Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 11 of 168
Found at i:3086391 original size:19 final size:19
Alignment explanation
Indices: 3086354--3086425 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
3086344 AATCATATCT
3086354 TCTAAGATTGCAT-TCATA
1 TCTAAGATTGCATATCATA
3086372 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3086391 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
3086410 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
3086426 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 13 0.25
19 38 0.75
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3087160 original size:91 final size:94
Alignment explanation
Indices: 3087047--3087415 Score: 440
Period size: 100 Copynumber: 3.8 Consensus size: 94
3087037 CAGTCTTTTA
**
3087047 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTACCAGG
1 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
3087112 GAAGTAAAATTCGCCATTGCGGC-T-TC-
66 GAAGTAAAATTCGCCATTGCGGCTTATCT
*
3087138 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGG
1 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
*
3087203 GAAGTAAAATTCGCCGTTTGCGGCTTTAATCTTTTT
66 GAAGTAAAATTCGCC-ATTGCGGC-TT-ATC----T
* * * * *
3087239 AATTGCAAAGTTGGGGAAACGAGATTTGCCGT-TTAGCTTCAATCTGTTCCACTACACCGCCAAG
1 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
** *
3087303 GAAGTAAAATTTTCCATTGCAGCTTCAATCTTTTT
66 GAAGTAAAATTCGCCATTGCGGCTT--ATC----T
* * * *
3087338 AATTGCAATGTTGGGGAAACTAGATTCGCCATCGTAGCTTCAATCTGTTCCACTACACTGTCAGG
1 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
*
3087403 GAAGTAAGATTCG
66 GAAGTAAAATTCG
3087416 TTGTTGCGAC
Statistics
Matches: 242, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
91 77 0.32
92 7 0.03
94 1 0.00
96 2 0.01
98 2 0.01
99 43 0.18
100 81 0.33
101 29 0.12
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (94 bp):
AATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGG
GAAGTAAAATTCGCCATTGCGGCTTATCT
Found at i:3087413 original size:50 final size:50
Alignment explanation
Indices: 3087272--3087415 Score: 119
Period size: 50 Copynumber: 2.9 Consensus size: 50
3087262 ATTTGCCGTT
* * * * ** *
3087272 TAGCTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAAATTTTCCATTG
1 TAGCTTCAATCTGTTCCACTACACTGTCAGGGAAGTAAGATTCGCCATCG
* * ** * * * ** *
3087322 CAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACT-AGATTCGCCATCG
1 TAGCTTCAATCTGTTCCACTACACTGTCAGGG-AAGTAAGATTCGCCATCG
3087372 TAGCTTCAATCTGTTCCACTACACTGTCAGGGAAGTAAGATTCG
1 TAGCTTCAATCTGTTCCACTACACTGTCAGGGAAGTAAGATTCG
3087416 TTGTTGCGAC
Statistics
Matches: 65, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
49 3 0.05
50 59 0.91
51 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (50 bp):
TAGCTTCAATCTGTTCCACTACACTGTCAGGGAAGTAAGATTCGCCATCG
Found at i:3087653 original size:167 final size:170
Alignment explanation
Indices: 3087359--3087751 Score: 446
Period size: 167 Copynumber: 2.3 Consensus size: 170
3087349 TGGGGAAACT
* * *
3087359 AGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC-ACTGTCAGGGAAGTAAGATT---CGTTGT
1 AGATTCGCCGTCGTAGCTTCAATCTGCTCGACTACAAC-GTCAGGGAAGTAAGATTCACCGTTGT
* * *
3087420 TGCGACTTTAATCTGCTCGACTGTAATGCCAAAGAGATAGGATTCACTACCCACATCTTCAATCC
65 TGCGACTTCAATCTGCTCGACTGTAATGCCAAAGAGATAAGATTCACTACCCACAGCTTCAATCC
3087485 GCTCCACTTCAGCTAATCCAAGCCTTAACGCCA-AGGAGATA
130 GCTCCACTTCAGCTAATCCAAGCCTTAACGCCAGA-GAGATA
*
3087526 AGATTCGCCGTCGTGGCTTCAATCTGCTCGACTACAACGTCAGGGAAGTAAGATTCACCGTT-TT
1 AGATTCGCCGTCGTAGCTTCAATCTGCTCGACTACAACGTCAGGGAAGTAAGATTCACCGTTGTT
** * * * *
3087590 G-G-CTTCAATCTATTTC-ATTGTAATGCCAAAGAGATAAGATTCGCTGCCCACAGCTTTAATCC
66 GCGACTTCAATCT-GCTCGACTGTAATGCCAAAGAGATAAGATTCACTACCCACAGCTTCAATCC
* * * *
3087652 GCTCCGCTTCAGCTATTTCAAGTCTTAACGCCAGAGAGATA
130 GCTCCACTTCAGCTAATCCAAGCCTTAACGCCAGAGAGATA
* * * * * * * *
3087693 AAATTCGCTGCCCTCAGCTTTAATCTACTCCG-CTATAACGTCAGGAAAGTAAGATTCAC
1 AGATTCGCCGTCGT-AGCTTCAATCTGCT-CGACTACAACGTCAGGGAAGTAAGATTCAC
3087752 AATCTTCAAC
Statistics
Matches: 192, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
167 141 0.73
168 42 0.22
169 5 0.03
170 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (170 bp):
AGATTCGCCGTCGTAGCTTCAATCTGCTCGACTACAACGTCAGGGAAGTAAGATTCACCGTTGTT
GCGACTTCAATCTGCTCGACTGTAATGCCAAAGAGATAAGATTCACTACCCACAGCTTCAATCCG
CTCCACTTCAGCTAATCCAAGCCTTAACGCCAGAGAGATA
Found at i:3087811 original size:44 final size:44
Alignment explanation
Indices: 3087748--3087958 Score: 271
Period size: 44 Copynumber: 5.0 Consensus size: 44
3087738 AAAGTAAGAT
*
3087748 TCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
3087792 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGG--
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* *
3087834 -----A--TTC-ACCTATTCCACTGCTGACTAGGGAGATAGGAT
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * *
3087870 TTACAATTTTCAAACTATTCCACTGCTGACCAGGGAGATAAGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* *
3087914 TTACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
3087958 T
1 T
3087959 AGGGTCATCG
Statistics
Matches: 149, Mismatches: 8, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
34 29 0.19
35 3 0.02
37 1 0.01
41 1 0.01
43 3 0.02
44 112 0.75
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
Found at i:3087847 original size:34 final size:34
Alignment explanation
Indices: 3087804--3087870 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
3087794 ACAATCTTCA
3087804 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
*
3087838 ACCTATTCCACTGCTGACTAGGGAGATAGGATT
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATT
3087871 TACAATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:3087889 original size:78 final size:78
Alignment explanation
Indices: 3087760--3087909 Score: 246
Period size: 78 Copynumber: 1.9 Consensus size: 78
3087750 ACAATCTTCA
*
3087760 ACCTATTCCACTGCTAACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTGCTGACCAG
3087825 GGAGATAGGATTC
66 GGAGATAGGATTC
* * * * *
3087838 ACCTATTCCACTGCTGACTAGGGAGATAGGATTTACAATTTTCAAACTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTGCTGACCAG
3087903 GGAGATA
66 GGAGATA
3087910 AGACTTACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (78 bp):
ACCTATTCCACTGCTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTGCTGACCAG
GGAGATAGGATTC
Found at i:3089345 original size:6 final size:6
Alignment explanation
Indices: 3089326--3089376 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
3089316 CCTTTTCCTC
* * *
3089326 TTCTTCT TTATTT TTCTTT TTCTTT TT-TCTT TTCTTT TTATTT TCCTTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT TTCTTT
3089375 TT
1 TT
3089377 TCCATCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
5 1 0.03
6 30 0.83
7 5 0.14
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:3089374 original size:24 final size:23
Alignment explanation
Indices: 3089318--3089378 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
3089308 TGGCCTCTCC
* *
3089318 TTTTCCTCTTCTTCTTTATTTTTC
1 TTTTCCT-TTTTTCTTTATTTTTA
* *
3089342 TTTTTCTTTTTTCTTTTCTTTTTA
1 TTTTCCTTTTTTC-TTTATTTTTA
3089366 TTTTCCTTTTTTC
1 TTTTCCTTTTTTC
3089379 CATCATCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCCTTTTTTCTTTATTTTTA
Found at i:3094112 original size:43 final size:47
Alignment explanation
Indices: 3094010--3094115 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 47
3094000 CCGCTTTAAC
*
3094010 AAATAA-CAATAATAAATACAACAATGACATAGAAATAATATAAACAT
1 AAATAAGCAA-AAAAAATACAACAATGACATAGAAATAATATAAACAT
* * * *
3094057 AAATAAGGAAAAAAAATA-AACAATGACAT-GTAA-AGTATCAA-AT
1 AAATAAGCAAAAAAAATACAACAATGACATAGAAATAATATAAACAT
*
3094100 AAATGAGCAAAAAAAA
1 AAATAAGCAAAAAAAA
3094116 AGACATTCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
43 16 0.31
44 6 0.12
45 3 0.06
46 11 0.22
47 13 0.25
48 2 0.04
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.18
Consensus pattern (47 bp):
AAATAAGCAAAAAAAATACAACAATGACATAGAAATAATATAAACAT
Found at i:3094738 original size:19 final size:19
Alignment explanation
Indices: 3094714--3094824 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
3094704 AATCATATCT
*
3094714 TCTAAGATTCCATATCATA
1 TCTAAGATTACATATCATA
* *
3094733 TCTAAGATTGCCTATCATA
1 TCTAAGATTACATATCATA
3094752 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
3094771 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
3094790 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
3094809 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
3094825 TTTGAAGATA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 85 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:3094760 original size:38 final size:38
Alignment explanation
Indices: 3094707--3094824 Score: 204
Period size: 38 Copynumber: 3.2 Consensus size: 38
3094697 ATTATAAAAT
*
3094707 CATATC-T-TCTAAGATTCCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATCATATCTAAGATTG
*
3094743 CCTATCATATCTAAGATTACATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATCATATCTAAGATTG
3094781 CATATCATATCTAAGATTACATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATCATATCTAAGATTG
3094819 CATATC
1 CATATC
3094825 TTTGAAGATA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
36 5 0.06
37 1 0.01
38 71 0.92
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (38 bp):
CATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:3095910 original size:69 final size:69
Alignment explanation
Indices: 3095815--3096027 Score: 300
Period size: 69 Copynumber: 3.1 Consensus size: 69
3095805 CATAGGTCTA
*
3095815 CTAGCTGCTTTAGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGGAACGTAGG
1 CTAGCTACTTTAGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGGAACGTAGG
3095880 TCCG
66 TCCG
* * * * * *
3095884 TTAGCTACTTTGGAGGTTGTGATCTTATATTGTCAAACCTTTATGACATCAGTTGGGAGCGTAGG
1 CTAGCTACTTTAGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGGAACGTAGG
*
3095949 TCTG
66 TCCG
* * ** * *
3095953 CTAGCTACTTTAGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATAAACTGGGAGCATAGG
1 CTAGCTACTTTAGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGGAACGTAGG
3096018 TCCG
66 TCCG
3096022 CTAGCT
1 CTAGCT
3096028 GTGTCGGAGC
Statistics
Matches: 125, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 125 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (69 bp):
CTAGCTACTTTAGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGGAACGTAGG
TCCG
Found at i:3098448 original size:16 final size:15
Alignment explanation
Indices: 3098427--3098461 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3098417 TAAAATTTTG
3098427 TATATCTAGATAAAAA
1 TATATCTAGA-AAAAA
*
3098443 TATATCTATAAAAAA
1 TATATCTAGAAAAAA
3098458 TATA
1 TATA
3098462 GACAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATATCTAGAAAAAA
Found at i:3102800 original size:41 final size:40
Alignment explanation
Indices: 3102750--3102843 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
3102740 GTTTTTTTAC
* * * *
3102750 TTTATATATTAGGCTTTAAATTAGCTCTTTAAATTTTAGA
1 TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
* * * *
3102790 TTTTAAATATTAAGTTTTAAATTGGATTTTTAGATTCTAGA
1 -TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
*
3102831 TTTAAATACTAAG
1 TTTAAATATTAAG
3102844 TTTTTTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 12 0.27
41 32 0.73
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (40 bp):
TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
Found at i:3105304 original size:43 final size:42
Alignment explanation
Indices: 3105119--3105332 Score: 148
Period size: 43 Copynumber: 5.0 Consensus size: 42
3105109 TTTCAAGTCA
* * *
3105119 AAGCAAAT-ATACTGGCACACGACA-TGCATTATCGGATGAATCG
1 AAGC-AATCATACTGGCACA-GA-AGTGCATCATCGGATAAACCG
* * * * * *
3105162 AAGCAATTATATTAGCACAGGAAGTGCATCATCGAACAAACTG
1 AAGCAATCATACTGGCACA-GAAGTGCATCATCGGATAAACCG
* * * * * *
3105205 AGGCAATTATACTAGCACACAAGGTGCGTCA-CTGGAAAAACCG
1 AAGCAATCATACTGGCACAGAA-GTGCATCATC-GGATAAACCG
* *
3105248 AAGCAATCATACTGGCACAGATAGTGCATTATTGGATAAACCG
1 AAGCAATCATACTGGCACAGA-AGTGCATCATCGGATAAACCG
* *
3105291 AAGCAATCATACTGGTACACATAA-TGCATCATCGAATAAACC
1 AAGCAATCATACTGG--CACAGAAGTGCATCATCGGATAAACC
3105333 AAAGTATAAA
Statistics
Matches: 135, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
42 7 0.05
43 121 0.90
44 2 0.01
45 5 0.04
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGCAATCATACTGGCACAGAAGTGCATCATCGGATAAACCG
Found at i:3112525 original size:24 final size:22
Alignment explanation
Indices: 3112481--3112526 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
3112471 ATGAAACATG
*
3112481 AAATATAATAGTTAAATTGTTA
1 AAATATAATAGTTAAAATGTTA
*
3112503 AAATATTAATTGTATAAAATGTTA
1 AAATA-TAATAGT-TAAAATGTTA
3112527 CAGAGTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATATAATAGTTAAAATGTTA
Found at i:3118095 original size:23 final size:23
Alignment explanation
Indices: 3118069--3118144 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
3118059 ATAAGTGTCA
3118069 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3118092 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3118115 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3118138 CACTGAT
1 CACTGAT
3118145 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3122784 original size:170 final size:171
Alignment explanation
Indices: 3122453--3122792 Score: 610
Period size: 170 Copynumber: 2.0 Consensus size: 171
3122443 TTGGAGTGGA
3122453 AGCAGCCTAAGAACGTGCCTGAGATCCGTAATTTTCTGGGACTGGATGGATATTATTGACGATTT
1 AGCAGCCTAAGAACGTGCCTGAGATCCGTAATTTTCTGGGACTGGATGGATATTATTGACGATTT
* *
3122518 GTAGAGGGTTTTTTTATTGATTGCAGTACCCTTGACTAAGCTGCTACGTAAGGGTGAACCGTTTA
66 GTAGAGGGTTTTTTTATTGATTGCAGCACCCTTGACTAAGCTGCTACGTAAGGATGAACCGTTTA
3122583 ACTAGACTGATGCACAGCAAGAGAGCTTTGAAAGCTCAAGC
131 ACTAGACTGATGCACAGCAAGAGAGCTTTGAAAGCTCAAGC
*
3122624 AGCAGCCTAAGAACGTGCCTGAGATCCGTAATTTTCTGGGACTGGGTGGATATTATTGACGATTT
1 AGCAGCCTAAGAACGTGCCTGAGATCCGTAATTTTCTGGGACTGGATGGATATTATTGACGATTT
* *
3122689 GTAGAGGG-TTTTTTATTGATTGCAGCACCCTTGACTAAGCTGCTACGTAAGGATGTACTGTTTA
66 GTAGAGGGTTTTTTTATTGATTGCAGCACCCTTGACTAAGCTGCTACGTAAGGATGAACCGTTTA
* *
3122753 ACTGGACTGATGCGCAGCAAGAGAGCTTTGAAAGCTCAAG
131 ACTAGACTGATGCACAGCAAGAGAGCTTTGAAAGCTCAAG
3122793 ACTGTACTAA
Statistics
Matches: 162, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
170 90 0.56
171 72 0.44
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (171 bp):
AGCAGCCTAAGAACGTGCCTGAGATCCGTAATTTTCTGGGACTGGATGGATATTATTGACGATTT
GTAGAGGGTTTTTTTATTGATTGCAGCACCCTTGACTAAGCTGCTACGTAAGGATGAACCGTTTA
ACTAGACTGATGCACAGCAAGAGAGCTTTGAAAGCTCAAGC
Found at i:3128802 original size:42 final size:42
Alignment explanation
Indices: 3128721--3128803 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3128711 TTTATCTTAG
* * * * *
3128721 AAAAAGAATTTTAAAAAGGAGAAGACAATCTTGGGTTGTTGA
1 AAAAAGAATTTAAAAAAGGAAAAGAAAATCATGGATTGTTGA
3128763 AAAAAGAATTTAAAAAAGGAAAAGATAAAT-ATGGATTGTTG
1 AAAAAGAATTTAAAAAAGGAAAAGA-AAATCATGGATTGTTG
3128804 GATTTACCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (42 bp):
AAAAAGAATTTAAAAAAGGAAAAGAAAATCATGGATTGTTGA
Found at i:3134331 original size:25 final size:25
Alignment explanation
Indices: 3134277--3134334 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3134267 TCTGTAAATT
* *
3134277 CTTTATGGCGATCTCTCTAAAAAGC
1 CTTTGTGGCAATCTCTCTAAAAAGC
**
3134302 CTTTGTGGCAATCTCTCTGGAAAGC
1 CTTTGTGGCAATCTCTCTAAAAAGC
3134327 CTTTGTGG
1 CTTTGTGG
3134335 TATATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (25 bp):
CTTTGTGGCAATCTCTCTAAAAAGC
Found at i:3134345 original size:25 final size:25
Alignment explanation
Indices: 3134297--3134372 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
3134287 ATCTCTCTAA
*
3134297 AAAGCCTTTGTGGCAATCTCTCTGG
1 AAAGCCTTTGTGGCAATCTATCTGG
*
3134322 AAAGCCTTTGTGGTATAT-TATCTGG
1 AAAGCCTTTGTGGCA-ATCTATCTGG
* * *
3134347 AGAGCCTTGGTGACAAGTC-ATCTGG
1 AAAGCCTTTGTGGCAA-TCTATCTGG
3134372 A
1 A
3134373 GAACCTATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.02
25 39 0.93
26 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (25 bp):
AAAGCCTTTGTGGCAATCTATCTGG
Found at i:3150744 original size:35 final size:36
Alignment explanation
Indices: 3150543--3150767 Score: 174
Period size: 37 Copynumber: 6.3 Consensus size: 36
3150533 CCACACATAT
* * * * * *
3150543 AGGGAGGCTTACGAGAGGTCCTACTCTCAGCACATA
1 AGGGAGGCTTATGAGAGGTCTTGCTCCCAACACATG
** * * * * *
3150579 AGGAGATACTTATGGGAGGTCCTGCTCCTAATATATGG
1 AGG-GAGGCTTATGAGAGGTCTTGCTCCCAACACAT-G
* *
3150617 AGGGCA--CTTATGAGGGGTCCTGCTCCCAACACAT-
1 AGGG-AGGCTTATGAGAGGTCTTGCTCCCAACACATG
* * *
3150651 AGGG-GGCTTATGGGAGGTCCTGCTCCCAACACAAAG
1 AGGGAGGCTTATGAGAGGTCTTGCTCCCAACAC-ATG
* *
3150687 GGGGAGGCTTATGAGAGGTCTTGCTTCCAACACATG
1 AGGGAGGCTTATGAGAGGTCTTGCTCCCAACACATG
*
3150723 AGGGAGGCTTA-GAGAGATCTTGCTCCCAACACATG
1 AGGGAGGCTTATGAGAGGTCTTGCTCCCAACACATG
3150758 -GCGGAGGCTT
1 AG-GGAGGCTT
3150768 GCAAGAGAAA
Statistics
Matches: 153, Mismatches: 27, Indels: 19
0.77 0.14 0.10
Matches are distributed among these distances:
34 29 0.19
35 31 0.20
36 41 0.27
37 48 0.31
38 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.22
Consensus pattern (36 bp):
AGGGAGGCTTATGAGAGGTCTTGCTCCCAACACATG
Found at i:3150764 original size:71 final size:71
Alignment explanation
Indices: 3150623--3150767 Score: 186
Period size: 71 Copynumber: 2.0 Consensus size: 71
3150613 ATGGAGGGCA
* * *
3150623 CTTATGAGGGGTCCTGCTCCCAACACATAGGGGGCTTATGGGAGGTCCTGCTCCCAACACAAAGG
1 CTTATGAGAGGTCCTGCTCCCAACACATAGGGGGCTTATGAGAGATCCTGCTCCCAACACAAAGG
*
3150688 GGGAGG
66 CGGAGG
* * * *
3150694 CTTATGAGAGGTCTTGCTTCCAACACATGAGGGAGGCTTA-GAGAGATCTTGCTCCCAACAC-AT
1 CTTATGAGAGGTCCTGCTCCCAACACAT-AGGG-GGCTTATGAGAGATCCTGCTCCCAACACAAA
3150757 GGCGGAGG
64 GGCGGAGG
3150765 CTT
1 CTT
3150768 GCAAGAGAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 36 0.56
72 22 0.34
73 6 0.09
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.21
Consensus pattern (71 bp):
CTTATGAGAGGTCCTGCTCCCAACACATAGGGGGCTTATGAGAGATCCTGCTCCCAACACAAAGG
CGGAGG
Found at i:3154245 original size:21 final size:21
Alignment explanation
Indices: 3154205--3154261 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3154195 GGTGGATCAA
* *
3154205 CTCTTATGAGCTTTTGTTCAG
1 CTCTTATGAGCTTCTATTCAG
* *
3154226 TTTTTATGAGCTTCTATTCAG
1 CTCTTATGAGCTTCTATTCAG
*
3154247 CTCTTATGAACTTCT
1 CTCTTATGAGCTTCT
3154262 GTTGGCGTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (21 bp):
CTCTTATGAGCTTCTATTCAG
Found at i:3154330 original size:40 final size:39
Alignment explanation
Indices: 3154243--3154342 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 39
3154233 GAGCTTCTAT
*
3154243 TCAGCTCTTATGAACTTCTGTTGGCGTGTTTCAGATGAC
1 TCAGCTCTTATGAACTTCTGTTGGCGTATTTCAGATGAC
* * * * *
3154282 CCAACTCTTATGAGCTTTTGTTTGGCGTATTTCAGTTGGA-
1 TCAGCTCTTATGAACTTCTG-TTGGCGTATTTCAGAT-GAC
*
3154322 TCAGCTCTTATGAATTTCTGT
1 TCAGCTCTTATGAACTTCTGT
3154343 CTGGTGTGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
39 17 0.35
40 29 0.60
41 2 0.04
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (39 bp):
TCAGCTCTTATGAACTTCTGTTGGCGTATTTCAGATGAC
Found at i:3171244 original size:2 final size:2
Alignment explanation
Indices: 3171237--3171267 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3171227 AGATAGCGAT
*
3171237 AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3171268 TTGGGACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3174412 original size:284 final size:285
Alignment explanation
Indices: 3173902--3174450 Score: 976
Period size: 284 Copynumber: 1.9 Consensus size: 285
3173892 AATGTGTCCA
3173902 TTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGGAAAGCAAAGAG
1 TTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGG-AAGCAAAGAG
* *
3173967 CAAAACTATCAGTAACAACATTGAAAACAGAACAGTTATATAAATCTTTAGCGCTCCATAGCTCA
65 CAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCA
* * *
3174032 GCTTTACAACTAGACAAATTCAAAGATAAATTAGTAACTGTATCTCAACTTTGACCCACAAGTTT
130 GCTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTC
3174097 ATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
195 ATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
3174162 ATAAATCTTTAGCAATTTCTCTTTTT
260 ATAAATCTTTAGCAATTTCTCTTTTT
* * *
3174188 TTTTTTTTTTGGTCAAATAAGATATTTACTCATAGCAATTTC-TCAAGAAAGTGG-AGCAAATAG
1 TTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGT-AAGAAAGAGGAAGCAAAGAG
3174251 CAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCA
65 CAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCA
*
3174316 GCTTTAAAACTAGGCAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTC
130 GCTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTC
*
3174381 ATCTTCTTCCATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
195 ATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
3174446 ATAAA
260 ATAAA
3174451 GGGAAACCCA
Statistics
Matches: 252, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
284 201 0.80
285 1 0.00
286 50 0.20
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (285 bp):
TTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGGAAGCAAAGAGC
AAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCAG
CTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTCA
TCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACAA
TAAATCTTTAGCAATTTCTCTTTTT
Found at i:3175209 original size:29 final size:28
Alignment explanation
Indices: 3175177--3175232 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3175167 GAAATTTTTT
*
3175177 TATAAAAATAGTAAAAAATTTATAAAATA
1 TATAAAAATA-TAAAAAAATTATAAAATA
*
3175206 TATAGAAATATAAAAAAATTATAAAAT
1 TATAAAAATATAAAAAAATTATAAAAT
3175233 TTTCTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (28 bp):
TATAAAAATATAAAAAAATTATAAAATA
Found at i:3175480 original size:16 final size:16
Alignment explanation
Indices: 3175459--3175489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3175449 TTTTATAAAA
3175459 TTTTACAATTTTTATT
1 TTTTACAATTTTTATT
*
3175475 TTTTACGATTTTTAT
1 TTTTACAATTTTTAT
3175490 AAAAAAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTACAATTTTTATT
Found at i:3175552 original size:16 final size:16
Alignment explanation
Indices: 3175493--3175596 Score: 70
Period size: 18 Copynumber: 6.0 Consensus size: 16
3175483 TTTTTATAAA
*
3175493 AAAATTCTAATT-TTTA
1 AAAATT-TAATTATTTT
3175509 ATAAATTTAATTAATTTTCT
1 A-AAATTTAATT-A-TTT-T
3175529 AAAATTTAATTATTTT
1 AAAATTTAATTATTTT
*
3175545 AAATTTTAATTATTTTTCT
1 AAAATTTAATTA--TTT-T
3175564 AAAATTT-ATTATTTTTCT
1 AAAATTTAATTA--TTT-T
3175582 AAAATTT-ATTATTTT
1 AAAATTTAATTATTTT
3175597 TTTATTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 17
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.01
16 21 0.27
17 8 0.10
18 26 0.34
19 20 0.26
20 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
AAAATTTAATTATTTT
Found at i:3175553 original size:35 final size:33
Alignment explanation
Indices: 3175528--3175596 Score: 63
Period size: 35 Copynumber: 2.0 Consensus size: 33
3175518 ATTAATTTTC
*
3175528 TAAAATTTAATTA-TTT-TAAATTTTAATTATTTTT
1 TAAAATTTAATTATTTTCTAAAATTT-ATTA--TTT
3175562 CTAAAATTT-ATTATTTTTCTAAAATTTATTATTT
1 -TAAAATTTAATTA-TTTTCTAAAATTTATTATTT
3175596 T
1 T
3175597 TTTATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
33 1 0.03
34 7 0.23
35 8 0.27
36 7 0.23
37 7 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (33 bp):
TAAAATTTAATTATTTTCTAAAATTTATTATTT
Found at i:3175606 original size:18 final size:18
Alignment explanation
Indices: 3175511--3175597 Score: 108
Period size: 18 Copynumber: 4.8 Consensus size: 18
3175501 AATTTTTAAT
*
3175511 AAATTTAATTAATTTTCTA
1 AAATTT-ATTATTTTTCTA
3175530 AAATTTA--ATTATTT-TA
1 AAATTTATTATT-TTTCTA
*
3175546 AATTTTAATTATTTTTCTA
1 AAATTT-ATTATTTTTCTA
3175565 AAATTTATTATTTTTCTA
1 AAATTTATTATTTTTCTA
3175583 AAATTTATTATTTTT
1 AAATTTATTATTTTT
3175598 TTATTATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.15
17 4 0.07
18 31 0.52
19 16 0.27
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTATTATTTTTCTA
Found at i:3175765 original size:108 final size:109
Alignment explanation
Indices: 3175651--3175864 Score: 297
Period size: 108 Copynumber: 2.0 Consensus size: 109
3175641 TTTTTGAAAA
* *
3175651 ATTTTGAGGGTCTTTGTGATGCATTTTGAAAGTTCAAATACTCAATTGAGTG-GAAAAAAA-AGG
1 ATTTTGAGGGTCTTTGTGATGCATTTTGAAAGTTCAAATACTCAATTAAGTGCAAAAAAAATAGG
* *
3175714 GGCTTAATTACTTTTTTTTAAGAAGTTTAAGGGTCTTTTTGATGC
66 GGCTTAATTACTTTTTTTGAAAAAGTTTAAGGG-CTTTTTGATGC
* * *
3175759 ATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTGCTCAATTAAGTGCAAAAAAAATTGA
1 ATTTTGAGGGTCTTTGTGATGCATTTTGAAAGTTCAAATACTCAATTAAGTGCAAAAAAAA-T-A
* * *
3175824 GGGGCTTGATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTT
64 GGGGCTTAATTACTTTTTTTGAAAAAGTTTAAGGGCTTTTT
3175865 ACACCATTAA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
108 48 0.52
109 7 0.08
111 6 0.07
112 31 0.34
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (109 bp):
ATTTTGAGGGTCTTTGTGATGCATTTTGAAAGTTCAAATACTCAATTAAGTGCAAAAAAAATAGG
GGCTTAATTACTTTTTTTGAAAAAGTTTAAGGGCTTTTTGATGC
Found at i:3175768 original size:22 final size:22
Alignment explanation
Indices: 3175743--3175787 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3175733 AAGAAGTTTA
3175743 AGGGTCTTTTTGATGCATTTTG
1 AGGGTCTTTTTGATGCATTTTG
3175765 AGGGTCTTTTTGATGCATTTTG
1 AGGGTCTTTTTGATGCATTTTG
3175787 A
1 A
3175788 AAGTTCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.49
Consensus pattern (22 bp):
AGGGTCTTTTTGATGCATTTTG
Found at i:3175990 original size:18 final size:19
Alignment explanation
Indices: 3175967--3176009 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3175957 TTACTATTAC
* *
3175967 TATTTTTGAT-TTTTTTTA
1 TATTTTTCATATTTTTATA
3175985 TA-TTTTCATATTTTTATA
1 TATTTTTCATATTTTTATA
3176003 TATTTTT
1 TATTTTT
3176010 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 11 0.52
19 4 0.19
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TATTTTTCATATTTTTATA
Found at i:3176386 original size:19 final size:20
Alignment explanation
Indices: 3176348--3176393 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3176338 TAATATTTTC
* *
3176348 TCATAAAAGGATATTCAAAA
1 TCATAAAAGAATATTAAAAA
3176368 TCATAAAA-AATATTAAAAA
1 TCATAAAAGAATATTAAAAA
*
3176387 TTATAAA
1 TCATAAA
3176394 TTATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (20 bp):
TCATAAAAGAATATTAAAAA
Found at i:3176451 original size:21 final size:21
Alignment explanation
Indices: 3176427--3176466 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3176417 AAACATATTT
*
3176427 AAAATTTTATAAAA-TTATATA
1 AAAATCTTA-AAAAGTTATATA
3176448 AAAATCTTAAAAAGTTATA
1 AAAATCTTAAAAAGTTATA
3176467 ATAATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATCTTAAAAAGTTATATA
Found at i:3176565 original size:32 final size:29
Alignment explanation
Indices: 3176525--3176590 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
3176515 AATAATTTGC
*
3176525 AAAAATTTATAAATTTAATAAAAATATATTT
1 AAAAATTTA-AAATTTAATAAAAA-ATATAT
*
3176556 AAAATATTTAAAATTTTATAAAAAATATAT
1 AAAA-ATTTAAAATTTAATAAAAAATATAT
3176586 AAAAA
1 AAAAA
3176591 ATCATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 1 0.03
30 9 0.28
31 17 0.53
32 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTAAAATTTAATAAAAAATATAT
Found at i:3176567 original size:21 final size:21
Alignment explanation
Indices: 3176542--3176600 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3176532 TATAAATTTA
3176542 ATAAAAATATATTTAAAATAT
1 ATAAAAATATATTTAAAATAT
* * * **
3176563 TTAAAATTTTATAAAAAATAT
1 ATAAAAATATATTTAAAATAT
3176584 ATAAAAA-ATCATTTAAA
1 ATAAAAATAT-ATTTAAA
3176601 CCCCTAAAAT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAAATATATTTAAAATAT
Found at i:3176589 original size:10 final size:10
Alignment explanation
Indices: 3176364--3176590 Score: 61
Period size: 10 Copynumber: 23.4 Consensus size: 10
3176354 AAGGATATTC
3176364 AAAATCATA-A
1 AAAAT-ATATA
3176374 AAAATAT-TA
1 AAAATATATA
3176383 AAAAT-TAT-
1 AAAATATATA
3176391 -AAAT-TAT-
1 AAAATATATA
* *
3176398 AAATTTTATA
1 AAAATATATA
*
3176408 AAATTA-ATA
1 AAAATATATA
*
3176417 AAACATATTTA
1 AAA-ATATATA
* *
3176428 AAATTTTATA
1 AAAATATATA
*
3176438 AAATTATATA
1 AAAATATATA
*
3176448 AAAATCT-TA
1 AAAATATATA
3176457 AAAAGT-TATA
1 AAAA-TATATA
* *
3176467 ATAATCAATCATT
1 AAAAT--AT-ATA
* *
3176480 AAAACATATG
1 AAAATATATA
*
3176490 AAAAT-CATA
1 AAAATATATA
3176499 AAAAT-TAT-
1 AAAATATATA
3176507 AAAAT-TATA
1 AAAATATATA
* * **
3176516 ATAATTTGCA
1 AAAATATATA
*
3176526 AAAATTTATA
1 AAAATATATA
**
3176536 AATTTA-ATA
1 AAAATATATA
*
3176545 AAAATATATTT
1 AAAATATA-TA
*
3176556 AAAATATTTA
1 AAAATATATA
* *
3176566 AAATTTTATAA
1 AAAATATAT-A
3176577 AAAATATATA
1 AAAATATATA
3176587 AAAA
1 AAAA
3176591 ATCATTTAAA
Statistics
Matches: 161, Mismatches: 38, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
7 7 0.04
8 12 0.07
9 46 0.29
10 67 0.42
11 23 0.14
12 1 0.01
13 5 0.03
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAATATATA
Found at i:3176592 original size:32 final size:31
Alignment explanation
Indices: 3176525--3176600 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
3176515 AATAATTTGC
**
3176525 AAAA-ATTTATAAATTTAATAAAAATATATTT
1 AAAATATTTA-AAATTTAATAAAAATATATAA
*
3176556 AAAATATTTAAAATTTTATAAAAAATATATAA
1 AAAATATTTAAAATTTAAT-AAAAATATATAA
3176588 AAAATCATTTAAA
1 AAAAT-ATTTAAA
3176601 CCCCTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 12 0.31
32 20 0.51
33 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
AAAATATTTAAAATTTAATAAAAATATATAA
Found at i:3180869 original size:31 final size:31
Alignment explanation
Indices: 3180830--3180903 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
3180820 AAGGAATCTG
* *
3180830 GTGAGTGGTTATTTGTGGGACTTAGAGGGAT
1 GTGAGTGGTTAATTATGGGACTTAGAGGGAT
* *
3180861 GTGGGTGGTTAATTATGGGACTTAGTGGGAT
1 GTGAGTGGTTAATTATGGGACTTAGAGGGAT
3180892 GTGAGTGGTTAA
1 GTGAGTGGTTAA
3180904 GAAATTATCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.03, G:0.42, T:0.35
Consensus pattern (31 bp):
GTGAGTGGTTAATTATGGGACTTAGAGGGAT
Found at i:3187187 original size:16 final size:14
Alignment explanation
Indices: 3187155--3187198 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3187145 CTTGGTTTTT
3187155 TCTTCTTTTTTTCTC
1 TCTT-TTTTTTTCTC
*
3187170 TCTTTTTTTTTCTT
1 TCTTTTTTTTTCTC
*
3187184 TCTCTTTTTTTCTC
1 TCTTTTTTTTTCTC
3187198 T
1 T
3187199 ATATGCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTTTTTCTC
Found at i:3187195 original size:10 final size:10
Alignment explanation
Indices: 3187150--3187198 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
3187140 GTTTTCTTGG
3187150 TTTTTTCTTCT
1 TTTTTTC-TCT
3187161 TTTTTTCTCT
1 TTTTTTCTCT
*
3187171 CTTTTT-T-T
1 TTTTTTCTCT
*
3187179 TTCTTTCTCT
1 TTTTTTCTCT
3187189 TTTTTTCTCT
1 TTTTTTCTCT
3187199 ATATGCGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 18 0.56
11 7 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:3187863 original size:27 final size:28
Alignment explanation
Indices: 3187833--3187891 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
3187823 TGGTAAATGA
*
3187833 TTTATTTTTAAGT-TATTTATATATT-AT
1 TTTATTTTT-AGTCGATTTATATATTAAT
*
3187860 TTTATTTTTAGTCGCTTTATATATTAAT
1 TTTATTTTTAGTCGATTTATATATTAAT
3187888 TTTA
1 TTTA
3187892 AAATTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 19 0.68
28 6 0.21
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTATTTTTAGTCGATTTATATATTAAT
Found at i:3193740 original size:13 final size:13
Alignment explanation
Indices: 3193722--3193751 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3193712 TTTGAGTAAA
3193722 AAAATGAAAAATG
1 AAAATGAAAAATG
3193735 AAAATGAAAAATG
1 AAAATGAAAAATG
3193748 AAAA
1 AAAA
3193752 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:3193754 original size:8 final size:7
Alignment explanation
Indices: 3193721--3193760 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
3193711 CTTTGAGTAA
3193721 AAAAATG
1 AAAAATG
3193728 AAAAATG
1 AAAAATG
3193735 -AAAATG
1 AAAAATG
3193741 AAAAATG
1 AAAAATG
3193748 AAAAAATG
1 -AAAAATG
3193756 AAAAA
1 AAAAA
3193761 GTAAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:3197261 original size:18 final size:18
Alignment explanation
Indices: 3197218--3197261 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3197208 GAATTGCAAG
*
3197218 TTTTCATTTTCATTTCCA
1 TTTTCATTCTCATTTCCA
**
3197236 TTCCCATTCTCATTTCCA
1 TTTTCATTCTCATTTCCA
3197254 TTTTCATT
1 TTTTCATT
3197262 TTTGGAAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTCATTCTCATTTCCA
Found at i:3197262 original size:12 final size:12
Alignment explanation
Indices: 3197218--3197262 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3197208 GAATTGCAAG
*
3197218 TTTTCATTTTCA
1 TTTTCATTTCCA
* *
3197230 TTTCCATTCCCA
1 TTTTCATTTCCA
*
3197242 TTCTCATTTCCA
1 TTTTCATTTCCA
3197254 TTTTCATTT
1 TTTTCATTT
3197263 TTGGAAACTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTCATTTCCA
Found at i:3200920 original size:23 final size:22
Alignment explanation
Indices: 3200894--3200945 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
3200884 TTTTTTTGAA
*
3200894 AATATTTATATTATTTTTAATTT
1 AATATTTAT-TTATTTATAATTT
3200917 AATACTTTATTTATTTATAATTT
1 AATA-TTTATTTATTTATAATTT
3200940 ATATAT
1 A-ATAT
3200946 AGATATCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTATTTATTTATAATTT
Found at i:3204425 original size:29 final size:29
Alignment explanation
Indices: 3204391--3204453 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
3204381 AATAAAATAT
3204391 TATCTAGATAAACATTAAATTAAATTTAA
1 TATCTAGATAAACATTAAATTAAATTTAA
*
3204420 TATCTAGATAAATATTAAATTAAATTTAA
1 TATCTAGATAAACATTAAATTAAATTTAA
3204449 TATCT
1 TATCT
3204454 CATATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (29 bp):
TATCTAGATAAACATTAAATTAAATTTAA
Found at i:3204437 original size:24 final size:23
Alignment explanation
Indices: 3204409--3204484 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
3204399 TAAACATTAA
3204409 ATTAAATTTAATATCTAGATAAAT
1 ATTAAA-TTAATATCTAGATAAAT
*
3204433 ATTAAATTAA-ATTTA-AT--AT
1 ATTAAATTAATATCTAGATAAAT
* * *
3204452 CTCATATTAATATCTAGATAAAT
1 ATTAAATTAATATCTAGATAAAT
3204475 ATTAAATTAA
1 ATTAAATTAA
3204485 ATTCATTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 9 0.22
20 4 0.10
21 4 0.10
22 4 0.10
23 13 0.32
24 6 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (23 bp):
ATTAAATTAATATCTAGATAAAT
Found at i:3204501 original size:37 final size:41
Alignment explanation
Indices: 3204418--3204501 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
3204408 AATTAAATTT
* * **
3204418 AATATCTAGATAAATATTAAATTAAATTTAATATCTCATATT
1 AATATCTAGATAAATATTAAATTAAATTT-ACATCTCAAAAC
3204460 AATATCTAGATAAATATTAAATTAAA-TT-CAT-T-AAAAC
1 AATATCTAGATAAATATTAAATTAAATTTACATCTCAAAAC
3204497 AATAT
1 AATAT
3204502 TATCTTTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 7 0.18
38 1 0.03
39 2 0.05
41 2 0.05
42 26 0.68
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (41 bp):
AATATCTAGATAAATATTAAATTAAATTTACATCTCAAAAC
Found at i:3206606 original size:22 final size:22
Alignment explanation
Indices: 3206572--3206652 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
3206562 TATTTATCCC
* *
3206572 TACTAAACCCTCATGGCTAACG
1 TACTAAGCTCTCATGGCTAACG
3206594 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGGCTAACG
** *
3206616 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGGCTAACG
3206638 TACTAAGCTCTCATG
1 TACTAAGCTCTCATG
3206653 TTTGAACGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (22 bp):
TACTAAGCTCTCATGGCTAACG
Found at i:3206653 original size:22 final size:22
Alignment explanation
Indices: 3206589--3206660 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
3206579 CCCTCATGGC
**
3206589 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGTT
3206611 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
*
3206633 TCACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGTT
3206655 TGAACG
1 T-AACG
3206661 GTCAAATCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 42 0.93
23 3 0.07
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGTT
Found at i:3207613 original size:42 final size:42
Alignment explanation
Indices: 3207567--3207650 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
3207557 ACTTTAAGTC
*
3207567 TAATAAACCTAAATTAATTTATAATTAA-ATTTAAATGTCAAT
1 TAATAAACCTAAATTAAATTATAA-TAATATTTAAATGTCAAT
* *
3207609 TAATAAATCTAAATTAAATTATAATAATATTTAGATGTCAAT
1 TAATAAACCTAAATTAAATTATAATAATATTTAAATGTCAAT
3207651 ACACTTTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (42 bp):
TAATAAACCTAAATTAAATTATAATAATATTTAAATGTCAAT
Found at i:3209029 original size:19 final size:20
Alignment explanation
Indices: 3208992--3209056 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
3208982 ATAAAAGTTT
*
3208992 TAAAAAATATATTTAAAAAAA
1 TAAAAAATATCTTT-AAAAAA
*
3209013 TAAAAAA-CTCTTT-AAAAA
1 TAAAAAATATCTTTAAAAAA
*
3209031 TAAAAAATATTTTTAAAAATA
1 TAAAAAATATCTTTAAAAA-A
3209052 TAAAA
1 TAAAA
3209057 GATGCTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 12 0.32
19 4 0.11
20 8 0.22
21 13 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAAATATCTTTAAAAAA
Found at i:3209031 original size:18 final size:19
Alignment explanation
Indices: 3208992--3209056 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 19
3208982 ATAAAAGTTT
*
3208992 TAAAAAATATATTTAAAAAAA
1 TAAAAAATATCTTT--AAAAA
*
3209013 TAAAAAA-CTCTTTAAAAA
1 TAAAAAATATCTTTAAAAA
*
3209031 TAAAAAATATTTTTAAAAA
1 TAAAAAATATCTTTAAAAA
3209050 TATAAAA
1 TA-AAAA
3209057 GATGCTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 12 0.32
19 11 0.29
20 8 0.21
21 7 0.18
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAATATCTTTAAAAA
Found at i:3209928 original size:35 final size:35
Alignment explanation
Indices: 3209882--3209951 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3209872 TGACACCCAA
*
3209882 ATCTCCTCTTCCCTAAAATATATTAATCATTTTCT
1 ATCTCCTCTTCCCTAAAATATATTAATAATTTTCT
3209917 ATCTCCTCTTCCCTAAAATATATTAATAATTTTCT
1 ATCTCCTCTTCCCTAAAATATATTAATAATTTTCT
3209952 CGAGAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (35 bp):
ATCTCCTCTTCCCTAAAATATATTAATAATTTTCT
Found at i:3216823 original size:20 final size:19
Alignment explanation
Indices: 3216794--3216833 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3216784 TCTTTTCAAG
3216794 TTTCACATCTCATTTCATCA
1 TTTCACATCTCATTTC-TCA
*
3216814 TTTCATATCTCATTTCTCA
1 TTTCACATCTCATTTCTCA
3216833 T
1 T
3216834 AATTCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCACATCTCATTTCTCA
Found at i:3218089 original size:3 final size:3
Alignment explanation
Indices: 3218081--3218145 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
3218071 ATGCATCCAC
3218081 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3218129 ATT ATT GTT ATT GTT AT
1 ATT ATT ATT ATT ATT AT
3218146 ATAACATAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3220556 original size:20 final size:20
Alignment explanation
Indices: 3220512--3220564 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
3220502 AGAAAAAGCT
*
3220512 GATTTAAAAAAAAAAGAAACC
1 GATTTAAAAAAAAAACAAA-C
3220533 GATTTAAAAAAAAGAACAAA-
1 GATTTAAAAAAAA-AACAAAC
*
3220553 GATTCAAAAAAA
1 GATTTAAAAAAA
3220565 TAAATTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 13 0.45
22 5 0.17
ACGTcount: A:0.68, C:0.08, G:0.09, T:0.15
Consensus pattern (20 bp):
GATTTAAAAAAAAAACAAAC
Found at i:3221306 original size:3 final size:3
Alignment explanation
Indices: 3221298--3221337 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
3221288 AAATTTGATG
* *
3221298 TTA TTA TTA TTA TTA TTA TTA TCA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3221338 ATTTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3221375 original size:25 final size:27
Alignment explanation
Indices: 3221336--3221415 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 27
3221326 TATTATTATT
*
3221336 ATATTTATATTTATATTTACTTATTTAA
1 ATATTAATA-TTATATTTACTTATTTAA
* * *
3221364 ATTTTAA-A-TATATTTGTCTTA-TTAT
1 ATATTAATATTATATTT-ACTTATTTAA
3221389 ATATTAATATTATTATTTACTTATTTA
1 ATATTAATATTA-TATTTACTTATTTA
3221416 TATCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
25 16 0.39
26 5 0.12
27 7 0.17
28 13 0.32
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTAATATTATATTTACTTATTTAA
Found at i:3222746 original size:30 final size:30
Alignment explanation
Indices: 3222693--3222774 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
3222683 GGATAACCTC
* * * **
3222693 GATATAATTTCAACTTGTTTGAGCAATTCT
1 GATATAATGTCAGCTTGTGTGAGCAACCCT
* *
3222723 GTTATAATGTCAGTTTGTGTGAGCAACCCT
1 GATATAATGTCAGCTTGTGTGAGCAACCCT
*
3222753 GATATACTGTCAGCTTGTGTGA
1 GATATAATGTCAGCTTGTGTGA
3222775 ACATCATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (30 bp):
GATATAATGTCAGCTTGTGTGAGCAACCCT
Found at i:3236939 original size:20 final size:20
Alignment explanation
Indices: 3236916--3236990 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
3236906 GTATGTTCCC
3236916 ATTAACTTATGTTAATTAAG
1 ATTAACTTATGTTAATTAAG
3236936 ATTATGAC-TA-GTTAATTAAG
1 ATTA--ACTTATGTTAATTAAG
* * *
3236956 ATTTAGTT-TAATTAATTAAG
1 ATTAACTTAT-GTTAATTAAG
3236976 ATTAA-TTAATGTTAA
1 ATTAACTT-ATGTTAA
3236991 AAAAAGTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 34 0.79
21 3 0.07
22 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTAACTTATGTTAATTAAG
Found at i:3247996 original size:28 final size:30
Alignment explanation
Indices: 3247958--3248027 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
3247948 GGTGGTCGAA
*
3247958 TTTGGGGATTTTATG-TAAGG-TTTTTGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
3247986 TTTGGGGATTTT-TGTTTAGGATTTCTGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
3248015 TTTGGAGATTTTA
1 TTTGGGGATTTTA
3248028 GGGATTGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 16 0.44
29 18 0.50
ACGTcount: A:0.17, C:0.01, G:0.27, T:0.54
Consensus pattern (30 bp):
TTTGGGGATTTTATGTTAAGGATTTCTGAT
Found at i:3248343 original size:21 final size:19
Alignment explanation
Indices: 3248313--3248368 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
3248303 AATCTTCAAG
*
3248313 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3248332 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
3248353 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3248369 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3248390 original size:23 final size:22
Alignment explanation
Indices: 3248313--3248391 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 22
3248303 AATCTTCAAG
* *
3248313 GATATACAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
3248335 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
3248353 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
3248375 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
3248392 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 11 0.23
22 8 0.17
23 12 0.25
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:3248629 original size:21 final size:21
Alignment explanation
Indices: 3248566--3248629 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
3248556 CTCTTGCGTT
*
3248566 ATTATTTTATGTGGTTTGT-T-
1 ATTATTTTAT-TGATTTGTATA
* *
3248586 CTTATTTTGTTGATCTGTGTATA
1 ATTATTTTATTGAT-T-TGTATA
3248609 ATTATTTTATTGATTTGTATA
1 ATTATTTTATTGATTTGTATA
3248630 TTTTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
21 9 0.26
22 2 0.06
23 12 0.34
ACGTcount: A:0.20, C:0.03, G:0.16, T:0.61
Consensus pattern (21 bp):
ATTATTTTATTGATTTGTATA
Found at i:3249325 original size:3 final size:3
Alignment explanation
Indices: 3249317--3249358 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3249307 TTATCTTTTC
3249317 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3249359 GTTCTTGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3253772 original size:17 final size:17
Alignment explanation
Indices: 3253750--3253782 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3253740 ATAACTGTCC
*
3253750 GCCAAACCCTAGAGTTT
1 GCCAAAACCTAGAGTTT
3253767 GCCAAAACCTAGAGTT
1 GCCAAAACCTAGAGTT
3253783 CACCAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (17 bp):
GCCAAAACCTAGAGTTT
Found at i:3253788 original size:17 final size:17
Alignment explanation
Indices: 3253751--3253789 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3253741 TAACTGTCCG
* **
3253751 CCAAACCCTAGAGTTTG
1 CCAAAACCTAGAGTTCA
3253768 CCAAAACCTAGAGTTCA
1 CCAAAACCTAGAGTTCA
3253785 CCAAA
1 CCAAA
3253790 TGGCGAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (17 bp):
CCAAAACCTAGAGTTCA
Found at i:3265842 original size:37 final size:37
Alignment explanation
Indices: 3265785--3265911 Score: 106
Period size: 37 Copynumber: 3.6 Consensus size: 37
3265775 CTGGTTATTA
* *
3265785 TATATTATG-ATTTTAGTAAATTCATA-TAAGAATAAT
1 TATATTAAGAATTTTATTAAATT-ATATTAAGAATAAT
*
3265821 TATATTAAGAATTTTATTAAATTATATTTAATAATAAT
1 TATATTAAGAATTTTATTAAATTATA-TTAAGAATAAT
* * * **
3265859 TATGTTAA-AATATGATTAAATTAT-TT-ATCAT--T
1 TATATTAAGAATTTTATTAAATTATATTAAGAATAAT
*
3265891 TATATTAATAATTTTATTAAA
1 TATATTAAGAATTTTATTAAA
3265912 ATTTAATAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
32 8 0.10
33 10 0.13
34 4 0.05
35 2 0.03
36 11 0.14
37 26 0.34
38 16 0.21
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (37 bp):
TATATTAAGAATTTTATTAAATTATATTAAGAATAAT
Found at i:3266093 original size:45 final size:44
Alignment explanation
Indices: 3266005--3266097 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
3265995 ATTACAACAT
*
3266005 CATTCCATTCAACCAAACACAAGGATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
3266049 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
3266094 CATT
1 CATT
3266098 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 23 0.51
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:3266100 original size:16 final size:16
Alignment explanation
Indices: 3266079--3266133 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
3266069 TTGAATTACT
*
3266079 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
3266095 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
3266111 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
3266127 ATTACAG
1 ATTACAG
3266134 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:3266582 original size:31 final size:32
Alignment explanation
Indices: 3266537--3266598 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
3266527 CCATTTTAAG
*
3266537 TATACATATTGAATCAAAATTAAAGTTTCATA
1 TATACATATTGAATCAAAATCAAAGTTTCATA
*
3266569 TATACAT-TTGAATCACAATCAAAGTTTCAT
1 TATACATATTGAATCAAAATCAAAGTTTCAT
3266599 GTGTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (32 bp):
TATACATATTGAATCAAAATCAAAGTTTCATA
Found at i:3268889 original size:16 final size:16
Alignment explanation
Indices: 3268868--3268913 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
3268858 TTGAATTACT
* *
3268868 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCA
3268884 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
3268900 ATTACAGCTCTATT
1 ATTACAGCTCTATT
3268914 ATAATATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:3281635 original size:3 final size:3
Alignment explanation
Indices: 3281627--3281652 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3281617 GAGTCTAAAA
3281627 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3281653 AGGAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3281846 original size:42 final size:42
Alignment explanation
Indices: 3281777--3281890 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 42
3281767 CCCAAAAAAG
*
3281777 GCGGCTCAAATATTGATTAGAACGGGGCATGAGGTGATCTGA
1 GCGGCTCAAATATTGATTAGAATGGGGCATGAGGTGATCTGA
*
3281819 GCGGCTCAAATATTGATCAGAATGGGGCATGAGGTGATCTGA
1 GCGGCTCAAATATTGATTAGAATGGGGCATGAGGTGATCTGA
* * * * *
3281861 ACAGTTCAAATTTTGATTAGATTGGGGCAT
1 GCGGCTCAAATATTGATTAGAATGGGGCAT
3281891 ATGACGATCT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (42 bp):
GCGGCTCAAATATTGATTAGAATGGGGCATGAGGTGATCTGA
Found at i:3282838 original size:11 final size:11
Alignment explanation
Indices: 3282822--3282847 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3282812 AGCATCCTAA
3282822 ACATCATTCAC
1 ACATCATTCAC
3282833 ACATCATTCAC
1 ACATCATTCAC
3282844 ACAT
1 ACAT
3282848 GTCTGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (11 bp):
ACATCATTCAC
Found at i:3283416 original size:9 final size:9
Alignment explanation
Indices: 3283399--3283453 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
3283389 GGTTAAAAAC
3283399 TAACCGAAT
1 TAACCGAAT
*
3283408 TAACTGAAT
1 TAACCGAAT
3283417 TAACCGAAT
1 TAACCGAAT
3283426 TAACCGAAT
1 TAACCGAAT
* *
3283435 CACCCGAAT
1 TAACCGAAT
3283444 TAACCGAAT
1 TAACCGAAT
3283453 T
1 T
3283454 GAATCACTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (9 bp):
TAACCGAAT
Found at i:3283504 original size:6 final size:6
Alignment explanation
Indices: 3283493--3283521 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3283483 ACTTTTAGAC
3283493 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
3283522 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:3283545 original size:20 final size:20
Alignment explanation
Indices: 3283477--3283534 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
3283467 ATTAAATTAT
* *
3283477 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
3283498 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
3283516 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
3283535 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:3283974 original size:41 final size:43
Alignment explanation
Indices: 3283918--3284112 Score: 139
Period size: 41 Copynumber: 4.5 Consensus size: 43
3283908 AAAATAAAAG
* *
3283918 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCG-CAT-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGACATGCAA
* * * * * * *
3283959 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAAAATTACAG
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCG--ACA-TGCAA
** ** * * *
3284005 ATCTTATCTCCCT-AAGCAGTGGTGGAGCAGATCGAAGATGGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCG-ACAT-GCAA
*
3284049 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCG-CAT-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGACATGCAA
* *
3284090 GTCTTATCTCCCTGAGGTTGCAG
1 ATCTTATCTCCCTGAAGTTGCAG
3284113 CGGAGCAGAC
Statistics
Matches: 119, Mismatches: 28, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
41 53 0.45
43 3 0.03
44 18 0.15
45 30 0.25
46 15 0.13
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGACATGCAA
Found at i:3284053 original size:131 final size:131
Alignment explanation
Indices: 3283918--3284189 Score: 445
Period size: 131 Copynumber: 2.1 Consensus size: 131
3283908 AAAATAAAAG
* *
3283918 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGC
* *** * *
3283983 GGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGATGGCA
66 GGAGCAGACCGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
3284048 A
131 A
*
3284049 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTGCAGC
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGC
*
3284114 GGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
66 GGAGCAGACCGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
*
3284179 G
131 A
3284180 ATCTTATCTC
1 ATCTTATCTC
3284190 CCTAAGCAGT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (131 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGC
GGAGCAGACCGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
A
Found at i:3284189 original size:44 final size:44
Alignment explanation
Indices: 3284001--3284390 Score: 260
Period size: 44 Copynumber: 8.9 Consensus size: 44
3283991 TTGAAAAATT
*
3284001 ACAGATCTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * * ** * * * * *
3284045 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCG--CATC
1 ACAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATG
* ** * * * *
3284088 A-AG-TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACCGAAGAATT
1 ACAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAG-ATG
3284132 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * * *
3284176 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGAT-TAAAATA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * * * * * *
3284219 AAAGATCTTATCTCTCTGAAG-TGTCAGTAGAGTAGATTG--CAT-
1 ACAGATCTTATCTCCCT-AAGCAGT-AGTGGAGCAGATCGAAGATG
* ** * * *
3284261 -CAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATT
1 ACAGATCTTATCTCCCTAA-GCAGTAGTGGAGCAGATCGAAG-ATG
* * *
3284306 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCTAATATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * * * *
3284350 GCAGATCTTATCTCCCTAGGCAGTAATAGAGCAGATTGAAG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
3284391 CCAGTAATCC
Statistics
Matches: 264, Mismatches: 66, Indels: 32
0.73 0.18 0.09
Matches are distributed among these distances:
40 2 0.01
41 52 0.20
42 3 0.01
43 25 0.09
44 103 0.39
45 50 0.19
46 29 0.11
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
Found at i:3284380 original size:130 final size:130
Alignment explanation
Indices: 3284136--3284428 Score: 324
Period size: 130 Copynumber: 2.2 Consensus size: 130
3284126 AGAATTACAG
** * *
3284136 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTA
1 ATCTTATCTCCCTAAGTTGCAGTGGAGCAGACCGAAGATGACAGATCTTATCTCCCTAAGCAGTA
* * * * * * *
3284201 GTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGTCAGTAGAGTAGATTGCA-TCAG-
66 GTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAAGAGTCAATAGAGCAGATTGAAGCCAGA
* *
3284264 GTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAG
1 ATCTTATCTCCCTAA-GTTGCAGTGGAGCAGACCGAAG-ATGACAGATCTTATCTCCCTAAGCAG
* * *** *
3284329 TAGTGGAGTAGATCTAATATGGCAGATCTTATCTCCCT-AGGCAGT-AATAGAGCAGATTGAAGC
64 TAGTGGAGCAGAT-TAAAATAAAAGATCTTATCTCCCTGAAG-AGTCAATAGAGCAGATTGAAGC
3284392 CAGTA
127 CAG-A
*
3284397 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 ATCTTATCTCCCT-AAGTTGCAGTGGAGCAGA
3284429 TTAAAATAAT
Statistics
Matches: 136, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
128 14 0.10
129 18 0.13
130 51 0.38
131 24 0.18
133 27 0.20
134 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (130 bp):
ATCTTATCTCCCTAAGTTGCAGTGGAGCAGACCGAAGATGACAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAAGAGTCAATAGAGCAGATTGAAGCCAGA
Found at i:3284414 original size:174 final size:174
Alignment explanation
Indices: 3283831--3284430 Score: 608
Period size: 174 Copynumber: 3.4 Consensus size: 174
3283821 AGAATTACAA
* *
3283831 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGAAATCCTATCTCCCTGAAGTTGCA
* * ** * * * * * * *
3283896 GTGGAG-CGAATTAAAATAAAAGATCTTATCTCTCTGAA-GTTGCAGTAGAGTAGATC---GCA-
66 GTAGAGTAG-ATT-GCAT--CAGGTCTTATCTCCCT-AAGGTTGCAGTGGAGCAGACCGAAGAAT
* ** * * *
3283955 T-CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGGT-TGAAAAATTACAG
126 TACAGATCTTATCTCCCT-AAGCAGTAGTGGAGTAGATCT--AAAATGACAG
* * ** * *
3284005 ATCTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGATGGCAAATCTTATCTCTCTGAAGTTGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAG-AAATCCTATCTCCCTGAAGTTGC
* * * *
3284070 AGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACCGAAGAATTACA
65 AGTAGAGTAGATTGCATCAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATTACA
* * *
3284135 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAG
130 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCTAAAATGACAG
* * * * * *
3284180 ATCTTATCTCCCTAAGCAGTAGTGGAGCGGATT-AAAATAAAAGATCTTATCTCTCTGAAG-TGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGAA-ATCCTATCTCCCTGAAGTTG-
3284243 CAGTAGAGTAGATTGCATCAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATTAC
64 CAGTAGAGTAGATTGCATCAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATTAC
* *
3284308 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCTAATATGGCAG
129 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCTAAAATGACAG
* * * * *
3284354 ATCTTATCTCCCTAGGCAGTAATAGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGAAATCCTATCTCCCTGAAGTTGCA
* *
3284419 GTGGAGCAGATT
66 GTAGAGTAGATT
3284431 AAAATAATAG
Statistics
Matches: 354, Mismatches: 59, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
171 1 0.00
172 26 0.07
173 4 0.01
174 218 0.62
175 74 0.21
176 16 0.05
177 15 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (174 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGAAATCCTATCTCCCTGAAGTTGCA
GTAGAGTAGATTGCATCAGGTCTTATCTCCCTAAGGTTGCAGTGGAGCAGACCGAAGAATTACAG
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCTAAAATGACAG
Found at i:3284833 original size:10 final size:10
Alignment explanation
Indices: 3284820--3284847 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3284810 AAATAAATAA
3284820 AAATAAAACC
1 AAATAAAACC
3284830 AAATAAAACC
1 AAATAAAACC
3284840 AAATAAAA
1 AAATAAAA
3284848 AATAATAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAACC
Found at i:3286082 original size:19 final size:20
Alignment explanation
Indices: 3286060--3286097 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3286050 AAATTAATTG
3286060 ATTTATTATTATTA-ATTTC
1 ATTTATTATTATTATATTTC
* *
3286079 ATTTGTTGTTATTATATTT
1 ATTTATTATTATTATATTT
3286098 AATAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTATTATTATTATATTTC
Found at i:3286109 original size:2 final size:2
Alignment explanation
Indices: 3286102--3286127 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3286092 ATATTTAATA
3286102 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
3286128 CAGTACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3287637 original size:16 final size:17
Alignment explanation
Indices: 3287618--3287652 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3287608 TTTTAAGTTA
3287618 TTCA-TTTTTATTTTAT
1 TTCATTTTTTATTTTAT
*
3287634 TTCATTTTTTTTTTTAT
1 TTCATTTTTTATTTTAT
3287651 TT
1 TT
3287653 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCATTTTTTATTTTAT
Found at i:3287660 original size:17 final size:18
Alignment explanation
Indices: 3287621--3287662 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3287611 TAAGTTATTC
3287621 ATTTTTATTTTATTTCATT
1 ATTTTT-TTTTATTTCATT
*
3287640 -TTTTTTTTTATTT-TTT
1 ATTTTTTTTTATTTCATT
3287656 ATTTTTT
1 ATTTTTT
3287663 ATAAATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 14 0.67
18 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (18 bp):
ATTTTTTTTTATTTCATT
Found at i:3294236 original size:56 final size:56
Alignment explanation
Indices: 3294148--3294257 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
3294138 TCTGTTTGTG
* *
3294148 TTTCAAATTTCTTTACTTTTGTTTTCTATTTTGATGTACTCCTGATATATAGGATA
1 TTTCAAATTTCTTTACTCTTGTTTGCTATTTTGATGTACTCCTGATATATAGGATA
* * * *
3294204 TTTCAAATTTCTTTGCTCTTGTTTGCTGTTTTGGTGTACTCTTGATATATAGGA
1 TTTCAAATTTCTTTACTCTTGTTTGCTATTTTGATGTACTCCTGATATATAGGA
3294258 GTTAGTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.53
Consensus pattern (56 bp):
TTTCAAATTTCTTTACTCTTGTTTGCTATTTTGATGTACTCCTGATATATAGGATA
Found at i:3297032 original size:16 final size:17
Alignment explanation
Indices: 3297006--3297039 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3296996 TGAGGAGGCA
3297006 TATATGGTTGTTTGAAT
1 TATATGGTTGTTTGAAT
3297023 TATA-GGTTGTTTGAAT
1 TATATGGTTGTTTGAAT
3297039 T
1 T
3297040 CTATCACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (17 bp):
TATATGGTTGTTTGAAT
Found at i:3300913 original size:126 final size:124
Alignment explanation
Indices: 3300708--3301018 Score: 344
Period size: 126 Copynumber: 2.5 Consensus size: 124
3300698 AGGCTAAATT
* * * * *
3300708 CATTCTTAAAGATCAAGCTTAAAAGGCCTTTGAAG-TGAATCATCAATCCAAGGA-CAAGTTTCA
1 CATTCTTAAAGATCAAGCTTAAAAGACCCTTGAAGCAGAATCATCCATCCAA-GATCAAGTCTCA
* *
3300771 AAGACCCTTGGTTAAAAGCTTTCCCCAATCTAGTTACACCAACATAAAAAAAGATAAAAACC
65 AAGAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAAC-TAAAAAAAGAT-AAAACC
* * *
3300833 CATTCTTTAGGATCAAG-TCTAAAAGACCCTTGAAGCAGAATCTTCCATCCAAGATCAAGTCTCA
1 CATTCTTAAAGATCAAGCT-TAAAAGACCCTTGAAGCAGAATCATCCATCCAAGATCAAGTCTCA
* ** * * * *
3300897 AATAACCTTGGATAAAAGCTTTTTCCGATCTAGTTGCACCAACTCAAAGAAGATAAAACC
65 AAGAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAACTAAAAAAAGATAAAACC
* * * *
3300957 CATTCTTCAATATCAAGCTTAGAAA-ACCCTTGAAGCAAAATCGTCCATCCCAA-ATCAAGTCT
1 CATTCTTAAAGATCAAGCTTA-AAAGACCCTTGAAGCAGAATCATCCAT-CCAAGATCAAGTCT
3301019 TGACAACCTT
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
124 53 0.34
125 48 0.30
126 57 0.36
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (124 bp):
CATTCTTAAAGATCAAGCTTAAAAGACCCTTGAAGCAGAATCATCCATCCAAGATCAAGTCTCAA
AGAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAACTAAAAAAAGATAAAACC
Found at i:3301685 original size:6 final size:6
Alignment explanation
Indices: 3301674--3301704 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3301664 TGGAACGAAG
3301674 CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC C
1 CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC C
3301705 ATTATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CTTCAC
Found at i:3303839 original size:11 final size:12
Alignment explanation
Indices: 3303822--3303855 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
3303812 TTTAGTACAT
3303822 TTATATTTTATA
1 TTATATTTTATA
3303834 TT-TATTTTA-A
1 TTATATTTTATA
3303844 TTATATTTTATA
1 TTATATTTTATA
3303856 ATAGGTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.15
11 14 0.70
12 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:3310391 original size:27 final size:27
Alignment explanation
Indices: 3310305--3310391 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
3310295 TTGGTTTTGA
3310305 TTTCAGACTAGAACAATATGTATTTAT
1 TTTCAGACTAGAACAATATGTATTTAT
* * * * *
3310332 TTTCATAATA-AAGCCCA-AGGTA-ATAT
1 TTTCAGACTAGAA--CAATATGTATTTAT
3310358 GATTTCAGACTAGAACAATATGTATTTAT
1 --TTTCAGACTAGAACAATATGTATTTAT
3310387 TTTCA
1 TTTCA
3310392 TAATATGTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 5 0.12
27 19 0.44
28 14 0.33
29 5 0.12
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (27 bp):
TTTCAGACTAGAACAATATGTATTTAT
Found at i:3312679 original size:24 final size:24
Alignment explanation
Indices: 3312643--3312718 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
3312633 TGAGGGTAAG
*
3312643 ATCTGATTCTGTAGT-TGATATTGC
1 ATCTGATTCTGTA-TATGAAATTGC
*
3312667 ATCTGACTT-TGTATCTGAAATTGC
1 ATCTGA-TTCTGTATATGAAATTGC
3312691 ATCTGATTCTGTATATGAAATTGC
1 ATCTGATTCTGTATATGAAATTGC
3312715 ATCT
1 ATCT
3312719 ATATTTGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.06
24 42 0.89
25 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (24 bp):
ATCTGATTCTGTATATGAAATTGC
Found at i:3314788 original size:40 final size:39
Alignment explanation
Indices: 3314693--3314788 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 39
3314683 AACCCAAACA
** *
3314693 CAATTACCCAACCCAATAAAACTAAAACTAAAGTTTATC
1 CAATTACCCAACCCAATAAAACTAAAACTAAAGACTACC
*
3314732 CAATTACCCAATCCAATAAAACTAAAACTAAAAGACTACC
1 CAATTACCCAACCCAATAAAACTAAAACT-AAAGACTACC
3314772 CAATTTA-CCAACCCAAT
1 CAA-TTACCCAACCCAAT
3314789 TTACTAAAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 28 0.56
40 19 0.38
41 3 0.06
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (39 bp):
CAATTACCCAACCCAATAAAACTAAAACTAAAGACTACC
Found at i:3314874 original size:9 final size:9
Alignment explanation
Indices: 3314862--3314920 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
3314852 AAAATAAAAA
3314862 AATTCGGGT
1 AATTCGGGT
3314871 AATTCGGGT
1 AATTCGGGT
*
3314880 ATTTTTC-GGT
1 A--ATTCGGGT
*
3314890 AATTCGGTT
1 AATTCGGGT
3314899 AATTCGGGT
1 AATTCGGGT
3314908 AATTCGGGT
1 AATTCGGGT
3314917 AATT
1 AATT
3314921 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:3317050 original size:11 final size:12
Alignment explanation
Indices: 3317033--3317062 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3317023 TTTCTACATT
3317033 TTTCTTCAGTTC
1 TTTCTTCAGTTC
3317045 -TTCTTCAGTTC
1 TTTCTTCAGTTC
3317056 TTTCTTC
1 TTTCTTC
3317063 TTTAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.60
Consensus pattern (12 bp):
TTTCTTCAGTTC
Found at i:3317062 original size:15 final size:14
Alignment explanation
Indices: 3317042--3317075 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3317032 TTTTCTTCAG
3317042 TTCTTCTTCAGTTCT
1 TTCTTCTTCAGTT-T
*
3317057 TTCTTCTTTAGTTT
1 TTCTTCTTCAGTTT
3317071 TTCTT
1 TTCTT
3317076 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.68
Consensus pattern (14 bp):
TTCTTCTTCAGTTT
Found at i:3318226 original size:9 final size:9
Alignment explanation
Indices: 3318208--3318300 Score: 132
Period size: 9 Copynumber: 10.3 Consensus size: 9
3318198 TCAGTTGAAC
3318208 TAAATCGGT
1 TAAATCGGT
*
3318217 TAAGTCGGT
1 TAAATCGGT
*
3318226 TAAGTCGGT
1 TAAATCGGT
3318235 TAAATCGGT
1 TAAATCGGT
*
3318244 TAAATTGGT
1 TAAATCGGT
*
3318253 TAAGTCGGT
1 TAAATCGGT
*
3318262 TAAATCAGT
1 TAAATCGGT
3318271 TAAATCGGT
1 TAAATCGGT
*
3318280 TAAGTCGGT
1 TAAATCGGT
3318289 TAAATCGGT
1 TAAATCGGT
3318298 TAA
1 TAA
3318301 TTTTTAACCA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (9 bp):
TAAATCGGT
Found at i:3318238 original size:27 final size:27
Alignment explanation
Indices: 3318208--3318300 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
3318198 TCAGTTGAAC
*
3318208 TAAATCGGTTAAGTCGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
*
3318235 TAAATCGGTTAAATTGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
*
3318262 TAAATCAGTTAAATCGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
3318289 TAAATCGGTTAA
1 TAAATCGGTTAA
3318301 TTTTTAACCA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (27 bp):
TAAATCGGTTAAATCGGTTAAGTCGGT
Found at i:3320237 original size:13 final size:13
Alignment explanation
Indices: 3320219--3320244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3320209 GGTGTTTCCA
3320219 AAAACCATTTGTT
1 AAAACCATTTGTT
3320232 AAAACCATTTGTT
1 AAAACCATTTGTT
3320245 TGCGTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:3343624 original size:21 final size:21
Alignment explanation
Indices: 3343592--3343636 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3343582 AAAAAATTAG
*
3343592 AATATAATAATTAAATTAAAA
1 AATATAATAATTAAAATAAAA
3343613 AATATTAA-AATTAAAATAAAA
1 AATA-TAATAATTAAAATAAAA
3343634 AAT
1 AAT
3343637 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATAATAATTAAAATAAAA
Found at i:3349374 original size:21 final size:21
Alignment explanation
Indices: 3349331--3349440 Score: 138
Period size: 21 Copynumber: 5.3 Consensus size: 21
3349321 CAAATACGCC
3349331 AACAGAAGCTCG-AA-AGCTT
1 AACAGAAGCTCGAAAGAGCTT
* *
3349350 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGAAAGAGCTT
3349371 AACAGAAGCTCGAAAGAGCTT
1 AACAGAAGCTCGAAAGAGCTT
*
3349392 AACAGAAGCTTGAAAGAGCTT
1 AACAGAAGCTCGAAAGAGCTT
*
3349413 AACAG-AGACTC-ATAAGAGTTT
1 AACAGAAG-CTCGA-AAGAGCTT
3349434 AACAGAA
1 AACAGAA
3349441 AGTAAAACAT
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
19 12 0.15
20 5 0.06
21 62 0.77
22 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGAAAGAGCTT
Found at i:3352514 original size:2 final size:2
Alignment explanation
Indices: 3352507--3352531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3352497 TAATTTTTGG
3352507 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3352532 GCAAAGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3356364 original size:3 final size:3
Alignment explanation
Indices: 3356356--3356381 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3356346 ACGGCACCAT
3356356 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
3356382 TCACCACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:3360141 original size:77 final size:77
Alignment explanation
Indices: 3360011--3360161 Score: 257
Period size: 77 Copynumber: 2.0 Consensus size: 77
3360001 AGGATCACTT
* *
3360011 GTTGTAAGTGTTTGAAGATAGTGGATATTTCTCACTGAGCTAACCTCAGCAAACGTAGAAAAACT
1 GTTGTAAGTGTTTGAAGATAGTGGATACTTCTCACTGAGCTAACCTCAACAAACGTAGAAAAACT
3360076 GAACAACATCAA
66 GAACAACATCAA
* * *
3360088 GTTGTAAGTGTTTGAAGATAGTGGATACTTCTCATTTAGCTAGCCTCAACAAACGTAGAAAAACT
1 GTTGTAAGTGTTTGAAGATAGTGGATACTTCTCACTGAGCTAACCTCAACAAACGTAGAAAAACT
3360153 GAACAACAT
66 GAACAACAT
3360162 AAACAAACTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (77 bp):
GTTGTAAGTGTTTGAAGATAGTGGATACTTCTCACTGAGCTAACCTCAACAAACGTAGAAAAACT
GAACAACATCAA
Found at i:3365537 original size:58 final size:58
Alignment explanation
Indices: 3365447--3365559 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
3365437 GTCATAACAA
*
3365447 CATGGTACAAGGTATAAGGTATATGGCGTAAGACCAT-GAATGAAAGATGTAATGGTGG
1 CATGGTACAAGGTATAAGGTATACGGCGTAAGACCATAG-ATGAAAGATGTAATGGTGG
* * * * *
3365505 CATGGTATAATGTATGAGGTATACGGTGTAAGACCATAGATGAAAGATGTTATGG
1 CATGGTACAAGGTATAAGGTATACGGCGTAAGACCATAGATGAAAGATGTAATGG
3365560 CATCCAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 47 0.98
59 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (58 bp):
CATGGTACAAGGTATAAGGTATACGGCGTAAGACCATAGATGAAAGATGTAATGGTGG
Found at i:3370301 original size:17 final size:20
Alignment explanation
Indices: 3370271--3370311 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
3370261 ATCAAATTTT
3370271 AATA-TTTAAGT-AAA-GAA
1 AATAGTTTAAGTAAAATGAA
3370288 AATAGTTTAA-TAAAATGAA
1 AATAGTTTAAGTAAAATGAA
3370307 AATAG
1 AATAG
3370312 AGATAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (20 bp):
AATAGTTTAAGTAAAATGAA
Found at i:3373451 original size:3 final size:3
Alignment explanation
Indices: 3373443--3373485 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3373433 GAAGATGACA
*
3373443 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3373486 AGTCCTTGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:3378854 original size:20 final size:22
Alignment explanation
Indices: 3378817--3378857 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3378807 AAAAGTATTT
3378817 TTATTTTATAAAATAAATTATA
1 TTATTTTATAAAATAAATTATA
3378839 TTATTTTA-AAAA-AAATTAT
1 TTATTTTATAAAATAAATTAT
3378858 CTTTTTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATTTTATAAAATAAATTATA
Found at i:3378865 original size:20 final size:20
Alignment explanation
Indices: 3378820--3378865 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3378810 AGTATTTTTA
* *
3378820 TTTTATAAAATAAATTATAT
1 TTTTTTAAAAAAAATTATAT
* *
3378840 TATTTTAAAAAAAATTATCT
1 TTTTTTAAAAAAAATTATAT
3378860 TTTTTT
1 TTTTTT
3378866 CGTTTAATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTAAAAAAAATTATAT
Found at i:3381145 original size:17 final size:18
Alignment explanation
Indices: 3381112--3381156 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3381102 AAAGGAGGAG
*
3381112 AAGCAAGAAGCAAGAAAC
1 AAGCAAAAAGCAAGAAAC
*
3381130 AAGCAAAAAG-AAGAAAG
1 AAGCAAAAAGCAAGAAAC
3381147 AAGCATAAAA
1 AAGCA-AAAA
3381157 AAAAAATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.67, C:0.11, G:0.20, T:0.02
Consensus pattern (18 bp):
AAGCAAAAAGCAAGAAAC
Done.