Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 131 of 206
Found at i:39638978 original size:26 final size:26
Alignment explanation
Indices: 39638940--39639029 Score: 128
Period size: 26 Copynumber: 3.4 Consensus size: 26
39638930 TGAACTCCTC
*
39638940 AGTTCACCAAAGTACTGGAAACCCTT
1 AGTTCACCGAAGTACTGGAAACCCTT
39638966 AGTTCACCGAAGTACTGGAAACCCTT
1 AGTTCACCGAAGTACTGGAAACCCTT
* *
39638992 AGTTCACCGAAGTA-TGGGTGAACCCCT
1 AGTTCACCGAAGTACT-GG-AAACCCTT
39639019 AGTTCACCGAA
1 AGTTCACCGAA
39639030 ACACTGGTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
25 1 0.02
26 41 0.69
27 17 0.29
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (26 bp):
AGTTCACCGAAGTACTGGAAACCCTT
Found at i:39639038 original size:27 final size:27
Alignment explanation
Indices: 39638927--39639038 Score: 97
Period size: 26 Copynumber: 4.2 Consensus size: 27
39638917 AATACTCTTT
*
39638927 TGGTGAACTCCTCAGTTCACC-AAAGTAC
1 TGGTGAACCCCT-AGTTCACCGAAA-TAC
* * *
39638955 TGG-AAACCCTTAGTTCACCGAAGTAC
1 TGGTGAACCCCTAGTTCACCGAAATAC
* * *
39638981 TGG-AAACCCTTAGTTCACCGAAGTA-
1 TGGTGAACCCCTAGTTCACCGAAATAC
*
39639006 TGGGTGAACCCCTAGTTCACCGAAACAC
1 T-GGTGAACCCCTAGTTCACCGAAATAC
39639034 TGGTG
1 TGGTG
39639039 TAGTGAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 1 0.01
26 38 0.53
27 29 0.40
28 4 0.06
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (27 bp):
TGGTGAACCCCTAGTTCACCGAAATAC
Found at i:39653163 original size:51 final size:50
Alignment explanation
Indices: 39653051--39653237 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
39653041 TATCATTCGA
* * *
39653051 TACACGTAGTAGCCTTCACATAGTACT-CACACGTGATCAAACTTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGG
* * *
39653100 TTCACGTAGTAGCCTGCACAAAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * * *
39653151 TACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-AACCT-TCCGG
* * *
39653202 TACACGTAGTAGCCTGCACTTTGTACTACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
39653238 TTTATAGGCA
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
49 24 0.21
50 13 0.11
51 77 0.66
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:39653181 original size:12 final size:13
Alignment explanation
Indices: 39653151--39653183 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
39653141 AGCCTTCCGG
39653151 TACACATAGTAGCC
1 TACACATAGTA-CC
39653165 TACACATAGTA-C
1 TACACATAGTACC
39653177 TACACAT
1 TACACAT
39653184 GTGACCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:39653231 original size:102 final size:100
Alignment explanation
Indices: 39653051--39653237 Score: 241
Period size: 102 Copynumber: 1.9 Consensus size: 100
39653041 TATCATTCGA
* * * * * *
39653051 TACACGTAGTAGCCTTCACATAGTACTCACACGTGATCAAACTTTCCGGTTCACGTAGTAGCCTG
1 TACACATAGTAGCCTACACATAGTACTCACACGTGACCAAACTATCCGATACACGTAGTAGCCTG
39653116 CACAAAGTACTACACACGTGACCAAAGCCTTCCGG
66 CACAAAGTACTACACACGTGACCAAAGCCTTCCGG
* *
39653151 TACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTAT-CGATACACGTAGTAGC
1 TACACATAGTAGCCTACACATAGTACT-CACACGTGACCA--AACTATCCGATACACGTAGTAGC
***
39653215 CTGCACTTTGTACTACACACGTG
63 CTGCACAAAGTACTACACACGTG
39653238 TTTATAGGCA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
100 25 0.34
101 10 0.14
102 34 0.47
103 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (100 bp):
TACACATAGTAGCCTACACATAGTACTCACACGTGACCAAACTATCCGATACACGTAGTAGCCTG
CACAAAGTACTACACACGTGACCAAAGCCTTCCGG
Found at i:39658981 original size:17 final size:17
Alignment explanation
Indices: 39658945--39658991 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
39658935 CATTGTCCCC
* *
39658945 AATGCACTAAC-ATGAA
1 AATGCAATAACAATAAA
* *
39658961 AATGTAATGACAATAAA
1 AATGCAATAACAATAAA
39658978 AATGCAATAACAAT
1 AATGCAATAACAAT
39658992 GTGTAGTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (17 bp):
AATGCAATAACAATAAA
Found at i:39659363 original size:7 final size:8
Alignment explanation
Indices: 39659346--39659371 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39659336 AAACTTGACC
39659346 AAAAATAA
1 AAAAATAA
39659354 AAAAATAA
1 AAAAATAA
39659362 AAAAATAA
1 AAAAATAA
39659370 AA
1 AA
39659372 TCACATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:39659402 original size:16 final size:16
Alignment explanation
Indices: 39659362--39659404 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
39659352 AAAAAAATAA
*
39659362 AAAAATAAAATCACAT
1 AAAAATAAATTCACAT
*
39659378 AATAATAAATTCA-AT
1 AAAAATAAATTCACAT
39659393 AAAAATTAAATT
1 AAAAA-TAAATT
39659405 TTTTCGACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATAAATTCACAT
Found at i:39664360 original size:13 final size:13
Alignment explanation
Indices: 39664342--39664377 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
39664332 AGGGGTCACA
39664342 CGGCCGTGTGGCC
1 CGGCCGTGTGGCC
39664355 CGGCCGTGTGGCC
1 CGGCCGTGTGGCC
*
39664368 AGGCCGTGTG
1 CGGCCGTGTG
39664378 ACTCACATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.33, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGCCGTGTGGCC
Found at i:39665874 original size:25 final size:25
Alignment explanation
Indices: 39665846--39665919 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
39665836 CCGAGTTGAA
39665846 TAATGGTAAGCTCATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAG
*
39665871 TAATGGTAAGCTTATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAG
* *
39665896 CAATGGTAAGCTCATAAGAGCTGA
1 TAATGGTAAGCTCATATGAGCTGA
39665920 AACTGATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (25 bp):
TAATGGTAAGCTCATATGAGCTGAG
Found at i:39670713 original size:44 final size:44
Alignment explanation
Indices: 39670663--39670800 Score: 199
Period size: 44 Copynumber: 3.1 Consensus size: 44
39670653 AAAGTAGGAG
39670663 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
1 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
* * *
39670707 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGT-A-TAAAAGTAGGA
1 TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAA--A-CA
39670752 GTCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
1 -TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
39670797 TCAG
1 TCAG
39670801 ATCCTTTTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.04
43 1 0.01
44 38 0.46
45 2 0.02
46 34 0.41
47 1 0.01
48 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
TCAGTTTAGAGACTCACCTGTTAGGTTCCAAGTCAGCATAAACA
Found at i:39670774 original size:46 final size:46
Alignment explanation
Indices: 39670645--39670785 Score: 209
Period size: 46 Copynumber: 3.1 Consensus size: 46
39670635 GATTAACATG
39670645 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
* * *
39670691 CAAGTCAGCATAA--A-CA-TCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGT-A-TAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
39670735 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
1 CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
39670781 CAAGT
1 CAAGT
39670786 CAGCATAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.04
43 1 0.01
44 34 0.41
45 2 0.02
46 39 0.47
47 1 0.01
48 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTATAAAAGTAGGAGTCAGTTTAGAGACTCACCTGTTAGGTTC
Found at i:39673997 original size:13 final size:14
Alignment explanation
Indices: 39673979--39674008 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39673969 TGAATGATCA
39673979 ATATATGCATG-AC
1 ATATATGCATGAAC
39673992 ATATATGCATGAAC
1 ATATATGCATGAAC
39674006 ATA
1 ATA
39674009 CATTTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
ATATATGCATGAAC
Found at i:39674130 original size:8 final size:8
Alignment explanation
Indices: 39674110--39674140 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
39674100 TTTATCCTAG
39674110 AAAATTAAT
1 AAAATT-AT
39674119 AAAATTAT
1 AAAATTAT
39674127 AAAATTAT
1 AAAATTAT
39674135 AAAATT
1 AAAATT
39674141 CACCCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:39674243 original size:17 final size:17
Alignment explanation
Indices: 39674203--39674237 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39674193 CGGTACTAAT
* *
39674203 TCACATTTCCATCGTCA
1 TCACCTTTCCATCATCA
39674220 TCACCTTTCCATCATCA
1 TCACCTTTCCATCATCA
39674237 T
1 T
39674238 TTCCTTGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.03, T:0.37
Consensus pattern (17 bp):
TCACCTTTCCATCATCA
Found at i:39675758 original size:31 final size:31
Alignment explanation
Indices: 39675722--39675804 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
39675712 GTAGTCTTGT
* * *
39675722 GTGTGAACAATCGGCAATGAGGAGTCTTTAG
1 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
39675753 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
1 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
39675784 GTGTGAACAATCAGCAATGAA
1 GTGTGAACAATCAGCAATGAA
39675805 AAGTAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (31 bp):
GTGTGAACAATCAGCAATGAAGAGCCTTTAG
Found at i:39677126 original size:6 final size:6
Alignment explanation
Indices: 39677108--39677137 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
39677098 GCAAATGGAT
39677108 CATTTC TCATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTT
39677138 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:39677383 original size:23 final size:24
Alignment explanation
Indices: 39677347--39677392 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
39677337 ATGATTTATA
*
39677347 ATTAAGTTTCAACT-TTTTTTCCT
1 ATTAAGTTTAAACTATTTTTTCCT
*
39677370 ATTAATTTTAAACTCATTTTTTC
1 ATTAAGTTTAAACT-ATTTTTTC
39677393 ACAAATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTAAGTTTAAACTATTTTTTCCT
Found at i:39681704 original size:40 final size:40
Alignment explanation
Indices: 39681659--39681760 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
39681649 TTCATAGCAA
* ** * *
39681659 ACTGAAGTGCAAATAAAGGCATGAATGTGCTATCAGAGCC
1 ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
* *
39681699 ACTGAAGTGCAAACAGAGGCACAAATGTGCGATCAAAGGC
1 ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
* *
39681739 ACCGAAGTACAAATAGAGGCAC
1 ACTGAAGTGCAAATAGAGGCAC
39681761 CGAAGTGAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (40 bp):
ACTGAAGTGCAAATAGAGGCACAAATGTGCGATCAAAGCC
Found at i:39681715 original size:20 final size:20
Alignment explanation
Indices: 39681659--39681716 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
39681649 TTCATAGCAA
* * *
39681659 ACTGAAGTGCAAATAAAGGC
1 ACTGAAGTGCAAACAGAGCC
* *
39681679 A-TGAATGTGCTATCAGAGCC
1 ACTGAA-GTGCAAACAGAGCC
39681699 ACTGAAGTGCAAACAGAG
1 ACTGAAGTGCAAACAGAG
39681717 GCACAAATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (20 bp):
ACTGAAGTGCAAACAGAGCC
Found at i:39682733 original size:16 final size:17
Alignment explanation
Indices: 39682708--39682740 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39682698 AGATGATGGC
*
39682708 ATTATTGTTTT-ATTTA
1 ATTATAGTTTTAATTTA
39682724 ATTATAGTTTTAATTTA
1 ATTATAGTTTTAATTTA
39682741 TAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
ATTATAGTTTTAATTTA
Found at i:39692279 original size:26 final size:26
Alignment explanation
Indices: 39692249--39692301 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
39692239 TTCACAAAAG
39692249 GCCTAAAGGTTTATGCATGATTTGGT
1 GCCTAAAGGTTTATGCATGATTTGGT
39692275 GCCTAAAGGTTTATGCATGATTTGGT
1 GCCTAAAGGTTTATGCATGATTTGGT
39692301 G
1 G
39692302 TTGGAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (26 bp):
GCCTAAAGGTTTATGCATGATTTGGT
Found at i:39693976 original size:26 final size:26
Alignment explanation
Indices: 39693917--39694008 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
39693907 GCTCGCCATG
* ***
39693917 AAGGCTTCCATTTCATATATTGTCACA
1 AAGGCTTCCATTTCAGATA-CACCACA
* *
39693944 AAGGCTTTCTTTTCAGATACACCACA
1 AAGGCTTCCATTTCAGATACACCACA
*
39693970 AAGGCTTCCATTTCAGATACTCCACA
1 AAGGCTTCCATTTCAGATACACCACA
*
39693996 AAGACTTCCATTT
1 AAGGCTTCCATTT
39694009 TCTGACGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 39 0.71
27 16 0.29
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (26 bp):
AAGGCTTCCATTTCAGATACACCACA
Found at i:39697001 original size:29 final size:29
Alignment explanation
Indices: 39696959--39697022 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
39696949 ATTTTTTTTT
*
39696959 TTTGTTTAAATTAGGCCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
*
39696988 TTTGTTCAAATTAGGTCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
*
39697017 ATTGTT
1 TTTGTT
39697023 TTCACATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
TTTGTTCAAATTAGGCCCTGAACTTGGCA
Found at i:39697069 original size:57 final size:58
Alignment explanation
Indices: 39696998--39697111 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 58
39696988 TTTGTTCAAA
* * * * ** *
39696998 TTAGGTCCTGAACTTGGCAATTGTTTTCACATTGGGGCTT-AAACTTTTTTT-TCCAAG
1 TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAA-TTTTTTTATCCAAG
*
39697055 TTAGGCCCTAAACTTGGTAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAA
1 TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAA
39697112 ATTGGTCCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
57 39 0.83
58 8 0.17
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (58 bp):
TTAGGCCCTAAACTTGGCAAATATTCCCACATTGGGACTTCAAATTTTTTTATCCAAG
Found at i:39697703 original size:15 final size:16
Alignment explanation
Indices: 39697683--39697712 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39697673 TAAATAAAAT
39697683 AAAATTT-TAATTTTA
1 AAAATTTCTAATTTTA
39697698 AAAATTTCTAATTTT
1 AAAATTTCTAATTTT
39697713 TTCATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTCTAATTTTA
Found at i:39697936 original size:20 final size:21
Alignment explanation
Indices: 39697899--39697938 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39697889 ATTATTAGAA
* *
39697899 AATTTAAAAATTTTAAAAATC
1 AATTTAAAAAGTTCAAAAATC
39697920 AATTT-AAAAGTTCAAAAAT
1 AATTTAAAAAGTTCAAAAAT
39697939 TTACAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
AATTTAAAAAGTTCAAAAATC
Found at i:39700527 original size:29 final size:30
Alignment explanation
Indices: 39700484--39700542 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
39700474 AAATTAGATC
* *
39700484 AAATCAAATTTTCATGTATAAAATTACACA
1 AAATCAAATATTCATATATAAAATTACACA
* *
39700514 AAATCAAA-ATTCATATATATAATTGCACA
1 AAATCAAATATTCATATATAAAATTACACA
39700543 TTAAACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAATATTCATATATAAAATTACACA
Found at i:39702754 original size:140 final size:142
Alignment explanation
Indices: 39702428--39702778 Score: 501
Period size: 142 Copynumber: 2.5 Consensus size: 142
39702418 ATATTGTTTC
* * *
39702428 AAGCTTGAAGCAACATAAAATAAAAAAATACAAATGTGAGTAGTAGAGGAATTGAACTCGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
* * *
39702493 -AAGGATGTAATTGCAACTATATAATCATCCAACAAAAGAACTAATATGTTAAAAAAAATTAATT
66 CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
39702557 AAAATTAAAAAAA
131 AAAATT-AAAAAA
* * * *
39702570 AAACTTGAAGCAACATGAAATAAAAAAATACAAATGTGAATAGGAAAGAAATTGAACTTGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
* * * * *
39702635 CAATGATGTATTTGCAACTATCTAACCATCTAACTAAAGAACTAACATATT-AAAAAAATTAATT
66 CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
*
39702699 AAAATT-TAAAA
131 AAAATTAAAAAA
* * *
39702710 AAGCCTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATCGAACCCGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
39702775 CAAG
66 CAAG
39702779 AATAAAAGAA
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
140 65 0.35
142 77 0.42
143 42 0.23
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (142 bp):
AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTCGAGACT
CAAGGATGTAATTGCAACTATATAACCATCCAACAAAAGAACTAACATATTAAAAAAAATTAATT
AAAATTAAAAAA
Found at i:39704578 original size:19 final size:17
Alignment explanation
Indices: 39704554--39704593 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
39704544 TAATAATTAA
39704554 AATAAAACCAAATTATCCT
1 AATAAAA-CAAATT-TCCT
*
39704573 AATAAAATAAATTTCCT
1 AATAAAACAAATTTCCT
39704590 AATA
1 AATA
39704594 TAATTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAACAAATTTCCT
Found at i:39704613 original size:3 final size:3
Alignment explanation
Indices: 39704605--39704640 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
39704595 AATTAAACTA
39704605 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39704641 CACAACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39706439 original size:20 final size:21
Alignment explanation
Indices: 39706396--39706475 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
39706386 ATAAACATTA
*
39706396 AATTAAACTTAATATTAAGAT
1 AATTAAATTTAATATTAAGAT
39706417 AA-TAAATTTAATATTAA-ATT
1 AATTAAATTTAATATTAAGA-T
*
39706437 AATTAAA--TACTATTAAGAT
1 AATTAAATTTAATATTAAGAT
39706456 AAGTATTAAATTTAAT-TTAA
1 -A--ATTAAATTTAATATTAA
39706476 TATTAAACTA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
19 10 0.21
20 19 0.40
21 6 0.12
22 6 0.12
23 4 0.08
24 3 0.06
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (21 bp):
AATTAAATTTAATATTAAGAT
Found at i:39712896 original size:18 final size:19
Alignment explanation
Indices: 39712873--39712918 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
39712863 CTGTGCTGCG
39712873 GCCGTGTGG-AAGGCCTAA
1 GCCGTGTGGAAAGGCCTAA
*
39712891 GCCGTGTGGAAAGGCCTAG
1 GCCGTGTGGAAAGGCCTAA
*
39712910 GTCGTGTGG
1 GCCGTGTGG
39712919 GGGTCAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (19 bp):
GCCGTGTGGAAAGGCCTAA
Found at i:39724065 original size:89 final size:88
Alignment explanation
Indices: 39723913--39724224 Score: 335
Period size: 89 Copynumber: 3.5 Consensus size: 88
39723903 TTGCCACCCT
* * * * * * *
39723913 TTTTCATAGTTCGATAGCCGAAGCTATTCCTTTTGATATTTTGATGGCC-ATCACCATCTCTTTT
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGA--ACTATCCCTTTT
* *
39723977 CATATTTGATGGTTGTCACTATCCC
64 CATATTTAATGGTCGTCACTATCCC
*
39724002 TTTTCATAGTTTGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAA-CTATCCCTTTTC
* *
39724067 ATAGTTCAATGGTCGTCACCATCCC
65 ATA-TTTAATGGTCGTCACTATCCC
* * * * * *
39724092 TTTTCATAGTT-GATGGCCGTCA-CCATCCTTTTTCATAATTTGATAGTCGAAACTATCCCTTTT
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCCTTTTCATAATTCGATAGCCG-AACTATCCCTTTT
* *
39724155 CATATTTCAATAGTCG-AAGCTATCCC
64 CATATTT-AATGGTCGTCA-CTATCCC
*
39724181 TTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGA
1 TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGA
39724225 CATTCGAAGC
Statistics
Matches: 186, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
88 4 0.02
89 125 0.67
90 57 0.31
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (88 bp):
TTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAACTATCCCTTTTCA
TATTTAATGGTCGTCACTATCCC
Found at i:39724125 original size:119 final size:119
Alignment explanation
Indices: 39723913--39724192 Score: 380
Period size: 119 Copynumber: 2.4 Consensus size: 119
39723903 TTGCCACCCT
* * * ** *
39723913 TTTTCATAGTTCGATAGCCGAAGCTATTCCTTTTGATATTTTGATGGCCATCACCATCTCTTTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
* ** * * *
39723978 ATATTTGATGGTTGTCACTATCCCTTTTCATAGTTTGATAGCCGAAGCTATCCC
66 ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
* * *
39724032 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCAATGGTCGTCACCATCCCTTTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
* *
39724097 ATAGTTGATGGCCGTCACCATCCTTTTTCATAATTTGATAGTCGAAACTATCCC
66 ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
* * *
39724151 TTTTCATATTTCAATAGTCGAAGCTATCCCTTTTGATAGTTC
1 TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTC
39724193 GATAGCCGAA
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
119 140 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (119 bp):
TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTGATAGTTCAATGGCCATCACCATCCCTTTTC
ATAGTTGATGGCCGTCACCATCCCTTTTCATAATTTGATAGCCGAAACTATCCC
Found at i:39724234 original size:30 final size:30
Alignment explanation
Indices: 39723913--39724224 Score: 242
Period size: 30 Copynumber: 10.5 Consensus size: 30
39723903 TTGCCACCCT
*
39723913 TTTTCATAGTTCGATAGCCGAAGCTATTCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * * * * *
39723943 TTTTGATATTTTGATGGCC-ATCA-CCATCTC
1 TTTTCATAGTTCGATAGCCGA--AGCTATCCC
* * ** *
39723973 TTTTCATA-TTTGATGGTTGTCA-CTATCCC
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
*
39724002 TTTTCATAGTTTGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
39724032 TTTTCATAATTCGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * * * *
39724062 TTTTCATAGTTCAATGGTCGTCA-CCATCCC
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
* * * *
39724092 TTTTCATAGTT-GATGGCCGTCA-CCATCCT
1 TTTTCATAGTTCGATAGCCG-AAGCTATCCC
* * * *
39724121 TTTTCATAATTTGATAGTCGAAACTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
* * *
39724151 TTTTCATATTTCAATAGTCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
39724181 TTTTGATAGTTCGATAGCCGAAGCTATCCC
1 TTTTCATAGTTCGATAGCCGAAGCTATCCC
*
39724211 TTTTCATAATTCGA
1 TTTTCATAGTTCGA
39724225 CATTCGAAGC
Statistics
Matches: 229, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
29 50 0.22
30 177 0.77
31 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTCATAGTTCGATAGCCGAAGCTATCCC
Found at i:39724245 original size:149 final size:147
Alignment explanation
Indices: 39723953--39724247 Score: 382
Period size: 149 Copynumber: 2.0 Consensus size: 147
39723943 TTTTGATATT
* * ** *
39723953 TTGATGGCCATCACCATCTCTTTTCATATTTGATGGTTGTCACTATCCCTTTTCATAGTTTGATA
1 TTGATGGCCATCACCATCTCTTTTCATATTTGATAGTCGAAACTATCCCTTTTCATAGTTTAATA
*
39724018 GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCAATGGTCGT
66 GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTCAAT-GTCGT
* *
39724083 CACCATCCCTTTTCATAG
130 AACCATACCTTTTCATAG
*
39724101 TTGATGGCCGTCACCATC-CTTTTTCATAATTTGATAGTCGAAACTATCCCTTTTCATA-TTTCA
1 TTGATGGCCATCACCATCTC-TTTTCAT-ATTTGATAGTCGAAACTATCCCTTTTCATAGTTT-A
* * *
39724164 ATAGTCGAAGCTATCCCTTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGACAT-
63 ATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTC-A-ATG
*
39724228 TCG-AAGCCATACTTTTTCAT
126 TCGTAA-CCATACCTTTTCAT
39724248 TGGTCGATGA
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
147 1 0.01
148 28 0.22
149 96 0.75
150 1 0.01
151 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (147 bp):
TTGATGGCCATCACCATCTCTTTTCATATTTGATAGTCGAAACTATCCCTTTTCATAGTTTAATA
GCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTCAATGTCGTA
ACCATACCTTTTCATAG
Found at i:39724255 original size:60 final size:60
Alignment explanation
Indices: 39724000--39724255 Score: 151
Period size: 60 Copynumber: 4.3 Consensus size: 60
39723990 TGTCACTATC
* * * * * * * *
39724000 CCTTTTCATAGTTTGATAGCCGAAGCTATCCCTTTTCATAATTCGATAGCCGAAGCTATC
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* * * * ** * * * * *
39724060 CCTTTTCATAGTTCAATGGTCGTCACCATCCCTTTTCATAGTTGATGGCCGTC--A-CCAT-
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCA--ACAGTCGAAGCCATA
** * * * * * *
39724118 CCTTTTTCATAATTTGATAGTCGAAACTATCCCTTTTCATATTTCAATAGTCGAAGCTATC
1 CC-TTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* * * * *
39724179 CCTTTTGATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCGACATTCGAAGCCATA
1 CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
* *
39724239 CTTTTTCATTGGTCGAT
1 CCTTTTCATAGGTCGAT
39724256 GACCGTCGAT
Statistics
Matches: 145, Mismatches: 44, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
57 3 0.02
58 2 0.01
59 38 0.26
60 98 0.68
61 2 0.01
62 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (60 bp):
CCTTTTCATAGGTCGATAGCCGAAACTATCCCTTTTCATAATTCAACAGTCGAAGCCATA
Found at i:39726191 original size:109 final size:109
Alignment explanation
Indices: 39726000--39726217 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
39725990 ATCACGGGAA
*
39726000 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTATCATCTGAAGATCCGATT
1 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
39726065 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
66 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
39726109 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
1 TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
39726174 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
66 CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
39726218 CCATAACCAG
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (109 bp):
TAAATCAAAATGTCATCTATGAATACTACCACAAACTGATCCAGCTACCATCTGAAGATCCGATT
CATCAAATCCATAAAAATAGCAGGTGCATTAGTAAGTCCGAAAG
Found at i:39728549 original size:23 final size:23
Alignment explanation
Indices: 39728511--39728591 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
39728501 ATCTACCTTG
*
39728511 TTTGGACAGC-TATTATACATCAA
1 TTTGGACAGCAT-TTATACACCAA
*
39728534 TTTGGACAGCATTTATATACCAA
1 TTTGGACAGCATTTATACACCAA
* ** *
39728557 ATTAAACATCATTTATACACCAAAA
1 TTTGGACAGCATTTATACACC--AA
39728582 TTTGGACAGC
1 TTTGGACAGC
39728592 TGATATACAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
23 35 0.80
24 1 0.02
25 8 0.18
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCATTTATACACCAA
Found at i:39728685 original size:69 final size:69
Alignment explanation
Indices: 39728540--39728760 Score: 327
Period size: 69 Copynumber: 3.2 Consensus size: 69
39728530 TCAATTTGGA
* * * * * * *
39728540 CAGCATTTATATACCAAATTAAACATCATTTATACACCAAAATTTGGACAGC-TGATATACAACA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTT-AACAGCAT-ATATACAACA
39728604 AATGGG
64 AATGGG
* *
39728610 CAGCATATACATACCAAATTGAGTAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
39728675 TGGG
66 TGGG
*
39728679 CAGCATATACGTACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
39728744 TGGG
66 TGGG
39728748 CAGCATATACATA
1 CAGCATATACATA
39728761 ATACATCATA
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
69 99 0.72
70 39 0.28
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (69 bp):
CAGCATATACATACCAAATTGAGCAACATTTTTACACCAAAATTTAACAGCATATATACAACAAA
TGGG
Found at i:39729618 original size:41 final size:41
Alignment explanation
Indices: 39729573--39729729 Score: 217
Period size: 41 Copynumber: 3.8 Consensus size: 41
39729563 TTGTATAAAA
* * * * *
39729573 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
39729614 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
39729655 CACCGGCACAGAA-CCTGCTAGGCATAACGCCTGATATAATT
1 CACCGGCACA-AAGCCTGCTAGGCATAAAGCCTGATATAATT
*
39729696 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
39729730 ACTTACAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
40 2 0.02
41 98 0.96
42 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:39732185 original size:13 final size:13
Alignment explanation
Indices: 39732169--39732193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39732159 TTTAAAAAAA
39732169 TTTTTTAAAATTT
1 TTTTTTAAAATTT
39732182 TTTTTTAAAATT
1 TTTTTTAAAATT
39732194 GGTGTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTAAAATTT
Found at i:39737455 original size:15 final size:15
Alignment explanation
Indices: 39737431--39737462 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39737421 TATGCTTGCA
*
39737431 AAATATAAAAGACAT
1 AAATACAAAAGACAT
39737446 AAATACAAAAGACAT
1 AAATACAAAAGACAT
39737461 AA
1 AA
39737463 TAGTGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:39744886 original size:71 final size:71
Alignment explanation
Indices: 39744793--39744930 Score: 174
Period size: 71 Copynumber: 1.9 Consensus size: 71
39744783 CTTTCCCCCC
* * ** *
39744793 AAAAATTTTACTTTCCCTCAAACCC-CACAACTTTTTTTCCTTTTATTTTTCCCCAAAAATTTTA
1 AAAAATTTTACTTTCCCCCAAACCCTCAAAAC-TTTTTTCCTTTT-GCTTCCCCCAAAAATTTTA
39744857 CTTCTCTT
64 CTTCTCTT
*
39744865 AAAAA-TTTAC-TTCCTCCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAACTTTTAC
1 AAAAATTTTACTTTCC-CCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAAATTTTAC
39744928 TTC
65 TTC
39744931 CTCCTAAACC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
70 23 0.40
71 25 0.43
72 10 0.17
ACGTcount: A:0.27, C:0.30, G:0.01, T:0.42
Consensus pattern (71 bp):
AAAAATTTTACTTTCCCCCAAACCCTCAAAACTTTTTTCCTTTTGCTTCCCCCAAAAATTTTACT
TCTCTT
Found at i:39746630 original size:37 final size:38
Alignment explanation
Indices: 39746584--39746674 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 38
39746574 TAGTTCCACA
*
39746584 AATT-TGGTGTGTAGGGTGGATGGGCTTAT-TATGGTCC
1 AATTGTGGTGTGTAGGGTGGATGGGCTT-TCTATAGTCC
* * *
39746621 TA-TGTGGTGTGCAGGGTGGATGGGCTTTCTTTAGTCC
1 AATTGTGGTGTGTAGGGTGGATGGGCTTTCTATAGTCC
39746658 AATTGTGGTGTGTAGGG
1 AATTGTGGTGTGTAGGG
39746675 GGCCAGAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 2 0.04
37 30 0.67
38 13 0.29
ACGTcount: A:0.14, C:0.09, G:0.40, T:0.37
Consensus pattern (38 bp):
AATTGTGGTGTGTAGGGTGGATGGGCTTTCTATAGTCC
Found at i:39756525 original size:266 final size:265
Alignment explanation
Indices: 39756027--39756556 Score: 1015
Period size: 266 Copynumber: 2.0 Consensus size: 265
39756017 CGCAGTGCTC
*
39756027 TTTGCTCCCTTCCGGTCATTCTCCTCTAGTTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
39756092 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
*
39756157 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
131 TATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
39756222 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
196 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
39756287 GTTTT
261 GTTTT
*
39756292 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGGTGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
39756357 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTCTTTTTGG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTT-TTTTTGG
*
39756422 GTATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCC
130 GTATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCA
39756487 CTCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACT
195 CTCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACT
39756552 TGTTT
260 TGTTT
39756557 ATCAAGGCTC
Statistics
Matches: 260, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
265 120 0.46
266 140 0.54
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (265 bp):
TTTGCTCCCTTCCGGTCATTCTCCTCTAATTGATGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
TATTAGTTAATTTTCTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
GTTTT
Found at i:39763782 original size:30 final size:30
Alignment explanation
Indices: 39763722--39763790 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
39763712 TCTACTTATA
*
39763722 TTTATTTTATTTTGTTTCATATTTATATTT
1 TTTATTTTATTTTGTTTCATATTTAAATTT
* **
39763752 TTTATTTTGTTTTGTTTTGT-TTTAAAATTT
1 TTTATTTTATTTTGTTTCATATTT-AAATTT
39763782 TTATATTTT
1 TT-TATTTT
39763791 TAATTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 24 0.73
31 6 0.18
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTGTTTCATATTTAAATTT
Found at i:39765430 original size:46 final size:44
Alignment explanation
Indices: 39765348--39765435 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 44
39765338 TTTTTATTTC
*
39765348 ATATTGTTTCAAGTTTTTTTAACTAATGTTTATAATTAATAAAT
1 ATATTGTTTCAAGTTTTTTTAACTAATCTTTATAATTAATAAAT
* * * *
39765392 ATATTGTTTTCAATTGTTTTTTAATTCATCTTTTTAATTAATAA
1 ATATTG-TTTCAAGT-TTTTTTAACTAATCTTTATAATTAATAA
39765436 CTCTTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 6 0.16
45 7 0.19
46 24 0.65
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (44 bp):
ATATTGTTTCAAGTTTTTTTAACTAATCTTTATAATTAATAAAT
Found at i:39766250 original size:28 final size:27
Alignment explanation
Indices: 39766204--39766261 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
39766194 TGTATCTCGG
39766204 TAAATATAAAAAAACAACATACTTATT
1 TAAATATAAAAAAACAACATACTTATT
* *
39766231 TAAATATTAAAAAAACAACATATTTCTT
1 TAAATA-TAAAAAAACAACATACTTATT
39766259 TAA
1 TAA
39766262 TTCCACTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAATATAAAAAAACAACATACTTATT
Found at i:39769140 original size:23 final size:23
Alignment explanation
Indices: 39769075--39769140 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
39769065 TCACATGTAT
*
39769075 TATTTATTTAAAATTTATATATG
1 TATTTATTTAAAATTTATATATA
**
39769098 TAATTTAATTT-ACTTCTTATATA-A
1 T-ATTT-ATTTAAAAT-TTATATATA
39769122 TATTTACTTTAAAATTTAT
1 TATTTA-TTTAAAATTTAT
39769141 TTAGATACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
22 1 0.03
23 12 0.36
24 9 0.27
25 11 0.33
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTTATTTAAAATTTATATATA
Found at i:39776178 original size:87 final size:87
Alignment explanation
Indices: 39776026--39776468 Score: 670
Period size: 87 Copynumber: 5.1 Consensus size: 87
39776016 AGATCAGTGA
* * *
39776026 AGATTGAAAACAAAGCCTTGCCTCCACCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATATTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
39776091 CTTCTTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
39776113 AGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAGCAAATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
39776178 CTTCCTGCATTGACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
39776200 AGATCGAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGTTGGTTAAAGATAGCAGATTTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
39776265 CTTCCTACATTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
** *
39776287 AGATAAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
39776352 CTTCCTGTGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
39776374 AAATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAAATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* ** *
39776439 CCTCCTGCGTCGACAGTGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
39776461 AGATCGAA
1 AGATCGAA
39776469 GATTACAAGT
Statistics
Matches: 320, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 320 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:39776222 original size:43 final size:43
Alignment explanation
Indices: 39776087--39776222 Score: 100
Period size: 45 Copynumber: 3.1 Consensus size: 43
39776077 ATAGCAGATA
* * * *
39776087 TTGCCTTCTTGCGTTAACAACGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
* * * * ** *
39776130 TTGCC-TCCAT-CGATTG-CAGTGGAGCTGGTTAAAGATAGCAAA-TC
1 TTGCCTTCC-TGC-ATTGACAGCGAAGCAGATCGAA-A-A-CAAAGCC
39776174 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
1 TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
39776217 TTGCCT
1 TTGCCT
39776223 CTATCGGTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 18
0.65 0.18 0.18
Matches are distributed among these distances:
42 17 0.26
43 17 0.26
44 13 0.20
45 19 0.29
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (43 bp):
TTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCC
Found at i:39776616 original size:44 final size:45
Alignment explanation
Indices: 39776563--39776759 Score: 132
Period size: 44 Copynumber: 4.2 Consensus size: 45
39776553 TGAAGCTAGT
*
39776563 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* * * * * *
39776607 GATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCATTAGATTGAAACCAGA
1 AATCTTATCTCCCTGAGATTACAGT-G-G-AG--CGGATTAAAAT--AA--AGA
* * * ** *
39776661 AATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGA
* *
39776705 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAGAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
*
39776749 GATCTTATCTC
1 AATCTTATCTC
39776760 TTTGAAGTTA
Statistics
Matches: 114, Mismatches: 26, Indels: 26
0.69 0.16 0.16
Matches are distributed among these distances:
43 3 0.03
44 63 0.55
45 3 0.03
46 1 0.01
47 2 0.02
49 12 0.11
50 2 0.02
51 4 0.04
52 1 0.01
53 3 0.03
54 20 0.18
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
Found at i:39777020 original size:50 final size:50
Alignment explanation
Indices: 39776868--39777030 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 50
39776858 AGTGGAACAA
* * * *
39776868 ATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
* *** * * * * ** *
39776918 ATTAAAGCTACAGTAGTGAATCTTACCTCCCAGGCAGTACAGTGGAACAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
* * *
39776968 ATTAAAGCCACAACGGTAAATCTTGCCTCCCTGACATTGTAGTTAAAAAG
1 ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
39777018 ATTAAAGCCACAA
1 ATTAAAGCCACAA
39777031 TGGCGAACTT
Statistics
Matches: 85, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (50 bp):
ATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCAGTTAAAAAG
Found at i:39777613 original size:14 final size:14
Alignment explanation
Indices: 39777590--39777624 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39777580 CAACACACAA
*
39777590 AAGAACAAAAAAGG
1 AAGAAAAAAAAAGG
39777604 AAGAAAAAAAAAGG
1 AAGAAAAAAAAAGG
39777618 -AGAAAAA
1 AAGAAAAA
39777625 TAGCAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAGG
Found at i:39778727 original size:23 final size:23
Alignment explanation
Indices: 39778662--39778727 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
39778652 TCACATGTAT
*
39778662 TATTTATTTAAAATTTATATATG
1 TATTTATTTAAAATTTATATATA
**
39778685 TATTTTAATTT-ACTTCTTATATA-A
1 TA-TTT-ATTTAAAAT-TTATATATA
39778709 TATTTACTTTAAAATTTAT
1 TATTTA-TTTAAAATTTAT
39778728 TTAGATACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
22 1 0.03
23 12 0.36
24 9 0.27
25 11 0.33
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTATTTAAAATTTATATATA
Found at i:39785395 original size:50 final size:50
Alignment explanation
Indices: 39785297--39785437 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 50
39785287 TATTGAGGTT
* * * *
39785297 ATGAGAGGTCCCACGTATGACCATGTCTGAGACATGGCGTTGGTACCGAG
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATTGGCACCGAG
* *
39785347 ATGAGAGGTCCCCCATAAGACCATGTCTGAGACATGGCATAT-GCACCGAT
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCAT-TGGCACCGAG
** ** * * *
39785397 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATT
1 ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATT
39785438 TGCAGTACAG
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.01
50 74 0.97
51 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGAGACATGGCATTGGCACCGAG
Found at i:39787566 original size:2 final size:2
Alignment explanation
Indices: 39787561--39787601 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39787551 TAATAAGGAA
39787561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39787602 CATACAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39789767 original size:26 final size:26
Alignment explanation
Indices: 39789738--39789795 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
39789728 TTAACGTGGT
*
39789738 TAAAATCATCAAAATTTTACCGAGGG
1 TAAAATCATCAAAATATTACCGAGGG
* * *
39789764 TAAAATCGTCAAAATATTACCTAGTG
1 TAAAATCATCAAAATATTACCGAGGG
39789790 TAAAAT
1 TAAAAT
39789796 TGGAGTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (26 bp):
TAAAATCATCAAAATATTACCGAGGG
Found at i:39793542 original size:14 final size:14
Alignment explanation
Indices: 39793523--39793551 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39793513 TACATTTTGA
39793523 TGGAGTCATATGTT
1 TGGAGTCATATGTT
39793537 TGGAGTCATATGTT
1 TGGAGTCATATGTT
39793551 T
1 T
39793552 AACTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (14 bp):
TGGAGTCATATGTT
Found at i:39795418 original size:40 final size:40
Alignment explanation
Indices: 39795364--39795448 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
39795354 CCTTTGACTT
*
39795364 TAAAA-CTTTTATCAACCTCTTTAGCTTCAATTTCAATAC
1 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
39795403 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
1 TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
39795443 TAAAAC
1 TAAAAC
39795449 AAAAAATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 5 0.11
40 39 0.89
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (40 bp):
TAAAACCTTTTATCAACCTCCTTAGCTTCAATTTCAATAC
Found at i:39798426 original size:37 final size:37
Alignment explanation
Indices: 39798362--39798470 Score: 114
Period size: 37 Copynumber: 3.0 Consensus size: 37
39798352 TGTACACAAG
* *
39798362 TAATCCAACC-AAAACATGCCAAGTGCTCCAAAGAGA
1 TAATCCAACCGATAACATGCCAAATGCTCCAAAGAGA
** * *
39798398 TAATCCAATTGATAACATGTCAAATGCT-CAGAAGAGT
1 TAATCCAACCGATAACATGCCAAATGCTCCA-AAGAGA
* * *
39798435 TAATCCAACCGATAACACGCCAAATGTTCCGAAGAG
1 TAATCCAACCGATAACATGCCAAATGCTCCAAAGAG
39798471 CTATACATCT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
36 10 0.17
37 47 0.81
38 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (37 bp):
TAATCCAACCGATAACATGCCAAATGCTCCAAAGAGA
Found at i:39807749 original size:20 final size:19
Alignment explanation
Indices: 39807688--39807747 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
39807678 GTCTCTCTCA
39807688 ATAAAAATTACAAAATAATTT
1 ATAAAAATT-CAAAAT-ATTT
*
39807709 -TTAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
*
39807727 ATAAAAATTCTAAA-ATTT
1 ATAAAAATTCAAAATATTT
39807745 ATA
1 ATA
39807748 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 11 0.31
19 17 0.49
20 7 0.20
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:39807769 original size:17 final size:18
Alignment explanation
Indices: 39807738--39807771 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39807728 TAAAAATTCT
*
39807738 AAAATTTATATATTTTTA
1 AAAATTTATAAATTTTTA
39807756 AAAATTT-TAAATTTTT
1 AAAATTTATAAATTTTT
39807772 TTTGCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATTTATAAATTTTTA
Found at i:39809287 original size:18 final size:18
Alignment explanation
Indices: 39809266--39809308 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
39809256 TTTTTCTAAA
*
39809266 CTCTTAACTCTCTCAAGT
1 CTCTCAACTCTCTCAAGT
*
39809284 CTCTCAACTCTCTCAATT
1 CTCTCAACTCTCTCAAGT
39809302 CTCTCAA
1 CTCTCAA
39809309 GTTTTGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.37
Consensus pattern (18 bp):
CTCTCAACTCTCTCAAGT
Found at i:39809305 original size:11 final size:9
Alignment explanation
Indices: 39809266--39809308 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
39809256 TTTTTCTAAA
*
39809266 CTCTTAACT
1 CTCTCAACT
*
39809275 CTCTCAAGT
1 CTCTCAACT
39809284 CTCTCAACT
1 CTCTCAACT
*
39809293 CTCTCAATT
1 CTCTCAACT
39809302 CTCTCAA
1 CTCTCAA
39809309 GTTTTGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.37
Consensus pattern (9 bp):
CTCTCAACT
Found at i:39823782 original size:7 final size:6
Alignment explanation
Indices: 39823761--39823792 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
39823751 ATTTTTCAGG
39823761 TCATTT TCATTT TCATTTT TCATTT TCATTT T
1 TCATTT TCATTT TCA-TTT TCATTT TCATTT T
39823793 GGAGAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TCATTT
Found at i:39823782 original size:13 final size:13
Alignment explanation
Indices: 39823764--39823792 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39823754 TTTCAGGTCA
39823764 TTTTCATTTTCAT
1 TTTTCATTTTCAT
39823777 TTTTCATTTTCAT
1 TTTTCATTTTCAT
39823790 TTT
1 TTT
39823793 GGAGAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:39823896 original size:57 final size:57
Alignment explanation
Indices: 39823777--39823894 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
39823767 TCATTTTCAT
** * ** *
39823777 TTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATTTTATTTTTCTA
1 TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATTTTATTTTTCCA
**
39823834 TTTTCATTTTCATTTTCAAGAAAACCTTAATCATTTCCAAAAGATTCTTATTTTTCCA
1 TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATT-TTATTTTTCCA
39823892 TTT
1 TTT
39823895 CACCATTTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 39 0.75
58 13 0.25
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (57 bp):
TTTTCATTTTCATTTTCAAGAAAACCACAATCATTTCCAAAAGATTTTATTTTTCCA
Found at i:39829935 original size:23 final size:23
Alignment explanation
Indices: 39829909--39829955 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39829899 CAGGATGGCG
39829909 CCAAAGTGCCAAG-AACAGGAGCA
1 CCAAAGTG-CAAGTAACAGGAGCA
*
39829932 CCAAAGTGCAAGTAACAGGGGCA
1 CCAAAGTGCAAGTAACAGGAGCA
39829955 C
1 C
39829956 TGATAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.40, C:0.26, G:0.28, T:0.06
Consensus pattern (23 bp):
CCAAAGTGCAAGTAACAGGAGCA
Found at i:39830175 original size:30 final size:30
Alignment explanation
Indices: 39830141--39830200 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39830131 TATTTTTAGA
*
39830141 AGCCACACGGGCTAGG-CACACGCCCGTGTG
1 AGCCACACGGGCT-GGACACACGCCCATGTG
*
39830171 AGCCACATGGGCTGGACACACGCCCATGTG
1 AGCCACACGGGCTGGACACACGCCCATGTG
39830201 CCAGCCCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.22, C:0.35, G:0.32, T:0.12
Consensus pattern (30 bp):
AGCCACACGGGCTGGACACACGCCCATGTG
Found at i:39837051 original size:15 final size:16
Alignment explanation
Indices: 39837031--39837065 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
39837021 AAGCAATTAC
39837031 GACATG-AAAATATAT
1 GACATGAAAAATATAT
39837046 GACATGAAAAAATATAT
1 GACATG-AAAAATATAT
39837063 GAC
1 GAC
39837066 CATGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (16 bp):
GACATGAAAAATATAT
Found at i:39843151 original size:13 final size:13
Alignment explanation
Indices: 39843135--39843200 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
39843125 TTTAAACCAA
*
39843135 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
39843148 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
39843161 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
**
39843174 ACTTTTCAAAATT
1 ACTTTTCAAAAGC
39843187 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39843200 A
1 A
39843201 ATGAAGAATT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39847658 original size:6 final size:6
Alignment explanation
Indices: 39847647--39847677 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
39847637 GAATGTCGTG
39847647 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
39847678 CAAATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:39848623 original size:14 final size:14
Alignment explanation
Indices: 39848606--39848635 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39848596 TTTTAAAGAA
*
39848606 TTCTTTTTCATATT
1 TTCTTTTACATATT
39848620 TTCTTTTACATATT
1 TTCTTTTACATATT
39848634 TT
1 TT
39848636 TAAAGGGTAT
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:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTTTACATATT
Found at i:39848810 original size:6 final size:6
Alignment explanation
Indices: 39848799--39848829 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
39848789 ATTTTTAATA
39848799 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
39848830 TAATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:39849051 original size:34 final size:34
Alignment explanation
Indices: 39849013--39849084 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
39849003 TGATTTTTAC
* * *
39849013 TTTTTGAA-TTTT-AAAGATTATTTTTTTCTTAATT
1 TTTTTAAATTTTTAAAAAATTATATTTTT-TT-ATT
39849047 TTTTTAAATTTTTAAAAAATTATATTTTTTTATT
1 TTTTTAAATTTTTAAAAAATTATATTTTTTTATT
39849081 TTTT
1 TTTT
39849085 AAAAGATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 14 0.42
35 6 0.18
36 13 0.39
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (34 bp):
TTTTTAAATTTTTAAAAAATTATATTTTTTTATT
Found at i:39849073 original size:26 final size:26
Alignment explanation
Indices: 39849044--39849130 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 26
39849034 TTTTTTCTTA
39849044 ATTTTTTTAAATTTTTAAAAAATTAT
1 ATTTTTTTAAATTTTTAAAAAATTAT
* *
39849070 ATTTTTTT-ATTTTTTAAAAGATTAT
1 ATTTTTTTAAATTTTTAAAAAATTAT
**
39849095 ATTTATTTTTTATTTTT-AAAAA-TAT
1 ATTT-TTTTAAATTTTTAAAAAATTAT
39849120 AATTTTTTTAA
1 -ATTTTTTTAA
39849131 TTGTTATGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
25 26 0.51
26 20 0.39
27 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (26 bp):
ATTTTTTTAAATTTTTAAAAAATTAT
Found at i:39849518 original size:21 final size:21
Alignment explanation
Indices: 39849494--39849534 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39849484 ATTATTTTTT
*
39849494 TAAAAAA-ATTTAATGAATTTC
1 TAAAAAATAATTAAT-AATTTC
39849515 TAAAAAATAATTAATAATTT
1 TAAAAAATAATTAATAATTT
39849535 GAAAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAATAATTAATAATTTC
Found at i:39849590 original size:71 final size:70
Alignment explanation
Indices: 39849517--39849799 Score: 530
Period size: 70 Copynumber: 4.0 Consensus size: 70
39849507 TGAATTTCTA
39849517 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
1 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
39849582 AAAAT
66 AAAAT
39849587 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
1 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
39849652 AAAAT
66 AAAAT
39849657 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
1 AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
39849722 AAAAT
66 AAAAT
39849727 AAAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTAATTAAT
1 -AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATA-TT--TTAAT
39849792 TTGTAAAA
62 TTGTAAAA
39849800 GTATTTTTCA
Statistics
Matches: 209, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
70 140 0.67
71 54 0.26
72 2 0.01
74 13 0.06
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (70 bp):
AAAAATAATTAATAATTTGAAAACTAATGTAATTATAAAATATTTTTAAAAATATTTTAATTTGT
AAAAT
Found at i:39856250 original size:31 final size:31
Alignment explanation
Indices: 39856179--39856253 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
39856169 TGAGTTGGTA
* * * *
39856179 CAATTATACACATGACACTTTGATTGTGGTT
1 CAATTATATACATGAAACTTTAATTGTGATT
* ** *
39856210 TAAAAATATACATGAAACTTTAATTTTGATT
1 CAATTATATACATGAAACTTTAATTGTGATT
39856241 CAATTATATACAT
1 CAATTATATACAT
39856254 TTAAAGAAAT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
CAATTATATACATGAAACTTTAATTGTGATT
Found at i:39860783 original size:154 final size:156
Alignment explanation
Indices: 39860583--39860882 Score: 516
Period size: 156 Copynumber: 1.9 Consensus size: 156
39860573 GTGTTTTTTC
39860583 ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
1 ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
* **
39860648 TTTATA-GGAGAGAGTGATCCTATGAGA-TTTTTTATTTAATAATTTTATTATTTTTCATTTCCT
66 TTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGACT
39860711 TCTATATTAAATTCTTAATAAAGCAA
131 TCTATATTAAATTCTTAATAAAGCAA
* * *
39860737 ATATACTATTTTTTTAAAAATGTATTCATT-AATTTTTTTATTGATGATATGTGCAGGATATATT
1 ATATACTA-TTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATT
39860801 ATTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGAC
65 ATTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGAC
39860866 TTCTATATTAAATTCTT
130 TTCTATATTAAATTCTT
39860883 TATGGAAAAT
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
154 47 0.34
155 40 0.29
156 50 0.36
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (156 bp):
ATATACTATTTTTAAAAAATGTATTCATTAAAATTTTTTATTGATGATATGTACAGGATATATTA
TTTATAGGGAGAGAGTGATCATATGAGATTTTTTTATTTAATAATTTTATTATTTTTCATTGACT
TCTATATTAAATTCTTAATAAAGCAA
Found at i:39864755 original size:15 final size:15
Alignment explanation
Indices: 39864735--39864764 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39864725 CCCAGTAAGT
39864735 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
39864750 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
39864765 ACTCCTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GTAACTTTTTGTAAC
Found at i:39867900 original size:42 final size:42
Alignment explanation
Indices: 39867804--39868001 Score: 240
Period size: 42 Copynumber: 4.7 Consensus size: 42
39867794 CAATGTCATA
* * * *
39867804 TCCCAGATATGGTCTTACATGCTATCACATATCGATGCCAATAG
1 TCCCAGACATGGTCTTACACG-AATCACATAACGATGCCAAT-G
*
39867848 --CCAG-CTATGGTCTTACACGAATCTCATAACGATGCCAATG
1 TCCCAGAC-ATGGTCTTACACGAATCACATAACGATGCCAATG
* *
39867888 TCCCAGACATGGTCTTACACGAATCTCATATCGATGCCAATG
1 TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
* *
39867930 TCCCAGACATGGTCTTACACGAATCACATAATGATGTCAATG
1 TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
* *
39867972 TCCCAAACATGATCTTACACGTAATCACAT
1 TCCCAGACATGGTCTTACACG-AATCACAT
39868002 CAAAGTATCC
Statistics
Matches: 137, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 17 0.12
42 110 0.80
43 9 0.07
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAATCACATAACGATGCCAATG
Found at i:39871477 original size:45 final size:45
Alignment explanation
Indices: 39871401--39871516 Score: 173
Period size: 46 Copynumber: 2.6 Consensus size: 45
39871391 TACGTATGAT
*
39871401 CACTTATCAC-TTGTCCCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCCTTGATCAGATAAGTGTAGCTAAGGCTAC
*
39871444 CACTTATCACTTTGTCACTTGGTCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTC-CTTGATCAGATAAGTGTAGCTAAGGCTAC
*
39871490 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTC-CTTGATCAGA
39871517 AGTACTCAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 10 0.15
44 5 0.08
45 19 0.29
46 31 0.48
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (45 bp):
CACTTATCACTTTGTCCTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:39875668 original size:64 final size:63
Alignment explanation
Indices: 39875558--39875676 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
39875548 TTTAAACTTA
* * * *
39875558 ATTATTTAAAATTATAAAAAAATATTTTTTAAATTTTAATTAAAAAAGTATAAATTTGTAAAAT
1 ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATA-AAATTTGTAAAAT
*
39875622 ATTATTCAAATTTAT-AAAAAATATTATATTAAA-TTAAATTAAAAAAAATAAAATT
1 ATTATTCAAAATTATAAAAAAATATT-TATTAAATTTAAATT-AAAAAAATAAAATT
39875677 AATAAAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
63 21 0.44
64 27 0.56
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (63 bp):
ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATAAAATTTGTAAAAT
Found at i:39875683 original size:63 final size:65
Alignment explanation
Indices: 39875558--39875688 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 65
39875548 TTTAAACTTA
* * * * **
39875558 ATTATTTAAAATTATAAAAAAATATTTTTTAAATTTTAATTAAAAAAGTATAAATTTGTAAAA-T
1 ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATATAAATTAATAAAACT
*
39875622 ATTATTCAAATTTAT-AAAAAATATTATATTAAA-TTAAATTAAAAAAA-ATAAAATTAATAAAA
1 ATTATTCAAAATTATAAAAAAATATT-TATTAAATTTAAATTAAAAAAATAT-AAATTAATAAAA
39875684 CT
64 CT
39875686 ATT
1 ATT
39875689 TAAAAATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
62 2 0.04
63 32 0.56
64 23 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (65 bp):
ATTATTCAAAATTATAAAAAAATATTTATTAAATTTAAATTAAAAAAATATAAATTAATAAAACT
Found at i:39882636 original size:22 final size:22
Alignment explanation
Indices: 39882594--39882636 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39882584 AATAGGGGAC
*
39882594 TTCTGTTACTAGTGCTATGATG
1 TTCTGTTACTAGTACTATGATG
* *
39882616 TTCTGTTATTAGTACTTTGAT
1 TTCTGTTACTAGTACTATGAT
39882637 ACTTCGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (22 bp):
TTCTGTTACTAGTACTATGATG
Found at i:39884450 original size:3 final size:3
Alignment explanation
Indices: 39884442--39884476 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39884432 GTTCCTAGAT
39884442 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39884477 TATTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39887896 original size:59 final size:58
Alignment explanation
Indices: 39887825--39887956 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 58
39887815 ATCATTTTAA
* *
39887825 TATTAAATTAATATAATAGTTA-T-CAAGATAAAAATTAGATTAAATTTAATATTAAATC
1 TATTAAAATAATATAATA-TTACTACAAGATAAAAATTAAATTAAATTTAATATTAAA-C
* *
39887883 TTATTAAAATAATAGAATATTATCTACAAGATAAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATATAATATTA-CTACAAGATAAAAATTAAATTAAATTTAATATTAAAC
*
39887943 CATTAAAATAATAT
1 TATTAAAATAATAT
39887957 CATTTTTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 3 0.05
59 28 0.44
60 2 0.03
61 31 0.48
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (58 bp):
TATTAAAATAATATAATATTACTACAAGATAAAAATTAAATTAAATTTAATATTAAAC
Found at i:39899106 original size:31 final size:31
Alignment explanation
Indices: 39899068--39899465 Score: 327
Period size: 31 Copynumber: 13.0 Consensus size: 31
39899058 ATATACATAT
*
39899068 TCATATACGAATCAGA-TTCAAG-AATGTATAA
1 TCATATACAAATCA-ATTTC-AGCAATGTATAA
* *
39899099 TCATATACAAATCAATTT-GGCAATGGATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* ** * * *
39899129 CCATATATGAATCAAGTTCGGGAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
*
39899160 TCATATACAAATTAA-TTCAGCAACT-TAT-A
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
* *
39899189 TCCATATACAATTCAATTTCAACAATGTATAA
1 T-CATATACAAATCAATTTCAGCAATGTATAA
* * *
39899221 CCATATACAAATTAATTTCAGCAAAGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* **
39899252 TCATATACGAATCAA-TTCAGCAACT-TATCT
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
39899282 TCATATACAAATCAATTTC-GACAATGTATAA
1 TCATATACAAATCAATTTCAG-CAATGTATAA
* *
39899313 CCATATACAAATAAATTTCAGCAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* * * **
39899344 TTATATACGAATCAA-TTCGGCAACT-TATCT
1 TCATATACAAATCAATTTCAGCAA-TGTATAA
* *
39899374 TCATATATAAATCAATTTC-GATAATGTATAA
1 TCATATACAAATCAATTTCAG-CAATGTATAA
* * *
39899405 CCATATACAAATAAATTTCAACAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
* * * *
39899436 TTATATACGAATTAA-TTCGGCAATGTATAA
1 TCATATACAAATCAATTTCAGCAATGTATAA
39899466 AACAATCAAA
Statistics
Matches: 291, Mismatches: 58, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
29 3 0.01
30 109 0.37
31 177 0.61
32 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (31 bp):
TCATATACAAATCAATTTCAGCAATGTATAA
Found at i:39899154 original size:61 final size:61
Alignment explanation
Indices: 39899069--39899465 Score: 297
Period size: 61 Copynumber: 6.5 Consensus size: 61
39899059 TATACATATT
* *
39899069 CATATACGAATCAGA-TTCAAG-AATGTATAATCATATACAAATCAATTTGGCAATGGATAAC
1 CATATACAAATCA-ATTTC-AGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
** * * * * ** *
39899130 CATATATGAATCAAGTTCGGGAATGTATAATCATATACAAATTAATTCAGCAACT-TATATC
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TGTATAAC
* * * * * * *
39899191 CATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAAAGTATAAT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* ** *
39899253 CATATACGAATCAA-TTCAGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
1 CATATACAAATCAATTTCAGCAA-TGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* * * * ***
39899314 CATATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCGGCAACT-TATCTT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TGTATAAC
* * * * ** *
39899375 CATATATAAATCAATTTC-GATAATGTATAACCATATACAAATAAATTTCAACAATGTATAAT
1 CATATACAAATCAATTTCAG-CAATGTATAATCATATACAAATCAATTT-GGCAATGTATAAC
* * * *
39899437 TATATACGAATTAA-TTCGGCAATGTATAA
1 CATATACAAATCAATTTCAGCAATGTATAA
39899466 AACAATCAAA
Statistics
Matches: 265, Mismatches: 58, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
60 3 0.01
61 194 0.73
62 68 0.26
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (61 bp):
CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
Found at i:39899225 original size:92 final size:92
Alignment explanation
Indices: 39899068--39899458 Score: 500
Period size: 92 Copynumber: 4.2 Consensus size: 92
39899058 ATATACATAT
** * *
39899068 TCATATACGAATCAGATTCAAG-AA-TGTATAATCATATACAAATCAATTT-GGCAATGGATAAC
1 TCATATACGAATCA-ATTC-AGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
** * * * *
39899130 CATATATGAATCAAGTTCGGGAATGTATAA
63 CATATACAAATAAATTTCAGCAATGTATAA
* * * * * *
39899160 TCATATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
* *
39899225 ATACAAATTAATTTCAGCAAAGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
39899252 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
39899317 ATACAAATAAATTTCAGCAATGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
* * * *
39899344 TTATATACGAATCAATTCGGCAACTTATCTTCATATATAAATCAATTTCGATAATGTATAACCAT
1 TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
*
39899409 ATACAAATAAATTTCAACAATGTATAA
66 ATACAAATAAATTTCAGCAATGTATAA
* * *
39899436 TTATATACGAATTAATTCGGCAA
1 TCATATACGAATCAATTCAGCAA
39899459 TGTATAAAAC
Statistics
Matches: 267, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
90 2 0.01
91 26 0.10
92 239 0.90
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (92 bp):
TCATATACGAATCAATTCAGCAACTTATCTTCATATACAAATCAATTTCGACAATGTATAACCAT
ATACAAATAAATTTCAGCAATGTATAA
Found at i:39913025 original size:21 final size:21
Alignment explanation
Indices: 39913001--39913044 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
39912991 GTCGTGTTGA
39913001 TATATAAAATCGGTTCTTTTC
1 TATATAAAATCGGTTCTTTTC
*
39913022 TATATAACATCGGTTCTTTTC
1 TATATAAAATCGGTTCTTTTC
39913043 TA
1 TA
39913045 GTTCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (21 bp):
TATATAAAATCGGTTCTTTTC
Found at i:39930157 original size:2 final size:2
Alignment explanation
Indices: 39930150--39930187 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39930140 CAGTTGGTAC
39930150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39930188 CTAAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39932720 original size:38 final size:38
Alignment explanation
Indices: 39932651--39932723 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
39932641 TGAATATACT
* * *
39932651 AAACGTGCTTAAAAGAGCAATGTCTATTGATTATATTG
1 AAACGTGCTTAAAAGAGCAATATCCACTGATTATATTG
* * *
39932689 AAACTTGCTTAAACGAGCGATATCCACTGATTATA
1 AAACGTGCTTAAAAGAGCAATATCCACTGATTATA
39932724 CAGAATGGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (38 bp):
AAACGTGCTTAAAAGAGCAATATCCACTGATTATATTG
Found at i:39932887 original size:135 final size:135
Alignment explanation
Indices: 39932641--39932888 Score: 372
Period size: 135 Copynumber: 1.8 Consensus size: 135
39932631 AGTTGAATAT
* * * *
39932641 TGAATATACTAAACGTGCTTAAAAGAGCAATGTCTATTGATTATATTGAAACTTGCTTAAACGAG
1 TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
* *
39932706 CGATATCCACTGATTATACAGAATGGGCTCAAATGAGCAATGTCTACTTGTACAAACGAGCAATA
66 CGATATCCACTGATTATACAGAATGGGCTCAAATGAGAAATATCTACTTGTACAAACGAGCAATA
39932771 TCTAC
131 TCTAC
* * * *
39932776 TGAATCTACTAAACGTGCTCAAAAGAGCAATGTTTATTGATTATACTGAAAGTCGGTCAAACGAG
1 TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
* *
39932841 TGATATTCACTGATTATACTA-AATGGGCTCAAATGAGAAATATCTACT
66 CGATATCCACTGATTATAC-AGAATGGGCTCAAATGAGAAATATCTACT
39932889 GAATATACTG
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
135 99 0.99
136 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (135 bp):
TGAATATACTAAACGTGCTCAAAAGAGCAATGTCTATTGATTATACTGAAACTCGCTCAAACGAG
CGATATCCACTGATTATACAGAATGGGCTCAAATGAGAAATATCTACTTGTACAAACGAGCAATA
TCTAC
Found at i:39932890 original size:37 final size:37
Alignment explanation
Indices: 39932758--39933007 Score: 182
Period size: 37 Copynumber: 6.7 Consensus size: 37
39932748 TCTACTTGTA
* * * *
39932758 CAAACGAGCAATATCTACTGAATCTACTAAACGTGCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
* * * * *
39932795 CAAAAGAGCAATGTTTATTGATTATACTGAAAGTCGG-T
1 CAAACGAGCAATATCTACTGATTATACT-AAA-TGGGCT
**
39932833 CAAACGAGTGATAT-TCACTGATTATACTAAATGGGCT
1 CAAACGAGCAATATCT-ACTGATTATACTAAATGGGCT
* * * * * **
39932870 CAAATGAGAAATATCTACTGAATATACTGAACGTTCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
* * * * *
39932907 CAAAAGAGAAATGTATACTGATTATACTAAAAT-TGCT
1 CAAACGAGCAATATCTACTGATTATACT-AAATGGGCT
* * *
39932944 CAAACAAGCAATATCCATTGATTATACTAAATGGGCT
1 CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
** *
39932981 CAAACGAGTGATATCTACTAATTATAC
1 CAAACGAGCAATATCTACTGATTATAC
39933008 GGAATGCATG
Statistics
Matches: 162, Mismatches: 44, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
36 7 0.04
37 126 0.78
38 28 0.17
39 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (37 bp):
CAAACGAGCAATATCTACTGATTATACTAAATGGGCT
Found at i:39937961 original size:19 final size:21
Alignment explanation
Indices: 39937918--39937969 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
39937908 ATATTTTTCT
* *
39937918 TTTATATTTTTAATCACTATT
1 TTTATATTTTTAATCAATATA
39937939 TTTA-ATTTTTAAT-AATATA
1 TTTATATTTTTAATCAATATA
39937958 TTTATATCTTTT
1 TTTATAT-TTTT
39937970 GCATAGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 11 0.41
21 8 0.30
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATATTTTTAATCAATATA
Found at i:39938393 original size:11 final size:11
Alignment explanation
Indices: 39938329--39938394 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 11
39938319 AAAAATAAAT
39938329 AAATTATA-AA
1 AAATTATATAA
39938339 AAATTGA-A-AA
1 AAATT-ATATAA
*
39938349 AAACTTATTTAA
1 AAA-TTATATAA
*
39938361 AAACTA-ATAGA
1 AAATTATATA-A
39938372 AAATTAT-TAA
1 AAATTATATAA
39938382 AAATTATATAA
1 AAATTATATAA
39938393 AA
1 AA
39938395 TTTAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
10 22 0.49
11 18 0.40
12 5 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (11 bp):
AAATTATATAA
Found at i:39938449 original size:19 final size:19
Alignment explanation
Indices: 39938425--39938466 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39938415 GAAGAAATAT
* * *
39938425 AAAAATTTTAAAATTTTAA
1 AAAAATTATAAAAGTGTAA
39938444 AAAAATTATAAAAGTGTAA
1 AAAAATTATAAAAGTGTAA
39938463 AAAA
1 AAAA
39938467 GTATAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAAGTGTAA
Found at i:39946627 original size:30 final size:30
Alignment explanation
Indices: 39946593--39946649 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
39946583 CTTGATTTGG
39946593 ACTTTGGCAAAATTATGA-TTTTGTCCCTAA
1 ACTTTGGCAAAATTAT-ACTTTTGTCCCTAA
* * *
39946623 ACTTTTGCATATTTATACTTTTGTCCC
1 ACTTTGGCAAAATTATACTTTTGTCCC
39946650 AAAGCTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (30 bp):
ACTTTGGCAAAATTATACTTTTGTCCCTAA
Found at i:39953630 original size:50 final size:49
Alignment explanation
Indices: 39953546--39953707 Score: 159
Period size: 50 Copynumber: 3.3 Consensus size: 49
39953536 ATGCAAGGCT
* * * *
39953546 TAATT-AGATGCAAACTAAATAAACAAATGAGTTACATAATGCATGACA
1 TAATTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
*
39953594 TAATTTAAGATGCAAACTTAATTAACATAGGTGTTACATAATGCATGACA
1 TAA-TTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
* ** * * * * *
39953644 TAATTAAAACACAAACTTTATTAACAT-GTGAGATGCTTTAATGCATGACT
1 TAATTAAGATGCAAACTTAATTAACATAG-GAGTTAC-ATAATGCATGACA
39953694 TAATTAA-ATGCAAA
1 TAATTAAGATGCAAA
39953708 ACACATAATG
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
48 4 0.04
49 31 0.33
50 59 0.63
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (49 bp):
TAATTAAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACA
Found at i:39962834 original size:25 final size:24
Alignment explanation
Indices: 39962774--39962839 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
39962764 CTCCTAAATT
* *
39962774 TTAATTTAATTATCTAATTTTTTAA
1 TTAATTAAATTAT-TAATATTTTAA
* *
39962799 TTTATTGAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTA-A
*
39962824 TTAATTAAATTTTTAA
1 TTAATTAAATTATTAA
39962840 GAAAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATTAAATTATTAATATTTTAA
Found at i:39967014 original size:18 final size:18
Alignment explanation
Indices: 39966991--39967026 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
39966981 TGAAAATACG
39966991 TGTTTGTCT-TGAAAACAT
1 TGTTTGT-TGTGAAAACAT
39967009 TGTTTGTTGTGAAAACAT
1 TGTTTGTTGTGAAAACAT
39967027 ATTTGTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTTTGTTGTGAAAACAT
Found at i:39967033 original size:17 final size:18
Alignment explanation
Indices: 39967000--39967033 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39966990 GTGTTTGTCT
*
39967000 TGAAAACATTGTTTGTTG
1 TGAAAACATTATTTGTTG
39967018 TGAAAACA-TATTTGTT
1 TGAAAACATTATTTGTT
39967034 TCCGTTAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (18 bp):
TGAAAACATTATTTGTTG
Found at i:39967592 original size:27 final size:27
Alignment explanation
Indices: 39967557--39967621 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
39967547 AGCAGAGCTG
39967557 CCAGT-ACAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTAAT-TGTGGCAAAGCCA
*
39967583 CCAGTAACAGTAATTGTGGCAGAGCCA
1 CCAGTAACAGTAATTGTGGCAAAGCCA
*
39967610 CCAATAACAGTA
1 CCAGTAACAGTA
39967622 CTTCTTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 5 0.14
27 28 0.80
28 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTAATTGTGGCAAAGCCA
Found at i:39981911 original size:11 final size:11
Alignment explanation
Indices: 39981895--39981919 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39981885 CATCAAAAAA
39981895 ATTATTTTAAT
1 ATTATTTTAAT
39981906 ATTATTTTAAT
1 ATTATTTTAAT
39981917 ATT
1 ATT
39981920 TACAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTAAT
Found at i:39990821 original size:15 final size:14
Alignment explanation
Indices: 39990787--39990822 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
39990777 GTAGATTTTG
*
39990787 ATGATTTTTGAGTC
1 ATGATTTTTGAGTA
39990801 ATGATTTTTGAGTA
1 ATGATTTTTGAGTA
39990815 ATGGATTT
1 AT-GATTT
39990823 AGCCATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (14 bp):
ATGATTTTTGAGTA
Found at i:39991467 original size:12 final size:12
Alignment explanation
Indices: 39991450--39991475 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39991440 GCTATTACAA
39991450 GGCCTAGCACAC
1 GGCCTAGCACAC
39991462 GGCCTAGCACAC
1 GGCCTAGCACAC
39991474 GG
1 GG
39991476 GCGTGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:40004894 original size:28 final size:28
Alignment explanation
Indices: 40004854--40004910 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40004844 GACCAGTTGA
40004854 AAGCACTATTGATCGAAGTACCCGTTCT
1 AAGCACTATTGATCGAAGTACCCGTTCT
40004882 AAGCACTATTGATCGAAGTACCCGTTCT
1 AAGCACTATTGATCGAAGTACCCGTTCT
40004910 A
1 A
40004911 GTTTAACCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (28 bp):
AAGCACTATTGATCGAAGTACCCGTTCT
Found at i:40007935 original size:39 final size:39
Alignment explanation
Indices: 40007881--40008113 Score: 333
Period size: 39 Copynumber: 6.0 Consensus size: 39
40007871 TAGTAGAAAA
40007881 CTGTTGTACTTCGGTACCCCTGAAT-GCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTG-ATCGCACTTACGTGCCC
*
40007920 CTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * * *
40007959 CGGTTGTACTTCGATACCCCTGATCGCTCTTAAGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * *
40007998 TTGTTGTACTTCGGTACCCTTGATCACACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* *
40008037 CTATTGTACTTCAGTACCCCTGATCGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
* * *
40008076 CTGTTGTACTTCGCTACCCTTGATCGCACTTTCGTGCC
1 CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCC
40008114 GTGGTTACGT
Statistics
Matches: 170, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 2 0.01
39 168 0.99
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (39 bp):
CTGTTGTACTTCGGTACCCCTGATCGCACTTACGTGCCC
Found at i:40012459 original size:70 final size:70
Alignment explanation
Indices: 40012368--40012571 Score: 223
Period size: 70 Copynumber: 2.9 Consensus size: 70
40012358 GTATGCCTAG
* * *
40012368 CACTATTCGAACGA-TTCGACAAATTATTACGCCCAGCGCTAGTAGGATAACCGACGATACTTGT
1 CACTAGTCGAACGAGTT-GACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGT
40012432 GCCCAT
65 GCCCAT
* * * * * * *
40012438 CACTAGTCGAATGAGTTGACAAATTAGTACGCCCAGTGCTACTCA-GATAACTGGCAATAGTTAT
1 CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGT-AGGATAACTGACGATAGTTGT
*
40012502 GTCCAT
65 GCCCAT
* * * * * *
40012508 CACTAGTCAAACAAGTTAACAAATTATTGCGCCCAGCACTAGTCGGATAACTGACGATAGTTGT
1 CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGT
40012572 CATCCGCAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
70 104 0.97
71 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (70 bp):
CACTAGTCGAACGAGTTGACAAATTATTACGCCCAGCGCTAGTAGGATAACTGACGATAGTTGTG
CCCAT
Found at i:40019873 original size:42 final size:43
Alignment explanation
Indices: 40019825--40019916 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 43
40019815 AATATTATTA
* *
40019825 TTTAATATTTACGATTCAATTATAATATTATATTGACTTTTAG
1 TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
* *
40019868 -TTAATATTTATGAGTCAATTATAATATTATATTGAATTTTTG
1 TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
40019910 TTTAATA
1 TTTAATA
40019917 ATTTTTGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 38 0.86
43 6 0.14
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (43 bp):
TTTAATATTTACGAGTCAATTATAATATTATATTGAATTTTAG
Found at i:40020810 original size:19 final size:19
Alignment explanation
Indices: 40020786--40020828 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40020776 ACTAAATTGA
*
40020786 ATAAAA-GGTAAAATTTTAG
1 ATAAAATGGTAAAATGTT-G
*
40020805 ATAAAATTGTAAAATGTTG
1 ATAAAATGGTAAAATGTTG
40020824 ATAAA
1 ATAAA
40020829 GAGTCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (19 bp):
ATAAAATGGTAAAATGTTG
Found at i:40035894 original size:19 final size:19
Alignment explanation
Indices: 40035870--40035908 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40035860 TTTTATTTGA
40035870 ACCTTTGCAATATTTAGTC
1 ACCTTTGCAATATTTAGTC
40035889 ACCTTTGCAATATTTAGTC
1 ACCTTTGCAATATTTAGTC
40035908 A
1 A
40035909 TCACTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (19 bp):
ACCTTTGCAATATTTAGTC
Found at i:40038835 original size:22 final size:22
Alignment explanation
Indices: 40038807--40038854 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
40038797 CCACTACCAA
*
40038807 ACCATCATACCACTACCTTAGC
1 ACCATCATACCACAACCTTAGC
* *
40038829 ACCATCATACTACAACCTTTGC
1 ACCATCATACCACAACCTTAGC
40038851 ACCA
1 ACCA
40038855 CCTTGAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.04, T:0.23
Consensus pattern (22 bp):
ACCATCATACCACAACCTTAGC
Found at i:40039199 original size:18 final size:19
Alignment explanation
Indices: 40039176--40039211 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40039166 TCATCCAATG
40039176 ATTAGATTCTCAA-AATCC
1 ATTAGATTCTCAACAATCC
*
40039194 ATTAGATTGTCAACAATC
1 ATTAGATTCTCAACAATC
40039212 ATAGCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (19 bp):
ATTAGATTCTCAACAATCC
Found at i:40041449 original size:30 final size:29
Alignment explanation
Indices: 40041393--40041582 Score: 139
Period size: 29 Copynumber: 6.5 Consensus size: 29
40041383 TGTTATGTCT
* * *
40041393 CTTTTCATATTCGATGGTCGAAACCATCA
1 CTTTTCATAATCGATGGTCGTAACCATCC
* *
40041422 CTTTTCATTAATCGATAGTCGTCACCATCC
1 CTTTTCA-TAATCGATGGTCGTAACCATCC
* * *
40041452 CTTTTCATAGTTGATGGTCGTTACCATCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
** * * * *
40041481 CTTTTCGCAATAGATAGCCG-AAGCTATCC
1 CTTTTCATAATCGATGGTCGTAA-CCATCC
* * * *
40041510 CGTTTCATATTCGATGGTCATCACCATCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
* * * * *
40041539 CTTTTCACAATTGATGGTCATCACCCTCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
*
40041568 ATTTTCATAATCGAT
1 CTTTTCATAATCGAT
40041583 AGCCGAAGCT
Statistics
Matches: 123, Mismatches: 35, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
28 1 0.01
29 97 0.79
30 25 0.20
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
CTTTTCATAATCGATGGTCGTAACCATCC
Done.