Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 161 of 168
Found at i:48262531 original size:2 final size:2
Alignment explanation
Indices: 48262520--48262562 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
48262510 GGCATGGAAT
48262520 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48262561 TA
1 TA
48262563 GAAGGAGCTN
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48266800 original size:10 final size:10
Alignment explanation
Indices: 48266778--48266857 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 10
48266768 TTTTTTGGTA
48266778 AAAAATTATTT
1 AAAAATTA-TT
48266789 AAAAATTATT
1 AAAAATTATT
* *
48266799 AACAATTATG
1 AAAAATTATT
*
48266809 AGAAATTATT
1 AAAAATTATT
*
48266819 AAATATATATTTT
1 AAA-A-AT-TATT
*
48266832 TAAAA-TATTT
1 AAAAATTA-TT
*
48266842 AAAAATGATT
1 AAAAATTATT
48266852 AAAAAT
1 AAAAAT
48266858 CATGCTTGGA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
9 1 0.02
10 33 0.62
11 11 0.21
12 3 0.06
13 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (10 bp):
AAAAATTATT
Found at i:48270259 original size:52 final size:52
Alignment explanation
Indices: 48270169--48270293 Score: 135
Period size: 52 Copynumber: 2.4 Consensus size: 52
48270159 AAGAAAACAT
* * * *
48270169 GCCTTGCAGGATGCATTTTCAGCTGATGCGGCAGAATGTTCTCTGAAAGTGC
1 GCCTTGCAGGACGCATTTTCAACTGATGCGGCAAAATGTTATCTGAAAGTGC
* * *
48270221 GCCTTGCAGGACGCGTTTTCAACTGA-GCTGGCAAAATGTTATTTGAAAGCGC
1 GCCTTGCAGGACGCATTTTCAACTGATGC-GGCAAAATGTTATCTGAAAGTGC
** * *
48270273 ATCTTGTAGGACGTATTTTCA
1 GCCTTGCAGGACGCATTTTCA
48270294 GAGAATATTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 2 0.03
52 58 0.97
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (52 bp):
GCCTTGCAGGACGCATTTTCAACTGATGCGGCAAAATGTTATCTGAAAGTGC
Found at i:48274331 original size:11 final size:11
Alignment explanation
Indices: 48274317--48274359 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
48274307 GTTATTTTTT
*
48274317 TATTGTTTTGC
1 TATTATTTTGC
*
48274328 TATTATTTCGC
1 TATTATTTTGC
* *
48274339 TCTTATATTGC
1 TATTATTTTGC
48274350 TATTATTTTG
1 TATTATTTTG
48274360 TTCTTAGTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (11 bp):
TATTATTTTGC
Found at i:48285042 original size:6 final size:6
Alignment explanation
Indices: 48285031--48285056 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48285021 CATGGATTGA
48285031 GGCATT GGCATT GGCATT GGCATT GG
1 GGCATT GGCATT GGCATT GGCATT GG
48285057 GGGATCAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.38, T:0.31
Consensus pattern (6 bp):
GGCATT
Found at i:48285398 original size:15 final size:16
Alignment explanation
Indices: 48285368--48285406 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
48285358 TAATAAAAAT
48285368 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
48285385 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
48285400 ATAATTT
1 ATAATTT
48285407 TTAGACGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:48285810 original size:18 final size:19
Alignment explanation
Indices: 48285789--48285824 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48285779 TGAGATTATG
48285789 AATAT-TAAAAAAAAATTA
1 AATATGTAAAAAAAAATTA
48285807 AATATGTAAAAAAAAATT
1 AATATGTAAAAAAAAATT
48285825 GATGTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AATATGTAAAAAAAAATTA
Found at i:48290473 original size:20 final size:20
Alignment explanation
Indices: 48290448--48290487 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48290438 AATGGGTAGG
48290448 AAATCTTGTAGAATAAGATT
1 AAATCTTGTAGAATAAGATT
48290468 AAATCTTGTAGAATAAGATT
1 AAATCTTGTAGAATAAGATT
48290488 TCTTAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (20 bp):
AAATCTTGTAGAATAAGATT
Found at i:48291142 original size:27 final size:27
Alignment explanation
Indices: 48291112--48291171 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
48291102 AGGTGGAAAA
* *
48291112 GTTTGTACTTGTTTCACTAGTTACAAT
1 GTTTGTACATGATTCACTAGTTACAAT
**
48291139 GTTTGTTGATGATTCACTAGTTACAAT
1 GTTTGTACATGATTCACTAGTTACAAT
*
48291166 GCTTGT
1 GTTTGT
48291172 TGATATTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (27 bp):
GTTTGTACATGATTCACTAGTTACAAT
Found at i:48291172 original size:27 final size:27
Alignment explanation
Indices: 48291124--48291175 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
48291114 TTGTACTTGT
*
48291124 TTCACTAGTTACAATGTTTGTTGATGA
1 TTCACTAGTTACAATGCTTGTTGATGA
48291151 TTCACTAGTTACAATGCTTGTTGAT
1 TTCACTAGTTACAATGCTTGTTGAT
48291176 ATTTGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (27 bp):
TTCACTAGTTACAATGCTTGTTGATGA
Found at i:48294412 original size:3 final size:3
Alignment explanation
Indices: 48294404--48294433 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
48294394 TATCTGAATA
48294404 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
48294434 ATAATTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:48296972 original size:2 final size:2
Alignment explanation
Indices: 48296965--48297000 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48296955 ACAACATTAT
48296965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48297001 AATCAGTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48302168 original size:12 final size:13
Alignment explanation
Indices: 48302153--48302184 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
48302143 ATGGCCGAAA
48302153 TAAAAAATTT-TT
1 TAAAAAATTTATT
48302165 TAAAAAATTTATT
1 TAAAAAATTTATT
48302178 TAAAAAA
1 TAAAAAA
48302185 ACACAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAAAATTTATT
Found at i:48303388 original size:12 final size:12
Alignment explanation
Indices: 48303371--48303395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48303361 AAAAAAATAT
48303371 TTTAATTTTTCG
1 TTTAATTTTTCG
48303383 TTTAATTTTTCG
1 TTTAATTTTTCG
48303395 T
1 T
48303396 ATTTTTTAGT
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTAATTTTTCG
Found at i:48308272 original size:19 final size:19
Alignment explanation
Indices: 48308237--48308275 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48308227 CTTATAATAA
*
48308237 ACACTTTTAAGGAAAAAAT
1 ACACTTTTAAGAAAAAAAT
48308256 ACACTTTTAA-AATAAAAAT
1 ACACTTTTAAGAA-AAAAAT
48308275 A
1 A
48308276 TTTCTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (19 bp):
ACACTTTTAAGAAAAAAAT
Found at i:48327884 original size:13 final size:13
Alignment explanation
Indices: 48327866--48327902 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
48327856 AAGAAATAGA
48327866 AACTGTACTTTCT
1 AACTGTACTTTCT
48327879 AACTGTACTTTCT
1 AACTGTACTTTCT
48327892 AACTGTA-TTTC
1 AACTGTACTTTC
48327903 ATATGTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (13 bp):
AACTGTACTTTCT
Found at i:48343620 original size:59 final size:58
Alignment explanation
Indices: 48343554--48343675 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 58
48343544 TACAATATTT
*
48343554 AACAGATAACAACAAAGTAGCAGTAATATAATAGCGAAACGGCACTAAAATATTGACAA
1 AACAGATAACAACAAAGTAGCAGTAATATAATAGCGAAACGGCACT-AAATAGTGACAA
* * *
48343613 AACAGATAACAACAAAGTAGTAGTAATATAATAGTGAAACGGCGCTAAATAGTGACAA
1 AACAGATAACAACAAAGTAGCAGTAATATAATAGCGAAACGGCACTAAATAGTGACAA
48343671 AACAG
1 AACAG
48343676 CGGCAAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 16 0.27
59 43 0.73
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (58 bp):
AACAGATAACAACAAAGTAGCAGTAATATAATAGCGAAACGGCACTAAATAGTGACAA
Found at i:48344151 original size:3 final size:3
Alignment explanation
Indices: 48344143--48344176 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
48344133 ACCGACTGAA
48344143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
48344177 CACATAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:48346952 original size:16 final size:16
Alignment explanation
Indices: 48346931--48346979 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
48346921 CGAGTGGAGA
*
48346931 GAGTTAATTTTGAATT
1 GAGTTAATTATGAATT
*
48346947 GAGTTAA-TATGGATT
1 GAGTTAATTATGAATT
48346962 GAGTTAATTCA-GAATT
1 GAGTTAATT-ATGAATT
48346978 GA
1 GA
48346980 AAATTTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.46
16 14 0.50
17 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (16 bp):
GAGTTAATTATGAATT
Found at i:48349497 original size:21 final size:21
Alignment explanation
Indices: 48349473--48349512 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48349463 CAAATTTGAT
48349473 TAAATAAAT-TATTAAAAATCG
1 TAAA-AAATATATTAAAAATCG
*
48349494 TAAAAATTATATTAAAAAT
1 TAAAAAATATATTAAAAAT
48349513 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAAAATATATTAAAAATCG
Found at i:48351476 original size:21 final size:21
Alignment explanation
Indices: 48351450--48351501 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
48351440 ATTGGGTGGA
48351450 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTTTGT
48351471 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTTTGT
*
48351492 TCAACTCTTA
1 TCAGCTCTTA
48351502 TAAGCTTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTTTGT
Found at i:48351507 original size:21 final size:21
Alignment explanation
Indices: 48351454--48351508 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
48351444 GGTGGATCAG
* *
48351454 CTCTTACGAGCTTTTGTTCAG
1 CTCTTACAAGCTTTTGTTCAA
*
48351475 CTCTTACGAGCTTTTGTTCAA
1 CTCTTACAAGCTTTTGTTCAA
*
48351496 CTCTTATAAGCTT
1 CTCTTACAAGCTT
48351509 CTATTCAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (21 bp):
CTCTTACAAGCTTTTGTTCAA
Found at i:48353440 original size:2 final size:2
Alignment explanation
Indices: 48353433--48353476 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
48353423 TAGTAATCTC
48353433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48353475 AT
1 AT
48353477 CTTTAGATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48353640 original size:2 final size:2
Alignment explanation
Indices: 48353633--48353677 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
48353623 AGCAAAGAAT
* *
48353633 AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AT AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
48353675 AC A
1 AC A
48353678 TATAATAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.44, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:48370129 original size:10 final size:9
Alignment explanation
Indices: 48370088--48370144 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
48370078 CATTGAGCAA
48370088 TTTTTTTAT
1 TTTTTTTAT
* *
48370097 GTTCTTTTAAC
1 -TT-TTTTTAT
*
48370108 TTTATTTAT
1 TTTTTTTAT
48370117 TTTTTTTAT
1 TTTTTTTAT
*
48370126 TTTTTTCA-
1 TTTTTTTAT
48370134 TTTTTTTAT
1 TTTTTTTAT
48370143 TT
1 TT
48370145 CTCTCTCTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
8 7 0.19
9 21 0.57
10 4 0.11
11 5 0.14
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:48370229 original size:16 final size:16
Alignment explanation
Indices: 48370208--48370239 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48370198 TTTCATTTGC
*
48370208 TAAAGAAATGAAAAAT
1 TAAAGAAATAAAAAAT
48370224 TAAAGAAATAAAAAAT
1 TAAAGAAATAAAAAAT
48370240 ATAGAAAAAC
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:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (16 bp):
TAAAGAAATAAAAAAT
Found at i:48370245 original size:15 final size:16
Alignment explanation
Indices: 48370208--48370246 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
48370198 TTTCATTTGC
*
48370208 TAAAGAAATGAAAAAT
1 TAAAGAAATGAAAAAA
48370224 TAAAGAAAT-AAAAAA
1 TAAAGAAATGAAAAAA
*
48370239 TATAGAAA
1 TAAAGAAA
48370247 AACTACGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (16 bp):
TAAAGAAATGAAAAAA
Found at i:48370321 original size:24 final size:24
Alignment explanation
Indices: 48370294--48370343 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
48370284 AAAAGAATGG
*
48370294 AAAGTAAAAGAAAA-AAAAAAGTTA
1 AAAG-AAAAGAAAAGAAAAAAATTA
* *
48370318 AAAGAATATAAAAGAAAAAAATTA
1 AAAGAAAAGAAAAGAAAAAAATTA
48370342 AA
1 AA
48370344 TTGATCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAGAAAAGAAAAGAAAAAAATTA
Found at i:48371938 original size:15 final size:15
Alignment explanation
Indices: 48371918--48371950 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48371908 GGAGGAGAAG
*
48371918 AAGAAGAAGAGAAAC
1 AAGAAGAAGAAAAAC
48371933 AAGAAGAAGAAAAAC
1 AAGAAGAAGAAAAAC
48371948 AAG
1 AAG
48371951 CAGGGCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAAAC
Found at i:48384124 original size:2 final size:2
Alignment explanation
Indices: 48384117--48384142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48384107 TTTTAGAGGA
48384117 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48384143 TTACGAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48384277 original size:11 final size:11
Alignment explanation
Indices: 48384261--48384291 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
48384251 TCCCAGTAGA
48384261 GTGTATAATGT
1 GTGTATAATGT
48384272 GTGTATAATGT
1 GTGTATAATGT
*
48384283 GTGAATAAT
1 GTGTATAAT
48384292 ATATTGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (11 bp):
GTGTATAATGT
Found at i:48403371 original size:3 final size:3
Alignment explanation
Indices: 48403363--48403424 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
48403353 AATAAGACAT
48403363 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48403411 TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TA
48403425 GTTTAACTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48404875 original size:16 final size:18
Alignment explanation
Indices: 48404836--48404869 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48404826 TAAGTTTATA
48404836 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
48404853 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
48404870 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:48407464 original size:12 final size:12
Alignment explanation
Indices: 48407447--48407471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48407437 CTAACAGCCC
48407447 CAGTATTAGGAG
1 CAGTATTAGGAG
48407459 CAGTATTAGGAG
1 CAGTATTAGGAG
48407471 C
1 C
48407472 CCTGATGTAT
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:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (12 bp):
CAGTATTAGGAG
Found at i:48408503 original size:21 final size:21
Alignment explanation
Indices: 48408453--48408504 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
48408443 AATTTAGTCC
*
48408453 TTAATATTTATTTTTTTGTTA
1 TTAATATTTATTTTTTTGTAA
*
48408474 TTTATATTTATATTTTTT-TAA
1 TTAATATTTAT-TTTTTTGTAA
*
48408495 TTAAAATTTA
1 TTAATATTTA
48408505 ATCATTAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTAATATTTATTTTTTTGTAA
Found at i:48438259 original size:29 final size:30
Alignment explanation
Indices: 48438217--48438275 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
48438207 ACAAAGACAT
48438217 ATTGGCTAAGTTCAAAG-ACCCTAATCCAG
1 ATTGGCTAAGTTCAAAGAACCCTAATCCAG
*
48438246 ATTGGTTAAGTTCAAAGAACCCTAATCCAG
1 ATTGGCTAAGTTCAAAGAACCCTAATCCAG
48438276 TCCCTGCCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (30 bp):
ATTGGCTAAGTTCAAAGAACCCTAATCCAG
Found at i:48441524 original size:2 final size:2
Alignment explanation
Indices: 48441519--48441546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48441509 CAAATTTAAA
48441519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48441547 TACACCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48443770 original size:38 final size:38
Alignment explanation
Indices: 48443719--48443794 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
48443709 TTAGTTATTA
48443719 GCGGTAAAAGCAAACATTAAGCGAATGTTTAAAGTATC
1 GCGGTAAAAGCAAACATTAAGCGAATGTTTAAAGTATC
48443757 GCGGTAAAAGCAAACATTAAGCGAATGTTTAAAGTATC
1 GCGGTAAAAGCAAACATTAAGCGAATGTTTAAAGTATC
48443795 AAATCATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (38 bp):
GCGGTAAAAGCAAACATTAAGCGAATGTTTAAAGTATC
Found at i:48450560 original size:26 final size:26
Alignment explanation
Indices: 48450507--48450563 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
48450497 AACTTGACAC
* *
48450507 TTTTTTCCTAATTTGGTACCTAAGCT
1 TTTTTTCCTAATTTGATACCTAAACT
**
48450533 TTTTTTCCTAATTTGATAGTTAAACT
1 TTTTTTCCTAATTTGATACCTAAACT
48450559 TTTTT
1 TTTTT
48450564 CTATTCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (26 bp):
TTTTTTCCTAATTTGATACCTAAACT
Found at i:48456378 original size:14 final size:15
Alignment explanation
Indices: 48456359--48456390 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
48456349 CTGTACAAAG
48456359 AATAAAATCGA-GTA
1 AATAAAATCGATGTA
48456373 AATAAAATCGATGTA
1 AATAAAATCGATGTA
48456388 AAT
1 AAT
48456391 CCAATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (15 bp):
AATAAAATCGATGTA
Found at i:48462382 original size:18 final size:17
Alignment explanation
Indices: 48462325--48462385 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
48462315 ATTGTATGAT
48462325 TTTTTAAATTATTTTAAA
1 TTTTTAAA-TATTTTAAA
* * *
48462343 -TTCTAATTATTTTAAG
1 TTTTTAAATATTTTAAA
48462359 TTTTTAAATATTTTATAA
1 TTTTTAAATATTTTA-AA
48462377 TTTTTAAAT
1 TTTTTAAAT
48462386 TATTAGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 8 0.23
17 17 0.49
18 10 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTTTAAATATTTTAAA
Found at i:48464229 original size:31 final size:32
Alignment explanation
Indices: 48464194--48464283 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 32
48464184 GGAGCCAATG
** *
48464194 ATTTGAAAGTTTAAATTTAAGTTATTGAAA-T
1 ATTTGAAAGTTTTTATTTAAGTCATTGAAATT
*
48464225 ATTTGAAATTTTTTATTTAAGTCATT-AAATT
1 ATTTGAAAGTTTTTATTTAAGTCATTGAAATT
*
48464256 ATTCGAAAGTTTTTATTTAAGTCATTGA
1 ATTTGAAAGTTTTTATTTAAGTCATTGA
48464284 GCTATTTGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.06
31 47 0.92
32 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (32 bp):
ATTTGAAAGTTTTTATTTAAGTCATTGAAATT
Found at i:48465527 original size:14 final size:16
Alignment explanation
Indices: 48465500--48465531 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
48465490 GTAAGGATAT
48465500 AATATAATATTTAAAA
1 AATATAATATTTAAAA
48465516 AATA-AATA-TTAAAA
1 AATATAATATTTAAAA
48465530 AA
1 AA
48465532 AAACGTGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATAATATTTAAAA
Found at i:48465532 original size:15 final size:16
Alignment explanation
Indices: 48465500--48465532 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48465490 GTAAGGATAT
*
48465500 AATATAATATTTAAAA
1 AATATAATATTAAAAA
48465516 AATA-AATATTAAAAA
1 AATATAATATTAAAAA
48465531 AA
1 AA
48465533 AACGTGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATAATATTAAAAA
Found at i:48466071 original size:21 final size:21
Alignment explanation
Indices: 48466013--48466073 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
48466003 CCATGTCTAC
48466013 TCCTTCC-TTTCTACTCTCACTT
1 TCCTTCCATTTCT-CTCTC-CTT
*
48466035 TCCTTCCTTTTC-CTCTCCTT
1 TCCTTCCATTTCTCTCTCCTT
48466055 T-CTCTCCATTTCTCTCTCC
1 TCCT-TCCATTTCTCTCTCC
48466074 CAACAACCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 11 0.31
22 7 0.20
23 4 0.11
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (21 bp):
TCCTTCCATTTCTCTCTCCTT
Found at i:48476106 original size:2 final size:2
Alignment explanation
Indices: 48476099--48476127 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48476089 GAATCAAATT
48476099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48476128 GATTCATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48482003 original size:2 final size:2
Alignment explanation
Indices: 48481967--48481991 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48481957 TTTGATGTAT
48481967 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
48481992 TAAAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48494221 original size:279 final size:279
Alignment explanation
Indices: 48493721--48494292 Score: 1117
Period size: 279 Copynumber: 2.1 Consensus size: 279
48493711 CTTTTCTAAG
48493721 CTACTATTTTTTGTTGTCGATAGTAATAACACCATTTAAATTTTTATCCCCTATTGATCAACTTT
1 CTACTATTTTTTGTTGTCGATAGTAATAACACCATTTAAATTTTTATCCCCTATTGATCAACTTT
48493786 GTTTATTTATCTGGTTTAATAGTCAAAATCCTTTACGTTTTCCAAGAATCCTTACATCCCCAGCA
66 GTTTATTTATCTGGTTTAATAGTCAAAATCCTTTACGTTTTCCAAGAATCCTTACATCCCCAGCA
48493851 ATCACTCTTCAACACCTACCCACTCTAGTCAAGAATGGACTGTCATATGTCACCCAATATTGTTC
131 ATCACTCTTCAACACCTACCCACTCTAGTCAAGAATGGACTGTCATATGTCACCCAATATTGTTC
48493916 CATAAAGTTTAGTGCTAAATTCCAACTTTTGTTAGATTGATGTAATTAATTTAACTAAGTAGGTT
196 CATAAAGTTTAGTGCTAAATTCCAACTTTTGTTAGATTGATGTAATTAATTTAACTAAGTAGGTT
48493981 TGAAAAAAAATAACAAAAT
261 TGAAAAAAAATAACAAAAT
48494000 CTACTATTTTTTGTTGTCGATAGTAATAACACCATTTAAATTTTTATCCCCTATTGATCAACTTT
1 CTACTATTTTTTGTTGTCGATAGTAATAACACCATTTAAATTTTTATCCCCTATTGATCAACTTT
48494065 GTTTATTTATCTGGTTTAATAGTCAAAATCCTTTACGTTTTCCAAGAATCCTTACATCCCCAGCA
66 GTTTATTTATCTGGTTTAATAGTCAAAATCCTTTACGTTTTCCAAGAATCCTTACATCCCCAGCA
48494130 ATCACTCTTCAACACCTACCCACTCTAGTCAAGAATGGACTGTCATATGTCACCCAATATTGTTC
131 ATCACTCTTCAACACCTACCCACTCTAGTCAAGAATGGACTGTCATATGTCACCCAATATTGTTC
48494195 CATAAAGTTTAGTGCTAAATTCCAACTTTTGTTAGATTGATGTAATTAATTTAACTAAGTAGGTT
196 CATAAAGTTTAGTGCTAAATTCCAACTTTTGTTAGATTGATGTAATTAATTTAACTAAGTAGGTT
48494260 TGAAAAAAAATAACAAAAT
261 TGAAAAAAAATAACAAAAT
* * *
48494279 ATAATATTATTTGT
1 CTACTATTTTTTGT
48494293 CACAATCCAA
Statistics
Matches: 290, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
279 290 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (279 bp):
CTACTATTTTTTGTTGTCGATAGTAATAACACCATTTAAATTTTTATCCCCTATTGATCAACTTT
GTTTATTTATCTGGTTTAATAGTCAAAATCCTTTACGTTTTCCAAGAATCCTTACATCCCCAGCA
ATCACTCTTCAACACCTACCCACTCTAGTCAAGAATGGACTGTCATATGTCACCCAATATTGTTC
CATAAAGTTTAGTGCTAAATTCCAACTTTTGTTAGATTGATGTAATTAATTTAACTAAGTAGGTT
TGAAAAAAAATAACAAAAT
Found at i:48508754 original size:29 final size:28
Alignment explanation
Indices: 48508675--48508754 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
48508665 AAACATATTT
* * *
48508675 AAAATTTTATAAAAATTCATAAAAATGTA
1 AAAATTATATAAAAATT-AGAAAAATCTA
*
48508704 AAACA-TATATAAAAA-AATGAAAAATCTA
1 AAA-ATTATATAAAAATTA-GAAAAATCTA
48508732 ATAAATTATATAAAAATTAGAAA
1 A-AAATTATATAAAAATTAGAAA
48508755 TTTAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.02
28 10 0.24
29 28 0.68
30 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (28 bp):
AAAATTATATAAAAATTAGAAAAATCTA
Found at i:48509234 original size:22 final size:22
Alignment explanation
Indices: 48509204--48509248 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
48509194 GGAACAAATA
48509204 AATAC-TTTTTTATATATTTATT
1 AATACTTTTTTTATA-ATTTATT
*
48509226 AATATTTTTTTTATAATTTATT
1 AATACTTTTTTTATAATTTATT
48509248 A
1 A
48509249 GAACTTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
AATACTTTTTTTATAATTTATT
Found at i:48515872 original size:28 final size:27
Alignment explanation
Indices: 48515824--48515880 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
48515814 GTAAGTTAAT
* * *
48515824 AATTAATAATTTGATAATTTTAGTAAC
1 AATTAATAAATTAATAATTTTACTAAC
48515851 AATTAATACAATTAATAATTTTACTAAC
1 AATTAATA-AATTAATAATTTTACTAAC
48515879 AA
1 AA
48515881 AATGTTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (27 bp):
AATTAATAAATTAATAATTTTACTAAC
Found at i:48515913 original size:17 final size:17
Alignment explanation
Indices: 48515877--48515916 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
48515867 AATTTTACTA
*
48515877 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
48515894 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
48515911 ACAAAA
1 ACAAAA
48515917 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:48515953 original size:16 final size:16
Alignment explanation
Indices: 48515934--48515990 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
48515924 AATTTGATAC
*
48515934 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
48515950 AATTTTGATAACAATT
1 AATTTTAATAACAATT
48515966 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
48515982 AGTTTTAAT
1 AATTTTAAT
48515991 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:48515974 original size:22 final size:23
Alignment explanation
Indices: 48515964--48516025 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
48515954 TTGATAACAA
* *
48515964 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
48515986 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
48516009 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
48516026 ACGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:48517361 original size:57 final size:57
Alignment explanation
Indices: 48517282--48517392 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 57
48517272 GGGTGATCCT
48517282 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCT-AGCCTGGACGGGTG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTG-GAAAATAGAT-TGAGCCTGGACGGGTG
* *
48517339 ATCTTGATATAGCCCTCTCGAAGAATATGTGGAAAATGGATTGAGCCTGGACGG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATTGAGCCTGGACGG
48517393 ATAATCTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
56 6 0.12
57 44 0.88
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (57 bp):
ATCTTGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATTGAGCCTGGACGGGTG
Found at i:48517828 original size:20 final size:20
Alignment explanation
Indices: 48517803--48517959 Score: 76
Period size: 20 Copynumber: 7.8 Consensus size: 20
48517793 TTTCTCGGAT
48517803 TTTTGGTACTTCCTCATATG
1 TTTTGGTACTTCCTCATATG
** **
48517823 TTTTGGTAAATCCTCATAAA
1 TTTTGGTACTTCCTCATATG
*
48517843 TTTTGGTATTTCCTCA-A-G
1 TTTTGGTACTTCCTCATATG
* *
48517861 TTTTACGATA-TTCTTTCATAAT-
1 TTTT--GGTACTTC-CTCAT-ATG
* *
48517883 TTTTGGCACTTCCTCCTA-G
1 TTTTGGTACTTCCTCATATG
*
48517902 TTTTTGCTA-TTCCCTCATAAT-
1 -TTTTGGTACTT-CCTCAT-ATG
* *
48517923 TTTTGGTACATCCTCATTTG
1 TTTTGGTACTTCCTCATATG
*
48517943 TTTTTGATACTTCCTCA
1 -TTTTGGTACTTCCTCA
48517960 AGTTTTATGG
Statistics
Matches: 101, Mismatches: 21, Indels: 29
0.67 0.14 0.19
Matches are distributed among these distances:
18 4 0.04
19 8 0.08
20 65 0.64
21 19 0.19
22 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTTGGTACTTCCTCATATG
Found at i:48518049 original size:20 final size:20
Alignment explanation
Indices: 48518020--48518057 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48518010 TACATTTAAG
* *
48518020 TTTTGGTACTTCCTCATAAA
1 TTTTGCTACTTCATCATAAA
48518040 TTTTGCTACTTCATCATA
1 TTTTGCTACTTCATCATA
48518058 TTTGTTGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTGCTACTTCATCATAAA
Found at i:48518075 original size:20 final size:19
Alignment explanation
Indices: 48518052--48518107 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
48518042 TTGCTACTTC
48518052 ATCATATTTGTTGGTACAT-T
1 ATCATATTT-TTGGTAC-TCT
* *
48518072 ATCATAATTCTCGGTACTCT
1 ATCAT-ATTTTTGGTACTCT
48518092 ATCATAATTTTTGGTA
1 ATCAT-ATTTTTGGTA
48518108 TAGTTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 26 0.87
21 3 0.10
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (19 bp):
ATCATATTTTTGGTACTCT
Found at i:48518452 original size:22 final size:23
Alignment explanation
Indices: 48518417--48518463 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
48518407 GTCCCTTTAA
* *
48518417 TTTTTGATATTTCCTTAT-ATTT
1 TTTTTGATACTTCCTCATGATTT
*
48518439 TTTTTGGTACTTCCTCATGATTT
1 TTTTTGATACTTCCTCATGATTT
48518462 TT
1 TT
48518464 GGTGGTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTTGATACTTCCTCATGATTT
Found at i:48529598 original size:27 final size:27
Alignment explanation
Indices: 48529568--48529634 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
48529558 CCTATCAGGT
48529568 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
* *
48529595 AGGCGCCAATGAAGGTGCCTCATATAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
48529622 AGGCGCCAATGAA
1 AGGCGCCAATGAA
48529635 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.31, T:0.13
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:48529733 original size:21 final size:21
Alignment explanation
Indices: 48529704--48529747 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
48529694 TGGATTAGTA
*
48529704 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
48529725 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
48529746 TT
1 TT
48529748 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:48530378 original size:8 final size:8
Alignment explanation
Indices: 48530365--48530455 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
48530355 CATACAAAAA
48530365 ATTACAAT
1 ATTACAAT
48530373 ATTACAAT
1 ATTACAAT
* *
48530381 ATATCCTAAC
1 AT-TAC-AAT
48530391 ATTACAAT
1 ATTACAAT
*
48530399 ATTCATACAAA
1 A-T--TACAAT
*
48530410 ATTACAAA
1 ATTACAAT
48530418 ATTACAAT
1 ATTACAAT
*
48530426 ATTCATACAAA
1 A-T--TACAAT
*
48530437 ATTATAAT
1 ATTACAAT
48530445 ATTACAAT
1 ATTACAAT
48530453 ATT
1 ATT
48530456 CATACAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
8 41 0.63
9 6 0.09
10 6 0.09
11 12 0.18
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (8 bp):
ATTACAAT
Found at i:48530415 original size:19 final size:19
Alignment explanation
Indices: 48530412--48530560 Score: 70
Period size: 19 Copynumber: 8.1 Consensus size: 19
48530402 CATACAAAAT
48530412 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
48530431 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
48530447 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
* *
48530462 -AAAAAAATACAATATTCA
1 TACAAAATTACAATATTCA
* *
48530480 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
*
48530498 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
48530521 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
48530541 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
48530560 T
1 T
48530561 TGGCGCCTCT
Statistics
Matches: 97, Mismatches: 15, Indels: 36
0.66 0.10 0.24
Matches are distributed among these distances:
14 8 0.08
15 1 0.01
16 11 0.11
17 3 0.03
18 10 0.10
19 38 0.39
20 12 0.12
21 2 0.02
22 5 0.05
23 5 0.05
25 2 0.02
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:48530427 original size:27 final size:26
Alignment explanation
Indices: 48530391--48530487 Score: 139
Period size: 27 Copynumber: 3.8 Consensus size: 26
48530381 ATATCCTAAC
48530391 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAA
*
48530418 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAA
48530445 ATTACAATATTCATAC-AAA--AAAA
1 ATTACAATATTCATACAAAATTAAAA
48530468 A-TACAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
48530488 ACTAATCCAA
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.22
23 6 0.09
24 1 0.02
26 3 0.05
27 41 0.63
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAA
Found at i:48530594 original size:27 final size:27
Alignment explanation
Indices: 48530556--48530622 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
48530546 AATTACAATA
48530556 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
* *
48530583 TTCATTGGCGCCTCTCTGTGAGGCAGC
1 TTCATTGGCGCCTCTCTATGAGGCACC
48530610 TTCATTGGCGCCT
1 TTCATTGGCGCCT
48530623 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.12, C:0.31, G:0.25, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:48533869 original size:117 final size:117
Alignment explanation
Indices: 48533663--48534140 Score: 734
Period size: 117 Copynumber: 4.1 Consensus size: 117
48533653 CACTAATGAC
* * ** *
48533663 ATCGATATCTTCATCGCTTTCAAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTT
1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
*
48533728 CTTCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
66 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
*
48533780 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAGGATTCTACCTACAGGTGTGCCTATTC
1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
*
48533845 CTCTGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
66 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
* *
48533897 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACATGTATGCCTATTC
1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
*
48533962 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTTAAT
66 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
*
48534014 ATCG--A----CATCACTTTTGAAGAGTTCAAATTTCAAGATTTTACCTACAGGTGTGCCTATTC
1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
* * * * * *
48534073 CTCCATCGGGACCTAATGAAAGTACATCATATCCACCTCCTCCATCGTTAAT
66 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
* *
48534125 ATCAACATCTTTATCA
1 ATCGACATCTTCATCA
48534141 ATTTCAAAAA
Statistics
Matches: 332, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
111 101 0.30
113 1 0.00
115 1 0.00
117 229 0.69
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (117 bp):
ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT
Found at i:48535470 original size:11 final size:12
Alignment explanation
Indices: 48535454--48535490 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
48535444 TTTAAAATTA
48535454 AAAAAGT-TTTT
1 AAAAAGTATTTT
48535465 AAAAAGTATTTT
1 AAAAAGTATTTT
48535477 -AAAA-TATTTT
1 AAAAAGTATTTT
48535487 AAAA
1 AAAA
48535491 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.25
11 14 0.58
12 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:48535484 original size:10 final size:10
Alignment explanation
Indices: 48535461--48535559 Score: 55
Period size: 10 Copynumber: 9.9 Consensus size: 10
48535451 TTAAAAAAGT
48535461 TTTTAAAAAGTA
1 TTTT-AAAA-TA
48535473 TTTTAAAATA
1 TTTTAAAATA
48535483 TTTT-AAA-A
1 TTTTAAAATA
*
48535491 --TTAAAAAA
1 TTTTAAAATA
* **
48535499 ATAAAAAAGTA
1 TTTTAAAA-TA
48535510 TTTTAAAATA
1 TTTTAAAATA
48535520 TTTTAAAATA
1 TTTTAAAATA
***
48535530 -AAAAAAAGTA
1 TTTTAAAA-TA
48535540 TTTTAAAAATA
1 TTTT-AAAATA
48535551 TTTTAAAAT
1 TTTTAAAAT
48535560 TAAAAAATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 2 0.03
9 7 0.10
10 29 0.43
11 16 0.24
12 8 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:48535567 original size:39 final size:39
Alignment explanation
Indices: 48535465--48535649 Score: 198
Period size: 38 Copynumber: 5.0 Consensus size: 39
48535455 AAAAGTTTTT
*
48535465 AAAAAGTATTTT-AAAATATTTTAAAATTAAAAAA-ATA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
48535502 AAAAAGTATTTT-AAAATA--TT----TT--AAAATAAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
48535532 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAT-AA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
**
48535570 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-ATT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
* **
48535608 AAAAAGTAAGTAAAAAAATATTTTAAAATTTTAAAAAATAAA
1 AAAAAGT-ATTTTAAAAATATTTTAAAA--TTAAAAAATAAA
48535650 TATATTTATT
Statistics
Matches: 125, Mismatches: 8, Indels: 25
0.79 0.05 0.16
Matches are distributed among these distances:
29 4 0.03
30 14 0.11
31 8 0.06
33 2 0.02
35 2 0.02
37 20 0.16
38 44 0.35
39 22 0.18
41 8 0.06
42 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (39 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
Found at i:48535585 original size:68 final size:68
Alignment explanation
Indices: 48535465--48535605 Score: 241
Period size: 68 Copynumber: 2.1 Consensus size: 68
48535455 AAAAGTTTTT
48535465 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAATAAAAAAGTATTTT-AAAATATTTTAAAAT
1 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAATAAAAAAGTATTTTAAAAATATTTTAAAAT
48535529 AAA
66 AAA
48535532 AAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAATAAAAAAAGTATTTTAAAAATATTTTAAA
1 AAAAAGTATTTT-AAAATATTTTAAAATTAAAAAAAT-AAAAAAGTATTTTAAAAATATTTTAAA
*
48535596 ATTAA
64 ATAAA
48535601 AAAAA
1 AAAAA
48535606 TTAAAAAGTA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
67 19 0.27
68 29 0.41
69 22 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (68 bp):
AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAATAAAAAAGTATTTTAAAAATATTTTAAAAT
AAA
Found at i:48544593 original size:19 final size:18
Alignment explanation
Indices: 48544563--48544618 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
48544553 ATTAATTTTT
*
48544563 AAAATTTTTAAAAAATTA
1 AAAATATTTAAAAAATTA
*
48544581 AAAAGTATTTAAAAAGTATA
1 AAAA-TATTTAAAAAAT-TA
*
48544601 AAAATATTT-TAAAATTA
1 AAAATATTTAAAAAATTA
48544618 A
1 A
48544619 TTAATTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 8 0.25
19 15 0.47
20 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
AAAATATTTAAAAAATTA
Found at i:48544602 original size:20 final size:19
Alignment explanation
Indices: 48544563--48544614 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
48544553 ATTAATTTTT
48544563 AAAAT-TTTTAAAAAATTA
1 AAAATATTTTAAAAAATTA
*
48544581 AAAAGTA-TTTAAAAAGTATA
1 AAAA-TATTTTAAAAAAT-TA
48544601 AAAATATTTTAAAA
1 AAAATATTTTAAAA
48544615 TTAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 12 0.41
20 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATATTTTAAAAAATTA
Found at i:48547690 original size:27 final size:24
Alignment explanation
Indices: 48547652--48547711 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 24
48547642 ATAAAAATTA
48547652 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATT-T-A-TTTTTTTATTT
48547679 ACCAAAATA-TTATTTTTTTATTT
1 ACCAAAATATTTATTTTTTTATTT
*
48547702 ACGAAAATAT
1 ACCAAAATAT
48547712 ACCAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 19 0.61
24 1 0.03
25 1 0.03
26 1 0.03
27 9 0.29
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (24 bp):
ACCAAAATATTTATTTTTTTATTT
Found at i:48547698 original size:23 final size:23
Alignment explanation
Indices: 48547668--48547711 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
48547658 ATATTATAAC
48547668 TTTTTTTATTTACCAAAATATTA
1 TTTTTTTATTTACCAAAATATTA
*
48547691 TTTTTTTATTTACGAAAATAT
1 TTTTTTTATTTACCAAAATAT
48547712 ACCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTTTATTTACCAAAATATTA
Found at i:48547810 original size:27 final size:27
Alignment explanation
Indices: 48547780--48547857 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
48547770 GGCCAATCAT
*
48547780 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
** *
48547807 ATTGTTGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
48547834 ATTGGCAGCACCAATGGTGCCAAA
1 ATTGGCGGCACCAATGGTGCCAAA
48547858 TGACTAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:48547960 original size:19 final size:18
Alignment explanation
Indices: 48547933--48548001 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 18
48547923 CAACTCATTT
48547933 TTTTATTTAATAACTCTA
1 TTTTATTTAATAACTCTA
*
48547951 TTTTAGTTTAATAA-ACTA
1 TTTTA-TTTAATAACTCTA
*
48547969 TTCTCATTTAATAACTCTA
1 TT-TTATTTAATAACTCTA
48547988 TTTTAATTTAATAA
1 TTTT-ATTTAATAA
48548002 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 19 0.44
19 24 0.56
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTTATTTAATAACTCTA
Found at i:48547969 original size:18 final size:18
Alignment explanation
Indices: 48547933--48548007 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 18
48547923 CAACTCATTT
*
48547933 TTTTATTTAATAACTCTA
1 TTTTATTTAATAACACTA
48547951 TTTTAGTTTAATAA-ACTA
1 TTTTA-TTTAATAACACTA
* *
48547969 TTCTCATTTAATAACTCTA
1 TT-TTATTTAATAACACTA
48547988 TTTTAATTTAATAA-ACTA
1 TTTT-ATTTAATAACACTA
48548006 TT
1 TT
48548008 AAGTAATACT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 24 0.50
19 24 0.50
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTTATTTAATAACACTA
Found at i:48547982 original size:37 final size:37
Alignment explanation
Indices: 48547937--48548007 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
48547927 TCATTTTTTT
*
48547937 ATTTAATAACTCTATTTTAGTTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
48547974 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
48548008 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:48548227 original size:19 final size:19
Alignment explanation
Indices: 48548203--48548264 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
48548193 TCTAATTAAG
48548203 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
48548222 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
48548240 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
48548259 TAATAA
1 TAATAA
48548265 ACTATTATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:48548232 original size:18 final size:18
Alignment explanation
Indices: 48548211--48548270 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
48548201 AGTAATAACT
48548211 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* * *
48548229 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
48548248 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
48548266 CTATT
1 CTATT
48548271 ATTACTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 20 0.57
19 15 0.43
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:48548279 original size:18 final size:17
Alignment explanation
Indices: 48548211--48548281 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
48548201 AGTAATAACT
48548211 CTATTTTAATTTAATAAA
1 CTATTTT-ATTTAATAAA
* *
48548229 CTATTCTCATTTAATAACT
1 CTATT-TTATTTAATAA-A
48548248 CTATTTTAATTTAATAAA
1 CTATTTT-ATTTAATAAA
*
48548266 CTATTATTACTTAATA
1 CTATT-TTATTTAATA
48548282 TTTTATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 27 0.61
19 17 0.39
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
CTATTTTATTTAATAAA
Found at i:48548280 original size:37 final size:37
Alignment explanation
Indices: 48548203--48548281 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
48548193 TCTAATTAAG
* *
48548203 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTATCACT
*
48548240 TAATAACTCTATTTTAATTTAATAAACTATTATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTATCACT
48548277 TAATA
1 TAATA
48548282 TTTTATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTATCACT
Found at i:48548299 original size:18 final size:18
Alignment explanation
Indices: 48548278--48548352 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
48548268 ATTATTACTT
*
48548278 AATATTTTATTAAATTAA
1 AATAATTTATTAAATTAA
* * *
48548296 AATAAAGTTATTAAATGAG
1 AAT-AATTTATTAAATTAA
*
48548315 AATAGTTTATTAAATTAA
1 AATAATTTATTAAATTAA
*
48548333 AATAGAGTTATTAAA-TAA
1 AATA-ATTTATTAAATTAA
48548351 AA
1 AA
48548353 AAATGGGTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 23 0.51
19 22 0.49
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AATAATTTATTAAATTAA
Found at i:48548308 original size:37 final size:36
Alignment explanation
Indices: 48548278--48548349 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
48548268 ATTATTACTT
*
48548278 AATATTTTATTAAATTAAAATAAAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAAAGTTATTAAAT-AG
*
48548315 AATAGTTTATTAAATTAAAATAGAGTTATTAAATA
1 AATAGTTTATTAAATTAAAATAAAGTTATTAAATA
48548350 AAAAAATGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.40
Consensus pattern (36 bp):
AATAGTTTATTAAATTAAAATAAAGTTATTAAATAG
Found at i:48548353 original size:19 final size:19
Alignment explanation
Indices: 48548284--48548352 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
48548274 ACTTAATATT
*
48548284 TTATTAAATTAAAATAAAG
1 TTATTAAATTAAAATAGAG
* * *
48548303 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
48548321 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
48548340 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
48548353 AAATGGGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 20 0.48
19 22 0.52
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:48548654 original size:19 final size:19
Alignment explanation
Indices: 48548578--48548647 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
48548568 ACTTAATAGT
*
48548578 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAATAGAG
* * *
48548597 TTATTAAATAAGAACA-AT
1 TTATTAAATAAAAATAGAG
*
48548615 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAATAGAG
48548634 TTATTAAATAAAAA
1 TTATTAAATAAAAA
48548648 ATGAGTTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (19 bp):
TTATTAAATAAAAATAGAG
Found at i:48548785 original size:295 final size:292
Alignment explanation
Indices: 48548233--48548826 Score: 1007
Period size: 295 Copynumber: 2.0 Consensus size: 292
48548223 AATAAACTAT
* * *
48548233 TCTCATTTAATAACTCTATTTTAATTTAATAAACTATTATTACTTAATATTTTATTAAATTAAAA
1 TCTCATTTAATAACTCTATTTTAATTTAAAAAACTAGTATTACTTAATAGTTTATTAAATTAAAA
* * * *
48548298 TAAAGTTATTAAATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGGGTTG
66 TAAAGTTATTAAATAAGAACAATTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTG
*
48548363 AAGGGGAATAAATAGAAAATAATAAATAAGGAGGGGCTTAGAAGGTAATTTAGGCCACATTTCAA
131 AAGGGGAATAAAAAGAAAATAATAAATAAGGAGGGGCTTAGAAGGTAATTTAGGCCACATTTCAA
48548428 TTTTAGTGCGCACACCAGCAATTCACTTTCAAAATTCAAAATGATAAATTTGCATGTCAGGTCCT
196 TTTTAGTGCGCACACCAGCAATTCACTTTCAAAATTCAAAATGATAAATTTGCATGTCAGGTCCT
48548493 TAAAACTGCAAATGGTCACTTAATTAGAATTC
261 TAAAACTGCAAATGGTCACTTAATTAGAATTC
*
48548525 TCTCATTTAATAACTCTATTTTAATTTTAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAA
1 TCTCATTTAATAACTCTATTTTAA-TTTAAAAAACT-AGTATTACTTAATAGTTTATTAAATTAA
*
48548590 AATAGAGTTATTAAATAAGAACAATTTATTAAATTAAAATAGAGTTATTAAAT-AAAAAATGAGT
64 AATAAAGTTATTAAATAAGAACAATTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGT
48548654 TGAAGGGGAATAAAAAGAAAAGAAAATAATAAATAAGGA-GGGCTTAGAAGGTAA-TTA-GCCAC
129 TGAAGGGGAAT----A-AAAAGAAAATAATAAATAAGGAGGGGCTTAGAAGGTAATTTAGGCCAC
48548716 ATTTCAATTTTAGTGCGCACACCAGCAATTCACTTTCAAAATTCAAAATGATAAATTTGCATGTC
189 ATTTCAATTTTAGTGCGCACACCAGCAATTCACTTTCAAAATTCAAAATGATAAATTTGCATGTC
48548781 AGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATTC
254 AGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATTC
48548820 TCTCATT
1 TCTCATT
48548827 NNNNNNNNNN
Statistics
Matches: 285, Mismatches: 10, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
292 24 0.08
293 30 0.11
294 75 0.26
295 116 0.41
296 3 0.01
297 16 0.06
298 21 0.07
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (292 bp):
TCTCATTTAATAACTCTATTTTAATTTAAAAAACTAGTATTACTTAATAGTTTATTAAATTAAAA
TAAAGTTATTAAATAAGAACAATTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTG
AAGGGGAATAAAAAGAAAATAATAAATAAGGAGGGGCTTAGAAGGTAATTTAGGCCACATTTCAA
TTTTAGTGCGCACACCAGCAATTCACTTTCAAAATTCAAAATGATAAATTTGCATGTCAGGTCCT
TAAAACTGCAAATGGTCACTTAATTAGAATTC
Found at i:48549238 original size:19 final size:19
Alignment explanation
Indices: 48549162--48549231 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
48549152 ACTTAATAGT
*
48549162 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAATAGAG
* * *
48549181 TTATTAAATAAGAACA-AT
1 TTATTAAATAAAAATAGAG
*
48549199 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAATAGAG
48549218 TTATTAAATAAAAA
1 TTATTAAATAAAAA
48549232 ATGAGTTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (19 bp):
TTATTAAATAAAAATAGAG
Found at i:48549391 original size:27 final size:27
Alignment explanation
Indices: 48549304--48549382 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
48549294 AATTTTAGTC
*
48549304 CTTTGGCACCATTGGTGCCGCCAATCA
1 CTTTGGCACCATTGGTGCCGCCAATCT
48549331 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
* *
48549358 CTTTGGCACCTTTGGTGTCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
48549383 GTGATTGGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.30
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:48549505 original size:25 final size:25
Alignment explanation
Indices: 48549471--48549520 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
48549461 TTTCGTAAAT
48549471 AATAAAAAAA-AGTAATATTTTGGTA
1 AATAAAAAAATA-TAATATTTTGGTA
48549496 AATAAAAAAATTATAATATTTTGGT
1 AATAAAAAAA-TATAATATTTTGGT
48549521 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.43
26 12 0.52
27 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (25 bp):
AATAAAAAAATATAATATTTTGGTA
Found at i:48549512 original size:26 final size:28
Alignment explanation
Indices: 48549457--48549520 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
48549447 TTTTTTTTGT
*
48549457 ATATTTTCGTAAATAATAAAAAAAAGTA
1 ATATTTTGGTAAATAATAAAAAAAAGTA
**
48549485 ATATTTTGGTAAATAA-AAAAATTA-TA
1 ATATTTTGGTAAATAATAAAAAAAAGTA
48549511 ATATTTTGGT
1 ATATTTTGGT
48549521 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.36
27 6 0.18
28 15 0.45
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAATAAAAAAAAGTA
Found at i:48552613 original size:25 final size:25
Alignment explanation
Indices: 48552567--48552615 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
48552557 AATCCATTGA
* *
48552567 AAATCTCAATTCGATTCGAAACCCT
1 AAATCTCAATCCCATTCGAAACCCT
48552592 AAATCTCAATCCCATTTC-AAACCC
1 AAATCTCAATCCCA-TTCGAAACCC
48552616 CAGACATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.27
Consensus pattern (25 bp):
AAATCTCAATCCCATTCGAAACCCT
Found at i:48558753 original size:13 final size:13
Alignment explanation
Indices: 48558735--48558763 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
48558725 TATTTGATAT
48558735 AATTTAAAATAAA
1 AATTTAAAATAAA
48558748 AATTTAAAATAAA
1 AATTTAAAATAAA
48558761 AAT
1 AAT
48558764 GAATATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:48562089 original size:2 final size:2
Alignment explanation
Indices: 48562082--48562130 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
48562072 NNNAATAATA
48562082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48562124 AT AT AT A
1 AT AT AT A
48562131 ACCATTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48564050 original size:73 final size:73
Alignment explanation
Indices: 48563969--48564118 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
48563959 GAAACATATC
48563969 GATCGATATGACTGATACTGATTTAATACTACAGTGGAGGTTATTTATGAGAGAGGTAGACTTGC
1 GATCGATATGACTGATACTGATTTAATACTACAGTGGAGGTTATTTATGAGAGAGGTAGACTTGC
48564034 CTTTGAGG
66 CTTTGAGG
48564042 GATCGATATGACTGATACTGATTTAATACTACAGTGGAGGTTATTTATGAGAGAGGTAGACTTGC
1 GATCGATATGACTGATACTGATTTAATACTACAGTGGAGGTTATTTATGAGAGAGGTAGACTTGC
48564107 CTTTGAGG
66 CTTTGAGG
48564115 GATC
1 GATC
48564119 TCATGATCCG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (73 bp):
GATCGATATGACTGATACTGATTTAATACTACAGTGGAGGTTATTTATGAGAGAGGTAGACTTGC
CTTTGAGG
Found at i:48572664 original size:31 final size:30
Alignment explanation
Indices: 48572597--48572665 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
48572587 ATGATAACGT
**
48572597 AAGTGACTAAAATGTAACATTTCAAACATA
1 AAGTGACTAAAATGTAACATGGCAAACATA
*
48572627 AA-TGACTAAAATGTAACCTGAGGCAAACA-A
1 AAGTGACTAAAATGTAACAT--GGCAAACATA
48572657 AAGTGACTA
1 AAGTGACTA
48572666 TTTTAATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAATGTAACATGGCAAACATA
Found at i:48573235 original size:21 final size:21
Alignment explanation
Indices: 48573199--48573248 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
48573189 GATTATGAGT
*
48573199 TTTAAG-TTTAAGGTTTA-AG
1 TTTAAGATTTAAAGTTTAGAG
*
48573218 ATTTAAGATTTAAAGTTTCGAG
1 -TTTAAGATTTAAAGTTTAGAG
48573240 TTTAAGATT
1 TTTAAGATT
48573249 CTGAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 18 0.69
22 2 0.08
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (21 bp):
TTTAAGATTTAAAGTTTAGAG
Found at i:48588469 original size:13 final size:13
Alignment explanation
Indices: 48588453--48588479 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48588443 GGAATCATAA
48588453 TACATTTCATGTG
1 TACATTTCATGTG
48588466 TACATTTCATGTG
1 TACATTTCATGTG
48588479 T
1 T
48588480 TGTAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TACATTTCATGTG
Found at i:48589658 original size:3 final size:3
Alignment explanation
Indices: 48589650--48589690 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
48589640 ACTATATACA
48589650 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
48589691 TATGATACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.34, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:48590831 original size:2 final size:2
Alignment explanation
Indices: 48590826--48590852 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48590816 TCTTACTTGC
48590826 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
48590853 GTTGCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48595133 original size:22 final size:21
Alignment explanation
Indices: 48595102--48595152 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
48595092 ATAAATATTT
*
48595102 TTTAAAATATA-ATA-ATAAA
1 TTTAAAATATATATATAAAAA
48595121 TTTAAAGATATATATATAAAAA
1 TTTAAA-ATATATATATAAAAA
48595143 TTTAAAATAT
1 TTTAAAATAT
48595153 TGTTGACGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 5 0.18
21 7 0.25
22 10 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTAAAATATATATATAAAAA
Found at i:48598417 original size:18 final size:16
Alignment explanation
Indices: 48598381--48598411 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48598371 CATTAAAAAT
*
48598381 ATATTAAAAAGTATTC
1 ATATTAAAAAATATTC
48598397 ATATTAAAAAATATT
1 ATATTAAAAAATATT
48598412 ATCATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATTAAAAAATATTC
Found at i:48599387 original size:13 final size:13
Alignment explanation
Indices: 48599369--48599431 Score: 99
Period size: 13 Copynumber: 4.8 Consensus size: 13
48599359 TCTTCATTGT
48599369 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
48599382 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
48599395 TATGGAAAAGTGC
1 TTTTGAAAAGTGC
*
48599408 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
48599421 TTTTGAAAAGT
1 TTTTGAAAAGT
48599432 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:48599863 original size:16 final size:16
Alignment explanation
Indices: 48599838--48599876 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
48599828 TTTTTTTATT
48599838 TTAA-CACAATTGTAA
1 TTAAGCACAATTGTAA
48599853 TTAAGCACAATTGTAA
1 TTAAGCACAATTGTAA
48599869 TTAAGCAC
1 TTAAGCAC
48599877 CAAGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (16 bp):
TTAAGCACAATTGTAA
Found at i:48603296 original size:17 final size:17
Alignment explanation
Indices: 48603241--48603304 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
48603231 TTTTTTTCAT
*
48603241 AAAAGTATTAAATATCATA
1 AAAAATATTAAATAT--TA
* *
48603260 AAAAA-ATTATAAAAAT-
1 AAAAATATTA-AATATTA
48603276 AAAAATATTAAATATTA
1 AAAAATATTAAATATTA
48603293 AAAAATATTAAA
1 AAAAATATTAAA
48603305 ATTGATACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.24
17 17 0.46
18 4 0.11
19 7 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAATATTAAATATTA
Found at i:48603418 original size:29 final size:30
Alignment explanation
Indices: 48603376--48603434 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
48603366 TAATAAATTA
* * *
48603376 TAAAATTTTATAAAATTAATAAAACTTATT
1 TAAAATATTATAAAATTAAAAAAACATATT
48603406 TAAAATATT-TAAAATTAAAAAAACATATT
1 TAAAATATTATAAAATTAAAAAAACATATT
48603435 AGAATTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAAATATTATAAAATTAAAAAAACATATT
Found at i:48604821 original size:23 final size:23
Alignment explanation
Indices: 48604794--48604915 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
48604784 AGTGTTATTG
*
48604794 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48604817 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48604840 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48604863 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48604886 AACAGCGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48604909 ATCAGTG
1 ATCAGTG
48604916 TTGCACTTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:48604849 original size:46 final size:46
Alignment explanation
Indices: 48604796--48604915 Score: 213
Period size: 46 Copynumber: 2.6 Consensus size: 46
48604786 TGTTATTGAT
*
48604796 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
48604842 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
* *
48604888 CAGCGGTAGCTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
48604916 TTGCACTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.29
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:48606683 original size:8 final size:9
Alignment explanation
Indices: 48606670--48606725 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
48606660 AATCTATTAG
48606670 ATTTTTAT-
1 ATTTTTATA
48606678 ATTTTTATA
1 ATTTTTATA
48606687 ATATTTTATA
1 AT-TTTTATA
48606697 ACTTTTTATA
1 A-TTTTTATA
*
48606707 AGTTTATATCA
1 A-TTTTTAT-A
48606718 ATTTTTAT
1 ATTTTTAT
48606726 TTTTAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.20
9 2 0.05
10 28 0.68
11 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:48610914 original size:23 final size:24
Alignment explanation
Indices: 48610870--48610916 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48610860 TGAAATTAAT
*
48610870 AAAATTAATAAAAATATTTTTTTC
1 AAAATTAATAAAAATATGTTTTTC
48610894 AAAA-TAAGTAAAAAT-TGTTTTTC
1 AAAATTAA-TAAAAATATGTTTTTC
48610917 CTTTGGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATTAATAAAAATATGTTTTTC
Found at i:48612957 original size:72 final size:73
Alignment explanation
Indices: 48612868--48613049 Score: 321
Period size: 72 Copynumber: 2.5 Consensus size: 73
48612858 ATCTGTGTTC
*
48612868 AATTAGGATTCATTGAAACCCAATTCGAATTTATAAACAAGAGTAATTAGACCCAAACTCCATTA
1 AATTAGGATTCACTGAAACCCAATTCGAATTTATAAACAAGAGTAATTAGACCCAAACTCCATTA
48612933 C-TTATTG
66 CGTTATTG
48612940 AATTAGGATTCACTGAAACCCAATTCGAATTTATAAACAAGAGTAATTAGACCCAAACTCCATTA
1 AATTAGGATTCACTGAAACCCAATTCGAATTTATAAACAAGAGTAATTAGACCCAAACTCCATTA
48613005 CGTTATTG
66 CGTTATTG
* * *
48613013 AATTAGGATTTACTGAAACCTAATTTGAATTTATAAA
1 AATTAGGATTCACTGAAACCCAATTCGAATTTATAAA
48613050 ATATTATATG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 65 0.62
73 40 0.38
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (73 bp):
AATTAGGATTCACTGAAACCCAATTCGAATTTATAAACAAGAGTAATTAGACCCAAACTCCATTA
CGTTATTG
Found at i:48614947 original size:3 final size:3
Alignment explanation
Indices: 48614939--48614963 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48614929 GCCTTTCTTG
48614939 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
48614964 AAAAAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:48632099 original size:144 final size:144
Alignment explanation
Indices: 48631895--48632184 Score: 553
Period size: 144 Copynumber: 2.0 Consensus size: 144
48631885 CTAGTATCAA
*
48631895 TAGTTATAATAAATCAAAATGAATTAATAAAAATACAACAAAAGTGGAAAAATTTCATGTAACAT
1 TAGTTATAATAAATCAAAATGAATTAATAAAAATACAACAAAAGTGGAAAAAATTCATGTAACAT
*
48631960 CCCCAATACCCTTGAGTTATGAACCATGTTAAATCAAGAGTAAATATTTTAGAATTTGAGAAGGT
66 CCCCAATACCCTTGAGTTATGAACCATGTTAAATCAAGAGTAAATATATTAGAATTTGAGAAGGT
48632025 TATAAGATAGAAGT
131 TATAAGATAGAAGT
*
48632039 TAGTTATAATAAATCAAAATGAATTAATAAAAATACAACAAAAGTGGAAAAAATTCATGTAGCAT
1 TAGTTATAATAAATCAAAATGAATTAATAAAAATACAACAAAAGTGGAAAAAATTCATGTAACAT
48632104 CCCCAATACCCTTGAGTTATGAACCATGTTAAATCAAGAGTAAATATATTAGAATTTGAGAAGGT
66 CCCCAATACCCTTGAGTTATGAACCATGTTAAATCAAGAGTAAATATATTAGAATTTGAGAAGGT
48632169 TATAAGATAGAAGT
131 TATAAGATAGAAGT
48632183 TA
1 TA
48632185 TCTTTGTTAG
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 143 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (144 bp):
TAGTTATAATAAATCAAAATGAATTAATAAAAATACAACAAAAGTGGAAAAAATTCATGTAACAT
CCCCAATACCCTTGAGTTATGAACCATGTTAAATCAAGAGTAAATATATTAGAATTTGAGAAGGT
TATAAGATAGAAGT
Found at i:48633025 original size:13 final size:13
Alignment explanation
Indices: 48633007--48633031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48632997 CAATATATTT
48633007 ATTAATTAAAAAC
1 ATTAATTAAAAAC
48633020 ATTAATTAAAAA
1 ATTAATTAAAAA
48633032 TTAAAACAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:48633051 original size:22 final size:20
Alignment explanation
Indices: 48633010--48633053 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
48633000 TATATTTATT
* *
48633010 AATTAAAAACATTAATTAAA
1 AATTAAAAACATGAAATAAA
48633030 AATTAAAACAACATGAAATAAA
1 AATT-AAA-AACATGAAATAAA
48633052 AA
1 AA
48633054 ATACAAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (20 bp):
AATTAAAAACATGAAATAAA
Found at i:48645932 original size:10 final size:11
Alignment explanation
Indices: 48645908--48645933 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48645898 TATATTTTTA
48645908 TTTTAAAATGT
1 TTTTAAAATGT
48645919 TTTTAAAATGT
1 TTTTAAAATGT
48645930 TTTT
1 TTTT
48645934 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
TTTTAAAATGT
Found at i:48646420 original size:26 final size:26
Alignment explanation
Indices: 48646372--48646421 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
48646362 TTCCTACTAA
*
48646372 AAATATTTTTTATAATAATAAACAAT
1 AAATATTTTTTATAATAAGAAACAAT
*
48646398 AAATATTTTTT-TATTATAGAAACA
1 AAATATTTTTTATAATA-AGAAACA
48646422 GTAGTTATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATATTTTTTATAATAAGAAACAAT
Found at i:48646821 original size:15 final size:14
Alignment explanation
Indices: 48646795--48646824 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
48646785 TAATTATAGT
48646795 TTAAATTATAATTA
1 TTAAATTATAATTA
48646809 TTAAATATATAATTA
1 TTAAAT-TATAATTA
48646824 T
1 T
48646825 CACAACCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTATAATTA
Found at i:48669249 original size:31 final size:29
Alignment explanation
Indices: 48669192--48669256 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
48669182 CTTTAATTAC
*
48669192 ATAAAATTAAAATTATATCATTTAATAAATT
1 ATAAAATTAAAATTATATCATGTAAT--ATT
48669223 ATAAAATT-AAATGTA-ACTCATGTAATATT
1 ATAAAATTAAAAT-TATA-TCATGTAATATT
48669252 ATAAA
1 ATAAA
48669257 CTGGTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 8 0.26
30 5 0.16
31 18 0.58
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAAAATTAAAATTATATCATGTAATATT
Found at i:48673950 original size:16 final size:17
Alignment explanation
Indices: 48673929--48673960 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
48673919 TTAATTATGA
48673929 AAAAAAATAA-AAAGAG
1 AAAAAAATAAGAAAGAG
48673945 AAAAAAATAAGAAAGA
1 AAAAAAATAAGAAAGA
48673961 AGAGGGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAATAAGAAAGAG
Done.