Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 14 of 226
Found at i:4979131 original size:30 final size:30
Alignment explanation
Indices: 4979097--4979158 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
4979087 CTTAACAAGT
4979097 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
4979127 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
4979157 AA
1 AA
4979159 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:4981052 original size:18 final size:19
Alignment explanation
Indices: 4981022--4981058 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4981012 TTTGCAAATC
4981022 AAATATTTATTATAAATTT
1 AAATATTTATTATAAATTT
*
4981041 AAATATTT-TTATTAATTT
1 AAATATTTATTATAAATTT
4981059 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATTTATTATAAATTT
Found at i:4981060 original size:19 final size:18
Alignment explanation
Indices: 4981022--4981094 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
4981012 TTTGCAAATC
*
4981022 AAATATTTATTATAAATTT
1 AAATATTT-TTATAATTTT
4981041 AAATATTTTTATTAATTTT
1 AAATATTTTTA-TAATTTT
*
4981060 AAAATAATTTTAATAATTTT
1 -AAAT-ATTTTTATAATTTT
* *
4981080 ATA-ATTATTATAATT
1 AAATATTTTTATAATT
4981095 ATTTGAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.22
18 3 0.07
19 16 0.35
20 11 0.24
21 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTTTTATAATTTT
Found at i:4981070 original size:20 final size:20
Alignment explanation
Indices: 4981041--4981103 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
4981031 TTATAAATTT
* *
4981041 AAATATTTTTATTAATTTTA
1 AAATAATTTTAATAATTTTA
4981061 AAATAATTTTAATAATTTTA
1 AAATAATTTTAATAATTTTA
* * * * *
4981081 TAATTATTATAATTATTTGA
1 AAATAATTTTAATAATTTTA
4981101 AAA
1 AAA
4981104 ACTACATTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATAATTTTAATAATTTTA
Found at i:4981074 original size:9 final size:9
Alignment explanation
Indices: 4981036--4981094 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
4981026 ATTTATTATA
*
4981036 AATTTAAAT
1 AATTTTAAT
* *
4981045 ATTTTTATT
1 AATTTTAAT
4981054 AATTTTAAAAT
1 AATTTT--AAT
4981065 AATTTTAAT
1 AATTTTAAT
4981074 AATTTT-AT
1 AATTTTAAT
4981082 AATTATT-AT
1 AATT-TTAAT
4981091 AATT
1 AATT
4981095 ATTTGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 6 0.14
9 28 0.67
11 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTAAT
Found at i:4981098 original size:29 final size:29
Alignment explanation
Indices: 4981028--4981098 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
4981018 AATCAAATAT
*
4981028 TTATTATAA-ATTTAAATATTTTTATTAA
1 TTATTATAATATTTAAATAATTTTATTAA
* *
4981056 TT-TTAAAATAATTTTAATAATTTTA-TAA
1 TTATTATAAT-ATTTAAATAATTTTATTAA
4981084 TTATTATAATTATTT
1 TTATTATAA-TATTT
4981099 GAAAAACTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 5 0.14
28 7 0.20
29 22 0.63
30 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTATTATAATATTTAAATAATTTTATTAA
Found at i:4982571 original size:37 final size:39
Alignment explanation
Indices: 4982529--4982607 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
4982519 TTAATATTAT
4982529 ATCAAT-AAAAAAA-GTTACACCCAACATTCCACTAATG
1 ATCAATAAAAAAAATGTTACACCCAACATTCCACTAATG
*
4982566 ATCAATAAAAAAAATGTTACACTCAACATTCCACTAATG
1 ATCAATAAAAAAAATGTTACACCCAACATTCCACTAATG
4982605 ATC
1 ATC
4982608 TAATGGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 6 0.15
38 7 0.18
39 26 0.67
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.24
Consensus pattern (39 bp):
ATCAATAAAAAAAATGTTACACCCAACATTCCACTAATG
Found at i:4983160 original size:21 final size:22
Alignment explanation
Indices: 4983136--4983186 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
4983126 ATCTTTCCAT
*
4983136 TTTTGTTTTC-AGGTATATTTC
1 TTTTGTTTTCGAGGTAGATTTC
* *
4983157 TTTTGTTTCCGAGTTAGATTTC
1 TTTTGTTTTCGAGGTAGATTTC
4983179 -TTTGTTTT
1 TTTTGTTTT
4983187 GTTGTTGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (22 bp):
TTTTGTTTTCGAGGTAGATTTC
Found at i:4984577 original size:69 final size:68
Alignment explanation
Indices: 4984453--4984585 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 68
4984443 CAATGGGTTC
*
4984453 GATAAAAGCTCTGATAGTCAAGTGAAAAAGAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGT
1 GATAAAAGCTCTGATAGTCAAGTGAAAAAGAGATCAAATGAAGATGCCCCAAAAGG-GATAAGGT
4984518 GTTT
65 GTTT
* * * ** *
4984522 GATAAAAGCTTTGAT-GATCAGGTGAAAAAGAGATCAAATGAAGTTTTCCCTAAAGGGATAAGGT
1 GATAAAAGCTCTGATAG-TCAAGTGAAAAAGAGATCAAATGAAGATGCCCCAAAAGGGATAAGGT
4984586 TGACAAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
68 9 0.16
69 47 0.84
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (68 bp):
GATAAAAGCTCTGATAGTCAAGTGAAAAAGAGATCAAATGAAGATGCCCCAAAAGGGATAAGGTG
TTT
Found at i:4984656 original size:158 final size:159
Alignment explanation
Indices: 4984255--4984812 Score: 926
Period size: 159 Copynumber: 3.5 Consensus size: 159
4984245 CAGGACTTAC
* * * * * *
4984255 GGGGATAAGGTTGATAAAAATGATGACAA--GGTGTCGGATAAACGCTCAGCT-GATCAGGTGAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGT-TC-GATAAAAGCTCTGATAG-TCAAGTG--
* *
4984317 AAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGTTGATC
61 AAA-AAGAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATC
*
4984382 AGGTGAAAAAGAGCTCAAATGAAGTTTTCCCTAAA
125 AGGTGAAAAAGAGATCAAATGAAGTTTTCCCTAAA
4984417 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
4984482 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
4984547 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
4984576 -GGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
4984640 GAGTTCAAATGAAGATGCCCCAAAAGAAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
4984705 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
*
4984734 GGGGATAAGGTTGACAAAAATAATGACAATGTGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
4984799 GAGCTCAAATGAAG
66 GAGTTCAAATGAAG
4984813 TTTTCCCATC
Statistics
Matches: 380, Mismatches: 12, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
158 157 0.41
159 169 0.44
160 3 0.01
162 45 0.12
163 3 0.01
164 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (159 bp):
GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
AAAAGAGATCAAATGAAGTTTTCCCTAAA
Found at i:4989932 original size:16 final size:15
Alignment explanation
Indices: 4989900--4989975 Score: 50
Period size: 15 Copynumber: 5.0 Consensus size: 15
4989890 AATTTTATTG
4989900 TTTTTTTATAATAAA
1 TTTTTTTATAATAAA
**
4989915 TTTTTTTATTGTATAA
1 TTTTTTTATAATA-AA
* *
4989931 TTGTTTT-TCATAAA
1 TTTTTTTATAATAAA
4989945 TTTGTTTGT-TAATATAA
1 TTT-TTT-TATAATA-AA
*
4989962 -ATTTTTATAATAAA
1 TTTTTTTATAATAAA
4989976 AATATTACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
15 25 0.52
16 14 0.29
17 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTTTTTATAATAAA
Found at i:4995038 original size:51 final size:51
Alignment explanation
Indices: 4994982--4995305 Score: 242
Period size: 51 Copynumber: 6.4 Consensus size: 51
4994972 TGTGGCATGG
* * * *
4994982 ACTGTGTGTAGGCCACTATATGAA-AGTGAAAG-TGTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAG-AAGCT-TTGGTCACGTGTGTAGT
* * *
4995033 ACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
** * * * * * *
4995084 ACTGTGTGAAGGCTACTACGTGAATCGATAA-ATAATGGTCACATGTGTAAT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCT-TTGGTCACGTGTGTAGT
** * *
4995135 ACTAAGTGAAGGCTACAATATGTACCGAGAAGCTTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
* * ** ** * * * *
4995186 ACTTTGTGAAGGTTACTACGTGAATTGATAA-ATGATGGTCACATGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCT-TTGGTCACGTGTGTAGT
** * * * * * *
4995237 ACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGTCACATATGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
*
4995288 ACTATGTGAAGGCTACTA
1 ACTGTGTGAAGGCTACTA
4995306 CGTGAATCGT
Statistics
Matches: 213, Mismatches: 54, Indels: 12
0.76 0.19 0.04
Matches are distributed among these distances:
50 2 0.01
51 206 0.97
52 5 0.02
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (51 bp):
ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
Found at i:4995159 original size:102 final size:102
Alignment explanation
Indices: 4995017--4995318 Score: 462
Period size: 102 Copynumber: 3.0 Consensus size: 102
4995007 GTGAAAGTGT
* **
4995017 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
*
4995082 GTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* *
4995119 TGGTCACATGTGTAATACTAAGTGAAGGCTACAATATGTACCGAGAAGCTTTGGTCACGTGTGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
* * * *
4995184 GTACTTTGTGAAGGTTACTACGTGAATTGATAAATGA
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * *
4995221 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGTCACATATGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
4995286 GTACTATGTGAAGGCTACTACGTGAATCG-TAAA
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAA
4995319 ACTTGATCAC
Statistics
Matches: 181, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
101 4 0.02
102 177 0.98
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
Found at i:4995374 original size:16 final size:16
Alignment explanation
Indices: 4995341--4995374 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4995331 GTATAGTGTT
* *
4995341 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
4995357 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
4995373 AA
1 AA
4995375 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:4998201 original size:21 final size:21
Alignment explanation
Indices: 4998175--4998215 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4998165 AGACGAGCAA
* *
4998175 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
4998196 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
4998216 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5000154 original size:16 final size:16
Alignment explanation
Indices: 5000121--5000154 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5000111 GGAGATTGTT
* *
5000121 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5000137 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5000153 AA
1 AA
5000155 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5002776 original size:18 final size:18
Alignment explanation
Indices: 5002755--5002797 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5002745 TTGAAATTTT
5002755 TAAAAATAT-AAAAATATA
1 TAAAAATATAAAAAATA-A
* *
5002773 TAAAATTTTAAAAAATAA
1 TAAAAATATAAAAAATAA
5002791 TAAAAAT
1 TAAAAAT
5002798 TGTTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATATAAAAAATAA
Found at i:5005835 original size:35 final size:35
Alignment explanation
Indices: 5005789--5005860 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
5005779 GTTATCTATA
5005789 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
5005824 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
5005859 TG
1 TG
5005861 ACATAATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
Found at i:5013884 original size:43 final size:43
Alignment explanation
Indices: 5013848--5013994 Score: 240
Period size: 43 Copynumber: 3.4 Consensus size: 43
5013838 TCCCGGACAG
5013848 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
5013891 GATCTTACACGAAAACACAGGTTGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
5013934 AGTCTTACACGAAAACACAAGTCGATGCCAACATCCTAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
5013977 GGTCTTACACGAAAACAC
1 GGTCTTACACGAAAACAC
5013995 TTATCAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.18
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
Found at i:5020413 original size:2 final size:2
Alignment explanation
Indices: 5020408--5020474 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
5020398 AATATATAAT
5020408 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5020450 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5020475 AACCCTAAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5030586 original size:16 final size:16
Alignment explanation
Indices: 5030565--5030633 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
5030555 GATTAGCTAT
*
5030565 TACACCACTAATCCAA
1 TACACCTCTAATCCAA
5030581 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
5030598 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5030614 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5030630 TACA
1 TACA
5030634 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5030609 original size:33 final size:32
Alignment explanation
Indices: 5030565--5030633 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
5030555 GATTAGCTAT
5030565 TACACCACTAATCCAATACACCTCTAATCCCAA
1 TACACCACTAATCCAATACACCTCTAAT-CCAA
*
5030598 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCACTAATCCAATACACCTCTAATCCAA
5030630 TACA
1 TACA
5030634 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (32 bp):
TACACCACTAATCCAATACACCTCTAATCCAA
Found at i:5045085 original size:27 final size:27
Alignment explanation
Indices: 5045055--5045109 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5045045 ATGATGAAAT
5045055 TGATACATGGAACAAAACATTACTTGA
1 TGATACATGGAACAAAACATTACTTGA
* *
5045082 TGATACATGGAACACAACATTAGTTGA
1 TGATACATGGAACAAAACATTACTTGA
5045109 T
1 T
5045110 CCATGATGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (27 bp):
TGATACATGGAACAAAACATTACTTGA
Found at i:5046423 original size:35 final size:35
Alignment explanation
Indices: 5046377--5046452 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
5046367 TATTTTATAC
* * *
5046377 TTAATTTTTATGGTT-CTTTATGATTATCCTGCCCA
1 TTAATTCTTAT-GTTGCATTATGATTACCCTGCCCA
5046412 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
1 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
*
5046447 TCAATT
1 TTAATT
5046453 TTTTTCATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (35 bp):
TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
Found at i:5056940 original size:2 final size:2
Alignment explanation
Indices: 5056933--5056967 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5056923 CACTAAACAT
* *
5056933 AC AC AC AC AT AC AC AC AC AT AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5056968 TATATGTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.43, G:0.00, T:0.06
Consensus pattern (2 bp):
AC
Found at i:5056944 original size:10 final size:10
Alignment explanation
Indices: 5056929--5056967 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
5056919 TGAGCACTAA
5056929 ACATACACAC
1 ACATACACAC
5056939 ACATACACAC
1 ACATACACAC
5056949 ACATACACAC
1 ACATACACAC
*
5056959 ACACACACA
1 ACATACACA
5056968 TATATGTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (10 bp):
ACATACACAC
Found at i:5062999 original size:27 final size:23
Alignment explanation
Indices: 5062946--5062993 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5062936 AACATAGCAC
5062946 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
5062969 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
5062992 TA
1 TA
5062994 GGTAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (23 bp):
TAAATAAAAGCAAGAAGGCATCT
Found at i:5066335 original size:19 final size:20
Alignment explanation
Indices: 5066305--5066346 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
5066295 ATATTATATA
5066305 CATAAGTAATTGTATTTATC
1 CATAAGTAATTGTATTTATC
5066325 CATAA-TAATTGTATTTATC
1 CATAAGTAATTGTATTTATC
5066344 CAT
1 CAT
5066347 GTATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (20 bp):
CATAAGTAATTGTATTTATC
Found at i:5068583 original size:11 final size:11
Alignment explanation
Indices: 5068567--5068592 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5068557 TAGAAGAGAC
5068567 GAAACAGGGGA
1 GAAACAGGGGA
5068578 GAAACAGGGGA
1 GAAACAGGGGA
5068589 GAAA
1 GAAA
5068593 GAAGAAAAAG
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:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:5069275 original size:18 final size:18
Alignment explanation
Indices: 5069252--5069300 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
5069242 ATGTGAGGTA
*
5069252 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
5069270 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
5069288 ATTATTATTATTA
1 AGTATTATTATTA
5069301 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:5069280 original size:3 final size:3
Alignment explanation
Indices: 5069254--5069301 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
5069244 GTGAGGTAAG
* * * *
5069254 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5069302 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:5069301 original size:12 final size:12
Alignment explanation
Indices: 5069254--5069301 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
5069244 GTGAGGTAAG
* *
5069254 TATTAATATTAG
1 TATTAGTATTAT
5069266 TATTAGTATTAT
1 TATTAGTATTAT
5069278 TATTAGTATTAT
1 TATTAGTATTAT
*
5069290 TATTATTATTAT
1 TATTAGTATTAT
5069302 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:5069496 original size:24 final size:24
Alignment explanation
Indices: 5069442--5069513 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
5069432 TGTGTGAAGT
*
5069442 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
5069465 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
5069490 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
5069514 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:5069716 original size:37 final size:39
Alignment explanation
Indices: 5069657--5069752 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5069647 CGGATAGATT
* * * *
5069657 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
5069694 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
5069733 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5069753 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:5071562 original size:78 final size:78
Alignment explanation
Indices: 5071477--5071632 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
5071467 TGATGATAGT
*
5071477 AAGCCCATTCTGATTTTCGGTTGATTCTCTGTTACCAACCCTGTTCTGATGACTAAGGCAATGCT
1 AAGCCCATTCTGATTTTCGGTTGATTCTCTGCTACCAACCCTGTTCTGATGACTAAGGCAATGCT
5071542 CAATATCTCAACG
66 CAATATCTCAACG
5071555 AAGCCCATTCTGATTTTCGGTTGATTCTCTGCTACCAACCCTGTTCTGATGACTAAGGCAATGCT
1 AAGCCCATTCTGATTTTCGGTTGATTCTCTGCTACCAACCCTGTTCTGATGACTAAGGCAATGCT
5071620 CAATATCTCAACG
66 CAATATCTCAACG
5071633 GACTCCATCG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (78 bp):
AAGCCCATTCTGATTTTCGGTTGATTCTCTGCTACCAACCCTGTTCTGATGACTAAGGCAATGCT
CAATATCTCAACG
Found at i:5072651 original size:12 final size:13
Alignment explanation
Indices: 5072624--5072649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5072614 TTTTAACTTC
5072624 ATCGAAAAAAAAA
1 ATCGAAAAAAAAA
5072637 ATCGAAAAAAAAA
1 ATCGAAAAAAAAA
5072650 TCTAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
ATCGAAAAAAAAA
Found at i:5078450 original size:3 final size:3
Alignment explanation
Indices: 5078442--5078474 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5078432 TTTTCTCCAT
5078442 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5078475 CTTTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:5080036 original size:64 final size:65
Alignment explanation
Indices: 5079962--5080096 Score: 236
Period size: 64 Copynumber: 2.1 Consensus size: 65
5079952 AATTAAGAGT
* *
5079962 TAATTTTTCTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTT-TTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
5080026 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
*
5080091 TTATTT
1 TAATTT
5080097 ATTTTATTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 44 0.66
65 23 0.34
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (65 bp):
TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
Found at i:5082810 original size:30 final size:30
Alignment explanation
Indices: 5082739--5082810 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5082729 CCACCCCAAG
* * *
5082739 TTTTTGAAAATTTTAGTTATACCCTTAAAA
1 TTTTTGAAAATTTTAATTAGACCCCTAAAA
* *
5082769 TTTTCTG-AAATTTTAATTAGGCCCCTCAAA
1 TTTT-TGAAAATTTTAATTAGACCCCTAAAA
5082799 TTTTTGAAAATT
1 TTTTTGAAAATT
5082811 ATTATTAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.06
30 31 0.89
31 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTTTGAAAATTTTAATTAGACCCCTAAAA
Found at i:5090648 original size:185 final size:185
Alignment explanation
Indices: 5090336--5090696 Score: 551
Period size: 185 Copynumber: 2.0 Consensus size: 185
5090326 ACTAATGATC
* *
5090336 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTGCCTTTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * *
5090401 TTGTTCCAACAATATTCACCAATATAGACACTTACTGGCTCTTCTTCATAGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* * *
5090466 AAACATGATCATTCATTCATTATTATTATCATCATTAATTTTTTTAATGGCATTT
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
* *
5090521 ATAACATTCTAATGATTCAAGGCCATTGCATGCATATATTTGATAAGCTCTCGTTGTTACCTCTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * * * ** *
5090586 TCGTTTCAACGATATTCACCAAAATAGACACTTGCTGTCTCATCTTTGTTGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* *
5090651 AAACATGATCATTTATTCTTTAGTATCATCATCATCAATTTTTTTA
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTA
5090697 CTGATGTATG
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
185 157 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (185 bp):
ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
Found at i:5093993 original size:43 final size:43
Alignment explanation
Indices: 5093945--5094031 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5093935 GACACACAGA
5093945 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
5093988 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
5094031 G
1 G
5094032 AACCAACCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (43 bp):
GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
Found at i:5115873 original size:91 final size:88
Alignment explanation
Indices: 5115777--5115962 Score: 205
Period size: 88 Copynumber: 2.1 Consensus size: 88
5115767 CATTTGAGTG
* * * * * *
5115777 CTTGAACTTTCACAATGTATTAAAAAGACCCTT-AAATTTTTTTTAAAAAAGTAATTAACACTCT
1 CTTGAACTTTCAAAATATATCAAAAAG-CCCTTCAAA-CTTTTTCAAAAAAGCAATT-ACAC-CT
5115841 GCTTTTATTTTTGCACTAAATTAGG-TA
62 GCTTTTATTTTTGCACTAAATT-GGATA
* * * *
5115868 CTTGAACTTTTAAAATATATCAAAAAGGCCTTCAAACTTTTTCAAAAAAGCAATTACTCCTTCTT
1 CTTGAACTTTCAAAATATATCAAAAAGCCCTTCAAACTTTTTCAAAAAAGCAATTACACCTGCTT
* *
5115933 TTTTTTTTGCACTCAATTGGATA
66 TTATTTTTGCACTAAATTGGATA
5115956 CTTGAAC
1 CTTGAAC
5115963 CACATCTAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
87 2 0.02
88 30 0.37
89 3 0.04
90 20 0.25
91 26 0.32
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (88 bp):
CTTGAACTTTCAAAATATATCAAAAAGCCCTTCAAACTTTTTCAAAAAAGCAATTACACCTGCTT
TTATTTTTGCACTAAATTGGATA
Found at i:5116207 original size:19 final size:20
Alignment explanation
Indices: 5116184--5116235 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
5116174 TTTATAACGT
5116184 CGTAAAAAAATTATGAAAA-G
1 CGTAAAAAAATTAT-AAAATG
*
5116204 -GTAAAGAAA-TATAAAATG
1 CGTAAAAAAATTATAAAATG
5116222 CGTAAAAAAATTAT
1 CGTAAAAAAATTAT
5116236 CGTACTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 16 0.59
20 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (20 bp):
CGTAAAAAAATTATAAAATG
Found at i:5116469 original size:20 final size:21
Alignment explanation
Indices: 5116446--5116485 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5116436 TATAAAAAAA
*
5116446 TTAC-AGTTTTTTATATTTTT
1 TTACGAGTTTTTTAAATTTTT
*
5116466 TTACGATTTTTTTAAATTTT
1 TTACGAGTTTTTTAAATTTT
5116486 AATAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTACGAGTTTTTTAAATTTTT
Found at i:5146784 original size:26 final size:27
Alignment explanation
Indices: 5146746--5146798 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
5146736 CTCCCAACTC
5146746 TTCTCTTCAA-TTTTTTTACTTTCCCT
1 TTCTCTTCAATTTTTTTTACTTTCCCT
*
5146772 TTCTCTTCTATTTTTTTTTACTTTCCC
1 TTCTCTTC-AATTTTTTTTACTTTCCC
5146799 CCTCCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
28 15 0.62
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.64
Consensus pattern (27 bp):
TTCTCTTCAATTTTTTTTACTTTCCCT
Found at i:5147320 original size:11 final size:12
Alignment explanation
Indices: 5147288--5147324 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
5147278 AAATAATTTA
5147288 ATAAATAAA-A-
1 ATAAATAAACAT
5147298 ATAAATAAACAT
1 ATAAATAAACAT
5147310 ATAAA-AAACAT
1 ATAAATAAACAT
5147321 ATAA
1 ATAA
5147325 TTTTCGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (12 bp):
ATAAATAAACAT
Found at i:5147579 original size:19 final size:20
Alignment explanation
Indices: 5147543--5147585 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5147533 CACTCGATTC
* *
5147543 AATTAAAAAAATGTAAATCA
1 AATTAAAAAAATGAAAATAA
*
5147563 AATTAAAATAAT-AAAATAA
1 AATTAAAAAAATGAAAATAA
5147582 AATT
1 AATT
5147586 CTCATTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
AATTAAAAAAATGAAAATAA
Found at i:5151535 original size:25 final size:25
Alignment explanation
Indices: 5151507--5151555 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5151497 AATATGTAAA
5151507 GTTAATTTAAAATTTTCATCGACCG
1 GTTAATTTAAAATTTTCATCGACCG
*
5151532 GTTAATTTAAAATTTTCATTGACC
1 GTTAATTTAAAATTTTCATCGACC
5151556 CAGTTGGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (25 bp):
GTTAATTTAAAATTTTCATCGACCG
Found at i:5160349 original size:6 final size:6
Alignment explanation
Indices: 5160340--5160366 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5160330 AACTCTTGCT
5160340 CTCTTG CTCTTG CTCTTG CTCTTG CTC
1 CTCTTG CTCTTG CTCTTG CTCTTG CTC
5160367 CAACGTCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.15, T:0.48
Consensus pattern (6 bp):
CTCTTG
Found at i:5166950 original size:63 final size:63
Alignment explanation
Indices: 5166851--5166976 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
5166841 TGGCCAAAAG
5166851 ACTTCAAAGACAAAGCGTAATGAAGGCCCTCGCCCTCACTGTTCCACCACAATCAAGAAGTAA
1 ACTTCAAAGACAAAGCGTAATGAAGGCCCTCGCCCTCACTGTTCCACCACAATCAAGAAGTAA
5166914 ACTTCAAAGACAAAGCGTAATGAAGGCCCTCGCCCTCACTGTTCCACCACAATCAAGAAGTAA
1 ACTTCAAAGACAAAGCGTAATGAAGGCCCTCGCCCTCACTGTTCCACCACAATCAAGAAGTAA
5166977 GTACAAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (63 bp):
ACTTCAAAGACAAAGCGTAATGAAGGCCCTCGCCCTCACTGTTCCACCACAATCAAGAAGTAA
Found at i:5169348 original size:3 final size:3
Alignment explanation
Indices: 5169340--5169380 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5169330 AATGGAAATA
5169340 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
5169381 ATATATATAT
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:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:5170316 original size:16 final size:16
Alignment explanation
Indices: 5170292--5170329 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5170282 TTTGGTTCGT
* *
5170292 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
5170308 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
5170324 TGTAAT
1 TGTAAT
5170330 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:5170374 original size:45 final size:44
Alignment explanation
Indices: 5170308--5170402 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5170298 GGATTAGAGG
* *
5170308 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
5170353 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
5170397 TGTAAT
1 TGTAAT
5170403 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:5170572 original size:25 final size:25
Alignment explanation
Indices: 5170540--5170594 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
5170530 TAATTTAATC
5170540 ATAT-TTAAACATAATTATT-ATT-AA
1 ATATATTAAACAT-ATT-TTAATTAAA
*
5170564 ATATATTAAATATATTTTAATTAAA
1 ATATATTAAACATATTTTAATTAAA
5170589 ATATAT
1 ATATAT
5170595 AATTTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 10 0.37
25 15 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATATTAAACATATTTTAATTAAA
Found at i:5170594 original size:18 final size:17
Alignment explanation
Indices: 5170573--5170607 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5170563 AATATATTAA
*
5170573 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5170591 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5170608 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5170666 original size:61 final size:59
Alignment explanation
Indices: 5170601--5170788 Score: 147
Period size: 61 Copynumber: 3.1 Consensus size: 59
5170591 ATATAATTTA
*
5170601 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
1 ATAAAATTCTTAATAATAAATATTCTTATATGAATTT-CT-AAATAATAATATATGATACT
* * ** *
5170662 ATAAAAGATAAT-TTGAAATGATTAATATT-AAATAT--ATTT-TAAATAA-AATATATGAT-TT
1 AT-AAA-AT--TCTT--AATAATAAATATTCTTATATGAATTTCTAAATAATAATATATGATACT
* * *
5170720 AATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAATAATAAATATTCTTATATGAA-TTTCT-AAATAATAATATATGATACT
5170782 ATAAAAT
1 ATAAAAT
5170789 ATAATTTAAC
Statistics
Matches: 98, Mismatches: 13, Indels: 32
0.69 0.09 0.22
Matches are distributed among these distances:
54 10 0.10
55 5 0.05
56 2 0.02
57 3 0.03
58 7 0.07
59 13 0.13
60 11 0.11
61 19 0.19
62 4 0.04
63 6 0.06
64 2 0.02
65 5 0.05
66 11 0.11
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTTAATAATAAATATTCTTATATGAATTTCTAAATAATAATATATGATACT
Found at i:5170714 original size:18 final size:17
Alignment explanation
Indices: 5170691--5170727 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5170681 GATTAATATT
5170691 AAATATAT--TTTAAATA
1 AAATATATGATTT-AATA
5170707 AAATATATGATTTAATA
1 AAATATATGATTTAATA
5170724 AAAT
1 AAAT
5170728 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 8 0.42
18 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:5170781 original size:120 final size:120
Alignment explanation
Indices: 5170566--5170840 Score: 401
Period size: 120 Copynumber: 2.3 Consensus size: 120
5170556 ATTATTAAAT
* *
5170566 ATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATA
1 ATATTAAATATATTTTAAATAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
* * *
5170631 TGAATTTACTCAAATAATAATATATGATACTATAAAAGATAATTTGAA-ATGATTA
66 TGAATTTACTAAAATAATAATATATAATACTATAAAAGATAATTT-AACATAATTA
* *
5170686 ATATTAAATATATTTTAAATAAAATATATGATTTAATAAAATTCTTAATATTAAATATTCTTATA
1 ATATTAAATATATTTTAAATAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
* * *
5170751 TGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTTAACATAATTA
66 TGAATTTACTAAAATAATAATATATAATACTATAAAAGATAATTTAACATAATTA
* **
5170806 TTATTAAATATAAGTT-AATAAAAATATATAATTTA
1 ATATTAAATATATTTTAAAT-AAAATATATAATTTA
5170841 TCATCATACT
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
119 5 0.04
120 134 0.96
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
ATATTAAATATATTTTAAATAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
TGAATTTACTAAAATAATAATATATAATACTATAAAAGATAATTTAACATAATTA
Found at i:5174896 original size:28 final size:28
Alignment explanation
Indices: 5174865--5174961 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
5174855 AAAAATAAAA
*
5174865 ATTTACTAAAATATTATAACTTTTTTTT
1 ATTTACCAAAATATTATAACTTTTTTTT
* *
5174893 ATTTACCAAAATATTACAATTTTTTTTT
1 ATTTACCAAAATATTATAACTTTTTTTT
5174921 ATTTACCAAAATA-TATAAAC-TTTTTTT
1 ATTTACCAAAATATTAT-AACTTTTTTTT
5174948 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5174962 ATCAAAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 22 0.35
28 40 0.65
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTACCAAAATATTATAACTTTTTTTT
Found at i:5175040 original size:27 final size:26
Alignment explanation
Indices: 5174986--5175070 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
5174976 TTGACACCAA
*
5174986 CCAATTAAATTGGCGGCACCAAAT-GTG
1 CCAAATAAATTGGCGGCACC--ATGGTG
*
5175013 CCAAATAAATTGGTGGCACCATTGGTG
1 CCAAATAAATTGGCGGCACCA-TGGTG
* *
5175040 CCAAAGT-CATTAGCGGCACCATGGTG
1 CCAAA-TAAATTGGCGGCACCATGGTG
5175066 CCAAA
1 CCAAA
5175071 AGAAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.02
26 11 0.22
27 37 0.74
28 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (26 bp):
CCAAATAAATTGGCGGCACCATGGTG
Found at i:5175171 original size:19 final size:19
Alignment explanation
Indices: 5175144--5175213 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
5175134 TCAACTCATT
*
5175144 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
5175163 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
5175181 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
5175200 TTTTAATTTAATAA
1 TTTTAATTTAATAA
5175214 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:5175194 original size:37 final size:37
Alignment explanation
Indices: 5175149--5175219 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
5175139 TCATTTTTTT
5175149 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
5175186 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
5175220 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:5175565 original size:20 final size:19
Alignment explanation
Indices: 5175526--5175566 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5175516 ACTTAATAGT
* *
5175526 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
5175545 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
5175565 TT
1 TT
5175567 GAAAGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:5175820 original size:37 final size:37
Alignment explanation
Indices: 5175773--5175843 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5175763 AGTATTACTT
*
5175773 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATACTTTATTAAATTAAAATAGAGTTATTAAATGAG
5175810 AATACTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATACTTTATTAAATTAAAATAGAGTTATTAAAT
5175844 AAAAAAATGA
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:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (37 bp):
AATACTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:5175831 original size:18 final size:18
Alignment explanation
Indices: 5175773--5175847 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
5175763 AGTATTACTT
*
5175773 AATAGTTTATTAAATTAA
1 AATAATTTATTAAATTAA
* * *
5175791 AATAGAGTTATTAAATGAG
1 AATA-ATTTATTAAATTAA
*
5175810 AATACTTTATTAAATTAA
1 AATAATTTATTAAATTAA
*
5175828 AATAGAGTTATTAAA-TAA
1 AATA-ATTTATTAAATTAA
5175846 AA
1 AA
5175848 AAATGAGTTG
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:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (18 bp):
AATAATTTATTAAATTAA
Found at i:5175848 original size:19 final size:19
Alignment explanation
Indices: 5175779--5175847 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
5175769 ACTTAATAGT
5175779 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * **
5175798 TTATTAAATGAGAATA-CT
1 TTATTAAATTAAAATAGAG
5175816 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
5175835 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
5175848 AAATGAGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.46
19 22 0.54
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:5175855 original size:20 final size:19
Alignment explanation
Indices: 5175779--5175856 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
5175769 ACTTAATAGT
* *
5175779 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
* * * **
5175798 TTATTAAATGAGAATA-CT
1 TTATTAAATAAAAAAAGAG
* *
5175816 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
5175835 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
5175855 TT
1 TT
5175857 GAAGGGGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
18 14 0.30
19 28 0.60
20 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:5175957 original size:26 final size:27
Alignment explanation
Indices: 5175921--5175971 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5175911 ATTTTTTTTC
*
5175921 CTTTGGCACC-ATGGTGCCGCCAATGA
1 CTTTGGCACCAATGGTGCCACCAATGA
5175947 CTTTGGCACCAATGGTGCCACCAAT
1 CTTTGGCACCAATGGTGCCACCAAT
5175972 TTATTTGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (27 bp):
CTTTGGCACCAATGGTGCCACCAATGA
Found at i:5176467 original size:27 final size:28
Alignment explanation
Indices: 5176413--5176482 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
5176403 TGTTTTTTAT
*
5176413 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAAT-AAAAAAAACTTGTA
*
5176442 ATATTTTGATAAAT-AAAAAAACTTGTA
1 ATATTTTGGTAAATAAAAAAAACTTGTA
5176469 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
5176483 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 25 0.66
29 13 0.34
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAACTTGTA
Found at i:5187328 original size:23 final size:23
Alignment explanation
Indices: 5187301--5187346 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5187291 TTTTTGTTAA
5187301 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
5187324 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
5187347 AATTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (23 bp):
GCCTGTATGTTCATTCATTTTGC
Found at i:5191623 original size:23 final size:25
Alignment explanation
Indices: 5191597--5191642 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5191587 TCATACATTA
5191597 TAAAAG-AAAATA-CAAAAAAAAAG
1 TAAAAGAAAAATATCAAAAAAAAAG
*
5191620 TAAAGGAAAAATATCAAAAAAAA
1 TAAAAGAAAAATATCAAAAAAAA
5191643 TGAAAATCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (25 bp):
TAAAAGAAAAATATCAAAAAAAAAG
Found at i:5205837 original size:11 final size:12
Alignment explanation
Indices: 5205809--5205839 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5205799 AAATTACTTT
5205809 TAAAAAATATTA
1 TAAAAAATATTA
*
5205821 TAAAAAATATTG
1 TAAAAAATATTA
5205833 TAAAAAA
1 TAAAAAA
5205840 GTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
TAAAAAATATTA
Found at i:5208150 original size:13 final size:13
Alignment explanation
Indices: 5208132--5208156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5208122 TTTAATAAAA
5208132 TTTTATATTTAAT
1 TTTTATATTTAAT
5208145 TTTTATATTTAA
1 TTTTATATTTAA
5208157 AAATTCTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATATTTAAT
Found at i:5223707 original size:46 final size:46
Alignment explanation
Indices: 5223635--5223790 Score: 264
Period size: 46 Copynumber: 3.5 Consensus size: 46
5223625 TAATCAGTGA
*
5223635 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
5223681 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5223727 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5223772 C-AGAGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
5223791 ATCATACGTA
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 19 0.18
46 71 0.66
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:5224384 original size:36 final size:36
Alignment explanation
Indices: 5224344--5224416 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5224334 TGGTAATGCC
5224344 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
5224380 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
5224416 T
1 T
5224417 GTTACACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.29
Consensus pattern (36 bp):
TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
Found at i:5224479 original size:11 final size:10
Alignment explanation
Indices: 5224436--5224483 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
5224426 ATAATAATGT
5224436 TATTAAATTA
1 TATTAAATTA
*
5224446 TATTTAA-TA
1 TATTAAATTA
5224455 -A-T-AATTA
1 TATTAAATTA
5224462 TATTAAATTA
1 TATTAAATTA
5224472 TGATTAAATTA
1 T-ATTAAATTA
5224483 T
1 T
5224484 TTATTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
6 2 0.06
7 3 0.09
8 2 0.06
9 3 0.09
10 12 0.38
11 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TATTAAATTA
Found at i:5226727 original size:4 final size:4
Alignment explanation
Indices: 5226718--5226744 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5226708 CGACCACCCT
5226718 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
5226745 TGCTTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:5227042 original size:24 final size:23
Alignment explanation
Indices: 5227017--5227092 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
5227007 TTCTCTTAAT
*
5227017 TTTTTTAAAGTTATAAAAATAAA
1 TTTTTTAAAATTATAAAAATAAA
* *
5227040 TTTTTAAAAATATTTAAAAATAAA
1 TTTTTTAAAAT-TATAAAAATAAA
* *
5227064 -TATTTAAAAATATAAAAAATAAA
1 TTTTTTAAAATTAT-AAAAATAAA
5227087 TTTTTT
1 TTTTTT
5227093 TTAAAATAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.05
23 25 0.60
24 15 0.36
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
TTTTTTAAAATTATAAAAATAAA
Found at i:5227047 original size:14 final size:13
Alignment explanation
Indices: 5227030--5227075 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
5227020 TTTAAAGTTA
5227030 TAAAAATAAATTTT
1 TAAAAATAAA-TTT
5227044 TAAAAAT--A-TT
1 TAAAAATAAATTT
5227054 TAAAAATAAATATT
1 TAAAAATAAAT-TT
5227068 TAAAAATA
1 TAAAAATA
5227076 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.32
12 2 0.07
14 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAAATAAATTT
Found at i:5227058 original size:23 final size:24
Alignment explanation
Indices: 5227031--5227091 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
5227021 TTAAAGTTAT
**
5227031 AAAAATAAATTTTTAAAAATATTT
1 AAAAATAAATTTTTAAAAATATAA
*
5227055 AAAAATAAATATTTAAAAATAT-A
1 AAAAATAAATTTTTAAAAATATAA
5227078 AAAAATAAATTTTT
1 AAAAATAAATTTTT
5227092 TTTAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAATAAATTTTTAAAAATATAA
Found at i:5229181 original size:20 final size:21
Alignment explanation
Indices: 5229136--5229185 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
5229126 ATTTTAAATT
*
5229136 TAAAAAA-TATGTAAAAATTA
1 TAAAAAATTATGTAAAAAGTA
*
5229156 T-TAAAATTAT-TAAAAAGTA
1 TAAAAAATTATGTAAAAAGTA
5229175 TAAAAAATTAT
1 TAAAAAATTAT
5229186 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAAAATTATGTAAAAAGTA
Found at i:5230087 original size:18 final size:18
Alignment explanation
Indices: 5230041--5230089 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
5230031 GACTTTGTAC
5230041 TTTTTCTTTTTAATCATT
1 TTTTTCTTTTTAATCATT
*
5230059 TTTATT-ATTTTATAT-ATT
1 TTT-TTCTTTTTA-ATCATT
5230077 TTTTTCTTTTTAA
1 TTTTTCTTTTTAA
5230090 CTTTCCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTTAATCATT
Found at i:5232595 original size:33 final size:33
Alignment explanation
Indices: 5232553--5232617 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
5232543 CTAAAAAAAC
*
5232553 CAATTGCAAACAATCTTTCAATAATGCTTTTAA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTAA
*
5232586 CAATTGCAAACAATCTTTTAACAATGCTTTTA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTA
5232618 TCATTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (33 bp):
CAATTGCAAACAATCTTTCAACAATGCTTTTAA
Found at i:5233095 original size:51 final size:51
Alignment explanation
Indices: 5233031--5233138 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
5233021 TTTTGATACT
5233031 TTTTCAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
1 TTTT-AGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
5233083 TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
1 TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
5233134 TTTTA
1 TTTTA
5233139 CTTGTATAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (51 bp):
TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
Found at i:5251011 original size:13 final size:14
Alignment explanation
Indices: 5250985--5251024 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
5250975 CGCTTAAGGG
5250985 ATTTACATCATTATT
1 ATTTACA-CATTATT
5251000 A-TTACACATTA-T
1 ATTTACACATTATT
5251012 ATTTACAC-TTATT
1 ATTTACACATTATT
5251025 TGGAAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 5 0.22
15 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTACACATTATT
Found at i:5254873 original size:3 final size:3
Alignment explanation
Indices: 5254865--5254900 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5254855 CAAGACATTA
5254865 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5254901 TTGCTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5260707 original size:6 final size:6
Alignment explanation
Indices: 5260696--5260724 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5260686 CTCTCTCCTG
5260696 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
1 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
5260725 GAGCAGTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (6 bp):
TCCAGC
Found at i:5268338 original size:104 final size:104
Alignment explanation
Indices: 5268158--5268345 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
5268148 GACAATTGAC
* *
5268158 CATTACTTATTGCTCGACTTTATGGCTCTTTGCCCTCCAAGGGTGAACTGTCCTCAAGCGTAATC
1 CATTACTTATTGCTCGACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAATC
*
5268223 CTAAACAATTGCCTACAAGTGTAATTCCAGACGATGGTT
66 CTAAACAATTGCCCACAAGTGTAATTCCAGACGATGGTT
*
5268262 CATTACTTATTGCT-GAACTTTATGGCT-TTTCACCCTCTAAGGGTGAACCGTCCTCAAGCGTAT
1 CATTACTTATTGCTCG-ACTTTATGGCTCTTT-ACCCTCCAAGGGTGAACCGTCCTCAAGCGTA-
* * *
5268325 TTCC-GAACGATTGCCCACAAG
63 ATCCTAAACAATTGCCCACAAG
5268346 CATAATCTCG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
103 4 0.05
104 67 0.91
105 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (104 bp):
CATTACTTATTGCTCGACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAATC
CTAAACAATTGCCCACAAGTGTAATTCCAGACGATGGTT
Found at i:5268369 original size:104 final size:104
Alignment explanation
Indices: 5268158--5268388 Score: 227
Period size: 104 Copynumber: 2.2 Consensus size: 104
5268148 GACAATTGAC
* *
5268158 CATTACTTATTGCTCG-ACTTTATGGCTCTTTGCCCTCCAAGGGTGAACTGTCCTCAAGCGTAAT
1 CATTACTTATTGCT-GAACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAAT
* ** * ****
5268222 CCTAAACAATTGCCTACAAGTGTAATTCCAGACGATGGTT
65 CCTAAACAATTGCCCACAAGCATAATTCCAGACAACAACT
* *
5268262 CATTACTTATTGCTGAACTTTATGGCT-TTTCACCCTCTAAGGGTGAACCGTCCTCAAGCGTATT
1 CATTACTTATTGCTGAACTTTATGGCTCTTT-ACCCTCCAAGGGTGAACCGTCCTCAAGCGTA-A
* * *
5268326 TCC-GAACGATTGCCCACAAGCATAATCTCGA-ACAACAACT
64 TCCTAAACAATTGCCCACAAGCATAAT-TCCAGACAACAACT
* * * *
5268366 CATTAATTGTTGCTCAATTTTAT
1 CATTACTTATTGCTGAACTTTAT
5268389 AACTCTCACA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
103 4 0.04
104 94 0.90
105 6 0.06
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (104 bp):
CATTACTTATTGCTGAACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAATC
CTAAACAATTGCCCACAAGCATAATTCCAGACAACAACT
Found at i:5276930 original size:3 final size:3
Alignment explanation
Indices: 5276924--5276956 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5276914 ATCATCATTG
5276924 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5276957 CTCAAAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5279294 original size:6 final size:7
Alignment explanation
Indices: 5279265--5279300 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
5279255 TAATTTGATG
5279265 AAATTTA
1 AAATTTA
5279272 AAATTTA
1 AAATTTA
5279279 AAATTTA
1 AAATTTA
5279286 AAA-TTA
1 AAATTTA
5279292 AAATCTTA
1 AAAT-TTA
5279300 A
1 A
5279301 TATTCGTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.22
7 17 0.63
8 4 0.15
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATTTA
Found at i:5283492 original size:85 final size:85
Alignment explanation
Indices: 5283349--5283522 Score: 287
Period size: 85 Copynumber: 2.0 Consensus size: 85
5283339 GAAGAAAAAG
* *
5283349 GATAGGTATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAGAATAATCACAATTAACAA
1 GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
*
5283414 GGTGC-CCTTACTGCTTTGCA
66 GGT-CACCTTACTGCATTGCA
* *
5283434 GATAGGCATGAAAAAAATCTAGGGTTTCCTTTTAAGTGAAGGATGAAAATAATCACAATTAACAA
1 GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
5283499 GGTCACCTTACTGCATTGCA
66 GGTCACCTTACTGCATTGCA
5283519 GATA
1 GATA
5283523 ACCTTTTTGA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 1 0.01
85 82 0.99
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (85 bp):
GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
GGTCACCTTACTGCATTGCA
Found at i:5286166 original size:59 final size:61
Alignment explanation
Indices: 5286069--5286256 Score: 238
Period size: 67 Copynumber: 3.0 Consensus size: 61
5286059 CAGCTCCAAT
* *
5286069 ATTAC-CAAAACATTACAAAAGCTGTAATAATTTGTGTAATTGGTTAATGTTTTGT-A-TA
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTGAGTA
*
5286127 ATTACACAAAACATTACGAAAGTTGTAATAATTTGTGTAATTGGGTAATGCTTTGTGTGATTGCG
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATG-TTT-TGTGA----G
5286192 TA
60 TA
* *
5286194 ATTACACAATACATTACAAAAGTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTA
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAA-TGTTTTGTG-AGTA
5286257 GAAGCTTATG
Statistics
Matches: 113, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
58 5 0.04
59 41 0.36
60 3 0.03
61 3 0.03
62 1 0.01
63 3 0.03
66 4 0.04
67 51 0.45
68 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (61 bp):
ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTGAGTA
Found at i:5286181 original size:20 final size:20
Alignment explanation
Indices: 5286158--5286195 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5286148 GTTGTAATAA
*
5286158 TTTGTGTAATTGGGTAATGC
1 TTTGTGTAATTGCGTAATGC
*
5286178 TTTGTGTGATTGCGTAAT
1 TTTGTGTAATTGCGTAAT
5286196 TACACAATAC
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:0.18, C:0.05, G:0.29, T:0.47
Consensus pattern (20 bp):
TTTGTGTAATTGCGTAATGC
Found at i:5286408 original size:110 final size:110
Alignment explanation
Indices: 5286215--5286421 Score: 396
Period size: 110 Copynumber: 1.9 Consensus size: 110
5286205 CATTACAAAA
*
5286215 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
1 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGCAGTAGAAGCTTATGGAAAGCTTATTTT
5286280 AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
66 AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
5286325 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGCAGTAGAAGCTTATGGAAAGCTTATTTT
1 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGCAGTAGAAGCTTATGGAAAGCTTATTTT
*
5286390 AGAAGCTCACCCTAAAAGTTCTTGCAACATTG
66 AGAAGCTCACCCTAAAAGTTCTCGCAACATTG
5286422 TGCAAGGGAT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (110 bp):
GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGCAGTAGAAGCTTATGGAAAGCTTATTTT
AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
Found at i:5303648 original size:20 final size:19
Alignment explanation
Indices: 5303610--5303649 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5303600 ATATTCACCT
* *
5303610 TAAAATGTGAAATCAAATA
1 TAAAATGTCAAAACAAATA
5303629 TAAAATGTCAAACACAAATA
1 TAAAATGTCAAA-ACAAATA
5303649 T
1 T
5303650 TATAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAATGTCAAAACAAATA
Found at i:5308190 original size:29 final size:28
Alignment explanation
Indices: 5308164--5308248 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 28
5308154 GAATAATAAA
*
5308164 TTTTTTTATTTTTTTATTTTTAAAATAC
1 TTTTTTTATTTTTTTAATTTTAAAATAC
* **
5308192 TTTTTTAAAAAATTTTTAATTTTAAAATAC
1 TTTTTT--TATTTTTTTAATTTTAAAATAC
5308222 TTTTTTTAATTTTTTTAATTTTAAAAT
1 TTTTTTT-ATTTTTTTAATTTTAAAAT
5308249 TTTTTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.13
29 17 0.36
30 24 0.51
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTTTATTTTTTTAATTTTAAAATAC
Found at i:5308215 original size:30 final size:30
Alignment explanation
Indices: 5308174--5308258 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
5308164 TTTTTTTATT
*
5308174 TTTTTATTTTTAAAATACTTTTTTAAAAAA
1 TTTTTAATTTTAAAATACTTTTTTAAAAAA
* **
5308204 TTTTTAATTTTAAAATACTTTTTT-TAATT
1 TTTTTAATTTTAAAATACTTTTTTAAAAAA
5308233 TTTTTAATTTTAAAAT--TTTTTTAAAA
1 TTTTTAATTTTAAAATACTTTTTTAAAA
5308259 TACTTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.12
28 2 0.04
29 18 0.37
30 23 0.47
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTTAATTTTAAAATACTTTTTTAAAAAA
Found at i:5308254 original size:29 final size:29
Alignment explanation
Indices: 5308164--5308254 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 29
5308154 GAATAATAAA
*
5308164 TTTTTTT-ATTTTTTTATTTTTAAAATACT
1 TTTTTTTAATTTTTTTAATTTTAAAATA-T
** ** *
5308193 TTTTTAAAAAATTTTTAATTTTAAAATAC
1 TTTTTTTAATTTTTTTAATTTTAAAATAT
5308222 TTTTTTTAATTTTTTTAATTTTAAAAT-T
1 TTTTTTTAATTTTTTTAATTTTAAAATAT
5308250 TTTTT
1 TTTTT
5308255 AAAATACTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 5 0.10
29 28 0.56
30 17 0.34
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:5308265 original size:29 final size:30
Alignment explanation
Indices: 5308174--5308266 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 30
5308164 TTTTTTTATT
*
5308174 TTTTTATTTTTAAAATACTTTTTTAAAA-AA
1 TTTTTAATTTTAAAATA-TTTTTTAAAATAA
* *
5308204 TTTTTAATTTTAAAATACTTTTTT-TAAT-T
1 TTTTTAATTTTAAAATA-TTTTTTAAAATAA
*
5308233 TTTTTAATTTTAAAAT-TTTTTTAAAATAC
1 TTTTTAATTTTAAAATATTTTTTAAAATAA
5308262 TTTTT
1 TTTTT
5308267 TTAATTTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 6 0.11
28 3 0.05
29 23 0.42
30 23 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAATTTTAAAATATTTTTTAAAATAA
Found at i:5309913 original size:67 final size:66
Alignment explanation
Indices: 5309790--5309915 Score: 148
Period size: 67 Copynumber: 1.9 Consensus size: 66
5309780 TAATACGAGT
* * * * *
5309790 TTAAGTATATTTAAATTTAAATTCTTTTAAGTATTGCAACAATAATAGTTTCAATTAAGCTAAGA
1 TTAAGTATATTCAAATTCAAATTCTTTTAAGTATTGCAACAACAACAATTTCAATTAAGCTAAGA
5309855 C
66 C
* *
5309856 TTAAGTGATATTCAAATTCACATTCTTTTGAA-TATTGCAATAACAACAATGTT-AATTAAG
1 TTAAGT-ATATTCAAATTCAAATTCTTTT-AAGTATTGCAACAACAACAAT-TTCAATTAAG
5309916 TTGAGATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
66 6 0.12
67 40 0.80
68 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (66 bp):
TTAAGTATATTCAAATTCAAATTCTTTTAAGTATTGCAACAACAACAATTTCAATTAAGCTAAGA
C
Found at i:5311617 original size:2 final size:2
Alignment explanation
Indices: 5311610--5311642 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5311600 CACAAGACTT
5311610 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5311643 TCCTAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5311838 original size:15 final size:14
Alignment explanation
Indices: 5311813--5311859 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
5311803 TATAATATCA
5311813 ATTTAATTTTTAAT
1 ATTTAATTTTTAAT
*
5311827 ATTTATATTTTTATT
1 ATTTA-ATTTTTAAT
*
5311842 AATTTACTTTTTAAT
1 -ATTTAATTTTTAAT
5311857 ATT
1 ATT
5311860 ATATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 8 0.29
15 15 0.54
16 5 0.18
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTAATTTTTAAT
Found at i:5313389 original size:13 final size:13
Alignment explanation
Indices: 5313371--5313422 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
5313361 CGGCTGATTG
5313371 TTAATTTGATTAA
1 TTAATTTGATTAA
* *
5313384 TTAATTTTATTTA
1 TTAATTTGATTAA
*
5313397 TTGATTTGATTAA
1 TTAATTTGATTAA
* *
5313410 TTGATTTTATTAA
1 TTAATTTGATTAA
5313423 CGATTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATTTGATTAA
Found at i:5327832 original size:19 final size:19
Alignment explanation
Indices: 5327803--5327839 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5327793 TGGGCTGATG
5327803 TTAATTTGGGCTTAGGGTTA
1 TTAATTTGGGCTT-GGGTTA
5327823 TTAA-TTGGGCTTGGGTT
1 TTAATTTGGGCTTGGGTT
5327840 GTTGTTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.46
Consensus pattern (19 bp):
TTAATTTGGGCTTGGGTTA
Found at i:5327848 original size:18 final size:19
Alignment explanation
Indices: 5327806--5327851 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
5327796 GCTGATGTTA
5327806 ATTTGGGCTTAGGGTTATT
1 ATTTGGGCTTAGGGTTATT
* *
5327825 AATTGGGCTT-GGGTTGTT
1 ATTTGGGCTTAGGGTTATT
*
5327843 GTTTGGGCT
1 ATTTGGGCT
5327852 GGTGTAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.11, C:0.07, G:0.37, T:0.46
Consensus pattern (19 bp):
ATTTGGGCTTAGGGTTATT
Found at i:5329759 original size:20 final size:21
Alignment explanation
Indices: 5329734--5329775 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5329724 GTCATCGTCC
*
5329734 GCTTTTCTTTTTCTTTT-TTT
1 GCTTTTCTATTTCTTTTCTTT
*
5329754 GCTTTTCTATTTGTTTTCTTT
1 GCTTTTCTATTTCTTTTCTTT
5329775 G
1 G
5329776 TTTCCGGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.02, C:0.14, G:0.10, T:0.74
Consensus pattern (21 bp):
GCTTTTCTATTTCTTTTCTTT
Found at i:5338009 original size:16 final size:16
Alignment explanation
Indices: 5337990--5338022 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5337980 GTTTTAGAGC
5337990 TATAAATATGTCAACA
1 TATAAATATGTCAACA
5338006 TATAAATATGTCAACA
1 TATAAATATGTCAACA
5338022 T
1 T
5338023 CGAAATTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (16 bp):
TATAAATATGTCAACA
Found at i:5338028 original size:16 final size:16
Alignment explanation
Indices: 5337993--5338028 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5337983 TTAGAGCTAT
*
5337993 AAATATGTCAACATAT
1 AAATATGTCAACATAG
*
5338009 AAATATGTCAACATCG
1 AAATATGTCAACATAG
5338025 AAAT
1 AAAT
5338029 TCAGTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (16 bp):
AAATATGTCAACATAG
Found at i:5341824 original size:29 final size:30
Alignment explanation
Indices: 5341765--5341822 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5341755 TCCGAGCCTT
*
5341765 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5341795 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5341823 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5342052 original size:13 final size:13
Alignment explanation
Indices: 5342034--5342065 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5342024 TTTCCAGCAA
5342034 TTATGAATTTATT
1 TTATGAATTTATT
5342047 TTATGAATTTATT
1 TTATGAATTTATT
*
5342060 TGATGA
1 TTATGA
5342066 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5342273 original size:50 final size:50
Alignment explanation
Indices: 5342160--5342401 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
5342150 ATTTGGGTAA
* * *
5342160 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
5342216 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5342266 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5342316 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
5342366 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5342402 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5342349 original size:100 final size:103
Alignment explanation
Indices: 5342160--5342409 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
5342150 ATTTGGGTAA
5342160 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
5342225 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
5342266 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5342328 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
5342366 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5342410 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:5344578 original size:45 final size:44
Alignment explanation
Indices: 5344528--5344801 Score: 381
Period size: 45 Copynumber: 6.1 Consensus size: 44
5344518 TAACGGTAGT
* *
5344528 AGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACATTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
*
5344573 GGTAACAGTATTCGACACACAAAGTG-TCGAATCGATAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCT-GAATCG-TAACAGTAAC
*
5344618 AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
*
5344663 GGTAACAGTATTCGACACACAAAGTG-TCGAATCGATAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCT-GAATCG-TAACAGTAAC
* *
5344708 AGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
* *
5344753 AGTAACAGTATTCGACACATAAAGTGCCGAATCAGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
5344798 AGTA
1 AGTA
5344802 GTCGGCACAT
Statistics
Matches: 208, Mismatches: 13, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
44 4 0.02
45 201 0.97
46 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (44 bp):
AGTAACAGTATTCGACACACAAAGTGCTGAATCGTAACAGTAAC
Found at i:5344650 original size:90 final size:90
Alignment explanation
Indices: 5344528--5344801 Score: 460
Period size: 90 Copynumber: 3.0 Consensus size: 90
5344518 TAACGGTAGT
*
5344528 AGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
5344593 AAAGTGTCGAATCGATAACAGTAAC
66 AAAGTGTCGAATCGATAACAGTAAC
5344618 AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
5344683 AAAGTGTCGAATCGATAACAGTAAC
66 AAAGTGTCGAATCGATAACAGTAAC
* * * * * *
5344708 AGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACAGTAACAGTAACAGTATTCGACACAT
1 AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
*
5344773 AAAGTGCCGAATC-AGTAACAGTAAC
66 AAAGTGTCGAATCGA-TAACAGTAAC
5344798 AGTA
1 AGTA
5344802 GTCGGCACAT
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
89 1 0.01
90 174 0.99
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (90 bp):
AGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAACATTAACGGTAACAGTATTCGACACAC
AAAGTGTCGAATCGATAACAGTAAC
Found at i:5344825 original size:38 final size:39
Alignment explanation
Indices: 5344611--5344828 Score: 150
Period size: 45 Copynumber: 5.2 Consensus size: 39
5344601 GAATCGATAA
* * *
5344611 CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAGTCGACACATAAAGTGCCGAAT
* * * *
5344650 CTGTAACATTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCGATAA
1 CAGTAAC----A--GTAACAGTAGTCGACACATAAAGTG-C----CGA-AT
* * *
5344701 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAA
1 CAGTAACAGTAACAGTAGTCGACACATAAAGTGCCGA------AT
*
5344746 CAGTAACAGTAACAGTATTCGACACATAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAGTCGACACATAAAGTGCCGAAT
* *
5344785 CAGTAACAGTAACAGTAGTCGGCACAT-AAGTGCCTAAT
1 CAGTAACAGTAACAGTAGTCGACACATAAAGTGCCGAAT
5344823 CAGTAA
1 CAGTAA
5344829 GCTGGCAAAT
Statistics
Matches: 153, Mismatches: 9, Indels: 35
0.78 0.05 0.18
Matches are distributed among these distances:
38 16 0.10
39 32 0.21
40 3 0.02
43 1 0.01
44 1 0.01
45 89 0.58
46 1 0.01
47 1 0.01
50 2 0.01
51 7 0.05
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (39 bp):
CAGTAACAGTAACAGTAGTCGACACATAAAGTGCCGAAT
Found at i:5348750 original size:9 final size:9
Alignment explanation
Indices: 5348733--5348777 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
5348723 TTTTTTCTCC
5348733 AAAACCCTA
1 AAAACCCTA
*
5348742 AAAATCCTA
1 AAAACCCTA
5348751 AAAACCCT-
1 AAAACCCTA
5348759 AAAACCCT-
1 AAAACCCTA
5348767 -AAACCCTA
1 AAAACCCTA
5348775 AAA
1 AAA
5348778 TCCAAAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.22
8 8 0.25
9 17 0.53
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:5348753 original size:8 final size:8
Alignment explanation
Indices: 5348733--5348786 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 8
5348723 TTTTTTCTCC
5348733 AAAACCCT
1 AAAACCCT
*
5348741 AAAAATCCT
1 -AAAACCCT
5348750 AAAAACCCT
1 -AAAACCCT
5348759 AAAACCCT
1 AAAACCCT
5348767 -AAACCCT
1 AAAACCCT
*
5348774 AAAATCC-
1 AAAACCCT
5348781 AAAACC
1 AAAACC
5348787 TACAAGTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 12 0.30
8 13 0.32
9 15 0.38
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAACCCT
Found at i:5357692 original size:2 final size:2
Alignment explanation
Indices: 5357685--5357740 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
5357675 CCCGCAAGAC
*
5357685 AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5357727 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
5357741 GGAGGACCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5366932 original size:20 final size:20
Alignment explanation
Indices: 5366904--5366943 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5366894 ATCTAAATGA
*
5366904 CAATACAATTACTTAACTTT
1 CAATACAATCACTTAACTTT
*
5366924 CAATTCAATCACTTAACTTT
1 CAATACAATCACTTAACTTT
5366944 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
CAATACAATCACTTAACTTT
Done.