Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 62 of 198
Found at i:18988408 original size:14 final size:14
Alignment explanation
Indices: 18988389--18988415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18988379 CTGTGTTAAT
18988389 TATGTGTGAAATTA
1 TATGTGTGAAATTA
18988403 TATGTGTGAAATT
1 TATGTGTGAAATT
18988416 TTCGTGAAAT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TATGTGTGAAATTA
Found at i:18990041 original size:41 final size:41
Alignment explanation
Indices: 18989995--18990093 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
18989985 AGGCTTGTGC
*
18989995 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACAATACGT
*
18990036 CTAGCAGGCTTAATACCGATGAAATATTTCAGACAATACGT
1 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACAATACGT
*
18990077 CTAGCAGGCCTAATGCC
1 CTAGCAGGCTTAATGCC
18990094 AGTGTACTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGATGAAATATTTCAGACAATACGT
Found at i:18996945 original size:14 final size:14
Alignment explanation
Indices: 18996926--18996954 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18996916 TTCTACGATG
18996926 TGCTTTATGTTACC
1 TGCTTTATGTTACC
18996940 TGCTTTATGTTACC
1 TGCTTTATGTTACC
18996954 T
1 T
18996955 AAATCGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TGCTTTATGTTACC
Found at i:19011986 original size:33 final size:32
Alignment explanation
Indices: 19011944--19012041 Score: 116
Period size: 33 Copynumber: 3.2 Consensus size: 32
19011934 AATATGAAGG
19011944 GGTTGCTAAGTGCTGATTCCCCGACTCTTTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTC-TTGGT
**
19011977 GGTTGCTAAGTGCTGATT-CCC--C-CAAGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCTTGGT
*
19012004 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTC-TTGGT
19012037 GGTTG
1 GGTTG
19012042 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 18 0.33
28 5 0.09
29 1 0.02
30 1 0.02
31 1 0.02
32 5 0.09
33 23 0.43
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCTTGGT
Found at i:19012007 original size:27 final size:29
Alignment explanation
Indices: 19011940--19012025 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 29
19011930 ATTGAATATG
19011940 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCT
1 AAGGGGTTGCTAAGTGCTGATT-CCC--CTCT
**
19011972 TTGGTGGTTGCTAAGTGCTGATTCCCC-C-
1 AAGG-GGTTGCTAAGTGCTGATTCCCCTCT
19012000 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
19012026 GATTCATTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
27 22 0.45
28 2 0.04
29 1 0.02
30 1 0.02
32 5 0.10
33 18 0.37
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.30
Consensus pattern (29 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCTCT
Found at i:19012218 original size:33 final size:33
Alignment explanation
Indices: 19012181--19012303 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 33
19012171 TCCCCCAAGG
19012181 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
19012214 GGTTGCTAAGTGCTGATTCCACC-ATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TC-----AT-TG---GT
* *
19012257 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
19012290 GGTTGCTAAGTGCT
1 GGTTGCTAAGTGCT
19012304 AAATCCACCG
Statistics
Matches: 74, Mismatches: 4, Indels: 24
0.73 0.04 0.24
Matches are distributed among these distances:
33 37 0.50
34 4 0.05
36 2 0.03
37 1 0.01
39 2 0.03
40 2 0.03
42 4 0.05
43 22 0.30
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:19015774 original size:155 final size:151
Alignment explanation
Indices: 19015516--19016225 Score: 611
Period size: 155 Copynumber: 4.9 Consensus size: 151
19015506 AAAGTTTTGA
* ** * *
19015516 TTTTTTAAAAAACAGAGAAAGTTTAGATTT-TAAAAAATAAAAAAATATGTTTTTTAGTCATTTT
1 TTTTTTAAAAAA-AGAGAAAGTTTAGATTTAAAAAAAATAAAACTATTTTTTTTTTAGTCATTTT
* *
19015580 AAAGGAAATTTTAAAATTTTAAAACAAAGTTTGATTTTTTTTCAGCTATTTCAAAATAAAAGCTT
65 AAAGGAAA-TTTAAAATTTTAAAACAAAATTTGA-TTTTTTTCAACTATTTCAAAATAAAAGCTT
19015645 TGATCTTTAAGAAAAATAGTTTTT
128 TGATCTTTAAGAAAAATAGTTTTT
* *
19015669 TTTTTTATAAAAAGAGAAAGTTTAGATTTAAAAAAAATGAAAACCTTTTTTTTTTTTAGTCATTT
1 TTTTTTAAAAAAAGAGAAAGTTTAGATTTAAAAAAAAT-AAAA-CTATTTTTTTTTTAGTCATTT
*
19015734 TAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGCT
64 TAAAGGAAA-TTTAAAATTTTAAAACAAAA-TTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
* * *
19015799 TTGATCTTTAATAAAAGTAG--TGT
127 TTGATCTTTAAGAAAAATAGTTTTT
**
19015822 TTTTTT----AAAGAGAAAGTTTAGATTTAAAAAAAAATAAAAATCTGCTTTTTTTTTAGTCATT
1 TTTTTTAAAAAAAGAGAAAGTTTAGATTT-AAAAAAAAT-AAAA-CTATTTTTTTTTTAGTCATT
* *
19015883 TT-----AAATTT-AAA-TTT-AAA-AAAA-TTGATTTTTTACAACTATTTCAAAATAAAAGATT
63 TTAAAGGAAATTTAAAATTTTAAAACAAAATTTGATTTTTTTCAACTATTTCAAAATAAAAGCTT
19015938 TGATCTTTAAGAAAAATAGTTTTT
128 TGATCTTTAAGAAAAATAGTTTTT
** ** * *
19015962 TTTTAAAAAAAAAAGAGAAAGTTTAGATTT---TTAAATAAAAATA-TGTTTTTTTAGTCATTTT
1 TTTT-TTAAAAAAAGAGAAAGTTTAGATTTAAAAAAAATAAAACTATTTTTTTTTTAGTCATTTT
** ** * *
19016023 AAATTTAAA-TT--AATTTT-------TTTTTGATTTTTTTCAATTATTTCAAAATAAAAGTTTT
65 AAA-GGAAATTTAAAATTTTAAAACAAAATTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTT
19016078 GATCTTTAAGAAAAATAG-TTTT
129 GATCTTTAAGAAAAATAGTTTTT
* ** * * *
19016100 TTTTTT----AAATAGAAAGTTTAGATTT--CTAAAATAAAA--ATATGTTTATTAGTCATTTTA
1 TTTTTTAAAAAAAGAGAAAGTTTAGATTTAAAAAAAATAAAACTATTTTTTTTTTAGTCATTTTA
** * * ** *
19016157 AAGGAAAATTTTAGATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTTGAAAT-AAAGTT
66 AAGG-AAA-TTTA-AAATTTTAAAACAAA-ATTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
19016221 TTGAT
127 TTGAT
19016226 TTTTTTTTAA
Statistics
Matches: 468, Mismatches: 53, Indels: 80
0.78 0.09 0.13
Matches are distributed among these distances:
132 1 0.00
133 38 0.08
134 9 0.02
135 2 0.00
138 77 0.16
139 51 0.11
140 14 0.03
141 7 0.01
142 5 0.01
143 8 0.02
144 6 0.01
145 33 0.07
146 24 0.05
149 19 0.04
150 33 0.07
152 17 0.04
153 26 0.06
154 4 0.01
155 89 0.19
156 5 0.01
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (151 bp):
TTTTTTAAAAAAAGAGAAAGTTTAGATTTAAAAAAAATAAAACTATTTTTTTTTTAGTCATTTTA
AAGGAAATTTAAAATTTTAAAACAAAATTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTGA
TCTTTAAGAAAAATAGTTTTT
Found at i:19016085 original size:139 final size:132
Alignment explanation
Indices: 19015760--19016158 Score: 462
Period size: 138 Copynumber: 2.9 Consensus size: 132
19015750 ATTTTAAAAC
* * * *
19015760 AAAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGCTTTGATCTTTAATAAAAGTAGTGTTTT
1 AAAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGATTTGATCTTTAAGAAAAATAGTTTTTT
* *
19015825 TTTAAAGAGAAAGTTTAGATTTAAAAAAAAATAAAAATCTGCTTTTTTTTTAGTCATTTTAAATT
66 TTTAAAGAGAAAGTTTAGATTT---ATAAAATAAAAATATG---TTTTTTTAGTCATTTTAAATT
19015890 TAAATTTA
125 TAAATTTA
** * *
19015898 AAAAAATTGATTTTTTACAACTATTTCAAAATAAAAGATTTGATCTTTAAGAAAAATAGTTTTTT
1 AAAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGATTTGATCTTTAAGAAAAATAGTTTTTT
*
19015963 TTTAAAAAAAAAAGAGAAAGTTTAGATTT-TTAAATAAAAATATGTTTTTTTAGTCATTTTAAAT
66 TTT-------AAAGAGAAAGTTTAGATTTATAAAATAAAAATATGTTTTTTTAGTCATTTTAAAT
19016027 TTAAA-TTA
124 TTAAATTTA
*** * *
19016035 ATTTTTTTTTGATTTTTTTCAATTATTTCAAAATAAAAGTTTTGATCTTTAAGAAAAATAGTTTT
1 A--AAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGATTTGATCTTTAAGAAAAATAG-TTT
* * *
19016100 TTTTTTAAATAGAAAGTTTAGATTTCTAAAATAAAAATATG-TTTATTAGTCATTTTAAA
63 TTTTTTAAAGAGAAAGTTTAGATTTATAAAATAAAAATATGTTTTTTTAGTCATTTTAAA
19016159 GGAAAATTTT
Statistics
Matches: 228, Mismatches: 22, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
133 35 0.15
134 14 0.06
137 4 0.02
138 85 0.37
139 50 0.22
140 9 0.04
141 12 0.05
145 19 0.08
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (132 bp):
AAAATTTTGATTTTTTTCAAATATTTCAAAATAAAAGATTTGATCTTTAAGAAAAATAGTTTTTT
TTTAAAGAGAAAGTTTAGATTTATAAAATAAAAATATGTTTTTTTAGTCATTTTAAATTTAAATT
TA
Found at i:19018316 original size:18 final size:19
Alignment explanation
Indices: 19018293--19018329 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19018283 AAGTTAAAGT
19018293 ATTACTTAAACT-AATTAA
1 ATTACTTAAACTAAATTAA
*
19018311 ATTACTTAACCTAAATTAA
1 ATTACTTAAACTAAATTAA
19018330 CTTGATGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTACTTAAACTAAATTAA
Found at i:19035360 original size:30 final size:31
Alignment explanation
Indices: 19035326--19035385 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19035316 AAACCTTTTA
19035326 TTTTCCCCCAAAA-TTTGTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTT-TACTCCCTTCCCAC
* *
19035356 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
19035386 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.20, C:0.40, G:0.02, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:19038120 original size:3 final size:3
Alignment explanation
Indices: 19038106--19038158 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
19038096 TCCTCAAGAC
*
19038106 CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
19038154 CAT CA
1 CAT CA
19038159 CTTCTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:19043584 original size:20 final size:20
Alignment explanation
Indices: 19043559--19043596 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19043549 GTTTTTAATT
19043559 GAAGTTAGATCGGGGAAATC
1 GAAGTTAGATCGGGGAAATC
19043579 GAAGTTAGATCGGGGAAA
1 GAAGTTAGATCGGGGAAA
19043597 GTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.37, T:0.18
Consensus pattern (20 bp):
GAAGTTAGATCGGGGAAATC
Found at i:19053045 original size:18 final size:18
Alignment explanation
Indices: 19053024--19053066 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
19053014 ATAATTTAAA
19053024 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
19053042 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
19053060 ATGTAAA
1 ATATAAA
19053067 AACAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:19064483 original size:78 final size:78
Alignment explanation
Indices: 19064393--19064553 Score: 261
Period size: 78 Copynumber: 2.1 Consensus size: 78
19064383 GGGAGCAACA
* *
19064393 AGAAATTTTTTAGAAGCTTAAGTTCGTGCTAACTCAAGCACCTGTTTTGATCTAGCCTAAGTCTG
1 AGAAATTTTTTAGAAGCTTAAGTTCGTGCTAACTCAAGCACCTGTTTTGATCCAACCTAAGTCTG
19064458 GGAAGGACTATAT
66 GGAAGGACTATAT
** * *
19064471 AGAAATTTTTTAGAAGCTTAAGTTCGTTTTGACTCAAGCACCTGTTTTGATCCAACCTGAGTCTG
1 AGAAATTTTTTAGAAGCTTAAGTTCGTGCTAACTCAAGCACCTGTTTTGATCCAACCTAAGTCTG
19064536 GGAAGGACTATAT
66 GGAAGGACTATAT
19064549 A-AAAT
1 AGAAAT
19064554 ACAATGATGC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 4 0.05
78 73 0.95
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (78 bp):
AGAAATTTTTTAGAAGCTTAAGTTCGTGCTAACTCAAGCACCTGTTTTGATCCAACCTAAGTCTG
GGAAGGACTATAT
Found at i:19069309 original size:24 final size:22
Alignment explanation
Indices: 19069266--19069382 Score: 86
Period size: 20 Copynumber: 5.5 Consensus size: 22
19069256 TAATATTTTA
*
19069266 ATTTATAATATTAATTTTAAAT
1 ATTTATAATATTAATATTAAAT
*
19069288 ATTTATAAGTAATTAATATTAATT
1 ATTTATAA-T-ATTAATATTAAAT
* *
19069312 ATTTATAAAATTTA-ATTATAAT
1 ATTTATAATATTAATATTA-AAT
*
19069334 A--TATAA-ACT-ATATTTAAAT
1 ATTTATAATATTAATA-TTAAAT
*
19069353 ATTTA-AATA-TAAAATTAAAT
1 ATTTATAATATTAATATTAAAT
*
19069373 ATTTGTAATA
1 ATTTATAATA
19069383 AGATATTGAC
Statistics
Matches: 77, Mismatches: 8, Indels: 21
0.73 0.08 0.20
Matches are distributed among these distances:
18 1 0.01
19 7 0.09
20 21 0.27
21 13 0.17
22 15 0.19
23 1 0.01
24 19 0.25
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTATAATATTAATATTAAAT
Found at i:19070364 original size:13 final size:13
Alignment explanation
Indices: 19070346--19070373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19070336 TTTAAATGCA
19070346 TTTAGGCCAACAT
1 TTTAGGCCAACAT
19070359 TTTAGGCCAACAT
1 TTTAGGCCAACAT
19070372 TT
1 TT
19070374 CAGAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
TTTAGGCCAACAT
Found at i:19073908 original size:12 final size:11
Alignment explanation
Indices: 19073881--19073913 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
19073871 TAAATCACAC
19073881 AATCCACAAAA
1 AATCCACAAAA
19073892 AATCCACAAATA
1 AATCCACAAA-A
19073904 AATCC-CAAAA
1 AATCCACAAAA
19073914 TAGATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.61, C:0.27, G:0.00, T:0.12
Consensus pattern (11 bp):
AATCCACAAAA
Found at i:19074261 original size:11 final size:10
Alignment explanation
Indices: 19074235--19074277 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
19074225 AGATACAGAG
19074235 ATAAAAAACT-
1 ATAAAAAA-TA
19074245 ATAAAAAATA
1 ATAAAAAATA
19074255 ATGAAAAAATA
1 AT-AAAAAATA
19074266 AT-AAAAATA
1 ATAAAAAATA
19074275 ATA
1 ATA
19074278 GTGCATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 10 0.33
10 10 0.33
11 10 0.33
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:19075328 original size:68 final size:68
Alignment explanation
Indices: 19075219--19075354 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
19075209 GACACCAAAT
19075219 CCCATAATACTAAAATGTCGAGTGATACCTCTAAGACAGAATGATATAGCTCGTGGGTCATCCCC
1 CCCATAATACTAAAATGTCGAGTGATACCTCTAAGACAGAATGATATAGCTCGTGGGTCATCCCC
19075284 AAC
66 AAC
19075287 CCCATAATACTAAAATGTCGAGTGATACCTCTAAGACAGAATGATATAGCTCGTGGGTCATCCCC
1 CCCATAATACTAAAATGTCGAGTGATACCTCTAAGACAGAATGATATAGCTCGTGGGTCATCCCC
19075352 AAC
66 AAC
19075355 GATAGCACTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (68 bp):
CCCATAATACTAAAATGTCGAGTGATACCTCTAAGACAGAATGATATAGCTCGTGGGTCATCCCC
AAC
Found at i:19082812 original size:21 final size:21
Alignment explanation
Indices: 19082772--19082821 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19082762 ACAATTATCT
* **
19082772 ATATCTGGCAGCTTGTCTACA
1 ATATCTGGTAGCTTACCTACA
*
19082793 TTATCTGGTAGCTTACCTACA
1 ATATCTGGTAGCTTACCTACA
19082814 ATAT-TGGT
1 ATATCTGGT
19082822 GTGTTAATGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
ATATCTGGTAGCTTACCTACA
Found at i:19104836 original size:9 final size:9
Alignment explanation
Indices: 19104822--19104867 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
19104812 TATATTTTGA
19104822 TATTCGAAT
1 TATTCGAAT
19104831 TATTCGAAT
1 TATTCGAAT
19104840 TATTCGAAT
1 TATTCGAAT
19104849 TATTC-AAGT
1 TATTCGAA-T
*
19104858 TAGTCGAAT
1 TATTCGAAT
19104867 T
1 T
19104868 TGAAAACTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
8 2 0.06
9 30 0.88
10 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19112953 original size:24 final size:24
Alignment explanation
Indices: 19112926--19112973 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19112916 AAATTAGTAA
19112926 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
19112950 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
19112974 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:19114918 original size:24 final size:24
Alignment explanation
Indices: 19114891--19114938 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19114881 AAATTAGTAA
19114891 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
19114915 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
19114939 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:19115784 original size:94 final size:94
Alignment explanation
Indices: 19115592--19115836 Score: 361
Period size: 94 Copynumber: 2.6 Consensus size: 94
19115582 TAGCTTTGAT
* * *
19115592 GTTGTCCGAATATGGTGTTAAAAATACT-TCTTAAATTGG-TTTTTCATGCTATCAGAGTAGAGT
1 GTTGTCCGAATATGGTGTTAAAAATACTGT-TTAAATTGGTTTTTTCATGCTGTCCGAATAGAGT
* *
19115655 ATTAACAGGCCGGAAATTTTGGTTATTTAT
65 ATTAACAGGCCGGAAATTTTGGTTATTCAG
* * *
19115685 TTTGTCCGAATATTGTGTTAAAAATACTGTTTAAATTGGTTTTTTCATGCTGTCCGAATAGGGTA
1 GTTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTTTCATGCTGTCCGAATAGAGTA
*
19115750 TTAACAGGCTGGAAATTTTGGTTATTCAG
66 TTAACAGGCCGGAAATTTTGGTTATTCAG
* *
19115779 GTTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTCT-ATGTTGTCCGAAT
1 GTTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTTTCATGCTGTCCGAAT
19115837 CTGGGGTTAA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
93 47 0.34
94 90 0.66
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (94 bp):
GTTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTTTCATGCTGTCCGAATAGAGTA
TTAACAGGCCGGAAATTTTGGTTATTCAG
Found at i:19115818 original size:47 final size:46
Alignment explanation
Indices: 19115686--19115848 Score: 152
Period size: 47 Copynumber: 3.5 Consensus size: 46
19115676 GTTATTTATT
*
19115686 TTGTCCGAATATTGTGTTAAAAATACTGTTTAAATTGGTTTTTTCATG
1 TTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGG--TTTTCATG
* * * * ** * *
19115734 CTGTCCGAATAGGGTATT-AACAGGCTG--GAAATTTTGGTTATTCAGG
1 TTGTCCGAATATGGTGTTAAAAATACTGTTTAAA--TTGGTT-TTCATG
19115780 TTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTCTATG
1 TTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTC-ATG
* *
19115827 TTGTCCGAATCTGGGGTTAAAA
1 TTGTCCGAATATGGTGTTAAAA
19115849 TTCTGCTCAA
Statistics
Matches: 89, Mismatches: 19, Indels: 15
0.72 0.15 0.12
Matches are distributed among these distances:
45 5 0.06
46 23 0.26
47 44 0.49
48 14 0.16
49 3 0.03
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (46 bp):
TTGTCCGAATATGGTGTTAAAAATACTGTTTAAATTGGTTTTCATG
Found at i:19116435 original size:51 final size:51
Alignment explanation
Indices: 19116353--19116531 Score: 198
Period size: 52 Copynumber: 3.5 Consensus size: 51
19116343 ATGTCAATCA
* * * *
19116353 TGGTTTTGCGGAGATTCGGTTGGGGTGTAAGGGGACTGTTATTTGGA-AAAT
1 TGGTTTTGCGGAGGTTCGGTTGGGATGTAAGGAGACTGTTATTT-GATAACT
* * * *
19116404 TGGTTTTGCGGTGGTTTGGTTGGGATTTAAGGAAACTGTTTATTTGATAACT
1 TGGTTTTGCGGAGGTTCGGTTGGGATGTAAGGAGACTG-TTATTTGATAACT
* * * *
19116456 TGGTTTTACGGAGGCTCGATTGGGATGTAAGGAGACTATTTATTTGATAACT
1 TGGTTTTGCGGAGGTTCGGTTGGGATGTAAGGAGACT-GTTATTTGATAACT
* *
19116508 TGGTTTTGCAGAGGTCCGGTTGGG
1 TGGTTTTGCGGAGGTTCGGTTGGG
19116532 TTAAAAGGAG
Statistics
Matches: 104, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 33 0.32
52 71 0.68
ACGTcount: A:0.20, C:0.08, G:0.35, T:0.38
Consensus pattern (51 bp):
TGGTTTTGCGGAGGTTCGGTTGGGATGTAAGGAGACTGTTATTTGATAACT
Found at i:19118656 original size:156 final size:146
Alignment explanation
Indices: 19118478--19119202 Score: 901
Period size: 142 Copynumber: 5.0 Consensus size: 146
19118468 GAGCACATAG
* *
19118478 ATATAATTAATATATGAATTTGATTCATACAAAATATCATTTGTATATATTTTACCCAATTTATT
1 ATAT-ATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCCAATTTATT
* *
19118543 AATATAAACATTTATACTAATTAATTTTTGTCAAAATATAAAAGATATGAAAATTAATATTCTTT
65 AATATAAACAGTTATATTAATTAATTTTTGTCAAAATATAAAAGATATGAAAATTAATATTCTTT
19118608 TGGAAAGAATATAATTAA
130 TGGAAAGAATATAATT-A
* * *
19118626 TATTTTGGATTAAATTAATATATGAATTTGATCCATCCAAAATATTAATTGTATATATTTTACCG
1 -A---T--A-T--ATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCC
* * ** *
19118691 AATTTATTAATATAAACAATTATATTAATTAA-TTTTGATCAAAATATAAAATATATTTAAGTTA
57 AATTTATTAATATAAACAGTTATATTAATTAATTTTTG-TCAAAATATAAAAGATATGAAAATTA
19118755 ATATTCTTTTGGAAAG-A-AT-A-T-
121 ATATTCTTTTGGAAAGAATATAATTA
* * *
19118776 A-AT-TTAATATATGAATTTAATTCATACAAAATATTAATTGTATACATTTTACCGAATTTATTA
1 ATATATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCCAATTTATTA
* ** * *
19118839 ATATAAACAGTTATATGAATTAATTTCGGTAAAAATATAAAAGACATGAAAATTAATATTCTTTT
66 ATATAAACAGTTATATTAATTAATTTTTGTCAAAATATAAAAGATATGAAAATTAATATTCTTTT
19118904 GGAAAGAATATAATTA
131 GGAAAGAATATAATTA
* *
19118920 ATATA-T-A-A-ATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTA
1 ATATATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCCAATTTATTA
** * * *
19118981 ATATAAACAGTTATATTAATTAATTTAAGCCAAAATATAAAAGACATGAAAATTAATATGCTTTT
66 ATATAAACAGTTATATTAATTAATTTTTGTCAAAATATAAAAGATATGAAAATTAATATTCTTTT
19119046 GGAAAGAATATAATT-
131 GGAAAGAATATAATTA
* * * *
19119061 A-ACA-T-ATATATGAATTTTATTCATACAAAATTTTAATTGTATATATTGTA-CCAATTTTATT
1 ATATATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCCAA-TTTATT
* *
19119122 AATATAAACAGGTAAATTAATTAATTTTTGTCAAAATATAAAAG-TCATGAAAATTAATATTCTT
65 AATATAAACAGTTATATTAATTAATTTTTGTCAAAATATAAAAGAT-ATGAAAATTAATATTCTT
19119186 TTGGAAAGAATATAATT
129 TTGGAAAGAATATAATT
19119203 CATTTTTCTA
Statistics
Matches: 509, Mismatches: 47, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
139 113 0.22
140 8 0.02
141 7 0.01
142 242 0.48
143 3 0.01
144 2 0.00
145 3 0.01
149 2 0.00
152 2 0.00
153 1 0.00
154 3 0.01
155 7 0.01
156 116 0.23
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.41
Consensus pattern (146 bp):
ATATATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCCAATTTATTA
ATATAAACAGTTATATTAATTAATTTTTGTCAAAATATAAAAGATATGAAAATTAATATTCTTTT
GGAAAGAATATAATTA
Found at i:19119390 original size:75 final size:76
Alignment explanation
Indices: 19119178--19119408 Score: 312
Period size: 75 Copynumber: 3.1 Consensus size: 76
19119168 ATGAAAATTA
* * *
19119178 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTATATTAAT-AGT
1 ATATTTTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA
*
19119242 GAAATAATTCT
66 GGAATAATTCT
* * * *
19119253 ATATTATTTTGGAAATAATATGATTCATTTTTCTAATTTTCCATTTGTCTTCTCTATTAATAAG-
1 ATATTTTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA
19119317 GGAATAATTCT
66 GGAATAATTCT
*
19119328 ATATTTTTTTGGAAA-AACTATAATTTC-TTTTTCTAACTTTCCTTTTGTCTTCTCTATTAATAA
1 ATATTTTTTTGGAAAGAA-TATAA-TTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAA
*
19119391 GAGG-ATAATCCT
64 GAGGAATAATTCT
19119403 A-ATTTT
1 ATATTTT
19119409 CCTCTTTAAT
Statistics
Matches: 141, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
74 7 0.05
75 127 0.90
76 7 0.05
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (76 bp):
ATATTTTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA
GGAATAATTCT
Found at i:19123993 original size:13 final size:13
Alignment explanation
Indices: 19123975--19124004 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19123965 TCCAGAAACT
19123975 ATGAATTTATTTC
1 ATGAATTTATTTC
*
19123988 ATGAATTTATTTG
1 ATGAATTTATTTC
19124001 ATGA
1 ATGA
19124005 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:19124175 original size:50 final size:50
Alignment explanation
Indices: 19124100--19124342 Score: 342
Period size: 50 Copynumber: 4.8 Consensus size: 50
19124090 ATTTGGGTAA
*
19124100 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
19124150 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
19124200 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
19124250 AGAGGTCCCCCGTATGACCATGTCTGGGACATGGCATGGGCGCCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
19124300 AGAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19124343 TGTTATTATC
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 137 0.82
51 31 0.18
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:19137925 original size:5 final size:5
Alignment explanation
Indices: 19137890--19137945 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
19137880 TGCCAAATTC
* * * *
19137890 TCTCT TTTC- TCTCT TC-CC TCTCT TCTTT TCTCT TCTCT TTTCT TCTCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT
19137938 TCCTCT TC
1 T-CTCT TC
19137946 ATTGTAGTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 6 0.15
5 29 0.73
6 5 0.12
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTCT
Found at i:19138658 original size:27 final size:27
Alignment explanation
Indices: 19138620--19138766 Score: 156
Period size: 27 Copynumber: 5.4 Consensus size: 27
19138610 GCGATTCATA
*
19138620 GGTAAAATGACTGAAATGCCCTCAAAG
1 GGTAAAATGACTGAAATACCCTCAAAG
* *
19138647 GGTAAAATGACTGAAATGCCC-CTGAAG
1 GGTAAAATGACTGAAATACCCTC-AAAG
*
19138674 GGTAAAATGACCGAAATACCCTCGAAA-
1 GGTAAAATGACTGAAATACCCTC-AAAG
* ** *
19138701 TGTAAAATGACCAAAATA-CTTCCAAAG
1 GGTAAAATGACTGAAATACCCT-CAAAG
* *
19138728 GGTAAAATGACTGAAATAACCTCATAG
1 GGTAAAATGACTGAAATACCCTCAAAG
19138755 GGTAAAATGACT
1 GGTAAAATGACT
19138767 ACTATACCCC
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.06
27 91 0.89
28 5 0.05
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCTCAAAG
Found at i:19138968 original size:26 final size:26
Alignment explanation
Indices: 19138938--19139018 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
19138928 TTTACCACAT
*
19138938 ATACTGTTACTGGCAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTCTACTGCG
* *
19138964 TTACTGTTACT-GCTAGCTTTACTGCG
1 ATACTGTTACTGGC-AGCTCTACTGCG
* *
19138990 ATACTATTACTGGCAGCTTTACTGCG
1 ATACTGTTACTGGCAGCTCTACTGCG
19139016 ATA
1 ATA
19139019 GTGGTGTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
25 2 0.04
26 44 0.92
27 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTCTACTGCG
Found at i:19145346 original size:5 final size:5
Alignment explanation
Indices: 19145311--19145366 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
19145301 TGCCAGATTC
* * *
19145311 TCTCT TTTC- TCTCT TC-CC TCTCT TCTAT TCTCT TCTCT TCTCT TCTTCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TC-TCT
*
19145360 CCTCT TC
1 TCTCT TC
19145367 ATTCTAGTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 6 0.15
5 30 0.75
6 4 0.10
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (5 bp):
TCTCT
Found at i:19145349 original size:15 final size:15
Alignment explanation
Indices: 19145329--19145371 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19145319 CTCTCTTCCC
19145329 TCTCTTCTATTCTCT
1 TCTCTTCTATTCTCT
*
19145344 TCTCTTCTCTTCTTCT
1 TCTCTTCTATTC-TCT
*
19145360 CCTCTTC-ATTCT
1 TCTCTTCTATTCT
19145372 AGTGCTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 14 0.58
16 9 0.38
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTCTTCTATTCTCT
Found at i:19146080 original size:27 final size:27
Alignment explanation
Indices: 19146038--19146293 Score: 234
Period size: 27 Copynumber: 9.5 Consensus size: 27
19146028 TGCAATTCAT
* *
19146038 GGGTAAAATGATTGAAATGCCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
19146065 GGGTAAAATGACTGAAATGCCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* *
19146092 GGGTAAAATGACTGAAAT-GCCTCTAAA
1 GGGTAAAATGACTGAAATACCCTC-GAA
* * * * *
19146119 TGTTAAAATTACCGAAATATCCTCGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
* * * *
19146146 TGGTAAAATGA-TAAAAATGCCCTTGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
* * * *
19146173 AGTTAAAATGACCGAAATACCCTTGAA
1 GGGTAAAATGACTGAAATACCCTCGAA
*
19146200 GGGTAAAATGA-TCGAAATTCCCTCGAA
1 GGGTAAAATGACT-GAAATACCCTCGAA
*
19146227 GGGTAAAATGACTGAAATACCC-CCATA
1 GGGTAAAATGACTGAAATACCCTCGA-A
* *
19146254 GGGTAAAATGACCGAAATACCC-CTATA
1 GGGTAAAATGACTGAAATACCCTCGA-A
19146281 GGGTAAAATGACT
1 GGGTAAAATGACT
19146294 CTTATGCCCA
Statistics
Matches: 191, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
26 6 0.03
27 180 0.94
28 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (27 bp):
GGGTAAAATGACTGAAATACCCTCGAA
Found at i:19146501 original size:26 final size:26
Alignment explanation
Indices: 19146470--19146548 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
19146460 CCACATATAC
* *
19146470 TGTTACTGGCAGCTCTGCTGCGTTAT
1 TGTTACTGGCAGCTTTGCTGCGATAT
* *
19146496 TGTTACTGGCAGCTTTACTGCGATAC
1 TGTTACTGGCAGCTTTGCTGCGATAT
*
19146522 TATTACTGGCAGCTTTGCTGCGATAT
1 TGTTACTGGCAGCTTTGCTGCGATAT
19146548 T
1 T
19146549 TGTGTGTTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTGCGATAT
Found at i:19154564 original size:22 final size:22
Alignment explanation
Indices: 19154536--19154579 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19154526 TGGAGTAGAA
19154536 CATAACTTATCCTTAAAGGCTT
1 CATAACTTATCCTTAAAGGCTT
*
19154558 CATAACTTATCCTTTAAGGCTT
1 CATAACTTATCCTTAAAGGCTT
19154580 GAAAAGCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (22 bp):
CATAACTTATCCTTAAAGGCTT
Found at i:19158377 original size:29 final size:29
Alignment explanation
Indices: 19158335--19158519 Score: 139
Period size: 29 Copynumber: 6.4 Consensus size: 29
19158325 TCATCGACCA
* * * *
19158335 ATGAAAAAGGATAGCTTTGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
19158364 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* * * *
19158393 ATAAAAAGGGAT-G-GT--GATGATCAATAACT
1 ATGAAAAGGGATAGCTTCGGCT-ATCGAT---T
* * * * * *
19158422 ATGAAAAGGGAT-GGTAACGACCATTGAAT
1 ATGAAAAGGGATAGCT-TCGGCTATCGATT
19158451 ATGAAAAGGGA-AGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
19158479 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
19158508 TTGAAAAGGGAT
1 ATGAAAAGGGAT
19158520 GGTGACGATC
Statistics
Matches: 121, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.02
26 5 0.04
27 1 0.01
28 20 0.17
29 90 0.74
32 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATT
Found at i:19158592 original size:29 final size:29
Alignment explanation
Indices: 19158355--19158592 Score: 121
Period size: 29 Copynumber: 8.2 Consensus size: 29
19158345 ATAGCTTTGG
* * *
19158355 CTATCAAATATGAAAAGGGATAGCTT-CGG
1 CTATCGAATATGAAAAGGGAT-GGTTACGA
* * * *
19158384 CTATCGATTATAAAAAGGGATGGTGATGA
1 CTATCGAATATGAAAAGGGATGGTTACGA
* *
19158413 TCAAT--AACTATGAAAAGGGATGGTAACGA
1 -CTATCGAA-TATGAAAAGGGATGGTTACGA
* * * * *
19158442 CCATTGAATATGAAAAGGGAAGCTT-CGG
1 CTATCGAATATGAAAAGGGATGGTTACGA
* * * *
19158470 CTATCGATTATGAAAAGGGATAGCTT-TGG
1 CTATCGAATATGAAAAGGGAT-GGTTACGA
* * *
19158499 CTATCGATTTTGAAAAGGGATGGTGACGA
1 CTATCGAATATGAAAAGGGATGGTTACGA
* * **
19158528 -TCATC-AATTAATAAAAAGGGTTGGTTTTGA
1 CT-ATCGAA-T-ATGAAAAGGGATGGTTACGA
* *
19158558 CCATCGAATATGAAAAGGGACGGTTACGA
1 CTATCGAATATGAAAAGGGATGGTTACGA
19158587 CTATCG
1 CTATCG
19158593 TTTAGCACAC
Statistics
Matches: 156, Mismatches: 41, Indels: 24
0.71 0.19 0.11
Matches are distributed among these distances:
28 29 0.19
29 102 0.65
30 23 0.15
31 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (29 bp):
CTATCGAATATGAAAAGGGATGGTTACGA
Found at i:19160776 original size:15 final size:15
Alignment explanation
Indices: 19160756--19160784 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19160746 TCGAGTAAGG
19160756 TGGGTTACAATTCTC
1 TGGGTTACAATTCTC
19160771 TGGGTTACAATTCT
1 TGGGTTACAATTCT
19160785 TTCTTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (15 bp):
TGGGTTACAATTCTC
Found at i:19168731 original size:23 final size:23
Alignment explanation
Indices: 19168705--19168749 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19168695 TGCTAAAACA
*
19168705 TGTAAGTTGTGGATAAACCACCT
1 TGTAAGTTATGGATAAACCACCT
*
19168728 TGTAGGTTATGGATAAACCACC
1 TGTAAGTTATGGATAAACCACC
19168750 AAATTTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (23 bp):
TGTAAGTTATGGATAAACCACCT
Found at i:19189331 original size:30 final size:30
Alignment explanation
Indices: 19189296--19189356 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
19189286 GGTACGGTAT
19189296 TTACAAAAAACTTCATGCATTATAAAGAGG
1 TTACAAAAAACTTCATGCATTATAAAGAGG
19189326 TTACAAAAAACTTCATGCATTATAAAGAGG
1 TTACAAAAAACTTCATGCATTATAAAGAGG
19189356 T
1 T
19189357 ATTTTGGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (30 bp):
TTACAAAAAACTTCATGCATTATAAAGAGG
Found at i:19189465 original size:16 final size:16
Alignment explanation
Indices: 19189444--19189480 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
19189434 TCTTTAGATT
19189444 TGAAAACTATAGACTG
1 TGAAAACTATAGACTG
*
19189460 TGAAAACTCTAGACTG
1 TGAAAACTATAGACTG
19189476 TGAAA
1 TGAAA
19189481 TCGATAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (16 bp):
TGAAAACTATAGACTG
Found at i:19210070 original size:12 final size:12
Alignment explanation
Indices: 19210055--19210083 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19210045 GAAAATATGA
19210055 CCCAAAACAATT
1 CCCAAAACAATT
19210067 CCCAAAACAATT
1 CCCAAAACAATT
19210079 CCCAA
1 CCCAA
19210084 TTGAGGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (12 bp):
CCCAAAACAATT
Found at i:19217484 original size:48 final size:48
Alignment explanation
Indices: 19217413--19217526 Score: 156
Period size: 48 Copynumber: 2.4 Consensus size: 48
19217403 ATGTGGCACG
* * *
19217413 GACTGTGTGCAAGCCACCAATATTCTGTTAAGATACAAGGGTGGTACA
1 GACTGTGTGCAGGCCACCAATATTCTGTTAAGACACAAAGGTGGTACA
** *
19217461 GACTGTGTGCAGGCCACCAATATTCTGTTATTACACAAAGGTGGTACG
1 GACTGTGTGCAGGCCACCAATATTCTGTTAAGACACAAAGGTGGTACA
* *
19217509 GACTATGTGTAGGCCACC
1 GACTGTGTGCAGGCCACC
19217527 GAGAAATCTG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (48 bp):
GACTGTGTGCAGGCCACCAATATTCTGTTAAGACACAAAGGTGGTACA
Found at i:19221148 original size:14 final size:14
Alignment explanation
Indices: 19221129--19221158 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19221119 AGTGAGAGAG
*
19221129 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
19221143 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
19221157 GA
1 GA
19221159 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:19225843 original size:20 final size:20
Alignment explanation
Indices: 19225795--19225843 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
19225785 CACTTTTCTC
*
19225795 TCTTCATTCCCTTTAATTGT
1 TCTTCATTTCCTTTAATTGT
*
19225815 TCTTCATTTCCTTTCATTGT
1 TCTTCATTTCCTTTAATTGT
19225835 TCTTCATTT
1 TCTTCATTT
19225844 TCTTCCCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.24, G:0.04, T:0.59
Consensus pattern (20 bp):
TCTTCATTTCCTTTAATTGT
Found at i:19232540 original size:13 final size:13
Alignment explanation
Indices: 19232522--19232546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19232512 CATTTGAATA
19232522 GTGTTTTAAATTT
1 GTGTTTTAAATTT
19232535 GTGTTTTAAATT
1 GTGTTTTAAATT
19232547 CTATCATGTT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
GTGTTTTAAATTT
Found at i:19232648 original size:29 final size:29
Alignment explanation
Indices: 19232616--19232744 Score: 127
Period size: 29 Copynumber: 4.4 Consensus size: 29
19232606 ACTATCGACC
* *
19232616 ATGAAATGGGATGGTGACGACCA-TCAATT
1 ATGAAAAGGGATGGTGATGACCATTCAA-T
* ** *
19232645 ATGAAAAGGGATGCTGAAAACCATTGAAT
1 ATGAAAAGGGATGGTGATGACCATTCAAT
* ** * *
19232674 ATGAAAAGGGATAGTTTTGACTATTGAAT
1 ATGAAAAGGGATGGTGATGACCATTCAAT
19232703 ATGAAAAGGGATGGTGATGACCA-TCGAAT
1 ATGAAAAGGGATGGTGATGACCATTC-AAT
19232732 ATGAAAAGGGATG
1 ATGAAAAGGGATG
19232745 ATTTCGACCA
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 1 0.01
29 77 0.95
30 3 0.04
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGATGACCATTCAAT
Found at i:19236606 original size:2 final size:2
Alignment explanation
Indices: 19236599--19236624 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19236589 GGAATAAACT
19236599 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
19236625 AAGCGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19239531 original size:6 final size:6
Alignment explanation
Indices: 19239520--19239545 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19239510 TACTCATCTT
19239520 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
19239546 AATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:19241170 original size:19 final size:20
Alignment explanation
Indices: 19241127--19241174 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
19241117 GATAGCAATT
*
19241127 TATAAAAATTAATATCAAAAT
1 TATAAAAATT-ATATCAAAAG
*
19241148 TATAAAAATT-TATTAAAAG
1 TATAAAAATTATATCAAAAG
19241167 TATAAAAA
1 TATAAAAA
19241175 AGTAGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TATAAAAATTATATCAAAAG
Found at i:19241497 original size:19 final size:18
Alignment explanation
Indices: 19241475--19241510 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19241465 ATTAGAAATT
19241475 ATTAAAATATTATAAAAAA
1 ATTAAAA-ATTATAAAAAA
*
19241494 ATTATAAATTATAAAAA
1 ATTAAAAATTATAAAAA
19241511 TTATAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTAAAAATTATAAAAAA
Found at i:19241504 original size:18 final size:17
Alignment explanation
Indices: 19241483--19241550 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 17
19241473 TTATTAAAAT
19241483 ATTATAAAAAAATTATAA
1 ATTAT-AAAAAATTATAA
19241501 ATTAT-AAAAATTAT-A
1 ATTATAAAAAATTATAA
* *
19241516 GTTATTAAAAATTATTAA
1 ATTATAAAAAATTA-TAA
19241534 ATGT-TAAAAAATT-TAA
1 AT-TATAAAAAATTATAA
19241550 A
1 A
19241551 ATTACAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.12
16 21 0.49
17 1 0.02
18 15 0.35
19 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTATAAAAAATTATAA
Found at i:19252842 original size:13 final size:13
Alignment explanation
Indices: 19252824--19252849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19252814 TGTCTTAATC
19252824 GCCTGGCCACACG
1 GCCTGGCCACACG
19252837 GCCTGGCCACACG
1 GCCTGGCCACACG
19252850 ACCGTGTGAC
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:0.15, C:0.46, G:0.31, T:0.08
Consensus pattern (13 bp):
GCCTGGCCACACG
Found at i:19255543 original size:20 final size:20
Alignment explanation
Indices: 19255518--19255556 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19255508 TTACTTCTTC
19255518 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
19255538 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
19255557 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:19255949 original size:50 final size:50
Alignment explanation
Indices: 19255757--19256003 Score: 194
Period size: 50 Copynumber: 4.8 Consensus size: 50
19255747 TGATAATAAT
* * * * * *
19255757 ATGCCAAAGCCATGTCCCAGACAGGGTCTTACATGGGATGTTTCCTGT-A
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCA
* * * * * * * *
19255806 TTGCCAATGCCATATCTCAGATATAGTCTTACATAGGAGT-TCTCATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATCTCA
* * * *
19255856 GTGCCCATGCCATGTCCCAGACATGGTCTTA-AGAGGGACCTCTCATCTCA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGATCTCTCATCTCA
*
19255906 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATCTCTCATAACCTCAATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCAT---CTC---A
** * *
19255962 ATATCAATTCCATGTCCTAGACATGGTCTTACATGGGATCTC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTC
19256004 ATTCCCTTAA
Statistics
Matches: 154, Mismatches: 33, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
49 36 0.23
50 77 0.50
53 3 0.02
56 38 0.25
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCA
Found at i:19260220 original size:17 final size:16
Alignment explanation
Indices: 19260198--19260229 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19260188 TTATAGATTA
19260198 TTGGAAGCTCGATCGGT
1 TTGGAAGCTC-ATCGGT
19260215 TTGGAAGCTCATCGG
1 TTGGAAGCTCATCGG
19260230 ATGATTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (16 bp):
TTGGAAGCTCATCGGT
Found at i:19262871 original size:20 final size:20
Alignment explanation
Indices: 19262839--19262941 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
19262829 TTCAACTATG
19262839 ATTAAACTTAATAACTTTAAT
1 ATTAAA-TTAATAACTTTAAT
*
19262860 ATTAAATTAATATAATACTTATCAAG
1 ATTAAATT-A-AT-A-ACTT-T-AAT
* *
19262886 ATAAATATTAGATTAAATTTAAT
1 ATTAA-ATTA-A-TAACTTTAAT
*
19262909 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATAACTTTAAT
19262929 ATTAAATTAATAA
1 ATTAAATTAATAA
19262942 AATACTATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 8 0.13
22 4 0.06
23 8 0.13
24 5 0.08
25 4 0.06
26 9 0.14
27 4 0.06
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (20 bp):
ATTAAATTAATAACTTTAAT
Found at i:19262958 original size:39 final size:37
Alignment explanation
Indices: 19262907--19262996 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 37
19262897 ATTAAATTTA
19262907 ATATTAAGATAATCACTTTAATATTAAATT-AATA-AAAT
1 ATATTAAGATAATCA--TTAA-ATTAAATTAAATATAAAT
*
19262945 ACTATTAAGATAATTATTAAATTAAATTAAATATTAAAT
1 A-TATTAAGATAATCATTAAATTAAATTAAATA-TAAAT
*
19262984 ATATTAAAATAAT
1 ATATTAAGATAAT
19262997 ATTTTTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
36 8 0.17
37 8 0.17
38 12 0.26
39 18 0.39
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (37 bp):
ATATTAAGATAATCATTAAATTAAATTAAATATAAAT
Found at i:19262979 original size:68 final size:69
Alignment explanation
Indices: 19262847--19262981 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 69
19262837 TGATTAAACT
* * *
19262847 TAATAACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATAACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATT
19262912 AAGA
66 AAGA
* * *
19262916 TAATCACTTTAATATTAAATTAATAAAATAC-TATTAAGATAATTATTAAATTAAATTAAATATT
1 TAATAACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATT
19262980 AA
66 AA
19262982 ATATATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 31 0.52
69 29 0.48
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (69 bp):
TAATAACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATT
AAGA
Found at i:19262994 original size:17 final size:17
Alignment explanation
Indices: 19262887--19262983 Score: 60
Period size: 17 Copynumber: 5.7 Consensus size: 17
19262877 CTTATCAAGA
*
19262887 TAAATATTAGATTAAAT
1 TAAATATTAAATTAAAT
*
19262904 TTAATATTAAGA-TAATCACT
1 TAAATATTAA-ATTAA--A-T
*
19262924 TTAATATTAAATT-AAT
1 TAAATATTAAATTAAAT
* *
19262940 AAAATACT--ATTAAGA-
1 TAAATATTAAATTAA-AT
*
19262955 TAATTATTAAATTAAAT
1 TAAATATTAAATTAAAT
19262972 TAAATATTAAAT
1 TAAATATTAAAT
19262984 ATATTAAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 8 0.13
17 28 0.46
18 1 0.02
19 3 0.05
20 12 0.20
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:19262997 original size:68 final size:69
Alignment explanation
Indices: 19262856--19262999 Score: 184
Period size: 68 Copynumber: 2.1 Consensus size: 69
19262846 TTAATAACTT
* * *
19262856 TAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGATAATC
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAGATAATC
***
19262921 ACTT
66 AAAA
* *
19262925 TAATATTAAATTAATAAAATAC-TATTAAGATAATTATTAAATTAAATTAAATATTAA-ATATAT
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAGATA-AT
*
19262988 TAAAA
65 CAAAA
19262993 TAATATT
1 TAATATT
19263000 TTTTAATAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 3 0.05
68 41 0.63
69 21 0.32
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (69 bp):
TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAGATAATC
AAAA
Found at i:19264297 original size:22 final size:22
Alignment explanation
Indices: 19264269--19264405 Score: 193
Period size: 22 Copynumber: 6.2 Consensus size: 22
19264259 TTTATTGTTC
*
19264269 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
19264291 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
19264313 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
19264335 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
19264357 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
19264379 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
19264401 AAACA
1 AAACA
19264406 AAAAGTTGTG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 103 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:19271145 original size:26 final size:26
Alignment explanation
Indices: 19271088--19271146 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
19271078 TATTTTCTCG
* * *
19271088 AAATTTTAGTAGGGGTAAAATTGTCA
1 AAATTTTACTAAGGGTAAAATCGTCA
*
19271114 AAATTTTACTAAGGGTAAAATCGTTA
1 AAATTTTACTAAGGGTAAAATCGTCA
*
19271140 ATATTTT
1 AAATTTT
19271147 GTTGGGGGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (26 bp):
AAATTTTACTAAGGGTAAAATCGTCA
Found at i:19272142 original size:29 final size:29
Alignment explanation
Indices: 19272100--19272157 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19272090 TTTCCATGTA
19272100 AGATTATTTTTTTATTTATAGAATTCTTG
1 AGATTATTTTTTTATTTATAGAATTCTTG
19272129 AGATTATTTTTTTATTTATAGAATTCTTG
1 AGATTATTTTTTTATTTATAGAATTCTTG
19272158 TGAGCCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (29 bp):
AGATTATTTTTTTATTTATAGAATTCTTG
Found at i:19278886 original size:19 final size:19
Alignment explanation
Indices: 19278850--19278886 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19278840 ACAAAGTAGA
* *
19278850 AAAAAATATTGATGCTAAG
1 AAAAAATATCGATACTAAG
19278869 AAAAAATATCGATACTAA
1 AAAAAATATCGATACTAA
19278887 ATTTGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAAAATATCGATACTAAG
Found at i:19297012 original size:57 final size:57
Alignment explanation
Indices: 19296936--19297045 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
19296926 TTTTACACTG
* * ***
19296936 ATTACCTTATACCTTGTACCTTGTTGCCATGGCATCTTTCATCCATGGTCTTATGCT
1 ATTACCTTATACCTCGTACCATGCAACCATGGCATCTTTCATCCATGGTCTTATGCT
*
19296993 ATTACCATT-TACCTCGTACCATGCAACCATGGCATCTTTCATCTATGGTCTTA
1 ATTACC-TTATACCTCGTACCATGCAACCATGGCATCTTTCATCCATGGTCTTA
19297046 CGTTACGTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 44 0.96
58 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (57 bp):
ATTACCTTATACCTCGTACCATGCAACCATGGCATCTTTCATCCATGGTCTTATGCT
Found at i:19299290 original size:40 final size:40
Alignment explanation
Indices: 19299208--19299328 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
19299198 ATGATGACAG
*
19299208 GAATAATTTTTAAAGAAAAAATGAAAG-AAAAATAATTAAAA
1 GAATAATTTTT-AAG-GAAAATGAAAGAAAAAATAATTAAAA
19299249 GAATAATTTTTAAGGAAAATGAAAGAAAAAATAATTAAAA
1 GAATAATTTTTAAGGAAAATGAAAGAAAAAATAATTAAAA
19299289 GAATAATTTTTAAGGAAAATGAAAGAAAAAATAATTAAAA
1 GAATAATTTTTAAGGAAAATGAAAGAAAAAATAATTAAAA
19299329 AGGGTTTGGT
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
39 10 0.13
40 57 0.73
41 11 0.14
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.25
Consensus pattern (40 bp):
GAATAATTTTTAAGGAAAATGAAAGAAAAAATAATTAAAA
Found at i:19303913 original size:25 final size:24
Alignment explanation
Indices: 19303875--19303970 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 24
19303865 GGTTATCGAT
19303875 TTCAGCTCGTATGAGCTTACCGTTA
1 TTCAGCTCG-ATGAGCTTACCGTTA
* *
19303900 TTCAGCTCGCATGAGCTTATCATTA
1 TTCAGCTCG-ATGAGCTTACCGTTA
*
19303925 TTCAGCTCAGATGAGCTTACCGTCA
1 TTCAGCTC-GATGAGCTTACCGTTA
* *
19303950 TTCAGCTTAGAGGAGCTTACC
1 TTCAGC-TCGATGAGCTTACC
19303971 ATTTACAGCT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
25 59 0.97
26 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (24 bp):
TTCAGCTCGATGAGCTTACCGTTA
Found at i:19303966 original size:50 final size:49
Alignment explanation
Indices: 19303874--19303994 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 49
19303864 GGGTTATCGA
* * * *
19303874 TTTCAGCTCGTATGAGCTTACCGTTATTCAGCTCGCATGAGCTTATCAT
1 TTTCAGCTCGTATGAGCTTACCGTCATTCAGCTAGCAGGAGCTTACCAT
19303923 TATTCAGCTCAG-ATGAGCTTACCGTCATTCAGCTTAG-AGGAGCTTACCAT
1 T-TTCAGCTC-GTATGAGCTTACCGTCATTCAGC-TAGCAGGAGCTTACCAT
* * *
19303973 TTACAGCTCGTAAGAGCATACC
1 TTTCAGCTCGTATGAGCTTACC
19303995 AATTCAGAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
48 1 0.02
49 17 0.28
50 40 0.66
51 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (49 bp):
TTTCAGCTCGTATGAGCTTACCGTCATTCAGCTAGCAGGAGCTTACCAT
Found at i:19309121 original size:17 final size:16
Alignment explanation
Indices: 19309085--19309144 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 16
19309075 GTGATGAATT
*
19309085 TATTGAATTTATATTA
1 TATTGAATTGATATTA
19309101 -ATTGAATTGATATATA
1 TATTGAATTGATAT-TA
19309117 TATTG-ATT-ATATTGA
1 TATTGAATTGATATT-A
19309132 TTATTTGAATTGA
1 -TA-TTGAATTGA
19309145 AATGAGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
14 1 0.03
15 17 0.47
16 7 0.19
17 7 0.19
18 3 0.08
19 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
TATTGAATTGATATTA
Found at i:19309130 original size:21 final size:22
Alignment explanation
Indices: 19309085--19309132 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
19309075 GTGATGAATT
*
19309085 TATTGA-ATTTATATTAATTGA
1 TATTGATATATATATTAATTGA
*
19309106 -ATTGATATATATATTGATT-A
1 TATTGATATATATATTAATTGA
19309126 TATTGAT
1 TATTGAT
19309133 TATTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TATTGATATATATATTAATTGA
Found at i:19309374 original size:40 final size:40
Alignment explanation
Indices: 19309265--19309404 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
19309255 GACTTCGAGT
* * * * *
19309265 CGATGAGACACTAGGTGTCAATTTACTACTTCGGACTAATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTC-GAATTATC
* * * *
19309306 CGATGAGGCACTAGGTG-CCAA-T-TTACTTCGATTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
*
19309343 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
* * *
19309383 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTAGGTGTCAAA
19309405 CTGGTGTGTT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
37 19 0.23
38 9 0.11
39 2 0.02
40 35 0.43
41 16 0.20
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
Found at i:19309638 original size:16 final size:16
Alignment explanation
Indices: 19309588--19309639 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
19309578 TTATATACTT
* *
19309588 ATGAATTGAGTATGGT
1 ATGAATTGAGTATTGC
*
19309604 ATGAAATGATGTATT-C
1 ATGAATTGA-GTATTGC
19309620 ATGAATTGAGTATTGC
1 ATGAATTGAGTATTGC
19309636 ATGA
1 ATGA
19309640 CTAATGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (16 bp):
ATGAATTGAGTATTGC
Found at i:19312293 original size:2 final size:2
Alignment explanation
Indices: 19312288--19312314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19312278 TTTAAAACTT
19312288 TA TA TA 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 T
19312315 CAATGTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19324062 original size:25 final size:25
Alignment explanation
Indices: 19324026--19324133 Score: 98
Period size: 24 Copynumber: 4.4 Consensus size: 25
19324016 CAGTTCGTGA
* * *
19324026 GAGCTTACCGTTATTCAGCTTGTAT
1 GAGCTTACCGTTACTCAACTCGTAT
*
19324051 GAGCTTATCGTTACTCAACTCGTAT
1 GAGCTTACCGTTACTCAACTCGTAT
* *
19324076 GAGCTTACAGATTA--CAACTCGTAG
1 GAGCTTACCG-TTACTCAACTCGTAT
* *
19324100 GAGCTTACCGATTA--CAGCTCGTAG
1 GAGCTTACCG-TTACTCAACTCGTAT
19324124 GAGCTTACCG
1 GAGCTTACCG
19324134 ATTCAGAGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
24 41 0.56
25 29 0.40
26 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGTTACTCAACTCGTAT
Found at i:19324098 original size:24 final size:24
Alignment explanation
Indices: 19324066--19324136 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
19324056 TATCGTTACT
* *
19324066 CAACTCGTATGAGCTTACAGATTA
1 CAACTCGTAGGAGCTTACCGATTA
19324090 CAACTCGTAGGAGCTTACCGATTA
1 CAACTCGTAGGAGCTTACCGATTA
*
19324114 CAGCTCGTAGGAGCTTACCGATT
1 CAACTCGTAGGAGCTTACCGATT
19324137 CAGAGCTCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (24 bp):
CAACTCGTAGGAGCTTACCGATTA
Found at i:19338809 original size:10 final size:10
Alignment explanation
Indices: 19338794--19338831 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
19338784 CATCATACAT
19338794 TGTGATTATA
1 TGTGATTATA
19338804 TGTGATTATA
1 TGTGATTATA
*
19338814 TGTGCTTATA
1 TGTGATTATA
19338824 TGTGATTA
1 TGTGATTA
19338832 ATATACGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (10 bp):
TGTGATTATA
Found at i:19342291 original size:31 final size:30
Alignment explanation
Indices: 19342255--19342323 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
19342245 CAATTTTCAT
*
19342255 AATTTTTATGAAA-ATCTGATAATTTTT-TATG
1 AATTTTTAT-AAATATCTAAT-ATTTTTCT-TG
*
19342286 AATTTTTATAAATATTTAATATTTTTCTTG
1 AATTTTTATAAATATCTAATATTTTTCTTG
19342316 AATTTTTA
1 AATTTTTA
19342324 ATATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
AATTTTTATAAATATCTAATATTTTTCTTG
Found at i:19342296 original size:20 final size:20
Alignment explanation
Indices: 19342246--19342296 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
19342236 TAGATTAATC
19342246 AATTTTCATAATTTTTATGA
1 AATTTTCATAATTTTTATGA
* * *
19342266 AAATCTGATAATTTTTTATG-
1 AATTTTCATAA-TTTTTATGA
*
19342286 AATTTTTATAA
1 AATTTTCATAA
19342297 ATATTTAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
AATTTTCATAATTTTTATGA
Found at i:19342311 original size:20 final size:19
Alignment explanation
Indices: 19342287--19342355 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
19342277 TTTTTTATGA
*
19342287 ATTTTTATAAATATTTAAT
1 ATTTTTTTAAATATTTAAT
* *
19342306 ATTTTTCTTGAATTTTTAATAT
1 ATTTTT-TTAAATATTT-A-AT
19342328 ATTTTTTTATAATATTTAGAT
1 ATTTTTTTA-AATATTTA-AT
19342349 -TTTTTTT
1 ATTTTTTT
19342356 TTGAATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 6 0.15
20 14 0.35
21 6 0.15
22 14 0.35
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTTTTAAATATTTAAT
Found at i:19343586 original size:10 final size:10
Alignment explanation
Indices: 19343563--19343598 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
19343553 AGTCATTTAT
19343563 AAATATGGACA
1 AAAT-TGGACA
*
19343574 AAATTGGAAA
1 AAATTGGACA
19343584 AAATTGGACA
1 AAATTGGACA
19343594 AAATT
1 AAATT
19343599 TTAAGTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (10 bp):
AAATTGGACA
Found at i:19344463 original size:73 final size:73
Alignment explanation
Indices: 19344344--19344491 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
19344334 AGCAGGCAAA
19344344 TAGACAAAGAAACATAAATAAAGTAAATTATCATGTGATGTGAGAGTGAGAGAGAGAGTGAGAGT
1 TAGACAAAGAAACATAAATAAAGTAAATTATCATGTGATGTGAGAGTGAGAGAGAGAGTGAGAGT
19344409 ATATATGT
66 ATATATGT
19344417 TAGACAAAGAAACATAAATAAAGTAAATTATCATGTGATGTGAGAGTGAGAGAGAGAGTGAGAGT
1 TAGACAAAGAAACATAAATAAAGTAAATTATCATGTGATGTGAGAGTGAGAGAGAGAGTGAGAGT
19344482 ATATATGT
66 ATATATGT
19344490 TA
1 TA
19344492 TTACTATTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.45, C:0.04, G:0.26, T:0.25
Consensus pattern (73 bp):
TAGACAAAGAAACATAAATAAAGTAAATTATCATGTGATGTGAGAGTGAGAGAGAGAGTGAGAGT
ATATATGT
Found at i:19344587 original size:2 final size:2
Alignment explanation
Indices: 19344580--19344606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19344570 TTTCTTCAAA
19344580 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
19344607 AAATCGCGCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19346176 original size:31 final size:32
Alignment explanation
Indices: 19346130--19346191 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
19346120 TTCCTTATAT
*
19346130 CAATTTATTGGGTAATTTTCAAGCTTTGATAG
1 CAATTTATTGGGTAATTTTCAAGCTCTGATAG
* *
19346162 CAATTTGTT-GGTAATTTTCGAGCTCTGATA
1 CAATTTATTGGGTAATTTTCAAGCTCTGATA
19346192 TTCGTTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (32 bp):
CAATTTATTGGGTAATTTTCAAGCTCTGATAG
Found at i:19348675 original size:120 final size:120
Alignment explanation
Indices: 19348538--19348855 Score: 627
Period size: 120 Copynumber: 2.6 Consensus size: 120
19348528 GAATTTTTGT
19348538 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
19348603 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
19348658 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
19348723 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
*
19348778 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
19348843 TAATTATGTTAAA
66 TAATTATGTTAAA
19348856 ATATGATTAA
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 197 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (120 bp):
TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
Found at i:19348685 original size:61 final size:61
Alignment explanation
Indices: 19348620--19348807 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
19348610 GTTAAATTAT
19348620 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
* * * * ** * ** * *
19348681 ATTTTATTA-AATTATATATTTTAATTAAAATATTTTTA-ATAATAAT-TATG-TTAAATT-A-T
1 ATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATAT-TGATT--ATTAAGA
19348740 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
19348801 ATTTTAT
1 ATTTTAT
19348808 TAAATTATAT
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
58 2 0.02
59 32 0.34
60 20 0.21
61 39 0.41
62 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
Found at i:19348952 original size:157 final size:157
Alignment explanation
Indices: 19348791--19349098 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
19348781 AAGAATATTG
* *
19348791 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATGTTAAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
* *
19348856 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
19348921 ATAATTTACCAAAACAAATTTCTGGTA
131 ATAATTTACCAAAACAAATTTCTGGTA
*
19348948 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
19349013 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
19349078 ATCATTTACCAAAACAAATTT
131 ATAATTTACCAAAACAAATTT
19349099 ATGCTAAGGG
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTCTGGTA
Found at i:19348986 original size:18 final size:17
Alignment explanation
Indices: 19348958--19348992 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19348948 ATTATTAAGA
*
19348958 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19348975 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19348993 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19349249 original size:16 final size:16
Alignment explanation
Indices: 19349228--19349263 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
19349218 GATTTGCTAT
19349228 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19349244 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19349260 TACA
1 TACA
19349264 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19351211 original size:22 final size:20
Alignment explanation
Indices: 19351172--19351213 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
19351162 TCAAATATTG
*
19351172 CAAATATTAAAATCTGAATT
1 CAAATATTAAAATATGAATT
19351192 CAAATATACTAAAATATGAATT
1 CAAATAT--TAAAATATGAATT
19351214 AATTAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
CAAATATTAAAATATGAATT
Found at i:19351225 original size:21 final size:22
Alignment explanation
Indices: 19351179--19351225 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
19351169 TTGCAAATAT
* *
19351179 TAAAATCTGAATTCAAATATAC
1 TAAAATATGAATTCAAATAAAC
*
19351201 TAAAATATGAATT-AATTAAAC
1 TAAAATATGAATTCAAATAAAC
19351222 TAAA
1 TAAA
19351226 CATAATTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (22 bp):
TAAAATATGAATTCAAATAAAC
Found at i:19362649 original size:135 final size:135
Alignment explanation
Indices: 19362407--19362672 Score: 478
Period size: 135 Copynumber: 2.0 Consensus size: 135
19362397 GTGATATTTT
19362407 AACATGTTACAAACTTCATATTGGTTGGTTTTGAATGCCTATTTATGCCATGGTTGTATGCACAT
1 AACATGTTACAAACTTCATATTGGTTGGTTTTGAATGCCTATTTATGCCATGGTTGTATGCACAT
* *
19362472 TGTTGAGCTTAGGTTGGTACCACTTTGGGTGAGAAATATGGCTTGGAAAATGGCCCATTTTGTCC
66 TGTTGAACTTAGGTTGGTACCACTTTGGGTGAGAAATATGGCTTGGAAAATAGCCCATTTTGTCC
19362537 ATACG
131 ATACG
* *
19362542 AACATGTTACAAACTTCATATTGGTTGGTTTTGAATGCCTATTTGTGCCATGGTTGTATGCATAT
1 AACATGTTACAAACTTCATATTGGTTGGTTTTGAATGCCTATTTATGCCATGGTTGTATGCACAT
* *
19362607 TGTTGAACTTAGGTTGGTATCACTTTGGGTGAGAAATATGGCTTGGAAAATAGCCTATTTTGTCC
66 TGTTGAACTTAGGTTGGTACCACTTTGGGTGAGAAATATGGCTTGGAAAATAGCCCATTTTGTCC
19362672 A
131 A
19362673 CACGGGCGTG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
135 125 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (135 bp):
AACATGTTACAAACTTCATATTGGTTGGTTTTGAATGCCTATTTATGCCATGGTTGTATGCACAT
TGTTGAACTTAGGTTGGTACCACTTTGGGTGAGAAATATGGCTTGGAAAATAGCCCATTTTGTCC
ATACG
Found at i:19365568 original size:16 final size:15
Alignment explanation
Indices: 19365549--19365578 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19365539 ATTTAATTGT
19365549 AACAAAATCTAAACAA
1 AACAAAAT-TAAACAA
19365565 AACAAAATTAAACA
1 AACAAAATTAAACA
19365579 TTTGAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.13
Consensus pattern (15 bp):
AACAAAATTAAACAA
Found at i:19372044 original size:19 final size:19
Alignment explanation
Indices: 19372035--19372095 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
19372025 AGAAAAAATC
* *
19372035 AAAATCAAAATTAAAATAA
1 AAAATCAAAATAAAAAGAA
*
19372054 AAAA-CAAAAAGAAAAAGAA
1 AAAATC-AAAATAAAAAGAA
* *
19372073 AAAATCAAAGTCAAAAGCAA
1 AAAATCAAAATAAAAAG-AA
19372093 AAA
1 AAA
19372096 GAGGAATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.03
19 26 0.79
20 6 0.18
ACGTcount: A:0.75, C:0.08, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAATCAAAATAAAAAGAA
Found at i:19372095 original size:38 final size:38
Alignment explanation
Indices: 19372016--19372095 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
19372006 AAAAGAAAAG
* * * *
19372016 AAAAGAAAAAGAAAAAATCAAAATCAAAATTAAAATAA
1 AAAACAAAAAGAAAAAATAAAAATCAAAATCAAAAGAA
* *
19372054 AAAACAAAAAGAAAAAGA-AAAAATCAAAGTCAAAAGCA
1 AAAACAAAAAGAAAAA-ATAAAAATCAAAATCAAAAGAA
19372092 AAAA
1 AAAA
19372096 GAGGAATCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.09
Consensus pattern (38 bp):
AAAACAAAAAGAAAAAATAAAAATCAAAATCAAAAGAA
Found at i:19372550 original size:14 final size:13
Alignment explanation
Indices: 19372519--19372553 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
19372509 GAAGAAGGAT
19372519 GAAAAATGAAAAA
1 GAAAAATGAAAAA
*
19372532 GAAAAATGAAAGA
1 GAAAAATGAAAAA
19372545 GTAAAAATG
1 G-AAAAATG
19372554 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:19373882 original size:43 final size:43
Alignment explanation
Indices: 19373835--19373971 Score: 118
Period size: 42 Copynumber: 3.2 Consensus size: 43
19373825 AGAAGCAGAT
19373835 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
* ** * * * * * * * *
19373878 CTTGCC-TCCAT-TAGTT-GTAGTGGAGCTGGTTGAAGACAGCAGAT
1 CTTGCCTTCC-TGCA-TTAACAGCGAAGCAGATCGAAAACA-AAG-C
19373922 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
19373965 CTTGCCT
1 CTTGCCT
19373972 CCATCGGTTG
Statistics
Matches: 65, Mismatches: 22, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
42 18 0.28
43 18 0.28
44 11 0.17
45 18 0.28
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
Found at i:19373956 original size:87 final size:87
Alignment explanation
Indices: 19373737--19374217 Score: 793
Period size: 87 Copynumber: 5.5 Consensus size: 87
19373727 CAGATTAATG
* * * *
19373737 AAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGTAGATCGAAAGCAAAGTCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
19373802 TCGATTGTAGTGGAGCTGGTTA
66 TCGGTTGTAGTGGAGCTGGTTA
19373824 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
** *
19373888 TTAGTTGTAGTGGAGCTGGTTG
66 TCGGTTGTAGTGGAGCTGGTTA
*
19373910 AAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
19373975 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGTAGTGGAGCTGGTTA
* *
19373997 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAACCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
19374062 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGTAGTGGAGCTGGTTA
*
19374084 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAACAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
19374149 TCGGTTGTAGTGGAGCTGGTTA
66 TCGGTTGTAGTGGAGCTGGTTA
* ** *
19374171 AAGATAGCAGATCTTGCCTTCTTGCATTGGCAGTGAAGCAGATCGAA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA
19374218 GCCAATAGTC
Statistics
Matches: 369, Mismatches: 24, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 78 0.21
87 291 0.79
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGTAGTGGAGCTGGTTA
Found at i:19374058 original size:43 final size:43
Alignment explanation
Indices: 19373922--19374058 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 43
19373912 GACAGCAGAT
* *
19373922 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAAC
* * * * * * * * *
19373965 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGATAGC-AGAT
1 CTTGCCTTCC-TGC-ATTAACAGCGAAGCAGATCAAA-A-A-CAAAAC
19374009 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAAC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAAC
19374052 CTTGCCT
1 CTTGCCT
19374059 CCATCGGTTG
Statistics
Matches: 65, Mismatches: 20, Indels: 18
0.63 0.19 0.17
Matches are distributed among these distances:
42 16 0.25
43 20 0.31
44 12 0.18
45 17 0.26
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAAC
Found at i:19374455 original size:45 final size:43
Alignment explanation
Indices: 19374353--19374560 Score: 152
Period size: 44 Copynumber: 4.7 Consensus size: 43
19374343 GCATCAGGTT
* * * *
19374353 TTATCTCCCTGAAGTCACAGTGGAGCAGATTAAGTGAGCAGGTC
1 TTATCTCCCTGAAGTTACAGTGGAGCAGATGAAGTGAACA-ATC
* * *
19374397 TTATC-CCGACTGAAGTTGCAGTGGGGCAGATCGAAGATGACCAATC
1 TTATCTCC--CTGAAGTTACAGTGGAGCAGAT-GAAG-TGAACAATC
* ** *
19374443 TTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCCAATAATC
1 TTATCTCCCTGAAGTTACAGTGGAGCAGA-TGAAGTGAACAATC
* ** * *
19374487 CTATCTCCCTGAAGTTGTAGTGGAG-AGGATTAAAGT-AATAGATC
1 TTATCTCCCTGAAGTTACAGTGGAGCA-GA-TGAAGTGAACA-ATC
* *
19374531 TTATCTCTCTGAAGTTACAGTAGAGCAGAT
1 TTATCTCCCTGAAGTTACAGTGGAGCAGAT
19374561 CGTATCAAGT
Statistics
Matches: 132, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
43 8 0.06
44 64 0.48
45 42 0.32
46 11 0.08
47 7 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTACAGTGGAGCAGATGAAGTGAACAATC
Found at i:19380079 original size:14 final size:14
Alignment explanation
Indices: 19380060--19380086 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19380050 TAATTTTAAT
19380060 TATGATTTGAAGTA
1 TATGATTTGAAGTA
19380074 TATGATTTGAAGT
1 TATGATTTGAAGT
19380087 TTTGTAATTT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TATGATTTGAAGTA
Found at i:19381001 original size:17 final size:18
Alignment explanation
Indices: 19380964--19381018 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 18
19380954 ATTAAGTTTA
*
19380964 AAAACAGAAAAAAAAAAC
1 AAAACAGAAAAAAAAATC
*
19380982 AAAACA-AAACAAAAATC
1 AAAACAGAAAAAAAAATC
*
19380999 -AAACATAAAAAAAAATC
1 AAAACAGAAAAAAAAATC
19381016 AAA
1 AAA
19381019 CTTGTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 5 0.16
17 19 0.59
18 8 0.25
ACGTcount: A:0.80, C:0.13, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAACAGAAAAAAAAATC
Found at i:19382523 original size:2 final size:2
Alignment explanation
Indices: 19382516--19382554 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19382506 GGACTATTTG
19382516 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA T
19382555 TCTTAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19383512 original size:15 final size:14
Alignment explanation
Indices: 19383489--19383520 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
19383479 TCTTCACAAT
19383489 TTTCTGCCTGCTTA
1 TTTCTGCCTGCTTA
19383503 TTTCTCGCCTGCTTA
1 TTTCT-GCCTGCTTA
19383518 TTT
1 TTT
19383521 TATTACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.06, C:0.28, G:0.12, T:0.53
Consensus pattern (14 bp):
TTTCTGCCTGCTTA
Found at i:19384433 original size:18 final size:17
Alignment explanation
Indices: 19384410--19384443 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19384400 AAAATATGAG
19384410 AAATGATGTTCACATTTC
1 AAATGATGTTCA-ATTTC
19384428 AAATGATGTTCAATTT
1 AAATGATGTTCAATTT
19384444 GATGGAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
AAATGATGTTCAATTTC
Found at i:19385013 original size:72 final size:72
Alignment explanation
Indices: 19384895--19385049 Score: 224
Period size: 72 Copynumber: 2.2 Consensus size: 72
19384885 TTTTCATCAG
* * * *
19384895 TAGTTATTTATGTTTAGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTA-T-AATCTAG
1 TAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTT-TGTACTAAAT-TAG
19384958 TTTTATTAA
64 TTTTATTAA
* *
19384967 TAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCCACTTATTTTTTACTAAATTAGTT
1 TAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTTTGTACTAAATTAGTT
19385032 TTATTAA
66 TTATTAA
19385039 TAGTTGTTTAT
1 TAGTTGTTTAT
19385050 ATGTGATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 3 0.04
72 69 0.92
73 3 0.04
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (72 bp):
TAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTTTGTACTAAATTAGTT
TTATTAA
Found at i:19387124 original size:13 final size:13
Alignment explanation
Indices: 19387106--19387167 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
19387096 ACACTCAAAA
19387106 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
19387119 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
*
19387132 TTTTCTACAA-CAC
1 TTTTC-AAAAGCAC
** *
19387145 TTTTCAAAAATAT
1 TTTTCAAAAGCAC
19387158 TTTTCAAAAG
1 TTTTCAAAAG
19387168 TAATAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 3 0.08
13 34 0.85
14 3 0.08
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:19387135 original size:26 final size:26
Alignment explanation
Indices: 19387106--19387167 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
19387096 ACACTCAAAA
*
19387106 TTTTCAAAAGCACTTTTCAAAAGTAC
1 TTTTCAAAAGCACTTTTCAAAAATAC
* *
19387132 TTTTCTACAA-CACTTTTCAAAAATAT
1 TTTTC-AAAAGCACTTTTCAAAAATAC
19387158 TTTTCAAAAG
1 TTTTCAAAAG
19387168 TAATAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.10
26 24 0.80
27 3 0.10
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAGCACTTTTCAAAAATAC
Found at i:19388115 original size:21 final size:22
Alignment explanation
Indices: 19388091--19388142 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 22
19388081 TTTAAAATAC
19388091 TTTAAAAATATTTTTTT-TATT
1 TTTAAAAATATTTTTTTATATT
*
19388112 TTT-AAAATATTTTTTTATGTT
1 TTTAAAAATATTTTTTTATATT
19388133 TATTAAAAAT
1 T-TTAAAAAT
19388143 CGGGCCGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 13 0.48
21 7 0.26
22 2 0.07
23 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTAAAAATATTTTTTTATATT
Found at i:19388126 original size:19 final size:20
Alignment explanation
Indices: 19388095--19388134 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19388085 AAATACTTTA
*
19388095 AAAATATTTTTTTTATTTTT
1 AAAATATTTTTTTTATGTTT
19388115 AAAATA-TTTTTTTATGTTT
1 AAAATATTTTTTTTATGTTT
19388134 A
1 A
19388135 TTAAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
AAAATATTTTTTTTATGTTT
Found at i:19391058 original size:17 final size:17
Alignment explanation
Indices: 19391036--19391068 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19391026 TCCTAGATTT
19391036 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
19391053 TGATACCTATATCTTT
1 TGATACCCATATCTTT
19391069 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:19395906 original size:13 final size:13
Alignment explanation
Indices: 19395890--19395915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19395880 TTATATATAA
19395890 TAAAAATTAAACC
1 TAAAAATTAAACC
19395903 TAAAAATTAAACC
1 TAAAAATTAAACC
19395916 CAATATGATT
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:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAATTAAACC
Found at i:19399371 original size:20 final size:20
Alignment explanation
Indices: 19399346--19399383 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19399336 AAGCTTATGC
19399346 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
19399366 TAAGTAAATGAAATGGAA
1 TAAGTAAATGAAATGGAA
19399384 TGGTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:19399379 original size:25 final size:25
Alignment explanation
Indices: 19399351--19399400 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19399341 TATGCTAAGT
*
19399351 AAATGAAATGGAAAGTAAGTAAATG
1 AAATGAAATGGAAAGAAAGTAAATG
* *
19399376 AAATGGAATGGTAAGAAAGTAAATG
1 AAATGAAATGGAAAGAAAGTAAATG
19399401 GAGTGGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (25 bp):
AAATGAAATGGAAAGAAAGTAAATG
Found at i:19405860 original size:44 final size:44
Alignment explanation
Indices: 19405796--19405910 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 44
19405786 ATGATCTACT
* * * *
19405796 CTACAACAATTTCAGAGAGATAAGATCT-GTGGATTTAATCTGTTC
1 CTACTACAAATTCAGGGAGATAAGAT-TAGTGGATTTAATCTG-CC
* * * *
19405841 C-ACTGCAAATTCAGGGAGATAGGATTATTGGCTTTAATCTGCC
1 CTACTACAAATTCAGGGAGATAAGATTAGTGGATTTAATCTGCC
* *
19405884 CTACTACAACTTAAGGGAGATAAGATT
1 CTACTACAAATTCAGGGAGATAAGATT
19405911 CGCCATCTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
43 3 0.05
44 52 0.93
45 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
CTACTACAAATTCAGGGAGATAAGATTAGTGGATTTAATCTGCC
Found at i:19406453 original size:133 final size:133
Alignment explanation
Indices: 19406260--19407288 Score: 1632
Period size: 133 Copynumber: 7.7 Consensus size: 133
19406250 TGCAGAAAGG
* * *
19406260 CAAGATCTACTTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
* * *
19406324 TACTTCATGCCAATACATGAAGATAAGATCTGCTTT-TTCCGATCTACTTCACCACCAGTATGGG
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT-CGATCTACTTCGCCACCAGTATGGG
19406388 AAGA
130 AAGA
* *
19406392 CAAGATCTGCGTCTTCGATCCACTTCACTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
*
19406457 TACTTCACGTCC-ATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGTCACCAGTATGGG
66 TACTTCACG-CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
19406521 AAGA
130 AAGA
* *
19406525 CAAGATCTGCATCTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTGGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
* * * *
19406590 TACTTCACGCCAATACATAAAGACAAGATCTACTTTCTTCGATCTACTTTGCCACCAATATGGGA
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
19406655 AGA
131 AGA
* *
19406658 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGAATCTGTTATCTTGGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
* * * * *
19406723 TACTTCATGCCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCGCCACAAGAATGGGA
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
19406788 AGA
131 AGA
* *
19406791 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAAACAGGATCTATTATCTTCGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
* * *
19406856 TACTTCACGCCAATACATGAAGACAATATCTGCTTTCTTTGATCTACTTTGCCACCAGTATGGGA
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
*
19406921 AAA
131 AGA
* *
19406924 CAAGATCTGCATCTTCGATCCACTTCGTTACCAATATAGGAAGACAGGATCTGATATCTTCGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
* *
19406989 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTATTGGA
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
19407054 AGA
131 AGA
* * * *
19407057 CAAGATTTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGATAGGATCTGTCATCTTCCATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
** *
19407122 TACTTCACGCCAATACATGAAGACAATTTCTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGA
66 TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
19407187 AGA
131 AGA
* * *
19407190 CAAGATCTTCATCTTCGATCCACTTCGCTACCAATATAGGAAGACATGATCTGTTATCTTGGATC
1 CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
*
19407255 TACTTCATGCCAATACATGAAGACAAGATCTGCT
66 TACTTCACGCCAATACATGAAGACAAGATCTGCT
19407289 ATTTTTTAGA
Statistics
Matches: 826, Mismatches: 67, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
132 26 0.03
133 796 0.96
134 4 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (133 bp):
CAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATC
TACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
AGA
Found at i:19422308 original size:11 final size:11
Alignment explanation
Indices: 19422292--19422317 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19422282 CATTATATTA
19422292 ATCCCAATACT
1 ATCCCAATACT
19422303 ATCCCAATACT
1 ATCCCAATACT
19422314 ATCC
1 ATCC
19422318 TTTAGCTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCCCAATACT
Done.