Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 133 of 228
Found at i:39813897 original size:36 final size:36
Alignment explanation
Indices: 39813854--39813937 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
39813844 AGAAATGAAA
*
39813854 GAAAAAGAAGATGAATGTGAGAATGAAAAGAAAATT
1 GAAAAAGAAGATGAATGTGAGAACGAAAAGAAAATT
*
39813890 GAAAAAGAAGATGAGTGTGAGAACGAAAAGAAAATT
1 GAAAAAGAAGATGAATGTGAGAACGAAAAGAAAATT
*
39813926 GAAAAAAAAGAT
1 GAAAAAGAAGAT
39813938 AAGTTTGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.60, C:0.01, G:0.25, T:0.14
Consensus pattern (36 bp):
GAAAAAGAAGATGAATGTGAGAACGAAAAGAAAATT
Found at i:39813976 original size:18 final size:18
Alignment explanation
Indices: 39813953--39814013 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
39813943 TGGTGAAATG
*
39813953 AAAGAAAAAGACATTGAA
1 AAAGAAAAAGAAATTGAA
**
39813971 AAAGAAAAAGAAATTGCT
1 AAAGAAAAAGAAATTGAA
* *
39813989 AAAGAACAGGAAATTGAA
1 AAAGAAAAAGAAATTGAA
39814007 AAAGAAA
1 AAAGAAA
39814014 TTGAAAGAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.66, C:0.05, G:0.18, T:0.11
Consensus pattern (18 bp):
AAAGAAAAAGAAATTGAA
Found at i:39815764 original size:20 final size:20
Alignment explanation
Indices: 39815739--39815806 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
39815729 TCCATGCAGT
39815739 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
39815759 TCAGCTCATTTGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* * *
39815779 TCAGCTCCCACGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
39815799 TCAGCTCA
1 TCAGCTCA
39815807 TTGCTGGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.24
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:39818854 original size:20 final size:20
Alignment explanation
Indices: 39818831--39818884 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39818821 AGTTTTTCCC
*
39818831 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
39818851 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
39818871 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
39818885 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:39818866 original size:30 final size:30
Alignment explanation
Indices: 39818831--39818904 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
39818821 AGTTTTTCCC
39818831 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
39818861 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
39818891 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
39818905 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:39818894 original size:20 final size:20
Alignment explanation
Indices: 39818831--39818895 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39818821 AGTTTTTCCC
* * * *
39818831 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
39818851 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
39818870 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
39818891 AGCTC
1 AGCTC
39818896 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:39830143 original size:23 final size:22
Alignment explanation
Indices: 39830091--39830143 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39830081 TCCACGTCTT
*
39830091 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39830113 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39830136 TTTCTTTT
1 TTTCTTTT
39830144 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39834401 original size:46 final size:46
Alignment explanation
Indices: 39834331--39834424 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
39834321 CAAAGAAAAG
*
39834331 ACCTCGACCCACTATCAAAAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAAAATGATAAGAACCTTGGTATATGATGA
**
39834377 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAAAATGATAAGAACCTTGGTATATGATGA
39834423 AC
1 AC
39834425 GCCACACTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAAAATGATAAGAACCTTGGTATATGATGA
Found at i:39839787 original size:14 final size:14
Alignment explanation
Indices: 39839768--39839795 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39839758 ATACATTGGA
39839768 TAGATTCATGCATG
1 TAGATTCATGCATG
39839782 TAGATTCATGCATG
1 TAGATTCATGCATG
39839796 GGAAGATGCA
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:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TAGATTCATGCATG
Found at i:39845648 original size:40 final size:40
Alignment explanation
Indices: 39845618--39845825 Score: 238
Period size: 40 Copynumber: 5.2 Consensus size: 40
39845608 GGACTAAGAT
* *
39845618 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* *
39845658 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** * *
39845698 CCGAAGGCATTCGTGCGAGTTGTTGAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
39845738 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * * *
39845778 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
39845817 CCGAAGGCA
1 CCGAAGGCA
39845826 ATTGAACGAG
Statistics
Matches: 151, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 32 0.21
40 119 0.79
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:39845702 original size:80 final size:80
Alignment explanation
Indices: 39845565--39845825 Score: 276
Period size: 80 Copynumber: 3.3 Consensus size: 80
39845555 TTGAATGCTG
* * * * * **
39845565 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCCT
* *
39845628 TTGTGCGAGATACTAAA
64 TCGTGCGAGTTACTAAA
* *
39845645 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTC
** *
39845710 GTGCGAGTTGTTGAA
66 GTGCGAGTTACTAAA
* * * * * *
39845725 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTCCCGAAGG-CATG
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTC
*
39845789 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
39845804 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCA
39845826 ATTGAACGAG
Statistics
Matches: 152, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
79 32 0.21
80 114 0.75
81 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCTTC
GTGCGAGTTACTAAA
Found at i:39845847 original size:79 final size:80
Alignment explanation
Indices: 39845618--39845862 Score: 219
Period size: 80 Copynumber: 3.1 Consensus size: 80
39845608 GGACTAAGAT
* * * * * ** * *
39845618 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAG-GAGCT
39845682 AAATCCGGGTTAAGTC
65 AAATCCGGGTTAAGTC
** * * * ** ** *
39845698 CCGAAGGCATTCGTGCGAGTTGTTGAAGCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
39845763 AATCCGGGTTACGTC
66 AATCCGGGTTAAGTC
* * *
39845778 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAATT-GAACGAGGAGCT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC-ATTCGAACGAGGAGCT
* *
39845841 ATATCC-GGTTAAATC
65 AAATCCGGGTTAAGTC
39845856 CCGAAGG
1 CCGAAGG
39845863 TACGTGAATT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 43 0.31
80 81 0.59
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:39856985 original size:18 final size:19
Alignment explanation
Indices: 39856948--39856986 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
39856938 TTTTTTCTAA
39856948 TTAATTTCGTAATATTTTT
1 TTAATTTCGTAATATTTTT
39856967 TTAATTTCG-AAT-TTTTT
1 TTAATTTCGTAATATTTTT
39856984 TTA
1 TTA
39856987 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
TTAATTTCGTAATATTTTT
Found at i:39858168 original size:20 final size:20
Alignment explanation
Indices: 39858124--39858168 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39858114 AATTAAAACT
39858124 GGACACAATTAATTAAGTTA
1 GGACACAATTAATTAAGTTA
* **
39858144 AGACACAATTAATTCGGTTA
1 GGACACAATTAATTAAGTTA
39858164 GGACA
1 GGACA
39858169 AGACACATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (20 bp):
GGACACAATTAATTAAGTTA
Found at i:39859618 original size:20 final size:21
Alignment explanation
Indices: 39859586--39859644 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
39859576 GAGCTAATAA
39859586 TGAGCTC-AATGAGCTGAA-T
1 TGAGCTCGAATGAGCTGAACT
**
39859605 TGAGCTCGTGTGAGCT-AACT
1 TGAGCTCGAATGAGCTGAACT
39859625 TGAGCTCGAATGAGCTGAAC
1 TGAGCTCGAATGAGCTGAAC
39859645 CACATGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.27
20 21 0.64
21 3 0.09
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
TGAGCTCGAATGAGCTGAACT
Found at i:39860782 original size:39 final size:39
Alignment explanation
Indices: 39860686--39860805 Score: 208
Period size: 38 Copynumber: 3.1 Consensus size: 39
39860676 TAAGACACAC
39860686 AATTAAA-ACACATATTAATGATGTTCAAACTAAGACAT
1 AATTAAAGACACATATTAATGATGTTCAAACTAAGACAT
39860724 AATT-AAGACACATATTAATGATGTTCAAACTAAGACAT
1 AATTAAAGACACATATTAATGATGTTCAAACTAAGACAT
* *
39860762 AATTAAAGACATATATTAATGATTTTCAAACTAAGACAT
1 AATTAAAGACACATATTAATGATGTTCAAACTAAGACAT
39860801 AATTA
1 AATTA
39860806 TATACTTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
37 2 0.03
38 39 0.50
39 37 0.47
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (39 bp):
AATTAAAGACACATATTAATGATGTTCAAACTAAGACAT
Found at i:39864135 original size:19 final size:20
Alignment explanation
Indices: 39864103--39864156 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
39864093 AACTAAAGTA
* *
39864103 AGCTAAAATGGAGCTT-GTG
1 AGCTAGAATTGAGCTTAGTG
*
39864122 AGCTAGGAA-TGAGCTTATTG
1 AGCTA-GAATTGAGCTTAGTG
39864142 AGCTAGAATTGAGCT
1 AGCTAGAATTGAGCT
39864157 AAATTGAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (20 bp):
AGCTAGAATTGAGCTTAGTG
Found at i:39864143 original size:20 final size:21
Alignment explanation
Indices: 39864120--39864176 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
39864110 ATGGAGCTTG
*
39864120 TGAGCTAGGAA-TGAGCT-TAT
1 TGAGCTA-GAATTGAGCTAAAT
39864140 TGAGCTAGAATTGAGCTAAAT
1 TGAGCTAGAATTGAGCTAAAT
*
39864161 TGAGCTTG-ATTGAGCT
1 TGAGCTAGAATTGAGCT
39864177 GGATCGAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 21 0.64
21 9 0.27
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (21 bp):
TGAGCTAGAATTGAGCTAAAT
Found at i:39864163 original size:10 final size:10
Alignment explanation
Indices: 39864138--39864176 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39864128 GAATGAGCTT
39864138 ATTGAGCTAGA
1 ATTGAGCTA-A
39864149 ATTGAGCTAA
1 ATTGAGCTAA
**
39864159 ATTGAGCTTG
1 ATTGAGCTAA
39864169 ATTGAGCT
1 ATTGAGCT
39864177 GGATCGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (10 bp):
ATTGAGCTAA
Found at i:39865641 original size:36 final size:36
Alignment explanation
Indices: 39865574--39865643 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
39865564 AGTTCAAAGA
* **
39865574 AGCTGTCACGGGTATTATTGATCGTGATTGGGCAGG
1 AGCTGTCACGGGTATAATTGATCAAGATTGGGCAGG
*
39865610 AGCTGTCACGGG-ACTAATTGATCAAGCTTGGGCA
1 AGCTGTCACGGGTA-TAATTGATCAAGATTGGGCA
39865644 TGCACTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (36 bp):
AGCTGTCACGGGTATAATTGATCAAGATTGGGCAGG
Found at i:39865831 original size:23 final size:23
Alignment explanation
Indices: 39865802--39865861 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
39865792 ACAAAGATTG
39865802 GTTTAACAAGGGATTAATTGGTT
1 GTTTAACAAGGGATTAATTGGTT
39865825 GTTTAACAAGGGATTAATTGGTT
1 GTTTAACAAGGGATTAATTGGTT
39865848 GTTTAACAAAGGGA
1 GTTTAAC-AAGGGA
39865862 CAGATGAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 30 0.83
24 6 0.17
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (23 bp):
GTTTAACAAGGGATTAATTGGTT
Found at i:39870258 original size:47 final size:47
Alignment explanation
Indices: 39870171--39870503 Score: 531
Period size: 47 Copynumber: 7.1 Consensus size: 47
39870161 CCCTTCGGGA
* ** * * * * *
39870171 CTTATCACATTTATGTACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*** *
39870218 CCCGTCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39870265 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39870312 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39870359 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39870406 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39870453 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39870500 CTTA
1 CTTA
39870504 CTATCATTTC
Statistics
Matches: 267, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 267 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39873718 original size:25 final size:25
Alignment explanation
Indices: 39873690--39873741 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
39873680 AAGGAATTCG
39873690 CACACACACAGTGCCTCTAATT-ATT
1 CACACACACAGTG-CTCTAATTCATT
* * *
39873715 CACATACATAGTGCTCTTATTCATT
1 CACACACACAGTGCTCTAATTCATT
39873740 CA
1 CA
39873742 TTAATACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (25 bp):
CACACACACAGTGCTCTAATTCATT
Found at i:39874014 original size:40 final size:40
Alignment explanation
Indices: 39873903--39874019 Score: 153
Period size: 40 Copynumber: 2.9 Consensus size: 40
39873893 CGAATACACG
* * * * * *
39873903 TCACCAGCATGATTGCTCTTCGGGATTTAGCACAGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
39873943 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
39873983 TCACTAGCATGAATGCTCTTCGGGACTTAGCCTGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
39874020 TTAGTAACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:39874448 original size:29 final size:29
Alignment explanation
Indices: 39874406--39874484 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
39874396 CTTAATAATC
* *
39874406 AACCACGCATACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39874436 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39874465 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39874485 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39874530 original size:43 final size:43
Alignment explanation
Indices: 39874466--39874611 Score: 274
Period size: 43 Copynumber: 3.4 Consensus size: 43
39874456 TGCATTTCAA
39874466 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
39874509 GCCCACACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
39874552 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
39874595 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
39874612 TGAAAACCAA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:39876701 original size:47 final size:47
Alignment explanation
Indices: 39876623--39876955 Score: 531
Period size: 47 Copynumber: 7.1 Consensus size: 47
39876613 CCCTTCGGGA
* * * * * * * *
39876623 CTTATCACATTTATGCACTTTAACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
39876670 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39876717 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39876764 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39876811 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39876858 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39876905 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39876952 CTTA
1 CTTA
39876956 CTATCATTTC
Statistics
Matches: 267, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 267 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39881361 original size:79 final size:81
Alignment explanation
Indices: 39881225--39881409 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39881215 TTGAATGATG
*
39881225 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39881289 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39881304 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39881366 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39881384 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39881410 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39881423 original size:40 final size:40
Alignment explanation
Indices: 39881226--39881409 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
39881216 TGAATGATGT
* * * *
39881226 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39881266 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
39881306 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39881344 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39881385 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39881410 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39881431 original size:79 final size:79
Alignment explanation
Indices: 39881226--39881442 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
39881216 TGAATGATGT
** * * * **
39881226 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
39881289 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
39881306 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
39881371 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
39881385 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
39881443 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:39886070 original size:50 final size:50
Alignment explanation
Indices: 39885990--39886187 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 50
39885980 TTTCTTGTAC
* * * **
39885990 TGCCAATACCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
39886040 TGCCCATGCCATGTCCCAGACATGGCCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
39886090 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
39886146 TGCCAATGCCATGTCCCAGACATGGTCTTAGATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39886188 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 80 0.66
53 2 0.02
56 40 0.33
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:39887492 original size:3 final size:3
Alignment explanation
Indices: 39887484--39887526 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39887474 ATTAAAACAC
39887484 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39887527 TGCGTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39892203 original size:37 final size:37
Alignment explanation
Indices: 39892143--39892220 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
39892133 TATTACGAAA
* *
39892143 TCTTACCCGGACATAATCTCCACACGA-AGTTATCGGG
1 TCTTACCCGGACAAAATCTCCACAC-ATAGTCATCGGG
39892180 TCTTACCCGGACAAAAT-TCCCACACATAGTCATCGGG
1 TCTTACCCGGACAAAATCT-CCACACATAGTCATCGGG
39892217 TCTT
1 TCTT
39892221 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCTCCACACATAGTCATCGGG
Found at i:39892410 original size:47 final size:47
Alignment explanation
Indices: 39892341--39892451 Score: 204
Period size: 47 Copynumber: 2.4 Consensus size: 47
39892331 CTTCGGGACT
39892341 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
* *
39892388 TATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
39892435 TATCACATATATACACT
1 TATCACATATATACACT
39892452 GTCTTGGCTG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
Found at i:39895957 original size:40 final size:40
Alignment explanation
Indices: 39895913--39896068 Score: 163
Period size: 40 Copynumber: 3.9 Consensus size: 40
39895903 CGAATACACG
* * * *
39895913 TCACCAGCATGATTGCTCTTTGGGACCTAGCCCGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
** *
39895953 TCACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * *
39895993 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATGG
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT-A
* *
39896034 TCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGA
39896069 CATCATTCAA
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
40 83 0.86
41 8 0.08
42 6 0.06
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:39896413 original size:29 final size:29
Alignment explanation
Indices: 39896374--39896452 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39896364 CTTAATAATC
*
39896374 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39896404 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39896433 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39896453 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39896495 original size:43 final size:43
Alignment explanation
Indices: 39896434--39896579 Score: 283
Period size: 43 Copynumber: 3.4 Consensus size: 43
39896424 TGCATTTCAA
39896434 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
39896477 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
39896520 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
39896563 GCCCACACACTTAGTGC
1 GCCCGCACACTTAGTGC
39896580 TGAAAACCAA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:39898497 original size:37 final size:37
Alignment explanation
Indices: 39898447--39898525 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
39898437 TTATTACGAA
* *
39898447 GTCTTACCCGGACATAA-TCTCCACACAAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACAAAGTCATCGG
**
39898484 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACAAAGTCATCGG
39898521 GTCTT
1 GTCTT
39898526 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACAAAGTCATCGG
Found at i:39898715 original size:47 final size:47
Alignment explanation
Indices: 39898646--39898756 Score: 195
Period size: 47 Copynumber: 2.4 Consensus size: 47
39898636 GTTCGGGACT
39898646 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
* * *
39898693 TATCACACATATACACTTTCACATTCATCATATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
39898740 TATCACATATATACACT
1 TATCACATATATACACT
39898757 GTCTTGGCTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCA
Found at i:39902448 original size:13 final size:13
Alignment explanation
Indices: 39902430--39902455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39902420 ACCTGAAAGC
39902430 AATTTAATTCATA
1 AATTTAATTCATA
39902443 AATTTAATTCATA
1 AATTTAATTCATA
39902456 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:39902870 original size:20 final size:21
Alignment explanation
Indices: 39902845--39902883 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39902835 TCAAACAAGC
39902845 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
39902865 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
39902884 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:39910729 original size:14 final size:14
Alignment explanation
Indices: 39910710--39910736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39910700 ATGCATCTCC
39910710 CATGCATGAATCTA
1 CATGCATGAATCTA
39910724 CATGCATGAATCT
1 CATGCATGAATCT
39910737 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:39918358 original size:15 final size:15
Alignment explanation
Indices: 39918338--39918392 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
39918328 ACTCTCATCA
*
39918338 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
39918353 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
39918368 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
39918382 TTCTTTT-TCTC
1 TTCTTTTCTCTC
39918393 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:39922610 original size:12 final size:12
Alignment explanation
Indices: 39922577--39922657 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
39922567 TTTCCACTCG
39922577 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
39922588 AGCTCTCTTTCA
1 ATTTCTTTTTCA
39922600 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
39922613 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
39922626 --TTCTCTTTCA
1 ATTTCTTTTTCA
39922636 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
39922648 ATCTCTTTTT
1 ATTTCTTTTT
39922658 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:39922618 original size:21 final size:20
Alignment explanation
Indices: 39922592--39922647 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
39922582 TTTTCAAGCT
39922592 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
39922613 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
39922628 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
39922648 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:39922718 original size:29 final size:28
Alignment explanation
Indices: 39922686--39922741 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
39922676 TTTTGAAATC
39922686 TCATTTTCATATTTTCTTT-TTCATTTCTT
1 TCATTTTC--ATTTTCTTTATTCATTTCTT
*
39922715 TCATTTTCATTTTCTTTATTCTTTTCT
1 TCATTTTCATTTTCTTTATTCATTTCT
39922742 CGCTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 8 0.32
29 8 0.32
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (28 bp):
TCATTTTCATTTTCTTTATTCATTTCTT
Found at i:39922721 original size:15 final size:15
Alignment explanation
Indices: 39922686--39922731 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
39922676 TTTTGAAATC
*
39922686 TCATTTTCATAT-TT
1 TCATTTTCATTTCTT
*
39922700 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
39922715 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
39922731 T
1 T
39922732 ATTCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 10 0.37
15 10 0.37
16 7 0.26
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:39923797 original size:20 final size:18
Alignment explanation
Indices: 39923767--39923825 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 18
39923757 CTTTTCACTT
39923767 CTTTTTTTCTTCTTTTTTA
1 CTTTTTTTCTT-TTTTTTA
39923786 CTTTTGTTTCTTTTTTTGCTCA
1 CTTTT-TTTCTTTTTTT--T-A
*
39923808 TTTCTTTTTCTTTTTTTT
1 CTT-TTTTTCTTTTTTTT
39923826 TCGAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 1 0.03
22 14 0.41
23 2 0.06
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (18 bp):
CTTTTTTTCTTTTTTTTA
Found at i:39925398 original size:20 final size:20
Alignment explanation
Indices: 39925375--39925421 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39925365 TGGTTAAAAT
39925375 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
* *
39925395 TGAGCTTACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
39925415 TGAGCTG
1 TGAGCTG
39925422 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:39926971 original size:37 final size:38
Alignment explanation
Indices: 39926921--39926996 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
39926911 CGCATTTCAT
39926921 AGCCTGCACAAAAAATAACGATGCGGTTCATG-TTCTA
1 AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
*
39926958 AGCCTGCACAAAAAATGACGATGCGGTTCATGTTTCTA
1 AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
39926996 A
1 A
39926997 CTTATTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 31 0.84
38 6 0.16
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (38 bp):
AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
Found at i:39933763 original size:12 final size:11
Alignment explanation
Indices: 39933741--39933765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39933731 TAAAAACAAA
39933741 TACTATTTTTT
1 TACTATTTTTT
39933752 TACTATTTTTT
1 TACTATTTTTT
39933763 TAC
1 TAC
39933766 AAACTTACTC
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:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (11 bp):
TACTATTTTTT
Found at i:39935085 original size:18 final size:19
Alignment explanation
Indices: 39935045--39935090 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
39935035 TTGTCCAATT
*
39935045 TTTAAAC-AAATTAATTAA
1 TTTAAACTAAATTAACTAA
*
39935063 CTTAAACTAAA-TAACTAA
1 TTTAAACTAAATTAACTAA
39935081 TTT-AACTAAA
1 TTTAAACTAAA
39935091 AGCAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAACTAAATTAACTAA
Found at i:39938761 original size:12 final size:12
Alignment explanation
Indices: 39938732--39938770 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39938722 TTGTTATTTC
*
39938732 TGTATTTGTATAT
1 TGTATATGTAT-T
39938745 TGTATATGTATT
1 TGTATATGTATT
*
39938757 TGTATCTGTATT
1 TGTATATGTATT
39938769 TG
1 TG
39938771 GGGTGGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (12 bp):
TGTATATGTATT
Found at i:39939917 original size:18 final size:20
Alignment explanation
Indices: 39939878--39939917 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39939868 GGATTGATGT
*
39939878 ATAAAATTTTATAATATTAG
1 ATAAAATTTGATAATATTAG
39939898 ATAAAATTTGA-AAT-TTAG
1 ATAAAATTTGATAATATTAG
39939916 AT
1 AT
39939918 GAGACTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
ATAAAATTTGATAATATTAG
Found at i:39953202 original size:10 final size:10
Alignment explanation
Indices: 39953189--39953226 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39953179 TTGTAGCTAA
39953189 ATTGAGCTCG
1 ATTGAGCTCG
39953199 ATTGAGCT-G
1 ATTGAGCTCG
39953208 ACTTGAGCTCG
1 A-TTGAGCTCG
*
39953219 AGTGAGCT
1 ATTGAGCT
39953227 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:39953206 original size:20 final size:20
Alignment explanation
Indices: 39953166--39953226 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39953156 ACCAATAAAA
39953166 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
39953186 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
39953206 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
39953226 T
1 T
39953227 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:39953227 original size:20 final size:20
Alignment explanation
Indices: 39953190--39953227 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39953180 TGTAGCTAAA
*
39953190 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
39953210 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
39953228 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:39955901 original size:29 final size:27
Alignment explanation
Indices: 39955869--39955937 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
39955859 GCAAGACTTT
*
39955869 TCACTTTTTTTTTAACTTGATTTTTTTGG
1 TCACTTTTTTTTT-ACTCGATTTTTTT-G
* *
39955898 TCACCTTTTTTTTTGCTCGATTTTTTTT
1 TCA-CTTTTTTTTTACTCGATTTTTTTG
39955926 TCACTTTTTTTT
1 TCACTTTTTTTT
39955938 GAATTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.25
28 3 0.08
29 14 0.39
30 10 0.28
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.68
Consensus pattern (27 bp):
TCACTTTTTTTTTACTCGATTTTTTTG
Found at i:39955946 original size:13 final size:13
Alignment explanation
Indices: 39955930--39955991 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
39955920 TTTTTTTCAC
39955930 TTTTTTTTGAATTT
1 TTTTTTTTGAA-TT
*
39955944 TTTTTTTCAATCAATT
1 TTTTTTT---TGAATT
39955960 TTTTTTTTCGAA-T
1 TTTTTTTT-GAATT
39955973 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
39955985 TTTTTTT
1 TTTTTTT
39955992 GTTACTCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
11 1 0.02
12 9 0.22
13 10 0.24
14 9 0.22
16 9 0.22
17 3 0.07
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:39955985 original size:11 final size:12
Alignment explanation
Indices: 39955959--39955992 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
39955949 TTCAATCAAT
39955959 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
39955972 TTTTTTTTTG-A
1 TTTTTTTTTGAA
39955983 TTTTTTTTTG
1 TTTTTTTTTG
39955993 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 1 0.05
13 9 0.43
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:39955991 original size:12 final size:13
Alignment explanation
Indices: 39955957--39955991 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
39955947 TTTTCAATCA
39955957 ATTTTTTTTTTCG
1 ATTTTTTTTTTCG
*
39955970 AATTTTTTTTT-G
1 ATTTTTTTTTTCG
39955982 ATTTTTTTTT
1 ATTTTTTTTT
39955992 GTTACTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTTCG
Found at i:39957400 original size:10 final size:10
Alignment explanation
Indices: 39957387--39957424 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39957377 TTGTAGCTAA
39957387 ATTGAGCTCG
1 ATTGAGCTCG
39957397 ATTGAGCT-G
1 ATTGAGCTCG
39957406 ACTTGAGCTCG
1 A-TTGAGCTCG
*
39957417 AGTGAGCT
1 ATTGAGCT
39957425 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:39957404 original size:20 final size:20
Alignment explanation
Indices: 39957364--39957424 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39957354 ACCAATAAAA
39957364 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
39957384 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
39957404 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
39957424 T
1 T
39957425 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:39957425 original size:20 final size:20
Alignment explanation
Indices: 39957388--39957425 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39957378 TGTAGCTAAA
*
39957388 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
39957408 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
39957426 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:39957615 original size:46 final size:45
Alignment explanation
Indices: 39957545--39957712 Score: 183
Period size: 46 Copynumber: 3.6 Consensus size: 45
39957535 GTATCACAAC
* **
39957545 GCATGTCCCAGACATGTCTAACACTGGCTAACATCTCAAGACCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG-CCGAT
* *** *
39957591 GCATGTCCCAAACATGTCTTACACTGGCTCTCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCAT-CTCAAGCCGAT
* * * *
39957637 GCATGTCCTAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAA-GCCGAT
39957683 GCCATGTCCCAGACATGGTCTTACACTGGC
1 G-CATGTCCCAGACAT-GTCTTACACTGGC
39957713 ACACAAATCT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
45 2 0.02
46 69 0.70
47 16 0.16
48 12 0.12
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (45 bp):
GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAGCCGAT
Found at i:39959790 original size:20 final size:20
Alignment explanation
Indices: 39959750--39959797 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39959740 ATAAGCTGGA
**
39959750 GTTGAGCTAGATGTGAACTT
1 GTTGAGCTAGAACTGAACTT
*
39959770 GTTGAGCTAGAACTGAGCTT
1 GTTGAGCTAGAACTGAACTT
*
39959790 GCTGAGCT
1 GTTGAGCT
39959798 GGTTGTGAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
GTTGAGCTAGAACTGAACTT
Found at i:39960410 original size:12 final size:12
Alignment explanation
Indices: 39960395--39960455 Score: 77
Period size: 12 Copynumber: 5.1 Consensus size: 12
39960385 GAAAAAGAAA
*
39960395 AAAAAGAGAGTG
1 AAAAAGAGATTG
*
39960407 AAAATGAGATTG
1 AAAAAGAGATTG
*
39960419 AAAAAGAAATTG
1 AAAAAGAGATTG
*
39960431 AAAAAGAGAATG
1 AAAAAGAGATTG
*
39960443 AAAAAGAGTTTG
1 AAAAAGAGATTG
39960455 A
1 A
39960456 GAGAGAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:39960445 original size:36 final size:33
Alignment explanation
Indices: 39960384--39960467 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 33
39960374 AAAAAGCCGA
* *
39960384 TGAAAAAGAAAAAAAAGAGAGTGAAAATGAGAT
1 TGAAAAAGAAAAAAAAGAGAATGAAAAAGAGAT
*
39960417 TGAAAAAGAAATTGAAAAAGAGAATGAAAAAGAGTT
1 TGAAAAAGAAA---AAAAAGAGAATGAAAAAGAGAT
* *
39960453 TGAGAGAGAAAAAAA
1 TGAAAAAGAAAAAAA
39960468 GTTGAACAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 15 0.35
36 28 0.65
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAAAGAAAAAAAAGAGAATGAAAAAGAGAT
Found at i:39960455 original size:24 final size:24
Alignment explanation
Indices: 39960384--39960455 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
39960374 AAAAAGCCGA
*
39960384 TGAAAAAGA-AA--AAAAAGAGAG
1 TGAAAAAGAGAATGAAAAAGAGAT
* * *
39960405 TGAAAATGAGATTGAAAAAGAAAT
1 TGAAAAAGAGAATGAAAAAGAGAT
*
39960429 TGAAAAAGAGAATGAAAAAGAGTT
1 TGAAAAAGAGAATGAAAAAGAGAT
39960453 TGA
1 TGA
39960456 GAGAGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.20
22 1 0.03
24 31 0.77
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (24 bp):
TGAAAAAGAGAATGAAAAAGAGAT
Found at i:39961165 original size:14 final size:14
Alignment explanation
Indices: 39961148--39961187 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39961138 CGAATGGAAT
*
39961148 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
39961162 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
39961176 GATACGAACAAA
1 GGTAGGAACAAA
39961188 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:39964156 original size:14 final size:14
Alignment explanation
Indices: 39964137--39964181 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
39964127 AACTCATCTT
*
39964137 AGTTTAATTAAATG
1 AGTTTAATTTAATG
39964151 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
39964164 AATTTAATTTAATG
1 AGTTTAATTTAATG
39964178 AGTT
1 AGTT
39964182 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:39968438 original size:30 final size:31
Alignment explanation
Indices: 39968404--39968500 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
39968394 AGCTCACTCC
*
39968404 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
39968434 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
39968464 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
39968494 TAGCTCA
1 TAGCTCA
39968501 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:39969173 original size:20 final size:22
Alignment explanation
Indices: 39969150--39969192 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
39969140 TTTTGTTGTC
39969150 TTTCCTCTCTTT-T-TCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
* *
39969170 TTTCTTTTCTTTCTCTCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
39969192 T
1 T
39969193 GATCTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCCTCTCTTTCTCTCTCATT
Found at i:39972874 original size:23 final size:22
Alignment explanation
Indices: 39972822--39972874 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39972812 TCCACGTCTT
*
39972822 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39972844 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39972867 TTTCTTTT
1 TTTCTTTT
39972875 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39976459 original size:15 final size:14
Alignment explanation
Indices: 39976439--39976486 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
39976429 CTCATTTTCA
39976439 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
39976454 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
39976468 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
39976483 TCTT
1 TCTT
39976487 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:39976491 original size:22 final size:21
Alignment explanation
Indices: 39976439--39976497 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
39976429 CTCATTTTCA
* *
39976439 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
39976460 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
39976481 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
39976498 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:39977422 original size:13 final size:13
Alignment explanation
Indices: 39977406--39977458 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
39977396 TCAATTTTGA
39977406 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
****
39977419 TTTTTTAATTCCGAA
1 TTTTTT--TTCTTCT
39977434 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
39977447 TTTTTTTTCTTC
1 TTTTTTTTCTTC
39977459 AATACTAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
13 21 0.70
15 9 0.30
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:39977525 original size:13 final size:12
Alignment explanation
Indices: 39977509--39977540 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
39977499 TTTTTTTTAT
39977509 TTTTTTTTCAAAA
1 TTTTTTTTC-AAA
39977522 TTTTTTTTCAAA
1 TTTTTTTTCAAA
39977534 TTTTTTT
1 TTTTTTT
39977541 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:39980526 original size:11 final size:9
Alignment explanation
Indices: 39980486--39980519 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
39980476 TTTTATTGAA
*
39980486 TTTTGTCTT
1 TTTTGACTT
39980495 TTTTGA-TT
1 TTTTGACTT
39980503 TTTTGACTT
1 TTTTGACTT
39980512 TTTTGACT
1 TTTTGACT
39980520 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.71
Consensus pattern (9 bp):
TTTTGACTT
Found at i:39983416 original size:34 final size:34
Alignment explanation
Indices: 39983373--39983439 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
39983363 GTCTAATATT
39983373 AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
1 AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
39983407 AGTGTGGGCCTTAGCCCATTATAGTAACAGTAT
1 AGTGTGGGCCTTAGCCCATTATAGTAACAGTAT
39983440 TAGAAATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (34 bp):
AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
Found at i:39984682 original size:15 final size:16
Alignment explanation
Indices: 39984636--39984684 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
39984626 TAACCCCATA
*
39984636 AAGTGAAAAGAGAAGA
1 AAGTGAAAAGAGAAGT
*
39984652 AAGTCAAAAGCAAGAAGT
1 AAGTGAAAAG--AGAAGT
39984670 AAG-GAAAAGAGAAGT
1 AAGTGAAAAGAGAAGT
39984685 CAAGAGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 5 0.18
18 8 0.29
ACGTcount: A:0.59, C:0.04, G:0.29, T:0.08
Consensus pattern (16 bp):
AAGTGAAAAGAGAAGT
Found at i:39988767 original size:15 final size:17
Alignment explanation
Indices: 39988739--39988772 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39988729 TTATTAATTT
39988739 TAAAAGGTTAAAT-ATA
1 TAAAAGGTTAAATAATA
39988755 TAAAAGG-TAAATAATA
1 TAAAAGGTTAAATAATA
39988771 TA
1 TA
39988773 TATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAAGGTTAAATAATA
Found at i:39989722 original size:43 final size:42
Alignment explanation
Indices: 39989661--39989790 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 42
39989651 ATAGGATTTT
*
39989661 GATATGTGTTCTCGTGTAAAACCACGTCTGGGACGTTGGCATC
1 GATATGTGAT-TCGTGTAAAACCACGTCTGGGACGTTGGCATC
* * * *
39989704 GATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATGTGATT-CGTGTAAAACCACGTCTGGGACGTTGGCATC
* * *
39989747 -ATATTTGATTCATGTAAAACC-CTATCTGGGACAG-TGGCATC
1 GATATGTGATTCGTGTAAAACCAC-GTCTGGGAC-GTTGGCATC
39989788 GAT
1 GAT
39989791 TTATCGATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
41 23 0.32
42 12 0.17
43 36 0.51
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
GATATGTGATTCGTGTAAAACCACGTCTGGGACGTTGGCATC
Found at i:39989775 original size:41 final size:42
Alignment explanation
Indices: 39989675--39989790 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 42
39989665 TGTGTTCTCG
** * *
39989675 TGTAAAACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAAACCATATCTGGGAC-ATGGCATCGATATGTGATTACA
* * *
39989718 TGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATT-CA
1 TGTAAAACCATATCTGGGACAT-GGCATCGATATGTGATTACA
*
39989759 TGTAAAACCCTATCTGGGACAGTGGCATCGAT
1 TGTAAAACCATATCTGGGACA-TGGCATCGAT
39989791 TTATCGATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 25 0.40
42 13 0.21
43 24 0.39
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAAACCATATCTGGGACATGGCATCGATATGTGATTACA
Found at i:39991877 original size:17 final size:18
Alignment explanation
Indices: 39991855--39991896 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39991845 CATGTTTACA
39991855 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
39991872 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
39991890 TGGTTGA
1 TGGTTGA
39991897 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:39993450 original size:16 final size:16
Alignment explanation
Indices: 39993429--39993460 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39993419 CATTCTGCAT
39993429 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39993445 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39993461 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:39995518 original size:18 final size:18
Alignment explanation
Indices: 39995497--39995556 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
39995487 GACCTCACTC
39995497 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
39995515 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
39995533 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
39995554 TCT
1 TCT
39995557 CGCTCACACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:39998075 original size:11 final size:12
Alignment explanation
Indices: 39998053--39998080 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39998043 AAAAAAAAAA
39998053 TTTTGAATTTTT
1 TTTTGAATTTTT
39998065 TTTTGAATTTTT
1 TTTTGAATTTTT
39998077 TTTT
1 TTTT
39998081 CAAATTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTGAATTTTT
Found at i:39999613 original size:16 final size:16
Alignment explanation
Indices: 39999592--39999623 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39999582 CATTCTGCAT
39999592 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39999608 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39999624 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:40004156 original size:12 final size:11
Alignment explanation
Indices: 40004139--40004190 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
40004129 AGTAAGTGAA
40004139 AAAAAAGTTTC
1 AAAAAAGTTTC
40004150 GAAAAAAG-TTC
1 -AAAAAAGTTTC
40004161 AAAAAAAAGTTTC
1 --AAAAAAGTTTC
**
40004174 AAAAAAAATTC
1 AAAAAAGTTTC
40004185 AAAAAA
1 AAAAAA
40004191 AAATTGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 18 0.51
12 14 0.40
13 3 0.09
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAAAAGTTTC
Found at i:40004169 original size:24 final size:24
Alignment explanation
Indices: 40004137--40004192 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
40004127 CAAGTAAGTG
* *
40004137 AAAAAAAAGTTTCGAAAAAAGTTC
1 AAAAAAAAGTTTCAAAAAAAATTC
40004161 AAAAAAAAGTTTCAAAAAAAATTC
1 AAAAAAAAGTTTCAAAAAAAATTC
40004185 AAAAAAAA
1 AAAAAAAA
40004193 ATTGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAAAAAAGTTTCAAAAAAAATTC
Found at i:40004191 original size:12 final size:12
Alignment explanation
Indices: 40004151--40004195 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
40004141 AAAAGTTTCG
*
40004151 AAAAAAGTTCAA
1 AAAAAAATTCAA
*
40004163 AAAAAAGTTTC-A
1 AAAAAA-ATTCAA
40004175 AAAAAAATTCAA
1 AAAAAAATTCAA
40004187 AAAAAAATT
1 AAAAAAATT
40004196 GAAACTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:40009301 original size:17 final size:18
Alignment explanation
Indices: 40009279--40009320 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40009269 CATGTTTACA
40009279 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
40009296 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
40009314 TGGTTGA
1 TGGTTGA
40009321 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:40015587 original size:14 final size:14
Alignment explanation
Indices: 40015568--40015617 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
40015558 CAAAAAAATC
40015568 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
*
40015582 AAAAAAAATTTGATTGA
1 AAAAAAAATTCGA---A
40015599 AAAAAAAATTC-AA
1 AAAAAAAATTCGAA
40015612 AAAAAA
1 AAAAAA
40015618 GTGAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
16 1 0.03
17 11 0.35
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:40015639 original size:26 final size:25
Alignment explanation
Indices: 40015609--40015668 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
40015599 AAAAAAAATT
**
40015609 CAAAAAAAAGTGAAAAAAAA-TCGAG
1 CAAAAAAAAGAAAAAAAAAAGT-GAG
40015634 CAAAAAAAAGAAAAAAAAAAGGTGAG
1 CAAAAAAAAGAAAAAAAAAA-GTGAG
40015660 CAAAAAAAA
1 CAAAAAAAA
40015669 TCAAGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 18 0.58
26 12 0.39
27 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (25 bp):
CAAAAAAAAGAAAAAAAAAAGTGAG
Found at i:40016727 original size:12 final size:12
Alignment explanation
Indices: 40016701--40016819 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
40016691 AAAGAAATTG
40016701 AAAGAAAAC-AA
1 AAAGAAAACGAA
40016712 AAAGAAAACGAA
1 AAAGAAAACGAA
*
40016724 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
40016736 ATTGCAAAA-G-A
1 AAAG-AAAACGAA
*
40016747 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
40016759 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
40016771 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
40016785 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
40016798 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
40016813 AAAGAAA
1 AAAGAAA
40016820 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
10 3 0.04
11 15 0.18
12 29 0.35
13 11 0.13
14 18 0.21
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:40016731 original size:18 final size:18
Alignment explanation
Indices: 40016705--40016807 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
40016695 AAATTGAAAG
*
40016705 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
40016723 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
40016741 AAAAG-AAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
40016758 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
40016776 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
40016797 AAAAGAAAAAG
1 AAAAGAAAAAG
40016808 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
17 15 0.23
18 31 0.48
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:40016733 original size:6 final size:6
Alignment explanation
Indices: 40016701--40016807 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
40016691 AAAGAAATTG
* * ** *
40016701 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
40016747 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
40016798 AAAGAA AAAG
1 AAAGAA AAAG
40016808 CGAAAAAAGA
Statistics
Matches: 74, Mismatches: 23, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
5 8 0.11
6 55 0.74
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:40016789 original size:14 final size:13
Alignment explanation
Indices: 40016768--40016805 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40016758 AAAAGTGAGA
40016768 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
40016780 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
40016795 GAAAAAGAAAA
1 GAAAAAGAAAA
40016806 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:40016819 original size:21 final size:21
Alignment explanation
Indices: 40016769--40016819 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
40016759 AAAGTGAGAG
*
40016769 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
40016790 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
40016811 AAAAAGAAA
1 AAAAAGAAA
40016820 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:40016859 original size:33 final size:33
Alignment explanation
Indices: 40016822--40016884 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40016812 AAAAGAAATT
40016822 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
40016855 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
40016885 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:40020796 original size:33 final size:33
Alignment explanation
Indices: 40020758--40020820 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40020748 GATTACTCAC
40020758 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
40020791 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
40020821 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:40020859 original size:18 final size:18
Alignment explanation
Indices: 40020835--40020878 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40020825 TCTTTTTTCG
* *
40020835 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
*
40020853 TTTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
40020871 CTTTTTCA
1 CTTTTTCA
40020879 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:40020874 original size:30 final size:27
Alignment explanation
Indices: 40020838--40020904 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 27
40020828 TTTTTCGCTT
*
40020838 TTTCTTTTTCAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
40020868 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
40020895 TTTCTTTTTC
1 TTTCTTTTTC
40020905 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
30 21 0.60
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:40020888 original size:12 final size:12
Alignment explanation
Indices: 40020838--40020937 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
40020828 TTTTTCGCTT
40020838 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
40020850 TTTTTTTTTC-A
1 TTTCTTTTTCAA
40020861 -TTC----TCAA
1 TTTCTTTTTCAA
40020868 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
40020880 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
40020895 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
40020907 TCACTTTTTCGA
1 TTTCTTTTTCAA
40020919 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
40020931 TCTCTTT
1 TTTCTTT
40020938 CTCCTTTTCT
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 3 0.05
10 2 0.03
11 1 0.02
12 39 0.59
13 7 0.11
14 7 0.11
15 4 0.06
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.67
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:40020946 original size:24 final size:24
Alignment explanation
Indices: 40020861--40020947 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
40020851 TTTTTTTTCA
* *
40020861 TTCTCAATTTCTTTTTCAATTTTCTT
1 TTCTCATTTTCTTTTTCAA-TCTC-T
** *
40020887 TTCTTCATTTTCTTTTTCTCTCACT
1 TTC-TCATTTTCTTTTTCAATCTCT
*
40020912 TTTTCGA-TTTCTTTTTCAATCTCT
1 TTCTC-ATTTTCTTTTTCAATCTCT
*
40020936 TTCTCCTTTTCT
1 TTCTCATTTTCT
40020948 CACTCAATGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
24 25 0.53
25 4 0.09
26 5 0.11
27 13 0.28
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.64
Consensus pattern (24 bp):
TTCTCATTTTCTTTTTCAATCTCT
Found at i:40024346 original size:17 final size:18
Alignment explanation
Indices: 40024324--40024365 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40024314 CATGTTTACA
40024324 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
40024341 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
40024359 TGGTTGA
1 TGGTTGA
40024366 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:40026627 original size:12 final size:13
Alignment explanation
Indices: 40026605--40026642 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
40026595 AGATTGTAAA
*
40026605 AAAATAAAATAAT
1 AAAATAAAATAAG
40026618 AAAA-AAAATAAG
1 AAAATAAAATAAG
40026630 AAAATGAAAATAA
1 AAAAT-AAAATAA
40026643 AAGAGAGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAATAAAATAAG
Found at i:40029230 original size:30 final size:30
Alignment explanation
Indices: 40029196--40029292 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40029186 TAAACTAAAA
*
40029196 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
40029226 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40029256 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40029285 ATGAGCTA
1 -TGAGCTA
40029293 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:40030509 original size:20 final size:20
Alignment explanation
Indices: 40030463--40030509 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40030453 AGCTCGTTTC
*
40030463 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
40030483 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40030503 CAGCTCA
1 CAGCTCA
40030510 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40034864 original size:20 final size:20
Alignment explanation
Indices: 40034841--40034887 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40034831 GGGTTAAAAT
*
40034841 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40034861 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40034881 TGAGCTG
1 TGAGCTG
40034888 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40037949 original size:17 final size:18
Alignment explanation
Indices: 40037927--40037960 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40037917 ACAACACTCC
*
40037927 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
40037944 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
40037961 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:40038682 original size:13 final size:13
Alignment explanation
Indices: 40038660--40038708 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
40038650 ATGCAATTTT
40038660 TTTTTCTTTTCAAA
1 TTTTT-TTTTCAAA
*
40038674 TTTTTTTTTTCAAT
1 -TTTTTTTTTCAAA
*
40038688 TTTTTTTTTCGAAC
1 TTTTTTTTTC-AAA
40038702 TTTTTTT
1 TTTTTTT
40038709 ACGTACCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 10 0.32
14 16 0.52
15 5 0.16
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:40038683 original size:14 final size:14
Alignment explanation
Indices: 40038659--40038708 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
40038649 TATGCAATTT
40038659 TTTTTTCTTTTCAAA
1 TTTTTT-TTTTCAAA
40038674 TTTTTTTTTTC-AA
1 TTTTTTTTTTCAAA
*
40038687 TTTTTTTTTTCGAAC
1 TTTTTTTTTTC-AAA
40038702 TTTTTTT
1 TTTTTTT
40038709 ACGTACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 13 0.41
14 5 0.16
15 14 0.44
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:40041763 original size:48 final size:48
Alignment explanation
Indices: 40041707--40041812 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
40041697 TTGTCTTTTC
*
40041707 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
40041755 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
40041803 TTTCTTTTTC
1 TTTCTTTTTC
40041813 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:40043775 original size:20 final size:20
Alignment explanation
Indices: 40043752--40043805 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40043742 AGTTTTTCCC
*
40043752 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40043772 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40043792 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40043806 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40043787 original size:30 final size:30
Alignment explanation
Indices: 40043752--40043825 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40043742 AGTTTTTCCC
40043752 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40043782 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40043812 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40043826 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40043815 original size:20 final size:20
Alignment explanation
Indices: 40043752--40043816 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40043742 AGTTTTTCCC
* * * *
40043752 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40043772 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40043791 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40043812 AGCTC
1 AGCTC
40043817 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40046433 original size:15 final size:16
Alignment explanation
Indices: 40046413--40046444 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40046403 AGAAAATGAA
40046413 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
40046428 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
40046444 A
1 A
40046445 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:40047848 original size:20 final size:20
Alignment explanation
Indices: 40047825--40047878 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40047815 AGTTTTTCCC
*
40047825 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40047845 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40047865 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40047879 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Done.