Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 1151237
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 79344 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:341498 original size:31 final size:31
Alignment explanation
Indices: 341455--341564 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
341445 GTGCCACCAA
* * * * *
341455 CTTGTGTAGGCTTTAACTCAGATGCCGTCAG
1 CTTGTGTGGGCTTTGACTCAGGTGTCGCCAG
* *
341486 CTTGTGTGGGCTTTGACTTAGGTGTCGCCAA
1 CTTGTGTGGGCTTTGACTCAGGTGTCGCCAG
341517 CTTGTGTGGGCTTTGACTCAGGTGTCGCCAG
1 CTTGTGTGGGCTTTGACTCAGGTGTCGCCAG
*
341548 CTTGTGCGGGCTTTGAC
1 CTTGTGTGGGCTTTGAC
341565 ATTCTAAGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.13, C:0.22, G:0.32, T:0.34
Consensus pattern (31 bp):
CTTGTGTGGGCTTTGACTCAGGTGTCGCCAG
Found at i:341819 original size:268 final size:268
Alignment explanation
Indices: 341286--341832 Score: 647
Period size: 268 Copynumber: 2.0 Consensus size: 268
341276 CAATTCGTGT
* * *
341286 AGGCTTTGATATTCTAAGGCTTAACTTCTTTAGAAAGGTGACAACTAATGTGGACTTGACTCAAA
1 AGGCTTTGACATTCTAAGGCTTAACTTCCTTAGAAAGGTGACAACTAATATGGACTTGACTCAAA
*** **
341351 TGCCGTTAGCTTGTACGGGCTTTAGCTAGAGTGCCATTAACTCGTGTGGGCTTTAAAAAAGAAAA
66 TGCCACCAGCTTGTACGGGCTTTAGCTAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAAGAAAA
* ** * *
341416 ATGTATCCTGCTCTTTGAGGACTGAACGGGTGCCACCAACTTGTGTAGGCTTTAACTCAGATGCC
131 AGGTATCCTGCTCTTTGAGGACTGAACGGGTGCCACCAACTTGTGTAGGCTTTAACAAAAAAGCC
* * ** * * * *
341481 GTCAGCTTGTGTGGGCTTTGACTTAGGTGTCGCCAACTTGTGTGGGCTTTGACTCAGGTGTCGCC
196 GTCAGCTTGTGAGGACTTAAAC-TAGGTGCCACCAACTTGTGTGGGCTTTAACTCAGGTGCCGCC
341546 AGCTTGTGC
260 AGCTTGTGC
* * * * *
341555 GGGCTTTGACATTCTAAGGCTTGAAC-TCCTTAGCAAGGTGCCAACTAATATGGACTTGACTTAG
1 AGGCTTTGACATTCTAAGGCTT-AACTTCCTTAGAAAGGTGACAACTAATATGGACTTGACTCAA
* *
341619 GTGTCACCAGCTTGTACGGGCTTTAGCTAGAGTGCCACCAACTCGTGT-GGCTTTAAAAAAGAAA
65 ATGCCACCAGCTTGTACGGGCTTTAGCTAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAAGAAA
* * ** * * *
341683 AAGGTATCTTGCTCTTTGAGGACTGAACGGGTGCTACTGACTTGTGTGGGGTTTAAAAGAAAAAA
130 AAGGTATCCTGCTCTTTGAGGACTGAACGGGTGCCACCAACTTGTGTAGGCTTT--AACAAAAAA
* * *
341748 G-CGTCATGCTATTTGAGGAC-TAAAC-GGGTGCCACCAACTTGTGTGGGCTTTAACT-TGGATG
193 GCCGTCA-GCT-TGTGAGGACTTAAACTAGGTGCCACCAACTTGTGTGGGCTTTAACTCAGG-TG
341809 CCGCCAGCTTGTGC
255 CCGCCAGCTTGTGC
341823 AGGCTTTGAC
1 AGGCTTTGAC
341833 TTGGGTGCCG
Statistics
Matches: 233, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
267 2 0.01
268 113 0.48
269 98 0.42
270 14 0.06
271 6 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (268 bp):
AGGCTTTGACATTCTAAGGCTTAACTTCCTTAGAAAGGTGACAACTAATATGGACTTGACTCAAA
TGCCACCAGCTTGTACGGGCTTTAGCTAGAGTGCCACCAACTCGTGTGGGCTTTAAAAAAGAAAA
AGGTATCCTGCTCTTTGAGGACTGAACGGGTGCCACCAACTTGTGTAGGCTTTAACAAAAAAGCC
GTCAGCTTGTGAGGACTTAAACTAGGTGCCACCAACTTGTGTGGGCTTTAACTCAGGTGCCGCCA
GCTTGTGC
Found at i:341860 original size:31 final size:31
Alignment explanation
Indices: 341773--341894 Score: 129
Period size: 31 Copynumber: 3.9 Consensus size: 31
341763 AGGACTAAAC
* * * * *
341773 GGGTGCCACCAACTTGTGTGGGCTTTAACTT
1 GGGTGCCGCCAGCTTGTGCGAGCTTTGACTT
*
341804 GGATGCCGCCAGCTTGTGC-AGGCTTTGACTT
1 GGGTGCCGCCAGCTTGTGCGA-GCTTTGACTT
* *
341835 GGGTGCCGCCAGTTTGTGCGAGCTTTGACTC
1 GGGTGCCGCCAGCTTGTGCGAGCTTTGACTT
* * *
341866 AGGTGCCGCTAGCTTATGCGAGCTTTGAC
1 GGGTGCCGCCAGCTTGTGCGAGCTTTGAC
341895 ATTCTAAGGC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 75 0.99
32 1 0.01
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (31 bp):
GGGTGCCGCCAGCTTGTGCGAGCTTTGACTT
Found at i:342011 original size:28 final size:28
Alignment explanation
Indices: 341969--342090 Score: 138
Period size: 28 Copynumber: 4.4 Consensus size: 28
341959 CACCAGTTTG
* *
341969 TGTGGGCTTTAAAAAGGTGCTACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
341997 TGTGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
342025 CGTGGTCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
342053 TGTGAGCTTT-AAAAGAATGCCATTGATT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
342081 TGTGGGCTTT
1 TGTGGGCTTT
342091 AGAGAGGGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
27 4 0.05
28 74 0.95
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:342118 original size:32 final size:32
Alignment explanation
Indices: 342081--342187 Score: 135
Period size: 32 Copynumber: 3.3 Consensus size: 32
342071 GCCATTGATT
* * *
342081 TGTGGGCTTTAGAGAGGGTTGCTACCGACTTG
1 TGTGGGCTTTAGAAAGGGTTGCCACCAACTTG
342113 TGTGGGCTTTAGAAAAGGGTTGCCACCAACTTG
1 TGTGGGCTTTAG-AAAGGGTTGCCACCAACTTG
* * *
342146 -GTGAGCTTTATAAAGGGTTGCCACTAACTTG
1 TGTGGGCTTTAGAAAGGGTTGCCACCAACTTG
*
342177 TATGGGCTTTA
1 TGTGGGCTTTA
342188 ACTCAGGTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
31 19 0.29
32 29 0.45
33 17 0.26
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTAGAAAGGGTTGCCACCAACTTG
Found at i:342298 original size:61 final size:61
Alignment explanation
Indices: 342164--342300 Score: 136
Period size: 61 Copynumber: 2.2 Consensus size: 61
342154 TATAAAGGGT
* * *
342164 TGCCACTAACTTGTATGGGCTTTAACTCAGGTGCTGCTAGTTCGTGCAGGCTTTAACTTAAG
1 TGCCAC-AACTCGTATAGGCTTTAACTCAGGTGCTGCCAGTTCGTGCAGGCTTTAACTTAAG
* ** * *
342226 TGCCGTCAACTCGTATAGGCTTT-ACTTGGGTGCTGCCAGCTT-GTGCGGGCTTTGAC-TAAGG
1 TGCC-ACAACTCGTATAGGCTTTAACTCAGGTGCTGCCAG-TTCGTGCAGGCTTTAACTTAA-G
342287 TGCCACAAACTCGT
1 TGCCAC-AACTCGT
342301 GTGAGCTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
60 4 0.06
61 37 0.60
62 20 0.32
63 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.31
Consensus pattern (61 bp):
TGCCACAACTCGTATAGGCTTTAACTCAGGTGCTGCCAGTTCGTGCAGGCTTTAACTTAAG
Found at i:342568 original size:40 final size:40
Alignment explanation
Indices: 342395--342660 Score: 150
Period size: 42 Copynumber: 6.5 Consensus size: 40
342385 TATTCTACTT
* *
342395 TTTGAGGACAAAGGAAAAAAAGAATGAAA-TGTGTCCTGCTC
1 TTTGAGGACAAAGGAAAAAGA-AAT-AAAGTGTGTCTTGCTC
* * * * * *
342436 TTTAAGGATAAAGTAAAAAAGGAAATGAAGTG-GATCCTACTC
1 TTTGAGGACAAAG-GAAAAA-GAAATAAAGTGTG-TCTTGCTC
* * * * * *
342478 CTTGAGGACAAAAGAAAAGGGAA-AAAG-GAATGCATCCTGCTT
1 TTTGAGGACAAAGGAAAAAGAAATAAAGTG--TG--TCTTGCTC
*
342520 TTTTAGGAC-AA-GAAAAATGGAAATAAAGTGTGTCTTGCTC
1 TTTGAGGACAAAGGAAAAA--GAAATAAAGTGTGTCTTGCTC
** * *
342560 TTTGAGGACAAAGGAAAAAGAAGGAAA-TGTGTTTTGTTC
1 TTTGAGGACAAAGGAAAAAGAAATAAAGTGTGTCTTGCTC
* * *
342599 TTTGAGGACTAAAAGTGAAAAAGAAATAAAGTGCGTCCTGCTA
1 TTTGAGGAC--AAAG-GAAAAAGAAATAAAGTGTGTCTTGCTC
342642 TTTGAGGACAAAAGGAAAA
1 TTTGAGGAC-AAAGGAAAA
342661 TAAAGAAATA
Statistics
Matches: 173, Mismatches: 34, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
38 1 0.01
39 22 0.13
40 28 0.16
41 32 0.18
42 68 0.39
43 21 0.12
44 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.23
Consensus pattern (40 bp):
TTTGAGGACAAAGGAAAAAGAAATAAAGTGTGTCTTGCTC
Found at i:342683 original size:82 final size:82
Alignment explanation
Indices: 342539--342695 Score: 192
Period size: 82 Copynumber: 1.9 Consensus size: 82
342529 AAGAAAAATG
* * * *** ** *
342539 GAAATAAAGTGTGTCTTGCTCTTTGAGGACAAAGGAAAAAGAAGGAAATGTGTTTTGTTCTTTGA
1 GAAATAAAGTGCGTCCTGCTATTTGAGGACAAAGGAAAAAGAAGGAAATACATCATGCTCTTTGA
*
342604 GGACTAAAAGTGAAAAA
66 AGACTAAAAGTGAAAAA
342621 GAAATAAAGTGCGTCCTGCTATTTGAGGACAAAAGGAAAATA-AA-GAAATACATCATGCTCTTT
1 GAAATAAAGTGCGTCCTGCTATTTGAGGAC-AAAGGAAAA-AGAAGGAAATACATCATGCTCTTT
342684 GAAGACTAAAAG
64 GAAGACTAAAAG
342696 GTACCACAGA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
82 51 0.81
83 11 0.17
84 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.25
Consensus pattern (82 bp):
GAAATAAAGTGCGTCCTGCTATTTGAGGACAAAGGAAAAAGAAGGAAATACATCATGCTCTTTGA
AGACTAAAAGTGAAAAA
Found at i:350515 original size:13 final size:13
Alignment explanation
Indices: 350497--350524 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
350487 ATACAAAGAT
350497 CAATGTATTGATA
1 CAATGTATTGATA
350510 CAATGTATTGATA
1 CAATGTATTGATA
350523 CA
1 CA
350525 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (13 bp):
CAATGTATTGATA
Found at i:350587 original size:13 final size:13
Alignment explanation
Indices: 350569--350652 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
350559 AGCTTCGTAG
350569 CGATACATTGTAT
1 CGATACATTGTAT
350582 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
350601 CGATACATTGTAT
1 CGATACATTGTAT
350614 CGATACAATACTTATGTAT
1 CGATAC---A--T-TGTAT
350633 CGATACATTGTAT
1 CGATACATTGTAT
350646 CGATACA
1 CGATACA
350653 AATTGTTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 28 0.47
14 1 0.02
15 2 0.03
16 4 0.07
17 2 0.03
18 1 0.02
19 21 0.36
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:350601 original size:19 final size:18
Alignment explanation
Indices: 350577--350639 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
350567 AGCGATACAT
350577 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
350596 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
350609 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
350628 TGTATCGATACA
1 TGTATCGATACA
350640 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:350610 original size:32 final size:32
Alignment explanation
Indices: 350569--350654 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
350559 AGCTTCGTAG
350569 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
350601 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
350633 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
350655 TTGTTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:355246 original size:20 final size:20
Alignment explanation
Indices: 355213--355292 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
355203 TTTTACCCAG
*
355213 ATGTATCTATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
355233 ATATATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
355253 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
355273 ATGTATCGATACATTATTTC
1 ATGTATCGATACATT-TTTC
355293 TTTTTACCTA
Statistics
Matches: 44, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 41 0.93
21 3 0.07
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:359401 original size:48 final size:48
Alignment explanation
Indices: 359337--359674 Score: 399
Period size: 48 Copynumber: 6.9 Consensus size: 48
359327 GTTAAACTTG
* * * * *
359337 AAGGTGACAATGTGCTGATTCAAGGCCGGCGACATTGGTCTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* * **
359385 AAGGTGCCAATATGCTGATTCAAGGTCAGCGATATTGGGCTTAAAGGT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* * * * * *
359433 GAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-C
* *
359482 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAA--GAC
* *
359533 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-C
* * *
359583 AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* *
359630 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
359675 AGAAGACGCC
Statistics
Matches: 246, Mismatches: 37, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
47 2 0.01
48 158 0.64
49 39 0.16
50 3 0.01
51 3 0.01
52 41 0.17
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (48 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
Found at i:359594 original size:149 final size:147
Alignment explanation
Indices: 359335--359676 Score: 501
Period size: 149 Copynumber: 2.3 Consensus size: 147
359325 CAGTTAAACT
* * * * * *
359335 TGAAGGTGACAATGTGCTGATTCAAGGCCGGCGACATTGGTCTT-AAA-GACAAGGTGCCAATAT
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGGACAAGGCGCCAATAT
* * * *
359398 GCTGATTCAAGGTCAGCGATATTGGGCTTAAAGGTGAGGTACCAATGTGCTGATTCAAGGCCAGC
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCAGC
359463 TACATTGGACTTAAAGA
131 TACATTGGACTTAAAGA
* *
359480 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAAGTGCCAAAGGCGCCAAT
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAG-GAC-AAGGCGCCAAT
*
359545 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTGCTGATTCAAGGCCA
64 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCA
359610 GCTACATTGGACTTAAAGA
129 GCTACATTGGACTTAAAGA
* * *
359629 -CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAAG
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAG
359677 AAGACGCCAC
Statistics
Matches: 176, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
145 38 0.22
146 3 0.02
148 46 0.26
149 89 0.51
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (147 bp):
TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGGACAAGGCGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCAGC
TACATTGGACTTAAAGA
Found at i:359751 original size:28 final size:28
Alignment explanation
Indices: 359694--359845 Score: 164
Period size: 28 Copynumber: 5.3 Consensus size: 28
359684 CACCAACTTG
*
359694 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* *
359723 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* **
359751 TGTGGGCTTTTAAAGATTGCTGCTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
359779 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
359807 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
*
359837 TGTAGGCTT
1 TGTGGGCTT
359846 AAAAGGAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.03
28 68 0.65
29 11 0.10
30 23 0.22
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:359848 original size:84 final size:84
Alignment explanation
Indices: 359694--359850 Score: 194
Period size: 84 Copynumber: 1.8 Consensus size: 84
359684 CACCAACTTG
* * * *
359694 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTAGGC-
359759 TTTAAAGATTGCTGCTGACT
65 TTTAAAGATTGCTGCTGACT
*
359779 TGTGGGCTTTT-AAAGG-TTGCCA-CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTA
1 TGTGGGCTTTTGAAAGGTTTG-CATC-AACTTGTGGGCTTTTG--AAGGGTGCCACTAACTTGTA
*
359841 GGCTTAAAAG
62 GGCTTTAAAG
359851 GAAAAAGAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
83 4 0.06
84 21 0.34
85 17 0.27
86 20 0.32
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTAGGCT
TTAAAGATTGCTGCTGACT
Found at i:359880 original size:34 final size:35
Alignment explanation
Indices: 359842--359909 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
359832 TAACTTGTAG
* * *
359842 GCTTA-AAAGGAAAAAGAGTGCTATGGAGTTGTGA
1 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGA
359876 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTG
1 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTG
359910 GACTTTGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (35 bp):
GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGA
Found at i:359937 original size:29 final size:29
Alignment explanation
Indices: 359886--360064 Score: 200
Period size: 29 Copynumber: 6.1 Consensus size: 29
359876 GCTTACAAAA
* * *
359886 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* *
359916 GGAAAAGATGCCACTGACTTGTGGGCTTC
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
359945 GAAAAATGGTGCCACTGATTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTT
* * *
359975 --AAAGGTTGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
360002 GAAAAAGATGGCACTGATTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
*
360031 GAAAAAGATGCCACTGACTTGTAGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
360061 GAAA
1 GAAA
360065 GGTGAGGAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 20 0.16
28 3 0.02
29 67 0.54
30 34 0.27
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:360006 original size:57 final size:57
Alignment explanation
Indices: 359886--360052 Score: 201
Period size: 57 Copynumber: 2.9 Consensus size: 57
359876 GCTTACAAAA
* * * * *
359886 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACTGACTTGTGGGCTTC
1 GAAAAAGA-TGCCACTGATTTGTGGGCTTT-AAAAAGATGCCACTGACTTGTGGACTTC
* * * *
359945 GAAAAATGGTGCCACTGATTTGTGGGCTTT-AAAGGTTGCCACTGACTTGTGGACTTT
1 GAAAAA-GATGCCACTGATTTGTGGGCTTTAAAAAGATGCCACTGACTTGTGGACTTC
*
360002 GAAAAAGATGGCACTGATTTGTGGGCTTTGAAAAAGATGCCACTGACTTGT
1 GAAAAAGATGCCACTGATTTGTGGGCTTT-AAAAAGATGCCACTGACTTGT
360053 AGGCTTTTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
56 21 0.23
57 29 0.31
58 18 0.19
59 24 0.26
60 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (57 bp):
GAAAAAGATGCCACTGATTTGTGGGCTTTAAAAAGATGCCACTGACTTGTGGACTTC
Found at i:361510 original size:11 final size:11
Alignment explanation
Indices: 361494--361564 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
361484 ATCCGGACCC
361494 TTTTTTTTAA-
1 TTTTTTTTAAT
*
361504 -TTTTTTT-GT
1 TTTTTTTTAAT
*
361513 TTTTTTTT-GT
1 TTTTTTTTAAT
* *
361523 TTTTTATTGAT
1 TTTTTTTTAAT
* *
361534 TTTTTATTATT
1 TTTTTTTTAAT
361545 TTTTTATTTAAT
1 TTTTT-TTTAAT
361557 TTTTTTTT
1 TTTTTTTT
361565 GCGGAGGACG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.14
10 16 0.32
11 18 0.36
12 9 0.18
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:372468 original size:14 final size:14
Alignment explanation
Indices: 372442--372483 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
372432 ACCTAATCCT
*
372442 AAAAA-AAATAAAA
1 AAAAACAAAAAAAA
372455 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
**
372469 AAACCCAAAAAAAA
1 AAAAACAAAAAAAA
372483 A
1 A
372484 CCTTTTCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:372472 original size:12 final size:12
Alignment explanation
Indices: 372442--372484 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
372432 ACCTAATCCT
*
372442 AAAAAAA-ATAA
1 AAAAAAACAAAA
372453 AAAAAAACAAAA
1 AAAAAAACAAAA
**
372465 AAAAAAACCCAA
1 AAAAAAACAAAA
372477 AAAAAAAC
1 AAAAAAAC
372485 CTTTTCACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:373175 original size:82 final size:83
Alignment explanation
Indices: 372984--373629 Score: 890
Period size: 82 Copynumber: 7.8 Consensus size: 83
372974 TGGCATTTTC
* * * *
372984 TTTTAAAGTCCACAACTCCGTGGTATCCTTTT-AAGTCCACAACTCTGTGGCATCCTTTTAAAGT
1 TTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
*
373048 CCACAACTCCGTGGCATCC
65 CCACAACTCCGTGGCATCG
* ** ***
373067 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAATTATGTGGCATTGTTTT-AAGT
1 TTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
* * * * *
373131 CCACAACTTCGTAGTACCC
65 CCACAACTCCGTGGCATCG
* *
373150 TTTAAAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
373215 CACAACTCCGTGGCATCG
66 CACAACTCCGTGGCATCG
* *
373233 TTTTAAGTCCACAACTCCGTGGTA-CCATTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
*
373297 CACAACTACGTGGCATCG
66 CACAACTCCGTGGCATCG
*
373315 TTTTAAGTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTTGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
373379 CACAACTCCGTGGCATCG
66 CACAACTCCGTGGCATCG
* *
373397 TTTTAAGTCCACAACTCCGTGGTA-CCATTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* *
373461 CACAACTACGTGGCATCA
66 CACAACTCCGTGGCATCG
*
373479 TTTTAAGTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* * *
373543 CACAACTCTGTGGCACCC
66 CACAACTCCGTGGCATCG
* * * * * * * *
373561 TTTTAAGTTCACAACTTCGTGGCATCCTTTTTAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
373626 CACA
66 CACA
373630 CAAGTCGGTG
Statistics
Matches: 508, Mismatches: 49, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
81 2 0.00
82 352 0.69
83 131 0.26
84 23 0.05
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (83 bp):
TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
CACAACTCCGTGGCATCG
Found at i:374082 original size:28 final size:28
Alignment explanation
Indices: 373020--374572 Score: 974
Period size: 28 Copynumber: 54.8 Consensus size: 28
373010 CCTTTTAAGT
* * *
373020 CCACAACTCTGTGGCATCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373048 CCACAACTCCGTGGCATCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373076 CCACAACTCCGTGGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* ** *
373104 CCACAA-TTATGTGGCA--TTGTTTTAAGT
1 CCACAAGTCA-GTGGCACCTT-TTCAAAGC
* * * * *
373131 CCACAACTTC-GTAGTACCCTTT-AAAGT
1 CCACAA-GTCAGTGGCACCTTTTCAAAGC
* *
373158 CCACAACTCCA-TGGCACCCTTTT-AAAGT
1 CCACAAGT-CAGTGGCA-CCTTTTCAAAGC
* * *
373186 CCACAACTCCGTGGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * *
373214 CCACAACTCCGTGGCATCGTTTT--AAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * * *
373241 CCACAACTCCGTGGTACCATTT-AAAGT
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
373268 CCACAACTCCGTGGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373296 CCACAACT-ACGTGGCATCGTTTT--AAGT
1 CCACAAGTCA-GTGGCA-CCTTTTCAAAGC
* * * *
373323 CCACAACTCCGTGGCACCCTTT-AAAGT
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * * *
373350 CCACAACTCCGTTGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * *
373378 CCACAACTCCGTGGCATCGTTTT--AAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * * *
373405 CCACAACTCCGTGGTACCATTT-AAAGT
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
373432 CCACAACTCCGTGGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373460 CCACAACT-ACGTGGCATCATTTT--AAGT
1 CCACAAGTCA-GTGGCA-CCTTTTCAAAGC
* * * *
373487 CCACAACTCCGTGGCACCCTTT-AAAGT
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
373514 CCACAACTCTGTGGCACCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373542 CCACAACTCTGTGGCACCCTTTT--AAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
373569 TCACAACTTC-GTGGCATCCTTTT-TAAGC
1 CCACAA-GTCAGTGGCA-CCTTTTCAAAGC
373597 CCACAAGTCAGTGGCACCCTTTT-AAAGCC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAG-C
*
373626 CACACAAGTCGGTGGCAACCTATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACCT-TTTCAAAG-C
* * *
373658 CACACAAGTCGGTGGCAACCCATTTGAAAGCC
1 C-CACAAGTCAGTGGC-A-CCTTTTCAAAG-C
* * *
373690 CACACAAGTCGGTGGCAACCCATTTCAAAAC
1 C-CACAAGTCAGTGGC-A-CCTTTTCAAAGC
*
373721 CCACAAATCAGTGGCACCCTTTT-AAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* *
373749 CCACAAATCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* *
373777 CCACAAGCCAGTGGCACTTTTTTCAAAGC
1 CCACAAGTCAGTGGCAC-CTTTTCAAAGC
373806 CCACACGAGTC-GATGGCAACCCTTTTCAAAGC
1 CCACA--AGTCAG-TGGC-A-CCTTTTCAAAGC
*
373838 CCACAAGTTAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
*
373866 CCACAAGTCTGTGGCAACACTTTTCAAAGC
1 CCACAAGTCAGTGGC-AC-CTTTTCAAAGC
* *
373896 CCACAAGTTAGTGGCATCC-TTTCGAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * *
373924 CCACAATTCAGTGGCACCCTTGCGAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
373952 CCACAATTCAGTGGCA-CTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
* *
373980 CTACAAGTCAGTGGCACCCTTTCAAAGCC
1 CCACAAGTCAGTGGCACCTTTTCAAAG-C
* *
374009 CACACAAGTCAGTGACACTCTTTTTAAAGCC
1 C-CACAAGTCAGTGGCAC-CTTTTCAAAG-C
*
374040 CACACAAGTTAGTGGCACCTTTTCAAAGC
1 C-CACAAGTCAGTGGCACCTTTTCAAAGC
*
374069 CCACAAGTCAGTGGCACCCTTTC-AAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* *
374096 CCACGAGTCAGTGGTACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
374124 CCACGAGTCAGTGGCA-CTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
*
374152 CCACAAGTTAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
374180 CCACGAGTTAGTGGCA-TTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
* *
374208 CCACAAGTTAGTGGCACCCTTTC-AAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* *
374235 CCACGAGTCAGTGGTACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
374263 CCACGAGTCAGTGGCA-CTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
374291 CCACAAGTCAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* **
374319 CCACGAGTCAGTGGCATTTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
374347 CCACGCAAGTCAGTGGCACCCTTTC-AAGC
1 CCA--CAAGTCAGTGGCACCTTTTCAAAGC
* *
374376 CCACGAGTCAGTGGTACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
374404 CCACGAGTCAGTGGCA-CTCTTTCAAAGC
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
374432 CCACAAGTCAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * **
374460 CCACGAGTCAATAGCATTTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
374488 CCACGCAAGTCAGTGGCACCCTTTT-AAAGC
1 CCA--CAAGTCAGTGGCA-CCTTTTCAAAGC
**
374518 CCACGCAAGTCAGTAACACTCTTTTCAAAGC
1 CCA--CAAGTCAGTGGCAC-CTTTTCAAAGC
* *
374549 CCACACGTATCAGTGGCAACTTTT
1 CCACAAG--TCAGTGGCACCTTTT
374573 TTTCAAAGCC
Statistics
Matches: 1309, Mismatches: 140, Indels: 150
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.00
26 19 0.01
27 281 0.21
28 678 0.52
29 48 0.04
30 142 0.11
31 59 0.05
32 77 0.06
33 3 0.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCTTTTCAAAGC
Found at i:374117 original size:55 final size:56
Alignment explanation
Indices: 373169--374572 Score: 1060
Period size: 55 Copynumber: 24.7 Consensus size: 56
373159 CACAACTCCA
* * * * * * *
373169 TGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * * * * * * * * *
373225 TGGCATCGTTT-TAAGTCCACAACTCCGTGGTACCATTT-AAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * * * * * *
373279 TGGCACCCTTTTAAAGTCCACAACT-ACGTGGCATCGTTTT--AAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCA-GTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * * * * *
373334 TGGCACCCTTT-AAAGTCCACAACTCCGTTGCACCCTTTT-AAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * * * * * * * * *
373389 TGGCATCGTTT-TAAGTCCACAACTCCGTGGTACCATTT-AAAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * * * * * *
373443 TGGCACCCTTTTAAAGTCCACAACT-ACGTGGCATCATTTT--AAGTCCACAACTCCG
1 TGGCACCCTTTCAAAGCCCACAAGTCA-GTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * * * * *
373498 TGGCACCCTTT-AAAGTCCACAACTCTGTGGCACCCTTTT-AAAGTCCACAACTCTG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* ** * *
373553 TGGCACCCTTT-TAAGTTCACAACTTC-GTGGCATCCTTTT-TAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAA-GTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* * *
373608 TGGCACCCTTTTAAAGCCCACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGG
1 TGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
* * * * *
373670 TGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAACCCACAAATCAG
1 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTTCAAAGCCCACAAGTCAG
* * * *
373732 TGGCACCCTTTTAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGCCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
** *
373788 TGGCACTTTTTTCAAAGCCCACACGAGTC-GATGGCAACCCTTTTCAAAGCCCACAAGTTAG
1 TGGCAC-CCTTTCAAAGCCCACA--AGTCAG-TGGC-A-CCTTTTCAAAGCCCACAAGTCAG
* * *
373849 TGGCATCCTTTCAAAGCCCACAAGTCTGTGGCAACACTTTTCAAAGCCCACAAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-AC-CTTTTCAAAGCCCACAAGTCAG
* * * * * * *
373907 TGGCATCCTTTCGAAGCCCACAATTCAGTGGCACCCTTGCGAAGCCCACAATTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
373963 TGGCACTCTTTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG-CC-CACAAGTCAG
* * * *
374021 TGACACTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAG
1 TGGCAC-CCTTTCAAAG-CC-CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
374080 TGGCACCCTTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * * *
374135 TGGCACTCTTTCAAAGCCCACAAGTTAGTGGCATCC-TTTCAAAGCCCACGAGTTAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
** * * *
374191 TGGCATTCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTC-AAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
374246 TGGTACCTTTTCAAAGCCCACGAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAG
* * **
374302 TGGCATCCTTTCAAAGCCCACGAGTCAGTGGCATTTTTTCAAAGCCCACGCAAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA--CAAGTCAG
* * *
374360 TGGCACCCTTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAG
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
* * *
374415 TGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACGAGTCAA
1 TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAG
* ***
374471 TAGCATTTTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTT-AAAGCCCACGCAAGTCAG
1 TGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTTCAAAGCCCA--CAAGTCAG
** * * *
374531 TAACACTCTTTTCAAAGCCCACACGTATCAGTGGCAACTTTT
1 TGGCAC-CCTTTCAAAGCCCACAAG--TCAGTGGCACCTTTT
374573 TTTCAAAGCC
Statistics
Matches: 1156, Mismatches: 138, Indels: 104
0.83 0.10 0.07
Matches are distributed among these distances:
54 108 0.09
55 326 0.28
56 285 0.25
57 61 0.05
58 147 0.13
59 42 0.04
60 44 0.04
61 76 0.07
62 25 0.02
63 6 0.01
64 34 0.03
65 2 0.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (56 bp):
TGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAG
Found at i:374437 original size:141 final size:139
Alignment explanation
Indices: 373427--374553 Score: 1043
Period size: 141 Copynumber: 7.9 Consensus size: 139
373417 GGTACCATTT
* * * * * * * *
373427 AAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-ACGTGGCATCATTTT--AAGTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA-GTGGCATC-TTTTCAAAGCCC
* * * * * * * * * * *
373489 ACAACTCCGTGGCACCCTTTAAAGTCCACAACTCTGTGGCACCCTTTT-AAAGTCCACAACTCTG
64 ACAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTA-CCTTTTCAAAGCCCACAAGTCAG
*
373553 TGGCACCCTTT-
128 TGGCACTCTTTC
* ** * ** *
373564 TAAGTTCACAACTTC-GTGGCATCCTTTTTAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCC
1 AAAGCCCACAA-GTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAG-CC
* * * * * * *
373627 ACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTGAAAGCCCA
63 -CACAAGTCAGTGGC-ACC-CTTTC-AAG-CC-CACGAGTCAGTGG-TA-CCTTTTCAAAG-CC-
* *
373692 CACAAGTCGGTGGCAACCCATTTC
118 CACAAGTCAGTGGC-ACTC-TTTC
* * * * * * *
373716 AAAACCCACAAATCAGTGGCACCCTTTTAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCAC
* ** *
373781 AAGCCAGTGGCACTTTTTTCAAAGCCCACACGAGTC-GATGGCAACCCTTTTCAAAGCCCACAAG
66 AAGTCAGTGGCAC-CCTTTC-AAG-CC-CACGAGTCAG-TGG-TA-CCTTTTCAAAGCCCACAAG
*
373845 TTAGTGGCA-TCCTTTC
124 TCAGTGGCACT-CTTTC
* * * * *
373861 AAAGCCCACAAGTCTGTGGCAACACTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCGAAGCCC
1 AAAGCCCACAAGTCAGTGGCATC-C-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCC
* * * * * *
373926 ACAATTCAGTGGCACCCTTGCGAAGCCCACAATTCAGTGGCA-CTCTTTCAAAGCCTACAAGTCA
64 ACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGTACCT-TTTCAAAGCCCACAAGTCA
*
373990 GTGGCACCCTTTC
127 GTGGCACTCTTTC
* * * * *
374003 AAAGCCCACACAAGTCAGTGACACTCTTTTTAAAGCCCACACAAGTTAGTGGCACCTTTTCAAAG
1 AAAG-CC-CACAAGTCAGTGGCA-TCCTTTCAAAG-CC-CACAAGTCAGTGGCATCTTTTCAAAG
*
374068 CCCACAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTC
61 CCCACAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACAAGTC
374133 AGTGGCACTCTTTC
126 AGTGGCACTCTTTC
* * *
374147 AAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACGAGTTAGTGGCAT-TCTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCT-TTTCAAAGCCCA
* *
374211 CAAGTTAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTG
65 CAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACAAGTCAGTG
374276 GCACTCTTTC
130 GCACTCTTTC
* *
374286 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCATTTTTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCA-
*
374351 GCAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGT
65 -CAAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACAAGTCAGT
374416 GGCACTCTTTC
129 GGCACTCTTTC
* * * *
374427 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAATAGCATTTTTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCA-
* ***
374492 GCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTAACACTCTTTTCAAAGCCCACA
65 -CAAGTCAGTGGCACCC-TTTCAAGCCCACG--AGTCAGTGGTAC-CTTTTCAAAGCCCACA
374554 CGTATCAGTG
Statistics
Matches: 854, Mismatches: 94, Indels: 76
0.83 0.09 0.07
Matches are distributed among these distances:
137 41 0.05
138 8 0.01
139 161 0.19
140 15 0.02
141 168 0.20
142 60 0.07
143 15 0.02
144 84 0.10
145 100 0.12
146 16 0.02
147 63 0.07
148 4 0.00
149 49 0.06
150 16 0.02
151 12 0.01
152 42 0.05
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (139 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCAC
AAGTCAGTGGCACCCTTTCAAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACAAGTCAGTGG
CACTCTTTC
Found at i:375189 original size:20 final size:20
Alignment explanation
Indices: 375160--375240 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
375150 TTTTTACCCA
375160 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
375180 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
375200 AATGTATCAATAAATTCTTC
1 AATGTATCGATACATTTTTC
375220 AATGTATCGATACATTATTTC
1 AATGTATCGATACATT-TTTC
375241 TTTTTACCTA
Statistics
Matches: 46, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:376460 original size:19 final size:19
Alignment explanation
Indices: 376436--376503 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
376426 GATTCAACAA
376436 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
376455 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
376470 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
376487 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
376504 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:376475 original size:13 final size:13
Alignment explanation
Indices: 376457--376481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
376447 ACATAAGTTT
376457 TGTATCGATACAA
1 TGTATCGATACAA
376470 TGTATCGATACA
1 TGTATCGATACA
376482 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:376479 original size:32 final size:32
Alignment explanation
Indices: 376438--376500 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
376428 TTCAACAATT
*
376438 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
376470 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
376501 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:376548 original size:20 final size:20
Alignment explanation
Indices: 376523--376577 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
376513 ACCAAGGAAA
*
376523 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
376543 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
376563 TGTATCGATACATTT
1 TGTATCGATACATTT
376578 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:379058 original size:28 final size:28
Alignment explanation
Indices: 379022--379098 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
379012 ATTTTTCACA
* * *
379022 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
379050 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
379078 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
379099 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:382646 original size:2 final size:2
Alignment explanation
Indices: 382639--382679 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
382629 GGATTTTCAA
382639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
382680 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:383643 original size:21 final size:23
Alignment explanation
Indices: 383610--383651 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
383600 CTTTTTTTTA
383610 TTTTTCTATTTATTT-ATAACTT
1 TTTTTCTATTTATTTCATAACTT
*
383632 TTTTTTTA-TTATTTCATAAC
1 TTTTTCTATTTATTTCATAAC
383652 CAAAGCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTCTATTTATTTCATAACTT
Found at i:385267 original size:3 final size:3
Alignment explanation
Indices: 385259--385293 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
385249 AAAAAGAGAG
385259 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
385294 ATAAATTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:385423 original size:15 final size:15
Alignment explanation
Indices: 385403--385446 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
385393 TCGCATAATT
385403 TATTTATTTATTTTA
1 TATTTATTTATTTTA
*
385418 TATTTATATA-TTTA
1 TATTTATTTATTTTA
385432 TATTATATTTTATTT
1 TATT-TA-TTTATTT
385447 AACATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 11 0.46
16 3 0.12
17 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTATTTATTTTA
Found at i:385424 original size:19 final size:19
Alignment explanation
Indices: 385400--385465 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
385390 AGATCGCATA
*
385400 ATTTATTTATTTATTTTAT
1 ATTTATTTATTTATATTAT
*
385419 ATTTATATATTTATATTAT
1 ATTTATTTATTTATATTAT
**
385438 ATTTTATTTA-ACATATTAT
1 A-TTTATTTATTTATATTAT
385457 A-TTATTTAT
1 ATTTATTTAT
385466 ATAATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.17
19 26 0.65
20 7 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTATTTATTTATATTAT
Found at i:385445 original size:24 final size:23
Alignment explanation
Indices: 385403--385468 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
385393 TCGCATAATT
385403 TATTTAT-TTATTTTATATTTATA
1 TATTTATATTATTTTATATTTA-A
385426 TATTTATATTATATTT-TATTTAA
1 TATTTATATTAT-TTTATATTTAA
*
385449 CATATTATATTATTTATATA
1 TAT-TTATATTATTT-TATA
385469 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 12 0.32
24 20 0.54
25 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATATTATTTTATATTTAA
Found at i:385844 original size:32 final size:33
Alignment explanation
Indices: 385804--385877 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
385794 TATGAATATA
*
385804 TAAATATATTAAAATTTATATAAAATAA-ATTAT
1 TAAATATATCAAAATTTATATAAAATAATATT-T
*
385837 T-AATATATCAAAATTTATATAATATAATATTT
1 TAAATATATCAAAATTTATATAAAATAATATTT
385869 TAAATATAT
1 TAAATATAT
385878 ATTAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 26 0.70
33 11 0.30
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
TAAATATATCAAAATTTATATAAAATAATATTT
Found at i:385861 original size:17 final size:16
Alignment explanation
Indices: 385813--385876 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
385803 ATAAATATAT
*
385813 TAAAATTTATATAAAA
1 TAAAATTTATATAATA
*
385829 TAAATTATTA-AT-ATA
1 TAAAAT-TTATATAATA
385844 TCAAAATTTATATAATA
1 T-AAAATTTATATAATA
*
385861 TAATATTT-TA-AATA
1 TAAAATTTATATAATA
385875 TA
1 TA
385877 TATTAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.15
15 8 0.20
16 19 0.47
17 7 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:385863 original size:5 final size:5
Alignment explanation
Indices: 385853--385954 Score: 99
Period size: 5 Copynumber: 20.8 Consensus size: 5
385843 ATCAAAATTT
* * *
385853 ATATA ATATA ATATT TTA-A ATATA TATTAAA ATATA A-A-A A-ATA ATATAA
1 ATATA ATATA ATATA ATATA ATATA -A-TATA ATATA ATATA ATATA ATAT-A
385902 ATATA ATATA AT-T- ATATTA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA
385951 ATAT
1 ATAT
385955 CAGATAATCT
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
3 5 0.06
4 6 0.07
5 58 0.71
6 10 0.12
7 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:385918 original size:39 final size:39
Alignment explanation
Indices: 385855--385952 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
385845 CAAAATTTAT
**
385855 ATAATATAATATTTTA-AATATATATTAAAAT-ATAAAAA
1 ATAATATAATATAATATAAT-TATATTAAAATAATAAAAA
* * *
385893 ATAATATAAATATAATATAATTATATTAATATAATATAAT
1 ATAATAT-AATATAATATAATTATATTAAAATAATAAAAA
385933 ATAATATAATATAATATAAT
1 ATAATATAATATAATATAAT
385953 ATCAGATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
38 7 0.13
39 30 0.58
40 15 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (39 bp):
ATAATATAATATAATATAATTATATTAAAATAATAAAAA
Found at i:385923 original size:63 final size:66
Alignment explanation
Indices: 385807--385929 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 66
385797 GAATATATAA
* *
385807 ATATATTAAAATTTATATAAAATAAATTATTAATATATCAAAATTTATATAATATAATATTTTAA
1 ATATATTAAAA-TTATAAAAAATAAATTATAAATATATCAAAATTTATATAATATAATATTTTAA
385872 AT
65 AT
*
385874 ATATATTAAAA-TATAAAAAAT-AA-TATAAATATAAT-ATAA-TTATATTAATATAATAT
1 ATATATTAAAATTATAAAAAATAAATTATAAATAT-ATCAAAATTTATA-TAATATAATAT
385930 AATATAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
62 5 0.10
63 22 0.43
64 4 0.08
65 9 0.18
67 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (66 bp):
ATATATTAAAATTATAAAAAATAAATTATAAATATATCAAAATTTATATAATATAATATTTTAAA
T
Found at i:385924 original size:49 final size:44
Alignment explanation
Indices: 385853--385954 Score: 116
Period size: 49 Copynumber: 2.2 Consensus size: 44
385843 ATCAAAATTT
*
385853 ATATAATATAATATTTTAAATATATATTAAAATATAAAAAATAATATAA
1 ATATAATATAATATATTAAATATA-A-TAAAATAT--AAAATAATAT-A
* *
385902 ATATAATATAATTATATT-AATATAATATAATATAATATAATATA
1 ATATAATATAA-TATATTAAATATAATAAAATATAAAATAATATA
385946 ATATAATAT
1 ATATAATAT
385955 CAGATAATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 10 0.20
45 9 0.18
47 7 0.14
48 1 0.02
49 17 0.35
50 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (44 bp):
ATATAATATAATATATTAAATATAATAAAATATAAAATAATATA
Found at i:386137 original size:20 final size:20
Alignment explanation
Indices: 386114--386186 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
386104 TATATATTCA
386114 TATATATTTATATAAAATTT
1 TATATATTTATATAAAATTT
*
386134 TATAT-TTTA-ATAATTTATTT
1 TATATATTTATATAA--AATTT
386154 TATATATATT-T-TAAAATATT
1 TATATAT-TTATATAAAAT-TT
*
386174 TATGTATTTATAT
1 TATATATTTATAT
386187 CATATTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
18 4 0.10
19 8 0.19
20 23 0.55
21 5 0.12
22 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TATATATTTATATAAAATTT
Found at i:386185 original size:24 final size:24
Alignment explanation
Indices: 386132--386186 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
386122 TATATAAAAT
* *
386132 TTTATATTTTAATAATTTATTTTA
1 TTTATATTTTAAAAATTTATTGTA
*
386156 TATATATTTTAAAATATTTA-TGTA
1 TTTATATTTTAAAA-ATTTATTGTA
386180 TTTATAT
1 TTTATAT
386187 CATATTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATATTTTAAAAATTTATTGTA
Found at i:386397 original size:22 final size:23
Alignment explanation
Indices: 386346--386399 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
386336 AGATTTAAAT
386346 ATATTTTTATATTTATGTATTTTA
1 ATATTTTTATATTTA-GTATTTTA
386370 AT-TTTTTATA-TTA-TATTTGTA
1 ATATTTTTATATTTAGTATTT-TA
*
386391 TTATTTTTA
1 ATATTTTTA
386400 AAATTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
21 3 0.11
22 9 0.33
23 8 0.30
24 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
ATATTTTTATATTTAGTATTTTA
Found at i:386966 original size:22 final size:20
Alignment explanation
Indices: 386941--386994 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
386931 ATAAAAAATT
386941 ATTTTTAT-ATTAATATTTATA
1 ATTTTTATAATTAA-ATTT-TA
386962 GA-TTTTATAATTAAATTTTA
1 -ATTTTTATAATTAAATTTTA
*
386982 ATTTTTTTAATTA
1 ATTTTTATAATTA
386995 TTAAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 10 0.34
22 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATTAAATTTTA
Found at i:386969 original size:21 final size:19
Alignment explanation
Indices: 386943--386986 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
386933 AAAAAATTAT
386943 TTTTAT-ATTAATATTTATAGA
1 TTTTATAATTAA-ATTT-TA-A
386964 TTTTATAATTAAATTTTAA
1 TTTTATAATTAAATTTTAA
386983 TTTT
1 TTTT
386987 TTTAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 10 0.45
22 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATAATTAAATTTTAA
Found at i:387601 original size:6 final size:6
Alignment explanation
Indices: 387592--387652 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
387582 TTATATAATT
* *
387592 ATATAA ATATAA ATATAA A-ATAA ATTATTAA ATAT-A TTATAA TATAAAA
1 ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATAA ATATAA -ATATAA
*
387641 ATATAA TTATAA
1 ATATAA ATATAA
387653 TACATACATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 9 0.20
6 25 0.56
7 7 0.16
8 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:387603 original size:14 final size:14
Alignment explanation
Indices: 387584--387632 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 14
387574 ATAGTTTTTT
387584 ATATAATTATATAA
1 ATATAATTATATAA
*
387598 ATATAAATATA-AA
1 ATATAATTATATAA
387611 ATA-AATTAT-TAA
1 ATATAATTATATAA
387623 ATAT-ATTATA
1 ATATAATTATA
387633 ATATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 15 0.50
13 5 0.17
14 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATTATATAA
Found at i:387633 original size:19 final size:17
Alignment explanation
Indices: 387592--387652 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
387582 TTATATAATT
387592 ATATAAATATAAATATA
1 ATATAAATATAAATATA
*
387609 AAATAAATTATTAAATATA
1 ATATAAA-TA-TAAATATA
* *
387628 TTATAATATAAAAATATA
1 ATATAA-ATATAAATATA
387646 ATTATAA
1 A-TATAA
387653 TACATACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.17
18 9 0.26
19 19 0.54
20 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATAAATATA
Found at i:387728 original size:16 final size:17
Alignment explanation
Indices: 387697--387728 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
387687 TATTTCATAT
387697 AATATTTTATAATATAA
1 AATATTTTATAATATAA
387714 AATATTTTA-AATATA
1 AATATTTTATAATATA
387729 GTTACGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTTTATAATATAA
Found at i:387969 original size:8 final size:7
Alignment explanation
Indices: 387942--387967 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
387932 TTATCGTAGC
387942 AAAAATA
1 AAAAATA
387949 AAAAATA
1 AAAAATA
387956 AAAAATA
1 AAAAATA
387963 AAAAA
1 AAAAA
387968 ATTTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:388048 original size:15 final size:15
Alignment explanation
Indices: 388030--388067 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
388020 TTTATCATAA
*
388030 TAATTTAAATTAAAT
1 TAATTTAAATTAAAC
388045 TAATTTAAATTAAAC
1 TAATTTAAATTAAAC
388060 T-ATTTAAA
1 TAATTTAAA
388068 AATTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTTAAATTAAAC
Found at i:388769 original size:23 final size:24
Alignment explanation
Indices: 388743--388788 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
388733 AACTAAATTA
*
388743 TTATTTTAA-TAATAAAAATATTT
1 TTATTTAAATTAATAAAAATATTT
388766 TTATTTAAATTTAATAAAAATAT
1 TTATTTAAA-TTAATAAAAATAT
388789 ATAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTTAAATTAATAAAAATATTT
Found at i:389632 original size:12 final size:12
Alignment explanation
Indices: 389615--389640 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
389605 ACCCAGATTG
389615 AAAATGGAAAAA
1 AAAATGGAAAAA
389627 AAAATGGAAAAA
1 AAAATGGAAAAA
389639 AA
1 AA
389641 TGGAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAATGGAAAAA
Found at i:389745 original size:12 final size:12
Alignment explanation
Indices: 389730--389756 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
389720 AAATGGGTGG
389730 AAAAAAGAAAGA
1 AAAAAAGAAAGA
389742 AAAAAAGAAAGA
1 AAAAAAGAAAGA
389754 AAA
1 AAA
389757 TTTGAGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:390825 original size:22 final size:22
Alignment explanation
Indices: 390800--390853 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
390790 TTAATAAAAA
* *
390800 TAATATATTAAATATAAAATTT
1 TAATATATTAAATAAAAAAATT
* *
390822 TAATATAATAATTAAAAAAATT
1 TAATATATTAAATAAAAAAATT
390844 TAATCATATT
1 TAAT-ATATT
390854 TTTAAATACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATATATTAAATAAAAAAATT
Found at i:391568 original size:16 final size:17
Alignment explanation
Indices: 391547--391590 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
391537 AAAAGAAGGG
391547 TTCATTTTTTTTA-TTT
1 TTCATTTTTTTTATTTT
391563 TTCA-TTTTTTTATTTT
1 TTCATTTTTTTTATTTT
*
391579 TTTATTTTTTTT
1 TTCATTTTTTTT
391591 CTACCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 7 0.28
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (17 bp):
TTCATTTTTTTTATTTT
Found at i:391589 original size:8 final size:8
Alignment explanation
Indices: 391552--391589 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
391542 AAGGGTTCAT
391552 TTTTTTTA
1 TTTTTTTA
*
391560 -TTTTTCA
1 TTTTTTTA
391567 TTTTTTTA
1 TTTTTTTA
391575 TTTTTTTA
1 TTTTTTTA
391583 TTTTTTT
1 TTTTTTT
391590 TCTACCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:391785 original size:16 final size:15
Alignment explanation
Indices: 391757--391799 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
391747 TGTGGTATAA
*
391757 ATATTAAATATAAATTT
1 ATATTTAATATAAA--T
391774 ATATTT-ATATAAAT
1 ATATTTAATATAAAT
391788 ATATTTAATATA
1 ATATTTAATATA
391800 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 7 0.29
17 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTAATATAAAT
Found at i:391799 original size:23 final size:21
Alignment explanation
Indices: 391773--391814 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
391763 AATATAAATT
391773 TATATTTATATAAATATATTTAA
1 TATATTTATA-AAAT-TATTTAA
*
391796 TATATTTTTAAAATTATTT
1 TATATTTATAAAATTATTT
391815 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTTATAAAATTATTTAA
Found at i:398695 original size:107 final size:107
Alignment explanation
Indices: 398559--398773 Score: 412
Period size: 107 Copynumber: 2.0 Consensus size: 107
398549 TTCATTTCAG
*
398559 ACCTATTTCATTCTCACAAAATGACTATTATATTATAATTTTATTCTATTCTAGTAAATCAAATA
1 ACCTATTTCATTCTCACAAAATGACTATTATATTATAATTTTATTCTATTCTAATAAATCAAATA
*
398624 TAAAGTAAATTGCTTTCACCAAGTATTTTGATTCGGAGCTTT
66 TAAAGTAAATTACTTTCACCAAGTATTTTGATTCGGAGCTTT
398666 ACCTATTTCATTCTCACAAAATGACTATTATATTATAATTTTATTCTATTCTAATAAATCAAATA
1 ACCTATTTCATTCTCACAAAATGACTATTATATTATAATTTTATTCTATTCTAATAAATCAAATA
398731 TAAAGTAAATTACTTTCACCAAGTATTTTGATTCGGAGCTTT
66 TAAAGTAAATTACTTTCACCAAGTATTTTGATTCGGAGCTTT
398773 A
1 A
398774 TCGACACTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (107 bp):
ACCTATTTCATTCTCACAAAATGACTATTATATTATAATTTTATTCTATTCTAATAAATCAAATA
TAAAGTAAATTACTTTCACCAAGTATTTTGATTCGGAGCTTT
Found at i:403978 original size:2 final size:2
Alignment explanation
Indices: 403971--404016 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
403961 AACTTCCTTC
403971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
404013 TA TA
1 TA TA
404017 AATTAATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:405147 original size:17 final size:18
Alignment explanation
Indices: 405127--405173 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
405117 TTTTTTAATT
*
405127 ATAATAATTTACCTT-AA
1 ATAATAATTTAACTTAAA
405144 ATAATAATTATAACTTAAA
1 ATAATAATT-TAACTTAAA
405163 ATAATATATTT
1 ATAATA-ATTT
405174 TGTATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 5 0.19
19 9 0.35
20 3 0.12
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATTTAACTTAAA
Found at i:405578 original size:31 final size:28
Alignment explanation
Indices: 405536--405613 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 28
405526 GTTAAACACA
405536 TTATA-AAAATTAAAATATTTAAAAATT
1 TTATATAAAATTAAAATATTTAAAAATT
* * *
405563 TATATAATATAAATTAATA-ACTTATAAATT
1 T-TAT-ATA-AAATTAAAATATTTAAAAATT
*
405593 TTATATAAAAATAAAATATTT
1 TTATATAAAATTAAAATATTT
405614 TTAATATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 8 0.20
28 9 0.22
29 4 0.10
30 11 0.28
31 8 0.20
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TTATATAAAATTAAAATATTTAAAAATT
Found at i:405772 original size:18 final size:19
Alignment explanation
Indices: 405741--405776 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
405731 TGCTTAACTC
405741 AATTCAAAAAATATATTTA
1 AATTCAAAAAATATATTTA
*
405760 AATT-AAAACATATATTT
1 AATTCAAAAAATATATTT
405777 TTATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAAAATATATTTA
Found at i:405816 original size:14 final size:14
Alignment explanation
Indices: 405797--405824 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
405787 TTAATTATAA
405797 AATATAAAAATATT
1 AATATAAAAATATT
405811 AATATAAAAATATT
1 AATATAAAAATATT
405825 TTTAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:407653 original size:14 final size:14
Alignment explanation
Indices: 407603--407663 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
407593 ATTTTGTAAA
* *
407603 TATATTATGTTAAT
1 TATATTATATTTAT
*
407617 TATATTTAAATTTAT
1 TATA-TTATATTTAT
*
407632 TATTTTATATTTAT
1 TATATTATATTTAT
* *
407646 TATATTATTTTTAG
1 TATATTATATTTAT
407660 TATA
1 TATA
407664 AAAAAATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 28 0.74
15 10 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TATATTATATTTAT
Found at i:407658 original size:20 final size:19
Alignment explanation
Indices: 407616--407656 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
407606 ATTATGTTAA
407616 TTATATTTAAATTTATTATT
1 TTATATTT-AATTTATTATT
407636 TTATATTT-ATTATATTATT
1 TTATATTTAATT-TATTATT
407655 TT
1 TT
407657 TAGTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 9 0.45
20 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATTTAATTTATTATT
Found at i:409459 original size:11 final size:11
Alignment explanation
Indices: 409443--409491 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
409433 TTACGTTTTT
409443 AATATTAAATA
1 AATATTAAATA
409454 AATATTAAATA
1 AATATTAAATA
* *
409465 ATTAATAAA-A
1 AATATTAAATA
409475 ATATATTTAAATA
1 A-ATA-TTAAATA
409488 AATA
1 AATA
409492 ATATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 2 0.06
11 20 0.65
12 7 0.23
13 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATTAAATA
Found at i:409488 original size:23 final size:24
Alignment explanation
Indices: 409449--409494 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
409439 TTTTAATATT
*
409449 AAATAAATATTAAATAATTAATAA
1 AAATAAATATTAAATAAATAATAA
*
409473 AAATATAT-TTAAATAAATAATA
1 AAATAAATATTAAATAAATAATA
409495 TAATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATATTAAATAAATAATAA
Found at i:409878 original size:20 final size:18
Alignment explanation
Indices: 409853--409897 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
409843 TATGATGTGA
*
409853 AAAAAATAATTAAGTATAAT
1 AAAAAATAA-TAA-CATAAT
409873 AAAAAAT-ATAACATAAT
1 AAAAAATAATAACATAAT
409890 AAAAAATA
1 AAAAAATA
409898 TAAAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 1 0.04
20 7 0.30
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAATAATAACATAAT
Found at i:409890 original size:17 final size:17
Alignment explanation
Indices: 409868--409900 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
409858 ATAATTAAGT
409868 ATAATAAAAAATATAAC
1 ATAATAAAAAATATAAC
409885 ATAATAAAAAATATAA
1 ATAATAAAAAATATAA
409901 AATATTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAATAAAAAATATAAC
Found at i:410080 original size:22 final size:20
Alignment explanation
Indices: 410040--410086 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
410030 ATATTATTAT
410040 TTAAAAAATTAAAATTAAAA
1 TTAAAAAATTAAAATTAAAA
* *
410060 TTAAAAATATTTATAATTAAAT
1 TTAAAAA-A-TTAAAATTAAAA
410082 TTAAA
1 TTAAA
410087 TCAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 1 0.04
22 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAAATTAAAATTAAAA
Found at i:410104 original size:26 final size:24
Alignment explanation
Indices: 410063--410111 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
410053 ATTAAAATTA
410063 AAAATATTTATAATTAAATTTAAATC
1 AAAATATTTATAATT--ATTTAAATC
* *
410089 AAAATATTTTTTATTATTTAAAT
1 AAAATATTTATAATTATTTAAAT
410112 AATAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAATATTTATAATTATTTAAATC
Found at i:413510 original size:19 final size:20
Alignment explanation
Indices: 413482--413519 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
413472 GGGTTTTTTT
413482 GTTAAATGTGAAA-GAGTTG
1 GTTAAATGTGAAACGAGTTG
*
413501 GTTAATTGTGAAACGAGTT
1 GTTAAATGTGAAACGAGTT
413520 CAACTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (20 bp):
GTTAAATGTGAAACGAGTTG
Found at i:416060 original size:1 final size:1
Alignment explanation
Indices: 416056--416163 Score: 144
Period size: 1 Copynumber: 108.0 Consensus size: 1
416046 CACAACAACA
* * * * * * * *
416056 CCCCCCACCCCCCCCCCCCACCCCCCCCCCCCCCCACACCACCCCCCCCCACCCCCCCCCACACC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
416121 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
416164 AACAAAAATC
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:501779 original size:2 final size:2
Alignment explanation
Indices: 501772--501802 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
501762 ATTATCAATA
501772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
501803 AACACCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:502549 original size:24 final size:24
Alignment explanation
Indices: 502519--502584 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
502509 ATTTTAAAAG
502519 TTTTAAA-A-TCAATAATATTTTATT
1 TTTTAAAGATTCAA-AA-ATTTTATT
*
502543 TTTTAAAGATTTAAAAATTTTATT
1 TTTTAAAGATTCAAAAATTTTATT
*
502567 TTTTAAATATTTCAAAAA
1 TTTTAAAGA-TTCAAAAA
502585 GAAATCTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 23 0.64
25 10 0.28
26 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTAAAGATTCAAAAATTTTATT
Found at i:502583 original size:25 final size:24
Alignment explanation
Indices: 502535--502584 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
502525 AATCAATAAT
502535 ATTTTATTTTTTAAAGATTTAAAA
1 ATTTTATTTTTTAAAGATTTAAAA
*
502559 ATTTTATTTTTTAAATATTTCAAAA
1 ATTTTATTTTTTAAAGATTT-AAAA
502584 A
1 A
502585 GAAATCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTATTTTTTAAAGATTTAAAA
Found at i:502866 original size:11 final size:11
Alignment explanation
Indices: 502846--502876 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
502836 AGCTTTACCG
502846 TTTTTATTTCTC
1 TTTTT-TTTCTC
502858 TTTTTTTTCTC
1 TTTTTTTTCTC
502869 TTTTTTTT
1 TTTTTTTT
502877 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:504747 original size:29 final size:27
Alignment explanation
Indices: 504699--504757 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
504689 AATGAAATTT
504699 AAGAAAAAATAAAAGAAGAGGT-GAAGA
1 AAGAAAAAATAAAAGAAGAGGTAG-AGA
504726 AAGAAAAAA-AAAAGTGAGAGAGGTAGAGA
1 AAGAAAAAATAAAA--GA-AGAGGTAGAGA
504755 AAG
1 AAG
504758 GAAGTTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 4 0.14
27 9 0.32
28 2 0.07
29 12 0.43
30 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (27 bp):
AAGAAAAAATAAAAGAAGAGGTAGAGA
Found at i:507093 original size:45 final size:44
Alignment explanation
Indices: 507041--507128 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
507031 CTCTCTTTCC
507041 CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTCTTTTTTT
1 CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCT-TTTTTTT
* *
507086 CTTCTCTCTCATTATGGTTAGCTTGCTTTTTTTCTCTTTTTTT
1 CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTTTTTTT
507129 CATCTTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 6 0.15
45 35 0.85
ACGTcount: A:0.07, C:0.24, G:0.09, T:0.60
Consensus pattern (44 bp):
CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTTTTTTTT
Found at i:509183 original size:19 final size:20
Alignment explanation
Indices: 509137--509194 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
509127 AAATTTAAGA
*
509137 AAAAAATAAAAAGAAGAGTG
1 AAAAAAGAAAAAGAAGAGTG
509157 AAAGAAAGAAAAA-AA-AGTG
1 AAA-AAAGAAAAAGAAGAGTG
**
509176 AGAAAAAGTTAAAGAAGAG
1 A-AAAAAGAAAAAGAAGAG
509195 GAAGTCGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 12 0.39
20 9 0.29
21 10 0.32
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (20 bp):
AAAAAAGAAAAAGAAGAGTG
Found at i:509393 original size:16 final size:15
Alignment explanation
Indices: 509369--509407 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
509359 GTTAGCTTGC
509369 TTTTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
509384 TTTTTCTTCTCTCTTT
1 TTTTT-TTCTCTCTTT
509400 TATTTTTT
1 T-TTTTTT
509408 TGATTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTCTCTTT
Found at i:510987 original size:19 final size:19
Alignment explanation
Indices: 510963--511001 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
510953 GAGTACAATC
* *
510963 ATTTAAATATATTAAAAAT
1 ATTTAAAAAAATTAAAAAT
510982 ATTTAAAAAAATTAAAAAT
1 ATTTAAAAAAATTAAAAAT
511001 A
1 A
511002 CATATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAAAAATTAAAAAT
Found at i:512772 original size:18 final size:19
Alignment explanation
Indices: 512735--512774 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
512725 AAACTATAAG
*
512735 TTTTGTAAAATATAATTAT
1 TTTTGGAAAATATAATTAT
*
512754 TTTTGGAAAATGTAA-TAT
1 TTTTGGAAAATATAATTAT
512772 TTT
1 TTT
512775 CTGTTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTTGGAAAATATAATTAT
Found at i:515255 original size:2 final size:2
Alignment explanation
Indices: 515248--515279 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
515238 CTCATGAATC
515248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
515280 GCATAACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515349 original size:28 final size:28
Alignment explanation
Indices: 515282--515341 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
515272 ATATATATGC
* * *
515282 ATAACCAAAACCAAACTGAATACTATAT
1 ATAACCAAAATCAAATTGAATACCATAT
515310 ATAACCAAAATCAAATTGAATACCATAT
1 ATAACCAAAATCAAATTGAATACCATAT
515338 ATAA
1 ATAA
515342 TTGAAATCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (28 bp):
ATAACCAAAATCAAATTGAATACCATAT
Found at i:518239 original size:9 final size:9
Alignment explanation
Indices: 518216--518259 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
518206 CATATGGTAA
518216 AAATTATAT
1 AAATTATAT
518225 -AA-TATAT
1 AAATTATAT
518232 AAATTATA-
1 AAATTATAT
518240 AAATTAATAT
1 AAATT-ATAT
518250 AAATTATAT
1 AAATTATAT
518259 A
1 A
518260 TTTTTAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.16
8 9 0.29
9 12 0.39
10 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTATAT
Found at i:520086 original size:15 final size:17
Alignment explanation
Indices: 520061--520102 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
520051 TGATATTAAT
520061 TATTAACATATTAAA-AA
1 TATTAA-ATATTAAATAA
520078 TA-TAAATA-TAAATAA
1 TATTAAATATTAAATAA
520093 TATTAAATAT
1 TATTAAATAT
520103 AATTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 9 0.41
17 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TATTAAATATTAAATAA
Found at i:520103 original size:22 final size:23
Alignment explanation
Indices: 520075--520117 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
520065 AACATATTAA
520075 AAATATAAATATAA-ATAATATT
1 AAATATAAATATAATATAATATT
*
520097 AAATATAATTATAATATAATA
1 AAATATAAATATAATATAATA
520118 AAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATATAAATATAATATAATATT
Found at i:521861 original size:22 final size:23
Alignment explanation
Indices: 521813--521864 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
521803 TTATTTTATG
***
521813 TAATATTAATTATAAAAATATTT
1 TAATATTAATTATAAAAATAAAA
521836 TAATATTAA-TATAAAAATAAAA
1 TAATATTAATTATAAAAATAAAA
521858 TAATATT
1 TAATATT
521865 TTAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATATTAATTATAAAAATAAAA
Found at i:522020 original size:19 final size:20
Alignment explanation
Indices: 521988--522027 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
521978 ATAAATTTTT
* *
521988 AAAAACTTTTAAAATATATA
1 AAAAACTTTAAAAAAATATA
522008 AAAAAC-TTAAAAAAATATA
1 AAAAACTTTAAAAAAATATA
522027 A
1 A
522028 TACACCTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAACTTTAAAAAAATATA
Found at i:527134 original size:79 final size:79
Alignment explanation
Indices: 527013--527247 Score: 228
Period size: 79 Copynumber: 2.9 Consensus size: 79
527003 TTATTGATTT
* * *
527013 TTTTATTTCCAAAACATCGAATTTTTTTACCATTGGGAATACTCCAACCCCGTTATTTTC-G-AG
1 TTTTATTTCCAAAATATC-AA-TTTTTCACCATCGGG-ATACTCCAACCCCGTTATTTTCTGAAG
527076 GAGATACTCCAATCC-CAA
63 G-GATACTCCAA-CCTCAA
* * *
527094 TTTTATTTCCAAAATATTAATTTTTCACCATCGAGGATACTCCAATCCCATTA-TTTCTGAAGGG
1 TTTTATTTCCAAAATATCAATTTTTCACCATCG-GGATACTCCAACCCCGTTATTTTCTGAAGGG
* * **
527158 ATATTGCAACCTCGG
65 ATACTCCAACCTCAA
* * * * *
527173 TTTTATTTTCAAAATATCAATATTTCACCATCGGGGATACACCAACCCTGTTATTTT-TAAAGGG
1 TTTTATTTCCAAAATATCAATTTTTCACCATC-GGGATACTCCAACCCCGTTATTTTCTGAAGGG
*
527237 ATACTTCAACC
65 ATACTCCAACC
527248 CTGGTTTTAT
Statistics
Matches: 128, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
78 6 0.05
79 95 0.74
80 11 0.09
81 16 0.12
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (79 bp):
TTTTATTTCCAAAATATCAATTTTTCACCATCGGGATACTCCAACCCCGTTATTTTCTGAAGGGA
TACTCCAACCTCAA
Found at i:527286 original size:79 final size:80
Alignment explanation
Indices: 527051--527377 Score: 235
Period size: 79 Copynumber: 4.1 Consensus size: 80
527041 ACCATTGGGA
* ** ** *
527051 ATACTCCAACCC-CGTTA-TTTTCGAGGAGATACTCCAATCC-CAATTTTATTTCCAAAATATT-
1 ATACTCCAACCCTCGCTATTTTTAAAGG-GATACTCCAA-CCTCGGTTTTATTTCTAAAATATTA
** * *
527112 AATTTTTCACCATCGAGG
64 AATTCCTCATC-TCGGGG
* ** * * * * *
527130 ATACTCCAATCC-CATTATTTCTGAAGGGATATTGCAACCTCGGTTTTATTT-TCAAAATATCAA
1 ATACTCCAACCCTCGCTATTTTTAAAGGGATACTCCAACCTCGGTTTTATTTCT-AAAATATTAA
*
527193 TATT--TCACCATCGGGG
65 -ATTCCTCATC-TCGGGG
* * * *
527209 ATACACCAACCCT-GTTATTTTTAAAGGGATACTTCAACC-CTGGTTTTATTTCTAAACTATTAA
1 ATACTCCAACCCTCGCTATTTTTAAAGGGATACTCCAACCTC-GGTTTTATTTCTAAAATATTAA
527272 ATTCCTCATCTCGGGG
65 ATTCCTCATCTCGGGG
** * * * *
527288 ATACTTTAA-CGTCGCTATTTTTGAGGGGATACTCCAACTTCGGTTTTATTTCTAAAATATTAAA
1 ATACTCCAACCCTCGCTATTTTTAAAGGGATACTCCAACCTCGGTTTTATTTCTAAAATATTAAA
* *
527352 TTTCTTATCTCGGGG
66 TTCCTCATCTCGGGG
527367 ATACTCCAACC
1 ATACTCCAACC
527378 TCAGTTTTAT
Statistics
Matches: 199, Mismatches: 36, Indels: 25
0.77 0.14 0.10
Matches are distributed among these distances:
78 8 0.04
79 174 0.87
80 14 0.07
81 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (80 bp):
ATACTCCAACCCTCGCTATTTTTAAAGGGATACTCCAACCTCGGTTTTATTTCTAAAATATTAAA
TTCCTCATCTCGGGG
Found at i:527448 original size:79 final size:79
Alignment explanation
Indices: 527365--527669 Score: 343
Period size: 79 Copynumber: 3.9 Consensus size: 79
527355 CTTATCTCGG
* * *
527365 GGATACTCCAACCTCAG-TTTTATTTCCAAAATATCGATTTTTCTCCATCGGGGAAACTCCAACC
1 GGATACTCCAACC-CAGTTTTTATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACC
*
527429 CTATTGTTTCTAAGA
65 CCATTGTTTCTAAGA
* * * *
527444 GGATACTCCAACCC-GATTTTTATTTTCAAAATATCGATCTTTCACCATTGGGGATACTCCAACC
1 GGATACTCCAACCCAG-TTTTTATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACC
*
527508 CCATTGTTTTCAAAGA
65 CCATTG-TTTCTAAGA
* *
527524 -GATACTCCAACCCCGTTTTTATTTCCAAACTATCAATTTTT-ACCATCGGGGATACTCCAACCC
1 GGATACTCCAACCCAGTTTTTATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCC
* **
527587 CATTATTT-TTTGA
66 CATTGTTTCTAAGA
* * * **
527600 GGGATACTCTAACCTC-GTTTTTATTTTCAAAATATCAAATTTTCACCATCCAGGATACTCCAAC
1 -GGATACTCCAACC-CAGTTTTTATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAAC
*
527664 CTCATT
64 CCCATT
527670 TTATTTCCAA
Statistics
Matches: 195, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
76 2 0.01
77 4 0.02
78 61 0.31
79 119 0.61
80 9 0.05
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (79 bp):
GGATACTCCAACCCAGTTTTTATTTCCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCC
CATTGTTTCTAAGA
Found at i:527599 original size:288 final size:286
Alignment explanation
Indices: 527078--527715 Score: 727
Period size: 288 Copynumber: 2.2 Consensus size: 286
527068 TTTTCGAGGA
** *
527078 GATACTCCAATCC-CAATTTTATTTCCAAAATATTAATTTTTCACCATCGAGGATACTCCAATCC
1 GATACTCCAA-CCTC-ATTTTATTTCCAAAATATCGATTTTTCACCATCGAGGAAACTCCAATCC
* *
527142 CATTATTTCTGAAGGGATATTGCAACCTCGGTTTTATTTTCAAAATATCAATATTTCACCATCGG
64 CATTATTTCTGAAGGGATACTCCAACCTCGGTTTTATTTTCAAAATATCAATATTTCACCATCGG
** * * * * *
527207 GGATACACCAACCCTGTTATTTTTAAAGGGATACTTCAACCCTGGTTTTATTTCTAAACTATTAA
129 GGATACACCAACCCCATTATTTTCAAAGAGATACTCCAACCCCGGTTTTATTTCCAAACTATTAA
* ** ** * *
527272 ATTCCTCATCTCGGGGATACTTTAACGTCGCTATTTTTGAGGGGATACTCCAACTTCGGTTTTA-
194 ATTCCTCACCTCGGGGATACTCCAACCCCACTATTTTTGA-GGGATACTCCAACCTCGGTTTTAT
* * * **
527336 TTTCTAAAATATTAAATTTCTTATC-TCGGG
258 TTTC-AAAATATCAAATTT-TCACCATCCAG
* *
527366 GATACTCCAACCTCAGTTTTATTTCCAAAATATCGATTTTTCTCCATCGGGGAAACTCCAA-CCC
1 GATACTCCAACCTCA-TTTTATTTCCAAAATATCGATTTTTCACCATCGAGGAAACTCCAATCCC
* * * * *
527430 TATTGTTTCT-AAGAGGATACTCCAACC-CGATTTTTATTTTCAAAATATCGATCTTTCACCATT
65 -ATTATTTCTGAAG-GGATACTCCAACCTCG-GTTTTATTTTCAAAATATCAATATTTCACCATC
* * *
527493 GGGGATACTCCAACCCCATTGTTTTCAAAGAGATACTCCAACCCCGTTTTTATTTCCAAACTA-T
127 GGGGATACACCAACCCCATTATTTTCAAAGAGATACTCCAACCCCGGTTTTATTTCCAAACTATT
* * * * * *
527557 CAATT-TTTACCATCGGGGATACTCCAACCCCATTATTTTTTGAGGGATACTCTAACCTCGTTTT
192 AAATTCCTCACC-TCGGGGATACTCCAACCCCACTA-TTTTTGAGGGATACTCCAACCTCGGTTT
527621 TATTTTCAAAATATCAAATTTTCACCATCCAG
255 TATTTTCAAAATATCAAATTTTCACCATCCAG
* *
527653 GATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCAT-TAGAGATACTCCAATCC
1 GATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCATCGAG-GAAACTCCAATCC
527716 TATTTTTATT
Statistics
Matches: 295, Mismatches: 44, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
285 1 0.00
286 45 0.15
287 86 0.29
288 163 0.55
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (286 bp):
GATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCATCGAGGAAACTCCAATCCCA
TTATTTCTGAAGGGATACTCCAACCTCGGTTTTATTTTCAAAATATCAATATTTCACCATCGGGG
ATACACCAACCCCATTATTTTCAAAGAGATACTCCAACCCCGGTTTTATTTCCAAACTATTAAAT
TCCTCACCTCGGGGATACTCCAACCCCACTATTTTTGAGGGATACTCCAACCTCGGTTTTATTTT
CAAAATATCAAATTTTCACCATCCAG
Found at i:527665 original size:51 final size:51
Alignment explanation
Indices: 527601--527770 Score: 204
Period size: 51 Copynumber: 3.4 Consensus size: 51
527591 ATTTTTTGAG
* * * *
527601 GGATACTCTAACCTCGTTTTTATTTTCAAAATATCAAATTTTCACCATCCA
1 GGATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCCA
* *
527652 GGATACTCCAACCTC-ATTTTATTTCCAAAATATCGATTTTTCACCAT-TA
1 GGATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCCA
* **
527701 GAGATACTCCAATCCT-ATTTTTATTTCCAAAATATCGATTTTTCACCATCGG
1 G-GATACTCCAA-CCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCCA
527753 GGATA-TACCAACCTCGTT
1 GGATACT-CCAACCTCGTT
527771 GTTTCTGAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
49 2 0.02
50 42 0.41
51 58 0.56
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (51 bp):
GGATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCCA
Found at i:527825 original size:180 final size:179
Alignment explanation
Indices: 527521--527844 Score: 465
Period size: 180 Copynumber: 1.8 Consensus size: 179
527511 TTGTTTTCAA
* *
527521 AGAGATACTCCAACCCCGTTTTTATTTCCAAACTATCAATTTTTACCATCGGGGATACTCCAACC
1 AGAGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTTTACCATCGGGGATACTCCAACC
* * * * *
527586 CCATTATTTTTTGAGGGATACTCTAACCTCGTTTTTATTTTCAAAATATCAAATTTTCACCATCC
66 CCATTAGTTTCTGAAGGATACTCTAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCAT-C
527651 A-GGATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCATT
130 AGGGATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCATT
* * *
527700 AGAGATACTCCAATCCTATTTTTATTTCCAAAATATCGATTTTTCACCATCGGGGATA-TACCAA
1 AGAGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTTT-ACCATCGGGGATACT-CCAA
* * *
527764 CCTCGTT-GTTTCTGAAAGGATACTCTAACCCCGTTTTTATTTCCAAAATATCAATTTTTCACCA
64 CCCCATTAGTTTCTG-AAGGATACTCTAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCA
*
527828 TCAGGGATACTTCAACC
128 TCAGGGATACTCCAACC
527845 CCGTTGTTTC
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
179 47 0.37
180 80 0.63
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (179 bp):
AGAGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTTTACCATCGGGGATACTCCAACC
CCATTAGTTTCTGAAGGATACTCTAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCATCA
GGGATACTCCAACCTCATTTTATTTCCAAAATATCGATTTTTCACCATT
Found at i:527960 original size:80 final size:78
Alignment explanation
Indices: 527703--527969 Score: 313
Period size: 79 Copynumber: 3.4 Consensus size: 78
527693 CACCATTAGA
* * * *
527703 GATACTCCAATCCTATTTTTATTTCCAAAATATCGATTTTTCACCATCGGGGATA-TACCAACCT
1 GATACTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACCATCGGGGATACT-CTAACCC
* *
527767 CGTTGTTTCTGAAAG
65 CGTTGTTT-TCAAGG
* * * *
527782 GATACTCTAACCCCGTTTTTATTTCCAAAATATCAATTTTTCACCATCAGGGATACT-TCAACCC
1 GATACTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACCATCGGGGATACTCT-AACCC
*
527846 CGTTGTTTCCGAAGG
65 CGTTGTTTTC-AAGG
* * *
527861 GATACTCCAACCCCTTTTTTATTTCCAAAATATCGATTTTATTACTATCGGGGATACTCTAACCC
1 GATACTCCAACCCCATTTTTATTTCCAAAATATCGATTTT-TCACCATCGGGGATACTCTAACCC
*
527926 CGTTATTTTCAAGG
65 CGTTGTTTTCAAGG
* *
527940 GAATACTCCAACTCCATTTTTATCTCCAAA
1 G-ATACTCCAACCCCATTTTTATTTCCAAA
527970 GTATTAAATT
Statistics
Matches: 160, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
79 106 0.66
80 53 0.33
81 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (78 bp):
GATACTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACCATCGGGGATACTCTAACCCC
GTTGTTTTCAAGG
Found at i:538747 original size:39 final size:39
Alignment explanation
Indices: 538691--538815 Score: 241
Period size: 39 Copynumber: 3.2 Consensus size: 39
538681 CAATTAACTA
538691 AAAATATATTTGATTTTGTAAAGAATACTTTGAAAAACAT
1 AAAATA-ATTTGATTTTGTAAAGAATACTTTGAAAAACAT
538731 AAAATAATTTGATTTTGTAAAGAATACTTTGAAAAACAT
1 AAAATAATTTGATTTTGTAAAGAATACTTTGAAAAACAT
538770 AAAATAATTTGATTTTGTAAAGAATACTTTGAAAAACAT
1 AAAATAATTTGATTTTGTAAAGAATACTTTGAAAAACAT
538809 AAAATAA
1 AAAATAA
538816 GTTTTCATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
39 79 0.93
40 6 0.07
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (39 bp):
AAAATAATTTGATTTTGTAAAGAATACTTTGAAAAACAT
Found at i:540631 original size:21 final size:21
Alignment explanation
Indices: 540605--540646 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
540595 AATCAACCAT
* *
540605 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
540626 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
540647 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:541119 original size:21 final size:23
Alignment explanation
Indices: 541095--541153 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
541085 ATTAGAGGAA
541095 AAAATGAATGAGTTAG-AAAA-G
1 AAAATGAATGAGTTAGCAAAATG
541116 AAAA-GAAATGAGTT-GCAAAATG
1 AAAATG-AATGAGTTAGCAAAATG
541138 AAAATG-ATGAGTTAGC
1 AAAATGAATGAGTTAGC
541154 TAATAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.06
21 23 0.70
22 7 0.21
23 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (23 bp):
AAAATGAATGAGTTAGCAAAATG
Found at i:543855 original size:10 final size:9
Alignment explanation
Indices: 543822--543860 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
543812 TTGTTATAAA
*
543822 TGAAGAAAT
1 TGAAAAAAT
543831 TGAAAAAAT
1 TGAAAAAAT
543840 TGAAAAAAT
1 TGAAAAAAT
543849 TGAAAAATAT
1 TGAAAAA-AT
543859 TG
1 TG
543861 GTATAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (9 bp):
TGAAAAAAT
Found at i:544580 original size:13 final size:13
Alignment explanation
Indices: 544562--544586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
544552 ATTTTGCTTA
544562 GTATCGATACATT
1 GTATCGATACATT
544575 GTATCGATACAT
1 GTATCGATACAT
544587 AAACTGGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:548056 original size:79 final size:79
Alignment explanation
Indices: 547896--548059 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
547886 TACTTTGGAG
* * * * *
547896 ATAAAAATGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGTAGTATCCCTGAGACGAAAATT
1 ATAAAAATAGGATTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCTGAGACGAAAATT
* *
547961 TTCATATTTTGAAA
66 TTAATATTTAGAAA
*
547975 ATAAAAATAGGATTAGAGTA-CCCCGTCAAAAATAATAGGGTTGGAGTATTCCC-GAGACGAGAA
1 ATAAAAATAGGATTAGAGTATCCCC-TCAAAAATAACAGGGTTGGAGTA-TCCCTGAGACGA-AA
548038 A-TTTAATATCTTAG-AA
63 ATTTTAATAT-TTAGAAA
548054 ATAAAA
1 ATAAAA
548060 CCAAGGGGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 4 0.05
79 59 0.81
80 10 0.14
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (79 bp):
ATAAAAATAGGATTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCTGAGACGAAAATT
TTAATATTTAGAAA
Found at i:548161 original size:79 final size:78
Alignment explanation
Indices: 548064--548405 Score: 353
Period size: 79 Copynumber: 4.3 Consensus size: 78
548054 ATAAAACCAA
* * * *
548064 GGGGATACTCCAACCCCGTTGTTTCCGAGGTAGTACTCCATCCCCGTTTTTATTTTCAAAATATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGA-TACTCCAACCCCATTTTTATTTTCAAAATATC
*
548129 GATTTTTCACCATC
65 AATTTTTCACCATC
* ** ** *
548143 GGGGATACTCCAATCCCGTTATTTTTGAGGAGATACTCCAACCTTATTTTTATTTCCAAAATATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGG-GATACTCCAACCCCATTTTTATTTTCAAAATATC
* **
548208 GATTTTTTTCCATC
65 AATTTTTCACCATC
* ** ** *
548222 AGGGATACTCCAACCTTGTTACTTTCAAAGGGATACTCCAACCTCATTTTTA-TTTCTAAAATAT
1 GGGGATACTCCAACCCCGTTA-TTTCCGAGGGATACTCCAACCCCATTTTTATTTTC-AAAATAT
*
548286 CAATTTTTTTCATCATC
64 CAA--TTTTTCACCATC
* * *
548303 AGGGATAGTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCAGTTTTATTTTCAAAATATC
1 GGGGATACTCCAACCCCGTTATTTCCG-AGGGATACTCCAACCCCATTTTTATTTTCAAAATATC
548368 AATTTTTCACCATC
65 AATTTTTCACCATC
* * * * *
548382 GAGGATGCACCAATCCTGTTATTT
1 GGGGATACTCCAACCCCGTTATTT
548406 TTTAGGGAAT
Statistics
Matches: 216, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
78 3 0.01
79 139 0.64
80 11 0.05
81 59 0.27
82 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGATACTCCAACCCCATTTTTATTTTCAAAATATCA
ATTTTTCACCATC
Found at i:548365 original size:160 final size:159
Alignment explanation
Indices: 548097--548445 Score: 381
Period size: 160 Copynumber: 2.2 Consensus size: 159
548087 TCCGAGGTAG
* * * * *
548097 TACTCCATCCCCG-TTTTTATTT-TCAAAATATCGATTTTTCACCATCGGGGATACTCCAATCCC
1 TACTCCAACCTCGATTTTTATTTCT-AAAATATCAATTTTTCACCATCAGGGATACTCCAACCCC
** ** * * **
548160 GTTATTTTTGAGGAGATACTCCAACCTTATTTTTATTTCCAAAATATCGATTTTTTTCCATC-AG
65 GTTATTTCCGAGGAGATACTCCAACCCCAGTTTTATTTCCAAAATATCAATTTTTCACCATCGA-
*
548224 GGATACTCCAA-CCTTGTTACTTTCAAAGGG-A
129 GGATACACCAATCC-TGTTA-TTTCAAAGGGAA
* *
548255 TACTCCAACCTC-ATTTTTATTTCTAAAATATCAATTTTTTTCATCATCAGGGATAGTCCAACCC
1 TACTCCAACCTCGATTTTTATTTCTAAAATATCAA--TTTTTCACCATCAGGGATACTCCAACCC
*
548319 CGTTATTTCCGAAGG-GATACTCCAACCCCAGTTTTATTTTCAAAATATCAATTTTTCACCATCG
64 CGTTATTTCCG-AGGAGATACTCCAACCCCAGTTTTATTTCCAAAATATCAATTTTTCACCATCG
* ***
548383 AGGATGCACCAATCCTGTTATTTTTTAGGGAA
128 AGGATACACCAATCCTGTTATTTCAAAGGGAA
*
548415 TACTCTAACCTCGA-TTTTATTTCTAAAATAT
1 TACTCCAACCTCGATTTTTATTTCTAAAATAT
548446 TAAATTCCTC
Statistics
Matches: 160, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
158 28 0.17
159 8 0.05
160 117 0.73
161 7 0.04
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (159 bp):
TACTCCAACCTCGATTTTTATTTCTAAAATATCAATTTTTCACCATCAGGGATACTCCAACCCCG
TTATTTCCGAGGAGATACTCCAACCCCAGTTTTATTTCCAAAATATCAATTTTTCACCATCGAGG
ATACACCAATCCTGTTATTTCAAAGGGAA
Found at i:548433 original size:79 final size:76
Alignment explanation
Indices: 548111--548510 Score: 306
Period size: 79 Copynumber: 5.1 Consensus size: 76
548101 CCATCCCCGT
* * * *
548111 TTTTATTTTCAAAATATCGATTTTTCACCATCGGGGATACTCCAATCCCGTTATTTTTGAGGAGA
1 TTTTATTTTCAAAATATCAATTTTTCACCATCGAGGATACTCCAA-CCTGTTATTTTTAAGG-GA
*
548176 TACTCCAACCTTA
64 TACTCCAACCTCA
* * ** **
548189 TTTTTATTTCCAAAATATCGATTTTTTTCCATC-AGGGATACTCCAACCTTGTTACTTTCAAAGG
1 -TTTTATTTTCAAAATATCAATTTTTCACCATCGA-GGATACTCCAACC-TGTTA-TTTTTAAGG
548253 GATACTCCAACCTCA
62 GATACTCCAACCTCA
* * * **
548268 TTTT-TATTTCTAAAATATCAATTTTTTTCATCATC-AGGGATAGTCCAACCCCGTTATTTCCGA
1 TTTTAT-TTTC-AAAATATCAA--TTTTTCACCATCGA-GGATACTCCAA-CCTGTTATTT-TTA
*
548331 AGGGATACTCCAACCCCA
59 AGGGATACTCCAACCTCA
* * *
548349 GTTTTATTTTCAAAATATCAATTTTTCACCATCGAGGATGCACCAATCCTGTTATTTTTTAGGGA
1 -TTTTATTTTCAAAATATCAATTTTTCACCATCGAGGATACTCCAA-CCTGTTATTTTTAAGGG-
*
548414 ATACTCTAACCTCGA
63 ATACTCCAACCTC-A
* ** ** *
548429 TTTTA-TTTCTAAAATATTAAATTCCTCGTC-TCGAGGATACTCCAACCTCGTTATTTTTTAGGG
1 TTTTATTTTC-AAAATA-TCAATTTTTCACCATCGAGGATACTCCAACCT-GTTA-TTTTTAAGG
* * *
548492 GGTACTCTAATCTCA
62 GATACTCCAACCTCA
548507 TTTT
1 TTTT
548511 TATTCCTAAA
Statistics
Matches: 263, Mismatches: 40, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
77 1 0.00
78 25 0.10
79 145 0.55
80 27 0.10
81 54 0.21
82 10 0.04
83 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (76 bp):
TTTTATTTTCAAAATATCAATTTTTCACCATCGAGGATACTCCAACCTGTTATTTTTAAGGGATA
CTCCAACCTCA
Found at i:548509 original size:239 final size:239
Alignment explanation
Indices: 548065--548556 Score: 565
Period size: 239 Copynumber: 2.1 Consensus size: 239
548055 TAAAACCAAG
* * * *
548065 GGGATACTCCAACCCCGTTGTTTCCGAGGTAGTACTCCATCCCCGTTTTTATTTTCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGAGTACTCCAACCCCGTTTTTATTTTCAAAATATCA
* * *
548130 ATTTTTCACCATCGGGGATACTCCAATCCCGTTATTTTTGAGGAGATACTCCAACCTTATTTTTA
66 ATTTTTCACCATCGAGGATACACCAATCCCGTTATTTTTGAGGAGATACTCCAACCTGATTTTTA
** * ** *
548195 TTTCCAAAATATCGATTTTTTTCCATCAGGGATACTCCAACCTTGTTACTTTCAAAGGGATACTC
131 TTTCCAAAATATAAATTCTCGTCCATCAGGGATACTCCAACCTCGTTACTTTCAAAGGGATACTC
*
548260 CAACCTCATTTTTATTTCTAAAATATCAATTTTTTTCATCATCA
196 CAACCTCATTTTTATTCCTAAAATATCAATTTTTTTCATCATCA
*
548304 GGGATAGTCCAACCCCGTTATTTCCGAAGGGA-TACTCCAACCCCAG-TTTTATTTTCAAAATAT
1 GGGATACTCCAACCCCGTTATTTCCG-AGGGAGTACTCCAACCCC-GTTTTTATTTTCAAAATAT
* * * *
548367 CAATTTTTCACCATCGAGGATGCACCAATCCTGTTATTTTTTAGG-GAATACTCTAACCTCGA-T
64 CAATTTTTCACCATCGAGGATACACCAATCCCGTTATTTTTGAGGAG-ATACTCCAACCT-GATT
* * ** *
548430 TTTATTTCTAAAATATTAAATTCCTCGT-C-TC-GAGGATACTCCAACCTCGTTATTTTTTAGGG
127 TTTATTTCCAAAATA-TAAATT-CTCGTCCATCAG-GGATACTCCAACCTCGTTACTTTCAAAGG
* * * * *
548492 GGTACTCTAATCTCATTTTTATTCCTAAAATATTGAA--ATTTTCATC-TC-
189 GATACTCCAACCTCATTTTTATTCCTAAAATA-TCAATTTTTTTCATCATCA
548540 GGAGATACTCCAACCCC
1 GG-GATACTCCAACCCC
548557 ATTTTTATCT
Statistics
Matches: 214, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
236 2 0.01
237 15 0.07
238 10 0.05
239 171 0.80
240 14 0.07
241 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (239 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGAGTACTCCAACCCCGTTTTTATTTTCAAAATATCA
ATTTTTCACCATCGAGGATACACCAATCCCGTTATTTTTGAGGAGATACTCCAACCTGATTTTTA
TTTCCAAAATATAAATTCTCGTCCATCAGGGATACTCCAACCTCGTTACTTTCAAAGGGATACTC
CAACCTCATTTTTATTCCTAAAATATCAATTTTTTTCATCATCA
Found at i:548512 original size:79 final size:78
Alignment explanation
Indices: 548380--548554 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 78
548370 TTTTTCACCA
* * *
548380 TCGAGGATGCACCAATCCTGTTATTTTTTAGGGAATACTCTAACCTCGATTTTATTTCTAAAATA
1 TCGAGGATACTCCAA-CCTGTTATTTTTTAGGGAATACTCTAACCTCGATTTTATTCCTAAAATA
*
548445 TT-AAATTCCTCGTC
65 TTGAAATT-CTCATC
** *
548459 TCGAGGATACTCCAACCTCGTTATTTTTTAGGGGGTACTCTAATCTC-ATTTTTATTCCTAAAAT
1 TCGAGGATACTCCAACCT-GTTATTTTTTAGGGAATACTCTAACCTCGA-TTTTATTCCTAAAAT
*
548523 ATTGAAATTTTCATC
64 ATTGAAATTCTCATC
548538 TCG-GAGATACTCCAACC
1 TCGAG-GATACTCCAACC
548555 CCATTTTTAT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
78 5 0.06
79 74 0.88
80 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (78 bp):
TCGAGGATACTCCAACCTGTTATTTTTTAGGGAATACTCTAACCTCGATTTTATTCCTAAAATAT
TGAAATTCTCATC
Found at i:548560 original size:51 final size:51
Alignment explanation
Indices: 548505--548610 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
548495 ACTCTAATCT
548505 CATTTTTAT-TCCTAAAATATTGAAA-TTTTCATCTC-GGAGATACTCCAACCC
1 CATTTTTATCTCC-AAAATATT-AAATTTTTCATC-CAGGAGATACTCCAACCC
* * *
548556 CATTTTTATCTCCAAAGTATTAAATTTTTCATCCAGGGATATACTCCAACTC
1 CATTTTTATCTCCAAAATATTAAATTTTTCATCCA-GGAGATACTCCAACCC
548608 CAT
1 CAT
548611 ACTCTGAAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
50 4 0.08
51 24 0.50
52 20 0.42
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (51 bp):
CATTTTTATCTCCAAAATATTAAATTTTTCATCCAGGAGATACTCCAACCC
Found at i:550082 original size:18 final size:19
Alignment explanation
Indices: 550046--550085 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
550036 CAATGAAAAC
550046 AAAAGCTCTTGGAAATTTG
1 AAAAGCTCTTGGAAATTTG
* *
550065 AAAA-CTCTTTGAACTTTG
1 AAAAGCTCTTGGAAATTTG
550083 AAA
1 AAA
550086 GCTTTGATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (19 bp):
AAAAGCTCTTGGAAATTTG
Found at i:550456 original size:19 final size:19
Alignment explanation
Indices: 550416--550467 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
550406 CAGTTTCATT
**
550416 TATCGATACAATTGTCCATG
1 TATCGATACAA-TGAACATG
550436 TATCGATACAATGAACATG
1 TATCGATACAATGAACATG
550455 TATCGATACAATG
1 TATCGATACAATG
550468 TATCGATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:550470 original size:13 final size:13
Alignment explanation
Indices: 550452--550478 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
550442 TACAATGAAC
550452 ATGTATCGATACA
1 ATGTATCGATACA
550465 ATGTATCGATACA
1 ATGTATCGATACA
550478 A
1 A
550479 AGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:550493 original size:33 final size:32
Alignment explanation
Indices: 550433--550497 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
550423 ACAATTGTCC
*
550433 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
550465 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
550498 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Done.