Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 37 of 332
Found at i:11322702 original size:54 final size:54
Alignment explanation
Indices: 11322620--11322762 Score: 223
Period size: 54 Copynumber: 2.6 Consensus size: 54
11322610 ATGGATCAAG
* *
11322620 ATACTTCTTATGTATATAATACAGACTTTGAAGAAGTACAATTTTATTTCATTT
1 ATACTTCTTATGTATATAATATAGACTTTGGAGAAGTACAATTTTATTTCATTT
* * *
11322674 ATACTTATTATGTATATAATATAGACTTTGGAGAAGTATAGTTTTATTTCATTT
1 ATACTTCTTATGTATATAATATAGACTTTGGAGAAGTACAATTTTATTTCATTT
* *
11322728 ATGCTTCTTATGTATATAATATAGGCTTTGGAGAA
1 ATACTTCTTATGTATATAATATAGACTTTGGAGAA
11322763 ATATTGTAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (54 bp):
ATACTTCTTATGTATATAATATAGACTTTGGAGAAGTACAATTTTATTTCATTT
Found at i:11330643 original size:143 final size:143
Alignment explanation
Indices: 11330385--11330660 Score: 401
Period size: 143 Copynumber: 1.9 Consensus size: 143
11330375 AAAGCAATCT
* * * *
11330385 CACTAGAAGTGCTCTCAATAAAAATCTCTAGGTTTTTAGAAACAATACTAGTTACATAGAAGTGT
1 CACTAGAAGTGCTCTCAAAAAAAATCTCCAAGTTTTCAGAAACAATACTAGTTACATAGAAGTGT
** * * *
11330450 GTAGAACCTATGTTTATCAAAGCAGTATGAGGTACATAAAAATAAAGAACGTACCCATGATAACA
66 GTAGAACCTATGTCGATCAAAACAGTATGAAGAACATAAAAATAAAGAACGTACCCATGATAACA
11330515 TCAATACCATTAC
131 TCAATACCATTAC
* * * *
11330528 CACTAGAAGTGCTCTTAAAAAAAATCTCCAAGTTTTCAGAAATAATACTAGTTATATAGGAGTGT
1 CACTAGAAGTGCTCTCAAAAAAAATCTCCAAGTTTTCAGAAACAATACTAGTTACATAGAAGTGT
**
11330593 GTAGAACCTATGTCGATCAAAACAGTAT-AAGAACATAAAAAATAAAGAACGTACCTGTGATAAC
66 GTAGAACCTATGTCGATCAAAACAGTATGAAGAACAT-AAAAATAAAGAACGTACCCATGATAAC
11330657 ATCA
130 ATCA
11330661 GGAGCATCTC
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
142 6 0.05
143 111 0.95
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (143 bp):
CACTAGAAGTGCTCTCAAAAAAAATCTCCAAGTTTTCAGAAACAATACTAGTTACATAGAAGTGT
GTAGAACCTATGTCGATCAAAACAGTATGAAGAACATAAAAATAAAGAACGTACCCATGATAACA
TCAATACCATTAC
Found at i:11334260 original size:12 final size:12
Alignment explanation
Indices: 11334243--11334267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11334233 AGAAAAGTTA
11334243 GTAGATATTTTT
1 GTAGATATTTTT
11334255 GTAGATATTTTT
1 GTAGATATTTTT
11334267 G
1 G
11334268 GTGATTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (12 bp):
GTAGATATTTTT
Found at i:11334710 original size:26 final size:26
Alignment explanation
Indices: 11334680--11334731 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11334670 AAATTGAAGA
11334680 AAAATTTTGAATTTTATAGAATACAT
1 AAAATTTTGAATTTTATAGAATACAT
11334706 AAAATTTTGAATTTTATAGAATACAT
1 AAAATTTTGAATTTTATAGAATACAT
11334732 GTGCTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (26 bp):
AAAATTTTGAATTTTATAGAATACAT
Found at i:11340329 original size:13 final size:13
Alignment explanation
Indices: 11340311--11340335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11340301 TTTATTGGAT
11340311 TTTTGTTATTTTA
1 TTTTGTTATTTTA
11340324 TTTTGTTATTTT
1 TTTTGTTATTTT
11340336 TTTGGTTTGG
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:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTGTTATTTTA
Found at i:11340894 original size:18 final size:18
Alignment explanation
Indices: 11340871--11340908 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11340861 ATGATTATCA
11340871 TGATGATTATGGGCTAGG
1 TGATGATTATGGGCTAGG
11340889 TGATGATTATGGGCTAGG
1 TGATGATTATGGGCTAGG
11340907 TG
1 TG
11340909 TTAAGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.39, T:0.34
Consensus pattern (18 bp):
TGATGATTATGGGCTAGG
Found at i:11342879 original size:14 final size:14
Alignment explanation
Indices: 11342846--11342879 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
11342836 CAAAAGTGGC
*
11342846 TATTTGTACTAAAA
1 TATTTGTAATAAAA
11342860 TA-TTGTAATAAAA
1 TATTTGTAATAAAA
11342873 TATTTGT
1 TATTTGT
11342880 GTGAAACGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (14 bp):
TATTTGTAATAAAA
Found at i:11345029 original size:39 final size:41
Alignment explanation
Indices: 11344993--11345071 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 41
11344983 TATTACAGAT
*
11344993 TCAGATACAGTTTA-GGCCTTAACCCAT-TCAGATACAGTC
1 TCAGATACAATTTAGGGCCTTAACCCATCTCAGATACAGTC
* *
11345032 TCAGATATAATTTAGGGCCTTAGCCCATCTCAGATACAGT
1 TCAGATACAATTTAGGGCCTTAACCCATCTCAGATACAGT
11345072 ATGCATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 12 0.34
40 12 0.34
41 11 0.31
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (41 bp):
TCAGATACAATTTAGGGCCTTAACCCATCTCAGATACAGTC
Found at i:11358007 original size:13 final size:13
Alignment explanation
Indices: 11357989--11358013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11357979 AATTCGATGG
11357989 GTGGATCAATATC
1 GTGGATCAATATC
11358002 GTGGATCAATAT
1 GTGGATCAATAT
11358014 TGTCTGAAGT
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:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
GTGGATCAATATC
Found at i:11358484 original size:13 final size:13
Alignment explanation
Indices: 11358449--11358478 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11358439 CTATTGAAAT
11358449 AATATGTTAAAAC
1 AATATGTTAAAAC
*
11358462 AATATGTTAACAC
1 AATATGTTAAAAC
11358475 AATA
1 AATA
11358479 ATTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (13 bp):
AATATGTTAAAAC
Found at i:11360525 original size:42 final size:43
Alignment explanation
Indices: 11360390--11360566 Score: 178
Period size: 43 Copynumber: 4.1 Consensus size: 43
11360380 GAAAAACGCA
* * * *
11360390 GCTATAGAACATGACCTTTAGTGGCG-TTTCTCACAAAAATACC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTC-CACACAAATGCC
* * * * **
11360433 GCTATAGAACATGACCTTTAGGGGCACTTTCCTCACAAATGTT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCACACAAATGCC
* *
11360476 GTTAAAGAACATAACCTTTAGCGGCGCTTTCC-CACAAATGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCACACAAATGCC
* * * * *
11360518 GTTAAAGAACATGACTTTTAGCGACGCTTTCCCCACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCACACAAATGCC
11360561 GCTAAA
1 GCTAAA
11360567 AGTCACGTCC
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 37 0.33
43 72 0.64
44 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTCCACACAAATGCC
Found at i:11360548 original size:85 final size:86
Alignment explanation
Indices: 11360395--11360556 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 86
11360385 ACGCAGCTAT
* * * * *
11360395 AGAACATGACCTTTAGTGGCGTTTCTCACAAAAATACCGCTATAGAACATGACCTTTAGGGGCAC
1 AGAACATAACCTTTAGCGGCGTTTCTCACAAAAATACCGCTAAAGAACATGACCTTTAGCGACAC
*
11360460 TTTCCTCACAAATGTTGTTAA
66 TTTCCCCACAAATGTTGTTAA
* * * * *
11360481 AGAACATAACCTTTAGCGGCGCTTTC-C-CACAAATGCCGTTAAAGAACATGACTTTTAGCGACG
1 AGAACATAACCTTTAGCGGCG-TTTCTCACAAAAATACCGCTAAAGAACATGACCTTTAGCGACA
11360544 CTTTCCCCACAAA
65 CTTTCCCCACAAA
11360557 CGCCGCTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 40 0.62
86 20 0.31
87 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (86 bp):
AGAACATAACCTTTAGCGGCGTTTCTCACAAAAATACCGCTAAAGAACATGACCTTTAGCGACAC
TTTCCCCACAAATGTTGTTAA
Found at i:11360581 original size:43 final size:43
Alignment explanation
Indices: 11360490--11360626 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 43
11360480 AAGAACATAA
* * * *
11360490 CCTTTAGCGGCGCTTT-CCCACAAATGCCG-TTAAAGAACATGA
1 CCTTTAGCGACGCTTTCCCCACAAATGCCGCTAAAAG-TCATGT
* * *
11360532 CTTTTAGCGACGCTTTCCCCACAAACGCCGCTAAAAGTCACGT
1 CCTTTAGCGACGCTTTCCCCACAAATGCCGCTAAAAGTCATGT
* * * * *
11360575 CCTTTAGCTACTCTTTTCCCAAAAAATGCAGCTAAAAGTCATGT
1 CCTTTAGCGACGC-TTTCCCCACAAATGCCGCTAAAAGTCATGT
*
11360619 TCTTTAGC
1 CCTTTAGC
11360627 ACCATTTTTC
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 14 0.18
43 25 0.33
44 37 0.49
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (43 bp):
CCTTTAGCGACGCTTTCCCCACAAATGCCGCTAAAAGTCATGT
Found at i:11360657 original size:43 final size:44
Alignment explanation
Indices: 11360545--11360666 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 44
11360535 TTAGCGACGC
* * * * *
11360545 TTTCCCCACAAACGCCGCTAAAAGTCACGTCCTTTAGCTACTCT
1 TTTCCCAAAAAACGCAGCTAAAAGTCATGTTCTTTAGCTACTCT
*
11360589 TTTCCCAAAAAATGCAGCTAAAAGTCATGTTCTTTAGC-AC-CAT
1 TTTCCCAAAAAACGCAGCTAAAAGTCATGTTCTTTAGCTACTC-T
* *
11360632 TTTTCCTAAAAACGCTA-CTAAAAGTCATGTTCTTT
1 TTTCCCAAAAAACGC-AGCTAAAAGTCATGTTCTTT
11360667 GGCAGCGTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.01
43 33 0.49
44 33 0.49
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (44 bp):
TTTCCCAAAAAACGCAGCTAAAAGTCATGTTCTTTAGCTACTCT
Found at i:11363489 original size:39 final size:39
Alignment explanation
Indices: 11363327--11363551 Score: 267
Period size: 40 Copynumber: 5.7 Consensus size: 39
11363317 GCTACTCGTT
* *
11363327 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
11363367 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
11363407 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
* *
11363447 CAAATGCCTTC-GGATCTTAGTCCGGATTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA
* * * * *
11363486 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
11363527 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
11363552 CATCATTCAA
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 41 0.25
40 115 0.69
41 11 0.07
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:11363511 original size:119 final size:120
Alignment explanation
Indices: 11363327--11363551 Score: 287
Period size: 119 Copynumber: 1.9 Consensus size: 120
11363317 GCTACTCGTT
* *
11363327 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGG
* *
11363392 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * **
11363447 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGTAACTCGTACAAATACCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGA-CTTAACCC
* * *
11363509 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
11363552 CATCATTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 3 0.03
119 59 0.66
120 28 0.31
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:11367618 original size:19 final size:20
Alignment explanation
Indices: 11367582--11367619 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11367572 TATTTGATAC
*
11367582 TTTTATTTATATATTAAATT
1 TTTTATTTATATAATAAATT
*
11367602 TTTTATTT-TTTAATAAAT
1 TTTTATTTATATAATAAAT
11367620 AATTATTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTTATATAATAAATT
Found at i:11367785 original size:23 final size:21
Alignment explanation
Indices: 11367740--11367788 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
11367730 TTATTATTTT
* *
11367740 AGAAAATATTTTTTTATAGAA
1 AGAAAATATTGTTTTATACAA
11367761 AGAAAATATTGTTTTATCACCAA
1 AGAAAATATTGTTTTAT-A-CAA
11367784 AGAAA
1 AGAAA
11367789 TAGGTGCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.67
22 1 0.04
23 7 0.29
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (21 bp):
AGAAAATATTGTTTTATACAA
Found at i:11371654 original size:37 final size:37
Alignment explanation
Indices: 11371604--11371676 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
11371594 AAGGTATGAC
11371604 CATTTTGAGAAAAAGAGGTCTTCTTACAATCACCAGT
1 CATTTTGAGAAAAAGAGGTCTTCTTACAATCACCAGT
11371641 CATTTTGAGAAAAAGAGGTCTTCTTACAATCACCAG
1 CATTTTGAGAAAAAGAGGTCTTCTTACAATCACCAG
11371677 ATTTGGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (37 bp):
CATTTTGAGAAAAAGAGGTCTTCTTACAATCACCAGT
Found at i:11373951 original size:76 final size:76
Alignment explanation
Indices: 11373799--11373956 Score: 196
Period size: 76 Copynumber: 2.1 Consensus size: 76
11373789 GCAGTTACAT
* * *
11373799 ATATGTGTAAGTGTAAGACCATAGCTAACCTATGGCAATGTGATAAAGTGTGTGATAATGGAAAG
1 ATATGTGCAAGTGCAAGACCATAGCTAACCTATGGCAATGTGATAAAGTGTGTGATAAGGGAAAG
*
11373864 GCCACGGTAAA
66 GCCACGATAAA
* * *
11373875 ATATGTGCAAGTGCAAGACTAGT-GCTAAGCTATGGCAATGTGATAAAGTGTGTGATCAGGGCAA
1 ATATGTGCAAGTGCAAGACCA-TAGCTAACCTATGGCAATGTGATAAAGTGTGTGATAAGGG-AA
* *
11373939 A-TCCATGATAAA
64 AGGCCACGATAAA
11373951 A-ATGTG
1 ATATGTG
11373957 TGCAAAACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
75 5 0.07
76 62 0.87
77 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (76 bp):
ATATGTGCAAGTGCAAGACCATAGCTAACCTATGGCAATGTGATAAAGTGTGTGATAAGGGAAAG
GCCACGATAAA
Found at i:11387727 original size:46 final size:45
Alignment explanation
Indices: 11387652--11387827 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
11387642 TGTAACCCGC
* * * *
11387652 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTT-GCAT
* * * *
11387698 CCATGAGTGAACTCTGACTCAACTCAACGAGTTCAGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC--GTTGCAT
* * *
11387748 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC-GTTGCAT
11387791 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
11387828 TGCCCAAACA
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 2 0.02
46 59 0.55
47 26 0.24
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTGCAT
Found at i:11387818 original size:93 final size:93
Alignment explanation
Indices: 11387659--11387831 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
11387649 CGCCCATAAG
* * * * *
11387659 CGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCTGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
11387724 ACGAGTTCAGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
* *
11387752 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
11387817 ACGAGTTCGGATGCC
66 ACGAGTTCAGATGCC
11387832 CAAACATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:11393051 original size:32 final size:32
Alignment explanation
Indices: 11393015--11393079 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
11393005 TTATATGTTC
11393015 ATTCAAAGCTGTCTACTTGAGTCATTGTCACT
1 ATTCAAAGCTGTCTACTTGAGTCATTGTCACT
11393047 ATTCAAAGCTGTCTACTTGAGTCATTGTCACT
1 ATTCAAAGCTGTCTACTTGAGTCATTGTCACT
11393079 A
1 A
11393080 AATTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (32 bp):
ATTCAAAGCTGTCTACTTGAGTCATTGTCACT
Found at i:11412392 original size:46 final size:46
Alignment explanation
Indices: 11412290--11412421 Score: 124
Period size: 46 Copynumber: 2.9 Consensus size: 46
11412280 ATAATCTCAC
** * * * * *
11412290 CCATAATGAACTCGGAACGCAACTCAAAGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTCAAAACACAAATCAACGAGTTCGGATGCTT-GCAT
*
11412336 CCATAATGAACTCAGAACACAAATCAACGAGTT-GGATGCTTGCAT
1 CCATAATGAACTCAAAACACAAATCAACGAGTTCGGATGCTTGCAT
* ** *
11412381 CCATAGGTGAACTCAAAATGCAACTCAACGAGTTCGGATGC
1 CCATA-ATGAACTCAAAACACAAATCAACGAGTTCGGATGC
11412422 CTCATAATTC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 13 0.18
46 53 0.74
47 6 0.08
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAATGAACTCAAAACACAAATCAACGAGTTCGGATGCTTGCAT
Found at i:11428362 original size:11 final size:11
Alignment explanation
Indices: 11428346--11428370 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11428336 TTTGTGGTAT
11428346 ATGTTGATACA
1 ATGTTGATACA
11428357 ATGTTGATACA
1 ATGTTGATACA
11428368 ATG
1 ATG
11428371 AAGTTGGAAT
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:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (11 bp):
ATGTTGATACA
Found at i:11435469 original size:13 final size:14
Alignment explanation
Indices: 11435451--11435479 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11435441 ATGTGATTTA
11435451 AAGGTT-AATTAGT
1 AAGGTTAAATTAGT
11435464 AAGGTTAAATTAGT
1 AAGGTTAAATTAGT
11435478 AA
1 AA
11435480 TTCAATAATT
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:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (14 bp):
AAGGTTAAATTAGT
Found at i:11437883 original size:3 final size:3
Alignment explanation
Indices: 11437875--11437914 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
11437865 AATAAAAGAT
*
11437875 ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11437915 GAACAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11439060 original size:20 final size:21
Alignment explanation
Indices: 11439023--11439065 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 21
11439013 GGCTAGCTGT
11439023 GTACGGAGGTGCTGACGTGGAG
1 GTACGGAGGT-CTGACGTGGAG
11439045 GTACGGAGGT-TGACGTGGAG
1 GTACGGAGGTCTGACGTGGAG
11439065 G
1 G
11439066 AGGCAGTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.19, C:0.12, G:0.51, T:0.19
Consensus pattern (21 bp):
GTACGGAGGTCTGACGTGGAG
Found at i:11439774 original size:45 final size:44
Alignment explanation
Indices: 11439611--11440108 Score: 318
Period size: 44 Copynumber: 11.0 Consensus size: 44
11439601 TTGTGACTTA
* * * * * *
11439611 TAGCTTTAATCTACCCCACTGCAACTTCAGGGAAATGAGATTCG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * * * *
11439655 TTATCTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGGTTTA
1 -TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * * *
11439700 TAGCTTTAATCTGCTCTATTGCAATTTCAACGAGATAAGATTTG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
*** * *
11439744 TTTTTTTTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTG
1 -TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * * * *
11439789 TGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTCG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * * * * * *
11439833 TGGCTTTAATCTACTTCACTGCAACTCCAGGGAGATAAGGTTTA
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * *
11439877 TGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTACCATG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT----TG
* * *
11439926 ATAACTTCAATCTG-TCCCACTGCAACTTCAAGG-GTATAAGAATTG
1 -TAGCTTTAATCTGCT-CCACTGCAACTTCAAGGAG-ATAAGATTTG
** * * ***
11439971 TAACTTGCTACTTAAATCTATTCCACTGCAACTTCAGGGAAATAAGATCCAC
1 T-A---GCT--TT-AATCTGCTCCACTGCAACTTCAAGGAGATAAGAT-TTG
* * * * * **
11440023 TATCTTCAA-CTTGTTCCACTGCAACTTCAGGGAGATAAGGTTAA
1 TAGCTTTAATC-TGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* *
11440067 TAGCTTTAATCTGCTTCACTGCAACTTTAAGGAGATAAGATT
1 TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
11440109 CACCATGGTA
Statistics
Matches: 355, Mismatches: 77, Indels: 43
0.75 0.16 0.09
Matches are distributed among these distances:
44 179 0.50
45 105 0.30
46 1 0.00
48 4 0.01
49 4 0.01
50 32 0.09
51 28 0.08
52 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
Found at i:11440005 original size:51 final size:51
Alignment explanation
Indices: 11439884--11440018 Score: 143
Period size: 51 Copynumber: 2.7 Consensus size: 51
11439874 TTATGGCTTT
* * *
11439884 AATCTACTCCACTGCAACTTC-AGGGAGATAAGATTTACCATGATAACTTC
1 AATCTATTCCACTGCAACTTCAAGGGAGATAAGATTTAACATGATAACTTA
* * * * *
11439934 AATCTGTCCCACTGCAACTTCAAGGG-TATAAGAATTGTAACTTGCT-ACTTA
1 AATCTATTCCACTGCAACTTCAAGGGAGATAAG-ATT-TAACATGATAACTTA
*
11439985 AATCTATTCCACTGCAACTTC-AGGGAAATAAGAT
1 AATCTATTCCACTGCAACTTCAAGGGAGATAAGAT
11440019 CCACTATCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 29 0.41
51 35 0.50
52 6 0.09
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (51 bp):
AATCTATTCCACTGCAACTTCAAGGGAGATAAGATTTAACATGATAACTTA
Found at i:11444750 original size:21 final size:21
Alignment explanation
Indices: 11444721--11444779 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
11444711 CCCTTAAAAT
*
11444721 GGGGCACACGCCCGTGTGGAA
1 GGGGAACACGCCCGTGTGGAA
11444742 GGGGAACACGCCCGTGTGGAA
1 GGGGAACACGCCCGTGTGGAA
*
11444763 GGGGAACACGGCCGTGT
1 GGGGAACACGCCCGTGT
11444780 TGATCGCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.44, T:0.10
Consensus pattern (21 bp):
GGGGAACACGCCCGTGTGGAA
Found at i:11450538 original size:47 final size:47
Alignment explanation
Indices: 11450469--11451006 Score: 815
Period size: 47 Copynumber: 11.4 Consensus size: 47
11450459 ATTGGTGTAC
* * *
11450469 AAAGTGTGTATATGTGATAAGGCCTAACGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* *
11450516 AAAGTGTATATATGTGATAAGGCCGAATGGCCAATGAGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* * * *
11450563 AAAGTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* *
11450610 AAGGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
11450657 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* *
11450704 AAAGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* *
11450751 AAAGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
*
11450798 AAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* * *
11450845 AAAGTGTATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* * * *
11450892 AAAGTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
* * ** *
11450939 AAGGTATATATATGTGATAAGGCCGAATGGCTAATGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
*
11450986 AAAGTGTATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
11451007 TCCCGAAGGG
Statistics
Matches: 448, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 448 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
AAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTG
Found at i:11450743 original size:22 final size:22
Alignment explanation
Indices: 11450715--11450790 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
11450705 AAGTGTGTAT
11450715 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ***
11450737 ATGTGATGAATGTGAAAGTGTGTAT
1 ATGTGAT-AAGGCCTAA-TG-GCCG
11450762 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
11450784 ATGTGAT
1 ATGTGAT
11450791 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 7 0.19
24 7 0.19
25 8 0.22
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:11452614 original size:39 final size:39
Alignment explanation
Indices: 11452564--11452650 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
11452554 GACTTAATGT
*
11452564 CTAGCAGGCCTCATGCCGGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTCATGCCGATGATAAATTCAGGTTTATAC
* *
11452603 CTAGCAGGCCTCGTGCCGATGATAAGTTCAGGTTTATAC
1 CTAGCAGGCCTCATGCCGATGATAAATTCAGGTTTATAC
11452642 CTAGCAGGC
1 CTAGCAGGC
11452651 TAATTACCGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (39 bp):
CTAGCAGGCCTCATGCCGATGATAAATTCAGGTTTATAC
Found at i:11459190 original size:14 final size:15
Alignment explanation
Indices: 11459166--11459195 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11459156 AGATATCAAA
11459166 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
11459181 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
11459195 A
1 A
11459196 AGTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:11459573 original size:13 final size:13
Alignment explanation
Indices: 11459555--11459594 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
11459545 GCTCGGTAGG
11459555 GACACGCCCATGT
1 GACACGCCCATGT
11459568 GACACGCCCATGT
1 GACACGCCCATGT
*
11459581 GACACGCCCGTGT
1 GACACGCCCATGT
11459594 G
1 G
11459595 CGATTACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:11470599 original size:17 final size:18
Alignment explanation
Indices: 11470571--11470607 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
11470561 CTAAAATTCA
11470571 AAAACATTTCTTATTTTG
1 AAAACATTTCTTATTTTG
*
11470589 AAAAC-TTTCTTTTTTTG
1 AAAACATTTCTTATTTTG
11470606 AA
1 AA
11470608 TAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (18 bp):
AAAACATTTCTTATTTTG
Found at i:11470985 original size:3 final size:3
Alignment explanation
Indices: 11470977--11471014 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
11470967 TAAATAAATA
*
11470977 AAT AAT AAT AAT AGAT AA- AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
11471015 GAACAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:11470998 original size:15 final size:15
Alignment explanation
Indices: 11470977--11471014 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
11470967 TAAATAAATA
11470977 AATAATAATAATAGAT
1 AATAATAATAATAG-T
11470993 AA-AATAATAATAGT
1 AATAATAATAATAGT
11471007 AATAATAA
1 AATAATAA
11471015 GAACAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 16 0.76
16 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AATAATAATAATAGT
Found at i:11471126 original size:21 final size:20
Alignment explanation
Indices: 11471101--11471149 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
11471091 AATATTTGAT
* *
11471101 AATAAAATAATAATGGAATAA
1 AATAAAATAAGAAGGGAA-AA
*
11471122 AATAACCATAAGAAGGGAAAA
1 AATAA-AATAAGAAGGGAAAA
11471143 AATAAAA
1 AATAAAA
11471150 ATACCAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.16
Consensus pattern (20 bp):
AATAAAATAAGAAGGGAAAA
Found at i:11471932 original size:25 final size:24
Alignment explanation
Indices: 11471892--11471953 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
11471882 TGTTTAAAAA
*
11471892 AATAAAAATAAA-ATGCACGAA-AT
1 AATAAAAAAAAAGATGCA-GAATAT
11471915 AATAAAAAAAGAAGATGCAGAATAT
1 AATAAAAAAA-AAGATGCAGAATAT
*
11471940 AAAAAAAAAAAAGA
1 AATAAAAAAAAAGA
11471954 GACCTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 16 0.47
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.13
Consensus pattern (24 bp):
AATAAAAAAAAAGATGCAGAATAT
Found at i:11473674 original size:29 final size:29
Alignment explanation
Indices: 11473642--11473697 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
11473632 CACAGAGGCG
* *
11473642 TGTGTGGCTATTTCCAAAGCACACGAGTA
1 TGTGTGGCCATTTCCAAAACACACGAGTA
*
11473671 TGTGTGGCCATTTTCAAAACACACGAG
1 TGTGTGGCCATTTCCAAAACACACGAG
11473698 CTAGTCACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (29 bp):
TGTGTGGCCATTTCCAAAACACACGAGTA
Found at i:11478395 original size:21 final size:21
Alignment explanation
Indices: 11478339--11478395 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
11478329 ATATTAATAT
11478339 AAAATATATTTTTATAAATTAA
1 AAAAT-TATTTTTATAAATTAA
* * *
11478361 AAAATAAATATTAT-AATTAA
1 AAAATTATTTTTATAAATTAA
11478381 AAAATTATTTGTTAT
1 AAAATTATTT-TTAT
11478396 TTGTAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.46
21 10 0.36
22 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATTATTTTTATAAATTAA
Found at i:11478956 original size:31 final size:32
Alignment explanation
Indices: 11478895--11478965 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
11478885 AAAAAATAAT
***
11478895 TTAA-TGACTTAAATAAAAAACTTTTGAATAG
1 TTAAGTGACTTAAATAAAAAACTTCCAAATAG
*
11478926 TTAAGTGACTTAAAT-GAAAACTTCCAAATAG
1 TTAAGTGACTTAAATAAAAAACTTCCAAATAG
*
11478957 TTCAGTGAC
1 TTAAGTGAC
11478966 CAAATTGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (32 bp):
TTAAGTGACTTAAATAAAAAACTTCCAAATAG
Found at i:11479629 original size:86 final size:85
Alignment explanation
Indices: 11479496--11479713 Score: 231
Period size: 86 Copynumber: 2.5 Consensus size: 85
11479486 AATTCTCAAT
* * * * *
11479496 TTTTTTTTAAAAAATAATTAAACCTTCTTTTTTTTTCATTCACTTGGGTACTTAAACTTTTACAA
1 TTTTTTTT-AAAAATAATT-AAGCTCCTTTTTTTTTCATTCAATTGGGTACTTAAACTTTCAAAA
**
11479561 TTTATCAAAAAGACCTTCAAAC
64 TACATCAAAAAGACCTTCAAAC
* *
11479583 TTTTTTTTAAAAATAATTAAGCTCCTGTTTTTTTTCATTTAATTGGGTACTTGAACTTTCAAAAT
1 TTTTTTTTAAAAATAATTAAGCTCCT-TTTTTTTTCATTCAATTGGGTACTTAAACTTTCAAAAT
* *
11479648 ACATCAAAAAGGCCTTTAAAC
65 ACATCAAAAAGACCTTCAAAC
** * * *
11479669 -TTTTTCAAAAAATGCAATTAAGCTCCTACTTTTTTGCACTCAATT
1 TTTTTTTTAAAAAT--AATTAAGCTCCT-TTTTTTTTCATTCAATT
11479714 AGATACTTGA
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
85 17 0.15
86 60 0.55
87 33 0.30
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (85 bp):
TTTTTTTTAAAAATAATTAAGCTCCTTTTTTTTTCATTCAATTGGGTACTTAAACTTTCAAAATA
CATCAAAAAGACCTTCAAAC
Found at i:11479869 original size:19 final size:19
Alignment explanation
Indices: 11479787--11479869 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
11479777 ACATGTGGCT
*
11479787 AAAATATGATAAAAGA-T-A
1 AAAATAT-ATAAAATATTAA
11479805 AAAATCA-ATAAAA-ATTATA
1 AAAAT-ATATAAAATATTA-A
* *
11479824 AAAATAAAT-AAATTTTAA
1 AAAATATATAAAATATTAA
11479842 TAAAATATATAAAATATTAA
1 -AAAATATATAAAATATTAA
*
11479862 AAATTATA
1 AAAATATA
11479870 ATATATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
16 1 0.02
17 7 0.13
18 10 0.19
19 27 0.51
20 8 0.15
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATATAAAATATTAA
Found at i:11479961 original size:18 final size:18
Alignment explanation
Indices: 11479914--11479967 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
11479904 AATTTTAACA
*
11479914 AAAAATA-TAAAAAATTT
1 AAAAATAGTAAAAAATAT
* *
11479931 AAAACTAGAAAAAAATAT
1 AAAAATAGTAAAAAATAT
*
11479949 AAAAATTGTAAAAAA-AT
1 AAAAATAGTAAAAAATAT
11479966 AA
1 AA
11479968 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAAATAGTAAAAAATAT
Found at i:11479994 original size:10 final size:10
Alignment explanation
Indices: 11479946--11480069 Score: 55
Period size: 9 Copynumber: 12.6 Consensus size: 10
11479936 TAGAAAAAAA
11479946 TATAAAAATT
1 TATAAAAATT
*
11479956 GTAAAAAAATAAT
1 -TATAAAAAT--T
*
11479969 TATAAAAAATC
1 TAT-AAAAATT
11479980 T-TAAAAATT
1 TATAAAAATT
11479989 TAT-AAAA-T
1 TATAAAAATT
*
11479997 TATAAAATTT
1 TATAAAAATT
* *
11480007 TAT-AAAGTCG
1 TATAAAAAT-T
*
11480017 TA-AGAAATT
1 TATAAAAATT
11480026 TAT-AAAATT
1 TATAAAAATT
* * *
11480035 TATAGAAGTA
1 TATAAAAATT
*
11480045 TAGAAAAA-T
1 TATAAAAATT
*
11480054 TATAAAATTT
1 TATAAAAATT
11480064 TATAAA
1 TATAAA
11480070 GCCGTAAGAA
Statistics
Matches: 82, Mismatches: 20, Indels: 23
0.66 0.16 0.18
Matches are distributed among these distances:
8 4 0.05
9 34 0.41
10 26 0.32
11 9 0.11
12 2 0.02
13 7 0.09
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (10 bp):
TATAAAAATT
Found at i:11480033 original size:29 final size:29
Alignment explanation
Indices: 11479996--11480089 Score: 122
Period size: 29 Copynumber: 3.3 Consensus size: 29
11479986 ATTTATAAAA
11479996 TTATAAAATTTTATAAAGTCGTAAGAAAT
1 TTATAAAATTTTATAAAGTCGTAAGAAAT
* *
11480025 TTATAAAA-TTTATAGAAGT-AT-AGAAAAA
1 TTATAAAATTTTATA-AAGTCGTAAG-AAAT
*
11480053 TTATAAAATTTTATAAAGCCGTAAGAAAT
1 TTATAAAATTTTATAAAGTCGTAAGAAAT
11480082 TTATAAAA
1 TTATAAAA
11480090 ATGTAAAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.04
28 21 0.38
29 30 0.55
30 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (29 bp):
TTATAAAATTTTATAAAGTCGTAAGAAAT
Found at i:11480037 original size:9 final size:9
Alignment explanation
Indices: 11479974--11480069 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
11479964 ATAATTATAA
11479974 AAAATCTTA-
1 AAAAT-TTAT
11479983 AAAATTTAT
1 AAAATTTAT
11479992 AAAA-TTAT
1 AAAATTTAT
11480000 AAAATTTTAT
1 AAAA-TTTAT
* *
11480010 AAAGTCGTA-
1 AAAAT-TTAT
11480019 AGAAATTTAT
1 A-AAATTTAT
11480029 AAAATTTAT
1 AAAATTTAT
* * *
11480038 AGAAGTATAG
1 A-AAATTTAT
*
11480048 AAAAATTAT
1 AAAATTTAT
11480057 AAAATTTTAT
1 AAAA-TTTAT
11480067 AAA
1 AAA
11480070 GCCGTAAGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
8 11 0.16
9 30 0.45
10 26 0.39
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (9 bp):
AAAATTTAT
Found at i:11480322 original size:18 final size:18
Alignment explanation
Indices: 11480300--11480335 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
11480290 TAAATGATCA
11480300 TTTTTATGCATTTTATAAT
1 TTTTTATG-ATTTTATAAT
11480319 TTTTTATGATTTTATAA
1 TTTTTATGATTTTATAA
11480336 AGTTTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTTATGATTTTATAAT
Found at i:11480341 original size:18 final size:19
Alignment explanation
Indices: 11480301--11480342 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
11480291 AAATGATCAT
**
11480301 TTTTATGCATTTTATAATT
1 TTTTATGCATTTTATAAAG
11480320 TTTTATG-ATTTTATAAAG
1 TTTTATGCATTTTATAAAG
11480338 TTTTA
1 TTTTA
11480343 CAATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTATGCATTTTATAAAG
Found at i:11480341 original size:19 final size:19
Alignment explanation
Indices: 11480300--11480341 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11480290 TAAATGATCA
*
11480300 TTTTTATGCATTTTATAAT
1 TTTTTATGCATTTTATAAG
11480319 TTTTTATG-ATTTTATAAAG
1 TTTTTATGCATTTTAT-AAG
11480338 TTTT
1 TTTT
11480342 ACAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATGCATTTTATAAG
Found at i:11480367 original size:21 final size:22
Alignment explanation
Indices: 11480338--11480382 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
11480328 TTTTATAAAG
*
11480338 TTTTACAATTTTTT-ATAATTT
1 TTTTACAATTTTTTAATAAATT
*
11480359 TTTTTCAATTTTTTAATAAATT
1 TTTTACAATTTTTTAATAAATT
11480381 TT
1 TT
11480383 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTACAATTTTTTAATAAATT
Found at i:11480380 original size:12 final size:10
Alignment explanation
Indices: 11480310--11480394 Score: 61
Period size: 10 Copynumber: 8.6 Consensus size: 10
11480300 TTTTTATGCA
11480310 TTTTATAATT
1 TTTTATAATT
*
11480320 TTTTATGA--
1 TTTTATAATT
**
11480328 TTTTATAAAG
1 TTTTATAATT
*
11480338 TTTTACAATT
1 TTTTATAATT
11480348 TTTTATAATT
1 TTTTATAATT
*
11480358 TTTTTTCAATT
1 TTTTAT-AATT
*
11480369 TTTTAATAA-A
1 TTTT-ATAATT
11480379 TTTTA-AATAT
1 TTTTATAAT-T
11480389 TTTTAT
1 TTTTAT
11480395 TAAAATTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
8 9 0.16
9 1 0.02
10 37 0.64
11 10 0.17
12 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:11480400 original size:21 final size:19
Alignment explanation
Indices: 11480360--11480404 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
11480350 TTATAATTTT
*
11480360 TTTTCAATTTTTTAATAAA
1 TTTTAAATTTTTTAATAAA
*
11480379 TTTTAAATATTTTTATTAAA
1 TTTTAAAT-TTTTTAATAAA
*
11480399 ATTTAA
1 TTTTAA
11480405 TAATTTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAATTTTTTAATAAA
Found at i:11484137 original size:15 final size:15
Alignment explanation
Indices: 11484119--11484159 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11484109 TCAACTAAAT
11484119 CATATTTAACTTTTA
1 CATATTTAACTTTTA
*
11484134 CATATATAACTTTTA
1 CATATTTAACTTTTA
*
11484149 TATATATTAAC
1 CATAT-TTAAC
11484160 ATAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (15 bp):
CATATTTAACTTTTA
Found at i:11487941 original size:27 final size:27
Alignment explanation
Indices: 11487911--11487996 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
11487901 AAATATTTTT
*
11487911 TATTTTTCTTGATTGGACATATATCAC
1 TATTTTTCTTGATTGGAAATATATCAC
* * ** * ***
11487938 TA-TTTTATTGGTTACAAATATTTTTT
1 TATTTTTCTTGATTGGAAATATATCAC
11487964 TATTTTTCTTGATTGGAAATATATCAC
1 TATTTTTCTTGATTGGAAATATATCAC
11487991 TATTTT
1 TATTTT
11487997 ATTGGTTATA
Statistics
Matches: 41, Mismatches: 17, Indels: 2
0.68 0.28 0.03
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (27 bp):
TATTTTTCTTGATTGGAAATATATCAC
Found at i:11487943 original size:26 final size:26
Alignment explanation
Indices: 11487914--11487996 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
11487904 TATTTTTTAT
*
11487914 TTTTCTTGATTGGACATATATCACTA
1 TTTTCTTGATTGGAAATATATCACTA
* * ** * ***
11487940 TTTTATTGGTTACAAATATTTTTTTA
1 TTTTCTTGATTGGAAATATATCACTA
11487966 TTTTTCTTGATTGGAAATATATCACTA
1 -TTTTCTTGATTGGAAATATATCACTA
11487993 TTTT
1 TTTT
11487997 ATTGGTTATA
Statistics
Matches: 39, Mismatches: 17, Indels: 2
0.67 0.29 0.03
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (26 bp):
TTTTCTTGATTGGAAATATATCACTA
Found at i:11487980 original size:53 final size:52
Alignment explanation
Indices: 11487901--11488004 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 52
11487891 TTTTCACGTT
*
11487901 AAATATTTTTTATTTTTCTTGATTGGACATATATCACTATTTTATTGGTTAC
1 AAATATTTTTTATTTTTCTTGATTGGAAATATATCACTATTTTATTGGTTAC
11487953 AAATATTTTTTTATTTTTCTTGATTGGAAATATATCACTATTTTATTGGTTA
1 AAATA-TTTTTTATTTTTCTTGATTGGAAATATATCACTATTTTATTGGTTA
11488005 TAAAAGGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 5 0.10
53 45 0.90
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.55
Consensus pattern (52 bp):
AAATATTTTTTATTTTTCTTGATTGGAAATATATCACTATTTTATTGGTTAC
Found at i:11492779 original size:30 final size:30
Alignment explanation
Indices: 11492738--11492798 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
11492728 TTTTCGAGCC
*
11492738 TAGGGGTAAAATCATAATTCTACAAAAGTT
1 TAGGGGCAAAATCATAATTCTACAAAAGTT
** * *
11492768 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAATCATAATTCTACAAAAGTT
11492798 T
1 T
11492799 GAGTTAGGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAATCATAATTCTACAAAAGTT
Found at i:11493664 original size:54 final size:54
Alignment explanation
Indices: 11493600--11493794 Score: 232
Period size: 54 Copynumber: 3.6 Consensus size: 54
11493590 TTGGTAAGAT
* *
11493600 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
* * * *
11493654 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTCACTATAAGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGT-TCTATAAGG-A
* * * * *
11493710 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
* * *
11493762 AAGGACACCACGTAAGACCATGTCAAGACATGG
1 AAGGATACCATGTAAGACCATGCCAAGACATGG
11493795 TAATAGTAAG
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 29 0.24
54 42 0.35
55 40 0.33
56 5 0.04
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
Found at i:11493729 original size:55 final size:54
Alignment explanation
Indices: 11493608--11493794 Score: 227
Period size: 55 Copynumber: 3.5 Consensus size: 54
11493598 ATAAGGATAT
* **
11493608 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGG-AAAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGG-ACC
* * *
11493662 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTCACTATAAGGCAAAGGTCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGT-TCTATAAGGCAAAGGACC
* * *
11493717 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC-AAGGACAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGAC-C
* *
11493770 CACGTAAGACCATGTCAAGACATGG
1 CATGTAAGACCATGCCAAGACATGG
11493795 TAATAGTAAG
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 5 0.04
53 30 0.26
54 35 0.30
55 40 0.35
56 5 0.04
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGACC
Found at i:11493805 original size:108 final size:109
Alignment explanation
Indices: 11493608--11493805 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 109
11493598 ATAAGGATAT
* *
11493608 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCACGTAAGACC
* *
11493673 ATGTCAAGACATGGCATTGATAAGTCACTATAAGGCAAAGGTCC
66 ATGTCAAGACATGGAATAGATAAGTCACTATAAGGCAAAGGTCC
* * * *
11493717 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGACACCACGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCACGTAAGACC
11493781 ATGTCAAGACATGGTAATAG-TAAGT
66 ATGTCAAGACATGG-AATAGATAAGT
11493806 TCAAAAAGGA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 41 0.51
109 39 0.49
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCACGTAAGACC
ATGTCAAGACATGGAATAGATAAGTCACTATAAGGCAAAGGTCC
Found at i:11497499 original size:39 final size:39
Alignment explanation
Indices: 11497451--11497586 Score: 191
Period size: 39 Copynumber: 3.5 Consensus size: 39
11497441 AAACAATCAA
* *
11497451 TAACAATCAATTATTCAGTGCAGTAATCTAGTCATTCAG
1 TAACTATCAATTATTCAGTGCAGTAATCTAGTTATTCAG
* * *
11497490 TAACTATCAAATATTCAGTGCAGTAGTCTAGTTATTCAA
1 TAACTATCAATTATTCAGTGCAGTAATCTAGTTATTCAG
* * *
11497529 TAACTATCAATTATTCAATACAGTAATTTAGTTATTCAG
1 TAACTATCAATTATTCAGTGCAGTAATCTAGTTATTCAG
*
11497568 TAACTAGCAATTATTCAGT
1 TAACTATCAATTATTCAGT
11497587 ATAGTAGTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (39 bp):
TAACTATCAATTATTCAGTGCAGTAATCTAGTTATTCAG
Found at i:11497527 original size:21 final size:20
Alignment explanation
Indices: 11497461--11497527 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
11497451 TAACAATCAA
11497461 TTATTCAGTGCAGTAATCTAG
1 TTATTCAGTGCAGT-ATCTAG
* * * *
11497482 TCATTCAGT-AACTATC-AA
1 TTATTCAGTGCAGTATCTAG
*
11497500 ATATTCAGTGCAGTAGTCTAG
1 TTATTCAGTGCAGTA-TCTAG
11497521 TTATTCA
1 TTATTCA
11497528 ATAACTATCA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 4 0.12
21 15 0.45
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (20 bp):
TTATTCAGTGCAGTATCTAG
Found at i:11497593 original size:78 final size:78
Alignment explanation
Indices: 11497447--11497594 Score: 215
Period size: 78 Copynumber: 1.9 Consensus size: 78
11497437 TATCAAACAA
* * * *
11497447 TCAATAACAATCAATTATTCAGTGCAGTAATCTAGTCATTCAGTAACTATCAAATATTCAGTGCA
1 TCAATAACAATCAATTATTCAATACAGTAATCTAGTCATTCAGTAACTAGCAAATATTCAGTACA
11497512 GTAGTCTAGTTAT
66 GTAGTCTAGTTAT
* * * * *
11497525 TCAATAACTATCAATTATTCAATACAGTAATTTAGTTATTCAGTAACTAGCAATTATTCAGTATA
1 TCAATAACAATCAATTATTCAATACAGTAATCTAGTCATTCAGTAACTAGCAAATATTCAGTACA
11497590 GTAGT
66 GTAGT
11497595 TTACCCTTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (78 bp):
TCAATAACAATCAATTATTCAATACAGTAATCTAGTCATTCAGTAACTAGCAAATATTCAGTACA
GTAGTCTAGTTAT
Found at i:11498624 original size:32 final size:33
Alignment explanation
Indices: 11498581--11498652 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
11498571 TATTTATCAT
11498581 ATAAAA-ATC-TTTTACAAATTA-ATAATAAATA
1 ATAAAATATCTTTTTACAAATTATAT-ATAAATA
*
11498612 ATAAAATATCTTTTTACTAATTATATATAAATA
1 ATAAAATATCTTTTTACAAATTATATATAAATA
11498645 ATACAAAT
1 ATA-AAAT
11498653 GTACTCATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.17
32 3 0.08
33 21 0.58
34 6 0.17
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAATATCTTTTTACAAATTATATATAAATA
Found at i:11498753 original size:29 final size:29
Alignment explanation
Indices: 11498711--11498767 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
11498701 GTCTTTTCTT
*
11498711 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
11498740 AATTTAATTT-ATAATATAATAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
11498768 AACAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:11498788 original size:37 final size:37
Alignment explanation
Indices: 11498721--11498812 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
11498711 AATTTATTTC
* * *
11498721 ATAATATAATAATATAATCAATTTAATTTATAATATA
1 ATAAAATAATAAAATAATCAATATAATTTATAATATA
*
11498758 ATAAAATAATAACAATAAT-AATATATTTTATAAT-TA
1 ATAAAATAATAA-AATAATCAATATAATTTATAATATA
* *
11498794 A-ACAATCATAAAA-AATCAA
1 ATAAAATAATAAAATAATCAA
11498813 AGATTTTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
33 3 0.06
34 4 0.09
35 8 0.17
36 3 0.06
37 24 0.51
38 5 0.11
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (37 bp):
ATAAAATAATAAAATAATCAATATAATTTATAATATA
Found at i:11500261 original size:23 final size:23
Alignment explanation
Indices: 11500229--11500280 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
11500219 TCGATTCAAA
11500229 AGTGTTAGAAAAGAAAGTTGAATC
1 AGTG-TAGAAAAGAAAGTTGAATC
*
11500253 AGTGTAGAAAGGAAAGTTGAATC
1 AGTGTAGAAAAGAAAGTTGAATC
11500276 AGTGT
1 AGTGT
11500281 CTGTTGTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.25
Consensus pattern (23 bp):
AGTGTAGAAAAGAAAGTTGAATC
Found at i:11506726 original size:11 final size:11
Alignment explanation
Indices: 11506703--11506736 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11506693 ATGTCAAATC
*
11506703 ATCAAGAATAA
1 ATCAAGAACAA
*
11506714 ATTAAGAACAA
1 ATCAAGAACAA
11506725 ATCAAGAACAA
1 ATCAAGAACAA
11506736 A
1 A
11506737 ACTAGATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAACAA
Found at i:11512189 original size:13 final size:13
Alignment explanation
Indices: 11512173--11512231 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
11512163 ACTAAATTTT
11512173 TCAAAAGTACTTC
1 TCAAAAGTACTTC
*
11512186 TCAAAAGTACTTTT
1 TCAAAAGTAC-TTC
* * *
11512200 TTATAA-CACTTC
1 TCAAAAGTACTTC
*
11512212 TCAAAAGTACTTT
1 TCAAAAGTACTTC
11512225 TCAAAAG
1 TCAAAAG
11512232 CATTGCCAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
12 6 0.17
13 23 0.66
14 6 0.17
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (13 bp):
TCAAAAGTACTTC
Found at i:11516071 original size:31 final size:31
Alignment explanation
Indices: 11515999--11516064 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
11515989 TTTGGTTCCT
11515999 ATTTGTAAAAATAGGAATGTCGGTTTCGTTC
1 ATTTGTAAAAATAGGAATGTCGGTTTCGTTC
11516030 ATTTGTAAAAATAGGAATGTCGGTTTCGTTC
1 ATTTGTAAAAATAGGAATGTCGGTTTCGTTC
11516061 ATTT
1 ATTT
11516065 TCAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (31 bp):
ATTTGTAAAAATAGGAATGTCGGTTTCGTTC
Found at i:11516453 original size:18 final size:18
Alignment explanation
Indices: 11516415--11516450 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11516405 GAGTATTATT
*
11516415 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
11516433 TAAAATTATAATATTAAA
1 TAAAATT-TAATATTAAA
11516451 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:11517996 original size:77 final size:77
Alignment explanation
Indices: 11517866--11518019 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
11517856 TTCAATGTAA
* *
11517866 AAAAAAAATTGATGGCAAACTACCCAAGTAAACCAAGGTTCAACATTTTTTGCGAACTTCTGTGT
1 AAAAAAAATTGATGGCAAACTACCCAAGTAAACCAAGGTTCAACATTTGTTGCGAACTTCTATGT
11517931 TTACGTTCCGTT
66 TTACGTTCCGTT
*
11517943 AAAAAAAATTGATGGCAAACTACCCAAGTAAACCAAGGTTCAGCATTTGTTGCGAACTTCTATGT
1 AAAAAAAATTGATGGCAAACTACCCAAGTAAACCAAGGTTCAACATTTGTTGCGAACTTCTATGT
11518008 TTACGTTCCGTT
66 TTACGTTCCGTT
11518020 TAGCTCACAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (77 bp):
AAAAAAAATTGATGGCAAACTACCCAAGTAAACCAAGGTTCAACATTTGTTGCGAACTTCTATGT
TTACGTTCCGTT
Found at i:11518124 original size:21 final size:21
Alignment explanation
Indices: 11518052--11518125 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
11518042 ACTCGTATGA
*
11518052 GTTTCAGTTTAACCC-TATTGG
1 GTTTCAGTTTAACCCTTA-CGG
* * * *
11518073 GTTTCCGTTTAGCTCTTTCGAG
1 GTTTCAGTTTAACCCTTACG-G
*
11518095 CTTT-AGTTTAACCCTTACGG
1 GTTTCAGTTTAACCCTTACGG
*
11518115 GTTTCCGTTTA
1 GTTTCAGTTTA
11518126 GCACTTATGT
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
20 4 0.11
21 29 0.76
22 5 0.13
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.45
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTACGG
Found at i:11518132 original size:21 final size:21
Alignment explanation
Indices: 11518071--11518132 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
11518061 TAACCCTATT
* *
11518071 GGGTTTCCGTTTAGCTCTTTC
1 GGGTTTCCGTTTAGCACTTAC
* * * *
11518092 GAGCTTT-AGTTTAACCCTTAC
1 G-GGTTTCCGTTTAGCACTTAC
11518113 GGGTTTCCGTTTAGCACTTA
1 GGGTTTCCGTTTAGCACTTA
11518133 TGTACTTCTG
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (21 bp):
GGGTTTCCGTTTAGCACTTAC
Found at i:11525889 original size:17 final size:17
Alignment explanation
Indices: 11525852--11525889 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11525842 AAAACGCTTT
*
11525852 AAAATTTTAAAAATATG
1 AAAATTTTAAAAATATA
*
11525869 AAAATTTTAAAAATTTA
1 AAAATTTTAAAAATATA
11525886 AAAA
1 AAAA
11525890 AAGTATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATTTTAAAAATATA
Found at i:11527532 original size:19 final size:19
Alignment explanation
Indices: 11527508--11527554 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11527498 TTTTTTTATA
11527508 TTTTAAAGATG-TTTAAAAT
1 TTTTAAA-ATGATTTAAAAT
* *
11527527 TTTTAAAATGATTTTATAT
1 TTTTAAAATGATTTAAAAT
11527546 TTTTAAAAT
1 TTTTAAAAT
11527555 TTAAGGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTAAAATGATTTAAAAT
Found at i:11528458 original size:51 final size:52
Alignment explanation
Indices: 11528391--11528493 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
11528381 ATCCCCCAAT
11528391 TCCATCCTTTTCATGGGGGTTCA-TTATCCTATTGTAAATTGAAATTACAGA
1 TCCATCCTTTTCATGGGGGTTCATTTATCCTATTGTAAATTGAAATTACAGA
*
11528442 TCCATCCTTTTCATGGGGGTTGATTTATCCTATTGTAAATTGAAATTACAGA
1 TCCATCCTTTTCATGGGGGTTCATTTATCCTATTGTAAATTGAAATTACAGA
11528494 CTTTTGTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 22 0.44
52 28 0.56
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (52 bp):
TCCATCCTTTTCATGGGGGTTCATTTATCCTATTGTAAATTGAAATTACAGA
Found at i:11530839 original size:26 final size:25
Alignment explanation
Indices: 11530802--11530859 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
11530792 TCTTTCTTCT
*
11530802 TCTTTCGTTTTC-TCAGAGAATATTTC
1 TCTTTCGATTTCTTCA-AGAA-ATTTC
11530828 TCTTTCGATTTCTTTCAAGAAATTTC
1 TCTTTCGATTTC-TTCAAGAAATTTC
11530854 TCTTTC
1 TCTTTC
11530860 TTGGAGCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.76
27 4 0.14
28 3 0.10
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.52
Consensus pattern (25 bp):
TCTTTCGATTTCTTCAAGAAATTTC
Found at i:11532080 original size:14 final size:12
Alignment explanation
Indices: 11532061--11532109 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
11532051 ATTTGGGGAG
11532061 AAGAAAGGAGAGAA
1 AAGAAA-GA-AGAA
11532075 AAGAAAGAAGAA
1 AAGAAAGAAGAA
11532087 AAGAAGAGAAGAA
1 AAGAA-AGAAGAA
11532100 GAAG-AAGAAG
1 -AAGAAAGAAG
11532110 GAGCAACCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 14 0.42
13 10 0.30
14 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAGAA
Found at i:11532094 original size:22 final size:22
Alignment explanation
Indices: 11532059--11532108 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
11532049 TCATTTGGGG
*
11532059 AGAAG-AAAGGAGAGAA-AAGAA
1 AGAAGAAAAGAAGAGAAGAAG-A
11532080 AGAAGAAAAGAAGAGAAGAAGA
1 AGAAGAAAAGAAGAGAAGAAGA
11532102 AGAAGAA
1 AGAAGAA
11532109 GGAGCAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 18 0.69
23 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (22 bp):
AGAAGAAAAGAAGAGAAGAAGA
Found at i:11532109 original size:17 final size:16
Alignment explanation
Indices: 11532059--11532109 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 16
11532049 TCATTTGGGG
*
11532059 AGAAGAAAGGAG-AGA
1 AGAAGAAAGAAGAAGA
11532074 A-AAGAAAGAAGAA-A
1 AGAAGAAAGAAGAAGA
11532088 AGAAGAGAAGAAGAAGA
1 AGAAGA-AAGAAGAAGA
11532105 AGAAG
1 AGAAG
11532110 GAGCAACCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 8 0.26
17 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAGAAAGAAGAAGA
Found at i:11532235 original size:11 final size:10
Alignment explanation
Indices: 11532221--11532254 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
11532211 GTATTTATTG
11532221 TTGATTTTAAT
1 TTGA-TTTAAT
11532232 TTGATTTAAT
1 TTGATTTAAT
11532242 TTAGATTTAAT
1 TT-GATTTAAT
11532253 TT
1 TT
11532255 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (10 bp):
TTGATTTAAT
Found at i:11532255 original size:11 final size:11
Alignment explanation
Indices: 11532226--11532255 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11532216 TATTGTTGAT
11532226 TTTAATTT-GA
1 TTTAATTTAGA
11532236 TTTAATTTAGA
1 TTTAATTTAGA
11532247 TTTAATTTA
1 TTTAATTTA
11532256 TAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (11 bp):
TTTAATTTAGA
Found at i:11532623 original size:17 final size:16
Alignment explanation
Indices: 11532600--11532645 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
11532590 TATCTTAATG
11532600 AAAAAATAAAATACGA
1 AAAAAATAAAATACGA
* *
11532616 AAAGAAATAGAATATGA
1 AAA-AAATAAAATACGA
*
11532633 AAAAAATACAATA
1 AAAAAATAAAATA
11532646 AAATACTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAATACGA
Found at i:11532645 original size:16 final size:16
Alignment explanation
Indices: 11532567--11532645 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
11532557 AAAATAGTAT
*
11532567 AAAAAAAGAAAATATG
1 AAAAAAATAAAATATG
***
11532583 AAAAAAATATCTTAATG
1 AAAAAAATAAAAT-ATG
*
11532600 -AAAAAATAAAATACG
1 AAAAAAATAAAATATG
*
11532615 AAAAGAAATAGAATATG
1 AAAA-AAATAAAATATG
*
11532632 AAAAAAATACAATA
1 AAAAAAATAAAATA
11532646 AAATACTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.04
16 30 0.61
17 17 0.35
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAAATATG
Found at i:11532956 original size:133 final size:133
Alignment explanation
Indices: 11532800--11533400 Score: 814
Period size: 133 Copynumber: 4.7 Consensus size: 133
11532790 TAAAATAAGA
* *
11532800 TAAAAAATAAAATACGAATATTTTAGAAATACAGATAATAAAGGGACAAAATTAGGGTTATATAA
1 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATATAA
*
11532865 AAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAATATAAAATACGAAAATAGTATA
66 AAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTATA
11532930 TTT
131 TTT
* * *
11532933 TAAAAAATAGAATCCGAATATTTTAGAAATAC-AA-AAT-TAGGG------TTA----TATAAAA
1 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATATAA
11532985 AAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTATA
66 AAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTATA
11533050 TTT
131 TTT
*
11533053 TAAAAAATAGAATCCGAATATTTTAG--------A-AAT------ACAAAATTAGGGTTATAT-A
1 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATATAA
*
11533102 AAAACACTAAAGTAATACATTTATGTACTAAAATAATAAGAT-AAAAATAAAATACAAAAATAGT
66 AAAACACTAAAGTAATACATTTATGTACT--AA-AATAAGATAAAAAATAAAATACGAAAATAGT
11533166 ATATTT
128 ATATTT
* * * **
11533172 TAAAAAATAAAATTCAAATATTTTAGAAATACAAATAATAAAGGGAAAAAATTAAAGTT-TATAA
1 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATAT-A
11533236 AAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTAT
65 AAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTAT
11533301 ATTT
130 ATTT
*
11533305 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGAGACAAAATTAGGGTTATATAA
1 TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATATAA
*
11533370 AAAACACTAAAGTTATACATTTATGTACTAA
66 AAAACACTAAAGTAATACATTTATGTACTAA
11533401 TAAATATTTA
Statistics
Matches: 414, Mismatches: 22, Indels: 64
0.83 0.04 0.13
Matches are distributed among these distances:
113 4 0.01
114 3 0.01
117 30 0.07
118 4 0.01
119 52 0.13
120 107 0.26
124 3 0.01
127 1 0.00
128 3 0.01
130 4 0.01
131 3 0.01
132 9 0.02
133 147 0.36
134 14 0.03
135 30 0.07
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (133 bp):
TAAAAAATAAAATCCGAATATTTTAGAAATACAAATAATAAAGGGACAAAATTAGGGTTATATAA
AAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAATAAAATACGAAAATAGTATA
TTT
Found at i:11533003 original size:120 final size:118
Alignment explanation
Indices: 11532845--11533339 Score: 733
Period size: 120 Copynumber: 4.0 Consensus size: 118
11532835 TAATAAAGGG
*
11532845 ACAAAATTAGGGTTATATAAAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAATA
1 ACAAAATTAGGGTTATATAAAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAA
*
11532910 TAAAATACGAAAATAGTATATTTTAAAAAATAGAATCCGAATATTTTAGAAAT
66 TAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGAAAT
11532963 ACAAAATTAGGGTTATATAAAAAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAA
1 ACAAAATTAGGGTTATAT--AAAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAA
*
11533028 AATAAAATACGAAAATAGTATATTTTAAAAAATAGAATCCGAATATTTTAGAAAT
64 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGAAAT
11533083 ACAAAATTAGGGTTATAT-AAAAACACTAAAGTAATACATTTATGTACTAAAATAATAAGAT-AA
1 ACAAAATTAGGGTTATATAAAAAACACTAAAGTAATACATTTATGTACT--AA-AATAAGATAAA
* * *
11533146 AAATAAAATACAAAAATAGTATATTTTAAAAAATAAAATTCAAATATTTTAGAAAT
63 AAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGAAAT
*
11533202 ACAAATAATAAAGGGAAAAAATTAAAGTTTATAAAAAAACACTAAAGTAATACATTTATGTACTA
1 AC-AA-AAT-TAGGG------TT--A---TAT-AAAAAACACTAAAGTAATACATTTATGTACTA
11533267 AAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGA
51 AAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGA
11533332 AAT
116 AAT
11533335 ACAAA
1 ACAAA
11533340 TAATAAAGAG
Statistics
Matches: 346, Mismatches: 9, Indels: 31
0.90 0.02 0.08
Matches are distributed among these distances:
117 30 0.09
118 18 0.05
119 58 0.17
120 127 0.37
121 3 0.01
122 4 0.01
128 2 0.01
130 1 0.00
131 1 0.00
132 10 0.03
133 62 0.18
135 30 0.09
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.28
Consensus pattern (118 bp):
ACAAAATTAGGGTTATATAAAAAACACTAAAGTAATACATTTATGTACTAAAATAAGATAAAAAA
TAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAGAAAT
Found at i:11533175 original size:23 final size:22
Alignment explanation
Indices: 11533149--11533213 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
11533139 AAGATAAAAA
*
11533149 TAAAATACAAAAATAGTATATTT
1 TAAAATACAAAAATA-AATATTT
* * *
11533172 TAAAAAATAAAATTCAAATATTT
1 TAAAATACAAAAAT-AAATATTT
11533195 TAGAAATACAAATAATAAA
1 TA-AAATACAAA-AATAAA
11533214 GGGAAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
23 19 0.59
24 11 0.34
25 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (22 bp):
TAAAATACAAAAATAAATATTT
Found at i:11539030 original size:26 final size:27
Alignment explanation
Indices: 11538993--11539045 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
11538983 TAGGGTGTCG
11538993 GTGCTGCCTCTGACAGAGGCAAGACCA
1 GTGCTGCCTCTGACAGAGGCAAGACCA
11539020 GTGC-GCCTCTGACAGAGGCAAGACCA
1 GTGCTGCCTCTGACAGAGGCAAGACCA
11539046 ATATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.13
Consensus pattern (27 bp):
GTGCTGCCTCTGACAGAGGCAAGACCA
Found at i:11539099 original size:18 final size:19
Alignment explanation
Indices: 11539063--11539102 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11539053 ATTATTATTA
11539063 TTTTTCAGATTCAATTTTT
1 TTTTTCAGATTCAATTTTT
11539082 TTTTTCAGATTCAATTTTT
1 TTTTTCAGATTCAATTTTT
11539101 TT
1 TT
11539103 AACAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTCAGATTCAATTTTT
Found at i:11539108 original size:18 final size:19
Alignment explanation
Indices: 11539068--11539110 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
11539058 TATTATTTTT
**
11539068 CAGATTCAATTTTTTTTTT
1 CAGATTCAATTTTTTTTAA
11539087 CAGATTCAA-TTTTTTTAA
1 CAGATTCAATTTTTTTTAA
11539105 CAGATT
1 CAGATT
11539111 TTGTCAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (19 bp):
CAGATTCAATTTTTTTTAA
Found at i:11542751 original size:131 final size:130
Alignment explanation
Indices: 11542491--11542829 Score: 402
Period size: 131 Copynumber: 2.6 Consensus size: 130
11542481 CAACGAAAAA
* * * * * * * *
11542491 AAATCGAAACCTAGCAC-AGTAGGGCACGATTCCTCGAATTTCTAGACATCGGACATTGCCTT-A
1 AAATCGCAACCCAGCACGA-TAGGGCACGATTCC-CGAATTGCCAAACATCGAACATTACCTTCG
* *
11542554 TTTT--AGAA--TTTAGAGAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAAC
64 TTTTAAAGAATTTTTAAAG-ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAAC
11542615 AGG
128 AGG
*
11542618 AAATCGCATCCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGT
1 AAATCGCAACCCAGCACGATAGGGCACGATT-CCCGAATTGCCAAACATCGAACATTACCTTCGT
* * * * * *
11542683 TTTGAATAATTTTTAAAGACATGAGTGAAATTCCAAAGGAATATTTGATTGTTTTGAACGAACGG
65 TTTAAAGAATTTTTAAAGACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAG
11542748 G
130 G
* * * * *
11542749 AAATTGTAACCCAGCACGATAGGGCACGATTCTCGAATTGCCAAACATCGAATATTGCCTTCGTT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCCGAATTGCCAAACATCGAACATTACCTTCGTT
11542814 TTAAAGAATTTTTAAA
66 TTAAAGAATTTTTAAA
11542830 TGAATAATTA
Statistics
Matches: 181, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
127 49 0.27
128 7 0.04
130 48 0.27
131 71 0.39
132 6 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (130 bp):
AAATCGCAACCCAGCACGATAGGGCACGATTCCCGAATTGCCAAACATCGAACATTACCTTCGTT
TTAAAGAATTTTTAAAGACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGG
Found at i:11547060 original size:40 final size:40
Alignment explanation
Indices: 11546976--11547199 Score: 251
Period size: 40 Copynumber: 5.6 Consensus size: 40
11546966 TTGAATGCTG
* *
11546976 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
** * * *
11547015 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
11547056 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
11547096 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* ** *
11547136 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
11547176 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
11547200 GAATGAGTTA
Statistics
Matches: 162, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
39 3 0.02
40 147 0.91
41 12 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11547189 original size:120 final size:120
Alignment explanation
Indices: 11546976--11547196 Score: 299
Period size: 120 Copynumber: 1.8 Consensus size: 120
11546966 TTGAATGCTG
* * *
11546976 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATTC
*
11547041 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
66 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
* **
11547096 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
11547157 ATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGGC
62 ATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGC
11547197 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
119 4 0.04
120 76 0.85
121 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
Found at i:11550523 original size:26 final size:26
Alignment explanation
Indices: 11550494--11550601 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
11550484 TGGTACAAAT
11550494 TGATAATAGG-TTAGGTAAATGTTCCA
1 TGATAAT-GGATTAGGTAAATGTTCCA
*
11550520 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
11550546 TGATAATGGGTTAGGTAAATGTCCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
11550572 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
11550598 TGAT
1 TGAT
11550602 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
25 2 0.03
26 73 0.97
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:11552264 original size:27 final size:26
Alignment explanation
Indices: 11552224--11552354 Score: 165
Period size: 27 Copynumber: 4.9 Consensus size: 26
11552214 AGGAAGCGTC
*
11552224 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
11552251 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
* *
11552278 CTGGTGGCTATGCCACGATTATCTAAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
11552305 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
11552332 CTGGTGGCTCTGCCACAATATCT
1 CTGGTGGCTCTGCCACATTATCT
11552355 ATATCTAGTG
Statistics
Matches: 93, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.11
27 80 0.86
28 3 0.03
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:11552307 original size:54 final size:53
Alignment explanation
Indices: 11552224--11552360 Score: 211
Period size: 54 Copynumber: 2.5 Consensus size: 53
11552214 AGGAAGCGTC
*
11552224 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCAC-ATTATCTAATCTGGTGGCTCTGCCACATATATCTATT
*
11552278 CTGGTGGCTATGCCACGATTATCTAATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTAATCTGGTGGCTCTGCCACATATATCTATT
* *
11552332 CTGGTGGCTCTGCCACAATATCTATATCT
1 CTGGTGGCTATGCCACATTATCTA-ATCT
11552361 AGTGACTTCT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 7 0.09
54 70 0.91
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTAATCTGGTGGCTCTGCCACATATATCTATT
Found at i:11558542 original size:26 final size:26
Alignment explanation
Indices: 11558513--11558620 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
11558503 TGGTACAAAT
11558513 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11558539 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11558565 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11558591 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11558617 TGAT
1 TGAT
11558621 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11560324 original size:54 final size:54
Alignment explanation
Indices: 11560242--11560382 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
11560232 AGGAAGCGTC
11560242 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
**
11560296 CTGGTGGCTATGCCATGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * *
11560350 CTGGTGGTTCTGCCACAA-TATTTGTATCTGGTG
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
11560383 ACTTCGTCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.06
54 74 0.94
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:11560378 original size:32 final size:27
Alignment explanation
Indices: 11560242--11560382 Score: 171
Period size: 27 Copynumber: 5.2 Consensus size: 27
11560232 AGGAAGCGTC
*
11560242 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
*
11560269 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
* *
11560296 CTGGTGGCTATGCCATGAT-TATCTGAT
1 CTGGTGGCTCTGCCA-CATATATCTGAT
*
11560323 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
* *
11560350 CTGGTGGTTCTGCCACA-ATATTTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
11560377 CTGGTG
1 CTGGTG
11560383 ACTTCGTCAC
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
26 8 0.08
27 88 0.89
28 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:11568906 original size:32 final size:32
Alignment explanation
Indices: 11568865--11568926 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
11568855 CTCTAGCTGC
*
11568865 ATTGTAATATCGAAGAACATGCAACACATTGT
1 ATTGTAATATCAAAGAACATGCAACACATTGT
*
11568897 ATTGTAATATCAAAGAACGTGCAACACATT
1 ATTGTAATATCAAAGAACATGCAACACATT
11568927 TTCATACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (32 bp):
ATTGTAATATCAAAGAACATGCAACACATTGT
Found at i:11577983 original size:26 final size:26
Alignment explanation
Indices: 11577954--11578003 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
11577944 TCATTATATA
11577954 GCTCTTCGTGAGCTTCCTAATTAAAG
1 GCTCTTCGTGAGCTTCCTAATTAAAG
* * *
11577980 GCTCTTTGTTAGCTTCTTAATTAA
1 GCTCTTCGTGAGCTTCCTAATTAA
11578004 TTAATCTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (26 bp):
GCTCTTCGTGAGCTTCCTAATTAAAG
Found at i:11580196 original size:26 final size:26
Alignment explanation
Indices: 11580144--11580210 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
11580134 AAAAAGTAAT
*
11580144 AGTGACAACTTTTGG-TTAGTAATCA
1 AGTGACAACTTTTGGTTTAGTAACCA
11580169 AGTGACAACTTTTGGTTTAGTAACCA
1 AGTGACAACTTTTGGTTTAGTAACCA
11580195 AGTGACAACTTTTGGT
1 AGTGACAACTTTTGGT
11580211 CACTTATAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 15 0.38
26 25 0.62
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (26 bp):
AGTGACAACTTTTGGTTTAGTAACCA
Found at i:11582819 original size:43 final size:43
Alignment explanation
Indices: 11582761--11582859 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
11582751 CCTAGACTTA
*
11582761 GTCTTACATGT-AATCAAACATCGATG-TCACTGTCCCAGACAGG
1 GTCTTACACGTAAATCAAACA-CGATGCTCA-TGTCCCAGACAGG
* * * * *
11582804 GTCTTACAC-TAAATCAGATACGATGCTGATGTCCCATACATG
1 GTCTTACACGTAAATCAAACACGATGCTCATGTCCCAGACAGG
11582846 GTCTTACACGTAAA
1 GTCTTACACGTAAA
11582860 CACATACCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 26 0.55
43 21 0.45
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
GTCTTACACGTAAATCAAACACGATGCTCATGTCCCAGACAGG
Found at i:11592244 original size:32 final size:32
Alignment explanation
Indices: 11592208--11592273 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
11592198 AAATTGTATA
*
11592208 TGCTTTTATGCTTTAATTAAATGTTGTGTTTG
1 TGCTTTTATGCTTGAATTAAATGTTGTGTTTG
11592240 TGCTTTTATGCTTGAATTAAATGTTGTGTTTG
1 TGCTTTTATGCTTGAATTAAATGTTGTGTTTG
11592272 TG
1 TG
11592274 AATTGCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (32 bp):
TGCTTTTATGCTTGAATTAAATGTTGTGTTTG
Found at i:11603110 original size:24 final size:24
Alignment explanation
Indices: 11603035--11603110 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
11603025 TCCATTTTCA
11603035 GGAAGCTCATAAAGAGCC-T-ATCG
1 GGAAGCTCAT-AAGAGCCATAATCG
* * * *
11603058 GGAAGCTTATCA-AGCTATATAACG
1 GGAAGCTCATAAGAGCCATA-ATCG
*
11603082 AGAAGCTCATAAGAGCCATAATCG
1 GGAAGCTCATAAGAGCCATAATCG
11603106 GGAAG
1 GGAAG
11603111 TTCACAAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 9 0.23
24 19 0.49
25 6 0.15
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCG
Found at i:11604736 original size:46 final size:46
Alignment explanation
Indices: 11604662--11604751 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
11604652 TTGTTGGTGT
* * *
11604662 GTGGGGATAAAAATGAATTTATGGTAAATTAACGAAAGCTTCAACG
1 GTGGGAATAAAAATGAATATATGATAAATTAACGAAAGCTTCAACG
*
11604708 GTGGGAATAAAAATGAATATATGATAAATTAACGAATGCTTCAA
1 GTGGGAATAAAAATGAATATATGATAAATTAACGAAAGCTTCAA
11604752 TTTAAGGTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (46 bp):
GTGGGAATAAAAATGAATATATGATAAATTAACGAAAGCTTCAACG
Found at i:11607823 original size:29 final size:28
Alignment explanation
Indices: 11607791--11607858 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
11607781 TAATTAGACT
11607791 TAAATTTTAAAATATAAAAAATA-AAAAAA
1 TAAATTTTAAAA-AT-AAAAATAGAAAAAA
* *
11607820 TAAATTTTTGAAAATAAAAATAGAAAAAC
1 TAAA-TTTTAAAAATAAAAATAGAAAAAA
*
11607849 TAAATATTAA
1 TAAATTTTAA
11607859 CTTTGTAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 11 0.33
29 15 0.45
30 7 0.21
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAATTTTAAAAATAAAAATAGAAAAAA
Found at i:11611611 original size:9 final size:9
Alignment explanation
Indices: 11611582--11611632 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
11611572 TTTCATTTCT
11611582 TTATTAAATA
1 TTATT-AATA
* *
11611592 TTCTTATTA
1 TTATTAATA
*
11611601 TTTTTAATA
1 TTATTAATA
11611610 TTATTAATA
1 TTATTAATA
*
11611619 TTATTACTA
1 TTATTAATA
11611628 TTATT
1 TTATT
11611633 TTATTTCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
9 31 0.89
10 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATTAATA
Found at i:11611614 original size:3 final size:3
Alignment explanation
Indices: 11611590--11611748 Score: 80
Period size: 3 Copynumber: 52.7 Consensus size: 3
11611580 CTTTATTAAA
* * * * *
11611590 TAT TCT TAT TAT TTT TAA TAT TAT TAA TAT TAT TAC TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
11611637 T-T CTAT TAT T-T TCAT TAT TAT TAC TGT TAG TAT TAT T-T TCAT TAA
1 TAT -TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* * * *
11611682 TAT TAT TTT TAT TAA CA- TAT TAAT TAT TCT TAAT GTAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT -TAT TAT TAT TAT
11611728 CTAGT T-T TAT TAT TAT TAT TA
1 -TA-T TAT TAT TAT TAT TAT TA
11611749 ACATTAGTGT
Statistics
Matches: 116, Mismatches: 25, Indels: 30
0.68 0.15 0.18
Matches are distributed among these distances:
2 11 0.09
3 91 0.78
4 12 0.10
5 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11611867 original size:3 final size:3
Alignment explanation
Indices: 11611859--11611893 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
11611849 TAGATTTCAA
*
11611859 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11611894 GTGTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:11612231 original size:15 final size:15
Alignment explanation
Indices: 11612213--11612242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11612203 TATTGTTATA
*
11612213 TTTATTATTATTACT
1 TTTATTATAATTACT
11612228 TTTATTATAATTACT
1 TTTATTATAATTACT
11612243 ACTATTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATAATTACT
Found at i:11612235 original size:24 final size:24
Alignment explanation
Indices: 11612197--11612253 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
11612187 TTATCGCTAA
* * * *
11612197 TATTACTATTGTTATATTTATTAT
1 TATTACTATTATTATAATTACTAC
*
11612221 TATTACTTTTATTATAATTACTAC
1 TATTACTATTATTATAATTACTAC
11612245 TATTACTAT
1 TATTACTAT
11612254 AGCTTTTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTACTATTATTATAATTACTAC
Found at i:11614172 original size:17 final size:16
Alignment explanation
Indices: 11614129--11614229 Score: 60
Period size: 17 Copynumber: 5.9 Consensus size: 16
11614119 ACTTCGTAAC
11614129 TTTGATGAGCTCGCAA
1 TTTGATGAGCTCGCAA
** *
11614145 TCTTGGGGAGCTCACACA
1 T-TTGATGAGCTCGCA-A
* *
11614163 TTTGATGAGCTTGCAGT
1 TTTGATGAGCTCGCA-A
*
11614180 TTTGAGTGAACTCGCAA
1 TTTGA-TGAGCTCGCAA
* *
11614197 CTTTG-TAGAGCTCACACT
1 -TTTGAT-GAGCTCGCA-A
11614215 TTTGATGAGCTCGCA
1 TTTGATGAGCTCGCA
11614230 GTCTTGCTAT
Statistics
Matches: 62, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
16 2 0.03
17 45 0.73
18 15 0.24
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (16 bp):
TTTGATGAGCTCGCAA
Found at i:11615242 original size:9 final size:9
Alignment explanation
Indices: 11615228--11615265 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
11615218 TAAATTTTTG
11615228 AATTCGAAT
1 AATTCGAAT
11615237 AATTCGAAT
1 AATTCGAAT
11615246 AATTCGAAT
1 AATTCGAAT
*
11615255 AATTTGAAT
1 AATTCGAAT
11615264 AA
1 AA
11615266 ACTAAATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (9 bp):
AATTCGAAT
Found at i:11623451 original size:28 final size:28
Alignment explanation
Indices: 11623420--11623547 Score: 184
Period size: 28 Copynumber: 4.6 Consensus size: 28
11623410 ATTAAAACAT
*
11623420 TTAGTGTGCGAGACTTTGATTATGGCAC
1 TTAGTGTGCGAGACATTGATTATGGCAC
* * *
11623448 TTAGTGTGTGAGATATTGATCATGGCAC
1 TTAGTGTGCGAGACATTGATTATGGCAC
* *
11623476 TTAGTGTGCGAGACAATGATTATTGCAC
1 TTAGTGTGCGAGACATTGATTATGGCAC
* *
11623504 TTAGTGTGAGAGACATTGATTGTGGCAC
1 TTAGTGTGCGAGACATTGATTATGGCAC
11623532 TTAGTGTGCGAGACAT
1 TTAGTGTGCGAGACAT
11623548 CAAGTATGCG
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
TTAGTGTGCGAGACATTGATTATGGCAC
Done.