Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 174 of 208
Found at i:53139766 original size:47 final size:49
Alignment explanation
Indices: 53139709--53139835 Score: 170
Period size: 49 Copynumber: 2.6 Consensus size: 49
53139699 ATTATGAAAT
*
53139709 TTCCGTGTAAGACCATATCTGGAATATGGCATCA-T-TGTGATATGTGA
1 TTCCGTGTAAGACCATATCTGGACTATGGCATCAGTATGTGATATGTGA
* * *
53139756 TTCCGTGTAAGACTATAGCTGGGCTATGGCATCAGTATGTGATATGTGA
1 TTCCGTGTAAGACCATATCTGGACTATGGCATCAGTATGTGATATGTGA
* *
53139805 TTACATGTAAGACCATAGT-TGGACTATGGCA
1 TTCCGTGTAAGACCATA-TCTGGACTATGGCA
53139836 ATGTGAAAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 30 0.44
48 1 0.01
49 37 0.54
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (49 bp):
TTCCGTGTAAGACCATATCTGGACTATGGCATCAGTATGTGATATGTGA
Found at i:53142501 original size:101 final size:102
Alignment explanation
Indices: 53142385--53142569 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
53142375 AAAGTGACGG
* ** *
53142385 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGTATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGAGTAGT
53142448 ACTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
*
53142486 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACATGAGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGAGTAGTA
* *
53142551 TTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
53142570 TGAATCCGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 40 0.53
102 31 0.41
103 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGAGTAGTA
CTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
Found at i:53142507 original size:51 final size:49
Alignment explanation
Indices: 53142383--53142567 Score: 192
Period size: 51 Copynumber: 3.7 Consensus size: 49
53142373 TGAAAGTGAC
* * *
53142383 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-G-TT
** * *
53142433 GGTCGTATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-TT
* * *
53142483 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTGAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT--T
* * *
53142535 GGTCACATGAGTAGTATTATGTGCATGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
53142568 TGTGAATCCG
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
50 41 0.37
51 69 0.62
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTT
Found at i:53142623 original size:43 final size:43
Alignment explanation
Indices: 53142575--53142706 Score: 180
Period size: 43 Copynumber: 3.1 Consensus size: 43
53142565 CTATGTGAAT
53142575 CCGTATCATTTAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
1 CCGTATCATTTAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
* * *
53142618 CCGTATC-CTTAACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-
1 CCGTATCATTTAA-TAT-AAAGGTGGTTGCTAAGTGCTGATTCCA
* *
53142660 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
1 CCGTATCATTTAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
53142703 CCGT
1 CCGT
53142707 GTAATGATTA
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
41 5 0.07
42 31 0.41
43 34 0.45
44 5 0.07
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (43 bp):
CCGTATCATTTAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
Found at i:53142695 original size:42 final size:42
Alignment explanation
Indices: 53142579--53142705 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
53142569 GTGAATCCGT
*
53142579 ATCATTTAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCA-TTAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGC
* * *
53142622 ATCCTTAACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-CCGC
1 ATCATTAA-TAT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGC
53142664 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCG
1 ATCATT-AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCG
53142706 TGTAATGATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
41 5 0.07
42 33 0.46
43 29 0.40
44 5 0.07
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
ATCATTAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGC
Found at i:53161307 original size:15 final size:15
Alignment explanation
Indices: 53161287--53161393 Score: 59
Period size: 15 Copynumber: 7.5 Consensus size: 15
53161277 TTTTTAAAAT
53161287 TTTTTTTAAAATTAA
1 TTTTTTTAAAATTAA
* **
53161302 TTTTTTT-AATTTTT
1 TTTTTTTAAAATTAA
*
53161316 TTTAATTTTAAAA--AT
1 TTT--TTTTAAAATTAA
*
53161331 TTTTTTTAAAATTAC
1 TTTTTTTAAAATTAA
53161346 TTTTTTT----TTAA
1 TTTTTTTAAAATTAA
**
53161357 -TTTTTTAATTTTTAA
1 TTTTTTTAA-AATTAA
*
53161372 TTTTTTTAAAAATAA
1 TTTTTTTAAAATTAA
53161387 TTTTTTT
1 TTTTTTT
53161394 TGGGTAATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
10 6 0.08
11 3 0.04
13 8 0.11
14 7 0.10
15 33 0.46
16 12 0.17
17 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTTAAAATTAA
Found at i:53161313 original size:45 final size:44
Alignment explanation
Indices: 53161264--53161393 Score: 171
Period size: 44 Copynumber: 3.0 Consensus size: 44
53161254 TTTTAATTTA
53161264 AATTTTTTTTAAATTTTTAAAATTTTTTTTAAAATTAATTTTTTT
1 AATTTTTTTT-AATTTTTAAAATTTTTTTTAAAATTAATTTTTTT
* *
53161309 AATTTTTTTTAATTTTAAAAATTTTTTTTAAAATTACTTTTTTT
1 AATTTTTTTTAATTTTTAAAATTTTTTTTAAAATTAATTTTTTT
*
53161353 --TTAATTTTTTAATTTTT--AA-TTTTTTTAAAAATAATTTTTTT
1 AATT--TTTTTTAATTTTTAAAATTTTTTTTAAAATTAATTTTTTT
53161394 TGGGTAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
41 20 0.26
42 4 0.05
44 44 0.56
45 10 0.13
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (44 bp):
AATTTTTTTTAATTTTTAAAATTTTTTTTAAAATTAATTTTTTT
Found at i:53161316 original size:8 final size:9
Alignment explanation
Indices: 53161298--53161380 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
53161288 TTTTTTAAAA
53161298 TTAATTTTT
1 TTAATTTTT
53161307 TTAATTTTTT
1 TTAA-TTTTT
*
53161317 TTAATTTTA
1 TTAATTTTT
**
53161326 AAAATTTTTT
1 TTAA-TTTTT
* **
53161336 TTAAAATTAC
1 TT-AATTTTT
53161346 TT--TTTTT
1 TTAATTTTT
53161353 TTAA-TTTT
1 TTAATTTTT
53161361 TTAA--TTT
1 TTAATTTTT
53161368 TTAATTTTT
1 TTAATTTTT
53161377 TTAA
1 TTAA
53161381 AAATAATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
7 11 0.20
8 8 0.15
9 17 0.31
10 17 0.31
11 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (9 bp):
TTAATTTTT
Found at i:53161317 original size:36 final size:36
Alignment explanation
Indices: 53161241--53161316 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
53161231 NNNNNNNNNC
*
53161241 TTTTTAAAATACTTTTTAATTTAAATTTTTTTTAAA
1 TTTTTAAAATACTTTTTAAATTAAATTTTTTTTAAA
** *
53161277 TTTTTAAAATTTTTTTTAAAATT-AA-TTTTTTTAAT
1 TTTTTAAAATACTTTTT-AAATTAAATTTTTTTTAAA
53161312 TTTTT
1 TTTTT
53161317 TTAATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 14 0.40
36 17 0.49
37 4 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (36 bp):
TTTTTAAAATACTTTTTAAATTAAATTTTTTTTAAA
Found at i:53161349 original size:25 final size:23
Alignment explanation
Indices: 53161263--53161342 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 23
53161253 TTTTTAATTT
53161263 AAATTTTTTTT-AAAT-TTTT-A
1 AAATTTTTTTTAAAATATTTTAA
**
53161283 AAATTTTTTTTAAAATTAATTTTTT
1 AAATTTTTTTTAAAA-T-ATTTTAA
*
53161308 TAATTTTTTTT---A-ATTTTAA
1 AAATTTTTTTTAAAATATTTTAA
53161327 AAATTTTTTTTAAAAT
1 AAATTTTTTTTAAAAT
53161343 TACTTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
19 15 0.33
20 11 0.24
21 3 0.07
22 3 0.07
24 4 0.09
25 10 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
AAATTTTTTTTAAAATATTTTAA
Found at i:53161394 original size:44 final size:42
Alignment explanation
Indices: 53161241--53161394 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 42
53161231 NNNNNNNNNC
*
53161241 TTTTT-AAAATACTTTTTAATTTAAATTTTTTTTAAATTTTTAAAATTT
1 TTTTTAAAAATAATTTTT--TTT-AATTTTTTTT-AATTTTT--AA-TT
* *
53161289 TTTTTAAAATTAA-TTTTTTTAATTTTTTTTAATTTTAAAAATTT
1 TTTTTAAAAATAATTTTTTTTAATTTTTTTTAATTTT--TAA-TT
* *
53161333 TTTTTAAAATTACTTTTTTTTTAA--TTTTTTAATTTTTAATT
1 TTTTTAAAAATA-ATTTTTTTTAATTTTTTTTAATTTTTAATT
53161374 TTTTTAAAAATAATTTTTTTT
1 TTTTTAAAAATAATTTTTTTT
53161395 GGGTAATTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
40 8 0.09
41 13 0.14
42 2 0.02
44 35 0.37
45 10 0.11
46 12 0.13
48 9 0.10
49 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (42 bp):
TTTTTAAAAATAATTTTTTTTAATTTTTTTTAATTTTTAATT
Found at i:53163188 original size:28 final size:27
Alignment explanation
Indices: 53163157--53163220 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
53163147 AAAACAGAAA
* *
53163157 CCTTTGTGGCAATGTATAAGAATGGAAG
1 CCTTTATGGCAATCTATAAG-ATGGAAG
* *
53163185 CCTTTATGGCGATCTATGAGATGGAAG
1 CCTTTATGGCAATCTATAAGATGGAAG
53163212 CCTTTATGG
1 CCTTTATGG
53163221 TGGTGATCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
CCTTTATGGCAATCTATAAGATGGAAG
Found at i:53166207 original size:234 final size:234
Alignment explanation
Indices: 53165790--53166249 Score: 875
Period size: 234 Copynumber: 2.0 Consensus size: 234
53165780 CTGACTCCTG
*
53165790 AGTGCTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTTGCTACTAATTTCTTGGATGAAGTAG
1 AGTGCTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
*
53165855 TAGTGACCTCTTTGCCACGAGTTTTCTTTAGAATAGATGAGATTTCCATGTCATGAAGATTTGAG
66 TAGTGACCTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATTTCCATGTCATGAAGATTTGAG
*
53165920 TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCAACTGGTAGTAGAAGAGGAAGCTAT
131 TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCAACTGGAAGTAGAAGAGGAAGCTAT
53165985 ATCAAGATTAGTGATGAGATTCTAATTTCAAGACCCCCA
196 ATCAAGATTAGTGATGAGATTCTAATTTCAAGACCCCCA
53166024 AGTGCTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
1 AGTGCTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
*
53166089 TAGTGACCTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATTTCCATGTCATGAAGGTTTGAG
66 TAGTGACCTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATTTCCATGTCATGAAGATTTGAG
*
53166154 TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCGACTGGAAGTAGAAGAGGAAGCTAT
131 TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCAACTGGAAGTAGAAGAGGAAGCTAT
53166219 ATCAAGATTAGTGATGAGATTCTAATTTCAA
196 ATCAAGATTAGTGATGAGATTCTAATTTCAA
53166250 AGAGGAAAGC
Statistics
Matches: 221, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
234 221 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (234 bp):
AGTGCTCTCTTCCCTCTAACCCTCTTCCTTGTTTTTTTTTGCTACTAATTTCTTGGATAAAGTAG
TAGTGACCTCTTTGCCACGAGTTCTCTTTAGAATAGATGAGATTTCCATGTCATGAAGATTTGAG
TGAGAAGGAAGTCATGTATCACCAATAAGAGAGTTAGCTCAACTGGAAGTAGAAGAGGAAGCTAT
ATCAAGATTAGTGATGAGATTCTAATTTCAAGACCCCCA
Found at i:53167814 original size:15 final size:16
Alignment explanation
Indices: 53167794--53167823 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53167784 ATTAAATTAA
53167794 TTAACC-AAATGCAAG
1 TTAACCTAAATGCAAG
53167809 TTAACCTAAATGCAA
1 TTAACCTAAATGCAA
53167824 ATGAAATGCA
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:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (16 bp):
TTAACCTAAATGCAAG
Found at i:53172206 original size:28 final size:28
Alignment explanation
Indices: 53172130--53172229 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
53172120 GAACACGGTA
* * *
53172130 GAAAATGGAAGCGTTTGTAGCAATCTAT
1 GAAAATGGAAGCCTTTGTGGTAATCTAT
53172158 GAAAATAGG-AGCCTTTGTGGTAATCTAT
1 GAAAAT-GGAAGCCTTTGTGGTAATCTAT
* *
53172186 GAAAATGGAAGCCTTTCTGGTAATCTAA
1 GAAAATGGAAGCCTTTGTGGTAATCTAT
*
53172214 GGAAA-GGAAGGCCTTT
1 GAAAATGGAA-GCCTTT
53172230 ATGATAAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.10
28 55 0.87
29 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (28 bp):
GAAAATGGAAGCCTTTGTGGTAATCTAT
Found at i:53174885 original size:38 final size:38
Alignment explanation
Indices: 53174843--53174925 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
53174833 TAAAGGGGTT
53174843 TATGCAATTAATTAAACTAAATGATTCTATCCTATATG
1 TATGCAATTAATTAAACTAAATGATTCTATCCTATATG
53174881 TATGCAATTAATTAAACTAAATGATTCTATCCTATATG
1 TATGCAATTAATTAAACTAAATGATTCTATCCTATATG
53174919 TATGCAA
1 TATGCAA
53174926 AATTTCAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (38 bp):
TATGCAATTAATTAAACTAAATGATTCTATCCTATATG
Found at i:53177424 original size:12 final size:12
Alignment explanation
Indices: 53177407--53177434 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53177397 TTAAATTTTA
53177407 ATCATCCTTCTC
1 ATCATCCTTCTC
53177419 ATCATCCTTCTC
1 ATCATCCTTCTC
53177431 ATCA
1 ATCA
53177435 CTTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (12 bp):
ATCATCCTTCTC
Found at i:53194775 original size:16 final size:17
Alignment explanation
Indices: 53194748--53194784 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
53194738 GCTAGCCCAA
53194748 AATTATAACCCAAACCT
1 AATTATAACCCAAACCT
53194765 AATTA-AACCCAAACCT
1 AATTATAACCCAAACCT
53194781 AATT
1 AATT
53194785 TGACCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTATAACCCAAACCT
Found at i:53195959 original size:23 final size:24
Alignment explanation
Indices: 53195905--53195962 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
53195895 ATTATTTTAT
* *
53195905 TATGTAGTATTATTTTAAGTTTCC
1 TATGTATTATTATTTTAAGTTTCA
*
53195929 TATATATTATTA-TTTAA-TTTCA
1 TATGTATTATTATTTTAAGTTTCA
53195951 TAATGTATTATT
1 T-ATGTATTATT
53195963 TTATATGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
TATGTATTATTATTTTAAGTTTCA
Found at i:53200695 original size:6 final size:6
Alignment explanation
Indices: 53200686--53200731 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
53200676 AAAAACGAAA
53200686 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
53200732 AAAGAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:53200780 original size:58 final size:56
Alignment explanation
Indices: 53200669--53200794 Score: 146
Period size: 58 Copynumber: 2.2 Consensus size: 56
53200659 GGGTTCAGAT
* * *
53200669 TCAAAAAAAAAACGAAAAAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAAAA
1 TCAAAAAAAAAAAGAAAAAAATCAAAATCAAAATAAAAAACAAAATC-AAATCAAAA
* * *
53200726 TCAAAAAAAGAAAAGAAAAAAATCAAAGTCAAAAGTAAAAAAGAGAAATC-AATCAAAG
1 TCAAAAAAA-AAAAGAAAAAAATCAAAATCAAAA-TAAAAAACA-AAATCAAATCAAAA
*
53200784 TCAAAATAAAA
1 TCAAAAAAAAA
53200795 TATGAAAAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 11 0.19
58 37 0.63
59 6 0.10
60 5 0.08
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.12
Consensus pattern (56 bp):
TCAAAAAAAAAAAGAAAAAAATCAAAATCAAAATAAAAAACAAAATCAAATCAAAA
Found at i:53200794 original size:28 final size:28
Alignment explanation
Indices: 53200669--53200794 Score: 114
Period size: 30 Copynumber: 4.4 Consensus size: 28
53200659 GGGTTCAGAT
* *
53200669 TCAAAA-AAAAAACGAAAAAAATCAAAA
1 TCAAAATAAAAAAAGAAAAAAATCAAAG
** *
53200696 TCAAAATCAAAATCAAA-ATCAAAATCAAAA
1 TCAAAAT-AAAA--AAAGAAAAAAATCAAAG
53200726 TCAAAA-AAAGAAAAGAAAAAAATCAAAG
1 TCAAAATAAA-AAAAGAAAAAAATCAAAG
**
53200754 TCAAAAGTAAAAAAGAGAAATCAATCAAAG
1 TCAAAA-TAAAAAA-AGAAAAAAATCAAAG
53200784 TCAAAATAAAA
1 TCAAAATAAAA
53200795 TATGAAAAGA
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.11
28 19 0.23
29 13 0.16
30 39 0.48
31 2 0.02
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.12
Consensus pattern (28 bp):
TCAAAATAAAAAAAGAAAAAAATCAAAG
Found at i:53201689 original size:13 final size:13
Alignment explanation
Indices: 53201658--53201711 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
53201648 GGGCACTCTA
53201658 AAAAAATGAAAAAT
1 AAAAAATG-AAAAT
* *
53201672 GAAAAATGAGAAT
1 AAAAAATGAAAAT
53201685 AAAAAATGAAAAT
1 AAAAAATGAAAAT
*
53201698 GAAAAATGGAAAAT
1 AAAAAAT-GAAAAT
53201712 GGAGAGGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 21 0.62
14 13 0.38
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:53201714 original size:7 final size:7
Alignment explanation
Indices: 53201659--53201712 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
53201649 GGCACTCTAA
53201659 AAAAATG
1 AAAAATG
53201666 AAAAATG
1 AAAAATG
53201673 AAAAATG
1 AAAAATG
* *
53201680 -AGAATA
1 AAAAATG
53201686 AAAAATG
1 AAAAATG
53201693 -AAAATG
1 AAAAATG
53201699 AAAAATG
1 AAAAATG
*
53201706 GAAAATG
1 AAAAATG
53201713 GAGAGGCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 10 0.25
7 30 0.75
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:53203303 original size:50 final size:50
Alignment explanation
Indices: 53203248--53203616 Score: 282
Period size: 50 Copynumber: 7.4 Consensus size: 50
53203238 CCCCAGGCGA
* * * *
53203248 TGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTGGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * * * * * **
53203298 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGG
1 TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC-GACAT
* * *
53203348 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * * * * *
53203398 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAAGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGA-C-AT
* *
53203448 TGCAGTGGAACAA-ATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACCT
1 TGCAGT-GAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* * * ** * ** *
53203498 TGCGGTTAAAAAGATTAAAGCTACAAT-AGCAAATCTTACTTCCTTGGCGA-
1 TGCAGTGAAAAAGATTAAAGCCAC-ATCAGTGAATCTTGCTTCCCCGAC-AT
* ** * * *
53203548 TGTAGTGAAGCAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
* *
53203598 TGCAGTTAAAAGGATTAAA
1 TGCAGTGAAAAAGATTAAA
53203617 ATCACAACGA
Statistics
Matches: 236, Mismatches: 71, Indels: 24
0.71 0.21 0.07
Matches are distributed among these distances:
49 17 0.07
50 201 0.85
51 18 0.08
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (50 bp):
TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
Found at i:53203633 original size:100 final size:100
Alignment explanation
Indices: 53203223--53203616 Score: 619
Period size: 100 Copynumber: 3.9 Consensus size: 100
53203213 CCGAAGAATT
* *
53203223 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTGGCT
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
53203288 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
*
53203323 ACAGCGAATCTTACTCCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
53203388 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * *
53203423 ACAGCGAATCTTACTCCCCAAGCGATGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCT
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* *
53203488 TCCCCGACCTTGCGGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * ** * *
53203523 ATAGCAAATCTTACTTCCTTGGCGATGTAGT-GAAGCAGATTAAAGCCACAACGGTGAATCTTGC
1 ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAA-CAGATTAAAGCCACATCGGTGAATCTTGC
* *
53203587 TTTCCCGACATTGCAGTTAAAAGGATTAAA
65 TTCCCCGACATTGCAGTTAAAAAGATTAAA
53203617 ATCACAACGA
Statistics
Matches: 270, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
99 3 0.01
100 267 0.99
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
ACAGCGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
Found at i:53204061 original size:16 final size:17
Alignment explanation
Indices: 53204034--53204065 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53204024 ACTAGCCCAA
53204034 AATTATAACCCAAACCC
1 AATTATAACCCAAACCC
53204051 AATTA-AACCCAAACC
1 AATTATAACCCAAACC
53204066 TAATCTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (17 bp):
AATTATAACCCAAACCC
Found at i:53205243 original size:23 final size:24
Alignment explanation
Indices: 53205191--53205246 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
53205181 TATTTTATTT
* *
53205191 TGTAGTATTATTTTAAGTTTCCTA
1 TGTATTATTATTTTAAGTTTCATA
*
53205215 TATATTATTA-TTTAA-TTTCATAA
1 TGTATTATTATTTTAAGTTTCAT-A
53205238 TGTATTATT
1 TGTATTATT
53205247 TTATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
24 8 0.30
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
TGTATTATTATTTTAAGTTTCATA
Found at i:53205329 original size:2 final size:2
Alignment explanation
Indices: 53205324--53205355 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53205314 CTTAATGCCC
53205324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53205356 TATTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53206944 original size:18 final size:18
Alignment explanation
Indices: 53206923--53206959 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53206913 ACTAAGTAAC
53206923 TTGTAACAATTAAGTTTT
1 TTGTAACAATTAAGTTTT
53206941 TTGTAACAATTAAGTTTT
1 TTGTAACAATTAAGTTTT
53206959 T
1 T
53206960 ATCAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTAACAATTAAGTTTT
Found at i:53211813 original size:43 final size:43
Alignment explanation
Indices: 53211743--53212056 Score: 334
Period size: 43 Copynumber: 7.3 Consensus size: 43
53211733 ACGTCGCTAA
* **
53211743 CTTTTGCGGCGCTTACACAAAAAAACGCCGCTAAAAATCATGTT
1 CTTTAGCGGCGCTTA-GGAAAAAAACGCCGCTAAAAATCATGTT
* * *
53211787 CTTTAGCGGC-ATTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT-AGGAAAAAAACGCCGCTAAAAATCATGTT
* *
53211830 CTGTAGCGGCGCTTA-GAAAAAAATGCCGC-AAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAA-ATCATGTT
* * **
53211872 CTTTAGCGGCGCTTA-GAAAAAAACTCCGCGAAATCTCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAATCATGTT
*
53211914 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAATCATGTT
* * * * *
53211957 CTTTAGCGGCGCTTTGGAATAAAACGCCTCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAATCATGTT
*** * *
53212000 CTTTAGCGGCGCTT-GTTCAAAAATGCCGCTAAAAGT-AGTGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAATCA-TGTT
*
53212042 CTTTAGCGGCACTTA
1 CTTTAGCGGCGCTTA
53212057 TTTCACAAAC
Statistics
Matches: 230, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.02
42 101 0.44
43 113 0.49
44 12 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAATCATGTT
Found at i:53211871 original size:42 final size:42
Alignment explanation
Indices: 53211743--53212056 Score: 307
Period size: 42 Copynumber: 7.4 Consensus size: 42
53211733 ACGTCGCTAA
* *
53211743 CTTTTGCGGCGCTTACACAAAAAAACGCCGCTAAAA-ATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGC-AAAAGATCATGTT
* * *
53211787 CTTTAGCGGC-ATTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT-A-GAAAAAAACGCCGCAAAAGATCATGTT
* *
53211830 CTGTAGCGGCGCTTAGAAAAAAATGCCGCAAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCAAAAGATCATGTT
* * **
53211872 CTTTAGCGGCGCTTAGAAAAAAACTCCGCGAAATCTCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCAAAAGATCATGTT
*
53211914 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCGCAAAAGATCATGTT
* * * *
53211957 CTTTAGCGGCGCTTTGGAATAAAACGCCTCTAAAAG-TAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGC-AAAAGATCATGTT
** *
53212000 CTTTAGCGGCGCTT-GTTCAAAAATGCCGCTAAAAG-T-AGTGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGC-AAAAGATCA-TGTT
*
53212042 CTTTAGCGGCACTTA
1 CTTTAGCGGCGCTTA
53212057 TTTCACAAAC
Statistics
Matches: 229, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.01
42 113 0.49
43 97 0.42
44 17 0.07
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCAAAAGATCATGTT
Found at i:53211913 original size:127 final size:129
Alignment explanation
Indices: 53211743--53212013 Score: 361
Period size: 127 Copynumber: 2.1 Consensus size: 129
53211733 ACGTCGCTAA
* *
53211743 CTTTTGCGGCGCTTACACAAAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGC-ATTAAGGAAA
1 CTTTAGCGGCGCTTA-ACAAAAAAACGCCGCGAAAAATCATGTTCTTTAGCGGCGATT-AGGAAA
* * *
53211807 TAAACGCCGCTAAAGATCATGTTCTGTAGCGGCGC-TTAGAAAAAAATGCCGC-AAAAGATCATG
64 AAAACGCCGCTAAAGATCATGTTCTGTAGCGGCGCTTTAGAAAAAAACGCCGCTAAAAG-TAATG
53211870 TT
128 TT
* * ** *
53211872 CTTTAGCGGCGCTT-AGAAAAAAACTCCGCGAAATCTCATGTTCTTTAGCGGCGCTTAGGAAAAA
1 CTTTAGCGGCGCTTAACAAAAAAACGCCGCGAAAAATCATGTTCTTTAGCGGCGATTAGGAAAAA
* * * *
53211936 AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAATAAAACGCCTCTAAAAGTAATGTT
66 AACGCCGCTAAAGATCATGTTCTGTAGCGGCGCTTTAGAAAAAAACGCCGCTAAAAGTAATGTT
53212000 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
53212014 GTTCAAAAAT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
127 72 0.58
128 35 0.28
129 18 0.14
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (129 bp):
CTTTAGCGGCGCTTAACAAAAAAACGCCGCGAAAAATCATGTTCTTTAGCGGCGATTAGGAAAAA
AACGCCGCTAAAGATCATGTTCTGTAGCGGCGCTTTAGAAAAAAACGCCGCTAAAAGTAATGTT
Found at i:53211934 original size:85 final size:86
Alignment explanation
Indices: 53211743--53212056 Score: 329
Period size: 85 Copynumber: 3.7 Consensus size: 86
53211733 ACGTCGCTAA
* ** *
53211743 CTTTTGCGGCGCTTACACAAAAAAACGCCGCTAAAA-ATCATGTTCTTTAGCGGC-ATTAAGGAA
1 CTTTAGCGGCGCTTA-GGAAAAAAACGCCGCTAAAAGATCATGTTCTTTAGCGGCGCTT-A-GAA
* *
53211806 ATAAACGCCGCTAAAGATCATGTT
63 AAAAACGCCGCTAAAAATCATGTT
* *
53211830 CTGTAGCGGCGCTTA-GAAAAAAATGCCGC-AAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
* * **
53211893 AACTCCGCGAAATCTCATGTT
66 AACGCCGCTAAAAATCATGTT
* *
53211914 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTTGGAATA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGATCATGTTCTTTAGCGGCGC-TTAGAAAA
* * *
53211978 AAACGCCTCTAAAAGTAATGTT
65 AAACGCCGCTAAAAATCATGTT
*** * *
53212000 CTTTAGCGGCGCTT-GTTCAAAAATGCCGCTAAAAG-T-AGTGTTCTTTAGCGGCACTTA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGATCA-TGTTCTTTAGCGGCGCTTA
53212057 TTTCACAAAC
Statistics
Matches: 194, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
84 43 0.22
85 96 0.49
86 42 0.22
87 13 0.07
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
AACGCCGCTAAAAATCATGTT
Found at i:53212535 original size:21 final size:21
Alignment explanation
Indices: 53212489--53212536 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
53212479 ATTTCTATCG
* *
53212489 CTGCTTCTCTCGCTGCGGCAT
1 CTGCTTCCCTCGCTGCCGCAT
* *
53212510 TTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCCGCAT
53212531 CTGCTT
1 CTGCTT
53212537 TAAGTTGTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.42, G:0.21, T:0.35
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCCGCAT
Found at i:53214884 original size:12 final size:12
Alignment explanation
Indices: 53214867--53214892 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53214857 GCCAGTTATG
53214867 TAAGTTATGTAT
1 TAAGTTATGTAT
53214879 TAAGTTATGTAT
1 TAAGTTATGTAT
53214891 TA
1 TA
53214893 GACAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TAAGTTATGTAT
Found at i:53214935 original size:9 final size:9
Alignment explanation
Indices: 53214900--53215211 Score: 349
Period size: 9 Copynumber: 35.2 Consensus size: 9
53214890 TTAGACAATA
53214900 ATGTAAGTT
1 ATGTAAGTT
*
53214909 A-GGAAGGTT
1 ATGTAA-GTT
53214918 ATGT-A-TT
1 ATGTAAGTT
53214925 ATGTAAGTT
1 ATGTAAGTT
53214934 ATGTAAGTT
1 ATGTAAGTT
53214943 ATGTAAGTT
1 ATGTAAGTT
53214952 ATGTAAGTT
1 ATGTAAGTT
*
53214961 ATTTAAGTT
1 ATGTAAGTT
53214970 ATGTAAGTT
1 ATGTAAGTT
53214979 ATGTAAGTT
1 ATGTAAGTT
* *
53214988 ATTTAATTT
1 ATGTAAGTT
53214997 ATGTAAGTT
1 ATGTAAGTT
53215006 ATGTATAAGTT
1 ATG--TAAGTT
53215017 ATGT-A-TT
1 ATGTAAGTT
*
53215024 ATGTAAATT
1 ATGTAAGTT
53215033 ATGTACTAAGTT
1 ATG---TAAGTT
53215045 ATGT-A-TT
1 ATGTAAGTT
* *
53215052 ATGTAAATA
1 ATGTAAGTT
*
53215061 ATTTAAGTT
1 ATGTAAGTT
*
53215070 AGGTAAGTT
1 ATGTAAGTT
53215079 ATGT-A-TT
1 ATGTAAGTT
53215086 ATGTAAGTT
1 ATGTAAGTT
*
53215095 ATTTAAGTT
1 ATGTAAGTT
53215104 ATGTAAGTT
1 ATGTAAGTT
53215113 ATGTAAGTT
1 ATGTAAGTT
* *
53215122 AGGTAGGTT
1 ATGTAAGTT
53215131 ATGT-A-TT
1 ATGTAAGTT
53215138 ATGTAAGTT
1 ATGTAAGTT
*
53215147 ATTTAAGTT
1 ATGTAAGTT
53215156 ATGTAAGTT
1 ATGTAAGTT
53215165 ATGTAAGTT
1 ATGTAAGTT
* *
53215174 ATTTAATTT
1 ATGTAAGTT
*
53215183 ATGTAAGGT
1 ATGTAAGTT
53215192 ATGTAAGTT
1 ATGTAAGTT
53215201 ATGTAAGTT
1 ATGTAAGTT
53215210 AT
1 AT
53215212 ATAATTTAAA
Statistics
Matches: 256, Mismatches: 30, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
7 30 0.12
8 11 0.04
9 197 0.77
10 1 0.00
11 9 0.04
12 8 0.03
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:53215384 original size:17 final size:18
Alignment explanation
Indices: 53215352--53215385 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53215342 TGATTGATAA
53215352 ATTTTGAAAAAAATATAG
1 ATTTTGAAAAAAATATAG
*
53215370 ATTTT-AAAAATATATA
1 ATTTTGAAAAAAATATA
53215386 TTAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTTGAAAAAAATATAG
Found at i:53215423 original size:9 final size:9
Alignment explanation
Indices: 53215409--53215443 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
53215399 TAAATATTTA
53215409 TAAGTTATG
1 TAAGTTATG
*
53215418 TAAGTTATA
1 TAAGTTATG
*
53215427 TAATTTATG
1 TAAGTTATG
53215436 TAAGTTAT
1 TAAGTTAT
53215444 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (9 bp):
TAAGTTATG
Found at i:53215434 original size:18 final size:18
Alignment explanation
Indices: 53215407--53215451 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
53215397 TATAAATATT
*
53215407 TATAAGTTATGTAAGTTA
1 TATAATTTATGTAAGTTA
53215425 TATAATTTATGTAAGTTA
1 TATAATTTATGTAAGTTA
53215443 TATAATTTA
1 TATAATTTA
53215452 AAAATTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TATAATTTATGTAAGTTA
Found at i:53216676 original size:22 final size:22
Alignment explanation
Indices: 53216651--53216697 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
53216641 AAAATTTTCT
53216651 TAAATTTTATACTGATTAAACC
1 TAAATTTTATACTGATTAAACC
53216673 TAAATTTTATACTGATTAAACC
1 TAAATTTTATACTGATTAAACC
53216695 TAA
1 TAA
53216698 GTAGAAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATTTTATACTGATTAAACC
Found at i:53218303 original size:21 final size:21
Alignment explanation
Indices: 53218279--53218329 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
53218269 ATAACCTAGA
53218279 CCCTAAACCACAACCCTTATC
1 CCCTAAACCACAACCCTTATC
53218300 CCCTAAACCACAACCCTTATC
1 CCCTAAACCACAACCCTTATC
53218321 CCCTAAACC
1 CCCTAAACC
53218330 CTAAATCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (21 bp):
CCCTAAACCACAACCCTTATC
Found at i:53222169 original size:25 final size:25
Alignment explanation
Indices: 53222141--53222199 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
53222131 GGCTCTTATA
*
53222141 AGCTTCCCGTTATACAGCTCGA-ATG
1 AGCTTCCCGTTACACAGCTC-ACATG
* **
53222166 AGCTTCCTGTTACATGGCTCACATG
1 AGCTTCCCGTTACACAGCTCACATG
53222191 AGCTTCCCG
1 AGCTTCCCG
53222200 ATTAATGGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTTCCCGTTACACAGCTCACATG
Found at i:53222207 original size:25 final size:25
Alignment explanation
Indices: 53222015--53222219 Score: 118
Period size: 24 Copynumber: 8.2 Consensus size: 25
53222005 TGACTTTTCG
* *
53222015 GAGCTTCCGGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAATGGCTC--TCAT
* * *
53222042 GAGCTTCCCAAATAATTGGCTTTC-T
1 GAGCTTCCCGATTAA-TGGCTCTCAT
*
53222067 AGAGCTTCCCGA-TATTGGCTCTC-T
1 -GAGCTTCCCGATTAATGGCTCTCAT
* * * *
53222091 GGAGCTTCCCGA-CATTGGCTCACTT
1 -GAGCTTCCCGATTAATGGCTCTCAT
* *
53222116 GAACTTCCCGATT-ATGGCTCTTAT
1 GAGCTTCCCGATTAATGGCTCTCAT
* ** **
53222140 AAGCTTCCCG-TTATACAGCTCGAAT
1 GAGCTTCCCGATTA-ATGGCTCTCAT
* *
53222165 GAGCTTCCTG-TTACATGGCTCACAT
1 GAGCTTCCCGATTA-ATGGCTCTCAT
*
53222190 GAGCTTCCCGATTAATGGCTCTCTT
1 GAGCTTCCCGATTAATGGCTCTCAT
53222215 GAGCT
1 GAGCT
53222220 ACCTGTTTAT
Statistics
Matches: 138, Mismatches: 33, Indels: 16
0.74 0.18 0.09
Matches are distributed among these distances:
23 2 0.01
24 53 0.38
25 52 0.38
26 15 0.11
27 12 0.09
28 4 0.03
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTCAT
Found at i:53231326 original size:30 final size:30
Alignment explanation
Indices: 53231292--53231354 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
53231282 ACTTAATAAG
53231292 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
53231322 CAAATGTCTTTAAAATAATTACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
53231352 CAA
1 CAA
53231355 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:53231905 original size:18 final size:18
Alignment explanation
Indices: 53231882--53231918 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53231872 TTGGTATACA
53231882 ATTATTCAAACTAATGGT
1 ATTATTCAAACTAATGGT
53231900 ATTATTCAAACTAATGGT
1 ATTATTCAAACTAATGGT
53231918 A
1 A
53231919 ATCTTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTATTCAAACTAATGGT
Found at i:53237718 original size:63 final size:63
Alignment explanation
Indices: 53237619--53237737 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
53237609 AAATACCTGT
* * *
53237619 AGAAGGTGTTGATGCAGGGCACAGTAGTTCATAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
1 AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
* ** * *
53237682 AGAAGGTGTTGATGCAAGGTATGGTGGTGCACAGTGTGGTGTTTGTGTAAAAATAA
1 AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAA
53237738 TGAGGTTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.29, C:0.08, G:0.34, T:0.29
Consensus pattern (63 bp):
AGAAGGTGTTGATGCAAGGCACAGTAGTGCACAGTGTGGTGCTTGTGTAAAAATAACAGGTGC
Found at i:53240652 original size:371 final size:371
Alignment explanation
Indices: 53239964--53240710 Score: 1138
Period size: 371 Copynumber: 2.0 Consensus size: 371
53239954 AACAATTCAC
* * * *
53239964 TTATTGCCTTCAGCTTTGCTTTCCATGAATTTCAATATGTGATGGAATATTTGAACTAGGGCTAC
1 TTATTGCCTTCAGCTTCGCTTTCCATGAATTTCAATATGTGATGGAACATTTGAACGAGGACTAC
* * *
53240029 ATATCAACTATTAGTAATGATACTGAAATTGTCAGATTTTCTCTAACCAACGGGATTATTCATTT
66 ATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTAATTT
* * * *
53240094 GCAAATAAGCTTGGAATCTATTTTGTGATGATCTCGCGTTAGTTGTGCAAGTATGAGGACTTTCA
131 GCAAATAAGCTTGGAATCTATTTTGTGATAATCTCGAGTTAGTTGTGCAAGTATAAGGACCTTCA
*
53240159 TATTTTTAAATTTCCCAATTTTGTTTCTTTTTCATCAATCCTACCTTGACCCTCCATTTATATCT
196 TATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATCCTACCTTGACCCTCCATTTATATCT
* * *
53240224 TCGTTACCGCTTTGACACTCACCAACATATTTGGTCATGGTAGAAATTACGACTTTGTAATCCAC
261 TCGTTACCACTTTAACACTCACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAATCCAC
* *
53240289 C-CAAAGTTTAAAGTTTTCTCCTTGAAAGCTCCTATAATGGCCTCCT
326 CTC-AAGTTTAAAGTTTTCTCCTTGAAAGCTCATATAATGGCCTCAT
* * ** *
53240335 TTATTGCCTTCAGCTTCGTTTTCTATGCCTTTCAATATGTGATGGAGCATTTGAATCGA-GACTA
1 TTATTGCCTTCAGCTTCGCTTTCCATGAATTTCAATATGTGATGGAACATTTGAA-CGAGGACTA
* * * * * *
53240399 CATATCAACTATTAGTAATGATACTAAAATTGTTATATTCTCTTTGATCGACGGGATTATTAATT
65 CATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTAATT
*
53240464 TGCAAATAAGCTTGGAATCTATTTTGTGATAATCTTGAGTTAGTTGTGCAAGTATAAGGACCTTC
130 TGCAAATAAGCTTGGAATCTATTTTGTGATAATCTCGAGTTAGTTGTGCAAGTATAAGGACCTTC
* *
53240529 ATATTTTCAAATTTCCTAATTTTGTTTCTTTTTCATCAATGCTACCTTGACCCTCCATTTATATC
195 ATATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATCCTACCTTGACCCTCCATTTATATC
* *
53240594 TTTGTTACCACTTTAACACTCACCAACATATTTGGTCATGGTAGAAATTGCAACTTTGTAATCCA
260 TTCGTTACCACTTTAACACTCACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAATCCA
* * *
53240659 CCTCGAGTTTAAAGTTTTCTCCTTGAAGGCTCATATAGTGGCCTCAT
325 CCTCAAGTTTAAAGTTTTCTCCTTGAAAGCTCATATAATGGCCTCAT
53240706 TTATT
1 TTATT
53240711 ATAAATTACA
Statistics
Matches: 338, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
371 335 0.99
372 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (371 bp):
TTATTGCCTTCAGCTTCGCTTTCCATGAATTTCAATATGTGATGGAACATTTGAACGAGGACTAC
ATATCAACTATTAGTAATGATACTAAAATTGTCAGATTCTCTCTAACCAACGGGATTATTAATTT
GCAAATAAGCTTGGAATCTATTTTGTGATAATCTCGAGTTAGTTGTGCAAGTATAAGGACCTTCA
TATTTTCAAATTTCCCAATTTTGTTTCTTTTTCATCAATCCTACCTTGACCCTCCATTTATATCT
TCGTTACCACTTTAACACTCACCAACATATTTGGTCATGGTAGAAATTACAACTTTGTAATCCAC
CTCAAGTTTAAAGTTTTCTCCTTGAAAGCTCATATAATGGCCTCAT
Found at i:53247743 original size:13 final size:13
Alignment explanation
Indices: 53247724--53247787 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
53247714 TAAACCAAAT
53247724 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
53247737 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
53247750 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
*
53247763 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
53247776 TTTTCAAAAGCA
1 TTTTCAAAAGCA
53247788 ATGAAGAACT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 5 0.12
13 32 0.78
14 4 0.10
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:53255046 original size:32 final size:31
Alignment explanation
Indices: 53255004--53255110 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
53254994 TCCCTAACTC
53255004 TTAATTTAATTTCTGAAAAATAGGATTGATT
1 TTAATTTAATTTCTGAAAAATAGGATTGATT
* * *
53255035 TTAATTTTAA-TT-AGAAAAATCGAGGAATTTCCTAACTC
1 TTAA-TTTAATTTCTGAAAAAT--AGG-A--T--TGA-TT
53255073 TTAATTTAATTTCTGAAAAATAGGATTGATT
1 TTAATTTAATTTCTGAAAAATAGGATTGATT
*
53255104 GTAATTT
1 TTAATTT
53255111 TGATTTGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
30 7 0.12
31 13 0.22
32 10 0.17
33 1 0.02
34 1 0.02
35 1 0.02
36 1 0.02
37 10 0.17
38 7 0.12
39 7 0.12
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (31 bp):
TTAATTTAATTTCTGAAAAATAGGATTGATT
Found at i:53255086 original size:69 final size:69
Alignment explanation
Indices: 53254975--53255111 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
53254965 ATTTCCTTTG
*
53254975 ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTTTAAT
1 ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTGTAAT
53255040 TTTA
66 TTTA
*
53255044 ATTAGAAAAATCGAGGAATTTCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTGTAAT
1 ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTGTAAT
53255109 TTT
66 TTT
53255112 GATTTGTGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (69 bp):
ATTAGAAAAATCGAGGAATTCCCTAACTCTTAATTTAATTTCTGAAAAATAGGATTGATTGTAAT
TTTA
Found at i:53259174 original size:21 final size:20
Alignment explanation
Indices: 53259148--53259187 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53259138 TTTTAGCATA
* *
53259148 TTTTAATTTATTTAACTAATT
1 TTTTAACTTAATTAA-TAATT
53259169 TTTTAACTTAATTAATAAT
1 TTTTAACTTAATTAATAAT
53259188 AATAAACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAACTTAATTAATAATT
Found at i:53259175 original size:12 final size:14
Alignment explanation
Indices: 53259150--53259181 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53259140 TTAGCATATT
53259150 TTAATTTATTTAAC
1 TTAATTTATTTAAC
53259164 -TAATTT-TTTAAC
1 TTAATTTATTTAAC
53259176 TTAATT
1 TTAATT
53259182 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTTATTTAAC
Found at i:53261231 original size:2 final size:2
Alignment explanation
Indices: 53261224--53261252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53261214 CAAAAACTTT
53261224 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 T
53261253 TATTTGAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53263949 original size:18 final size:18
Alignment explanation
Indices: 53263908--53263950 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
53263898 AAAAACTGTT
* * *
53263908 TTTACATATATTAATATA
1 TTTATATATATTAACAAA
*
53263926 TATATATATATTAACAAA
1 TTTATATATATTAACAAA
53263944 TTTATAT
1 TTTATAT
53263951 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATTAACAAA
Found at i:53269458 original size:21 final size:22
Alignment explanation
Indices: 53269424--53269467 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
53269414 GGGAGTAAGG
53269424 TTCTATATTTGGTTTTATATGT
1 TTCTATATTTGGTTTTATATGT
53269446 TTCTATA-TTGGTTTTATATGT
1 TTCTATATTTGGTTTTATATGT
53269467 T
1 T
53269468 AATGACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.18, C:0.05, G:0.14, T:0.64
Consensus pattern (22 bp):
TTCTATATTTGGTTTTATATGT
Found at i:53271484 original size:21 final size:23
Alignment explanation
Indices: 53271460--53271504 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
53271450 GTAAAAAAAG
*
53271460 TAAATATAGAT-TAAAAA-ATTT
1 TAAATATAAATATAAAAATATTT
*
53271481 TAAATGTAAATATAAAAATATTT
1 TAAATATAAATATAAAAATATTT
53271504 T
1 T
53271505 TAAGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATATAAATATAAAAATATTT
Found at i:53290241 original size:40 final size:41
Alignment explanation
Indices: 53290170--53290252 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 41
53290160 TGTACGTTTA
*
53290170 AAAATAACATAAAATAAAAAAAAATTATATACTTTGAAGCT
1 AAAATAACATAAAATAAAAAAAAATTATATACTTTGAAACT
* *
53290211 AAAATAACATACAAT-AAAAAAAATTGTATACTTTGAAACT
1 AAAATAACATAAAATAAAAAAAAATTATATACTTTGAAACT
53290251 AA
1 AA
53290253 TAACAATAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 25 0.64
41 14 0.36
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (41 bp):
AAAATAACATAAAATAAAAAAAAATTATATACTTTGAAACT
Found at i:53297842 original size:42 final size:42
Alignment explanation
Indices: 53297796--53297915 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 42
53297786 AGCTAAACAA
* * *
53297796 AAACCCATAAGGGTTGAACAGAAGCTCGTAAAAGCTTAACGG
1 AAACCCATAAGAGTTAAACAGAAGCTCGTAAAAGCTGAACGG
* *
53297838 AAACCCATAAGAGTTAAACAAAAGCTC-AAAAGAGCTGAACGG
1 AAACCCATAAGAGTTAAACAGAAGCTCGTAAA-AGCTGAACGG
* * * *
53297880 AAACTCATATGAGTTAAATAGAAGCTCGTAAGAGCT
1 AAACCCATAAGAGTTAAACAGAAGCTCGTAAAAGCT
53297916 ACATAGAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.05
42 60 0.92
43 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AAACCCATAAGAGTTAAACAGAAGCTCGTAAAAGCTGAACGG
Found at i:53307648 original size:6 final size:6
Alignment explanation
Indices: 53307592--53307656 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
53307582 AGATGATAAC
* * * *
53307592 GAAGAC GAAGAG GAAGTG GAAGAG CAGAACGAA GAAGAG GAAGAC GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG --GAA-GAG GAAGAG GAAGAG GAAGAG
*
53307643 GAAGAG GAGGAG GA
1 GAAGAG GAAGAG GA
53307657 GGAAGAGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 40 0.83
7 3 0.06
8 3 0.06
9 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.45, T:0.02
Consensus pattern (6 bp):
GAAGAG
Found at i:53309215 original size:17 final size:16
Alignment explanation
Indices: 53309195--53309233 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53309185 TAGTATATTT
53309195 TTTTATTAGTTATAAAA
1 TTTTATT-GTTATAAAA
*
53309212 TTTTAATGTTATAAAA
1 TTTTATTGTTATAAAA
*
53309228 TATTAT
1 TTTTAT
53309234 ATTTAGTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTTATTGTTATAAAA
Found at i:53309622 original size:18 final size:17
Alignment explanation
Indices: 53309595--53309634 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
53309585 AATTTTATAA
53309595 AAAAACTTATAAATAATAT
1 AAAAACTTATAAAT--TAT
53309614 AAAAA-TTATAAATTAT
1 AAAAACTTATAAATTAT
53309630 AAAAA
1 AAAAA
53309635 AAAGTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAACTTATAAATTAT
Found at i:53309635 original size:18 final size:19
Alignment explanation
Indices: 53309589--53309636 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
53309579 ATTTAAAATT
53309589 TTATAAAAAAACTTATAAA
1 TTATAAAAAAACTTATAAA
* *
53309608 TAATATAAAAA-TTATAAA
1 TTATAAAAAAACTTATAAA
53309626 TTATAAAAAAA
1 TTATAAAAAAA
53309637 AGTCTAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTATAAAAAAACTTATAAA
Found at i:53310132 original size:18 final size:18
Alignment explanation
Indices: 53310065--53310132 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
53310055 CAATAAATGA
*
53310065 ATTTTCATAATTCTAT-AT
1 ATTTTAATAATT-TATAAT
* *
53310083 ATTTTAATATTTTATTAGT
1 ATTTTAATAATTTA-TAAT
*
53310102 -TTTTAA-AAATTATAAT
1 ATTTTAATAATTTATAAT
53310118 ATTTTAATAATTTAT
1 ATTTTAATAATTTAT
53310133 TAGAACTCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 3 0.08
17 12 0.31
18 23 0.59
19 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (18 bp):
ATTTTAATAATTTATAAT
Found at i:53310580 original size:18 final size:19
Alignment explanation
Indices: 53310536--53310576 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
53310526 CATTTTTGAA
53310536 ATTTTTAT-TGATATTATT
1 ATTTTTATATGATATTATT
*
53310554 ATTATTATAT-ATATT-TT
1 ATTTTTATATGATATTATT
53310571 ATTTTT
1 ATTTTT
53310577 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 12 0.60
19 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTATATGATATTATT
Found at i:53310777 original size:29 final size:29
Alignment explanation
Indices: 53310709--53310777 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
53310699 TTAATGATAT
*
53310709 TGGCTCAATTAGGTGCAAATTTAGTGTAG
1 TGGCTCAATTGGGTGCAAATTTAGTGTAG
* *
53310738 -GAGCTCAATTGGGTGCAGATTTGGTGTAG
1 TG-GCTCAATTGGGTGCAAATTTAGTGTAG
53310767 TGGCTCAATTG
1 TGGCTCAATTG
53310778 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (29 bp):
TGGCTCAATTGGGTGCAAATTTAGTGTAG
Found at i:53317783 original size:24 final size:24
Alignment explanation
Indices: 53317751--53317798 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53317741 GTAATATTGG
53317751 GTGCATAGGTGATTAACTTCATTA
1 GTGCATAGGTGATTAACTTCATTA
53317775 GTGCATAGGTGATTAACTTCATTA
1 GTGCATAGGTGATTAACTTCATTA
53317799 CCTGATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (24 bp):
GTGCATAGGTGATTAACTTCATTA
Found at i:53338028 original size:2 final size:2
Alignment explanation
Indices: 53338023--53338052 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
53338013 TCTCTCTCTC
53338023 TA TA TA TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
53338053 CACCTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53339885 original size:16 final size:16
Alignment explanation
Indices: 53339854--53339890 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53339844 ATATGAAGAA
53339854 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
53339870 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
53339886 TATTA
1 TATTA
53339891 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:53341430 original size:6 final size:6
Alignment explanation
Indices: 53341419--53341458 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
53341409 GTGACCCAAC
53341419 CCATAA CCATAA CCATAA CCATAA CCATAA CCATAA CCAT
1 CCATAA CCATAA CCATAA CCATAA CCATAA CCATAA CCAT
53341459 TCTCTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATAA
Found at i:53344550 original size:114 final size:114
Alignment explanation
Indices: 53344217--53344551 Score: 505
Period size: 114 Copynumber: 3.0 Consensus size: 114
53344207 CAGGGGAACC
* * * *
53344217 AAGTTCAATGATAATCCCACATTTTACATGTTAATAAAAACAAGTTAGACCAGCAAAGCAGCAAT
1 AAGTTGAATGATGATTCCACATTTTACATGTTAATAAAAACAAGTTAGAGCAGCAAAGCAGCAAT
* ** *
53344282 AATTTTACATGT--AAGAAATATTTGGTTCATAGTTAGAATATGCGGGC
66 ATTTTTACATGTAAAAGAAATATTTGGTTCATAGTTAGAATATGCAAGA
*
53344329 AAGTTGAATGATGATTCCACATTTTACATGTTACTAAAAACAAGTTAGAGCAGCAAAGCAGCAAT
1 AAGTTGAATGATGATTCCACATTTTACATGTTAATAAAAACAAGTTAGAGCAGCAAAGCAGCAAT
*
53344394 ATTTTTACATGTAAAAGAAATATTTGGTTCATAATTAGAATATGCAAGA
66 ATTTTTACATGTAAAAGAAATATTTGGTTCATAGTTAGAATATGCAAGA
* * *
53344443 AAGTTGAATGATGATTCCACATTTTACGTGTTAATAGAAACAAATTAGAGCAGCAAAGCAGCAAT
1 AAGTTGAATGATGATTCCACATTTTACATGTTAATAAAAACAAGTTAGAGCAGCAAAGCAGCAAT
* *
53344508 ATTTTTACATATAAAAGAAACATTTGGTTCATAGTT-GAAATATG
66 ATTTTTACATGTAAAAGAAATATTTGGTTCATAGTTAG-AATATG
53344552 AGCACACCAG
Statistics
Matches: 203, Mismatches: 17, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
112 71 0.35
113 1 0.00
114 131 0.65
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (114 bp):
AAGTTGAATGATGATTCCACATTTTACATGTTAATAAAAACAAGTTAGAGCAGCAAAGCAGCAAT
ATTTTTACATGTAAAAGAAATATTTGGTTCATAGTTAGAATATGCAAGA
Found at i:53345654 original size:25 final size:25
Alignment explanation
Indices: 53345626--53345673 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53345616 AAATTTTAAA
53345626 TTTAATTTT-TCATTATAATATAACT
1 TTTAATTTTATCATTATAA-ATAACT
*
53345651 TTTAATTTTATTATTATAAATAA
1 TTTAATTTTATCATTATAAATAA
53345674 AAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTAATTTTATCATTATAAATAACT
Found at i:53346936 original size:20 final size:20
Alignment explanation
Indices: 53346911--53346967 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 20
53346901 TTCTCCTTAT
53346911 TTATATTAATTAAAATTAAA
1 TTATATTAATTAAAATTAAA
* * **
53346931 TTATATATAGTAAAAATTATT
1 TTATAT-TAATTAAAATTAAA
*
53346952 TTA-ATTACTTAAAATT
1 TTATATTAATTAAAATT
53346968 TTTATAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 9 0.30
20 8 0.27
21 13 0.43
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATATTAATTAAAATTAAA
Found at i:53347583 original size:6 final size:6
Alignment explanation
Indices: 53347572--53347605 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
53347562 GTGACCCAAC
53347572 CCATAA CCATAA CCATAA CCATAA CCATAA CCAT
1 CCATAA CCATAA CCATAA CCATAA CCATAA CCAT
53347606 TCTTTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (6 bp):
CCATAA
Found at i:53351712 original size:46 final size:46
Alignment explanation
Indices: 53351638--53351869 Score: 374
Period size: 46 Copynumber: 5.0 Consensus size: 46
53351628 ACATTGCTAT
* * *
53351638 AACTCAGTATGATTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATG-GTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* * *
53351685 AACTCAGTATGGTTTTCTTTACTGAAATACCACACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53351731 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53351777 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* * *
53351823 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53351869 A
1 A
53351870 CTTTGCCATG
Statistics
Matches: 174, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
46 163 0.94
47 11 0.06
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
Found at i:53353981 original size:21 final size:21
Alignment explanation
Indices: 53353957--53353998 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53353947 CTTTTTGTTC
*
53353957 AATTAATTACCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
53353978 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
53353999 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:53363810 original size:19 final size:20
Alignment explanation
Indices: 53363774--53363821 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53363764 AGATGACATA
53363774 TAAATATTTAATTAATATTT
1 TAAATATTTAATTAATATTT
* *
53363794 TAAATTTTTAA-TAATATTA
1 TAAATATTTAATTAATATTT
*
53363813 AAAATATTT
1 TAAATATTT
53363822 GTTTTCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATTTAATTAATATTT
Found at i:53363919 original size:30 final size:28
Alignment explanation
Indices: 53363861--53363919 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
53363851 AATTTAGTGA
*
53363861 TTTTAAATTTTAAAAATAATTTATATAT
1 TTTTAAATTTTAAAAATAATTTAAATAT
53363889 TTTTAAATTTTTTAAAAATTAA-TTAAATAT
1 TTTTAAA--TTTTAAAAA-TAATTTAAATAT
53363919 T
1 T
53363920 GACATGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
30 17 0.63
31 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTAAATTTTAAAAATAATTTAAATAT
Found at i:53364469 original size:11 final size:11
Alignment explanation
Indices: 53364452--53364481 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
53364442 TTTTATTTTT
53364452 TAATTTTAAAA
1 TAATTTTAAAA
*
53364463 TACTTTTAAAA
1 TAATTTTAAAA
53364474 TAATTTTA
1 TAATTTTA
53364482 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:53370849 original size:20 final size:20
Alignment explanation
Indices: 53370824--53370863 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53370814 TCGACTGCCA
53370824 AATTATAAATAAATTTTGAG
1 AATTATAAATAAATTTTGAG
53370844 AATTATAAATAAATTTTGAG
1 AATTATAAATAAATTTTGAG
53370864 TAATAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AATTATAAATAAATTTTGAG
Found at i:53370875 original size:18 final size:19
Alignment explanation
Indices: 53370828--53370875 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
53370818 CTGCCAAATT
*
53370828 ATAAATAAATTTTGAGAATT
1 ATAAATAAATTTTGAG-ATA
53370848 ATAAATAAATTTTGAG-TA
1 ATAAATAAATTTTGAGATA
*
53370866 ATAAACAAAT
1 ATAAATAAAT
53370876 CGGTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (19 bp):
ATAAATAAATTTTGAGATA
Found at i:53372860 original size:21 final size:22
Alignment explanation
Indices: 53372819--53372865 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
53372809 TTGAATCTCC
*
53372819 AATACATTCAAAACATTTAA-T
1 AATACATACAAAACATTTAATT
*
53372840 AATACATAGAAAAC-TTGTAATT
1 AATACATACAAAACATT-TAATT
53372862 AATA
1 AATA
53372866 TATATTCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 15 0.68
22 5 0.23
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (22 bp):
AATACATACAAAACATTTAATT
Found at i:53375278 original size:21 final size:21
Alignment explanation
Indices: 53375254--53375293 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53375244 AGAATTGTCA
* *
53375254 AAATAGTTTGAGGAGAAATAG
1 AAATAGATTGAAGAGAAATAG
*
53375275 AAATGGATTGAAGAGAAAT
1 AAATAGATTGAAGAGAAAT
53375294 TTAGAGCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATAGATTGAAGAGAAATAG
Found at i:53382201 original size:42 final size:42
Alignment explanation
Indices: 53382094--53382204 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
53382084 CAAAAAGGCG
* * *
53382094 GCTCAAATATTGATTGGAATAGGGCATGAGGTAATCTGAGCG
1 GCTCAAATATTGATTAGAATGGGGCATGAGGTAATCTGAGCA
* ** *
53382136 GCTCAAATATTAACCAGAATGGGGCATGAGGTGATCTGAGCA
1 GCTCAAATATTGATTAGAATGGGGCATGAGGTAATCTGAGCA
* * *
53382178 GTTCAAATTTTGATTAGATTGGGGCAT
1 GCTCAAATATTGATTAGAATGGGGCAT
53382205 ATGACGATCT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.28
Consensus pattern (42 bp):
GCTCAAATATTGATTAGAATGGGGCATGAGGTAATCTGAGCA
Found at i:53383390 original size:43 final size:43
Alignment explanation
Indices: 53383343--53383886 Score: 293
Period size: 43 Copynumber: 12.3 Consensus size: 43
53383333 ACAGATCTTA
* * *
53383343 TCTCCCTAAGCAGTAGTGGAGCAAATTGAAGACCCCATCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
* * * * *** * *
53383386 TCTCCCTAAGTAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTG-AA-AACCCCAG-CCTTG
* *
53383432 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CCCAGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
* * * * *** * *
53383474 TCTTCCTGAGCAGTAGTGGAGTAGGTTGAAATAAATACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTG-AA-AACCCCAG-CCTTG
* * *
53383520 TCTCCCTAGGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
* *
53383563 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
* * * * **** * *
53383606 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATATAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTG---AAAACCCCAG-CCTTG
*
53383653 TCTCCCTAAGCAGTAGTGGAGCAGATAGAAAACCCCAGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
* * * * *** ** *
53383696 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATATTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTG---AAAACCCCAG-CCTTG
* *
53383743 TCTCCCTAAGCAGTAGTGGAGCAGA-TCAAAGACCCCAGCCTTC
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAA-ACCCCAGCCTTG
* ** * * * *** ** *
53383786 TCTCCCTCAGCAACAATGGAGTAGGTTGAAAAATTACATATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTG-AAAACCCCA-GCCTTG
* * *
53383831 TCTCCCTAAGCAGTAGTAGAGCAGA-TCAAAGACACCAGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAA-ACCCCAGCCTTG
* *
53383874 CCTCCCTGAGCAG
1 TCTCCCTAAGCAG
53383887 CAGTAGACGA
Statistics
Matches: 362, Mismatches: 119, Indels: 40
0.69 0.23 0.08
Matches are distributed among these distances:
42 26 0.07
43 163 0.45
44 26 0.07
45 34 0.09
46 64 0.18
47 49 0.14
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (43 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAAACCCCAGCCTTG
Found at i:53383533 original size:88 final size:89
Alignment explanation
Indices: 53383290--53383583 Score: 482
Period size: 89 Copynumber: 3.3 Consensus size: 89
53383280 GAAACCACAA
* *
53383290 AGCCTTGTCTCCCTGAGTAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
* *
53383355 GTAGTGGAGCAAATTGAAGACCCC
66 GTAGTGGAGCAGATCGAAGACCCC
* *
53383379 ATCCTTGTCTCCCTAAGTAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
53383444 GTAGTGGAGCAGATCGAAGA-CCC
66 GTAGTGGAGCAGATCGAAGACCCC
* * * *
53383467 AGCCTTGTCTTCCTGAGCAGTAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAGGCA
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
53383532 GTAGTGGAGCAGATCGAAGACCCC
66 GTAGTGGAGCAGATCGAAGACCCC
*
53383556 AGCCTTGTCTCCCTAAGCAGTAGTGGAG
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAG
53383584 CAGATCGAAG
Statistics
Matches: 192, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 82 0.43
89 110 0.57
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (89 bp):
AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAATAAATACAGATCTTATCTCCCTAAGCA
GTAGTGGAGCAGATCGAAGACCCC
Found at i:53383659 original size:47 final size:47
Alignment explanation
Indices: 53383606--53383763 Score: 162
Period size: 47 Copynumber: 3.4 Consensus size: 47
53383596 CCCAGCCTTG
* *
53383606 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATATAGATCTTA
1 TCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATCTTA
* * * * *** * *
53383653 TCTCCCTAAGCAGTAGTGGAGCA-GAT--AGAAAACCCCAG-CCTTG
1 TCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATCTTA
* *
53383696 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATATTA
1 TCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATCTTA
*
53383743 TCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGCAGTGGAG
53383764 CAGATCAAAG
Statistics
Matches: 83, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
43 23 0.28
44 9 0.11
46 10 0.12
47 41 0.49
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (47 bp):
TCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATCTTA
Found at i:53383670 original size:90 final size:90
Alignment explanation
Indices: 53383563--53383890 Score: 509
Period size: 90 Copynumber: 3.7 Consensus size: 90
53383553 CCCAGCCTTG
*
53383563 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
*
53383628 AGGTTGAAAAAAAATATAGATCTTA
66 AGGTTGAAAAAAAATACAGATCTTA
*
53383653 TCTCCCTAAGCAGTAGTGGAGCAGAT-AGAAAACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAGCAGATCA-AAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAG
*
53383717 TAGGTTGAAAAAAAATACAGATATTA
65 TAGGTTGAAAAAAAATACAGATCTTA
* * * *
53383743 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTCTCTCCCTCAGCAACAATGGAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
* *
53383808 AGGTTG--AAAAATTACATATCTTA
66 AGGTTGAAAAAAAATACAGATCTTA
* * *
53383831 TCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACACCAGCCTTGCCTCCCTGAGCAGCAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGT
53383891 AGACGAAGCG
Statistics
Matches: 217, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
88 67 0.31
90 149 0.69
91 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (90 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
AGGTTGAAAAAAAATACAGATCTTA
Found at i:53383688 original size:133 final size:131
Alignment explanation
Indices: 53383432--53383716 Score: 471
Period size: 133 Copynumber: 2.2 Consensus size: 131
53383422 ACAGATCTTA
* *
53383432 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCAGCCTTGTCTTCCTGAGCAGTAGTGGAGTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTA
* * * *
53383497 GGTTGAAATAAATACAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTT
66 GGTTGAAAAAAATACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAAACCCCAGCCTT
53383562 G
131 G
53383563 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
*
53383628 AGGTTGAAAAAAAATATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAAACCCCAGCC
65 AGGTTG-AAAAAAATACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAAACCCCAGCC
53383693 TTG
129 TTG
* *
53383696 TCTCCCTGAGCAGCAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAG
53383717 TAGGTTGAAA
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 32 0.22
132 36 0.25
133 75 0.52
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (131 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTA
GGTTGAAAAAAATACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAAACCCCAGCCTT
G
Found at i:53383756 original size:180 final size:178
Alignment explanation
Indices: 53383563--53383890 Score: 514
Period size: 178 Copynumber: 1.8 Consensus size: 178
53383553 CCCAGCCTTG
* * * * *
53383563 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTCTCTCCCTCAGCAACAATGGAGT
* * *
53383628 AGGTTGAAAAAAAATATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-AGAAAACCCCAGC
66 AGGTTG--AAAAAATACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCA-AAAACACCAGC
*
53383692 CTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATATTA
128 CTTGCCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATATTA
53383743 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTCTCTCCCTCAGCAACAATGGAGT
1 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTCTCTCCCTCAGCAACAATGGAGT
* * *
53383808 AGGTTGAAAAATTACATATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACACCAGCCTT
66 AGGTTGAAAAAATACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAAACACCAGCCTT
53383873 GCCTCCCTGAGCAGCAGT
131 GCCTCCCTGAGCAGCAGT
53383891 AGACGAAGCG
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
178 68 0.50
179 1 0.01
180 66 0.49
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (178 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAGCCTTCTCTCCCTCAGCAACAATGGAGT
AGGTTGAAAAAATACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAAACACCAGCCTT
GCCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAAAAATACAGATATTA
Found at i:53383989 original size:41 final size:41
Alignment explanation
Indices: 53383912--53383989 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 41
53383902 ATTAAAATAA
** * *
53383912 CAGATCTTATCTCTTTGAAGTTATAGTAGAGGAGATCACAT
1 CAGATCTTATCTCCCTGAAGTTACAGCAGAGGAGATCACAT
* * *
53383953 CAGATCTTATCTCCCTGAAGTTGCAGCGGAGTAGATC
1 CAGATCTTATCTCCCTGAAGTTACAGCAGAGGAGATC
53383990 GAAGAAGCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
CAGATCTTATCTCCCTGAAGTTACAGCAGAGGAGATCACAT
Found at i:53384323 original size:17 final size:16
Alignment explanation
Indices: 53384272--53384327 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
53384262 ATACATTTCA
*
53384272 AAAAAACAAA-CAAAT
1 AAAAAATAAATCAAAT
53384287 AAAAAATATAAT-AAAT
1 AAAAAATA-AATCAAAT
53384303 -AAAAATAAATCCAAAT
1 AAAAAATAAAT-CAAAT
53384319 AAAAAATAA
1 AAAAAATAA
53384328 TATTAAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 3 0.09
15 14 0.40
16 10 0.29
17 8 0.23
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATAAATCAAAT
Found at i:53384334 original size:23 final size:23
Alignment explanation
Indices: 53384294--53384347 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
53384284 AATAAAAAAT
*
53384294 ATAATAAATAAAAATAAA-TCCAA
1 ATAAAAAATAAAAATAAAGTCC-A
* *
53384317 ATAAAAAATAATATTAAAGGTCCA
1 ATAAAAAATAAAAATAAA-GTCCA
53384341 ATAAAAA
1 ATAAAAA
53384348 CAGTCCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 15 0.58
24 8 0.31
25 3 0.12
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (23 bp):
ATAAAAAATAAAAATAAAGTCCA
Found at i:53387991 original size:2 final size:2
Alignment explanation
Indices: 53387984--53388012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53387974 ATTAAATTAG
53387984 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 T
53388013 GTTCTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53388225 original size:66 final size:64
Alignment explanation
Indices: 53388068--53388249 Score: 172
Period size: 66 Copynumber: 2.8 Consensus size: 64
53388058 CCGATTATGT
* * * * *
53388068 ATATATGTGTTTTAAATTCTATAAGTT-AAAAAAATGTATGAATTGTATATATATGTGTTAGCCA
1 ATATATGTG-TTGAGATTCTATAAGTTGAAAAAATTGTATGAATTATATATATATATGTTAGCCA
* * * * * *
53388132 ATGTATGTTTTGAG-CTCTATAAATTGAAACAAATTGTATAAATTATATATATATATATTTAGCC
1 ATATATGTGTTGAGATTCTATAAGTTGAAA-AAATTGTATGAATTATATATATATAT-GTTAGCC
53388196 AA
64 -A
** *
53388198 ATATATGTGTTGAGATTC-ATAAGTTGAATGTAATTATATGAATTATATATAT
1 ATATATGTGTTGAGATTCTATAAGTTGAA-AAAATTGTATGAATTATATATAT
53388250 GTTAGTCGAA
Statistics
Matches: 93, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
62 9 0.10
63 6 0.06
64 29 0.31
65 6 0.06
66 41 0.44
67 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (64 bp):
ATATATGTGTTGAGATTCTATAAGTTGAAAAAATTGTATGAATTATATATATATATGTTAGCCA
Found at i:53397671 original size:2 final size:2
Alignment explanation
Indices: 53397664--53397695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53397654 NNNNNNTTAG
53397664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53397696 GCCATGCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53398835 original size:23 final size:23
Alignment explanation
Indices: 53398809--53398852 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53398799 CCTATTTTTC
*
53398809 CTTTTT-CTTTTCTTTCTTTCTTT
1 CTTTTTCCTTTT-TTCCTTTCTTT
53398832 CTTTTTCCTTTTTTCCTTTCT
1 CTTTTTCCTTTTTTCCTTTCT
53398853 CTATTCGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
CTTTTTCCTTTTTTCCTTTCTTT
Found at i:53409632 original size:25 final size:24
Alignment explanation
Indices: 53409599--53409645 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
53409589 AGAGAGAATT
*
53409599 TTATTTTATTTAATATTAATATCA
1 TTATTTTATTCAATATTAATATCA
53409623 TTATATTTATTCAATATTAATAT
1 TTAT-TTTATTCAATATTAATAT
53409646 GAAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTATTCAATATTAATATCA
Found at i:53417230 original size:18 final size:18
Alignment explanation
Indices: 53417207--53417259 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
53417197 AATATATATG
*
53417207 AAAATCTCTGAAGGATTT
1 AAAATCCCTGAAGGATTT
**
53417225 AAAATCCCAAAATGGATTT
1 AAAATCCCTGAA-GGATTT
53417244 AAAATCCCTGAAGGAT
1 AAAATCCCTGAAGGAT
53417260 AAAGAGTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (18 bp):
AAAATCCCTGAAGGATTT
Found at i:53419327 original size:20 final size:20
Alignment explanation
Indices: 53419289--53419327 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53419279 AAAATTTATA
*
53419289 TTTTTTGAAAAATTATAAAT
1 TTTTTTGAAAAAATATAAAT
* *
53419309 TTTTTTTAAAAAATCTAAA
1 TTTTTTGAAAAAATATAAA
53419328 CAATATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTTTTGAAAAAATATAAAT
Found at i:53419946 original size:15 final size:14
Alignment explanation
Indices: 53419908--53419946 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
53419898 ATTTCATCTG
53419908 TGTATATTATTTCT
1 TGTATATTATTTCT
*
53419922 TGTAACATTATTTCTT
1 TGT-ATATTATTTC-T
53419938 TGTATATTA
1 TGTATATTA
53419947 AATCACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 14 0.67
16 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (14 bp):
TGTATATTATTTCT
Found at i:53420351 original size:2 final size:2
Alignment explanation
Indices: 53420291--53420335 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
53420281 TTTACTATCT
53420291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53420333 TA T
1 TA T
53420336 TACATTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53444252 original size:338 final size:338
Alignment explanation
Indices: 53443631--53444307 Score: 1189
Period size: 338 Copynumber: 2.0 Consensus size: 338
53443621 GGGCACAAAA
*
53443631 TCCTAACAAGCATATGTTTGAAGACAGTAGTTTACATTCAATTTTGGAAAGATTATTGATTTCAT
1 TCCTAACAAGCATATGTTTGAAGACAGTAGTTTACATTCAATTTTGAAAAGATTATTGATTTCAT
53443696 GAATCACTAGTGCATTGATAATGATGAGTTTGGTGAATCCAGTGATGAGATTACCAAGTAGCTCA
66 GAATCACTAGTGCATTGATAATGATGAGTTTGGTGAATCCAGTGATGAGATTACCAAGTAGCTCA
*
53443761 CTACTAGAATTCAAGCAACATGTACAAATGGGCAAGATTTCAAAACTTTAAATCTATCACTAACT
131 CTACTAGAATTCAAGCAACATGTACAAATGGGCAAGATTTCAAAACTTTAAATCTACCACTAACT
53443826 TATGCTACTTCACATGCAATTGCTACTGGAAATTGGTTTCCTAATAACCAAAGAAATGTGATAAC
196 TATGCTACTTCACATGCAATTGCTACTGGAAATTGGTTTCCTAATAACCAAAGAAATGTGATAAC
53443891 CAAGAAAACGGGATAAATGATATTCAATAAGATTGTGAAGCACACTAAGATAAACAATCTAAGCT
261 CAAGAAAACGGGATAAATGATATTCAATAAGATTGTGAAGCACACTAAGATAAACAATCTAAGCT
53443956 TGTCCTTGCCATT
326 TGTCCTTGCCATT
* *
53443969 TCCTAACAAGCATATGTTTGAAGAC-GCTAGTTTACATTTAGTTTTGAAAAGATTATTGATTTCA
1 TCCTAACAAGCATATGTTTGAAGACAG-TAGTTTACATTCAATTTTGAAAAGATTATTGATTTCA
*
53444033 TGAATCACTAGTGCATTGATAATGATGAGTTTGGTGAATCCTGTGATGAGATTACCAAGTAGCTC
65 TGAATCACTAGTGCATTGATAATGATGAGTTTGGTGAATCCAGTGATGAGATTACCAAGTAGCTC
* ** *
53444098 ACTACT-GAAATTCCAGCAACATGTACAAATGGGCAAGATTTCAAGGCTTTATATCTACCACTAA
130 ACTACTAG-AATTCAAGCAACATGTACAAATGGGCAAGATTTCAAAACTTTAAATCTACCACTAA
*
53444162 CTTATGCTAC-TCTACATGCAATTTCTACTGGAAATTGGTTTCCTAATAACCAAAGAAATGTGAT
194 CTTATGCTACTTC-ACATGCAATTGCTACTGGAAATTGGTTTCCTAATAACCAAAGAAATGTGAT
* **
53444226 AACTAAGAAAACGGGATAGCTGATATTCAATAAGATTGTGAAGCACACTAAGATAAACAATCTAA
258 AACCAAGAAAACGGGATAAATGATATTCAATAAGATTGTGAAGCACACTAAGATAAACAATCTAA
53444291 GCTTGTCCTTGCCATT
323 GCTTGTCCTTGCCATT
53444307 T
1 T
53444308 ACATCCTTAA
Statistics
Matches: 323, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
337 4 0.01
338 319 0.99
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (338 bp):
TCCTAACAAGCATATGTTTGAAGACAGTAGTTTACATTCAATTTTGAAAAGATTATTGATTTCAT
GAATCACTAGTGCATTGATAATGATGAGTTTGGTGAATCCAGTGATGAGATTACCAAGTAGCTCA
CTACTAGAATTCAAGCAACATGTACAAATGGGCAAGATTTCAAAACTTTAAATCTACCACTAACT
TATGCTACTTCACATGCAATTGCTACTGGAAATTGGTTTCCTAATAACCAAAGAAATGTGATAAC
CAAGAAAACGGGATAAATGATATTCAATAAGATTGTGAAGCACACTAAGATAAACAATCTAAGCT
TGTCCTTGCCATT
Found at i:53444794 original size:37 final size:37
Alignment explanation
Indices: 53444753--53444824 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
53444743 AATGTTTTTA
**
53444753 TTGATGAATCTTAGTTGAGCTTCTTATGTTGTTCTAT
1 TTGATGAATCTTAAATGAGCTTCTTATGTTGTTCTAT
53444790 TTGATGAATCTTAAATGAGCTTCTTATGTTGTTCT
1 TTGATGAATCTTAAATGAGCTTCTTATGTTGTTCT
53444825 GTTTTTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (37 bp):
TTGATGAATCTTAAATGAGCTTCTTATGTTGTTCTAT
Found at i:53455095 original size:19 final size:19
Alignment explanation
Indices: 53455065--53455103 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
53455055 GAAAGAGATT
53455065 AATTTAATTTTATATAAATA
1 AATTTAATTTTATA-AAATA
53455085 AATTT-ATTTTATAAAATA
1 AATTTAATTTTATAAAATA
53455103 A
1 A
53455104 TGTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTAATTTTATAAAATA
Found at i:53455155 original size:17 final size:18
Alignment explanation
Indices: 53455133--53455169 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53455123 GTTCTTTTTA
*
53455133 ATAAATTT-AATAATTAT
1 ATAAATTTAAAAAATTAT
53455150 ATAAATTTAAAAAATTAT
1 ATAAATTTAAAAAATTAT
53455168 AT
1 AT
53455170 TAAGTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAATTTAAAAAATTAT
Found at i:53458922 original size:6 final size:6
Alignment explanation
Indices: 53458911--53458937 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53458901 AAGGCTGAAG
53458911 TTTCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTT
53458938 TCCAATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCAT
Found at i:53466268 original size:22 final size:21
Alignment explanation
Indices: 53466240--53466315 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
53466230 TTCTAATCAA
*
53466240 ATAAAAAAATATTTACAATTTT
1 ATAAAAAAATA-TTAAAATTTT
*
53466262 ATAAAAAACTATTAAAATTTT
1 ATAAAAAAATATTAAAATTTT
*
53466283 ATAAAAACCATA--AAAA--TT
1 ATAAAAA-AATATTAAAATTTT
53466301 ATAAAAAAATATTAA
1 ATAAAAAAATATTAA
53466316 GATTAATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 2 0.04
20 4 0.09
21 16 0.35
22 12 0.26
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAAAATATTAAAATTTT
Found at i:53466269 original size:21 final size:21
Alignment explanation
Indices: 53466240--53466315 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
53466230 TTCTAATCAA
* *
53466240 ATAAAAAAATATTTACAATTTT
1 ATAAAAAACTA-TTAAAATTTT
53466262 ATAAAAAACTATTAAAATTTT
1 ATAAAAAACTATTAAAATTTT
* *
53466283 AT-AAAAACCA-TAAAA-ATT
1 ATAAAAAACTATTAAAATTTT
*
53466301 ATAAAAAAATATTAA
1 ATAAAAAACTATTAA
53466316 GATTAATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.09
19 11 0.24
20 10 0.22
21 11 0.24
22 10 0.22
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAAACTATTAAAATTTT
Found at i:53466290 original size:20 final size:20
Alignment explanation
Indices: 53466256--53466315 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
53466246 AAATATTTAC
53466256 AATTTTATAAAAAACTATTAA
1 AATTTTAT-AAAAACTATTAA
* *
53466277 AATTTTATAAAAACCATAAA
1 AATTTTATAAAAACTATTAA
* *
53466297 AATTATA-AAAAAATATTAA
1 AATTTTATAAAAACTATTAA
53466316 GATTAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 9 0.27
20 16 0.48
21 8 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTTATAAAAACTATTAA
Found at i:53466303 original size:39 final size:39
Alignment explanation
Indices: 53466260--53466348 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
53466250 ATTTACAATT
* *
53466260 TTATAAAAAACTATTAAAATTTTATAAAAAC-CATAAAAA
1 TTATAAAAAAATATTAAAA-TTAATAAAAACTCATAAAAA
* * *
53466299 TTATAAAAAAATATTAAGATTAATATAAACTTATAAAAA
1 TTATAAAAAAATATTAAAATTAATAAAAACTCATAAAAA
53466338 TTATAAAAAAA
1 TTATAAAAAAA
53466349 ATCATAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 9 0.20
39 35 0.80
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (39 bp):
TTATAAAAAAATATTAAAATTAATAAAAACTCATAAAAA
Found at i:53466304 original size:9 final size:9
Alignment explanation
Indices: 53466281--53466346 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
53466271 TATTAAAATT
53466281 TTATAAAAA
1 TTATAAAAA
**
53466290 CCATAAAAA
1 TTATAAAAA
53466299 TTATAAAAAA
1 TTAT-AAAAA
* * *
53466309 ATATTAAGA
1 TTATAAAAA
*
53466318 TTAATATAAAC
1 TT-ATA-AAAA
53466329 TTATAAAAA
1 TTATAAAAA
53466338 TTATAAAAA
1 TTATAAAAA
53466347 AAATCATAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
9 25 0.60
10 13 0.31
11 4 0.10
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (9 bp):
TTATAAAAA
Found at i:53471874 original size:21 final size:21
Alignment explanation
Indices: 53471859--53471928 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
53471849 CCTTATGGGT
*
53471859 TTCTGTTCAGCTCTTACAAGC
1 TTCTGTTCAGCTCTTATAAGC
* * * * *
53471880 TTCTATTCAACCCTTATAGGT
1 TTCTGTTCAGCTCTTATAAGC
* * *
53471901 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTATAAGC
53471922 TTCTGTT
1 TTCTGTT
53471929 TAGCCTTCAA
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATAAGC
Found at i:53471923 original size:42 final size:42
Alignment explanation
Indices: 53471774--53471930 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 42
53471764 TCGTGTTTAC
* * * *
53471774 TTTCCGTTTAGCTCTCACGAACTTCTGTTTAACTCATATTA-G
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTTAACCCTTA-TAGG
* * *
53471816 TTTCCGTTCAGCTCT-ATTGAGCTTTTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTCA-CGAGCTTCTGTTTAACCCTTATAGG
* * * * *
53471858 TTTCTGTTCAGCTCTTACAAGCTTCTATTCAACCCTTATAGG
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTTAACCCTTATAGG
* * *
53471900 TTTCTGTTTAGCTCTCATGAGCTTCTGTTTA
1 TTTCCGTTCAGCTCTCACGAGCTTCTGTTTA
53471931 GCCTTCAAGC
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 2 0.02
42 89 0.97
43 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.45
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTCACGAGCTTCTGTTTAACCCTTATAGG
Found at i:53474101 original size:22 final size:21
Alignment explanation
Indices: 53474061--53474102 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53474051 CTAACCTTAT
53474061 CTTTCTTCTTTCTTTCTTTCC
1 CTTTCTTCTTTCTTTCTTTCC
53474082 CTTT-TTCTTTTCTTTTCTTTC
1 CTTTCTTC-TTTC-TTTCTTTC
53474103 TGTTTCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTCTTCTTTCTTTCTTTCC
Found at i:53477082 original size:18 final size:17
Alignment explanation
Indices: 53477058--53477134 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
53477048 AAATTAGAAA
*
53477058 AAAAATATAAAAATCAT
1 AAAAATATAAAAATTAT
*
53477075 ACAAAATATAAAATTTTAT
1 A-AAAATATAAAA-ATTAT
53477094 AAAAATCATAAAAATTAT
1 AAAAAT-ATAAAAATTAT
*
53477112 -AAAATATACAAAAATAT
1 AAAAATATA-AAAATTAT
53477129 AAAAAT
1 AAAAAT
53477135 TTTATTGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
16 3 0.06
17 13 0.25
18 25 0.49
19 10 0.20
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATATAAAAATTAT
Found at i:53477094 original size:28 final size:28
Alignment explanation
Indices: 53477063--53477135 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
53477053 AGAAAAAAAA
53477063 TATAAAAATCATACAAAA-TATAAAATTT
1 TATAAAAATCATA-AAAATTATAAAATTT
*
53477091 TATAAAAATCATAAAAATTATAAAA-TA
1 TATAAAAATCATAAAAATTATAAAATTT
*
53477118 TACAAAAAT-ATAAAAATT
1 TATAAAAATCATAAAAATT
53477136 TTATTGTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.21
27 13 0.31
28 20 0.48
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (28 bp):
TATAAAAATCATAAAAATTATAAAATTT
Found at i:53477125 original size:10 final size:9
Alignment explanation
Indices: 53477057--53477133 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 9
53477047 AAAATTAGAA
53477057 AAAAAATAT
1 AAAAAATAT
53477066 -AAAAATCAT
1 AAAAAAT-AT
*
53477075 ACAAAATAT
1 AAAAAATAT
* *
53477084 -AAAATTTT
1 AAAAAATAT
53477092 ATAAAAATCAT
1 A-AAAAAT-AT
53477103 -AAAAAT-T
1 AAAAAATAT
*
53477110 ATAAAATAT
1 AAAAAATAT
53477119 ACAAAAATAT
1 A-AAAAATAT
53477129 AAAAA
1 AAAAA
53477134 TTTTATTGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
7 1 0.02
8 16 0.31
9 16 0.31
10 18 0.35
11 1 0.02
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAAATAT
Found at i:53477306 original size:89 final size:85
Alignment explanation
Indices: 53477191--53477399 Score: 255
Period size: 89 Copynumber: 2.4 Consensus size: 85
53477181 GAGCAGGGGC
* * *
53477191 TTAATTGC-TTTTTTGAAAAATTTTGAGGGACTTTTTGATGCATTTTGAAAGTTCGAGTAC-CTA
1 TTAATTGCTTTTTTTGAAAAAGTTTGAGGGACTTTTTGATACATTTTGAAAGTTCAAGTACTC-A
* *
53477254 ATTGAGTGGAAAAAAAAGCATGAGT
65 ATTAAGTGCAAAAAAAA--A-G-GT
* * *
53477279 TTAATTGCTTTTTTTGAAGAAGCTTGAGGGTCTTTTTGATACATTTTGAAAGTTCAAGTACTCAA
1 TTAATTGCTTTTTTTGAAAAAGTTTGAGGGACTTTTTGATACATTTTGAAAGTTCAAGTACTCAA
53477344 TTAAGTGCAAAAAAAAAGGT
66 TTAAGTGCAAAAAAAAAGGT
*
53477364 TTAATTG-TTTTTTCTTAAAAAGTTTGA-GGACTTTTT
1 TTAATTGCTTTTTT-TGAAAAAGTTTGAGGGACTTTTT
53477400 ACACACTTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
84 14 0.13
85 19 0.18
86 1 0.01
87 1 0.01
88 8 0.08
89 62 0.58
90 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (85 bp):
TTAATTGCTTTTTTTGAAAAAGTTTGAGGGACTTTTTGATACATTTTGAAAGTTCAAGTACTCAA
TTAAGTGCAAAAAAAAAGGT
Found at i:53479874 original size:18 final size:18
Alignment explanation
Indices: 53479851--53479893 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53479841 GAATAGATTT
53479851 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
53479869 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
53479887 TTAATTA
1 TTAATTA
53479894 CATATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Done.