Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 20 of 27
Found at i:3222067 original size:64 final size:63
Alignment explanation
Indices: 3221630--3222082 Score: 269
Period size: 64 Copynumber: 7.4 Consensus size: 63
3221620 TTCCAATGCC
* * * * **
3221630 CACAAGTCAGTGACATCC-TTTTCAGAG-CC-CACAAGTCAGTGGCATCC--TTCAAAG-CC-
1 CACAAGTCGGTGGCACCCTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCAAAGTCCA
* * *
3221686 CACAAGTCAAG-GGCA-CC-TTTTCAAAG-CC-CACAAGTTAGTGGCATCATTTTATCAAAG-CC
1 CACAAGTC-GGTGGCACCCTTTTTCAAAGCCCACACAAGTTGGTGGCATC-CTTT-TCAAAGTCC
3221745 -
63 A
* * * * * **
3221745 CACAAAT-AGTGGCATCTTTTTTCAAAGCTCACA-AA-TCAGTGGCATCCTTTTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCTTTTTCAAAGCCCACACAAGTTGGTGGCATCC-TTTTCAAAGTCCA
* * *
3221804 CATAAGTCAGTGGCA--CTTTTTCAAAG-CC-CACAAGTTAGTGGCATCCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCAAAGTCCA
* * * * * * * *
3221861 CATAAG-CTGATGGCACCTCTTTTTAAAAGTCTACACAAGTTGGTGGCAACCCTTTAAAAGTCCA
1 CACAAGTC-GGTGGCACC-CTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCAAAGTCCA
* * * * *
3221925 CACAAGTCGATGGTACCTCTTTTTAAAAGTCCACACAAGTTGGT-GCTATCGTTTTCCAAAAGTC
1 CACAAGTCGGTGGCACC-CTTTTTCAAAGCCCACACAAGTTGGTGGC-ATCCTTTT-C-AAAGTC
*
3221989 GA
62 CA
* *
3221991 CACAAGTTGGTGGCAACCC-TTTTCAAAGCCCACACAAGTCGGTGGCAATCCTTTTCAAAGTCCA
1 CACAAGTCGGTGGC-ACCCTTTTTCAAAGCCCACACAAGTTGGTGGC-ATCCTTTTCAAAGTCCA
*
3222055 CACAAGCCGGTGGCAACCCTTTTTCAAA
1 CACAAGTCGGTGGC-ACCCTTTTTCAAA
3222083 ACACCACTTT
Statistics
Matches: 327, Mismatches: 41, Indels: 49
0.78 0.10 0.12
Matches are distributed among these distances:
55 28 0.09
56 14 0.04
57 29 0.09
58 26 0.08
59 28 0.09
60 39 0.12
61 4 0.01
62 25 0.08
63 4 0.01
64 68 0.21
65 31 0.09
66 28 0.09
67 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (63 bp):
CACAAGTCGGTGGCACCCTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCAAAGTCCA
Found at i:3223161 original size:49 final size:50
Alignment explanation
Indices: 3223108--3223221 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 50
3223098 TGAACAGCAC
* *
3223108 ATGTATCGATACATTCTA-TTTTTACCCAAATGTATTGATACATTTTTCA
1 ATGTATCGATACATTCTATTTTTTACCCAAATATATCGATACATTTTTCA
* * *
3223157 ATGTATCTATACATTCTATTTTTTTACCCAGATATATCGATACTTTTTTCA
1 ATGTATCGATACATTCTA-TTTTTTACCCAAATATATCGATACATTTTTCA
*
3223208 AGGTATCGATACAT
1 ATGTATCGATACAT
3223222 CTAGTTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 17 0.30
51 39 0.70
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (50 bp):
ATGTATCGATACATTCTATTTTTTACCCAAATATATCGATACATTTTTCA
Found at i:3227310 original size:22 final size:22
Alignment explanation
Indices: 3227280--3227324 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3227270 GCAATAGGTC
3227280 TCCTCTTTTTGT-CATTTTTTAT
1 TCCTCTTTTT-TACATTTTTTAT
* *
3227302 TCCTTTTTTTTACTTTTTTTAT
1 TCCTCTTTTTTACATTTTTTAT
3227324 T
1 T
3227325 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (22 bp):
TCCTCTTTTTTACATTTTTTAT
Found at i:3227494 original size:14 final size:14
Alignment explanation
Indices: 3227455--3227508 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
3227445 TAAAATTATC
3227455 TTGTAAAAATT-AA
1 TTGTAAAAATTAAA
*
3227468 -TGAAAAGAATTAAA
1 TTGTAAA-AATTAAA
3227482 TTGTAAAAATTAAAA
1 TTGTAAAAATT-AAA
*
3227497 CT-TAAAAATTAA
1 TTGTAAAAATTAA
3227509 GATAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
12 5 0.15
13 6 0.18
14 14 0.41
15 9 0.26
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (14 bp):
TTGTAAAAATTAAA
Found at i:3228028 original size:157 final size:157
Alignment explanation
Indices: 3227712--3228253 Score: 424
Period size: 157 Copynumber: 3.4 Consensus size: 157
3227702 ATATTAGAAG
* * * ** *
3227712 AATTTTAAAAATTTTAAA-CAGAGAAAAA-TCTTCCGAAAACATTTTTGGAGTAGAAAA-CTCAG
1 AATTTTAAAAATTTAAAACCA-AGAAAAATTCCTCCAAAAACATTTACGGAGTAGAAAACCCCA-
* * * *
3227774 TTTTTCAAAAATAGAGAATTTCAA-ACAGAAAAAT-CAAAACTCATGAAGATGAATTAATTTTTC
64 TATTTCGAAAATAGAGAATTTCAAGA-A-AAAAATGAAAAACT--T-AA-ATGAA-T-ACTTTT-
* *
3227837 AAAATTGATTTAGTGTGAATTAAATAATAATATTTTAT
120 AAAACTGATTTAATGTGAATTAAATAATAATATTTTAT
* ** * *
3227875 AAATTTTAAAAATTTTAAACCAAGAAAAATTCCTTTAAAAACATTTACGGAGTAGAAAACTCTAT
1 -AATTTTAAAAATTTAAAACCAAGAAAAATTCCTCCAAAAACATTTACGGAGTAGAAAACCCCAT
* * * ** *
3227940 ATTTTGGAAACAT-GAGAATTTTGAGGAAAAAAATTCAAAAC-T-CATGAAT-CTTTTAAAACTG
65 A-TTTCGAAA-ATAGAGAA-TTTCAAGAAAAAAATGAAAAACTTAAATGAATACTTTTAAAACTG
** *
3228001 ATTTAATGTGAATCGAATAATAATATTTGAT
127 ATTTAATGTGAATTAAATAATAATATTTTAT
* * * * * * *
3228032 GATTTATAAAAATTAAAAACCAA-AAGAAATCCCCCCAAAAACATTTACAGAGCAGAAAACCCCG
1 AATTT-TAAAAATTTAAAACCAAGAA-AAATTCCTCCAAAAACATTTACGGAGTAGAAAACCCCA
*
3228096 TATTTCGAAAATAGAGAATTTCAAGAAAAAAATGAAAAACTTATGAAAATGAATGAATTTTTATA
64 TATTTCGAAAATAGAGAATTTCAAGAAAAAAATGAAAAAC-T-T--AAATGAAT--ACTTTTA-A
*
3228161 AACTGATTTAATATGAATTAAATAATAATATTTTAT
122 AACTGATTTAATGTGAATTAAATAATAATATTTTAT
** *
3228197 GAATTTTAAAAA-TTAAAACTGAGAAAAA-TCTCTCCGAAAACATTTACGGAGTAGAAA
1 -AATTTTAAAAATTTAAAACCAAGAAAAATTC-CTCCAAAAACATTTACGGAGTAGAAA
3228254 CTGCATGTTT
Statistics
Matches: 301, Mismatches: 53, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
155 20 0.07
156 18 0.06
157 79 0.26
158 5 0.02
160 1 0.00
161 11 0.04
163 1 0.00
164 63 0.21
165 67 0.22
166 22 0.07
167 13 0.04
168 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (157 bp):
AATTTTAAAAATTTAAAACCAAGAAAAATTCCTCCAAAAACATTTACGGAGTAGAAAACCCCATA
TTTCGAAAATAGAGAATTTCAAGAAAAAAATGAAAAACTTAAATGAATACTTTTAAAACTGATTT
AATGTGAATTAAATAATAATATTTTAT
Found at i:3228211 original size:165 final size:162
Alignment explanation
Indices: 3227775--3228253 Score: 444
Period size: 157 Copynumber: 3.0 Consensus size: 162
3227765 AAAACTCAGT
* *
3227775 TTTTCAAAAATAGAGAATTTCAA-ACAGAAAAATCAAAACTCATGAAGATGAATTAATTTTTCAA
1 TTTTCGAAAATAGAGAATTTCAAGA-A-AAAAATCAAAACT-ATGAAAATGAA-TAATTTTT-AA
* * * **
3227839 AATTGATTTAGTGTGAATTAAATAATAATATTTTATAAATTTTAAAAATTTTAAACCAAGAAAAA
61 AACTGATTTAATGTGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAA
* *** * * * *
3227904 TTCCTTTAAAAACATTTACGGAGTAGAAAACTCTATA
126 TCCCCCCAAAAACATTTACAGAGCAGAAAACCCCATA
* * * * *
3227941 TTTTGGAAACAT-GAGAATTTTGAGGAAAAAAATTCAAAAC--T---CATGAAT--CTTTTAAAA
1 TTTTCGAAA-ATAGAGAA-TTTCAAGAAAAAAA-TCAAAACTATGAAAATGAATAATTTTTAAAA
** *
3227998 CTGATTTAATGTGAATCGAATAATAATATTTGATG-ATTTATAAAAATTAAAAACCAA-AAGAAA
63 CTGATTTAATGTGAATTAAATAATAATATTTTATGAATTT-TAAAAATTAAAAACCAAGAA-AAA
*
3228061 TCCCCCCAAAAACATTTACAGAGCAGAAAACCCCGTA
126 TCCCCCCAAAAACATTTACAGAGCAGAAAACCCCATA
*
3228098 -TTTCGAAAATAGAGAATTTCAAGAAAAAAATGAAAAACTTATGAAAATGAATGAATTTTTATAA
1 TTTTCGAAAATAGAGAATTTCAAGAAAAAAAT-CAAAAC-TATGAAAATGAAT-AATTTTTA-AA
* **
3228162 ACTGATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATT-AAAACTGAGAAAAAT
62 ACTGATTTAATGTGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAAT
* * * * *
3228226 CTCTCCGAAAACATTTACGGAGTAGAAA
127 CCCCCCAAAAACATTTACAGAGCAGAAA
3228254 CTGCATGTTT
Statistics
Matches: 253, Mismatches: 40, Indels: 42
0.76 0.12 0.13
Matches are distributed among these distances:
154 1 0.00
155 19 0.08
156 18 0.07
157 79 0.31
158 5 0.02
160 1 0.00
161 11 0.04
164 39 0.15
165 44 0.17
166 21 0.08
167 14 0.06
168 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (162 bp):
TTTTCGAAAATAGAGAATTTCAAGAAAAAAATCAAAACTATGAAAATGAATAATTTTTAAAACTG
ATTTAATGTGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCC
CCAAAAACATTTACAGAGCAGAAAACCCCATA
Found at i:3228280 original size:165 final size:162
Alignment explanation
Indices: 3227636--3228377 Score: 367
Period size: 164 Copynumber: 4.6 Consensus size: 162
3227626 TATTATATGT
* * * * * * *
3227636 AAAAAAATCAAAAAAT-A-AGAAATAAATTGAATTTTGCAAAACTGATTTACTGGGAGTTTAATA
1 AAAAAAATCAAAAACTCATA-AAATAAAATGAATTTT-TAAAACTGATTTAATGTGAATTAAATA
* * * ** * ***
3227699 ACAATA-TTAGAAGAATTTTAAAAATTTTAAA-CAGAGAA-AAAT-CTTCCGAAAACATTTTTGG
64 ATAATATTTA-ATGAATTTTAAAAA-TTAAAACCA-A-AAGAAATCCCCCCAAAAACATTTACAG
* *
3227760 AGTAGAAAACTCA-GTTTTTCA-AAAATAGAGAATT-TCAA
125 AGCAGAAAAC-CACGTATTT-AGAAAATAGAGAATTCT-AA
* * * * *
3227798 ACAGAAAAATC-AAAACTCATGAAGAT-GAATTAATTTTTCAAAATTGATTTAGTGTGAATTAAA
1 A-A-AAAAATCAAAAACTCAT-AAAATAAAATGAATTTTT-AAAACTGATTTAATGTGAATTAAA
* * * * *** *
3227861 TAATAATATTTTATAAATTTTAAAAATTTTAAACCAAGAA-AAATTCCTTTAAAAACATTTACGG
62 TAATAATATTTAATGAATTTTAAAAA-TTAAAACCAA-AAGAAATCCCCCCAAAAACATTTACAG
* *
3227925 AGTAGAAAACTCTA--TATTTTGGAAACAT-GAGAATT-T--
125 AGCAGAAAAC-C-ACGTA-TTTAGAAA-ATAGAGAATTCTAA
** ** * * * **
3227961 TGAGGAA--AAAAATTCA-AAACT--CATGAATCTTTTAAAACTGATTTAATGTGAATCGAATAA
1 AAAAAAATCAAAAACTCATAAAATAAAATGAAT-TTTTAAAACTGATTTAATGTGAATTAAATAA
*
3228021 TAATATTTGATG-ATTTATAAAAATTAAAAACCAAAAGAAATCCCCCCAAAAACATTTACAGAGC
65 TAATATTTAATGAATTT-TAAAAATT-AAAACCAAAAGAAATCCCCCCAAAAACATTTACAGAGC
* *
3228085 AGAAAACCCCGTATTTCGAAAATAGAGAATT-TCAA
128 AGAAAACCACGTATTTAGAAAATAGAGAATTCT-AA
* * * *
3228120 GAAAAAAATGAAAAACTTATGAAAAT-GAATGAATTTTTATAAACTGATTTAATATGAATTAAAT
1 -AAAAAAATCAAAAACTCAT-AAAATAAAATGAATTTTTA-AAACTGATTTAATGTGAATTAAAT
* * * * * * *
3228184 AATAATATTTTATGAATTTTAAAAATTAAAACTGAGAA-AAATCTCTCCGAAAACATTTACGGAG
63 AATAATATTTAATGAATTTTAAAAATTAAAAC-CAAAAGAAATCCCCCCAAAAACATTTACAGAG
* * * *
3228248 TAG-AAACTGCATGT-TTTAGCAATATGGAGAATTCTAA
127 CAGAAAAC--CACGTATTTAG-AAAATAGAGAATTCTAA
* * * * * *
3228285 AAGAAAATCAATAACTCATAACATAAAAGGAATTTTTAAAAATTGATTTAATGGTG-ATTAAATG
1 AAAAAAATCAAAAACTCATAAAATAAAATGAATTTTT-AAAACTGATTTAAT-GTGAATTAAATA
* *
3228349 ATAATATTTAAGGAATTTT-AGAATTAAAA
64 ATAATATTTAATGAATTTTAAAAATTAAAA
3228378 GCTTAGGAAA
Statistics
Matches: 456, Mismatches: 84, Indels: 79
0.74 0.14 0.13
Matches are distributed among these distances:
155 2 0.00
156 24 0.05
157 81 0.18
158 7 0.02
160 10 0.02
161 3 0.01
162 8 0.02
163 23 0.05
164 172 0.38
165 103 0.23
166 21 0.05
167 2 0.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (162 bp):
AAAAAAATCAAAAACTCATAAAATAAAATGAATTTTTAAAACTGATTTAATGTGAATTAAATAAT
AATATTTAATGAATTTTAAAAATTAAAACCAAAAGAAATCCCCCCAAAAACATTTACAGAGCAGA
AAACCACGTATTTAGAAAATAGAGAATTCTAA
Found at i:3230366 original size:58 final size:57
Alignment explanation
Indices: 3230272--3230389 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 57
3230262 TACCTTTTAT
* *
3230272 TCTTACAAACCTCTCCATGTGTTCCATTTGTTTGCAAGGTCTACATTGAATATTAGG
1 TCTTACAAACCTCTCCATGTGTCCCATTTGTTTGCAAGCTCTACATTGAATATTAGG
*
3230329 TCTTGCAAACCCTCTCCATGTG-CCCTATTTGTTTGCAAGCTCTACATTGAATATTAGG
1 TCTTACAAA-CCTCTCCATGTGTCCC-ATTTGTTTGCAAGCTCTACATTGAATATTAGG
3230387 TCT
1 TCT
3230390 AAACCAATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 10 0.18
58 46 0.82
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (57 bp):
TCTTACAAACCTCTCCATGTGTCCCATTTGTTTGCAAGCTCTACATTGAATATTAGG
Found at i:3234704 original size:16 final size:16
Alignment explanation
Indices: 3234678--3234723 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
3234668 AAATTTTTGA
*
3234678 ATCATTTTTGAGTTCGG
1 ATCA-TTTTGAGTTCAG
*
3234695 ATTATTTTGAGTTCAG
1 ATCATTTTGAGTTCAG
3234711 ATCATTTTGAGTT
1 ATCATTTTGAGTT
3234724 TGAATCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.50
Consensus pattern (16 bp):
ATCATTTTGAGTTCAG
Found at i:3234730 original size:16 final size:16
Alignment explanation
Indices: 3234673--3234765 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
3234663 TTTTAAAATT
3234673 TTTGAATCATTTTTGAG
1 TTTGAATCA-TTTTGAG
* * *
3234690 TTCGGATTATTTTGAG
1 TTTGAATCATTTTGAG
*
3234706 -TTCAGATCATTTTGAG
1 TTTGA-ATCATTTTGAG
3234722 TTTGAATCATTTT-AGG
1 TTTGAATCATTTTGA-G
* * *
3234738 TTTGTATTATTTTAAG
1 TTTGAATCATTTTGAG
* *
3234754 TTCGAGTCATTT
1 TTTGAATCATTT
3234766 CAGATTCGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
15 2 0.03
16 46 0.79
17 10 0.17
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTGAATCATTTTGAG
Found at i:3234756 original size:48 final size:49
Alignment explanation
Indices: 3234673--3234765 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
3234663 TTTTAAAATT
* *
3234673 TTTGAATCATTTTTGAGTTCGGATTATTTTGAGTTC-AGATCATTTTGAG
1 TTTGAATCATTTTAGAGTTCGGATTATTTTAAGTTCGAG-TCATTTTGAG
* *
3234722 TTTGAATCATTTTAG-GTTTGTATTATTTTAAGTTCGAGTCATTT
1 TTTGAATCATTTTAGAGTTCGGATTATTTTAAGTTCGAGTCATTT
3234766 CAGATTCGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 23 0.59
49 16 0.41
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (49 bp):
TTTGAATCATTTTAGAGTTCGGATTATTTTAAGTTCGAGTCATTTTGAG
Found at i:3235735 original size:29 final size:29
Alignment explanation
Indices: 3235698--3235755 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3235688 TTGAGTTTAG
*
3235698 ATTTGAATTAATTAATTGAATTTTTTAAA
1 ATTTGAATTAATTAATTAAATTTTTTAAA
*
3235727 ATTTGAATTAATTTATTAAATTTTTTAAA
1 ATTTGAATTAATTAATTAAATTTTTTAAA
3235756 TTCAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTTGAATTAATTAATTAAATTTTTTAAA
Found at i:3235763 original size:28 final size:29
Alignment explanation
Indices: 3235703--3235765 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
3235693 TTTAGATTTG
* **
3235703 AATTAATTAATTGAATTTTTTAAAATTTG
1 AATTAATTAATTAAATTTTTTAAAATTCA
*
3235732 AATTAATTTATTAAATTTTTT-AAATTCA
1 AATTAATTAATTAAATTTTTTAAAATTCA
3235760 AATTAA
1 AATTAA
3235766 AATTTACAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
AATTAATTAATTAAATTTTTTAAAATTCA
Found at i:3238176 original size:120 final size:119
Alignment explanation
Indices: 3238011--3238238 Score: 296
Period size: 120 Copynumber: 1.9 Consensus size: 119
3238001 CAAAGTGAAA
* * * * * * *
3238011 AAAATATAATCTAATCCACTTTCGAGGGAAATCATTATGGCACTTAGCATGTGACACAAGCCTTT
1 AAAATATAATCTAATCCACTTTCAAAGAAAATCATGATAGCACTTACCATATGACACAAGCCTTT
* * *
3238076 AAACCCTTAGATG-TCTTCAGTGGACGAGTTTAGTCTTGTGAGGGAACAAAGCAAG
66 AAACCCCTAGATGTTCTT-AGTGGAAGAG-TTAGTCTTGTAAGGGAACAAAGCAAG
* * * * *
3238131 AAAATCTAATCTAATCCGCTTTCAAAGAAAATCATGGTAGTACTTACCATATGACATAAGCCTTT
1 AAAATATAATCTAATCCACTTTCAAAGAAAATCATGATAGCACTTACCATATGACACAAGCCTTT
3238196 AAACCCCTAGATGTTCTTAGTGGAAGAGTTAGTCTTGTAAGGG
66 AAACCCCTAGATGTTCTTAGTGGAAGAGTTAGTCTTGTAAGGG
3238239 TTTAACAAGA
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
119 14 0.15
120 74 0.80
121 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (119 bp):
AAAATATAATCTAATCCACTTTCAAAGAAAATCATGATAGCACTTACCATATGACACAAGCCTTT
AAACCCCTAGATGTTCTTAGTGGAAGAGTTAGTCTTGTAAGGGAACAAAGCAAG
Found at i:3241380 original size:27 final size:27
Alignment explanation
Indices: 3241342--3241402 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
3241332 CAGAGCCTGT
3241342 GATCAAAGTAAACAATTACGTTAGTCC
1 GATCAAAGTAAACAATTACGTTAGTCC
3241369 GATCAAAGTAAACAATTACGTTAGTCC
1 GATCAAAGTAAACAATTACGTTAGTCC
*
3241396 AATCAAA
1 GATCAAA
3241403 TATTAACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (27 bp):
GATCAAAGTAAACAATTACGTTAGTCC
Found at i:3242104 original size:2 final size:2
Alignment explanation
Indices: 3242097--3242122 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3242087 TGTTTTCTTT
3242097 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3242123 ACAATATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3247172 original size:360 final size:359
Alignment explanation
Indices: 3246493--3247574 Score: 1966
Period size: 360 Copynumber: 3.0 Consensus size: 359
3246483 CAACAAGCTG
* * *
3246493 ATGGACACTTCAACATCTACATTAGACTCACCTATACACTTCCTAATGAGTTTCAACAAAGCTCC
1 ATGGACACTTAAACA-CAACATTAGACTCACCTATACACTTCCTAATGACTTTCAACAAAGCTCC
* * *
3246558 ACAAGGTAGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCTAAAATAGC
65 ACAAGTTAGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGC
3246623 TCTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATT
130 TCTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATT
3246688 AAACCTCTACCCACTCATTGATTAAAAACTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTT
195 AAACCTCTACCCACTCATTGATT-AAAACTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTT
3246753 TACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAA
259 TACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAA
3246818 CTAATTAACCATAAACATGTTCTAAACACAAAAATA
324 CTAATTAACCATAAACATGTTCTAAACACAAAAATA
* *
3246854 ATGGCCACTTAAACACAACATTAGACTCACCTATACACTTCCTAATGACTTTCAATAAAGCTCCA
1 ATGGACACTTAAACACAACATTAGACTCACCTATACACTTCCTAATGACTTTCAACAAAGCTCCA
*
3246919 CAAGTTGGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGCT
66 CAAGTTAGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGCT
3246984 CTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATTA
131 CTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATTA
*
3247049 AACCTCTACCCACTCATTTATTAAAGACTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTTT
196 AACCTCTACCCACTCATTGATTAAA-ACTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTTT
3247114 ACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAAC
260 ACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAAC
*
3247179 TAATTGACCATAAACATGTTCTAAACACAAAAATA
325 TAATTAACCATAAACATGTTCTAAACACAAAAATA
*
3247214 ATGGACACTTAAACACAACATTAGACTAACCTATACACTTCCTAATGACTTTCAACAAAGCTCCA
1 ATGGACACTTAAACACAACATTAGACTCACCTATACACTTCCTAATGACTTTCAACAAAGCTCCA
*
3247279 CAAGTTATGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGCT
66 CAAGTTAGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGCT
* * * *
3247344 CTAAGCTCCAGCTTTTTATCAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATTT
131 CTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATTA
3247409 AACCTCTACCCACTCATTGATTAAAAGCTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTTT
196 AACCTCTACCCACTCATTGATTAAAA-CTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTTT
3247474 ACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAAC
260 ACACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAAC
*
3247539 TAATTACCCATAAACATGTTCTAAACACAAAAATA
325 TAATTAACCATAAACATGTTCTAAACACAAAAATA
3247574 A
1 A
3247575 CTTAGCTGAA
Statistics
Matches: 696, Mismatches: 23, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
359 4 0.01
360 679 0.98
361 13 0.02
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (359 bp):
ATGGACACTTAAACACAACATTAGACTCACCTATACACTTCCTAATGACTTTCAACAAAGCTCCA
CAAGTTAGGTTAATAAAAACTAGTGAAAACACATAGAAATTATTTTTTTAATCTCCAAATTAGCT
CTAAACTCAAGCTTTTTATTAAATGTCCCCTAGTTGTTCATTGAAGAACTTACTTCAAAAAATTA
AACCTCTACCCACTCATTGATTAAAACTTGTTCTTGGTGGTTCTTTTGTGAAATTAAGTTTTTTA
CACATCTAATTCTAAACAAGCATTTTAACAAACACGTAGTATACTACCTATTATATCTATCAACT
AATTAACCATAAACATGTTCTAAACACAAAAATA
Found at i:3250447 original size:19 final size:21
Alignment explanation
Indices: 3250401--3250454 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
3250391 TTTCAACAAT
3250401 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
3250422 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
3250441 TTGTATCGATACAA
1 TTGTATCGATACAA
3250455 TGTATCGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:3250508 original size:20 final size:20
Alignment explanation
Indices: 3250483--3250632 Score: 77
Period size: 20 Copynumber: 7.7 Consensus size: 20
3250473 TTGCCAAGGA
3250483 AATGTATCGATACTTTATTC
1 AATGTATCGATACTTTATTC
3250503 AATGTATCGATAC---A-T-
1 AATGTATCGATACTTTATTC
*
3250518 --TGTATCGATACATTATTC
1 AATGTATCGATACTTTATTC
3250536 AATGTATCGATACATTGTA-TC
1 AATGTATCGATAC-TT-TATTC
* * *
3250557 GATATATTGAT-CTTTATATC
1 AATGTATCGATACTTTAT-TC
* * * **
3250577 GATATATCTGGGA-ATTTTACCC
1 AATGTATC---GATACTTTATTC
*
3250599 AGATGTATCGATACATTATTC
1 A-ATGTATCGATACTTTATTC
3250620 AATGTATCGATAC
1 AATGTATCGATAC
3250633 ATGTAGGCAA
Statistics
Matches: 99, Mismatches: 14, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
13 11 0.11
16 2 0.02
17 2 0.02
18 2 0.02
19 2 0.02
20 48 0.48
21 17 0.17
22 3 0.03
23 12 0.12
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACTTTATTC
Found at i:3250523 original size:13 final size:13
Alignment explanation
Indices: 3250505--3250565 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
3250495 CTTTATTCAA
3250505 TGTATCGATACAT
1 TGTATCGATACAT
3250518 TGTATCGATACA-
1 TGTATCGATACAT
*
3250530 T-TAT---T-CAA
1 TGTATCGATACAT
3250538 TGTATCGATACAT
1 TGTATCGATACAT
*
3250551 TGTATCGATATAT
1 TGTATCGATACAT
3250564 TG
1 TG
3250566 ATCTTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 3 0.08
11 3 0.08
12 2 0.05
13 28 0.70
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3250527 original size:33 final size:33
Alignment explanation
Indices: 3250485--3250560 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
3250475 GCCAAGGAAA
*
3250485 TGTATCGATACTTTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
3250518 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
3250551 TGTATCGATA
1 TGTATCGATA
3250561 TATTGATCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:3251492 original size:21 final size:20
Alignment explanation
Indices: 3251461--3251506 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
3251451 GTTAACAGCC
* *
3251461 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTCAG
3251481 CTATGTTTCATGCATTTTCAG
1 C-ATGTTTCATGCATTTTCAG
3251502 CATGT
1 CATGT
3251507 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (20 bp):
CATGTTTCATGCATTTTCAG
Found at i:3254957 original size:9 final size:9
Alignment explanation
Indices: 3254943--3255000 Score: 62
Period size: 9 Copynumber: 6.1 Consensus size: 9
3254933 CCATTTCATA
3254943 TTTTTTTCT
1 TTTTTTTCT
3254952 TTTTTTTCT
1 TTTTTTTCT
**
3254961 TTTTCATCT
1 TTTTTTTCT
3254970 TTTTTTTCCT
1 TTTTTTT-CT
*
3254980 TTCTTCTTCT
1 TT-TTTTTCT
3254990 TTTTCTTTCT
1 TTTT-TTTCT
3255000 T
1 T
3255001 CTTCCCCACC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 23 0.57
10 13 0.32
11 4 0.10
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:3254972 original size:26 final size:29
Alignment explanation
Indices: 3254936--3254994 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3254926 AGCCACTCCA
*
3254936 TTTCATA-TTTTTTT-CTTT-TTTTTCTT
1 TTTCATATTTTTTTTCCTTTCTTCTTCTT
*
3254962 TTTCATCTTTTTTTTCCTTTCTTCTTCTT
1 TTTCATATTTTTTTTCCTTTCTTCTTCTT
3254991 TTTC
1 TTTC
3254995 TTTCTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 7 0.25
28 4 0.14
29 11 0.39
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTCATATTTTTTTTCCTTTCTTCTTCTT
Found at i:3254974 original size:20 final size:20
Alignment explanation
Indices: 3254951--3255004 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3254941 TATTTTTTTC
3254951 TTTTTTTTCTTT-TTCATCT
1 TTTTTTTTCTTTCTTCATCT
* *
3254970 TTTTTTTCCTTTCTTCTTCT
1 TTTTTTTTCTTTCTTCATCT
*
3254990 TTTTCTTTC-TTCTTC
1 TTTTTTTTCTTTCTTC
3255005 CCCACCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTTTCTTCATCT
Found at i:3254992 original size:16 final size:16
Alignment explanation
Indices: 3254973--3255004 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3254963 TTCATCTTTT
3254973 TTTTCCTTTCTTCTTC
1 TTTTCCTTTCTTCTTC
*
3254989 TTTTTCTTTCTTCTTC
1 TTTTCCTTTCTTCTTC
3255005 CCCACCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTCCTTTCTTCTTC
Found at i:3255675 original size:11 final size:11
Alignment explanation
Indices: 3255659--3255687 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3255649 ATTCATTTTC
3255659 TTTTTTTTGTT
1 TTTTTTTTGTT
3255670 TTTTTTTTGTT
1 TTTTTTTTGTT
3255681 TTTTTTT
1 TTTTTTT
3255688 CATATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:3256286 original size:86 final size:86
Alignment explanation
Indices: 3256176--3256824 Score: 771
Period size: 86 Copynumber: 7.5 Consensus size: 86
3256166 CATCAACTTG
* * * * * *
3256176 TGTGGGCTTTTG-AAAGGATT-CCATTAACTTGTGAGCTTTGAAAA-GATGCCACTTACTTATGG
1 TGTGGGC-TTTGAAAAGG-TTGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGG
* * * *
3256238 GCTTTAAAAGGGTGTCACTAACT
64 GCTTTGAAAGGATGCCACTGACT
* * * * *
3256261 TGTGGGCTTTGAAAAAGGTTACCATTGACTTGTGGGATTTGAGAA-GATGCCACTGACTTGTGGG
1 TGTGGGCTTTG-AAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGG
*
3256325 CTTTGAGAAGG-TGCCACTCACT
65 CTTTGA-AAGGATGCCACTGACT
* *
3256347 TGTGGGCTTTGAAAAGGGTTGCCACTCACTTGTGGGCTTTGAAAAGGGTTGCCACTAACTTGTGG
1 TGTGGGCTTTGAAAA-GGTTGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACTTGTGG
3256412 GCTTTGAAAGGATGCCACTGACT
64 GCTTTGAAAGGATGCCACTGACT
* * * * *
3256435 TGTGGGCTTTGAGAAGG-AGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCTACTGGCTTATGGG
1 TGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACTTGTGGG
3256499 CTTTGAAAGGATGCCACTGACT
65 CTTTGAAAGGATGCCACTGACT
* *
3256521 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTACCA-TCGACTTGTGG
1 TGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACT-GACTTGTGG
3256584 GCTTTGAGAA-GATGCCACTGACT
64 GCTTTGA-AAGGATGCCACTGACT
* * *
3256607 TGTGAGCTTTGAGAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACTAACTTGTGGG
1 TGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACTTGTGGG
3256671 CTTTGAAAGGATGCCACTGACT
65 CTTTGAAAGGATGCCACTGACT
* * **
3256693 TGTGGGCTTTGAGAAGGGTTGCTACTGACTTGTGCACTTTGAAAAGGGTTGCCACTGACTTGTGG
1 TGTGGGCTTTGA-AAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACTTGTGG
*
3256758 GCTTTGAAAGGATGCCAGTGACT
64 GCTTTGAAAGGATGCCACTGACT
** * *
3256781 TGTGGGCTTTGAAAA-GAAGCCATTGACTTGTGAGCTTTGAAAAG
1 TGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAG
3256825 AAGCCATATT
Statistics
Matches: 499, Mismatches: 49, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
84 4 0.01
85 21 0.04
86 329 0.66
87 22 0.04
88 123 0.25
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (86 bp):
TGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGC
TTTGAAAGGATGCCACTGACT
Found at i:3256325 original size:58 final size:57
Alignment explanation
Indices: 3256176--3256822 Score: 711
Period size: 58 Copynumber: 11.2 Consensus size: 57
3256166 CATCAACTTG
* * * * * *
3256176 TGTGGGCTTTTGAAAGGATTCCATTAACTTGTGAGCTTTGAAAA-GATGCCACTTACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
* * * * * * *
3256233 TATGGGCTTTAAAAGGGTGTCACTAACTTGTGGGCTTTGAAAAAGGTTACCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAAGGTTGCCACTGACT
* * *
3256291 TGTGGGATTTGAGAA-GATGCCACTGACTTGTGGGCTTTGAGAAGG-TGCCACTCACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
* * *
3256347 TGTGGGCTTTGAAAAGGGTTGCCACTCACTTGTGGGCTTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACT
* *
3256407 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGG-AGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
* * * * *
3256463 TGTGGGCTTTGAAAAGGGTTGCTACTGGCTTATGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
*
3256521 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTACCA-TCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACT-GACT
* *
3256579 TGTGGGCTTTGAGAA-GATGCCACTGACTTGTGAGCTTTGAGAAGG-TGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
* * *
3256635 TGTGGGCTTTGAAAAGGGTTGCCACTAACTTGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
* * **
3256693 TGTGGGCTTTGAGAAGGGTTGCTACTGACTTGTGCACTTTGAAAAGGGTTGCCACTGACT
1 TGTGGGCTTTGA-AA-GGATGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACTGACT
* ** *
3256753 TGTGGGCTTTGAAAGGATGCCAGTGACTTGTGGGCTTTGAAAA-GAAGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
*
3256809 TGTGAGCTTTGAAA
1 TGTGGGCTTTGAAA
3256823 AGAAGCCATA
Statistics
Matches: 503, Mismatches: 64, Indels: 47
0.82 0.10 0.08
Matches are distributed among these distances:
56 131 0.26
57 41 0.08
58 271 0.54
59 14 0.03
60 46 0.09
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACTGACT
Found at i:3256831 original size:28 final size:28
Alignment explanation
Indices: 3256176--3256830 Score: 650
Period size: 28 Copynumber: 22.8 Consensus size: 28
3256166 CATCAACTTG
* * * *
3256176 TGTGGGCTTTTGAAAGGATTCCATTAACT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* *
3256205 TGTGAGCTTTGAAAAGATGCCACTTACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * * *
3256233 TATGGGCTTT-AAAAGGGTGTCACTAACT
1 TGTGGGCTTTGAAAA-GATGCCACTGACT
* * *
3256261 TGTGGGCTTTGAAAAAGGTTACCATTGACT
1 TGTGGGCTTTG-AAAA-GATGCCACTGACT
* *
3256291 TGTGGGATTTGAGAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
3256319 TGTGGGCTTTGAGAAGGTGCCACTCACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
3256347 TGTGGGCTTTGAAAAGGGTTGCCACTCACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* *
3256377 TGTGGGCTTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
*
3256407 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
3256435 TGTGGGCTTTGAGAAGGA-GCCACTGACT
1 TGTGGGCTTTGA-AAAGATGCCACTGACT
* * *
3256463 TGTGGGCTTTGAAAAGGGTTGCTACTGGCT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* *
3256493 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
3256521 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
3256549 TGTGGGCTTTGAAAAGGGTTACCA-TCGACT
1 TGTGGGCTTTGAAAA--GATGCCACT-GACT
*
3256579 TGTGGGCTTTGAGAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
3256607 TGTGAGCTTTGAGAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
3256635 TGTGGGCTTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
*
3256665 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* * *
3256693 TGTGGGCTTTGAGAAGGGTTGCTACTGACT
1 TGTGGGCTTTGA-AA-AGATGCCACTGACT
** *
3256723 TGTGCACTTTGAAAAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAAA--GATGCCACTGACT
* *
3256753 TGTGGGCTTTGAAAGGATGCCAGTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
3256781 TGTGGGCTTTGAAAAGAAGCCATTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
* *
3256809 TGTGAGCTTTGAAAAGAAGCCA
1 TGTGGGCTTTGAAAAGATGCCA
3256831 TATTGACAAA
Statistics
Matches: 537, Mismatches: 70, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.01
28 317 0.59
29 21 0.04
30 193 0.36
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:3257661 original size:13 final size:13
Alignment explanation
Indices: 3257643--3257669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3257633 ACAAACAGTA
3257643 AATGTATCGATAC
1 AATGTATCGATAC
3257656 AATGTATCGATAC
1 AATGTATCGATAC
3257669 A
1 A
3257670 TAAGTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3257739 original size:21 final size:21
Alignment explanation
Indices: 3257713--3257773 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3257703 AGCTACTGCC
3257713 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
3257734 AAGGAAGTGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
3257755 --GTAAAATGTATCGATACAT
1 AAG-GAAATGTATCGATACAT
3257774 CGATCTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 20 0.56
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:3257766 original size:20 final size:19
Alignment explanation
Indices: 3257717--3257773 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
3257707 ACTGCCAAGG
3257717 AAATGTATCGATACA-TTA
1 AAATGTATCGATACATTTA
3257735 AGGAAGTGTATCGATACATTGTA
1 A--AA-TGTATCGATACATT-TA
3257758 AAATGTATCGATACAT
1 AAATGTATCGATACAT
3257774 CGATCTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.03
20 15 0.44
21 14 0.41
22 1 0.03
23 3 0.09
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AAATGTATCGATACATTTA
Found at i:3258928 original size:729 final size:730
Alignment explanation
Indices: 3257839--3259288 Score: 2355
Period size: 729 Copynumber: 2.0 Consensus size: 730
3257829 CAATGTATCG
* * ** *
3257839 ATACCTTCAGGCATTTTTGACCACTTCGAGCCATTTTTTTGCTTTTCCATTGTTCATTCAGAACA
1 ATACATTCAGGCATTTTTGACCACTTCGAGCCATTTTTGTGCTTCGCCATTGTTCATTCAAAACA
*
3257904 TGTTTTTAACACACATTTTGCATCTAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTC
66 TGTTTTTAACACACATTTTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTC
* ** *
3257969 GGAATGGAATTTAAACATGTTTTAAGATCAAATTTGCAAAAAAGCTGAATGTTATTTTCCACCAA
131 GGAATGCAATTTAAACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAA
* * *
3258034 AGGACATGTTAGATTTTTTCGAATTCTGGCAGTTTCAAGTTCAAGACCACCACTGCATTGTAGAA
196 AGGACATGTCAGATTTTTTCGAATTCTGGCAGTCTCAAGTTCAAGACCACCACTGCATTGCAGAA
*
3258099 CCAATGGCAATGAGGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATCC
261 CCAATGGCAATGAGGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATAC
*
3258164 CATTATGCCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCATGATTATAAGTAGTGGCTGTTGG
326 CATAATGCCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCATGATTATAAGTAGTGGCTGTTGG
*
3258229 CTCAGC-AAAAAGGATCCTTTTTTGGGGGAGAGAAAAAA-CAGTTTTCCAGCAGCAAGAAACCCT
391 CTCAGCAAAAAAGGATCCTTTTTT--GGGAGA-AAAAAAGCAATTTTCCAGCAGCAAGAAACCCT
* *
3258292 TAGGAAATCTTTTAGCAAC-AAAAAACC-AAAAACAC-AAAAAAATACTATTCCATTGGTTTTCC
453 TAGGAAATCCTTTAGCAACAAAAAAACCAAAAAACACAAAAAAAACACTATTCCATTGG-TTT-C
* * * * * *
3258354 AACACTCCATTTCCGTAGCTCCAAAAACCACTACCAAAGGACCTCCAAAAACTCCATATTCCTTA
516 AA-ACTCCATTCCCGCAGATCCAAAAACCACCACCAAAGAACCTCCAAAAACTCCATATTCCTCA
* * *
3258419 CACTTTCA-CCCTAGAACAG-CTCCTCTCTCAACCAT-ACTACCCAAAAGCTACCTCTTTTCATC
580 CACTTTCATCCCCA-AACAGCCT-CTCCCT-AACCATGACTACCCAAAAGCTACCTCATTTCATC
* *
3258481 CTTTTCTTGCTAAATAATAGCAAAGAGAGGGAGAAAACTAGGCCAACAACATTTATTCCGATAAA
642 CTTTTCTTGCTAAATAATAGCAAAGAGAGGGAGAAAACTAGGCCAACAACATTTATTCCAAGAAA
*
3258546 CAAGGAAAGTTCAAGCTCTTTGGT
707 CAAGGAAAGCTCAAGCTCTTTGGT
*
3258570 ATACATTCAGGCATTTTTGACTACTTCGAGCCATTTTTGTGCTTCGCCATTGTTCATTCAAAACA
1 ATACATTCAGGCATTTTTGACCACTTCGAGCCATTTTTGTGCTTCGCCATTGTTCATTCAAAACA
3258635 TGTTTTTAACACACATTTTGCATCCAGAATCATT-G-AATCATGCTAAGATTCATCCTTAGGGTC
66 TGTTTTTAACACACATTTTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTC
*
3258698 GGAATGCAATTTAAACATGTTTTATGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAA
131 GGAATGCAATTTAAACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAA
* *
3258763 AGGACATGTCAGA-TTTTTCTGAATTCTGGCAGTCTCAGGTTCAGGACCACCACTGCATTGCAGA
196 AGGACATGTCAGATTTTTTC-GAATTCTGGCAGTCTCAAGTTCAAGACCACCACTGCATTGCAGA
3258827 ACCAATGGCAATGAGGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATA
260 ACCAATGGCAATGAGGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATA
* *
3258892 CCATAATGCCCTTGGTTTGTCCTCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
325 CCATAATGCCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCATGATTATAAGTAGTGGCTGTTG
*
3258957 GCTCAGCAAAAAAGGATCCTTTTTTTGGAGAAAAAAAGCAATTTTCCAGCAGCAAGAAACCCTTA
390 GCTCAGCAAAAAAGGATCCTTTTTTGGGAGAAAAAAAGCAATTTTCCAGCAGCAAGAAACCCTTA
3259022 GGAAATCCTTTAGCAACAAAAAAACCAAAAAACACAAAAAAAAACACTATTCCATTGGTTTCAAA
455 GGAAATCCTTTAGCAACAAAAAAACCAAAAAACAC-AAAAAAAACACTATTCCATTGGTTTCAAA
3259087 CTCCATTCCCGCAGATCCAAAAACCACCACCAAAGAACCTCCAAAAACTCCATATTCCTCACACT
519 CTCCATTCCCGCAGATCCAAAAACCACCACCAAAGAACCTCCAAAAACTCCATATTCCTCACACT
* * *
3259152 TTCATCCCCAAACAGCCTCTCCCTTAGCTTGACTACCCAAAAGCTACCTCATTTCATCCTTTTCT
584 TTCATCCCCAAACAGCCTCTCCCTAACCATGACTACCCAAAAGCTACCTCATTTCATCCTTTTCT
*
3259217 TGCTAAATAATAGCAAAGAGAGGGAGAAAACTAGGCCAACAACTTTTATTCCAAGAAACAAGGAA
649 TGCTAAATAATAGCAAAGAGAGGGAGAAAACTAGGCCAACAACATTTATTCCAAGAAACAAGGAA
3259282 AGCTCAA
714 AGCTCAA
3259289 ACTTTGGTAT
Statistics
Matches: 668, Mismatches: 41, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
727 6 0.01
728 56 0.08
729 456 0.68
730 35 0.05
731 95 0.14
732 20 0.03
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (730 bp):
ATACATTCAGGCATTTTTGACCACTTCGAGCCATTTTTGTGCTTCGCCATTGTTCATTCAAAACA
TGTTTTTAACACACATTTTGCATCCAGAATCATTAGAAATCATGCTAAGATTCATCCTTAGGGTC
GGAATGCAATTTAAACATGTTTTAAGATCAAATTTGCAAAAAAGCCAAATGTCATTTTCCACCAA
AGGACATGTCAGATTTTTTCGAATTCTGGCAGTCTCAAGTTCAAGACCACCACTGCATTGCAGAA
CCAATGGCAATGAGGGGCAGCCTGAGCTGGTGGCTGGTTGCCTCCTTGGGCAAAAGGGAAAATAC
CATAATGCCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCATGATTATAAGTAGTGGCTGTTGG
CTCAGCAAAAAAGGATCCTTTTTTGGGAGAAAAAAAGCAATTTTCCAGCAGCAAGAAACCCTTAG
GAAATCCTTTAGCAACAAAAAAACCAAAAAACACAAAAAAAACACTATTCCATTGGTTTCAAACT
CCATTCCCGCAGATCCAAAAACCACCACCAAAGAACCTCCAAAAACTCCATATTCCTCACACTTT
CATCCCCAAACAGCCTCTCCCTAACCATGACTACCCAAAAGCTACCTCATTTCATCCTTTTCTTG
CTAAATAATAGCAAAGAGAGGGAGAAAACTAGGCCAACAACATTTATTCCAAGAAACAAGGAAAG
CTCAAGCTCTTTGGT
Found at i:3260925 original size:52 final size:53
Alignment explanation
Indices: 3260868--3261202 Score: 199
Period size: 52 Copynumber: 6.4 Consensus size: 53
3260858 CAATTGTTCA
* *
3260868 TAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* * *
3260920 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* ** * ** * * ** *
3260972 CAATCAAGGATACTCCAACCTCG---TTATTTCATCGGGGATACTCCAA--CCCCGT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTC--C--AAAAACACCAATTTTCCTT
* * * * * *** *
3261024 TACCTCCAAGGGGATATTCTAACCCCGACTTTATTTCC-AAAATATTGA-TTT-CTCA
1 TA-AT-C--GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCT-T
*
3261079 TAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
** * * * *
3261131 TAATCGGGGATACTCCAATTCCAATTTTATTTCAAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* *
3261183 CAATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
3261203 TCGTTATTTC
Statistics
Matches: 208, Mismatches: 56, Indels: 38
0.69 0.19 0.13
Matches are distributed among these distances:
49 7 0.03
50 1 0.00
51 32 0.15
52 99 0.48
53 40 0.19
54 6 0.03
55 2 0.01
56 13 0.06
57 1 0.00
59 7 0.03
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.32
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
Found at i:3261036 original size:28 final size:28
Alignment explanation
Indices: 3260979--3261050 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
3260969 TCACAATCAA
* * * *
3260979 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTCCATAGG
3261007 GGATACTCCAACCCCGTTACCTCCA-AGG
1 GGATACTCCAACCCCGTTA-CTCCATAGG
* *
3261035 GGATATTCTAACCCCG
1 GGATACTCCAACCCCG
3261051 ACTTTATTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTCCATAGG
Found at i:3261229 original size:211 final size:211
Alignment explanation
Indices: 3260865--3261312 Score: 754
Period size: 211 Copynumber: 2.1 Consensus size: 211
3260855 TCTCAATTGT
*
3260865 TCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCTTTAATCGGGGA
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
* *
3260930 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCG
66 TACTCCAACTCCAATTTTATTTCAAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCG
* * * *
3260995 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATATTCTAACCCCGACTTTATTT
131 TTATTTCATCGGGGACACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGACTTTATTC
*
3261060 CCAAAATATTGATTTC
196 CCAAAATATTCATTTC
3261076 TCATAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACCAATTTTCCTTTAATCGGGG
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCTTTAATCGGGG
* *
3261140 ATACTCCAATTCCAATTTTATTTCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTC
65 ATACTCCAACTCCAATTTTATTTCAAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTC
* *
3261205 GTTATTTCATCGGGGACACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATT
130 GTTATTTCATCGGGGACACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGACTTTATT
3261270 CCCAAAATATTCATTTC
195 CCCAAAATATTCATTTC
**
3261287 TCATAATTAGGGATACTCCAACCCCG
1 TCATAATCGGGGATACTCCAACCCCG
3261313 TTATTTCCGA
Statistics
Matches: 222, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
210 4 0.02
211 218 0.98
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (211 bp):
TCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
TACTCCAACTCCAATTTTATTTCAAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCG
TTATTTCATCGGGGACACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTCATTTC
Found at i:3261365 original size:79 final size:79
Alignment explanation
Indices: 3261217--3261419 Score: 212
Period size: 79 Copynumber: 2.6 Consensus size: 79
3261207 TATTTCATCG
* ** *
3261217 GGGACACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTC
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATTC
* **
3261282 ATTTCTCATAATTA
66 ATTTCTCACAACCA
* * * * * *
3261296 GGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAATCCCGATTTTTTTTCC-TAATCA-T
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATT
*
3261359 CGATTTCTCACAACCG
65 C-ATTTCTCACAACCA
* * * *
3261375 GGGATGCTCTAACCCCGTTATTTTCAAGGGGATACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
3261420 TTATTATCTC
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 5 0.05
79 97 0.95
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATTC
ATTTCTCACAACCA
Found at i:3263502 original size:4 final size:4
Alignment explanation
Indices: 3263493--3263525 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
3263483 TATTTTGAGG
*
3263493 TATT TATT TATT TATT TATT TATT GATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
3263526 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:3273876 original size:10 final size:10
Alignment explanation
Indices: 3273836--3273878 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
3273826 CTTCTCTTCT
3273836 AAAAAAAAA-
1 AAAAAAAAAG
*
3273845 ACAAAAAAAAC
1 A-AAAAAAAAG
3273856 AAAGAAAAAAG
1 AAA-AAAAAAG
3273867 AAAAAAAAAG
1 AAAAAAAAAG
3273877 AA
1 AA
3273879 TCTGCTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 1 0.03
10 19 0.63
11 10 0.33
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3274952 original size:55 final size:54
Alignment explanation
Indices: 3274859--3275023 Score: 244
Period size: 55 Copynumber: 3.0 Consensus size: 54
3274849 ATGCCTTTTC
*
3274859 CCTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG
1 CCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACG
*
3274913 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
3274968 CTTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGACG
1 C-CTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
3275023 C
1 C
3275024 TCTCTCCTTT
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
54 5 0.05
55 86 0.84
56 11 0.11
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (54 bp):
CCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:3275106 original size:55 final size:54
Alignment explanation
Indices: 3275038--3275566 Score: 621
Period size: 55 Copynumber: 9.4 Consensus size: 54
3275028 TCCTTTCACC
*
3275038 CTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3275091 CCTTTCAGTACTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
3275146 CTTCTCAGTCCTCAAAGAGCAGAACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTT-TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
3275201 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTTTAAAGCCCACAGAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3275256 CTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAGGCCCACACAAGTTGGTGACA
1 CTTTC-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3275311 TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
3275366 TTTTCCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* ** *
3275421 TTTTCCAGTAGTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGTGC-
1 CTTT-CAGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGT-G-GCA
* **
3275483 CTTTCAGTCCTCAAAGAGTAGGACGCCTTTCCTTTTCAAAGCCCACATGAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACG-----CC-TTTCAAAGCCCACACAAGTTGGTGGCA
*
3275543 CTTTTTAGTCCTCAAAGAGCAGGA
1 C-TTTCAGTCCTCAAAGAGCAGGA
3275567 TGCACCTTAT
Statistics
Matches: 412, Mismatches: 42, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
54 9 0.02
55 306 0.74
56 1 0.00
57 1 0.00
59 4 0.01
60 6 0.01
61 75 0.18
62 8 0.02
63 2 0.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (54 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:3275162 original size:149 final size:149
Alignment explanation
Indices: 3274892--3275332 Score: 465
Period size: 149 Copynumber: 2.9 Consensus size: 149
3274882 TGGCACTTCC
* * *
3274892 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCACTTTCCAGTACTCAA
* * * *
3274957 AGAGCAGGACACTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGAC
66 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAAC
3275022 GCTCTCTCCTTTCACCCTT
131 GCTCTCTCCTTTCACCCTT
3275041 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCACCTTT-CAGTACTCA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCA-CTTTCCAGTACTCA
**
3275105 AAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAA
65 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAA
* * ** **
3275170 CGCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
130 CG-C--T-----CTCTC-C---TT--TCACCCTT
* * * * *
3275204 TCCAGTCCTCAAAGAGCAGGACGCTTTTTAAAGCCCACAGAAGTTGGTGGCAC-TTCCTAGTCCT
1 T--AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCACTTTCC-AGTACT
* * * * *
3275268 CAAAGAGCAGGACGCCTTTCAAGGCCCACACAAGTTGGTGACA-TTTTCCAGTCCTCAAAGAGCA
63 CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT-CAGTCCTCAAAGAGCA
3275332 G
127 G
3275333 GATGCCTTTC
Statistics
Matches: 247, Mismatches: 25, Indels: 24
0.83 0.08 0.08
Matches are distributed among these distances:
149 118 0.48
150 4 0.02
152 1 0.00
157 3 0.01
158 1 0.00
161 2 0.01
163 7 0.03
164 5 0.02
165 106 0.43
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (149 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGGGGCACTTTCCAGTACTCAA
AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAAC
GCTCTCTCCTTTCACCCTT
Found at i:3276035 original size:13 final size:13
Alignment explanation
Indices: 3276017--3276042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3276007 TACACCAAGT
3276017 ATGTATCGATACA
1 ATGTATCGATACA
3276030 ATGTATCGATACA
1 ATGTATCGATACA
3276043 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3278295 original size:21 final size:21
Alignment explanation
Indices: 3278262--3278306 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3278252 TTGCAAGTTG
*
3278262 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3278284 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3278304 AAA
1 AAA
3278307 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3280129 original size:15 final size:15
Alignment explanation
Indices: 3280109--3280139 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3280099 TAAAAATGTC
*
3280109 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3280124 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3280139 C
1 C
3280140 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3283424 original size:13 final size:13
Alignment explanation
Indices: 3283406--3283457 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
3283396 ATAATCACCC
3283406 TGTATCGATACAA
1 TGTATCGATACAA
3283419 TGTATCGATACAA
1 TGTATCGATACAA
3283432 TGTATCGATACAA
1 TGTATCGATACAA
3283445 TGTATCGATACAA
1 TGTATCGATACAA
3283458 AGAAAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3284000 original size:55 final size:55
Alignment explanation
Indices: 3283916--3284238 Score: 366
Period size: 55 Copynumber: 5.7 Consensus size: 55
3283906 AAAATATCAG
* *
3283916 AAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAGGCCCACAC
1 AAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC
*
3283971 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACAC
1 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC
* *
3284026 GAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACAC
1 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC
*
3284081 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACAC
1 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACAC
* * *
3284142 AAGTTGGTGGTGC-CTTT-CAGTCCTCAAAGAGTAGGACGCCTTTCCTTTTCAAAGCCCACAT
1 AAGTTGGT-G-GCATTTTCCAGTCCTCAAAGAGCAGGACG-----CC-TTTCAAAGCCCACAC
* * *
3284203 GAGTTGGTGGCACTTTT-TAGTCCTCAAATAGCAGGA
1 AAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
3284239 TGCACCTTAT
Statistics
Matches: 233, Mismatches: 18, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
55 133 0.57
56 4 0.02
57 1 0.00
59 4 0.02
60 5 0.02
61 76 0.33
62 8 0.03
63 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (55 bp):
AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAC
Found at i:3284110 original size:110 final size:111
Alignment explanation
Indices: 3283916--3284241 Score: 408
Period size: 110 Copynumber: 2.8 Consensus size: 111
3283906 AAAATATCAG
* * *
3283916 AAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAGGCCCACACAAGTTGGTGG
1 AAGTTGGTGGCATTTCC-AGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
3283981 CATTTTCCAGTCCTCAAAGAGCAGGATGC-CTTT-CAAAGCCCACAC
65 CATTTTCCAGTCCTCAAAGAGCAGGATGCTCTTTGCAAAGCCCACAC
*
3284026 GAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
1 AAGTTGGTGGCA-TTTCCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
3284091 CATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACAC
65 CATTTTCCAGTCCTCAAAGAGCAGGATG----CTCTTTGCAAAGCCCACAC
* **
3284142 AAGTTGGTGGTGCCTTT-CAGTCCTCAAAGAGTAGGACGCCTTTCCTTTTCAAAGCCCACATGAG
1 AAGTTGGT-G-GCATTTCCAGTCCTCAAAGAGTAGGACG-----CC-TTTCAAAGCCCACACAAG
* *
3284206 TTGGTGGCACTTTT-TAGTCCTCAAATAGCAGGATGC
58 TTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGC
3284242 ACCTTATTTT
Statistics
Matches: 190, Mismatches: 10, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
110 84 0.44
111 4 0.02
114 1 0.01
115 4 0.02
116 40 0.21
117 4 0.02
118 3 0.02
121 2 0.01
122 44 0.23
123 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (111 bp):
AAGTTGGTGGCATTTCCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
ATTTTCCAGTCCTCAAAGAGCAGGATGCTCTTTGCAAAGCCCACAC
Found at i:3284707 original size:13 final size:13
Alignment explanation
Indices: 3284689--3284714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3284679 TACACCAAGT
3284689 ATGTATCGATACA
1 ATGTATCGATACA
3284702 ATGTATCGATACA
1 ATGTATCGATACA
3284715 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3285500 original size:42 final size:41
Alignment explanation
Indices: 3285450--3285553 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 41
3285440 CTTTTTCACG
*
3285450 TTGTCCTCAAGAAGCAGGACACT-TTCCTTTTCTTCTTTGCCT
1 TTGTCCTCAAGAAGCAGGACACTATTCC-ATTC-TCTTTGCCT
* * * *
3285492 TTGTCCTCAAGGAGCAAGAC-CTATTTCATTCTCTTTTCCT
1 TTGTCCTCAAGAAGCAGGACACTATTCCATTCTCTTTGCCT
* *
3285532 TTGTCCTCAAAAAGTAGGACAC
1 TTGTCCTCAAGAAGCAGGACAC
3285554 CCCTTCCATT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 24 0.47
41 6 0.12
42 21 0.41
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (41 bp):
TTGTCCTCAAGAAGCAGGACACTATTCCATTCTCTTTGCCT
Found at i:3286274 original size:32 final size:32
Alignment explanation
Indices: 3286224--3286296 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
3286214 ACAAACCGTA
* *
3286224 AATATATCAATACATAAGTGTTGTATCGATGC
1 AATATATCGATACATAAGTGTTGTATCGATAC
* *
3286256 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATATATCGATACATAAGTGTTGTATCGATAC
3286288 AATATATCG
1 AATATATCG
3286297 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
AATATATCGATACATAAGTGTTGTATCGATAC
Found at i:3286338 original size:13 final size:13
Alignment explanation
Indices: 3286320--3286345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3286310 GCCAAGGAAA
3286320 TGTATCGATACAT
1 TGTATCGATACAT
3286333 TGTATCGATACAT
1 TGTATCGATACAT
3286346 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3288687 original size:52 final size:52
Alignment explanation
Indices: 3288598--3288911 Score: 180
Period size: 52 Copynumber: 6.0 Consensus size: 52
3288588 TTCTCAAACC
* * **
3288598 CCGATTTTATTTTC-AAAACACTAATTTTTCTTTAATCGGGGATACTCCAACT
1 CCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATCGGGGATACTCCAACT
*
3288650 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAAC-
1 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACT
** * * *** *
3288701 CTCG---TTATTTCATCGGGGATACTCCAACCCCGTT-AC-CTCTGAGGGGATACTCCAAC-
1 C-CGATTTTATTTC--C--AAAAACACCAA--TTTTTCACAATC---GGGGATACTCCAACT
** * * *** * *
3288757 CCTGGCTTTA-TTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACT
1 CC-GATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACT
* * * **
3288809 CCGGTTTTATTT-CTAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
1 CCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATCGGGGATACTCCAACT
* *
3288861 CCGATTTTATTTCCAAAAACACTAATTTTTCACAATCAGGGATACTCCAAC
1 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
3288912 CTCGTTATTT
Statistics
Matches: 197, Mismatches: 44, Indels: 42
0.70 0.16 0.15
Matches are distributed among these distances:
49 7 0.04
51 33 0.17
52 85 0.43
53 40 0.20
54 7 0.04
55 3 0.02
56 16 0.08
58 3 0.02
59 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACT
Found at i:3288720 original size:28 final size:28
Alignment explanation
Indices: 3288684--3288758 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
3288674 ATTTTTCACA
* * **
3288684 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
3288712 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
*
3288740 -TGAGGGGATACTCCAACCC
1 AT-CGGGGATACTCCAACCC
3288759 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:3288957 original size:28 final size:28
Alignment explanation
Indices: 3288899--3288971 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
3288889 TTCACAATCA
* ** **
3288899 GGGATACTCCAACCTCGTTATTTCATCG
1 GGGATACTCCAACCCCGTTACATCAGAG
*
3288927 GGGATACTCCAACCCCGTTACATCCGAG
1 GGGATACTCCAACCCCGTTACATCAGAG
3288955 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
3288972 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTACATCAGAG
Found at i:3288966 original size:211 final size:211
Alignment explanation
Indices: 3288602--3289018 Score: 739
Period size: 211 Copynumber: 2.0 Consensus size: 211
3288592 CAAACCCCGA
* *
3288602 TTTTATTTTCAAAACACTAATTTTTCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAA
1 TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAA
3288667 AACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCC
66 AACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCC
* * *
3288732 GTTACCTCTGAGGGGATACTCCAACCCTGGCTTTATTCCCAAAATATTGATTTCTCATAATCGGG
131 GTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCGGG
3288797 GATACTCCAACTCCGG
196 GATACTCCAACTCCGG
3288813 TTTTA-TTTCTAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAA
1 TTTTATTTTC-AAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAA
*
3288877 AAACACTAATTTTTCACAATC-AGGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACC
65 AAACACCAATTTTTCACAATCGA-GGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACC
*
3288941 CCGTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTG
129 CCGTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCG
3289006 GGGATACTCCAAC
194 GGGATACTCCAAC
3289019 CCCGTTATTT
Statistics
Matches: 197, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
210 5 0.03
211 192 0.97
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (211 bp):
TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAA
AACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCC
GTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCGGG
GATACTCCAACTCCGG
Found at i:3289037 original size:107 final size:107
Alignment explanation
Indices: 3288674--3289050 Score: 376
Period size: 107 Copynumber: 3.6 Consensus size: 107
3288664 AAAAACACCA
* * * * * *
3288674 ATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCT
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCATAGGGGATACTCCAACCCCGTTACAT
* *
3288739 CTGAGGGGATACTCCAACCCTGGCTTTATTCCCAAAATATTG
66 CCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
* * * ** *
3288781 ATTTCTCATAATCGGGGATACTCCAACTCCGGTTTTATTTC-TA----AAACACCAATTTTCCTT
1 ATTTCTCATAATCGGGGATACTCCAAC-CCCG--TTATTTCATAGGGGATACTCCAA--CCCCGT
* ** * * * *
3288841 TA-AT-C--GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACTA
61 TACATCCGAGGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTG
* * * * *
3288885 ATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACAT
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCATAGGGGATACTCCAACCCCGTTACAT
3288950 CCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
66 CCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
* * *
3288992 ATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTCTTAGGGGATACTCCAATCCCG
1 ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCATAGGGGATACTCCAACCCCG
3289051 ATTTTTTTTC
Statistics
Matches: 208, Mismatches: 47, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
101 7 0.03
102 1 0.00
103 22 0.11
104 39 0.19
105 9 0.04
106 9 0.04
107 90 0.43
108 23 0.11
109 1 0.00
110 7 0.03
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (107 bp):
ATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCATAGGGGATACTCCAACCCCGTTACAT
CCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
Found at i:3289074 original size:79 final size:79
Alignment explanation
Indices: 3288925--3289106 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 79
3288915 GTTATTTCAT
** *
3288925 CGGGGATACTCCAACCCCGTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
3288990 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* ** * * * * *
3289004 TGGGGATACTCCAACCCCGTTATTTCTTAGGGGATACTCCAATCCCGATTTTTTTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
3289068 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
3289083 CGGGGATACTCCAACCCCGTTATT
1 CGGGGATACTCCAACCCCGTTATT
3289107 ATCTCCAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 3 0.03
79 84 0.97
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:3290852 original size:19 final size:20
Alignment explanation
Indices: 3290819--3290863 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3290809 GACCCCTCTT
*
3290819 TTTTTGTATTATTTTTTTGG
1 TTTTTGTATTATTTTTTTGC
*
3290839 TTTTTGT-TTTTTTTTTTGC
1 TTTTTGTATTATTTTTTTGC
3290858 TTTTTG
1 TTTTTG
3290864 AGAATGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.80
Consensus pattern (20 bp):
TTTTTGTATTATTTTTTTGC
Found at i:3297675 original size:593 final size:594
Alignment explanation
Indices: 3296485--3297675 Score: 2195
Period size: 594 Copynumber: 2.0 Consensus size: 594
3296475 GGATTCGCAA
*
3296485 CAATATTAGGTCCTTGATTTGTCCTGAACTGCAGCACCTTCGAGTCAATGAGACTTTGCACTTTT
1 CAATATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCAATGAGACTTTGCACTTTT
*
3296550 TTTTAAGGGCAATGCAACTTTCGATGTCATGCCCCGCTGCCCAAGCATGATACTCACATTGAGCA
66 TTTTAAGGGCAATGCAACTTTCGATGTCATGCCCCGCTACCCAAGCATGATACTCACATTGAGCA
3296615 TTGGGATTGTACAATTATAGATATGGAGGCTTCTTCTCTAGGACATACTCAGGGACCACCAGATG
131 TTGGGATTGTACAATTATAGATATGGAGGCTTCTTCTCTAGGACATACTCAGGGACCACCAGATG
3296680 ACTTTGTAGAAGAGTCTAGTAAAGTTCTTTATATGTTATGGGAATGGGGTCAAATGATGGTCTTT
196 ACTTTGTAGAAGAGTCTAGTAAAGTTCTTTATATGTTATGGGAATGGGGTCAAATGATGGTCTTT
3296745 GCTGATTTGTGCCTTGGTTACTTGGCACACCATTGGTTAGTTGAATGGTGTTTCGATGATTTTAT
261 GCTGATTTGTGCCTTGGTTACTTGGCACACCATTGGTTAGTTGAATGGTGTTTCGATGATTTTAT
3296810 GGTGGGTAGTCAGGTGGTGGATGATTTTGTGGTGGGTTTTGGTGGAATTGTAAAGGTTGGGTTGT
326 GGTGGGTAGTCAGGTGGTGGATGATTTTGTGGTGGGTTTTGGTGGAATTGTAAAGGTTGGGTTGT
3296875 AATTTATAGCATAAACTGGTTGATGAGGCATTGTAGCAGACGAATAGGGTGTATTTGGGTAGCGA
391 AATTTATAGCATAAACTGGTTGATGAGGCATTGTAGCAGACGAATAGGGTGTATTTGGGTAGCGA
* *
3296940 AACTTAGATCTTTAGCAATGCTTAGGGTTAGCATAACTTATGGTATTAGCTTTCCCTTTTTTTTT
456 AAATTAGATCTTTAGCAATGCCTAGGGTTAGCATAACTTATGGTATTAGCTTTCCCTTTTTTTTT
* *
3297005 CTTAGTAGCGGTAGGCTTTTTGCTTATTCTCGATGACTCTCCCATCAACATTCTGCCACTCTTAA
521 CTTAGTAGCGGTAGGCTTTTTGCTTATTCCCAATGACTCTCCCATCAACATTCTGCCACTCTTAA
*
3297070 TCGCGGCAT
586 TCGCGACAT
* *
3297079 CAATATTAGGTCCTTGATTTGTCCCGAATTGCAGCACCTTCGAGTCGATGAGACTTTGCACTTTT
1 CAATATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCAATGAGACTTTGCACTTTT
3297144 TTTTAAGGGCAATGCAACTTTCGATGTCATGCCCCGCTACCCAAGCATGATACTCACATTGAGCA
66 TTTTAAGGGCAATGCAACTTTCGATGTCATGCCCCGCTACCCAAGCATGATACTCACATTGAGCA
3297209 TTGGGATTGTACAATTATAGATATGGAGGCTTCTTCTCTAGGACATACTCAGGGACCACCAGATG
131 TTGGGATTGTACAATTATAGATATGGAGGCTTCTTCTCTAGGACATACTCAGGGACCACCAGATG
* *
3297274 ACTTTGTAGCAGAGTGTAGTAAAGTTCTTTATATGTTATGGGAATGGGGTCAAATGATGGTCTTT
196 ACTTTGTAGAAGAGTCTAGTAAAGTTCTTTATATGTTATGGGAATGGGGTCAAATGATGGTCTTT
* * *
3297339 GCTGATTTGTGCCTTGGTTATTTGGCACACCATTGGTTGGTTGAGTGGTGTTTCGATGATTTTAT
261 GCTGATTTGTGCCTTGGTTACTTGGCACACCATTGGTTAGTTGAATGGTGTTTCGATGATTTTAT
3297404 GGTGGGTAGTCAGGTGGTGGATGATTTTGTGGTGGG-TTTGGTGGAATTGTAAAGGTTGGGTTGT
326 GGTGGGTAGTCAGGTGGTGGATGATTTTGTGGTGGGTTTTGGTGGAATTGTAAAGGTTGGGTTGT
* * * *
3297468 AATTTGTAGCATAAGCTGGTTGATGAGGCGTTGTAGCCGACGAATAGGGTGTATTTGGGTAGCGA
391 AATTTATAGCATAAACTGGTTGATGAGGCATTGTAGCAGACGAATAGGGTGTATTTGGGTAGCGA
*
3297533 AAATTAGATCTTTAGCATTGCCTAGGGTTAGCATAACTTATGGTATTAGCTTTCCCTTTTTTTTT
456 AAATTAGATCTTTAGCAATGCCTAGGGTTAGCATAACTTATGGTATTAGCTTTCCCTTTTTTTTT
*
3297598 CTTAGTAGCGGTAGGCTTTTTGCTTATTCCCAATGACTTTCCCATCAACATTCTGCCACTCTTAA
521 CTTAGTAGCGGTAGGCTTTTTGCTTATTCCCAATGACTCTCCCATCAACATTCTGCCACTCTTAA
3297663 TCGCGACAT
586 TCGCGACAT
3297672 CAAT
1 CAAT
3297676 CATTTCGCCA
Statistics
Matches: 577, Mismatches: 20, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
593 225 0.39
594 352 0.61
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (594 bp):
CAATATTAGGTCCTTGATTTGTCCCGAACTGCAGCACCTTCGAGTCAATGAGACTTTGCACTTTT
TTTTAAGGGCAATGCAACTTTCGATGTCATGCCCCGCTACCCAAGCATGATACTCACATTGAGCA
TTGGGATTGTACAATTATAGATATGGAGGCTTCTTCTCTAGGACATACTCAGGGACCACCAGATG
ACTTTGTAGAAGAGTCTAGTAAAGTTCTTTATATGTTATGGGAATGGGGTCAAATGATGGTCTTT
GCTGATTTGTGCCTTGGTTACTTGGCACACCATTGGTTAGTTGAATGGTGTTTCGATGATTTTAT
GGTGGGTAGTCAGGTGGTGGATGATTTTGTGGTGGGTTTTGGTGGAATTGTAAAGGTTGGGTTGT
AATTTATAGCATAAACTGGTTGATGAGGCATTGTAGCAGACGAATAGGGTGTATTTGGGTAGCGA
AAATTAGATCTTTAGCAATGCCTAGGGTTAGCATAACTTATGGTATTAGCTTTCCCTTTTTTTTT
CTTAGTAGCGGTAGGCTTTTTGCTTATTCCCAATGACTCTCCCATCAACATTCTGCCACTCTTAA
TCGCGACAT
Found at i:3298583 original size:13 final size:13
Alignment explanation
Indices: 3298565--3298589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3298555 ATTACTCAAA
3298565 TGTATCGATACAT
1 TGTATCGATACAT
3298578 TGTATCGATACA
1 TGTATCGATACA
3298590 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3298642 original size:52 final size:52
Alignment explanation
Indices: 3298598--3298726 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
3298588 CACTGATCTT
3298598 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
3298650 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
3298702 GGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3298727 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:3310565 original size:51 final size:51
Alignment explanation
Indices: 3310457--3310572 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
3310447 AAAATAACGG
*
3310457 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTATTTTAGAAATAAGACCGA
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAGTATTTTAGAAATAAAACCGA
* * * *
3310508 GGTTGGAGTATCCCCGATGGTGGAAAA-TAGATGTTTTAGAAATAAAATC-A
1 GGTTGGAGTATCCCCAATGGTGAAAAATTAG-TATTTTAGAAATAAAACCGA
*
3310558 GGATTGGAGCATCCC
1 GG-TTGGAGTATCCC
3310573 TTCAAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 6 0.11
51 51 0.89
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATGGTGAAAAATTAGTATTTTAGAAATAAAACCGA
Found at i:3310593 original size:79 final size:77
Alignment explanation
Indices: 3310510--3310791 Score: 307
Period size: 79 Copynumber: 3.6 Consensus size: 77
3310500 AAGACCGAGG
* *
3310510 TTGGAGTATCCCCGATGGTGGAAAATAGATGTTTTAGAAATAAAATCAGGATTGGAGCATCCCTT
1 TTGGAGTATCCCCGATGGTGGAAAATAGGTGTTTTAGAAATAAAATC-GGATTGGAGTATCCCTT
3310575 CAAAAATAACGGGA
65 -AAAAATAACGGGA
* * * * * *
3310589 TTGGAGTATGCCTGATTGTGAAAAATCA-GTGTTTTAGAAATAAAATCGGGGTTAGAGTATCCTC
1 TTGGAGTATCCCCGATGGTGGAAAAT-AGGTGTTTTAGAAATAAAATC-GGATTGGAGTATCC-C
* *
3310653 TTAGAAATAACGGGT
63 TTAAAAATAACGGGA
* *
3310668 TTGGAGTATCCCCGATGGT-GAAAATTTGGTATTTTAGAAATAAAATCGGAGTTGGAGTATCTCC
1 TTGGAGTATCCCCGATGGTGGAAAA-TAGGTGTTTTAGAAATAAAATCGGA-TTGGAGTATC-CC
* *
3310732 TAAAAAATAACGGGG
63 TTAAAAATAACGGGA
* * * * *
3310747 TTGGAGTATCCCCGATGATGGAGAGTTGGCGTTTTAGAAATAAAA
1 TTGGAGTATCCCCGATGGTGGAAAATAGGTGTTTTAGAAATAAAA
3310792 ACATCAATGA
Statistics
Matches: 169, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
78 6 0.04
79 155 0.92
80 8 0.05
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (77 bp):
TTGGAGTATCCCCGATGGTGGAAAATAGGTGTTTTAGAAATAAAATCGGATTGGAGTATCCCTTA
AAAATAACGGGA
Found at i:3313226 original size:21 final size:20
Alignment explanation
Indices: 3313200--3313275 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
3313190 ATATAATGAA
3313200 AAATGTATCGATACAAACAGT
1 AAATGTATCGATACAAA-AGT
* ** *
3313221 AAATGTATTGATACATTTACT
1 AAATGTATCGATACA-AAAGT
* *
3313242 GAATGTATCGATAC-AATGT
1 AAATGTATCGATACAAAAGT
3313261 AAATGTATCGATACA
1 AAATGTATCGATACA
3313276 TTTCCTCGGC
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
19 14 0.33
21 28 0.67
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACAAAAGT
Found at i:3313274 original size:40 final size:42
Alignment explanation
Indices: 3313201--3313278 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 42
3313191 TATAATGAAA
*
3313201 AATGTATCGATACAAACAGTAAATGTATTGATACATTTACTG
1 AATGTATCGATACAAACAGTAAATGTATCGATACATTTACTG
*
3313243 AATGTATCGATAC-AA-TGTAAATGTATCGATACATTT
1 AATGTATCGATACAAACAGTAAATGTATCGATACATTT
3313279 CCTCGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 19 0.56
41 2 0.06
42 13 0.38
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (42 bp):
AATGTATCGATACAAACAGTAAATGTATCGATACATTTACTG
Found at i:3314534 original size:13 final size:13
Alignment explanation
Indices: 3314516--3314540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3314506 ACATTTGGTC
3314516 ATGTATCGATACA
1 ATGTATCGATACA
3314529 ATGTATCGATAC
1 ATGTATCGATAC
3314541 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3315123 original size:22 final size:22
Alignment explanation
Indices: 3315096--3315140 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3315086 TTTTCTTTTC
3315096 TCTCCCCCTTAATGAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
3315118 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
3315140 T
1 T
3315141 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:3317018 original size:13 final size:13
Alignment explanation
Indices: 3317000--3317037 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3316990 ATAAACCCTT
*
3317000 TGTATCGATACAC
1 TGTATCGATACAA
3317013 TGTATCGATACAA
1 TGTATCGATACAA
3317026 TGTATCGATACA
1 TGTATCGATACA
3317038 GAGAGTGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3318676 original size:13 final size:13
Alignment explanation
Indices: 3318658--3318715 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
3318648 TTCAATGATT
3318658 TGTATCGATACAA
1 TGTATCGATACAA
3318671 TGTATCGATACATAA
1 TGTATCGATAC--AA
3318686 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
3318703 TGTATCGCTACAA
1 TGTATCGATACAA
3318716 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3318831 original size:52 final size:52
Alignment explanation
Indices: 3318787--3318915 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
3318777 CACTGATCTT
3318787 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
** * *
3318839 TGTATCGATACATATAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
*
3318891 TGTATCGATATATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3318916 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
Found at i:3325704 original size:429 final size:429
Alignment explanation
Indices: 3324905--3325757 Score: 1661
Period size: 429 Copynumber: 2.0 Consensus size: 429
3324895 ATCCCTCCAA
*
3324905 GCTTGTCAAGACGAATCAATAAGGGCTTCCAAGCAATGCGACTTAGAGTGGTAGGCAACAGTCGA
1 GCTTGTCAAGACGAATCAATAAGGGCTTCCAAGCAACGCGACTTAGAGTGGTAGGCAACAGTCGA
*
3324970 CCAAGTACATCTGAACTACCAAGCACAACGTCAGCACCTCACTGAGCAAATTCAGATGGCTCAAC
66 CCAAGTACATCTGAACTACCAAGCACAACGTCAGCACCTCACTAAGCAAATTCAGATGGCTCAAC
3325035 TAGAGGCAGATGACATGGTTGAAGGAGCTCGATCCATAAGACGTGATATTGTCCCCGTTGGGAAT
131 TAGAGGCAGATGACATGGTTGAAGGAGCTCGATCCATAAGACGTGATATTGTCCCCGTTGGGAAT
* *
3325100 CACGGGTAACTGTTTTTAACTTTTCTTGATCGTGTGATTACACAGTATAATCACGTTAGATATTT
196 CACGGGTAACTATTTTTAACTTTTCTTGATCGCGTGATTACACAGTATAATCACGTTAGATATTT
3325165 TCAGATGTAACCGTGTTGTAAAAATGAAAAAAAAAACTTCTTTTGTGGTTCTATGAATGATGTTA
261 TCAGATGTAACCGTGTTGTAAAAATGAAAAAAAAAACTTCTTTTGTGGTTCTATGAATGATGTTA
3325230 TTGACGAAGCTATTCCAAGAATCAATTGTCTCTACTGCATATGCATATTCAATCTCACTTCATTA
326 TTGACGAAGCTATTCCAAGAATCAATTGTCTCTACTGCATATGCATATTCAATCTCACTTCATTA
3325295 GTTCCTACACTTACATCAATCATTCCTAGCGCAATAAGG
391 GTTCCTACACTTACATCAATCATTCCTAGCGCAATAAGG
3325334 GCTTGTCAAGACGAATCAATAAGGGCTTCCAAGCAACGCGACTTAGAGTGGTAGGCAACAGTCGA
1 GCTTGTCAAGACGAATCAATAAGGGCTTCCAAGCAACGCGACTTAGAGTGGTAGGCAACAGTCGA
3325399 CCAAGTACATCTGAACTACCAAGCACAACGTCAGCACCTCACTAAGCAAATTCAGATGGCTCAAC
66 CCAAGTACATCTGAACTACCAAGCACAACGTCAGCACCTCACTAAGCAAATTCAGATGGCTCAAC
3325464 TAGAGGCAGATGACATGGTTGAAGGAGCTCGATCCATAAGACGTGATATTGTCCCCGTTGGGAAT
131 TAGAGGCAGATGACATGGTTGAAGGAGCTCGATCCATAAGACGTGATATTGTCCCCGTTGGGAAT
3325529 CACGGGTAACTATTTTTAACTTTTCTTGATCGCGTGATTACACAGTATAATCACGTTAGATATTT
196 CACGGGTAACTATTTTTAACTTTTCTTGATCGCGTGATTACACAGTATAATCACGTTAGATATTT
3325594 TCAGATGTAACCGTGTTGTAAAAATGAAAAAAAAAACTTCTTTTGTGGTTCTATGAATGATGTTA
261 TCAGATGTAACCGTGTTGTAAAAATGAAAAAAAAAACTTCTTTTGTGGTTCTATGAATGATGTTA
*
3325659 TTGACGAAGCTGTTCCAAGAATCAATTGTCTCTACTGCATATGCATATTCAATCTCACTTCATTA
326 TTGACGAAGCTATTCCAAGAATCAATTGTCTCTACTGCATATGCATATTCAATCTCACTTCATTA
3325724 GTTCCTACACTTACATCAATCATTCCTAGCGCAA
391 GTTCCTACACTTACATCAATCATTCCTAGCGCAA
3325758 CACCTCATTA
Statistics
Matches: 419, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 419 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (429 bp):
GCTTGTCAAGACGAATCAATAAGGGCTTCCAAGCAACGCGACTTAGAGTGGTAGGCAACAGTCGA
CCAAGTACATCTGAACTACCAAGCACAACGTCAGCACCTCACTAAGCAAATTCAGATGGCTCAAC
TAGAGGCAGATGACATGGTTGAAGGAGCTCGATCCATAAGACGTGATATTGTCCCCGTTGGGAAT
CACGGGTAACTATTTTTAACTTTTCTTGATCGCGTGATTACACAGTATAATCACGTTAGATATTT
TCAGATGTAACCGTGTTGTAAAAATGAAAAAAAAAACTTCTTTTGTGGTTCTATGAATGATGTTA
TTGACGAAGCTATTCCAAGAATCAATTGTCTCTACTGCATATGCATATTCAATCTCACTTCATTA
GTTCCTACACTTACATCAATCATTCCTAGCGCAATAAGG
Found at i:3333261 original size:13 final size:13
Alignment explanation
Indices: 3333243--3333268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3333233 CAATTTTTTG
3333243 TGTATCGATACAT
1 TGTATCGATACAT
3333256 TGTATCGATACAT
1 TGTATCGATACAT
3333269 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3333353 original size:20 final size:20
Alignment explanation
Indices: 3333328--3333400 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3333318 CAACTTTTTT
3333328 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3333348 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3333369 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3333389 ATGTATCGATAC
1 ATGTATCGATAC
3333401 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3333366 original size:41 final size:41
Alignment explanation
Indices: 3333307--3333400 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3333297 CTGCCAAGAA
*
3333307 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3333348 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3333389 ATGTATCGATAC
1 ATGTATCGATAC
3333401 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3333382 original size:21 final size:21
Alignment explanation
Indices: 3333307--3333382 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3333297 CTGCCAAGAA
* *
3333307 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3333328 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3333348 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3333369 ATGTATCGATACAT
1 ATGTATCGATACAT
3333383 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3338661 original size:13 final size:13
Alignment explanation
Indices: 3338643--3338668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3338633 CAATTTTTTG
3338643 TGTATCGATACAT
1 TGTATCGATACAT
3338656 TGTATCGATACAT
1 TGTATCGATACAT
3338669 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3338753 original size:20 final size:20
Alignment explanation
Indices: 3338728--3338800 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3338718 CAACTTTTTT
3338728 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3338748 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3338769 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3338789 ATGTATCGATAC
1 ATGTATCGATAC
3338801 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3338766 original size:41 final size:41
Alignment explanation
Indices: 3338707--3338800 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3338697 CTGCCAAGAA
*
3338707 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3338748 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3338789 ATGTATCGATAC
1 ATGTATCGATAC
3338801 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3338782 original size:21 final size:21
Alignment explanation
Indices: 3338707--3338782 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3338697 CTGCCAAGAA
* *
3338707 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3338728 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3338748 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3338769 ATGTATCGATACAT
1 ATGTATCGATACAT
3338783 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3342328 original size:13 final size:13
Alignment explanation
Indices: 3342310--3342336 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3342300 TACATTTTAT
3342310 AATGTATCGATAC
1 AATGTATCGATAC
3342323 AATGTATCGATAC
1 AATGTATCGATAC
3342336 A
1 A
3342337 TTTGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3342333 original size:33 final size:34
Alignment explanation
Indices: 3342291--3342357 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
3342281 TTTTGCCTGC
*
3342291 ATGTATCGATACATTTTA-TAATGTATCGATACA
1 ATGTATCGATACATTTGAGTAATGTATCGATACA
3342324 ATGTATCGATACATTTGAGTAATGTATCGATACA
1 ATGTATCGATACATTTGAGTAATGTATCGATACA
3342358 TTTTTTGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (34 bp):
ATGTATCGATACATTTGAGTAATGTATCGATACA
Found at i:3342414 original size:33 final size:33
Alignment explanation
Indices: 3342377--3342443 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3342367 AGTAGCTTAA
3342377 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3342410 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3342443 A
1 A
3342444 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3342417 original size:13 final size:13
Alignment explanation
Indices: 3342399--3342423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3342389 CAAAAAAATA
3342399 TGTATCGATACAT
1 TGTATCGATACAT
3342412 TGTATCGATACA
1 TGTATCGATACA
3342424 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3348122 original size:19 final size:19
Alignment explanation
Indices: 3348100--3348211 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 19
3348090 GGTGTTCTCC
3348100 ACAAAAAAAAAACAAACAA
1 ACAAAAAAAAAACAAACAA
3348119 ACAAAAAAAAAGA-AGAA-AA
1 ACAAAAAAAAA-ACA-AACAA
* *
3348138 A-AAAACAACAACAAAACAA
1 ACAAAAAAAAAAC-AAACAA
*
3348157 A-AAAAAAGAAAAAAAACAAA
1 ACAAAAAA-AAAACAAAC-AA
*
3348177 ACAAAACAATAAA-AAACAA
1 ACAAAA-AAAAAACAAACAA
3348196 ACAAATAAAAAAACAA
1 ACAAA-AAAAAAACAA
3348212 CAATAAAAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
17 1 0.01
18 9 0.12
19 40 0.53
20 16 0.21
21 7 0.09
22 2 0.03
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (19 bp):
ACAAAAAAAAAACAAACAA
Found at i:3348137 original size:29 final size:30
Alignment explanation
Indices: 3348103--3348220 Score: 125
Period size: 31 Copynumber: 3.8 Consensus size: 30
3348093 GTTCTCCACA
*
3348103 AAAAAAAAAC-AAACAAACAAAAAAAAAGAAG
1 AAAAAAAAACAAAACAAA-ACAAAAAAA-AAG
3348134 AAAAAAAAACAACAACAAAACAAAAAAAAAG
1 AAAAAAAAACAA-AACAAAACAAAAAAAAAG
* *
3348165 -AAAAAAAACAAAACAAAACAATAAAAAAC
1 AAAAAAAAACAAAACAAAACAAAAAAAAAG
*
3348194 AAACAAATAAA-AAAACAACAATAAAAA
1 AAA-AAA-AAACAAAACAA-AACAAAAA
3348221 GGGTCCGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
29 16 0.21
30 13 0.17
31 23 0.30
32 18 0.24
33 6 0.08
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.03
Consensus pattern (30 bp):
AAAAAAAAACAAAACAAAACAAAAAAAAAG
Found at i:3348141 original size:31 final size:31
Alignment explanation
Indices: 3348102--3348211 Score: 125
Period size: 34 Copynumber: 3.4 Consensus size: 31
3348092 TGTTCTCCAC
3348102 AAAAAAAAAAC-AAACAAACAAAAAAAAAGA
1 AAAAAAAAAACAAAACAAACAAAAAAAAAGA
3348132 AGAAAAAAAAACAACAACAAAACAAAAAAAAAGAA
1 A-AAAAAAAAACAA-AAC-AAACAAAAAAAAAG-A
* *
3348167 AAAAAACAAAACAAAACAATA-AAAAACAAACA
1 AAAAAA-AAAACAAAACAA-ACAAAAAAAAAGA
*
3348199 AATAAAAAAACAA
1 AAAAAAAAAACAA
3348212 CAATAAAAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
30 1 0.01
31 17 0.24
32 7 0.10
33 13 0.19
34 23 0.33
35 9 0.13
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.02
Consensus pattern (31 bp):
AAAAAAAAAACAAAACAAACAAAAAAAAAGA
Found at i:3348148 original size:34 final size:32
Alignment explanation
Indices: 3348102--3348214 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 32
3348092 TGTTCTCCAC
3348102 AAAAAAAAAACAAACAAACAAAAAAAAAGAAGA
1 AAAAAAAAAACAAACAAACAAAAAAAAAGAA-A
3348135 AAAAAAAACAAC-AACAAAACAAAAAAAAAGAAA
1 AAAAAAAA-AACAAAC-AAACAAAAAAAAAGAAA
* * *
3348168 AAAAACAAAACAAAACAATA-AAAAACAAACAAA
1 AAAAAAAAAAC-AAACAA-ACAAAAAAAAAGAAA
*
3348201 TAAAAAAACAACAA
1 -AAAAAAAAAACAA
3348215 TAAAAAGGGT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
32 3 0.04
33 34 0.49
34 32 0.46
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (32 bp):
AAAAAAAAAACAAACAAACAAAAAAAAAGAAA
Found at i:3348214 original size:19 final size:17
Alignment explanation
Indices: 3348102--3348208 Score: 87
Period size: 17 Copynumber: 6.3 Consensus size: 17
3348092 TGTTCTCCAC
3348102 AAAAAAAAAACAAACAA
1 AAAAAAAAAACAAACAA
* *
3348119 ACAAAAAAAAA-GAAGAA
1 A-AAAAAAAAACAAACAA
*
3348136 AAAAAAACAAC-AACAA
1 AAAAAAAAAACAAACAA
*
3348152 AACAAAAAAAA-AGA-AA
1 AA-AAAAAAAACAAACAA
*
3348168 AAAAACAAAACAAAACAA
1 AAAAAAAAAAC-AAACAA
* *
3348186 TAAAAAACAAACAAATAA
1 -AAAAAAAAAACAAACAA
3348204 AAAAA
1 AAAAA
3348209 CAACAATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
15 7 0.10
16 18 0.25
17 21 0.30
18 16 0.23
19 9 0.13
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAACAAACAA
Found at i:3348220 original size:1 final size:1
Alignment explanation
Indices: 3348102--3348208 Score: 61
Period size: 1 Copynumber: 107.0 Consensus size: 1
3348092 TGTTCTCCAC
* * * * * * * * * *
3348102 AAAAAAAAAACAAACAAACAAAAAAAAAGAAGAAAAAAAAACAACAACAAAACAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
3348167 AAAAAACAAAACAAAACAATAAAAAACAAACAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3348209 CAACAATAAA
Statistics
Matches: 72, Mismatches: 34, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:3349732 original size:27 final size:27
Alignment explanation
Indices: 3349661--3349962 Score: 363
Period size: 27 Copynumber: 10.8 Consensus size: 27
3349651 ACCTTTTTCG
* * *
3349661 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAATCAGTGGCAAC--CTTC
*
3349690 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
3349717 AAAGCCCAAAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
3349744 AAAAGCCCACAAAT-TGTGGCAACCTTC
1 -AAAGCCCACAAATCAGTGGCAACCTTC
* * *
3349771 AAAAGCCCACAAGTTAGTGGCACCCTTTTTC
1 -AAAGCCCACAAATCAGTGGCAACC---TTC
3349802 AAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
3349829 AAAGTCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
3349856 AAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
* *
3349883 AAAAGCCCACAAGTCAGTGGCACCCTTTTTC
1 -AAAGCCCACAAATCAGTGGCAACC---TTC
3349914 AAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
* *
3349941 AAAAGCCCACAAGTCCGTGGCA
1 -AAAGCCCACAAATCAGTGGCA
3349963 TCTTTTTCCT
Statistics
Matches: 243, Mismatches: 20, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
27 111 0.46
28 61 0.25
29 22 0.09
30 43 0.18
31 6 0.02
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:3349819 original size:85 final size:82
Alignment explanation
Indices: 3349661--3349962 Score: 385
Period size: 85 Copynumber: 3.6 Consensus size: 82
3349651 ACCTTTTTCG
* * *
3349661 AAAGCCCACAAGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCA
1 AAAGCCCACAAATCAGTGGCAAC--CTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCA
*
3349725 AAAATCAGTGGCAACCTTC
64 CAAATCAGTGGCAACCTTC
* * *
3349744 AAAAGCCCACAAAT-TGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAGCC
1 -AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACC---TTCAAAGCC
3349808 CACAAATCAGTGGCAACCTTC
62 CACAAATCAGTGGCAACCTTC
* *
3349829 AAAGTCCACAAATCAGTGGCAACCTTC-AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCAC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTC-AAAGCCCAC
* *
3349893 AAGTCAGTGGCACCCTTTTTC
65 AAATCAGTGGCAACC---TTC
*
3349914 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCA
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCA
3349963 TCTTTTTCCT
Statistics
Matches: 191, Mismatches: 17, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
81 6 0.03
82 44 0.23
83 7 0.04
84 45 0.24
85 70 0.37
86 19 0.10
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.18
Consensus pattern (82 bp):
AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACA
AATCAGTGGCAACCTTC
Found at i:3349857 original size:112 final size:112
Alignment explanation
Indices: 3349661--3349962 Score: 500
Period size: 112 Copynumber: 2.7 Consensus size: 112
3349651 ACCTTTTTCG
* *
3349661 AAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAGCCCA
* *
3349725 AAAATCAGTGGCAACCTTCAAAAGCCCACAAAT-TGTGGCAACCTTCA
66 CAAATCAGTGGCAACCTTC-AAAGCCCACAAATCAGTGGCAACCTTCA
* *
3349772 AAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAGTCCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAGCCCA
3349837 CAAATCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCAACCTTCA
66 CAAATCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCAACCTTCA
3349884 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTC-AAAGCCC
* *
3349949 ACAAGTCCGTGGCA
65 ACAAATCAGTGGCA
3349963 TCTTTTTCCT
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
111 33 0.19
112 127 0.71
113 18 0.10
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.18
Consensus pattern (112 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAGCCCA
CAAATCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCAACCTTCA
Found at i:3349985 original size:33 final size:32
Alignment explanation
Indices: 3349943--3350010 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
3349933 CAACCTTCAA
** * *
3349943 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACCCCGTGGC-GCCTTTTCCTTTT
3349976 AAGCCCACAACCCCGTGGCGCCTTTTCCTTTT
1 AAGCCCACAACCCCGTGGCGCCTTTTCCTTTT
3350008 AAG
1 AAG
3350011 TCCATAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.19, C:0.34, G:0.16, T:0.31
Consensus pattern (32 bp):
AAGCCCACAACCCCGTGGCGCCTTTTCCTTTT
Found at i:3350007 original size:32 final size:33
Alignment explanation
Indices: 3349943--3350032 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 33
3349933 CAACCTTCAA
** * *
3349943 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACCCCGTGGCAGCCTTTTCCTTTT
3349976 AAGCCCACAACCCCGTGGC-GCCTTTTCCTTTT
1 AAGCCCACAACCCCGTGGCAGCCTTTTCCTTTT
* * **
3350008 AAGTCCATAACTTCGTGGCA-CCTTT
1 AAGCCCACAACCCCGTGGCAGCCTTT
3350033 AAGCCCAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 31 0.65
33 17 0.35
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (33 bp):
AAGCCCACAACCCCGTGGCAGCCTTTTCCTTTT
Found at i:3350143 original size:33 final size:33
Alignment explanation
Indices: 3350064--3350144 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
3350054 GAGTCAGCAT
* * *
3350064 ATTGGCACCTTTTCTTTTTTAAGTCCATAACTC
1 ATTGGCACCTTTTCTTTTATAAGCCCACAACTC
*
3350097 -TGTGGCACTCCTTTTCTTTTATAAGCCCACAAGTC
1 AT-TGGCA--CCTTTTCTTTTATAAGCCCACAACTC
3350132 ATTGGCACCTTTT
1 ATTGGCACCTTTT
3350145 TCAAAAGCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
32 1 0.03
33 11 0.28
35 27 0.68
36 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (33 bp):
ATTGGCACCTTTTCTTTTATAAGCCCACAACTC
Found at i:3350278 original size:49 final size:49
Alignment explanation
Indices: 3350225--3350442 Score: 256
Period size: 49 Copynumber: 4.4 Consensus size: 49
3350215 TTGCTGACCA
* * *
3350225 TGAATTAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCT
1 TGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCT
* * *
3350274 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTCGTTGGCCT
1 TGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCT
* * * * *
3350323 AGAATCAGCACATTGGCACCTTCACCTTTAAGCCCAGTATCGCTGGCCT
1 TGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCT
* * * **
3350372 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCATTGGCCT
1 TGAATCAGCACATTGGCACC-T--TCATCTTTAAGA-CCAATGTCGCTGGCCT
3350425 TGAATCAGCACATTGGCA
1 TGAATCAGCACATTGGCA
3350443 TTCTTCTCAT
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
49 102 0.73
50 1 0.01
52 9 0.06
53 28 0.20
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCT
Found at i:3356726 original size:13 final size:13
Alignment explanation
Indices: 3356708--3356733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3356698 CAATTTTTTG
3356708 TGTATCGATACAT
1 TGTATCGATACAT
3356721 TGTATCGATACAT
1 TGTATCGATACAT
3356734 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3357422 original size:38 final size:38
Alignment explanation
Indices: 3357388--3357511 Score: 248
Period size: 38 Copynumber: 3.3 Consensus size: 38
3357378 CAAATTTGTA
3357388 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
1 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
3357426 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
1 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
3357464 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
1 CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
3357502 CATTCTCCCC
1 CATTCTCCCC
3357512 TTTATCTCCC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 86 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (38 bp):
CATTCTCCCCCTTAATAAAATAATTGTAGCAATTTACG
Found at i:3357460 original size:76 final size:78
Alignment explanation
Indices: 3357356--3357511 Score: 246
Period size: 76 Copynumber: 2.0 Consensus size: 78
3357346 TTTTATTTCT
**
3357356 CCCTTAATCAAAATAAATTTAACAAATTTGTACATTCTCCCCCTTAATAAAATAATTGTAGCAAT
1 CCCTTAATCAAAATAAATTTAACAAATTTACACATTCTCCCCCTTAATAAAATAATTGTAGCAAT
3357421 TTACGCATTCTCC
66 TTACGCATTCTCC
* *
3357434 CCCTTAAT-AAAAT-AATTGTAGC-AATTTACGCATTCTCCCCCTTAATAAAATAATTGTAGCAA
1 CCCTTAATCAAAATAAATT-TAACAAATTTACACATTCTCCCCCTTAATAAAATAATTGTAGCAA
3357496 TTTACGCATTCTCC
65 TTTACGCATTCTCC
3357510 CC
1 CC
3357512 TTTATCTCCC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
76 57 0.78
77 8 0.11
78 8 0.11
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.34
Consensus pattern (78 bp):
CCCTTAATCAAAATAAATTTAACAAATTTACACATTCTCCCCCTTAATAAAATAATTGTAGCAAT
TTACGCATTCTCC
Found at i:3357557 original size:21 final size:21
Alignment explanation
Indices: 3357516--3357559 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3357506 CTCCCCTTTA
* *
3357516 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
3357537 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
3357558 TC
1 TC
3357560 ATATTCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:3360389 original size:15 final size:15
Alignment explanation
Indices: 3360369--3360399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3360359 ATTTCGTTTG
*
3360369 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3360384 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3360399 G
1 G
3360400 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3364373 original size:13 final size:13
Alignment explanation
Indices: 3364355--3364380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3364345 CAATTTTTTG
3364355 TGTATCGATACAT
1 TGTATCGATACAT
3364368 TGTATCGATACAT
1 TGTATCGATACAT
3364381 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3367770 original size:20 final size:21
Alignment explanation
Indices: 3367723--3367775 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3367713 GCCAATGACC
*
3367723 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
3367744 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
3367764 TGTATCGATACA
1 TGTATCGATACA
3367776 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:3367781 original size:13 final size:13
Alignment explanation
Indices: 3367763--3367787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3367753 ACATTTGGTC
3367763 ATGTATCGATACA
1 ATGTATCGATACA
3367776 ATGTATCGATAC
1 ATGTATCGATAC
3367788 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3368146 original size:34 final size:34
Alignment explanation
Indices: 3368108--3368207 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
3368098 AAAAAACTTA
* * *
3368108 TGAAATTTCTTAAAACATCTTTAAGAGATGCTTG
1 TGAAATTTCTTAAAACATCCTCAAGAGAAGCTTG
*
3368142 TGAAATCTCTTAAAACATCCTCAAGAGAAGCTTG
1 TGAAATTTCTTAAAACATCCTCAAGAGAAGCTTG
*
3368176 TGAAATTTCTTAAAATATCCTCAAGA-AAGCTT
1 TGAAATTTCTTAAAACATCCTCAAGAGAAGCTT
3368208 ATATGAAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 6 0.10
34 54 0.90
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (34 bp):
TGAAATTTCTTAAAACATCCTCAAGAGAAGCTTG
Found at i:3372326 original size:28 final size:28
Alignment explanation
Indices: 3372286--3372340 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3372276 TACTTGATTA
*
3372286 TCTAAAGAATATTTTTATTTTA-TATATT
1 TCTAAACAATA-TTTTATTTTATTATATT
3372314 TCTAAACAATATTTTATTTTATTATAT
1 TCTAAACAATATTTTATTTTATTATAT
3372341 AAAAAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.56
Consensus pattern (28 bp):
TCTAAACAATATTTTATTTTATTATATT
Found at i:3374579 original size:154 final size:157
Alignment explanation
Indices: 3374267--3374777 Score: 411
Period size: 156 Copynumber: 3.3 Consensus size: 157
3374257 AAGTTCAAAG
** * * * *
3374267 AAAATTACGAAAATACTTCTA-AAGGATACCTTCGACATGAAAGTAT-CTAATA-CCCTAAAAAG
1 AAAATTACGAAAATACCCCTAGGA-GATACCTTCGACGTGAAAGTATCCCAGTACCCCT-AAAAG
* *
3374329 ACTTAAAAAGGACTATAAAAGAGATGAATATATCCTAAATACCCACTTTTGGCATAAAAGCAGAC
64 ACTTAAAAGGGACTATAAAAGAGATGAATATATCCTAAATACCCACCTTTGGCATAAAAGCAGAC
* * *
3374394 TCGGTTATAACCTAGGACTCGATTCT-GA
129 TCGATGATAACCTAGGACTCGATTCTAAA
* * * *
3374422 AAAATTACGAAAATTCCCCTAGGGGATATC-TCGACGTGAAAGTATCCCAGTACCCCTAAAGGAC
1 AAAATTACGAAAATACCCCTAGGAGATACCTTCGACGTGAAAGTATCCCAGTACCCCTAAAAGAC
* * **
3374486 TTAAAAGGGACTATAAAAGGGATGAA-CTATCC-AGAATACCCACCTTTGGCATAAAAGTGGA-T
66 TTAAAAGGGACTATAAAAGAGATGAATATATCCTA-AATACCCACCTTTGGCATAAAAGCAGACT
* * * *
3374548 CCGATGATAACTTAGGATTTGGTTCTAAAA
130 -CGATGATAACCTAGGACTCGATTCT-AAA
* * * * *
3374578 AAAATTATGAAAATACCCTTAGGAGATGCCTTCGACGT-ACAAGTA-CCCGGTGCCCCTAAAAGA
1 AAAATTACGAAAATACCCCTAGGAGATACCTTCGACGTGA-AAGTATCCCAGTACCCCTAAAAGA
* * * ** * ** *
3374641 CTTAGAAA-GG--TTTGAAATGGGATGAACCTATCCTAACTGTCCATCTTTGGCATAAAAGCAGA
65 CTTA-AAAGGGACTAT-AAAAGAGATGAATATATCCTAAATACCCACCTTTGGCATAAAAGCAGA
* ** * * * *
3374703 CCCGATGGCAACATAGGAATCAATT-TTAA
128 CTCGATGATAACCTAGGACTCGATTCTAAA
* * * *
3374732 GAAATTACAAAAATACCCCTATGAGTATACCTTCGACGTAAAAGTA
1 AAAATTACGAAAATACCCCTAGGAG-ATACCTTCGACGTGAAAGTA
3374778 CCTGATATCC
Statistics
Matches: 285, Mismatches: 55, Indels: 32
0.77 0.15 0.09
Matches are distributed among these distances:
153 2 0.01
154 86 0.30
155 86 0.30
156 95 0.33
157 16 0.06
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (157 bp):
AAAATTACGAAAATACCCCTAGGAGATACCTTCGACGTGAAAGTATCCCAGTACCCCTAAAAGAC
TTAAAAGGGACTATAAAAGAGATGAATATATCCTAAATACCCACCTTTGGCATAAAAGCAGACTC
GATGATAACCTAGGACTCGATTCTAAA
Found at i:3378848 original size:54 final size:54
Alignment explanation
Indices: 3378790--3378897 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
3378780 TGCTTGGGTA
*
3378790 TCGATACAAATGAGAAGAAAAGGCTCAAACAGTTTTAAATAGTGGCCCTGTATC
1 TCGATACAAATGAGAAGAAAAGGCTCAAACAGTTTTAAATAGTAGCCCTGTATC
3378844 TCGATACAAATGAGAAGAAAAGGCTCAAACAGTTTTAAATAGTAGCCCTGTATC
1 TCGATACAAATGAGAAGAAAAGGCTCAAACAGTTTTAAATAGTAGCCCTGTATC
3378898 AATACAATGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (54 bp):
TCGATACAAATGAGAAGAAAAGGCTCAAACAGTTTTAAATAGTAGCCCTGTATC
Found at i:3378977 original size:20 final size:21
Alignment explanation
Indices: 3378947--3378985 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3378937 TCTGAGTTTT
*
3378947 TTCAGATGTATTGATACATCA
1 TTCAGATGTATCGATACATCA
3378968 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
3378986 TCTGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:3385182 original size:19 final size:19
Alignment explanation
Indices: 3385134--3385189 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3385124 CTGCCAATTT
*
3385134 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAG
*
3385154 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
*
3385173 CATGTGTCGATACAATG
1 CATGTATCGATACAATG
3385190 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:3386528 original size:22 final size:23
Alignment explanation
Indices: 3386503--3386545 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3386493 TGTTGTTTTA
*
3386503 CTATTTG-TTGCTGTTTTGCTTG
1 CTATTTGTTTGCTGCTTTGCTTG
3386525 CTATTTGTTTGCTGCTTTGCT
1 CTATTTGTTTGCTGCTTTGCT
3386546 ATTGGCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.05, C:0.16, G:0.21, T:0.58
Consensus pattern (23 bp):
CTATTTGTTTGCTGCTTTGCTTG
Found at i:3387061 original size:25 final size:25
Alignment explanation
Indices: 3387023--3387090 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
3387013 CTGCGGTTTG
* * *
3387023 TCGTTACTTCCTTCTTCATCAATTA
1 TCGTTGCTTGCTTCTTCAGCAATTA
** *
3387048 TCGTTGCTTGCTTCTTCAGCTGTTG
1 TCGTTGCTTGCTTCTTCAGCAATTA
*
3387073 CCGTTGCTTGCTTCTTCA
1 TCGTTGCTTGCTTCTTCA
3387091 ACTACTGCTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.10, C:0.28, G:0.15, T:0.47
Consensus pattern (25 bp):
TCGTTGCTTGCTTCTTCAGCAATTA
Found at i:3387103 original size:25 final size:25
Alignment explanation
Indices: 3387049--3387110 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
3387039 CATCAATTAT
* **
3387049 CGTTGCTTGCTTCTTCAGCTGTTGC
1 CGTTGCTTGCTTCTTCAACTACTGC
3387074 CGTTGCTTGCTTCTTCAACTACTGC
1 CGTTGCTTGCTTCTTCAACTACTGC
*
3387099 TGTTGCTTGCTT
1 CGTTGCTTGCTT
3387111 TGCTGTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.06, C:0.27, G:0.21, T:0.45
Consensus pattern (25 bp):
CGTTGCTTGCTTCTTCAACTACTGC
Found at i:3387593 original size:19 final size:19
Alignment explanation
Indices: 3387569--3387606 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3387559 TACTCATGGT
3387569 AGTTGCTGCATGCTTATTC
1 AGTTGCTGCATGCTTATTC
*
3387588 AGTTGCTGCATGTTTATTC
1 AGTTGCTGCATGCTTATTC
3387607 TTCCACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (19 bp):
AGTTGCTGCATGCTTATTC
Found at i:3387902 original size:16 final size:16
Alignment explanation
Indices: 3387858--3387896 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3387848 TTTAATTTTG
3387858 ATTTTTTGATTTTCTT
1 ATTTTTTGATTTTCTT
*
3387874 ATTTTTTGATTTTTTT
1 ATTTTTTGATTTTCTT
3387890 ATTTTTT
1 ATTTTTT
3387897 TGTTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (16 bp):
ATTTTTTGATTTTCTT
Found at i:3387935 original size:14 final size:14
Alignment explanation
Indices: 3387846--3387959 Score: 79
Period size: 14 Copynumber: 7.7 Consensus size: 14
3387836 TTTTGAAGAA
* *
3387846 TTTTTAATTTTGAT
1 TTTTTATTTTTTAT
3387860 TTTTTGATTTTCTTAT
1 TTTTT-ATTTT-TTAT
3387876 TTTTTGATTTTTTTAT
1 TTTTT-A-TTTTTTAT
*
3387892 TTTTT-TGTTTTGAT
1 TTTTTAT-TTTTTAT
* **
3387906 TTTTTAATGATT-T
1 TTTTTATTTTTTAT
3387919 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
*
3387933 TTTTTATTATTATAT
1 TTTTTATT-TTTTAT
3387948 TATTATTATTTT
1 T-TT-TTATTTT
3387960 AATTTTATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
13 11 0.14
14 27 0.34
15 10 0.12
16 23 0.29
17 9 0.11
ACGTcount: A:0.18, C:0.01, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:3387936 original size:16 final size:16
Alignment explanation
Indices: 3387853--3387943 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 16
3387843 GAATTTTTAA
*
3387853 TTTTGATTTTTTGA-TT
1 TTTTTATTTTTT-ATTT
*
3387869 TTCTTATTTTTTGA-TT
1 TTTTTATTTTTT-ATTT
3387885 TTTTTATTTTTT-TGTT
1 TTTTTATTTTTTAT-TT
* *
3387901 TTGATTT-TTTAATGATTT
1 TT--TTTATTT-TTTATTT
3387919 TTTTTATTTTTTATTT
1 TTTTTATTTTTTATTT
3387935 TTTATTATT
1 TTT-TTATT
3387944 ATATTATTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
16 40 0.67
17 11 0.18
18 8 0.13
19 1 0.02
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:3389173 original size:20 final size:20
Alignment explanation
Indices: 3389148--3389197 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3389138 ACCCTAAAAA
**
3389148 GTATCGATACACCTTCAAAT
1 GTATCGATACACCACCAAAT
**
3389168 GTATCGATACATGACCAAAT
1 GTATCGATACACCACCAAAT
3389188 GTATCGATAC
1 GTATCGATAC
3389198 TTGTTAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACACCACCAAAT
Done.