Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 54 of 59
Found at i:19539827 original size:20 final size:20
Alignment explanation
Indices: 19539802--19539873 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
19539792 ATTGAATAAT
19539802 TTAAATATTAATATTTAAAA
1 TTAAATATTAATATTTAAAA
*
19539822 TTAAATATTAA-ATTT---T
1 TTAAATATTAATATTTAAAA
* *
19539838 TTAATTTTTGAATATTTGAAAA
1 TTAAATATT-AATATTT-AAAA
19539860 -TAAATATTAATATT
1 TTAAATATTAATATT
19539874 CATCAAACCT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.17
17 2 0.05
18 4 0.10
19 4 0.10
20 17 0.43
21 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAAATATTAATATTTAAAA
Found at i:19545449 original size:27 final size:28
Alignment explanation
Indices: 19545392--19545449 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
19545382 GAAAAAATAT
* *
19545392 CCTGGTGGTGGAAAATTACGATTTTGCC
1 CCTGGTGGTGGAAAATTACCATTTTGAC
19545420 CCTGG-GGTGGCAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACCATTTTGAC
19545447 CCT
1 CCT
19545450 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACCATTTTGAC
Found at i:19545520 original size:20 final size:20
Alignment explanation
Indices: 19545495--19545540 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19545485 CTTCTAAACC
19545495 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
19545515 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
19545535 TCAAAT
1 TCAAAT
19545541 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:19545942 original size:15 final size:18
Alignment explanation
Indices: 19545904--19545943 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
19545894 TATTTTTTTA
19545904 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
19545922 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
19545937 ATTTTAA
1 ATTTTAA
19545944 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:19547255 original size:67 final size:67
Alignment explanation
Indices: 19547142--19547385 Score: 257
Period size: 67 Copynumber: 3.7 Consensus size: 67
19547132 GCTGGCTGAA
* * * * *
19547142 TTAATTTTCAAGTGTTGTGCTCTTAACTTTCAAGTGTTATGCTTTTAAATTTCAAGTGTTGTGCT
1 TTAACTTTCAAGTGTTATGCTTTTAACTTTCAAGTGTTATGTTTTTAAATTTCAAGTGTTATGCT
19547207 CT
66 CT
* **
19547209 TTAACTTTCAAGTGTTATGCTTTTGAA-TTTCAAGTGTCATGTTTTTAGTTTTCAAGTGTTATGC
1 TTAACTTTCAAGTGTTATGCTTTT-AACTTTCAAGTGTTATGTTTTTAAATTTCAAGTGTTATGC
19547273 TC-
65 TCT
* * * *
19547275 TTAACTTTCAAGTGCTT-TGTTTTTAATTTTCAAGTGTTACGTTTTTAAA-TTCAAGTGTTACGC
1 TTAACTTTCAAGTG-TTATGCTTTTAACTTTCAAGTGTTATGTTTTTAAATTTCAAGTGTTATGC
19547338 T-T
65 TCT
* * * ** * *
19547340 TTAATTTTCAAATGTTAT-TTTTTATTTTTCAAGTGCTATGCTTTTA
1 TTAACTTTCAAGTGTTATGCTTTTAACTTTCAAGTGTTATGTTTTTA
19547386 TTTTTCAATA
Statistics
Matches: 152, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
64 26 0.17
65 29 0.19
66 38 0.25
67 57 0.38
68 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (67 bp):
TTAACTTTCAAGTGTTATGCTTTTAACTTTCAAGTGTTATGTTTTTAAATTTCAAGTGTTATGCT
CT
Found at i:19547387 original size:22 final size:22
Alignment explanation
Indices: 19547142--19547393 Score: 260
Period size: 22 Copynumber: 11.5 Consensus size: 22
19547132 GCTGGCTGAA
* *
19547142 TTAATTTTCAAGTGTTGTGCTC
1 TTAATTTTCAAGTGTTATGCTT
*
19547164 TTAACTTTCAAGTGTTATGCTT
1 TTAATTTTCAAGTGTTATGCTT
* *
19547186 TTAAATTTCAAGTGTTGTGCTCT
1 TTAATTTTCAAGTGTTATGCT-T
*
19547209 TTAACTTTCAAGTGTTATGCTT
1 TTAATTTTCAAGTGTTATGCTT
* *
19547231 TTGAA-TTTCAAGTGTCATGTTT
1 TT-AATTTTCAAGTGTTATGCTT
* *
19547253 TTAGTTTTCAAGTGTTATGCTC
1 TTAATTTTCAAGTGTTATGCTT
* *
19547275 TTAACTTTCAAGTGCTT-TGTTT
1 TTAATTTTCAAGTG-TTATGCTT
* *
19547297 TTAATTTTCAAGTGTTACGTTT
1 TTAATTTTCAAGTGTTATGCTT
* *
19547319 TTAA-ATTCAAGTGTTACGCTT
1 TTAATTTTCAAGTGTTATGCTT
* *
19547340 TTAATTTTCAAATGTTAT-TTT
1 TTAATTTTCAAGTGTTATGCTT
* *
19547361 TTATTTTTCAAGTGCTATGCTT
1 TTAATTTTCAAGTGTTATGCTT
*
19547383 TTATTTTTCAA
1 TTAATTTTCAA
19547394 TAGGGTAGTA
Statistics
Matches: 194, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
21 39 0.20
22 131 0.68
23 24 0.12
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (22 bp):
TTAATTTTCAAGTGTTATGCTT
Found at i:19548027 original size:257 final size:256
Alignment explanation
Indices: 19547571--19548075 Score: 922
Period size: 257 Copynumber: 2.0 Consensus size: 256
19547561 ATATATATAT
* *
19547571 ATATAGACTGTGCAAGTTTCCATTAAATTGGTTTGGTTAATTCAATTAATGAGGTCGATTAATTT
1 ATATAGACTGTGCAAGTTTCCATTAAATTGGTTTGGTTAATTCAATTAAGGAGGTCAATTAATTT
* *
19547636 GAGTAACTTAATTGGTTTCCCTTTTGAATTTTTTTTCAATTAATAGAATTAACCAATTTATAGAT
66 GAGTAACTTAATTGGTTTCCATTTTGAATTTTTTTTCAATCAATAGAATTAACCAATTTATAGAT
19547701 GACCAATGAAAAAGTGTACTCCGTGGGAACCAAATTGACAACCACCTTGTTAAAAGCCAAGCGCT
131 GACCAATGAAAAAGTGTACTCCGTGGGAACCAAATTGACAACCACCTTGTTAAAAGCCAAGCGCT
19547766 CTACCAACCGAGTCTTTGTTTAAATTATTGTAGTTTAGACTTTATAATTAATTAAACATCA
196 CTACCAACCGAGTCTTTGTTTAAATTATTGTAGTTTAGACTTTATAATTAATTAAACATCA
*
19547827 NATATAGACTGTGCAA-TTTCGATTAAATTGGTTTGGTTAATTCAATTAAGGAGGTCAATTAATT
1 -ATATAGACTGTGCAAGTTTCCATTAAATTGGTTTGGTTAATTCAATTAAGGAGGTCAATTAATT
* *
19547891 TGATTAACTTAATTGGTTTCCATTTTGAATTTTTTTTTCGATCAATAGAATTAACCAATTTATAG
65 TGAGTAACTTAATTGGTTTCCATTTTGAA-TTTTTTTTCAATCAATAGAATTAACCAATTTATAG
19547956 ATGACCAATGAAAAAGTGTACTCCGTGGGAACCAAATTGACAACCACCTTGTTAAAAGCCAAGCG
129 ATGACCAATGAAAAAGTGTACTCCGTGGGAACCAAATTGACAACCACCTTGTTAAAAGCCAAGCG
19548021 CTCTACCAACCGAGTCTTTGTTTAAATTATTGTAGTTTAGACTTTATAATTAATT
194 CTCTACCAACCGAGTCTTTGTTTAAATTATTGTAGTTTAGACTTTATAATTAATT
19548076 TTGTGTCCAA
Statistics
Matches: 240, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
256 72 0.30
257 168 0.70
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (256 bp):
ATATAGACTGTGCAAGTTTCCATTAAATTGGTTTGGTTAATTCAATTAAGGAGGTCAATTAATTT
GAGTAACTTAATTGGTTTCCATTTTGAATTTTTTTTCAATCAATAGAATTAACCAATTTATAGAT
GACCAATGAAAAAGTGTACTCCGTGGGAACCAAATTGACAACCACCTTGTTAAAAGCCAAGCGCT
CTACCAACCGAGTCTTTGTTTAAATTATTGTAGTTTAGACTTTATAATTAATTAAACATCA
Found at i:19550259 original size:34 final size:32
Alignment explanation
Indices: 19550221--19550321 Score: 80
Period size: 34 Copynumber: 3.0 Consensus size: 32
19550211 TCAAAAACCA
19550221 ACAGCACAAAGCCCCTTTTGTCCTTCACAATCC
1 ACAGCACAAAGCCCCTTTT-TCCTTCACAATCC
* *
19550254 GACAGCA-AACAACCTCCATTTTTCCTGCACAGA-CC
1 -ACAGCACAA-AGCC-CC-TTTTTCCTTCACA-ATCC
* *
19550289 AGTAGCACAAAGCCCCTTTTATCTTTCACAATC
1 A-CAGCACAAAGCCCCTTTT-TCCTTCACAATC
19550322 TAGCAGCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
33 7 0.13
34 20 0.38
35 19 0.36
36 7 0.13
ACGTcount: A:0.30, C:0.36, G:0.10, T:0.25
Consensus pattern (32 bp):
ACAGCACAAAGCCCCTTTTTCCTTCACAATCC
Found at i:19552665 original size:13 final size:13
Alignment explanation
Indices: 19552647--19552671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19552637 AGAGAAATTG
19552647 TGATTTTATAAAA
1 TGATTTTATAAAA
19552660 TGATTTTATAAA
1 TGATTTTATAAA
19552672 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19554080 original size:15 final size:16
Alignment explanation
Indices: 19554062--19554106 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
19554052 AGATCAGATA
19554062 TTTGGATTTTAAAG-C
1 TTTGGATTTTAAAGTC
*
19554077 TTTGAATTTTAAAGTC
1 TTTGGATTTTAAAGTC
19554093 TTTGG-TTTTAAAGT
1 TTTGGATTTTAAAGT
19554107 TGTTTTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (16 bp):
TTTGGATTTTAAAGTC
Found at i:19554159 original size:5 final size:5
Alignment explanation
Indices: 19554149--19554188 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
19554139 CCCCAAGTCT
* *
19554149 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA AGTTA TGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
19554189 GATTGAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
AGTTA
Found at i:19557930 original size:19 final size:20
Alignment explanation
Indices: 19557903--19557948 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
19557893 AGGAGACAAG
*
19557903 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
19557922 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
19557941 ATAATATT
1 ATAATATT
19557949 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:19559780 original size:13 final size:13
Alignment explanation
Indices: 19559762--19559786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19559752 AGAGAAATTG
19559762 TGATTTTATAAAA
1 TGATTTTATAAAA
19559775 TGATTTTATAAA
1 TGATTTTATAAA
19559787 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19566164 original size:25 final size:25
Alignment explanation
Indices: 19566136--19566183 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
19566126 TACATGGGCC
19566136 CACTAATGAACAAAAGTAGTAAATA
1 CACTAATGAACAAAAGTAGTAAATA
19566161 CACTAATGAACAAAAGTAGTAAA
1 CACTAATGAACAAAAGTAGTAAA
19566184 GACAGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (25 bp):
CACTAATGAACAAAAGTAGTAAATA
Found at i:19567005 original size:17 final size:17
Alignment explanation
Indices: 19566979--19567014 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19566969 AATTTATAAA
19566979 AATTCAATTTATTTTAT
1 AATTCAATTTATTTTAT
*
19566996 AATTCTATTTATTTTAT
1 AATTCAATTTATTTTAT
19567013 AA
1 AA
19567015 ATTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTCAATTTATTTTAT
Found at i:19569933 original size:68 final size:68
Alignment explanation
Indices: 19569824--19570058 Score: 231
Period size: 68 Copynumber: 3.4 Consensus size: 68
19569814 AAGAGGAATT
* * *
19569824 CAAAGGAAGAGATCATGGTGATGTTTTCAAAATCTTTAAGGGTGAGTGACTCAAACACAGCCCGA
1 CAAAGGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGTGAGTGACTCAAACACAGCCCGA
19569889 GAC
66 GAC
* * *****
19569892 CAAAGGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGTGGGAGAGA-TGATGGTGATGTT
1 CAAAGGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT--GAGTGACTCAAACACA-G--
** * *
19569956 TTCAAAATC
61 CCCGAGA-C
* * *
19569965 TATAAGGGTGA-ATGATGGTGATGTTTTCAAAATCTATAAGGGTGAGTGACACAAACACAGCCCG
1 CA-AAGGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGTGAGTGACTCAAACACAGCCCG
*
19570029 AGAT
65 AGAC
19570033 CAAAGGGAGAGATGATGGTGATGTTT
1 CAAAGGGAGAGATGATGGTGATGTTT
19570059 GTGTATTTTA
Statistics
Matches: 127, Mismatches: 31, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
67 7 0.06
68 56 0.44
69 6 0.05
70 6 0.05
71 6 0.05
72 5 0.04
73 34 0.27
74 7 0.06
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (68 bp):
CAAAGGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGTGAGTGACTCAAACACAGCCCGA
GAC
Found at i:19569944 original size:39 final size:39
Alignment explanation
Indices: 19569896--19570008 Score: 191
Period size: 39 Copynumber: 3.0 Consensus size: 39
19569886 CGAGACCAAA
19569896 GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
1 GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
19569935 GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
1 GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
19569974 ----GA-ATGATGGTGATGTTTTCAAAATCTATAAGGGT
1 GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
19570008 G
1 G
19570009 AGTGACACAA
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
34 32 0.44
35 2 0.03
39 39 0.53
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (39 bp):
GGGAGAGATGATGGTGATGTTTTCAAAATCTATAAGGGT
Found at i:19573757 original size:24 final size:23
Alignment explanation
Indices: 19573709--19573757 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
19573699 AAATAATTTT
*
19573709 TTAATATTATAAAAGTGAGAAAA
1 TTAATATTATAAAAGTGACAAAA
*
19573732 TTAAGTATT-TAAAAGATGACATAA
1 TTAA-TATTATAAAAG-TGACAAAA
19573756 TT
1 TT
19573758 TTGAAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (23 bp):
TTAATATTATAAAAGTGACAAAA
Found at i:19587439 original size:18 final size:19
Alignment explanation
Indices: 19587400--19587439 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
19587390 TTAATATTTT
19587400 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
19587419 AATATTATTTTATTC-TAA
1 AATATTATTTTATTCATAA
19587437 AAT
1 AAT
19587440 TCTCCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:19588979 original size:18 final size:19
Alignment explanation
Indices: 19588956--19588994 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19588946 TTTCTTGATC
19588956 TCCTGTTTCAGATTCA-TT
1 TCCTGTTTCAGATTCAGTT
*
19588974 TCCTGTTTCAGTTTCAGTT
1 TCCTGTTTCAGATTCAGTT
19588993 TC
1 TC
19588995 AGTTCCAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (19 bp):
TCCTGTTTCAGATTCAGTT
Found at i:19588987 original size:6 final size:6
Alignment explanation
Indices: 19588960--19589016 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
19588950 TTGATCTCCT
* * * *
19588960 GTTTCA GATTCA -TTTCCT GTTTCA GTTTCA GTTTCA GTTCCA GTTCCA
1 GTTTCA GTTTCA GTTT-CA GTTTCA GTTTCA GTTTCA GTTTCA GTTTCA
*
19589008 GTTCCA GTT
1 GTTTCA GTT
19589017 CAACTCTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
5 2 0.05
6 39 0.89
7 3 0.07
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.46
Consensus pattern (6 bp):
GTTTCA
Found at i:19589017 original size:6 final size:6
Alignment explanation
Indices: 19588982--19589017 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19588972 TTTCCTGTTT
* *
19588982 CAGTTT CAGTTT CAGTTC CAGTTC CAGTTC CAGTTC
1 CAGTTC CAGTTC CAGTTC CAGTTC CAGTTC CAGTTC
19589018 AACTCTCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (6 bp):
CAGTTC
Found at i:19592525 original size:22 final size:21
Alignment explanation
Indices: 19592486--19592527 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19592476 AAAAGAATCC
19592486 AAATCTAAATAAAATAAAATA
1 AAATCTAAATAAAATAAAATA
* *
19592507 AAATCCTAAATCAACTAAAAT
1 AAAT-CTAAATAAAATAAAAT
19592528 TAGAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATCTAAATAAAATAAAATA
Found at i:19592525 original size:27 final size:28
Alignment explanation
Indices: 19592468--19592534 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
19592458 AGTCCTAATA
19592468 AAAATAAGAAAAGAATCCAAATCTAAAT
1 AAAATAAGAAAAGAATCCAAATCTAAAT
*
19592496 AAAATAA-AATAA-AATCCTAAATC-AACT
1 AAAATAAGAA-AAGAATCC-AAATCTAAAT
*
19592523 AAAATTAGAAAA
1 AAAATAAGAAAA
19592535 ACTAAATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.66, C:0.10, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAATAAGAAAAGAATCCAAATCTAAAT
Found at i:19594272 original size:29 final size:29
Alignment explanation
Indices: 19594213--19594274 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
19594203 TGGTTGGTTG
* * * *
19594213 TTCTTTCCCTTTTTTCTCTTTTTTCTTTT
1 TTCTTTCCCTTCTTCCTCTCTTTTCTCTT
19594242 TTCTTTCTCCTTCTTCCTCTCTTTTC-CTT
1 TTCTTTC-CCTTCTTCCTCTCTTTTCTCTT
19594271 TTCT
1 TTCT
19594275 CCAACCGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (29 bp):
TTCTTTCCCTTCTTCCTCTCTTTTCTCTT
Found at i:19594488 original size:25 final size:29
Alignment explanation
Indices: 19594436--19594498 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
19594426 TCTTCTTTTA
19594436 TCTTTCTTGGCCCACTGCTCTCCTTTCTC
1 TCTTTCTTGGCCCACTGCTCTCCTTTCTC
* * *
19594465 TCTTTCTTGGCTCACTGTTCTTCTTTCTC
1 TCTTTCTTGGCCCACTGCTCTCCTTTCTC
19594494 TCTTT
1 TCTTT
19594499 TTTCTCCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.03, C:0.35, G:0.10, T:0.52
Consensus pattern (29 bp):
TCTTTCTTGGCCCACTGCTCTCCTTTCTC
Found at i:19594609 original size:14 final size:14
Alignment explanation
Indices: 19594551--19594610 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
19594541 CGCTCTAATT
*
19594551 TTTCTCTTTCT-TC
1 TTTCTTTTTCTCTC
19594564 TTT-TCTTTTC-CTC
1 TTTCT-TTTTCTCTC
* * *
19594577 TTTCCTTCTCTGTC
1 TTTCTTTTTCTCTC
19594591 TTTCTTTTTCTCTC
1 TTTCTTTTTCTCTC
19594605 TTTCTT
1 TTTCTT
19594611 GGCCCGCAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
12 1 0.03
13 16 0.44
14 19 0.53
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTCTTTTTCTCTC
Found at i:19594682 original size:77 final size:77
Alignment explanation
Indices: 19594511--19594685 Score: 183
Period size: 77 Copynumber: 2.3 Consensus size: 77
19594501 TCTCCTCTTT
* * * * *
19594511 TCCTTCTTCCTTCTCTCTTGCTTGGCCCGCCGCTCTAATTTTTCTCTTTCTTCTTTTCTTTTCCT
1 TCCTGCTT-CTTCTCTCTTTCTTGGCCCGCAGCTCTAATTTTTCTCTTTCTTCTTCTCTCTTCCT
* * * **
19594576 CTTTCCTTCTCTG
65 CCTCCCCTCTCAC
* * * *
19594589 TCTTTCTTTTTCTCTCTTTCTTGGCCCGCAGCTCT-CTTTTCTCTCTTTCTTCTTCTCTCTTCCT
1 TCCTGCTTCTTCTCTCTTTCTTGGCCCGCAGCTCTAATTTT-TCTCTTTCTTCTTCTCTCTTCCT
19594653 CCTCCCCTCTCAC
65 CCTCCCCTCTCAC
19594666 TCCCTGCTTCTT-TCTCTTTC
1 T-CCTGCTTCTTCTCTCTTTC
19594686 GTTTCTTCTT
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
76 4 0.05
77 62 0.77
78 14 0.17
ACGTcount: A:0.02, C:0.39, G:0.06, T:0.53
Consensus pattern (77 bp):
TCCTGCTTCTTCTCTCTTTCTTGGCCCGCAGCTCTAATTTTTCTCTTTCTTCTTCTCTCTTCCTC
CTCCCCTCTCAC
Found at i:19594745 original size:2 final size:2
Alignment explanation
Indices: 19594740--19594770 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19594730 ACTGATCCTT
*
19594740 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19594771 TTGCTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:19595197 original size:7 final size:7
Alignment explanation
Indices: 19595139--19595197 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
19595129 TTATTTTATA
19595139 TTTATTT
1 TTTATTT
*
19595146 ATTATTT
1 TTTATTT
*
19595153 TTTATGT
1 TTTATTT
19595160 TTTAGTTT
1 TTTA-TTT
19595168 TTTATTT
1 TTTATTT
*
19595175 CATTA-TT
1 -TTTATTT
*
19595182 ATT-TTT
1 TTTATTT
19595188 TTTATTT
1 TTTATTT
19595195 TTT
1 TTT
19595198 TGAAATAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.17
7 26 0.62
8 9 0.21
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTATTT
Found at i:19595776 original size:122 final size:122
Alignment explanation
Indices: 19595517--19595778 Score: 389
Period size: 122 Copynumber: 2.1 Consensus size: 122
19595507 GTTTTAGGAG
* * *
19595517 TGTACCCGAAGGTTTTAGAAGAAAAGGTTGTTCCTCATCTCAGAATGAGGCTATATAATTTTGAA
1 TGTACCCGAAGGTTTTAGAAGAAAAGGTTGGTCCTCATCTCAGAATGAGGCTACATAACTTTGAA
* * *
19595582 GAAATCTTGAAACTAATTACCCAGAGGTTTTAAGAATGTACTTGGAGGTTTTGAAGA
66 GAAATCTTGAAACTAATTACCCAAAGGTTTTAAGAATGTACTTGGAGGTTTAGAAAA
* * * *
19595639 CGTACCCAAAGGTTTTAGAAGAAAATGTTGGTCCTCATCTCAGAATGAGGCTACGTAACTTTGAA
1 TGTACCCGAAGGTTTTAGAAGAAAAGGTTGGTCCTCATCTCAGAATGAGGCTACATAACTTTGAA
* * *
19595704 GAAATCTTGAAACTAATTGCTCAAAGGTTTTAAGTATGTACTTGGAGGTTTAGAAAA
66 GAAATCTTGAAACTAATTACCCAAAGGTTTTAAGAATGTACTTGGAGGTTTAGAAAA
*
19595761 TGTACCCGCAAGTTTTTA
1 TGTACCCG-AAGGTTTTA
19595779 AGATGTACCC
Statistics
Matches: 123, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
122 115 0.93
123 8 0.07
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (122 bp):
TGTACCCGAAGGTTTTAGAAGAAAAGGTTGGTCCTCATCTCAGAATGAGGCTACATAACTTTGAA
GAAATCTTGAAACTAATTACCCAAAGGTTTTAAGAATGTACTTGGAGGTTTAGAAAA
Found at i:19595796 original size:21 final size:21
Alignment explanation
Indices: 19595731--19595797 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
19595721 TGCTCAAAGG
**
19595731 TTTTAAGTATGTACTTGGAGGT
1 TTTTAAG-ATGTACCCGGAGGT
** * * *
19595753 TTAGAAAATGTACCCGCAAGT
1 TTTTAAGATGTACCCGGAGGT
19595774 TTTTAAGATGTACCCGGAGGT
1 TTTTAAGATGTACCCGGAGGT
19595795 TTT
1 TTT
19595798 AGAAGAAAAG
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (21 bp):
TTTTAAGATGTACCCGGAGGT
Found at i:19595909 original size:21 final size:20
Alignment explanation
Indices: 19595864--19595923 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
19595854 TGAAACTAAT
* * *
19595864 TACCCAAAGGTTTTAGGAATA
1 TACCCAGAGGTTTTA-AAATG
*
19595885 TACCCGGAGGTTTTGAAAATG
1 TACCCAGAGGTTTT-AAAATG
*
19595906 TACCTAGAGGTTTTAAAA
1 TACCCAGAGGTTTTAAAA
19595924 GAAAATGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.12
21 27 0.84
22 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
TACCCAGAGGTTTTAAAATG
Found at i:19595919 original size:143 final size:143
Alignment explanation
Indices: 19595599--19595919 Score: 430
Period size: 143 Copynumber: 2.2 Consensus size: 143
19595589 TGAAACTAAT
* * *
19595599 TACCCAGAGGTTTT-AAGAATGTACTTGGAGGTTTTGAAGACGTACCCAAAGGTTTTAGAAGAAA
1 TACCCGGAGGTTTTGAA-AATGTACCTAGAGGTTTTGAAGACGTACCCAAAGGTTTTAGAAGAAA
* * * *
19595663 ATGTTGGTCCTCATCTCAGAATGAGGCTACGTAACTTTGAAGAAATCTTGAAACTAATTGCTCAA
65 AGGTTGGTCCTCATCTCAAAATGAGGCTACGTAACTTTGAAGAAATCTTGAAACTAATTACCCAA
* *
19595728 AGGTTTTAAGTATG
130 AGGTTTTAAGAATA
** * * * * * **
19595742 TACTTGGAGGTTTAGAAAATGTACC-CGCAAGTTTTTAAGATGTACCCGGAGGTTTTAGAAGAAA
1 TACCCGGAGGTTTTGAAAATGTACCTAG-AGGTTTTGAAGACGTACCCAAAGGTTTTAGAAGAAA
*
19595806 AGGTTGGTCCTCATCTCAAAATGAGGCTATGTAACTTTGAAGAAATCTTGAAACTAATTACCCAA
65 AGGTTGGTCCTCATCTCAAAATGAGGCTACGTAACTTTGAAGAAATCTTGAAACTAATTACCCAA
*
19595871 AGGTTTTAGGAATA
130 AGGTTTTAAGAATA
19595885 TACCCGGAGGTTTTGAAAATGTACCTAGAGGTTTT
1 TACCCGGAGGTTTTGAAAATGTACCTAGAGGTTTT
19595920 AAAAGAAAAT
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
142 1 0.01
143 147 0.97
144 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (143 bp):
TACCCGGAGGTTTTGAAAATGTACCTAGAGGTTTTGAAGACGTACCCAAAGGTTTTAGAAGAAAA
GGTTGGTCCTCATCTCAAAATGAGGCTACGTAACTTTGAAGAAATCTTGAAACTAATTACCCAAA
GGTTTTAAGAATA
Found at i:19596000 original size:22 final size:22
Alignment explanation
Indices: 19595967--19596026 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
19595957 CATAACTAAT
* *
19595967 TACCCGGA-GGTTTAGGAGAATA
1 TACCTGGAGGGTTTAGAAG-ATA
*
19595989 TACCT-GAGGGTTTTGAAGATA
1 TACCTGGAGGGTTTAGAAGATA
19596010 TACCTGGAGGGTTTAGA
1 TACCTGGAGGGTTTAGA
19596027 GGAAAAGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (22 bp):
TACCTGGAGGGTTTAGAAGATA
Found at i:19597243 original size:19 final size:19
Alignment explanation
Indices: 19597219--19597256 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19597209 CCATTTGACT
19597219 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
*
19597238 TATTGGAGTATTATTTGAG
1 TATTGGAGTATGATTTGAG
19597257 GTTGAGAACT
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:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:19604455 original size:25 final size:25
Alignment explanation
Indices: 19604421--19604469 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
19604411 ATGCTACCCT
19604421 TCAAATATCTAAGGATACGTTTAGC
1 TCAAATATCTAAGGATACGTTTAGC
*
19604446 TCAAATATCTTAGGATACGTTTAG
1 TCAAATATCTAAGGATACGTTTAG
19604470 ATGTAGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (25 bp):
TCAAATATCTAAGGATACGTTTAGC
Found at i:19606214 original size:28 final size:28
Alignment explanation
Indices: 19606181--19606237 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19606171 AATTTAATAA
19606181 ACATTTCAAAGGTTTCAAACTTAAGTTT
1 ACATTTCAAAGGTTTCAAACTTAAGTTT
19606209 ACATTTCAAAGGTTTCAAACTTAAGTTT
1 ACATTTCAAAGGTTTCAAACTTAAGTTT
19606237 A
1 A
19606238 AGAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
ACATTTCAAAGGTTTCAAACTTAAGTTT
Found at i:19608759 original size:38 final size:40
Alignment explanation
Indices: 19608673--19608775 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
19608663 ACCCGGCTCA
*
19608673 TGTACATCCCCCCACATCGTGCACATAGCTGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCTAGCACCATCG
* * * *
19608713 TGTGCATCCCCCCACACCGTGCACA-ATC-AGTACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCTAGCACCATCG
*
19608751 TGTACATCCCCCCAAATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
19608776 CGAGCACTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 30 0.55
39 2 0.04
40 23 0.42
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGCTAGCACCATCG
Found at i:19615738 original size:4 final size:4
Alignment explanation
Indices: 19615729--19615767 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
19615719 ATTCTATTAC
*
19615729 ACAT ACAT ACAT ACAT ACAT ACAT ATCTAT ATAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A-C-AT ACAT ACAT A
19615768 TATATATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 27 0.87
5 1 0.03
6 3 0.10
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (4 bp):
ACAT
Found at i:19628561 original size:20 final size:20
Alignment explanation
Indices: 19628536--19628575 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19628526 TGTCCTTTAG
19628536 CAGTATGTTACATAGGACGT
1 CAGTATGTTACATAGGACGT
19628556 CAGTATGTTACATAGGACGT
1 CAGTATGTTACATAGGACGT
19628576 TAGACAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
CAGTATGTTACATAGGACGT
Found at i:19641069 original size:30 final size:30
Alignment explanation
Indices: 19641033--19641100 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
19641023 TCATAAAGAT
19641033 TTATTTGACTCAAAATAAAAGTAGAAAGGC
1 TTATTTGACTCAAAATAAAAGTAGAAAGGC
** * * *
19641063 TTATTTGGTTTAAAATAAAAGTATAAAGGT
1 TTATTTGACTCAAAATAAAAGTAGAAAGGC
19641093 TTATTTGA
1 TTATTTGA
19641101 ATTTTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (30 bp):
TTATTTGACTCAAAATAAAAGTAGAAAGGC
Found at i:19641560 original size:14 final size:14
Alignment explanation
Indices: 19641541--19641586 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
19641531 AAATCTACTA
19641541 ATTTTTATTATATT
1 ATTTTTATTATATT
* *
19641555 ATTTTT-TTGT-TA
1 ATTTTTATTATATT
19641567 ATTTTTATTATATAT
1 ATTTTTATTATAT-T
19641582 ATTTT
1 ATTTT
19641587 ATTTGGGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 7 0.28
15 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (14 bp):
ATTTTTATTATATT
Found at i:19641575 original size:26 final size:28
Alignment explanation
Indices: 19641539--19641591 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
19641529 ATAAATCTAC
19641539 TAATTTTTATTATAT-TATTTT-TTTGT
1 TAATTTTTATTATATATATTTTATTTGT
19641565 TAATTTTTATTATATATATTTTATTTG
1 TAATTTTTATTATATATATTTTATTTG
19641592 GGGATAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 15 0.60
27 6 0.24
28 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (28 bp):
TAATTTTTATTATATATATTTTATTTGT
Found at i:19642629 original size:3 final size:3
Alignment explanation
Indices: 19642621--19642647 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19642611 TAGCATTAAA
19642621 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
19642648 GTTAGAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19642861 original size:15 final size:14
Alignment explanation
Indices: 19642836--19642869 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
19642826 TTTATAATTT
19642836 TATAATAATTATAA
1 TATAATAATTATAA
*
19642850 TATAATTAATTATAT
1 TATAA-TAATTATAA
19642865 TATAA
1 TATAA
19642870 ATATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAATAATTATAA
Found at i:19648689 original size:12 final size:12
Alignment explanation
Indices: 19648672--19648696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19648662 CACTGTACAC
19648672 TCTCAAATCAAG
1 TCTCAAATCAAG
19648684 TCTCAAATCAAG
1 TCTCAAATCAAG
19648696 T
1 T
19648697 TAGTAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (12 bp):
TCTCAAATCAAG
Found at i:19650723 original size:103 final size:103
Alignment explanation
Indices: 19650542--19650745 Score: 327
Period size: 103 Copynumber: 2.0 Consensus size: 103
19650532 TTAAGGAGCA
* *
19650542 AATGCATGCATATATGGTCCCTTTGCCATTGATTATTTCAACTTCCAAAGTGACACTTTTACAAC
1 AATGCATGCATATATGGTCCCTTTGCCATTGATTATTTCAACTTCCAAAGAGACACTCTTACAAC
*
19650607 TTGGTATTGACTTTCTTCTTATCTGGAAAATGCTATAT
66 TTGCTATTGACTTTCTTCTTATCTGGAAAATGCTATAT
* * * * *
19650645 AATGCATGCGTATATGTTCCCTTTGCTATTGATTGTTTCAACTTCCAAAGAGACACTCTTACAGC
1 AATGCATGCATATATGGTCCCTTTGCCATTGATTATTTCAACTTCCAAAGAGACACTCTTACAAC
*
19650710 TTGCTATTTACTTTCTTCTTATCTGGAAAATGCTAT
66 TTGCTATTGACTTTCTTCTTATCTGGAAAATGCTAT
19650746 CTAAGGTCTC
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 92 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (103 bp):
AATGCATGCATATATGGTCCCTTTGCCATTGATTATTTCAACTTCCAAAGAGACACTCTTACAAC
TTGCTATTGACTTTCTTCTTATCTGGAAAATGCTATAT
Found at i:19654531 original size:79 final size:78
Alignment explanation
Indices: 19654438--19654612 Score: 190
Period size: 79 Copynumber: 2.2 Consensus size: 78
19654428 TTATCCCTTG
* * * *
19654438 AGATAATTTGAAGATAATATT-TAAATTGAACCGATTAAAATTTAATTATTGATCATCTAATTTA
1 AGATAATTTAAAGATAATATTATAAATTGAACCAATCAAAATTTAATCATTGATCATCTAATTTA
*
19654502 TTTCTAAATAAATCA
66 TCTCT-AAT-AATCA
** ** * *
19654517 AGATAATTTAAAGATAATATTCATATTTTTTACTAATCAAAATTTAATCATTGGTCATCTAATTT
1 AGATAATTTAAAGATAATATT-ATAAATTGAACCAATCAAAATTTAATCATTGATCATCTAATTT
*
19654582 ATCTCTAATAATTA
65 ATCTCTAATAATCA
* *
19654596 TGATAATTTAGAGATAA
1 AGATAATTTAAAGATAA
19654613 AAATCAAATT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 39 0.49
80 3 0.04
81 38 0.47
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (78 bp):
AGATAATTTAAAGATAATATTATAAATTGAACCAATCAAAATTTAATCATTGATCATCTAATTTA
TCTCTAATAATCA
Found at i:19655305 original size:32 final size:32
Alignment explanation
Indices: 19655264--19655324 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
19655254 GAGATCTTCT
19655264 TCCTCCATCCCCAAATCATCAGCTATTTTTCA
1 TCCTCCATCCCCAAATCATCAGCTATTTTTCA
19655296 TCCTCCATCCCCAAATCATCAGCTATTTT
1 TCCTCCATCCCCAAATCATCAGCTATTTT
19655325 GTCTGGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.38, G:0.03, T:0.34
Consensus pattern (32 bp):
TCCTCCATCCCCAAATCATCAGCTATTTTTCA
Found at i:19659051 original size:19 final size:20
Alignment explanation
Indices: 19659023--19659065 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
19659013 AGGGTCAAGG
*
19659023 CACCTGGGCGTTGT-AAAGA
1 CACCTAGGCGTTGTGAAAGA
19659042 CACCTAGGCGTTGTGAAAGA
1 CACCTAGGCGTTGTGAAAGA
19659062 CACC
1 CACC
19659066 AATCGTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (20 bp):
CACCTAGGCGTTGTGAAAGA
Found at i:19659115 original size:40 final size:40
Alignment explanation
Indices: 19659062--19659140 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
19659052 TTGTGAAAGA
19659062 CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAAT
1 CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAAT
*
19659102 CACCAATCTTGACAAGGTTGAAAACCCCACTAAGGTGAA
1 CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAA
19659141 AAATAGCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (40 bp):
CACCAATCGTGACAAGGTTGAAAACCCCACTAAGGTGAAT
Found at i:19659519 original size:3 final size:3
Alignment explanation
Indices: 19659496--19659563 Score: 86
Period size: 3 Copynumber: 22.7 Consensus size: 3
19659486 CTCATGCGTC
* *
19659496 AAT AAT -AT ACAT AA- AAA AAT AAT AAT AAT AACA AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
19659541 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
19659564 ATATATAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.07
3 49 0.84
4 5 0.09
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:19659573 original size:8 final size:7
Alignment explanation
Indices: 19659512--19659575 Score: 61
Period size: 6 Copynumber: 9.9 Consensus size: 7
19659502 ATACATAAAA
19659512 AAATAAT
1 AAATAAT
19659519 -AATAAT
1 AAATAAT
19659525 AACA-AAT
1 AA-ATAAT
19659532 -AATAAT
1 AAATAAT
19659538 -AATAAT
1 AAATAAT
19659544 -AATAAT
1 AAATAAT
19659550 -AATAAT
1 AAATAAT
19659556 -AATAAT
1 AAATAAT
19659562 AAATATAT
1 AAATA-AT
19659570 AAATAA
1 AAATAA
19659576 AGCAATAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
5 1 0.02
6 34 0.65
7 9 0.17
8 8 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATAAT
Found at i:19660416 original size:26 final size:25
Alignment explanation
Indices: 19660376--19660424 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
19660366 ATGTGAGGCT
19660376 GAAAGTTGGGCAGTAGATAGATATTTG
1 GAAAGTTGGGCAGTA-ATA-ATATTTG
*
19660403 GAAA-TTGGGTAGTAATAATATT
1 GAAAGTTGGGCAGTAATAATATT
19660425 GTTTTCTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 9 0.43
27 4 0.19
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.33
Consensus pattern (25 bp):
GAAAGTTGGGCAGTAATAATATTTG
Found at i:19663423 original size:40 final size:40
Alignment explanation
Indices: 19663366--19663443 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
19663356 TATGAAAGAA
*
19663366 ACCAATCGTGGCGAGGTTGAAAACCCCACTAAGGTGAATC
1 ACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAATC
*
19663406 ACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAA
1 ACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAA
19663444 AAATAACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (40 bp):
ACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAATC
Found at i:19666087 original size:40 final size:41
Alignment explanation
Indices: 19666029--19666108 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
19666019 TTATAAAAAA
* *
19666029 CACCAATCGTGGCGAGGTTGAAAA-CCCCACTAAAGTGAAT
1 CACCAATCGTGACAAGGTTGAAAACCCCCACTAAAGTGAAT
* *
19666069 CACCAATCTTGACAAGGTTGAAAACCCCCACTAAGGTGAA
1 CACCAATCGTGACAAGGTTGAAAACCCCCACTAAAGTGAA
19666109 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (41 bp):
CACCAATCGTGACAAGGTTGAAAACCCCCACTAAAGTGAAT
Found at i:19667895 original size:112 final size:112
Alignment explanation
Indices: 19667698--19667918 Score: 424
Period size: 112 Copynumber: 2.0 Consensus size: 112
19667688 TCATTGAAGT
19667698 ATTTTCTTTTATGTTGGGTGGATCTTCTCCAAGAACCATTCTTACTTTAGATGTTAAGATTACCA
1 ATTTTCTTTTATGTTGGGTGGATCTTCTCCAAGAACCATTCTTACTTTAGATGTTAAGATTACCA
19667763 CTCTTAATTTCTCTAATATGGAAAATGGAGGGTGATGATGTTATGGA
66 CTCTTAATTTCTCTAATATGGAAAATGGAGGGTGATGATGTTATGGA
* *
19667810 ATTTTCTTTTATGTTGGGTGGATCTTCTCCGAGAACCATTCTTACTTTAGATGTTAAGATTACCG
1 ATTTTCTTTTATGTTGGGTGGATCTTCTCCAAGAACCATTCTTACTTTAGATGTTAAGATTACCA
19667875 CTCTTAATTTCTCTAATATGGAAAATGGAGGGTGATGATGTTAT
66 CTCTTAATTTCTCTAATATGGAAAATGGAGGGTGATGATGTTAT
19667919 AAATATATGG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (112 bp):
ATTTTCTTTTATGTTGGGTGGATCTTCTCCAAGAACCATTCTTACTTTAGATGTTAAGATTACCA
CTCTTAATTTCTCTAATATGGAAAATGGAGGGTGATGATGTTATGGA
Found at i:19669741 original size:14 final size:15
Alignment explanation
Indices: 19669723--19669763 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
19669713 TTATTTTTAC
19669723 TATATATTTTTTAAA
1 TATATATTTTTTAAA
19669738 -ATAT-TTTATTTAAA
1 TATATATTT-TTTAAA
*
19669752 TAGATATTTTTT
1 TATATATTTTTT
19669764 TTATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 6 0.27
16 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TATATATTTTTTAAA
Found at i:19669781 original size:45 final size:48
Alignment explanation
Indices: 19669697--19669798 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 48
19669687 ATAAATTTAA
**
19669697 TATTTAAATATTTGATTTATTTTTACTATATATTTTTTAAAATA-TTT
1 TATTTAAATAGATGATTTATTTTTACTATATATTTTTTAAAATACTTT
* *
19669744 TATTTAAATAGAT-ATTT-TTTTTATTAT-TATTATTTTAAATTACTTT
1 TATTTAAATAGATGATTTATTTTTACTATATATT-TTTTAAAATACTTT
19669790 TA-TTAAATA
1 TATTTAAATA
19669799 ATCAACTTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 4 0.08
45 25 0.51
46 9 0.18
47 11 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (48 bp):
TATTTAAATAGATGATTTATTTTTACTATATATTTTTTAAAATACTTT
Found at i:19694406 original size:21 final size:23
Alignment explanation
Indices: 19694368--19694409 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
19694358 CAGTTTCACT
*
19694368 CTCTCTCTCTCTCTACTTAAGAG
1 CTCTCTCTCTCTCCACTTAAGAG
19694391 CTCTC-CTC-CTCCACTTAAG
1 CTCTCTCTCTCTCCACTTAAG
19694410 CACCTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 3 0.17
23 5 0.28
ACGTcount: A:0.17, C:0.40, G:0.07, T:0.36
Consensus pattern (23 bp):
CTCTCTCTCTCTCCACTTAAGAG
Found at i:19738668 original size:20 final size:20
Alignment explanation
Indices: 19738640--19738679 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19738630 ATTTATATAT
* * *
19738640 AATTTTTATTTTTTTAATAA
1 AATTATTATTATTATAATAA
19738660 AATTATTATTATTATAATAA
1 AATTATTATTATTATAATAA
19738680 CTCTAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTATTATTATTATAATAA
Found at i:19746202 original size:2 final size:2
Alignment explanation
Indices: 19746190--19746232 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19746180 TGGATGCCAG
*
19746190 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19746232 A
1 A
19746233 CATGATAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19752148 original size:116 final size:116
Alignment explanation
Indices: 19751964--19752378 Score: 568
Period size: 116 Copynumber: 3.6 Consensus size: 116
19751954 AAAAAAAATA
* ** * *
19751964 ATATGGTGACAAAA-TA--TTTT-TTGTTGATAAATTTGTAATTTTTAAAAATGAATTAGTCATT
1 ATATGGTGA-AAAAGTATCTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGAATTAGTCATT
* * *
19752025 TTAAGGTACACAATTTGAGATTTATTATTTTCGATTCGAAATTAAAGAGGTG
65 TTAAGGTACACAACTTGAGATTTATTATTCTCGATTCGGAATTAAAGAGGTG
* *
19752077 ATATGGTGAAAAAGTATTTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGGATTAGTCATTT
1 ATATGGTGAAAAAGTATCTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGAATTAGTCATTT
* * * * * *
19752142 TAAGGTACACAAGTTGGGGTTTATTATTCTCGATTCGGAATTAACGAAGTA
66 TAAGGTACACAACTTGAGATTTATTATTCTCGATTCGGAATTAAAGAGGTG
* * * *
19752193 ATATGGTGAGAAAGTATCTTTTGTTGCTAATAAATTTATGGTTTGCAAGAATGAATTAGTCATTT
1 ATATGGTGAAAAAGTATCTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGAATTAGTCATTT
* *
19752258 TAAGGTACACAACTTGAGATTTATTATTCTCGATTTGGAATTAAGGAGGTG
66 TAAGGTACACAACTTGAGATTTATTATTCTCGATTCGGAATTAAAGAGGTG
* * *
19752309 ATATGGTGACAAAGTATCTTTTGTTGTTGATAAATTTGTGGTTTTGAAGAATGAATTAGTCATTT
1 ATATGGTGAAAAAGTATCTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGAATTAGTCATTT
19752374 TAAGG
66 TAAGG
19752379 ATTTGAATAA
Statistics
Matches: 265, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
112 4 0.02
113 11 0.04
115 4 0.02
116 246 0.93
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (116 bp):
ATATGGTGAAAAAGTATCTTTTGTTGTTGATAAATTTATGGTTTTCAAGAATGAATTAGTCATTT
TAAGGTACACAACTTGAGATTTATTATTCTCGATTCGGAATTAAAGAGGTG
Found at i:19753110 original size:16 final size:16
Alignment explanation
Indices: 19753089--19753122 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19753079 TCCTCAACTC
19753089 AAAGAAAAAAAAGACA
1 AAAGAAAAAAAAGACA
* *
19753105 AAAGAAAGAAAATACA
1 AAAGAAAAAAAAGACA
19753121 AA
1 AA
19753123 TAATTAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAAAGACA
Found at i:19753861 original size:31 final size:32
Alignment explanation
Indices: 19753803--19753867 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
19753793 ATCATAATAA
*
19753803 TGCCACGTGACACTACCACATCATCATGTCGG
1 TGCCACGTGACACTACCACATCATCATGTAGG
* **
19753835 TGCCACGTGACA-TGCCATGTCATCATGTAGG
1 TGCCACGTGACACTACCACATCATCATGTAGG
19753866 TG
1 TG
19753868 TCATGTCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (32 bp):
TGCCACGTGACACTACCACATCATCATGTAGG
Found at i:19764810 original size:3 final size:3
Alignment explanation
Indices: 19764802--19764827 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19764792 CGCAAACCAA
19764802 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
19764828 ACAAGAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:19771186 original size:3 final size:3
Alignment explanation
Indices: 19771178--19771215 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19771168 ATAACCATCT
19771178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19771216 TGGATAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19774634 original size:2 final size:2
Alignment explanation
Indices: 19774625--19774655 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19774615 GTGTGTGTGT
19774625 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19774656 ATATCTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19776524 original size:14 final size:14
Alignment explanation
Indices: 19776492--19776529 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19776482 TGCATCACCA
*
19776492 AATTT-TATATTGC
1 AATTTCTATTTTGC
19776505 AATTTCTATTTTGC
1 AATTTCTATTTTGC
*
19776519 ATTTTCTATTT
1 AATTTCTATTT
19776530 GAGAACTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.61
Consensus pattern (14 bp):
AATTTCTATTTTGC
Found at i:19779218 original size:25 final size:24
Alignment explanation
Indices: 19779179--19779250 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 24
19779169 ACTTTTAATA
19779179 AAATATTAATATTAAATTATAAAT
1 AAATATTAATATTAAATTATAAAT
19779203 AAATATTAATATTTAAATTATAAAT
1 AAATATTAATA-TTAAATTATAAAT
* * * *
19779228 TATTAATAA-AATAAATTATAAAT
1 AAATATTAATATTAAATTATAAAT
19779251 TATTCCTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 12 0.28
24 12 0.28
25 19 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTAATATTAAATTATAAAT
Found at i:19783831 original size:24 final size:24
Alignment explanation
Indices: 19783804--19783860 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 24
19783794 TTATTTTATT
*
19783804 TTATTTTGAAACATTAATAATTGA
1 TTATTTTAAAACATTAATAATTGA
*
19783828 TTATTTGTTTAAAATATTAATAATTGA
1 TTA--T-TTTAAAACATTAATAATTGA
*
19783855 TGATTT
1 TTATTT
19783861 AATTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
26 1 0.04
27 20 0.74
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
TTATTTTAAAACATTAATAATTGA
Found at i:19783987 original size:7 final size:7
Alignment explanation
Indices: 19783970--19784055 Score: 53
Period size: 7 Copynumber: 12.6 Consensus size: 7
19783960 ATAATTGATC
19783970 ATTTAAAT
1 ATTT-AAT
19783978 ATTTAAT
1 ATTTAAT
19783985 ATTT--T
1 ATTTAAT
19783990 ATTT-AT
1 ATTTAAT
19783996 AGTTTAAT
1 A-TTTAAT
*
19784004 TTTTAAT
1 ATTTAAT
19784011 ATTTTAA-
1 A-TTTAAT
19784018 ACTATTAAT
1 A-T-TTAAT
19784027 ATTT--T
1 ATTTAAT
19784032 ATTT-AT
1 ATTTAAT
19784038 AATTTAAT
1 -ATTTAAT
19784046 A-TTAAT
1 ATTTAAT
19784052 ATTT
1 ATTT
19784056 TATTAAAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.15
6 9 0.14
7 27 0.42
8 18 0.28
9 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (7 bp):
ATTTAAT
Found at i:19784003 original size:19 final size:19
Alignment explanation
Indices: 19783978--19784048 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 19
19783968 TCATTTAAAT
19783978 ATTTAATATTTTATTTATA
1 ATTTAATATTTTATTTATA
* *
19783997 GTTTAAT-TTTTAATATTTTAA
1 ATTTAATATTTT-AT-TTAT-A
19784018 ACTATTAATATTTTATTTATA
1 A-T-TTAATATTTTATTTATA
19784039 ATTTAATATT
1 ATTTAATATT
19784049 AATATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.10
19 16 0.38
20 4 0.10
21 3 0.07
22 4 0.10
23 7 0.17
24 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTAATATTTTATTTATA
Found at i:19784017 original size:42 final size:41
Alignment explanation
Indices: 19783971--19784057 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 41
19783961 TAATTGATCA
* *
19783971 TTTAAA-TATTTAATATTTTATTTATAGTTTAATTTTTAATAT
1 TTTAAACTA-TTAATATTTTATTTATAATTTAA-TATTAATAT
19784013 TTTAAACTATTAATATTTTATTTATAATTTAATATTAATAT
1 TTTAAACTATTAATATTTTATTTATAATTTAATATTAATAT
19784054 TTTA
1 TTTA
19784058 TTAAAAGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
41 12 0.29
42 28 0.67
43 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (41 bp):
TTTAAACTATTAATATTTTATTTATAATTTAATATTAATAT
Found at i:19790106 original size:2 final size:2
Alignment explanation
Indices: 19790099--19790166 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
19790089 TATAGTAAGG
19790099 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19790141 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
19790167 AGAAATTAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19791612 original size:2 final size:2
Alignment explanation
Indices: 19791605--19791631 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19791595 TAATATTAAC
19791605 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19791632 AGCTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19793215 original size:14 final size:15
Alignment explanation
Indices: 19793198--19793230 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19793188 AAAAATATAT
19793198 AAAAAAAAAGA-GAA
1 AAAAAAAAAGATGAA
*
19793212 AAAAAAAATGATGAA
1 AAAAAAAAAGATGAA
19793227 AAAA
1 AAAA
19793231 GAAAGGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAAAAAGATGAA
Found at i:19794521 original size:2 final size:2
Alignment explanation
Indices: 19794514--19794564 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19794504 AATATAGGAG
19794514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19794556 TA TA TA TA T
1 TA TA TA TA T
19794565 GTTTATATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19795154 original size:15 final size:16
Alignment explanation
Indices: 19795134--19795163 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19795124 ATATATATAT
19795134 ATATATATA-ATAAAA
1 ATATATATACATAAAA
19795149 ATATATATACATAAA
1 ATATATATACATAAA
19795164 TTTATGAAAA
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATATATACATAAAA
Found at i:19800995 original size:22 final size:21
Alignment explanation
Indices: 19800953--19801032 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
19800943 AAACACCTAA
*
19800953 AAAATAAATGAAAAAATTAAATT
1 AAAATAAAT-AAAATA-TAAATT
* *
19800976 ATAATAAAATAAAATATAAAGT
1 AAAAT-AAATAAAATATAAATT
* *
19800998 AAAATAAATAAATAAATAAATA
1 AAAATAAATAAA-ATATAAATT
* *
19801020 AAAAGAAAAAAAA
1 AAAATAAATAAAA
19801033 AGGAAGAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 8 0.17
22 25 0.54
23 9 0.20
24 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAATAAATAAAATATAAATT
Found at i:19801008 original size:4 final size:4
Alignment explanation
Indices: 19800950--19801021 Score: 51
Period size: 4 Copynumber: 17.0 Consensus size: 4
19800940 TGTAAACACC
*
19800950 TAAA -AAA TAAA TGAAA -AAA TTAAA TTATAA TAAAA TAAA -ATA TAAA
1 TAAA TAAA TAAA T-AAA TAAA -TAAA -TA-AA T-AAA TAAA TAAA TAAA
19800996 GTAAAA TAAA TAAA TAAA TAAA TAAA
1 -T-AAA TAAA TAAA TAAA TAAA TAAA
19801022 AAGAAAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
3 8 0.14
4 28 0.49
5 15 0.26
6 6 0.11
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:19801645 original size:27 final size:27
Alignment explanation
Indices: 19801614--19801685 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
19801604 GTCTTGTGGT
*
19801614 GGCCGATGGGTAGAGAGAAGGTGGAGA
1 GGCCGACGGGTAGAGAGAAGGTGGAGA
*
19801641 GGCCGGCGGGTAGAGAGAAGGTGGAGA
1 GGCCGACGGGTAGAGAGAAGGTGGAGA
* *
19801668 GGTCGACGGCTAGAGAGA
1 GGCCGACGGGTAGAGAGA
19801686 GAAAATGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.11, G:0.51, T:0.10
Consensus pattern (27 bp):
GGCCGACGGGTAGAGAGAAGGTGGAGA
Found at i:19814610 original size:62 final size:62
Alignment explanation
Indices: 19814497--19814786 Score: 262
Period size: 62 Copynumber: 4.9 Consensus size: 62
19814487 GCATAAAGAA
* * * * *
19814497 TTAAATCGAACCTGTTGTGAGAAAGTTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAATTTCAATTTTGT
* * *
19814559 TTAAATCGAACCTGTTATGAGATAGGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAATTTCAATTTTGT
* *
19814621 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAATCTA-G-A----AA---T-T
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAATTTCAATTTTGT
* ** * * * * * * *
19814673 TT-AATTGAATTTATTCTAATATGGGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAATTTCAATTTTGT
** * * *
19814734 TTAAATCGAATTTGTTGTGAGATAGGTTGAGCC-AAGATTAAATCTAGAAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAA-ATTAAGTCTAGGAATTT
19814787 TAATCGGATT
Statistics
Matches: 180, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
51 31 0.17
52 4 0.02
53 2 0.01
56 2 0.01
57 2 0.01
60 2 0.01
61 6 0.03
62 131 0.73
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (62 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAATTTCAATTTTGT
Found at i:19814781 original size:113 final size:113
Alignment explanation
Indices: 19814583--19814884 Score: 451
Period size: 113 Copynumber: 2.7 Consensus size: 113
19814573 TTATGAGATA
*
19814583 GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAACCTGTTGTGAGATAGGT
1 GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAACTTGTTGTGAGATAGGT
*
19814648 CGAGCCTAGATTAAATCTAGAAATTTTAATTGAATTTATTCTAATATG
66 CGAGCCTAGATTAAATCTAGAAATTTTAATCGAATTTATTCTAATATG
*
19814696 GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAATTTGTTGTGAGATAGGT
1 GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAACTTGTTGTGAGATAGGT
* * * *
19814761 TGAGCCAAGATTAAATCTAGAAATTTTAATCGGATTTGTTCTAATATG
66 CGAGCCTAGATTAAATCTAGAAATTTTAATCGAATTTATTCTAATATG
* * ** * * * * * *
19814809 GGTCAAGCCTAGATCGAGTCTAGAAATTTCATTTTTGTTTAAATCGAACTTATTTTGAGATAAGT
1 GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAACTTGTTGTGAGATAGGT
19814874 CGAGCCTAGAT
66 CGAGCCTAGAT
19814885 CAATTTGATT
Statistics
Matches: 169, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 169 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (113 bp):
GGTCGAGCCTAAATTTAGTTTAGGAATTTCAATTTTGTTTAAATCGAACTTGTTGTGAGATAGGT
CGAGCCTAGATTAAATCTAGAAATTTTAATCGAATTTATTCTAATATG
Found at i:19815018 original size:5 final size:5
Alignment explanation
Indices: 19814995--19815065 Score: 53
Period size: 5 Copynumber: 14.8 Consensus size: 5
19814985 AGACACCTAA
* * *
19814995 AAAAT -AAAT GAAA- AAATT AAATT AAAAT AAAAT AAAAT ATAAAGT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAA-T AAAAT
*
19815045 -AAAT AAAA- AAAAG AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA
19815066 AGAGAAGGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
4 18 0.32
5 31 0.54
6 6 0.11
7 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:19815037 original size:22 final size:20
Alignment explanation
Indices: 19815007--19815052 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
19814997 AATAAATGAA
*
19815007 AAAATTAAATTAAAATAAAAT
1 AAAATTAAAGTAAAAT-AAAT
19815028 AAAATATAAAGTAAAATAAAT
1 AAAAT-TAAAGTAAAATAAAT
19815049 AAAA
1 AAAA
19815053 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATTAAAGTAAAATAAAT
Found at i:19815048 original size:16 final size:16
Alignment explanation
Indices: 19815007--19815053 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19814997 AATAAATGAA
19815007 AAAATTAAAT-TAAAAT
1 AAAA-TAAATATAAAAT
*
19815023 AAAATAAAATATAAAGT
1 AAAAT-AAATATAAAAT
19815040 AAAATAAATA-AAAA
1 AAAATAAATATAAAA
19815054 AAAGAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAATAAATATAAAAT
Found at i:19815053 original size:10 final size:10
Alignment explanation
Indices: 19814994--19815062 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 10
19814984 TAGACACCTA
19814994 AAAAATAAAT
1 AAAAATAAAT
19815004 GAAAAAATTAAAT
1 --AAAAA-TAAAT
*
19815017 TAAAATAAAAT
1 AAAAAT-AAAT
19815028 AAAATATAAAGT
1 AAAA-ATAAA-T
19815040 -AAAATAAAT
1 AAAAATAAAT
*
19815049 AAAAA-AAAG
1 AAAAATAAAT
19815058 AAAAA
1 AAAAA
19815063 AAAAGAGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.18
10 10 0.20
11 17 0.35
12 8 0.16
13 5 0.10
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:19815053 original size:22 final size:22
Alignment explanation
Indices: 19814995--19815054 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
19814985 AGACACCTAA
*
19814995 AAAATAAATGAAAAAATTAAATT
1 AAAATAAAT-AAAAAATTAAAGT
*
19815018 AAAATAAA-ATAAAATATAAAGT
1 AAAATAAATAAAAAAT-TAAAGT
19815040 AAAATAAATAAAAAA
1 AAAATAAATAAAAAA
19815055 AAGAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 6 0.19
22 13 0.41
23 13 0.41
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAATAAATAAAAAATTAAAGT
Found at i:19819635 original size:2 final size:2
Alignment explanation
Indices: 19819630--19819659 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19819620 AAAAAAATAC
*
19819630 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19819660 AAATATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19828531 original size:2 final size:2
Alignment explanation
Indices: 19828526--19828558 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19828516 ATATATATAT
19828526 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19828559 GGTTGCCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19840538 original size:18 final size:17
Alignment explanation
Indices: 19840495--19840538 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
19840485 TTCCTTCTTC
19840495 TTTTTTTTTTTTAATTA
1 TTTTTTTTTTTTAATTA
*
19840512 TTCTCTTTTTTTTAATTA
1 TT-TTTTTTTTTTAATTA
*
19840530 TTTTATTTT
1 TTTTTTTTT
19840539 ATATTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTTTTAATTA
Found at i:19840543 original size:12 final size:12
Alignment explanation
Indices: 19840528--19840552 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19840518 TTTTTTTAAT
19840528 TATTTTATTTTA
1 TATTTTATTTTA
19840540 TATTTTATTTTA
1 TATTTTATTTTA
19840552 T
1 T
19840553 TATATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:19840545 original size:22 final size:22
Alignment explanation
Indices: 19840520--19840567 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
19840510 TATTCTCTTT
*
19840520 TTTTTA-ATTATTTTA-TTTTA
1 TTTTTATATTATTATATTTTTA
*
19840540 TATTTTATTTTATTATATTTTTA
1 T-TTTTATATTATTATATTTTTA
19840563 TTTTT
1 TTTTT
19840568 TGAGGTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 5 0.22
22 11 0.48
23 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTATATTATTATATTTTTA
Found at i:19840567 original size:17 final size:17
Alignment explanation
Indices: 19840527--19840566 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
19840517 TTTTTTTTAA
*
19840527 TTATTTTATTTTATATT
1 TTATTTTATTATATATT
19840544 TTATTTTATTATAT-TT
1 TTATTTTATTATATATT
19840560 TTATTTT
1 TTATTTT
19840567 TTGAGGTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTTTATTATATATT
Found at i:19843067 original size:2 final size:2
Alignment explanation
Indices: 19843062--19843094 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19843052 ATATATATAT
19843062 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19843095 GGACGGNTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19847071 original size:18 final size:18
Alignment explanation
Indices: 19847039--19847100 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
19847029 ATATATGGAT
*
19847039 AAATAGAATAGAAATAAAA
1 AAATA-AATAAAAATAAAA
*
19847058 AAATAAATAAAAATAATA
1 AAATAAATAAAAATAAAA
*
19847076 ATATAAATTAAAAAATTAAAA
1 AAATAAA-T-AAAAA-TAAAA
19847097 AAAT
1 AAAT
19847101 TTTAAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 17 0.49
19 6 0.17
20 5 0.14
21 7 0.20
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAATAAAA
Found at i:19857794 original size:15 final size:15
Alignment explanation
Indices: 19857774--19857805 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19857764 TATGGAAGTA
19857774 CCGCATAATATAATC
1 CCGCATAATATAATC
19857789 CCGCATAATATAATC
1 CCGCATAATATAATC
19857804 CC
1 CC
19857806 CTCTAAGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (15 bp):
CCGCATAATATAATC
Found at i:19861370 original size:98 final size:98
Alignment explanation
Indices: 19861201--19861396 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
19861191 CTAATGCGTG
19861201 GGCAACTTGTAAAGTATTATTGCACTAGCAATTTAACAATCCCTCAAAGGCACCAACAGCATCTG
1 GGCAACTTGTAAAGTATTATTGCACTAGCAATTTAACAATCCCTCAAAGGCACCAACAGCATCTG
19861266 TAGCTAGCATCCACAACCCCCTCTGCCCCACAA
66 TAGCTAGCATCCACAACCCCCTCTGCCCCACAA
19861299 GGCAACTTGTAAAGTATTATTGCACTAGCAATTTAACAATCCCTCAAAGGCACCAACAGCATCTG
1 GGCAACTTGTAAAGTATTATTGCACTAGCAATTTAACAATCCCTCAAAGGCACCAACAGCATCTG
19861364 TAGCTAGCATCCACAACCCCCTCTGCCCCACAA
66 TAGCTAGCATCCACAACCCCCTCTGCCCCACAA
19861397 TTTCTCAGAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (98 bp):
GGCAACTTGTAAAGTATTATTGCACTAGCAATTTAACAATCCCTCAAAGGCACCAACAGCATCTG
TAGCTAGCATCCACAACCCCCTCTGCCCCACAA
Found at i:19866759 original size:22 final size:24
Alignment explanation
Indices: 19866690--19866759 Score: 74
Period size: 26 Copynumber: 2.9 Consensus size: 24
19866680 TATGGGTCAA
19866690 AAAAATTAATAATTTTAATTA-ATT
1 AAAAATTAATAA-TTTAATTATATT
*
19866714 AAATAATTTTATATATTTAATTATA-T
1 AAA-AA-TTAATA-ATTTAATTATATT
19866740 -AAAATTAATAATTTAATTAT
1 AAAAATTAATAATTTAATTAT
19866760 CAATAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 10 0.25
23 5 0.12
24 5 0.12
25 4 0.10
26 14 0.35
27 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAAATTAATAATTTAATTATATT
Found at i:19866872 original size:15 final size:17
Alignment explanation
Indices: 19866842--19866881 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
19866832 GAATTAAATC
19866842 ATAAAATAATTTTATTA
1 ATAAAATAATTTTATTA
19866859 ATAAAA-AA-TTTATTA
1 ATAAAATAATTTTATTA
19866874 AGTAAAAT
1 A-TAAAAT
19866882 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATAAAATAATTTTATTA
Found at i:19868041 original size:27 final size:27
Alignment explanation
Indices: 19867989--19868041 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19867979 ACAAGCTCAT
* *
19867989 AAAAATTGAATTATAACTTTCAAAAAA
1 AAAAATTGAAGTATAACTGTCAAAAAA
*
19868016 AAAAATTGAAGTATAACATGTGAAAA
1 AAAAATTGAAGTATAAC-TGTCAAAA
19868042 TTAGGGATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.26
Consensus pattern (27 bp):
AAAAATTGAAGTATAACTGTCAAAAAA
Found at i:19877296 original size:19 final size:21
Alignment explanation
Indices: 19877258--19877296 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19877248 AAGTTTGAAT
*
19877258 AAACCAATGGATAAGCAATAA
1 AAACCAATGGATAAGAAATAA
19877279 AAACCAATGGA-AA-AAATA
1 AAACCAATGGATAAGAAATA
19877297 TTAATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 2 0.12
21 11 0.65
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (21 bp):
AAACCAATGGATAAGAAATAA
Found at i:19887106 original size:21 final size:20
Alignment explanation
Indices: 19887067--19887106 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19887057 AAGTGAATTA
*
19887067 TTTTAATTTTATGTTATTTC
1 TTTTAATTTTATATTATTTC
*
19887087 TTTTAATTTGTTTATTATTT
1 TTTTAATTT-TATATTATTT
19887107 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTAATTTTATATTATTTC
Found at i:19889277 original size:20 final size:22
Alignment explanation
Indices: 19889233--19889279 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19889223 TTTCTTCTCC
**
19889233 TTTTTCTCTCTATTTTTTTTCT
1 TTTTTCTCTCTATTTTCCTTCT
19889255 TTTTTCTCTCT-TTTTCCTT-T
1 TTTTTCTCTCTATTTTCCTTCT
19889275 TTTTT
1 TTTTT
19889280 AATTTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTCTCTATTTTCCTTCT
Found at i:19889358 original size:21 final size:21
Alignment explanation
Indices: 19889233--19889358 Score: 80
Period size: 21 Copynumber: 5.8 Consensus size: 21
19889223 TTTCTTCTCC
19889233 TTTTTCTCTCTATTTT-TTTTCT
1 TTTTTCTCTCT-TTTTCTTTT-T
*
19889255 TTTTTCTCTCTTTTTCCTTTT
1 TTTTTCTCTCTTTTTCTTTTT
** * *
19889276 TTTTAATTTATTCTTCTCATCTTTT
1 TTTTTCTCTCTT-TT-TC-T-TTTT
* * *
19889301 ATTTTATC-CTTTCTT-TTCTCT
1 TTTTTCTCTCTTT-TTCTT-TTT
19889322 TTTTTC-CTCTTTTTCTTTTT
1 TTTTTCTCTCTTTTTCTTTTT
19889342 TTTTTCTCTCTTTTTCT
1 TTTTTCTCTCTTTTTCT
19889359 CGCTTTTTTC
Statistics
Matches: 80, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
20 12 0.15
21 36 0.45
22 16 0.20
23 4 0.05
24 3 0.04
25 9 0.11
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCTCTCTTTTTCTTTTT
Found at i:19889365 original size:21 final size:20
Alignment explanation
Indices: 19889320--19889368 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
19889310 TTTCTTTTCT
**
19889320 CTTTTTTCCTCTTTTTCTTT
1 CTTTTTTCCTCTTTTTCTCG
*
19889340 TTTTTTTCTCTCTTTTTCTCG
1 CTTTTTTC-CTCTTTTTCTCG
19889361 CTTTTTTC
1 CTTTTTTC
19889369 AATTTTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (20 bp):
CTTTTTTCCTCTTTTTCTCG
Found at i:19889394 original size:87 final size:88
Alignment explanation
Indices: 19889227--19889390 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 88
19889217 AAACATTTTC
* *
19889227 TTCTCCTTTTTCTCTCTATTTTTTTTCTTTTTTCTCTCTTTTTCCTTTTTTTTAATTTATTCTTC
1 TTCTCCTTTTTCTCTCTATTTTTTTTCTTTTTTCTCTCTTTTTCCCTTTTTTCAATTTATTCTTC
19889292 TCATCTTTTATTTTATCCTTTCTT
66 T-ATCTTTTATTTTATCCTTTCTT
*
19889316 TTCTCTTTTTTC-CTCT-TTTTCTTTT-TTTTTTCTCTCTTTTTCTCGCTTTTTTCAATTT-TTC
1 TTCTCCTTTTTCTCTCTATTTT-TTTTCTTTTTTCTCTCTTTTTC-C-CTTTTTTCAATTTATTC
19889377 TTCT-TC-TTTATTTT
63 TTCTATCTTTTATTTT
19889391 TTATTTTTGT
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
85 8 0.12
86 2 0.03
87 21 0.30
88 16 0.23
89 22 0.32
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (88 bp):
TTCTCCTTTTTCTCTCTATTTTTTTTCTTTTTTCTCTCTTTTTCCCTTTTTTCAATTTATTCTTC
TATCTTTTATTTTATCCTTTCTT
Found at i:19890017 original size:31 final size:29
Alignment explanation
Indices: 19889979--19890045 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
19889969 TTTTCTTCAT
*
19889979 TTTTTTTCCATTTTTTGATACTTTTTCTCTC
1 TTTTTTTCC-TTCTTTG-TACTTTTTCTCTC
* * *
19890010 TTTTTTTCCTTCTTTGTATTTTTTTTCTT
1 TTTTTTTCCTTCTTTGTACTTTTTCTCTC
19890039 TTTTTTT
1 TTTTTTT
19890046 TAATTTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.53
30 6 0.19
31 9 0.28
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTTTTTCCTTCTTTGTACTTTTTCTCTC
Found at i:19890849 original size:23 final size:23
Alignment explanation
Indices: 19890813--19890868 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
19890803 TCTAGTTGAC
* *
19890813 TAGAATAACAATTCCTAATTCTAT
1 TAGAATAA-GATTCCTAATTATAT
* *
19890837 TAGGATAAGATTCTTAATTATAT
1 TAGAATAAGATTCCTAATTATAT
19890860 TAGAATAAG
1 TAGAATAAG
19890869 GTTATTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
TAGAATAAGATTCCTAATTATAT
Found at i:19894793 original size:14 final size:14
Alignment explanation
Indices: 19894774--19894800 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19894764 CCACTCAAAG
19894774 AAAAAAGAAATCGA
1 AAAAAAGAAATCGA
19894788 AAAAAAGAAATCG
1 AAAAAAGAAATCG
19894801 CTGAACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAAAAGAAATCGA
Found at i:19901723 original size:2 final size:2
Alignment explanation
Indices: 19901679--19901706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19901669 AATTTAAACC
19901679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19901707 GATAACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19904467 original size:14 final size:14
Alignment explanation
Indices: 19904448--19904481 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19904438 ACAAAAAAAA
19904448 AAAAAGAGAA-AGAG
1 AAAAAGA-AAGAGAG
19904462 AAAAAGAAAGAGAG
1 AAAAAGAAAGAGAG
19904476 AAAAAG
1 AAAAAG
19904482 GTGTGGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAGAG
Found at i:19911380 original size:19 final size:20
Alignment explanation
Indices: 19911340--19911382 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19911330 TTTATTGTTC
*
19911340 AAGGACAAAACTAAAAAGGA
1 AAGGAAAAAACTAAAAAGGA
19911360 AAGGAAAAAAC-AAGAAA-GA
1 AAGGAAAAAACTAA-AAAGGA
19911379 AAGG
1 AAGG
19911383 TTACCACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.07, G:0.23, T:0.02
Consensus pattern (20 bp):
AAGGAAAAAACTAAAAAGGA
Found at i:19914002 original size:38 final size:38
Alignment explanation
Indices: 19913958--19914031 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
19913948 CACATTCTGG
*
19913958 GTAAAAGAACAATCAATATTGAAATGCATAGTATTCGC
1 GTAAAAGAACAATCAATATTAAAATGCATAGTATTCGC
*
19913996 GTAAAAGAACAATTAATATTAAAATGCATAGTATTC
1 GTAAAAGAACAATCAATATTAAAATGCATAGTATTC
19914032 TATTTTGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (38 bp):
GTAAAAGAACAATCAATATTAAAATGCATAGTATTCGC
Found at i:19914858 original size:25 final size:25
Alignment explanation
Indices: 19914815--19914929 Score: 134
Period size: 25 Copynumber: 4.7 Consensus size: 25
19914805 TTAATAATTG
19914815 ATAA-TTAATATTAATA-TTTATTT
1 ATAATTTAATATTAATATTTTATTT
*
19914838 ATAATTTAATCATTAACATTTTA---
1 ATAATTTAAT-ATTAATATTTTATTT
19914861 A-AATATTAATATTAATATTTTATTT
1 ATAAT-TTAATATTAATATTTTATTT
*
19914886 ATAATTTAAAATTAATATTTTATTT
1 ATAATTTAATATTAATATTTTATTT
19914911 ATAATTTAAAATATTAATA
1 ATAATTT--AATATTAATA
19914930 ATTGATAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
22 14 0.18
23 10 0.13
24 5 0.06
25 33 0.42
26 7 0.09
27 9 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTTAATATTAATATTTTATTT
Found at i:19914874 original size:22 final size:22
Alignment explanation
Indices: 19914835--19914882 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19914825 TTAATATTTA
*
19914835 TTTATAATTTAATCATTAACAT
1 TTTAAAATTTAATCATTAACAT
*
19914857 TTTAAAATATTAAT-ATTAATAT
1 TTTAAAAT-TTAATCATTAACAT
19914879 TTTA
1 TTTA
19914883 TTTATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAATTTAATCATTAACAT
Found at i:19914874 original size:47 final size:47
Alignment explanation
Indices: 19914818--19914907 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
19914808 ATAATTGATA
*
19914818 ATTAATATTAATA-TTTATTTATAATTTAATCATTAACATTTTAAAAT
1 ATTAATATTAATATTTTATTTATAATTTAA-AATTAACATTTTAAAAT
*
19914865 ATTAATATTAATATTTTATTTATAATTTAAAATTAATATTTTA
1 ATTAATATTAATATTTTATTTATAATTTAAAATTAACATTTTA
19914908 TTTATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
47 24 0.60
48 16 0.40
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (47 bp):
ATTAATATTAATATTTTATTTATAATTTAAAATTAACATTTTAAAAT
Found at i:19914929 original size:58 final size:57
Alignment explanation
Indices: 19914857--19914972 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 57
19914847 TCATTAACAT
*
19914857 TTTAAAATATTAAT-ATTAAT-ATT-TTATTTATAATTTAAAATTAATATTTTATTTATAA
1 TTTAAAATATTAATAATTAATAATTATT-TTTA-AATTTAAAA-TAATAATTT-TTTATAA
* *
19914915 TTTAAAATATTAATAATTGATAATTATTTTTAAATTTAAAATATTAATTTTTTATAA
1 TTTAAAATATTAATAATTAATAATTATTTTTAAATTTAAAATAATAATTTTTTATAA
19914972 T
1 T
19914973 ATATTATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
57 8 0.15
58 21 0.40
59 14 0.27
60 7 0.13
61 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (57 bp):
TTTAAAATATTAATAATTAATAATTATTTTTAAATTTAAAATAATAATTTTTTATAA
Done.