Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 14 of 343
Found at i:4899151 original size:13 final size:12
Alignment explanation
Indices: 4899122--4899154 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
4899112 TTTATTTTAT
4899122 TTTATTTTAAAA
1 TTTATTTTAAAA
4899134 TTTATTTTAAAA
1 TTTATTTTAAAA
4899146 TATTATTTT
1 T-TTATTTT
4899155 TGGGGCGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:4900374 original size:20 final size:21
Alignment explanation
Indices: 4900334--4900375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4900324 ATACATGAAA
* *
4900334 TTAAAAAAAATAACTCTTAAT
1 TTAAAAAAAATAACACGTAAT
4900355 TTAAAAAAAATAA-ACGTAAT
1 TTAAAAAAAATAACACGTAAT
4900375 T
1 T
4900376 ATCTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAAAAAAAATAACACGTAAT
Found at i:4904077 original size:32 final size:33
Alignment explanation
Indices: 4904011--4904080 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
4904001 AAATTTAGAC
*
4904011 GATTAATACAAATACTTGAAAAAAATTAGGATT
1 GATTAATACAAATACTTGAAAAAAATTAGAATT
* *
4904044 GATTAATACAAATCCTTG-AAGAAATTAGAATT
1 GATTAATACAAATACTTGAAAAAAATTAGAATT
4904076 GATTA
1 GATTA
4904081 GAAATTTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (33 bp):
GATTAATACAAATACTTGAAAAAAATTAGAATT
Found at i:4905214 original size:28 final size:27
Alignment explanation
Indices: 4905183--4905251 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
4905173 TACAATTAAT
4905183 TAATGTTTTGTATAATTGTTTAATTACA
1 TAATGTTTTGTATAATT-TTTAATTACA
*
4905211 TAATAAGTTATTG--TAATTTTTAATTGCA
1 TAAT--GTT-TTGTATAATTTTTAATTACA
*
4905239 TAATATTTTGTAT
1 TAATGTTTTGTAT
4905252 GATTAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 1 0.03
28 17 0.50
29 5 0.15
30 3 0.09
31 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (27 bp):
TAATGTTTTGTATAATTTTTAATTACA
Found at i:4915505 original size:14 final size:15
Alignment explanation
Indices: 4915478--4915506 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4915468 AATTTTATGA
4915478 ATTTCATGATGTGTT
1 ATTTCATGATGTGTT
4915493 ATTTCAT-ATGTGTT
1 ATTTCATGATGTGTT
4915507 GATGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (15 bp):
ATTTCATGATGTGTT
Found at i:4915699 original size:50 final size:51
Alignment explanation
Indices: 4915622--4915750 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
4915612 GACCATGGCA
4915622 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
* *
4915673 A-AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
4915723 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
4915751 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 44 0.63
51 26 0.37
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:4915764 original size:31 final size:31
Alignment explanation
Indices: 4915726--4915905 Score: 263
Period size: 31 Copynumber: 5.8 Consensus size: 31
4915716 ACAAATGACA
*
4915726 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
4915757 AGTGAAAAGTGGTAGCTTCTGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4915788 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
* *
4915819 AGTGAAAAGTGGTAGCTCCGGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
4915850 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4915881 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
4915906 AAGTGACAAG
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
30 2 0.01
31 131 0.98
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:4916079 original size:42 final size:42
Alignment explanation
Indices: 4916024--4916136 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
4916014 TATGTGATTC
* * *
4916024 GTGTAAGATCATAGCTGGGCTATGGTATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATATGAAGAT
*
4916066 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
* **
4916108 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
4916137 GAGAAAACGA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
Found at i:4923106 original size:23 final size:23
Alignment explanation
Indices: 4923025--4923110 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
4923015 CTGATCAGAG
*
4923025 TACGACACATAAAGTGCCT-AAA
1 TACGACACACAAAGTGCCTGAAA
* *
4923047 -ACGACACACGAGGTGCCTG--A
1 TACGACACACAAAGTGCCTGAAA
* *
4923067 TACGACACACGAGGTGCCTGAAA
1 TACGACACACAAAGTGCCTGAAA
*
4923090 TACGACACATAAAGTGCCTGA
1 TACGACACACAAAGTGCCTGA
4923111 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.63
23 19 0.35
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
TACGACACACAAAGTGCCTGAAA
Found at i:4923510 original size:15 final size:15
Alignment explanation
Indices: 4923482--4923539 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
4923472 TCATATATAT
*
4923482 TATATAATTAAATCAA
1 TATA-AATTCAATCAA
4923498 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
4923513 AATAATTTCAATCAA
1 TATAAATTCAATCAA
4923528 TATAAATTCAAT
1 TATAAATTCAAT
4923540 AAATTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:4924825 original size:5 final size:5
Alignment explanation
Indices: 4924817--4924843 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4924807 TCTTTAGTTT
4924817 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
4924844 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:4930237 original size:21 final size:21
Alignment explanation
Indices: 4930213--4930277 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
4930203 AAATCTAACT
4930213 GAAGCACAAAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
** *
4930234 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACAAAAGTGCTAAACG
*
4930252 GAAGCACATAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
4930273 GAAGC
1 GAAGC
4930278 CCGAATGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACAAAAGTGCTAAACG
Found at i:4930253 original size:39 final size:39
Alignment explanation
Indices: 4930207--4930295 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
4930197 AACCCGAAAT
4930207 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
* *
4930246 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAATG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
4930285 CTAACTGAAGC
1 CTAACTGAAGC
4930296 TCATCAGAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (39 bp):
CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
Found at i:4930288 original size:19 final size:19
Alignment explanation
Indices: 4930225--4930288 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4930215 AGCACAAAAG
4930225 TGCTAAACGGAAGCCCGAA
1 TGCTAAACGGAAGCCCGAA
* * **
4930244 GGCT-AACTGAAGCACATAA
1 TGCTAAACGGAAGC-CCGAA
4930263 GTGCTAAACGGAAGCCCGAA
1 -TGCTAAACGGAAGCCCGAA
4930283 TGCTAA
1 TGCTAA
4930289 CTGAAGCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 8 0.24
19 12 0.35
20 6 0.18
21 8 0.24
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (19 bp):
TGCTAAACGGAAGCCCGAA
Found at i:4938202 original size:19 final size:18
Alignment explanation
Indices: 4938178--4938217 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4938168 TTATATTTTT
*
4938178 AAAATATCAATTATTATAA
1 AAAATATCAA-TATGATAA
*
4938197 AAAATATTAATATGATAA
1 AAAATATCAATATGATAA
4938215 AAA
1 AAA
4938218 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATATCAATATGATAA
Found at i:4939260 original size:8 final size:8
Alignment explanation
Indices: 4939223--4939251 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4939213 TGAAGTAATC
4939223 ATTATTAT
1 ATTATTAT
4939231 ATTATTAT
1 ATTATTAT
4939239 ATTATTAT
1 ATTATTAT
4939247 ATTAT
1 ATTAT
4939252 ATTAGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTATTAT
Found at i:4939332 original size:16 final size:16
Alignment explanation
Indices: 4939311--4939343 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4939301 ATAGAAAATG
4939311 GAATAGAAAAAGAACA
1 GAATAGAAAAAGAACA
*
4939327 GAATAGAAAACGAACA
1 GAATAGAAAAAGAACA
4939343 G
1 G
4939344 GAGAGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.09, G:0.21, T:0.06
Consensus pattern (16 bp):
GAATAGAAAAAGAACA
Found at i:4940832 original size:15 final size:15
Alignment explanation
Indices: 4940808--4940857 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
4940798 TTCAAGATAG
*
4940808 AGAAACCCAGAATAA
1 AGAAATCCAGAATAA
4940823 AGAAATCCAGAATAA
1 AGAAATCCAGAATAA
* *
4940838 AGAGATCCAGGATAA
1 AGAAATCCAGAATAA
4940853 AGAAA
1 AGAAA
4940858 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AGAAATCCAGAATAA
Found at i:4940866 original size:15 final size:15
Alignment explanation
Indices: 4940800--4940866 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
4940790 ACCGGAATTT
*
4940800 CAAGATAGAGAAACC
1 CAAGATAAAGAAACC
*
4940815 C-AGAATAAAGAAATC
1 CAAG-ATAAAGAAACC
* *
4940830 C-AGAATAAAGAGATC
1 CAAG-ATAAAGAAACC
*
4940845 CAGGATAAAGAAACC
1 CAAGATAAAGAAACC
4940860 CAAGATA
1 CAAGATA
4940867 CGATACTATG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
14 2 0.05
15 40 0.93
16 1 0.02
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.10
Consensus pattern (15 bp):
CAAGATAAAGAAACC
Found at i:4942274 original size:10 final size:10
Alignment explanation
Indices: 4942259--4942292 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
4942249 AACTTTCATC
4942259 TCACATATTA
1 TCACATATTA
4942269 TCACATATTA
1 TCACATATTA
4942279 TCACATATGTA
1 TCACATAT-TA
4942290 TCA
1 TCA
4942293 TAAACTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (10 bp):
TCACATATTA
Found at i:4948328 original size:40 final size:39
Alignment explanation
Indices: 4948284--4948444 Score: 128
Period size: 39 Copynumber: 4.1 Consensus size: 39
4948274 CAAATCCAAT
4948284 CACCACCACAAA-GCATGCGGGACTTTAAGCCCGAATATAA
1 CACCACCACAAATGCATGCGGGAC-TT-AGCCCGAATATAA
* * * * *
4948324 CACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAA
1 CACCACCACAAATGCATGCGGGACTTAGCCCGAATATAA
* * * * * * *
4948363 CACCAGCAC-GATGCCTTCGGGGCTTAGCTCGGATATAA
1 CACCACCACAAATGCATGCGGGACTTAGCCCGAATATAA
* * * * * *
4948401 CACCAGCACGAATGCCTTCGGGGCTTAGCCCGGATATAA
1 CACCACCACAAATGCATGCGGGACTTAGCCCGAATATAA
4948440 CACCA
1 CACCA
4948445 AATCATATAA
Statistics
Matches: 110, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
38 36 0.33
39 53 0.48
40 13 0.12
41 8 0.07
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.17
Consensus pattern (39 bp):
CACCACCACAAATGCATGCGGGACTTAGCCCGAATATAA
Found at i:4948386 original size:38 final size:38
Alignment explanation
Indices: 4948311--4948444 Score: 223
Period size: 39 Copynumber: 3.5 Consensus size: 38
4948301 CGGGACTTTA
* *
4948311 AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCAC-GATGCCTTCGGGGCTT
4948350 AGCCCGGATATAACACCAGCACGATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGATGCCTTCGGGGCTT
*
4948388 AGCTCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACG-ATGCCTTCGGGGCTT
4948427 AGCCCGGATATAACACCA
1 AGCCCGGATATAACACCA
4948445 AATCATATAA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 37 0.41
39 53 0.59
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (38 bp):
AGCCCGGATATAACACCAGCACGATGCCTTCGGGGCTT
Found at i:4950458 original size:19 final size:19
Alignment explanation
Indices: 4950434--4950474 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4950424 GTTATAATAT
*
4950434 TAATATTCCTTTAATATTA
1 TAATATTCATTTAATATTA
*
4950453 TAATATTCATTTCATATTA
1 TAATATTCATTTAATATTA
4950472 TAA
1 TAA
4950475 AACAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTCATTTAATATTA
Found at i:4952875 original size:130 final size:132
Alignment explanation
Indices: 4952719--4953074 Score: 563
Period size: 135 Copynumber: 2.7 Consensus size: 132
4952709 GTATCTGACT
* * * *
4952719 TGCTCTACTCTTGTTCAACGGAGATAAGATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGTG
1 TGCTCTGCTCTTGCTCAACGAAGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTGCTCAGTG
* *
4952784 AAGATAAGGCTGATGATTAGAATCTGCTCCATCATCAGTACGT-G-AAGATTCACCAAAATTCGA
66 AAGATAAGGCTGATGATTGGAATCTGCTCCATCACCAGTACGTGGAAAGATTCACCAAAATTCGA
4952847 TC
131 TC
*
4952849 TGCTCTGCTCTTGCTCAACGAAGATAAGATCTGCTATATTTAACCTGCTTCACTCCTGCTCAGTG
1 TGCTCTGCTCTTGCTCAACGAAGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTGCTCAGTG
* *
4952914 AAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCAGTACGTGGAGATAAGATTCGCCAAAATT
66 AAGATAAGGCTGATGATTGGAATCTGCTCCATCACCAGTACGT-G-GA-AAGATTCACCAAAATT
4952979 CGATC
128 CGATC
* * *
4952984 TGCTCCGCTCCTGCTCAGCGAAGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTGCTCAGTG
1 TGCTCTGCTCTTGCTCAACGAAGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTGCTCAGTG
4953049 AAGATAAGGCTGATGATTGGAATCTG
66 AAGATAAGGCTGATGATTGGAATCTG
4953075 TTATATGTAG
Statistics
Matches: 208, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
130 100 0.48
133 1 0.00
135 107 0.51
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (132 bp):
TGCTCTGCTCTTGCTCAACGAAGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTGCTCAGTG
AAGATAAGGCTGATGATTGGAATCTGCTCCATCACCAGTACGTGGAAAGATTCACCAAAATTCGA
TC
Found at i:4953191 original size:13 final size:13
Alignment explanation
Indices: 4953175--4953227 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
4953165 CTCCTAAACT
4953175 ACCCCACTAAGCC
1 ACCCCACTAAGCC
*
4953188 ACCCCACTAACTCC
1 ACCCCACTAA-GCC
*
4953202 ATCACCCTACTAAGCT
1 A-C-CCC-ACTAAGCC
4953218 ACCCCACTAA
1 ACCCCACTAA
4953228 CTCTATTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 15 0.45
14 6 0.18
15 2 0.06
16 5 0.15
17 5 0.15
ACGTcount: A:0.32, C:0.49, G:0.04, T:0.15
Consensus pattern (13 bp):
ACCCCACTAAGCC
Found at i:4953216 original size:30 final size:30
Alignment explanation
Indices: 4953175--4953242 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
4953165 CTCCTAAACT
*
4953175 ACCCCACTAAGCCACCCCACTAACTCCATC
1 ACCCTACTAAGCCACCCCACTAACTCCATC
* * *
4953205 ACCCTACTAAGCTACCCCACTAACTCTATT
1 ACCCTACTAAGCCACCCCACTAACTCCATC
4953235 ACCCTACT
1 ACCCTACT
4953243 TGTCACCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.29, C:0.47, G:0.03, T:0.21
Consensus pattern (30 bp):
ACCCTACTAAGCCACCCCACTAACTCCATC
Found at i:4953605 original size:3 final size:3
Alignment explanation
Indices: 4953597--4953729 Score: 82
Period size: 3 Copynumber: 45.0 Consensus size: 3
4953587 AGGGGGAGAG
4953597 TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT T-T TAT TACT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * *
4953639 TAC TAT TAT T-T TA- TAT ATATT TAT TAC CAT TATT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TA-T TA-T TAT TAT TAT
* * * * * * *
4953686 TAG TAA CA- TAT TGT TAT TTT TAT TAT TAT AAT TTT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4953730 AATGGCACTA
Statistics
Matches: 101, Mismatches: 18, Indels: 22
0.72 0.13 0.16
Matches are distributed among these distances:
2 13 0.13
3 74 0.73
4 13 0.13
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4955127 original size:133 final size:133
Alignment explanation
Indices: 4954890--4955902 Score: 1722
Period size: 133 Copynumber: 7.6 Consensus size: 133
4954880 TTGGAACTTT
* * ** * *
4954890 ATCTGCTCCGCTCTTGCTCAACGAAGATAAGATCTGCAATTTAGCCTGCT-CACTCTTGCTCAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
* *
4954954 GAAGATAAGGCTGATGATTGGAATCTGCTCTATTGCCGGTACGTGGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955019 TTG
131 TTG
* * *
4955022 ATCTGCTCCGCTCCTACTCAGCGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTTAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
* *
4955087 GAAAATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATATGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955152 TTG
131 TTG
4955155 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
*
4955220 GAAGATAAGGCTGATGATTAGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955285 TTG
131 TTG
* *
4955288 ATCTGCTCCGCTCCTGCTCAATGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTGCTCAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
*
4955353 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATATGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955418 TTG
131 TTG
4955421 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
*
4955486 GAAGATAAGGCTGATGATTAGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955551 TTG
131 TTG
*
4955554 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTGCTCAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
*
4955619 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACCTGGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955684 TTG
131 TTG
* * * * *
4955687 ATTTGCTCTGCTCTTGCTCAGCGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTTAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
* *
4955752 GAAAATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATATGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
4955817 TTG
131 TTG
* * * * *
4955820 ATCTGCTCCGCTCTTGCTCAGCGAAGATAAGACCTGGTATTTAGCCTGTTCCACTCCTGCTAAGT
1 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
*
4955885 AAAGATAAGGCTGATGAT
66 GAAGATAAGGCTGATGAT
4955903 ATCTGTAATC
Statistics
Matches: 834, Mismatches: 46, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
132 44 0.05
133 790 0.95
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (133 bp):
ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
TTG
Found at i:4955345 original size:43 final size:44
Alignment explanation
Indices: 4955017--4955627 Score: 239
Period size: 43 Copynumber: 13.8 Consensus size: 44
4955007 ATTCACCAAA
* * * *
4955017 ATTT-GATCTGCTCCGCTCCTACTCAGCGAAGATAAGACCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * * * *
4955060 ATTTAG-CCTGCTCCACTCCTACTTAGTGAAAATAAG-GCTGAT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * * * * ** *
4955102 GA-TTGGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATATGATTCACCAAA
1 -ATTTAG-ATCTGCTCCACTC-CTGCTCA-GTGAAGATAAGA--C-CTGAT
* ** *
4955150 ATTT-GATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * *
4955193 ATTTAG-CCTGCTCCACTCCTACTCAGTGAAGATAAG-GCTGAT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * * ** *
4955235 GA-TTAGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATAAGATTCACCAAA
1 -ATTTAG-ATCTGCTCCACTC-CTGCTCA-GTGAAGATAAGA--C-CTGAT
* * *
4955283 ATTT-GATCTGCTCCGCTCCTGCTCAATGAAGATAAGACCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* *
4955326 ATTTAG-CCTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGAT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * * * * ** *
4955368 GA-TTGGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATATGATTCACCAAA
1 -ATTTAG-ATCTGCTCCACTC-CTGCTCA-GTGAAGATAAGA--C-CTGAT
* ** *
4955416 ATTT-GATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * *
4955459 ATTTAG-CCTGCTCCACTCCTACTCAGTGAAGATAAG-GCTGAT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
* * * ** *
4955501 GA-TTAGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATAAGATTCACCAAA
1 -ATTTAG-ATCTGCTCCACTC-CTGCTCA-GTGAAGATAAGA--C-CTGAT
* ** *
4955549 ATTT-GATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTGGT
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
*
4955592 ATTTAG-CCTGCTCCACTCCTGCTCAGTGAAGATAAG
1 ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAG
4955628 GCTGATGATT
Statistics
Matches: 404, Mismatches: 111, Indels: 106
0.65 0.18 0.17
Matches are distributed among these distances:
42 30 0.07
43 168 0.42
44 87 0.22
46 83 0.21
47 20 0.05
48 16 0.04
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
ATTTAGATCTGCTCCACTCCTGCTCAGTGAAGATAAGACCTGAT
Found at i:4963640 original size:21 final size:21
Alignment explanation
Indices: 4963614--4963658 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4963604 GCTGGCTCAT
*
4963614 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGAGACTCCAG
*
4963635 CATGTTTTTCTGAGACTCCAG
1 CATGTTGTTCTGAGACTCCAG
4963656 CAT
1 CAT
4963659 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGAGACTCCAG
Found at i:4968009 original size:13 final size:14
Alignment explanation
Indices: 4967989--4968029 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
4967979 GTAAACGGTA
4967989 AAAT-AAATA-AAT
1 AAATAAAATATAAT
*
4968001 AAATAAAATATGAT
1 AAATAAAATATAAT
4968015 AAA-AAAATATAAT
1 AAATAAAATATAAT
4968028 AA
1 AA
4968030 GTATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 16 0.64
14 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
AAATAAAATATAAT
Found at i:4968038 original size:22 final size:22
Alignment explanation
Indices: 4967990--4968039 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4967980 TAAACGGTAA
*
4967990 AATAAATAAATAAATAAAATAT
1 AATAAAAAAATAAATAAAATAT
* *
4968012 GATAAAAAAATATAAT-AAGTAT
1 AATAAAAAAATA-AATAAAATAT
4968034 AATAAA
1 AATAAA
4968040 CTATATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AATAAAAAAATAAATAAAATAT
Found at i:4968347 original size:12 final size:11
Alignment explanation
Indices: 4968271--4968385 Score: 53
Period size: 12 Copynumber: 10.3 Consensus size: 11
4968261 AAATTAAATG
4968271 AAAATAA-ATA
1 AAAATAATATA
*
4968281 AAAATAATAATG
1 AAAATAAT-ATA
*
4968293 AAAATGATATA
1 AAAATAATATA
4968304 ATAAGTATAATA-A
1 A-AA--ATAATATA
* * *
4968317 ATAATAGTGTA
1 AAAATAATATA
4968328 AAAA-AATATA
1 AAAATAATATA
4968338 ATAAATAATA-A
1 A-AAATAATATA
*
4968349 GAAAATAATTTAA
1 -AAAATAATAT-A
*
4968362 AAAATGATAGTA
1 AAAATAATA-TA
4968374 AAAA-AA-ATA
1 AAAATAATATA
4968383 AAA
1 AAA
4968386 TAGTAATAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
9 5 0.06
10 17 0.22
11 19 0.24
12 29 0.37
13 4 0.05
14 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (11 bp):
AAAATAATATA
Found at i:4970410 original size:20 final size:21
Alignment explanation
Indices: 4970382--4970420 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4970372 GACCCCTGCA
4970382 TTTAAGAAAAATTT-TGAAAT
1 TTTAAGAAAAATTTCTGAAAT
*
4970402 TTTACGAAAAATTTCTGAA
1 TTTAAGAAAAATTTCTGAA
4970421 GTACCCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTAAGAAAAATTTCTGAAAT
Found at i:4971913 original size:13 final size:13
Alignment explanation
Indices: 4971897--4971934 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4971887 TACTTTATGT
4971897 TATTATATTATTA
1 TATTATATTATTA
*
4971910 TATTATATTATAA
1 TATTATATTATTA
*
4971923 TAAT-TATTATTA
1 TATTATATTATTA
4971935 CTTAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:4972215 original size:13 final size:14
Alignment explanation
Indices: 4972199--4972227 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4972189 AATAAACTTC
4972199 ATAAATATTT-TTA
1 ATAAATATTTATTA
4972212 ATAAATATTTATTA
1 ATAAATATTTATTA
4972226 AT
1 AT
4972228 CCGTTTGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTATTA
Found at i:4972646 original size:15 final size:15
Alignment explanation
Indices: 4972626--4972658 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4972616 TTTTTTACTG
4972626 TTTTCTTGCTT-TTTT
1 TTTTCTTG-TTATTTT
4972641 TTTTCTTGTTATTTT
1 TTTTCTTGTTATTTT
4972656 TTT
1 TTT
4972659 GCACTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTGTTATTTT
Found at i:4972655 original size:14 final size:15
Alignment explanation
Indices: 4972626--4972658 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4972616 TTTTTTACTG
*
4972626 TTTTCTTGCTTTTTT
1 TTTTCTTGCTTATTT
4972641 TTTTCTTG-TTATTT
1 TTTTCTTGCTTATTT
4972655 TTTT
1 TTTT
4972659 GCACTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTGCTTATTT
Found at i:4983659 original size:13 final size:13
Alignment explanation
Indices: 4983641--4983679 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4983631 ATGTGAACAA
4983641 TATTATTTAAAAT
1 TATTATTTAAAAT
*
4983654 TATTATTTAAATTT
1 TATTATTTAAA-AT
4983668 TATTA-TTAAAAT
1 TATTATTTAAAAT
4983680 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 1 0.04
13 16 0.70
14 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:4983672 original size:14 final size:14
Alignment explanation
Indices: 4983641--4983680 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4983631 ATGTGAACAA
4983641 TATTATTTAAA-AT
1 TATTATTTAAATAT
*
4983654 TATTATTTAAATTT
1 TATTATTTAAATAT
*
4983668 TATTATTAAAATA
1 TATTATTTAAATA
4983681 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATTTAAATAT
Found at i:4983709 original size:19 final size:19
Alignment explanation
Indices: 4983687--4983755 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
4983677 AATAAAATTA
4983687 AAATATTAAATAATTTATT
1 AAATATTAAATAATTTATT
*
4983706 AAATAATAAATTATATTTATT
1 AAATATTAAA-TA-ATTTATT
4983727 --ATATT-AATAATTTATT
1 AAATATTAAATAATTTATT
*
4983743 ATATGATTAAATA
1 AAAT-ATTAAATA
4983756 TAAATAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 7 0.17
17 2 0.05
18 4 0.10
19 16 0.38
20 6 0.14
21 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
AAATATTAAATAATTTATT
Found at i:4983734 original size:22 final size:21
Alignment explanation
Indices: 4983687--4983760 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
4983677 AATAAAATTA
*
4983687 AAATATTAAA-TA-ATTTATT
1 AAATAATAAATTATATTTATT
4983706 AAATAATAAATTATATTTATT
1 AAATAATAAATTATATTTATT
* * *
4983727 ATATTAATAATTTATTATATGATT
1 A-AATAATAAATTA-TAT-TTATT
4983751 AAAT-ATAAAT
1 AAATAATAAAT
4983761 AATTAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 9 0.20
20 2 0.05
21 8 0.18
22 15 0.34
23 5 0.11
24 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
AAATAATAAATTATATTTATT
Found at i:4995142 original size:16 final size:16
Alignment explanation
Indices: 4995121--4995153 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4995111 AAACTGAATG
*
4995121 ATTTCTTAGAGTTCCC
1 ATTTCTTAGAGTACCC
4995137 ATTTCTTAGAGTACCC
1 ATTTCTTAGAGTACCC
4995153 A
1 A
4995154 AGAGGCGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (16 bp):
ATTTCTTAGAGTACCC
Found at i:4996759 original size:17 final size:17
Alignment explanation
Indices: 4996722--4996759 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4996712 TAGAAAACTG
*
4996722 TATTCTCAATTAATTTG
1 TATTCTCAATTAATTTC
4996739 TATTCTCAATT-ATTTAC
1 TATTCTCAATTAATTT-C
4996756 TATT
1 TATT
4996760 AATTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTCTCAATTAATTTC
Found at i:5002345 original size:23 final size:20
Alignment explanation
Indices: 5002307--5002352 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
5002297 ATTCAATTTA
5002307 TTTTATTATATCTATAAATATT
1 TTTTATTATATCTAT--ATATT
*
5002329 TTTTATTTATATTTATATATT
1 TTTTA-TTATATCTATATATT
5002350 TTT
1 TTT
5002353 GTTCGCTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTATATCTATATATT
Found at i:5002348 original size:21 final size:22
Alignment explanation
Indices: 5002307--5002352 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
5002297 ATTCAATTTA
5002307 TTTTATTATATCTATAAATATT
1 TTTTATTATATCTATAAATATT
*
5002329 TTTTATTTATAT-T-TATATATT
1 TTTTA-TTATATCTATAAATATT
5002350 TTT
1 TTT
5002353 GTTCGCTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 6 0.27
23 6 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATATCTATAAATATT
Found at i:5003855 original size:45 final size:45
Alignment explanation
Indices: 5003791--5003876 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
5003781 AAGTATGCGA
5003791 AACCAATGCCAAAGTTTAAATCATTGAGTTTACACTTGGGAAAGT
1 AACCAATGCCAAAGTTTAAATCATTGAGTTTACACTTGGGAAAGT
5003836 AACCAATGCCAAAGTTTAAATCATTGAGTTTACACTTGGGA
1 AACCAATGCCAAAGTTTAAATCATTGAGTTTACACTTGGGA
5003877 TCTCTAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (45 bp):
AACCAATGCCAAAGTTTAAATCATTGAGTTTACACTTGGGAAAGT
Found at i:5016346 original size:9 final size:9
Alignment explanation
Indices: 5016334--5016358 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5016324 TAAATATAAT
5016334 ATATTAAAA
1 ATATTAAAA
5016343 ATATTAAAA
1 ATATTAAAA
5016352 ATATTAA
1 ATATTAA
5016359 GATAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATTAAAA
Found at i:5017169 original size:5 final size:5
Alignment explanation
Indices: 5017145--5017243 Score: 56
Period size: 5 Copynumber: 18.2 Consensus size: 5
5017135 AGCAGCCCCT
* * *
5017145 TTTTA CTTTA CTTTA CTTTTA TTTTA TATTTA TTATA TTTATA TTTATA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA T-TTTA TTTTA TTT-TA TTT-TA
* * *
5017194 TTTATA TTATA TTTATA TTTTCTAA TTTT- TCTAA TTTTA TTTTA TTTTA
1 TTT-TA TTTTA TTT-TA -TTT-T-A TTTTA TTTTA TTTTA TTTTA TTTTA
5017243 T
1 T
5017244 AAAAATGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.03
5 38 0.50
6 28 0.37
7 7 0.09
8 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (5 bp):
TTTTA
Found at i:5017176 original size:6 final size:6
Alignment explanation
Indices: 5017162--5017213 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
5017152 TTACTTTACT
5017162 TTTAT- TTTATA -TT-TA -TTATA TTTATA TTTATA TTTATA -TTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
5017205 TTTATA TTT
1 TTTATA TTT
5017214 TCTAATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.09
5 14 0.33
6 25 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:5017205 original size:23 final size:21
Alignment explanation
Indices: 5017162--5017213 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 21
5017152 TTACTTTACT
5017162 TTTAT-TTTATATTTATTATA
1 TTTATATTTATATTTATTATA
5017182 TTTATATTTATATTTATATTATA
1 TTTATATTTATA-TT-TATTATA
5017205 TTTATATTT
1 TTTATATTT
5017214 TCTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.17
21 6 0.21
22 2 0.07
23 16 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATATTTATATTTATTATA
Found at i:5017210 original size:11 final size:11
Alignment explanation
Indices: 5017162--5017212 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
5017152 TTACTTTACT
*
5017162 TTTATTTTATA
1 TTTATATTATA
5017173 -TT-TATTATA
1 TTTATATTATA
5017182 TTTATATTTATA
1 TTTATA-TTATA
5017194 TTTATATTATA
1 TTTATATTATA
5017205 TTTATATT
1 TTTATATT
5017213 TTCTAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 6 0.17
10 4 0.11
11 15 0.42
12 11 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATTATA
Found at i:5017344 original size:21 final size:22
Alignment explanation
Indices: 5017306--5017352 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5017296 ATTATAACTT
*
5017306 TTAAATATAAAATATT-AAAAA
1 TTAAAAATAAAATATTAAAAAA
5017327 TTAAAAATACAAAT-TTAAAAAA
1 TTAAAAATA-AAATATTAAAAAA
5017349 TTAA
1 TTAA
5017353 TTTGAATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATAAAATATTAAAAAA
Found at i:5017660 original size:3 final size:3
Alignment explanation
Indices: 5017617--5017650 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5017607 TTAAAATTCA
* *
5017617 ATT ATC ATT ATT ATT ACT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5017651 AAATATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:5018847 original size:12 final size:12
Alignment explanation
Indices: 5018832--5018865 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5018822 TCATTTATTT
5018832 TTTTATAATTAA
1 TTTTATAATTAA
5018844 TTTTAGTAATTAA
1 TTTTA-TAATTAA
*
5018857 TTTTTTAAT
1 TTTTATAAT
5018866 CAATCACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTATAATTAA
Found at i:5027733 original size:19 final size:18
Alignment explanation
Indices: 5027700--5027736 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5027690 ACATAATTTA
5027700 TAATTTTAAAAAAATTAT
1 TAATTTTAAAAAAATTAT
*
5027718 TAATTATTATAAAAATTAT
1 TAATT-TTAAAAAAATTAT
5027737 CAGTATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTTAAAAAAATTAT
Found at i:5030361 original size:44 final size:44
Alignment explanation
Indices: 5030274--5030361 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 44
5030264 TTTTTTCATA
* * ** *
5030274 ATATATTAATAATATTTTATATTTTTAATTTTTTTTGTATTTTT
1 ATATATCAATAATATTTTATATATTTAATTAATTTTATATTTTT
5030318 ATATATCAATAATATTTT-TATAATTTAA-TAATTTTATAGTTTTT
1 ATATATCAATAATATTTTATAT-ATTTAATTAATTTTATA-TTTTT
5030362 CCATTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
43 10 0.27
44 27 0.73
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (44 bp):
ATATATCAATAATATTTTATATATTTAATTAATTTTATATTTTT
Found at i:5030400 original size:19 final size:19
Alignment explanation
Indices: 5030364--5030400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5030354 TAGTTTTTCC
**
5030364 ATTTTTTATAATTTTTTGA
1 ATTTTTTATAATAGTTTGA
5030383 ATTTTTTATAATAGTTTG
1 ATTTTTTATAATAGTTTG
5030401 TTTTTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
ATTTTTTATAATAGTTTGA
Found at i:5032067 original size:30 final size:30
Alignment explanation
Indices: 5032033--5032094 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
5032023 TAACAAGCAA
*
5032033 AAATGTCTCTAAAATAAAAACAAATTTAAC
1 AAATGTCTCTAAAATAAAAACAAAATTAAC
* *
5032063 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGTCTCTAAAATAAAAACAAAATTAAC
5032093 AA
1 AA
5032095 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGTCTCTAAAATAAAAACAAAATTAAC
Found at i:5033237 original size:19 final size:20
Alignment explanation
Indices: 5033196--5033248 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
5033186 ACATCCACTT
*
5033196 AATAATAAAAATA--TTTAG
1 AATAAAAAAAATATTTTTAG
5033214 AATAAAAAAAATATTTTTAG
1 AATAAAAAAAATATTTTTAG
5033234 -AT-AAAAAAATATTTT
1 AATAAAAAAAATATTTT
5033249 CATTAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 25 0.78
19 2 0.06
20 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AATAAAAAAAATATTTTTAG
Found at i:5033288 original size:21 final size:22
Alignment explanation
Indices: 5033258--5033299 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5033248 TCATTAAATT
*
5033258 ATTTAAATATTTAA-AAATATC
1 ATTTAAATATTAAATAAATATC
*
5033279 ATTTATATATTAAATAAATAT
1 ATTTAAATATTAAATAAATAT
5033300 ATATATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAATATTAAATAAATATC
Found at i:5034148 original size:20 final size:20
Alignment explanation
Indices: 5034110--5034148 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5034100 TATTAAAATA
*
5034110 GTTACATTTATTTACTTTAG
1 GTTACATTTAATTACTTTAG
5034130 GTTACATTTTAATTA-TTTA
1 GTTACA-TTTAATTACTTTA
5034149 TGTTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (20 bp):
GTTACATTTAATTACTTTAG
Found at i:5051108 original size:131 final size:131
Alignment explanation
Indices: 5050848--5051093 Score: 415
Period size: 131 Copynumber: 1.9 Consensus size: 131
5050838 AATTTAGAGA
*
5050848 ACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCTAGCAC
1 ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCTAGCAC
* *
5050913 GATAGGGCACGGTTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTGAGGAGTTTTTAAA
66 GATAGAGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTGAGGAGTTTTTAAA
5050978 G
131 G
* *
5050979 ACATGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAATCC-AGCA
1 ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAA-CCTAGCA
*
5051043 CGATAGAGCACGATT-CCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTT
65 CGATAGAGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTT
5051094 AGTGATTTTT
Statistics
Matches: 108, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
130 35 0.32
131 71 0.66
132 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (131 bp):
ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCTAGCAC
GATAGAGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTGAGGAGTTTTTAAA
G
Found at i:5052019 original size:19 final size:19
Alignment explanation
Indices: 5051980--5052030 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
5051970 GCCTAAGTAG
* *
5051980 ATATATGTATACATTATATA
1 ATATATG-ATAAATTAAATA
*
5052000 ATGTATGATAAATTAAATA
1 ATATATGATAAATTAAATA
5052019 ATATATGATAAA
1 ATATATGATAAA
5052031 ACCCTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATATGATAAATTAAATA
Found at i:5052498 original size:14 final size:14
Alignment explanation
Indices: 5052479--5052508 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5052469 TTTCAACACC
5052479 AATACTCACGGCTT
1 AATACTCACGGCTT
5052493 AATACTCACGGCTT
1 AATACTCACGGCTT
5052507 AA
1 AA
5052509 AACGACGCCG
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:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (14 bp):
AATACTCACGGCTT
Found at i:5052697 original size:116 final size:116
Alignment explanation
Indices: 5052493--5052711 Score: 420
Period size: 116 Copynumber: 1.9 Consensus size: 116
5052483 CTCACGGCTT
5052493 AATACTCACGGCTTAAAACGACGCCGTTTTACGCATATATATAAACCCAAAATTTGCCCTAAAAT
1 AATACTCACGGCTTAAAACGACGCCGTTTTACGCATATATATAAACCCAAAATTTGCCCTAAAAT
5052558 TTCATTCAGCATGTCATTTGCTCAAAGAGCCTTAAAGCAAATTCCAACACC
66 TTCATTCAGCATGTCATTTGCTCAAAGAGCCTTAAAGCAAATTCCAACACC
*
5052609 AATACTCACGGCTTGAAACGACGCCGTTTTACGCATATATATAAACCCAAAATTTGCCCTAAAAT
1 AATACTCACGGCTTAAAACGACGCCGTTTTACGCATATATATAAACCCAAAATTTGCCCTAAAAT
*
5052674 TTCATTCGGCATGTCATTTGCTCAAAGAGCCTTAAAGC
66 TTCATTCAGCATGTCATTTGCTCAAAGAGCCTTAAAGC
5052712 CCCCTTTCGA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 101 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (116 bp):
AATACTCACGGCTTAAAACGACGCCGTTTTACGCATATATATAAACCCAAAATTTGCCCTAAAAT
TTCATTCAGCATGTCATTTGCTCAAAGAGCCTTAAAGCAAATTCCAACACC
Found at i:5053676 original size:7 final size:8
Alignment explanation
Indices: 5053659--5053687 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5053649 TAAACTTGAG
5053659 AAATAAAA
1 AAATAAAA
5053667 AAATAAAA
1 AAATAAAA
5053675 AAATAAAA
1 AAATAAAA
5053683 AAATA
1 AAATA
5053688 TTATGTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATAAAA
Found at i:5057989 original size:30 final size:30
Alignment explanation
Indices: 5057955--5058017 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5057945 AATCAACAAG
5057955 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAATTAA
*
5057985 CAAATGCCTTTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAATTAA
5058015 CAA
1 CAA
5058018 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAATAAAATTAA
Found at i:5058457 original size:17 final size:17
Alignment explanation
Indices: 5058435--5058468 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5058425 ATTGAATCTC
5058435 TTTAATCATATTTATTA
1 TTTAATCATATTTATTA
* *
5058452 TTTAATTATTTTTATTA
1 TTTAATCATATTTATTA
5058469 GCTTACTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATCATATTTATTA
Found at i:5059256 original size:15 final size:16
Alignment explanation
Indices: 5059236--5059265 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5059226 TAAATATAAT
5059236 TTTAAAA-ATAAAGTA
1 TTTAAAAGATAAAGTA
5059251 TTTAAAAGATAAAGT
1 TTTAAAAGATAAAGT
5059266 TAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (16 bp):
TTTAAAAGATAAAGTA
Found at i:5067541 original size:21 final size:21
Alignment explanation
Indices: 5067515--5067555 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5067505 ATCTGCTCAA
* *
5067515 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5067536 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5067556 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5072687 original size:31 final size:31
Alignment explanation
Indices: 5072629--5072687 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5072619 GCTTAACATG
* **
5072629 AAAATAATTATTTAATTTAAGTTTTAATATA
1 AAAATAATTATTTAATTCAAGAGTTAATATA
5072660 AAAATAATTA-TTAAGTTCAAGAGTTAAT
1 AAAATAATTATTTAA-TTCAAGAGTTAAT
5072688 TTAGACAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (31 bp):
AAAATAATTATTTAATTCAAGAGTTAATATA
Found at i:5075072 original size:4 final size:4
Alignment explanation
Indices: 5075063--5075087 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5075053 TTAAAGTTTC
5075063 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
5075088 TAACAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:5090469 original size:31 final size:31
Alignment explanation
Indices: 5090423--5090482 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5090413 ATCACTCAAT
* *
5090423 TATTTGAAAATTTTTATTTAAATCATTGAAC
1 TATTTAAAAAATTTTATTTAAATCATTGAAC
*
5090454 TATTTAAAAAATTTTATTTAAGTCATTGA
1 TATTTAAAAAATTTTATTTAAATCATTGA
5090483 GTTGTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (31 bp):
TATTTAAAAAATTTTATTTAAATCATTGAAC
Found at i:5091545 original size:9 final size:11
Alignment explanation
Indices: 5091523--5091547 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5091513 TTATATCTAC
5091523 ATATCATTTAT
1 ATATCATTTAT
5091534 ATATCATTTAT
1 ATATCATTTAT
5091545 ATA
1 ATA
5091548 CTATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATCATTTAT
Found at i:5095315 original size:48 final size:48
Alignment explanation
Indices: 5095260--5095355 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
5095250 GAATTAAAGG
5095260 ATGTTTTAAACTAAGACTAATTATCTAATTGGCTAAGATTACGACAGA
1 ATGTTTTAAACTAAGACTAATTATCTAATTGGCTAAGATTACGACAGA
5095308 ATGTTTTAAACTAAGACTAATTATCTAATTGGCTAAGATTACGACAGA
1 ATGTTTTAAACTAAGACTAATTATCTAATTGGCTAAGATTACGACAGA
5095356 GATAAATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (48 bp):
ATGTTTTAAACTAAGACTAATTATCTAATTGGCTAAGATTACGACAGA
Found at i:5105974 original size:47 final size:47
Alignment explanation
Indices: 5105915--5106261 Score: 568
Period size: 47 Copynumber: 7.4 Consensus size: 47
5105905 GATGTACAAG
* *
5105915 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
5105962 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
5106009 GTGTGTATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
5106056 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
5106103 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
5106150 GTGTATATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTAAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
5106197 GTGTGTATATGTGATAAGGCCTAATGTCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
5106244 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
5106262 TCCCGAAGGG
Statistics
Matches: 281, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 281 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
Found at i:5118582 original size:35 final size:35
Alignment explanation
Indices: 5118538--5118657 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 35
5118528 AATATTTAAG
* * *
5118538 ATAACTTCACATATATCCGAGTATACAATTTCAAT
1 ATAACTTCACATGTATCCGAATATACAAATTCAAT
* *
5118573 ATAAGTTCACATGTAAT-CAAATACTA-AAATTCAAT
1 ATAACTTCACATGT-ATCCGAATA-TACAAATTCAAT
* * *
5118608 ATAACCTCACATGTAGCCGAATATACAAGTTCAAT
1 ATAACTTCACATGTATCCGAATATACAAATTCAAT
5118643 ATAAGCTT-ACATGTA
1 ATAA-CTTCACATGTA
5118658 CTTACCTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
34 3 0.04
35 60 0.87
36 6 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (35 bp):
ATAACTTCACATGTATCCGAATATACAAATTCAAT
Found at i:5124896 original size:11 final size:11
Alignment explanation
Indices: 5124882--5124926 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5124872 AGATAAATAT
5124882 TATTTTATTAA
1 TATTTTATTAA
*
5124893 TATTTTAATAATA
1 TATTTT-ATTA-A
*
5124906 TATTTTATTAT
1 TATTTTATTAA
5124917 TATTTTATTA
1 TATTTTATTA
5124927 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5124909 original size:24 final size:24
Alignment explanation
Indices: 5124877--5124932 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
5124867 TAATTAGATA
5124877 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
5124902 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
5124926 AGTATAT
1 AATATAT
5124933 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:5127110 original size:46 final size:46
Alignment explanation
Indices: 5127058--5127285 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
5127048 AGTGTGCTCT
**
5127058 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
5127104 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
5127150 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
5127196 GTGACATGAAAAGAATAAGACTATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
5127242 ATGACA-GAAAATGAGTAAGACCATAGCTGAAAGACACTATGGCA
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
5127286 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5128753 original size:35 final size:35
Alignment explanation
Indices: 5128691--5128828 Score: 129
Period size: 35 Copynumber: 3.9 Consensus size: 35
5128681 CACATATGGA
* * * * *
5128691 CGAATATGCATATTTAAGATAACTTCACATATATC
1 CGAATATACAAATTCAATATAACTTCACATGTATC
* * *
5128726 CGAGTATACAATTTCAATATAAGTTCACATGTAAT-
1 CGAATATACAAATTCAATATAACTTCACATGT-ATC
* *
5128761 CGAATACTA-AAATTCAATATAACCTCACATGTAGC
1 CGAATA-TACAAATTCAATATAACTTCACATGTATC
*
5128796 CGAATATACAAGTTCAATATAAGCTT-ACATGTA
1 CGAATATACAAATTCAATATAA-CTTCACATGTA
5128829 CTTACCTATG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
34 3 0.04
35 74 0.89
36 6 0.07
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (35 bp):
CGAATATACAAATTCAATATAACTTCACATGTATC
Found at i:5135676 original size:36 final size:36
Alignment explanation
Indices: 5135635--5135707 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5135625 TTCGAACAAG
5135635 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
1 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
5135671 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
1 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
5135707 T
1 T
5135708 CACGTTGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (36 bp):
TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
Found at i:5138939 original size:46 final size:44
Alignment explanation
Indices: 5138798--5138939 Score: 119
Period size: 46 Copynumber: 3.1 Consensus size: 44
5138788 CGCCCATAAT
*
5138798 TGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AG
* * * * *
5138845 CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTCG--GATGC-CAACCATCTAG
5138891 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAG
5138937 TGA
1 TGA
5138940 CATGTCACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 29 0.38
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (44 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAG
Found at i:5141851 original size:20 final size:20
Alignment explanation
Indices: 5141799--5141853 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
5141789 ATGTGACAAA
* *
5141799 AAAAATGATAAAAA-ATAAT
1 AAAAATCATAAAAATTTAAT
*
5141818 AAAAATCATTAAAATTTAAT
1 AAAAATCATAAAAATTTAAT
5141838 AAATAATC-TAAAAATT
1 AAA-AATCATAAAAATT
5141854 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATCATAAAAATTTAAT
Found at i:5141877 original size:23 final size:24
Alignment explanation
Indices: 5141847--5141892 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5141837 TAAATAATCT
5141847 AAAAATTATTAAAAT-T-TAGAAAA
1 AAAAATTA-TAAAATATATAGAAAA
5141870 AAAAATTATAAAATATATAGAAA
1 AAAAATTATAAAATATATAGAAA
5141893 TATAGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAATTATAAAATATATAGAAAA
Found at i:5147591 original size:14 final size:13
Alignment explanation
Indices: 5147575--5147599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5147565 CAAAAACATT
5147575 TTTTCAAAAGTAG
1 TTTTCAAAAGTAG
5147588 TTTTCAAAAGTA
1 TTTTCAAAAGTA
5147600 TTATCAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGTAG
Found at i:5150891 original size:18 final size:17
Alignment explanation
Indices: 5150868--5150903 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5150858 TAAGTTGAGA
*
5150868 CCCAAATATTAATTTAAC
1 CCCAAAT-TTAATGTAAC
5150886 CCCAAATTTAATGTAAC
1 CCCAAATTTAATGTAAC
5150903 C
1 C
5150904 ATGGACTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.31
Consensus pattern (17 bp):
CCCAAATTTAATGTAAC
Found at i:5156836 original size:21 final size:21
Alignment explanation
Indices: 5156802--5156841 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5156792 TGTATAAATT
*
5156802 AGAAAGATTTGAGATTGGAACC
1 AGAAAGATCTGAGA-TGGAACC
5156824 AGAAA-ATCTGAGATGGAA
1 AGAAAGATCTGAGATGGAA
5156842 AGCATGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (21 bp):
AGAAAGATCTGAGATGGAACC
Found at i:5157580 original size:19 final size:20
Alignment explanation
Indices: 5157542--5157580 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5157532 AATGAAATTA
5157542 AAAATAATATAAATTGATTT
1 AAAATAATATAAATTGATTT
5157562 AAAATGAATA-AAATT-ATTT
1 AAAAT-AATATAAATTGATTT
5157581 GTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATAATATAAATTGATTT
Found at i:5167434 original size:18 final size:18
Alignment explanation
Indices: 5167411--5167455 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5167401 AGTCTAGATT
5167411 TTTAAAAATTAAAAA-AA
1 TTTAAAAATTAAAAATAA
*
5167428 CTTTAAAAA-TAAAAATTA
1 -TTTAAAAATTAAAAATAA
5167446 TTTAAAAATT
1 TTTAAAAATT
5167456 CATTTTCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAAAATTAAAAATAA
Found at i:5167575 original size:20 final size:20
Alignment explanation
Indices: 5167550--5167600 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5167540 ATTTATTTAT
* *
5167550 TAAAATAATATTTTTATAGA
1 TAAAATAATATTCTTATAAA
*
5167570 TAAAATAATAATCTTATAAA
1 TAAAATAATATTCTTATAAA
*
5167590 TAAAAAAATAT
1 TAAAATAATAT
5167601 ACGGGGAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATAATATTCTTATAAA
Found at i:5168855 original size:21 final size:21
Alignment explanation
Indices: 5168825--5168864 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5168815 CTGTGAGGAT
*
5168825 ATAATTAAAATTTTAAAAAAC
1 ATAATAAAAATTTTAAAAAAC
*
5168846 ATAATAAAAATTTTCAAAA
1 ATAATAAAAATTTTAAAAA
5168865 TTTTGTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAAAAATTTTAAAAAAC
Found at i:5170706 original size:16 final size:15
Alignment explanation
Indices: 5170664--5170707 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5170654 TTTATCAGTA
5170664 TTATTTTAGTTTAAAT
1 TTATTTTA-TTTAAAT
**
5170680 AAATTTTATTTAAAT
1 TTATTTTATTTAAAT
5170695 TTATTTTGATTTA
1 TTATTTT-ATTTA
5170708 GATCCAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTATTTTATTTAAAT
Found at i:5171114 original size:22 final size:22
Alignment explanation
Indices: 5171069--5171122 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5171059 TGTCACACAA
* *
5171069 AAGATTTTAATAGAATAAATTT
1 AAGATTTTAACAGAATAAACTT
*
5171091 AACGATTTTAACA-AATAGACTT
1 AA-GATTTTAACAGAATAAACTT
*
5171113 AAAATTTTAA
1 AAGATTTTAA
5171123 ACCCAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (22 bp):
AAGATTTTAACAGAATAAACTT
Found at i:5173931 original size:29 final size:33
Alignment explanation
Indices: 5173891--5173953 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 33
5173881 AGCCTATATC
5173891 TTTATAATTTTTAA-AAGATT-AAAT-TAATTT
1 TTTATAATTTTTAAGAAGATTAAAATATAATTT
*
5173921 TTTAT-ATTTTTAAGAGGATTAAAATATAATTT
1 TTTATAATTTTTAAGAAGATTAAAATATAATTT
5173953 T
1 T
5173954 ATCATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.28
30 10 0.34
31 4 0.14
32 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (33 bp):
TTTATAATTTTTAAGAAGATTAAAATATAATTT
Found at i:5173955 original size:30 final size:29
Alignment explanation
Indices: 5173891--5173953 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
5173881 AGCCTATATC
5173891 TTTATAATTTTTAAAAGATTAAATTAATT
1 TTTATAATTTTTAAAAGATTAAATTAATT
*
5173920 TTT-TATATTTTTAAGAGGATTAAAATATAATT
1 TTTATA-ATTTTTAA-AAGATT-AAAT-TAATT
5173952 TT
1 TT
5173954 ATCATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.07
29 11 0.38
30 5 0.17
31 4 0.14
32 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (29 bp):
TTTATAATTTTTAAAAGATTAAATTAATT
Found at i:5174090 original size:31 final size:31
Alignment explanation
Indices: 5174055--5174113 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5174045 AATGAAACTT
*
5174055 TAACTTTAATAAAAA-TATATAAATAATTTAA
1 TAACTTAAATAAAAACT-TATAAATAATTTAA
*
5174086 TAACTTAAATAAAAACTTTTAAATAATT
1 TAACTTAAATAAAAACTTATAAATAATT
5174114 CAACAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (31 bp):
TAACTTAAATAAAAACTTATAAATAATTTAA
Found at i:5174998 original size:29 final size:30
Alignment explanation
Indices: 5174954--5175010 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5174944 GAGATAATTT
* *
5174954 GACAAAAAATACAAATTAAAAATTAAAAGA
1 GACAAAAAATACAAATAAAAAACTAAAAGA
*
5174984 GACAAAAAA-ATAAATAAAAAACTAAAA
1 GACAAAAAATACAAATAAAAAACTAAAA
5175011 TATATAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (30 bp):
GACAAAAAATACAAATAAAAAACTAAAAGA
Found at i:5186605 original size:21 final size:21
Alignment explanation
Indices: 5186581--5186623 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
5186571 GTTAAGGTGA
5186581 AAAAATTATAATA-ATT-TTTTT
1 AAAAA-TA-AATATATTATTTTT
5186602 AAAAATAAATATATTATTTTT
1 AAAAATAAATATATTATTTTT
5186623 A
1 A
5186624 TAATATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAATAAATATATTATTTTT
Found at i:5188121 original size:16 final size:16
Alignment explanation
Indices: 5188088--5188121 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5188078 GGCTAGTGTT
* *
5188088 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5188104 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5188120 AA
1 AA
5188122 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5190942 original size:21 final size:21
Alignment explanation
Indices: 5190916--5190956 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5190906 AGACGAGCAA
* *
5190916 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5190937 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5190957 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5192894 original size:16 final size:16
Alignment explanation
Indices: 5192861--5192894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5192851 GGAGATTGTT
* *
5192861 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5192877 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5192893 AA
1 AA
5192895 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5196974 original size:107 final size:107
Alignment explanation
Indices: 5196841--5197057 Score: 355
Period size: 107 Copynumber: 2.0 Consensus size: 107
5196831 ATCTTTATCT
* *
5196841 TAATAGGGCTCAAACTCTTATGTCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
1 TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
* *
5196906 ACTTACTTGTTTATTGAA-GAACATATATTTGAGAGTGTAAAG
66 ACTTACCTGTTCATTGAATG-ACATATATTTGAGAGTGTAAAG
* *
5196948 TAATAGGCCTCAAACTCTTATATCTTAGATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAGC
1 TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
*
5197013 ACTTACCTGTTCATTGAATGACATGTATTTGAGAGTGTAAAG
66 ACTTACCTGTTCATTGAATGACATATATTTGAGAGTGTAAAG
5197055 TAA
1 TAA
5197058 ATTGATATCA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 101 0.99
108 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (107 bp):
TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
ACTTACCTGTTCATTGAATGACATATATTTGAGAGTGTAAAG
Found at i:5199229 original size:22 final size:21
Alignment explanation
Indices: 5199204--5199255 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
5199194 CATTATTTAG
*
5199204 TTATATGAATACTAAATTTTTT
1 TTAT-TGAAAACTAAATTTTTT
*
5199226 TTATTTAAAACTAAA-TTTTT
1 TTATTGAAAACTAAATTTTTT
*
5199246 TTATTTAAAA
1 TTATTGAAAA
5199256 ACGTAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.54
21 9 0.32
22 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATTGAAAACTAAATTTTTT
Found at i:5199257 original size:21 final size:21
Alignment explanation
Indices: 5199214--5199255 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
5199204 TTATATGAAT
5199214 ACTAAATTTTTTTTATTTAAA
1 ACTAAATTTTTTTTATTTAAA
5199235 ACTAAA-TTTTTTTATTTAAA
1 ACTAAATTTTTTTTATTTAAA
5199255 A
1 A
5199256 ACGTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTAAATTTTTTTTATTTAAA
Found at i:5199486 original size:30 final size:30
Alignment explanation
Indices: 5199449--5199518 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
5199439 ATATATGAAG
5199449 AATATTAAATTATTATTAAAATAAAATTGA
1 AATATTAAATTATTATTAAAATAAAATTGA
*
5199479 ATTATTAAATTATTATTAAAATAAAATTGA
1 AATATTAAATTATTATTAAAATAAAATTGA
5199509 AATATTAAAT
1 AATATTAAAT
5199519 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
AATATTAAATTATTATTAAAATAAAATTGA
Found at i:5206976 original size:21 final size:22
Alignment explanation
Indices: 5206938--5206978 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5206928 CGTTTGATAA
*
5206938 TTATTAAAAAAATATGAAAATT
1 TTATTAAAAAAACATGAAAATT
*
5206960 TTATT-AAAAAACGTGAAAA
1 TTATTAAAAAAACATGAAAA
5206979 ATTATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (22 bp):
TTATTAAAAAAACATGAAAATT
Found at i:5210223 original size:83 final size:83
Alignment explanation
Indices: 5210121--5210302 Score: 258
Period size: 83 Copynumber: 2.2 Consensus size: 83
5210111 GACACATATG
* * ** *
5210121 AAATATTTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTACTTATGTAATTCG-GAA
1 AAATAATTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTAATTACATAATTCGAAAA
*
5210185 AACATTTTACATTTGAAA
66 AACATTCTACATTTGAAA
*
5210203 AAATAAATTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTAATTACATAGTTCGAAA
1 AAAT-AATTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTAATTACATAATTCGAAA
* *
5210268 AAACATTCTACGTTTGAAT
65 AAACATTCTACATTTGAAA
5210287 AAATAATGTAGTGTCA
1 AAATAAT-TAGTGTCA
5210303 TAAAATTAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
82 4 0.05
83 55 0.62
84 29 0.33
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (83 bp):
AAATAATTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTAATTACATAATTCGAAAA
AACATTCTACATTTGAAA
Found at i:5211846 original size:23 final size:23
Alignment explanation
Indices: 5211818--5211865 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5211808 TTTTTTAAAG
5211818 TTTGATTGTATTTATCTATGGGT
1 TTTGATTGTATTTATCTATGGGT
5211841 TTTGATTGTATTTATCTATGGGT
1 TTTGATTGTATTTATCTATGGGT
5211864 TT
1 TT
5211866 ATTATTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.58
Consensus pattern (23 bp):
TTTGATTGTATTTATCTATGGGT
Found at i:5217914 original size:80 final size:79
Alignment explanation
Indices: 5217781--5217930 Score: 246
Period size: 80 Copynumber: 1.9 Consensus size: 79
5217771 CCAAAAATTG
* *
5217781 ATTTGATCACAGCCTTCTACTACTTGCGTCCCAGTTAGCATTGATATTGGTACAACTTTTTGAGA
1 ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAAC-TTTTGAGA
5217846 TTAAAAGTTGTGTTA
65 TTAAAAGTTGTGTTA
* * *
5217861 ATTTGATTACAGCCTTCAACTACTTGCGTCACAGTTAGTATTGATTTTGGTACAACTTTTGAGAT
1 ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAACTTTTGAGAT
5217926 TAAAA
66 TAAAA
5217931 CAATGCTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 14 0.22
80 51 0.78
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (79 bp):
ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAACTTTTGAGAT
TAAAAGTTGTGTTA
Found at i:5219539 original size:13 final size:14
Alignment explanation
Indices: 5219521--5219549 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5219511 TAAATATGAC
5219521 TTTTTA-AAAATAA
1 TTTTTAGAAAATAA
5219534 TTTTTAGAAAATAA
1 TTTTTAGAAAATAA
5219548 TT
1 TT
5219550 AGCTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTTTAGAAAATAA
Found at i:5233207 original size:5 final size:5
Alignment explanation
Indices: 5233197--5233239 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
5233187 AACGTATTAT
* * *
5233197 ACCGC ACCGC ACTGT ACCGC ACCGT ACCGC ACCGC ACCGC ACC
1 ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACC
5233240 ACCGCTCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.21, C:0.53, G:0.19, T:0.07
Consensus pattern (5 bp):
ACCGC
Found at i:5237482 original size:15 final size:15
Alignment explanation
Indices: 5237462--5237502 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
5237452 TTAAGATCCC
5237462 TTATAAATTATGAAA
1 TTATAAATTATGAAA
*
5237477 TTATAAATTAATGTAA
1 TTATAAATT-ATGAAA
*
5237493 TGATAAATTA
1 TTATAAATTA
5237503 CTTTATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TTATAAATTATGAAA
Found at i:5238030 original size:22 final size:23
Alignment explanation
Indices: 5237997--5238056 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
5237987 ATCATGATTC
*
5237997 TAAAACAT-TAAATAATTT-ATA
1 TAAAAAATATAAATAATTTCATA
*
5238018 TAAAAAATATAAATATTTTCATA
1 TAAAAAATATAAATAATTTCATA
* *
5238041 AAAAAAACAATAAATA
1 TAAAAAA-TATAAATA
5238057 TTGGAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.22
22 9 0.28
23 9 0.28
24 7 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAAATATAAATAATTTCATA
Found at i:5238035 original size:21 final size:21
Alignment explanation
Indices: 5237997--5238045 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5237987 ATCATGATTC
*
5237997 TAAAACATTAAATAATTTAT-A
1 TAAAAAATTAAATAATTT-TCA
5238018 TAAAAAATATAAAT-ATTTTCA
1 TAAAAAAT-TAAATAATTTTCA
5238039 TAAAAAA
1 TAAAAAA
5238046 AACAATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAATTAAATAATTTTCA
Found at i:5238053 original size:24 final size:23
Alignment explanation
Indices: 5237998--5238058 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
5237988 TCATGATTCT
* * *
5237998 AAAACATTAAATAATTTATATAA
1 AAAACAATAAATATTTTATAAAA
*
5238021 AAAA-TATAAATATTTTCATAAAA
1 AAAACAATAAATATTTT-ATAAAA
5238044 AAAACAATAAATATT
1 AAAACAATAAATATT
5238059 GGAACTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 9 0.29
23 13 0.42
24 9 0.29
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAACAATAAATATTTTATAAAA
Found at i:5238548 original size:6 final size:6
Alignment explanation
Indices: 5238539--5238576 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5238529 TTTATTTTAT
*
5238539 TTAATA TTAATA TTAATA TTAATA TTTAT- TTAATA TTA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTA
5238577 TTTTGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTAATA
Found at i:5246558 original size:29 final size:29
Alignment explanation
Indices: 5246526--5246630 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 29
5246516 ATTTATTTTG
5246526 TTAT-TCTAATACTATTTTTATTTATCTAT
1 TTATATCTAATACTATTTTTATTT-TCTAT
* * *
5246555 TTATATTTCA-ACTATTATTATATTTCTAT
1 TTATATCTAATACTATTTTTAT-TTTCTAT
* * **
5246584 TTAT-TATATTTTTATTTTTA-TTTCTAT
1 TTATATCTAATACTATTTTTATTTTCTAT
*
5246611 TTATATACTAATATTATTTT
1 TTATAT-CTAATACTATTTT
5246631 CATTATTACA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
27 11 0.19
28 3 0.05
29 40 0.68
30 5 0.08
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.64
Consensus pattern (29 bp):
TTATATCTAATACTATTTTTATTTTCTAT
Found at i:5246577 original size:17 final size:15
Alignment explanation
Indices: 5246555--5246594 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
5246545 ATTTATCTAT
5246555 TTATATTTCAACTATTA
1 TTATATTTCAA-T-TTA
*
5246572 TTATATTTCTATTTA
1 TTATATTTCAATTTA
5246587 TTATATTT
1 TTATATTT
5246595 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTCAATTTA
Done.