
Found at i:28203328 original size:23 final size:23
Alignment explanation
Indices: 28203293--28203338 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28203283 GCCAAGATTG
* *
28203293 TTACCATATTGATTTTGATACTA
1 TTACCAAACTGATTTTGATACTA
28203316 TTACCAAACTGATTTTGATACTA
1 TTACCAAACTGATTTTGATACTA
28203339 AAATGCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (23 bp):
TTACCAAACTGATTTTGATACTA
Found at i:28215575 original size:29 final size:30
Alignment explanation
Indices: 28215516--28215573 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28215506 TCCGAGCCTT
*
28215516 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28215546 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28215574 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28215803 original size:13 final size:13
Alignment explanation
Indices: 28215785--28215816 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28215775 TTTCCAGCAA
28215785 TTATGAATTTATT
1 TTATGAATTTATT
28215798 TTATGAATTTATT
1 TTATGAATTTATT
*
28215811 TGATGA
1 TTATGA
28215817 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28215991 original size:50 final size:50
Alignment explanation
Indices: 28215911--28216147 Score: 370
Period size: 50 Copynumber: 4.7 Consensus size: 50
28215901 ATTTGGGTAA
*
28215911 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* *
28215961 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
*
28216011 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
*
28216061 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
*
28216112 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGC
28216148 TTTGGCATGT
Statistics
Matches: 181, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
49 1 0.01
50 98 0.54
51 82 0.45
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.17
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:28216048 original size:26 final size:26
Alignment explanation
Indices: 28216019--28216147 Score: 72
Period size: 26 Copynumber: 5.0 Consensus size: 26
28216009 CGAGAGGTCC
28216019 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
* ** * **
28216045 CATG--GGCACCATCAC-GAGAACATCC
1 CATGTAAG-ACCATGTCTG-GGACATGG
28216070 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
* ** * **
28216096 CATG--GGCACCATCAC-GAGAACATCC
1 CATGTAAG-ACCATGTCTG-GGACATGG
28216121 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
28216147 C
1 C
28216148 TTTGGCATGT
Statistics
Matches: 69, Mismatches: 24, Indels: 20
0.61 0.21 0.18
Matches are distributed among these distances:
24 4 0.06
25 30 0.43
26 31 0.45
27 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (26 bp):
CATGTAAGACCATGTCTGGGACATGG
Found at i:28216055 original size:25 final size:25
Alignment explanation
Indices: 28216027--28216107 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
28216017 CCCATGTAAG
28216027 ACCATGTCTGGGACATGGCATGGGC
1 ACCATGTCTGGGACATGGCATGGGC
** * ** *
28216052 ACCATCAC-GAGAACATCCCATGTAAG-
1 ACCATGTCTG-GGACATGGCATG--GGC
28216078 ACCATGTCTGGGACATGGCATGGGC
1 ACCATGTCTGGGACATGGCATGGGC
28216103 ACCAT
1 ACCAT
28216108 CACGAGAACA
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
24 2 0.05
25 20 0.51
26 15 0.38
27 2 0.05
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (25 bp):
ACCATGTCTGGGACATGGCATGGGC
Found at i:28216124 original size:25 final size:25
Alignment explanation
Indices: 28216045--28216124 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
28216035 TGGGACATGG
28216045 CATGGGCACCATCACGAGAACATCC
1 CATGGGCACCATCACGAGAACATCC
* ** * **
28216070 CATGTAAG-ACCATGTCTG-GGACATGG
1 CATG--GGCACCATCAC-GAGAACATCC
28216096 CATGGGCACCATCACGAGAACATCC
1 CATGGGCACCATCACGAGAACATCC
28216121 CATG
1 CATG
28216125 TAAGACCATG
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 2 0.05
25 19 0.50
26 15 0.39
27 2 0.05
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (25 bp):
CATGGGCACCATCACGAGAACATCC
Found at i:28220363 original size:13 final size:13
Alignment explanation
Indices: 28220345--28220376 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28220335 TTTCCAGAAA
28220345 TTATGAATTTATT
1 TTATGAATTTATT
28220358 TTATGAATTTATT
1 TTATGAATTTATT
*
28220371 TGATGA
1 TTATGA
28220377 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28232994 original size:21 final size:21
Alignment explanation
Indices: 28232968--28233008 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28232958 TTTTAGAAAT
*
28232968 TGTTAGATTTCATGGCGTATA
1 TGTTAGATTTAATGGCGTATA
28232989 TGTTAGATTTAATGGCGTAT
1 TGTTAGATTTAATGGCGTAT
28233009 TGCTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (21 bp):
TGTTAGATTTAATGGCGTATA
Found at i:28236283 original size:27 final size:27
Alignment explanation
Indices: 28236253--28236405 Score: 162
Period size: 27 Copynumber: 5.7 Consensus size: 27
28236243 TTAGAGTTCG
* *
28236253 CCACAAAGACGATTCTTTCAGATTTTT
1 CCACAAAGGCTATTCTTTCAGATTTTT
28236280 CCACAAAGGCTATTCTTTCAGATTTTT
1 CCACAAAGGCTATTCTTTCAGATTTTT
* * **
28236307 CCACAAAGGCTATTCTTTCAAAGTTCA
1 CCACAAAGGCTATTCTTTCAGATTTTT
* * *
28236334 CCATAAAGGCTATTCTTTCAGAGTTCT
1 CCACAAAGGCTATTCTTTCAGATTTTT
* ** * * **
28236361 CCATAAAGATTATTCTTTTAGAGTTCG
1 CCACAAAGGCTATTCTTTCAGATTTTT
28236388 CCACAAAGGCTATTCTTT
1 CCACAAAGGCTATTCTTT
28236406 GTTGTCGTGT
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (27 bp):
CCACAAAGGCTATTCTTTCAGATTTTT
Found at i:28236322 original size:54 final size:54
Alignment explanation
Indices: 28236245--28236405 Score: 196
Period size: 54 Copynumber: 3.0 Consensus size: 54
28236235 TAGTCCATTT
* * * **
28236245 AGAGTTCGCCACAAAGACGATTCTTTCAGATTTTTCCACAAAGGCTATTCTTTC
1 AGAGTTCTCCACAAAGACTATTCTTTCAGAGTTCACCACAAAGGCTATTCTTTC
* * * * *
28236299 AGATTTTTCCACAAAGGCTATTCTTTCAAAGTTCACCATAAAGGCTATTCTTTC
1 AGAGTTCTCCACAAAGACTATTCTTTCAGAGTTCACCACAAAGGCTATTCTTTC
* * * *
28236353 AGAGTTCTCCATAAAGATTATTCTTTTAGAGTTCGCCACAAAGGCTATTCTTT
1 AGAGTTCTCCACAAAGACTATTCTTTCAGAGTTCACCACAAAGGCTATTCTTT
28236406 GTTGTCGTGT
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (54 bp):
AGAGTTCTCCACAAAGACTATTCTTTCAGAGTTCACCACAAAGGCTATTCTTTC
Found at i:28236787 original size:22 final size:22
Alignment explanation
Indices: 28236744--28236787 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28236734 CATATACAAC
* *
28236744 CATACTCCAACATTTCAGTACT
1 CATACACCAACATCTCAGTACT
28236766 CATACACCAATCATCTCA-TACT
1 CATACACCAA-CATCTCAGTACT
28236788 TCAATTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (22 bp):
CATACACCAACATCTCAGTACT
Found at i:28241058 original size:17 final size:18
Alignment explanation
Indices: 28241036--28241076 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28241026 TTTTCCTGGG
28241036 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
28241053 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
28241070 CCCAAAA
1 CCCAAAA
28241077 TAAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.56, C:0.34, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:28242495 original size:3 final size:3
Alignment explanation
Indices: 28242489--28242518 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28242479 ATTATTCTAT
28242489 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28242519 TATTAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:28245984 original size:331 final size:331
Alignment explanation
Indices: 28245382--28246043 Score: 1270
Period size: 331 Copynumber: 2.0 Consensus size: 331
28245372 CCAATCACTG
*
28245382 TGGGCAGGCCAAAGACGGAAACCACCAGCCATCAGAGCCCTTTAAAGTAAGAATCCAGAGTGAAC
1 TGGGCAGGCCAAAGACGGAAACCACCAGCCATCAGAGCCCTTTAAAGTAAGAATCCAGAGTGAAA
* *
28245447 CCAGGTCCCGAGAAGCTCCAGTTCACACCAATTTCGACGTCATATAAGTAGCTGTATCAAAGCTT
66 CCAGGTACCGAGAAGCTCCAGTTCACACCAATTTCGACGTCATATAAGGAGCTGTATCAAAGCTT
28245512 GTTCGATGCGTATGTTGTTGCTCCTCATTACTTAAAACCCATACAGCCTCCATATCCCAAATGGT
131 GTTCGATGCGTATGTTGTTGCTCCTCATTACTTAAAACCCATACAGCCTCCATATCCCAAATGGT
28245577 ATGACATGAACACACAATGTGACTACCACGCGGGAATTACGGGGCATTCAATAGAGAATTGCATT
196 ATGACATGAACACACAATGTGACTACCACGCGGGAATTACGGGGCATTCAATAGAGAATTGCATT
*
28245642 GCCTTCAAGAAGCTAGTCGAAAAATTCATCAACATGGGTATTGTCAAGTTGTGTGACTCATCTAG
261 GCCTTCAAGAAGCTAGTCGAAAAATTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAG
28245707 TGCAGA
326 TGCAGA
*
28245713 TGGGCAGGCCAAAGACGGAAACCACCAGCCATCAGAGCCCTTTAAAGTAAGAATCTAGAGTGAAA
1 TGGGCAGGCCAAAGACGGAAACCACCAGCCATCAGAGCCCTTTAAAGTAAGAATCCAGAGTGAAA
28245778 CCAGGTACCGAGAAGCTCCAGTTCACACCAATTTCGACGTCATATAAGGAGCTGTATCAAAGCTT
66 CCAGGTACCGAGAAGCTCCAGTTCACACCAATTTCGACGTCATATAAGGAGCTGTATCAAAGCTT
28245843 GTTCGATGCGTATGTTGTTGCTCCTCATTACTTAAAACCCATACAGCCTCCATATCCCAAATGGT
131 GTTCGATGCGTATGTTGTTGCTCCTCATTACTTAAAACCCATACAGCCTCCATATCCCAAATGGT
*
28245908 ATGACATGAACGCACAATGTGACTACCACGCGGGAATTACGGGGCATTCAATAGAGAATTGCATT
196 ATGACATGAACACACAATGTGACTACCACGCGGGAATTACGGGGCATTCAATAGAGAATTGCATT
28245973 GCCTTCAAGAAGCTAGTCGAAAAATTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAG
261 GCCTTCAAGAAGCTAGTCGAAAAATTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAG
28246038 TGCAGA
326 TGCAGA
28246044 AAGCCATCTA
Statistics
Matches: 325, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
331 325 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (331 bp):
TGGGCAGGCCAAAGACGGAAACCACCAGCCATCAGAGCCCTTTAAAGTAAGAATCCAGAGTGAAA
CCAGGTACCGAGAAGCTCCAGTTCACACCAATTTCGACGTCATATAAGGAGCTGTATCAAAGCTT
GTTCGATGCGTATGTTGTTGCTCCTCATTACTTAAAACCCATACAGCCTCCATATCCCAAATGGT
ATGACATGAACACACAATGTGACTACCACGCGGGAATTACGGGGCATTCAATAGAGAATTGCATT
GCCTTCAAGAAGCTAGTCGAAAAATTCATCAACATGGGTATTGTCAAGTTGGGTGACTCATCTAG
TGCAGA
Found at i:28247062 original size:9 final size:9
Alignment explanation
Indices: 28247048--28247076 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28247038 TTCAGACTCA
28247048 AAAAAAATC
1 AAAAAAATC
28247057 -AAAAAATC
1 AAAAAAATC
28247065 AAAAAAATC
1 AAAAAAATC
28247074 AAA
1 AAA
28247077 GTCAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:28247103 original size:6 final size:6
Alignment explanation
Indices: 28247080--28247138 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
28247070 AATCAAAGTC
* * *
28247080 AAAATAG AAAAA- AAAAAG AAAAAG GAAAA- AAGAAG AAAAAG TAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
28247127 TAAAAG TAAAAG
1 AAAAAG AAAAAG
28247139 GAGAGGTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.18
6 33 0.73
7 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:28247110 original size:17 final size:17
Alignment explanation
Indices: 28247088--28247140 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
28247078 TCAAAATAGA
28247088 AAAAAAAAAGAAAAAGG
1 AAAAAAAAAGAAAAAGG
* *
28247105 AAAAAAGAAGAAAAAGT
1 AAAAAAAAAGAAAAAGG
* *
28247122 AAAAGTAAAAGTAAAAGG
1 AAAA-AAAAAGAAAAAGG
28247140 A
1 A
28247141 GAGGTCAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGG
Found at i:28249784 original size:50 final size:50
Alignment explanation
Indices: 28249722--28249998 Score: 351
Period size: 50 Copynumber: 5.5 Consensus size: 50
28249712 ACAGTTAAAA
*
28249722 AGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCATTGCAATGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28249772 AGATTGAAGCTACAGCAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* * *
28249822 AGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28249872 AGATTGAAGCTACAACAGCGAATCTTACTTCCAT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28249922 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
*
28249972 AGATTGAAGCCACAACAGCGGATCTTA
1 AGATTGAAGCTACAACAGCGGATCTTA
28249999 GTGGAACAGA
Statistics
Matches: 191, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
49 2 0.01
50 187 0.98
51 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
Found at i:28249855 original size:100 final size:100
Alignment explanation
Indices: 28249616--28249998 Score: 555
Period size: 100 Copynumber: 3.9 Consensus size: 100
28249606 AACCATAGTC
* * * *
28249616 TGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTTACCTTTC-CAGGCAGTGCAGTGGAACAG
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTA-CTTTCTTA-GCATTGCAGTGGAACAG
* *
28249679 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA-
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* * *
28249715 -G---TTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCATTGCAATGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCATTGCAGTGGAACAGAT
*
28249776 TGAAGCTACAGCAGCGGATCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
*
28249811 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCATTGCAGTGGAACAGAT
* *
28249876 TGAAGCTACAACAGCGAATCTTACTTCCATGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* *
28249911 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCATTGCAGTGGAACAGAT
*
28249976 TGAAGCCACAACAGCGGATCTTA
66 TGAAGCTACAACAGCGGATCTTA
28249999 GTGGAACAGA
Statistics
Matches: 257, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
95 55 0.21
96 27 0.11
97 1 0.00
98 1 0.00
100 173 0.67
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (100 bp):
TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCATTGCAGTGGAACAGAT
TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
Found at i:28250002 original size:34 final size:34
Alignment explanation
Indices: 28249964--28250032 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
28249954 TTAGCGTTGC
*
28249964 AGTGGAACAGATTGAAGCCACAACAGCGGATCTT
1 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
28249998 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
1 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
28250032 A
1 A
28250033 CTTTCTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (34 bp):
AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
Found at i:28250033 original size:84 final size:84
Alignment explanation
Indices: 28249922--28250081 Score: 284
Period size: 84 Copynumber: 1.9 Consensus size: 84
28249912 GCAATTAAAA
* *
28249922 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
1 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
28249987 CAGCGGATCTTAGTGGAAC
66 CAGCGGATCTTAGTGGAAC
* *
28250006 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
28250071 CAGCGGATCTT
66 CAGCGGATCTT
28250082 GCTTCCCCGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (84 bp):
AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
CAGCGGATCTTAGTGGAAC
Found at i:28250161 original size:50 final size:50
Alignment explanation
Indices: 28250101--28250280 Score: 177
Period size: 50 Copynumber: 3.6 Consensus size: 50
28250091 GCAATTAAAA
* * *
28250101 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
* ** * ** *
28250151 AGATTAAAGCTACAACGGTAAATCTT-CTTTCCCTGAC-ATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTT-CCAGACGA-TGCAATGGAAT
* * * *
28250201 AGATTGAAG-TCACAATGGCGAATCTTACTTCCCAGAAGATGTAATGGAAT
1 AGATTGAAGCT-ACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
*
28250251 AGATTGAAGCTACGACGGCGAATCTTACTT
1 AGATTGAAGCTACAACGGCGAATCTTACTT
28250281 CCCCAACATT
Statistics
Matches: 101, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
49 5 0.05
50 91 0.90
51 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
Found at i:28250176 original size:95 final size:95
Alignment explanation
Indices: 28250045--28250285 Score: 261
Period size: 100 Copynumber: 2.5 Consensus size: 95
28250035 TTCTTAGTGT
* * *
28250045 TGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTTCCCC-GGCAATTAAAAAGATTGAA
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTT-CTTCCCCAGGCAATTAAAAAGATTGAA
* ** *
28250109 G-CTACAACGGCGAATCTTACTTTCCAGGCGG
65 GTC-ACAACGGCGAATCTTACTTCCCAGAAGA
* ** *
28250140 TGCAGTGGAATAGATTAAAGCTACAACGGTAAATCTTCTTTCCCTGACATTGCAATTAAAAAGAT
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTC-TTCCC---CA-GGCAATTAAAAAGAT
*
28250205 TGAAGTCACAATGGCGAATCTTACTTCCCAGAAGA
61 TGAAGTCACAACGGCGAATCTTACTTCCCAGAAGA
* * *
28250240 TGTAATGGAATAGATTGAAGCTACGACGGCGAATCTTACTTCCCCA
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTT-CTTCCCCA
28250286 ACATTGTAGT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
94 1 0.01
95 36 0.30
97 2 0.02
98 1 0.01
100 78 0.65
101 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (95 bp):
TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTCTTCCCCAGGCAATTAAAAAGATTGAAG
TCACAACGGCGAATCTTACTTCCCAGAAGA
Found at i:28250257 original size:279 final size:281
Alignment explanation
Indices: 28249616--28250260 Score: 734
Period size: 279 Copynumber: 2.3 Consensus size: 281
28249606 AACCATAGTC
* * *
28249616 TGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTTACCTTT-CCAG-GCAGTGCAGTGGAACA
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTA-CTTTCCCAGAG-A-TGCAATGGAACA
* * * *
28249678 GATTGAAGCTACAACAGCGGATCTT-GCTTCCCCGACAGTTAAAAAGATTGAAGCTACAACAGTG
63 GATTGAAGCCACAACAGCGGATCTTAG--T----G---G---AACAGATTGAAGCCACAACAGAG
*
28249742 GATCTTACTTTCTTAGCATTGCAATGGAACAGATTGAAGCTACAGCAGCGGATCTTACTTCCCTG
116 GATCTTACTTTCTTAGCATTGCAATGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCC--
* * *
28249807 ACATTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAAC
179 ACA-GGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCTCAGCGGTGCAGTGGAAC
* *
28249872 AGATTGAAGCTACAACAGCGAATCTTACTTCCATGACAT
243 AGATTAAAGCTACAACAGCAAATCTTACTTCCATGACAT
* ** * * *
28249911 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCCAGAGATGCAATGGAACAGAT
28249976 TGAAGCCACAACAGCGGATCTTAGTGGAACAGATTGAAGCCACAACAGAGGATCTTACTTTCTTA
66 TGAAGCCACAACAGCGGATCTTAGTGGAACAGATTGAAGCCACAACAGAGGATCTTACTTTCTTA
** * *
28250041 GTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTTCCC-C-GGCAATTAAAAAGA
131 GCATTGCAATGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCACAGGCAATTAAAAAGA
* * *
28250104 TTGAAGCTACAACGGCGAATCTTACTTTC-CAGGCGGTGCAGTGGAATAGATTAAAGCTACAACG
196 TTGAAGCTACAACAGCGAATCTTACTTTCTCA-GCGGTGCAGTGGAACAGATTAAAGCTACAACA
* *
28250168 GTAAATCTT-CTTTCCCTGACAT
260 GCAAATCTTAC-TTCCATGACAT
** * *
28250190 TGCAATTAAAAAGATTGAAG-TCACAATGGCGAATCTTAC-TTCCCAGAAGATGTAATGGAATAG
1 TGCAATTAAAAAGATTGAAGCT-ACAACAGCGAATCTTACTTTCCCAG-AGATGCAATGGAACAG
28250253 ATTGAAGC
64 ATTGAAGC
28250261 TACGACGGCG
Statistics
Matches: 307, Mismatches: 35, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
278 8 0.03
279 139 0.45
281 1 0.00
284 78 0.25
287 1 0.00
290 1 0.00
294 1 0.00
295 47 0.15
296 30 0.10
297 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (281 bp):
TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCCAGAGATGCAATGGAACAGAT
TGAAGCCACAACAGCGGATCTTAGTGGAACAGATTGAAGCCACAACAGAGGATCTTACTTTCTTA
GCATTGCAATGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCACAGGCAATTAAAAAGA
TTGAAGCTACAACAGCGAATCTTACTTTCTCAGCGGTGCAGTGGAACAGATTAAAGCTACAACAG
CAAATCTTACTTCCATGACAT
Found at i:28250305 original size:50 final size:50
Alignment explanation
Indices: 28250091--28250306 Score: 152
Period size: 50 Copynumber: 4.3 Consensus size: 50
28250081 TGCTTCCCCG
* * **
28250091 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTT-TCCAGGCGGT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCA-ACATT
* ** * * ** **
28250141 GCAGTGGAATAGATTAAAGCTACAACGGTAAATCTT-CTTTCCCTGACATT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCCAACATT
* * *
28250191 GCAATTAAAAAGATTGAAG-TCACAATGGCGAATCTTACTTCCCAGAAGA-T
1 GCAATTAAAAAGATTGAAGCT-ACAACGGCGAATCTTACTTCCC-CAACATT
* ** * *
28250241 GTAATGGAATAGATTGAAGCTACGACGGCGAATCTTACTTCCCCAACATT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATT
* * *
28250291 GTAGTTAAACAGATTG
1 GCAATTAAAAAGATTG
28250307 GAGATGGCAG
Statistics
Matches: 123, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
49 5 0.04
50 113 0.92
51 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (50 bp):
GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATT
Found at i:28250380 original size:18 final size:18
Alignment explanation
Indices: 28250357--28250391 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28250347 GATCGCAGGT
*
28250357 AGTCCTATCTCCCTAAGC
1 AGTCCTATCACCCTAAGC
28250375 AGTCCTATCACCCTAAG
1 AGTCCTATCACCCTAAG
28250392 TAGTAGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (18 bp):
AGTCCTATCACCCTAAGC
Found at i:28250622 original size:132 final size:132
Alignment explanation
Indices: 28250375--28251006 Score: 994
Period size: 132 Copynumber: 4.8 Consensus size: 132
28250365 CTCCCTAAGC
** * * * *
28250375 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCATCCTAAGCAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * * *
28250440 AGTGGAGCAGATCGAAAATGGTGAATCTTATCTTCGCAATACAGTAGAGAAGCAGATTTAAGTCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
28250505 TT
131 TT
* ** * * * *
28250507 TGTCCTATCACCCTAAGTAGTAGTGGAGTAGATTGAATATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * *
28250572 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAAGCAAATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
28250637 TT
131 TT
* * * *
28250639 AGTCTTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGCAGATTCTGTCACCTTAAACAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
28250704 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
28250769 TT
131 TT
* *
28250771 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTACAGATTCTGTCACCCTAAGTAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
*
28250836 AGTGGAGCAGATCGAATATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
28250901 TT
131 TT
* *
28250903 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTACAGATTCTGTCACCCTAAGTAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
28250968 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
28251007 GTGGAATGAA
Statistics
Matches: 467, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 467 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (132 bp):
AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
TT
Found at i:28251210 original size:17 final size:18
Alignment explanation
Indices: 28251188--28251229 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
28251178 TTTTCCTGGG
28251188 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
28251205 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
28251222 CCCAAAAC
1 CCCAAAAC
28251230 AAATTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.55, C:0.36, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:28253335 original size:2 final size:2
Alignment explanation
Indices: 28253328--28253368 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28253318 CTGTGTATGA
28253328 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
28253369 ATCGATCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:28257679 original size:6 final size:6
Alignment explanation
Indices: 28257670--28257701 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28257660 CACGCCTTTG
28257670 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CC
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CC
28257702 CATTGCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTTCA
Found at i:28260469 original size:29 final size:30
Alignment explanation
Indices: 28260432--28260488 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28260422 TCCGAGCCTT
*
28260432 GGGGAAAAAT-GTAATTATGTAAAAGTTTA
1 GGGGAAAAATCGTAATTATGAAAAAGTTTA
* *
28260461 GGGGCAAAATCGTAATTTTGAAAAAGTT
1 GGGGAAAAATCGTAATTATGAAAAAGTT
28260489 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.30
Consensus pattern (30 bp):
GGGGAAAAATCGTAATTATGAAAAAGTTTA
Found at i:28260897 original size:50 final size:50
Alignment explanation
Indices: 28260822--28261121 Score: 402
Period size: 50 Copynumber: 5.9 Consensus size: 50
28260812 CATTTGGGTA
* *
28260822 GAGAGGTCTCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
28260872 GAGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCGTTGGCATTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC----G--TTGGCACCGAGAT
* * **
28260928 GAGAGGTCCCATATAAGACCATGTCTGAGACATGGCACTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
28260978 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * * *
28261028 GTGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
** *
28261078 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28261122 TGTTATGATC
Statistics
Matches: 222, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
50 140 0.63
51 35 0.16
54 1 0.00
56 46 0.21
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:28261007 original size:106 final size:104
Alignment explanation
Indices: 28260822--28261122 Score: 414
Period size: 106 Copynumber: 2.9 Consensus size: 104
28260812 CATTTGGGTA
* * *
28260822 GAGAGGTCTCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGAGATGAGAGGTCCCATGTA
*
28260887 AGGCCATGTCTGGGACATGGCGTTGGCATTGGCACCGAGAT
65 AGACCATGTCTGGGACATGGC-TTGGCATTGGCACCGAGAT
* *
28260928 GAGAGGTCCCATATAAGACCATGTCTGAGACATGGCACTGGCACCGAGATGAGAGGTCCCATGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGGCACCGAGATGAGAGGTCCCATGTA
28260993 AGACCATGTCTGGGACATGGC---G--TTGGCACCGAGAT
65 AGACCATGTCTGGGACATGGCTTGGCATTGGCACCGAGAT
* * * **
28261028 GTGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT-GGCACCGAGATGAG-AGGTCCCATGT
28261093 AAGACCATGTCTGGGACATGGCTTTGGCAT
64 AAGACCATGTCTGGGACATGGC-TTGGCAT
28261123 GTTATGATCA
Statistics
Matches: 173, Mismatches: 13, Indels: 17
0.85 0.06 0.08
Matches are distributed among these distances:
99 1 0.01
100 59 0.34
101 31 0.18
102 1 0.01
105 1 0.01
106 79 0.46
107 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (104 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCTTGGCATTGGCACCGAGAT
Found at i:28283728 original size:26 final size:27
Alignment explanation
Indices: 28283684--28283737 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28283674 TGGATCCGTA
*
28283684 TGTTACTTGTTTTTGTTAATTTTAATT
1 TGTTACTTGTTTTTGTTAATTTCAATT
* *
28283711 TGTTTCTT-TTTTTTTTAATTTCAATT
1 TGTTACTTGTTTTTGTTAATTTCAATT
28283737 T
1 T
28283738 ACTAAGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.17, C:0.06, G:0.07, T:0.70
Consensus pattern (27 bp):
TGTTACTTGTTTTTGTTAATTTCAATT
Found at i:28289895 original size:19 final size:20
Alignment explanation
Indices: 28289873--28289917 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
28289863 AAAAAATACA
28289873 AAAAAATTA-AAATATTT-AT
1 AAAAAATTACAAAT-TTTCAT
28289892 AAAAAATTACAAATTTTCAT
1 AAAAAATTACAAATTTTCAT
28289912 AAAAAA
1 AAAAAA
28289918 AATTTCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTACAAATTTTCAT
Found at i:28292270 original size:22 final size:21
Alignment explanation
Indices: 28292245--28292292 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
28292235 ACTTATGTTT
28292245 TAAAA-TTCAAAAAATAAATGAA
1 TAAAATTTCAAAAAATAAA--AA
*
28292267 TAAAATTTCTAAAAATAAAAA
1 TAAAATTTCAAAAAATAAAAA
28292288 TAAAA
1 TAAAA
28292293 GTTTGGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 12 0.50
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAAATTTCAAAAAATAAAAA
Found at i:28293010 original size:9 final size:9
Alignment explanation
Indices: 28292996--28293023 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28292986 TTATTGTTAG
28292996 TGTGAATAT
1 TGTGAATAT
28293005 TGTGAATAT
1 TGTGAATAT
28293014 TGTGAATAT
1 TGTGAATAT
28293023 T
1 T
28293024 ATTTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (9 bp):
TGTGAATAT
Found at i:28294677 original size:17 final size:16
Alignment explanation
Indices: 28294627--28294689 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 16
28294617 GGGTAAGAAG
28294627 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG--AAA
*
28294646 TAAAAAGTTTTGGGAAA
1 T-AAAAGTTTAGGGAAA
28294663 TAAAAGTTTGAGGGAAA
1 TAAAAGTTT-AGGGAAA
28294680 GTAAATAGTT
1 -TAAA-AGTT
28294690 GGAGTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 8 0.21
17 10 0.26
18 4 0.11
19 8 0.21
20 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (16 bp):
TAAAAGTTTAGGGAAA
Found at i:28296053 original size:7 final size:8
Alignment explanation
Indices: 28296036--28296060 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28296026 ATGAAATTAT
28296036 AAAAATAA
1 AAAAATAA
28296044 AAAAATAA
1 AAAAATAA
28296052 AAAAATAA
1 AAAAATAA
28296060 A
1 A
28296061 TTATGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:28296389 original size:19 final size:19
Alignment explanation
Indices: 28296365--28296404 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28296355 ACTAATTACA
28296365 AAGCTTAAATCATCTCCCT
1 AAGCTTAAATCATCTCCCT
28296384 AAGCTTAAATCATCTCCCT
1 AAGCTTAAATCATCTCCCT
28296403 AA
1 AA
28296405 CGGGTAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (19 bp):
AAGCTTAAATCATCTCCCT
Found at i:28299121 original size:43 final size:43
Alignment explanation
Indices: 28299073--28299159 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
28299063 ATAATGTCAT
*
28299073 TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
1 TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
* *
28299116 TAGTTAGTCTAAATATTTAATACTGTTAACTGTTTCAATAAAA
1 TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
28299159 T
1 T
28299160 TGTTTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (43 bp):
TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
Done.