Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 147 of 172
Found at i:42262908 original size:7 final size:7
Alignment explanation
Indices: 42262896--42262922 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42262886 TATAAAAGAA
42262896 AATGGGT
1 AATGGGT
42262903 AATGGGT
1 AATGGGT
42262910 AATGGGT
1 AATGGGT
42262917 AATGGG
1 AATGGG
42262923 AGAAGCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.44, T:0.26
Consensus pattern (7 bp):
AATGGGT
Found at i:42264321 original size:22 final size:23
Alignment explanation
Indices: 42264271--42264324 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
42264261 TCCAAACAAT
42264271 AAATTTTATTTACAAAATCATAA
1 AAATTTTATTTACAAAATCATAA
42264294 AAATTTTATTTACAAAATCATAA
1 AAATTTTATTTACAAAATCATAA
*
42264317 AATTTTTA
1 AAATTTTA
42264325 AAAATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTTTATTTACAAAATCATAA
Found at i:42272086 original size:15 final size:15
Alignment explanation
Indices: 42272066--42272099 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42272056 ACCAAGGAAC
* *
42272066 GGAAAGAGAGGAGGA
1 GGAAAGAAAGGAAGA
42272081 GGAAAGAAAGGAAGA
1 GGAAAGAAAGGAAGA
42272096 GGAA
1 GGAA
42272100 TGTGAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGGAAGA
Found at i:42273889 original size:42 final size:42
Alignment explanation
Indices: 42273838--42273924 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
42273828 ACTCTCGAAT
42273838 GATGAAGAATTGCATGTGCTTGATCTCCTTTAGAGGTTCAAG
1 GATGAAGAATTGCATGTGCTTGATCTCCTTTAGAGGTTCAAG
42273880 GATGAAGAATTGCATGTGCTTGATCTCCTTTAGAGGTTCAAG
1 GATGAAGAATTGCATGTGCTTGATCTCCTTTAGAGGTTCAAG
42273922 GAT
1 GAT
42273925 TTTTACAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (42 bp):
GATGAAGAATTGCATGTGCTTGATCTCCTTTAGAGGTTCAAG
Found at i:42281421 original size:22 final size:22
Alignment explanation
Indices: 42281391--42281433 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42281381 TTGAATATAA
42281391 TTAACATA-TATTAATTTATTAAT
1 TTAACATATTA-TAATTT-TTAAT
42281414 TTAA-ATATTATAATTTTTAA
1 TTAACATATTATAATTTTTAA
42281434 ATAATAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAACATATTATAATTTTTAAT
Found at i:42284196 original size:19 final size:20
Alignment explanation
Indices: 42284154--42284201 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
42284144 AAATTATTTA
* *
42284154 TAAAATTTAATTTAAACATG
1 TAAAATATATTTTAAACATG
* *
42284174 TAAACTATATTTTAAATAT-
1 TAAAATATATTTTAAACATG
42284193 TAAAATATA
1 TAAAATATA
42284202 ATATTTCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATATATTTTAAACATG
Found at i:42284649 original size:12 final size:12
Alignment explanation
Indices: 42284632--42284664 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
42284622 CGACCCGCCC
42284632 ATATTAATTTTT
1 ATATTAATTTTT
42284644 ATATT-ATTTTT
1 ATATTAATTTTT
42284655 ATA-TAATTTT
1 ATATTAATTTT
42284665 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:42284823 original size:30 final size:30
Alignment explanation
Indices: 42284789--42284851 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
42284779 ACTTAATAAG
*
42284789 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTATAAAATAATAACAAAATTAA
**
42284819 CAAATGTCTATAAAATAATAACAAAATTAA
1 CAAATACCTATAAAATAATAACAAAATTAA
42284849 CAA
1 CAA
42284852 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTATAAAATAATAACAAAATTAA
Found at i:42285235 original size:23 final size:23
Alignment explanation
Indices: 42285205--42285252 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
42285195 TGTGTCTAGA
* *
42285205 GGTGCTCATGGGCCGGGCGGGCC
1 GGTGCTCATGGGCAGGGCGGCCC
42285228 GGTGCTCATGGGCAGGGCGGCCC
1 GGTGCTCATGGGCAGGGCGGCCC
42285251 GG
1 GG
42285253 CCCGACGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.06, C:0.29, G:0.52, T:0.12
Consensus pattern (23 bp):
GGTGCTCATGGGCAGGGCGGCCC
Found at i:42285403 original size:26 final size:26
Alignment explanation
Indices: 42285367--42285424 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
42285357 AATATAATAA
* *
42285367 ATTTTTTTA-TTTTTATTTTTAAAAT
1 ATTTTTTTATTTTTTAATTTAAAAAT
42285392 ACTTTTTTTATTTTTTAATTTAAAAAT
1 A-TTTTTTTATTTTTTAATTTAAAAAT
42285419 ATTTTT
1 ATTTTT
42285425 AAAATACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.03
26 13 0.45
27 15 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTTTTTATTTTTTAATTTAAAAAT
Found at i:42285407 original size:33 final size:33
Alignment explanation
Indices: 42285369--42285482 Score: 97
Period size: 38 Copynumber: 3.3 Consensus size: 33
42285359 TATAATAAAT
*
42285369 TTTTTTATTTTTATTTTTAAAATACTTTTTTTA
1 TTTTTTATTTATATTTTTAAAATACTTTTTTTA
*
42285402 TTTTTTAATTTAAAAATATTTTTAAAATACTTTTTTTC
1 TTTTTT-ATTT----ATATTTTTAAAATACTTTTTTTA
* ** *
42285440 TAATTTTA-AAATA-TTTTAAAATACTTTTTTAA
1 T-TTTTTATTTATATTTTTAAAATACTTTTTTTA
42285472 TTTTTTTATTT
1 -TTTTTTATTT
42285483 TTAAAATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
32 22 0.35
33 10 0.16
34 4 0.06
38 23 0.37
39 4 0.06
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTTTTATTTATATTTTTAAAATACTTTTTTTA
Found at i:42285457 original size:32 final size:32
Alignment explanation
Indices: 42285402--42285469 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
42285392 ACTTTTTTTA
42285402 TTTTTTAATTTAAAAATATTTTTAAAATACTT
1 TTTTTTAATTTAAAAATATTTTTAAAATACTT
*
42285434 TTTTTCTAATTTTAAAATA-TTTTAAAATACTT
1 TTTTT-TAATTTAAAAATATTTTTAAAATACTT
42285466 TTTT
1 TTTT
42285470 AATTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTTTAATTTAAAAATATTTTTAAAATACTT
Found at i:42295619 original size:31 final size:31
Alignment explanation
Indices: 42295584--42295686 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
42295574 GTTTGCGATG
42295584 TAATAACTTGATTCTACAAACTGTTTATTTA
1 TAATAACTTGATTCTACAAACTGTTTATTTA
* * *** *
42295615 TAATAAGC-TGATACTTATAATTACTGTTTGCGATG
1 TAATAA-CTTGATTC-TACAA--ACTGTTT-ATTTA
42295650 TAATAACTTGATTCTACAAACTGTTTATTTA
1 TAATAACTTGATTCTACAAACTGTTTATTTA
42295681 TAATAA
1 TAATAA
42295687 GCTGATACTT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
31 18 0.33
32 12 0.22
34 12 0.22
35 12 0.22
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (31 bp):
TAATAACTTGATTCTACAAACTGTTTATTTA
Found at i:42295642 original size:34 final size:34
Alignment explanation
Indices: 42295603--42295705 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 34
42295593 GATTCTACAA
42295603 ACTGTTTATTTATAATAAGCTGATACTTATAATT
1 ACTGTTTATTTATAATAAGCTGATACTTATAATT
*** * * *
42295637 ACTGTTTGCGATGTAATAA-CTTGATTC-TACAA--
1 ACTGTTT-ATTTATAATAAGC-TGATACTTATAATT
42295669 ACTGTTTATTTATAATAAGCTGATACTTATAATT
1 ACTGTTTATTTATAATAAGCTGATACTTATAATT
42295703 ACT
1 ACT
42295706 CGAAATTATA
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
31 12 0.24
32 12 0.24
34 15 0.29
35 12 0.24
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (34 bp):
ACTGTTTATTTATAATAAGCTGATACTTATAATT
Found at i:42295654 original size:66 final size:66
Alignment explanation
Indices: 42295573--42295705 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
42295563 AACTTTAATT
42295573 TGTTTGCGATGTAATAACTTGATTCTACAAACTGTTTATTTATAATAAGCTGATACTTATAATTA
1 TGTTTGCGATGTAATAACTTGATTCTACAAACTGTTTATTTATAATAAGCTGATACTTATAATTA
42295638 C
66 C
42295639 TGTTTGCGATGTAATAACTTGATTCTACAAACTGTTTATTTATAATAAGCTGATACTTATAATTA
1 TGTTTGCGATGTAATAACTTGATTCTACAAACTGTTTATTTATAATAAGCTGATACTTATAATTA
42295704 C
66 C
42295705 T
1 T
42295706 CGAAATTATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (66 bp):
TGTTTGCGATGTAATAACTTGATTCTACAAACTGTTTATTTATAATAAGCTGATACTTATAATTA
C
Found at i:42295675 original size:32 final size:32
Alignment explanation
Indices: 42295573--42295675 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
42295563 AACTTTAATT
42295573 TGTTTGCGATGTAATAACTTGATTCTACAAAC
1 TGTTTGCGATGTAATAACTTGATTCTACAAAC
*** * * *
42295605 TGTTT-ATTTATAATAAGC-TGATACTTATAATTAC
1 TGTTTGCGATGTAATAA-CTTGATTC-TACAA--AC
42295639 TGTTTGCGATGTAATAACTTGATTCTACAAAC
1 TGTTTGCGATGTAATAACTTGATTCTACAAAC
42295671 TGTTT
1 TGTTT
42295676 ATTTATAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
31 12 0.23
32 17 0.32
34 12 0.23
35 12 0.23
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (32 bp):
TGTTTGCGATGTAATAACTTGATTCTACAAAC
Found at i:42296835 original size:17 final size:16
Alignment explanation
Indices: 42296806--42296852 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
42296796 AAAGACTTTT
42296806 AATATAAATATATTATTA
1 AATATAAA-ATATTA-TA
42296824 AATATAAAATATTATA
1 AATATAAAATATTATA
*
42296840 AATCTAAAA-ATTA
1 AATATAAAATATTA
42296853 AATATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
17 6 0.21
18 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAAATATTATA
Found at i:42297049 original size:18 final size:19
Alignment explanation
Indices: 42297006--42297054 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
42296996 GTGAAAAGAA
*
42297006 AATTTTTATATAAAATATAT
1 AATTTTTAAAT-AAATATAT
42297026 AA--TTTAAATAAATA-AT
1 AATTTTTAAATAAATATAT
42297042 AATTTTTAAATAA
1 AATTTTTAAATAA
42297055 TGTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 15 0.58
20 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTTTAAATAAATATAT
Found at i:42297140 original size:22 final size:22
Alignment explanation
Indices: 42297096--42297141 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42297086 TAAATAAATA
**
42297096 TTATTTTTAAAAAGCTAGCTTT
1 TTATTTTTAAAAAAATAGCTTT
42297118 TTATTTTTAAAAAAATAG-TTT
1 TTATTTTTAAAAAAATAGCTTT
42297139 TTA
1 TTA
42297142 AAGAGATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (22 bp):
TTATTTTTAAAAAAATAGCTTT
Found at i:42298021 original size:40 final size:40
Alignment explanation
Indices: 42297964--42298051 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
42297954 TTTAATCCTC
* *
42297964 TCAATTTCCTTCTAAAATTCTCTCAAACCCATATTTAATT
1 TCAATTTCATTCCAAAATTCTCTCAAACCCATATTTAATT
*
42298004 TCAATTTCATTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCATTCCAAAATTCTCTCAAACCCATATTTAATT
42298044 TCAATTTC
1 TCAATTTC
42298052 CCCTCAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (40 bp):
TCAATTTCATTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:42298104 original size:30 final size:31
Alignment explanation
Indices: 42298064--42298127 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
42298054 CTCAATTTCA
*
42298064 TTTTTGAAAATAATTTTAAA-TTTTTTATAT
1 TTTTTAAAAATAATTTTAAATTTTTTTATAT
42298094 TTTTTAAAAATAATTTTAAATTTTTTTATAT
1 TTTTTAAAAATAATTTTAAATTTTTTTATAT
42298125 TTT
1 TTT
42298128 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTTAAAAATAATTTTAAATTTTTTTATAT
Found at i:42299890 original size:18 final size:18
Alignment explanation
Indices: 42299864--42299898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42299854 AGGTGTGTTT
* *
42299864 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
42299882 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
42299899 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:42300865 original size:29 final size:30
Alignment explanation
Indices: 42300806--42300863 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42300796 TCCGAGCCTT
*
42300806 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
42300836 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
42300864 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:42301093 original size:13 final size:13
Alignment explanation
Indices: 42301075--42301106 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42301065 TTTCCAGCAA
42301075 TTATGAATTTATT
1 TTATGAATTTATT
42301088 TTATGAATTTATT
1 TTATGAATTTATT
*
42301101 TGATGA
1 TTATGA
42301107 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:42301314 original size:50 final size:50
Alignment explanation
Indices: 42301201--42301442 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
42301191 ATTTGGGTAA
* * *
42301201 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
42301257 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42301307 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42301357 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
42301407 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42301443 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:42301390 original size:100 final size:103
Alignment explanation
Indices: 42301201--42301450 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
42301191 ATTTGGGTAA
42301201 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
42301266 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
42301307 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
42301369 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
42301407 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42301451 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:42308597 original size:14 final size:14
Alignment explanation
Indices: 42308578--42308604 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42308568 TTCCAGCAAT
42308578 TATGAATTTATTTA
1 TATGAATTTATTTA
42308592 TATGAATTTATTT
1 TATGAATTTATTT
42308605 GATGATGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATGAATTTATTTA
Found at i:42308817 original size:50 final size:50
Alignment explanation
Indices: 42308704--42308945 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
42308694 ATTTGGGTAA
* * *
42308704 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
42308760 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42308810 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42308860 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
42308910 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42308946 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:42308893 original size:100 final size:103
Alignment explanation
Indices: 42308704--42308953 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
42308694 ATTTGGGTAA
42308704 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
42308769 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
42308810 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
42308872 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
42308910 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42308954 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:42310605 original size:25 final size:25
Alignment explanation
Indices: 42310577--42310645 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
42310567 TTTAAATTTA
*
42310577 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
42310602 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
42310627 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
42310646 ACCTTAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:42310664 original size:18 final size:18
Alignment explanation
Indices: 42310641--42310883 Score: 276
Period size: 18 Copynumber: 13.5 Consensus size: 18
42310631 TTTGATGTAA
*
42310641 TAAAAACCTTAATTTAAT
1 TAAAAACCCTAATTTAAT
42310659 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
* * *
42310677 TAAAAACCTTAACTTAGT
1 TAAAAACCCTAATTTAAT
42310695 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
*
42310713 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAATTTAAT
*
42310731 AAAAAAACCCTAATTTAAT
1 -TAAAAACCCTAATTTAAT
* *
42310750 TAAAAATCCTAACTTAAT
1 TAAAAACCCTAATTTAAT
42310768 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
*
42310786 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAATTTAAT
**
42310804 TAAAAACCCTAACCCTAA-
1 TAAAAACCCTAA-TTTAAT
**** *
42310822 CCCTAA-CCTAACTTAAT
1 TAAAAACCCTAATTTAAT
*
42310839 TAAAAACACC-AACTTAAT
1 TAAAAAC-CCTAATTTAAT
*
42310857 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAATTTAAT
42310875 TAAAAACCC
1 TAAAAACCC
42310884 AAACCCAAAT
Statistics
Matches: 193, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
16 4 0.02
17 9 0.05
18 158 0.82
19 22 0.11
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAACCCTAATTTAAT
Found at i:42310688 original size:36 final size:36
Alignment explanation
Indices: 42310641--42311009 Score: 326
Period size: 36 Copynumber: 10.0 Consensus size: 36
42310631 TTTGATGTAA
* *
42310641 TAAAAACCTTAATTTAATTAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
* *
42310677 TAAAAACCTTAACTTAGTTAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
*
42310713 TAAAAACCCTAACTTAATAAAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT-TAAAAACCCTAATTTAAT
*
42310750 TAAAAATCCTAACTTAATTAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
**
42310786 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA-
1 TAAAAACCCTAACTTAATTAAAAACCCTAA-TTTAAT
**** *
42310822 CCCTAA-CCTAACTTAATTAAAAACACC-AACTTAAT
1 TAAAAACCCTAACTTAATTAAAAAC-CCTAATTTAAT
42310857 TAAAAACCCTAACTTAATTAAAAACCC--A---AA-
1 TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
*** *
42310887 CCCAAA-TCTAACTTAATTAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACTTAATTAAAAA--C---CCTAATTTAAT
*
42310927 TAAAAATCCTAACCTTAACTTAACTTAATTAAAAACCTAATTTAAT
1 TAAAAA--C---CC-TAACTTAA-TT-A--AAAACCCTAATTTAAT
* *
42310973 TAAAAATCCTAACTTAATTAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
42311009 T
1 T
42311010 TTACTAGCCA
Statistics
Matches: 275, Mismatches: 31, Indels: 54
0.76 0.09 0.15
Matches are distributed among these distances:
29 16 0.06
30 3 0.01
31 3 0.01
34 7 0.03
35 24 0.09
36 134 0.49
37 37 0.13
38 1 0.00
39 4 0.01
40 11 0.04
41 2 0.01
46 18 0.07
47 8 0.03
48 2 0.01
49 1 0.00
51 4 0.01
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (36 bp):
TAAAAACCCTAACTTAATTAAAAACCCTAATTTAAT
Found at i:42310763 original size:73 final size:71
Alignment explanation
Indices: 42310641--42310883 Score: 310
Period size: 73 Copynumber: 3.4 Consensus size: 71
42310631 TTTGATGTAA
* * * *
42310641 TAAAAACCTTAATTTAATTAAAAACCCTAATTTAATTAAAAACCTTAACTTAGTTAAAAACCCTA
1 TAAAAACCCTAACTTAATAAAAAACCCTAATTTAATTAAAAACC-TAACTTAATTAAAAACCCTA
42310706 ATTTAAT
65 ATTTAAT
42310713 TAAAAACCCTAACTTAATAAAAAAACCCTAATTTAATTAAAAATCCTAACTTAATTAAAAACCCT
1 TAAAAACCCTAACTTAAT-AAAAAACCCTAATTTAATTAAAAA-CCTAACTTAATTAAAAACCCT
42310778 AATTTAAT
64 AATTTAAT
* ** ****
42310786 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA-CCCTAACCTAACTTAATTAAAAACACC-
1 TAAAAACCCTAACTTAATAAAAAACCCTAA-TTTAATTAAAAACCTAACTTAATTAAAAAC-CCT
*
42310849 AACTTAAT
64 AATTTAAT
*
42310857 TAAAAACCCTAACTTAATTAAAAACCC
1 TAAAAACCCTAACTTAATAAAAAACCC
42310884 AAACCCAAAT
Statistics
Matches: 155, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
71 52 0.34
72 31 0.20
73 70 0.45
74 2 0.01
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (71 bp):
TAAAAACCCTAACTTAATAAAAAACCCTAATTTAATTAAAAACCTAACTTAATTAAAAACCCTAA
TTTAAT
Found at i:42310873 original size:71 final size:72
Alignment explanation
Indices: 42310641--42311009 Score: 308
Period size: 73 Copynumber: 5.3 Consensus size: 72
42310631 TTTGATGTAA
* * ** * *
42310641 TAAAAACCTTAATTTAATTAAAAACCCTAA-TTTAATTAAAAACCTTAACTTAGTTAAAAACCCT
1 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAATCAAAAACC-TAACTTAATTAAAAACCCT
42310705 AATTTAAT
65 AATTTAAT
* ** *
42310713 TAAAAACCCTAACTTAATAAAAAAACCCTAA-TTTAATTAAAAATCCTAACTTAATTAAAAACCC
1 TAAAAACCCTAACTTAAT-TAAAAACCCTAACCCTAATCAAAAA-CCTAACTTAATTAAAAACCC
42310777 TAATTTAAT
64 TAATTTAAT
***
42310786 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA-CCCTAACCTAACTTAATTAAAAACACC-
1 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAATCAAAAACCTAACTTAATTAAAAAC-CCT
*
42310849 AACTTAAT
65 AATTTAAT
* *
42310857 TAAAAACCCTAACTTAATTAAAAACCC-AAACC----C--AAATCTAACTTAATTAAAAACCCTA
1 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAATCAAAAACCTAACTTAATTAAAAA--C--
42310915 ACCTAATTTAAT
62 -CCTAATTTAAT
* * * * * * *
42310927 TAAAAATCCTAAC---CTT---AA-CTTAA-CTTAATTAAAAACCTAATTTAATTAAAAATCCTA
1 TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAATCAAAAACCTAACTTAATTAAAAACCCTA
*
42310984 ACTTAAT
66 ATTTAAT
42310991 TAAAAACCCTAACTTAATT
1 TAAAAACCCTAACTTAATT
42311010 TTACTAGCCA
Statistics
Matches: 251, Mismatches: 27, Indels: 43
0.78 0.08 0.13
Matches are distributed among these distances:
63 2 0.01
64 26 0.10
65 18 0.07
67 6 0.02
69 21 0.08
70 23 0.09
71 52 0.21
72 31 0.12
73 70 0.28
74 2 0.01
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (72 bp):
TAAAAACCCTAACTTAATTAAAAACCCTAACCCTAATCAAAAACCTAACTTAATTAAAAACCCTA
ATTTAAT
Found at i:42310900 original size:47 final size:47
Alignment explanation
Indices: 42310849--42310978 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 47
42310839 TAAAAACACC
42310849 AACTTAATTAAAAACCCTAACTTAATTAAAAACCCAAACCCAAA-TCT
1 AACTTAATTAAAAACCCTAACTTAATTAAAAACCCAAACCCAAACT-T
* * **
42310896 AACTTAATTAAAAACCCTAACCTAATTTAATTAAAAATCCTAACCTTAACTT
1 AACTTAATTAAAAACCCTAA-C----TTAATTAAAAACCCAAACCCAAACTT
*
42310948 AACTTAATTAAAAA-CCTAATTTAATTAAAAA
1 AACTTAATTAAAAACCCTAACTTAATTAAAAA
42310979 TCCTAACTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
46 11 0.15
47 20 0.28
48 1 0.01
51 5 0.07
52 34 0.47
53 1 0.01
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (47 bp):
AACTTAATTAAAAACCCTAACTTAATTAAAAACCCAAACCCAAACTT
Found at i:42310912 original size:23 final size:23
Alignment explanation
Indices: 42310820--42310978 Score: 95
Period size: 23 Copynumber: 7.1 Consensus size: 23
42310810 CCCTAACCCT
*
42310820 AACCCTAACCTAACTTAATTAAA
1 AACCCAAACCTAACTTAATTAAA
42310843 AA--C--ACC-AACTTAATTAAA
1 AACCCAAACCTAACTTAATTAAA
* * *
42310861 AACCCTAACTTAA-TTAA-AAACCCA
1 AACCCAAACCTAACTTAATTAA---A
*
42310885 AACCCAAATCTAACTTAATTAAA
1 AACCCAAACCTAACTTAATTAAA
* *
42310908 AACCCTAACCTAATTTAATTAAA
1 AACCCAAACCTAACTTAATTAAA
* * *
42310931 AATCCTAACCTTAACTTAACTTAATT
1 AACCCAAACC-TAACTTAA-TTAA-A
*
42310957 AA---AAACCTAATTTAATTAAA
1 AACCCAAACCTAACTTAATTAAA
42310977 AA
1 AA
42310979 TCCTAACTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
18 14 0.13
19 3 0.03
20 3 0.03
21 7 0.06
22 13 0.12
23 38 0.35
24 18 0.17
25 8 0.07
26 4 0.04
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCCAAACCTAACTTAATTAAA
Found at i:42310940 original size:29 final size:28
Alignment explanation
Indices: 42310864--42310966 Score: 99
Period size: 29 Copynumber: 3.8 Consensus size: 28
42310854 AATTAAAAAC
* *
42310864 CCTAACTTAATTAAAAACCCAAACCCAAA
1 CCTAACTTAATTAAAAA-CCTAACCCTAA
*
42310893 TCTAACTTAATT--AAA---AACCCTAA
1 CCTAACTTAATTAAAAACCTAACCCTAA
* *
42310916 CCTAATTTAATTAAAAATCCTAACCTTAA
1 CCTAACTTAATTAAAAA-CCTAACCCTAA
*
42310945 CTTAACTTAATTAAAAACCTAA
1 CCTAACTTAATTAAAAACCTAA
42310967 TTTAATTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
23 17 0.28
25 3 0.05
27 3 0.05
28 5 0.08
29 33 0.54
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (28 bp):
CCTAACTTAATTAAAAACCTAACCCTAA
Found at i:42310983 original size:18 final size:17
Alignment explanation
Indices: 42310947--42311009 Score: 99
Period size: 18 Copynumber: 3.6 Consensus size: 17
42310937 AACCTTAACT
42310947 TAACTTAATTAAAAACC
1 TAACTTAATTAAAAACC
*
42310964 TAATTTAATTAAAAATCC
1 TAACTTAATTAAAAA-CC
42310982 TAACTTAATTAAAAACCC
1 TAACTTAATTAAAAA-CC
42311000 TAACTTAATT
1 TAACTTAATT
42311010 TTACTAGCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 14 0.33
18 28 0.67
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (17 bp):
TAACTTAATTAAAAACC
Found at i:42310990 original size:23 final size:23
Alignment explanation
Indices: 42310894--42310991 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
42310884 AAACCCAAAT
* *
42310894 CTAACTTAATTAAAAACCCTAAC
1 CTAATTTAATTAAAAATCCTAAC
42310917 CTAATTTAATTAAAAATCCTAAC
1 CTAATTTAATTAAAAATCCTAAC
*
42310940 CTTAACTTAACTTAATTAAA----AAC
1 C-TAATTTAA-TTAA--AAATCCTAAC
42310963 CTAATTTAATTAAAAATCCTAAC
1 CTAATTTAATTAAAAATCCTAAC
*
42310986 TTAATT
1 CTAATT
42310992 AAAAACCCTA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.05
21 4 0.06
22 7 0.11
23 34 0.55
24 7 0.11
25 4 0.06
27 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (23 bp):
CTAATTTAATTAAAAATCCTAAC
Found at i:42311056 original size:26 final size:26
Alignment explanation
Indices: 42311020--42311111 Score: 78
Period size: 26 Copynumber: 3.4 Consensus size: 26
42311010 TTACTAGCCA
42311020 TTAACACAATTGTTGGACTTAATAAT
1 TTAACACAATTGTTGGACTTAATAAT
* * * * * *
42311046 TTAACATAATTTGAT-AATTTTACTAACCA
1 TTAACACAA-TTGTTGGA-CTTAATAA--T
42311075 TTAACACAATTGTTGGACTTAATAAT
1 TTAACACAATTGTTGGACTTAATAAT
*
42311101 TTAACATAATT
1 TTAACACAATT
42311112 TGATAATTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
26 19 0.40
27 10 0.21
28 10 0.21
29 9 0.19
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (26 bp):
TTAACACAATTGTTGGACTTAATAAT
Found at i:42311064 original size:55 final size:54
Alignment explanation
Indices: 42311005--42311512 Score: 446
Period size: 55 Copynumber: 9.0 Consensus size: 54
42310995 AACCCTAACT
* * *
42311005 TAATTTTACTAGCCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATT-TTGGACTTAATAATTTTACATAATTTGA
* *
42311060 TAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATT-TTGGACTTAATAATTTTACATAATTTGA
42311115 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTTT-GGACTTAATAATTTTACATAATTTGA
** * *
42311170 TAATTTTACCTAATTTAATTAA-AAATTTTTTGG-CTTAATAATTTTACATAATTTTACA
1 TAATTTTA-CTAA--CCATTAACAAA-ATTTTGGACTTAATAATTTTACATAA-TTT-GA
* * *
42311228 TAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGG-CTTAATAATTTTACATAATTTGA
1 TAATTT--T-A-CTAACC-A--TTAA-CAAAA---TTTTGGACTTAATAATTTTACATAATTTGA
42311292 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC--------A
1 TAATTTTACTAACCATTAACAAAATTTT-GGACTTAATAATTTTACATAATTTGA
*
42311339 TAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTTTG-GACTTAATAATTTTACATAATTTGA
*** *
42311394 TAATTTTACCTAGTTTAATTAAAAAAATTTTGG-CTTAATAATTTTACATAATTATACATAATTT
1 TAATTTTA-CTA--ACCATTAACAAAATTTTGGAC-T--TAA---TA-AT--TT-TACATAATTT
42311458 GA
53 GA
*
42311460 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAAAAATTTTACATAATTT
1 TAATTTTACTAACCATTAACAAAATTTT-GGACTTAATAATTTTACATAATTT
42311513 TACATAATGT
Statistics
Matches: 382, Mismatches: 27, Indels: 88
0.77 0.05 0.18
Matches are distributed among these distances:
46 1 0.00
47 44 0.12
53 4 0.01
54 4 0.01
55 145 0.38
56 32 0.08
57 14 0.04
58 32 0.08
59 5 0.01
60 6 0.02
61 4 0.01
62 10 0.03
63 15 0.04
64 13 0.03
65 9 0.02
66 44 0.12
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (54 bp):
TAATTTTACTAACCATTAACAAAATTTTGGACTTAATAATTTTACATAATTTGA
Found at i:42311174 original size:18 final size:18
Alignment explanation
Indices: 42311151--42311185 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42311141 TTGGGACTTA
42311151 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
42311169 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
42311186 AATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:42311222 original size:10 final size:10
Alignment explanation
Indices: 42311207--42311233 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42311197 TTTTGGCTTA
42311207 ATAATTTTAC
1 ATAATTTTAC
42311217 ATAATTTTAC
1 ATAATTTTAC
42311227 ATAATTT
1 ATAATTT
42311234 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:42311229 original size:66 final size:66
Alignment explanation
Indices: 42311151--42311289 Score: 260
Period size: 66 Copynumber: 2.1 Consensus size: 66
42311141 TTGGGACTTA
42311151 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAATTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAATTTTTTGGCTTAATAATTTTA
42311216 C
66 C
* *
42311217 ATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGCTTAATAATTTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAATTTTTTGGCTTAATAATTTTA
42311282 C
66 C
42311283 ATAATTT
1 ATAATTT
42311290 GATAATTTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (66 bp):
ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAATTTTTTGGCTTAATAATTTTA
C
Found at i:42311319 original size:21 final size:21
Alignment explanation
Indices: 42311293--42311366 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
42311283 ATAATTTGAT
*
42311293 AATTTTACTAACCATTAACAA
1 AATTTTACTAACAATTAACAA
* * *
42311314 AATTTTGGGACTTAATAATTTTACAT
1 AATTTT---AC-TAACAA-TTAACAA
*
42311340 AATTTTACTAACTATTAACAA
1 AATTTTACTAACAATTAACAA
42311361 AATTTT
1 AATTTT
42311367 GCGACTTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
21 17 0.43
22 4 0.10
23 2 0.05
24 2 0.05
25 4 0.10
26 11 0.28
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTTTACTAACAATTAACAA
Found at i:42311344 original size:26 final size:25
Alignment explanation
Indices: 42311314--42311391 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
42311304 CCATTAACAA
42311314 AATTTTGGGACTTAATAATTTTACAT
1 AATTTT-GGACTTAATAATTTTACAT
* *
42311340 AATTTT--AC-TAACT-A-TTAACAA
1 AATTTTGGACTTAA-TAATTTTACAT
42311361 AATTTTGCGACTTAATAATTTTACAT
1 AATTTTG-GACTTAATAATTTTACAT
42311387 AATTT
1 AATTT
42311392 GATAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 11 0.27
22 4 0.10
23 3 0.07
24 3 0.07
25 4 0.10
26 16 0.39
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.45
Consensus pattern (25 bp):
AATTTTGGACTTAATAATTTTACAT
Found at i:42311350 original size:47 final size:47
Alignment explanation
Indices: 42311291--42311391 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
42311281 ACATAATTTG
*
42311291 ATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
1 ATAATTTTACTAACCATTAACAAAATTTTGCGACTTAATAATTTTAC
*
42311338 ATAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTAC
1 ATAATTTTACTAACCATTAACAAAATTTTGCGACTTAATAATTTTAC
42311385 ATAATTT
1 ATAATTT
42311392 GATAATTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (47 bp):
ATAATTTTACTAACCATTAACAAAATTTTGCGACTTAATAATTTTAC
Found at i:42311397 original size:65 final size:64
Alignment explanation
Indices: 42311328--42311520 Score: 208
Period size: 65 Copynumber: 3.1 Consensus size: 64
42311318 TTGGGACTTA
42311328 ATAATTTTACATAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTACATAATTT-
1 ATAATTTTACATAATTTTACTAAC-ATTAACAAAATTTTG-GACTTAATAATTTTACATAATTTA
*
42311392 G
64 C
* * *
42311393 ATAATTTTACCT-A-GTT--T-A-ATTAAAAAAATTTTGG-CTTAATAATTTTACATAATTATAC
1 ATAATTTTACATAATTTTACTAACATTAACAAAATTTTGGACTTAATAATTTTACATAATT-TAC
* *
42311451 ATAA-TTT-GATAATTTTACTAACCATTAACAAAATTTTGGGACTTAAAAATTTTACATAATTTT
1 ATAATTTTACATAATTTTACTAA-CATTAACAAAATTTT-GGACTTAATAATTTTACATAA-TTT
42311514 AC
63 AC
42311516 ATAAT
1 ATAAT
42311521 GTTAGATTTG
Statistics
Matches: 106, Mismatches: 9, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
56 21 0.20
57 6 0.06
58 20 0.19
60 2 0.02
61 2 0.02
63 15 0.14
64 3 0.03
65 35 0.33
66 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (64 bp):
ATAATTTTACATAATTTTACTAACATTAACAAAATTTTGGACTTAATAATTTTACATAATTTAC
Found at i:42311400 original size:158 final size:164
Alignment explanation
Indices: 42311005--42311515 Score: 496
Period size: 177 Copynumber: 3.1 Consensus size: 164
42310995 AACCCTAACT
* * * *
42311005 TAATTTTACTAGCCATTAACACAATTGTTG-GACTTAATAATTTAACATAATTTGATAATTTTA-
1 TAATTTTACTAACTATTAACAAAATT-TTGCGACTTAATAATTTTACATAATTTGATAATTTTAC
*** * *
42311068 CTA--ACCATTAACACAATTGTTGGAC-T-TAA-TA-AT-TTA-ACATAATTTGATAATTTTACT
65 CTAGTTTAATTAAAAAAATT-TTGG-CTTATAATTACATATTATACATAATTTGATAATTTTACT
*
42311125 AACCATTAACAAAATTTTGGGACTTAATAATTTTACA
128 AACCATTAACAAAATTTTGGGACTTAAAAATTTTACA
* * * ** *
42311162 TAATTTGATAATTTTACCTAATTTAATTAAAAATTTTTTGGCTTAATAATTTTACATAATTTTAC
1 TAATTT--T-A--CTAACT-A-TTAA--CAAAATTTTGCGAC-T--------TA-ATAATTTTAC
***
42311227 ATAATTTGATAATTTTACCTAGTTTAATTAAAATTTTTTTGGC-T-TAA-TA-AT-TT-TACATA
47 ATAATTTGATAATTTTACCTAGTTTAATTAAAAAAATTTTGGCTTATAATTACATATTATACATA
*
42311286 ATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACA
112 ATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAAAAATTTTACA
42311339 TAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACC
1 TAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACC
42311404 TAGTTTAATTAAAAAAATTTTGGCTTAATAATTTTACATAATTATACATAATTTGATAATTTTAC
66 TAGTTTAATTAAAAAAATTTTGGCTT-ATAA--TTACAT-ATTATACATAATTTGATAATTTTAC
42311469 TAACCATTAACAAAATTTTGGGACTTAAAAATTTTACA
127 TAACCATTAACAAAATTTTGGGACTTAAAAATTTTACA
42311507 TAATTTTAC
1 TAATTTTAC
42311516 ATAATGTTAG
Statistics
Matches: 295, Mismatches: 25, Indels: 57
0.78 0.07 0.15
Matches are distributed among these distances:
157 6 0.02
158 50 0.17
159 4 0.01
160 1 0.00
161 3 0.01
162 3 0.01
163 1 0.00
164 6 0.02
165 4 0.01
166 7 0.02
167 4 0.01
168 77 0.26
170 4 0.01
171 1 0.00
172 4 0.01
174 1 0.00
175 3 0.01
176 26 0.09
177 78 0.26
178 4 0.01
179 8 0.03
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (164 bp):
TAATTTTACTAACTATTAACAAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACC
TAGTTTAATTAAAAAAATTTTGGCTTATAATTACATATTATACATAATTTGATAATTTTACTAAC
CATTAACAAAATTTTGGGACTTAAAAATTTTACA
Found at i:42311486 original size:224 final size:226
Alignment explanation
Indices: 42311005--42311512 Score: 724
Period size: 224 Copynumber: 2.2 Consensus size: 226
42310995 AACCCTAACT
* * * *
42311005 TAATTTTACTAGCCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGATAATTTTACT
1 TAATTTTACTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTACT
* *
42311070 AACCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGATAATTTTACTAACCATTAAC
66 AACCATTAACAAAATTGTTGGACTTAATAATTT---ATAA--TCATAATTTTACTAACCATTAAC
* **
42311135 AAAATTTTGGGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAATTTTT
126 AAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTT
*
42311200 TGGCTTAATAATTTTACATAATTTTACATAATTTGA
191 TGGCTTAATAATTTTACATAATTATACATAATTTGA
** *
42311236 TAATTTTACCT-A-GTTTAATTAAAATTTTTTTGG-CTTAATAATTTTACATAATTTGATAATTT
1 TAATTTTA-CTAACCATTAA-CAAAA--TTTTTGGACTTAATAATTTTACATAATTTGATAATTT
*
42311298 TACTAACCATTAACAAAATT-TTGGGACTTAATAATTT-T-A-CATAATTTTACTAACTATTAAC
62 TACTAACCATTAACAAAATTGTT-GGACTTAATAATTTATAATCATAATTTTACTAACCATTAAC
*
42311359 AAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACCTAGTTTAATTAAAAAAATTT
126 AAAATTTTGCGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTT
42311424 TGGCTTAATAATTTTACATAATTATACATAATTTGA
191 TGGCTTAATAATTTTACATAATTATACATAATTTGA
* *
42311460 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAAAAATTTTACATAATTT
1 TAATTTTACTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTT
42311513 TACATAATGT
Statistics
Matches: 249, Mismatches: 20, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
222 6 0.02
223 22 0.09
224 129 0.52
225 4 0.02
227 1 0.00
228 1 0.00
230 4 0.02
231 13 0.05
232 63 0.25
233 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (226 bp):
TAATTTTACTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTACT
AACCATTAACAAAATTGTTGGACTTAATAATTTATAATCATAATTTTACTAACCATTAACAAAAT
TTTGCGACTTAATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTTTGGCT
TAATAATTTTACATAATTATACATAATTTGA
Found at i:42314441 original size:11 final size:13
Alignment explanation
Indices: 42314420--42314451 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42314410 AATAAATTAA
42314420 TAAAATATCAT-T
1 TAAAATATCATAT
42314432 TAAAAT-TCATAT
1 TAAAATATCATAT
42314444 TAAAATAT
1 TAAAATAT
42314452 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 13 0.72
13 1 0.06
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:42317222 original size:124 final size:124
Alignment explanation
Indices: 42317002--42317351 Score: 578
Period size: 124 Copynumber: 2.8 Consensus size: 124
42316992 CCCAAACTTG
*
42317002 CTACTGTAGTAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
42317067 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTGAAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTGACATGAC
* * *
42317126 CTACTGTAGCAAAATCGCATCCACGAGGTCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
42317191 TAGAGGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTGACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTGACATGAC
42317250 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAAGT-GCATCCTG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAA-TAGCATCCTG
* *
42317314 GTAGAATCGATTTTATACTATTTGAC-CAAAAACGTCAA
65 GTAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
42317352 CTCGAAATAA
Statistics
Matches: 210, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
124 208 0.99
125 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTGACATGAC
Found at i:42320368 original size:15 final size:16
Alignment explanation
Indices: 42320348--42320380 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
42320338 TAACTGGAAA
42320348 AATATATTTTA-TATT
1 AATATATTTTATTATT
42320363 AATATATTTTATTATT
1 AATATATTTTATTATT
42320379 AA
1 AA
42320381 ACTTAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATATTTTATTATT
Found at i:42320612 original size:8 final size:8
Alignment explanation
Indices: 42320599--42320625 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42320589 AATTACATAA
42320599 AAATAATT
1 AAATAATT
42320607 AAATAATT
1 AAATAATT
42320615 AAATAATT
1 AAATAATT
42320623 AAA
1 AAA
42320626 AGAAGAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATAATT
Found at i:42331776 original size:10 final size:10
Alignment explanation
Indices: 42331746--42331776 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42331736 TGTGTTGTGC
42331746 TTATATATAT
1 TTATATATAT
*
42331756 ATATATATAT
1 TTATATATAT
42331766 TTATATATAT
1 TTATATATAT
42331776 T
1 T
42331777 GTGTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATATAT
Found at i:42335135 original size:3 final size:3
Alignment explanation
Indices: 42335127--42335167 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
42335117 TAATCATTAA
* * *
42335127 AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42335168 AATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:42336009 original size:15 final size:15
Alignment explanation
Indices: 42335983--42336020 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 15
42335973 TTTTTTTACT
42335983 TATATAATATAATATAA
1 TATATAATA-AA-ATAA
42336000 TATATAATAAAATAA
1 TATATAATAAAATAA
42336015 TATATA
1 TATATA
42336021 TAGCATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATATAATAAAATAA
Found at i:42336021 original size:17 final size:17
Alignment explanation
Indices: 42335983--42336022 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42335973 TTTTTTTACT
*
42335983 TATATAATATAATATAA
1 TATATAATAAAATATAA
42336000 TATATAATAAAATA-ATA
1 TATATAATAAAATATA-A
42336017 TATATA
1 TATATA
42336023 GCATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAATAAAATATAA
Found at i:42339375 original size:24 final size:24
Alignment explanation
Indices: 42339341--42339425 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
42339331 GAAGAATTTT
*
42339341 CTCCTAGGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
* * *
42339365 CTTCGATGGGAGCAAGGGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
42339389 CTCCTATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
42339413 CTCCTATGGGAGC
1 CTCCTATGGGAGC
42339426 TTCAAATCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.20
Consensus pattern (24 bp):
CTCCTATGGGAGCAAGAGGTGGTC
Found at i:42341594 original size:89 final size:89
Alignment explanation
Indices: 42341487--42341660 Score: 244
Period size: 89 Copynumber: 2.0 Consensus size: 89
42341477 AGCTCTTTTT
* * *
42341487 TTTTTTTTTGCACTCAATT-GAGCACTTGAACTTTTAAAATGCATCAAAAAGGCCCTCAAACTTC
1 TTTTTTTTTGCACTCAATTAG-GCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTC
42341551 TTCAAAAGAAGCAATAAAGCCCCTAC
65 TTC-AAAGAAGCAATAAAGCCCCTAC
* * *
42341577 TTTTTTTTT-CACTCAATTAGGTACTTGAACTTTCAAAATGCCTCAAAAAGACCCTCAAAATTTT
1 TTTTTTTTTGCACTCAATTAGGCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCT
* *
42341641 TCAAATAAGCAATTAAGCCC
66 TCAAAGAAGCAATAAAGCCC
42341661 ATGGTCTTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 16 0.21
89 49 0.65
90 10 0.13
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (89 bp):
TTTTTTTTTGCACTCAATTAGGCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTCT
TCAAAGAAGCAATAAAGCCCCTAC
Found at i:42341750 original size:18 final size:17
Alignment explanation
Indices: 42341720--42341769 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
42341710 AAATTCTAAT
42341720 AAAATTTTTAAAAATTA
1 AAAATTTTTAAAAATTA
42341737 AAAATTTATTAAAAATTA
1 AAAATTT-TTAAAAATTA
* *
42341755 GAATTTTTTATAAAA
1 AAAATTTTTA-AAAA
42341770 ATCTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAAATTTTTAAAAATTA
Found at i:42341771 original size:47 final size:46
Alignment explanation
Indices: 42341681--42341787 Score: 110
Period size: 47 Copynumber: 2.3 Consensus size: 46
42341671 TAAAAATTAG
* *
42341681 AAAAATTAAAAATTTTTAGAAAAATTATTAAATTCTAATAAAATTTTT
1 AAAAATTAAAAATTTTTA-AAAAATTATGAAATTCTAATAAAA-TCTT
* * *
42341729 AAAAATTAAAAATTTATT-AAAAATTA-GAATTTTTTATAAAAATCTT
1 AAAAATTAAAAATTT-TTAAAAAATTATGAAATTCTAAT-AAAATCTT
42341775 AAAAATATAAAAA
1 AAAAAT-TAAAAA
42341788 AAATTGTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 16 0.31
47 18 0.35
48 15 0.29
49 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (46 bp):
AAAAATTAAAAATTTTTAAAAAATTATGAAATTCTAATAAAATCTT
Found at i:42341808 original size:19 final size:18
Alignment explanation
Indices: 42341719--42341809 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 18
42341709 TAAATTCTAA
42341719 TAAAATTTT-TAAAAA-T
1 TAAAATTTTATAAAAATT
*
42341735 TAAAAATTTATTAAAAA-T
1 TAAAATTTTA-TAAAAATT
*
42341753 TAGAATTTTTTATAAAAATCT
1 TA-AA-ATTTTATAAAAAT-T
* * *
42341774 TAAAAATATAAAAAAAATT
1 T-AAAATTTTATAAAAATT
42341793 GTAAAATTTTATAAAAA
1 -TAAAATTTTATAAAAA
42341810 AGCATAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
16 8 0.14
18 9 0.16
19 21 0.37
20 14 0.25
21 4 0.07
22 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAAATTTTATAAAAATT
Found at i:42341955 original size:9 final size:9
Alignment explanation
Indices: 42341941--42342092 Score: 64
Period size: 9 Copynumber: 16.1 Consensus size: 9
42341931 TTTTGATACG
42341941 ATAATTTTT
1 ATAATTTTT
42341950 ATAATTTTTTT
1 ATAA--TTTTT
* *
42341961 ATGATATTT
1 ATAATTTTT
42341970 AT-ATTTCTT
1 ATAATTT-TT
42341979 -TACATTTTGT
1 ATA-ATTTT-T
42341989 ATAATTTGCTT
1 ATAATTT--TT
* *
42342000 ATGA-CTTT
1 ATAATTTTT
*
42342008 ATAAAATTTT
1 AT-AATTTTT
42342018 ATAATTTTT
1 ATAATTTTT
*
42342027 -TATATTTCT
1 ATA-ATTTTT
42342036 AT-ATATTTT
1 ATAAT-TTTT
42342045 ATAATTTTT
1 ATAATTTTT
*
42342054 GACAATTTTT
1 -ATAATTTTT
*
42342064 ATAAAATTTT
1 AT-AATTTTT
*
42342074 ACAATTTTT
1 ATAATTTTT
42342083 -TATATTTTT
1 ATA-ATTTTT
42342092 A
1 A
42342093 ACGATTTTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 37
0.67 0.10 0.23
Matches are distributed among these distances:
8 13 0.12
9 47 0.44
10 33 0.31
11 14 0.13
12 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:42342027 original size:10 final size:10
Alignment explanation
Indices: 42342014--42342091 Score: 58
Period size: 10 Copynumber: 8.3 Consensus size: 10
42342004 CTTTATAAAA
42342014 TTTTATAATT
1 TTTTATAATT
42342024 TTTTAT-A-T
1 TTTTATAATT
* *
42342032 TTCTAT-ATA
1 TTTTATAATT
42342041 TTTTATAATT
1 TTTTATAATT
* *
42342051 TTTGACAA-T
1 TTTTATAATT
**
42342060 TTTTATAAAA
1 TTTTATAATT
*
42342070 TTTTACAATT
1 TTTTATAATT
42342080 TTTTAT-ATT
1 TTTTATAATT
42342089 TTT
1 TTT
42342092 AACGATTTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
8 7 0.13
9 19 0.37
10 26 0.50
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:42342030 original size:20 final size:20
Alignment explanation
Indices: 42342005--42342086 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
42341995 TGCTTATGAC
*
42342005 TTTATAAAATTTTATAATTT
1 TTTATAAAATTTTACAATTT
* *
42342025 TTTAT---ATTTCTA-TATAT
1 TTTATAAAATTT-TACAATTT
*
42342042 TTTAT-AATTTTTGACAA-TT
1 TTTATAAAATTTT-ACAATTT
42342061 TTTATAAAATTTTACAATTT
1 TTTATAAAATTTTACAATTT
42342081 TTTATA
1 TTTATA
42342087 TTTTTAACGA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 12 0.24
18 3 0.06
19 14 0.29
20 20 0.41
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (20 bp):
TTTATAAAATTTTACAATTT
Found at i:42342099 original size:19 final size:18
Alignment explanation
Indices: 42342014--42342102 Score: 72
Period size: 19 Copynumber: 4.8 Consensus size: 18
42342004 CTTTATAAAA
*
42342014 TTTTATAATTTTTTATAT
1 TTTTACAATTTTTTATAT
* * *
42342032 TTCTA-TATATTTTATAAT
1 TTTTACAATTTTTTAT-AT
* *
42342050 TTTTGACAATTTTTATAAAA
1 TTTT-ACAATTTTT-TATAT
42342070 TTTTACAATTTTTTATAT
1 TTTTACAATTTTTTATAT
*
42342088 TTTTAACGATTTTTT
1 TTTT-ACAATTTTTT
42342103 TTCTATTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 8 0.15
18 16 0.29
19 19 0.35
20 10 0.18
21 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTACAATTTTTTATAT
Found at i:42357746 original size:29 final size:30
Alignment explanation
Indices: 42357687--42357744 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42357677 TCCGAGCCTT
*
42357687 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
42357717 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
42357745 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:42357974 original size:13 final size:13
Alignment explanation
Indices: 42357956--42357987 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42357946 TTTCCAGAAA
42357956 TTATGAATTTATT
1 TTATGAATTTATT
42357969 TTATGAATTTATT
1 TTATGAATTTATT
*
42357982 TGATGA
1 TTATGA
42357988 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:42358195 original size:50 final size:50
Alignment explanation
Indices: 42358082--42358323 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
42358072 ATTTGGGTAA
* * *
42358082 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
42358138 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42358188 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42358238 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
42358288 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42358324 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:42358271 original size:100 final size:103
Alignment explanation
Indices: 42358082--42358331 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
42358072 ATTTGGGTAA
42358082 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
42358147 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
42358188 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
42358250 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
42358288 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42358332 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:42359959 original size:28 final size:28
Alignment explanation
Indices: 42359917--42360038 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
42359907 TTTCGACACC
* *
42359917 AAGTGTGCAAATTTAATTGTAAAGCACT
1 AAGTGTGCGAGTTTAATTGTAAAGCACT
42359945 AAGTGTGCGAGTTTAATTGTAAAGCACT
1 AAGTGTGCGAGTTTAATTGTAAAGCACT
* *
42359973 AAGTGTGCGAGTTTAATGGCAAAGCACT
1 AAGTGTGCGAGTTTAATTGTAAAGCACT
* * *
42360001 AAGTGTGCGAGTTTGATTATTGAA-CACT
1 AAGTGTGCGAGTTTAATT-GTAAAGCACT
42360029 AAGTGTGCGA
1 AAGTGTGCGA
42360039 ACTTATTAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
28 82 0.98
29 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (28 bp):
AAGTGTGCGAGTTTAATTGTAAAGCACT
Found at i:42360797 original size:23 final size:23
Alignment explanation
Indices: 42360743--42360898 Score: 156
Period size: 23 Copynumber: 6.7 Consensus size: 23
42360733 TGCTACATAT
*
42360743 ATGCTGCCCAATTTTGGTGA-ATAA
1 ATGCTGTCCAATTTT-GT-ATATAA
*
42360767 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCCAATTTTGTATATAA
*
42360790 ATGCTGTCCAATTTTGTGTATAA
1 ATGCTGTCCAATTTTGTATATAA
* * * *
42360813 GTGCTGTCCAA-ATTGCTACATAT
1 ATGCTGTCCAATTTTG-TATATAA
*
42360836 ATGCTGCCCAATTTTGGTGA-ATAA
1 ATGCTGTCCAATTTT-GT-ATATAA
*
42360860 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCCAATTTTGTATATAA
*
42360883 ATGCTGTCAAATTTTG
1 ATGCTGTCCAATTTTG
42360899 ATGATAATAA
Statistics
Matches: 110, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.05
23 69 0.63
24 34 0.31
25 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
ATGCTGTCCAATTTTGTATATAA
Found at i:42360805 original size:47 final size:47
Alignment explanation
Indices: 42360743--42360898 Score: 217
Period size: 47 Copynumber: 3.3 Consensus size: 47
42360733 TGCTACATAT
42360743 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAC
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAC
* * * * * *
42360790 ATGCTGTCCAATTTT-GTGTATAAGTGCTGTCCAA-ATTGCTACATAT
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTG-TATATAC
42360836 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAC
1 ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAC
* *
42360883 ATGCTGTCAAATTTTG
1 ATGCTGCCCAATTTTG
42360899 ATGATAATAA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
45 3 0.03
46 36 0.39
47 50 0.54
48 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (47 bp):
ATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATAC
Found at i:42360846 original size:93 final size:93
Alignment explanation
Indices: 42360729--42360898 Score: 331
Period size: 93 Copynumber: 1.8 Consensus size: 93
42360719 TAATGGTCAA
42360729 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
42360794 TGTCCAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
42360822 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
42360887 TGTCAAATTTTG
66 TGTCAAATTTTG
42360899 ATGATAATAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (93 bp):
AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:42360869 original size:70 final size:68
Alignment explanation
Indices: 42360767--42360895 Score: 181
Period size: 70 Copynumber: 1.9 Consensus size: 68
42360757 TGGTGAATAA
* * *
42360767 ATGCTGTCCAATTTTGTATATACATGCTGTCCAATTTTGTGTATA-AGTGCTGTCCAAATTGCTA
1 ATGCTGCCCAATTTTGTATATAAATGCTGTCCAATTTTGTATATACA-TGCTGT-CAAATTGCTA
42360831 CATAT
64 CATAT
42360836 ATGCTGCCCAATTTTGGTGA-ATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATT
1 ATGCTGCCCAATTTT-GT-ATATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATT
42360896 TTGATGATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
69 20 0.37
70 32 0.59
71 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (68 bp):
ATGCTGCCCAATTTTGTATATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTGCTACA
TAT
Found at i:42361504 original size:23 final size:23
Alignment explanation
Indices: 42361456--42361505 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
42361446 ATTCATGCGA
* *
42361456 TCTATTTCTTTTACTTCATCGTT
1 TCTATTTATTTTACTTCATCGGT
*
42361479 TCTATTTATTTT-CATTCATTGGT
1 TCTATTTATTTTAC-TTCATCGGT
42361502 TCTA
1 TCTA
42361506 CATGCAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.16, C:0.18, G:0.06, T:0.60
Consensus pattern (23 bp):
TCTATTTATTTTACTTCATCGGT
Found at i:42370434 original size:22 final size:20
Alignment explanation
Indices: 42370402--42370441 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
42370392 TATTAAATAT
*
42370402 ATATATATTTTATTTTTAAA
1 ATATATATTTTAGTTTTAAA
42370422 ATATACTAGTTTTAGTTTTA
1 ATATA-TA-TTTTAGTTTTA
42370442 TTTTAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATATATATTTTAGTTTTAAA
Found at i:42370527 original size:40 final size:38
Alignment explanation
Indices: 42370477--42370603 Score: 103
Period size: 40 Copynumber: 3.1 Consensus size: 38
42370467 TGTTACAACA
*
42370477 ATTAATACAATTAACAATTAATAATTTTACTAACAAAAT
1 ATTAGTACAATTAACAATTAATAATTTTA-TAACAAAAT
* * * *
42370516 ATTAGTAACAATTAATAATGAATAATTTGATAATTTTAGTAACA-
1 ATTAGT-ACAATTAACAATTAATAATTTTATAA---CA--AA-AT
*
42370560 ATTAATACAATTAACAATTAATAATTTTATTAACAAAAT
1 ATTAGTACAATTAACAATTAATAATTTTA-TAACAAAAT
*
42370599 GTTAG
1 ATTAG
42370604 ATTTTACAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
38 1 0.01
39 13 0.19
40 20 0.30
41 1 0.01
42 1 0.01
43 20 0.30
44 10 0.15
45 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (38 bp):
ATTAGTACAATTAACAATTAATAATTTTATAACAAAAT
Found at i:42370668 original size:16 final size:16
Alignment explanation
Indices: 42370649--42370689 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
42370639 AATTTGATAC
42370649 AATTTTAATAACAATT
1 AATTTTAATAACAATT
42370665 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
42370681 AGTTTTAAT
1 AATTTTAAT
42370690 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:42370691 original size:22 final size:23
Alignment explanation
Indices: 42370663--42370724 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
42370653 TTAATAACAA
* *
42370663 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
42370685 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
42370708 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
42370725 ACGGGCCGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:42372551 original size:15 final size:14
Alignment explanation
Indices: 42372531--42372568 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
42372521 AAAAAAAATG
42372531 AATTAATAAACCTT
1 AATTAATAAACCTT
42372545 AAATTAATAAA-CTT
1 -AATTAATAAACCTT
42372559 -ATTAATAAAC
1 AATTAATAAAC
42372569 ATTTTTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
14 3 0.14
15 10 0.45
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAATAAACCTT
Found at i:42372564 original size:12 final size:13
Alignment explanation
Indices: 42372531--42372568 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
42372521 AAAAAAAATG
42372531 AATTAATAAACCTT
1 AATTAATAAA-CTT
42372545 AAATTAATAAACTT
1 -AATTAATAAACTT
42372559 -ATTAATAAAC
1 AATTAATAAAC
42372569 ATTTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTAATAAACTT
Found at i:42373586 original size:41 final size:41
Alignment explanation
Indices: 42373529--42373610 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
42373519 TGGCATGGCT
42373529 TCACTCACGGTAGTTTAAACCCTAAAATTATAGCTCGATAA
1 TCACTCACGGTAGTTTAAACCCTAAAATTATAGCTCGATAA
42373570 TCACTCACGGTAGTTTAAACCCTAAAATTATAGCTCGATAA
1 TCACTCACGGTAGTTTAAACCCTAAAATTATAGCTCGATAA
42373611 AAATTAGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (41 bp):
TCACTCACGGTAGTTTAAACCCTAAAATTATAGCTCGATAA
Found at i:42381757 original size:21 final size:23
Alignment explanation
Indices: 42381733--42381775 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42381723 CATTAAAGTT
42381733 TTCTCA-CG-ACAGTTTTGTTTA
1 TTCTCATCGCACAGTTTTGTTTA
* *
42381754 TTCTTATGGCACAGTTTTGTTT
1 TTCTCATCGCACAGTTTTGTTT
42381776 GCTTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 1 0.06
23 12 0.67
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (23 bp):
TTCTCATCGCACAGTTTTGTTTA
Found at i:42382515 original size:20 final size:19
Alignment explanation
Indices: 42382486--42382534 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
42382476 ATATGTAAAT
42382486 TTTTTATTTTTT-ATTATAC
1 TTTTTATTTTTTGA-TATAC
*
42382505 TTTTTAGTTTTTTGATATAT
1 TTTTTA-TTTTTTGATATAC
42382525 TTTTTATTTT
1 TTTTTATTTT
42382535 GGTCAGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTGATATAC
Found at i:42385929 original size:21 final size:20
Alignment explanation
Indices: 42385900--42385940 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
42385890 GGAGGGCACT
*
42385900 CTGAAAAGTTAATATATATTA
1 CTGAAAAGTTAA-ATACATTA
*
42385921 CTGAGAAGTTAAATACATTA
1 CTGAAAAGTTAAATACATTA
42385941 TCCATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (20 bp):
CTGAAAAGTTAAATACATTA
Found at i:42392541 original size:14 final size:15
Alignment explanation
Indices: 42392520--42392554 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42392510 GCTTAAGTAC
42392520 TAAAAAAAGTCACTG
1 TAAAAAAAGTCACTG
42392535 TAAAAAAAGTCACTG
1 TAAAAAAAGTCACTG
42392550 TAAAA
1 TAAAA
42392555 TAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (15 bp):
TAAAAAAAGTCACTG
Found at i:42396219 original size:18 final size:17
Alignment explanation
Indices: 42396198--42396231 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42396188 AAGACAACAA
*
42396198 TAAAATAATTTGAAATTT
1 TAAAAAAATTT-AAATTT
42396216 TAAAAAAATTTAAATT
1 TAAAAAAATTTAAATT
42396232 ATAACATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAAAATTTAAATTT
Found at i:42404743 original size:26 final size:27
Alignment explanation
Indices: 42404698--42404749 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
42404688 AAATCCCAAA
*
42404698 TTTTCTTCCTTTGCTTCCCT-TTTTCT
1 TTTTCTTCCTTTGCTCCCCTGTTTTCT
42404724 TTTTCTTTCCTTT-CTCCCCTGTTTTC
1 TTTTC-TTCCTTTGCTCCCCTGTTTTC
42404750 GTTTGCCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTCTTCCTTTGCTCCCCTGTTTTCT
Found at i:42405973 original size:30 final size:30
Alignment explanation
Indices: 42405937--42406107 Score: 111
Period size: 31 Copynumber: 5.8 Consensus size: 30
42405927 TTGTTTCAAA
*
42405937 AAAAATTAATAGGGATATTTTAGATAATAT
1 AAAAATTAATAGGGATAATTTAGATAATAT
** * *
42405967 AAAAATTAATATAGATATTTTAGGTAGCATA-
1 AAAAATTAATAGGGATAATTTAGATA--ATAT
* * * * *
42405998 AAAAATCAATAGGGGTAATTTAGACATTAAC
1 AAAAATTAATAGGGATAATTTAGATAAT-AT
* * *
42406029 AAAAATAAATAGGTG-TATTTTAGGTAATAT
1 AAAAATTAATAGG-GATAATTTAGATAATAT
**
42406059 AAAAA--AGCAGGGATAATTTAGA-AAT-T
1 AAAAATTAATAGGGATAATTTAGATAATAT
* *
42406085 AAAACTTAATAAGGATAATTTAG
1 AAAAATTAATAGGGATAATTTAG
42406108 TTATATTTTA
Statistics
Matches: 108, Mismatches: 25, Indels: 18
0.72 0.17 0.12
Matches are distributed among these distances:
26 5 0.05
27 4 0.04
28 24 0.22
29 1 0.01
30 30 0.28
31 40 0.37
32 4 0.04
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAAATTAATAGGGATAATTTAGATAATAT
Found at i:42410588 original size:109 final size:108
Alignment explanation
Indices: 42410387--42410597 Score: 332
Period size: 109 Copynumber: 1.9 Consensus size: 108
42410377 CCAACTCATC
* * *
42410387 TTGGTATAATCATCAATGAAAACCATGCAATACTTGCTCTCTTTGAGCGACAAAGTTGTGTGAGA
1 TTGGTATAATCATCAATAAAAACCATGCAATACTTACTCTCTTTGAGCGACAAAGTTGTGTCAGA
**
42410452 TCTAGTCAAGTCCATGTAGATTAATTTAAGTTTTTCAGACATT
66 TCTAACCAAGTCCATGTAGATTAATTTAAGTTTTTCAGACATT
* * *
42410495 TTGGTATAATCATCAATAAAAACTATGCAATACTTACTCTCTTTTGAGTGACAAAGTTTTGTCAG
1 TTGGTATAATCATCAATAAAAACCATGCAATACTTACTCTC-TTTGAGCGACAAAGTTGTGTCAG
*
42410560 ATCTAACCAGGTCCATGTAGATTAATTTAAGTTTTTCA
65 ATCTAACCAAGTCCATGTAGATTAATTTAAGTTTTTCA
42410598 ATAACTCTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 38 0.41
109 55 0.59
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (108 bp):
TTGGTATAATCATCAATAAAAACCATGCAATACTTACTCTCTTTGAGCGACAAAGTTGTGTCAGA
TCTAACCAAGTCCATGTAGATTAATTTAAGTTTTTCAGACATT
Found at i:42417097 original size:18 final size:19
Alignment explanation
Indices: 42417063--42417098 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42417053 AAAATGAAAG
*
42417063 TTTTGTATACTTTTTTTTC
1 TTTTGTATACATTTTTTTC
42417082 TTTTGTA-ACATTTTTTT
1 TTTTGTATACATTTTTTT
42417099 GAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.72
Consensus pattern (19 bp):
TTTTGTATACATTTTTTTC
Found at i:42422062 original size:32 final size:33
Alignment explanation
Indices: 42421976--42422062 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 33
42421966 AAAAAAAACT
*
42421976 AAAGTTGATATTTGTTATCATTTTACAAAATTG
1 AAAGTTGATATTTGTTATCATTTCACAAAATTG
*
42422009 AAA-TTG-TAATTTGTTACCATTTCACAAAA-TG
1 AAAGTTGAT-ATTTGTTATCATTTCACAAAATTG
**
42422040 AAAGTTGATATTCATTATCATTT
1 AAAGTTGATATTTGTTATCATTT
42422063 TACATATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 6 0.13
32 36 0.78
33 4 0.09
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (33 bp):
AAAGTTGATATTTGTTATCATTTCACAAAATTG
Found at i:42423841 original size:11 final size:11
Alignment explanation
Indices: 42423825--42423911 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
42423815 TCAATTATTT
42423825 TCTCAATTTCC
1 TCTCAATTTCC
*
42423836 TCTCAATTTGC
1 TCTCAATTTCC
*
42423847 TCTCAAATTCC
1 TCTCAATTTCC
42423858 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
42423869 TCTCAA-ATCC
1 TCTCAATTTCC
* **
42423879 -AT--ATTTAA
1 TCTCAATTTCC
*
42423887 TCTCAATTTGC
1 TCTCAATTTCC
42423898 TCTCAATTTCC
1 TCTCAATTTCC
42423909 TCT
1 TCT
42423912 TAAATTTCTC
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.07
11 41 0.75
12 5 0.09
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:42424146 original size:21 final size:22
Alignment explanation
Indices: 42424102--42424147 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42424092 TTTTCTCCAA
**
42424102 AACCCTAAAAACCCTAAACTCT
1 AACCCTAAAAACCAAAAACTCT
42424124 AACCCTAAAAACCAAAAAC-CT
1 AACCCTAAAAACCAAAAACTCT
42424145 AAC
1 AAC
42424148 ATGGGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (22 bp):
AACCCTAAAAACCAAAAACTCT
Found at i:42425383 original size:19 final size:17
Alignment explanation
Indices: 42425349--42425383 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
42425339 TTAAAATAGT
42425349 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
42425366 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
42425384 TCTAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:42440827 original size:6 final size:6
Alignment explanation
Indices: 42440816--42440843 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42440806 GGTTCTTTGT
42440816 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCT
42440844 CACACGCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTTC
Found at i:42444682 original size:4 final size:4
Alignment explanation
Indices: 42444673--42444702 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
42444663 GTCACAATAT
*
42444673 ATAG ATAG ATAG ATAA ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
42444703 GAGAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:42447919 original size:36 final size:35
Alignment explanation
Indices: 42447854--42447928 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
42447844 ATATGAAGAT
* * *
42447854 TAATTTTTTAAATGGTTCGTAGTTATTTCTTTCGTA
1 TAATCTTTTAAATGGTTCATAGTTATTTCTCTCG-A
* *
42447890 TAATCTTTTAAATGGTTCATGGTTGTTTCTCTCGA
1 TAATCTTTTAAATGGTTCATAGTTATTTCTCTCGA
42447925 TAAT
1 TAAT
42447929 GTGAATTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.52
Consensus pattern (35 bp):
TAATCTTTTAAATGGTTCATAGTTATTTCTCTCGA
Found at i:42461125 original size:26 final size:27
Alignment explanation
Indices: 42461066--42461125 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
42461056 ATTTTTAGAA
42461066 TTAATGATAAATAAAATATTAAAAAAT
1 TTAATGATAAATAAAATATTAAAAAAT
***
42461093 TAATAATGATAAATGGTAT-TTAAAAAAT
1 T--TAATGATAAATAAAATATTAAAAAAT
42461121 TTAAT
1 TTAAT
42461126 ATCACTGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 1 0.04
28 10 0.36
29 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (27 bp):
TTAATGATAAATAAAATATTAAAAAAT
Found at i:42472968 original size:228 final size:227
Alignment explanation
Indices: 42472562--42473209 Score: 755
Period size: 228 Copynumber: 2.8 Consensus size: 227
42472552 CTTTGAAGAA
* * *
42472562 GATGCAGATCTTTGTGAAAACCCTTACCGGCAAGACCATAACACTCGAGGTCGAAAGCTCCGACA
1 GATGCAGATCTTTGTCAAAA-CCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * *
42472627 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCCGACCAGCAGCGTCTC
65 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTC
* ** * * ** *
42472692 ATTTTCGCTGGCAAACAGCTCGAAGACGGTCGGACCCTT-GCCGATTATAACATCCAGAAAGAAT
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGA-CCTTGGCTGATTATAACATCCAGAAAGAAT
42472756 CCACCCTCCACCTCGTCTT-ACGCCTTCGTGG-GG
194 CCACCCTCCACCTCGTCTTGA-GCCTTCGTGGAGG
* * * *
42472789 GCATGCAAATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGAC
1 G-ATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGAC
* * *
42472854 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGCATCCCACCTGACCAACAGCGTTT
64 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCT
* *
42472919 GATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAATATCCA-AAAGGAA
129 CATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAA-GAA
* * * *
42472983 TCCACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
193 TCCACCCTCCACCTCGTCTTGAGCCTTCGTGGAGG
* * * * * * * * *
42473018 GATGCAGATTTTTGTCAAGACTTTGACCGGCAAAACAATCACCTTGGAGGTTGAAAGCTCCGATA
1 GATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * * * * ** *
42473083 CCATTGACAATGTTAAGGCAAAGATTCAGGATAAGGAAGGAATCCCACCTGATCAGCAAAGGCTC
65 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTC
* * * *
42473148 ATCTTTGCCGGCAAACAATTGGAAGATGGGAGGACTTTGGCTGATTATAACATTCAGAAAGA
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGA
42473210 GTCTACACTT
Statistics
Matches: 355, Mismatches: 59, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
227 12 0.03
228 336 0.95
229 7 0.02
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (227 bp):
GATGCAGATCTTTGTCAAAACCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACAC
CATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTCA
TCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCC
ACCCTCCACCTCGTCTTGAGCCTTCGTGGAGG
Found at i:42484161 original size:23 final size:24
Alignment explanation
Indices: 42484116--42484168 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
42484106 GTTCGTTTGA
*
42484116 AACATGTTCATGAATATTAAATT-
1 AACATGTTCATGAACATTAAATTG
42484139 AACATGTTCATGAACA-TATAATTG
1 AACATGTTCATGAACATTA-AATTG
42484163 AACATG
1 AACATG
42484169 CTCACAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 19 0.70
24 6 0.22
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (24 bp):
AACATGTTCATGAACATTAAATTG
Found at i:42484769 original size:21 final size:21
Alignment explanation
Indices: 42484739--42484789 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
42484729 ACTGCTACAT
42484739 TAAA-TTTCAATACCCAATCA
1 TAAATTTTCAATACCCAATCA
42484759 TAAATTTTCAATACCCAATCA
1 TAAATTTTCAATACCCAATCA
42484780 TAAATTTTCA
1 TAAATTTTCA
42484790 TTTTACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATTTTCAATACCCAATCA
Found at i:42486191 original size:51 final size:50
Alignment explanation
Indices: 42486055--42486243 Score: 238
Period size: 51 Copynumber: 3.7 Consensus size: 50
42486045 AAAGTGAAAG
* * *
42486055 TGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAGCAGA-A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* *
42486104 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * * * *
42486155 -GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAA
1 TG-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-A
42486207 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
42486244 TGTGAACTGG
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 4 0.03
50 40 0.34
51 72 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
Found at i:42486247 original size:102 final size:101
Alignment explanation
Indices: 42486061--42486247 Score: 313
Period size: 101 Copynumber: 1.8 Consensus size: 101
42486051 AAAGTGATGG
* *
42486061 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAGCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCAGAATGATAGGTCACATGTGTAGTAC
42486126 TATGTGCAGGCTACTATGTGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGTGTACCGGATAGCTTCGA
* *
42486162 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAATGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTA--GCAGAATGATAGGTCACATGTGTAGT
42486226 ACTATGTGCAGGCTACTATGTG
64 ACTATGTGCAGGCTACTATGTG
42486248 AACTGGTATC
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
101 36 0.45
102 36 0.45
103 8 0.10
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAGCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGTGTACCGGATAGCTTCGA
Found at i:42486491 original size:16 final size:16
Alignment explanation
Indices: 42486470--42486501 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42486460 TGATTGAAAG
*
42486470 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
42486486 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
42486502 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:42486821 original size:10 final size:10
Alignment explanation
Indices: 42486806--42486830 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42486796 TTTTCAAAAG
42486806 AAATAAACAA
1 AAATAAACAA
42486816 AAATAAACAA
1 AAATAAACAA
42486826 AAATA
1 AAATA
42486831 TCATCTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (10 bp):
AAATAAACAA
Found at i:42488762 original size:17 final size:17
Alignment explanation
Indices: 42488740--42488774 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
42488730 GAATGGTCTC
*
42488740 TGTTTCTTTTCTTCTTT
1 TGTTTCTTTTATTCTTT
42488757 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
42488774 T
1 T
42488775 ATTTTATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:42494726 original size:20 final size:19
Alignment explanation
Indices: 42494690--42494729 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42494680 ATTTATTTTA
**
42494690 TTAAAAAATTAAAATATTT
1 TTAAAAAAAAAAAATATTT
42494709 TTAAAAAAAAAAAGATATTT
1 TTAAAAAAAAAAA-ATATTT
42494729 T
1 T
42494730 CTTTCACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAAAAAAAAAATATTT
Found at i:42501454 original size:53 final size:53
Alignment explanation
Indices: 42501344--42501478 Score: 141
Period size: 53 Copynumber: 2.6 Consensus size: 53
42501334 TCAGGGTTGA
* * * *
42501344 CAAGTTCAAGTACCGAATCAGTCAAAAAAAAGTACCAAATTAGGAAAAAAGAGT
1 CAAGTTCAAGTACCAAATCAGACAAAAAAAAGGACCAAATTA-GAAAAAAGACT
* * ** *
42501398 CAAGTTTAAGTACCAAATTAGACTAAAAAAAAGGGTCAAATTA-AAAAAAGTCT
1 CAAGTTCAAGTACCAAATCAGAC-AAAAAAAAGGACCAAATTAGAAAAAAGACT
*
42501451 CAAGTTCAAGTACTAAATCA-A-AAAAAAA
1 CAAGTTCAAGTACCAAATCAGACAAAAAAA
42501479 GTGTCAAGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
50 7 0.10
52 1 0.01
53 25 0.37
54 19 0.28
55 16 0.24
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (53 bp):
CAAGTTCAAGTACCAAATCAGACAAAAAAAAGGACCAAATTAGAAAAAAGACT
Found at i:42501736 original size:24 final size:24
Alignment explanation
Indices: 42501704--42501752 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42501694 GATGATATGA
42501704 ATGAAACATTAGTTTCCTAAATTG
1 ATGAAACATTAGTTTCCTAAATTG
42501728 ATGAAACATTAGTTTCCTAAATTG
1 ATGAAACATTAGTTTCCTAAATTG
42501752 A
1 A
42501753 GCCTACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (24 bp):
ATGAAACATTAGTTTCCTAAATTG
Found at i:42506842 original size:49 final size:47
Alignment explanation
Indices: 42506727--42506820 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
42506717 AGGTGGAGTG
*
42506727 ATAATAAATTTGTATTTTAATATAATTGAACACACACATGATCTTTA
1 ATAATAATTTTGTATTTTAATATAATTGAACACACACATGATCTTTA
42506774 ATAATAATTTTGTATTTTAATATAATTGAACACACACATGATCTTTA
1 ATAATAATTTTGTATTTTAATATAATTGAACACACACATGATCTTTA
42506821 TATCTATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (47 bp):
ATAATAATTTTGTATTTTAATATAATTGAACACACACATGATCTTTA
Found at i:42507349 original size:26 final size:25
Alignment explanation
Indices: 42507311--42507370 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
42507301 GATCCAAAAC
* *
42507311 CTTAAACCTTGAACCCTGGACCCGAA
1 CTTAAACCATGAA-CCTGAACCCGAA
*
42507337 CTTAAACCATGAACCTGAACCCTAA
1 CTTAAACCATGAACCTGAACCCGAA
42507362 CTTCAAACC
1 CTT-AAACC
42507371 CTAAACATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (25 bp):
CTTAAACCATGAACCTGAACCCGAA
Found at i:42508595 original size:58 final size:58
Alignment explanation
Indices: 42508474--42508599 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
42508464 GGGACCCTCT
* * * * * *
42508474 GTGAACCTTTTGGGCTCTCAACGGAGGTAAGGCATATCTTCAATATCTTGGCCCTTTA
1 GTGAACCCTTTGGGATCTCAACGAAGGTAAGACATATCTTCAATATCTTAGACCTTTA
* ** * *
42508532 ATGAACCCTTTGGGATCTCAGTGAAGGTGAGACATATCTTCAATAT-TTAGACCTCTTC
1 GTGAACCCTTTGGGATCTCAACGAAGGTAAGACATATCTTCAATATCTTAGACCT-TTA
42508590 GTGAACCCTT
1 GTGAACCCTT
42508600 CGATCACTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 6 0.11
58 49 0.89
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (58 bp):
GTGAACCCTTTGGGATCTCAACGAAGGTAAGACATATCTTCAATATCTTAGACCTTTA
Found at i:42511880 original size:16 final size:17
Alignment explanation
Indices: 42511859--42511896 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42511849 ATTAAGATTT
* *
42511859 TTACTTTCTT-CTTTAC
1 TTACTTGCTTGCTTAAC
42511875 TTACTTGCTTGCTTAAC
1 TTACTTGCTTGCTTAAC
42511892 TTACT
1 TTACT
42511897 CATTCGTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (17 bp):
TTACTTGCTTGCTTAAC
Found at i:42512218 original size:50 final size:50
Alignment explanation
Indices: 42512125--42512270 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
42512115 TTTCCTGTAC
* * * * * **
42512125 TGCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* * * * *
42512175 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* *
42512225 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGATCTCTCATA
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACCTCTCATA
42512271 GTCTCAATGA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:42517456 original size:112 final size:104
Alignment explanation
Indices: 42517308--42517605 Score: 296
Period size: 112 Copynumber: 2.8 Consensus size: 104
42517298 AAATTTTTTT
42517308 TTTTACATTTTGGGCTATCATTGGCCAACACCAGTATACGAAAAAATTCAAAAGAAATTTATTTT
1 TTTTACATTTTGGGCTATCATTGGCCAACACCAGTATACGAAAAAATT------AAATTT-TTTT
*
42517373 TTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATATATAAAAAA
59 TT-GTGGTGGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAA
* * * *
42517420 TTTTACATTTTGGGCTCTCATTTGCCGGA-ACCAGTATACGAAAAAATTTAATTTTTTTTTGTGG
1 TTTTACATTTTGGGCTATCATTGGCC-AACACCAGTATACGAAAAAATTAAATTTTTTTTTGTGG
* ****
42517484 TGGCCTGGCAATGGCCGGCACCACCTTTATGTA-AATTTTT
65 TGGCCTGGCAATGGCCGGCACCACCTTTATATATAA-AAAA
* * ** * *
42517524 TTTATATATTTTGGGCTGTCATTGGCTGGA-ACTAGTATATGAAAAAATTTTAAATTTTTTTTTG
1 TTT-TACATTTTGGGCTATCATTGGC-CAACACCAGTATACGAAAAAA--TTAAATTTTTTTTTG
42517588 CTGGTGGCCTGGCAATGG
62 -TGGTGGCCTGGCAATGG
42517606 TCAACACCGC
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
103 2 0.01
104 38 0.23
105 42 0.26
106 5 0.03
107 14 0.09
108 17 0.10
112 43 0.27
113 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (104 bp):
TTTTACATTTTGGGCTATCATTGGCCAACACCAGTATACGAAAAAATTAAATTTTTTTTTGTGGT
GGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAA
Found at i:42517485 original size:104 final size:104
Alignment explanation
Indices: 42517274--42517605 Score: 326
Period size: 105 Copynumber: 3.1 Consensus size: 104
42517264 GCTGGCCTAT
* **** *
42517274 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTACATTTTGGGCTATCATTGGCC-AACA
1 CAATGGCCGGCACCACCTTTATATAAA--TAAAATTTTACATTTTGGGCTATCATTGGCCGGA-A
*
42517338 CCAGTATACGAAAAAATTCAAAAGAAATTTATTTTTTGGTGGTGGCCTGG
63 CCAGTATACGAAAAAATT------TAATTT-TTTTTT-GTGGTGGCCTGG
* * *
42517388 CAATGGCTGGCACCACCTTTATATATAA-AAAATTTTACATTTTGGGCTCTCATTTGCCGGAACC
1 CAATGGCCGGCACCACCTTTATATA-AATAAAATTTTACATTTTGGGCTATCATTGGCCGGAACC
42517452 AGTATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
65 AGTATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
* **** * * * *
42517492 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATATATTTTGGGCTGTCATTGGCTGGAACT
1 CAATGGCCGGCACCACCTTTATATAAATAAAATTT-TACATTTTGGGCTATCATTGGCCGGAACC
*
42517557 AGTATATGAAAAAATTTTAAATTTTTTTTTGCTGGTGGCCTGG
65 AGTATACGAAAAAA-TTT-AATTTTTTTTTG-TGGTGGCCTGG
42517600 CAATGG
1 CAATGG
42517606 TCAACACCGC
Statistics
Matches: 189, Mismatches: 22, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
103 2 0.01
104 38 0.20
105 43 0.23
106 8 0.04
107 12 0.06
108 17 0.09
112 43 0.23
113 1 0.01
114 23 0.12
115 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (104 bp):
CAATGGCCGGCACCACCTTTATATAAATAAAATTTTACATTTTGGGCTATCATTGGCCGGAACCA
GTATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
Found at i:42517571 original size:105 final size:103
Alignment explanation
Indices: 42517274--42517797 Score: 395
Period size: 108 Copynumber: 4.8 Consensus size: 103
42517264 GCTGGCCTAT
**
42517274 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTACATTTTGGGCTATCATTGGCCAACAC
1 CAATGGCCGGCACCACCTTTATGTAAA--TTTTTTTTTACATTTTGGGCTATCATTGGCGGA-AC
*
42517339 CAGTATACGAAAAAATTCAAAAGAAATTTATTTTTTGGTGGTGGCCTGG
63 CAGTATACGAAAAAATT------TAATTT-TTTTTT-GTGGTGGCCTGG
* * **** * *
42517388 CAATGGCTGGCACCACCTTTATATATAA-AAAATTTTACATTTTGGGCTCTCATTTGCCGGAACC
1 CAATGGCCGGCACCACCTTTATGTA-AATTTTTTTTTACATTTTGGGCTATCA-TTGGCGGAACC
42517452 AGTATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
64 AGTATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
* * *
42517492 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTATATATTTTGGGCTGTCATTGGCTGGAACT
1 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTT-TACATTTTGGGCTATCATTGGC-GGAACC
*
42517557 AGTATATGAAAAAATTTTAAATTTTTTTTTGCTGGTGGCCTGG
64 AGTATACGAAAAAA-TTT-AATTTTTTTTTG-TGGTGGCCTGG
* ** * * *
42517600 CAATGGTCAACACCGCCTTTATGTAAAAAAGAGAAATTTTTTTTTTACATTTT-GGCTGTTATTG
1 CAATGGCCGGCACCACCTTTATGT---------AAA-TTTTTTTTTACATTTTGGGCTATCATTG
* * *** * * *
42517664 GCCGGCACCAGTATACGAAAAAATTCAAAAAAAAATTTTTGGTAGTGACCTGG
56 G-CGGAACCAGTATACGAAAAAATT----TAATTTTTTTTTGTGGTGGCCTGG
* * * * * *
42517717 CAATGACCGGCACCACGTTTATGTAATTTTTTTTTTACATTTTGGGTTGTCATTGGCCGACACCA
1 CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTACATTTTGGGCTATCATTGGCGGA-ACCA
**
42517782 GTATATAAAAAAATTT
65 GTATACGAAAAAATTT
42517798 TAAAAAAAAT
Statistics
Matches: 333, Mismatches: 52, Indels: 60
0.75 0.12 0.13
Matches are distributed among these distances:
103 2 0.01
104 42 0.13
105 39 0.12
106 8 0.02
107 30 0.09
108 60 0.18
112 38 0.11
113 5 0.02
114 23 0.07
115 4 0.01
116 28 0.08
117 38 0.11
118 16 0.05
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (103 bp):
CAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTACATTTTGGGCTATCATTGGCGGAACCAG
TATACGAAAAAATTTAATTTTTTTTTGTGGTGGCCTGG
Done.