Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 166 of 313
Found at i:52069460 original size:15 final size:15
Alignment explanation
Indices: 52069440--52069496 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
52069430 ATTCAAAATT
52069440 AATATTTTAATAATA
1 AATATTTTAATAATA
*
52069455 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
52069474 AATATATTAATAATA
1 AATATTTTAATAATA
*
52069489 AATGTTTT
1 AATATTTT
52069497 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:52069656 original size:15 final size:16
Alignment explanation
Indices: 52069636--52069671 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
52069626 TAACATTGTT
*
52069636 ATTTTGTTTTTGTCA-
1 ATTTTGTTGTTGTCAC
52069651 ATTTTGTTGTTGTCAC
1 ATTTTGTTGTTGTCAC
52069667 ATTTT
1 ATTTT
52069672 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.64
Consensus pattern (16 bp):
ATTTTGTTGTTGTCAC
Found at i:52071196 original size:25 final size:26
Alignment explanation
Indices: 52071148--52071196 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
52071138 ATTAGAGCTT
* *
52071148 TCTAGAGATTTTATCTCTTTCTTTTC
1 TCTAGAGATTTTATCTATTCCTTTTC
52071174 TCTAGAG-TTTTATCTATTCCTTT
1 TCTAGAGATTTTATCTATTCCTTT
52071197 CTTTTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.57
Consensus pattern (26 bp):
TCTAGAGATTTTATCTATTCCTTTTC
Found at i:52071197 original size:24 final size:26
Alignment explanation
Indices: 52071148--52071198 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
52071138 ATTAGAGCTT
* *
52071148 TCTAGAGATTTTATCTCTTTCTTTTC
1 TCTAGAGATTTTATCTCATTCCTTTC
52071174 TCTAGAG-TTTTATCT-ATTCCTTTC
1 TCTAGAGATTTTATCTCATTCCTTTC
52071198 T
1 T
52071199 TTTTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.57
Consensus pattern (26 bp):
TCTAGAGATTTTATCTCATTCCTTTC
Found at i:52073781 original size:20 final size:20
Alignment explanation
Indices: 52073758--52073797 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52073748 TAATAATAAT
52073758 AATA-GTAAAATAAATAAAAG
1 AATATGTAAAA-AAATAAAAG
*
52073778 AATATTTAAAAAAATAAAAG
1 AATATGTAAAAAAATAAAAG
52073798 GGAAAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
AATATGTAAAAAAATAAAAG
Found at i:52080798 original size:50 final size:50
Alignment explanation
Indices: 52080682--52080925 Score: 373
Period size: 50 Copynumber: 4.9 Consensus size: 50
52080672 GATAATAACA
* * ** *
52080682 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
52080733 AGCCCATGCCATGTCCCAGACATGGTCCTAC-GGAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCGG
52080783 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
52080833 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
52080883 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
52080926 TACCCAAATG
Statistics
Matches: 177, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 147 0.83
51 30 0.17
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.24
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:52082775 original size:15 final size:15
Alignment explanation
Indices: 52082760--52082789 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
52082750 TTAAATCTAA
52082760 TAAAAGTAAAAATAAT
1 TAAAA-TAAAAATAAT
52082776 TAAAATAAAAATAA
1 TAAAATAAAAATAA
52082790 CAGTACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAAATAAAAATAAT
Found at i:52084250 original size:90 final size:88
Alignment explanation
Indices: 52084146--52084316 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 88
52084136 TGAATTTATG
*
52084146 AAAAATCTCAATTTTTTAAAATAATAACTGGATTAGGTTGTTTTTTTTTGTAAAATTACAGGG-T
1 AAAAATCTCAATTTTTTAAAATAATAACTGGATTAGG--CTTTTTTTTTGTAAAATTAC-GGGAT
*
52084210 TGGG-CAGAAATAATAAAAATGCTATA
63 TGGGCCA-AAATAACAAAAATGCTATA
** *
52084236 AAAAATCTTGATTTTTTAAAATAATTACTGGATTAGGCTTTTTTTTTGTAAAATTACGGGATTGG
1 AAAAATCTCAATTTTTTAAAATAATAACTGGATTAGGCTTTTTTTTTGTAAAATTACGGGATTGG
52084301 GCCAAAATAACAAAAA
66 GCCAAAATAACAAAAA
52084317 AGCTTCTAGC
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
87 3 0.04
88 35 0.47
89 2 0.03
90 34 0.46
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (88 bp):
AAAAATCTCAATTTTTTAAAATAATAACTGGATTAGGCTTTTTTTTTGTAAAATTACGGGATTGG
GCCAAAATAACAAAAATGCTATA
Found at i:52084525 original size:23 final size:23
Alignment explanation
Indices: 52084478--52084525 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52084468 TTGTGCAGGG
*
52084478 TTTTGAAGTTTTTTCATTATATT
1 TTTTGAAGTTTTTTCATAATATT
* *
52084501 TTTTTAAGTTTTTTTATAAT-TT
1 TTTTGAAGTTTTTTCATAATATT
52084523 TTT
1 TTT
52084526 GATATGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTTGAAGTTTTTTCATAATATT
Found at i:52084902 original size:18 final size:18
Alignment explanation
Indices: 52084876--52084911 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52084866 ATTTTAAAAA
52084876 AAAAGTTGAGAGAGAAAT
1 AAAAGTTGAGAGAGAAAT
* *
52084894 AAAATTTGAGTGAGAAAT
1 AAAAGTTGAGAGAGAAAT
52084912 TAGAAGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (18 bp):
AAAAGTTGAGAGAGAAAT
Found at i:52087247 original size:25 final size:27
Alignment explanation
Indices: 52087198--52087247 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
52087188 GGATGGGTTA
*
52087198 TTAATTGAATTGAATATTTTTTTAACT
1 TTAATCGAATTGAATATTTTTTTAACT
52087225 TTAATCGAATT-AA-ATTTTTTTAA
1 TTAATCGAATTGAATATTTTTTTAA
52087248 ATATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 10 0.45
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (27 bp):
TTAATCGAATTGAATATTTTTTTAACT
Found at i:52088232 original size:13 final size:13
Alignment explanation
Indices: 52088199--52088226 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52088189 TAACTATTAT
52088199 TTAATATAGTTAA
1 TTAATATAGTTAA
52088212 TTAATATAGTTAA
1 TTAATATAGTTAA
52088225 TT
1 TT
52088227 TTTATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTAATATAGTTAA
Found at i:52089033 original size:6 final size:7
Alignment explanation
Indices: 52089018--52089042 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52089008 AATTATTTTC
52089018 AAAATAA
1 AAAATAA
52089025 AAAATAA
1 AAAATAA
52089032 AAAATAA
1 AAAATAA
52089039 AAAA
1 AAAA
52089043 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:52089276 original size:22 final size:22
Alignment explanation
Indices: 52089251--52089304 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
52089241 ACATATGGAT
52089251 TTGAGAGAAATTT-AGAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
52089273 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
52089295 TTGAGA-AAAT
1 TTGAGAGAAAT
52089305 AATTGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:52089969 original size:14 final size:15
Alignment explanation
Indices: 52089950--52089988 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
52089940 GTAATTTTAT
52089950 ATTTTATATATAA-A
1 ATTTTATATATAATA
*
52089964 ATTTTATAAATAATA
1 ATTTTATATATAATA
*
52089979 AATTTATATA
1 ATTTTATATA
52089989 ATCTAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTTATATATAATA
Found at i:52090451 original size:18 final size:17
Alignment explanation
Indices: 52090424--52090458 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52090414 AAAAATCACC
*
52090424 TGAATTAATTTTTCATTT
1 TGAATGAATTTTT-ATTT
52090442 TGAATGAATTTTTATTT
1 TGAATGAATTTTTATTT
52090459 AATTATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (17 bp):
TGAATGAATTTTTATTT
Found at i:52092319 original size:246 final size:246
Alignment explanation
Indices: 52091885--52092378 Score: 988
Period size: 246 Copynumber: 2.0 Consensus size: 246
52091875 TCATGACATC
52091885 AGAGCCTCCGGAAGTAGTGAAGGCAAGGAATGATAATTCTCATAAAACGAATTTTCCGGATTCAC
1 AGAGCCTCCGGAAGTAGTGAAGGCAAGGAATGATAATTCTCATAAAACGAATTTTCCGGATTCAC
52091950 CTGAGCCAATATATGGGACTCAGTTCTTGCCGAGGAAGTTTAAAATTGCTGTCACTGTGCCAACT
66 CTGAGCCAATATATGGGACTCAGTTCTTGCCGAGGAAGTTTAAAATTGCTGTCACTGTGCCAACT
52092015 GATAACTCGGTGGATATCCTCACAAATGATATTGGTGTTGTGGTAGTTTCTGATGATAACGGGGA
131 GATAACTCGGTGGATATCCTCACAAATGATATTGGTGTTGTGGTAGTTTCTGATGATAACGGGGA
52092080 GCCTCAGGGATTGAACATCTATGTAAGTCTACTGTGTGACTTAAGAAATCA
196 GCCTCAGGGATTGAACATCTATGTAAGTCTACTGTGTGACTTAAGAAATCA
52092131 AGAGCCTCCGGAAGTAGTGAAGGCAAGGAATGATAATTCTCATAAAACGAATTTTCCGGATTCAC
1 AGAGCCTCCGGAAGTAGTGAAGGCAAGGAATGATAATTCTCATAAAACGAATTTTCCGGATTCAC
52092196 CTGAGCCAATATATGGGACTCAGTTCTTGCCGAGGAAGTTTAAAATTGCTGTCACTGTGCCAACT
66 CTGAGCCAATATATGGGACTCAGTTCTTGCCGAGGAAGTTTAAAATTGCTGTCACTGTGCCAACT
52092261 GATAACTCGGTGGATATCCTCACAAATGATATTGGTGTTGTGGTAGTTTCTGATGATAACGGGGA
131 GATAACTCGGTGGATATCCTCACAAATGATATTGGTGTTGTGGTAGTTTCTGATGATAACGGGGA
52092326 GCCTCAGGGATTGAACATCTATGTAAGTCTACTGTGTGACTTAAGAAATCA
196 GCCTCAGGGATTGAACATCTATGTAAGTCTACTGTGTGACTTAAGAAATCA
52092377 AG
1 AG
52092379 TTTTTTTTTT
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 248 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (246 bp):
AGAGCCTCCGGAAGTAGTGAAGGCAAGGAATGATAATTCTCATAAAACGAATTTTCCGGATTCAC
CTGAGCCAATATATGGGACTCAGTTCTTGCCGAGGAAGTTTAAAATTGCTGTCACTGTGCCAACT
GATAACTCGGTGGATATCCTCACAAATGATATTGGTGTTGTGGTAGTTTCTGATGATAACGGGGA
GCCTCAGGGATTGAACATCTATGTAAGTCTACTGTGTGACTTAAGAAATCA
Found at i:52098718 original size:6 final size:6
Alignment explanation
Indices: 52098707--52098736 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
52098697 ATTAAAGGTT
52098707 TTAAAA TTAAAA TTAAAA TTAAAA TATAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA T-TAAA
52098737 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:52102155 original size:13 final size:13
Alignment explanation
Indices: 52102137--52102164 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52102127 ACATGATGCA
52102137 AATTGAAGTCTAT
1 AATTGAAGTCTAT
52102150 AATTGAAGTCTAT
1 AATTGAAGTCTAT
52102163 AA
1 AA
52102165 GATCAGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (13 bp):
AATTGAAGTCTAT
Found at i:52103812 original size:37 final size:37
Alignment explanation
Indices: 52103751--52103896 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
52103741 TACGTATGAT
* *
52103751 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
52103786 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
52103823 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
52103860 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
52103897 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:52103913 original size:46 final size:46
Alignment explanation
Indices: 52103860--52104128 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
52103850 TAAGTGTAGC
* **
52103860 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
52103906 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
52103952 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
52104004 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
52104050 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
52104102 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
52104129 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:52103979 original size:52 final size:52
Alignment explanation
Indices: 52103903--52104122 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
52103893 TAGCTAAAGC
* *
52103903 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
52103956 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
52104008 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
52104054 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
52104106 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
52104123 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:52104025 original size:98 final size:98
Alignment explanation
Indices: 52103860--52104128 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
52103850 TAAGTGTAGC
* * *
52103860 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
52103925 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
52103959 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
52104024 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
52104057 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
52104122 GATCAGA
66 GATCAGA
52104129 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:52113079 original size:21 final size:21
Alignment explanation
Indices: 52113053--52113093 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52113043 GTAAAAAATT
52113053 TTCTTGTTGTATCGAGACATG
1 TTCTTGTTGTATCGAGACATG
* *
52113074 TTCTTGTTGTTTTGAGACAT
1 TTCTTGTTGTATCGAGACAT
52113094 TAAGGTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (21 bp):
TTCTTGTTGTATCGAGACATG
Found at i:52113925 original size:28 final size:28
Alignment explanation
Indices: 52113880--52113984 Score: 124
Period size: 28 Copynumber: 3.8 Consensus size: 28
52113870 GTAACAGTAT
*
52113880 AGTGTGGGCCTT--CCCAATATAGAAAC
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
* * *
52113906 AGAGTAGGCCTTAGCCCAATACAGAAAT
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
**
52113934 AGTGTGGGCCTTAAACCAATACAGAAAC
1 AGTGTGGGCCTTAGCCCAATACAGAAAC
* *
52113962 AGTGTGGGCCTAAGCCCGATACA
1 AGTGTGGGCCTTAGCCCAATACA
52113985 ATATCAATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.16
28 54 0.84
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGAAAC
Found at i:52113963 original size:56 final size:54
Alignment explanation
Indices: 52113878--52113984 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 54
52113868 CAGTAACAGT
* * *
52113878 ATAGTGTGGGCCTTCCCAATATAGAAACAGAGTAGGCCTTAGCCCAATACAGAA
1 ATAGTGTGGGCCTTACCAATACAGAAACAGAGTAGGCCTAAGCCCAATACAGAA
* * *
52113932 ATAGTGTGGGCCTTAAACCAATACAGAAACAGTGTGGGCCTAAGCCCGATACA
1 ATAGTGTGGGCCTT--ACCAATACAGAAACAGAGTAGGCCTAAGCCCAATACA
52113985 ATATCAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 14 0.31
56 31 0.69
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (54 bp):
ATAGTGTGGGCCTTACCAATACAGAAACAGAGTAGGCCTAAGCCCAATACAGAA
Found at i:52114265 original size:32 final size:32
Alignment explanation
Indices: 52114195--52114461 Score: 263
Period size: 32 Copynumber: 8.4 Consensus size: 32
52114185 AAATGACTAC
* * * *
52114195 AAGCCATAAGT-ACAATAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* **
52114226 AAGCCATCAGTAGCAGTGTTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
52114258 CAA-CCATCAGTAACGGTAACATGATCGGCACA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
52114290 AAGCCATCAGTAGCAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
52114322 CAGCCATCAGTAATAGTGAA-ATGATCGGCACA
1 AAGCCATCAGTAACAGT-AATATGATCGGCACA
* * * *
52114354 CAGTCATCAGTAACTGTAATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
52114386 AAACCATCAGTAAC-GATACTATGATCGACACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
* *
52114418 AAGCCATCAGTAACGGTACTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
52114450 AAGCCATTAGTA
1 AAGCCATCAGTA
52114462 GCATCGCAGC
Statistics
Matches: 194, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
31 15 0.08
32 175 0.90
33 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:52114494 original size:26 final size:26
Alignment explanation
Indices: 52114464--52114515 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
52114454 CATTAGTAGC
*
52114464 ATCGCAGCAAAGTTACCAGCAACAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
*
52114490 ATCGCAGCAAAGCTACCAGTAACAGT
1 ATCGCAGCAAAGCTACCAGCAACAGT
52114516 GATTGTGGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (26 bp):
ATCGCAGCAAAGCTACCAGCAACAGT
Found at i:52114639 original size:24 final size:24
Alignment explanation
Indices: 52114606--52114739 Score: 160
Period size: 24 Copynumber: 5.6 Consensus size: 24
52114596 CTATGCACGG
** *
52114606 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATTTAAATCACAGACA
*
52114630 AATCAATCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
*
52114654 AATCAGTCATTTAAATCATAGACA
1 AATCAGTCATTTAAATCACAGACA
* * *
52114678 AATCAGTCATTTACATCTCAAACA
1 AATCAGTCATTTAAATCACAGACA
* * *
52114702 AATCATTCATTTACATCACAGGCA
1 AATCAGTCATTTAAATCACAGACA
*
52114726 AATCAATCATTTAA
1 AATCAGTCATTTAA
52114740 CCCTGAGGGG
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 94 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:52114728 original size:72 final size:72
Alignment explanation
Indices: 52114606--52114739 Score: 196
Period size: 72 Copynumber: 1.9 Consensus size: 72
52114596 CTATGCACGG
*
52114606 AATCAGTCATACAAATCACAAACAAATCAATCATTTAAATCACAGACAAATCAGTCATTTAAATC
1 AATCAGTCATACAAATCACAAACAAATCAATCATTTAAATCACAGACAAATCAATCATTTAAATC
52114671 ATAGACA
66 ATAGACA
** * * * * *
52114678 AATCAGTCATTTACATCTCAAACAAATCATTCATTTACATCACAGGCAAATCAATCATTTAA
1 AATCAGTCATACAAATCACAAACAAATCAATCATTTAAATCACAGACAAATCAATCATTTAA
52114740 CCCTGAGGGG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (72 bp):
AATCAGTCATACAAATCACAAACAAATCAATCATTTAAATCACAGACAAATCAATCATTTAAATC
ATAGACA
Found at i:52114775 original size:27 final size:27
Alignment explanation
Indices: 52114731--52114797 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
52114721 AGGCAAATCA
*
52114731 ATCATTTAACCCT-GAGGGGTAAAATA-G
1 ATCATTTTACCCTAGAGGGG--AAATACG
* *
52114758 -TCATTTTACCCTATAGGGGAATTACG
1 ATCATTTTACCCTAGAGGGGAAATACG
52114784 ATCATTTTACCCTA
1 ATCATTTTACCCTA
52114798 CAAGGGAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 12 0.35
27 18 0.53
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (27 bp):
ATCATTTTACCCTAGAGGGGAAATACG
Found at i:52114804 original size:27 final size:27
Alignment explanation
Indices: 52114758--52114823 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
52114748 GGTAAAATAG
* * *
52114758 TCATTTTACCCTATAGGGGAATTACGA
1 TCATTTTACCCTACAAGGGAATTAAGA
* *
52114785 TCATTTTACCCTACAAGGGAGTTAAGG
1 TCATTTTACCCTACAAGGGAATTAAGA
52114812 TCATTTTACCCT
1 TCATTTTACCCT
52114824 TTTAGGGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
TCATTTTACCCTACAAGGGAATTAAGA
Found at i:52114830 original size:27 final size:27
Alignment explanation
Indices: 52114757--52114830 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
52114747 GGGTAAAATA
*
52114757 GTCATTTTACCC-TATAGGGGAATTACG
1 GTCATTTTACCCTTATA-GGGAATTAAG
* * *
52114784 ATCATTTTACCC-TACAAGGGAGTTAAG
1 GTCATTTTACCCTTA-TAGGGAATTAAG
*
52114811 GTCATTTTACCCTTTTAGGG
1 GTCATTTTACCCTTATAGGG
52114831 TATTCCAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 36 0.95
28 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTTATAGGGAATTAAG
Found at i:52115109 original size:19 final size:19
Alignment explanation
Indices: 52115069--52115109 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52115059 AGCCCATTGA
**
52115069 GCCCACATGGCCCATTTTG
1 GCCCACATGGCCCATTACG
*
52115088 GCCCACGTGGCCCATTACG
1 GCCCACATGGCCCATTACG
52115107 GCC
1 GCC
52115110 TAAGCCCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.20
Consensus pattern (19 bp):
GCCCACATGGCCCATTACG
Found at i:52127722 original size:16 final size:16
Alignment explanation
Indices: 52127701--52127732 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52127691 GTTTTGTTGC
*
52127701 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52127717 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
52127733 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52127929 original size:46 final size:43
Alignment explanation
Indices: 52127856--52127954 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
52127846 AATAATAACA
*
52127856 GATACACGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAAT
* *
52127902 GATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAAT
52127946 GATACCGGT
1 GATACCGGT
52127955 TCACATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 13 0.27
45 2 0.04
46 24 0.50
47 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAAT
Found at i:52128014 original size:51 final size:51
Alignment explanation
Indices: 52127950--52128150 Score: 266
Period size: 51 Copynumber: 4.0 Consensus size: 51
52127940 ATTAATGATA
* *
52127950 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
52128001 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * *
52128052 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
* *
52128102 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
52128151 TTCACTTTCA
Statistics
Matches: 130, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
49 4 0.03
50 42 0.32
51 81 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (51 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:52128141 original size:101 final size:102
Alignment explanation
Indices: 52127958--52128142 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
52127948 TACCGGTTCA
*
52127958 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCTGCA
52128023 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
52128060 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACATAGTAGCCTGC
52128123 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
52128143 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 39 0.50
102 35 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:52128166 original size:101 final size:102
Alignment explanation
Indices: 52127950--52128142 Score: 300
Period size: 102 Copynumber: 1.9 Consensus size: 102
52127940 ATTAATGATA
*
52127950 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACATAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGT
*
52128015 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
* * * * *
52128052 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAG
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACATAG
52128115 TAGCCTGCACATAGTACTACACACGTGA
65 TAGCCTGCACATAGTACTACACACGTGA
52128143 CCATCACTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
101 39 0.46
102 41 0.49
103 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGT
AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
Found at i:52128435 original size:31 final size:31
Alignment explanation
Indices: 52128378--52128436 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
52128368 AAAAATCACA
* *
52128378 TTTTAGAAAAATTACATTTTTTCCCCTAAAG
1 TTTTACAAAAATTACATTTTTGCCCCTAAAG
*
52128409 TTTTACAAAAATTATGA-TTTTGCCCCTA
1 TTTTACAAAAATTA-CATTTTTGCCCCTA
52128437 GGCTCAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (31 bp):
TTTTACAAAAATTACATTTTTGCCCCTAAAG
Found at i:52130970 original size:13 final size:13
Alignment explanation
Indices: 52130952--52130976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52130942 ATAATAGGCA
52130952 AGAAAATAAAAGC
1 AGAAAATAAAAGC
52130965 AGAAAATAAAAG
1 AGAAAATAAAAG
52130977 TGTTTTCAAT
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:0.72, C:0.04, G:0.16, T:0.08
Consensus pattern (13 bp):
AGAAAATAAAAGC
Found at i:52132197 original size:104 final size:104
Alignment explanation
Indices: 52132017--52132226 Score: 420
Period size: 104 Copynumber: 2.0 Consensus size: 104
52132007 CTATTGATAA
52132017 ATTTATTTTTAAAAAAGTAGTTTTTAATGAAAATTTGGATCAATCAAATGAAAGTTTGCATGTCC
1 ATTTATTTTTAAAAAAGTAGTTTTTAATGAAAATTTGGATCAATCAAATGAAAGTTTGCATGTCC
52132082 ATGAGAATGATGAAATTAATGATCTAAATGAGCCGAATG
66 ATGAGAATGATGAAATTAATGATCTAAATGAGCCGAATG
52132121 ATTTATTTTTAAAAAAGTAGTTTTTAATGAAAATTTGGATCAATCAAATGAAAGTTTGCATGTCC
1 ATTTATTTTTAAAAAAGTAGTTTTTAATGAAAATTTGGATCAATCAAATGAAAGTTTGCATGTCC
52132186 ATGAGAATGATGAAATTAATGATCTAAATGAGCCGAATG
66 ATGAGAATGATGAAATTAATGATCTAAATGAGCCGAATG
52132225 AT
1 AT
52132227 GTGCCAAATG
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (104 bp):
ATTTATTTTTAAAAAAGTAGTTTTTAATGAAAATTTGGATCAATCAAATGAAAGTTTGCATGTCC
ATGAGAATGATGAAATTAATGATCTAAATGAGCCGAATG
Found at i:52133609 original size:28 final size:28
Alignment explanation
Indices: 52133574--52133647 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
52133564 TGACTTTCGA
52133574 CACTAAGTGTGCGAGTTTAATTGG-AAAG
1 CACTAAGTGTGCGAGTTTAA-TGGAAAAG
* *
52133602 CAGTAAGTGTGGGAGTTTAATGGAAAAG
1 CACTAAGTGTGCGAGTTTAATGGAAAAG
52133630 CACTAAGTGTGCGAGTTT
1 CACTAAGTGTGCGAGTTT
52133648 GATTATTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 3 0.07
28 38 0.93
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.28
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATGGAAAAG
Found at i:52134450 original size:47 final size:47
Alignment explanation
Indices: 52134390--52134611 Score: 167
Period size: 47 Copynumber: 4.7 Consensus size: 47
52134380 TTATGCTTAA
*
52134390 ATGCTGCACAATTTCTTGTATATAAATGCTG-CTCAATTTGTTGTATAT
1 ATGCTGC-CAATTTGTTGTATATAAATGCTGTC-CAATTTGTTGTATAT
* * * * *
52134438 TTGCTGCCAATTTGTTTTATAT-AA-GCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCAATTTGTTGTATATAAATGCTGTCCAA--TTTGTTGTATAT
* * *
52134485 ATGCTGCTCAATTTGTTG--TGTAATTGCTGTCCAATTTGTTGTGTAT
1 ATGCTGC-CAATTTGTTGTATATAAATGCTGTCCAATTTGTTGTATAT
* * * *
52134531 AAGCTGTCCAATTTTGGTGCA-A-AAATGCTG-CTCAATATGTTGTATAT
1 ATGCTG-CCAA-TTTGTTGTATATAAATGCTGTC-CAATTTGTTGTATAT
*
52134578 ATGCTGCCTAAATTGTTGTATAT--ATGCTGTCCAA
1 ATGCTGCC-AATTTGTTGTATATAAATGCTGTCCAA
52134612 ATTTTGGTGT
Statistics
Matches: 135, Mismatches: 24, Indels: 32
0.71 0.13 0.17
Matches are distributed among these distances:
45 7 0.05
46 39 0.29
47 65 0.48
48 24 0.18
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42
Consensus pattern (47 bp):
ATGCTGCCAATTTGTTGTATATAAATGCTGTCCAATTTGTTGTATAT
Found at i:52134488 original size:70 final size:69
Alignment explanation
Indices: 52134413--52134631 Score: 303
Period size: 70 Copynumber: 3.1 Consensus size: 69
52134403 TCTTGTATAT
*
52134413 AAATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGG
1 AAATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAA-TTTTGG
52134478 TGTAA
65 TGTAA
* * *
52134483 AAATGCTGCTCAATTTGTTGTGTAATTGCTGTCCAATTTGTTGTGTATAAGCTGTCCAATTTTGG
1 AAATGCTGCTCAATTTGTTGTATATTTGCTG-CCAATTTGTTGTATATAAGCTGTCCAATTTTGG
*
52134548 TGCAA
65 TGTAA
* * * *
52134553 AAATGCTGCTCAATATGTTGTATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAAATTTTG
1 AAATGCTGCTCAATTTGTTGTATATTTGCTGCC-AATTTGTTGTATATAAGCTGTCC-AATTTTG
*
52134618 GTGTGA
64 GTGTAA
*
52134624 AATTGCTG
1 AAATGCTG
52134632 TTTAGTTTGG
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
69 2 0.02
70 86 0.66
71 43 0.33
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (69 bp):
AAATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTGGT
GTAA
Found at i:52134614 original size:23 final size:22
Alignment explanation
Indices: 52134390--52134611 Score: 158
Period size: 23 Copynumber: 9.5 Consensus size: 22
52134380 TTATGCTTAA
*
52134390 ATGCTGCACAATTTCTTGTATAT
1 ATGCTGC-CAATTTGTTGTATAT
52134413 AAATGCTGCTCAATTTGTTGTATAT
1 --ATGCTGC-CAATTTGTTGTATAT
* *
52134438 TTGCTGCCAATTTGTTTTATAT
1 ATGCTGCCAATTTGTTGTATAT
* * * *
52134460 AAGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTG-CCAA--TTTGTTGTATAT
*
52134485 ATGCTGCTCAATTTGTTGTGTA-
1 ATGCTGC-CAATTTGTTGTATAT
*
52134507 ATTGCTGTCCAATTTGTTGTGTAT
1 A-TGCTG-CCAATTTGTTGTATAT
* * * * *
52134531 AAGCTGTCCAATTTTGGTGCAAAA
1 ATGCTG-CCAA-TTTGTTGTATAT
*
52134555 ATGCTGCTCAATATGTTGTATAT
1 ATGCTGC-CAATTTGTTGTATAT
*
52134578 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCC-AATTTGTTGTATAT
52134601 ATGCTGTCCAA
1 ATGCTG-CCAA
52134612 ATTTTGGTGT
Statistics
Matches: 158, Mismatches: 28, Indels: 24
0.75 0.13 0.11
Matches are distributed among these distances:
22 20 0.13
23 81 0.51
24 20 0.13
25 37 0.23
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42
Consensus pattern (22 bp):
ATGCTGCCAATTTGTTGTATAT
Found at i:52137588 original size:20 final size:19
Alignment explanation
Indices: 52137563--52137617 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
52137553 CATTTAAAAA
52137563 AATTTATTTTATAATAACAT
1 AATTTATTTTATAATAA-AT
* *
52137583 AATTTACTTTGTAA-AAAT
1 AATTTATTTTATAATAAAT
* *
52137601 AATATATTTTTTAATAA
1 AATTTATTTTATAATAA
52137618 TTTTTCAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 13 0.45
19 4 0.14
20 12 0.41
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTTATTTTATAATAAAT
Found at i:52140986 original size:31 final size:31
Alignment explanation
Indices: 52140950--52141009 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
52140940 ATTTAATGGA
* *
52140950 GAGTGACCAAAATATAAACGATCTAAAACGT
1 GAGTGACCAAAATAAAAACAATCTAAAACGT
*
52140981 GAGTGACCAAAATAAAAATAATCTAAAAC
1 GAGTGACCAAAATAAAAACAATCTAAAAC
52141010 ATTAGTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.18
Consensus pattern (31 bp):
GAGTGACCAAAATAAAAACAATCTAAAACGT
Found at i:52151454 original size:27 final size:27
Alignment explanation
Indices: 52151419--52151473 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
52151409 AAACTCTTCT
*
52151419 AAAAGAAAACTC-AAGAAAATTTCTTG
1 AAAAGAAAACTCAAAGAAAATTTATTG
52151445 AAAAGAAAAACTCAAAGAAAATTTATTG
1 AAAAG-AAAACTCAAAGAAAATTTATTG
52151473 A
1 A
52151474 CTCAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 5 0.19
27 7 0.27
28 14 0.54
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (27 bp):
AAAAGAAAACTCAAAGAAAATTTATTG
Found at i:52167624 original size:27 final size:27
Alignment explanation
Indices: 52167587--52167648 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
52167577 AATTATTTAT
***
52167587 ATATATTTGCATGAACTTGATTTTCAC
1 ATATATTTGCATGAACTTGATGGGCAC
52167614 ATATATTTGCATGAACTTGATGGGCAC
1 ATATATTTGCATGAACTTGATGGGCAC
52167641 ATATATTT
1 ATATATTT
52167649 AAAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
ATATATTTGCATGAACTTGATGGGCAC
Found at i:52168978 original size:21 final size:21
Alignment explanation
Indices: 52168940--52168979 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52168930 GTTTAATCTG
*
52168940 TTCAAAACACGATCAAACATA
1 TTCAAAACACGATAAAACATA
* *
52168961 TTCAAAACATGCTAAAACA
1 TTCAAAACACGATAAAACA
52168980 ATCATCCTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
TTCAAAACACGATAAAACATA
Found at i:52170544 original size:7 final size:7
Alignment explanation
Indices: 52170532--52170557 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52170522 TTTCAATTTC
52170532 ATATTGA
1 ATATTGA
52170539 ATATTGA
1 ATATTGA
52170546 ATATTGA
1 ATATTGA
52170553 ATATT
1 ATATT
52170558 TAAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
ATATTGA
Found at i:52171001 original size:4 final size:4
Alignment explanation
Indices: 52170984--52171033 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
52170974 CGTGCGTCTC
**
52170984 TTCT TTCT CCCT TTCT TTCT TTCT ATT-T TTCT TTC- TT-T TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
52171030 TTCT
1 TTCT
52171034 AATTTCTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.16
4 30 0.79
5 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:52175077 original size:22 final size:22
Alignment explanation
Indices: 52175045--52175086 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52175035 CAATTAAATA
*
52175045 AAAATTTACGTGCAACTATTATG
1 AAAATTTACGTACAAC-ATTATG
52175068 AAAA-TTACGTACAACATTA
1 AAAATTTACGTACAACATTA
52175087 GAACTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAATTTACGTACAACATTATG
Found at i:52175322 original size:21 final size:21
Alignment explanation
Indices: 52175298--52175344 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
52175288 ATGTTCACTT
*
52175298 TTATATCA-TAAAATAAACAAA
1 TTATAT-ATTAAAATAAAAAAA
52175319 TTAT-TATTAAAATAAAAAAA
1 TTATATATTAAAATAAAAAAA
52175339 -TATATA
1 TTATATA
52175345 CTAGTCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 15 0.65
21 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
TTATATATTAAAATAAAAAAA
Found at i:52176282 original size:13 final size:13
Alignment explanation
Indices: 52176266--52176292 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52176256 AATTTTTGGT
52176266 GGCAAGAGAGGGA
1 GGCAAGAGAGGGA
52176279 GGCAAGAGAGGGA
1 GGCAAGAGAGGGA
52176292 G
1 G
52176293 TATCGTCGAT
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:0.37, C:0.07, G:0.56, T:0.00
Consensus pattern (13 bp):
GGCAAGAGAGGGA
Found at i:52178661 original size:19 final size:19
Alignment explanation
Indices: 52178637--52178677 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
52178627 TAGACCATCC
52178637 AACGAAGAGTTTGAATCAT
1 AACGAAGAGTTTGAATCAT
52178656 AACGAAGAGTTTGAATCAT
1 AACGAAGAGTTTGAATCAT
52178675 AAC
1 AAC
52178678 ATATGGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (19 bp):
AACGAAGAGTTTGAATCAT
Found at i:52184851 original size:25 final size:25
Alignment explanation
Indices: 52184823--52184877 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
52184813 ACGTCAGAAA
52184823 AAGGA-ATCATTTGTGGCGATCTATG
1 AAGGATATC-TTTGTGGCGATCTATG
*
52184848 AAGGGATTGTCTTTGTGGCGATCTATG
1 AA-GGA-TATCTTTGTGGCGATCTATG
52184875 AAG
1 AAG
52184878 AATGGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.08
26 4 0.15
27 18 0.69
28 2 0.08
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (25 bp):
AAGGATATCTTTGTGGCGATCTATG
Found at i:52185620 original size:20 final size:20
Alignment explanation
Indices: 52185587--52185626 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52185577 CCAACCCTCA
*
52185587 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
52185607 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
52185627 TTACCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:52185911 original size:39 final size:39
Alignment explanation
Indices: 52185850--52185925 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
52185840 GAATTTCATA
*
52185850 TTTTATCTTTAAGATAAATTTT-ATTAAAAAATCACATTT
1 TTTTATATTTAAGATAAATTTTAATTAAAAAAT-ACATTT
* ** *
52185889 TTTTATATTTAATATATTTTTTAATTTAAAAATACAT
1 TTTTATATTTAAGATAAATTTTAATTAAAAAATACAT
52185926 AATGACAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 22 0.71
40 9 0.29
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (39 bp):
TTTTATATTTAAGATAAATTTTAATTAAAAAATACATTT
Found at i:52186052 original size:19 final size:19
Alignment explanation
Indices: 52186028--52186065 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52186018 AAAGTTAATA
*
52186028 ACAAATTTGATTACGGTGG
1 ACAAATTTAATTACGGTGG
52186047 ACAAATTTAATTACGGTGG
1 ACAAATTTAATTACGGTGG
52186066 GTGACAGTGG
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:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ACAAATTTAATTACGGTGG
Found at i:52191346 original size:29 final size:30
Alignment explanation
Indices: 52191287--52191346 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
52191277 CAGATTTCGG
* * *
52191287 GAGCCACACGGGCTGGGCACATAGCCATGT
1 GAGCCACACGGGCTGGCCACACAACCATGT
*
52191317 GAGCCCCACGGGCT-GCCACACAACCATGT
1 GAGCCACACGGGCTGGCCACACAACCATGT
52191346 G
1 G
52191347 CCAGACCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.23, C:0.35, G:0.30, T:0.12
Consensus pattern (30 bp):
GAGCCACACGGGCTGGCCACACAACCATGT
Found at i:52196679 original size:27 final size:27
Alignment explanation
Indices: 52196640--52197054 Score: 416
Period size: 27 Copynumber: 15.6 Consensus size: 27
52196630 AGACCCTAAA
*
52196640 ATAGG-TAAAATGACCAAAATACCCCC
1 ATAGGATAAAATGACCGAAATACCCCC
* * *
52196666 ATAGGATAGAATGACCAAAATACCCTC
1 ATAGGATAAAATGACCGAAATACCCCC
*
52196693 ATAGGATAAAATGATCGAAATACCCCC
1 ATAGGATAAAATGACCGAAATACCCCC
* * *
52196720 ATAAGATAGAATGATCGAAATA-CCCC
1 ATAGGATAAAATGACCGAAATACCCCC
52196746 ATAGGATAAAATGACCGAAATACCCCC
1 ATAGGATAAAATGACCGAAATACCCCC
* * *
52196773 ATAGGTTAAAATGATCGAAATACCCCT
1 ATAGGATAAAATGACCGAAATACCCCC
* * ** *
52196800 ATAGGGTAAAATAACTAAAATACCCCT
1 ATAGGATAAAATGACCGAAATACCCCC
* * *
52196827 ATAGGGTACAATGACTGAAATACCCCC
1 ATAGGATAAAATGACCGAAATACCCCC
*
52196854 ATAGGATAAAATGACTGAAATACCCCC
1 ATAGGATAAAATGACCGAAATACCCCC
* * * *
52196881 ATAAGATAGAATGACTGAAATACCCTC
1 ATAGGATAAAATGACCGAAATACCCCC
* * *
52196908 ATATGG-TAAACTGGCCGAAATACCCCT
1 ATA-GGATAAAATGACCGAAATACCCCC
* *
52196935 ATATGG-TAGAATGATCGAAATA-CCCC
1 ATA-GGATAAAATGACCGAAATACCCCC
* * *
52196961 ATAGGGTAGAATGACTGAAATA-CCCC
1 ATAGGATAAAATGACCGAAATACCCCC
*
52196987 ATAAGG-TAGAATGACCGAAATA-CCCC
1 AT-AGGATAAAATGACCGAAATACCCCC
*
52197013 ATAAGG-TAGAATGACCGAAATACCCCC
1 AT-AGGATAAAATGACCGAAATACCCCC
*
52197040 ATAGGGTAAAATGAC
1 ATAGGATAAAATGAC
52197055 TATTATACCC
Statistics
Matches: 338, Mismatches: 44, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
25 2 0.01
26 98 0.29
27 237 0.70
28 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
ATAGGATAAAATGACCGAAATACCCCC
Found at i:52211329 original size:24 final size:24
Alignment explanation
Indices: 52211297--52211348 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
52211287 CGTTCATGAA
*
52211297 GGCATTATAAGTAAGGGCATCAGG
1 GGCATTATAAGTAACGGCATCAGG
52211321 GGCATTATAAGTAACGGCATCAGG
1 GGCATTATAAGTAACGGCATCAGG
52211345 GGCA
1 GGCA
52211349 ATTCCAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (24 bp):
GGCATTATAAGTAACGGCATCAGG
Found at i:52221521 original size:62 final size:60
Alignment explanation
Indices: 52221424--52221543 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 60
52221414 GATCCACACA
52221424 GCCTAAGCATTTCCACACGAGCTGGGCACACACCCGTGTAAGACACACAGGCTAGTCACATG
1 GCCTAAGCATTTCCACACGAGCTGGGCACACACCCGTGT--GACACACAGGCTAGTCACATG
*
52221486 GCCTAAGCATTTCCACACGAGCTGGGCACACACCCGTGTGAGACACAGGCTAGTCACA
1 GCCTAAGCATTTCCACACGAGCTGGGCACACACCCGTGTGACACACAGGCTAGTCACA
52221544 CGCCCCTGTG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 18 0.32
62 39 0.68
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (60 bp):
GCCTAAGCATTTCCACACGAGCTGGGCACACACCCGTGTGACACACAGGCTAGTCACATG
Found at i:52222989 original size:89 final size:91
Alignment explanation
Indices: 52222798--52223008 Score: 246
Period size: 89 Copynumber: 2.3 Consensus size: 91
52222788 TTGAATATTT
* * * * * *
52222798 TGGCATGTTATCAGTTGGAAAGCTTTTATGAGCAAACTAACGTGTTACCGTGGGAGAATGTTTGG
1 TGGCATGTTATCGGTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTTAG
* *
52222863 CCTACGGGCTTTGCACTATGTGCATC
66 CATACGAGCTTTGCACTATGTGCATC
** * * *
52222889 TGGTTTATTATCGGTTGGAAAGCTCTTATGAG-AAACTAGCATGTTATC-AGGGAAAATGTTTAG
1 TGGCATGTTATCGGTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTTAG
* * * *
52222952 CATATGAGTTTTTCCCTATGTGCATC
66 CATACGAGCTTTGCACTATGTGCATC
*
52222978 TGGCATGTTATCGATTGGAAAGCTCTTATGA
1 TGGCATGTTATCGGTTGGAAAGCTCTTATGA
52223009 ACAATCCGAT
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 59 0.60
90 13 0.13
91 27 0.27
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (91 bp):
TGGCATGTTATCGGTTGGAAAGCTCTTATGAGCAAACTAACATGTTACCGAGGGAAAATGTTTAG
CATACGAGCTTTGCACTATGTGCATC
Found at i:52223645 original size:15 final size:15
Alignment explanation
Indices: 52223620--52223654 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52223610 AACTCTATTT
*
52223620 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
52223634 TAATTAATATTAAGA
1 TAATTAATATTAAGA
52223649 TAATTA
1 TAATTA
52223655 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:52226169 original size:76 final size:76
Alignment explanation
Indices: 52226051--52226195 Score: 227
Period size: 76 Copynumber: 1.9 Consensus size: 76
52226041 TCATTAGCCA
*
52226051 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATGTAATGCAA
1 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
52226116 GATATTAGTTG
66 GATATTAGTTG
* * * * * *
52226127 TTTGGGGTGTATTTAGACACTTATTGTTTAGGGATTTTTATGTAAAGATATTGTATATAATGTAA
1 TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
52226192 GATA
66 GATA
52226196 GGGGAGAGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (76 bp):
TTTGGGGTGCATTTAAACACTCATTATTTAGGGATTTTTATGTAAAGATATTATATATAATGCAA
GATATTAGTTG
Found at i:52227199 original size:3 final size:3
Alignment explanation
Indices: 52227191--52227269 Score: 99
Period size: 3 Copynumber: 26.3 Consensus size: 3
52227181 AAGTAAACAG
* *
52227191 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA -AA TTAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
*
52227239 TAA TAA TAA TAA TAGA -AT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T
52227270 CTTAAGTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52233536 original size:211 final size:211
Alignment explanation
Indices: 52232982--52233610 Score: 976
Period size: 211 Copynumber: 3.0 Consensus size: 211
52232972 GAATGAGAAG
* * *
52232982 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGGATGATATTCAATCC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* *
52233047 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTGCATCATTCGGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* * *
52233112 TGAGCTATGTTACCCAGGCTC-AGTGGATCTTGGTTGCTGACATTTGTCTAACACTGATATGGTA
131 TGAGCTATGTTACCCAGGCTCAAGT-GATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
*
52233176 AACCTTTCGAAGTGAAT
195 AACCTTTCTAAGTGAAT
* *
52233193 C-TTTATTTGTTTGCGTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAGTTC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* * *
52233257 TCTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTTGGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* * * *
52233322 TGAGCTATGTTAGCCACGCTCAAGTGACTCTTGGATGCTGACTTTTGTCCAACACTGGTATGCTA
131 TGAGCTATGTTACCCAGGCTCAAGTGA-TCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
*
52233387 AACCTTTCTAGGTGAAT
195 AACCTTTCTAAGTGAAT
*
52233404 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAAGGTTGCAAAAAGAATGATCTTCAATTC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
* * *
52233469 TTTCATGTACTTTATTTCCCATTGAATGTGG-TTTTTCAATTTTTTTTCTTTACTTCATTCAGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
* * *
52233533 TGAGGTATGTTACCCAGGCTCAAGTCAATCTTGGATGCTGACATTTGTCCAACCCTGATATGCTA
131 TGAGCTATGTTACCCAGGCTCAAGT-GATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
52233598 AACCTTTCTAAGT
195 AACCTTTCTAAGT
52233611 TTTTCATATA
Statistics
Matches: 379, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
210 139 0.37
211 149 0.39
212 91 0.24
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (211 bp):
CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAATTC
TTTCATGTACTTTATTTCCCATTGAATGTGGCTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
TGAGCTATGTTACCCAGGCTCAAGTGATCTTGGATGCTGACATTTGTCCAACACTGATATGCTAA
ACCTTTCTAAGTGAAT
Found at i:52245378 original size:49 final size:49
Alignment explanation
Indices: 52245285--52245386 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 49
52245275 TAGGCTCTCA
* *
52245285 AGTTATACTCCAACCTGTTAACACATAACCACCGTCAATGGGGAGCCCT
1 AGTTATACTCCAACCTGTTAACACATAACCACCATCAATGGGGAGCCCG
* * * *
52245334 AGTTATACTTCAACCT-TTGACTATATAACCACCATGAACT-GGGAGCCCG
1 AGTTATACTCCAACCTGTTAAC-ACATAACCACCATCAA-TGGGGAGCCCG
52245383 AGTT
1 AGTT
52245387 GTAATTCGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.09
49 40 0.89
50 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (49 bp):
AGTTATACTCCAACCTGTTAACACATAACCACCATCAATGGGGAGCCCG
Found at i:52255218 original size:17 final size:16
Alignment explanation
Indices: 52255196--52255229 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
52255186 GTTATTGAAC
*
52255196 ATTGTCATTGCATTGTT
1 ATTGTCATCGCA-TGTT
52255213 ATTGTCATCGCATGTT
1 ATTGTCATCGCATGTT
52255229 A
1 A
52255230 ATCTTAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (16 bp):
ATTGTCATCGCATGTT
Found at i:52266682 original size:50 final size:50
Alignment explanation
Indices: 52266607--52266709 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
52266597 TGAAATCGGT
52266607 CTTACATTTCTTGCTCAGGCTTCCTTACCAATGCACTTATGGGCACATAC
1 CTTACATTTCTTGCTCAGGCTTCCTTACCAATGCACTTATGGGCACATAC
52266657 CTTACATTTCTTGCTCAGGCTTCCTTACCAATGCACTTATGGGCACATAC
1 CTTACATTTCTTGCTCAGGCTTCCTTACCAATGCACTTATGGGCACATAC
52266707 CTT
1 CTT
52266710 TCTCAATGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (50 bp):
CTTACATTTCTTGCTCAGGCTTCCTTACCAATGCACTTATGGGCACATAC
Found at i:52272275 original size:16 final size:16
Alignment explanation
Indices: 52272254--52272284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52272244 TTCACTATTA
*
52272254 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
52272270 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
52272285 ACATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:52272684 original size:571 final size:567
Alignment explanation
Indices: 52271604--52272722 Score: 1440
Period size: 571 Copynumber: 2.0 Consensus size: 567
52271594 GAAATGTGTC
** *
52271604 CATATTGTAGTAAACATTTAACTGTTTTCTATGTATTTGAACGATGAATAAATAAATAAAGTTAA
1 CATATTGTAGTAAACATGCAACTGTTTTCTATGTATTTAAACGATGAATAAATAAATAAAGTTAA
* * * *
52271669 TTTCACATTTCACTGTTATATCTTTTATGTTTCTATCTTTCATGTTTTGCATACATAGCAAAATT
66 ATTCACATTTCACTATTATATCTTTTATGTTTCTATCTTTCATATTTTACATACATAGCAAAATT
* * * *
52271734 ATGACAAGAAAATATTAGCTCATTGATTGTTTAAGTTCAAACTGATGATAAGTGGAACTGTAAGA
131 ATGACAAGAAAATATTAGCTCATTAATTGTTAAAGTTCAAACTGAAGATAAGTGGAACTGTAACA
* * **
52271799 ACATTTACATTACGAGAAGACAACTTACTTCAGTAGATAATCTAAACAAGTCTGTAATCGTGTAA
196 ACATTTACATTACGAAAAGACAACTTACTTCAGTAGATAATCTAAAAAAGTCTGTAATCGCATAA
* * * *
52271864 AAGAATCAAAGTTAGCGTTTAATTTAAATACTTAGAAAGATTAGTATGTCGTCTACAATTCCAAC
261 AAGAATCAAAGTGAGCGTTTAATTCAAACACTGAGAAAGATTAGTATGTCGTCTACAATTCCAAC
* *
52271929 CGGGGAGATGACTAGTCTTGACTACCGAAGTAGTTGAATCCACGGGTAGAGACATAGATGTATTC
326 CGGGGAGATGACTAGTCTTGACTACCGAAGCAGTTGAATCCACGAGTAGAGACATAGATGTATTC
* * **
52271994 ATTGAAAGAATGATACATTGGACTGAAACCAAGATAAATTAATTCTAAATTCGTTTGTGAATTAA
391 ATTGAAAGAATGATACATTGCACTGAAACCAAGATAAATTAATTCTAAATCCACTTGTGAATTAA
* * * *
52272059 TACACTTGTGAAGTTCATTGTGTGATTTTCCTAAATCCTGAGTTAGCCACTGACCATGCGTATGT
456 TACACTTGTGAAGTTCATGGTGTGATTTTCCTAAATCCTAAGTTAACCACTGACCATGCGTATGC
*
52272124 AACTCATATGCTTTAATATAAGTGGAGGCTTTTTAAGGAAATGAGCT
521 AACTCATATGCTTTAATATAAGTCGAGGCTTTTTAAGGAAATGAGCT
* *
52272171 CATATTGTAGTAAACATGCAACTGTTTTCTATTTATTTAAATGATGAATAAATAAATAAAGTTAA
1 CATATTGTAGTAAACATGCAACTGTTTTCTATGTATTTAAACGATGAATAAATAAATAAAGTTAA
* * * * * **
52272236 ATTCACATTTCACTATTATGTCTTTTGTAT-TTTTTGTCTTTTATATTTTACATGCATAGTGAAA
66 ATTCACATTTCACTATTATATC-TTT-TATGTTTCTATCTTTCATATTTTACATACATAGCAAAA
* * * *
52272300 TTATGGCAATAAAATATTAGCTCATTAATTGTCTAAAGTTCAAACTGAAGATAAGTGGCATTGTA
129 TTATGACAAGAAAATATTAGCTCATTAATTGT-TAAAGTTCAAACTGAAGATAAGTGGAACTGT-
* * * * *
52272365 AACAACGTTTATATTGCGAAAAATACAACTTACTTCGGTAGATAATCTAAAAAAGT-TCGTAATA
192 AACAACATTTACATTACG-AAAAGACAACTTACTTCAGTAGATAATCTAAAAAAGTCT-GTAAT-
* * * *
52272429 C-CATAAAAGAATTAAAGTGAG-GATTTGATTCAAACACTGAGAATGATTATTATGTCGTCTACA
254 CGCATAAAAGAATCAAAGTGAGCG-TTTAATTCAAACACTGAGAAAGATTAGTATGTCGTCTACA
* ** ** * * * *
52272492 ATTTCAATTGGGGAGATGGTTAGTCTTGGCTATCGAAGCAGTTGACTCCACGAGTGGAGACATAG
318 ATTCCAACCGGGGAGATGACTAGTCTTGACTACCGAAGCAGTTGAATCCACGAGTAGAGACATAG
* ** * * *
52272557 ATGTATTGATTGGTAGAATGATACATTGCTCT-AAACCCAAGATGAATTAATTCTGAATCCACTT
383 ATGTATTCATTGAAAGAATGATACATTGCACTGAAA-CCAAGATAAATTAATTCTAAATCCACTT
* * **
52272621 GTGAATTAATTCACTTGTGACGTTCATGGTGTGATTTAT-CTAAATCCTAAGTTAATTACTGACC
447 GTGAATTAATACACTTGTGAAGTTCATGGTGTGATTT-TCCTAAATCCTAAGTTAACCACTGACC
* * *
52272685 ATGCGTATGCAATTCATGTGCTTTGATATAAGTCGAGG
511 ATGCGTATGCAACTCATATGCTTTAATATAAGTCGAGG
52272723 ATTATGCTCT
Statistics
Matches: 468, Mismatches: 74, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
567 79 0.17
568 58 0.12
569 30 0.06
570 19 0.04
571 280 0.60
572 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (567 bp):
CATATTGTAGTAAACATGCAACTGTTTTCTATGTATTTAAACGATGAATAAATAAATAAAGTTAA
ATTCACATTTCACTATTATATCTTTTATGTTTCTATCTTTCATATTTTACATACATAGCAAAATT
ATGACAAGAAAATATTAGCTCATTAATTGTTAAAGTTCAAACTGAAGATAAGTGGAACTGTAACA
ACATTTACATTACGAAAAGACAACTTACTTCAGTAGATAATCTAAAAAAGTCTGTAATCGCATAA
AAGAATCAAAGTGAGCGTTTAATTCAAACACTGAGAAAGATTAGTATGTCGTCTACAATTCCAAC
CGGGGAGATGACTAGTCTTGACTACCGAAGCAGTTGAATCCACGAGTAGAGACATAGATGTATTC
ATTGAAAGAATGATACATTGCACTGAAACCAAGATAAATTAATTCTAAATCCACTTGTGAATTAA
TACACTTGTGAAGTTCATGGTGTGATTTTCCTAAATCCTAAGTTAACCACTGACCATGCGTATGC
AACTCATATGCTTTAATATAAGTCGAGGCTTTTTAAGGAAATGAGCT
Found at i:52275121 original size:28 final size:28
Alignment explanation
Indices: 52275082--52275146 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
52275072 ACCATTACTT
52275082 AAAACCTCTTTAACCTCTAATTCTTTCA
1 AAAACCTCTTTAACCTCTAATTCTTTCA
*
52275110 AAAACCTCTTTAACCTCTAATTCTTTTA
1 AAAACCTCTTTAACCTCTAATTCTTTCA
*
52275138 AAATCCTCT
1 AAAACCTCT
52275147 AAATTTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAACCTCTTTAACCTCTAATTCTTTCA
Found at i:52290661 original size:14 final size:14
Alignment explanation
Indices: 52290642--52290680 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52290632 TTATAAATTT
*
52290642 TATTATTTATTGTA
1 TATTATTTATAGTA
*
52290656 TATTATTTGTAGTA
1 TATTATTTATAGTA
52290670 TA-TATTTATAG
1 TATTATTTATAG
52290681 GATAGGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (14 bp):
TATTATTTATAGTA
Found at i:52297281 original size:25 final size:25
Alignment explanation
Indices: 52297252--52297301 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52297242 AATTACAGTT
*
52297252 TTAAAAATTTATAAATTAT-AAAAAA
1 TTAAAAA-TAATAAATTATCAAAAAA
*
52297277 TTAAAAATAATAAATTTTCAAAAAA
1 TTAAAAATAATAAATTATCAAAAAA
52297302 AAAATACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TTAAAAATAATAAATTATCAAAAAA
Found at i:52309337 original size:21 final size:21
Alignment explanation
Indices: 52309313--52309356 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52309303 TGATGGTCAG
* *
52309313 GGTATTTATTGTCTCAGGTGT
1 GGTATTCATTGTCTCAAGTGT
52309334 GGTATTCATTGTCTCAAGTGT
1 GGTATTCATTGTCTCAAGTGT
52309355 GG
1 GG
52309357 CTTAGGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.43
Consensus pattern (21 bp):
GGTATTCATTGTCTCAAGTGT
Found at i:52318559 original size:33 final size:33
Alignment explanation
Indices: 52318513--52318611 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
52318503 GATCGATCAA
* * *
52318513 AATTTGAG-AAGGAGACAGATGTACAGCCGGTG
1 AATTTGGGAAAGGAGACAAATGTACAGTCGGTG
*
52318545 AATTTGGGAAAGGAGACAAATGTACATTCGGTG
1 AATTTGGGAAAGGAGACAAATGTACAGTCGGTG
*
52318578 AATTTGGGACAGGAGACAAATGTACAGTCGGTG
1 AATTTGGGAAAGGAGACAAATGTACAGTCGGTG
52318611 A
1 A
52318612 CAGAACATCC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 7 0.12
33 53 0.88
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.21
Consensus pattern (33 bp):
AATTTGGGAAAGGAGACAAATGTACAGTCGGTG
Found at i:52320306 original size:45 final size:45
Alignment explanation
Indices: 52320242--52320351 Score: 202
Period size: 45 Copynumber: 2.4 Consensus size: 45
52320232 ATTGGGCTCT
* *
52320242 CTAGAATTGTTCAGCCCAAAATTCGGACCAGCATTTGTTTGCCCA
1 CTAGAATTGTTTAGCCCAAAATTCGAACCAGCATTTGTTTGCCCA
52320287 CTAGAATTGTTTAGCCCAAAATTCGAACCAGCATTTGTTTGCCCA
1 CTAGAATTGTTTAGCCCAAAATTCGAACCAGCATTTGTTTGCCCA
52320332 CTAGAATTGTTTAGCCCAAA
1 CTAGAATTGTTTAGCCCAAA
52320352 CGGCTGGCCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (45 bp):
CTAGAATTGTTTAGCCCAAAATTCGAACCAGCATTTGTTTGCCCA
Found at i:52323492 original size:16 final size:16
Alignment explanation
Indices: 52323471--52323506 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
52323461 TTTGGTTCGC
52323471 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52323487 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52323503 TGTA
1 TGTA
52323507 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52323652 original size:15 final size:15
Alignment explanation
Indices: 52323632--52323662 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52323622 AATACCCTTA
52323632 GCATAAATTTGTTTT
1 GCATAAATTTGTTTT
52323647 GCATAAATTTGTTTT
1 GCATAAATTTGTTTT
52323662 G
1 G
52323663 GTAAATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (15 bp):
GCATAAATTTGTTTT
Found at i:52323778 original size:18 final size:17
Alignment explanation
Indices: 52323757--52323791 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52323747 TTATTATTAA
*
52323757 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52323775 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52323792 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52323799 original size:79 final size:79
Alignment explanation
Indices: 52323716--52323959 Score: 207
Period size: 79 Copynumber: 3.1 Consensus size: 79
52323706 TTATTATCAA
*
52323716 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
52323781 TTTAATAAAATTCT
66 TTTAATAAAATTCT
* ** * * **** * * * **
52323795 TAATAATTAGCA-GAAAT-TTGTTTTGGTA-AATTATTATT-ATTGTTATTTAAATTTTAATA-A
1 TAATAAATA--ATTTAATCATATTTAAACATAATTATTATTAAAT-ATATTTTAATTAAAATATA
* * * *
52323855 -GA-TTATTAATA-TCAA
63 TAATTTAATAAAATTC-T
*
52323870 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
52323935 TTTAATAAAATTCT
66 TTTAATAAAATTCT
*
52323949 TAATAATTAAT
1 TAATAAATAAT
52323960 ATTCTTATAT
Statistics
Matches: 114, Mismatches: 39, Indels: 24
0.64 0.22 0.14
Matches are distributed among these distances:
73 1 0.01
74 5 0.04
75 20 0.18
76 23 0.20
77 6 0.05
78 24 0.21
79 30 0.26
80 5 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (79 bp):
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
TTTAATAAAATTCT
Found at i:52323911 original size:154 final size:156
Alignment explanation
Indices: 52323651--52323957 Score: 555
Period size: 154 Copynumber: 2.0 Consensus size: 156
52323641 TGTTTTGCAT
* *
52323651 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAA-GATTATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
52323716 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
65 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
52323781 TTTAATAAAATTCTTAATAATTAGCAG
130 TTTAATAAAATTCTTAATAATTAGCAG
52323808 AAATTTGTTTTGGT-AA-ATTATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAAT
1 AAATTTGTTTTGGTAAAGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAAT
52323871 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAAT
66 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAAT
52323936 TTAATAAAATTCTTAATAATTA
131 TTAATAAAATTCTTAATAATTA
52323958 ATATTCTTAT
Statistics
Matches: 146, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 130 0.89
156 2 0.01
157 14 0.10
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (156 bp):
AAATTTGTTTTGGTAAAGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTAATATCAAT
AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAAT
TTAATAAAATTCTTAATAATTAGCAG
Found at i:52323928 original size:16 final size:16
Alignment explanation
Indices: 52323891--52323932 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52323881 TTAATCATAT
*
52323891 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52323907 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52323922 TTAAAATATAT
1 TTAAAATATAT
52323933 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52323939 original size:14 final size:15
Alignment explanation
Indices: 52323900--52323941 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52323890 TTTAAACATA
*
52323900 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52323915 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52323929 A-TATAATTTAATA
1 ATTATAATTAAATA
52323942 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52324030 original size:125 final size:121
Alignment explanation
Indices: 52323894--52324190 Score: 397
Period size: 125 Copynumber: 2.4 Consensus size: 121
52323884 ATCATATTTA
*
52323894 AACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATAATT-TAATTAAAATATATAATTTAATAAAATTCTTAATAAATA
* * *
52323958 ATATTCTTATATGAATTTACTCAAATCATAATATATAATATGATACTGTAAAATATAAA-AT-
65 AAATTCTTATATGAATTTACTCAAATC---ATA-AT-ATATGATACTATAAAAGA-AAATATC
**
52324019 AACATAATTATTATTAAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
* *
52324084 AATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTC
66 AATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATATC
* * *
52324140 AA-ATAATTAATATTAAATATGATTTAATT-AAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATT
52324191 TAAAATTATT
Statistics
Matches: 156, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
119 24 0.15
120 40 0.26
121 4 0.03
122 3 0.02
125 82 0.53
126 3 0.02
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (121 bp):
AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
AATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATATC
Found at i:52324171 original size:15 final size:15
Alignment explanation
Indices: 52324151--52324189 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
52324141 AATAATTAAT
52324151 ATTAAATATGATTTA
1 ATTAAATATGATTTA
52324166 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
52324183 ATAAAAT
1 ATTAAAT
52324190 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:52324176 original size:17 final size:17
Alignment explanation
Indices: 52324156--52324189 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52324146 TTAATATTAA
*
52324156 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
52324173 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
52324190 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:52328092 original size:25 final size:25
Alignment explanation
Indices: 52328058--52328138 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
52328048 AATATTGATT
52328058 AGTCCTTATTTTAATAAAATATTAA
1 AGTCCTTATTTTAATAAAATATTAA
* *
52328083 AGTCCTTATTTTAAT-TATTGATT--
1 AGTCCTTATTTTAATAAAAT-ATTAA
52328106 AGTCCTTATTTTAATAAAATATTAA
1 AGTCCTTATTTTAATAAAATATTAA
52328131 AGTCCTTA
1 AGTCCTTA
52328139 NGACTTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 18 0.38
24 4 0.08
25 26 0.54
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (25 bp):
AGTCCTTATTTTAATAAAATATTAA
Found at i:52328111 original size:48 final size:48
Alignment explanation
Indices: 52328021--52328138 Score: 206
Period size: 48 Copynumber: 2.5 Consensus size: 48
52328011 ATTTCTTGAT
52328021 TTTTAATAAAATATTAAAGT-C--ATTTTAAATATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAAATATTGATTAGTCCTTA
*
52328066 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAAATATTGATTAGTCCTTA
52328114 TTTTAATAAAATATTAAAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTA
52328139 NGACTTCAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
45 20 0.29
46 1 0.01
48 48 0.70
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (48 bp):
TTTTAATAAAATATTAAAGTCCTTATTTTAAATATTGATTAGTCCTTA
Found at i:52328120 original size:23 final size:23
Alignment explanation
Indices: 52328042--52328120 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
52328032 TATTAAAGTC
*
52328042 ATTTTAAATATTGATTAGTCCTT
1 ATTTTAATTATTGATTAGTCCTT
* *
52328065 ATTTTAATAAAAT-ATTAAAGTCCTT
1 ATTTTAAT-TATTGATT--AGTCCTT
52328090 ATTTTAATTATTGATTAGTCCTT
1 ATTTTAATTATTGATTAGTCCTT
52328113 ATTTTAAT
1 ATTTTAAT
52328121 AAAATATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 25 0.53
24 4 0.09
25 18 0.38
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTTTAATTATTGATTAGTCCTT
Found at i:52328786 original size:23 final size:23
Alignment explanation
Indices: 52328758--52328841 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
52328748 AACATAAACA
*
52328758 AATCAACACAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
*
52328781 AATCAAAACAATTTCCAGCAGCC
1 AATCAAAACAATTTCCAGCAGAC
* *
52328804 AATCATACCAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
52328827 AATCAAAACAATTTC
1 AATCAAAACAATTTC
52328842 AGAACAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (23 bp):
AATCAAAACAATTTCCAGCAGAC
Found at i:52328869 original size:22 final size:21
Alignment explanation
Indices: 52328827--52328872 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
52328817 TCCAGCAGAC
* *
52328827 AATCAAAACAATTTCAGAACA
1 AATCAAAACAATATCAAAACA
*
52328848 AATCAAGACCAATATCAAAACA
1 AATCAA-AACAATATCAAAACA
52328870 AAT
1 AAT
52328873 GCAACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (21 bp):
AATCAAAACAATATCAAAACA
Found at i:52329781 original size:32 final size:34
Alignment explanation
Indices: 52329740--52329803 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
52329730 CTTTTCGATT
* *
52329740 TTCTTTTAA-GAGAATGGTTTTATAAT-GTGACA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
52329772 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
52329804 AATTATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.32
33 15 0.54
34 4 0.14
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (34 bp):
TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
Found at i:52331316 original size:25 final size:25
Alignment explanation
Indices: 52331288--52331368 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
52331278 TATTATTTAT
52331288 TTATCTTATTATTTTTCACATGCAA
1 TTATCTTATTATTTTTCACATGCAA
***
52331313 TTATCTTATT-GGGTT---AT-CTAA
1 TTATCTTATTATTTTTCACATGC-AA
*
52331334 GTATCTTATTATTTTTCACATGCAA
1 TTATCTTATTATTTTTCACATGCAA
52331359 TTATCTTATT
1 TTATCTTATT
52331369 GGGTTATCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 1 0.02
21 13 0.31
22 2 0.05
24 2 0.05
25 23 0.55
26 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (25 bp):
TTATCTTATTATTTTTCACATGCAA
Found at i:52331356 original size:46 final size:46
Alignment explanation
Indices: 52331289--52331382 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
52331279 ATTATTTATT
52331289 TATCTTATTATTTTTCACATGCAATTATCTTATTGGGTTATCTAAG
1 TATCTTATTATTTTTCACATGCAATTATCTTATTGGGTTATCTAAG
52331335 TATCTTATTATTTTTCACATGCAATTATCTTATTGGGTTATCTAAG
1 TATCTTATTATTTTTCACATGCAATTATCTTATTGGGTTATCTAAG
52331381 TA
1 TA
52331383 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.50
Consensus pattern (46 bp):
TATCTTATTATTTTTCACATGCAATTATCTTATTGGGTTATCTAAG
Found at i:52339012 original size:59 final size:57
Alignment explanation
Indices: 52338898--52339067 Score: 175
Period size: 59 Copynumber: 3.0 Consensus size: 57
52338888 CGTAAAAATG
* * * * *
52338898 AGCCTTTGTGGCTATCTC--TGAAAGGACGCCTTTAT-GATAATCTCTATTAAAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGA-AATCTCTATTAAAAGGA
*
52338953 AGCCTTTGTGGCAATCTCTATTAAAAGGAAGCCTTTTGTGGAAATCTCTATTAAAAGGA
1 AGCCTTTGTGGCAATCTCTATT-AAAGGAAGCC-CTTGTGGAAATCTCTATTAAAAGGA
** * * ** *
52339012 AGCCTTTGTGGTTATCTTTGTTAAAGGAAGCCCTTGTGGCGATCTCTGTTAAAAGG
1 AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGAAATCTCTATTAAAAGG
52339068 GTGTCTTTGA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
55 17 0.17
57 21 0.21
58 19 0.19
59 39 0.40
60 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (57 bp):
AGCCTTTGTGGCAATCTCTATTAAAGGAAGCCCTTGTGGAAATCTCTATTAAAAGGA
Found at i:52339035 original size:29 final size:29
Alignment explanation
Indices: 52338898--52339067 Score: 177
Period size: 29 Copynumber: 6.0 Consensus size: 29
52338888 CGTAAAAATG
* *
52338898 AGCCTTTGTGGCTATCTC---TGAAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAAGGA
* * **
52338924 CGCCTTTATGATAATCTCTATTAAAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAAGGA
52338953 AGCCTTTGTGGCAATCTCTATTAAAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAAGGA
*
52338982 AGCCTTTTGTGGAAATCTCTATTAAAAGGA
1 AGCC-TTTGTGGCAATCTCTATTAAAAGGA
** * *
52339012 AGCCTTTGTGGTTATCTTTGTT-AAAGGA
1 AGCCTTTGTGGCAATCTCTATTAAAAGGA
* * *
52339040 AGCCCTTGTGGCGATCTCTGTTAAAAGG
1 AGCCTTTGTGGCAATCTCTATTAAAAGG
52339068 GTGTCTTTGA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
26 13 0.11
28 24 0.20
29 55 0.46
30 28 0.23
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (29 bp):
AGCCTTTGTGGCAATCTCTATTAAAAGGA
Found at i:52345538 original size:24 final size:24
Alignment explanation
Indices: 52345506--52345553 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52345496 GGAAAAAAGA
52345506 AAACTTATTTAGTGAATTCCACAT
1 AAACTTATTTAGTGAATTCCACAT
52345530 AAACTTATTTAGTGAATTCCACAT
1 AAACTTATTTAGTGAATTCCACAT
52345554 GATAATACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (24 bp):
AAACTTATTTAGTGAATTCCACAT
Found at i:52353570 original size:17 final size:18
Alignment explanation
Indices: 52353535--52353573 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52353525 AATTTAACTT
52353535 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
* *
52353553 TAATT-AATTTTTTTAAA
1 TAATTAAATTATTTAAAA
52353570 TAAT
1 TAAT
52353574 AAACAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:52353928 original size:22 final size:21
Alignment explanation
Indices: 52353903--52353944 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
52353893 TTATGAATCC
52353903 GGGGTT-CATGATTTGAGGGTTT
1 GGGGTTGCATG-TTTG-GGGTTT
52353925 GGGGTTGCATGTTTGGGGTT
1 GGGGTTGCATGTTTGGGGTT
52353945 CGGGTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.10, C:0.05, G:0.45, T:0.40
Consensus pattern (21 bp):
GGGGTTGCATGTTTGGGGTTT
Found at i:52360511 original size:23 final size:23
Alignment explanation
Indices: 52360471--52360515 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52360461 ATAGAAAAAG
*
52360471 ATATATATGCAACGATATATATT
1 ATATATATGAAACGATATATATT
52360494 ATATATTATGAAAC-ATATATAT
1 ATATA-TATGAAACGATATATAT
52360516 ATTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATATGAAACGATATATATT
Found at i:52362651 original size:92 final size:92
Alignment explanation
Indices: 52362494--52363055 Score: 1115
Period size: 92 Copynumber: 6.1 Consensus size: 92
52362484 GTTTAAAAGC
52362494 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52362559 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
52362586 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52362651 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
52362678 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52362743 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
52362770 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52362835 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
*
52362862 ATTCATTTACATATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52362927 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
52362954 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
52363019 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
52363046 ATTCATTTAC
1 ATTCATTTAC
52363056 ATAACACATA
Statistics
Matches: 468, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 468 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (92 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATAT
Found at i:52363075 original size:9 final size:9
Alignment explanation
Indices: 52363052--52363436 Score: 136
Period size: 9 Copynumber: 44.9 Consensus size: 9
52363042 ATATATTCAT
52363052 TTACATAAC
1 TTACATAAC
52363061 --ACATAAC
1 TTACATAAC
52363068 TTACATAAC
1 TTACATAAC
* *
52363077 CTACTTAA-
1 TTACATAAC
*
52363085 -TATATAAC
1 TTACATAAC
*
52363093 TTGCATAAC
1 TTACATAAC
* *
52363102 TTAAATAAG
1 TTACATAAC
*
52363111 TTACGTAA-
1 TTACATAAC
52363119 TAATACATAA-
1 T--TACATAAC
*
52363129 -TACACAAC
1 TTACATAAC
*
52363137 TTACAT-GC
1 TTACATAAC
* *
52363145 GTAAATAA-
1 TTACATAAC
* *
52363153 -TACAGAGC
1 TTACATAAC
52363161 TTACATAAC
1 TTACATAAC
*
52363170 TTACATACC
1 TTACATAAC
* *
52363179 CTACATAAA
1 TTACATAAC
* *
52363188 TTAAATAAG
1 TTACATAAC
*
52363197 TTACATAAAA
1 TTACAT-AAC
* *
52363207 ATACATACC
1 TTACATAAC
* *
52363216 CTACATAAA
1 TTACATAAC
* *
52363225 TTAAATAAG
1 TTACATAAC
52363234 TTACATAA-
1 TTACATAAC
*
52363242 TAATACATACC
1 T--TACATAAC
*
52363253 CTACATAAC
1 TTACATAAC
52363262 TTACATAA-
1 TTACATAAC
*
52363270 -GACATAAC
1 TTACATAAC
*
52363278 TTTCATAA-
1 TTACATAAC
*
52363286 -TACACAAC
1 TTACATAAC
**
52363294 TTACGCAAC
1 TTACATAAC
52363303 TTACATAA-
1 TTACATAAC
*
52363311 -GACATAAC
1 TTACATAAC
*
52363319 TTACAT--G
1 TTACATAAC
*
52363326 TGTAAATAA-
1 T-TACATAAC
**
52363335 -TACATATT
1 TTACATAAC
52363343 TTACATAAC
1 TTACATAAC
52363352 TTACATAA-
1 TTACATAAC
*
52363360 -GACATAAC
1 TTACATAAC
*
52363368 TTACATAAG
1 TTACATAAC
*
52363377 TTTCATAA-
1 TTACATAAC
* *
52363385 -TACACATC
1 TTACATAAC
**
52363393 TTACGCAAC
1 TTACATAAC
*
52363402 TTACACAAC
1 TTACATAAC
52363411 TTACATAAC
1 TTACATAAC
52363420 TTACATAAC
1 TTACATAAC
52363429 TTACATAA
1 TTACATAA
52363437 TGTATATCTT
Statistics
Matches: 273, Mismatches: 73, Indels: 60
0.67 0.18 0.15
Matches are distributed among these distances:
7 55 0.20
8 11 0.04
9 188 0.69
10 19 0.07
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (9 bp):
TTACATAAC
Found at i:52363215 original size:37 final size:37
Alignment explanation
Indices: 52363171--52363270 Score: 173
Period size: 37 Copynumber: 2.7 Consensus size: 37
52363161 TTACATAACT
52363171 TACATACCCTACATAAATTAAATAAGTTACATAAAAA
1 TACATACCCTACATAAATTAAATAAGTTACATAAAAA
*
52363208 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAAAAA
* *
52363245 TACATACCCTACATAACTTACATAAG
1 TACATACCCTACATAAATTAAATAAG
52363271 ACATAACTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAAAAA
Found at i:52363274 original size:16 final size:16
Alignment explanation
Indices: 52363255--52363376 Score: 82
Period size: 16 Copynumber: 8.0 Consensus size: 16
52363245 TACATACCCT
52363255 ACATAACTTACATAAG
1 ACATAACTTACATAAG
* *
52363271 ACATAACTTTCATAAT
1 ACATAACTTACATAAG
*
52363287 ACACAACTTAC----G
1 ACATAACTTACATAAG
52363299 -C--AACTTACATAAG
1 ACATAACTTACATAAG
**
52363312 ACATAACTTACATGTG
1 ACATAACTTACATAAG
* **
52363328 TAAATAA--TACATATTTT
1 -ACATAACTTACATA--AG
52363345 ACATAACTTACATAAG
1 ACATAACTTACATAAG
52363361 ACATAACTTACATAAG
1 ACATAACTTACATAAG
52363377 TTTCATAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
9 7 0.09
11 1 0.01
13 1 0.01
14 1 0.01
15 5 0.06
16 54 0.67
17 6 0.07
18 6 0.07
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (16 bp):
ACATAACTTACATAAG
Found at i:52363303 original size:25 final size:25
Alignment explanation
Indices: 52363275--52363406 Score: 70
Period size: 25 Copynumber: 5.3 Consensus size: 25
52363265 CATAAGACAT
* *
52363275 AACTTTCATAATACACAACTTACGC
1 AACTTACATAAGACACAACTTACGC
*
52363300 AACTTACATAAGACATAACTTA--C
1 AACTTACATAAGACACAACTTACGC
** * * * ** **
52363323 ATGTGTAAATAATACATATTTTACAT
1 AACT-TACATAAGACACAACTTACGC
* **
52363349 AACTTACATAAGACATAACTTACAT
1 AACTTACATAAGACACAACTTACGC
* * * *
52363374 AAGTTTCATAATACACATCTTACGC
1 AACTTACATAAGACACAACTTACGC
52363399 AACTTACA
1 AACTTACA
52363407 CAACTTACAT
Statistics
Matches: 79, Mismatches: 25, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
23 3 0.04
24 14 0.18
25 60 0.76
26 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.31
Consensus pattern (25 bp):
AACTTACATAAGACACAACTTACGC
Found at i:52369000 original size:66 final size:66
Alignment explanation
Indices: 52368880--52369004 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
52368870 GAGGCAACAT
*
52368880 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCTAGCTACAACTGAAAGCAGATCCAGCA
1 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATCCAGCA
52368945 G
66 G
* * *
52368946 CGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGC-AGCAGCTTAAAGCAGAT
1 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGAT
52369005 GCGGCAACAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
65 1 0.02
66 48 0.91
67 4 0.08
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATCCAGCA
G
Found at i:52369018 original size:66 final size:66
Alignment explanation
Indices: 52368882--52369021 Score: 176
Period size: 66 Copynumber: 2.1 Consensus size: 66
52368872 GGCAACATCG
* *
52368882 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCTAGCTACAACTGAAAGCAGATCCAGCAGC
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATCCAGCAAC
*
52368947 G
66 A
* * * * *
52368948 AGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGC-AGCAGCTTAAAGCAGATGCGGCA
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATCCAGCA
52369011 ACA
64 ACA
52369014 AGAGAAGC
1 AGAGAAGC
52369022 AGAGACGGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.02
66 59 0.92
67 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATCCAGCAAC
A
Found at i:52369023 original size:21 final size:21
Alignment explanation
Indices: 52368997--52369041 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
52368987 CAGCAGCTTA
52368997 AAGCAGATG-CGGCAACAAGAG
1 AAGCAGA-GACGGCAACAAGAG
* *
52369018 AAGCAGAGACGGCAGCGAGAG
1 AAGCAGAGACGGCAACAAGAG
52369039 AAG
1 AAG
52369042 TACAGGCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.42, C:0.18, G:0.38, T:0.02
Consensus pattern (21 bp):
AAGCAGAGACGGCAACAAGAG
Found at i:52369054 original size:21 final size:21
Alignment explanation
Indices: 52369030--52369084 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
52369020 GCAGAGACGG
* *
52369030 CAGCGAGAGAAGTACAGGCTA
1 CAGCGAGGGAAGCACAGGCTA
*
52369051 CAGCGAGGGAAGCAGAGGCTA
1 CAGCGAGGGAAGCACAGGCTA
52369072 CAGCGAGGGAAGC
1 CAGCGAGGGAAGC
52369085 CGAGCAGCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.40, T:0.05
Consensus pattern (21 bp):
CAGCGAGGGAAGCACAGGCTA
Found at i:52369486 original size:43 final size:43
Alignment explanation
Indices: 52369439--52369886 Score: 301
Period size: 43 Copynumber: 10.3 Consensus size: 43
52369429 AGGTGTTGGC
* * * *
52369439 CTTTAGTGGCATTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
52369482 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
52369525 CTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * *
52369568 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCG-TTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
52369612 CTATT-GCGGCGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * * *
52369655 CTTTCGTGGCGTTTTTGGTCAAAGTGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *** * * ** *
52369698 CTATTAGCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGAT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** *
52369742 CTTTAGCGTTAGCGGCGCTTGT-CCCAAAAACGCCGCTAAAGATCAGGGT
1 C--T----TTAGCGGCGTTTGTGGTC-AAAGCGCCGCTAAAGATCAGGGT
* **** * * ****
52369791 CTTTAGCGGCGCTTCCACT-AAAGCACCGCTAAAGGTCTTACT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
52369833 CTTCAGCGGCGTTTGTGCT-AGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTAAAGATCAGGGT
52369876 CTTTAGCGGCG
1 CTTTAGCGGCG
52369887 ATTTTTTTAA
Statistics
Matches: 307, Mismatches: 86, Indels: 24
0.74 0.21 0.06
Matches are distributed among these distances:
42 33 0.11
43 177 0.58
44 61 0.20
45 2 0.01
46 1 0.00
47 1 0.00
49 32 0.10
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:52369611 original size:130 final size:129
Alignment explanation
Indices: 52369439--52369712 Score: 318
Period size: 130 Copynumber: 2.1 Consensus size: 129
52369429 AGGTGTTGGC
* *
52369439 CTTTAGTGGCATTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTAGCGGCGTTTGTGGAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTATT-GCGGCGTTTGAGGAAA
* * *
52369503 AAGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGT
65 AAGCGCCACTAAAGATCA-GGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGG
52369567 T
129 T
* * * * **
52369568 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGGA
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCTATTGCGGCGTTTGAGGAAA
* * * * * * * *
52369633 AAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTTTGGTCAAAGTGCCGCTATAGATCAGGGT
65 AAGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGGT
*
52369698 CTATTAGCGGCGTTT
1 CT-TTAGTGGCGTTT
52369713 GAGAAAAAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
129 16 0.13
130 92 0.76
131 13 0.11
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (129 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTATTGCGGCGTTTGAGGAAAA
AGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGGT
Found at i:52369624 original size:87 final size:88
Alignment explanation
Indices: 52369459--52369734 Score: 371
Period size: 87 Copynumber: 3.2 Consensus size: 88
52369449 ATTTTTGGTC
* * * ** * * *
52369459 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCG-TTTGTGGAAAAAGCGCCACTAAAGATCATG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGG
*
52369523 GTCT-TTAGCGGCGTTTGTGGGG
66 GTCTATTAGCGGCGTTTGAGGGG
* *
52369545 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGG
52369610 GTCTATT-GCGGCGTTTGAGGGG
66 GTCTATTAGCGGCGTTTGAGGGG
* *
52369632 AAAGCGCCGCTAAAGATTAGGTTCTTTCGTGGCGTTTT-TGGTCAAAGTGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGG
***
52369696 GTCTATTAGCGGCGTTTGAGAAA
66 GTCTATTAGCGGCGTTTGAGGGG
*
52369719 AAAACGCCGCTAAAGA
1 AAAGCGCCGCTAAAGA
52369735 CCCTGATCTT
Statistics
Matches: 168, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
86 61 0.36
87 105 0.62
88 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (88 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAGATCAGG
GTCTATTAGCGGCGTTTGAGGGG
Found at i:52370010 original size:22 final size:22
Alignment explanation
Indices: 52369982--52370024 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52369972 CTACGGCGCT
*
52369982 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
52370004 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
52370025 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:52371420 original size:79 final size:79
Alignment explanation
Indices: 52371289--52371437 Score: 235
Period size: 79 Copynumber: 1.9 Consensus size: 79
52371279 GCTTATATAC
*
52371289 AGATAAAACATATCAGAACATACTAGTTGCACACATAATTAACAAATCAAAACATGCTATTGGCA
1 AGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTATTGGCA
52371354 TATTCCCCATATGT
66 TATTCCCCATATGT
* * * * * *
52371368 AGATAAAACATATTAGAACATACTAATTGTACATATAGTTAACAGATCAAAACATGCTATTGGTA
1 AGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTATTGGCA
52371433 TATTC
66 TATTC
52371438 GACCATCACA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (79 bp):
AGATAAAACATATCAGAACATACTAATTGCACACATAATTAACAAATCAAAACATGCTATTGGCA
TATTCCCCATATGT
Found at i:52372446 original size:11 final size:11
Alignment explanation
Indices: 52372430--52372454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52372420 TATAGAACCC
52372430 TAAAAATAGTT
1 TAAAAATAGTT
52372441 TAAAAATAGTT
1 TAAAAATAGTT
52372452 TAA
1 TAA
52372455 TTTGAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAAAAATAGTT
Done.