Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 52 of 208
Found at i:20160994 original size:30 final size:30
Alignment explanation
Indices: 20160960--20161021 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
20160950 TGATACTATT
* *
20160960 AACATTTAATGTCTGATTCAGTGATCGTTA
1 AACATTTAATGTCTGATCCAGTGATCATTA
*
20160990 AACATTTAATGTTTGATCCAGTGATCATTA
1 AACATTTAATGTCTGATCCAGTGATCATTA
20161020 AA
1 AA
20161022 GTTAGTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (30 bp):
AACATTTAATGTCTGATCCAGTGATCATTA
Found at i:20161094 original size:21 final size:21
Alignment explanation
Indices: 20161065--20161106 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20161055 GATACCTGGT
*
20161065 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGACACTTTTTG
*
20161086 AAAATGTATCGACACTTTTTG
1 AAAAGGTATCGACACTTTTTG
20161107 TAATTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGACACTTTTTG
Found at i:20187095 original size:18 final size:18
Alignment explanation
Indices: 20187068--20187160 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
20187058 TACGACCGTT
20187068 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
20187086 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
20187104 TACAGTACTATTTACGTA
1 TACGGTACTATTCACGTA
**
20187122 TACGACACTATTCACGTA
1 TACGGTACTATTCACGTA
*
20187140 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
20187158 TAC
1 TAC
20187161 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:20193799 original size:116 final size:115
Alignment explanation
Indices: 20193670--20194007 Score: 525
Period size: 119 Copynumber: 3.0 Consensus size: 115
20193660 TTTTATATTT
20193670 TTCTCTCAGCACTCTACAATTTTTATTTTTTTACTTATTATTAATAATTATTATTTTAAAAAATT
1 TTCTCTCAGCACTCTACAATTTTTATTTTTTTACTTATTATTAATAATTATTATTTTAAAAAATT
20193735 AAAATT-TTCTTTTTGGTGTTTCATAAGACTACTTTATAATAATAAAAAAAA
66 -AAATTGTTCTTTTTGGTGTTTCATAAGACTACTTT-TAATAATAAAAAAAA
*
20193786 TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTATTTAAAAAA
1 TTCTCTCAGCACTCTACAATTTTTA--TTT-TTTTACTTATTATTAATAATTATTATTTTAAAAA
* *
20193851 ATTAAATTGTTCTTTTTGGTGTTTCATAAGACTAC-TTT-CTAATAAAAAATA
63 ATTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTTAATAATAAAAAAAA
20193902 TTCTCTCAGCACTCTACAA----T-TTTTTTTACTTATTATTAATAATTATTA-TTTAAAAAATT
1 TTCTCTCAGCACTCTACAATTTTTATTTTTTTACTTATTATTAATAATTATTATTTTAAAAAATT
20193961 AAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAA-AAAAA
66 AAATTGTTCTTTTTGGTGTTTCATAAGACTACTTT-TAATAATAAAAA
20194008 TAACAATTTA
Statistics
Matches: 210, Mismatches: 5, Indels: 21
0.89 0.02 0.09
Matches are distributed among these distances:
107 42 0.20
108 27 0.13
109 9 0.04
110 3 0.01
112 1 0.00
116 55 0.26
117 1 0.00
118 10 0.05
119 62 0.30
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (115 bp):
TTCTCTCAGCACTCTACAATTTTTATTTTTTTACTTATTATTAATAATTATTATTTTAAAAAATT
AAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTTAATAATAAAAAAAA
Found at i:20213358 original size:12 final size:12
Alignment explanation
Indices: 20213341--20213365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20213331 AAAAATTAAT
20213341 TTTAATTATTCA
1 TTTAATTATTCA
20213353 TTTAATTATTCA
1 TTTAATTATTCA
20213365 T
1 T
20213366 CTTTTTTAAT
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAATTATTCA
Found at i:20214290 original size:22 final size:22
Alignment explanation
Indices: 20214263--20214330 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
20214253 ATTTTGAAAA
*
20214263 ATTATTTATTTATAATTTTAAT
1 ATTATTTATTAATAATTTTAAT
* * *
20214285 ATTATTAATATGAT-ATTTTTAT
1 ATTATTTAT-TAATAATTTTAAT
* *
20214307 TTTATTTCTTAATAATTTTAAT
1 ATTATTTATTAATAATTTTAAT
20214329 AT
1 AT
20214331 GTTAATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
ATTATTTATTAATAATTTTAAT
Found at i:20214319 original size:35 final size:36
Alignment explanation
Indices: 20214262--20214341 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
20214252 AATTTTGAAA
20214262 AATTATTTATTTATAATTTTAAT-ATTATTAATATGAT
1 AATT-TTTATTTATAATTTTAATAATT-TTAATATGAT
* *
20214299 -ATTTTTATTT-TATTTCTTAATAATTTTAATATGTT
1 AATTTTTATTTATAATT-TTAATAATTTTAATATGAT
20214334 AATTTTTA
1 AATTTTTA
20214342 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 4 0.11
35 21 0.55
36 13 0.34
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (36 bp):
AATTTTTATTTATAATTTTAATAATTTTAATATGAT
Found at i:20219026 original size:21 final size:22
Alignment explanation
Indices: 20218966--20219029 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
20218956 CAGAAGCAGT
* *
20218966 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
20218988 A-ACGACACACT-T-GATGCCT-A
1 ATACGACACA-TATAG-TGCCTGA
20219008 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
20219030 TCCGCAAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:20221343 original size:47 final size:47
Alignment explanation
Indices: 20221292--20221387 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
20221282 TTTTGTAGTG
* *
20221292 TTAATTATATTTTTTAATCAAACAATATAAGTAATATAAAATATTGT
1 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
20221339 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
1 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
20221386 TT
1 TT
20221388 GAAGACCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (47 bp):
TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
Found at i:20227386 original size:137 final size:137
Alignment explanation
Indices: 20227224--20227498 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
20227214 TGGCATTCTC
20227224 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
* * **
20227289 TTTGTGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTTTAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
20227354 TATTTTA
131 TATTTTA
20227361 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
20227426 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
20227491 TATTTTA
131 TATTTTA
20227498 T
1 T
20227499 GTGTGAAATT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (137 bp):
TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
TATTTTA
Found at i:20242676 original size:136 final size:137
Alignment explanation
Indices: 20242515--20242788 Score: 514
Period size: 136 Copynumber: 2.0 Consensus size: 137
20242505 TGGCATTCTC
20242515 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
* * *
20242580 TTTGTGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTT-TAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
20242644 TATTTTA
131 TATTTTA
20242651 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
20242716 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
20242781 TATTTTA
131 TATTTTA
20242788 T
1 T
20242789 GTGTGAAATT
Statistics
Matches: 134, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 116 0.87
137 18 0.13
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (137 bp):
TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
TATTTTA
Found at i:20250076 original size:18 final size:18
Alignment explanation
Indices: 20250055--20250094 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20250045 CGAAGTGTTG
* *
20250055 GAGGATGATGGTGATGAT
1 GAGGACGATGGCGATGAT
20250073 GAGGACGATGGCGATGAT
1 GAGGACGATGGCGATGAT
20250091 GAGG
1 GAGG
20250095 GTGGTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.47, T:0.20
Consensus pattern (18 bp):
GAGGACGATGGCGATGAT
Found at i:20259073 original size:14 final size:14
Alignment explanation
Indices: 20259053--20259090 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20259043 CTTTAGGATC
20259053 ATTATAATTTTAAA
1 ATTATAATTTTAAA
* *
20259067 TTTATAATTATAAA
1 ATTATAATTTTAAA
20259081 ATTAT-ATTTT
1 ATTATAATTTT
20259091 GATCCCTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATAATTTTAAA
Found at i:20259274 original size:19 final size:20
Alignment explanation
Indices: 20259236--20259281 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
20259226 GACAAATTAT
* *
20259236 ATATTATAATATATATTTTA
1 ATATTATAATATAGACTTTA
20259256 ATATTA-AATATAGACTTTA
1 ATATTATAATATAGACTTTA
*
20259275 ATGTTAT
1 ATATTAT
20259282 TTAAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (20 bp):
ATATTATAATATAGACTTTA
Found at i:20259928 original size:20 final size:20
Alignment explanation
Indices: 20259903--20259983 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
20259893 ATTTAATTAT
20259903 AAAAATTAT-AAAAAGTCATA
1 AAAAATTATCAAAAA-TCATA
*
20259923 AAAAATTATCAAAAACCATA
1 AAAAATTATCAAAAATCATA
* *
20259943 TAAAATTAT-AAATAATCAGA
1 AAAAATTATCAAA-AATCATA
* *
20259963 TAAAATTATCAAAAATAATA
1 AAAAATTATCAAAAATCATA
20259983 A
1 A
20259984 TAATTACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.06
20 40 0.78
21 8 0.16
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATCAAAAATCATA
Found at i:20260094 original size:16 final size:16
Alignment explanation
Indices: 20260048--20260094 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
20260038 AAAGATATAA
20260048 ATAAATCTAATAAAAT
1 ATAAATCTAATAAAAT
* * *
20260064 ATAATTGTAAAAAAAT
1 ATAAATCTAATAAAAT
20260080 ATAAAAT-TAATAAAA
1 AT-AAATCTAATAAAA
20260095 CATATTTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAAATCTAATAAAAT
Found at i:20260610 original size:9 final size:9
Alignment explanation
Indices: 20260596--20260745 Score: 56
Period size: 9 Copynumber: 16.0 Consensus size: 9
20260586 TATATCGATG
20260596 TTAATATTT
1 TTAATATTT
20260605 TTAATATTT
1 TTAATATTT
* *
20260614 TTCAAGAATT
1 TT-AATATTT
*
20260624 CTAATATGTT
1 TTAATAT-TT
**
20260634 TTTTTATTT
1 TTAATATTT
*
20260643 TAAATATTT
1 TTAATATTT
* *
20260652 TAAATAGGTT
1 TTAATA-TTT
20260662 TTATATAGTTT
1 TTA-ATA-TTT
20260673 ATTAGAT-TTT
1 -TTA-ATATTT
20260683 TT-ATATTT
1 TTAATATTT
*
20260691 TT-ATAATAT
1 TTAAT-ATTT
**
20260700 TT-ATAAGT
1 TTAATATTT
*
20260708 TTAATAATT
1 TTAATATTT
**
20260717 TTATATAAAAT
1 TTA-AT-ATTT
20260728 TTAATATTT
1 TTAATATTT
20260737 TTAATATTT
1 TTAATATTT
20260746 ATTTATTATA
Statistics
Matches: 109, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 56 0.51
10 23 0.21
11 12 0.11
12 5 0.05
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (9 bp):
TTAATATTT
Found at i:20260745 original size:28 final size:26
Alignment explanation
Indices: 20260678--20260745 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
20260668 AGTTTATTAG
* *
20260678 ATTTTTTATATTTTTATAATATTTAT
1 ATTTTTAATATTTTTATAAAATTTAT
**
20260704 AAGTTTAATAATTTTATATAAAATTTAAT
1 ATTTTTAAT-ATTTT-TATAAAATTT-AT
20260733 ATTTTTAATATTT
1 ATTTTTAATATTT
20260746 ATTTATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.18
27 5 0.15
28 13 0.39
29 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
ATTTTTAATATTTTTATAAAATTTAT
Found at i:20281612 original size:55 final size:56
Alignment explanation
Indices: 20281528--20281707 Score: 145
Period size: 58 Copynumber: 3.2 Consensus size: 56
20281518 CATTTTGGGA
* * * *
20281528 CTTGAACTTGACAAATTTTTTCATATTGGGG-TCT-AATTTTTTGTCCAAGTTAGGT
1 CTTGAACTTGACAAATTTCTTCATATTGGGGCT-TAAATTTTTTATCCAAGTCAGGC
*
20281583 CTTGAACTTGATAAATATTCTT-ATATTGGGGCTTGAAAATTTTTTATCCAAGTCAGGC
1 CTTGAACTTGACAAAT-TTCTTCATATTGGGGCTT--AAATTTTTTATCCAAGTCAGGC
* ** * * * *
20281641 CTTGAACTT-AGCAAATATCCCCACATTGAGGCTTGAAATTTTTT-TGCCCAAGTTAGGG
1 CTTGAACTTGA-CAAATTTCTTCATATTGGGGCTT-AAATTTTTTAT--CCAAGTCAGGC
20281699 CTTGAACTT
1 CTTGAACTT
20281708 AGCAAATATT
Statistics
Matches: 102, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
55 25 0.25
56 6 0.06
57 12 0.12
58 59 0.58
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (56 bp):
CTTGAACTTGACAAATTTCTTCATATTGGGGCTTAAATTTTTTATCCAAGTCAGGC
Found at i:20281645 original size:58 final size:58
Alignment explanation
Indices: 20281562--20281716 Score: 186
Period size: 58 Copynumber: 2.7 Consensus size: 58
20281552 ATTGGGGTCT
* * * ** * *
20281562 AATTTTTTGTCCAAGTTAGGTCTTGAACTT-GATAAATATTCTTATATTGGGGCTTGAA
1 AATTTTTTGTCCAAGTTAGGCCTTGAACTTAG-CAAATATCCCCACATTGAGGCTTGAA
* *
20281620 AATTTTTTATCCAAGTCAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAA
1 AATTTTTTGTCCAAGTTAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAA
* * *
20281678 ATTTTTTTGCCCAAGTTAGGGCTTGAACTTAGCAAATAT
1 AATTTTTTGTCCAAGTTAGGCCTTGAACTTAGCAAATAT
20281717 TCCTAAAGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 81 0.99
59 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (58 bp):
AATTTTTTGTCCAAGTTAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAA
Found at i:20301893 original size:32 final size:31
Alignment explanation
Indices: 20301831--20301924 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
20301821 AGGCAAATTA
*
20301831 CAAGAGTAATTGAATCTTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
20301862 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
* * *
20301894 AAAGAGTAAATGAATTCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
20301925 AAAATTATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 30 0.52
32 28 0.48
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:20305105 original size:19 final size:18
Alignment explanation
Indices: 20305065--20305124 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
20305055 GGTAGGCAAC
**
20305065 TTTT-TTTTTTTGCGCTT
1 TTTTGTTTTTTTGCTTTT
*
20305082 GTTTGCTTTTTTTGCTTTT
1 TTTTG-TTTTTTTGCTTTT
20305101 TTTTGTTGTTTTTGCTGTTT
1 TTTTGTT-TTTTTGCT-TTT
20305121 TTTT
1 TTTT
20305125 TTTGCTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 23 0.66
20 7 0.20
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTTTTGCTTTT
Found at i:20305772 original size:31 final size:31
Alignment explanation
Indices: 20305679--20305774 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
20305669 GGCAAATTAC
*
20305679 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
*
20305710 AAGAATAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
20305742 AAGAGTAATTGAATTCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
20305773 AA
1 AA
20305775 ACTATCTAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:20311288 original size:23 final size:24
Alignment explanation
Indices: 20311262--20311306 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
20311252 TTTTTTTAAA
*
20311262 AAAAATTTGATGATA-TAATTTTT
1 AAAAATTTGATGAGATTAATTTTT
* *
20311285 AAAATTTTTATGAGATTAATTT
1 AAAAATTTGATGAGATTAATTT
20311307 ACCAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATTTGATGAGATTAATTTTT
Found at i:20313917 original size:17 final size:18
Alignment explanation
Indices: 20313895--20313929 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20313885 GGTGGATAAG
20313895 AAATAATGCCTA-TTTTT
1 AAATAATGCCTAGTTTTT
20313912 AAATAATGCCTAGTTTTT
1 AAATAATGCCTAGTTTTT
20313930 TTAGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (18 bp):
AAATAATGCCTAGTTTTT
Found at i:20334695 original size:80 final size:80
Alignment explanation
Indices: 20334599--20334758 Score: 266
Period size: 80 Copynumber: 2.0 Consensus size: 80
20334589 GTCCGGCTCG
*
20334599 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGCTTGGGCAA
1 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGCTTGAGCAA
* *
20334664 AAAAACGAGGCCCGT
66 AAAAAAGAGACCCGT
** *
20334679 ACGGCCTGCCTGAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGTTTGAGCAA
1 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGCTTGAGCAA
20334744 AAAAAAGAGACCCGT
66 AAAAAAGAGACCCGT
20334759 TTAAAAAACG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.17
Consensus pattern (80 bp):
ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGCTTGAGCAA
AAAAAAGAGACCCGT
Found at i:20334863 original size:14 final size:14
Alignment explanation
Indices: 20334839--20334882 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
20334829 TAAATATATA
20334839 TTTTA-TTTTTATT
1 TTTTATTTTTTATT
20334852 TTTTATTTTTTAATT
1 TTTTATTTTTT-ATT
* *
20334867 TTTAATTTTTAATT
1 TTTTATTTTTTATT
20334881 TT
1 TT
20334883 AAAATACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
15 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTATTTTTTATT
Found at i:20334884 original size:6 final size:7
Alignment explanation
Indices: 20334839--20334882 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
20334829 TAAATATATA
20334839 TTTT-AT
1 TTTTAAT
*
20334845 TTTTATT
1 TTTTAAT
*
20334852 TTTTATT
1 TTTTAAT
20334859 TTTTAAT
1 TTTTAAT
20334866 TTTTAAT
1 TTTTAAT
20334873 TTTTAAT
1 TTTTAAT
20334880 TTT
1 TTT
20334883 AAAATACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTAAT
Found at i:20334954 original size:67 final size:64
Alignment explanation
Indices: 20334829--20334955 Score: 141
Period size: 67 Copynumber: 1.9 Consensus size: 64
20334819 TCGAATATAA
* * **
20334829 TAAATATATATTTTATTTTTATTTTTTATTTTTTAATTTTTAATTTTTAATTTTAAAATACTTT
1 TAAATATATATTTTATTTTTATTTTTTATTTTTTAATTTTTAAATGTTAATTAAAAAATACTTT
* *
20334893 TAAA-ATAT-TTTTATTTTTATTTTATTATTTTTAAAATAATTTTTTAATGTTTATTAAAAAATA
1 TAAATATATATTTTATTTTTATTTT-TTATTTTT----TAATTTTTAAATGTTAATTAAAAAATA
20334956 GGCCGGGCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
62 15 0.29
63 12 0.23
64 4 0.08
67 21 0.40
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (64 bp):
TAAATATATATTTTATTTTTATTTTTTATTTTTTAATTTTTAAATGTTAATTAAAAAATACTTT
Found at i:20339754 original size:5 final size:5
Alignment explanation
Indices: 20339746--20339776 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
20339736 ATAAATAAGT
20339746 TATTA TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
20339777 TATATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:20339859 original size:16 final size:19
Alignment explanation
Indices: 20339816--20339866 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
20339806 ATGGAAATTG
20339816 AAACGAAAACAGAGAAGCAA
1 AAACGAAAA-AGAGAAGCAA
20339836 AAACGAAAAAGA-AAG-AA
1 AAACGAAAAAGAGAAGCAA
20339853 AAA-GAAAAAGAGAA
1 AAACGAAAAAGAGAA
20339867 AGAAGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
18 3 0.10
19 3 0.10
20 9 0.30
ACGTcount: A:0.73, C:0.08, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAGCAA
Found at i:20339866 original size:18 final size:19
Alignment explanation
Indices: 20339816--20339870 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
20339806 ATGGAAATTG
20339816 AAACGAAAACAGAG-AAGCAA
1 AAACGAAAA-AGAGAAAG-AA
20339836 AAACG-AAAA-AGAAAGAA
1 AAACGAAAAAGAGAAAGAA
20339853 AAA-GAAAAAGAGAAAGAA
1 AAACGAAAAAGAGAAAGAA
20339871 GGAAGCCCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 11 0.34
18 12 0.38
19 3 0.09
20 5 0.16
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAAGAA
Found at i:20340802 original size:27 final size:25
Alignment explanation
Indices: 20340746--20340803 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20340736 ACTTTAGTGC
* * *
20340746 GCTCTCTGATTATTAGCATGCTGGT
1 GCTCTCTGATTACTAGCACGCAGGT
20340771 GCTCTCTGATTACTAGCACGTCA-GT
1 GCTCTCTGATTACTAGCACG-CAGGT
*
20340796 GTTCTCTG
1 GCTCTCTG
20340804 TTTAGCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGCAGGT
Found at i:20340818 original size:22 final size:22
Alignment explanation
Indices: 20340784--20340827 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20340774 CTCTGATTAC
20340784 TAGCACGTCAGTGTTCTCTGTT
1 TAGCACGTCAGTGTTCTCTGTT
* *
20340806 TAGCACTTTAGTGTTCTCTGTT
1 TAGCACGTCAGTGTTCTCTGTT
20340828 CATTAGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (22 bp):
TAGCACGTCAGTGTTCTCTGTT
Found at i:20341919 original size:17 final size:17
Alignment explanation
Indices: 20341897--20341935 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20341887 TGCGGATGAA
*
20341897 AAATGCCCTTGGCTGAT
1 AAATGCCCTTGACTGAT
* *
20341914 AAATGCTCTTGACTGGT
1 AAATGCCCTTGACTGAT
20341931 AAATG
1 AAATG
20341936 GACCTCGTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (17 bp):
AAATGCCCTTGACTGAT
Found at i:20347147 original size:37 final size:36
Alignment explanation
Indices: 20347071--20347144 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
20347061 TTAGTTCAGT
*
20347071 TTCACTTTTTCACTTTCAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCACAATTCAATT-AAAA
*
20347108 TTCACTTTTCCATTTTTCAAGTCA-ATATTCAATTAAA
1 TTCACTTTTCCA-CTTTCAA-TCACA-ATTCAATTAAA
20347145 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 11 0.34
38 10 0.31
39 11 0.34
ACGTcount: A:0.34, C:0.22, G:0.01, T:0.43
Consensus pattern (36 bp):
TTCACTTTTCCACTTTCAATCACAATTCAATTAAAA
Found at i:20347474 original size:21 final size:23
Alignment explanation
Indices: 20347445--20347486 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20347435 TCGAAATAGC
*
20347445 TTCTGTTCTTTTTC-TTATTTGT
1 TTCTGTTCTTTTACTTTATTTGT
20347467 TTCT-TTCTTTTACTTTATTT
1 TTCTGTTCTTTTACTTTATTT
20347487 TATTTGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (23 bp):
TTCTGTTCTTTTACTTTATTTGT
Found at i:20351892 original size:40 final size:40
Alignment explanation
Indices: 20351814--20351924 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
20351804 ATAAGAATAT
* *
20351814 GTATGTGTATATAAATTATATGAAAATATAAAACATATAA
1 GTATGTGTATATAAATTATAAGAAAATAAAAAACATATAA
* **
20351854 GTATGTGTATAT-ATTTATAAG-AAATAAAAAATGTATATA
1 GTATGTGTATATAAATTATAAGAAAATAAAAAACATATA-A
*
20351893 GATATATAG-ATATAAATTATAA-AAAATAAAAA
1 G-TATGT-GTATATAAATTATAAGAAAATAAAAA
20351925 TATAACAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
38 13 0.22
39 9 0.15
40 20 0.34
41 17 0.29
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.34
Consensus pattern (40 bp):
GTATGTGTATATAAATTATAAGAAAATAAAAAACATATAA
Found at i:20352021 original size:21 final size:22
Alignment explanation
Indices: 20351985--20352027 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20351975 TAAATGAGCA
20351985 AATAACAGTAATAATAATTAAT
1 AATAACAGTAATAATAATTAAT
*
20352007 AATAACAGT-ATAATATTTAAT
1 AATAACAGTAATAATAATTAAT
20352028 TTATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
AATAACAGTAATAATAATTAAT
Found at i:20355360 original size:67 final size:67
Alignment explanation
Indices: 20355239--20355370 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
20355229 TTTTCAATTC
* * *
20355239 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGCTTACCAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCTG
20355304 CA
66 CA
* * *
20355306 AGAGTGCACCCTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCTG
20355371 TAATATAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:20364618 original size:6 final size:6
Alignment explanation
Indices: 20364607--20364631 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20364597 AAAAATATAA
20364607 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
20364632 TATATTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:20379412 original size:34 final size:35
Alignment explanation
Indices: 20379354--20379420 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
20379344 CAAATATCAG
20379354 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
20379389 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
20379421 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20385897 original size:16 final size:16
Alignment explanation
Indices: 20385876--20385916 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
20385866 CATCTATAAT
*
20385876 ACACACACA-GACACAG
1 ACACACACATG-CACAC
20385892 ACACACACATGCACAC
1 ACACACACATGCACAC
20385908 ACACACACA
1 ACACACACA
20385917 CGGAGTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.41, G:0.07, T:0.02
Consensus pattern (16 bp):
ACACACACATGCACAC
Found at i:20388345 original size:21 final size:21
Alignment explanation
Indices: 20388319--20388384 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
20388309 GATCTGATAG
20388319 GAGATTATACGAAGAATATAA
1 GAGATTATACGAAGAATATAA
* * * *
20388340 GAGATTATATGAAG-CT-GAG
1 GAGATTATACGAAGAATATAA
20388359 GAGATTATACGAAGAATATAA
1 GAGATTATACGAAGAATATAA
20388380 GAGAT
1 GAGAT
20388385 ACGAACAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 14 0.40
20 2 0.06
21 19 0.54
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (21 bp):
GAGATTATACGAAGAATATAA
Found at i:20394282 original size:99 final size:99
Alignment explanation
Indices: 20394092--20394387 Score: 502
Period size: 99 Copynumber: 3.0 Consensus size: 99
20394082 GGCGAAAGCC
* * * *
20394092 GCATCCTCTTTGCTGCTGGTTGCTCGGATAACTCTGCCAGAGAATCATTGACAATGATGGCCTCC
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGAC---GATAGCCTCC
20394157 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
63 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
* *
20394194 GCATCCTCTTTGCTGCCAGTTGCTCAGATAATTCTGCAAGAGAATCATTGACGATAGCCTCCTTG
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGACGATAGCCTCCTTG
20394259 TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
66 TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
*
20394293 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGACAATAGCCTCCTTG
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGACGATAGCCTCCTTG
20394358 TTTTCAGCCACTTCAGAATCTTGATTCAAT
66 TTTTCAGCCACTTCAGAATCTTGATTCAAT
20394388 GCTTCAGCCA
Statistics
Matches: 185, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
99 138 0.75
102 47 0.25
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (99 bp):
GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGACGATAGCCTCCTTG
TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
Found at i:20408182 original size:20 final size:20
Alignment explanation
Indices: 20408133--20408187 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
20408123 AAATCATTGC
20408133 AATATATGTAAAAACAATTT
1 AATATATGTAAAAACAATTT
* *
20408153 AA-A-ATATAAAAA-ATTATT
1 AATATATGTAAAAACAAT-TT
20408171 AATATATGTAAAAACAA
1 AATATATGTAAAAACAA
20408188 ATTTCTGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
19 2 0.07
20 10 0.37
21 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (20 bp):
AATATATGTAAAAACAATTT
Found at i:20408231 original size:32 final size:32
Alignment explanation
Indices: 20408195--20408269 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
20408185 CAAATTTCTG
* * *
20408195 GAAAATATTTT-CAGGAAATCTATCAAACAGCA
1 GAAAATATTTTACA-CAAATCAATCAAACACCA
* *
20408227 GAAAATATTTTACACAATTCAATCAAATACCA
1 GAAAATATTTTACACAAATCAATCAAACACCA
20408259 GAAAATATTTT
1 GAAAATATTTT
20408270 TCAATAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (32 bp):
GAAAATATTTTACACAAATCAATCAAACACCA
Found at i:20408313 original size:34 final size:34
Alignment explanation
Indices: 20408260--20408325 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
20408250 CAAATACCAG
*
20408260 AAAATATTTTTCAATAAATCATTTTACAGAAAAGT
1 AAAATATTTTTCAAGAAATCATTTTAC-GAAAAGT
*
20408295 AAAATA-TTTTCCAGAAATCATTTTACGAAAA
1 AAAATATTTTTCAAGAAATCATTTTACGAAAA
20408326 ACATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 18 0.62
35 6 0.21
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (34 bp):
AAAATATTTTTCAAGAAATCATTTTACGAAAAGT
Found at i:20408614 original size:17 final size:18
Alignment explanation
Indices: 20408580--20408614 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20408570 CTAAATTTTG
20408580 AAATCTAAAAAGTAAAAA
1 AAATCTAAAAAGTAAAAA
*
20408598 AAATCTTAAAA-TAAAAA
1 AAATCTAAAAAGTAAAAA
20408615 TATAAAAACT
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:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATCTAAAAAGTAAAAA
Found at i:20411610 original size:21 final size:22
Alignment explanation
Indices: 20411585--20411626 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
20411575 TCATTGGCTC
20411585 ATAC-TCTCTTAAGCAAATTGG
1 ATACTTCTCTTAAGCAAATTGG
*
20411606 ATACTTTCTCTTAAGCGAATT
1 ATAC-TTCTCTTAAGCAAATT
20411627 TTGATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (22 bp):
ATACTTCTCTTAAGCAAATTGG
Found at i:20417451 original size:14 final size:15
Alignment explanation
Indices: 20417424--20417452 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20417414 CAATTATATG
20417424 TTATAAAAATGTTAT
1 TTATAAAAATGTTAT
20417439 TTATAAAAA-GTTAT
1 TTATAAAAATGTTAT
20417453 GGCCAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
TTATAAAAATGTTAT
Found at i:20422136 original size:15 final size:15
Alignment explanation
Indices: 20422118--20422147 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20422108 ATATTATAAT
*
20422118 TATAATAAAATAAAG
1 TATAATAAAAGAAAG
20422133 TATAATAAAAGAAAG
1 TATAATAAAAGAAAG
20422148 AGAACATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
TATAATAAAAGAAAG
Found at i:20437706 original size:6 final size:7
Alignment explanation
Indices: 20437687--20437715 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
20437677 GATTTATCTT
20437687 TTAAAAA
1 TTAAAAA
20437694 TTAAAAA
1 TTAAAAA
20437701 TTAAAAA
1 TTAAAAA
20437708 TTAAAAA
1 TTAAAAA
20437715 T
1 T
20437716 ATAAGAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:20454047 original size:20 final size:20
Alignment explanation
Indices: 20454022--20454074 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
20454012 TTAATAATGA
*
20454022 TAAAAAAATAAGTTAATCTT
1 TAAAAAAATAAGTTAATATT
*
20454042 TAAAAAAATTAATTTAATATT
1 TAAAAAAA-TAAGTTAATATT
20454063 TAAAAAATATAA
1 TAAAAAA-ATAA
20454075 ATATATAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAAATAAGTTAATATT
Found at i:20455151 original size:102 final size:105
Alignment explanation
Indices: 20454936--20455206 Score: 370
Period size: 104 Copynumber: 2.6 Consensus size: 105
20454926 CGGGGCCAAA
* *
20454936 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCAACACCCCTTTTCTACAATAA
1 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAA-AA
* * * * *
20455001 TTTTTTTTTTTACTTTTGGTGTGTCAATAGTCGGCACCAGT
65 TTATTTTTTTTACTTTTGGTCTGTCAATAGCCAGAACCAGT
* * * *
20455042 ATACGAAAAAAGT-AAAAAAAATTT-GATGGCCTCGCAATGGCCGGCACCCCCTTTATACAAAA-
1 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAAT
* * *
20455104 TATTTTTTTTCCTTTTGGTCTTTCAATGGCCAGAACCAGT
66 TATTTTTTTTACTTTTGGTCTGTCAATAGCCAGAACCAGT
*
20455144 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGTCGACA-CCCCTTTCTACAAAA
1 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAA
20455207 AAAAATTTAC
Statistics
Matches: 144, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
102 45 0.31
103 27 0.19
104 48 0.33
105 11 0.08
106 13 0.09
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (105 bp):
ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAAT
TATTTTTTTTACTTTTGGTCTGTCAATAGCCAGAACCAGT
Found at i:20455327 original size:104 final size:104
Alignment explanation
Indices: 20455212--20455458 Score: 252
Period size: 104 Copynumber: 2.4 Consensus size: 104
20455202 CAAAAAAAAA
* **** * *
20455212 TTTACTTTTTTCGTATACTGGTGCTGACCATTGACAGACA-AAAAGT-AATTTTTTTTTGTATAA
1 TTTACTTTTTTCGTATACTGGTGCCGACCATTGACAGACACAAAAGTAAAAAAATTATTGTAGAA
* *
20455275 AGGGGGTGCCAACCATTGTCAGGCCATCCCCCCAA-TTTTTT
66 AGGGGGTGCCAACCATTGCCAGGCCA---CCCAAATTTTTTT
* * * * *
20455316 TTTACTTTTTTCGTATACTAGTGCCGGCTATTAACACA-ACAAAAGTAAAAAAAATTATTGTAGA
1 TTTACTTTTTTCGTATACTGGTGCCGACCATTGACAGACACAAAAGT-AAAAAAATTATTGTAGA
**
20455380 AAGGGGGTGCCGGCCATTGCCAGGCCACCCAAATTTTTTT
65 AAGGGGGTGCCAACCATTGCCAGGCCACCCAAATTTTTTT
* *
20455420 TTTACTTTTTTCGTATTCTGGTGCGGGA-CATTGACAGAC
1 TTTACTTTTTTCGTATACTGGTGC-CGACCATTGACAGAC
20455459 CAACACTCAA
Statistics
Matches: 114, Mismatches: 23, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
103 6 0.05
104 73 0.64
105 1 0.01
106 34 0.30
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (104 bp):
TTTACTTTTTTCGTATACTGGTGCCGACCATTGACAGACACAAAAGTAAAAAAATTATTGTAGAA
AGGGGGTGCCAACCATTGCCAGGCCACCCAAATTTTTTT
Found at i:20455472 original size:106 final size:104
Alignment explanation
Indices: 20455265--20455530 Score: 259
Period size: 106 Copynumber: 2.5 Consensus size: 104
20455255 AGTAATTTTT
** * *
20455265 TTTTGTATAAAGGGGGTGCCAACCATTGTCAGGCCATCCCCCCAATTTTTTTTTACTTTTTTCGT
1 TTTTGTATAAAGGGGGTGCCGGCCATTGCCAGGCCA--CCCCAAATTTTTTTTTACTTTTTTCGT
*
20455330 ATACTAGTGCCGGCTATTAACACAACAAAAGT-AAAAAAAA
64 ATACTAGTGCCGGCTATTAACACAACAAAACTAAAAAAAAA
*
20455370 TTATTGTAGAAAGGGGGTGCCGGCCATTGCCAGGCCA-CCCAAATTTTTTTTTTACTTTTTTCGT
1 TT-TTGTATAAAGGGGGTGCCGGCCATTGCCAGGCCACCCCAAA-TTTTTTTTTACTTTTTTCGT
* * * * * * *
20455434 ATTCTGGTGCGGGAC-ATTGACAGACCAACACTCAAAAAAAAAA
64 ATACTAGTGCCGG-CTATTAACACAACAAAACT--AAAAAAAAA
* * * * * *
20455477 TTTCGTATAATGGGGGTGTCGGCCATTGACAAGCCAGCACCCAAAATTTTTTTT
1 TTTTGTATAAAGGGGGTGCCGGCCATTGCCAGGCCA-C-CCCAAATTTTTTTTT
20455531 CCCGTTTTCT
Statistics
Matches: 132, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
103 5 0.04
104 42 0.32
105 3 0.02
106 58 0.44
107 10 0.08
108 8 0.06
109 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (104 bp):
TTTTGTATAAAGGGGGTGCCGGCCATTGCCAGGCCACCCCAAATTTTTTTTTACTTTTTTCGTAT
ACTAGTGCCGGCTATTAACACAACAAAACTAAAAAAAAA
Found at i:20464139 original size:41 final size:41
Alignment explanation
Indices: 20464082--20464276 Score: 345
Period size: 41 Copynumber: 4.8 Consensus size: 41
20464072 AGGCTAAGCG
20464082 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
20464123 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
*
20464164 CCTAGCAGGCTACATGCCGGTGATTTGAATCGGGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
* * *
20464205 CCTAGCAGGCTACGTGCCGATGATCTGAATCAGGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
*
20464246 CCTAGCAGGCTACGTGCCGGTGATCTGAATC
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATC
20464277 AAGCTATAAG
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 148 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
Found at i:20466949 original size:22 final size:22
Alignment explanation
Indices: 20466855--20466949 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
20466845 TAGTATACTT
*
20466855 TTATTTTAAA-TTATCATAAATA
1 TTATTTTAAACTTATCAT-ATTA
20466877 TTA-TTTAAACTTATCATA-TA
1 TTATTTTAAACTTATCATATTA
* * * **
20466897 TCCTAATTTAAAATTTATCATGTGC
1 T--T-ATTTTAAACTTATCATATTA
*
20466922 TAATTTTAAACTTATCATATTA
1 TTATTTTAAACTTATCATATTA
20466944 TTATTT
1 TTATTT
20466950 AGATTTATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.05
21 7 0.13
22 31 0.56
23 1 0.02
24 12 0.22
25 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTTTAAACTTATCATATTA
Found at i:20472044 original size:40 final size:42
Alignment explanation
Indices: 20471994--20472076 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 42
20471984 TAAACATTAA
*
20471994 AAAATTATTTTAAAAATAAAAAA-AAATAA-AAAAATAT-TTT
1 AAAAGTATTTTAAAAATAAAAAATAAA-AATAAAAATATATTT
*
20472034 AAAAGTATTTTAAAATTAAAAAATAAAAATAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAATATATTT
20472076 A
1 A
20472077 TTATATTCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 23 0.61
41 11 0.29
42 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (42 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAATATATTT
Found at i:20474033 original size:4 final size:4
Alignment explanation
Indices: 20474021--20474051 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20474011 TAAAATAAAT
*
20474021 ATTA TTTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
20474052 TCTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
ATTA
Found at i:20474059 original size:16 final size:16
Alignment explanation
Indices: 20474026--20474074 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
20474016 TAAATATTAT
** *
20474026 TTAATTAATTAATTAA
1 TTAATTAATTTCTCAA
20474042 TTAATTAATTTCTCAA
1 TTAATTAATTTCTCAA
*
20474058 TTAAATAATTTTCTCAA
1 TTAATTAA-TTTCTCAA
20474075 CCTAATTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATTAATTTCTCAA
Found at i:20479885 original size:18 final size:19
Alignment explanation
Indices: 20479864--20479903 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20479854 TAATTTTTTC
20479864 TTTTTTAACTT-AAGCTTT
1 TTTTTTAACTTGAAGCTTT
* *
20479882 TTTTTTAATTTGAATCTTT
1 TTTTTTAACTTGAAGCTTT
20479901 TTT
1 TTT
20479904 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTAACTTGAAGCTTT
Found at i:20499239 original size:38 final size:39
Alignment explanation
Indices: 20499184--20499306 Score: 163
Period size: 38 Copynumber: 3.3 Consensus size: 39
20499174 CAGGCTAGCG
*
20499184 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTATAA
1 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCGGGTATAA
20499223 -CTAGCAGGCTAAGTGCC-GTGATTTGAATC-GGTA-AA
1 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCGGGTATAA
20499258 CCTAG-AGGCTACA-TG-CGGTGA-TTGAATCGGGTTATAA
1 CCTAGCAGGCTA-AGTGCCGGTGATTTGAATCGGG-TATAA
20499295 CCTAGCAGGCTA
1 CCTAGCAGGCTA
20499307 CGTCGGATCT
Statistics
Matches: 76, Mismatches: 1, Indels: 15
0.83 0.01 0.16
Matches are distributed among these distances:
34 8 0.11
35 16 0.21
36 11 0.14
37 19 0.25
38 22 0.29
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (39 bp):
CCTAGCAGGCTAAGTGCCGGTGATTTGAATCGGGTATAA
Found at i:20499327 original size:36 final size:38
Alignment explanation
Indices: 20499184--20499353 Score: 178
Period size: 37 Copynumber: 4.6 Consensus size: 38
20499174 CAGGCTAGCG
*
20499184 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTATAA
1 CCTAGCAGGCTACGTG-CGGTGATTTGAATCGGTTATAA
* *
20499223 -CTAGCAGGCTAAGTGCCGTGATTTGAATCGG-TA-AA
1 CCTAGCAGGCTACGTGCGGTGATTTGAATCGGTTATAA
*
20499258 CCTAG-AGGCTACATGCGGTGA-TTGAATCGGGTTATAA
1 CCTAGCAGGCTACGTGCGGTGATTTGAATC-GGTTATAA
* *
20499295 CCTAGCAGGCTACGT-C-G-GATCTGAATCAGGTTAAAAA
1 CCTAGCAGGCTACGTGCGGTGATTTGAATC-GGTT-ATAA
20499332 CCTAGCA-GCTACGTGCCGGTGA
1 CCTAGCAGGCTACGTG-CGGTGA
20499354 CTGATAGCTA
Statistics
Matches: 111, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
34 7 0.06
35 19 0.17
36 26 0.23
37 33 0.30
38 23 0.21
39 1 0.01
40 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (38 bp):
CCTAGCAGGCTACGTGCGGTGATTTGAATCGGTTATAA
Found at i:20501994 original size:22 final size:22
Alignment explanation
Indices: 20501900--20501994 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
20501890 TAGTATACTT
*
20501900 TTATTTTAAA-TTATCATAAATA
1 TTATTTTAAACTTATCAT-ATTA
20501922 TTA-TTTAAACTTATCATA-TA
1 TTATTTTAAACTTATCATATTA
* * * **
20501942 TCCTAATTTAAAATTTATCATGTGC
1 T--T-ATTTTAAACTTATCATATTA
*
20501967 TAATTTTAAACTTATCATATTA
1 TTATTTTAAACTTATCATATTA
20501989 TTATTT
1 TTATTT
20501995 AGATTATTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.05
21 7 0.13
22 31 0.56
23 1 0.02
24 12 0.22
25 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTTTAAACTTATCATATTA
Found at i:20507030 original size:28 final size:28
Alignment explanation
Indices: 20506961--20507032 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
20506951 GACCCATTTT
20506961 TAATAAACATTAAAAAATTATTTTAAAAA
1 TAATAAA-ATTAAAAAATTATTTTAAAAA
* * *
20506990 TAAAAAAAATAAAAAA-TATTTTAAAAG
1 TAATAAAATTAAAAAATTATTTTAAAAA
*
20507017 TATTTAAAATTAAAAA
1 TA-ATAAAATTAAAAA
20507033 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 12 0.33
28 18 0.50
29 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (28 bp):
TAATAAAATTAAAAAATTATTTTAAAAA
Found at i:20507880 original size:18 final size:19
Alignment explanation
Indices: 20507845--20507882 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
20507835 ATAATAACCA
20507845 TTAATTAATATTTATTAAT
1 TTAATTAATATTTATTAAT
*
20507864 TTAATTAA-ATTTTTTAAT
1 TTAATTAATATTTATTAAT
20507882 T
1 T
20507883 AACATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATTAATATTTATTAAT
Found at i:20508992 original size:4 final size:4
Alignment explanation
Indices: 20508980--20509010 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20508970 TAAAATAAAT
*
20508980 ATTA TTTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
20509011 TCTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
ATTA
Found at i:20509018 original size:16 final size:16
Alignment explanation
Indices: 20508985--20509033 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
20508975 TAAATATTAT
** *
20508985 TTAATTAATTAATTAA
1 TTAATTAATTTCTCAA
20509001 TTAATTAATTTCTCAA
1 TTAATTAATTTCTCAA
*
20509017 TTAAATAATTTTCTCAA
1 TTAATTAA-TTTCTCAA
20509034 CCTAATTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATTAATTTCTCAA
Found at i:20510614 original size:24 final size:21
Alignment explanation
Indices: 20510575--20510628 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
20510565 CTCAATTAAC
*
20510575 TAAAATTATTTAATTTAAAATT
1 TAAAATTTTTTAATTTAAAA-T
*
20510597 TAAAATTTTATTACATTTTAAAT
1 TAAAATTTT-TTA-ATTTAAAAT
*
20510620 CAAAATTTT
1 TAAAATTTT
20510629 CTCAAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.30
23 12 0.44
24 7 0.26
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATTTTTTAATTTAAAAT
Found at i:20514800 original size:17 final size:18
Alignment explanation
Indices: 20514780--20514817 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20514770 ATAATTTTTC
20514780 TTTTTAACTT-AAGCTTT
1 TTTTTAACTTGAAGCTTT
* *
20514797 TTTTTAATTTGAATCTTT
1 TTTTTAACTTGAAGCTTT
20514815 TTT
1 TTT
20514818 AATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTTAACTTGAAGCTTT
Found at i:20524079 original size:44 final size:44
Alignment explanation
Indices: 20524023--20524521 Score: 223
Period size: 44 Copynumber: 11.5 Consensus size: 44
20524013 CCGAAAATCC
20524023 TATCTCCCTGAAGTTGTAGTGGAGCGA-ATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACC-CAGATCT
** * *****
20524067 TATCTCTTTGAAGTTGTAGTAGAGC-AGA-TCGTGTCCAG-TCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCAGATCT
* *
20524108 TATCTCCCTGAAATTGTAGTGGGGC-AGACTATATAAA-CCA-ATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGA-T-TA-AAACCCAGATCT
* * * * * * *
20524152 TATCTCCATGAAGTTGCAGTGGAAC-AGATTAAAGCCAATAATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCA-GATCT
* **
20524196 TATCTCCCTGAAGTTGCAGTGGAGCG-GATTAAAACTAAGGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCA-GATCT
* * * * *** *
20524240 GATCTCTCTGAAGTTGCAGTTGAGC-AGA-TCGCATCCAG-TCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCAGATCT
* * ** * *
20524281 CATCTCCATGAAGTTGTAGTGGAGC-AGACAGAAGAAACCA-ATCA
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGA-TTAA-AACCCAGATCT
* * * *
20524325 TATCTCCTTAAATTTGCAGTGGAGCG-GATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACC-CAGATCT
* * *****
20524369 TATCTCTCTGAAGTTGTAGTAGAGCG-GA-TCGTGTCCAG-TCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCAGATCT
* * * * *
20524410 TGTCTCCCTGAAGTTGCAGTGGGGC-AGACTAAATAAACCA-ATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGA-TTAA-AACCCAGATCT
* * * *
20524454 TATCTCTCTGAAGTTGCAGTGGAGC-AGATTGAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCGAGATT-AA-AACCCAGATCT
* *
20524498 TATCGCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGTAGTGGAG
20524522 TGGATCAAAA
Statistics
Matches: 340, Mismatches: 91, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
41 79 0.23
42 14 0.04
43 14 0.04
44 233 0.69
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGTAGTGGAGCGAGATTAAAACCCAGATCT
Found at i:20524180 original size:85 final size:85
Alignment explanation
Indices: 20524023--20524305 Score: 218
Period size: 85 Copynumber: 3.3 Consensus size: 85
20524013 CCGAAAATCC
* ** *
20524023 TATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAACCACAGATCTTATCTCTTTGAAGTTGTAGTA
1 TATCTCCCTGAAATTGTAGTGGAGCGAATTAAAACCACAGATCTTATCTCCATGAAGTTGCAGTA
*
20524088 GAGCAGATCGTGTCCAGTCT
66 GAACAGATCGTGTCCAGTCT
* *
20524108 TATCTCCCTGAAATTGTAGTGGGGCAGACTATATAAA-C-CA-ATCTTATCTCCATGAAGTTGCA
1 TATCTCCCTGAAATTGTAGTGGAGC-GAAT-TA-AAACCACAGATCTTATCTCCATGAAGTTGCA
* *** * *
20524170 GTGGAACAGATTAAAG-CCAATAATCC
63 GTAGAACAGA-TCGTGTCC---AGTCT
* * * * *
20524196 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTA-AGGATCTGATCTCTC-TGAAGTTGCAG
1 TATCTCCCTGAAATTGTAGTGGAGCGAATTAAAACCACA-GATCTTATCTC-CATGAAGTTGCAG
* * **
20524259 TTGAGCAGATCGCATCCAGTCT
64 TAGAACAGATCGTGTCCAGTCT
* * *
20524281 CATCTCCATGAAGTTGTAGTGGAGC
1 TATCTCCCTGAAATTGTAGTGGAGC
20524306 AGACAGAAGA
Statistics
Matches: 154, Mismatches: 31, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
85 80 0.52
86 10 0.06
87 6 0.04
88 57 0.37
89 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (85 bp):
TATCTCCCTGAAATTGTAGTGGAGCGAATTAAAACCACAGATCTTATCTCCATGAAGTTGCAGTA
GAACAGATCGTGTCCAGTCT
Found at i:20524286 original size:129 final size:128
Alignment explanation
Indices: 20524153--20524483 Score: 387
Period size: 129 Copynumber: 2.6 Consensus size: 128
20524143 AACCAATCTT
* * * *
20524153 ATCTCCATGAAGTTGCAGTGGAACAGATTAAAGCCAA-TAATCCTATCTCCCTGAAGTTGCAGTG
1 ATCTCCATGAAGTTGCAGTGGAGCAGA-TAAAG-AAACCAATCATATCTCCCTGAAGTTGCAGTG
* *
20524217 GAGCGGATTAAAACTA-AGGATCTGATCTCTCTGAAGTTGCAGTTGAGCAGATCGCATCCAGTCT
64 GAGCGGATTAAAACCACA-GATCTGATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCT
20524281 C
128 C
* * * * *
20524282 ATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAACCAATCATATCTCCTTAAATTTGCAGTGG
1 ATCTCCATGAAGTTGCAGTGGAGCAGATA-AAGAAACCAATCATATCTCCCTGAAGTTGCAGTGG
* * * ** *
20524347 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAGTAGAGCGGATCGTGTCCAGTCTT
65 AGCGGATTAAAACCACAGATCTGATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTC
* * * * * *
20524411 GTCTCCCTGAAGTTGCAGTGGGGCAGACTAAATAAACCAATCTTATCTCTCTGAAGTTGCAGTGG
1 ATCTCCATGAAGTTGCAGTGGAGCAGA-TAAAGAAACCAATCATATCTCCCTGAAGTTGCAGTGG
*
20524476 AGCAGATT
65 AGCGGATT
20524484 GAAGAAACCA
Statistics
Matches: 169, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
128 3 0.02
129 164 0.97
130 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (128 bp):
ATCTCCATGAAGTTGCAGTGGAGCAGATAAAGAAACCAATCATATCTCCCTGAAGTTGCAGTGGA
GCGGATTAAAACCACAGATCTGATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTC
Found at i:20524321 original size:173 final size:173
Alignment explanation
Indices: 20524017--20524397 Score: 480
Period size: 173 Copynumber: 2.2 Consensus size: 173
20524007 GTGAAACCGA
* * *
20524017 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAACCACAGATCTTATCTCTTTGAAGTT
1 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACAGATCTGATCTCTCTGAAGTT
* ** * * * * *
20524082 GTAGTAGAGCAGATCGTGTCCAGTCTTATCTCCCTGAAATTGTAGTGGGGCAGACTATATAAACC
66 GCAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACTAAAGAAACC
* * *
20524147 AATCTTATCTCCATGAAGTTGCAGTGGAACAGATTAAAGCCA-
131 AATCATATCTCCATAAAGTTGCAGTGGAACAGATTAAAACCAC
* *
20524189 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTA-AGGATCTGATCTCTCTGAAG
1 A-AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACA-GATCTGATCTCTCTGAAG
* *
20524253 TTGCAGTTGAGCAGATCGCATCCAGTCTCATCTCCATGAAGTTGTAGTGGAGCAGAC-AGAAGAA
64 TTGCAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACTA-AAGAA
* * * *
20524317 ACCAATCATATCTCCTTAAATTTGCAGTGGAGCGGATTAAAACCAC
128 ACCAATCATATCTCCATAAAGTTGCAGTGGAACAGATTAAAACCAC
* * * *
20524363 AGATCTTATCTCTCTGAAGTTGTAGTAGAGCGGAT
1 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGAT
20524398 CGTGTCCAGT
Statistics
Matches: 178, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
172 3 0.02
173 174 0.98
174 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACAGATCTGATCTCTCTGAAGTT
GCAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACTAAAGAAACC
AATCATATCTCCATAAAGTTGCAGTGGAACAGATTAAAACCAC
Found at i:20524509 original size:129 final size:129
Alignment explanation
Indices: 20524153--20524527 Score: 327
Period size: 129 Copynumber: 2.9 Consensus size: 129
20524143 AACCAATCTT
* * * * * * *
20524153 ATCTCCATGAAGTTGCAGTGGAACAGATTA-AAGCCAA-TAATCCTATCTCCCTGAAGTTGCAGT
1 ATCTCCATGAAGTTGCAGTGGAGCAGA-CAGAAG-AAACCAATCATATCTCCTTAAAGTTGCAGT
* * * * *
20524216 GGAGCGGATT-AAAACTA-AGGAT-CTGATCTCTCTGAAGTTGCAGTTGAGCAGATCGCATCCAG
64 GGAGCAGATTAAAAAC-ACA-GATCCT-ATCGCCCTGAAGTTGCAGTAGAGCGGATCGCATCCAG
20524278 TCTC
126 TCTC
* *
20524282 ATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAACCAATCATATCTCCTTAAATTTGCAGTGG
1 ATCTCCATGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCATATCTCCTTAAAGTTGCAGTGG
* * * * * * ** *
20524347 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAGTAGAGCGGATCGTGTCCAGTCTT
66 AGCAGATTAAAAACACAGATCCTATCGCCCTGAAGTTGCAGTAGAGCGGATCGCATCCAGTCTC
* * * * * *
20524411 GTCTCCCTGAAGTTGCAGTGGGGCAGACTA-AATAAACCAATCTTATCT-CTCTGAAGTTGCAGT
1 ATCTCCATGAAGTTGCAGTGGAGCAGAC-AGAAGAAACCAATCATATCTCCT-TAAAGTTGCAGT
* *
20524474 GGAGCAGATTGAAGAAAC-CA-ATCCTATCGCCCTGAAGTTGCAGTGGAGTGGATC
64 GGAGCAGATT-AA-AAACACAGATCCTATCGCCCTGAAGTTGCAGTAGAGCGGATC
20524528 AAAATGATGG
Statistics
Matches: 204, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
128 5 0.02
129 185 0.91
130 11 0.05
131 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (129 bp):
ATCTCCATGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCATATCTCCTTAAAGTTGCAGTGG
AGCAGATTAAAAACACAGATCCTATCGCCCTGAAGTTGCAGTAGAGCGGATCGCATCCAGTCTC
Found at i:20526535 original size:18 final size:19
Alignment explanation
Indices: 20526498--20526538 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20526488 TTATTTCAAC
20526498 TTATTTCAAAATTGTTAAT
1 TTATTTCAAAATTGTTAAT
* *
20526517 TTATTTTAATATT-TTAAT
1 TTATTTCAAAATTGTTAAT
20526535 TTAT
1 TTAT
20526539 ATATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATTTCAAAATTGTTAAT
Found at i:20527310 original size:23 final size:23
Alignment explanation
Indices: 20527284--20527327 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20527274 TTATAACTTT
20527284 TTTTATTTACCAAAAAATATATA
1 TTTTATTTACCAAAAAATATATA
*
20527307 TTTTATTTACCAAAATATATA
1 TTTTATTTACCAAAAAATATA
20527328 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTTATTTACCAAAAAATATATA
Found at i:20527519 original size:10 final size:10
Alignment explanation
Indices: 20527500--20527535 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
20527490 AGGTGCTACG
*
20527500 GAAAAGAAGA
1 GAAAAAAAGA
20527510 GAAAAAAAGA
1 GAAAAAAAGA
*
20527520 GAAAAGAAGA
1 GAAAAAAAGA
20527530 GAAAAA
1 GAAAAA
20527536 GAAGGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:20527600 original size:19 final size:21
Alignment explanation
Indices: 20527562--20527600 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
20527552 AATAATTGAT
*
20527562 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
20527583 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
20527601 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:20528243 original size:18 final size:18
Alignment explanation
Indices: 20528220--20528264 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20528210 TTGACATGGT
20528220 TGGTGGTGAAGAAGAAGG
1 TGGTGGTGAAGAAGAAGG
*
20528238 TGGTGGCGAAGAAGAAGG
1 TGGTGGTGAAGAAGAAGG
*
20528256 TGATGGTGA
1 TGGTGGTGA
20528265 TCATAGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.49, T:0.18
Consensus pattern (18 bp):
TGGTGGTGAAGAAGAAGG
Found at i:20529474 original size:20 final size:20
Alignment explanation
Indices: 20529449--20529489 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20529439 AGATTATAAG
20529449 AATGCAGACTGGAAGAGACA
1 AATGCAGACTGGAAGAGACA
20529469 AATGCAGACTGGAAGAGACA
1 AATGCAGACTGGAAGAGACA
20529489 A
1 A
20529490 GTCGTGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.29, T:0.10
Consensus pattern (20 bp):
AATGCAGACTGGAAGAGACA
Found at i:20534040 original size:5 final size:5
Alignment explanation
Indices: 20534032--20534177 Score: 64
Period size: 5 Copynumber: 30.6 Consensus size: 5
20534022 TTTTCTCTTC
* * * *
20534032 TCCTT TCCTT TCCTT TTCTT TCC-T T-CTT T-CTT TCTTTT TTCTT CTGCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC-CTT TCCTT -TCCTT
* * *
20534081 TCCTT TTCTT CTTCTT T-CTT T-CTT T-TTT TCTCTT CTCCTT TCCTT
1 TCCTT TCCTT -TCCTT TCCTT TCCTT TCCTT TC-CTT -TCCTT TCCTT
* * * *
20534126 TTCTT TCC-T TCTTT TTCTT T-CTT TCCTC TCC-T TCCTT T-CTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
20534171 T-CTT TCC
1 TCCTT TCC
20534178 CTCTCCTTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
3 1 0.01
4 41 0.37
5 51 0.46
6 17 0.15
7 2 0.02
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (5 bp):
TCCTT
Found at i:20534062 original size:4 final size:4
Alignment explanation
Indices: 20534046--20534176 Score: 85
Period size: 4 Copynumber: 32.0 Consensus size: 4
20534036 TTCCTTTCCT
*
20534046 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTGC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * *
20534092 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* *
20534139 TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
20534177 CCTCTCCTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
3 13 0.13
4 68 0.66
5 15 0.15
6 7 0.07
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:20534112 original size:79 final size:78
Alignment explanation
Indices: 20533977--20534176 Score: 225
Period size: 79 Copynumber: 2.5 Consensus size: 78
20533967 AAATTACTTT
* * *
20533977 TTTTTCTTTTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTT-TCC
1 TTTTTC-TTTCTTTCCTCTCCTT-CCT-TTCTTCTTCTT-TCTTTCTTTTCTCTTCT-CTTCTCC
20534040 TTTCCTTTTCTTTCCTTC
61 TTTCCTTTTCTTTCCTTC
* *
20534058 TTTCTTTCTTT-TTTCTTCTGCTTTCCTTTTCTTCTTCTTTCTTTCTTTT-T-TTCTCTTCTCCT
1 -TT-TTTCTTTCTTTCCTCT-CCTTCC-TTTCTTCTTCTTTCTTTCTTTTCTCTTCTCTTCTCCT
20534120 TTCCTTTTCTTTCCTTC
62 TTCCTTTTCTTTCCTTC
20534137 TTTTTCTTTCTTTCCTCTCCTTCCTTTC-T-TTCTTTCTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCTTTCTTCTTCTTTCTTTC
20534177 CCTCTCCTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
74 11 0.10
75 1 0.01
76 4 0.04
77 12 0.11
78 12 0.11
79 25 0.24
80 1 0.01
81 13 0.12
82 19 0.18
83 8 0.08
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.69
Consensus pattern (78 bp):
TTTTTCTTTCTTTCCTCTCCTTCCTTTCTTCTTCTTTCTTTCTTTTCTCTTCTCTTCTCCTTTCC
TTTTCTTTCCTTC
Found at i:20534169 original size:40 final size:39
Alignment explanation
Indices: 20533985--20534172 Score: 135
Period size: 40 Copynumber: 4.7 Consensus size: 39
20533975 TTTTTTTCTT
20533985 TTTTTTCCT-TCCTTCCCTCTTC-TTC-TT-CTTCTTTTT-
1 TTTTTTCCTCTCCTT-CCT-TTCTTTCTTTCCTTCTTTTTC
*
20534021 TTTTTCTCTTCTCCTTTCCTTTCCTTTTCTTTCCTTCTTTCTTTC
1 TTTTT-TCCTCTCC-TTCCTTT-C-TTTCTTTCCTTC-TT-TTTC
* * *
20534066 TTTTTTCTTCTGCTTTCCTTT-TCTTC-TT-CTT-TCTTTC
1 TTTTTTCCTCT-CCTTCCTTTCT-TTCTTTCCTTCTTTTTC
* *
20534103 TTTTTTTCTCTTC-TCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TTTTTTCCTCTCCTTCCTTT-C-TTTCTTTCCTTCTTTTTC
20534143 TTTCTTTCCTCTCCTTCCTTTCTTTCTTTC
1 TTT-TTTCCTCTCCTTCCTTTCTTTCTTTC
20534173 TTTCCCTCTC
Statistics
Matches: 121, Mismatches: 10, Indels: 38
0.72 0.06 0.22
Matches are distributed among these distances:
35 6 0.05
36 5 0.04
37 21 0.17
38 11 0.09
39 5 0.04
40 22 0.18
41 14 0.12
42 13 0.11
43 2 0.02
44 16 0.13
45 6 0.05
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTTCCTCTCCTTCCTTTCTTTCTTTCCTTCTTTTTC
Found at i:20534180 original size:27 final size:27
Alignment explanation
Indices: 20534130--20534185 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
20534120 TTCCTTTTCT
*
20534130 TTCCTTCTTTTTCTTTCTTTCCTCTCC
1 TTCCTTCTCTTTCTTTCTTTCCTCTCC
20534157 TTCCTT-TCTTTCTTTCTTTCCCTCTCC
1 TTCCTTCTCTTTCTTTCTTT-CCTCTCC
20534184 TT
1 TT
20534186 TTGCCCGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (27 bp):
TTCCTTCTCTTTCTTTCTTTCCTCTCC
Found at i:20534259 original size:27 final size:26
Alignment explanation
Indices: 20534219--20534290 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
20534209 CCTTTTTATG
* *
20534219 CATTGGTGCTGCCAATGGTATTCGCAC
1 CATTGGTGCCGCCAATGCT-TTCGCAC
*
20534246 CATTGGTGCCGCCAATAGCTTTGGCAC
1 CATTGGTGCCGCCAAT-GCTTTCGCAC
*
20534273 CTTTGGTGCCGCCAATGC
1 CATTGGTGCCGCCAATGC
20534291 CATTGGCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.05
27 36 0.90
28 2 0.05
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (26 bp):
CATTGGTGCCGCCAATGCTTTCGCAC
Found at i:20538713 original size:3 final size:3
Alignment explanation
Indices: 20538705--20538735 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20538695 ATTTTCATCT
*
20538705 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20538736 AGTACTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20538914 original size:20 final size:21
Alignment explanation
Indices: 20538878--20538917 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20538868 AAAAAATATT
*
20538878 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAATAAA
20538899 AATAATA-TTTAATAAATAA
1 AATAATATTTTAATAAATAA
20538918 GATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATATTTTAATAAATAAA
Found at i:20538970 original size:3 final size:3
Alignment explanation
Indices: 20538962--20538995 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
20538952 TAAATCTCAC
*
20538962 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20538996 ACTTTTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:20541363 original size:7 final size:7
Alignment explanation
Indices: 20541351--20541379 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20541341 TGTTCAAAAT
20541351 AGAAAGA
1 AGAAAGA
20541358 AGAAAGA
1 AGAAAGA
20541365 AGAAAGA
1 AGAAAGA
20541372 AG-AAGA
1 AGAAAGA
20541378 AG
1 AG
20541380 CAAATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:20548476 original size:87 final size:87
Alignment explanation
Indices: 20548329--20548676 Score: 464
Period size: 87 Copynumber: 4.0 Consensus size: 87
20548319 TTTGAGGTGA
* *
20548329 ATGTTTATTTGTCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGGTTCTA-CTTTGTCCACATTC
1 ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTC-AGCTTTGTCCACATTC
* *
20548393 GTTTCCTGCTGAAGCAGATTCTT
65 ATTTCCTGCTGAACCAGATTCTT
* * * * *
20548416 TTGTTTATTTTCCGTAAATGATTCTTGCTTCTTCCCTTTCTCTGATTCAGCTTTGTCCACATTCG
1 ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
*
20548481 TTTCCTGCTGAACCGGATTCTT
66 TTTCCTGCTGAACCAGATTCTT
* * *
20548503 ATGTTTATTTGCTGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATCCA
1 ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
* *
20548568 TTTCCTGCTGAACCGGATTCCT
66 TTTCCTGCTGAACCAGATTCTT
* * ** * *
20548590 ATGTCTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCACCTTCCGCTTTGTCCACTTTCA
1 ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
* * *
20548655 TTTCCTTCTGCAGCAGATTCTT
66 TTTCCTGCTGAACCAGATTCTT
20548677 GGTTCAGAGA
Statistics
Matches: 231, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 1 0.00
87 230 1.00
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.45
Consensus pattern (87 bp):
ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
TTTCCTGCTGAACCAGATTCTT
Found at i:20552062 original size:9 final size:9
Alignment explanation
Indices: 20552050--20552083 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20552040 CGTCATCACA
*
20552050 TTCATCGTC
1 TTCATCATC
*
20552059 TTCATAATC
1 TTCATCATC
20552068 TTCATCATC
1 TTCATCATC
20552077 TTCATCA
1 TTCATCA
20552084 GACTCATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (9 bp):
TTCATCATC
Found at i:20563231 original size:19 final size:20
Alignment explanation
Indices: 20563193--20563232 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
20563183 TTTTGACTAT
20563193 TTATTTTTTACTCTTAAATTTC
1 TTATTTTTTACTC-T-AATTTC
20563215 TTATTTTTTACTC-AATTT
1 TTATTTTTTACTCTAATTT
20563233 TGTAGGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
22 13 0.72
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTTTACTCTAATTTC
Found at i:20567004 original size:46 final size:45
Alignment explanation
Indices: 20566937--20567176 Score: 304
Period size: 46 Copynumber: 5.5 Consensus size: 45
20566927 TTTGAGTACT
* *
20566937 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
20566983 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
20567019 TCTGATCAAGAGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
20567065 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
20567111 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
20567156 TCTGATC-AGGGAC-AAGTGATA
1 TCTGATCAAGTGACAAAGTGATA
20567177 GGTGATCATA
Statistics
Matches: 174, Mismatches: 10, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
36 30 0.17
37 2 0.01
40 2 0.01
42 2 0.01
43 8 0.05
44 5 0.03
45 22 0.13
46 103 0.59
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:20567014 original size:36 final size:36
Alignment explanation
Indices: 20566973--20567045 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
20566963 GGTAGCTTTA
*
20566973 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
*
20567009 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
20567045 G
1 G
20567046 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
Found at i:20567074 original size:82 final size:86
Alignment explanation
Indices: 20566937--20567163 Score: 320
Period size: 82 Copynumber: 2.6 Consensus size: 86
20566927 TTTGAGTACT
* *
20566937 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
20567002 GAT-A-AG-T-GCTACACTTA
66 GATAAGAGCTAGCTACACTTA
* *
20567019 TCTGATCAAGAGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
20567084 GATAAGTGGTAGCCTTAGCTACACTTA
66 GATAA---G-AG-C-TAGCTACACTTA
*
20567111 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTATCTGATCA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCA
20567164 GGGACAAGTG
Statistics
Matches: 129, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
82 64 0.50
83 1 0.01
88 2 0.02
91 21 0.16
92 41 0.32
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (86 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGAGCTAGCTACACTTA
Found at i:20574945 original size:12 final size:12
Alignment explanation
Indices: 20574928--20574952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20574918 GGTGTTCATT
20574928 CGGTTAACCGAC
1 CGGTTAACCGAC
20574940 CGGTTAACCGAC
1 CGGTTAACCGAC
20574952 C
1 C
20574953 CGAAATTACT
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:20575127 original size:9 final size:9
Alignment explanation
Indices: 20575113--20575164 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
20575103 TTTGGTTAAA
20575113 AATTACCCG
1 AATTACCCG
20575122 AATTACCCG
1 AATTACCCG
20575131 AATTACCCG
1 AATTACCCG
*
20575140 AATTAACCG
1 AATTACCCG
* *
20575149 AATTAACTG
1 AATTACCCG
20575158 AATTACC
1 AATTACC
20575165 GAAAAATACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:20575310 original size:39 final size:39
Alignment explanation
Indices: 20575267--20575376 Score: 211
Period size: 39 Copynumber: 2.8 Consensus size: 39
20575257 TGGGTTGTCT
20575267 TTTAGTTTTAGTTTTATTGGATTGGGTAATTGGGTAAAC
1 TTTAGTTTTAGTTTTATTGGATTGGGTAATTGGGTAAAC
20575306 TTTAGTTTTAGTTTTATTGGATTGGGTAATTGGGTAAAC
1 TTTAGTTTTAGTTTTATTGGATTGGGTAATTGGGTAAAC
*
20575345 TTTAGTTTTAGTTTTATTGGGTTGGGTAATTG
1 TTTAGTTTTAGTTTTATTGGATTGGGTAATTG
20575377 AGTTTGGGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (39 bp):
TTTAGTTTTAGTTTTATTGGATTGGGTAATTGGGTAAAC
Found at i:20579048 original size:12 final size:12
Alignment explanation
Indices: 20579031--20579057 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20579021 GATAGGGGAA
20579031 TTTCTTTTCTTT
1 TTTCTTTTCTTT
20579043 TTTCTTTTCTTT
1 TTTCTTTTCTTT
20579055 TTT
1 TTT
20579058 AGATTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:20592796 original size:12 final size:13
Alignment explanation
Indices: 20592774--20592802 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20592764 AGTTTTTGCC
20592774 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
20592787 CTTTTT-TTTTTT
1 CTTTTTCTTTTTT
20592799 CTTT
1 CTTT
20592803 AATTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:20599318 original size:13 final size:13
Alignment explanation
Indices: 20599300--20599325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20599290 GTTTAAGTTT
20599300 TATTAGATAAATA
1 TATTAGATAAATA
20599313 TATTAGATAAATA
1 TATTAGATAAATA
20599326 CAAACTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TATTAGATAAATA
Found at i:20604616 original size:23 final size:22
Alignment explanation
Indices: 20604586--20604630 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
20604576 CATACAATAA
20604586 ATATTTAAATTT-AAATTGAATT
1 ATATTTAAATTTGAAA-TGAATT
*
20604608 ATATGTTAATTTTGAAATGAATT
1 ATAT-TTAAATTTGAAATGAATT
20604631 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATATTTAAATTTGAAATGAATT
Found at i:20610546 original size:19 final size:20
Alignment explanation
Indices: 20610519--20610557 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
20610509 GATTTAAAAT
*
20610519 TTTAATTTTT-TTTATTAAA
1 TTTAATTTTTATTCATTAAA
*
20610538 TTTAGTTTTTATTCATTAAA
1 TTTAATTTTTATTCATTAAA
20610558 ATAATATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTAATTTTTATTCATTAAA
Found at i:20617304 original size:50 final size:50
Alignment explanation
Indices: 20617229--20617426 Score: 243
Period size: 50 Copynumber: 3.8 Consensus size: 50
20617219 GATAATAACA
* *
20617229 TGCCAAAGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
20617279 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
20617329 TGCCCATGTCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
20617384 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
20617427 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 83 0.66
53 2 0.02
54 1 0.01
55 2 0.02
56 38 0.30
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:20617421 original size:106 final size:100
Alignment explanation
Indices: 20617238--20617426 Score: 279
Period size: 106 Copynumber: 1.8 Consensus size: 100
20617228 ATGCCAAAGC
* *
20617238 CATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTCCCAGACATG
20617303 GTATTACATGGGACCTCTCGTCTCGGTGCCCATGT
66 GTATTACATGGGACCTCTCGTCTCGGTGCCCATGT
*
20617338 CATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAATGCCATGTCCCA
1 CATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-AGG-TGCCAACGCCATGTCCCA
* *
20617403 GACATGGTCTTACATGGGATCTCT
60 GACATGGTATTACATGGGACCTCT
20617427 TTACCCAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
100 33 0.42
103 3 0.04
104 1 0.01
105 2 0.03
106 39 0.50
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (100 bp):
CATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTCCCAGACATG
GTATTACATGGGACCTCTCGTCTCGGTGCCCATGT
Found at i:20617542 original size:13 final size:13
Alignment explanation
Indices: 20617521--20617552 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20617511 GCTTGGATCA
*
20617521 TCATCAAATAAAT
1 TCATAAAATAAAT
20617534 TCATAAAATAAAT
1 TCATAAAATAAAT
20617547 TCATAA
1 TCATAA
20617553 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:20617800 original size:30 final size:30
Alignment explanation
Indices: 20617764--20617821 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
20617754 CCTCGACTCT
*
20617764 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
20617794 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
20617822 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:20619655 original size:72 final size:73
Alignment explanation
Indices: 20619540--20619695 Score: 170
Period size: 72 Copynumber: 2.2 Consensus size: 73
20619530 ATATAACTTA
* * ** * * *
20619540 AATAAACGGTTTTACTTAATATCGTAACTCAATGAATTGAACTAAA-ATAGCATTTTTAAAAACA
1 AATAAACGGTTCTAATTAATATCAAAACTCAATAAATTCAACTAAATATAACATTTTTAAAAACA
*
20619604 CATAATTG
66 CACAATTG
* * * * * *
20619612 AATAAACGGTTCTAATTAATATCAAAATTTAATAAATTCAACTAAATTTAACCTTTTTTAAAACG
1 AATAAACGGTTCTAATTAATATCAAAACTCAATAAATTCAACTAAATATAACATTTTTAAAAACA
20619677 CACAATTG
66 CACAATTG
*
20619685 AATAAGCGGTT
1 AATAAACGGTT
20619696 TTACTATGTA
Statistics
Matches: 68, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 38 0.56
73 30 0.44
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (73 bp):
AATAAACGGTTCTAATTAATATCAAAACTCAATAAATTCAACTAAATATAACATTTTTAAAAACA
CACAATTG
Found at i:20619791 original size:58 final size:57
Alignment explanation
Indices: 20619726--20619840 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 57
20619716 AATGGTTCCA
* *
20619726 CTTAATATAAAAACTCAATAAATTAAACTAAATT-AGCCTTTTTAAAAATGCATAATTG
1 CTTAATATAAAAACTCAATAAATCAAACTAAATTAAG-CTTCTT-AAAATGCATAATTG
* ** *
20619784 CTTAATATCAAATTTCAATAAATCAAACTAAATTAAGCTTCTTAAAATGTATAATTG
1 CTTAATATAAAAACTCAATAAATCAAACTAAATTAAGCTTCTTAAAATGCATAATTG
20619841 AATCAACGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 13 0.26
58 35 0.70
59 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (57 bp):
CTTAATATAAAAACTCAATAAATCAAACTAAATTAAGCTTCTTAAAATGCATAATTG
Found at i:20621885 original size:28 final size:23
Alignment explanation
Indices: 20621826--20621875 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
20621816 TTCCTTTCCT
20621826 TGTTCTTTTGAGTTTTGTTTAAA
1 TGTTCTTTTGAGTTTTGTTTAAA
20621849 TGTTCTTTTGAGTTTTGTTTAAA
1 TGTTCTTTTGAGTTTTGTTTAAA
20621872 TGTT
1 TGTT
20621876 TGATTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (23 bp):
TGTTCTTTTGAGTTTTGTTTAAA
Found at i:20622857 original size:77 final size:79
Alignment explanation
Indices: 20622716--20622877 Score: 274
Period size: 77 Copynumber: 2.0 Consensus size: 79
20622706 AAAAGGTAAA
20622716 TGAGCCCTGGTGGTCCATAAATGATCGATTTAACTTTGTTTACTTGCTAATATGGTTTGAATTTG
1 TGAGCCCTGGTGGTCCATAAATGATCG---T-ACTTTGTTTACTTGCTAATATGGTTTGAATTTG
20622781 CAGGAAAGAGTGATGAAG
62 CAGGAAAGAGTGATGAAG
20622799 TGAGCCCTGGTGGTCCATAAATGATCG-A-TTTGTTTACTTGCTAATATGGTTTGAATTTGCAGG
1 TGAGCCCTGGTGGTCCATAAATGATCGTACTTTGTTTACTTGCTAATATGGTTTGAATTTGCAGG
20622862 AAAGAGTGATGAAG
66 AAAGAGTGATGAAG
20622876 TG
1 TG
20622878 TGTGGAAGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
77 51 0.65
78 1 0.01
83 27 0.34
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (79 bp):
TGAGCCCTGGTGGTCCATAAATGATCGTACTTTGTTTACTTGCTAATATGGTTTGAATTTGCAGG
AAAGAGTGATGAAG
Found at i:20623136 original size:2 final size:2
Alignment explanation
Indices: 20623129--20623153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20623119 CATCAAACAA
20623129 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
20623154 AAAACACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20623683 original size:77 final size:77
Alignment explanation
Indices: 20623602--20623756 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
20623592 GTAATGGGCT
20623602 TGGATGGGCTATAAAAGAAATAGTAAGATTGTGTGGATTATTATTTTCTGACAATAAAAAAGCAT
1 TGGATGGGCTATAAAAGAAATAGTAAGATTGTGTGGATTATTATTTTCTGACAATAAAAAAGCAT
20623667 TAAATTAACTGG
66 TAAATTAACTGG
20623679 TGGATGGGCTATAAAAGAAATAGTAAGATTGTGTGGATTATTATTTTCTGACAATAAAAAAGCAT
1 TGGATGGGCTATAAAAGAAATAGTAAGATTGTGTGGATTATTATTTTCTGACAATAAAAAAGCAT
20623744 TAAATTAACTGG
66 TAAATTAACTGG
20623756 T
1 T
20623757 CACATGGAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (77 bp):
TGGATGGGCTATAAAAGAAATAGTAAGATTGTGTGGATTATTATTTTCTGACAATAAAAAAGCAT
TAAATTAACTGG
Found at i:20625480 original size:16 final size:16
Alignment explanation
Indices: 20625443--20625482 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20625433 TTAATAAAAT
* *
20625443 TAAAACTAACTGTTAT
1 TAAAATTAACTGTTAG
*
20625459 TAAAATTAATTGTTAG
1 TAAAATTAACTGTTAG
20625475 TAAAATTA
1 TAAAATTA
20625483 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTAACTGTTAG
Found at i:20625552 original size:66 final size:67
Alignment explanation
Indices: 20625471--20625614 Score: 245
Period size: 68 Copynumber: 2.1 Consensus size: 67
20625461 AAATTAATTG
* *
20625471 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATATAACATTT
20625535 GA
66 GA
*
20625537 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATATAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATATAACATT
20625602 TGA
65 TGA
20625605 TTAGTAAAAT
1 TTAGTAAAAT
20625615 AAACTTGATG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATATAACATTT
GA
Found at i:20625567 original size:9 final size:9
Alignment explanation
Indices: 20625555--20625582 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20625545 TTTATCAAAT
20625555 TATTAATTG
1 TATTAATTG
20625564 TATTAATTG
1 TATTAATTG
20625573 TATTAATTG
1 TATTAATTG
20625582 T
1 T
20625583 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Done.