Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 182 of 425
Found at i:55256855 original size:30 final size:30
Alignment explanation
Indices: 55256821--55256917 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
55256811 TAAACTAAAA
*
55256821 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAACTCGTGAGCTAAAGT
* * * * *
55256851 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAACTCGTGAGCTAAAGT
* *
55256881 TGAGCTAAGGTTTAACTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAACTCGTGAGCT-AAAGT
55256911 TGAGCTA
1 TGAGCTA
55256918 GGGGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAACTCGTGAGCTAAAGT
Found at i:55259069 original size:30 final size:29
Alignment explanation
Indices: 55259025--55259095 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
55259015 TCTTTTGTTG
*
55259025 CAATTTCTTTTTCA-TCTTCTTTTTCACTCT
1 CAATTTC-TTTTCATTC-TCTTTTTCAATCT
55259055 CAAATTTCTTTTCATTCTCTTTTTCAATCT
1 C-AATTTCTTTTCATTCTCTTTTTCAATCT
*
55259085 CATTTTCTTTT
1 CAATTTCTTTT
55259096 TTCTTTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.24
30 20 0.54
31 8 0.22
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (29 bp):
CAATTTCTTTTCATTCTCTTTTTCAATCT
Found at i:55259175 original size:5 final size:5
Alignment explanation
Indices: 55259165--55259227 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
55259155 CTTTTGCCTC
*
55259165 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-CTTT T-C-TTT
55259213 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
55259228 GTTTTCTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.58
6 12 0.24
7 5 0.10
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:55260207 original size:17 final size:16
Alignment explanation
Indices: 55260172--55260207 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55260162 ATTACAACTT
*
55260172 GAATTTTTTTTAATTC
1 GAATTTTTTTTAATAC
55260188 GAATTTTTTTTAACTAC
1 GAATTTTTTTTAA-TAC
55260205 GAA
1 GAA
55260208 CCTATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
GAATTTTTTTTAATAC
Found at i:55261743 original size:30 final size:30
Alignment explanation
Indices: 55261709--55261805 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
55261699 TAAACTAAAA
55261709 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
55261739 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
55261769 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
55261799 TGAGCTA
1 TGAGCTA
55261806 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:55263382 original size:18 final size:18
Alignment explanation
Indices: 55263361--55263398 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55263351 ACATGACATA
*
55263361 CACTGTTTACTGTTACTG
1 CACTATTTACTGTTACTG
*
55263379 CACTATTTATTGTTACTG
1 CACTATTTACTGTTACTG
55263397 CA
1 CA
55263399 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (18 bp):
CACTATTTACTGTTACTG
Found at i:55270379 original size:28 final size:26
Alignment explanation
Indices: 55270324--55270436 Score: 136
Period size: 27 Copynumber: 4.2 Consensus size: 26
55270314 AGCATGGCTG
* *
55270324 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
55270350 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
55270378 CCAGAACAGATATATGTTGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
55270405 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
55270433 CCAG
1 CCAG
55270437 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.08
27 38 0.50
28 32 0.42
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:55270409 original size:55 final size:54
Alignment explanation
Indices: 55270324--55270436 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 54
55270314 AGCATGGCTG
*
55270324 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAGCCA
* *
55270378 CCAGAACAGATATATGTTG-CAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATG-TGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
55270433 CCAG
1 CCAG
55270437 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
54 19 0.36
55 32 0.60
56 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
Found at i:55271029 original size:31 final size:31
Alignment explanation
Indices: 55270991--55271055 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
55270981 CATACTAACC
55270991 CCTTACCATATTCGGCCAATAACTCCTTAGG
1 CCTTACCATATTCGGCCAATAACTCCTTAGG
55271022 CCTTACCATATTCGGCCAATAACTCCTTAGG
1 CCTTACCATATTCGGCCAATAACTCCTTAGG
55271053 CCT
1 CCT
55271056 CGGATAGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.12, T:0.29
Consensus pattern (31 bp):
CCTTACCATATTCGGCCAATAACTCCTTAGG
Found at i:55273487 original size:11 final size:10
Alignment explanation
Indices: 55273472--55273510 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55273462 TTTTTTTCGA
55273472 TTTTTTTATT
1 TTTTTTTATT
55273482 TATTTTTTATT
1 T-TTTTTTATT
* *
55273493 TTTTTTGAAT
1 TTTTTTTATT
55273503 TTTTTTTA
1 TTTTTTTA
55273511 ACTTGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:55280426 original size:11 final size:11
Alignment explanation
Indices: 55280420--55280449 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
55280410 TATTTTTTAT
55280420 TTTTTTTTGAA
1 TTTTTTTTGAA
55280431 TTTTTTTTGAA
1 TTTTTTTTGAA
55280442 TTTTTTTT
1 TTTTTTTT
55280450 AACTTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:55280864 original size:14 final size:14
Alignment explanation
Indices: 55280817--55280864 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
55280807 GTACGAATGG
*
55280817 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
55280831 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
55280845 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
55280859 ATTGGT
1 AATGGT
55280865 CGGTTTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:55283375 original size:28 final size:26
Alignment explanation
Indices: 55283320--55283432 Score: 145
Period size: 27 Copynumber: 4.2 Consensus size: 26
55283310 AGCATGGCTG
* *
55283320 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
55283346 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
55283374 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
55283401 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
55283429 CCAG
1 CCAG
55283433 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
26 6 0.08
27 39 0.50
28 33 0.42
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:55283403 original size:55 final size:54
Alignment explanation
Indices: 55283320--55283432 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 54
55283310 AGCATGGCTG
*
55283320 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAGCCA
* * *
55283374 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
55283429 CCAG
1 CCAG
55283433 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 19 0.36
55 34 0.64
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
Found at i:55291220 original size:27 final size:26
Alignment explanation
Indices: 55291165--55291270 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 26
55291155 CTGCCAAAAT
* * *
55291165 AGATAATGTGACAGAGTCACTAGATAC
1 AGATAATGTGGCAGAGCCACCAGA-AC
55291192 AGATAATCGTGGCAGAGCCACCAGAAC
1 AGATAAT-GTGGCAGAGCCACCAGAAC
*
55291219 AGATATATGTGGCAGAGCCACCAGATC
1 AGATA-ATGTGGCAGAGCCACCAGAAC
*
55291246 AGATAATTTGTGGCATAGCCACCAG
1 AGATAA--TGTGGCAGAGCCACCAG
55291271 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.01
27 37 0.53
28 32 0.46
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
AGATAATGTGGCAGAGCCACCAGAAC
Found at i:55291259 original size:55 final size:54
Alignment explanation
Indices: 55291165--55291270 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 54
55291155 CTGCCAAAAT
* *
55291165 AGATAATGTGACAGAGTCACTAGATACAGATAATCGTGGCAGAGCCACCAGAAC
1 AGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAGAAC
* * *
55291219 AGATATATGTGGCAGAGCCACCAGAT-CAGATAATTTGTGGCATAGCCACCAG
1 AGATA-ATGTGACAGAGCCACCAGATACAGATAA-TCGTGGCAGAGCCACCAG
55291271 GACGCTTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 12 0.27
55 33 0.73
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (54 bp):
AGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAGAAC
Found at i:55291266 original size:28 final size:28
Alignment explanation
Indices: 55291171--55291270 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
55291161 AAATAGATAA
* * *
55291171 TGTGACAGAGTCACTAGATACAGATAA-T
1 TGTGGCAGAGCCACCAGAT-CAGATAATT
* * *
55291199 CGTGGCAGAGCCACCAGAACAGAT-ATA
1 TGTGGCAGAGCCACCAGATCAGATAATT
55291226 TGTGGCAGAGCCACCAGATCAGATAATT
1 TGTGGCAGAGCCACCAGATCAGATAATT
*
55291254 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
55291271 GACGCTTCCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.02
27 27 0.45
28 32 0.53
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGATCAGATAATT
Found at i:55295698 original size:25 final size:25
Alignment explanation
Indices: 55295666--55295713 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
55295656 TACAGGTATG
55295666 TATACTAAACTCTCGAATAGGACTA
1 TATACTAAACTCTCGAATAGGACTA
55295691 TATACTAAACTCTCGAATAGGAC
1 TATACTAAACTCTCGAATAGGAC
55295714 CTTGAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (25 bp):
TATACTAAACTCTCGAATAGGACTA
Found at i:55296734 original size:18 final size:18
Alignment explanation
Indices: 55296711--55296763 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
55296701 TGGCCCGTTA
55296711 CAGTAACAGTAAACAGTG
1 CAGTAACAGTAAACAGTG
*
55296729 CAGTAACAGTAAATAGTG
1 CAGTAACAGTAAACAGTG
55296747 CAGTAACAGTAAACAGT
1 CAGTAACAGTAAACAGT
55296764 ATGCAAGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (18 bp):
CAGTAACAGTAAACAGTG
Found at i:55297165 original size:30 final size:30
Alignment explanation
Indices: 55297070--55297166 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
55297060 AGCTCACTCC
* * *
55297070 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCAAGAGCTAAAGCT
* * * **
55297100 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAG-CT
*
55297130 CAGCTCAACTTTAGCTCAAGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
55297160 TAGCTCA
1 TAGCTCA
55297167 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
Found at i:55298854 original size:12 final size:11
Alignment explanation
Indices: 55298832--55298888 Score: 73
Period size: 12 Copynumber: 5.2 Consensus size: 11
55298822 AAAGTTATAC
55298832 AATTC-AAAAA
1 AATTCAAAAAA
55298842 AATTCGAAAAAA
1 AATTC-AAAAAA
55298854 AATTC-AAAAA
1 AATTCAAAAAA
55298864 AATTCAAAAAA
1 AATTCAAAAAA
*
55298875 AAATCTAAAAAA
1 AATTC-AAAAAA
55298887 AA
1 AA
55298889 GGTGTTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
10 15 0.36
11 9 0.21
12 18 0.43
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.18
Consensus pattern (11 bp):
AATTCAAAAAA
Found at i:55298857 original size:22 final size:22
Alignment explanation
Indices: 55298832--55298888 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
55298822 AAAGTTATAC
*
55298832 AATTCAAAAAAATTCGAAAAAA
1 AATTCAAAAAAATTCAAAAAAA
55298854 AATTCAAAAAAATTCAAAAAAA
1 AATTCAAAAAAATTCAAAAAAA
*
55298876 AATCTAAAAAAAA
1 AAT-TCAAAAAAA
55298889 GGTGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.18
Consensus pattern (22 bp):
AATTCAAAAAAATTCAAAAAAA
Found at i:55298862 original size:9 final size:10
Alignment explanation
Indices: 55298832--55298875 Score: 70
Period size: 10 Copynumber: 4.2 Consensus size: 10
55298822 AAAGTTATAC
55298832 AATTCAAAAA
1 AATTCAAAAA
55298842 AATTCGAAAAAA
1 AATTC--AAAAA
55298854 AATTCAAAAA
1 AATTCAAAAA
55298864 AATTCAAAAA
1 AATTCAAAAA
55298874 AA
1 AA
55298876 AATCTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 22 0.69
12 10 0.31
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.18
Consensus pattern (10 bp):
AATTCAAAAA
Found at i:55299890 original size:12 final size:12
Alignment explanation
Indices: 55299870--55299900 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55299860 AAAAGCCTTT
55299870 GAAAA-GAAAAA
1 GAAAATGAAAAA
55299881 GAAAATGAAAAA
1 GAAAATGAAAAA
55299893 GAAAATGA
1 GAAAATGA
55299901 GATTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:55299892 original size:18 final size:18
Alignment explanation
Indices: 55299871--55299922 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
55299861 AAAGCCTTTG
55299871 AAAAGAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
* * *
55299889 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
55299907 AAAAGAGAACGAAAAT
1 AAAAGAAAAAGAAAAT
55299923 AAATTTGAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:55299911 original size:30 final size:30
Alignment explanation
Indices: 55299875--55299956 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
55299865 CCTTTGAAAA
*
55299875 GAAAAAGAAAATGAAAAAGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAAAATGAGAGT
* * **
55299905 GAAAAAGAGAACGAAAATA-AATTTGAGAGT
1 GAAAAAGAAAATGAAAA-AGAAAATGAGAGT
*
55299935 GAAAAAGAAGATGAAAAAGAAA
1 GAAAAAGAAAATGAAAAAGAAA
55299957 TTGAAACAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (30 bp):
GAAAAAGAAAATGAAAAAGAAAATGAGAGT
Found at i:55302089 original size:30 final size:30
Alignment explanation
Indices: 55302055--55302151 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
55302045 AGCTCACTCC
*
55302055 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
55302085 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
55302115 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
55302145 TAGCTCA
1 TAGCTCA
55302152 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:55305936 original size:19 final size:17
Alignment explanation
Indices: 55305893--55305936 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
55305883 CTTCATTAAG
55305893 TCTTTATTCAAAAATAA
1 TCTTTATTCAAAAATAA
*
55305910 TTTTTATTCAAAAATATTA
1 TCTTTATTCAAAAATA--A
55305929 TCTTTATT
1 TCTTTATT
55305937 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TCTTTATTCAAAAATAA
Found at i:55311335 original size:45 final size:46
Alignment explanation
Indices: 55311285--55311408 Score: 189
Period size: 45 Copynumber: 2.7 Consensus size: 46
55311275 GTCTGTACCG
55311285 TTTAGTGGTTTACCCACATCATATTAGCAACTTTTT-TCCGCACCA
1 TTTAGTGGTTTACCCACATCATATTAGCAACTTTTTATCCGCACCA
* * *
55311330 TTTAGTGTTTTATCCACATCATATTAGCAA-TTTTTATCTGCACCA
1 TTTAGTGGTTTACCCACATCATATTAGCAACTTTTTATCCGCACCA
* *
55311375 TTTAGTGGTTTACCCACACCGTATTAGCAACTTT
1 TTTAGTGGTTTACCCACATCATATTAGCAACTTT
55311409 CATTTGCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
44 5 0.07
45 62 0.89
46 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (46 bp):
TTTAGTGGTTTACCCACATCATATTAGCAACTTTTTATCCGCACCA
Found at i:55311340 original size:21 final size:21
Alignment explanation
Indices: 55311316--55311381 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
55311306 TATTAGCAAC
55311316 TTTTTTCCGCACCATTTAGTG
1 TTTTTTCCGCACCATTTAGTG
* * * **
55311337 TTTTATCCACATCATATTAGCAA
1 TTTTTTCCGCACCAT-TTAG-TG
*
55311360 TTTTTATCTGCACCATTTAGTG
1 TTTTT-TCCGCACCATTTAGTG
55311382 GTTTACCCAC
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
21 12 0.39
22 4 0.13
23 8 0.26
24 7 0.23
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (21 bp):
TTTTTTCCGCACCATTTAGTG
Found at i:55311363 original size:23 final size:23
Alignment explanation
Indices: 55311293--55311363 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 23
55311283 CGTTTAGTGG
*
55311293 TTTACCCACATCATATTAGCAACT
1 TTTATCCACATCATATTAGCAA-T
* * * **
55311317 TTTTTCCGCACCAT-TTAG-TGT
1 TTTATCCACATCATATTAGCAAT
55311338 TTTATCCACATCATATTAGCAAT
1 TTTATCCACATCATATTAGCAAT
55311361 TTT
1 TTT
55311364 TATCTGCACC
Statistics
Matches: 34, Mismatches: 11, Indels: 5
0.68 0.22 0.10
Matches are distributed among these distances:
21 12 0.35
22 4 0.12
23 8 0.24
24 10 0.29
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (23 bp):
TTTATCCACATCATATTAGCAAT
Found at i:55311364 original size:24 final size:24
Alignment explanation
Indices: 55311293--55311367 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
55311283 CGTTTAGTGG
*
55311293 TTTACCCACATCATATTAGCAACTT
1 TTTATCCACATCATATTAGCAA-TT
* *
55311318 TTT-TCCGCACCAT-TTAG---TGT
1 TTTATCCACATCATATTAGCAAT-T
55311338 TTTATCCACATCATATTAGCAATT
1 TTTATCCACATCATATTAGCAATT
55311362 TTTATC
1 TTTATC
55311368 TGCACCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 8 0.21
22 4 0.10
23 4 0.10
24 14 0.36
25 4 0.10
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.43
Consensus pattern (24 bp):
TTTATCCACATCATATTAGCAATT
Found at i:55314532 original size:14 final size:14
Alignment explanation
Indices: 55314513--55314540 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55314503 TAAAACGATT
55314513 ATAGTTCACACGAA
1 ATAGTTCACACGAA
55314527 ATAGTTCACACGAA
1 ATAGTTCACACGAA
55314541 CTTACCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ATAGTTCACACGAA
Found at i:55317276 original size:20 final size:20
Alignment explanation
Indices: 55317238--55317276 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55317228 TTAATTTAAT
*
55317238 AAATTTTTATAATTATTTAC
1 AAATTTTTAGAATTATTTAC
55317258 AAATTTTTAAGAATT-TTTA
1 AAATTTTT-AGAATTATTTA
55317277 TAATATTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
AAATTTTTAGAATTATTTAC
Found at i:55317339 original size:35 final size:34
Alignment explanation
Indices: 55317293--55317367 Score: 123
Period size: 35 Copynumber: 2.2 Consensus size: 34
55317283 TCTGAATCAC
*
55317293 ATTCAAAATGAAATCTAGACAACTATTTGTCAAAG
1 ATTCACAATGAAATCTAGACAACTATTTGTC-AAG
*
55317328 ATTCACAATGAAATCTAGACAACTATTTGTCGAG
1 ATTCACAATGAAATCTAGACAACTATTTGTCAAG
55317362 ATTCAC
1 ATTCAC
55317368 GTGAGCTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 8 0.21
35 30 0.79
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (34 bp):
ATTCACAATGAAATCTAGACAACTATTTGTCAAG
Found at i:55317529 original size:22 final size:22
Alignment explanation
Indices: 55317496--55317537 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55317486 ATGATGTGAA
*
55317496 TAAAAATATTATGTAACAAATAT
1 TAAAAATATTATATAA-AAATAT
55317519 TAAAAAT-TTATATAAAAAT
1 TAAAAATATTATATAAAAAT
55317538 CAAATGGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATATTATATAAAAATAT
Found at i:55322398 original size:16 final size:16
Alignment explanation
Indices: 55322377--55322410 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
55322367 ATCAAAGGCA
55322377 TGACAGAAATCTCAAT
1 TGACAGAAATCTCAAT
55322393 TGACAGAAATCTCAAT
1 TGACAGAAATCTCAAT
55322409 TG
1 TG
55322411 GTAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (16 bp):
TGACAGAAATCTCAAT
Found at i:55323547 original size:23 final size:20
Alignment explanation
Indices: 55323521--55323572 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 20
55323511 TTTGAGAAAA
55323521 AGAAAAATAAGAAGAAGAGAAGG
1 AGAAAAATAAGAAG--GAGAA-G
* *
55323544 AGAAAGAGAAGAAGGAGAAG
1 AGAAAAATAAGAAGGAGAAG
55323564 AGGAAAAAT
1 A-GAAAAAT
55323573 GAATATGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
23 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (20 bp):
AGAAAAATAAGAAGGAGAAG
Found at i:55324210 original size:59 final size:59
Alignment explanation
Indices: 55324117--55324255 Score: 233
Period size: 59 Copynumber: 2.4 Consensus size: 59
55324107 TGTTGTTGTT
*
55324117 TACAAATTGCTTAACACTTGGTATACATGACTGCTAGTTAGAAAAGATAACAATTGATA
1 TACAAATTGCTTAACAGTTGGTATACATGACTGCTAGTTAGAAAAGATAACAATTGATA
* * *
55324176 TACAAATTGCTTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAGTTGGTA
1 TACAAATTGCTTAACAGTTGGTATACATGACTGCTAGTTAGAAAAGATAACAATTGATA
*
55324235 TATAAATTGCTTAACAGTTGG
1 TACAAATTGCTTAACAGTTGG
55324256 ATAACAAATA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 75 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (59 bp):
TACAAATTGCTTAACAGTTGGTATACATGACTGCTAGTTAGAAAAGATAACAATTGATA
Found at i:55324706 original size:21 final size:21
Alignment explanation
Indices: 55324654--55324707 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
55324644 AGCTTCTTGA
* *
55324654 TGAGTTGGGGCAGTAGGTATC
1 TGAGTTGGGGTAGTAGGTAAC
55324675 TGAGTTGGGGTAGTAGGTAAC
1 TGAGTTGGGGTAGTAGGTAAC
55324696 TGAGTTGGGGTA
1 TGAGTTGGGGTA
55324708 CCCTTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.06, G:0.44, T:0.30
Consensus pattern (21 bp):
TGAGTTGGGGTAGTAGGTAAC
Found at i:55325517 original size:42 final size:43
Alignment explanation
Indices: 55325398--55325617 Score: 297
Period size: 43 Copynumber: 5.2 Consensus size: 43
55325388 AAAAAAAAAC
* *
55325398 TCATTGCATGCATATTAAAAAATAGGCAACAG---ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
55325438 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* * *
55325481 TCATTGCATGCACATTAAAAAA-AGTAAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
55325523 TCATTGCATCCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* * * *
55325566 TCATTGCATACATATTAAAAAA-ATTCAATAGCTTTCGAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
55325608 TCAGTGCATG
1 TCATTGCATG
55325618 TGATCAGCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
40 30 0.19
42 62 0.39
43 67 0.42
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:55325539 original size:85 final size:85
Alignment explanation
Indices: 55325431--55325616 Score: 300
Period size: 85 Copynumber: 2.2 Consensus size: 85
55325421 AGGCAACAGA
* *
55325431 CCAACAATCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAATCATTGCATGCACAT
1 CCAACAATCATTGCATCCATATTAAAAAATAGTCAACAACTTTCCAACAATCATTGCATACACAT
55325496 TAAAAAAAGTAAATAGCTTT
66 TAAAAAAAGTAAATAGCTTT
* *
55325516 CCAACAATCATTGCATCCATATTAAAAAATAGTCAACAGCTTTCCAACAATCATTGCATACATAT
1 CCAACAATCATTGCATCCATATTAAAAAATAGTCAACAACTTTCCAACAATCATTGCATACACAT
* *
55325581 TAAAAAAATTCAATAGCTTT
66 TAAAAAAAGTAAATAGCTTT
* *
55325601 CGAACAATCAGTGCAT
1 CCAACAATCATTGCAT
55325617 GTGATCAGCA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (85 bp):
CCAACAATCATTGCATCCATATTAAAAAATAGTCAACAACTTTCCAACAATCATTGCATACACAT
TAAAAAAAGTAAATAGCTTT
Found at i:55327279 original size:15 final size:15
Alignment explanation
Indices: 55327259--55327287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55327249 ATGCATCACT
55327259 ATCACTACCAGACAC
1 ATCACTACCAGACAC
55327274 ATCACTACCAGACA
1 ATCACTACCAGACA
55327288 TGTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.07, T:0.14
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:55329288 original size:40 final size:40
Alignment explanation
Indices: 55329152--55329305 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
55329142 GTGTGCATGA
* *
55329152 GCAAATTGTGATATCCGGGCTAAGTCCC-AAGGACATTTAT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGG-CATTTGT
* * ** * *
55329192 GCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * *
55329232 GCAAGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * * *
55329272 GCAAATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGC
55329306 CTTGGTGCGG
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 89 0.96
41 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
Found at i:55337456 original size:40 final size:40
Alignment explanation
Indices: 55337320--55337473 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
55337310 GTGTGCATGA
* *
55337320 GCAAATTGTGATATCCGGGCTAAGTCCCG-AGGACATTTAT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGG-CATTTGT
* * ** * *
55337360 GCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * *
55337400 GCAAGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * * *
55337440 GCAAATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGC
55337474 CTTGGTGCGG
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 90 0.97
41 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
Found at i:55339156 original size:48 final size:48
Alignment explanation
Indices: 55339047--55339215 Score: 250
Period size: 48 Copynumber: 3.5 Consensus size: 48
55339037 AATAAACATC
* * *
55339047 ATGGTAGATATACACAATAAACATCAGTTTGATAAT-GCATTCATACA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
* *
55339094 ATGGCAGATTTACACAATACGCATCAATTTGATAATGGCATTCATACA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
55339142 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
* * * *
55339190 ATGGCAGAAACAAACAATAAACATCA
1 ATGGCAGATATACACAATACACATCA
55339216 TGCACATGGC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 31 0.28
48 79 0.72
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (48 bp):
ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
Found at i:55339376 original size:6 final size:6
Alignment explanation
Indices: 55339252--55339375 Score: 113
Period size: 6 Copynumber: 20.7 Consensus size: 6
55339242 AAATAATCCT
* * * * * *
55339252 AAATCA AAATCC AAATCG AAATCA AAATCA AATTCT AAATCT AAATCG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* ** * * *
55339300 AGATCA AAATTG GAATCA AAATCA AAATCA AAATCA AAATCG AAATTA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * *
55339348 AAATCA AAATCA GAATCG AAATTA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAAT
55339376 TGAAATAGAA
Statistics
Matches: 93, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.57, C:0.15, G:0.06, T:0.22
Consensus pattern (6 bp):
AAATCA
Found at i:55340241 original size:3 final size:3
Alignment explanation
Indices: 55340233--55340293 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
55340223 TTAGGATGAG
55340233 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55340281 ATT ATT ATAT ATT
1 ATT ATT AT-T ATT
55340294 TTTCAATTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:55354938 original size:18 final size:18
Alignment explanation
Indices: 55354917--55354953 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55354907 TAGTATCCTT
55354917 CGGTTCCCAAGTAGCTTC
1 CGGTTCCCAAGTAGCTTC
55354935 CGGTTCCCAAGTAGCTTC
1 CGGTTCCCAAGTAGCTTC
55354953 C
1 C
55354954 TCTATACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.35, G:0.22, T:0.27
Consensus pattern (18 bp):
CGGTTCCCAAGTAGCTTC
Found at i:55356190 original size:55 final size:54
Alignment explanation
Indices: 55356131--55356253 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 54
55356121 TGTGGACAAC
*
55356131 ACTGACTTTTAAACACGGCCATGGCACACGCCCGTGTGGACTACCCGTGTTCAAT
1 ACTGACTTTTAAA-ACGGCCATGGCACACGCCCGTGTGGACTACCCGTGTCCAAT
** * * * * *
55356186 ACTGACTTTGGGAAATGGCTATGGGACACGCCCGTGTGGCCTACCCGTGTCCTAT
1 ACTGACTTT-TAAAACGGCCATGGCACACGCCCGTGTGGACTACCCGTGTCCAAT
* *
55356241 ACTAACTTATAAA
1 ACTGACTTTTAAA
55356254 TTAAACATCC
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
54 2 0.04
55 51 0.93
56 2 0.04
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (54 bp):
ACTGACTTTTAAAACGGCCATGGCACACGCCCGTGTGGACTACCCGTGTCCAAT
Found at i:55362222 original size:20 final size:19
Alignment explanation
Indices: 55362186--55362236 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
55362176 AAGGGCTATT
*
55362186 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
55362205 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
55362225 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
55362237 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:55362863 original size:45 final size:45
Alignment explanation
Indices: 55362681--55363036 Score: 274
Period size: 45 Copynumber: 8.0 Consensus size: 45
55362671 TTGATATTAA
*
55362681 GTGATATATGTGAGAAATCCGAACTTGTTGAGTTGGTCCAAGTTC
1 GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
* * * * **
55362726 ATGATATATGTGA-AGCATCTGAGCT-GTTGAGTTGGTCTGAGTTC
1 GTGATATATGTGAGA-AATCCGAACTCGTTGAGTTGGTCCAAGTTC
* * ** * * * * ***
55362770 ATTATCGATGCGAG-CATCCGAGCACGTTGAGTTGGTCTGCGTTC
1 GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
** * * *
55362814 GTGATATATGTGAGAAATCTAAACTTGTTGAGTTTGTCCAAGTTT
1 GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
* **
55362859 GTGATATATGTGA-AGCATCCGAACTCGTTGAGTTGGTCTGAGTTC
1 GTGATATATGTGAGA-AATCCGAACTCGTTGAGTTGGTCCAAGTTC
* * * * * * *
55362904 ATTATAGATGCGAG-CATCCGAGCTCGTTGAGTTGGTCCGAGTTC
1 GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
** * *
55362948 GTGATATATGTGAGAAATTTGAACTTGTTGAGTTGTTCCAAGTTC
1 GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
* * * *
55362993 GTGATATAAGTGA-AGCATCCGAGCTCGTTGAATTGGTCCAAGTT
1 GTGATATATGTGAGA-AATCCGAACTCGTTGAGTTGGTCCAAGTT
55363037 TATTATGGAT
Statistics
Matches: 241, Mismatches: 62, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
43 8 0.03
44 94 0.39
45 139 0.58
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (45 bp):
GTGATATATGTGAGAAATCCGAACTCGTTGAGTTGGTCCAAGTTC
Found at i:55363042 original size:134 final size:134
Alignment explanation
Indices: 55362681--55363030 Score: 551
Period size: 134 Copynumber: 2.6 Consensus size: 134
55362671 TTGATATTAA
* * * *
55362681 GTGATATATGTGAGAAATCCGAACTTGTTGAGTTGGTCCAAGTTCATGATATATGTGAAGCATCT
1 GTGATATATGTGAGAAATCTGAACTTGTTGAGTTGTTCCAAGTTCGTGATATATGTGAAGCATCC
* * *
55362746 GAGCT-GTTGAGTTGGTCTGAGTTCATTATCGATGCGAGCATCCGAGCACGTTGAGTTGGTCTGC
66 GAGCTCGTTGAGTTGGTCTGAGTTCATTATAGATGCGAGCATCCGAGCACGTTGAGTTGGTCCGA
55362810 GTTC
131 GTTC
* *
55362814 GTGATATATGTGAGAAATCTAAACTTGTTGAGTT-TGTCCAAGTTTGTGATATATGTGAAGCATC
1 GTGATATATGTGAGAAATCTGAACTTGTTGAGTTGT-TCCAAGTTCGTGATATATGTGAAGCATC
* *
55362878 CGAACTCGTTGAGTTGGTCTGAGTTCATTATAGATGCGAGCATCCGAGCTCGTTGAGTTGGTCCG
65 CGAGCTCGTTGAGTTGGTCTGAGTTCATTATAGATGCGAGCATCCGAGCACGTTGAGTTGGTCCG
55362943 AGTTC
130 AGTTC
* *
55362948 GTGATATATGTGAGAAATTTGAACTTGTTGAGTTGTTCCAAGTTCGTGATATAAGTGAAGCATCC
1 GTGATATATGTGAGAAATCTGAACTTGTTGAGTTGTTCCAAGTTCGTGATATATGTGAAGCATCC
*
55363013 GAGCTCGTTGAATTGGTC
66 GAGCTCGTTGAGTTGGTC
55363031 CAAGTTTATT
Statistics
Matches: 197, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
133 62 0.31
134 134 0.68
135 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (134 bp):
GTGATATATGTGAGAAATCTGAACTTGTTGAGTTGTTCCAAGTTCGTGATATATGTGAAGCATCC
GAGCTCGTTGAGTTGGTCTGAGTTCATTATAGATGCGAGCATCCGAGCACGTTGAGTTGGTCCGA
GTTC
Found at i:55369424 original size:30 final size:30
Alignment explanation
Indices: 55369389--55369449 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
55369379 TTGGAGAGTT
* *
55369389 ACTTAAATAGATGGTCTTTAGTGTATAACC
1 ACTTAAACAGATGGTCTTTAGTATATAACC
*
55369419 ACTTAACCAGATGGTCTTTAGTATATAACC
1 ACTTAAACAGATGGTCTTTAGTATATAACC
55369449 A
1 A
55369450 TGAACTCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (30 bp):
ACTTAAACAGATGGTCTTTAGTATATAACC
Found at i:55393689 original size:31 final size:31
Alignment explanation
Indices: 55393654--55393732 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
55393644 TATCAGAACT
* *
55393654 AGAATCAAAATGAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
* * *
55393685 AGAATTAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
55393716 AGTATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
55393733 GTGAATACAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:55393899 original size:27 final size:26
Alignment explanation
Indices: 55393851--55393910 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
55393841 GCGAGGCTGC
*
55393851 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55393878 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
55393904 TAGATAT
1 CAGATAT
55393911 ATATATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55393914 original size:2 final size:2
Alignment explanation
Indices: 55393907--55393936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55393897 ACCAGAATAG
55393907 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
55393937 GTGGCGAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55394017 original size:27 final size:26
Alignment explanation
Indices: 55393969--55394020 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
55393959 GCGAGGCTGC
*
55393969 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
55393995 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
55394021 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55394287 original size:27 final size:27
Alignment explanation
Indices: 55394257--55394666 Score: 493
Period size: 27 Copynumber: 15.2 Consensus size: 27
55394247 AACACCCTAG
* * *
55394257 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
*
55394284 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
55394311 GGGTAAAATAATAATTCTGTCAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* * * *
55394338 AGGTAAAA-CGATAATTCTATAAATTGA
1 GGGTAAAATAG-TAATTCTGTAAATCGA
* *
55394365 GGGAAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
**
55394392 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
55394419 GGGTAAAATAGTAATTTTGTAAATCAA
1 GGGTAAAATAGTAATTCTGTAAATCGA
*
55394446 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* * * *
55394473 GGGTAAAACAATAATTCTATCAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
*
55394500 GGGTAAAAT-GATAATTCTGTCAATCGA
1 GGGTAAAATAG-TAATTCTGTAAATCGA
55394527 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
*
55394554 GGGTAAAATAATAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
** *
55394581 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
** *
55394608 GGGTAAAACGGTAATAT-TGTAAATTGA
1 GGGTAAAATAGTAAT-TCTGTAAATCGA
* *
55394635 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
55394662 GGGTA
1 GGGTA
55394667 CTTTGGTAAT
Statistics
Matches: 333, Mismatches: 44, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.00
27 329 0.99
28 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (27 bp):
GGGTAAAATAGTAATTCTGTAAATCGA
Found at i:55394703 original size:27 final size:28
Alignment explanation
Indices: 55394673--55394895 Score: 138
Period size: 27 Copynumber: 8.2 Consensus size: 28
55394663 GGTACTTTGG
*
55394673 TAATTTTACAAGTCGA-GGGTATTTCAA
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* *
55394700 TAATTTTACAGGTCGA-GGGTATTTTAG
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * * *
55394727 TAATTTCACAAATC-AGGGGTATGTTGA
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * *
55394754 TAATTTTACAA-ACTAGGGGTATTTTGA
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * * **
55394781 TAATTTTACAA-ACCAGTGGTATTTTGG
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * **
55394808 TAATTTTACAA-ACTAGGGGTATTTTGG
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * * * *
55394835 TAATTTTATAA-ACTAAGGGTATTTTAG
1 TAATTTTACAAGTCGAGGGGTATTTTAA
* * **
55394862 TAATTTTACAA-ACCAGGGGTATTTTGG
1 TAATTTTACAAGTCGAGGGGTATTTTAA
55394889 TAATTTT
1 TAATTTT
55394896 GTAAACCAAG
Statistics
Matches: 170, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 168 0.99
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (28 bp):
TAATTTTACAAGTCGAGGGGTATTTTAA
Found at i:55394729 original size:81 final size:79
Alignment explanation
Indices: 55394644--55394933 Score: 278
Period size: 81 Copynumber: 3.6 Consensus size: 79
55394634 AGGGTAAAAC
* * * * * *
55394644 AGTAATTCTATAAATC-GAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTA
1 AGTAATTTTACAAATCAG-GGGTATTTTGGTAATTTTACAA-ACAAGGGTATTTTAATAATTTTA
** *
55394708 CAGGTCGAGGGTATTTT
64 CA-AACCAGGGTATTTT
* * * * *
55394725 AGTAATTTCACAAATCAGGGGTATGTTGATAATTTTACAAACTAGGGGTATTTTGATAATTTTAC
1 AGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAAC-AAGGGTATTTTAATAATTTTAC
55394790 AAACCAGTGGTATTTT
65 AAACCAG-GGTATTTT
* * *
55394806 GGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTATAAACTAAGGGTATTTTAGTAATTTTA
1 AGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAAC-AAGGGTATTTTAATAATTTTA
55394870 CAAACCAGGGGTATTTT
64 CAAACCA-GGGTATTTT
* ** * * * *
55394887 GGTAATTTTGTAAACCAAGAGTATTTTGGTAATTTTACAAACCAGGG
1 AGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACAAGGG
55394934 GTATGTTGGT
Statistics
Matches: 175, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
80 9 0.05
81 163 0.93
82 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (79 bp):
AGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACAAGGGTATTTTAATAATTTTACA
AACCAGGGTATTTT
Found at i:55394774 original size:54 final size:54
Alignment explanation
Indices: 55394662--55394948 Score: 301
Period size: 54 Copynumber: 5.3 Consensus size: 54
55394652 TATAAATCGA
* ** * ** ***
55394662 GGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAGGTC-G
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAG
* * * * * *
55394715 AGGGTATTTTAGTAATTTCACAAATCAGGGGTATGTTGATAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAG
* * *
55394770 GGGTATTTTGATAATTTTACAAACC-AGTGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAAG-GGTATTTTGATAATTTTACAAACCAG
* *
55394824 GGGTATTTTGGTAATTTTATAAACTAAGGGTATTTT-AGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGA-TAATTTTACAAACCAG
** * *
55394878 GGGTATTTTGGTAATTTTGTAAACCAAGAGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAG
*
55394932 GGGTATGTTGGTAATTT
1 GGGTATTTTGGTAATTT
55394949 GGTAAACTAA
Statistics
Matches: 198, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 194 0.98
55 3 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAG
Found at i:55394955 original size:27 final size:27
Alignment explanation
Indices: 55394716--55394948 Score: 304
Period size: 27 Copynumber: 8.6 Consensus size: 27
55394706 TACAGGTCGA
* * *
55394716 GGGTATTTTAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
55394743 GGGTATGTTGATAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
55394770 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
55394797 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
55394824 GGGTATTTTGGTAATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAG
*
55394851 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
55394878 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
*
55394905 GAGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
55394932 GGGTATGTTGGTAATTT
1 GGGTATTTTGGTAATTT
55394949 GGTAAACTAA
Statistics
Matches: 178, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 178 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:55396931 original size:6 final size:6
Alignment explanation
Indices: 55396901--55396994 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
55396891 AAGAAACATT
* * *
55396901 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
55396950 ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
55396995 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.06
6 57 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:55396959 original size:31 final size:31
Alignment explanation
Indices: 55396922--55396994 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
55396912 AATCAAAATG
*
55396922 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
*
55396953 AGAATCAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
*
55396984 AAAATCAGAAT
1 AGAATCAGAAT
55396995 GTGAATGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATC
Found at i:55397160 original size:27 final size:26
Alignment explanation
Indices: 55397112--55397171 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
55397102 GCGAGGCTGC
*
55397112 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55397139 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
55397165 CAGATAT
1 CAGATAT
55397172 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55397175 original size:2 final size:2
Alignment explanation
Indices: 55397168--55397203 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55397158 ACCAGAACAG
55397168 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
55397204 GTGTGGCGAA
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):
AT
Found at i:55397556 original size:27 final size:27
Alignment explanation
Indices: 55397526--55397962 Score: 543
Period size: 27 Copynumber: 16.2 Consensus size: 27
55397516 AACACCCTAG
** * *
55397526 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55397553 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
55397580 GGGTAAAATAGTAATTTTGTAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55397607 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
55397634 AGGTAAAAC-GATAATTCTATAAATTGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* *
55397661 GGGTAAAACAGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
55397688 GGGTAAAACGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
**
55397715 GGGTAAAATTGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55397742 GGGTAAAACAATAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55397769 GGGTAAAACAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55397796 GGGTAAAACAGTAATTTTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55397823 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55397850 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55397877 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * **
55397904 GGGTAAAACGGTAATTTTGTAAATTAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
55397931 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55397958 CGGTA
1 GGGTA
55397963 TTTTGGTAAT
Statistics
Matches: 360, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.00
27 358 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:55397984 original size:27 final size:27
Alignment explanation
Indices: 55397959--55398217 Score: 261
Period size: 27 Copynumber: 9.6 Consensus size: 27
55397949 GTAAATCGAC
*
55397959 GGTATTTTGGTAATTTTACAAGTCGA-G
1 GGTATTTTGGTAATTTTACAA-ACGAGG
*** **
55397986 GGTATTTCAATAATTTTACAGGTCGA-G
1 GGTATTTTGGTAATTTTACA-AACGAGG
*** * *
55398013 GGTATTCCAGTAATTTCACAAATGAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* *
55398040 GGTATTTTGGTAATTTTATAAACTAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* *
55398067 GGTATTTTGATAATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
*
55398094 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* * *
55398121 GGTATTTTGGTAATTTTATAAACCAAG
1 GGTATTTTGGTAATTTTACAAACGAGG
* * * * *
55398148 AGTATTTTAGTAATTTTATAAACTAAG
1 GGTATTTTGGTAATTTTACAAACGAGG
*
55398175 GGTATTTTGGTAATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
55398202 GGTATTTTGGTAATTT
1 GGTATTTTGGTAATTT
55398218 GGTAAACTAA
Statistics
Matches: 197, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 195 0.99
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACGAGG
Found at i:55398070 original size:54 final size:54
Alignment explanation
Indices: 55398022--55398226 Score: 302
Period size: 54 Copynumber: 3.8 Consensus size: 54
55398012 GGGTATTCCA
* **
55398022 GTAATTTCACAAATGAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
* *
55398076 ATAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
* * * * *
55398130 GTAATTTTATAAACCAAGAGTATTTTAGTAATTTTATAAACTAAGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
**
55398184 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTA
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTA
55398227 AAGTATTCTA
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 133 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (54 bp):
GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
Found at i:55398224 original size:27 final size:27
Alignment explanation
Indices: 55398037--55398217 Score: 263
Period size: 27 Copynumber: 6.7 Consensus size: 27
55398027 TTCACAAATG
*
55398037 AGGGGTATTTTGGTAATTTTATAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55398064 AGGGGTATTTTGATAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55398091 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
55398118 AGGGGTATTTTGGTAATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
* * * *
55398145 AAGAGTATTTTAGTAATTTTATAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55398172 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
55398199 AGGGGTATTTTGGTAATTT
1 AGGGGTATTTTGGTAATTT
55398218 GGTAAACTAA
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTATAAACC
Found at i:55400199 original size:6 final size:6
Alignment explanation
Indices: 55400169--55400256 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
55400159 AAGAAACATT
* * *
55400169 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * *
55400218 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA AACAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
55400257 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.06
6 49 0.79
7 7 0.11
8 2 0.03
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:55400223 original size:25 final size:25
Alignment explanation
Indices: 55400190--55400256 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
55400180 AATCAAAATG
*
55400190 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
55400215 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
55400240 AGAATCAAAAACAGAAT
1 AGAATCAGAATCAGAAT
55400257 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.16
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:55400422 original size:27 final size:26
Alignment explanation
Indices: 55400374--55400433 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
55400364 GCGAGGCTGC
*
55400374 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
55400401 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
55400427 CAGATAT
1 CAGATAT
55400434 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55400437 original size:2 final size:2
Alignment explanation
Indices: 55400430--55400457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55400420 ACCAGAACAG
55400430 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
55400458 GTGTGGCGAA
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:55400810 original size:27 final size:27
Alignment explanation
Indices: 55400780--55401216 Score: 552
Period size: 27 Copynumber: 16.2 Consensus size: 27
55400770 AACACCCTAG
** * *
55400780 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55400807 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55400834 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55400861 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
55400888 AGGTAAAAC-GATAATTCTATAAATTGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
*
55400915 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55400942 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
**
55400969 GGGTAAAATTGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55400996 GGGTAAAATAATAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55401023 GGGTAAAACAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
55401050 GGGTAAAACGGTAATTTTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55401077 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55401104 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
55401131 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * **
55401158 GGGTAAAACGGTAATTTTGTAAATTAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
55401185 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
55401212 CGGTA
1 GGGTA
55401217 TTTTGGTAAT
Statistics
Matches: 360, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.00
27 358 0.99
28 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:55401238 original size:27 final size:27
Alignment explanation
Indices: 55401213--55401471 Score: 261
Period size: 27 Copynumber: 9.6 Consensus size: 27
55401203 GTAAATCGAC
*
55401213 GGTATTTTGGTAATTTTACAAGTCGA-G
1 GGTATTTTGGTAATTTTACAA-ACGAGG
*** **
55401240 GGTATTTCAATAATTTTACAGGTCGA-G
1 GGTATTTTGGTAATTTTACA-AACGAGG
*** * *
55401267 GGTATTCCAGTAATTTCACAAATGAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* *
55401294 GGTATTTTGGTAATTTTATAAACTAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* *
55401321 GGTATTTTGTTAATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
*
55401348 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
* * *
55401375 GGTATTTTGGTAATTTTATAAACCAAG
1 GGTATTTTGGTAATTTTACAAACGAGG
* * * * *
55401402 AGTATTTTAGTAATTTTATAAACTAAG
1 GGTATTTTGGTAATTTTACAAACGAGG
*
55401429 GGTATTTTGGTAATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACGAGG
55401456 GGTATTTTGGTAATTT
1 GGTATTTTGGTAATTT
55401472 GGTAAACTAA
Statistics
Matches: 197, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 195 0.99
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACGAGG
Found at i:55401324 original size:54 final size:54
Alignment explanation
Indices: 55401276--55401480 Score: 302
Period size: 54 Copynumber: 3.8 Consensus size: 54
55401266 GGGTATTCCA
* **
55401276 GTAATTTCACAAATGAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
* *
55401330 TTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
* * * * *
55401384 GTAATTTTATAAACCAAGAGTATTTTAGTAATTTTATAAACTAAGGGTATTTTG
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
**
55401438 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTA
1 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTA
55401481 AAGTATTCTA
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 133 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.40
Consensus pattern (54 bp):
GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
Found at i:55401478 original size:27 final size:27
Alignment explanation
Indices: 55401291--55401471 Score: 263
Period size: 27 Copynumber: 6.7 Consensus size: 27
55401281 TTCACAAATG
*
55401291 AGGGGTATTTTGGTAATTTTATAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55401318 AGGGGTATTTTGTTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55401345 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
55401372 AGGGGTATTTTGGTAATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
* * * *
55401399 AAGAGTATTTTAGTAATTTTATAAACT
1 AGGGGTATTTTGGTAATTTTATAAACC
* *
55401426 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTATAAACC
55401453 AGGGGTATTTTGGTAATTT
1 AGGGGTATTTTGGTAATTT
55401472 GGTAAACTAA
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTATAAACC
Found at i:55402431 original size:12 final size:12
Alignment explanation
Indices: 55402414--55402440 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55402404 ATAACCTAAG
55402414 AAATACAAAACC
1 AAATACAAAACC
55402426 AAATACAAAACC
1 AAATACAAAACC
55402438 AAA
1 AAA
55402441 ACTCTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.22, G:0.00, T:0.07
Consensus pattern (12 bp):
AAATACAAAACC
Found at i:55403618 original size:16 final size:16
Alignment explanation
Indices: 55403599--55403638 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
55403589 TTGGAGTAGG
* *
55403599 GCTGTAATTAAATATA
1 GCTGTAATGAAATAGA
*
55403615 GCTGTAATGGAATAGA
1 GCTGTAATGAAATAGA
55403631 GCTGTAAT
1 GCTGTAAT
55403639 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (16 bp):
GCTGTAATGAAATAGA
Found at i:55403809 original size:25 final size:26
Alignment explanation
Indices: 55403780--55403829 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
55403770 TAAGTAGATA
*
55403780 ATTATTGTT-ATTAAATTTTAATAAG
1 ATTATTGTTAAATAAATTTTAATAAG
*
55403805 ATTATTGTTAAATATATTTTAATAA
1 ATTATTGTTAAATAAATTTTAATAA
55403830 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
ATTATTGTTAAATAAATTTTAATAAG
Found at i:55403870 original size:61 final size:59
Alignment explanation
Indices: 55403805--55403947 Score: 166
Period size: 58 Copynumber: 2.4 Consensus size: 59
55403795 TTTTAATAAG
* * *
55403805 ATTATTGTTAAATATATTTTAATAAAAATAAAAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATTAAATATATTTTAATAAAAAT---AATAAATAATTTAATAACATTCTTAACATA
* * * *
55403866 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATATTTTAATAAAAATAATAAATAATTTAATAACATTCTTAACATA
55403924 ATTATTATTAAGA-ATATTTTAATA
1 ATTATTATTAA-ATATATTTTAATA
55403948 TAAAGTTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
57 18 0.26
58 26 0.37
59 1 0.01
60 5 0.07
61 20 0.29
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATATTTTAATAAAAATAATAAATAATTTAATAACATTCTTAACATA
Found at i:55403945 original size:58 final size:58
Alignment explanation
Indices: 55403794--55403947 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 58
55403784 TTGTTATTAA
* * *
55403794 ATTTTAATA-AGATTATTGTTAAATATATTTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATATTTTAAT-AAAAT--AAATAAATAATTTAATAAC
* * * *
55403855 ATTTTAACATAATTATTATTAAATACAATTTAATAAAAT-AATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATATTTTAATAAAATAAATAAATAATTTAATAAC
55403912 ATTCTTAATATAATTATTATTAAGA-ATATTTTAATA
1 ATT-TTAATATAATTATTATTAA-ATATATTTTAATA
55403948 TAAAGTTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
57 18 0.22
58 27 0.34
59 1 0.01
60 5 0.06
61 28 0.35
62 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATATTTTAATAAAATAAATAAATAATTTAATAAC
Found at i:55403965 original size:28 final size:26
Alignment explanation
Indices: 55403855--55403970 Score: 90
Period size: 28 Copynumber: 4.2 Consensus size: 26
55403845 ATTTAATCAT
*
55403855 ATTTTAACATAATTATTATTAA-ATACA
1 ATTTTAATATAATTATTATTAAGA-A-A
* * * *
55403882 ATTTAATAAAATAATATATAATTTAATAAC
1 ATTT--TAATATAAT-TATTA-TTAAGAAA
*
55403912 ATTCTTAATATAATTATTATTAAGAAT
1 ATT-TTAATATAATTATTATTAAGAAA
55403939 ATTTTAATATAAAGTTATTATTAAGAAA
1 ATTTTAATAT-AA-TTATTATTAAGAAA
55403967 ATTT
1 ATTT
55403971 CAATGCCTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
26 7 0.10
27 15 0.21
28 21 0.29
29 16 0.22
30 7 0.10
31 6 0.08
32 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTTTAATATAATTATTATTAAGAAA
Found at i:55406746 original size:28 final size:28
Alignment explanation
Indices: 55406706--55406762 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55406696 CTACAGGCAG
55406706 TGAGGGGCAATGGTGTTTAGGGCTTTGT
1 TGAGGGGCAATGGTGTTTAGGGCTTTGT
55406734 TGAGGGGCAATGGTGTTTAGGGCTTTGT
1 TGAGGGGCAATGGTGTTTAGGGCTTTGT
55406762 T
1 T
55406763 AATGGAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.07, G:0.42, T:0.37
Consensus pattern (28 bp):
TGAGGGGCAATGGTGTTTAGGGCTTTGT
Found at i:55406755 original size:16 final size:16
Alignment explanation
Indices: 55406708--55406755 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
55406698 ACAGGCAGTG
55406708 AGGGGCAATGGTGTTT
1 AGGGGCAATGGTGTTT
* *
55406724 A-GGGC--T-TTGTTG
1 AGGGGCAATGGTGTTT
55406736 AGGGGCAATGGTGTTT
1 AGGGGCAATGGTGTTT
55406752 AGGG
1 AGGG
55406756 CTTTGTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 8
0.67 0.11 0.22
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
15 5 0.21
16 9 0.38
ACGTcount: A:0.17, C:0.06, G:0.46, T:0.31
Consensus pattern (16 bp):
AGGGGCAATGGTGTTT
Found at i:55409026 original size:40 final size:40
Alignment explanation
Indices: 55408967--55409174 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
55408957 CAATTGAATG
* * * *
55408967 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
55409007 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * **
55409047 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55409087 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
55409127 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
55409167 ATATCCGG
1 ATATCCGG
55409175 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
39 2 0.01
40 136 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:55409105 original size:80 final size:80
Alignment explanation
Indices: 55408969--55409174 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 80
55408959 ATTGAATGAT
* * ** * * *
55408969 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCCA-
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CAT
*
55409033 TTGTGCTAGT-GACCAC
65 TTGTGCAAGTCGACC-C
* * *
55409049 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
** *
55409114 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGACCC
* *
55409129 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
55409175 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 103 0.96
81 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGACCC
Found at i:55414775 original size:40 final size:40
Alignment explanation
Indices: 55414713--55414930 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
55414703 AAGGCAAGTA
* * * * *
55414713 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
55414752 CCTTCGGGACATAGCCCGGATATAGTAACTCACACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55414792 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
55414832 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55414872 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55414912 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55414931 TTATCATCCA
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 148 0.92
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55423844 original size:17 final size:17
Alignment explanation
Indices: 55423823--55423866 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
55423813 TGAATTGTAT
55423823 ATTGAATTGAAAGTGAA
1 ATTGAATTGAAAGTGAA
*
55423840 TTTG-ATATGAAAGTGAA
1 ATTGAAT-TGAAAGTGAA
55423857 ATTGAATTGA
1 ATTGAATTGA
55423867 TAACTGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (17 bp):
ATTGAATTGAAAGTGAA
Found at i:55423847 original size:23 final size:22
Alignment explanation
Indices: 55423813--55423868 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
55423803 TATATTGAGT
*
55423813 TGAATTGTATATTG-AATTGAAAG
1 TGAATTG-ATA-TGAAAGTGAAAG
*
55423836 TGAATTTGATATGAAAGTGAAAT
1 TGAA-TTGATATGAAAGTGAAAG
55423859 TGAATTGATA
1 TGAATTGATA
55423869 ACTGGAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 8 0.28
23 18 0.62
24 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (22 bp):
TGAATTGATATGAAAGTGAAAG
Found at i:55424047 original size:23 final size:23
Alignment explanation
Indices: 55424017--55424100 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
55424007 CTTAATGCTT
*
55424017 TTCTGGTGTGTTTAGGTA-GATTA
1 TTCTGGTGTGTTT-GGGAGGATTA
55424040 TTCTGGTGTGTTTGGGAGGATTA
1 TTCTGGTGTGTTTGGGAGGATTA
* *
55424063 TTTTGGTGTGTTT-GGATGGATCA
1 TTCTGGTGTGTTTGGGA-GGATTA
55424086 TTCT-GTGGTGTTTGG
1 TTCTGGT-GTGTTTGG
55424101 TTGGAATTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
22 8 0.15
23 44 0.83
24 1 0.02
ACGTcount: A:0.12, C:0.05, G:0.36, T:0.48
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGAGGATTA
Found at i:55426410 original size:49 final size:48
Alignment explanation
Indices: 55426338--55426512 Score: 242
Period size: 49 Copynumber: 3.5 Consensus size: 48
55426328 TGAGGTCACG
*
55426338 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATTGGTCGCA
* * * * *
55426387 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGAAAACTGTGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CGATAA-T-TGGTCGCA
*
55426438 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATTGGTCGCA
55426487 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
55426513 TGCATACCAG
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
49 66 0.60
50 4 0.04
51 40 0.36
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCA
Found at i:55426461 original size:51 final size:49
Alignment explanation
Indices: 55426331--55426525 Score: 239
Period size: 49 Copynumber: 3.9 Consensus size: 49
55426321 ACTATTGTGA
* ** *
55426331 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
55426380 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-GAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTAC-CAGATAA-T-T
* * *
55426431 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
55426480 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
55426526 GCTTCGGCTA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
49 80 0.65
50 4 0.03
51 40 0.32
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:55426511 original size:100 final size:100
Alignment explanation
Indices: 55426333--55426515 Score: 330
Period size: 100 Copynumber: 1.8 Consensus size: 100
55426323 TATTGTGAGG
* *
55426333 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGTAGTACT
55426398 AAGTGCAGGCTACTATGCGTACTCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACTCGAAAACTGTGA
* *
55426433 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGTAGTACT
55426498 AAGTGCAGGCTACTATGC
66 AAGTGCAGGCTACTATGC
55426516 ATACCAGATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACTCGAAAACTGTGA
Found at i:55428827 original size:40 final size:40
Alignment explanation
Indices: 55428700--55428829 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
55428690 ATGCTGGAAA
* *
55428700 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
55428740 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
55428780 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
55428820 TTATATCCGG
1 TTATATCCGG
55428830 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:55432484 original size:28 final size:30
Alignment explanation
Indices: 55432452--55432519 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
55432442 GTATCGTATC
55432452 TTGGGTTTCTT-TAT-TCT-GATTTCTTTAT
1 TTGGGTTTCTTCTATCT-TGGATTTCTTTAT
55432480 TTGGGTTT-TTCTATCTTGGATTTCTTTAT
1 TTGGGTTTCTTCTATCTTGGATTTCTTTAT
* *
55432509 TCGGTTTTCTT
1 TTGGGTTTCTT
55432520 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 12 0.35
29 18 0.53
30 2 0.06
ACGTcount: A:0.09, C:0.12, G:0.16, T:0.63
Consensus pattern (30 bp):
TTGGGTTTCTTCTATCTTGGATTTCTTTAT
Found at i:55432519 original size:14 final size:14
Alignment explanation
Indices: 55432457--55432519 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
55432447 GTATCTTGGG
*
55432457 TTTCTTTATTCTGA
1 TTTCTTTATTCGGA
* *
55432471 TTTCTTTATTTGGG
1 TTTCTTTATTCGGA
*
55432485 TTT-TTCTATCTTGGA
1 TTTCTT-TAT-TCGGA
*
55432500 TTTCTTTATTCGGT
1 TTTCTTTATTCGGA
55432514 TTTCTT
1 TTTCTT
55432520 GTTATCTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
13 2 0.05
14 26 0.65
15 10 0.25
16 2 0.05
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTCTTTATTCGGA
Found at i:55434254 original size:49 final size:48
Alignment explanation
Indices: 55434182--55434354 Score: 238
Period size: 51 Copynumber: 3.5 Consensus size: 48
55434172 GTGAGGTCAC
55434182 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATTGGTCGCAT
* * * * * *
55434231 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAA-T-TGGTCGCAT
* *
55434282 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAATTATTGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCAT
55434330 GTGTAGTACTAAGTGCAGGCTACTA
1 GTGTAGTACTAAGTGCAGGCTACTA
55434355 TGCATACCAG
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
48 31 0.29
49 34 0.32
50 7 0.07
51 35 0.33
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (48 bp):
GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCAT
Found at i:55434304 original size:51 final size:49
Alignment explanation
Indices: 55434182--55434354 Score: 224
Period size: 49 Copynumber: 3.5 Consensus size: 49
55434172 GTGAGGTCAC
* * *
55434182 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAATTGGTCGCAT
* * * *
55434231 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGT
1 GTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAA-T-TGGTCGCAT
* *
55434282 GTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC-AATTATTGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAA-AATTGGTCGCAT
55434330 GTGTAGTACTAAGTGCAGGCTACTA
1 GTGTAGTACTAAGTGCAGGCTACTA
55434355 TGCATACCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
48 31 0.29
49 38 0.35
50 4 0.04
51 35 0.32
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAATTGGTCGCAT
Found at i:55434356 original size:99 final size:100
Alignment explanation
Indices: 55434182--55434362 Score: 328
Period size: 99 Copynumber: 1.8 Consensus size: 100
55434172 GTGAGGTCAC
*
55434182 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGC
*
55434247 AGGCTACTATGCGTACCCGAAAACTGTGATCACGT
66 AGGCTACTATGCATACCCGAAAACTGTGATCACGT
*
55434282 GTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AATTATTGGTCGCATGTGTAGTACTAAGTGC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGC
55434346 AGGCTACTATGCATACC
66 AGGCTACTATGCATACC
55434363 AGATAGCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
99 45 0.58
100 33 0.42
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGC
AGGCTACTATGCATACCCGAAAACTGTGATCACGT
Found at i:55437392 original size:43 final size:43
Alignment explanation
Indices: 55437331--55437453 Score: 192
Period size: 43 Copynumber: 2.9 Consensus size: 43
55437321 TGTAACACAT
* *
55437331 CCATAATGAACTCGGACCTCTCAATGATCTCGGATGCTTGCAC
1 CCATAATGAACTCGGACCTCTCAACGAGCTCGGATGCTTGCAC
* *
55437374 CCATAATGAACTCAGACCTCTCAACGAGCTCGGATGCTTGCAT
1 CCATAATGAACTCGGACCTCTCAACGAGCTCGGATGCTTGCAC
* *
55437417 CCATAATGAACTCGGACCTCTCAACAAGCTCGAATGC
1 CCATAATGAACTCGGACCTCTCAACGAGCTCGGATGC
55437454 CACATATCTC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
CCATAATGAACTCGGACCTCTCAACGAGCTCGGATGCTTGCAC
Found at i:55443307 original size:8 final size:8
Alignment explanation
Indices: 55443294--55443323 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
55443284 AGATCGGCAC
55443294 AAGCCGAA
1 AAGCCGAA
55443302 AAGCCGAA
1 AAGCCGAA
*
55443310 ATGCCGAA
1 AAGCCGAA
55443318 AAGCCG
1 AAGCCG
55443324 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:55443810 original size:54 final size:54
Alignment explanation
Indices: 55443709--55443853 Score: 220
Period size: 54 Copynumber: 2.7 Consensus size: 54
55443699 TGGAGGAAGC
*
55443709 GTCCTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAA-TTATCTGATCTGGTGGCTCTACCACATATATCT
*
55443764 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
* * *
55443818 GTTCTGGTGGCTCTGCCACGA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
55443854 ACTTCGTCAC
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
53 6 0.07
54 57 0.68
55 21 0.25
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
Found at i:55443850 original size:27 final size:27
Alignment explanation
Indices: 55443712--55443871 Score: 159
Period size: 27 Copynumber: 5.9 Consensus size: 27
55443702 AGGAAGCGTC
* *
55443712 CTGGTGGCTATGCCACAATTTATCT-AAT
1 CTGGTGGCTCTGCCACAA--TATCTGTAT
* *
55443740 CTGGTGGCTCTACCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
55443767 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
55443794 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
55443821 CTGGTGGCTCTGCCACGATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
55443848 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
55443872 GCAGCCTCGC
Statistics
Matches: 112, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.09
27 85 0.76
28 16 0.14
29 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:55443865 original size:81 final size:81
Alignment explanation
Indices: 55443712--55443871 Score: 191
Period size: 81 Copynumber: 2.0 Consensus size: 81
55443702 AGGAAGCGTC
* * *
55443712 CTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTCTACCACATATATCTGTCCTGGTGGCTA
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTACCACAGATATCTGTCCTGGTGACTA
55443777 TGCCACAATTATCTGAT
66 TGCCACAA-TATCTGAT
* ** * *
55443794 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCAC-GATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTACCACAGATATCTGT-CCTGGTGACT
*
55443857 -TCGTCACAATATCTG
65 AT-GCCACAATATCTG
55443872 GCAGCCTCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
80 15 0.22
81 37 0.55
82 15 0.22
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (81 bp):
CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTACCACAGATATCTGTCCTGGTGACTA
TGCCACAATATCTGAT
Found at i:55447733 original size:23 final size:23
Alignment explanation
Indices: 55447699--55447812 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 23
55447689 CACTTAGTGC
55447699 TATTCT-AGTGTGTTTGGGTGGAT
1 TATTCTGA-TGTGTTTGGGTGGAT
* *
55447722 TATTCTGATGTGCTTGGGAGGAT
1 TATTCTGATGTGTTTGGGTGGAT
* * *
55447745 TATTTTGGTGTGTTTGGATGGAT
1 TATTCTGATGTGTTTGGGTGGAT
* * *
55447768 AACTCT-AGTGTGTTT-AGTGGAAT
1 TATTCTGA-TGTGTTTGGGTGG-AT
* * *
55447791 CATTCTGGTGTGTTTGGTTGGA
1 TATTCTGATGTGTTTGGGTGGA
55447813 ATTCGTATAT
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
22 3 0.04
23 61 0.90
24 4 0.06
ACGTcount: A:0.16, C:0.06, G:0.33, T:0.45
Consensus pattern (23 bp):
TATTCTGATGTGTTTGGGTGGAT
Found at i:55450657 original size:39 final size:40
Alignment explanation
Indices: 55450522--55450660 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
55450512 GGATATAACG
* * * *
55450522 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCTG-TTATAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCAGATT-TAGTA
* *
55450562 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCAGATTTAGTA
* * *
55450602 ACTCGCACAAATGCCTTCGGG-CTTAGCCCAGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCAGATTTAGTA
*
55450641 ACTCGCACGAACGCCTTCGG
1 ACTCGCACGAATGCCTTCGG
55450661 ATCTTAGTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 32 0.37
40 50 0.58
41 4 0.05
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCAGATTTAGTA
Found at i:55458600 original size:40 final size:40
Alignment explanation
Indices: 55458555--55458693 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
55458545 GGATATAACG
*
55458555 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCC-GGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTAAA-CCCGGGTT-TAGTA
* *
55458595 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTAAACCCGGGTTTAGTA
* * * *
55458635 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGGACTAAACCCGGGTTTAGTA
* *
55458674 ACTCGCACGAACGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
55458694 ATCTTAGTCC
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.38
40 49 0.56
41 6 0.07
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTAAACCCGGGTTTAGTA
Found at i:55458676 original size:79 final size:81
Alignment explanation
Indices: 55458530--55458746 Score: 223
Period size: 79 Copynumber: 2.7 Consensus size: 81
55458520 AATCACGTAT
*** * **
55458530 CTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGGGACAAAGCCCGG-TTATA
1 CTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATA
*
55458592 GTAACTCGCACGAATGC
65 GTAACTCGCACGAACGC
* *
55458609 CTTCGGGA-CTTAACCCGGGTTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATT-TA
1 CTTC-GGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATA
*
55458671 TTAACTCGCACGAACGC
65 GTAACTCGCACGAACGC
** * **
55458688 CTTCGGATCTTAGTCCGGATATAGTCACTTAACACAAA-GCCTTCGGGACTTAGCCCGGA
1 CTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
55458747 CATCATTCAA
Statistics
Matches: 114, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 62 0.54
80 49 0.43
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATAG
TAACTCGCACGAACGC
Found at i:55461627 original size:40 final size:40
Alignment explanation
Indices: 55461568--55461735 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
55461558 CATTTGAATG
* * *
55461568 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
55461608 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * **
55461648 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
55461688 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
55461728 ATATCCGG
1 ATATCCGG
55461736 TTAAATCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.03
40 99 0.93
41 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:55468821 original size:12 final size:13
Alignment explanation
Indices: 55468804--55468835 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55468794 GCAAATGTTA
55468804 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
55468816 AGTTTTGATGCAT
1 AGTTTTGATGCAT
55468829 -GTTTTGA
1 AGTTTTGA
55468836 AATGTGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:55474328 original size:25 final size:21
Alignment explanation
Indices: 55474300--55474349 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
55474290 GTTTGTGATA
55474300 TGTGAATTTATATCTGTACAGTTTC
1 TGTG-ATTTA-AT-TGT-CAGTTTC
*
55474325 TGTGATTTAATTGTCTGTTTC
1 TGTGATTTAATTGTCAGTTTC
55474346 TGTG
1 TGTG
55474350 CTTAATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 2 0.08
24 5 0.21
25 4 0.17
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.52
Consensus pattern (21 bp):
TGTGATTTAATTGTCAGTTTC
Found at i:55476242 original size:40 final size:40
Alignment explanation
Indices: 55476187--55476368 Score: 296
Period size: 40 Copynumber: 4.6 Consensus size: 40
55476177 TATTTGAATG
*
55476187 ATATCCGGGCTAAGTCCCGAAGGCATTTGTACTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
55476227 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
55476267 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
55476307 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
55476347 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
55476369 TACTTGGGTT
Statistics
Matches: 135, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.10
40 119 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:55478143 original size:27 final size:28
Alignment explanation
Indices: 55478113--55478169 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
55478103 ATTTTTGATG
55478113 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
55478140 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
55478169 A
1 A
55478170 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:55479210 original size:12 final size:13
Alignment explanation
Indices: 55479193--55479224 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55479183 GCAAATGTTA
55479193 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
55479205 AGTTTTGATGCAT
1 AGTTTTGATGCAT
55479218 -GTTTTGA
1 AGTTTTGA
55479225 AATGTGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:55481469 original size:40 final size:39
Alignment explanation
Indices: 55481310--55481471 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
55481300 TGTGTATGAA
*
55481310 TGTGCGAATTGTGATA-CCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
55481348 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
55481387 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
55481426 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
55481466 TGTGCG
1 TGTGCG
55481472 GGTTACCATA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 15 0.13
39 81 0.72
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:55481487 original size:40 final size:39
Alignment explanation
Indices: 55481310--55481502 Score: 244
Period size: 39 Copynumber: 4.9 Consensus size: 39
55481300 TGTGTATGAA
* *
55481310 TGTGCGAATTGTGATA-CCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
55481348 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
55481387 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
55481426 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
55481466 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
55481503 GTTTGAACGA
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
38 15 0.11
39 81 0.59
40 41 0.30
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.23
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:55489273 original size:39 final size:39
Alignment explanation
Indices: 55489219--55489381 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
55489209 TGTGTATGAA
*
55489219 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
55489258 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
55489297 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
55489336 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
55489376 TGTGCG
1 TGTGCG
55489382 GGTTACCATA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Done.