Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 44 of 213
Found at i:11758850 original size:17 final size:18
Alignment explanation
Indices: 11758818--11758853 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
11758808 ATATTATTTT
11758818 TTAATTATTTAAAATATA
1 TTAATTATTTAAAATATA
*
11758836 TTAATT-TTTATAATATA
1 TTAATTATTTAAAATATA
11758853 T
1 T
11758854 GACAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATTTAAAATATA
Found at i:11764892 original size:44 final size:42
Alignment explanation
Indices: 11764744--11764897 Score: 127
Period size: 42 Copynumber: 3.6 Consensus size: 42
11764734 CGTACAATGA
*
11764744 CAACGTCCTAGACGTGGTCTTACATGTAATCAAATAACGAT-C
1 CAACGTCCTAGACGTGGTCTTACATGTAATCAAA-ATCGATGC
** * * *
11764786 CATTGTCCCAGATAG-GGTCTTACATGTAATC-ATATACGATGC
1 CAACGTCCTAGA-CGTGGTCTTACATGTAATCAAAAT-CGATGC
* * * * *
11764828 CAATGT-CTCCGACATTGTCTTACACGTAAATCTAAAATCGATGC
1 CAACGTCCT-AGACGTGGTCTTACATGT-AATC-AAAATCGATGC
11764872 CAACGTCCTAGACGTGGTCTTACATG
1 CAACGTCCTAGACGTGGTCTTACATG
11764898 ATATCACATA
Statistics
Matches: 84, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.01
41 6 0.07
42 43 0.51
43 5 0.06
44 24 0.29
45 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
CAACGTCCTAGACGTGGTCTTACATGTAATCAAAATCGATGC
Found at i:11770176 original size:29 final size:30
Alignment explanation
Indices: 11770117--11770174 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11770107 TCCGAGCCTT
*
11770117 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
11770147 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
11770175 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:11770404 original size:13 final size:13
Alignment explanation
Indices: 11770386--11770417 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11770376 TTTCCAGCAA
11770386 TTATGAATTTATT
1 TTATGAATTTATT
11770399 TTATGAATTTATT
1 TTATGAATTTATT
*
11770412 TGATGA
1 TTATGA
11770418 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:11770599 original size:50 final size:50
Alignment explanation
Indices: 11770496--11770683 Score: 259
Period size: 50 Copynumber: 3.6 Consensus size: 50
11770486 ATACGAATCA
*
11770496 TGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--GAGAGGTCCCC
* *
11770552 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCCCC
* *
11770602 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCCCC
* *
11770652 TATAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
11770684 TGTTATTATC
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
50 86 0.70
52 1 0.01
53 3 0.02
55 2 0.02
56 31 0.25
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.22
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCCCC
Found at i:11775620 original size:3 final size:3
Alignment explanation
Indices: 11775607--11775639 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
11775597 GCCGGTGAGT
11775607 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
11775640 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:11788210 original size:18 final size:18
Alignment explanation
Indices: 11788187--11788229 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11788177 GTTCAATGTG
11788187 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
11788205 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
11788223 TAATTAA
1 TAATTAA
11788230 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:11790245 original size:8 final size:8
Alignment explanation
Indices: 11790232--11790296 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
11790222 ATCACAATTT
11790232 AATAAACA
1 AATAAACA
11790240 AATAAACGA
1 AATAAAC-A
*
11790249 AATGAAATA
1 AAT-AAACA
* *
11790258 ATTGAACA
1 AATAAACA
11790266 AATAAACA
1 AATAAACA
* *
11790274 AACATACA
1 AATAAACA
11790282 AATAAACA
1 AATAAACA
11790290 AATAAAC
1 AATAAAC
11790297 CAACAACACC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 35 0.78
9 7 0.16
10 3 0.07
ACGTcount: A:0.68, C:0.12, G:0.05, T:0.15
Consensus pattern (8 bp):
AATAAACA
Found at i:11790506 original size:13 final size:13
Alignment explanation
Indices: 11790488--11790517 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11790478 TAACATAGTT
11790488 TAAAATAAATAAA
1 TAAAATAAATAAA
11790501 TAAAATAAATAAA
1 TAAAATAAATAAA
11790514 -AAAA
1 TAAAA
11790518 CACAGAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:11793557 original size:104 final size:103
Alignment explanation
Indices: 11793384--11793792 Score: 489
Period size: 104 Copynumber: 3.9 Consensus size: 103
11793374 AGTTGTTTGA
* * * * *
11793384 GAGTTGCGATCTTTAAATCAGCTAACTCAAAAGAACT-TAGTTGCGAGCTTAACTCAGCTAACTT
1 GAGTTGCGAGC-TTAACTCAGCTAACTC-AAATAACTGGAGTTGCGAGCTTAACTCAGCTAACAT
* * *
11793448 TTAATCATCAGCTGGGAATGTAGGTTCGCGAGCTGTTTCG
64 TTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
* *
11793488 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAGGTTGCGAGCTTAACTCAGCTAACCTT
1 GAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGGA-GTTGCGAGCTTAACTCAGCTAACATT
* * * *
11793553 TAATCATTAGTTGGGAACGTAGGTCAGCAAGTTGTTTCG
65 TAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
** * * * * *
11793592 GAGTTATGAGCTTAACTCGGCTAACTCAAATAATTGGAGTTGTGAGCTTAACTCATCCAACATTT
1 GAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGGAGTTGCGAGCTTAACTCAGCTAACATTT
* * * * *
11793657 AATCATCAATTGGGAACATAGGTCCACGAGCTACTTT-A
66 AATCATCAGTTGGGAACGTAGGTCCGCGAGCT-GTTTCG
* * *
11793695 GAGTTGTGAGCTTAACTCAGCTAACTCAAATAACTGGTGGTTTCGAGCTTAACTCAGCTAACATT
1 GAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGG-AGTTGCGAGCTTAACTCAGCTAACATT
*
11793760 TAATCATCAGTTGGGAACGTAAGTCCGCGAGCT
65 TAATCATCAGTTGGGAACGTAGGTCCGCGAGCT
11793793 ATTTTAAAGG
Statistics
Matches: 260, Mismatches: 41, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
102 7 0.03
103 97 0.37
104 156 0.60
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (103 bp):
GAGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGGAGTTGCGAGCTTAACTCAGCTAACATTT
AATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
Found at i:11793884 original size:69 final size:67
Alignment explanation
Indices: 11793760--11793969 Score: 231
Period size: 69 Copynumber: 3.0 Consensus size: 67
11793750 AGCTAACATT
* * * * * * **
11793760 TAATCATCAGTTGGGAACGTAAGTCCGCGAGCTATTTTAAAGGCTACGATATTAAATCAGCGAGC
1 TAAT-ATCAGCTGGGAACGTAGGTCCGCAAGCT-GTTT-GAGGCTGCGATATTAAATCAATGAGC
11793825 CTTTA
63 CTTTA
* *
11793830 TAATATCAGCTGGGAACGTAGGTCCGTAAGCTGTTTGAGGGGCTGCGATCTTAAATCAATGAGCC
1 TAATATCAGCTGGGAACGTAGGTCCGCAAGCTGTTTGA--GGCTGCGATATTAAATCAATGAGCC
11793895 TTTA
64 TTTA
* * * *
11793899 TAATATCAACTAGGAACGTAGGTCCGCAAGCTGCTTTTGAGGTTGCGATTTTAAATCAATGAGCC
1 TAATATCAGCTGGGAACGTAGGTCCGCAAGCTG--TTTGAGGCTGCGATATTAAATCAATGAGCC
11793964 TTTA
64 TTTA
11793968 TA
1 TA
11793970 TAGAAGGTCG
Statistics
Matches: 121, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
67 1 0.01
68 3 0.02
69 108 0.89
70 4 0.03
71 5 0.04
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (67 bp):
TAATATCAGCTGGGAACGTAGGTCCGCAAGCTGTTTGAGGCTGCGATATTAAATCAATGAGCCTT
TA
Found at i:11794838 original size:15 final size:15
Alignment explanation
Indices: 11794818--11794847 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11794808 CAAAATTTTG
11794818 ACAAGAACATAACAA
1 ACAAGAACATAACAA
11794833 ACAAGAACATAACAA
1 ACAAGAACATAACAA
11794848 TGTGATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
ACAAGAACATAACAA
Found at i:11795140 original size:15 final size:15
Alignment explanation
Indices: 11795115--11795149 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11795105 GACTCTATTT
*
11795115 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
11795129 TAATTAATATTAAGA
1 TAATTAATATTAAGA
11795144 TAATTA
1 TAATTA
11795150 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:11812434 original size:22 final size:22
Alignment explanation
Indices: 11812373--11812436 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
11812363 ACCACACTAG
* *
11812373 AGAGCA-CGTAGTGCT-AAGCAG
1 AGAGCACCGAAGTGCTGAA-CAA
* **
11812394 AGAGCACTGAAGTATTGAACAA
1 AGAGCACCGAAGTGCTGAACAA
11812416 AGAGCACCGAAGTGCTGAACA
1 AGAGCACCGAAGTGCTGAACA
11812437 TGTACAAGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 6 0.18
22 25 0.76
23 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (22 bp):
AGAGCACCGAAGTGCTGAACAA
Found at i:11813972 original size:58 final size:57
Alignment explanation
Indices: 11813840--11813972 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 57
11813830 TTTAATTCAT
* * **
11813840 ATAATAATTATATTAAGAATTTTATTAAAGTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AGTATGGTTAAAGTATATATTATTTTATTAAATTATATTTA
* * * *
11813898 ATAATAATTATGTTAAAGTATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAAGTATGGTTAAAGTATATATTA-TTTTATTAAATTATATTTA
11813956 ATAATAATCT-TATTAAA
1 ATAATAAT-TATATTAAA
11813973 ATTTAATAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 16 0.25
58 47 0.73
59 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (57 bp):
ATAATAATTATATTAAAGTATGGTTAAAGTATATATTATTTTATTAAATTATATTTA
Found at i:11815760 original size:32 final size:32
Alignment explanation
Indices: 11815699--11815763 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
11815689 TCCTCCCTTC
***
11815699 TCCATTTCTTTTAGTGTAATTTTTCTATGTTT
1 TCCATTTCTTTTAACATAATTTTTCTATGTTT
11815731 TCCATTTCTTTTAACATAACTTTTT-TATGTTT
1 TCCATTTCTTTTAACATAA-TTTTTCTATGTTT
11815763 T
1 T
11815764 TGAAACAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (32 bp):
TCCATTTCTTTTAACATAATTTTTCTATGTTT
Found at i:11820370 original size:18 final size:16
Alignment explanation
Indices: 11820347--11820381 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11820337 AATTTAACTT
11820347 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
11820365 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
11820381 T
1 T
11820382 TATAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:11831646 original size:16 final size:18
Alignment explanation
Indices: 11831624--11831668 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
11831614 TTATTATTTG
*
11831624 TTTTATAATATTTTAA-A
1 TTTTATAATATTTAAACA
11831641 -TTTAT-AT-TTTAAACA
1 TTTTATAATATTTAAACA
11831656 TTTTATAATATTT
1 TTTTATAATATTT
11831669 GTTTATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 10 0.43
17 2 0.09
18 3 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAATATTTAAACA
Found at i:11836419 original size:21 final size:23
Alignment explanation
Indices: 11836390--11836445 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
11836380 ATATTTACTT
*
11836390 TATAGAATATTTAG-TTTTATTAG
1 TATA-AATATTTAGCATTTATTAG
11836413 TATAATATATTTAGCATTTATTAG
1 TATAA-ATATTTAGCATTTATTAG
11836437 TATAAATAT
1 TATAAATAT
11836446 CTTTGTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 13 0.43
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (23 bp):
TATAAATATTTAGCATTTATTAG
Found at i:11836456 original size:25 final size:24
Alignment explanation
Indices: 11836396--11836445 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11836386 ACTTTATAGA
*
11836396 ATATTTAG-TTTTATTAGTATAAT
1 ATATTTAGCATTTATTAGTATAAT
11836419 ATATTTAGCATTTATTAGTATAA-
1 ATATTTAGCATTTATTAGTATAAT
11836442 ATAT
1 ATAT
11836446 CTTTGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGTATAAT
Found at i:11842647 original size:6 final size:6
Alignment explanation
Indices: 11842636--11842668 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11842626 TAAGTGAAGT
11842636 AAAAA- AAAAA- AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
11842669 TGCACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:11844956 original size:30 final size:30
Alignment explanation
Indices: 11844910--11845033 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
11844900 TTTTATTATG
*
11844910 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
11844941 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
11844971 CCAATATTTTATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
11845001 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11845031 CCA
1 CCA
11845034 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:11844965 original size:15 final size:15
Alignment explanation
Indices: 11844920--11845027 Score: 71
Period size: 15 Copynumber: 7.2 Consensus size: 15
11844910 CCAATATCTC
11844920 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
11844935 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
11844950 GATACCCATATCTTT
1 GATACCCATATCTTT
* *
11844965 GACTTTCCAATAT-TTT
1 GA--TACCCATATCTTT
11844981 -ATACCCATATCTTT
1 GATACCCATATCTTT
** * *
11844995 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
11845010 GATACCCATATCTTT
1 GATACCCATATCTTT
11845025 GAT
1 GAT
11845028 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
13 7 0.10
14 11 0.16
15 31 0.46
16 11 0.16
17 7 0.10
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:11849645 original size:30 final size:30
Alignment explanation
Indices: 11849599--11849692 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
11849589 TTTTATTATG
*
11849599 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
11849630 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
11849660 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11849690 CCA
1 CCA
11849693 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:11849654 original size:15 final size:15
Alignment explanation
Indices: 11849609--11849686 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
11849599 CCAATATCTC
11849609 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
11849624 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
11849639 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
11849654 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
11849669 GATACCCATATCTTT
1 GATACCCATATCTTT
11849684 GAT
1 GAT
11849687 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:11859113 original size:23 final size:22
Alignment explanation
Indices: 11859068--11859113 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
11859058 GAGAAATACA
* *
11859068 TATTTTAATTTTAATTTTTATT
1 TATTTTAATTTTAACTTTAATT
*
11859090 TATTTGTATTTTTAACTTTAATT
1 TATTT-TAATTTTAACTTTAATT
11859113 T
1 T
11859114 TTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTAATTTTAACTTTAATT
Found at i:11859128 original size:29 final size:29
Alignment explanation
Indices: 11859070--11859129 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
11859060 GAAATACATA
* *
11859070 TTTTAATTTTAATTTTTATTTATTTGTAT
1 TTTTAACTTTAATTTTTATATATTTGTAT
11859099 TTTTAACTTTAATTTTTATATATATT-TAT
1 TTTTAACTTTAATTTTTATATAT-TTGTAT
11859128 TT
1 TT
11859130 ATTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTAACTTTAATTTTTATATATTTGTAT
Found at i:11859153 original size:14 final size:14
Alignment explanation
Indices: 11859084--11859141 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
11859074 AATTTTAATT
*
11859084 TTTATTTATTTGTA
1 TTTATTTATTTATA
*
11859098 TTT-TTAACTTTA-A
1 TTTATTTA-TTTATA
*
11859111 -TT-TTTATATATA
1 TTTATTTATTTATA
11859123 TTTATTTATTTATA
1 TTTATTTATTTATA
11859137 TTTAT
1 TTTAT
11859142 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 6 0.17
14 20 0.57
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:11859309 original size:6 final size:7
Alignment explanation
Indices: 11859293--11859323 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11859283 ATACGTACCC
11859293 AAAATCA
1 AAAATCA
11859300 AAAATCA
1 AAAATCA
11859307 AAAATCA
1 AAAATCA
*
11859314 AAAATTA
1 AAAATCA
11859321 AAA
1 AAA
11859324 CCCAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATCA
Found at i:11865394 original size:36 final size:36
Alignment explanation
Indices: 11865328--11865406 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
11865318 ATCTTTGCTG
* * * *
11865328 GAGGATTCACATGGTGCAACAAATTGGGCTTTACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
* *
11865364 GAGGGTTCACATGGTGCAGCGAACTAGGCTTCACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
*
11865400 AAGGGTT
1 GAGGGTT
11865407 TGCATAATGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (36 bp):
GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
Found at i:11866752 original size:17 final size:17
Alignment explanation
Indices: 11866723--11866882 Score: 87
Period size: 17 Copynumber: 9.4 Consensus size: 17
11866713 CGCCTAACAT
*
11866723 AGCTCGCACCTTTGGTG
1 AGCTCGCAGCTTTGGTG
*
11866740 A-CTTCGCAGCTTTGATG
1 AGC-TCGCAGCTTTGGTG
*
11866757 AGCTCGCAGCCTTGGTG
1 AGCTCGCAGCTTTGGTG
* * *
11866774 AGCTCACA-ATATTGATG
1 AGCTCGCAGCT-TTGGTG
*
11866791 AGATCGCAG-TCTTGGTG
1 AGCTCGCAGCT-TTGGTG
*
11866808 AGCTCGTA-CATTTGAG-G
1 AGCTCGCAGC-TTTG-GTG
* **
11866825 AGCTCACAATTTTGGTG
1 AGCTCGCAGCTTTGGTG
*
11866842 AGCTCGCAACTTTAGGTG
1 AGCTCGCAGCTTT-GGTG
** * *
11866860 AGCTTACATCTTTGGTA
1 AGCTCGCAGCTTTGGTG
11866877 AGCTCG
1 AGCTCG
11866883 TACCTTTGGG
Statistics
Matches: 108, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
16 2 0.02
17 89 0.82
18 17 0.16
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (17 bp):
AGCTCGCAGCTTTGGTG
Found at i:11866861 original size:18 final size:17
Alignment explanation
Indices: 11866824--11866863 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11866814 TACATTTGAG
*
11866824 GAGCTCACAATTTTGGT
1 GAGCTCACAATTTAGGT
*
11866841 GAGCTCGCAACTTTAGGT
1 GAGCTCACAA-TTTAGGT
11866859 GAGCT
1 GAGCT
11866864 TACATCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (17 bp):
GAGCTCACAATTTAGGT
Found at i:11870417 original size:51 final size:51
Alignment explanation
Indices: 11870332--11870436 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
11870322 TAAAGTTAGT
* * *
11870332 TGATGAGGTTTAAAATAAGTTACTTGTGTAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
11870383 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
11870434 TGA
1 TGA
11870437 ATTTGAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (51 bp):
TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
Found at i:11870422 original size:26 final size:26
Alignment explanation
Indices: 11870342--11870423 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
11870332 TGATGAGGTT
*
11870342 TAAAATAAGTTACTTGTGTAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
* * * **
11870368 TAAAA-ATGTTAACCATG-ATA-AGGCT
1 TAAAATAAGTT-A-CTTGTATAGTGGAA
11870393 TAAAATAAGTTACTTGTATAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
11870419 TAAAA
1 TAAAA
11870424 ATGTTAACCA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAATAAGTTACTTGTATAGTGGAA
Found at i:11878230 original size:14 final size:14
Alignment explanation
Indices: 11878211--11878241 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11878201 GGAATGAAAA
*
11878211 TATTTTTTTCTCTT
1 TATTTTTTTCTATT
11878225 TATTTTTTTCTATT
1 TATTTTTTTCTATT
11878239 TAT
1 TAT
11878242 ACAGGCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTTTCTATT
Found at i:11878897 original size:16 final size:15
Alignment explanation
Indices: 11878876--11878905 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11878866 AAGTTTATTC
11878876 ATATATATATATTTAG
1 ATATATAT-TATTTAG
11878892 ATATATATTATTTA
1 ATATATATTATTTA
11878906 TACTTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATATATTATTTAG
Found at i:11886859 original size:18 final size:19
Alignment explanation
Indices: 11886821--11886858 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
11886811 TTAACTTTTC
11886821 TTATTTTTATCAAATTATT
1 TTATTTTTATCAAATTATT
11886840 TTATTTTT-TC-AATTATT
1 TTATTTTTATCAAATTATT
11886857 TT
1 TT
11886859 TTTCAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 2 0.11
19 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTTATCAAATTATT
Found at i:11899702 original size:17 final size:18
Alignment explanation
Indices: 11899680--11899715 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
11899670 GACAACCACG
11899680 TCTTTTTTTTT-TCTTTT
1 TCTTTTTTTTTGTCTTTT
11899697 TCTTTTTTTTTGTCTTTT
1 TCTTTTTTTTTGTCTTTT
11899715 T
1 T
11899716 GCATGCATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (18 bp):
TCTTTTTTTTTGTCTTTT
Found at i:11900732 original size:17 final size:17
Alignment explanation
Indices: 11900681--11900732 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
11900671 ATGGAAACAT
* * *
11900681 AATCTTCAAGGATATGT
1 AATCTTAAAAGATATGC
*
11900698 AATCTTAGATATGATATGC
1 AATCTTA-A-AAGATATGC
11900717 AATCTTAAAAGATATG
1 AATCTTAAAAGATATG
11900733 ATTCTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
AATCTTAAAAGATATGC
Found at i:11913451 original size:44 final size:44
Alignment explanation
Indices: 11913383--11913582 Score: 198
Period size: 44 Copynumber: 4.6 Consensus size: 44
11913373 AATCGTTACA
*
11913383 CGGTGGAATCAGCACTTAGTAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
*
11913427 CGGTGGAATTAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
* * * ** ** *
11913471 CGATGGAATCAGTACTTAGCAACCACCTTATAATC-AATTAT-A
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
* ** *
11913513 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATT--AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCA-TGTTCAAAGGATCC
11913555 CGGTGGAATCAGCACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
11913583 TTATTGTTAG
Statistics
Matches: 131, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
40 2 0.02
41 18 0.14
42 13 0.10
43 25 0.19
44 73 0.56
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
Found at i:11936933 original size:42 final size:42
Alignment explanation
Indices: 11936869--11936969 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
11936859 AGCTGAACAG
*
11936869 AAACCCATAAGGGTTAATCTGAAGCTCAGAAA-AGATAAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCA-AAAGAGATAAACTA
* * * * *
11936911 AAACCCATTAGGGTTAAACTGAAGCTCAAAAGAGCTGAATTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGATAAACTA
11936953 AAACCCATAAGGGTTAA
1 AAACCCATAAGGGTTAA
11936970 TCTAAAACTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 3 0.06
42 48 0.94
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.20
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGATAAACTA
Found at i:11936982 original size:21 final size:20
Alignment explanation
Indices: 11936953--11937006 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
11936943 AGCTGAATTG
* *
11936953 AAACCCATAAGGGTTAATCTA
1 AAACTCATAAGAGTTAA-CTA
*
11936974 AAACTCATATGAGTTAACTA
1 AAACTCATAAGAGTTAACTA
* *
11936994 AAGCTCATGAGAG
1 AAACTCATAAGAG
11937007 CTAAACTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
AAACTCATAAGAGTTAACTA
Found at i:11942082 original size:15 final size:16
Alignment explanation
Indices: 11942042--11942093 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
11942032 GTCCTGTTTG
** *
11942042 TTATTTTTGCTATTAA
1 TTATTTTTATTATTTA
*
11942058 TTAATTTTATTATTT-
1 TTATTTTTATTATTTA
11942073 TTATTTTTATTATTTA
1 TTATTTTTATTATTTA
11942089 TTATT
1 TTATT
11942094 ATTACTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTTTATTATTTA
Found at i:11942085 original size:3 final size:3
Alignment explanation
Indices: 11942064--11942125 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
11942054 TTAATTAATT
* * * * *
11942064 TTA TTA TTT TTA TTT TTA TTA TTTA TTA TTA TTA CTC TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
11942110 TTGA -TA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA T
11942126 GTTTGGTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11942088 original size:22 final size:22
Alignment explanation
Indices: 11942063--11942108 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
11942053 ATTAATTAAT
* * *
11942063 TTTATTATTTTTATTTTTATTA
1 TTTATTATTATTACTCTTATTA
11942085 TTTATTATTATTACTCTTATTA
1 TTTATTATTATTACTCTTATTA
11942107 TT
1 TT
11942109 GTTGATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTATTATTACTCTTATTA
Found at i:11942964 original size:10 final size:10
Alignment explanation
Indices: 11942949--11942979 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
11942939 TATTAATTAA
11942949 TTTTATTATT
1 TTTTATTATT
11942959 TTTTATTATT
1 TTTTATTATT
11942969 TATTTATTATT
1 T-TTTATTATT
11942980 ACTCTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTATTATT
Found at i:11951166 original size:34 final size:35
Alignment explanation
Indices: 11951111--11951177 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11951101 CAAACACCAG
*
11951111 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
11951146 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11951178 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11954524 original size:19 final size:20
Alignment explanation
Indices: 11954500--11954540 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
11954490 ATACAAAAAA
11954500 TTATAAAAAT-TTTGATTTT
1 TTATAAAAATCTTTGATTTT
*
11954519 TTATAAAAATCTTTTATTTT
1 TTATAAAAATCTTTGATTTT
11954539 TT
1 TT
11954541 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATAAAAATCTTTGATTTT
Found at i:11954541 original size:29 final size:28
Alignment explanation
Indices: 11954509--11954626 Score: 77
Period size: 28 Copynumber: 4.3 Consensus size: 28
11954499 ATTATAAAAA
*
11954509 TTTTGATTTTTTATAAAA-ATCTTTTATTT
1 TTTTAATTTTTTA-AAAATAT-TTTTATTT
**
11954538 TTTTAATTTTTTAAAAATATTTTTATAC
1 TTTTAATTTTTTAAAAATATTTTTATTT
* ** *
11954566 TTTT--TTATAAAAAAATA-TTTTATAT
1 TTTTAATTTTTTAAAAATATTTTTATTT
* * *
11954591 TTTTAACTTTTTATATAA-ATTTTTA-AT
1 TTTTAATTTTTTA-AAAATATTTTTATTT
11954618 TTTTAATTT
1 TTTTAATTT
11954627 ATGCTTTTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
25 11 0.15
26 10 0.14
27 14 0.20
28 22 0.31
29 14 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTAATTTTTTAAAAATATTTTTATTT
Found at i:11954558 original size:22 final size:23
Alignment explanation
Indices: 11954533--11954594 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
11954523 AAAAATCTTT
*
11954533 TATTTTTTTAATTTTTTA-AAAA
1 TATTTTTATAATTTTTTATAAAA
*
11954555 TATTTTTATACTTTTTTATAAAAA
1 TATTTTTATAATTTTTTAT-AAAA
*
11954579 AATATTTTAT-ATTTTT
1 TAT-TTTTATAATTTTT
11954595 AACTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.48
24 11 0.33
25 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTTATAATTTTTTATAAAA
Found at i:11965763 original size:22 final size:23
Alignment explanation
Indices: 11965719--11965769 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
11965709 ATGAATGTTG
*
11965719 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT-ACATATAATTAT
11965743 TTTAAATTTAT-CATATAATTAT
1 TTTAAATTTATACATATAATTAT
11965765 TTTAA
1 TTTAA
11965770 GTTTCATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 15 0.58
24 11 0.42
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAATTTATACATATAATTAT
Found at i:11971080 original size:29 final size:29
Alignment explanation
Indices: 11971013--11971096 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
11971003 GTTTAGATTC
11971013 AAAAAAAATCAA--AAA--CAAAAG-AAA
1 AAAAAAAATCAATCAAAGTCAAAAGTAAA
**
11971037 AAAAAAAGAAAAATCAAAGTCAAAAGTAAA
1 AAAAAAA-ATCAATCAAAGTCAAAAGTAAA
11971067 AAAAAAAATCAATCAAAGTCAAAA-TAAA
1 AAAAAAAATCAATCAAAGTCAAAAGTAAA
11971095 AA
1 AA
11971097 TATGAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 7 0.14
25 3 0.06
27 3 0.06
28 6 0.12
29 21 0.42
30 10 0.20
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (29 bp):
AAAAAAAATCAATCAAAGTCAAAAGTAAA
Found at i:11973405 original size:87 final size:88
Alignment explanation
Indices: 11973284--11973505 Score: 261
Period size: 87 Copynumber: 2.5 Consensus size: 88
11973274 AGATCAGTGA
* * *
11973284 AGATCGAAAACA-AAGCCTTGCCTCCTTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTTG
1 AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTG
* * *
11973348 CCTCCCTAAG-CAATAGTGGAGC
66 CCTCCCTAAGTCAACAGCGAAGC
* * *
11973370 AGATCGAAGATACTAA-CCTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTT
1 AGATCGAAGACAC-AAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTT
* ** * *
11973434 GCCTTCCTGCGTCGACGGCGAAGC
65 GCCTCCCTAAGTCAACAGCGAAGC
* * *
11973458 AGATGGAAGGCACAAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTT
1 AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTT
11973506 GAATATTGGA
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
86 10 0.09
87 54 0.48
88 49 0.43
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (88 bp):
AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTG
CCTCCCTAAGTCAACAGCGAAGC
Found at i:11973422 original size:43 final size:44
Alignment explanation
Indices: 11973299--11973508 Score: 124
Period size: 44 Copynumber: 4.8 Consensus size: 44
11973289 GAAAACAAAG
* * *
11973299 CCTTGCCTCCTTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGA
1 CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCGAA
* ** **** * * *
11973343 TCTTGCCTCCCTAAGCAATAGTGGAGCAGATCGAAGATA-CTAA
1 CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCGAA
*
11973386 CCTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGC-AGA
1 CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCGA-A
* * * * * * * * **
11973430 TCTTGCCTTCCT-GCGTCGACGGCGAAGCAGATGGAAGGCA-C-AA
1 CCTTGCCTCCCTCG-GTTG-CAGTGGAGCAGGTTGAAGATAGCGAA
*
11973473 GCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAA
1 -CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAA
11973509 TATTGGAAAT
Statistics
Matches: 117, Mismatches: 43, Indels: 13
0.68 0.25 0.08
Matches are distributed among these distances:
43 45 0.38
44 58 0.50
45 14 0.12
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (44 bp):
CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCGAA
Found at i:11973676 original size:131 final size:130
Alignment explanation
Indices: 11973514--11974350 Score: 777
Period size: 131 Copynumber: 6.3 Consensus size: 130
11973504 TTGAATATTG
* *
11973514 GAAATTACAGATCTTATCTCCTTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTC
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTC
* ** * * * *
11973579 CCTAGGAGTAGGGAAATAGATTTAAGCCACAAGTCCTATTTCTCTGAGCAACAGTGGAATATGTT
66 CCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAGCAGCAGTGGAATAGGTT
* *
11973644 GTAAACTACAGATCTTATCTCCCTAAGAAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTT
1 G-AAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTT
* * *
11973709 CCCCAGGAGTAGGGAAGCAAATTTAAGCCACAAGTCCTATCTCCCTG-GCCAACA-TGGAATATG
65 CCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAG-CAGCAGTGGAATAGG
11973772 TT
129 TT
** * * * ***
11973774 GGGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGC-AGATCTCGCCTT
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGA-ATCTTATCTT
* ** * * * ** *
11973838 CCTGC-GTCG-ACGGCGAAGCAGATCTAAGGCACAAG-CGT-TGCCTCCCTCG-GTTGTAGTGGA
65 CC-CCAGGAGTA-GG-GAAGCAGATTTAAGCCACAAGTCCTAT--CTCCCT-GAGCAGCAGTGGA
*
11973898 GCAGGTTGAAGATT
124 --A---T--AGGTT
*
11973912 GGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTT
1 -GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTT
* * *
11973977 CCCCAGGAGTAGGGAAACAGATTTAAGCTACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGT
65 CCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAGCAGCAGTGGAATAGGT
11974042 T
130 T
* *
11974043 GGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATAGCGAATCTTATCTT
1 -GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTT
* *
11974108 CCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCT-AGTCAGTAGTGAAATAGG
65 CCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAG-CAGCAGTGGAATAGG
11974172 TT
129 TT
** * * * * * * *
11974174 GGGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-TGACGGATTTTA-CCT
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAG-CGAATCTTATCTT
* * * ** * * * *
11974237 -CCCTGTG-GTTACAGTGG-AGTACATAGAAGCCAGTAA-TTCTATATCCCTGGGCAGCAGTGGA
65 CCCCAG-GAG-T--AG-GGAAGCAGATTTAAGCCA-CAAGTCCTATCTCCCTGAGCAGCAGTGGA
* *
11974298 ATTGATT
124 ATAGGTT
*
11974305 GAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
1 GAA-ATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
11974351 GGATGGCAGA
Statistics
Matches: 583, Mismatches: 90, Indels: 66
0.79 0.12 0.09
Matches are distributed among these distances:
128 8 0.01
129 64 0.11
130 91 0.16
131 272 0.47
132 45 0.08
133 2 0.00
136 2 0.00
137 1 0.00
138 34 0.06
139 61 0.10
140 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (130 bp):
GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTC
CCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAGCAGCAGTGGAATAGGTT
Found at i:11974027 original size:399 final size:400
Alignment explanation
Indices: 11973418--11974222 Score: 1396
Period size: 399 Copynumber: 2.0 Consensus size: 400
11973408 GGAGTAGGTT
* *
11973418 GAAGATAGCAGATCTTGCCTTCCTGCGTCGACGGCGAAGCAGATGGAAGGCACAAGCCTTGCCTC
1 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
* *
11973483 CCTCGGTTGTAGTGGAGCAGGTTGAATATTGGAAATTACAGATCTTATCTCCTTAAGCAATAGTG
66 CCTCGGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
* *
11973548 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAATAGATTTAAGCCACAAGT
131 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
* * *
11973613 CCTATTTCTCTGAGCAACAGTGGAATATGTTGTAAACTACAGATCTTATCTCCCTAAGAAATAGT
196 CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGAAATAGT
11973678 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAAG
* * *
11973743 TCCTATCTCCCTGGCCAACA-TGGAATATGTTGGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
326 TCCTATCTCCCTAGCCAACAGTGAAATAGGTTGGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
11973807 GGAGCAGATC
391 GGAGCAGATC
* *
11973817 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCTAAGGCACAAGCGTTGCCTC
1 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
11973882 CCTCGGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
66 CCTCGGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
*
11973947 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCTACAAGT
131 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
* *
11974012 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGCAATAGT
196 CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGAAATAGT
* *
11974077 GGAGCAGATCGAAGATAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAAG
* **
11974142 TCCTATCTCCCTAGTCAGTAGTGAAATAGGTTGGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
326 TCCTATCTCCCTAGCCAACAGTGAAATAGGTTGGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
11974207 GGAGTAGATC
391 GGAGCAGATC
11974217 GAAGAT
1 GAAGAT
11974223 GACGGATTTT
Statistics
Matches: 382, Mismatches: 23, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
399 325 0.85
400 57 0.15
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (400 bp):
GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
CCTCGGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGAAATAGT
GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAAG
TCCTATCTCCCTAGCCAACAGTGAAATAGGTTGGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATC
Found at i:11974663 original size:50 final size:50
Alignment explanation
Indices: 11974609--11974867 Score: 231
Period size: 50 Copynumber: 5.2 Consensus size: 50
11974599 GCAATGGAAC
* *
11974609 AGATTAACGCCACAACGACGAATCTTGCTTCCCAGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGACGAATCTTACTTCCCAGACATTGCAGTTAAAA
* ** * * *
11974659 AGATTAAAGCTACAAC-AGCGAATCTTACTTCTTA-AGCAGTGCAGTGAAAT
1 AGATTAAAGCCACAACGA-CGAATCTTACTTCCCAGA-CATTGCAGTTAAAA
* * * * *
11974709 AGATTAAAGCCACAACGATGAATCTTGCTTCCCCGACATCGCATTTAAAA
1 AGATTAAAGCCACAACGACGAATCTTACTTCCCAGACATTGCAGTTAAAA
* ** * ** *
11974759 AGATTAAAGCCACAAC-A-GCAAGTCTTACTTCTCA-AGCGGTGCAATGGAAC
1 AGATTAAAGCCACAACGACG-AA-TCTTACTTCCCAGA-CATTGCAGTTAAAA
* * *
11974809 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAAC
1 AGATTAAAGCCACAACGACGAATCTTACTTCCCAGACATTGCAGTTAAAA
11974859 AGATTAAAG
1 AGATTAAAG
11974868 TTACGAGTTA
Statistics
Matches: 162, Mismatches: 37, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
48 1 0.01
49 6 0.04
50 149 0.92
51 5 0.03
52 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGACGAATCTTACTTCCCAGACATTGCAGTTAAAA
Found at i:11974757 original size:100 final size:100
Alignment explanation
Indices: 11974597--11974867 Score: 391
Period size: 100 Copynumber: 2.7 Consensus size: 100
11974587 TTCCCTGGCG
* * *
11974597 GTGCAATGGAACAGATTAACGCCACAACGACGAATCTTGCTTCCCAGACATTGCAGTTAAAAAGA
1 GTGCAATGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* *
11974662 TTAAAGCTACAACAGCGAA-TCTTACTTCTTAAGCA
66 TTAAAGCCACAACAGC-AAGTCTTACTTCTCAAGCA
* * * * *
11974697 GTGCAGTGAAATAGATTAAAGCCACAACGATGAATCTTGCTTCCCCGACATCGCATTTAAAAAGA
1 GTGCAATGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
*
11974762 TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCG
66 TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCA
* * * *
11974797 GTGCAATGGAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAACAGA
1 GTGCAATGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
11974862 TTAAAG
66 TTAAAG
11974868 TTACGAGTTA
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 2 0.01
100 148 0.99
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (100 bp):
GTGCAATGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCA
Found at i:11976421 original size:22 final size:22
Alignment explanation
Indices: 11976377--11976435 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
11976367 ATGAATGTTG
*
11976377 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
11976401 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
11976423 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
11976436 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:11979296 original size:43 final size:43
Alignment explanation
Indices: 11979258--11979484 Score: 235
Period size: 43 Copynumber: 5.3 Consensus size: 43
11979248 ATGCACTTCA
* *
11979258 TGTGCCAGTATATTTACTTTGGTTCGTCCGATGATGCAC--TG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * * *
11979299 TGTGCCAGCATATTTGTTTTGGTTCGTTCGATAATGTACTGTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * *
11979342 TGTGCCAATATATTTGCTTCGGTTCATCCGGTGATGCACTGTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * ** * * *
11979385 TCTGTCAGTATATTTGCTTCAATTCGTCTGATAATGCACTATG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* *
11979428 TGTGCCAGTATATTTGCTTCAGTTCGTCCGATGATGCGA-TATG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGC-ACTGTG
*
11979471 TGTGCCAATATATT
1 TGTGCCAGTATATT
11979485 CACTTTGATT
Statistics
Matches: 152, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 33 0.22
43 118 0.78
44 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (43 bp):
TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
Found at i:11986895 original size:28 final size:27
Alignment explanation
Indices: 11986862--11986960 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
11986852 TAATGAGATT
11986862 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
11986889 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
11986918 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
11986946 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
11986961 TACTTATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 56 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:11987938 original size:25 final size:24
Alignment explanation
Indices: 11987903--11988175 Score: 193
Period size: 25 Copynumber: 11.5 Consensus size: 24
11987893 ATTTAATGTA
*
11987903 TAATGTTGTCCAATTTTGAGCATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
*
11987928 TATTGCTGTCCAATTTTGAGTATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
* *
11987953 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
11987974 ATAATGCTGTCCAATTTTGAGTATAT
1 -TAATGCTGTCCAATTTTGAG-ATAT
* *
11988000 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
*
11988021 ATAATGCTGTCCAATTTTAAGTATAT
1 -TAATGCTGTCCAATTTTGAG-ATAT
* *
11988047 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
* *
11988068 ATAATGCTATCAAATTTTGAGTATATT
1 -TAATGCTGTCCAATTTTGAG-ATA-T
*
11988095 TAA-GCTGTCTAA-TTTGATG-TA-
1 TAATGCTGTCCAATTTTGA-GATAT
11988116 TAATGCTGTCC-ATTTTGAGCATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
*
11988140 TATTGCTGTCCAA-TTTGATGA-A-
1 TAATGCTGTCCAATTTTGA-GATAT
11988162 TAATTGCTGTCCAA
1 TAA-TGCTGTCCAA
11988176 AACAGGGTTG
Statistics
Matches: 200, Mismatches: 23, Indels: 52
0.73 0.08 0.19
Matches are distributed among these distances:
21 14 0.07
22 41 0.20
23 33 0.17
24 39 0.19
25 61 0.31
26 11 0.05
27 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (24 bp):
TAATGCTGTCCAATTTTGAGATAT
Found at i:11987982 original size:47 final size:47
Alignment explanation
Indices: 11987931--11988175 Score: 350
Period size: 47 Copynumber: 5.2 Consensus size: 47
11987921 AGCATATTAT
11987931 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
11987978 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
*
11988025 TGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
* * * * * * *
11988072 TGCTATCAAATTTTGAGTATATTTAAGCTGTCTAATTTGATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
* * * *
11988119 TGCTGTCC-ATTTTGAGCATATT-ATTGCTGTCCAATTTGATGAATAA
1 TGCTGTCCAATTTTGAGTATATTGA-TGCTGTCCATTTTAATGTATAA
11988165 TTGCTGTCCAA
1 -TGCTGTCCAA
11988176 AACAGGGTTG
Statistics
Matches: 180, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 32 0.18
47 146 0.81
48 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (47 bp):
TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
Found at i:11987985 original size:72 final size:70
Alignment explanation
Indices: 11987894--11988155 Score: 270
Period size: 72 Copynumber: 3.7 Consensus size: 70
11987884 TTTGTTATAA
*
11987894 TTTAATGTATAATGTTGTCCAATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATTGATGC
1 TTTAATGTATAATGCTGTCC-ATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATT-ATGC
11987959 TGTCCAT
64 TGTCCAT
* *
11987966 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCC-ATTTTAATGTATA--ATG
1 TTTAATGTATAATGCTGTCC-ATTTTGAGCATATT-ATTGCTGTCCAATTTTGA-GTATATTATG
11988027 CTGTCCAAT
63 CTGTCC-AT
* * * *
11988036 TTTAA-GTATATTGATGCTGTCCATTTT-A--ATGTATAATGCTATCAAATTTTGAGTATATTTA
1 TTTAATGTATA---ATGCTGTCCATTTTGAGCATAT-TATTGCTGTCCAATTTTGAGTATA-TTA
* * *
11988097 AGCTGTCTAA
61 TGCTGTCCAT
*
11988107 TTTGATGTATAATGCTGTCCATTTTGAGCATATTATTGCTGTCCAATTT
1 TTTAATGTATAATGCTGTCCATTTTGAGCATATTATTGCTGTCCAATTT
11988156 GATGAATAAT
Statistics
Matches: 159, Mismatches: 15, Indels: 33
0.77 0.07 0.16
Matches are distributed among these distances:
68 4 0.03
69 40 0.25
70 15 0.09
71 29 0.18
72 70 0.44
73 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (70 bp):
TTTAATGTATAATGCTGTCCATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATTATGCTG
TCCAT
Found at i:12009352 original size:15 final size:15
Alignment explanation
Indices: 12009332--12009382 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12009322 AAATTTTTTA
12009332 AAATTATAAAAATAT
1 AAATTATAAAAATAT
* *
12009347 AAATTATTAAAGTAAT
1 AAATTATAAAAAT-AT
* *
12009363 AACTTATAAAAACAT
1 AAATTATAAAAATAT
12009378 AAATT
1 AAATT
12009383 TAATTTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:12013676 original size:44 final size:43
Alignment explanation
Indices: 12013628--12013783 Score: 109
Period size: 44 Copynumber: 3.4 Consensus size: 43
12013618 TCATTCCAAC
12013628 CCACTGCAACTTCAGAGGTATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGAGG-ATAGGATTTGTAGCTTCATCTTGCT
* * * * ***
12013672 CCACTGTAACTTTAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAAC-
1 CCACTGCAACTTCA-GAGGATAGGA---T-T-T-GTAGCTTCA-TCTTGCT
* *
12013722 CCACTGCCACTTCAGGGGCATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGAGG-ATAGGATTTGTAGCTTCATCTTGCT
* *
12013766 CCATTGTAACTTCA-AGGA
1 CCACTGCAACTTCAGAGGA
12013784 GATAAGATTC
Statistics
Matches: 82, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
42 1 0.01
43 5 0.06
44 37 0.45
45 4 0.05
46 1 0.01
47 2 0.02
48 1 0.01
49 3 0.04
50 25 0.30
51 3 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (43 bp):
CCACTGCAACTTCAGAGGATAGGATTTGTAGCTTCATCTTGCT
Found at i:12013831 original size:94 final size:94
Alignment explanation
Indices: 12013567--12013833 Score: 347
Period size: 94 Copynumber: 2.8 Consensus size: 94
12013557 GTGTCACAGT
* ** * ** * *
12013567 TTCATATTGCTCCATTACAGCTTCAAGGAGATAAGATTTGTTGTTGTAGTTTCATTCCAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
* *
12013632 TGCAACTTCAGAGGTATAGGATTTGTAGC
66 TGCAACTTCAGGGGCATAGGATTTGTAGC
* * * * *
12013661 TTCATCTTGCTCCACTGTAACTT-TAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAACCCA
1 TTCATCTTGCTCCATTGTAACTTCAAGG-AGATAAGATTTACTATTGTAGCTTCATTCCAACCCA
*
12013725 CTGCCACTTCAGGGGCATAGGATTTGTAGC
65 CTGCAACTTCAGGGGCATAGGATTTGTAGC
* *
12013755 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTCACTATTGTAGCTTCATTCAAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
*
12013820 TACAACTTCAGGGG
66 TGCAACTTCAGGGG
12013834 GACTGGAGTT
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
93 3 0.02
94 141 0.96
95 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (94 bp):
TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
TGCAACTTCAGGGGCATAGGATTTGTAGC
Found at i:12022810 original size:20 final size:20
Alignment explanation
Indices: 12022764--12022801 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12022754 AATTTTCTCC
*
12022764 TCTTCCAACTTCTCTATCCT
1 TCTTCTAACTTCTCTATCCT
12022784 TCTTCTAACTTCTCTATC
1 TCTTCTAACTTCTCTATC
12022802 TTTTTTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (20 bp):
TCTTCTAACTTCTCTATCCT
Found at i:12025676 original size:13 final size:13
Alignment explanation
Indices: 12025660--12025686 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12025650 ATTAGTACTT
12025660 ATAATAATTAATG
1 ATAATAATTAATG
12025673 ATAATAATTAATG
1 ATAATAATTAATG
12025686 A
1 A
12025687 CCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATAATTAATG
Found at i:12026948 original size:15 final size:15
Alignment explanation
Indices: 12026928--12026957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12026918 AATTTTAAGT
12026928 TTTGGGCTATTGGGC
1 TTTGGGCTATTGGGC
*
12026943 TTTGGGCTGTTGGGC
1 TTTGGGCTATTGGGC
12026958 CTTTTGGGTC
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:0.03, C:0.13, G:0.43, T:0.40
Consensus pattern (15 bp):
TTTGGGCTATTGGGC
Found at i:12027187 original size:19 final size:20
Alignment explanation
Indices: 12027150--12027187 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12027140 ATATATAAGA
* *
12027150 TAAATAAAACTAGTCTAAAC
1 TAAATAAAACTAATATAAAC
12027170 TAAA-AAAACTAATATAAA
1 TAAATAAAACTAATATAAA
12027188 TAAGAATTAA
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:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAATAAAACTAATATAAAC
Found at i:12028758 original size:30 final size:31
Alignment explanation
Indices: 12028724--12028783 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
12028714 AAACCTTTTA
*
12028724 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
12028754 TTTTCCTCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
12028784 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:12045374 original size:44 final size:44
Alignment explanation
Indices: 12045195--12045500 Score: 130
Period size: 44 Copynumber: 7.0 Consensus size: 44
12045185 CAGATCATTA
* * *
12045195 AAGATAACAGATCTTATCTCCCTAAGCACTCGTGGAGCAGATCG
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATTG
* * * * * *
12045239 AAGA-CGAAAAAACTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
1 AAGATAG-CAGATCTTATC-TCCCTAAGCACTAGT-GG-AGCAGATTG
** * * * * * *
12045283 AAGCCACCA-AGCATTGTCTCCCTGAGCAGC-AGTGGAGTAGGTTG
1 AAGATAGCAGATC-TTATCTCCCTAAGCA-CTAGTGGAGCAGATTG
* *
12045327 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGAAGATCG
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATTG
* * * *
12045371 AAGA-CGACAAATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTT
1 AAGATAG-CAGATCTTATC-TCCCTAAGCACTAGTGG--AGCAGATTG
** * ** ** * * *
12045415 AAGCCACCAGGCCTCGTCTCCCTGAGCAGC-AGTGGAGGAGGTTG
1 AAGATAGCAGATCTTATCTCCCTAAGCA-CTAGTGGAGCAGATTG
*
12045459 AAGATAGCAGATATTATCTCCCTAAGCACTAGTGGAGCAGAT
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGAT
12045501 CGAAAATGAC
Statistics
Matches: 181, Mismatches: 59, Indels: 44
0.64 0.21 0.15
Matches are distributed among these distances:
42 9 0.05
43 15 0.08
44 137 0.76
45 12 0.07
46 8 0.04
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (44 bp):
AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATTG
Found at i:12045434 original size:132 final size:131
Alignment explanation
Indices: 12045195--12045635 Score: 557
Period size: 132 Copynumber: 3.4 Consensus size: 131
12045185 CAGATCATTA
* * * *
12045195 AAGATAACAGATCTTATCTCCCTAAGCACTCGTGGAGCAGATCGAAGACGAAAAAACTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
* * *
12045260 CCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGAAAGCAGATTTAAGCCACCAGGC-CTGTCTCCCTGAGCAGCAGTGGAGTAGGT
12045325 TG
130 TG
*
12045327 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGAAGATCGAAGACGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
*
12045392 CCAAGATAGTGGAAAGCAGATTTAAGCCACCAGGCCTCGTCTCCCTGAGCAGCAGTGGAGGAGGT
66 CCAAGATAGTGGAAAGCAGATTTAAGCCACCAGGCCT-GTCTCCCTGAGCAGCAGTGGAGTAGGT
12045457 TG
130 TG
* * * * *
12045459 AAGATAGCAGATATTATCTCCCTAAGCACTAGTGGAGCAGATCGAAAATGACGAATCATATCTTC
1 AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATCTT-
* * * * * * * * *
12045524 CCCAGGAGTAG-GGAAA-CAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGG
65 TCCAAGA-TAGTGGAAAGCAGATTTAAGCCACCAGGCCTGTCTCCCTGAGCAGCAGTGGAGTAGG
12045587 TTGG
129 TT-G
* * **
12045591 AA-ATTA-CAGATCTTATCTCCCTAAGCATTAGCGGAGTGGATCGAA
1 AAGA-TAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAA
12045636 TACGGTGAAT
Statistics
Matches: 274, Mismatches: 30, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
131 59 0.22
132 202 0.74
133 10 0.04
134 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (131 bp):
AAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
CCAAGATAGTGGAAAGCAGATTTAAGCCACCAGGCCTGTCTCCCTGAGCAGCAGTGGAGTAGGTT
G
Found at i:12049169 original size:171 final size:171
Alignment explanation
Indices: 12048875--12049203 Score: 482
Period size: 171 Copynumber: 1.9 Consensus size: 171
12048865 CTCAAACGCT
* * *
12048875 GCAATAGACCCTGATCTATAGCGGCGTTTCTACCACAAACGCCACTAAAGAACCTATTCTTTAGC
1 GCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGC
* * *
12048940 GGCGCTTTCCCTCAAACGCCGCAATTGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCAC
66 GGCGCTTTCCCACAAACGCCGCAATAGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCAC
*
12049005 TAAAGAACC-TATTCTTTAGCGGTGCTTTCCCCTCAAACATC
131 TAAAGAACCTTA-TCTTTAGCGCTGCTTTCCCCTCAAACATC
12049046 GCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGC
1 GCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGC
* * * * *** *
12049111 GGCGCTTTCCCACAAACGCTGCTAA-AGACCATGATCTTTAGTGGCGTTTTTTCCACAAACGCCG
66 GGCGCTTTCCCACAAACGCCGC-AATAGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCA
*
12049175 CTAAAGACCCTTATCTTTAGCGCTGCTTT
130 CTAAAGAACCTTATCTTTAGCGCTGCTTT
12049204 GACCAAAAAC
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
171 136 0.97
172 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (171 bp):
GCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGC
GGCGCTTTCCCACAAACGCCGCAATAGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCAC
TAAAGAACCTTATCTTTAGCGCTGCTTTCCCCTCAAACATC
Found at i:12049203 original size:85 final size:85
Alignment explanation
Indices: 12048846--12049196 Score: 456
Period size: 85 Copynumber: 4.1 Consensus size: 85
12048836 AAGATCAGGG
** * * *
12048846 TCTTTAGCGGCATTTTTCTCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGTTTCTACCAC
1 TCTTTAGCGGC-GCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
12048911 AAACGCCACTAAAGAACCTAT
65 AAACGCCACTAAAGAACCTAT
* *
12048932 TCTTTAGCGGCGCTTTCCCTCAAACGCCGCAATTGACCCTGATCTATAGCGGCGCTTCGACCACA
1 TCTTTAGCGGCGCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACA
12048997 AACGCCACTAAAGAACCTAT
66 AACGCCACTAAAGAACCTAT
* *
12049017 TCTTTAGCGGTGCTTTCCCCTCAAAC-ATCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCA
1 TCTTTAGCGGCGCTTT-CCCTCAAACGCT-GCAATAGACCCTGATCTATAGCGGCGCTTCGACCA
*
12049081 CAAACGCCACTAAAGAACCTAA
64 CAAACGCCACTAAAGAACCTAT
* * * * * ***
12049103 TCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA-AGACCATGATCTTTAGTGGCGTTTTTTCCAC
1 TCTTTAGCGGCGCTTTCCCTCAAACGCTGC-AATAGACCCTGATCTATAGCGGCGCTTCGACCAC
* *
12049167 AAACGCCGCTAAAGACCCT-T
65 AAACGCCACTAAAGAACCTAT
12049187 ATCTTTAGCG
1 -TCTTTAGCG
12049197 CTGCTTTGAC
Statistics
Matches: 235, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
85 142 0.60
86 93 0.40
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACA
AACGCCACTAAAGAACCTAT
Found at i:12049222 original size:43 final size:43
Alignment explanation
Indices: 12048880--12049223 Score: 281
Period size: 43 Copynumber: 8.0 Consensus size: 43
12048870 ACGCTGCAAT
* *
12048880 AGACCCTGATCTATAGCGGCG-TTTCTACCACAAACGCCACTAA
1 AGACCCTGATCTTTAGCGGCGCTTT-GACCACAAACGCCACTAA
* * * *
12048923 AGAACCT-ATTCTTTAGCGGCGCTTT-CCCTCAAACGCCGC-AA
1 AGACCCTGA-TCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* * *
12048964 TTGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAA
1 -AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* * ** * ** *
12049008 AGAACCT-ATTCTTTAGCGGTGCTTTCCCCTCAAACATCGC-AA
1 AGACCCTGA-TCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* *
12049050 TAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAA
1 -AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* * * **
12049094 AGAACCTAATCTTTAGCGGCGCTTT-CCCACAAACGCTGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* * * ** *
12049136 AGACCATGATCTTTAGTGGCGTTTTTTCCACAAACGCCGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
* * *
12049179 AGACCCTTATCTTTAGC-GCTGCTTTGACCAAAAACACCACTAA
1 AGACCCTGATCTTTAGCGGC-GCTTTGACCACAAACGCCACTAA
12049222 AG
1 AG
12049224 GCCAACACCT
Statistics
Matches: 233, Mismatches: 56, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
41 2 0.01
42 70 0.30
43 153 0.66
44 8 0.03
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (43 bp):
AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA
Found at i:12049247 original size:85 final size:85
Alignment explanation
Indices: 12049078--12049247 Score: 182
Period size: 85 Copynumber: 2.0 Consensus size: 85
12049068 GGCGCTTCGA
* * * ** *
12049078 CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCACAAACGCTGCTAAAGACCAT
1 CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACACCACTAAAGACCAA
* * * *
12049143 GATCTTTAGTGGCGTTTTTT
66 CACCTTTAGTGACGATTTTT
* * * *
12049163 CCACAAACGCCGCTAAAGACCCTTATCTTTAGC-GCTGCTTTGACCAAAAACACCACTAAAGGCC
1 CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGC-GCTTT-ACCAAAAACACCACTAAAGACC
12049227 AACACCTTTAGTGAC-ATTTTT
64 AACACCTTTAGTGACGATTTTT
12049248 TTAAAAATTG
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
84 2 0.03
85 40 0.58
86 27 0.39
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (85 bp):
CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACACCACTAAAGACCAA
CACCTTTAGTGACGATTTTT
Found at i:12049661 original size:21 final size:21
Alignment explanation
Indices: 12049595--12049662 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
12049585 CACTTTAGCC
* *
12049595 TCTGCTTCCCTCGCTGCAGCA
1 TCTGCTTCTCTCGCTGCCGCA
* * * * *
12049616 TGTACTTCTCTCGCTACCACC
1 TCTGCTTCTCTCGCTGCCGCA
*
12049637 TCTGCTTCTCTTGCTGCCGCA
1 TCTGCTTCTCTCGCTGCCGCA
12049658 TCTGC
1 TCTGC
12049663 ATTAAGCTGT
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
TCTGCTTCTCTCGCTGCCGCA
Found at i:12049744 original size:66 final size:66
Alignment explanation
Indices: 12049634--12049804 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 66
12049624 TCTCGCTACC
* * * * * *
12049634 ACCTCTGCTTCTCTTGCTGCCGCATCTGCATTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTT
1 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-GTT
12049698 GA
65 GA
* *
12049700 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTG
1 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTG
12049765 A
66 A
* * * * * *
12049766 ACATCATCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
12049805 GTAATTTGCT
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 85 0.96
67 4 0.04
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (66 bp):
ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTG
A
Found at i:12055255 original size:16 final size:16
Alignment explanation
Indices: 12055234--12055325 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
12055224 ATTAAGCTAC
12055234 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
12055250 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* * *
12055266 GAAAATTATGTAAGTTGT
1 GTAAGTTATGT-A-TTAT
* *
12055284 GT-A-TTATGAAATAT
1 GTAAGTTATGTATTAT
*
12055298 GTAAGTTATGTAAGT-T
1 GTAAGTTATGT-ATTAT
12055314 GTAAGTTATGTA
1 GTAAGTTATGTA
12055326 AGTTGTAAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 45 0.75
17 4 0.07
18 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:12055273 original size:25 final size:24
Alignment explanation
Indices: 12055245--12055309 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
12055235 TAAGTTATGT
*
12055245 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATG-AA
*
12055270 ATTATGTAAGTTGTGTATTATGAA
1 ATTATGTAAGTTATGTATTATGAA
12055294 A-TATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
12055310 AGTTGTAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 14 0.38
24 3 0.08
25 20 0.54
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (24 bp):
ATTATGTAAGTTATGTATTATGAA
Found at i:12055307 original size:32 final size:32
Alignment explanation
Indices: 12055271--12055709 Score: 104
Period size: 31 Copynumber: 13.5 Consensus size: 32
12055261 ATTATGAAAA
*
12055271 TTATGTAAGTTGTGTATTATGAAATATGTAAG
1 TTATGTAAGTTATGTATTATGAAATATGTAAG
*
12055303 TTATGTAAG-T-TGTAAGTTATGTAAGT-TGTAAG
1 TTATGTAAGTTATGT-A-TTATG-AAATATGTAAG
**
12055335 TTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAG
1 TTATGTAAGTTATGT-A-TTATG---AA-A-T-ATGTAAG
* *
12055375 TTATGTAAGTTATGTA-TATTAACTAAT-TAAG
1 TTATGTAAGTTATGTATTATGAAAT-ATGTAAG
* ** *
12055406 TTATGTAATTTATGAATAATTAAAAAAAATGTAAG
1 TTATGTAAGTTATG--T-ATTATGAAATATGTAAG
12055441 TTATGTAAG-T-TGTAAGTTATGTATAATAT-TAA-
1 TTATGTAAGTTATGT-A-TTATG-A-AATATGTAAG
** *
12055473 TTAACTAAGTTATGTAATTTATGTATAATATTAATGTATG
1 TTATGTAAGTTATGT-A-TTATG---AA-A-T-ATGTAAG
* * *
12055513 TTATGTAATTTATGTA-TATTAACTAAT-TAAG
1 TTATGTAAGTTATGTATTATGAAAT-ATGTAAG
*
12055544 TTATGTAATTTATG---TAT--AATAT-T-A-
1 TTATGTAAGTTATGTATTATGAAATATGTAAG
* * **
12055568 --ATGTAAGTTATGTATAATATTAATTAACTAAG
1 TTATGTAAGTTATGTAT--TATGAAATATGTAAG
* * *
12055600 TTATGTAATTTATGTATAAT--ATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAT-ATGTAAG
* * *
12055631 TTATGTAATTTATGTA-TATTAATTAAT-TAAG
1 TTATGTAAGTTATGTATTATGAAAT-ATGTAAG
* * *
12055662 TTATGTAATTTATGTATAAT--ATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAT-ATGTAAG
**
12055693 TTATGTATTTTATGTAT
1 TTATGTAAGTTATGTAT
12055710 ATTAATTAAT
Statistics
Matches: 323, Mismatches: 39, Indels: 91
0.71 0.09 0.20
Matches are distributed among these distances:
22 11 0.03
25 1 0.00
26 3 0.01
27 5 0.02
29 6 0.02
30 15 0.05
31 101 0.31
32 55 0.17
33 12 0.04
34 46 0.14
35 17 0.05
36 6 0.02
37 7 0.02
38 3 0.01
39 4 0.01
40 31 0.10
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (32 bp):
TTATGTAAGTTATGTATTATGAAATATGTAAG
Found at i:12055309 original size:9 final size:9
Alignment explanation
Indices: 12055234--12055677 Score: 120
Period size: 9 Copynumber: 51.3 Consensus size: 9
12055224 ATTAAGCTAC
12055234 GTAAGTTAT
1 GTAAGTTAT
12055243 GT-A-TTAT
1 GTAAGTTAT
12055250 GTAAGTTAT
1 GTAAGTTAT
*
12055259 -TTA-TTAT
1 GTAAGTTAT
* *
12055266 GAAAATTAT
1 GTAAGTTAT
*
12055275 GTAAGTTGT
1 GTAAGTTAT
12055284 GT-A-TTAT
1 GTAAGTTAT
*
12055291 G-AA-ATAT
1 GTAAGTTAT
12055298 GTAAGTTAT
1 GTAAGTTAT
12055307 GTAAG-T-T
1 GTAAGTTAT
12055314 GTAAGTTAT
1 GTAAGTTAT
12055323 GTAAG-T-T
1 GTAAGTTAT
*
12055330 GTAAGTTAA
1 GTAAGTTAT
*
12055339 CTAAGTTAT
1 GTAAGTTAT
*
12055348 GTAATTTAT
1 GTAAGTTAT
*
12055357 GTATAATATTAAT
1 G--TAA-GTT-AT
12055370 GTAAGTTAT
1 GTAAGTTAT
12055379 GTAAGTTAT
1 GTAAGTTAT
12055388 GT-A--TAT
1 GTAAGTTAT
* *
12055394 -TAACTAAT
1 GTAAGTTAT
12055402 -TAAGTTAT
1 GTAAGTTAT
*
12055410 GTAATTTAT
1 GTAAGTTAT
12055419 GAATAA-TTA-
1 G--TAAGTTAT
* ***
12055428 -AAAAAAAT
1 GTAAGTTAT
12055436 GTAAGTTAT
1 GTAAGTTAT
12055445 GTAAG-T-T
1 GTAAGTTAT
12055452 GTAAGTTAT
1 GTAAGTTAT
*
12055461 GTATA-ATAT
1 GTA-AGTTAT
*
12055470 -TAA-TTAA
1 GTAAGTTAT
*
12055477 CTAAGTTAT
1 GTAAGTTAT
*
12055486 GTAATTTAT
1 GTAAGTTAT
*
12055495 GTATAATATTAAT
1 G--TAA-GTT-AT
*
12055508 GTATGTTAT
1 GTAAGTTAT
*
12055517 GTAATTTAT
1 GTAAGTTAT
12055526 GT-A--TAT
1 GTAAGTTAT
* *
12055532 -TAACTAAT
1 GTAAGTTAT
12055540 -TAAGTTAT
1 GTAAGTTAT
*
12055548 GTAATTTAT
1 GTAAGTTAT
*
12055557 GTATAATATTAAT
1 G--TAA-GTT-AT
12055570 GTAAGTTAT
1 GTAAGTTAT
*
12055579 GTATA-ATAT
1 GTA-AGTTAT
*
12055588 -TAA-TTAA
1 GTAAGTTAT
*
12055595 CTAAGTTAT
1 GTAAGTTAT
*
12055604 GTAATTTAT
1 GTAAGTTAT
*
12055613 GTATAATATTAAT
1 G--TAA-GTT-AT
12055626 GTAAGTTAT
1 GTAAGTTAT
*
12055635 GTAATTTAT
1 GTAAGTTAT
12055644 GT-A--TAT
1 GTAAGTTAT
12055650 -TAA-TTAAT
1 GTAAGTT-AT
12055658 -TAAGTTAT
1 GTAAGTTAT
*
12055666 GTAATTTAT
1 GTAAGTTAT
12055675 GTA
1 GTA
12055678 TAATATTAAT
Statistics
Matches: 328, Mismatches: 54, Indels: 106
0.67 0.11 0.22
Matches are distributed among these distances:
5 3 0.01
6 14 0.04
7 45 0.14
8 50 0.15
9 157 0.48
10 13 0.04
11 26 0.08
12 8 0.02
13 12 0.04
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:12055327 original size:25 final size:26
Alignment explanation
Indices: 12055295--12055386 Score: 83
Period size: 25 Copynumber: 3.8 Consensus size: 26
12055285 TATTATGAAA
*
12055295 TATGTAAGTTATGTAAGTT-GTAAGT
1 TATGTAAGTTATGTAAGTTACTAAGT
12055320 TATGTAAG-T-TGTAAGTTAACTAAGT
1 TATGTAAGTTATGTAAGTT-ACTAAGT
* *
12055345 TATGTAATTTATGT-A--TAAT-A-T
1 TATGTAAGTTATGTAAGTTACTAAGT
12055366 TAATGTAAGTTATGTAAGTTA
1 T-ATGTAAGTTATGTAAGTTA
12055387 TGTATATTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
21 2 0.04
22 13 0.24
23 11 0.20
24 2 0.04
25 22 0.40
26 2 0.04
27 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (26 bp):
TATGTAAGTTATGTAAGTTACTAAGT
Found at i:12055345 original size:16 final size:16
Alignment explanation
Indices: 12055271--12055337 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
12055261 ATTATGAAAA
*
12055271 TTATGTAAGTTGTGTA-
1 TTATGTAAGTTGT-AAG
*
12055287 TTATG-AAATATGTAAG
1 TTATGTAAGT-TGTAAG
12055303 TTATGTAAGTTGTAAG
1 TTATGTAAGTTGTAAG
12055319 TTATGTAAGTTGTAAG
1 TTATGTAAGTTGTAAG
12055335 TTA
1 TTA
12055338 ACTAAGTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 4 0.09
16 38 0.84
17 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTGTAAG
Found at i:12055378 original size:31 final size:31
Alignment explanation
Indices: 12055340--12055719 Score: 391
Period size: 31 Copynumber: 12.0 Consensus size: 31
12055330 GTAAGTTAAC
12055340 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* * *
12055371 TAAGTTATGTAAGTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATAAT-ATTAATG
* **
12055402 TAAGTTATGTAATTTATGAATAATTAAAAAAAATG
1 TAAGTTATGTAATTTATG--T-A-TAATATTAATG
*
12055437 TAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAAC
1 TAAGTTATGTAA----T---TTATGTATAATATTAA-T--G
12055478 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* * *
12055509 TATGTTATGTAATTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATAAT-ATTAATG
12055540 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* * *
12055571 TAAGTTATGT-A--TA-ATATTA-ATTAA-C
1 TAAGTTATGTAATTTATGTATAATATTAATG
12055596 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
*
12055627 TAAGTTATGTAATTTATGTATATTAATTAAT-
1 TAAGTTATGTAATTTATGTATAAT-ATTAATG
12055658 TAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATG
* *
12055689 TAAGTTATGTATTTTATGTATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAAT-ATTAAT
12055720 TAAATGATAT
Statistics
Matches: 293, Mismatches: 29, Indels: 53
0.78 0.08 0.14
Matches are distributed among these distances:
25 10 0.03
26 6 0.02
27 4 0.01
28 4 0.01
29 4 0.01
30 17 0.06
31 161 0.55
32 22 0.08
33 2 0.01
34 21 0.07
35 14 0.05
37 1 0.00
38 6 0.02
39 3 0.01
40 1 0.00
41 12 0.04
42 5 0.02
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (31 bp):
TAAGTTATGTAATTTATGTATAATATTAATG
Found at i:12055414 original size:62 final size:62
Alignment explanation
Indices: 12055335--12055722 Score: 509
Period size: 62 Copynumber: 6.1 Consensus size: 62
12055325 AAGTTGTAAG
* *
12055335 TTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTATGTATATTAA
1 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
* * **
12055397 CTAATTAAGTTATGTAATTTATGAATAATTAAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATG
1 TTAATTAAGTTATGTAATTTATG--T-A-TAATATTAATGTAAGTTATGTAA----T---TTATG
12055462 TATAATATTAA
55 --T-ATATTAA
* *
12055473 TTAACTAAGTTATGTAATTTATGTATAATATTAATGTATGTTATGTAATTTATGTATATTAA
1 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
*
12055535 CTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGT-A--TA---ATATTAA
1 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
*
12055591 TTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
1 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
*
12055653 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATTTTATGTATATTAA
1 TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
12055715 TTAATTAA
1 TTAATTAA
12055723 ATGATATGTA
Statistics
Matches: 287, Mismatches: 19, Indels: 40
0.83 0.05 0.12
Matches are distributed among these distances:
56 51 0.18
57 1 0.00
59 4 0.01
61 1 0.00
62 146 0.51
63 1 0.00
64 1 0.00
65 6 0.02
66 20 0.07
68 1 0.00
72 19 0.07
73 6 0.02
74 1 0.00
75 1 0.00
76 28 0.10
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (62 bp):
TTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATATTAA
Found at i:12055461 original size:138 final size:138
Alignment explanation
Indices: 12055296--12055681 Score: 528
Period size: 138 Copynumber: 2.9 Consensus size: 138
12055286 ATTATGAAAT
*
12055296 ATGTAAGTTATGTAAGTTGTAAGTTATGTA-AGT-TGTAAGTTAACTAAGTTATGTAATTTATGT
1 ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATAT-TAA-TTAACTAAGTTATGTAATTTATGT
12055359 ATAATATTAATGTAAGTTATGTAAGTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATA
64 ATAATATTAATGTAAGTTATGTAAGTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATA
12055424 ATTAAAAAAA
129 ATTAAAAAAA
12055434 ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
* *
12055499 AATATTAATGTATGTTATGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATG--T-A-
66 AATATTAATGTAAGTTATGTAAGTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATAAT
*
12055560 T----AAT
131 TAAAAAAA
*
12055564 AT-T-A---ATGTAAG-T-T-AT----GTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
* * *
12055617 AATATTAATGTAAGTTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAAT
66 AATATTAATGTAAGTTATGTAAGTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATAAT
12055682 ATTAATGTAA
Statistics
Matches: 235, Mismatches: 7, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
118 95 0.40
120 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 1 0.00
125 7 0.03
128 1 0.00
129 1 0.00
130 4 0.02
134 1 0.00
135 1 0.00
136 1 0.00
138 113 0.48
139 5 0.02
140 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.46
Consensus pattern (138 bp):
ATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
AATATTAATGTAAGTTATGTAAGTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATAAT
TAAAAAAA
Found at i:12055516 original size:22 final size:22
Alignment explanation
Indices: 12055491--12055591 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
12055481 GTTATGTAAT
12055491 TTATGTATAATATTAATGTATG
1 TTATGTATAATATTAATGTATG
*
12055513 TTATG--TAAT-TT-ATGTATA
1 TTATGTATAATATTAATGTATG
** *
12055531 TTAACTAATTAA-GTT-ATGTAAT-
1 TTATGT-A-TAATATTAATGT-ATG
*
12055553 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATGTATG
12055575 TTATGTATAATATTAAT
1 TTATGTATAATATTAAT
12055592 TAACTAAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
18 9 0.14
19 2 0.03
20 7 0.11
21 4 0.06
22 39 0.62
23 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.50
Consensus pattern (22 bp):
TTATGTATAATATTAATGTATG
Found at i:12055588 original size:118 final size:118
Alignment explanation
Indices: 12055451--12055700 Score: 482
Period size: 118 Copynumber: 2.1 Consensus size: 118
12055441 TTATGTAAGT
*
12055451 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTATGTTA
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
12055516 TGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATAATATTAA
66 TGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATAATATTAA
12055569 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
*
12055634 TGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
66 TGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATAATATTAA
12055687 TGTAAGTTATGTAT
1 TGTAAGTTATGTAT
12055701 TTTATGTATA
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 130 1.00
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (118 bp):
TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTA
TGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:12055605 original size:25 final size:22
Alignment explanation
Indices: 12055553--12055606 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
12055543 GTTATGTAAT
*
12055553 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATCTAAG
12055575 TTATGTATAATATTAATTAACTAAG
1 TTATGTATAATATTAA-T--CTAAG
12055600 TTATGTA
1 TTATGTA
12055607 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
25 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATGTATAATATTAATCTAAG
Found at i:12055634 original size:22 final size:21
Alignment explanation
Indices: 12055600--12055700 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 21
12055590 ATTAACTAAG
*
12055600 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
12055621 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
12055640 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
12055662 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
12055683 TTAATGTAAGTTATGTAT
1 TT-ATGTAAGTTATGTAT
12055701 TTTATGTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 23
0.71 0.03 0.25
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 7 0.11
21 8 0.12
22 38 0.58
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTATGTAAGTTATGTATAATA
Found at i:12060891 original size:15 final size:15
Alignment explanation
Indices: 12060871--12060908 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12060861 TTGAAATTAA
12060871 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
12060886 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
12060901 CCCTAAAT
1 CCCTAAAT
12060909 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:12061414 original size:41 final size:39
Alignment explanation
Indices: 12061369--12061682 Score: 129
Period size: 41 Copynumber: 7.8 Consensus size: 39
12061359 AGGTAAATAC
* *
12061369 ATTAGCGACGCTTAGATACAAACGCCGCTGAAGACAAGAGA
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGAC-A-AGA
* * * * * *
12061410 ATTAGTGGCTCTCAGTTAAAAACGCCGCTAAAGATTCAAGC
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA--CAAGA
* *
12061451 ATTAGCGACGCTT-GTATAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGACGCTTAG-ATAAAAACGCCGCTAAAGA--CAAGA
* ** * * * *
12061492 ATTAGTGGTGCGTAGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA--CAAGA
* * * * * *
12061533 ATTAGCGGCACATAGACAAAAACGCCGCTAAAGATCTGAGC
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA-C-AAGA
** * * *
12061574 ATTAGCGGTGCTTAG------AGGCCGCTAAAGACTCGAGC
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA--CAAGA
* * * *
12061609 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCGGAGC
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA-C-AAGA
* * *
12061650 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGACGCTTAGATAAAAACGCCGCTAAAG
12061683 GTTTAAAAAA
Statistics
Matches: 226, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
35 30 0.13
36 2 0.01
40 4 0.02
41 187 0.83
42 2 0.01
43 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (39 bp):
ATTAGCGACGCTTAGATAAAAACGCCGCTAAAGACAAGA
Found at i:12061474 original size:82 final size:82
Alignment explanation
Indices: 12061368--12061682 Score: 249
Period size: 82 Copynumber: 3.9 Consensus size: 82
12061358 AAGGTAAATA
* * **
12061368 CATTAGCGACGCTTAGATACAAACGCCGCTGAAGACAAGAGAATTAGTGGCT-C-TCAGTTAAAA
1 CATTAGCGACGCTTAGATAAAAACGCCGCTAAAGACAAGAGAATTAGTGG-TGCGT-AGACAAAA
*
12061431 ACGCCGCTAAAGATTCAAG
64 ACGCCGCTAAAGATCCAAG
** *
12061450 CATTAGCGACGCTT-GTATAAAAACGCCGCTAAAGACCCGAGCATTAGTGGTGCGTAGACAAAAA
1 CATTAGCGACGCTTAG-ATAAAAACGCCGCTAAAGACAAGAGAATTAGTGGTGCGTAGACAAAAA
*
12061514 CGCCGCTAAAGATCCGAG
65 CGCCGCTAAAGATCCAAG
* * * * * * * *
12061532 CATTAGCGGCACATAGACAAAAACGCCGCTAAAGATC-TGAGCATTAGCGGTGCTTAG------A
1 CATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA-CAAGAGAATTAGTGGTGCGTAGACAAAAA
* *
12061590 GGCCGCTAAAGA-CTCGAG
65 CGCCGCTAAAGATC-CAAG
* * * * * * * *
12061608 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATC-GGAGCATTAGCGGCGCTTACACAAAAA
1 CATTAGCGACGCTTAGATAAAAACGCCGCTAAAGA-CAAGAGAATTAGTGGTGCGTAGACAAAAA
12061672 CGCCGCTAAAG
65 CGCCGCTAAAG
12061683 GTTTAAAAAA
Statistics
Matches: 198, Mismatches: 23, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
75 1 0.01
76 68 0.34
81 2 0.01
82 124 0.63
83 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (82 bp):
CATTAGCGACGCTTAGATAAAAACGCCGCTAAAGACAAGAGAATTAGTGGTGCGTAGACAAAAAC
GCCGCTAAAGATCCAAG
Found at i:12061626 original size:76 final size:76
Alignment explanation
Indices: 12061430--12061663 Score: 265
Period size: 76 Copynumber: 3.0 Consensus size: 76
12061420 CTCAGTTAAA
* * * *
12061430 AACGCCGCTAAAGATTCAAGCATTAGCGACGCTT-GTATAAAAACGCCGCTAAAGACCCGAGCAT
1 AACGCCGCTAAAGA-TCGAGCATTAGCGGCGCTTAG-ACAAAAACGCCGCTAAAGATCCGAGCAT
* *
12061494 TAGTGGTGCGTAG
64 TAGCGGTGCTTAG
* * *
12061507 ACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCACATAGACAAAAACGCCGCTAAAGATCTGA
1 -----AACGCCGCTAAAGAT-CGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGA
12061572 GCATTAGCGGTGCTTAG
60 GCATTAGCGGTGCTTAG
* *
12061589 -AGGCCGCTAAAGACTCGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCGGAGCATT
1 AACGCCGCTAAAGA-TCGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATT
*
12061653 AGCGGCGCTTA
65 AGCGGTGCTTA
12061664 CACAAAAACG
Statistics
Matches: 135, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
76 68 0.50
77 1 0.01
81 1 0.01
82 64 0.47
83 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (76 bp):
AACGCCGCTAAAGATCGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTA
GCGGTGCTTAG
Found at i:12061852 original size:40 final size:40
Alignment explanation
Indices: 12061729--12061855 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
12061719 GGTTTTTTGT
** * *
12061729 GGCGCTTTATATAAAACGCCGCTAATTC-CTATTTTTAGC
1 GGCGCTTTGGATAAATCGCCGCTAATGCTCTATTTTTAGC
* * **
12061768 GGCGCTTCCGGAT-AATCGCCGCTGATGCTCTACCTTTAGC
1 GGCGCTT-TGGATAAATCGCCGCTAATGCTCTATTTTTAGC
* * * *
12061808 GGCGCTTTGGCTAAATCGCCGCTAATGCTCGATTTTTTGT
1 GGCGCTTTGGATAAATCGCCGCTAATGCTCTATTTTTAGC
12061848 GGCGCTTT
1 GGCGCTTT
12061856 TGTTCCAAAC
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
39 22 0.32
40 47 0.68
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (40 bp):
GGCGCTTTGGATAAATCGCCGCTAATGCTCTATTTTTAGC
Found at i:12062223 original size:21 final size:21
Alignment explanation
Indices: 12062184--12062225 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
12062174 GTACATGCAT
*
12062184 ACATATATTTTTATAATATTG
1 ACATATATTTTAATAATATTG
12062205 ACATATATTTATAATATATAT
1 ACATATATTT-TAATA-ATAT
12062226 GCATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
ACATATATTTTAATAATATTG
Found at i:12062721 original size:108 final size:108
Alignment explanation
Indices: 12062523--12062723 Score: 330
Period size: 108 Copynumber: 1.9 Consensus size: 108
12062513 AGAAAATTTT
* * * * *
12062523 TTTCTAAATAAGGCAATGTTTTGCGTCTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATATTTTACATCTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
*
12062588 CGGTTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
*
12062631 TTTCAAAACAAGGCAATATTTTACATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATATTTTACATCTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
*
12062696 CGATTTCTCGTTCGACTAAATAGCCAAA
66 CGATTTCTCGTTCGACCAAATAGCCAAA
12062724 TATCCTCTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 85 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (108 bp):
TTTCAAAACAAGGCAATATTTTACATCTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
Found at i:12063731 original size:9 final size:9
Alignment explanation
Indices: 12063714--12063750 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12063704 TGAGTTTTCA
12063714 AATTCGAAT
1 AATTCGAAT
*
12063723 AACTCGAAT
1 AATTCGAAT
12063732 AATTCGAAT
1 AATTCGAAT
12063741 AATTCGAAT
1 AATTCGAAT
12063750 A
1 A
12063751 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12063999 original size:30 final size:31
Alignment explanation
Indices: 12063965--12064025 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
12063955 AAACCTTTTA
*
12063965 TTTTCCCCCAAAATTTTTACTCCC-TCCCAT
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
* *
12063995 TTTTCCCCTAAAACTTTTATTCCCTTCCCAT
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
12064026 CTCACCTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
Found at i:12064776 original size:5 final size:5
Alignment explanation
Indices: 12064766--12064791 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12064756 CTCGAAAATT
12064766 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12064792 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12068168 original size:34 final size:34
Alignment explanation
Indices: 12068130--12068200 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
12068120 TATTACATAC
* *
12068130 ATAAA-TAATTATATTTTATCCAATATAAAAATAA
1 ATAAATTAATTAT-TTTTATCCAATAAAAAAACAA
* **
12068164 ATAAATTTATTATTTTTATTGAATAAAAAAACAA
1 ATAAATTAATTATTTTTATCCAATAAAAAAACAA
12068198 ATA
1 ATA
12068201 CCAAATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (34 bp):
ATAAATTAATTATTTTTATCCAATAAAAAAACAA
Found at i:12068989 original size:18 final size:19
Alignment explanation
Indices: 12068953--12068995 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
12068943 GGTTTTTTAC
12068953 AAAAATATTATAAAAAATA
1 AAAAATATTATAAAAAATA
*
12068972 AAAAATATTA-AAATAATA
1 AAAAATATTATAAAAAATA
*
12068990 TAAAAT
1 AAAAAT
12068996 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATTATAAAAAATA
Found at i:12069699 original size:144 final size:141
Alignment explanation
Indices: 12069541--12069818 Score: 468
Period size: 144 Copynumber: 2.0 Consensus size: 141
12069531 AATACATTTA
*
12069541 AAAAAAATACTATTTTCGTATTTTATTATTTTACTTTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
*
12069606 TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACTCTTATTTCGG-TCCTTTATTCGTATT
66 TCATTTAGTGTGTTTTTTAAATAAA--TTAAAAAAAAC-CTTATTTCGGCT-CTTTATTCGTACT
12069670 TTTTTCCCTTTCAAT
127 TTTTTCCCTTTCAAT
*
12069685 AAAAATATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
* *
12069750 TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAATCCTTATTTCGGCTCTTTGTTCGTACTTTTT
66 TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCTTATTTCGGCTCTTTATTCGTACTTTTT
12069815 TCCC
131 TCCC
12069819 CGGATTTTAT
Statistics
Matches: 128, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
141 29 0.23
142 11 0.09
144 88 0.69
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.51
Consensus pattern (141 bp):
AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCTTATTTCGGCTCTTTATTCGTACTTTTT
TCCCTTTCAAT
Found at i:12073214 original size:20 final size:20
Alignment explanation
Indices: 12073172--12073214 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12073162 ACACTTTAAA
* * *
12073172 AAATATATAATATTTCTTTT
1 AAATATATAATATATATTAT
*
12073192 AAATTTATAATATATATTAT
1 AAATATATAATATATATTAT
12073212 AAA
1 AAA
12073215 ATTCTGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATATAATATATATTAT
Found at i:12076974 original size:20 final size:20
Alignment explanation
Indices: 12076949--12076986 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12076939 GGACCATGCA
*
12076949 AAACAATGTTGTTTTACCCT
1 AAACAATGCTGTTTTACCCT
12076969 AAACAATGCTGTTTTACC
1 AAACAATGCTGTTTTACC
12076987 TTGATCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
AAACAATGCTGTTTTACCCT
Found at i:12077708 original size:8 final size:9
Alignment explanation
Indices: 12077687--12077716 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12077677 TAAAAAGTAT
*
12077687 TTTTTATAA
1 TTTTTAAAA
12077696 TTTTTAAAA
1 TTTTTAAAA
12077705 TTTTTAAAA
1 TTTTTAAAA
12077714 TTT
1 TTT
12077717 CAAAAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:12083072 original size:3 final size:3
Alignment explanation
Indices: 12083064--12083166 Score: 188
Period size: 3 Copynumber: 34.3 Consensus size: 3
12083054 CCAATACACT
*
12083064 GAA GAA GAA TAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
12083112 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12083160 GAA GAA G
1 GAA GAA G
12083167 TCCTCAACTG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:12084473 original size:12 final size:12
Alignment explanation
Indices: 12084456--12084480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12084446 GGTGTTCAGT
12084456 CGGTTAACCGAC
1 CGGTTAACCGAC
12084468 CGGTTAACCGAC
1 CGGTTAACCGAC
12084480 C
1 C
12084481 CGAAATTCTT
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:12084657 original size:9 final size:9
Alignment explanation
Indices: 12084641--12084747 Score: 151
Period size: 9 Copynumber: 11.4 Consensus size: 9
12084631 TTTGGTTAAA
12084641 AATTACCCG
1 AATTACCCG
*
12084650 ACTTACCCG
1 AATTACCCG
12084659 AATTACCCG
1 AATTACCCG
*
12084668 ACTTACCCG
1 AATTACCCG
12084677 AATTACCCG
1 AATTACCCG
12084686 AAAATTACCCG
1 --AATTACCCG
12084697 AATTACCCG
1 AATTACCCG
12084706 AATTACCCG
1 AATTACCCG
*
12084715 AAAATTACCCA
1 --AATTACCCG
12084726 AATTACCCG
1 AATTACCCG
12084735 AATTACCCG
1 AATTACCCG
12084744 AATT
1 AATT
12084748 GAATCACTAC
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
9 71 0.81
11 17 0.19
ACGTcount: A:0.36, C:0.33, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:12084699 original size:38 final size:37
Alignment explanation
Indices: 12084640--12084747 Score: 155
Period size: 38 Copynumber: 2.9 Consensus size: 37
12084630 TTTTGGTTAA
* * *
12084640 AAATTACCCGACTTACCCGAATTACCCGACTTACCCG
1 AAATTACCCAAATTACCCGAATTACCCGAATTACCCG
12084677 -AATTACCCGAAAATTACCCGAATTACCCGAATTACCCG
1 AAATTACCC--AAATTACCCGAATTACCCGAATTACCCG
12084715 AAAATTACCCAAATTACCCGAATTACCCGAATT
1 -AAATTACCCAAATTACCCGAATTACCCGAATT
12084748 GAATCACTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
36 8 0.12
38 48 0.75
40 8 0.12
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.22
Consensus pattern (37 bp):
AAATTACCCAAATTACCCGAATTACCCGAATTACCCG
Found at i:12084702 original size:29 final size:28
Alignment explanation
Indices: 12084642--12084745 Score: 156
Period size: 29 Copynumber: 3.7 Consensus size: 28
12084632 TTGGTTAAAA
*
12084642 ATTACCCGACTTACCCG-AATTACCCGA
1 ATTACCCGAATTACCCGAAATTACCCGA
*
12084669 CTTACCCGAATTACCCGAAAATTACCCGA
1 ATTACCCGAATTACCCG-AAATTACCCGA
*
12084698 ATTACCCGAATTACCCGAAAATTACCCAA
1 ATTACCCGAATTACCCG-AAATTACCCGA
12084727 ATTACCCGAATTACCCGAA
1 ATTACCCGAATTACCCGAA
12084746 TTGAATCACT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 15 0.21
28 2 0.03
29 54 0.76
ACGTcount: A:0.36, C:0.34, G:0.10, T:0.21
Consensus pattern (28 bp):
ATTACCCGAATTACCCGAAATTACCCGA
Found at i:12084777 original size:17 final size:17
Alignment explanation
Indices: 12084755--12084852 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
12084745 ATTGAATCAC
12084755 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
12084772 TACATAAATATTTGAATCAC
1 TACAT--A-ATTAAAAACAT
*
12084792 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
12084809 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
12084829 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
12084846 TACATAA
1 TACATAA
12084853 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 30 0.54
18 1 0.02
19 1 0.02
20 24 0.43
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:12084853 original size:37 final size:37
Alignment explanation
Indices: 12084746--12084861 Score: 198
Period size: 37 Copynumber: 3.2 Consensus size: 37
12084736 ATTACCCGAA
* * *
12084746 TTGAATCACTACATAATTAAAAACATTACATAAATAT
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12084783 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12084820 TTGAATCACTACATAATTAAAAATATTACATAAGTC-
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12084856 TTGAAT
1 TTGAAT
12084862 TAACACATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 70 0.92
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAATATTACATAAGTCT
Found at i:12084929 original size:24 final size:24
Alignment explanation
Indices: 12084902--12084960 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
12084892 ATTCTCCATT
*
12084902 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
12084926 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
12084950 TATCTCCATTT
1 TATATCCATTT
12084961 GCATTAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:12087897 original size:8 final size:8
Alignment explanation
Indices: 12087884--12087908 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12087874 AAATGTTCGC
12087884 ATTTAATT
1 ATTTAATT
12087892 ATTTAATT
1 ATTTAATT
12087900 ATTTAATT
1 ATTTAATT
12087908 A
1 A
12087909 ACAATATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:12088043 original size:27 final size:27
Alignment explanation
Indices: 12088013--12088092 Score: 160
Period size: 27 Copynumber: 3.0 Consensus size: 27
12088003 AAAGATGAAA
12088013 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
12088040 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
12088067 GAAAAAATTAAGACAATAGTATACAA
1 GAAAAAATTAAGACAATAGTATACAA
12088093 CGACATGATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.21
Consensus pattern (27 bp):
GAAAAAATTAAGACAATAGTATACAAT
Found at i:12088351 original size:19 final size:19
Alignment explanation
Indices: 12088327--12088378 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
12088317 TTATTACTAA
12088327 CATAAAAGTAAGCAAAACC
1 CATAAAAGTAAGCAAAACC
** *
12088346 CATAAATAAAAAGAAAAACC
1 CATAAA-AGTAAGCAAAACC
12088366 CATAAAAGTAAGC
1 CATAAAAGTAAGC
12088379 TGAAAGCACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.12
Consensus pattern (19 bp):
CATAAAAGTAAGCAAAACC
Done.