Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 95 of 214
Found at i:27399027 original size:27 final size:27
Alignment explanation
Indices: 27398987--27399042 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
27398977 CAGTAACAGA
* *
27398987 ACAGAACAATGTGGGCTTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
27399014 ACAGAACAAGGTGGGCCTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
27399041 AC
1 AC
27399043 CACATCAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (27 bp):
ACAGAACAAGGTGGGCCTTAGCCCAAT
Found at i:27399628 original size:27 final size:27
Alignment explanation
Indices: 27399534--27399632 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
27399524 TCCAAACTGA
* * * *
27399534 GGGTATTTTGATAATTTTGCAATTCAG
1 GGGTACTTTGGTAATTTTACAAATCAG
*
27399561 GGGTACTTTGGTAATTTTTCAAATCAG
1 GGGTACTTTGGTAATTTTACAAATCAG
* *
27399588 GGGTACTTCGGTAATTTTACAAGTC-G
1 GGGTACTTTGGTAATTTTACAAATCAG
* *
27399614 AGGGTATTTTAGTAATTTT
1 -GGGTACTTTGGTAATTTT
27399633 GTAAACCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 60 0.98
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.42
Consensus pattern (27 bp):
GGGTACTTTGGTAATTTTACAAATCAG
Found at i:27399664 original size:26 final size:27
Alignment explanation
Indices: 27399616--27399700 Score: 122
Period size: 26 Copynumber: 3.2 Consensus size: 27
27399606 ACAAGTCGAG
27399616 GGTATTTTAGTAATTTTGTAAACCAAA
1 GGTATTTTAGTAATTTTGTAAACCAAA
27399643 GGTATTTTAGT-ATTTTGTAAACC-AA
1 GGTATTTTAGTAATTTTGTAAACCAAA
* *
27399668 GAGTATTTCAGTAATTTTTTAAACCAAA
1 G-GTATTTTAGTAATTTTGTAAACCAAA
27399696 -GTATT
1 GGTATT
27399701 CTAAATAGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
25 3 0.06
26 26 0.49
27 22 0.42
28 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTGTAAACCAAA
Found at i:27402953 original size:23 final size:23
Alignment explanation
Indices: 27402918--27402963 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
27402908 AACTTGATTT
* *
27402918 TGCCTCAATGGCATCACAAAATA
1 TGCCACAAAGGCATCACAAAATA
27402941 TGCCACAAAGGCATCACAAAATA
1 TGCCACAAAGGCATCACAAAATA
27402964 CACCACGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (23 bp):
TGCCACAAAGGCATCACAAAATA
Found at i:27409049 original size:13 final size:14
Alignment explanation
Indices: 27409026--27409054 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27409016 GTTCTCACAC
27409026 TCATCTTCTTTTTT
1 TCATCTTCTTTTTT
27409040 TCAT-TTCTTTTTT
1 TCATCTTCTTTTTT
27409053 TC
1 TC
27409055 GTCTCTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (14 bp):
TCATCTTCTTTTTT
Found at i:27409050 original size:36 final size:36
Alignment explanation
Indices: 27408924--27409038 Score: 205
Period size: 36 Copynumber: 3.2 Consensus size: 36
27408914 CTTCTTTCGT
* *
27408924 TTCTTTTTCAATTTTCTTTTTGTTCTCACACTCGTC
1 TTCTTTTTCAATTTTCTTTTCGTTCTCACACTCATC
27408960 TTC-TTTTCAATTTTCTTTTCGTTCTCACACTCATC
1 TTCTTTTTCAATTTTCTTTTCGTTCTCACACTCATC
27408995 TTCTTTTTCAATTTTCTTTTCGTTCTCACACTCATC
1 TTCTTTTTCAATTTTCTTTTCGTTCTCACACTCATC
27409031 TTCTTTTT
1 TTCTTTTT
27409039 TTCATTTCTT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 33 0.43
36 43 0.57
ACGTcount: A:0.12, C:0.26, G:0.03, T:0.58
Consensus pattern (36 bp):
TTCTTTTTCAATTTTCTTTTCGTTCTCACACTCATC
Found at i:27410231 original size:18 final size:18
Alignment explanation
Indices: 27410197--27410239 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27410187 TAATGCCAAA
*
27410197 TGATGTGATCCGGCTCGG
1 TGATGTGATCCGACTCGG
*
27410215 TGATGTGAGT-CGACTCGT
1 TGATGTGA-TCCGACTCGG
27410233 TGATGTG
1 TGATGTG
27410240 CCCGATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.14, C:0.16, G:0.37, T:0.33
Consensus pattern (18 bp):
TGATGTGATCCGACTCGG
Found at i:27411502 original size:20 final size:20
Alignment explanation
Indices: 27411477--27411520 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
27411467 TTAAACGAGC
*
27411477 TGAATTAAGCCCATGTGAGT
1 TGAATTAAACCCATGTGAGT
*
27411497 TGAATTAAACTCATGTGAGT
1 TGAATTAAACCCATGTGAGT
27411517 TGAA
1 TGAA
27411521 CTGAGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
TGAATTAAACCCATGTGAGT
Found at i:27418683 original size:40 final size:40
Alignment explanation
Indices: 27418652--27418888 Score: 143
Period size: 40 Copynumber: 5.9 Consensus size: 40
27418642 TGTACATTAT
* *
27418652 TGCCCCTGTTTGTACTTCGCTACCCCTAAATGCACATGCA
1 TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACATGCA
* * * * *
27418692 TGCTCCTATTTGTACTTTGGTACCCCTAAATGAACATACG
1 TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACATGCA
* * * * * *
27418732 TGCTCCTATTTGTACTTCAG-TACCCTTGAATGCACATACG
1 TGCCCCTATTTGTACTTC-GCTACCCCTAAATGAACATGCA
*** * * * * **
27418772 TGCTTTTGTTTGTACTTTGGTACCCCTGAATGAACATAAA
1 TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACATGCA
* * * * * * * *
27418812 TGCTCCTGTTTATACTTCGGTACCCTTGAATGCATATGCA
1 TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACATGCA
* * * * *
27418852 TGCTCCTATTTGTACTTTGGTACCCCTGAATGCACAT
1 TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACAT
27418889 TCGTGCTTTA
Statistics
Matches: 162, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
39 1 0.01
40 160 0.99
41 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (40 bp):
TGCCCCTATTTGTACTTCGCTACCCCTAAATGAACATGCA
Found at i:27418784 original size:80 final size:79
Alignment explanation
Indices: 27418660--27418895 Score: 310
Period size: 80 Copynumber: 2.9 Consensus size: 79
27418650 ATTGCCCCTG
* * *
27418660 TTTGTACTTCGCTACCCCTAAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTAAATGA
1 TTTGTACTTCG-TACCCTTGAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGA
27418725 ACATACGTGCTCCTA
65 ACATACGTGCTCCTA
* * ** *
27418740 TTTGTACTTCAGTACCCTTGAATGCACATACGTGCTTTTGTTTGTACTTTGGTACCCCTGAATGA
1 TTTGTACTTC-GTACCCTTGAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGA
** *
27418805 ACATAAATGCTCCTG
65 ACATACGTGCTCCTA
* * *
27418820 TTTATACTTCGGTACCCTTGAATGCATATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGC
1 TTTGTACTTC-GTACCCTTGAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGA
*
27418885 ACATTCGTGCT
65 ACATACGTGCT
27418896 TTAAATGAAC
Statistics
Matches: 132, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
80 131 0.99
81 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (79 bp):
TTTGTACTTCGTACCCTTGAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGAA
CATACGTGCTCCTA
Found at i:27418875 original size:120 final size:120
Alignment explanation
Indices: 27418658--27418897 Score: 309
Period size: 120 Copynumber: 2.0 Consensus size: 120
27418648 TTATTGCCCC
* ** * *
27418658 TGTTTGTACTTCGCTACCCCTAAATGCACATGCATGCTCCTATTTGTACTTTGGTACCCCTAAAT
1 TGTTTGTACTTCGCTACCCCTAAATGAACATAAATGCTCCTATTTATACTTCGGTACCCCTAAAT
* *
27418723 GAACATACGTGCTCCTATTTGTACTTCAGTACCCTTGAATGCACATACGTGCTTT
66 GAACATACATGCTCCTATTTGTACTTCAGTACCCCTGAATGCACATACGTGCTTT
* * * * * *
27418778 TGTTTGTACTTTGGTACCCCTGAATGAACATAAATGCTCCTGTTTATACTTCGGTACCCTTGAAT
1 TGTTTGTACTTCGCTACCCCTAAATGAACATAAATGCTCCTATTTATACTTCGGTACCCCTAAAT
* * * ** *
27418843 GCATATGCATGCTCCTATTTGTACTTTGGTACCCCTGAATGCACATTCGTGCTTT
66 GAACATACATGCTCCTATTTGTACTTCAGTACCCCTGAATGCACATACGTGCTTT
27418898 AAATGAACTT
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (120 bp):
TGTTTGTACTTCGCTACCCCTAAATGAACATAAATGCTCCTATTTATACTTCGGTACCCCTAAAT
GAACATACATGCTCCTATTTGTACTTCAGTACCCCTGAATGCACATACGTGCTTT
Found at i:27434373 original size:6 final size:6
Alignment explanation
Indices: 27434358--27434390 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
27434348 AAGCATCTAT
*
27434358 GAAAAA GAAAAG GAAAAG GAAAAG GAAAAG GAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAA
27434391 CACTTTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:27447737 original size:78 final size:78
Alignment explanation
Indices: 27447629--27447794 Score: 260
Period size: 78 Copynumber: 2.1 Consensus size: 78
27447619 TGCTTAATTC
** * *
27447629 TAAATTTAGTCCCGAATTCAAGACTAATTTTAATACTCGTATTTAACCTCAAATTTTTATACTAA
1 TAAATTTAGTCCCGAAACCAAGACTAATTTTAATACCCATATTTAACCTCAAATTTTTATACTAA
27447694 TTTTACTCTAAGA
66 TTTTACTCTAAGA
* * *
27447707 TAAATTTAGTCCCTAAACCAATACTGATTTTAATACCCATATTTAACCTCAAATTTTTATACTAA
1 TAAATTTAGTCCCGAAACCAAGACTAATTTTAATACCCATATTTAACCTCAAATTTTTATACTAA
*
27447772 TTTTACTCTAAGC
66 TTTTACTCTAAGA
27447785 TAAATTTAGT
1 TAAATTTAGT
27447795 TCTCTATTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.41
Consensus pattern (78 bp):
TAAATTTAGTCCCGAAACCAAGACTAATTTTAATACCCATATTTAACCTCAAATTTTTATACTAA
TTTTACTCTAAGA
Found at i:27448129 original size:14 final size:14
Alignment explanation
Indices: 27448106--27448135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27448096 CGTCGGTCTC
27448106 TTCTTGTTCTTTCT
1 TTCTTGTTCTTTCT
*
27448120 TTCTTTTTCTTTCT
1 TTCTTGTTCTTTCT
27448134 TT
1 TT
27448136 TAATTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (14 bp):
TTCTTGTTCTTTCT
Found at i:27451461 original size:25 final size:25
Alignment explanation
Indices: 27451432--27451502 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
27451422 CCTCTCTAGA
** *
27451432 GCCATATAACGGGAAGCTCATGTGT
1 GCCATATAACGGGAAGCTCATCCGG
* * *
27451457 GCCATGTAACGAGAAGCTTATCCGG
1 GCCATATAACGGGAAGCTCATCCGG
* *
27451482 GCTATATAACAGGAAGCTCAT
1 GCCATATAACGGGAAGCTCAT
27451503 AAGAGCCATA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (25 bp):
GCCATATAACGGGAAGCTCATCCGG
Found at i:27451521 original size:24 final size:25
Alignment explanation
Indices: 27451492--27451539 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
27451482 GCTATATAAC
27451492 AGGAAGCTCATAAGAGCC-ATAATT
1 AGGAAGCTCATAAGAGCCAATAATT
*
27451516 AGGAAGCTCATACGAGCCAATAAT
1 AGGAAGCTCATAAGAGCCAATAAT
27451540 GGGTAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (25 bp):
AGGAAGCTCATAAGAGCCAATAATT
Found at i:27451665 original size:26 final size:26
Alignment explanation
Indices: 27451632--27451682 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
27451622 CAGAGAAACA
*
27451632 TTAATCAGGAAGCTCAGAAAGAGCCT
1 TTAATCAGGAAGCTCACAAAGAGCCT
*
27451658 TTAATCAGGAAGCTCACTAAGAGCC
1 TTAATCAGGAAGCTCACAAAGAGCC
27451683 ATATATCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAGCCT
Found at i:27456604 original size:50 final size:50
Alignment explanation
Indices: 27456498--27456606 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
27456488 ATGTCTCACA
* ** *
27456498 TAAGACCATGCCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGCCTGGGACATGGCGTGGGCACCGAGATGAGAACTCCCACG
* * * *
27456548 TGAGACCATGTCTGGGACATGG-GATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGCCTGGGACATGGCG-TGGGCACCGAGATGAGAACTCCCACG
27456598 TAAGACCAT
1 TAAGACCAT
27456607 ATTTGGGATG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (50 bp):
TAAGACCATGCCTGGGACATGGCGTGGGCACCGAGATGAGAACTCCCACG
Found at i:27458503 original size:17 final size:17
Alignment explanation
Indices: 27458481--27458513 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27458471 GTTAGTGCAC
*
27458481 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
27458498 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
27458514 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:27459497 original size:17 final size:16
Alignment explanation
Indices: 27459477--27459510 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27459467 CGATTCAGCC
27459477 CAAAATTCATAATTTTG
1 CAAAATT-ATAATTTTG
*
27459494 CAAAATTGTAATTTTG
1 CAAAATTATAATTTTG
27459510 C
1 C
27459511 CACTACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (16 bp):
CAAAATTATAATTTTG
Found at i:27460050 original size:20 final size:20
Alignment explanation
Indices: 27460019--27460073 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
27460009 TCCATTCCAA
*
27460019 TCCATGTCACATATTGCATT
1 TCCATTTCACATATTGCATT
* *
27460039 TCCATTTTACATATTGTATT
1 TCCATTTCACATATTGCATT
27460059 TCCATTTCACATATT
1 TCCATTTCACATATT
27460074 TAAATTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (20 bp):
TCCATTTCACATATTGCATT
Found at i:27460421 original size:16 final size:16
Alignment explanation
Indices: 27460400--27460451 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
27460390 CCAATCTCAT
27460400 ATATATACATTATCAC
1 ATATATACATTATCAC
* *
27460416 ATATATTCAAT-TCA-
1 ATATATACATTATCAC
27460430 ATAT-TCACATTATCAC
1 ATATAT-ACATTATCAC
27460446 ATATAT
1 ATATAT
27460452 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.04
14 7 0.25
15 6 0.21
16 13 0.46
17 1 0.04
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATACATTATCAC
Found at i:27463807 original size:25 final size:25
Alignment explanation
Indices: 27463768--27463837 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
27463758 ACATTTCACC
* *
27463768 CACAACTCGTGAGAGTATACCAATT
1 CACAGCTCGTGAGAGCATACCAATT
* *
27463793 TACAGCTCGTGAGAGCATACCGATT
1 CACAGCTCGTGAGAGCATACCAATT
* *
27463818 CACAGCTCATGTGAGCATAC
1 CACAGCTCGTGAGAGCATAC
27463838 AGGTACATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (25 bp):
CACAGCTCGTGAGAGCATACCAATT
Found at i:27471336 original size:15 final size:15
Alignment explanation
Indices: 27471316--27471352 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
27471306 AGAGACACGG
27471316 GTGTGTGTCTCAGCC
1 GTGTGTGTCTCAGCC
27471331 GTGTGTGTCTCAGCC
1 GTGTGTGTCTCAGCC
27471346 GTGTGTG
1 GTGTGTG
27471353 ACACACAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.22, G:0.38, T:0.35
Consensus pattern (15 bp):
GTGTGTGTCTCAGCC
Found at i:27482051 original size:45 final size:44
Alignment explanation
Indices: 27481987--27482175 Score: 186
Period size: 45 Copynumber: 4.2 Consensus size: 44
27481977 CTACTACGTG
* *
27481987 CACCGGGTAGCATTGATTATAATGGTGGTTGTTGTATGCTGATTC
1 CACCGGGTATCATTGATTATAA-GGTGGTTGTTGTGTGCTGATTC
* *
27482032 CACCGGGTATCATTGATTATAAAGGTGGTTATTGTGTGTTGATTC
1 CACCGGGTATCATTGATTAT-AAGGTGGTTGTTGTGTGCTGATTC
* * * * *
27482077 CACCGGGTACCATTGATTATGAAGGTGGCTT-CTATGTCCTGGTTC
1 CACCGGGTATCATTGATTAT-AAGGTGG-TTGTTGTGTGCTGATTC
** * *
27482122 CACCTAGTATCATTGACTATAAGGGTGG-TGCTGTGTGCTGA-TC
1 CACCGGGTATCATTGATTATAA-GGTGGTTGTTGTGTGCTGATTC
*
27482165 CACCGTGTATC
1 CACCGGGTATC
27482176 TGTTATTATT
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
43 12 0.10
44 10 0.08
45 94 0.78
46 4 0.03
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.35
Consensus pattern (44 bp):
CACCGGGTATCATTGATTATAAGGTGGTTGTTGTGTGCTGATTC
Found at i:27482143 original size:90 final size:89
Alignment explanation
Indices: 27481987--27482150 Score: 206
Period size: 90 Copynumber: 1.8 Consensus size: 89
27481977 CTACTACGTG
* * * * *
27481987 CACCGGGTAGCATTGATTATAATGGTGGTTGTTGTATGCTGATTCCACCGGGTATCATTGATTAT
1 CACCGGGTACCATTGATTATAATGGTGGTTCTTG-ATCCTGATTCCACCGAGTATCATTGACTAT
27482052 AAAGGTGGTTATTGTGTGTTGATTC
65 AAAGGTGGTTATTGTGTGTTGATTC
* *
27482077 CACCGGGTACCATTGATTATGAA-GGTGGCTTCTATG-TCCTGGTTCCACCTAGTATCATTGACT
1 CACCGGGTACCATTGATTAT-AATGGTGG-TTCT-TGATCCTGATTCCACCGAGTATCATTGACT
*
27482140 ATAAGGGTGGT
63 ATAAAGGTGGT
27482151 GCTGTGTGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
90 56 0.89
91 5 0.08
92 2 0.03
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (89 bp):
CACCGGGTACCATTGATTATAATGGTGGTTCTTGATCCTGATTCCACCGAGTATCATTGACTATA
AAGGTGGTTATTGTGTGTTGATTC
Found at i:27484728 original size:76 final size:76
Alignment explanation
Indices: 27484633--27484832 Score: 194
Period size: 78 Copynumber: 2.6 Consensus size: 76
27484623 GAAATTAGGG
* * *
27484633 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
27484696 TATGTAA-TTATAT
64 TATG-AATTTATAT
* * * * * * *
27484709 ATGTATATGATAGACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAGA
1 ATGTATATGATAGATTCG-A-ATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGA
27484774 TATGAATTTATAT
64 TATGAATTTATAT
* *
27484787 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
27484833 TTATATTGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
76 36 0.36
77 10 0.10
78 54 0.54
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:27485286 original size:41 final size:41
Alignment explanation
Indices: 27485224--27485417 Score: 316
Period size: 41 Copynumber: 4.7 Consensus size: 41
27485214 TAGGCTTAGC
27485224 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* * *
27485265 GCTTAGCAAGCTAAGTACCGGTGATCTGAATCAGGCTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG-TTATAA
* * *
27485307 GCCTAGCAGGCTAAGTGCCAGTGAACTGAATTAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
27485348 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
27485389 GCCTAGCAGGCTAAGTGCCGGTGAATCTG
1 GCCTAGCAGGCTAAGTGCCGGTG-ATCTG
27485418 TTTAAACTAA
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
41 99 0.71
42 40 0.29
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
Found at i:27485363 original size:83 final size:82
Alignment explanation
Indices: 27485224--27485413 Score: 317
Period size: 83 Copynumber: 2.3 Consensus size: 82
27485214 TAGGCTTAGC
* *
27485224 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAGCTTAGCAAGCTAAGTACCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAAGCTAAGTACCGGTGA
27485289 TCTGAATCAGGCTTATAA
66 TCTGAATCAGG-TTATAA
* * * *
27485307 GCCTAGCAGGCTAAGTGCCAGTGAACTGAATTAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAAGCTAAGTACCGGTGA
27485372 TCTGAATCAGGTTATAA
66 TCTGAATCAGGTTATAA
27485389 GCCTAGCAGGCTAAGTGCCGGTGAA
1 GCCTAGCAGGCTAAGTGCCGGTGAA
27485414 TCTGTTTAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 30 0.30
83 70 0.70
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAAGCTAAGTACCGGTGA
TCTGAATCAGGTTATAA
Found at i:27485654 original size:34 final size:34
Alignment explanation
Indices: 27485585--27485658 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 34
27485575 TTGTTGGATA
*
27485585 TATATATGTATGCATTCGGCATATGTGGATTATAAG
1 TATATATG-ATGCATTCGGCACATGT-GATTATAAG
27485621 TATATATG-TGCATTCGGCACATGT-ACTTGATAAG
1 TATATATGATGCATTCGGCACATGTGA-TT-ATAAG
27485655 TATA
1 TATA
27485659 AATATATGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 1 0.03
33 2 0.06
34 24 0.69
36 8 0.23
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (34 bp):
TATATATGATGCATTCGGCACATGTGATTATAAG
Found at i:27491247 original size:40 final size:40
Alignment explanation
Indices: 27491157--27491250 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
27491147 CGTTTGGATA
* *
27491157 AAAAATGCCGCTAAAAATCGAGCATTAGCGACGCTTTTCG
1 AAAAATGCCGCTAAAAATCGAACATTAGCGACGCTTATCG
* * *
27491197 AAAAACGCCGCTAAAGATCGAACATTAGCGGCGCGTTAT-G
1 AAAAATGCCGCTAAAAATCGAACATTAGCGACGC-TTATCG
*
27491237 GAAAATGCCGCTAA
1 AAAAATGCCGCTAA
27491251 GAATAAGCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAAATGCCGCTAAAAATCGAACATTAGCGACGCTTATCG
Found at i:27491394 original size:41 final size:41
Alignment explanation
Indices: 27491331--27491622 Score: 225
Period size: 41 Copynumber: 7.1 Consensus size: 41
27491321 CTTTCGGGGT
*
27491331 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTTAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGC
* *
27491372 TTTAGCGGCGTTTTTGGGAAAGCCCCGCTAATGCTTAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGC
* * *
27491413 TTTAGCGGCTTTTTTTGAGAAAGCGGCGCTAATG-TTCAGGGA
1 TTTAGCGGC-GTTTTTGAGAAAGCGCCGCTAATGCTT-AGGGC
* * * * * *
27491455 TTTAGCTGCGTTTTTTATG-AGGCACCGCTAATGCTCAAGGC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTTAGGGC
* * * * ** * * * *
27491496 TTTAGCGGCATTTCCTAAAAAAATGCCACGAATGCTCAAGGC
1 TTTAGCGGCGTTT-TTGAGAAAGCGCCGCTAATGCTTAGGGC
* * * ***
27491538 TTTAGCGGCGTTTTTGTGTAAGCACCGCTAATGCTCT--CTT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT-TAGGGC
* *
27491578 TTTAGCGGCGTTTTCT-AAAAAGCGCCGCTAATGCTTAGGGA
1 TTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTTAGGGC
27491619 TTTA
1 TTTA
27491623 AAATAATTTA
Statistics
Matches: 191, Mismatches: 50, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
39 1 0.01
40 29 0.15
41 97 0.51
42 64 0.34
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGC
Found at i:27491469 original size:83 final size:82
Alignment explanation
Indices: 27491331--27491622 Score: 243
Period size: 83 Copynumber: 3.5 Consensus size: 82
27491321 CTTTCGGGGT
* * *
27491331 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCG-TTTTTGGGAAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGATTTAGCGGCGTTTTTTAGG-AAGC
* * *
27491395 CCCGCTAATGCTTAGGGC
65 ACCGCTAATGCTCAAGGC
* * * * *
27491413 TTTAGCGGCTTTTTTTGAGAAAGCGGCGCTAATG-TTCAGGGATTTAGCTGCGTTTTTTATGAGG
1 TTTAGCGGC-GTTTTTGAGAAAGCGCCGCTAATGCTT-AGGGATTTAGCGGCGTTTTTTAGGAAG
27491477 CACCGCTAATGCTCAAGGC
64 CACCGCTAATGCTCAAGGC
* * * * ** * * * * * *
27491496 TTTAGCGGCATTTCCTAAAAAAATGCCACGAATGCTCAAGGCTTTAGCGGCGTTTTTGT-GTAAG
1 TTTAGCGGCGTTT-TTGAGAAAGCGCCGCTAATGCTTAGGGATTTAGCGGCGTTTTT-TAGGAAG
****
27491560 CACCGCTAATGCTC-TCTT
64 CACCGCTAATGCTCAAGGC
*
27491578 TTTAGCGGCGTTTTCT-AAAAAGCGCCGCTAATGCTTAGGGATTTA
1 TTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTTAGGGATTTA
27491623 AAATAATTTA
Statistics
Matches: 163, Mismatches: 40, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
81 22 0.13
82 27 0.17
83 106 0.65
84 8 0.05
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTAGGGATTTAGCGGCGTTTTTTAGGAAGCA
CCGCTAATGCTCAAGGC
Found at i:27497521 original size:43 final size:44
Alignment explanation
Indices: 27497420--27497724 Score: 369
Period size: 43 Copynumber: 7.1 Consensus size: 44
27497410 AGAACGTACT
* *
27497420 TTTAGCGGCGTTTGT-GATAAAAGCGCC-GCTAAAAATCATG-TC
1 TTTAGCGGCGTTTGTGGGT-AAAGCGCCAGCTAAAGATCATGTTC
* *
27497462 TTTAGTGGCGTTTGTGGGTAAAGC-ACAGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
* * * * * *
27497505 TTTAGTGGCATTTGTGGGCAAAGTGCC-TCTAAAGATCATGTTT
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
*
27497548 TTTAGCGGCGTTTATGGGTAAAGCGCC-GCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
* * **
27497591 TTTAGCGGCGTTT-TTGATAAAAGCGCCAG-TAAATCTCATGTTC
1 TTTAGCGGCGTTTGTGGGT-AAAGCGCCAGCTAAAGATCATGTTC
*
27497634 TTTAGCGGCGTTTGTGGGTAAAGCGCCA-CTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
*
27497677 TTTAGCGGCGTTTGTGGGTAAAGCGTC-GCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
27497720 TTTAG
1 TTTAG
27497725 TGGTGTTTTT
Statistics
Matches: 227, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.00
42 34 0.15
43 187 0.82
44 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGGGTAAAGCGCCAGCTAAAGATCATGTTC
Found at i:27497648 original size:129 final size:128
Alignment explanation
Indices: 27497419--27497734 Score: 413
Period size: 129 Copynumber: 2.5 Consensus size: 128
27497409 AAGAACGTAC
* * * *
27497419 TTTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAAATCATG-TCTTTAGTGGCGTTTGTGGGTA
1 TTTTAGCGGCGTTTGTGGGT-AAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTT-TTGATA
* * *
27497482 AAGCACAGCTAAAGATCATGTTCTTTAGTGGCATTTGTGGGCAAAGTGCCTCTAAAGATCATGTT
64 AAGCACAGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGCAAAGCGCCACTAAAGATCATGTT
* *
27497547 TTTTAGCGGCGTTTATGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTGATAAA
1 TTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTGAT-AA
* ** * * *
27497612 AGCGCCAG-TAAATCTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCGCCACTAAAGGTCATGTT
65 AGC-ACAGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGCAAAGCGCCACTAAAGATCATGTT
* * *
27497676 CTTTAGCGGCGTTTGTGGGTAAAGCGTCGCTAAAGATCATGTTCTTTAGTGGTGTTTTT
1 TTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTT
27497735 TCACATAAAC
Statistics
Matches: 164, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
128 38 0.23
129 123 0.75
130 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (128 bp):
TTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTGATAAA
GCACAGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGCAAAGCGCCACTAAAGATCATGTT
Found at i:27501037 original size:50 final size:50
Alignment explanation
Indices: 27500936--27501030 Score: 118
Period size: 50 Copynumber: 1.9 Consensus size: 50
27500926 ACACCACAGG
**** * *
27500936 TCGTATGAGCTTACCAATTTCTAACTTGTGAGAGCTTATCGATTCTCAGC
1 TCGTATGAGCTTACCAATTTCTAACTCAACAGAGCATACCGATTCTCAGC
* *
27500986 TCGTATGAGCTTACCGATTTCTAGCTCAACAGAGCATACCGATTC
1 TCGTATGAGCTTACCAATTTCTAACTCAACAGAGCATACCGATTC
27501031 ATAGCTCTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (50 bp):
TCGTATGAGCTTACCAATTTCTAACTCAACAGAGCATACCGATTCTCAGC
Found at i:27505071 original size:25 final size:25
Alignment explanation
Indices: 27505024--27505083 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
27505014 CGTTCCGACC
**
27505024 CACAGCTCGTGAGAGCTTACCGATT
1 CACAGCTCGTGAGAGCAGACCGATT
* * *
27505049 TACAGCTCGTGAGGGCAGGCCGATT
1 CACAGCTCGTGAGAGCAGACCGATT
*
27505074 CACAACTCGT
1 CACAGCTCGT
27505084 ATGAGCATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (25 bp):
CACAGCTCGTGAGAGCAGACCGATT
Found at i:27509352 original size:17 final size:17
Alignment explanation
Indices: 27509330--27509384 Score: 110
Period size: 17 Copynumber: 3.2 Consensus size: 17
27509320 GTCTCAACCA
27509330 TGTGAGGCACACGACCG
1 TGTGAGGCACACGACCG
27509347 TGTGAGGCACACGACCG
1 TGTGAGGCACACGACCG
27509364 TGTGAGGCACACGACCG
1 TGTGAGGCACACGACCG
27509381 TGTG
1 TGTG
27509385 TCCCCTACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.15
Consensus pattern (17 bp):
TGTGAGGCACACGACCG
Found at i:27510162 original size:41 final size:38
Alignment explanation
Indices: 27510089--27510171 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
27510079 ATTATTTATT
* * * *
27510089 TATTTATTAGAATATTAAAAAATTATTATTAATTCAAA
1 TATTAATTAGAATAATAAAAAATTAATATTAATTAAAA
27510127 TATTAATTAGAATAATAATAAAATTTAATATTTAATTAAAA
1 TATTAATTAGAATAATAA-AAAA-TTAATA-TTAATTAAAA
27510168 TATT
1 TATT
27510172 TTATCCAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 16 0.42
39 4 0.11
40 5 0.13
41 13 0.34
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (38 bp):
TATTAATTAGAATAATAAAAAATTAATATTAATTAAAA
Found at i:27516779 original size:25 final size:25
Alignment explanation
Indices: 27516745--27516795 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
27516735 TTGTTTATTC
27516745 ATCCCTTTGTAATCCCGATCAAGTG
1 ATCCCTTTGTAATCCCGATCAAGTG
*
27516770 ATCCCTTTGTAATCTCGATCAAGTG
1 ATCCCTTTGTAATCCCGATCAAGTG
27516795 A
1 A
27516796 GTTCCATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (25 bp):
ATCCCTTTGTAATCCCGATCAAGTG
Found at i:27517672 original size:18 final size:19
Alignment explanation
Indices: 27517659--27517694 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27517649 TATTGAAAGT
27517659 GAAAA-AAAATTTGAAAAA
1 GAAAAGAAAATTTGAAAAA
*
27517677 GAAAAGAAAATTGGAAAA
1 GAAAAGAAAATTTGAAAA
27517695 GAGATTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (19 bp):
GAAAAGAAAATTTGAAAAA
Found at i:27530780 original size:8 final size:8
Alignment explanation
Indices: 27530769--27530793 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27530759 TTAAAAAAAA
27530769 TTAAAATT
1 TTAAAATT
27530777 TTAAAATT
1 TTAAAATT
27530785 TTAAAATT
1 TTAAAATT
27530793 T
1 T
27530794 CCCAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:27531910 original size:21 final size:21
Alignment explanation
Indices: 27531881--27531930 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
27531871 TAGAATAATT
27531881 TTTTATATTTTTGGAA-TTATAA
1 TTTT-TATTTTT-GAATTTATAA
* *
27531903 TTTTTATTTTTTAATTTTTAA
1 TTTTTATTTTTGAATTTATAA
27531924 TTTTTAT
1 TTTTTAT
27531931 AATATTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTTGAATTTATAA
Found at i:27531915 original size:7 final size:7
Alignment explanation
Indices: 27531900--27531929 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
27531890 TTTGGAATTA
27531900 TAATTTT
1 TAATTTT
*
27531907 TATTTTT
1 TAATTTT
27531914 TAATTTT
1 TAATTTT
27531921 TAATTTT
1 TAATTTT
27531928 TA
1 TA
27531930 TAATATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TAATTTT
Found at i:27532290 original size:17 final size:17
Alignment explanation
Indices: 27532268--27532315 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
27532258 AACTATTACC
27532268 TAATATTATAATAT-AAA
1 TAATA-TATAATATCAAA
*
27532285 TAATATATAATTTCAAA
1 TAATATATAATATCAAA
*
27532302 TAATTACATAATAT
1 TAA-TATATAATAT
27532316 GTTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 11 0.42
18 8 0.31
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATATAATATCAAA
Found at i:27532710 original size:3 final size:3
Alignment explanation
Indices: 27532702--27532740 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27532692 GCCCTTTTGT
27532702 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27532741 AATTGGTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27536527 original size:23 final size:23
Alignment explanation
Indices: 27536498--27536619 Score: 185
Period size: 23 Copynumber: 5.3 Consensus size: 23
27536488 ATAAGTGCCA
*
27536498 CACTGATATGTAGCCGGAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27536521 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27536544 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
27536567 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
27536590 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
27536613 CACTGAT
1 CACTGAT
27536620 CAATAACATT
Statistics
Matches: 91, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.02
23 88 0.97
24 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:27536565 original size:46 final size:46
Alignment explanation
Indices: 27536498--27536619 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
27536488 ATAAGTGCCA
* * *
27536498 CACTGATATGTAGCCGGAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
27536544 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
*
27536590 CACTGAATTGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
27536620 CAATAACATT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
Found at i:27536863 original size:18 final size:17
Alignment explanation
Indices: 27536837--27536875 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
27536827 ATTTTCCTTC
27536837 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
27536854 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
27536872 CACA
1 CACA
27536876 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:27539562 original size:26 final size:26
Alignment explanation
Indices: 27539533--27539589 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
27539523 CTATTTTTTT
* * *
27539533 AATAAATACCAAAAATTTATTTTAAA
1 AATAAAAACAAAAAAATTATTTTAAA
*
27539559 AATAAAAAATAAAAAAATTATTTTAAA
1 AAT-AAAAACAAAAAAATTATTTTAAA
27539586 AATA
1 AATA
27539590 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAAAAACAAAAAAATTATTTTAAA
Found at i:27542026 original size:51 final size:51
Alignment explanation
Indices: 27541971--27542312 Score: 318
Period size: 51 Copynumber: 6.7 Consensus size: 51
27541961 GTGAAAGTGT
* * *
27541971 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACCTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * ** * * * *
27542022 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* *
27542073 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * ** * * * *
27542124 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* * *
27542175 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACTG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATA-A
* * *
27542225 TGATCACGTGTGTAGTACTATGTGAAGGCTATTATGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * *
27542274 TTGATCACGTGTGTAATACTATGTGAAGGCTCCTACGTG
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
27542313 TATCGAATGA
Statistics
Matches: 232, Mismatches: 53, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
50 81 0.35
51 149 0.64
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
Found at i:27542129 original size:102 final size:102
Alignment explanation
Indices: 27541970--27542318 Score: 492
Period size: 102 Copynumber: 3.4 Consensus size: 102
27541960 AGTGAAAGTG
*
27541970 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACCTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
27542035 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
27542072 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
27542137 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * *
27542174 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA-CTG-TAAA-ACTTGATCACGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATC-GATAAATA-ATGGTCACATGT
* ** * * **
27542236 GTAGTACTATGTGAAGGCTATTATGTGAACCGTA-AA-AA
64 GTAGTACTAAGTGAAGGCTACAATATGTACCG-AGAAGCT
* * * * *
27542274 TTGATCACGTGTGTAATACTATGTGAAGGCTCCTACGTGTATCGA
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
27542319 ATGATAATAG
Statistics
Matches: 226, Mismatches: 16, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
100 38 0.17
101 44 0.19
102 144 0.64
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
Found at i:27543227 original size:5 final size:5
Alignment explanation
Indices: 27543217--27543269 Score: 70
Period size: 5 Copynumber: 10.6 Consensus size: 5
27543207 TGCTTGATGA
* * * *
27543217 AATGG AATGG AATGG AATGG TATGA AATGG AATAG TATGG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
27543267 AAT
1 AAT
27543270 ATATATATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:27544883 original size:18 final size:19
Alignment explanation
Indices: 27544862--27544897 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27544852 GTATACAGAG
*
27544862 GTAATAATAG-TTTGGAAA
1 GTAAAAATAGTTTTGGAAA
27544880 GTAAAAATAGTTTTGGAA
1 GTAAAAATAGTTTTGGAA
27544898 GAAAAATTAG
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:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (19 bp):
GTAAAAATAGTTTTGGAAA
Found at i:27545869 original size:54 final size:54
Alignment explanation
Indices: 27545789--27545895 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
27545779 GATAAATTTA
27545789 AAAAAAAAACTAAAGTGATGTTTCCTTTGCAAGTTTGAGAAACATTACATGGTT
1 AAAAAAAAACTAAAGTGATGTTTCCTTTGCAAGTTTGAGAAACATTACATGGTT
27545843 AAAAAAAAACTAAAGTGATGTTTCCTTTGCAAGTTTGAGAAACATTACATGGT
1 AAAAAAAAACTAAAGTGATGTTTCCTTTGCAAGTTTGAGAAACATTACATGGT
27545896 AATCTAAGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (54 bp):
AAAAAAAAACTAAAGTGATGTTTCCTTTGCAAGTTTGAGAAACATTACATGGTT
Found at i:27547006 original size:16 final size:16
Alignment explanation
Indices: 27546985--27547016 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27546975 ACTTTAGGGG
27546985 CAAAAATGTAATTTTT
1 CAAAAATGTAATTTTT
*
27547001 CAAAAATGTGATTTTT
1 CAAAAATGTAATTTTT
27547017 GGACTGGATT
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:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
CAAAAATGTAATTTTT
Found at i:27547293 original size:51 final size:51
Alignment explanation
Indices: 27547237--27547686 Score: 371
Period size: 51 Copynumber: 8.9 Consensus size: 51
27547227 AGTGAAAGTG
* *
27547237 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA
* * * ** * * * *
27547288 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATA
* * *
27547339 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTATTACGTGAATCGATAAATA
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA
* * * ** * * * *
27547390 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATA
* *
27547441 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAT-A
* * * * *
27547493 -TAGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA--TA
* * * *
27547543 TTAGTCACATATGGAGTACTATGTGAAGGCTACTACGT-AA-CTATAAA-A
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA
* * * * *
27547591 CTTGATCACGTGTGTAGTACTGTATGAAGGCTATTACGTGAATCGCA-AAA-A
1 -TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-ATAAATA
* * * * *
27547642 TTGATCACGTGTGTAGTACTATGTGAAGACTACTATGTGTATCGA
1 TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
27547687 ATGATAATAG
Statistics
Matches: 311, Mismatches: 74, Indels: 30
0.75 0.18 0.07
Matches are distributed among these distances:
49 33 0.11
50 49 0.16
51 225 0.72
52 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TTGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA
Found at i:27547396 original size:102 final size:102
Alignment explanation
Indices: 27547237--27547580 Score: 571
Period size: 102 Copynumber: 3.4 Consensus size: 102
27547227 AGTGAAAGTG
*
27547237 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
27547302 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* *
27547339 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTATTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
27547404 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * *
27547441 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATAGTCACATGTGT
1 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
27547506 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * * *
27547543 TTAGTCACATATGGAGTACTATGTGAAGGCTACTACGT
1 TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGT
27547581 AACTATAAAA
Statistics
Matches: 229, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 229 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
TTGGTCACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
Found at i:27548595 original size:5 final size:5
Alignment explanation
Indices: 27548585--27548647 Score: 81
Period size: 5 Copynumber: 12.6 Consensus size: 5
27548575 TGCTTGATGA
* * * *
27548585 AATGG AATGG AATGG AATGG TATGA AATGG AATAG TATGG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
*
27548635 TATGG AATGG AAT
1 AATGG AATGG AAT
27548648 ATATATATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:27548613 original size:15 final size:15
Alignment explanation
Indices: 27548585--27548647 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
27548575 TGCTTGATGA
*
27548585 AATGGAATGGAATGG
1 AATGGTATGGAATGG
*
27548600 AATGGTATGAAATGG
1 AATGGTATGGAATGG
*
27548615 AATAGTATGGAATGG
1 AATGGTATGGAATGG
27548630 AATGGTATGGAATGG
1 AATGGTATGGAATGG
27548645 AAT
1 AAT
27548648 ATATATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (15 bp):
AATGGTATGGAATGG
Found at i:27552207 original size:25 final size:25
Alignment explanation
Indices: 27552166--27552237 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 25
27552156 TCCTATACAT
** *
27552166 GTATGCTCACATGAGCTGTGAATTG
1 GTATGCTCACACAAGCTGTGAATCG
* ** * *
27552191 GTATGCTCGCGTAAGCTATGGATCG
1 GTATGCTCACACAAGCTGTGAATCG
27552216 GTATGCTCACACAAGCTGTGAA
1 GTATGCTCACACAAGCTGTGAA
27552238 AATGGGCCTG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACAAGCTGTGAATCG
Found at i:27558100 original size:34 final size:34
Alignment explanation
Indices: 27558049--27558115 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
27558039 GCATTTTTGA
* *
27558049 ACTGTACTGAGATGGGCTGAAGCCCAA-ACTGTC
1 ACTGTACTGAAAAGGGCTGAAGCCCAAGACTGTC
* *
27558082 ACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 ACTG-TACTGAAAAGGGCTGAAGCCCAAGACTGT
27558116 TCAACTGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 4 0.14
34 19 0.68
35 5 0.18
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (34 bp):
ACTGTACTGAAAAGGGCTGAAGCCCAAGACTGTC
Found at i:27562704 original size:28 final size:28
Alignment explanation
Indices: 27562673--27562726 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
27562663 ATTCAAGTCC
27562673 AATTGATTCTTTTCTTGATCTAAATAAT
1 AATTGATTCTTTTCTTGATCTAAATAAT
27562701 AATTGATTCTTTTCTTGATCTAAATA
1 AATTGATTCTTTTCTTGATCTAAATA
27562727 TTTCAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.50
Consensus pattern (28 bp):
AATTGATTCTTTTCTTGATCTAAATAAT
Found at i:27563924 original size:754 final size:757
Alignment explanation
Indices: 27562445--27563952 Score: 2368
Period size: 754 Copynumber: 2.0 Consensus size: 757
27562435 AATGACATAA
27562445 CATTTGTATCCTAAGCATTCTCTAGGTTCAAACGAGACTTTTGTCGTCAAATATTCAATTATCGA
1 CATTTGTATCCTAAGCATTCTCTAGGTTCAAACGAGACTTTTGTCGTCAAATATTCAATTATCGA
*
27562510 ATTATTACCGAATTAATTGTAAAAAATATAATATTAACAAATAATCAACCAAAATAACATTTAAT
66 ATTATTACCGAATCAATTGTAAAAAATATAATATTAACAAATAATCAACCAAAATAACATTTAAT
* * * *
27562575 AAATATAAAATTCATACGACCTTACCTCGACCACAGCGGTTCTATCAACAAAAGTCGAGAATTAA
131 AAATATAAAATTCATACAAACTTACCTCGACCACAACGGTTCTATCAACAAAAGTAGAGAATTAA
* * *
27562640 TCTAAGACTTTCGCTTTTCCTCGATTCAAGTCCAATTGATTCTTTTCTTGATCTAAATAATAATT
196 TCCAAGACTTTCGCTTTTCCTCAATTCAAGTCCAATTGATTCTTTTCCTGATCTAAATAATAATT
* * *
27562705 GATTCTTTTCTTGATCTAAATATTTCAATTGACTACAATTATCCAATTCAAACCTATAATCCATA
261 GATAC--TTC-TAATCTAAATATGTCAATTGACTACAATTATCCAATTCAAACCTATAATCCATA
27562770 TTAACATGAAATTAAAAAATTAACCCTAACATTTTAACTTTTTATCGTTTAGCCCATAAATCTAA
323 TTAACATGAAATTAAAAAATTAACCCTAACATTTTAACTTTTTATCGTTTAGCCCATAAATCTAA
*
27562835 ATCTTATAATTTAACCAATAAAATAAAATATCATAATACCCAAATATTCTTAAGGGTCCAAACAA
388 ATATTATAATTTAACCAATAAAATAAAATATCATAATACCCAAATATTCTTAAGGGTCCAAACAA
27562900 CCCCTAACTTTCTCTAATTCACAACATTAACCATGAATTTTACTATTTTCACCATTAAGTCCTTA
453 CCCCTAACTTTCTCTAATTCACAACATTAACCATGAATTTTACTATTTTCACCATTAAGTCCTTA
* *
27562965 AAATTTAAATTCATCAAAAATTACTTAACAAAACATGTTTATCTAACAATTAGACTTAATAATCT
518 AAATTTAAATTCATCAAAAATTACTTAACAAAACATGTTTATCTAACAATTAAACTTAATAATAT
* * * *
27563030 ATCAAACAAATTCACAAATATTATTAAATCATTCATGGTGAAACCCTAAAATTTTTATAACATGA
583 ATCAAAAAAATTCACAAATATCATTAAATCATTCATAGTAAAACCCTAAAATTTTTATAACATGA
* * *
27563095 CAGTTCAACCCCCAAGTTAAGTAGATTAAGCTAAAATGAGTTCAAAAACATAAAAAAATCATTAA
648 CAATTCAACCCCCAAGCTAAGTAGATTAAGCTAAAACGAGTTCAAAAACAT-AAAAAATCATTAA
** *
27563160 AATGGGGTTAAAAAACCTCACCATGCACCAAATGAAACTGACATGT
712 AACAGGGTTAAAAAACCTCACCATGCACCAAAGGAAACTGACATGT
* *
27563206 CATTTGTATCCTAAGCATTCTCTAGGTTCAAATGGGACTTTTGTCGTCAAATATTCAATTATCGA
1 CATTTGTATCCTAAGCATTCTCTAGGTTCAAACGAGACTTTTGTCGTCAAATATTCAATTATCGA
* * *
27563271 ATTATTATCGAATCAATTGTAAAAAATATAATGTTAACAAATAATCAACCAAAATAACATTTAGT
66 ATTATTACCGAATCAATTGTAAAAAATATAATATTAACAAATAATCAACCAAAATAACATTTAAT
* *
27563336 AAATATAAAATTTATACAAACTTACCTCGACCACAACGGTTGTATCAACAAAAGTAGAGAATTAA
131 AAATATAAAATTCATACAAACTTACCTCGACCACAACGGTTCTATCAACAAAAGTAGAGAATTAA
* * *
27563401 TCCGAGAC-TTCTGTTTTTCCTCAATTCGAG-CCTAATTGATTCTTTTCCTGATCTAAATAATAA
196 TCCAAGACTTTC-GCTTTTCCTCAATTCAAGTCC-AATTGATTCTTTTCCTGATCTAAATAATAA
* *
27563464 TTTA-AC-TC-AAT-TAAATATGTCAATTGACTACAATTATTCAATTCAAACCTATAATCCATAT
259 TTGATACTTCTAATCTAAATATGTCAATTGACTACAATTATCCAATTCAAACCTATAATCCATAT
* * * *
27563525 TAACGTGAAATTACAAAATTACCCCTAACATTTTAACTTTTTATCGTTTAGCCCCTAAATCTAAA
324 TAACATGAAATTAAAAAATTAACCCTAACATTTTAACTTTTTATCGTTTAGCCCATAAATCTAAA
* * * * * *
27563590 TATTATAATTTAACTAGTAAAATAAAATATCATAATACCCAAATATTTTTAAGGTTCCAAGCAGC
389 TATTATAATTTAACCAATAAAATAAAATATCATAATACCCAAATATTCTTAAGGGTCCAAACAAC
27563655 CCCTAACTTTCTCTAATTCACAACATTAACCATGAATTTTACTATTTTCACCATTAAGTCCTTAA
454 CCCTAACTTTCTCTAATTCACAACATTAACCATGAATTTTACTATTTTCACCATTAAGTCCTTAA
* *
27563720 ACTTTAAATTCATTAAAAATTACTTTAA-AAAACATGTTTATCTAACAATTAAACTTAATAATAT
519 AATTTAAATTCATCAAAAATTAC-TTAACAAAACATGTTTATCTAACAATTAAACTTAATAATAT
* **
27563784 TTCAAAAAAAATTCACAAATATCATTAAATCATTCA-AGTAAAAGCCCTAAAATTTTTATAAGTT
583 ATC-AAAAAAATTCACAAATATCATTAAATCATTCATAGTAAAA-CCCTAAAATTTTTATAACAT
* * * *
27563848 TACAATTCAACCCTCGAGCTAAGTAGATTAAGCTAAAACGAGTTCAGAAACAT-AAAAATCATTA
646 GACAATTCAACCCCCAAGCTAAGTAGATTAAGCTAAAACGAGTTCAAAAACATAAAAAATCATT-
27563912 AAAACAGGGTTAAAAAACCTCACCATGCACCAAAGGAAACT
710 AAAACAGGGTTAAAAAACCTCACCATGCACCAAAGGAAACT
27563953 TTTCAGAATT
Statistics
Matches: 686, Mismatches: 55, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
753 10 0.01
754 332 0.48
755 100 0.15
757 2 0.00
760 6 0.01
761 236 0.34
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (757 bp):
CATTTGTATCCTAAGCATTCTCTAGGTTCAAACGAGACTTTTGTCGTCAAATATTCAATTATCGA
ATTATTACCGAATCAATTGTAAAAAATATAATATTAACAAATAATCAACCAAAATAACATTTAAT
AAATATAAAATTCATACAAACTTACCTCGACCACAACGGTTCTATCAACAAAAGTAGAGAATTAA
TCCAAGACTTTCGCTTTTCCTCAATTCAAGTCCAATTGATTCTTTTCCTGATCTAAATAATAATT
GATACTTCTAATCTAAATATGTCAATTGACTACAATTATCCAATTCAAACCTATAATCCATATTA
ACATGAAATTAAAAAATTAACCCTAACATTTTAACTTTTTATCGTTTAGCCCATAAATCTAAATA
TTATAATTTAACCAATAAAATAAAATATCATAATACCCAAATATTCTTAAGGGTCCAAACAACCC
CTAACTTTCTCTAATTCACAACATTAACCATGAATTTTACTATTTTCACCATTAAGTCCTTAAAA
TTTAAATTCATCAAAAATTACTTAACAAAACATGTTTATCTAACAATTAAACTTAATAATATATC
AAAAAAATTCACAAATATCATTAAATCATTCATAGTAAAACCCTAAAATTTTTATAACATGACAA
TTCAACCCCCAAGCTAAGTAGATTAAGCTAAAACGAGTTCAAAAACATAAAAAATCATTAAAACA
GGGTTAAAAAACCTCACCATGCACCAAAGGAAACTGACATGT
Found at i:27566933 original size:15 final size:15
Alignment explanation
Indices: 27566915--27566967 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
27566905 AATAATTTAA
27566915 ATATTAATATTAATT
1 ATATTAATATTAATT
27566930 ATATTAAT-TTAACTT
1 ATATTAATATTAA-TT
* *
27566945 ATA-AAATCTT-ATT
1 ATATTAATATTAATT
27566958 ATATTAATAT
1 ATATTAATAT
27566968 GAAATCGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 12 0.38
15 15 0.47
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTAATATTAATT
Found at i:27567027 original size:11 final size:11
Alignment explanation
Indices: 27567011--27567035 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27567001 ATAATTGAGA
27567011 AATTAAATTAT
1 AATTAAATTAT
27567022 AATTAAATTAT
1 AATTAAATTAT
27567033 AAT
1 AAT
27567036 ATATTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAAATTAT
Found at i:27569637 original size:16 final size:15
Alignment explanation
Indices: 27569612--27569641 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27569602 GTCATGTGTC
27569612 TTTTTTTTAAATATG
1 TTTTTTTTAAATATG
27569627 TTTTGTTTTAAATAT
1 TTTT-TTTTAAATAT
27569642 TTTACTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTTTTTAAATATG
Found at i:27580862 original size:33 final size:33
Alignment explanation
Indices: 27580820--27580895 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
27580810 TACACTTTAT
*
27580820 TTGGCGTGTTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
27580853 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
*
27580886 TTAGTGTGTT
1 TTGGTGTGTT
27580896 TAAGGGATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.14, C:0.09, G:0.33, T:0.43
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
Found at i:27580904 original size:33 final size:33
Alignment explanation
Indices: 27580834--27580928 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
27580824 CGTGTTGGTT
***
27580834 GGATTAGCTCTTATGAGCATTGGTGTGTTGGTT
1 GGATTAGCTCTTATGAGCATTGGTGTGTTGAAG
* *
27580867 GGATTAGCTCTTATGAGCATTAGTGTGTTTAAG
1 GGATTAGCTCTTATGAGCATTGGTGTGTTGAAG
* * *
27580900 GGATTGGCTCGTGTGAGCATCTGGTGTGT
1 GGATTAGCTCTTATGAGCAT-TGGTGTGT
27580929 AAGATTCAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
33 45 0.87
34 7 0.13
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.39
Consensus pattern (33 bp):
GGATTAGCTCTTATGAGCATTGGTGTGTTGAAG
Found at i:27583730 original size:230 final size:230
Alignment explanation
Indices: 27583327--27583787 Score: 780
Period size: 230 Copynumber: 2.0 Consensus size: 230
27583317 CACTAAACCG
* * * *
27583327 ACCCACTTTTTAGAGCATTTGAAACATCACTAGTTTCAATTCAAAATGAGGTGCCTTGATATTCG
1 ACCCACTATTTAGAGCATTTAAAACATCACTAGTTTCAATTCAAAATAAGGTGCCTTGATATTCA
* *
27583392 GCCTCTTAACTCCCGAATTTAATTCATTGAAGAGTAGCAAAGCGTATTCTCTTATGGCATGATCC
66 GCCTCCTAACTCCCGAATTTAATTCATTGAAGAGTAGCAAAGCGTATTCTCTTATGGCAGGATCC
27583457 CTATCATCAACAATAAGGATTACGTTGTACATATGATTGACTCCATTACCTTGTCCACCATTTTG
131 CTATCATCAACAATAAGGATTACGTTGTACATATGATTGACTCCATTACCTTGTCCACCATTTTG
27583522 ATTTCCAAGGTCCAT-CTCAACTTGTCTTCAAGCAA
196 ATTTCCAAGGTCCATCCT-AACTTGTCTTCAAGCAA
* *
27583557 ACCCACTATTTAGAGCATTTAAAACATCAGTGGTTTCAATTCAAAATAAGGTGCCTTGATATTCA
1 ACCCACTATTTAGAGCATTTAAAACATCACTAGTTTCAATTCAAAATAAGGTGCCTTGATATTCA
* * * *
27583622 GCCTCCTGACTCCTGAATTTAATTCATTGAAGAGTAGCAAAGCGTATTGTCTTATGGTAGGATCC
66 GCCTCCTAACTCCCGAATTTAATTCATTGAAGAGTAGCAAAGCGTATTCTCTTATGGCAGGATCC
* *
27583687 CTATCATCAACAATAAGGATTAGGTTGTACATATGATTGACTCCATTACCTTGTCCATCATTTTG
131 CTATCATCAACAATAAGGATTACGTTGTACATATGATTGACTCCATTACCTTGTCCACCATTTTG
27583752 ATTTCCAAGGTCCATCCTAACTTGTCTTCAAGCAA
196 ATTTCCAAGGTCCATCCTAACTTGTCTTCAAGCAA
27583787 A
1 A
27583788 TCTCTCGCAT
Statistics
Matches: 216, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
230 214 0.99
231 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (230 bp):
ACCCACTATTTAGAGCATTTAAAACATCACTAGTTTCAATTCAAAATAAGGTGCCTTGATATTCA
GCCTCCTAACTCCCGAATTTAATTCATTGAAGAGTAGCAAAGCGTATTCTCTTATGGCAGGATCC
CTATCATCAACAATAAGGATTACGTTGTACATATGATTGACTCCATTACCTTGTCCACCATTTTG
ATTTCCAAGGTCCATCCTAACTTGTCTTCAAGCAA
Found at i:27589502 original size:20 final size:21
Alignment explanation
Indices: 27589449--27589488 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27589439 AAATAATGAC
27589449 AAAAGTATCGATACCTTTTCA
1 AAAAGTATCGATACCTTTTCA
*
27589470 AAAAGTATTGATACCTTTT
1 AAAAGTATCGATACCTTTT
27589489 ACCAGGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAGTATCGATACCTTTTCA
Found at i:27589967 original size:250 final size:250
Alignment explanation
Indices: 27589526--27590027 Score: 862
Period size: 250 Copynumber: 2.0 Consensus size: 250
27589516 GGTCACTGAA
* *
27589526 ATATGCATTAATTACAAAAAATATAGACACTCAATGTTGTAGGTGTATTTAATGAACTGGTATTT
1 ATATGCATTAATTACAAAAAATATAGACACTCAATGTTGTAGGTGAATTTAATCAACTGGTATTT
* * *
27589591 CCATCCCAATAGCTATATCCAATTCGTTAACAACCAGAACGAGTGGAAATCAATTAGAGAGTGTA
66 CCATCCCAACAGCTATATCCAATTCGTAAACAACCAGAACGAGTGGAAATCAATTAGAGAGTATA
27589656 AATATCATATTCCAAAAGTCCCACAACAACAAGAGATATGTGCAAAGCTTAAAGATCAATAAAAA
131 AATATCATATTCCAAAAGTCCCACAACAACAAGAGATATGTGCAAAGCTTAAAGATCAATAAAAA
*
27589721 CAACCTAAGAGCTTAATTCTTTCATACCTTTTCTTGTAAACACTTATGAGCTTTC
196 CAACCTAAGAGCTTAATTCTTTCATACCTGTTCTTGTAAACACTTATGAGCTTTC
* * *
27589776 ATATGCATTAATTACAAAAAATATCA-ATACTCAATGTTGTAGGTGAATTTAATCAGCTGTTATT
1 ATATGCATTAATTACAAAAAATAT-AGACACTCAATGTTGTAGGTGAATTTAATCAACTGGTATT
* *
27589840 TCCATCCCAACGGCTATATCCAATTCGTAAACAACCAGAACGATTGGAAATCAATTAGAGAGTAT
65 TCCATCCCAACAGCTATATCCAATTCGTAAACAACCAGAACGAGTGGAAATCAATTAGAGAGTAT
**
27589905 AAATATCATATTCCAAAAGTCCCACAAGTACAAGAGATATGTGCAAAGCTTAAAGATCAATAAAA
130 AAATATCATATTCCAAAAGTCCCACAACAACAAGAGATATGTGCAAAGCTTAAAGATCAATAAAA
*
27589970 ACAACTTAAGAGCTTAATTCTTTCATACCTGTTCTTGTAAACACTTATGAGCTTTC
195 ACAACCTAAGAGCTTAATTCTTTCATACCTGTTCTTGTAAACACTTATGAGCTTTC
27590026 AT
1 AT
27590028 TGTATTCATT
Statistics
Matches: 237, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
250 236 1.00
251 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (250 bp):
ATATGCATTAATTACAAAAAATATAGACACTCAATGTTGTAGGTGAATTTAATCAACTGGTATTT
CCATCCCAACAGCTATATCCAATTCGTAAACAACCAGAACGAGTGGAAATCAATTAGAGAGTATA
AATATCATATTCCAAAAGTCCCACAACAACAAGAGATATGTGCAAAGCTTAAAGATCAATAAAAA
CAACCTAAGAGCTTAATTCTTTCATACCTGTTCTTGTAAACACTTATGAGCTTTC
Found at i:27591673 original size:27 final size:27
Alignment explanation
Indices: 27591643--27591705 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
27591633 CCATAAAGGT
27591643 GTTCCTTTCATAATGCGCCACATAGAC
1 GTTCCTTTCATAATGCGCCACATAGAC
** * * *
27591670 GTTCCTTTTGTATTGTGCCACATAGGC
1 GTTCCTTTCATAATGCGCCACATAGAC
*
27591697 ATTCCTTTC
1 GTTCCTTTC
27591706 TTAACGTGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (27 bp):
GTTCCTTTCATAATGCGCCACATAGAC
Found at i:27598176 original size:26 final size:26
Alignment explanation
Indices: 27598137--27598206 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
27598127 CCTTTCATCG
* *
27598137 TTGCTTACACGAGCTGTGAAATGGGC
1 TTGCTCACATGAGCTGTGAAATGGGC
27598163 TTGCTCACATGAGCTGTGAAATGGGC
1 TTGCTCACATGAGCTGTGAAATGGGC
27598189 TTGCTCACATGAGCTGTG
1 TTGCTCACATGAGCTGTG
27598207 GGTCAGAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (26 bp):
TTGCTCACATGAGCTGTGAAATGGGC
Found at i:27609420 original size:17 final size:19
Alignment explanation
Indices: 27609394--27609435 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27609384 GACCCTTAAC
27609394 TTTTCATT-AA-TTATACA
1 TTTTCATTAAACTTATACA
* *
27609411 TTTTCCTTAAACTTTTACA
1 TTTTCATTAAACTTATACA
27609430 TTTTCA
1 TTTTCA
27609436 CAATTTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTCATTAAACTTATACA
Found at i:27611166 original size:23 final size:23
Alignment explanation
Indices: 27611139--27611193 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
27611129 AATACAATAT
27611139 GATCAAATTCAAAATAATTCATG
1 GATCAAATTCAAAATAATTCATG
27611162 GATCAAATTCAAAATAATTCATG
1 GATCAAATTCAAAATAATTCATG
*
27611185 TATCAAATT
1 GATCAAATT
27611194 AAACTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (23 bp):
GATCAAATTCAAAATAATTCATG
Found at i:27615603 original size:19 final size:20
Alignment explanation
Indices: 27615558--27615629 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
27615548 TCTCAACAAA
*
27615558 AAAAATACAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
27615578 AAAAATTCAAAATAATTTT-
1 AAAAATTCAAAATAATTTTC
* **
27615597 TAAAATTCAAAAT-ATTTAA
1 AAAAATTCAAAATAATTTTC
27615616 AAAAATTACAAAAT
1 AAAAATT-CAAAAT
27615630 TTATATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.09
19 18 0.39
20 24 0.52
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Found at i:27615641 original size:26 final size:26
Alignment explanation
Indices: 27615608--27615658 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
27615598 AAAATTCAAA
27615608 ATATTTAAAAAAATTACAAAATTTAT
1 ATATTTAAAAAAATTACAAAATTTAT
* *
27615634 ATATTTAAAAAAATTATAAATTTTA
1 ATATTTAAAAAAATTACAAAATTTA
27615659 AAAAAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATTTAAAAAAATTACAAAATTTAT
Found at i:27615671 original size:18 final size:18
Alignment explanation
Indices: 27615637--27615671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27615627 AATTTATATA
*
27615637 TTTAAAAAAATTATAAAT
1 TTTAAAAAAAATATAAAT
*
27615655 TTTAAAAAAAATCTAAA
1 TTTAAAAAAAATATAAA
27615672 GAACATATAA
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAAAAAAAATATAAAT
Found at i:27617582 original size:25 final size:25
Alignment explanation
Indices: 27617548--27617599 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
27617538 AAATGTGCTC
27617548 CAGGGTTTCTAAGATCTGAAAATGG
1 CAGGGTTTCTAAGATCTGAAAATGG
27617573 CAGGGTTTCTAAGATCTGAAAATGG
1 CAGGGTTTCTAAGATCTGAAAATGG
27617598 CA
1 CA
27617600 ATGGGAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (25 bp):
CAGGGTTTCTAAGATCTGAAAATGG
Found at i:27626735 original size:5 final size:5
Alignment explanation
Indices: 27626725--27626772 Score: 87
Period size: 5 Copynumber: 9.6 Consensus size: 5
27626715 AACAATTATT
*
27626725 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAAGC AAACC AAA
1 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAA
27626773 TCACTTAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.62, C:0.35, G:0.02, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:27627110 original size:21 final size:21
Alignment explanation
Indices: 27627084--27627131 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27627074 AACCAACCGA
27627084 ACACCA-CTCCAGCCACCCTGC
1 ACACCAGC-CCAGCCACCCTGC
* *
27627105 ACACCAGCCTATCCACCCTGC
1 ACACCAGCCCAGCCACCCTGC
27627126 ACACCA
1 ACACCA
27627132 TAAAGGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.54, G:0.08, T:0.10
Consensus pattern (21 bp):
ACACCAGCCCAGCCACCCTGC
Found at i:27629250 original size:39 final size:39
Alignment explanation
Indices: 27629184--27629260 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
27629174 AAATGCGATC
*
27629184 AGGGCTACTGAAGTACAATAGGAGCACGTAAGCGCAATT
1 AGGGCTACCGAAGTACAATAGGAGCACGTAAGCGCAATT
* * *
27629223 AGGGGTACCGAAGTAC-ATCAGGGGCACGTAAGTGCAAT
1 AGGGCTACCGAAGTACAAT-AGGAGCACGTAAGCGCAAT
27629261 CAGAGGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.17
Consensus pattern (39 bp):
AGGGCTACCGAAGTACAATAGGAGCACGTAAGCGCAATT
Found at i:27634167 original size:31 final size:31
Alignment explanation
Indices: 27634129--27634192 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
27634119 TGGTATCGAT
27634129 AATTAGCATTCTATTTCTCGCCTAAAATCCA
1 AATTAGCATTCTATTTCTCGCCTAAAATCCA
27634160 AATTAGCATTCTATTTCTCGCCTAAAATCCA
1 AATTAGCATTCTATTTCTCGCCTAAAATCCA
27634191 AA
1 AA
27634193 CTCAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (31 bp):
AATTAGCATTCTATTTCTCGCCTAAAATCCA
Found at i:27643560 original size:11 final size:13
Alignment explanation
Indices: 27643543--27643576 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
27643533 CAATTTCACA
27643543 GAAAATTTCG-TC
1 GAAAATTTCGTTC
27643555 -AAAATTTCGTTC
1 GAAAATTTCGTTC
27643567 GAAAATTTCG
1 GAAAATTTCG
27643577 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 2 0.10
13 9 0.45
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (13 bp):
GAAAATTTCGTTC
Found at i:27644825 original size:103 final size:102
Alignment explanation
Indices: 27644646--27644846 Score: 287
Period size: 103 Copynumber: 2.0 Consensus size: 102
27644636 AATATAAAAA
* * * * * *
27644646 GGGTTGCTAAGTGTTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTG
1 GGGTTACTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTTG
* * *
27644711 GAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAG
66 AAATATAAA-GGGGTTGCTAAATGCTAATTCCCCCAAG
27644749 GGGTTACTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTT-
1 GGGTTACTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTTG
*
27644813 AAATGTGAAAGGGGTTGCTAAATGCTAATTCCCC
66 AAATAT-AAAGGGGTTGCTAAATGCTAATTCCCC
27644847 GAATAACTGG
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 26 0.30
103 61 0.70
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (102 bp):
GGGTTACTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTTG
AAATATAAAGGGGTTGCTAAATGCTAATTCCCCCAAG
Found at i:27652990 original size:18 final size:19
Alignment explanation
Indices: 27652955--27653003 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
27652945 TATTAGAAGT
* *
27652955 TTTGAAATAGTGAAAAAAG
1 TTTGAAATAATAAAAAAAG
*
27652974 TTTGAAATAATAAAAAAAT
1 TTTGAAATAATAAAAAAAG
27652993 TTTGAAA-AATA
1 TTTGAAATAATA
27653004 TACGAAGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTGAAATAATAAAAAAAG
Found at i:27653057 original size:11 final size:10
Alignment explanation
Indices: 27653038--27653067 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
27653028 AATTGAAGTT
27653038 GAAAAAAAAA
1 GAAAAAAAAA
27653048 GAAGAAAAAAA
1 GAA-AAAAAAA
27653059 GAAAAAAAA
1 GAAAAAAAA
27653068 TTGATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:27653656 original size:21 final size:21
Alignment explanation
Indices: 27653632--27653693 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
27653622 GTTTACAATG
*
27653632 ACAACGAGGACGTTTACCTCC
1 ACAACGAGGACGTTCACCTCC
* *
27653653 ACAATGAGGCCGTTCACCTCC
1 ACAACGAGGACGTTCACCTCC
** * *
27653674 ACCTCGAGGCCGATCACCTC
1 ACAACGAGGACGTTCACCTC
27653694 ATGTTCCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.39, G:0.19, T:0.18
Consensus pattern (21 bp):
ACAACGAGGACGTTCACCTCC
Found at i:27656253 original size:26 final size:26
Alignment explanation
Indices: 27656224--27656277 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
27656214 ACATATAATT
*
27656224 TACACATCATGTATC-TATATATCATG
1 TACAAATCAT-TATCATATATATCATG
* *
27656250 TACAAATCATTTTCATATATCTCATG
1 TACAAATCATTATCATATATATCATG
27656276 TA
1 TA
27656278 AATACCTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.41
Consensus pattern (26 bp):
TACAAATCATTATCATATATATCATG
Found at i:27656468 original size:25 final size:25
Alignment explanation
Indices: 27656435--27656519 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
27656425 ACGAGCTGTA
* *
27656435 AACGATAAGCTCCTCCAAACTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
* *
27656460 AATGGTAAGGTCCTCCAAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
*
27656485 AACGGTAAGCACCTCCAAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
*
27656510 AACGATAAGC
1 AACGGTAAGC
27656520 ACATACGAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCAAGCTGAAT
Found at i:27656520 original size:25 final size:25
Alignment explanation
Indices: 27656435--27656544 Score: 112
Period size: 25 Copynumber: 4.4 Consensus size: 25
27656425 ACGAGCTGTA
* *
27656435 AACGATAAGCTCCTCCAAACTGAAT
1 AACGATAAGCACCTCCAAGCTGAAT
* * **
27656460 AATGGTAAGGTCCTCCAAGCTGAAT
1 AACGATAAGCACCTCCAAGCTGAAT
*
27656485 AACGGTAAGCACCTCCAAGCTGAAT
1 AACGATAAGCACCTCCAAGCTGAAT
* * * *
27656510 AACGATAAGCACATACGAGCTGAGT
1 AACGATAAGCACCTCCAAGCTGAAT
*
27656535 ATCGATAAGC
1 AACGATAAGC
27656545 TCATAAGAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (25 bp):
AACGATAAGCACCTCCAAGCTGAAT
Found at i:27656531 original size:50 final size:49
Alignment explanation
Indices: 27656422--27656532 Score: 114
Period size: 50 Copynumber: 2.2 Consensus size: 49
27656412 CATGTATGCT
* * * * **
27656422 CATACGAGCTGTAAACGATAAGCTCCTCCAAACTGAATAATGGTAAGGT
1 CATACGAGCTGAAAACGATAAGCACCTCCAAACTGAATAACGATAAGCA
* * * * *
27656471 CCTCCAAGCTGAATAACGGTAAGCACCTCCAAGCTGAATAACGATAAGCA
1 CATACGAGCTGAA-AACGATAAGCACCTCCAAACTGAATAACGATAAGCA
27656521 CATACGAGCTGA
1 CATACGAGCTGA
27656533 GTATCGATAA
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
49 9 0.19
50 38 0.81
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (49 bp):
CATACGAGCTGAAAACGATAAGCACCTCCAAACTGAATAACGATAAGCA
Found at i:27656549 original size:25 final size:25
Alignment explanation
Indices: 27656477--27656555 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
27656467 AGGTCCTCCA
* * *
27656477 AGCTGAATAACGGTAAGCACCTCCA-
1 AGCTGAATAACGATAAGCACAT-AAG
*
27656502 AGCTGAATAACGATAAGCACATACG
1 AGCTGAATAACGATAAGCACATAAG
* * *
27656527 AGCTGAGTATCGATAAGCTCATAAG
1 AGCTGAATAACGATAAGCACATAAG
27656552 AGCT
1 AGCT
27656556 AAAATCAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (25 bp):
AGCTGAATAACGATAAGCACATAAG
Found at i:27668840 original size:16 final size:16
Alignment explanation
Indices: 27668819--27668855 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
27668809 GTAAAAGTTA
27668819 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
27668835 ATATAACATTTATAAT
1 ATATAAAATTTATAAT
27668851 A-ATAA
1 ATATAA
27668856 TAAAAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:27670255 original size:29 final size:29
Alignment explanation
Indices: 27670200--27670261 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
27670190 CATAATTTAA
*
27670200 CATAAAAAGTCCCAAATAGAAATAAAGTT
1 CATAAAAAGTCCCAAATAGAAATAAAGTC
*
27670229 CATAAAAA-T-CCAAATCATAAATAAAAGTC
1 CATAAAAAGTCCCAAAT-AGAAAT-AAAGTC
27670258 CATA
1 CATA
27670262 TTTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 6 0.21
29 17 0.59
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.21
Consensus pattern (29 bp):
CATAAAAAGTCCCAAATAGAAATAAAGTC
Found at i:27670516 original size:19 final size:20
Alignment explanation
Indices: 27670489--27670528 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
27670479 ATGATCATGT
*
27670489 CAATGCATATTTTGT-AAAA
1 CAATACATATTTTGTGAAAA
27670508 CAATACATATTTTGTGAAAA
1 CAATACATATTTTGTGAAAA
27670528 C
1 C
27670529 GGTCCTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
CAATACATATTTTGTGAAAA
Found at i:27674888 original size:35 final size:35
Alignment explanation
Indices: 27674844--27674916 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
27674834 TTACTTCACA
27674844 AAATACATGCACAAATTCAGGTTCTATGTTGCAAC
1 AAATACATGCACAAATTCAGGTTCTATGTTGCAAC
27674879 AAATACATGCACAAATTCAGGTTCTATGTTGCAAC
1 AAATACATGCACAAATTCAGGTTCTATGTTGCAAC
27674914 AAA
1 AAA
27674917 AGTATGCGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
AAATACATGCACAAATTCAGGTTCTATGTTGCAAC
Found at i:27706064 original size:34 final size:34
Alignment explanation
Indices: 27706026--27706104 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
27706016 TATCACTTTT
* * *
27706026 TGGATAGTATCGCTTAGCAAATAGTATCGTCTAG
1 TGGATAGTATCGCCTAGCAAATAGTACCGACTAG
* **
27706060 TGGATAGTATTGCCTAGTGAATAGTACCGACTAG
1 TGGATAGTATCGCCTAGCAAATAGTACCGACTAG
*
27706094 TGGACAGTATC
1 TGGATAGTATC
27706105 TACTAGCAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (34 bp):
TGGATAGTATCGCCTAGCAAATAGTACCGACTAG
Found at i:27706066 original size:17 final size:17
Alignment explanation
Indices: 27706046--27706110 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
27706036 CGCTTAGCAA
*
27706046 ATAGTATCGTCTAGTGG
1 ATAGTATCGACTAGTGG
* * *
27706063 ATAGTATTGCCTAGTGA
1 ATAGTATCGACTAGTGG
*
27706080 ATAGTACCGACTAGTGG
1 ATAGTATCGACTAGTGG
* *
27706097 ACAGTATCTACTAG
1 ATAGTATCGACTAG
27706111 CAGGCAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (17 bp):
ATAGTATCGACTAGTGG
Found at i:27710055 original size:43 final size:43
Alignment explanation
Indices: 27709994--27710075 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
27709984 TTTATTTTAA
27709994 CATAGCCATGGGTTTTGCTGACCCTAACGATGTTTAGTCCGAC
1 CATAGCCATGGGTTTTGCTGACCCTAACGATGTTTAGTCCGAC
27710037 CATAGCCATGGGTTTTGCTGACCCTAACGATGTTTAGTC
1 CATAGCCATGGGTTTTGCTGACCCTAACGATGTTTAGTC
27710076 TGACTCGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (43 bp):
CATAGCCATGGGTTTTGCTGACCCTAACGATGTTTAGTCCGAC
Found at i:27710059 original size:22 final size:22
Alignment explanation
Indices: 27709994--27710059 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
27709984 TTTATTTTAA
27709994 CATAGCCATGGGTTTTGCTGAC
1 CATAGCCATGGGTTTTGCTGAC
* * * * *
27710016 CCTAACGAT--GTTTAGTCCGAC
1 CATAGCCATGGGTTTTG-CTGAC
27710037 CATAGCCATGGGTTTTGCTGAC
1 CATAGCCATGGGTTTTGCTGAC
27710059 C
1 C
27710060 CTAACGATGT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
20 5 0.16
21 10 0.32
22 11 0.35
23 5 0.16
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (22 bp):
CATAGCCATGGGTTTTGCTGAC
Found at i:27710078 original size:21 final size:21
Alignment explanation
Indices: 27710011--27710079 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
27710001 ATGGGTTTTG
27710011 CTGACCCTAACGATGTTTAGT
1 CTGACCCTAACGATGTTTAGT
* * * * *
27710032 CCGACCATAGCCATGGGTTTTG-
1 CTGACCCTAACGAT--GTTTAGT
27710054 CTGACCCTAACGATGTTTAGT
1 CTGACCCTAACGATGTTTAGT
27710075 CTGAC
1 CTGAC
27710080 TCGTACCATA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 5 0.14
21 15 0.43
22 10 0.29
23 5 0.14
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (21 bp):
CTGACCCTAACGATGTTTAGT
Found at i:27711873 original size:18 final size:18
Alignment explanation
Indices: 27711836--27711890 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
27711826 ATCCTATAAA
* * *
27711836 TAGTTTGAATTTTATCTT
1 TAGTTTAAATTTGATTTT
27711854 TAGTTTAAATTTGATTTT
1 TAGTTTAAATTTGATTTT
27711872 TA----AAATTTGATTTT
1 TAGTTTAAATTTGATTTT
27711886 TAGTT
1 TAGTT
27711891 GATATTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 14 0.45
18 17 0.55
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (18 bp):
TAGTTTAAATTTGATTTT
Found at i:27711879 original size:14 final size:14
Alignment explanation
Indices: 27711860--27711887 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27711850 TCTTTAGTTT
27711860 AAATTTGATTTTTA
1 AAATTTGATTTTTA
27711874 AAATTTGATTTTTA
1 AAATTTGATTTTTA
27711888 GTTGATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
AAATTTGATTTTTA
Found at i:27713164 original size:16 final size:16
Alignment explanation
Indices: 27713140--27713174 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27713130 GAAAGAACCA
27713140 TCTAATATTTTATTAT
1 TCTAATATTTTATTAT
* *
27713156 TCTATTATTTTATTTT
1 TCTAATATTTTATTAT
27713172 TCT
1 TCT
27713175 GGCTAAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTAATATTTTATTAT
Found at i:27718840 original size:18 final size:18
Alignment explanation
Indices: 27718803--27718840 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
27718793 TAAATGATGA
27718803 ATTTAAAGTATTAGTTGTT
1 ATTTAAAGTATTA-TTGTT
27718822 ATTTAAAAGTATT-TTGTT
1 ATTT-AAAGTATTATTGTT
27718840 A
1 A
27718841 ACTGATCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
ATTTAAAGTATTATTGTT
Found at i:27719507 original size:40 final size:39
Alignment explanation
Indices: 27719452--27719563 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 39
27719442 AAATGAATAA
* *
27719452 GTACCCCTGTTTGCACATTAGTGCCCCTATTTATACTTCG
1 GTACCCTTATTTGCACATTAGTGCCCCTATTTA-ACTTCG
* * *
27719492 GTACCCTTATTTGCACATCAGTGCCCCTGATTGAACTTTG
1 GTACCCTTATTTGCACATTAGTGCCCCT-ATTTAACTTCG
* * *
27719532 GTACCCCTGA-ATGCACATTTGTGCCCCTATTT
1 GTA-CCCTTATTTGCACATTAGTGCCCCTATTT
27719564 GCATTTCGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.05
40 48 0.80
41 9 0.15
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (39 bp):
GTACCCTTATTTGCACATTAGTGCCCCTATTTAACTTCG
Found at i:27719566 original size:20 final size:20
Alignment explanation
Indices: 27719455--27719566 Score: 59
Period size: 20 Copynumber: 5.6 Consensus size: 20
27719445 TGAATAAGTA
*
27719455 CCCCTGTTTGCACATTAGTG
1 CCCCTATTTGCACATTAGTG
** * *
27719475 CCCCTATTTATAC-TTCGGTA
1 CCCCTATTTGCACATT-AGTG
* *
27719495 CCCTTATTTGCACATCAGTG
1 CCCCTATTTGCACATTAGTG
* * * *
27719515 CCCCTGA-TTGAACTTTGGTA
1 CCCCT-ATTTGCACATTAGTG
* *
27719535 CCCCTGA-ATGCACATTTGTG
1 CCCCT-ATTTGCACATTAGTG
27719555 CCCCTATTTGCA
1 CCCCTATTTGCA
27719567 TTTCGGTGCC
Statistics
Matches: 65, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
19 3 0.05
20 60 0.92
21 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (20 bp):
CCCCTATTTGCACATTAGTG
Found at i:27719620 original size:20 final size:20
Alignment explanation
Indices: 27719512--27719620 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
27719502 TTGCACATCA
*
27719512 GTGCCCCTGATTGAACTTTG
1 GTGCCCCTGATTGCACTTTG
* *
27719532 GTACCCCTGAATGCACATTT-
1 GTGCCCCTGATTGCAC-TTTG
27719552 GTGCCCCT-ATTTGCA-TTTCG
1 GTGCCCCTGA-TTGCACTTT-G
* * *
27719572 GTGCCCCTGATCGCTCATT-
1 GTGCCCCTGATTGCACTTTG
27719591 -TGCACTCCTGATTGCACTTTG
1 GTGC-C-CCTGATTGCACTTTG
27719612 GTGCCCCTG
1 GTGCCCCTG
27719621 TTATGCATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 6 0.09
19 2 0.03
20 50 0.74
21 7 0.10
22 3 0.04
ACGTcount: A:0.14, C:0.31, G:0.21, T:0.34
Consensus pattern (20 bp):
GTGCCCCTGATTGCACTTTG
Found at i:27722401 original size:11 final size:11
Alignment explanation
Indices: 27722385--27722409 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27722375 ACAAATAATA
27722385 TAAATAAGTTT
1 TAAATAAGTTT
27722396 TAAATAAGTTT
1 TAAATAAGTTT
27722407 TAA
1 TAA
27722410 TGTACTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
TAAATAAGTTT
Found at i:27722831 original size:20 final size:20
Alignment explanation
Indices: 27722730--27722872 Score: 81
Period size: 20 Copynumber: 7.2 Consensus size: 20
27722720 ACACACTAGT
*
27722730 TTGTGGACAAGCCACCAGTA
1 TTGTGGATAAGCCACCAGTA
* * * * *
27722750 TTGTAGATAAACTACTAGAA
1 TTGTGGATAAGCCACCAGTA
* * *
27722770 ATGTCGACAAGCCACCAGTA
1 TTGTGGATAAGCCACCAGTA
** * * *
27722790 TTGCAGATAAACTATC-GATA
1 TTGTGGATAAGCCACCAG-TA
*
27722810 TTATGGATAAGCCACCAGTA
1 TTGTGGATAAGCCACCAGTA
** * **
27722830 TTGCAGATAAACTGCCAGTA
1 TTGTGGATAAGCCACCAGTA
*
27722850 TTGTGGACAAGCCACCAGTA
1 TTGTGGATAAGCCACCAGTA
27722870 TTG
1 TTG
27722873 CAGACAAGCT
Statistics
Matches: 83, Mismatches: 38, Indels: 4
0.66 0.30 0.03
Matches are distributed among these distances:
19 1 0.01
20 81 0.98
21 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGTGGATAAGCCACCAGTA
Found at i:27722885 original size:40 final size:40
Alignment explanation
Indices: 27722730--27722903 Score: 206
Period size: 40 Copynumber: 4.3 Consensus size: 40
27722720 ACACACTAGT
* * *
27722730 TTGTGGACAAGCCACCAGTATTGTAGATAAACTACTAGAA
1 TTGTGGACAAGCCACCAGTATTGCAGATAAACTACCAGTA
* * *
27722770 ATGTCGACAAGCCACCAGTATTGCAGATAAACTATC-GATA
1 TTGTGGACAAGCCACCAGTATTGCAGATAAACTACCAG-TA
* * *
27722810 TTATGGATAAGCCACCAGTATTGCAGATAAACTGCCAGTA
1 TTGTGGACAAGCCACCAGTATTGCAGATAAACTACCAGTA
* * *
27722850 TTGTGGACAAGCCACCAGTATTGCAGACAAGCTGCCAGTA
1 TTGTGGACAAGCCACCAGTATTGCAGATAAACTACCAGTA
* *
27722890 ATGTGAACAAGCCA
1 TTGTGGACAAGCCA
27722904 TCAATGTTGC
Statistics
Matches: 114, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.98
41 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (40 bp):
TTGTGGACAAGCCACCAGTATTGCAGATAAACTACCAGTA
Found at i:27722887 original size:20 final size:20
Alignment explanation
Indices: 27722824--27722889 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
27722814 GGATAAGCCA
* *
27722824 CCAGTATTGCAGATAAACTG
1 CCAGTATTGCAGACAAGCTG
** **
27722844 CCAGTATTGTGGACAAGCCA
1 CCAGTATTGCAGACAAGCTG
27722864 CCAGTATTGCAGACAAGCTG
1 CCAGTATTGCAGACAAGCTG
27722884 CCAGTA
1 CCAGTA
27722890 ATGTGAACAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (20 bp):
CCAGTATTGCAGACAAGCTG
Found at i:27722899 original size:20 final size:20
Alignment explanation
Indices: 27722841--27722901 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
27722831 TGCAGATAAA
* *
27722841 CTGCCAGTATTGTGGACAAG
1 CTGCCAGTAATGTGAACAAG
**
27722861 CCACCAGT-AT-TGCAGACAAG
1 CTGCCAGTAATGTG-A-ACAAG
27722881 CTGCCAGTAATGTGAACAAG
1 CTGCCAGTAATGTGAACAAG
27722901 C
1 C
27722902 CATCAATGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 23 0.74
21 3 0.10
22 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (20 bp):
CTGCCAGTAATGTGAACAAG
Found at i:27722914 original size:40 final size:40
Alignment explanation
Indices: 27722731--27722929 Score: 141
Period size: 40 Copynumber: 5.0 Consensus size: 40
27722721 CACACTAGTT
* * * * * * *
27722731 TGTGGACAAGCCACCAGTATTGTAGATAAACTACTAGAAA
1 TGTGAACAAGCCACCAATATTGCAGACAAACTGCCAGTAA
* * ** *
27722771 TGTCG-ACAAGCCACCAGTATTGCAGATAAACTATC-GATAT
1 TGT-GAACAAGCCACCAATATTGCAGACAAACTGCCAG-TAA
* * * * * *
27722811 TATGGATAAGCCACCAGTATTGCAGATAAACTGCCAGTAT
1 TGTGAACAAGCCACCAATATTGCAGACAAACTGCCAGTAA
* * *
27722851 TGTGGACAAGCCACCAGTATTGCAGACAAGCTGCCAGTAA
1 TGTGAACAAGCCACCAATATTGCAGACAAACTGCCAGTAA
* * * *
27722891 TGTGAACAAGCCATCAATGTTGCAGACAAATTGTCAGTA
1 TGTGAACAAGCCACCAATATTGCAGACAAACTGCCAGTA
27722930 CCTCCTCCTT
Statistics
Matches: 134, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.01
40 130 0.97
41 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
TGTGAACAAGCCACCAATATTGCAGACAAACTGCCAGTAA
Found at i:27729820 original size:38 final size:38
Alignment explanation
Indices: 27729769--27729842 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
27729759 AGCAAGTTAG
27729769 TGGTGGCATGATTTCGTTGAAATTAGTATATAAGTGCA
1 TGGTGGCATGATTTCGTTGAAATTAGTATATAAGTGCA
27729807 TGGTGGCATGATTTCGTTGAAATTAGTATATAAGTG
1 TGGTGGCATGATTTCGTTGAAATTAGTATATAAGTG
27729843 TATATTAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.27, T:0.38
Consensus pattern (38 bp):
TGGTGGCATGATTTCGTTGAAATTAGTATATAAGTGCA
Found at i:27730206 original size:34 final size:35
Alignment explanation
Indices: 27730161--27730244 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 35
27730151 GACGGCAGCA
* * *
27730161 ATTAGAGTTTTAATTTTATTTATTTTCTTTATTAT
1 ATTAGAGTTTTAATTTTACTTATTTTCTCTATCAT
27730196 A-TAGAGTTTTAATTTTACTTATTTTCTCTATCAT
1 ATTAGAGTTTTAATTTTACTTATTTTCTCTATCAT
*
27730230 ATTAG-GTTTTTATTT
1 ATTAGAGTTTTAATTT
27730245 CCTTTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 40 0.91
35 4 0.09
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.62
Consensus pattern (35 bp):
ATTAGAGTTTTAATTTTACTTATTTTCTCTATCAT
Found at i:27731673 original size:44 final size:45
Alignment explanation
Indices: 27731585--27731674 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
27731575 GCAGCAATTC
* *
27731585 GAGTTTTAGTTTTATTTATTTTCTTTATTATATCAGGTTTTTATTT
1 GAGTTTTAGTTTTACTTA-TTTCTCTATTATATCAGGTTTTTATTT
*
27731631 GAGTTTTAGTTTTACTTA-TTCTCTATTATATTAGGTTTTTATTT
1 GAGTTTTAGTTTTACTTATTTCTCTATTATATCAGGTTTTTATTT
27731675 CCTTTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 24 0.59
46 17 0.41
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (45 bp):
GAGTTTTAGTTTTACTTATTTCTCTATTATATCAGGTTTTTATTT
Found at i:27740183 original size:26 final size:26
Alignment explanation
Indices: 27740154--27740209 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
27740144 CAATATATGA
27740154 CTCTTTGTGAGCTTCCTGATTAAAGG
1 CTCTTTGTGAGCTTCCTGATTAAAGG
* *
27740180 CTCTTTGTGAGCTTCTTGATTAATGG
1 CTCTTTGTGAGCTTCCTGATTAAAGG
27740206 CTCT
1 CTCT
27740210 CCGGAGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCTGATTAAAGG
Done.