Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 217 of 316
Found at i:71127249 original size:180 final size:177
Alignment explanation
Indices: 71126929--71127469 Score: 571
Period size: 180 Copynumber: 3.0 Consensus size: 177
71126919 CGTTGAGTTA
* * * * *
71126929 TTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA--AG
1 TTTTCAATTTATG-CTTTC-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
* * * *
71126992 ACGCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTTTGTGTTTCAAAAAAATCAGCTCATATTGC
64 ACGCTGAGGTATTTTCAATTTCTGTTTTTCAA-TTTTGT-TTTCAAAAAAATCAACTCATATTGC
* * *
71127057 AAGTGGTGAGTTGAGCCTTGACTCACACGCTGAGGTGTTTTCAAATTTTGT
127 GAGAGGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAAATTTTGT
* *
71127108 TTTTCAAATTT-TGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGAC
1 TTTTC-AATTTATG-CTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
* *
71127172 ACGCTGAGATATTTTCAATTTCTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGC
64 ACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTT-TGTTT-TCAAAAAAATCAACTCATATTGC
* *
71127237 GAGAGGTGAGTTGAGCCTCAGA-TCACACGCCGAGGTATTTTCAATTGATTTT-T
127 GAGAGGTGAGTTGAGCCT-TGACTCACACGCTGAGGTATTTTCAA---ATTTTGT
* * *
71127290 TTTTCAATTTATGCTTTGC-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTCAATTTATGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--AC
** * ** * *
71127354 ATACCGAGGTATTTTCAAAATCTGTTTTACAAATTTTGTTTT---AAAAATCAACTCATATTGTG
64 ACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTTGTTTTCAAAAAAATCAACTCATATTGCG
* * ** *
71127416 AGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTC-AATTTCTGT
128 AGAGGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAAATTT-TGT
71127466 TTTT
1 TTTT
71127470 AATGTCTAGT
Statistics
Matches: 308, Mismatches: 38, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
174 4 0.01
175 1 0.00
176 5 0.02
177 2 0.01
178 88 0.29
179 17 0.06
180 132 0.43
181 12 0.04
182 37 0.12
183 10 0.03
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (177 bp):
TTTTCAATTTATGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTTGTTTTCAAAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAAATTTTGT
Found at i:71128187 original size:30 final size:30
Alignment explanation
Indices: 71128151--71128219 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
71128141 CTAGCCTTTG
*
71128151 CCACCACCAACTCCACTAGTCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
71128181 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
71128211 CCACCACCA
1 CCACCACCA
71128220 CTTGTACCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:71128801 original size:25 final size:26
Alignment explanation
Indices: 71128761--71128833 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
71128751 ATTCTAAATT
* *
71128761 CTATATTACGTATATATATATATTATA
1 CTATATTATGTATATATATAT-TAATA
* *
71128788 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
*
71128813 CTATATTATTTATATATATAT
1 CTATATTATGTATATATATAT
71128834 ATATTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 20 0.53
26 2 0.05
27 16 0.42
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:71128879 original size:22 final size:22
Alignment explanation
Indices: 71128849--71128956 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
71128839 TTTTTACATG
*
71128849 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
71128871 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
71128896 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
71128919 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
71128939 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
71128957 ATGTAGTATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:71128905 original size:25 final size:24
Alignment explanation
Indices: 71128855--71128941 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
71128845 CATGTTATCT
*
71128855 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
71128881 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
** * *
71128906 TACATA-TTTTTAA-TATTATCACG
1 TATGTATTTTTTAACTA-TATTATG
*
71128929 TATTTATTTTTTA
1 TATGTATTTTTTA
71128942 TATATGTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 10 0.20
24 17 0.33
25 15 0.29
26 7 0.14
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:71128923 original size:20 final size:20
Alignment explanation
Indices: 71128898--71128956 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
71128888 TTTTTACACT
71128898 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
71128918 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
71128941 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
71128957 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:71129095 original size:16 final size:15
Alignment explanation
Indices: 71129071--71129105 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
71129061 TAATTATTAT
71129071 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
71129087 TATTTTAATATTTTA
1 TATTCTAATATTTTA
71129102 TATT
1 TATT
71129106 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:71130717 original size:13 final size:13
Alignment explanation
Indices: 71130699--71130725 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
71130689 TCTTACGATT
71130699 GAACTTTCACTTA
1 GAACTTTCACTTA
71130712 GAACTTTCACTTA
1 GAACTTTCACTTA
71130725 G
1 G
71130726 TGAAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (13 bp):
GAACTTTCACTTA
Found at i:71132996 original size:10 final size:11
Alignment explanation
Indices: 71132972--71133005 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
71132962 TGAGCTCATG
71132972 ATAT-TGTGAT
1 ATATGTGTGAT
71132982 ATATGTGTGAT
1 ATATGTGTGAT
71132993 -TATGTGTGAT
1 ATATGTGTGAT
71133003 ATA
1 ATA
71133006 CAAGTGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (11 bp):
ATATGTGTGAT
Found at i:71136279 original size:29 final size:29
Alignment explanation
Indices: 71136244--71136317 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
71136234 GTTGTGAGAT
* *
71136244 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
71136273 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
71136302 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
71136318 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:71139315 original size:26 final size:27
Alignment explanation
Indices: 71139279--71139336 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
71139269 TGTGAGTACG
71139279 TGTAAGACCATAGCTGGGCTATGACA-
1 TGTAAGACCATAGCTGGGCTATGACAT
* *
71139305 TGTAAGACCATAGCTGGGTTATGGCAT
1 TGTAAGACCATAGCTGGGCTATGACAT
71139332 TGTAA
1 TGTAA
71139337 TCCCATGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
TGTAAGACCATAGCTGGGCTATGACAT
Found at i:71141004 original size:29 final size:28
Alignment explanation
Indices: 71140968--71141045 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
71140958 TCATGAGATT
71140968 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
71140998 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
71141025 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
71141046 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:71141263 original size:174 final size:174
Alignment explanation
Indices: 71140998--71141499 Score: 932
Period size: 174 Copynumber: 2.9 Consensus size: 174
71140988 AAATTGTACA
*
71140998 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
71141063 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
71141128 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * *
71141172 GCCCTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTGAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
71141237 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
*
71141302 TTTTGGACAGCAGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
71141346 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
71141411 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
71141476 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
71141500 ACCTTGAGTT
Statistics
Matches: 316, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 316 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:71142970 original size:48 final size:48
Alignment explanation
Indices: 71142914--71143128 Score: 295
Period size: 48 Copynumber: 4.5 Consensus size: 48
71142904 GGGGTGTTAC
* *
71142914 AGACCATGTCTGGGACATGGCATTGGCATCGGTATGTGATCCTATGTA
1 AGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTA
*
71142962 AGACCATGTCTGGGACATGGCATTGGCATTGATATGTGATCCCATGTA
1 AGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTA
* *
71143010 AGACCATGTCTGGGACATGACATTGGCATCGATATATGATCCCATGTA
1 AGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTA
* * * * * ** *
71143058 AGACCATATCTGGGATATGGCCTTGTCATCGTTATGTGATTTCGTGTA
1 AGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTA
* *
71143106 AGACTATGTCTGGAACATGGCAT
1 AGACCATGTCTGGGACATGGCAT
71143129 CGATATGAGA
Statistics
Matches: 146, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (48 bp):
AGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTA
Found at i:71143168 original size:42 final size:42
Alignment explanation
Indices: 71143084--71143171 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
71143074 ATGGCCTTGT
* * * *
71143084 CATCGTTATGTGATTTCGTGTAAGACTATGTCTGGAACATGG
1 CATCGATATGAGACTTCGTGTAAGACCATGTCTGGAACATGG
71143126 CATCGATATGAGACTTCGTGTAAGACCATAGT-TGG-ACTATGG
1 CATCGATATGAGACTTCGTGTAAGACCAT-GTCTGGAAC-ATGG
71143168 CATC
1 CATC
71143172 AAGTAAACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 2 0.05
42 36 0.90
43 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
CATCGATATGAGACTTCGTGTAAGACCATGTCTGGAACATGG
Found at i:71146487 original size:20 final size:20
Alignment explanation
Indices: 71146457--71146501 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
71146447 CTGTTTTGTT
*
71146457 ATGGG-CCAACTGTATTGAA
1 ATGGGCCCAACTGTATTAAA
*
71146476 ATGGGCCCAACTGTGTTAAA
1 ATGGGCCCAACTGTATTAAA
71146496 ATGGGC
1 ATGGGC
71146502 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:71152597 original size:42 final size:42
Alignment explanation
Indices: 71152520--71152602 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
71152510 CATGAAATAT
* * *
71152520 CATATCGACGCCATGTCCCTGACATGGTCTTATACGAAATCA
1 CATATCGACGCCATATCCCTGACATAGTCTCATACGAAATCA
* * *
71152562 CATATCGAGGCCATAT-CCTGGATATAGTCTCATACGGAATC
1 CATATCGACGCCATATCCCT-GACATAGTCTCATACGAAATC
71152603 TTAATAACCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.09
42 31 0.91
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (42 bp):
CATATCGACGCCATATCCCTGACATAGTCTCATACGAAATCA
Found at i:71161646 original size:16 final size:17
Alignment explanation
Indices: 71161614--71161646 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
71161604 AAGTTCTGAC
*
71161614 TAAAACATAAAAGAAAA
1 TAAAACATAAAAAAAAA
71161631 TAAAAC-TAAAAAAAAA
1 TAAAACATAAAAAAAAA
71161647 AGCAGTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (17 bp):
TAAAACATAAAAAAAAA
Found at i:71161877 original size:20 final size:21
Alignment explanation
Indices: 71161848--71161906 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
71161838 TCAAGCTTTA
*
71161848 TGGCTCAACACAA-GTTGATG
1 TGGCTCAACACAAGGCTGATG
* *
71161868 TGGCTTAACACAAGGCTGTTG
1 TGGCTCAACACAAGGCTGATG
*
71161889 TGGCTCAACACAATGCTG
1 TGGCTCAACACAAGGCTG
71161907 CGTGTTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (21 bp):
TGGCTCAACACAAGGCTGATG
Found at i:71164200 original size:14 final size:14
Alignment explanation
Indices: 71164181--71164210 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
71164171 TAATTATTTT
71164181 AATTAAAATAATTA
1 AATTAAAATAATTA
71164195 AATTAAAATAATTA
1 AATTAAAATAATTA
71164209 AA
1 AA
71164211 ATAGAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAAATAATTA
Found at i:71164200 original size:18 final size:18
Alignment explanation
Indices: 71164160--71164200 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
71164150 AATAGTAATT
* *
71164160 ATTAATTTAAATAATTAT
1 ATTAATTAAAATAATTAA
*
71164178 TTTAATTAAAATAATTAA
1 ATTAATTAAAATAATTAA
71164196 ATTAA
1 ATTAA
71164201 AATAATTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATTAAAATAATTAA
Found at i:71164267 original size:3 final size:3
Alignment explanation
Indices: 71164259--71164289 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
71164249 ATTTACTCTT
71164259 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
71164290 AGAGACCCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:71166962 original size:89 final size:91
Alignment explanation
Indices: 71166796--71167011 Score: 253
Period size: 89 Copynumber: 2.4 Consensus size: 91
71166786 TTAAGAAAGT
* * * ** *
71166796 AAAAAG-CCATCAAACTTTTTCAAAAAAAACAATTAAGTCTCTGTTTTTTTTTTTGCACTCATTT
1 AAAAAGACCCTCAAACCTTTTCAAAAAAAACAATTAAGTCTCTCTACTTTTTTTTGCACTCAATT
*
71166860 GGGTACTTAAACTTTTAAAATGCATA
66 GGGTACTTAAACTTTCAAAATGCATA
** * *
71166886 AAAAATTCCCTCAAACCTTTTCGAAGAAAACAATTAAGTC-C-CTACTTTTTTTTGCACTCAATT
1 AAAAAGACCCTCAAACCTTTTCAAAAAAAACAATTAAGTCTCTCTACTTTTTTTTGCACTCAATT
* * *
71166949 GGGTATTTGAACTTTCAAAATGCATC
66 GGGTACTTAAACTTTCAAAATGCATA
*
71166975 AAAAAGACCCTCAAA-C-TTTAAAAAAAAAGCAATTAAG
1 AAAAAGACCCTCAAACCTTTTCAAAAAAAA-CAATTAAG
71167012 CTCCTGCTTA
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
87 9 0.08
88 9 0.08
89 53 0.50
90 6 0.06
91 29 0.27
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (91 bp):
AAAAAGACCCTCAAACCTTTTCAAAAAAAACAATTAAGTCTCTCTACTTTTTTTTGCACTCAATT
GGGTACTTAAACTTTCAAAATGCATA
Found at i:71167106 original size:9 final size:9
Alignment explanation
Indices: 71167079--71167179 Score: 57
Period size: 10 Copynumber: 10.7 Consensus size: 9
71167069 TTAAATTTTA
71167079 ATAAAAATT
1 ATAAAAATT
71167088 CATTAAAAATT
1 -A-TAAAAATT
*
71167099 AGAAAAA-T
1 ATAAAAATT
71167107 ATAAAAATCGT
1 ATAAAAAT--T
*
71167118 A-AAAAAAT
1 ATAAAAATT
71167126 ATAAAAAATT
1 AT-AAAAATT
*
71167136 ATAAAATTTT
1 ATAAAA-ATT
71167146 ATAAAAATCGT
1 ATAAAAAT--T
*
71167157 A-AAAAACT
1 ATAAAAATT
71167165 AT-AAAATAT
1 ATAAAAAT-T
71167174 ATAAAA
1 ATAAAA
71167180 GTATTAAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
8 15 0.21
9 13 0.18
10 31 0.44
11 12 0.17
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:71167123 original size:19 final size:19
Alignment explanation
Indices: 71167101--71167170 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
71167091 TAAAAATTAG
71167101 AAAAATATAAAAATCGTAA
1 AAAAATATAAAAATCGTAA
**
71167120 AAAAATATAAAAAATTATAA
1 AAAAATAT-AAAAATCGTAA
***
71167140 AATTTTATAAAAATCGTAA
1 AAAAATATAAAAATCGTAA
*
71167159 AAAACTATAAAA
1 AAAAATATAAAA
71167171 TATATAAAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 26 0.65
20 14 0.35
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAAATCGTAA
Found at i:71167125 original size:39 final size:38
Alignment explanation
Indices: 71167092--71167170 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 38
71167082 AAAATTCATT
71167092 AAAAATTAGAAAA-ATATAAAAATCGTAAAAAAATATA
1 AAAAATTAGAAAATATATAAAAATCGTAAAAAAATATA
* * *
71167129 AAAAATTATAAAATTTTATAAAAATCGTAAAAAACTATA
1 AAAAATTAGAAAA-TATATAAAAATCGTAAAAAAATATA
71167168 AAA
1 AAA
71167171 TATATAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 12 0.32
39 25 0.68
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (38 bp):
AAAAATTAGAAAATATATAAAAATCGTAAAAAAATATA
Found at i:71168516 original size:29 final size:29
Alignment explanation
Indices: 71168482--71168539 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
71168472 ATTTTTAAAG
71168482 TAAAACTAATTATTTTATGTATAAATGGT
1 TAAAACTAATTATTTTATGTATAAATGGT
71168511 TAAAACTAATTATTTTATGTATAAATGGT
1 TAAAACTAATTATTTTATGTATAAATGGT
71168540 CATTATATGT
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:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (29 bp):
TAAAACTAATTATTTTATGTATAAATGGT
Found at i:71168627 original size:22 final size:22
Alignment explanation
Indices: 71168602--71168654 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
71168592 TTTTATTTCT
*
71168602 TTTTATATATATTTTATAATAA
1 TTTTATATATAGTTTATAATAA
* * *
71168624 TTTTAAATATAGTTTATTATAC
1 TTTTATATATAGTTTATAATAA
71168646 TTATTATAT
1 TT-TTATAT
71168655 TTTATTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTATATATAGTTTATAATAA
Found at i:71180481 original size:45 final size:45
Alignment explanation
Indices: 71180429--71180636 Score: 165
Period size: 45 Copynumber: 4.6 Consensus size: 45
71180419 AATAATCAGC
71180429 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAAT
* ** ** *
71180474 CTTATCTTCACTGAGCAGGAGTGAAGCAGG-TCAAATTTTGGCAAGT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAA-CATACCAAAT
* * * ** * * * **
71180520 CTTATCTCCA-TGTATC-GGCAATGGAGCAGATTTCAGC-CACC-AGC
1 CTTATCTTCACTG-AGCAGG-AGTGGAGCAG-GCTAAACATACCAAAT
* *
71180564 CTTATCTTAACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAAT
*
71180609 CTTATCTTCACTGAGCAGGAGTGAAGCA
1 CTTATCTTCACTGAGCAGGAGTGGAGCA
71180637 AATCAAATTT
Statistics
Matches: 121, Mismatches: 32, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
43 3 0.02
44 25 0.21
45 67 0.55
46 24 0.20
47 1 0.01
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAAT
Found at i:71180544 original size:135 final size:135
Alignment explanation
Indices: 71180292--71180779 Score: 709
Period size: 135 Copynumber: 3.6 Consensus size: 135
71180282 CAGATATCAT
* * *
71180292 CAGCCTTATCTTTACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACCAGATCTTATCTTCACTGAGT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
* * * * *
71180355 AGGAGTGAAGCAGATCGAATTTTGATG-AA-TCTTATCTCCACGTACCGGCGATGGAGCAGATTC
66 AGGAGTGAAGCAGATCAAATTTTG--GCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTT
*** *
71180418 CAATAAT
129 CAGCCAC
71180425 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
*
71180490 AGGAGTGAAGCAGGTCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
71180555 GCCAC
131 GCCAC
* *
71180560 CAGCCTTATCTTAACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
* * *
71180625 AGGAGTGAAGCAAATCAAATTTTGGCAAGTCTTATCTCCATGTATCGACAATGGAGCAGATTTTA
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
71180690 GCCAC
131 GCCAC
* * **
71180695 CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATA-CAAATCTTATCTTCGCTGATT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
71180759 AGGAGT-AGAGCAGATCAAATT
66 AGGAGTGA-AGCAGATCAAATT
71180780 ACAGCAGACC
Statistics
Matches: 324, Mismatches: 26, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
133 40 0.12
134 38 0.12
135 246 0.76
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (135 bp):
CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAAATCTTATCTTCACTGAGC
AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
GCCAC
Found at i:71180979 original size:62 final size:62
Alignment explanation
Indices: 71180882--71181014 Score: 266
Period size: 62 Copynumber: 2.1 Consensus size: 62
71180872 CACAGGCAAA
71180882 ATTGGTCCCTTATAGTCTTTGCTCTATTCTTGTTACACAATAATGAGCAAAGAGGGGCAGCT
1 ATTGGTCCCTTATAGTCTTTGCTCTATTCTTGTTACACAATAATGAGCAAAGAGGGGCAGCT
71180944 ATTGGTCCCTTATAGTCTTTGCTCTATTCTTGTTACACAATAATGAGCAAAGAGGGGCAGCT
1 ATTGGTCCCTTATAGTCTTTGCTCTATTCTTGTTACACAATAATGAGCAAAGAGGGGCAGCT
71181006 ATTGGTCCC
1 ATTGGTCCC
71181015 AATTCATTCC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (62 bp):
ATTGGTCCCTTATAGTCTTTGCTCTATTCTTGTTACACAATAATGAGCAAAGAGGGGCAGCT
Found at i:71182439 original size:12 final size:12
Alignment explanation
Indices: 71182402--71182440 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
71182392 TTTTATTTCT
71182402 TTTTATATATATA
1 TTTTATATATA-A
71182415 TTTTATA-ATAA
1 TTTTATATATAA
*
71182426 TTTTAAATATAA
1 TTTTATATATAA
71182438 TTT
1 TTT
71182441 ATTATACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 7 0.29
12 10 0.42
13 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTATATATAA
Found at i:71182464 original size:23 final size:23
Alignment explanation
Indices: 71182437--71182482 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
71182427 TTTAAATATA
71182437 ATTTATTATA-CTTATTATATTTT
1 ATTTATTATATCTTATT-TATTTT
*
71182460 ATTTATTATATTTTATTTATTTT
1 ATTTATTATATCTTATTTATTTT
71182483 TTCCTACCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTATATCTTATTTATTTT
Found at i:71182465 original size:14 final size:14
Alignment explanation
Indices: 71182448--71182480 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
71182438 TTTATTATAC
71182448 TTATTATATTTTAT
1 TTATTATATTTTAT
71182462 TTATTATATTTTAT
1 TTATTATATTTTAT
71182476 TTATT
1 TTATT
71182481 TTTTCCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATATTTTAT
Found at i:71183539 original size:19 final size:18
Alignment explanation
Indices: 71183515--71183591 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 18
71183505 GTCGTTAATT
71183515 TTTTATGATTTTTATAAAA
1 TTTTAT-ATTTTTATAAAA
71183534 TTTTATATTTTTTATTAAAA
1 TTTTATA-TTTTTA-TAAAA
* *
71183554 TTTAATAATTTTTCTAAAA
1 TTTTAT-ATTTTTATAAAA
*
71183573 -TTTAT-TATTTAT-AAA
1 TTTTATATTTTTATAAAA
71183588 TTTT
1 TTTT
71183592 TTCTAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.06
16 8 0.16
18 5 0.10
19 17 0.35
20 15 0.31
21 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTTATATTTTTATAAAA
Found at i:71183546 original size:20 final size:19
Alignment explanation
Indices: 71183522--71183576 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
71183512 ATTTTTTATG
*
71183522 ATTTTTATAAAATTTTATA
1 ATTTTTATAAAATTTAATA
*
71183541 TTTTTTATTAAAATTTAATA
1 ATTTTTA-TAAAATTTAATA
*
71183561 ATTTTTCTAAAATTTA
1 ATTTTTATAAAATTTA
71183577 TTATTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAAATTTAATA
Found at i:71185854 original size:14 final size:14
Alignment explanation
Indices: 71185831--71185867 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
71185821 CATCATTTAA
71185831 AAATTAAAAAAATT
1 AAATTAAAAAAATT
*
71185845 AAATTTAAAAAATT
1 AAATTAAAAAAATT
71185859 AAA-TAAAAA
1 AAATTAAAAA
71185868 TATACGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATTAAAAAAATT
Found at i:71195049 original size:8 final size:8
Alignment explanation
Indices: 71195036--71195065 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
71195026 AAAATTAAAT
71195036 ATGAATAA
1 ATGAATAA
71195044 ATGAATAA
1 ATGAATAA
71195052 ATGAATGAA
1 ATGAAT-AA
71195061 ATGAA
1 ATGAA
71195066 AACTCTAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (8 bp):
ATGAATAA
Found at i:71206064 original size:21 final size:21
Alignment explanation
Indices: 71206038--71206077 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71206028 TGTGTTAAAA
*
71206038 GAGGCATACGACC-GTGTGTCC
1 GAGGCACACG-CCTGTGTGTCC
71206059 GAGGCACACGCCTGTGTGT
1 GAGGCACACGCCTGTGTGT
71206078 ACTAGGGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (21 bp):
GAGGCACACGCCTGTGTGTCC
Found at i:71206896 original size:22 final size:22
Alignment explanation
Indices: 71206837--71206884 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
71206827 ATATGTCCAA
* * *
71206837 AAAAGAAAAAGAAAATTAAAATT
1 AAAAGTAAAAGTAAA-TCAAATT
71206860 AAAAGTAAAAGTAAATCAAATT
1 AAAAGTAAAAGTAAATCAAATT
71206882 AAA
1 AAA
71206885 TATACAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (22 bp):
AAAAGTAAAAGTAAATCAAATT
Found at i:71208286 original size:22 final size:20
Alignment explanation
Indices: 71208238--71208286 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
71208228 TAAAAAATGT
71208238 TGAAATGTTGAAAAACTTGA
1 TGAAATGTTGAAAAACTTGA
*
71208258 -AACAATGTTGAAGAAATCTTGA
1 TGA-AATGTTGAA-AAA-CTTGA
71208280 TGAAATG
1 TGAAATG
71208287 GTGTTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 3 0.13
22 9 0.39
23 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (20 bp):
TGAAATGTTGAAAAACTTGA
Found at i:71208494 original size:20 final size:19
Alignment explanation
Indices: 71208471--71208524 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
71208461 GTATCGGTAT
71208471 TTTTAAAAGGGTATTGATAA
1 TTTTAAAA-GGTATTGATAA
**
71208491 TTTTATAAAATTATTGATAA
1 TTTTA-AAAGGTATTGATAA
71208511 TTTTAAAATGGTAT
1 TTTTAAAA-GGTAT
71208525 CAATACCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (19 bp):
TTTTAAAAGGTATTGATAA
Found at i:71211560 original size:23 final size:25
Alignment explanation
Indices: 71211532--71211586 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
71211522 AGCCCTGAAA
71211532 AGCTTCCTAAT-A-GGCTCTTTGTG
1 AGCTTCCTAATAATGGCTCTTTGTG
*
71211555 AGCTTCCCTATTAATGGCTCTTTGTG
1 AGCTT-CCTAATAATGGCTCTTTGTG
71211581 AGCTTC
1 AGCTTC
71211587 TTGTTACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 5 0.18
25 2 0.07
26 16 0.57
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (25 bp):
AGCTTCCTAATAATGGCTCTTTGTG
Found at i:71219794 original size:18 final size:17
Alignment explanation
Indices: 71219767--71219803 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
71219757 CTTATATCCA
*
71219767 TCATATTAAAGTCATAT
1 TCATATTAAAATCATAT
71219784 TCATAATTAAAATCATAT
1 TCAT-ATTAAAATCATAT
71219802 TC
1 TC
71219804 CATTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (17 bp):
TCATATTAAAATCATAT
Found at i:71221464 original size:28 final size:28
Alignment explanation
Indices: 71221431--71221512 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
71221421 TTTGAATCAT
**
71221431 TCAATATTTCGCACACTAAGTTTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
71221459 TCAATATCTT-GCACACTAAGTGCCATTC
1 TCAATAT-TTCGCACACTAAGTGCCATTC
* *
71221487 TCAATATTTCGTACACTGAGTGCCAT
1 TCAATATTTCGCACACTAAGTGCCAT
71221513 ATTTGATTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.04
28 44 0.92
29 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:71222836 original size:13 final size:13
Alignment explanation
Indices: 71222818--71222843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71222808 TTTTCTAAAC
71222818 CCACTTGAACTTA
1 CCACTTGAACTTA
71222831 CCACTTGAACTTA
1 CCACTTGAACTTA
71222844 ATAAATTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
CCACTTGAACTTA
Found at i:71225440 original size:64 final size:64
Alignment explanation
Indices: 71225359--71225538 Score: 177
Period size: 67 Copynumber: 2.8 Consensus size: 64
71225349 AGAAATTATG
* * *
71225359 ATGTAGCTAGGTCGCATGGGTAATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
71225423 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
71225488 AA
63 AA
* * * *
71225490 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGA
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGA
71225539 AAGCCGAACT
Statistics
Matches: 93, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 21 0.23
65 7 0.08
66 16 0.17
67 31 0.33
68 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:71231249 original size:21 final size:22
Alignment explanation
Indices: 71231216--71231256 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
71231206 TTCATTTATG
*
71231216 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
71231237 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
71231257 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:71231713 original size:28 final size:28
Alignment explanation
Indices: 71231672--71231740 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
71231662 TTCAATATTT
**
71231672 CACTAAGTTTCATTCTCAATATCTT-GCA
1 CACTAAGTGCCATTCTCAATAT-TTCGCA
*
71231700 CACTAAGTGCCATTCTCAATATTTCGTA
1 CACTAAGTGCCATTCTCAATATTTCGCA
*
71231728 CACTGAGTGCCAT
1 CACTAAGTGCCAT
71231741 ATTTGATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (28 bp):
CACTAAGTGCCATTCTCAATATTTCGCA
Found at i:71235203 original size:30 final size:29
Alignment explanation
Indices: 71235169--71235420 Score: 152
Period size: 30 Copynumber: 8.5 Consensus size: 29
71235159 TAATCGAAAT
*
71235169 TATCCCTTTTCATAGTTCGATAGCCGAAGC
1 TATCCCTTTTCATAATTCGATAGCCGAA-C
* * * *
71235199 TATCCCTTTTCATAATTTGATGGTCGTCAC
1 TATCCCTTTTCATAATTCGATAGCCG-AAC
* * * ** * * * *
71235229 CATCTCTTTTTATTGTTTGATGGTCGTCAC
1 TATCCCTTTTCATAATTCGATAGCCG-AAC
*
71235259 TATCCCTTTTCATAATT-GATAGCCGGAGC
1 TATCCCTTTTCATAATTCGATAGCC-GAAC
*
71235288 TATCCCTTTTCATAGA-TCGATAGCCAAAGC
1 TATCCCTTTTCATA-ATTCGATAGCCGAA-C
* * * *
71235318 CATCCCTTTTCATAATTTGATGGTC-ATCAC
1 TATCCCTTTTCATAATTCGATAGCCGA--AC
* * * *
71235348 CATCCCTTTTCATTATTCGATAGTCGTCAC
1 TATCCCTTTTCATAATTCGATAGCCG-AAC
*
71235378 CATCCCTTTTCATAATT-GATAGCCGAAGC
1 TATCCCTTTTCATAATTCGATAGCCGAA-C
*
71235407 TGTCCCTTTTCATA
1 TATCCCTTTTCATA
71235421 GATTGATGAT
Statistics
Matches: 177, Mismatches: 34, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.01
29 44 0.25
30 130 0.73
31 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (29 bp):
TATCCCTTTTCATAATTCGATAGCCGAAC
Found at i:71235238 original size:60 final size:60
Alignment explanation
Indices: 71235170--71235394 Score: 217
Period size: 60 Copynumber: 3.8 Consensus size: 60
71235160 AATCGAAATT
*
71235170 ATCCCTTTTCATAGTTCGATAGCCG-AAGCTATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATAGCCGTAA-CCATCCCTTTTCATAATTTGATGGTCGTCACC
* * * * * * * * * * * *
71235230 ATCTCTTTTTATTGTTTGATGGTCGTCACTATCCCTTTTCATAA-TTGATAGCCG-GAGCT
1 ATCCCTTTTCATAGTTCGATAGCCGTAACCATCCCTTTTCATAATTTGATGGTCGTCA-CC
* * *
71235289 ATCCCTTTTCATAGATCGATAGCC-AAAGCCATCCCTTTTCATAATTTGATGGTCATCACC
1 ATCCCTTTTCATAGTTCGATAGCCGTAA-CCATCCCTTTTCATAATTTGATGGTCGTCACC
* *
71235349 ATCCCTTTTCATTA-TTCGATAGTCGTCACCATCCCTTTTCATAATT
1 ATCCCTTTTCA-TAGTTCGATAGCCGTAACCATCCCTTTTCATAATT
71235395 GATAGCCGAA
Statistics
Matches: 128, Mismatches: 30, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
58 2 0.02
59 41 0.32
60 80 0.62
61 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (60 bp):
ATCCCTTTTCATAGTTCGATAGCCGTAACCATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:71235321 original size:89 final size:89
Alignment explanation
Indices: 71235169--71235428 Score: 267
Period size: 89 Copynumber: 2.9 Consensus size: 89
71235159 TAATCGAAAT
* * ***
71235169 TATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCGTCA-CCATC
1 TATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAA-TTGATAG-CCAAAGCCATC
* * ** *
71235233 TCTTTTTATTGTTTGATGGTCGTCAC
64 CCTTTTCATAATTTGATGGTCATCAC
* *
71235259 TATCCCTTTTCATAATT-GATAGCCGGAGCTATCCCTTTTCATAGATCGATAGCCAAAGCCATCC
1 TATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATA-ATTGATAGCCAAAGCCATCC
71235323 CTTTTCATAATTTGATGGTCATCAC
65 CTTTTCATAATTTGATGGTCATCAC
* * * * * * **
71235348 CATCCCTTTTCATTATTCGATAGTCGTCA-CCATCCCTTTTCATAATTGATAGCCGAAGCTGTCC
1 TATCCCTTTTCATAATTCGATAGCCG-AAGCTATCCCTTTTCATAATTGATAGCCAAAGCCATCC
71235412 CTTTTCATAGA-TTGATG
65 CTTTTCATA-ATTTGATG
71235429 ATCGCCATTA
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
88 2 0.01
89 102 0.71
90 39 0.27
91 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (89 bp):
TATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTGATAGCCAAAGCCATCCC
TTTTCATAATTTGATGGTCATCAC
Found at i:71235339 original size:119 final size:119
Alignment explanation
Indices: 71235169--71235423 Score: 402
Period size: 119 Copynumber: 2.1 Consensus size: 119
71235159 TAATCGAAAT
* * * * *
71235169 TATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCT
1 TATCCCTTTTCATAGATCGATAGCCAAAGCCATCCCTTTTCATAATTTGATGGTCATCACCATCC
* * * * * *
71235234 CTTTTTATTGTTTGATGGTCGTCACTATCCCTTTTCATAATTGATAGCCGGAGC
66 CTTTTCATTATTCGATAGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGC
71235288 TATCCCTTTTCATAGATCGATAGCCAAAGCCATCCCTTTTCATAATTTGATGGTCATCACCATCC
1 TATCCCTTTTCATAGATCGATAGCCAAAGCCATCCCTTTTCATAATTTGATGGTCATCACCATCC
71235353 CTTTTCATTATTCGATAGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGC
66 CTTTTCATTATTCGATAGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGC
*
71235407 TGTCCCTTTTCATAGAT
1 TATCCCTTTTCATAGAT
71235424 TGATGATCGC
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 124 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (119 bp):
TATCCCTTTTCATAGATCGATAGCCAAAGCCATCCCTTTTCATAATTTGATGGTCATCACCATCC
CTTTTCATTATTCGATAGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGC
Found at i:71241268 original size:17 final size:17
Alignment explanation
Indices: 71241239--71241383 Score: 56
Period size: 16 Copynumber: 8.4 Consensus size: 17
71241229 TTAACACCCC
*
71241239 AATTTTAAT-TTATTTT
1 AATTTTTATATTATTTT
71241255 AATTTTTATATTA-TTT
1 AATTTTTATATTATTTT
**
71241271 -ATTTTTAT-TT-TACT
1 AATTTTTATATTATTTT
* *
71241285 AATTAATTA-ATTAATTT
1 AATT-TTTATATTATTTT
*
71241302 AGTGTTCTTATACTTATATTTTT
1 AAT-TT-TTATA--T-TA-TTTT
*
71241325 AATTTTTTTA-TATTTT
1 AATTTTTATATTATTTT
71241341 AATTTTTA-ATATACTTTT
1 AATTTTTATAT-TA-TTTT
71241359 ATTATTTTTATTATTATTTT
1 A--ATTTTTA-TATTATTTT
71241379 -ATTTT
1 AATTTT
71241384 ACTATTTCTA
Statistics
Matches: 96, Mismatches: 13, Indels: 39
0.65 0.09 0.26
Matches are distributed among these distances:
14 3 0.03
15 12 0.12
16 27 0.28
17 15 0.16
18 9 0.09
19 1 0.01
20 11 0.11
21 7 0.07
22 6 0.06
23 5 0.05
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (17 bp):
AATTTTTATATTATTTT
Found at i:71241367 original size:20 final size:20
Alignment explanation
Indices: 71241342--71241381 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
71241332 TTATATTTTA
71241342 ATTTTTAATA-TACTTTTATT
1 ATTTTTAATATTA-TTTTATT
*
71241362 ATTTTTATTATTATTTTATT
1 ATTTTTAATATTATTTTATT
71241382 TTACTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTAATATTATTTTATT
Found at i:71241495 original size:14 final size:14
Alignment explanation
Indices: 71241476--71241503 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71241466 TATTATTGAG
71241476 TTTATTATTTTTAT
1 TTTATTATTTTTAT
71241490 TTTATTATTTTTAT
1 TTTATTATTTTTAT
71241504 CTTTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTATTTTTAT
Found at i:71244497 original size:6 final size:6
Alignment explanation
Indices: 71244486--71244533 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
71244476 TAATTTAGCC
* *
71244486 ATTTTA ATTTT- ATTGT- A-TTTA ATTTTA ATTTTA ATTTTA TTTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
71244531 ATT
1 ATT
71244534 ACTAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 2 0.06
5 6 0.17
6 28 0.78
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:71244548 original size:19 final size:18
Alignment explanation
Indices: 71244503--71244542 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
71244493 TTTTATTGTA
* *
71244503 TTTAATTTTAATTTTAAT
1 TTTATTTTTAATTCTAAT
71244521 TTTATTTTTAATTACTAAT
1 TTTATTTTTAATT-CTAAT
71244540 TTT
1 TTT
71244543 TCTTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTTTTAATTCTAAT
Found at i:71247792 original size:26 final size:27
Alignment explanation
Indices: 71247741--71247801 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
71247731 TCACCCTAAT
**
71247741 TTTATTTT-ATTTTAATTGTTATATTA
1 TTTATTTTAATTTTAATAATTATATTA
*
71247767 TTTATTTTAATTTTACTAATTA-ATTA
1 TTTATTTTAATTTTAATAATTATATTA
* *
71247793 ATTAATTTA
1 TTTATTTTA
71247802 GTATTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTATTTTAATTTTAATAATTATATTA
Found at i:71247860 original size:14 final size:14
Alignment explanation
Indices: 71247838--71247896 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
71247828 TTTTATATAC
*
71247838 TTTTATTATTTTTA
1 TTTTCTTATTTTTA
*
71247852 TTTTCTTATTTCTA
1 TTTTCTTATTTTTA
71247866 TTTT-TTATTTTT-
1 TTTTCTTATTTTTA
*
71247878 TCTTTCGTATTTTTTA
1 T-TTTCTTA-TTTTTA
71247894 TTT
1 TTT
71247897 ATTTTTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 1 0.03
13 10 0.27
14 18 0.49
15 7 0.19
16 1 0.03
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTCTTATTTTTA
Found at i:71247860 original size:27 final size:26
Alignment explanation
Indices: 71247825--71247877 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
71247815 TATATTCTTA
71247825 ATTTTTTATATACT-TTTATTATTTTT
1 ATTTTTTAT-TACTATTTATTATTTTT
* *
71247851 ATTTTCTTATTTCTATTTTTTATTTTT
1 ATTTT-TTATTACTATTTATTATTTTT
71247878 TCTTTCGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
ATTTTTTATTACTATTTATTATTTTT
Found at i:71247870 original size:21 final size:21
Alignment explanation
Indices: 71247846--71247896 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
71247836 ACTTTTATTA
71247846 TTTTTATTTTCTTATTTC-TAT
1 TTTTTATTTT-TTATTTCGTAT
*
71247867 TTTTTATTTTTTCTTTCGTAT
1 TTTTTATTTTTTATTTCGTAT
71247888 TTTTTATTT
1 TTTTTATTT
71247897 ATTTTTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTTATTTTTTATTTCGTAT
Found at i:71247874 original size:7 final size:7
Alignment explanation
Indices: 71247846--71247896 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
71247836 ACTTTTATTA
71247846 TTTTTAT
1 TTTTTAT
71247853 TTTCTTA-
1 TTT-TTAT
*
71247860 TTTCTAT
1 TTTTTAT
71247867 TTTTTAT
1 TTTTTAT
*
71247874 TTTTTCT
1 TTTTTAT
**
71247881 TTCGTAT
1 TTTTTAT
71247888 TTTTTAT
1 TTTTTAT
71247895 TT
1 TT
71247897 ATTTTTACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 2 0.06
7 29 0.85
8 3 0.09
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTAT
Found at i:71247981 original size:13 final size:12
Alignment explanation
Indices: 71247949--71247995 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
71247939 TATTATTGAG
71247949 TTTATTATTATTAT
1 TTTATT-TT-TTAT
71247963 TTTATTTTTTAT
1 TTTATTTTTTAT
71247975 CTTTATTTTTTAT
1 -TTTATTTTTTAT
*
71247988 TTTGTTTT
1 TTTATTTT
71247996 AGTTGTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.35
13 14 0.45
14 6 0.19
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:71248012 original size:25 final size:24
Alignment explanation
Indices: 71247953--71248015 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
71247943 ATTGAGTTTA
71247953 TTATTATTATTTTATTTTTTATCT
1 TTATTATTATTTTATTTTTTATCT
* * *
71247977 TTATTTTTTATTTTGTTTTAGTTGT-T
1 TTA-TTATTATTTTATTTT--TTATCT
71248003 TTATTATTATTTT
1 TTATTATTATTTT
71248016 TCTCTTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.09
25 22 0.69
26 4 0.12
27 3 0.09
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (24 bp):
TTATTATTATTTTATTTTTTATCT
Found at i:71248095 original size:31 final size:31
Alignment explanation
Indices: 71248057--71248120 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
71248047 AGATTCATGA
71248057 TTGTTTCTAATCGAGTTATAACCCCTTAATT
1 TTGTTTCTAATCGAGTTATAACCCCTTAATT
71248088 TTGTTTCTAATCGAGTTATAACCCCTTAATT
1 TTGTTTCTAATCGAGTTATAACCCCTTAATT
71248119 TT
1 TT
71248121 CTTTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (31 bp):
TTGTTTCTAATCGAGTTATAACCCCTTAATT
Found at i:71252872 original size:45 final size:45
Alignment explanation
Indices: 71252808--71252898 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
71252798 CAATGAGACA
*
71252808 AAGAATATTAAAACTCCCTGGATCTTCTAGTTTGTTGGGTAGTTT
1 AAGAATATTAAAACTCCCTGGATCTTCTAGTTTGTTGGGCAGTTT
71252853 AAGAATATTAAAACTCCCTGGATCTTCTAGTTTGTTGGGCAGTTT
1 AAGAATATTAAAACTCCCTGGATCTTCTAGTTTGTTGGGCAGTTT
71252898 A
1 A
71252899 TTTTAGAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (45 bp):
AAGAATATTAAAACTCCCTGGATCTTCTAGTTTGTTGGGCAGTTT
Found at i:71254696 original size:25 final size:24
Alignment explanation
Indices: 71254668--71254725 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
71254658 AAACAGAAGA
* *
71254668 AAAAATAAAATATAAAATTTAAATT
1 AAAAATAAAATATAAAA-ATAAAAT
71254693 AAAACA-AAAATATAAAAATAAAAT
1 AAAA-ATAAAATATAAAAATAAAAT
71254717 -AAAATAAAA
1 AAAAATAAAA
71254726 ATGGCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 7 0.24
24 5 0.17
25 15 0.52
26 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAATAAAATATAAAAATAAAAT
Found at i:71254726 original size:25 final size:25
Alignment explanation
Indices: 71254667--71254727 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
71254657 CAAACAGAAG
* *
71254667 AAAAAATAAAATATAAAATTTAAATT
1 AAAAAA-AAAATATAAAATATAAAAT
*
71254693 AAAACAAAAATATAAAA-ATAAAAT
1 AAAAAAAAAATATAAAATATAAAAT
*
71254717 AAAATAAAAAT
1 AAAAAAAAAAT
71254728 GGCTAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 15 0.48
25 11 0.35
26 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAAAAAATATAAAATATAAAAT
Found at i:71263460 original size:42 final size:43
Alignment explanation
Indices: 71263344--71263462 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
71263334 GTTGGTACTA
* *
71263344 ATCTGAA-TTATCGTGTAAGACCGTGTCTGGGACACAAGCATCG
1 ATCTGAATTTA-CATGTAAGACCATGTCTGGGACACAAGCATCG
* *
71263387 ATTTGAAATTTACGTGTAAGACCATGTCTGGGACATC-AGCATCG
1 ATCTG-AATTTACATGTAAGACCATGTCTGGGACA-CAAGCATCG
*
71263431 TATCTG-A-TTACATGTAAGACCACGTCTGGGAC
1 -ATCTGAATTTACATGTAAGACCATGTCTGGGAC
71263463 GTTGGCATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
42 23 0.34
43 5 0.07
44 31 0.46
45 8 0.12
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
ATCTGAATTTACATGTAAGACCATGTCTGGGACACAAGCATCG
Found at i:71263649 original size:89 final size:89
Alignment explanation
Indices: 71263524--71263701 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
71263514 TGACAAAGTA
71263524 TGAAATATGAAAATGAACATGTGAAATGTGTAATCTATACAGGTATGTTTGTATCGTACTTAATT
1 TGAAATATGAAAATGAACATGTGAAATGTGTAATCTATACAGGTATGTTTGTATCGTACTTAATT
71263589 TCTGAATATGAAAGACTCTGTTTT
66 TCTGAATATGAAAGACTCTGTTTT
71263613 TGAAATATGAAAATGAACATGTGAAATGTGTAATCTATACAGGTATGTTTGTATCGTACTTAATT
1 TGAAATATGAAAATGAACATGTGAAATGTGTAATCTATACAGGTATGTTTGTATCGTACTTAATT
71263678 TCTGAATATGAAAGACTCTGTTTT
66 TCTGAATATGAAAGACTCTGTTTT
71263702 CTGCGAAGTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (89 bp):
TGAAATATGAAAATGAACATGTGAAATGTGTAATCTATACAGGTATGTTTGTATCGTACTTAATT
TCTGAATATGAAAGACTCTGTTTT
Found at i:71266583 original size:326 final size:327
Alignment explanation
Indices: 71265989--71266641 Score: 1299
Period size: 326 Copynumber: 2.0 Consensus size: 327
71265979 GCACCATTTT
71265989 TTATATATTAGCCACTCCCCATAATGTCTCATATAACTTGCATCTTATTCAATAAAAAAAAAAAA
1 TTATATATTAGCCACTCCCCATAATGTCTCATATAACTTGCATCTTATTCAATAAAAAAAAAAAA
71266054 AAAACTCACATGCTGTTCCATGGTCGACGTTCTCAGCAATTTGTCAAAAAGTGATGCAACCTATA
66 AAAACTCACATGCTGTTCCATGGTCGACGTTCTCAGCAATTTGTCAAAAAGTGATGCAACCTATA
71266119 TAAGAATTCGAAGTCAATAAAGTAACAACGATGACAGTAGTTTTGAAACATCAGAAAAGCAGTCA
131 TAAGAATTCGAAGTCAATAAAGTAACAACGATGACAGTAGTTTTGAAACATCAGAAAAGCAGTCA
71266184 GAGTCCGATCGAGTGTCGACCAAGGGCCCTTCTCAGCCGATTGCATGTAACCTTGGAGAGGATAT
196 GAGTCCGATCGAGTGTCGACCAAGGGCCCTTCTCAGCCGATTGCATGTAACCTTGGAGAGGATAT
71266249 TGGTGCTTCTGTGAGGTAATGGGAACACCAAGTGCTAGACCTTGTTGCCCATAGTGTTGAGGCGC
261 TGGTGCTTCTGTGAGGTAATGGGAACACCAAGTGCTAGACCTTGTTGCCCATAGTGTTGAGGCGC
71266314 TG
326 TG
71266316 TTATATATTAGCCACTCCCCATAATGTCTCATATAACTTGCATCTTATTCAAT-AAAAAAAAAAA
1 TTATATATTAGCCACTCCCCATAATGTCTCATATAACTTGCATCTTATTCAATAAAAAAAAAAAA
71266380 AAAACTCACATGCTGTTCCATGGTCGACGTTCTCAGCAATTTGTCAAAAAGTGATGCAACCTATA
66 AAAACTCACATGCTGTTCCATGGTCGACGTTCTCAGCAATTTGTCAAAAAGTGATGCAACCTATA
71266445 TAAGAATTCGAAGTCAATAAAGTAACAACGATGACAGTAGTTTTGAAACATCAGAAAAGCAGTCA
131 TAAGAATTCGAAGTCAATAAAGTAACAACGATGACAGTAGTTTTGAAACATCAGAAAAGCAGTCA
71266510 GAGTCCGATCGAGTGTCGACCAAGGGCCCTTCTCAGCCGATTGCATGTAACCTTGGAGAGGATAT
196 GAGTCCGATCGAGTGTCGACCAAGGGCCCTTCTCAGCCGATTGCATGTAACCTTGGAGAGGATAT
71266575 TGGTGCTTCTGTGAGGTAATGGGAACACCAAGTGCTAGACCTTGTTGCCCATAGTGTTGAGGCGC
261 TGGTGCTTCTGTGAGGTAATGGGAACACCAAGTGCTAGACCTTGTTGCCCATAGTGTTGAGGCGC
71266640 TG
326 TG
71266642 CCGAGTTTGG
Statistics
Matches: 326, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
326 273 0.84
327 53 0.16
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (327 bp):
TTATATATTAGCCACTCCCCATAATGTCTCATATAACTTGCATCTTATTCAATAAAAAAAAAAAA
AAAACTCACATGCTGTTCCATGGTCGACGTTCTCAGCAATTTGTCAAAAAGTGATGCAACCTATA
TAAGAATTCGAAGTCAATAAAGTAACAACGATGACAGTAGTTTTGAAACATCAGAAAAGCAGTCA
GAGTCCGATCGAGTGTCGACCAAGGGCCCTTCTCAGCCGATTGCATGTAACCTTGGAGAGGATAT
TGGTGCTTCTGTGAGGTAATGGGAACACCAAGTGCTAGACCTTGTTGCCCATAGTGTTGAGGCGC
TG
Found at i:71271145 original size:24 final size:25
Alignment explanation
Indices: 71271106--71271162 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
71271096 AGGTCTTTTA
71271106 ACAAAAAAAAAGCACAAATCTGTTG
1 ACAAAAAAAAAGCACAAATCTGTTG
*
71271131 ACAAAAAAAAA-CACAAATCTGTTT
1 ACAAAAAAAAAGCACAAATCTGTTG
71271155 A-AAAAAAA
1 ACAAAAAAA
71271163 GGATTTGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.23
24 13 0.42
25 11 0.35
ACGTcount: A:0.63, C:0.14, G:0.07, T:0.16
Consensus pattern (25 bp):
ACAAAAAAAAAGCACAAATCTGTTG
Found at i:71271273 original size:3 final size:3
Alignment explanation
Indices: 71271267--71271292 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
71271257 TGCTGCGATG
71271267 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
71271293 GGGCGGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:71272068 original size:21 final size:21
Alignment explanation
Indices: 71272023--71272070 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
71272013 TTTTTACTTC
*
71272023 AATAAA-CATTAAAAATAAAT
1 AATAAATCAATAAAAATAAAT
*
71272043 TATAAATCAATAAAAATATAA-
1 AATAAATCAATAAAAATA-AAT
71272064 AATAAAT
1 AATAAAT
71272071 ACAAACATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAATCAATAAAAATAAAT
Found at i:71274893 original size:27 final size:27
Alignment explanation
Indices: 71274863--71274999 Score: 181
Period size: 27 Copynumber: 5.1 Consensus size: 27
71274853 GTCACTAGAT
71274863 ACAGATATATGTGGCATAGCCACCAGG
1 ACAGATATATGTGGCATAGCCACCAGG
*
71274890 ACAGATATATGTGGCAAAGCCACCA-G
1 ACAGATATATGTGGCATAGCCACCAGG
*
71274916 ATCAGATA-ATTGTGGTATAGCCACCAGG
1 A-CAGATATA-TGTGGCATAGCCACCAGG
* *
71274944 ATAGATATATGTGGCAGAGCCACCA-G
1 ACAGATATATGTGGCATAGCCACCAGG
*
71274970 ATCAGATATTTGTGGCATAGCCACCAGG
1 A-CAGATATATGTGGCATAGCCACCAGG
71274998 AC
1 AC
71275000 GCTTCCTCTA
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
26 5 0.05
27 85 0.89
28 5 0.05
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (27 bp):
ACAGATATATGTGGCATAGCCACCAGG
Found at i:71274922 original size:54 final size:54
Alignment explanation
Indices: 71274859--71274999 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
71274849 TGAAGTCACT
71274859 AGATACAGATATATGTGGCATAGCCACCAGGACAGATATATGTGGCAAAGCCACC
1 AGAT-CAGATATATGTGGCATAGCCACCAGGACAGATATATGTGGCAAAGCCACC
* * *
71274914 AGATCAGATA-ATTGTGGTATAGCCACCAGGATAGATATATGTGGCAGAGCCACC
1 AGATCAGATATA-TGTGGCATAGCCACCAGGACAGATATATGTGGCAAAGCCACC
*
71274968 AGATCAGATATTTGTGGCATAGCCACCAGGAC
1 AGATCAGATATATGTGGCATAGCCACCAGGAC
71275000 GCTTCCTCTA
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
53 1 0.01
54 73 0.94
55 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (54 bp):
AGATCAGATATATGTGGCATAGCCACCAGGACAGATATATGTGGCAAAGCCACC
Found at i:71277150 original size:40 final size:41
Alignment explanation
Indices: 71277103--71277314 Score: 333
Period size: 40 Copynumber: 5.3 Consensus size: 41
71277093 TTTAAGATCA
*
71277103 AGCATTAG-GGCATTTTTAAGAAAGCGCTGCTAAAGATCTG
1 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
*
71277143 AGCATTAGTGGCATTTTTAAGAAAGCGCCGCTAAAGATC-G
1 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
71277183 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATC-G
1 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
*
71277223 AGCATTAGCGGCATTTTTAAGAAAGCGTCGCTAAAGATCTG
1 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
* ** *
71277264 AGCACTAGCGGCGCTTTTAAGAAAGCACCGCTAAAGAT-TG
1 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
71277304 AGCATTAGCGG
1 AGCATTAGCGG
71277315 TGCTTTTTTA
Statistics
Matches: 161, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 98 0.61
41 63 0.39
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTG
Found at i:71277205 original size:81 final size:81
Alignment explanation
Indices: 71277096--71277314 Score: 336
Period size: 81 Copynumber: 2.7 Consensus size: 81
71277086 CGGCGTTTTT
* * *
71277096 AAGATCAAGCATTAG-GGCATTTTTAAGAAAGCGCTGCTAAAGATCTGAGCATTAGTGGCATTTT
1 AAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTGAGCATTAGCGGCATTTT
71277160 TAAGAAAGCGCCGCTA
66 TAAGAAAGCGCCGCTA
71277176 AAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATC-GAGCATTAGCGGCATTTT
1 AAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTGAGCATTAGCGGCATTTT
*
71277240 TAAGAAAGCGTCGCTA
66 TAAGAAAGCGCCGCTA
* ** *
71277256 AAGATCTGAGCACTAGCGGCGCTTTTAAGAAAGCACCGCTAAAGAT-TGAGCATTAGCGG
1 AAGATC-GAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTGAGCATTAGCGG
71277315 TGCTTTTTTA
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
80 52 0.41
81 76 0.59
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (81 bp):
AAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCTGAGCATTAGCGGCATTTT
TAAGAAAGCGCCGCTA
Found at i:71277335 original size:40 final size:38
Alignment explanation
Indices: 71277103--71277343 Score: 261
Period size: 40 Copynumber: 6.0 Consensus size: 38
71277093 TTTAAGATCA
71277103 AGCATTAG-GGCATTTTTAAGAAAGCGCTGCTAAAGATCTG
1 AGCATTAGCGGCATTTTTAAGAAAGC-C-GCTAAAGAT-TG
* *
71277143 AGCATTAGTGGCATTTTTAAGAAAGCGCCGCTAAAGATCG
1 AGCATTAGCGGCATTTTTAAGAAA--GCCGCTAAAGATTG
*
71277183 AGCATTAGCGGCATTTTTAAGAAAGCGCCGCTAAAGATCG
1 AGCATTAGCGGCATTTTTAAGAAA--GCCGCTAAAGATTG
71277223 AGCATTAGCGGCATTTTTAAGAAAGCGTCGCTAAAGATCTG
1 AGCATTAGCGGCATTTTTAAGAAAGC--CGCTAAAGAT-TG
* **
71277264 AGCACTAGCGGCGCTTTTAAGAAAGCACCGCTAAAGATTG
1 AGCATTAGCGGCATTTTTAAGAAAG--CCGCTAAAGATTG
*
71277304 AGCATTAGCGGTGCTTTTTTAA-AAATGCCGCTAAAAGATT
1 AGCATTAGC-G-GCATTTTTAAGAAA-GCCGCT-AAAGATT
71277344 AAACAGAACT
Statistics
Matches: 180, Mismatches: 9, Indels: 23
0.85 0.04 0.11
Matches are distributed among these distances:
38 2 0.01
40 97 0.54
41 68 0.38
42 10 0.06
43 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (38 bp):
AGCATTAGCGGCATTTTTAAGAAAGCCGCTAAAGATTG
Found at i:71277338 original size:121 final size:120
Alignment explanation
Indices: 71277096--71277314 Score: 350
Period size: 121 Copynumber: 1.8 Consensus size: 120
71277086 CGGCGTTTTT
* * *
71277096 AAGATCAAGCATTAGGGCATTTTTAAGAAAGCGCTGCTAAAGATCTGAGCATTAGTGGCATTTTT
1 AAGATCAAGCATTAGGGCATTTTTAAGAAAGCGCTGCTAAAGATCTGAGCACTAGCGGCACTTTT
*
71277161 AAGAAAGCGCCGCTAAAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTA
66 AAGAAAGCACCGCTAAAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTA
* *
71277216 AAGATCGAGCATTAGCGGCATTTTTAAGAAAGCG-TCGCTAAAGATCTGAGCACTAGCGGCGCTT
1 AAGATCAAGCATTAG-GGCATTTTTAAGAAAGCGCT-GCTAAAGATCTGAGCACTAGCGGCACTT
*
71277280 TTAAGAAAGCACCGCTAAAGATTGAGCATTAGCGG
64 TTAAGAAAGCACCGCTAAAGATCGAGCATTAGCGG
71277315 TGCTTTTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
120 15 0.17
121 75 0.83
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (120 bp):
AAGATCAAGCATTAGGGCATTTTTAAGAAAGCGCTGCTAAAGATCTGAGCACTAGCGGCACTTTT
AAGAAAGCACCGCTAAAGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCGCTA
Found at i:71278170 original size:22 final size:21
Alignment explanation
Indices: 71278080--71278166 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
71278070 CGCCAGACCC
71278080 TAAATCTCAAATCATAAACCCT
1 TAAATCTCAAATCATAAA-CCT
* *
71278102 TAAAACT-ATAAACGATAAACCT
1 TAAATCTCA-AATC-ATAAACCT
* * * *
71278124 T-AATCCCAACACCCTAAACCC
1 TAAATCTCAA-ATCATAAACCT
71278145 TAAATCTCAAATCATAAACCT
1 TAAATCTCAAATCATAAACCT
71278166 T
1 T
71278167 TAAAACTCCA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
21 21 0.43
22 23 0.47
23 5 0.10
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAATCTCAAATCATAAACCT
Found at i:71278186 original size:65 final size:65
Alignment explanation
Indices: 71278067--71278213 Score: 177
Period size: 65 Copynumber: 2.3 Consensus size: 65
71278057 ATATCTCTTT
* * * * **
71278067 AAACGCCAGACCCTAAATCTCAAATCATAAACCCTTAAAACTATAAACGATAAACCTTAATCCCA
1 AAACCCCAAACCCTAAATCTCAAATCATAAACCCTTAAAACTACAAACCATAAACCCCAATCCCA
* * * * * * *
71278132 ACACCCTAAACCCTAAATCTCAAATCATAAACCTTTAAAACTCCAACCCTTAAACCCCAATCCTA
1 AAACCCCAAACCCTAAATCTCAAATCATAAACCCTTAAAACTACAAACCATAAACCCCAATCCCA
71278197 AAACCCCAAACCCTAAA
1 AAACCCCAAACCCTAAA
71278214 ACTAACTTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.19
Consensus pattern (65 bp):
AAACCCCAAACCCTAAATCTCAAATCATAAACCCTTAAAACTACAAACCATAAACCCCAATCCCA
Found at i:71278191 original size:14 final size:14
Alignment explanation
Indices: 71278167--71278215 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
71278157 CATAAACCTT
*
71278167 TAAAACTCCAACCC
1 TAAAACCCCAACCC
* *
71278181 TTAAACCCCAATCC
1 TAAAACCCCAACCC
71278195 TAAAACCCCAAACCC
1 TAAAACCCC-AACCC
71278210 TAAAAC
1 TAAAAC
71278216 TAACTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (14 bp):
TAAAACCCCAACCC
Found at i:71278475 original size:8 final size:8
Alignment explanation
Indices: 71278464--71278512 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
71278454 AAAATCTTTA
71278464 AAAAAATT
1 AAAAAATT
71278472 AAAAAATT
1 AAAAAATT
71278480 -AAAAATT
1 AAAAAATT
71278487 AAAAAATT
1 AAAAAATT
* *
71278495 TAAAACTT
1 AAAAAATT
*
71278503 AAAAATTT
1 AAAAAATT
71278511 AA
1 AA
71278513 TATTTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 7 0.19
8 29 0.81
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:71278485 original size:15 final size:15
Alignment explanation
Indices: 71278465--71278512 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
71278455 AAATCTTTAA
71278465 AAAAATTAAAAAATT
1 AAAAATTAAAAAATT
71278480 AAAAATTAAAAAATTT
1 AAAAATTAAAAAA-TT
* *
71278496 AAAACTTAAAAATTT
1 AAAAATTAAAAAATT
71278511 AA
1 AA
71278513 TATTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:71278519 original size:15 final size:15
Alignment explanation
Indices: 71278466--71278519 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
71278456 AATCTTTAAA
* *
71278466 AAAATTAAAAAATTA
1 AAAATTTAAAAATTT
*
71278481 AAAATTAAAAAATTT
1 AAAATTTAAAAATTT
*
71278496 AAAACTTAAAAATTT
1 AAAATTTAAAAATTT
*
71278511 AATATTTAA
1 AAAATTTAA
71278520 TATTTTAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTTAAAAATTT
Found at i:71280577 original size:37 final size:37
Alignment explanation
Indices: 71280527--71280605 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
71280517 TTATTACGAA
* *
71280527 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
71280564 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
71280601 GTCTT
1 GTCTT
71280606 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:71280802 original size:47 final size:47
Alignment explanation
Indices: 71280724--71281009 Score: 437
Period size: 47 Copynumber: 6.1 Consensus size: 47
71280714 CCCTTCGGGA
* * * * * * *
71280724 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
71280771 CCTGTCACATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
71280818 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
71280865 CTTATCACATATATACACTTTCACATTCATCACATCGGCTGTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
71280912 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
71280959 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
71281006 CTTA
1 CTTA
71281010 CTATCATTTC
Statistics
Matches: 224, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 224 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:71283389 original size:154 final size:154
Alignment explanation
Indices: 71283109--71283416 Score: 571
Period size: 154 Copynumber: 2.0 Consensus size: 154
71283099 GTAAGATAGA
* **
71283109 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAGTTTGCTTTCTTCATCA
1 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTCCCTTCATCA
71283174 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGATGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGATGTATAGTTTTTA
71283239 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
*
71283263 TTGATTTCATTGATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTCCCTTCATCA
1 TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTCCCTTCATCA
*
71283328 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGTTGTATAGTTTTTA
66 ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGATGTATAGTTTTTA
71283393 TTTTATCTTATATTCTGCAGAATG
131 TTTTATCTTATATTCTGCAGAATG
71283417 GGGATGATTC
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 149 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (154 bp):
TTGATTTCACTGATTTTAGGCTTGAATTTTACGTTCTTCAAAGAAAAAATTTGCTCCCTTCATCA
ACTGTCATTTTATATGGTAGCAGACATTGATACCTTTGATAGCATTCTGTGATGTATAGTTTTTA
TTTTATCTTATATTCTGCAGAATG
Found at i:71287489 original size:18 final size:19
Alignment explanation
Indices: 71287468--71287506 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
71287458 TATTGATATC
71287468 TTTA-TATTTAATTTAATT
1 TTTATTATTTAATTTAATT
* *
71287486 TTTATTATTTATTTTAGTT
1 TTTATTATTTAATTTAATT
71287505 TT
1 TT
71287507 GATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTATTTAATTTAATT
Found at i:71289165 original size:14 final size:11
Alignment explanation
Indices: 71289134--71289175 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
71289124 AAGTCTTCAA
71289134 ATTATTTTTAT
1 ATTATTTTTAT
71289145 ATTATTTTTAT
1 ATTATTTTTAT
*
71289156 GATT-TTATTTAA
1 -ATTATT-TTTAT
71289168 ATTATTTT
1 ATTATTTT
71289176 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:71294845 original size:83 final size:83
Alignment explanation
Indices: 71294628--71295056 Score: 759
Period size: 83 Copynumber: 5.1 Consensus size: 83
71294618 GTAAGGACAT
* * * *
71294628 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAATCATATCTGCAAGGTCCTCGACTTGTTCC
1 CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
71294693 TTGTAAGCACAAGGATGC
66 TTGTAAGCACAAGGATGC
71294711 CTAAACCATCTTGAGTCATGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTT
1 C-AAACCATCTTGAGTC-TGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTT
*
71294776 CCTTGTAAGCACAAGTATGC
64 CCTTGTAAGCACAAGGATGC
*
71294796 CAAACCATCTTGAGTCTGTTTGAGAATATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
1 CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
71294861 TTGTAAGCACAAGGATGC
66 TTGTAAGCACAAGGATGC
*
71294879 CAAACCATCTTAAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
1 CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
71294944 TTGTAAGCACAAGGATGC
66 TTGTAAGCACAAGGATGC
71294962 CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
1 CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
* *
71295027 TTGTAAGTACAAGGATGT
66 TTGTAAGCACAAGGATGC
71295045 CAAACCATCTTG
1 CAAACCATCTTG
71295057 GATCTGCTTC
Statistics
Matches: 332, Mismatches: 12, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
83 239 0.72
84 29 0.09
85 64 0.19
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (83 bp):
CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
TTGTAAGCACAAGGATGC
Found at i:71295576 original size:119 final size:119
Alignment explanation
Indices: 71294980--71295573 Score: 1017
Period size: 119 Copynumber: 5.0 Consensus size: 119
71294970 CTTGAGTCTG
* * * * ** * *
71294980 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGTACAAGGATGT
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* * *
71295045 CAAACCATCTTGGATCTGCTTCAGTATAAACATTTGAAGGTTAGATCTACTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
71295099 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
71295164 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
71295218 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
71295283 CAAATCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
71295337 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* *
71295402 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTACTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
71295456 TTTGAGAACGTCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
71295521 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
71295574 CTTCGATCTG
Statistics
Matches: 452, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 452 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:71295613 original size:44 final size:44
Alignment explanation
Indices: 71295565--71295744 Score: 186
Period size: 44 Copynumber: 4.1 Consensus size: 44
71295555 TGAAGGTTAG
71295565 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
* *
71295609 ATCTGCTATCTTC-AACTTGTTCCCAATAAACACAGGGATGCC--
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCAA
** * * * * * * * *
71295651 ATGCTGAAATCTGCAATCTGCTTCGCTGTAAGCATAGGAATGCCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGATGCCAA
* *
71295697 ATCTGCTATCTTTGATCTGTTCCCTATAAACATAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
71295741 ATCT
1 ATCT
71295745 TATTTCTTTG
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
42 2 0.02
43 12 0.11
44 80 0.74
45 12 0.11
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:71296612 original size:20 final size:20
Alignment explanation
Indices: 71296589--71296649 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
71296579 TCACCTTGGC
*
71296589 CTCTCCATTTTTTCTTTTTT
1 CTCTTCATTTTTTCTTTTTT
* *
71296609 CTCTTTATTTTTTTCTCTTTT
1 CTCTTCA-TTTTTTCTTTTTT
*
71296630 CTTTTC-TTTCTTTCTTTTTT
1 CTCTTCATTT-TTTCTTTTTT
71296650 TTTGAAATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
21 16 0.48
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.75
Consensus pattern (20 bp):
CTCTTCATTTTTTCTTTTTT
Found at i:71296620 original size:21 final size:20
Alignment explanation
Indices: 71296596--71296649 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
71296586 GGCCTCTCCA
71296596 TTTTTTCTTTTTTCTCTTTAT
1 TTTTTTCTTTTTTCT-TTTAT
* *
71296617 TTTTTTCTCTTTTCTTTTCT
1 TTTTTTCTTTTTTCTTTTAT
*
71296637 TTCTTTCTTTTTT
1 TTTTTTCTTTTTT
71296650 TTTGAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTTTTAT
Found at i:71296622 original size:14 final size:13
Alignment explanation
Indices: 71296598--71296650 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
71296588 CCTCTCCATT
71296598 TTTTCTTTTTTCTC
1 TTTT-TTTTTTCTC
71296612 TTTATTTTTTTCTC
1 TTT-TTTTTTTCTC
71296626 TTTTCTTTTCTT-TC
1 TTTT-TTTT-TTCTC
71296640 TTTCTTTTTTT
1 TTT-TTTTTTT
71296651 TTGAAATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.09
14 28 0.80
15 4 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:71305123 original size:25 final size:26
Alignment explanation
Indices: 71305068--71305133 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
71305058 ACATAAAAAT
* * *
71305068 ATGTATGTAAACAAATAAATAACTTA
1 ATGTATTTAAATAAATAAATAACGTA
*
71305094 A-GTATTTAAATAAATAGATAA-GTA
1 ATGTATTTAAATAAATAAATAACGTA
71305118 ATGTA-TTAATATAAAT
1 ATGTATTTAA-ATAAAT
71305134 TGAATGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.21
25 26 0.76
26 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (26 bp):
ATGTATTTAAATAAATAAATAACGTA
Found at i:71305249 original size:21 final size:20
Alignment explanation
Indices: 71305143--71305286 Score: 117
Period size: 20 Copynumber: 6.8 Consensus size: 20
71305133 TTGAATGTTT
* *
71305143 AAATAAAAAAAATAATAAAT
1 AAATAAAAAAAAAAATAAAA
** *
71305163 TGATAAAAAAAAAAAAAAAA
1 AAATAAAAAAAAAAATAAAA
* *
71305183 AAAAAAAAAAAAAAAAAAAA
1 AAATAAAAAAAAAAATAAAA
* *
71305203 AAAAAAAAATAAAAAAAAAAGA
1 AAATAAAAA-AAAAAATAAA-A
71305225 AAATAAAAAGAAAAAATAAAA
1 AAATAAAAA-AAAAAATAAAA
*
71305246 AAATAAATAATAAAAATATAAAG
1 AAATAAA-AA-AAAAA-ATAAAA
* *
71305269 AATTAAAATAAAATAATA
1 AAATAAAA-AAAAAAATA
71305287 GACAGAAATA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
20 41 0.39
21 21 0.20
22 30 0.29
23 12 0.12
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (20 bp):
AAATAAAAAAAAAAATAAAA
Found at i:71305261 original size:1 final size:1
Alignment explanation
Indices: 71305167--71305248 Score: 119
Period size: 1 Copynumber: 82.0 Consensus size: 1
71305157 ATAAATTGAT
* * *
71305167 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAGAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
71305232 AAGAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAA
71305249 TAAATAATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.94, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:71305276 original size:44 final size:44
Alignment explanation
Indices: 71305168--71305270 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 44
71305158 TAAATTGATA
71305168 AAAAA-AAAAAAAAAA-AAAA--AAAAAAAAAAAAAAAA-AAAA
1 AAAAATAAAAAAAAAAGAAAATAAAAAAAAAAAAAAAAAAAAAA
* * *
71305207 AAAAATAAAAAAAAAAGAAAATAAAAAGAAAAAATAAAAAAATA
1 AAAAATAAAAAAAAAAGAAAATAAAAAAAAAAAAAAAAAAAAAA
* *
71305251 AATAATAAAAATATAAAGAA
1 AAAAATAAAAA-AAAAAGAA
71305271 TTAAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
39 5 0.09
40 10 0.19
41 4 0.08
43 14 0.26
44 13 0.25
45 7 0.13
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (44 bp):
AAAAATAAAAAAAAAAGAAAATAAAAAAAAAAAAAAAAAAAAAA
Found at i:71305336 original size:16 final size:17
Alignment explanation
Indices: 71305300--71305340 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
71305290 AGAAATAATA
71305300 AATTAAAAATGAAAGCTG
1 AATT-AAAATGAAAGCTG
*
71305318 AATTAAAATGATA-CTG
1 AATTAAAATGAAAGCTG
71305334 AA-TAAAA
1 AATTAAAA
71305341 ACTAAAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 8 0.36
18 4 0.18
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (17 bp):
AATTAAAATGAAAGCTG
Found at i:71305341 original size:16 final size:17
Alignment explanation
Indices: 71305303--71305341 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
71305293 AATAATAAAT
71305303 TAAAAATGAAAGCTGAA
1 TAAAAATGAAAGCTGAA
* *
71305320 TTAAAATGATA-CTGAA
1 TAAAAATGAAAGCTGAA
71305336 TAAAAA
1 TAAAAA
71305342 CTAAAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (17 bp):
TAAAAATGAAAGCTGAA
Found at i:71307520 original size:49 final size:50
Alignment explanation
Indices: 71307459--71307587 Score: 181
Period size: 49 Copynumber: 2.6 Consensus size: 50
71307449 GGCTATTCTG
*
71307459 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCTA
1 GTACGCATAGTAGCCTGCACTTAGTACTACACA-GCGATCCAAGTTATCGA
* * * * *
71307508 GTACACATAGTAGCCTACACTTAGTACTACACAGTGATCGAAGTTATCGG
1 GTACGCATAGTAGCCTGCACTTAGTACTACACAGCGATCCAAGTTATCGA
71307558 GTACGCATAGTAGCCTGCACTTAGTACTAC
1 GTACGCATAGTAGCCTGCACTTAGTACTAC
71307588 GCCACAATAG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
48 3 0.04
49 34 0.49
50 33 0.47
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (50 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACAGCGATCCAAGTTATCGA
Found at i:71307870 original size:25 final size:27
Alignment explanation
Indices: 71307824--71307877 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
71307814 TCATACAACC
*
71307824 CATGTAATAGTAATTTAACATTC-ATT
1 CATGTAATAATAATTTAACATTCAATT
**
71307850 CATGTAA-AATAATTTGCCATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
71307876 CA
1 CA
71307878 CATGACACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAATAATAATTTAACATTCAATT
Found at i:71309377 original size:25 final size:25
Alignment explanation
Indices: 71309344--71309439 Score: 131
Period size: 25 Copynumber: 3.8 Consensus size: 25
71309334 AGCATGGCTG
* *
71309344 CAGAACAGATAA-GTTGAAGAGCAC
1 CAGAACAGATAATGTGGCAGAGCAC
71309368 CAGATACAGATAATCGTGGCAGAGCCAC
1 CAGA-ACAGATAAT-GTGGCAGAG-CAC
71309396 CAGAACAGATAATGTGGCAGAGCAC
1 CAGAACAGATAATGTGGCAGAGCAC
*
71309421 CAGATCAGATAATGTGGCA
1 CAGAACAGATAATGTGGCA
71309440 TGCCACCAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
24 4 0.06
25 29 0.45
26 9 0.14
27 16 0.25
28 7 0.11
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.15
Consensus pattern (25 bp):
CAGAACAGATAATGTGGCAGAGCAC
Found at i:71309406 original size:52 final size:50
Alignment explanation
Indices: 71309344--71309448 Score: 149
Period size: 52 Copynumber: 2.1 Consensus size: 50
71309334 AGCATGGCTG
*
71309344 CAGAACAGATAA-GTTGAAGAGCACCAGATACAGATAATCGTGGCAGAGCCAC
1 CAGAACAGATAATGTGGAAGAGCACCAGAT-CAGATAAT-GTGGCA-AGCCAC
* *
71309396 CAGAACAGATAATGTGGCAGAGCACCAGATCAGATAATGTGGCATGCCAC
1 CAGAACAGATAATGTGGAAGAGCACCAGATCAGATAATGTGGCAAGCCAC
71309446 CAG
1 CAG
71309449 GATGTTTCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 8 0.16
51 6 0.12
52 20 0.41
53 15 0.31
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (50 bp):
CAGAACAGATAATGTGGAAGAGCACCAGATCAGATAATGTGGCAAGCCAC
Found at i:71309446 original size:25 final size:24
Alignment explanation
Indices: 71309365--71309448 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 24
71309355 AGTTGAAGAG
71309365 CACCAGATACAGATAATCGTGGCAGAGC
1 CACCAGAT-CAGATAAT-GTGGC--AGC
* *
71309393 CACCAGAACAGATAATGTGGCAGAG
1 CACCAGATCAGATAATGTGGCAG-C
71309418 CACCAGATCAGATAATGTGGCATGC
1 CACCAGATCAGATAATGTGGCA-GC
71309443 CACCAG
1 CACCAG
71309449 GATGTTTCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.04
25 27 0.54
26 6 0.12
27 8 0.16
28 7 0.14
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.14
Consensus pattern (24 bp):
CACCAGATCAGATAATGTGGCAGC
Found at i:71326771 original size:17 final size:16
Alignment explanation
Indices: 71326744--71326777 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
71326734 TTATTAACCC
71326744 AAATTAAATTAGATAT
1 AAATTAAATTAGATAT
*
71326760 AAATTAAAATTAGTTAT
1 AAATT-AAATTAGATAT
71326777 A
1 A
71326778 TTATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATTAAATTAGATAT
Found at i:71330517 original size:40 final size:39
Alignment explanation
Indices: 71330466--71330595 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 39
71330456 GTAATCATAC
* *
71330466 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
71330506 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
*
71330546 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTC-CACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
71330585 AATGCCTTCGG
1 AATGCCTTCGG
71330596 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 17 0.21
40 63 0.79
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:71330639 original size:79 final size:79
Alignment explanation
Indices: 71330464--71330648 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 79
71330454 TAGTAATCAT
* * *
71330464 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
71330529 AATTAGTATCTCGC
66 AATTAGTATCTAGC
**
71330543 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTC-CACAAATGCCTTC-GGATCTTAGTC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGGA-CTTAACC
71330605 CGG-ATATAGTCA-CTTAGC
63 CGGAAT-TAGT-ATC-TAGC
*
71330623 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
71330649 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
78 5 0.05
79 53 0.57
80 35 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTATCTAGC
Found at i:71338383 original size:39 final size:40
Alignment explanation
Indices: 71338340--71338507 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
71338330 CTCGTTCAAG
* * * *
71338340 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
71338379 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
71338419 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
71338459 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
71338499 TGCCTTCGG
1 TGCCTTCGG
71338508 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:71338491 original size:80 final size:80
Alignment explanation
Indices: 71338375--71338560 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
71338365 AGTAACTCAT
* * *
71338375 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
71338439 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
71338454 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
71338518 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
71338535 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
71338561 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:71338520 original size:40 final size:40
Alignment explanation
Indices: 71338377--71338560 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
71338367 TAACTCATAC
* *
71338377 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
71338417 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
71338457 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
71338497 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
71338538 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
71338561 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:71341822 original size:21 final size:22
Alignment explanation
Indices: 71341798--71341838 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
71341788 ATATTAACTT
* *
71341798 AAATTATAATT-ACTTAAATAA
1 AAATCATAATTGACTCAAATAA
71341819 AAATCATAATTGACTCAAAT
1 AAATCATAATTGACTCAAAT
71341839 GTGAAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATCATAATTGACTCAAATAA
Found at i:71345072 original size:14 final size:14
Alignment explanation
Indices: 71345055--71345102 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
71345045 TAGATAATTT
*
71345055 TATTTTTATTTTAA
1 TATTTTTAATTTAA
71345069 TATTTTTAATTTAA
1 TATTTTTAATTTAA
71345083 -ATTTTTACATTCTAA
1 TATTTTTA-ATT-TAA
71345098 T-TTTT
1 TATTTT
71345103 CGTTTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 16 0.53
15 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTAATTTAA
Found at i:71346853 original size:48 final size:48
Alignment explanation
Indices: 71346782--71347091 Score: 360
Period size: 48 Copynumber: 6.5 Consensus size: 48
71346772 CATGTCACTA
* *
71346782 ATGCCATGTCTCC-GACATGGTCTTACATGAATC-CACATATCATCGCCG
1 ATGCCATGTC-CCAGACATGGTCTTACA-CAAGCACACATATCATCGCCG
*** * *
71346830 ATGCCATGTCCCAGACATGGTCTTACATTGGCACACAAATCATCGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
*** * * **
71346878 ATGCCATGTCCCAGACATGGTCTTACATTGGCACATATATTATAACCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
* * * *
71346926 ATGCTATGTCCCAGACATAGTCTTACACAGGCACATATATCA-CTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATC-GCCG
*
71346974 ATGCCATGTCCCAGACATGGTCTTACACAAGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
* *
71347022 ATGCCATGTCCCAGACATTGTCTTACAC-AG-ACACATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
*
71347068 ATGCCATGTCCCAGAAATGGTCTT
1 ATGCCATGTCCCAGACATGGTCTT
71347092 TTTTATCAAT
Statistics
Matches: 231, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
46 36 0.16
47 5 0.02
48 189 0.82
49 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATCGCCG
Found at i:71347112 original size:18 final size:18
Alignment explanation
Indices: 71347086--71347120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
71347076 TCCCAGAAAT
*
71347086 GGTCTTTTTTATCAATTA
1 GGTCCTTTTTATCAATTA
71347104 GGTCCTTTTTATCAATT
1 GGTCCTTTTTATCAATT
71347121 TCACCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (18 bp):
GGTCCTTTTTATCAATTA
Found at i:71360701 original size:19 final size:19
Alignment explanation
Indices: 71360667--71360703 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
71360657 ACCTACCAGA
71360667 AGTAAATAAAAGAAAATTT
1 AGTAAATAAAAGAAAATTT
71360686 AGTAATATAAAA-AAAATT
1 AGTAA-ATAAAAGAAAATT
71360704 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (19 bp):
AGTAAATAAAAGAAAATTT
Done.