Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 64 of 143
Found at i:20787259 original size:80 final size:82
Alignment explanation
Indices: 20787121--20787352 Score: 265
Period size: 80 Copynumber: 2.9 Consensus size: 82
20787111 GGGTATTGAC
* * **
20787121 TATATGGACCCTCCGATGGCTGAGATTTTGCATATGTTGTGGATTCTTGACAGCTTGTGTGAGCA
1 TATA-GGACCCTCCGATGGCTGAGATCTTACATATGTTGCAGATTCTTGACAGCTTGTGTGAGCA
*
20787186 GCATCGA-GAGTGGATAA
65 GCATCGATGAGTAGATAA
* * * *
20787203 TA-AGGACCCTCCAATGGCTGAGAACCTACATATGTTGCAGATTCTTGACAGCTTGTGTGAGTAG
1 TATAGGACCCTCCGATGGCTGAGATCTTACATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAG
20787267 CATC-ATGAGTAGATAA
66 CATCGATGAGTAGATAA
* * * * * * *
20787283 TATA-GACCGTATCGATGGTTGGGATCTTACATATGTTGCAGTTTCTTGATAGCTTGTGTAAGCA
1 TATAGGACCCT-CCGATGGCTGAGATCTTACATATGTTGCAGATTCTTGACAGCTTGTGTGAGCA
*
20787347 ACATCG
65 GCATCG
20787353 TATACTGGTT
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
79 1 0.01
80 73 0.58
81 49 0.39
82 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (82 bp):
TATAGGACCCTCCGATGGCTGAGATCTTACATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAG
CATCGATGAGTAGATAA
Found at i:20792744 original size:81 final size:80
Alignment explanation
Indices: 20792554--20792756 Score: 266
Period size: 80 Copynumber: 2.5 Consensus size: 80
20792544 TGAGATTTTA
* * *
20792554 CATATGTTGCAGATTCTTGACAACTTGTGTGAGCAGCATCGAGAGTGGATAATAAGGACCCTCTT
1 CATATGTTGCAGATTCTTGACAACTTGTGTGAGCAGCATCGTGACTGGATAATAAGGACCCTCAT
*
20792619 ATGATTGAGATCCTG
66 ATGATGGAGATCCTG
* * * *
20792634 CATATGTTGCGGATTCTTGACAACTTGTGTGGGCAGCATCGTGACTGGATAATATGGACCGT-AT
1 CATATGTTGCAGATTCTTGACAACTTGTGTGAGCAGCATCGTGACTGGATAATAAGGACCCTCAT
20792698 A-GATGGCTAGGATCCTG
66 ATGATGG--A-GATCCTG
* * *
20792715 CATATGTTGCAGTTTCCTGACAACTTGTGTGAGTAGCATCGT
1 CATATGTTGCAGATTCTTGACAACTTGTGTGAGCAGCATCGT
20792757 ATACTGGTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
78 4 0.04
79 2 0.02
80 57 0.53
81 44 0.41
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (80 bp):
CATATGTTGCAGATTCTTGACAACTTGTGTGAGCAGCATCGTGACTGGATAATAAGGACCCTCAT
ATGATGGAGATCCTG
Found at i:20792816 original size:26 final size:26
Alignment explanation
Indices: 20792763--20792816 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
20792753 TCGTATACTG
* *
20792763 GTTAAATTCTGTCTGGGCTCGTAAGA
1 GTTAAATTCTGTCTGGACTCATAAGA
* *
20792789 GTTAAGTTCTGTCTGGACTCATATGA
1 GTTAAATTCTGTCTGGACTCATAAGA
20792815 GT
1 GT
20792817 GAAAATTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (26 bp):
GTTAAATTCTGTCTGGACTCATAAGA
Found at i:20793896 original size:22 final size:22
Alignment explanation
Indices: 20793843--20793890 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
20793833 ACAGGACCAA
20793843 TGTCACGACACCCTAGTGCCTG
1 TGTCACGACACCCTAGTGCCTG
20793865 TGTCACGACACCCTAGTGCCTG
1 TGTCACGACACCCTAGTGCCTG
20793887 TGTC
1 TGTC
20793891 GTGACATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (22 bp):
TGTCACGACACCCTAGTGCCTG
Found at i:20793971 original size:21 final size:21
Alignment explanation
Indices: 20793947--20793989 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20793937 GTGTCGCAAA
*
20793947 ATCCAATGGCTGTGTCACGAC
1 ATCCAATGGCTATGTCACGAC
** *
20793968 ATCCCGTGGCTATGTCGCGAC
1 ATCCAATGGCTATGTCACGAC
20793989 A
1 A
20793990 CTAAAGGCAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (21 bp):
ATCCAATGGCTATGTCACGAC
Found at i:20794916 original size:16 final size:17
Alignment explanation
Indices: 20794887--20794919 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20794877 TATACTAATT
20794887 TTTTTTCAAATTTTTTA
1 TTTTTTCAAATTTTTTA
*
20794904 TTTTTT-AATTTTTTTA
1 TTTTTTCAAATTTTTTA
20794920 AAAATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCAAATTTTTTA
Found at i:20803443 original size:30 final size:30
Alignment explanation
Indices: 20803223--20803461 Score: 252
Period size: 30 Copynumber: 8.0 Consensus size: 30
20803213 GAATACGAGA
*
20803223 TCAAAATGTAAATTTGGAAAAGTTTAGGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTA-GGGG
* *
20803254 TAAAAATGTAATTTTAGG-AAAG-CTAGGGG
1 TCAAAATGTAATTTT-GGAAAAGTTTAGGGG
* * * *
20803283 TCAAAATGTGATTGTGGAGAAGTTTAGGGT
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGG
* * *
20803313 TAAAACATG--ATTTTGGAAAAGTTTAAGGT
1 TCAAA-ATGTAATTTTGGAAAAGTTTAGGGG
* * *
20803342 TCAAAATCTATTTTTGGAAAAATTTAGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGG
*
20803372 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGG
* *
20803402 TTAAAATGTAATTTTGGACAAGTTTAGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGG
* *
20803432 TCAAAATGTAATTTTTGAGAAGTTTGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTT-AGGG
20803462 TTAAAATATG
Statistics
Matches: 172, Mismatches: 29, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.02
29 40 0.23
30 102 0.59
31 24 0.14
32 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTAGGGG
Found at i:20805150 original size:17 final size:17
Alignment explanation
Indices: 20805087--20805155 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 17
20805077 TAAATGGACT
20805087 TTTAAATTTAAA-TAAA
1 TTTAAATTTAAAGTAAA
20805103 TTTAAATTTAAATGTATTGGACA
1 TTTAAATTTAAA-GTA----A-A
20805126 TTTAAAATTTAAAGTAAA
1 TTT-AAATTTAAAGTAAA
20805144 TTTAAATTTAAA
1 TTTAAATTTAAA
20805156 ATTTGTCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
16 12 0.27
17 9 0.20
18 6 0.13
19 1 0.02
22 1 0.02
23 7 0.16
24 9 0.20
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:20811084 original size:20 final size:20
Alignment explanation
Indices: 20811052--20811111 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
20811042 ATTTTGAAGT
20811052 GTTAAAATAATTTTGACTTG
1 GTTAAAATAATTTTGACTTG
* *
20811072 GTTCAAATGATTTTGACTTG
1 GTTAAAATAATTTTGACTTG
* * *
20811092 TTTAAAATCATTTTAACTTG
1 GTTAAAATAATTTTGACTTG
20811112 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (20 bp):
GTTAAAATAATTTTGACTTG
Found at i:20817867 original size:11 final size:11
Alignment explanation
Indices: 20817851--20817883 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
20817841 TTTTTGCTAA
20817851 ATATTAATTAT
1 ATATTAATTAT
20817862 ATATTAATTAT
1 ATATTAATTAT
*
20817873 A-ATTTATTAT
1 ATATTAATTAT
20817883 A
1 A
20817884 GTCAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTAATTAT
Found at i:20819462 original size:189 final size:189
Alignment explanation
Indices: 20819138--20819518 Score: 726
Period size: 189 Copynumber: 2.0 Consensus size: 189
20819128 GTGAAAAAAT
20819138 AAGTCTTTTATTGACTTTAGGGTCGATTGAGGCTTAAAGGTTGGCAAACGAACTTCGTGAGTGTG
1 AAGTCTTTTATTGACTTTAGGGTCGATTGAGGCTTAAAGGTTGGCAAACGAACTTCGTGAGTGTG
* *
20819203 CAGGAGACCATTAGAGGATGAACTACATCGAAGCTGATCATTATGTCACAACATGAGACAAGATA
66 CAGGAGACCATTAAAGGATGAACTACATCGAAGCTGATCATTATGTCACAACATGAGACAAGAGA
20819268 TGTAGCAACATAGGGACAAGAACCAAAGAATCTTGAAGTTGTCTTCTATGTCACGACAC
131 TGTAGCAACATAGGGACAAGAACCAAAGAATCTTGAAGTTGTCTTCTATGTCACGACAC
20819327 AAGTCTTTTATTGACTTTAGGGTCGATTGAGGCTTAAAGGTTGGCAAACGAACTTCGTGAGTGTG
1 AAGTCTTTTATTGACTTTAGGGTCGATTGAGGCTTAAAGGTTGGCAAACGAACTTCGTGAGTGTG
20819392 CAGGAGACCATTAAAGGATGAACTACATCGAAGCTGATCATTATGTCACAACATGAGACAAGAGA
66 CAGGAGACCATTAAAGGATGAACTACATCGAAGCTGATCATTATGTCACAACATGAGACAAGAGA
* *
20819457 TGTAGCATCATAGGGACAAGAACCAAAGAATCTTGAAGTTGTCTTCTATGTCAGGACAC
131 TGTAGCAACATAGGGACAAGAACCAAAGAATCTTGAAGTTGTCTTCTATGTCACGACAC
20819516 AAG
1 AAG
20819519 CACATGTCGG
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (189 bp):
AAGTCTTTTATTGACTTTAGGGTCGATTGAGGCTTAAAGGTTGGCAAACGAACTTCGTGAGTGTG
CAGGAGACCATTAAAGGATGAACTACATCGAAGCTGATCATTATGTCACAACATGAGACAAGAGA
TGTAGCAACATAGGGACAAGAACCAAAGAATCTTGAAGTTGTCTTCTATGTCACGACAC
Found at i:20819830 original size:22 final size:22
Alignment explanation
Indices: 20819786--20819831 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20819776 TCTTTGTAAT
*
20819786 TTAGGTTTAATTATTTCTTTTC
1 TTAGGTTTAATTATTTCTGTTC
*
20819808 TTAGGTTTTAGTTATTT-TGTTC
1 TTAGG-TTTAATTATTTCTGTTC
20819830 TT
1 TT
20819832 TTGTTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (22 bp):
TTAGGTTTAATTATTTCTGTTC
Found at i:20822001 original size:73 final size:73
Alignment explanation
Indices: 20821910--20822103 Score: 203
Period size: 74 Copynumber: 2.6 Consensus size: 73
20821900 CACTGTTGTT
* * *
20821910 GTGTCGCTCCATAGAGTCGATAAACCATCATCACGGTGTCTCTCTAGTGAGCAAGTCTATTATCA
1 GTGTAGCTCCATAGAGTCGATAAACCATCGTCACGGTGTCTCTCTAGTGAGCAAGTCTATTACCA
*
20821975 CCGTTGCA
66 CCGTAGCA
* * *** * *
20821983 GTTTCA-CTCCATAGAGTCGATAGACCATCGTCATAATGTCGCCTTTAGTGAGCAAGTCTATTAC
1 GTGT-AGCTCCATAGAGTCGATAAACCATCGTCACGGTGTC-TCTCTAGTGAGCAAGTCTATTAC
* * *
20822047 CGCTGTAGCG
64 CACCGTAGCA
* *
20822057 GTGTAGCTCCATAGAGTCAATATACCATCGTCACGGTGT-TGCTCTAG
1 GTGTAGCTCCATAGAGTCGATAAACCATCGTCACGGTGTCT-CTCTAG
20822104 CGAGTCATTC
Statistics
Matches: 95, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
73 38 0.40
74 57 0.60
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (73 bp):
GTGTAGCTCCATAGAGTCGATAAACCATCGTCACGGTGTCTCTCTAGTGAGCAAGTCTATTACCA
CCGTAGCA
Found at i:20835676 original size:195 final size:194
Alignment explanation
Indices: 20835292--20835739 Score: 526
Period size: 195 Copynumber: 2.3 Consensus size: 194
20835282 TATCAGTAAT
* * * * * * *
20835292 CGATGTTGCTCACATGAACTGTCGAGGACTCGCAACGTATGCAGTACCCCAGCCATCGGTACGGT
1 CGATGCTGCTCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGAT
* * * * * *
20835357 GCCTGTCTGTACTATAAACTCTTCCCTACCGATGTTGCTCACACGAGCTGTCGAGAGTATGCATA
66 ACCTG-CTGCACTATAAACTCTTCCCTAACGATGCTGCTCACACGAGCTGTCCAGAATATGCATA
* * *
20835422 AAGCATAGTCTCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGAGTCA
130 AAGCATAATCTCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCA
* * * *
20835487 TGATGCTGCTCAAATGAGTTGTCGAGGACTCGCAACATATGCGGTGCCTCAGCCATCGATACGAT
1 CGATGCTGCTCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGAT
* * *
20835552 ATCTG-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCCAGAATATGCACTT
66 ACCTGCTGCACTATAAACTCTTCCCTAACGATGCTGCTCACACGAGCTGTCCAGAATATGCA-TA
* * * * *
20835614 ATGCATAAATCTCAACCATCGTAGGGCCTGTAATCCATTCTTGGATTC-TTTACTCATTTCTCGA
130 AAGCAT-AATCTCAACCATCGTAGGGCCTATAATCCATT-TAGGATCCATAT-CTC-TTTCTCGA
20835678 CTCA
191 CTCA
* * * *
20835682 CGATACTGCTCACACGAGCTGTGGAGGACTCGCAACATATGTGGTACCTCAGCCATCG
1 CGATGCTGCTCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
20835740 CGTCGGTTTC
Statistics
Matches: 212, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
191 42 0.20
192 9 0.04
193 34 0.16
194 9 0.04
195 118 0.56
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (194 bp):
CGATGCTGCTCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGAT
ACCTGCTGCACTATAAACTCTTCCCTAACGATGCTGCTCACACGAGCTGTCCAGAATATGCATAA
AGCATAATCTCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCA
Found at i:20836234 original size:16 final size:16
Alignment explanation
Indices: 20836210--20836241 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20836200 TCCTTACAAA
*
20836210 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
20836226 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
20836242 AAAAATCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:20841713 original size:45 final size:45
Alignment explanation
Indices: 20841517--20842135 Score: 602
Period size: 46 Copynumber: 14.1 Consensus size: 45
20841507 TCTTTTGTGA
* * * *
20841517 GATGGTAGTTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGA-TTAGGGGTAAAAGATTG
* *
20841563 GATGGTGGCTTCAATCTGC-CCTTATTGACTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCC-TCTTGA-TTAGGGGTAAAAGATTG
* * * * *
20841609 GATAGTGGCTTCAATTTTCCCCTTTTGATTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGA-TTAGGGGTAAAAGATTG
* ** * * * * *
20841655 GATAGTGATTTCAATATGCTGCTCTTTATTAGGAGTAAAAGATCG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
20841700 GATGGTGGCTTCAATCTGC-CCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
*
20841744 GATGGTAGCTTCAATCTGC-CTCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTC-CTCTTGA-TTAGGGGTAAAAGATTG
* * * *
20841790 GATGGTGGCTTTAATCTACTCCTCTTGATTCGGAGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
*
20841835 GATGGTGGCTTCAATCTGC-CTTTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTC-CTCTTGATTAGGGGTAAAAGATTG
* * * * *
20841880 GATAGTGACTTCAACCTACCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGA-TTAGGGGTAAAAGATTG
* * * * *
20841926 GATAGTGGTTTCAATCTGCCCCTCTTGACTTAAGGATAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGA-TTAGGGGTAAAAGATTG
* * *
20841972 GATGGT--TTTTAATCTGC-CCTC-TGGTTA-GGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
* *
20842012 GATGGT--TTTCAATCTGC-CCTC-TGGTTA-GGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
* *
20842052 GATGGT--CTTCAACCTGC-CCTC-TGGTTA-GGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
*
20842092 GATGGT--CTTCAATCTGC-CCTCTAG-TTA-GGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
20842132 GATG
1 GATG
20842136 TGGTGGTGTA
Statistics
Matches: 503, Mismatches: 61, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
40 129 0.26
41 4 0.01
42 2 0.00
43 4 0.01
44 51 0.10
45 113 0.22
46 197 0.39
47 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCTCCTCTTGATTAGGGGTAAAAGATTG
Found at i:20842566 original size:98 final size:101
Alignment explanation
Indices: 20842194--20842648 Score: 414
Period size: 101 Copynumber: 4.6 Consensus size: 101
20842184 TTCATTATTG
* * * *
20842194 TAGTTTTAATCCGCTTCAC-GGTAACTTCAAGAAGATAGGATTTGGTGTTGTAGCCTCATCTTAC
1 TAGTTTTAATCCGCTTCACTAGTAACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC
* * *
20842258 TCCACTGTAATTTTAGGGAGATAAAGATTTGCCACTGT
66 TCCACTGCAACTTCAGGGAGATAAAGATTTGCCAC--T
* ** * * * *
20842296 TAGTTTTAATTC-AATCCCTA-CAACTTTATGG-ATATAGGATTTGGTGTTGTAGCCTT-ATCTT
1 TAGTTTTAATCCGCTTCACTAGTAACTTCA-GGAAGATAGGATTTGGTGTTGTAG-CTTCATCTT
* *
20842357 GCTCCACTACAACTTCAGGGAGATAAAGATTTACCACTGT
64 GCTCCACTGCAACTTCAGGGAGATAAAGATTTGCCAC--T
* * * * * ** *
20842397 TAGTTTTAATCTG-ATCCCT-GTAACTTCAGGGATATAGGATTTGGAATTGTAGTTTCATCTTGC
1 TAGTTTTAATCCGCTTCACTAGTAACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC
* *
20842460 TCCACTGCATCTTCAGGGAGATAAAGATTTGCTAC-
66 TCCACTGCAACTTCAGGGAGATAAAGATTTGCCACT
20842495 T-GTTTTAATCCGCTTCACTAG-AACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC
1 TAGTTTTAATCCGCTTCACTAGTAACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC
** * ***
20842558 TCTGCTGCAACTTCAGGGAGATAAATATTTGTTGC-
66 TCCACTGCAACTTCAGGGAGATAAAGATTTGCCACT
* * * * * * *
20842593 TA-TTTTAATCTGCTTC-GTTGCAACTTTAGGAAGATAGGATTTGGTGTGGTAACTTC
1 TAGTTTTAATCCGCTTCACTAGTAACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTC
20842649 GCTCCATTCC
Statistics
Matches: 295, Mismatches: 47, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
97 12 0.04
98 117 0.40
99 1 0.00
100 4 0.01
101 147 0.50
102 14 0.05
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (101 bp):
TAGTTTTAATCCGCTTCACTAGTAACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC
TCCACTGCAACTTCAGGGAGATAAAGATTTGCCACT
Found at i:20842572 original size:50 final size:49
Alignment explanation
Indices: 20842516--20842648 Score: 121
Period size: 48 Copynumber: 2.7 Consensus size: 49
20842506 GCTTCACTAG
*
20842516 AACTTCAGGAAGATAGGATTTGGTGTTGTAGCTTCATCTTGC-TCTGCTGC
1 AACTTCAGGAAGATAGGATTTGGTGTTGTAACTTCATC-TGCTTC-GCTGC
* * ** * *
20842566 AACTTCAGGGAGATA-AATATT--TGTTGCTATTTTAATCTGCTTCGTTGC
1 AACTTCAGGAAGATAGGAT-TTGGTGTTG-TAACTTCATCTGCTTCGCTGC
* *
20842614 AACTTTAGGAAGATAGGATTTGGTGTGGTAACTTC
1 AACTTCAGGAAGATAGGATTTGGTGTTGTAACTTC
20842649 GCTCCATTCC
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
48 27 0.42
49 17 0.27
50 20 0.31
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (49 bp):
AACTTCAGGAAGATAGGATTTGGTGTTGTAACTTCATCTGCTTCGCTGC
Found at i:20844601 original size:16 final size:16
Alignment explanation
Indices: 20844584--20844620 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
20844574 CATCTTGACT
20844584 TTTTTC-TTTCTTTCC
1 TTTTTCTTTTCTTTCC
20844599 TTTTTCTTTTCTTT--
1 TTTTTCTTTTCTTTCC
20844613 TTTTTCTT
1 TTTTTCTT
20844621 CTTTTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 7 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTTTCC
Found at i:20844628 original size:12 final size:13
Alignment explanation
Indices: 20844583--20844628 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 13
20844573 TCATCTTGAC
20844583 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
20844596 TCCTTTTTCTTTTCTT
1 T--TTTTTC-TTTCTT
20844612 TTTTTTC-TTCTT
1 TTTTTTCTTTCTT
20844624 TTTTT
1 TTTTT
20844629 GGGGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.33
13 1 0.03
14 6 0.20
15 6 0.20
16 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:20844628 original size:20 final size:19
Alignment explanation
Indices: 20844583--20844628 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
20844573 TCATCTTGAC
20844583 TTTTTTCTTTCTTTCCTTT
1 TTTTTTCTTTCTTTCCTTT
* *
20844602 TTCTTTTCTTTTTTTTCTTCT
1 TT-TTTTCTTTCTTTCCTT-T
20844623 TTTTTT
1 TTTTTT
20844629 GGGGTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTCTTTCCTTT
Found at i:20850862 original size:108 final size:108
Alignment explanation
Indices: 20850561--20850870 Score: 390
Period size: 108 Copynumber: 2.9 Consensus size: 108
20850551 AATTACTTTG
* * *
20850561 GTCAGTTTATTTGACTAGCACTGGGCGCAAATATTTGTTGGTATATCTAACTAGAGTTGGGCTCA
1 GTCAGTTTATTCGACTAGCACTGGGCGC-AATA-TTGTTGGTTTATCCAACTAGAGTTGGGCTCA
* * *
20850626 -TTATTAATATCATTAGTTTATCTGACTAGTGCTGGGCACACATTT
64 CTT-TTAATATCGTTAGTTTATCTGACTAGTGCTAGGAACACATTT
* * * * * **
20850671 GTGAGTTTATCCGACTAGCGCTGGGCGCAATATCGTTGGTTAATCCAACTAGAACTGGGCTCACT
1 GTCAGTTTATTCGACTAGCACTGGGCGCAATATTGTTGGTTTATCCAACTAGAGTTGGGCTCACT
* ** *
20850736 ATTT-ATTTCGCCAATTTATCTGACTAGTGCTAGGAACACATTT
66 -TTTAATATCGTTAGTTTATCTGACTAGTGCTAGGAACACATTT
* *
20850779 GTCAGTTTATTCGACTAGCACTGGGTGCAATATTGTTGGTTTATCCAACTAGAGTTGTGCTCACT
1 GTCAGTTTATTCGACTAGCACTGGGCGCAATATTGTTGGTTTATCCAACTAGAGTTGGGCTCACT
*
20850844 TTTAATATCGTTAGTTTATCCGACTAG
66 TTTAATATCGTTAGTTTATCTGACTAG
20850871 CATTGGGCGC
Statistics
Matches: 166, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
107 3 0.02
108 131 0.79
109 7 0.04
110 25 0.15
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (108 bp):
GTCAGTTTATTCGACTAGCACTGGGCGCAATATTGTTGGTTTATCCAACTAGAGTTGGGCTCACT
TTTAATATCGTTAGTTTATCTGACTAGTGCTAGGAACACATTT
Found at i:20855791 original size:108 final size:107
Alignment explanation
Indices: 20855669--20855941 Score: 270
Period size: 108 Copynumber: 2.6 Consensus size: 107
20855659 CGCAAACATT
* *
20855669 TGTTGG-TATATCCAACTAGAGCTGGACTTA-TTATTAATATCGTCAGTTTATCTGACTAGTGCT
1 TGTTGGTTA-ATCCAACTAGAGCTGGGCTCACTT-TTAATATCGTCAGTTTATCTGACTAGTGCT
* *
20855732 -GAACACACATT-TGTC-GATTTATCTGACTAGTGCTGAGCGCAATA
64 CG-ACACACATTAT-TCAG-TTTATCCGACTAGCGCTGAGCGCAATA
* * * * * * *
20855776 TCGTTGGTTAATCCAACTAGATCTGGGCTCAGTTTTTATTTCGTCAGTTTATCTTACTAATGTTC
1 T-GTTGGTTAATCCAACTAGAGCTGGGCTCACTTTTAATATCGTCAGTTTATCTGACTAGTGCTC
* * * * *
20855841 GGCATACATTATTCAGTTTATCCGACTAGCGTTGGGCGCATTA
65 GACACACATTATTCAGTTTATCCGACTAGCGCTGAGCGCAATA
* * * *
20855884 TGTT-GTTTATCCAACTAGTGCTGGGCTCACTTTTAATATTGTCGGTTTATCTGACTAG
1 TGTTGGTTAATCCAACTAGAGCTGGGCTCACTTTTAATATCGTCAGTTTATCTGACTAG
20855942 CACTGGGCGC
Statistics
Matches: 135, Mismatches: 25, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
106 44 0.33
107 4 0.03
108 80 0.59
109 7 0.05
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (107 bp):
TGTTGGTTAATCCAACTAGAGCTGGGCTCACTTTTAATATCGTCAGTTTATCTGACTAGTGCTCG
ACACACATTATTCAGTTTATCCGACTAGCGCTGAGCGCAATA
Found at i:20874255 original size:26 final size:26
Alignment explanation
Indices: 20874056--20874295 Score: 243
Period size: 26 Copynumber: 9.2 Consensus size: 26
20874046 AAGCCTTGAA
20874056 CCGGTGAATAAATAGCTA-GCTTCGAG
1 CCGGTGAATAAATAGC-AGGCTTCGAG
* *
20874082 CCAGTGAATAAATATCAGGCTTCGAG
1 CCGGTGAATAAATAGCAGGCTTCGAG
* *
20874108 CCGATGAATATATAGCAGGCCTT-GAG
1 CCGGTGAATAAATAGCAGG-CTTCGAG
* *
20874134 CCAGTGAATAATTAGCAGGCTTCGAG
1 CCGGTGAATAAATAGCAGGCTTCGAG
* * *
20874160 CCGATGAATAAATAGTAGGCTTTGAG
1 CCGGTGAATAAATAGCAGGCTTCGAG
* * *
20874186 CCGATGAACATATAGCAGGCCTT-GAG
1 CCGGTGAATAAATAGCAGG-CTTCGAG
*
20874212 CCGGTGAATAATTAGCAGGCTTCGAG
1 CCGGTGAATAAATAGCAGGCTTCGAG
** *
20874238 TTGGTGAATAAATAGCAGGCTTAGAG
1 CCGGTGAATAAATAGCAGGCTTCGAG
* * * * *
20874264 CTGTTGATTATATAGCAGGCTTCGTG
1 CCGGTGAATAAATAGCAGGCTTCGAG
20874290 CCGGTG
1 CCGGTG
20874296 TACAGTTGAC
Statistics
Matches: 175, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
25 7 0.04
26 162 0.93
27 6 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (26 bp):
CCGGTGAATAAATAGCAGGCTTCGAG
Found at i:20874295 original size:78 final size:78
Alignment explanation
Indices: 20874036--20874283 Score: 336
Period size: 78 Copynumber: 3.2 Consensus size: 78
20874026 ATCGTAAACA
* * * * *
20874036 AATATATAGCAAGCCTTGAACCGGTGAATAAATAGCTA-GCTTCGAGCCAGTGAATAAATATCAG
1 AATATATAGCAGGCCTTGAGCCGGTGAATAATTAGC-AGGCTTCGAGCCGGTGAATAAATAGCAG
*
20874100 GCTTCGAGCCGATG
65 GCTTAGAGCCGATG
* * *
20874114 AATATATAGCAGGCCTTGAGCCAGTGAATAATTAGCAGGCTTCGAGCCGATGAATAAATAGTAGG
1 AATATATAGCAGGCCTTGAGCCGGTGAATAATTAGCAGGCTTCGAGCCGGTGAATAAATAGCAGG
*
20874179 CTTTGAGCCGATG
66 CTTAGAGCCGATG
* **
20874192 AACATATAGCAGGCCTTGAGCCGGTGAATAATTAGCAGGCTTCGAGTTGGTGAATAAATAGCAGG
1 AATATATAGCAGGCCTTGAGCCGGTGAATAATTAGCAGGCTTCGAGCCGGTGAATAAATAGCAGG
* *
20874257 CTTAGAGCTGTTG
66 CTTAGAGCCGATG
*
20874270 ATTATATAGCAGGC
1 AATATATAGCAGGC
20874284 TTCGTGCCGG
Statistics
Matches: 149, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 1 0.01
78 148 0.99
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (78 bp):
AATATATAGCAGGCCTTGAGCCGGTGAATAATTAGCAGGCTTCGAGCCGGTGAATAAATAGCAGG
CTTAGAGCCGATG
Found at i:20881329 original size:52 final size:52
Alignment explanation
Indices: 20881257--20881495 Score: 263
Period size: 52 Copynumber: 4.6 Consensus size: 52
20881247 AACAAATATA
* * *
20881257 TAGCAGGCCTT-GAGCAAGTGAATAAATAGCAGG-CTTCAGCCCGGTGAATAAA
1 TAGCAGG-CTTCGAGCCAGTGAATAAATAGCAGGCCTTGAG-CCGGTGAATAAT
* * *
20881309 TATCAGGCTTCTAGCCAGTGAATATATAGCAGGCCTTGAGCCGGTGAATAAT
1 TAGCAGGCTTCGAGCCAGTGAATAAATAGCAGGCCTTGAGCCGGTGAATAAT
* * *
20881361 TAGCAGGCTTCGAGCTAGTGAATATATAGCAGGCCTTGAGCCGGTGAGTAAT
1 TAGCAGGCTTCGAGCCAGTGAATAAATAGCAGGCCTTGAGCCGGTGAATAAT
* * * * *
20881413 TAGCAAGCTTCGAGCC-GATGAATAAGTAGCAGGCTTTGAGCTGGTG-ATCAT
1 TAGCAGGCTTCGAGCCAG-TGAATAAATAGCAGGCCTTGAGCCGGTGAATAAT
*
20881464 ATAGCAGGCCTT-GAGCCAGTGAATAATTAGCA
1 -TAGCAGG-CTTCGAGCCAGTGAATAAATAGCA
20881496 ATCTTCGAAT
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
51 7 0.04
52 145 0.90
53 9 0.06
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (52 bp):
TAGCAGGCTTCGAGCCAGTGAATAAATAGCAGGCCTTGAGCCGGTGAATAAT
Found at i:20881382 original size:78 final size:78
Alignment explanation
Indices: 20881251--20881488 Score: 261
Period size: 78 Copynumber: 3.1 Consensus size: 78
20881241 TTAGTAAACA
** * *
20881251 AATATATAGCAGGCCTTGAGCAAGTGAATAAATAGCAGGCTTC-AGCCCGGTGAATAAATATCAG
1 AATATATAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAG-CTGGTGAATAAATAGCAG
*
20881315 G-CTTCTAGCCAGTG
65 GCCTT-GAGCCAGTG
* * *
20881329 AATATATAGCAGGCCTTGAGCCGGTGAATAATTAGCAGGCTTCGAGCTAGTGAATATATAGCAGG
1 AATATATAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCTGGTGAATAAATAGCAGG
*
20881394 CCTTGAGCCGGTG
66 CCTTGAGCCAGTG
* * * * * *
20881407 AGTA-ATTAGCAAG-CTTCGAGCCGATGAATAAGTAGCAGGCTTTGAGCTGGTG-ATCATATAGC
1 AATATA-TAGCAGGCCTT-GAGCCGGTGAATAAATAGCAGGCTTCGAGCTGGTGAAT-AAATAGC
20881469 AGGCCTTGAGCCAGTG
63 AGGCCTTGAGCCAGTG
20881485 AATA
1 AATA
20881489 ATTAGCAATC
Statistics
Matches: 138, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
77 6 0.04
78 127 0.92
79 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (78 bp):
AATATATAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCTGGTGAATAAATAGCAGG
CCTTGAGCCAGTG
Found at i:20881491 original size:78 final size:78
Alignment explanation
Indices: 20881275--20881550 Score: 256
Period size: 78 Copynumber: 3.5 Consensus size: 78
20881265 CTTGAGCAAG
* ** * * *
20881275 TGAATAAATAGCAGGCTTC-AGCCCGGTGAATAAATATCAGG-CTTCTAGCCAGTGAAT-ATATA
1 TGAATAAGTAGCAGGCTTCGAG-CTAGTGAATATATAGCAGGCCTT-GAGCCAGTGAATAAT-TA
* *
20881337 GCAGGCCTT-GAGCCGG
63 GCAAG-CTTCGAGCCGA
* * *
20881353 TGAATAATTAGCAGGCTTCGAGCTAGTGAATATATAGCAGGCCTTGAGCCGGTGAGTAATTAGCA
1 TGAATAAGTAGCAGGCTTCGAGCTAGTGAATATATAGCAGGCCTTGAGCCAGTGAATAATTAGCA
20881418 AGCTTCGAGCCGA
66 AGCTTCGAGCCGA
* *
20881431 TGAATAAGTAGCAGGCTTTGAGCTGGTG-ATCATATAGCAGGCCTTGAGCCAGTGAATAATTAGC
1 TGAATAAGTAGCAGGCTTCGAGCTAGTGAAT-ATATAGCAGGCCTTGAGCCAGTGAATAATTAGC
* *** *
20881495 AATCTTCGAATTGG
65 AAGCTTCGAGCCGA
* * * * * *
20881509 TGAATAAATAGTAGGCTTCGAACCAGTGATTATATAGAAGGC
1 TGAATAAGTAGCAGGCTTCGAGCTAGTGAATATATAGCAGGC
20881551 TTCGTGTCGG
Statistics
Matches: 164, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
77 5 0.03
78 151 0.92
79 8 0.05
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (78 bp):
TGAATAAGTAGCAGGCTTCGAGCTAGTGAATATATAGCAGGCCTTGAGCCAGTGAATAATTAGCA
AGCTTCGAGCCGA
Found at i:20881537 original size:26 final size:26
Alignment explanation
Indices: 20881251--20881554 Score: 217
Period size: 26 Copynumber: 11.7 Consensus size: 26
20881241 TTAGTAAACA
* *
20881251 AATATATAGCAGGCCTT-GAGCAAGTG
1 AATAAATAGCAGG-CTTCGAGCCAGTG
*
20881277 AATAAATAGCAGGCTTC-AGCCCGGTG
1 AATAAATAGCAGGCTTCGAG-CCAGTG
* *
20881303 AATAAATATCAGGCTTCTAGCCAGTG
1 AATAAATAGCAGGCTTCGAGCCAGTG
* *
20881329 AATATATAGCAGGCCTT-GAGCCGGTG
1 AATAAATAGCAGG-CTTCGAGCCAGTG
* *
20881355 AATAATTAGCAGGCTTCGAGCTAGTG
1 AATAAATAGCAGGCTTCGAGCCAGTG
* *
20881381 AATATATAGCAGGCCTT-GAGCCGGTG
1 AATAAATAGCAGG-CTTCGAGCCAGTG
* * *
20881407 AGTAATTAGCAAGCTTCGAGCC-GATG
1 AATAAATAGCAGGCTTCGAGCCAG-TG
* * **
20881433 AATAAGTAGCAGGCTTTGAGCTGGTG
1 AATAAATAGCAGGCTTCGAGCCAGTG
*
20881459 -ATCATATAGCAGGCCTT-GAGCCAGTG
1 AAT-AAATAGCAGG-CTTCGAGCCAGTG
* ** ****
20881485 AATAATTAGCAATCTTCGAATTGGTG
1 AATAAATAGCAGGCTTCGAGCCAGTG
* *
20881511 AATAAATAGTAGGCTTCGAACCAGTG
1 AATAAATAGCAGGCTTCGAGCCAGTG
* * *
20881537 ATTATATAGAAGGCTTCG
1 AATAAATAGCAGGCTTCG
20881555 TGTCGGTGCA
Statistics
Matches: 217, Mismatches: 48, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
25 17 0.08
26 186 0.86
27 14 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (26 bp):
AATAAATAGCAGGCTTCGAGCCAGTG
Found at i:20891512 original size:21 final size:20
Alignment explanation
Indices: 20891487--20891537 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
20891477 AACTTGAGGA
* *
20891487 AAAGAAGGAAAATGAGGAAG
1 AAAGAAGGAAAAAGAAGAAG
*
20891507 AGAAGAAAGAAAAAGAAGAAG
1 A-AAGAAGGAAAAAGAAGAAG
20891528 AAGAGAAGGA
1 AA-AGAAGGA
20891538 TGAAGAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (20 bp):
AAAGAAGGAAAAAGAAGAAG
Found at i:20898445 original size:12 final size:12
Alignment explanation
Indices: 20898427--20898460 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
20898417 TTATTATCAA
20898427 TTTTTTCTTT-C
1 TTTTTTCTTTCC
20898438 TTTCTTTCTTTCC
1 TTT-TTTCTTTCC
20898451 TTTTTTCTTT
1 TTTTTTCTTT
20898461 TATGCGACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 14 0.67
13 4 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTTCC
Found at i:20899393 original size:3 final size:3
Alignment explanation
Indices: 20899368--20899427 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
20899358 GGGCAACATT
* *
20899368 TTC TTC TTT TTC TTCC TTC -TC TTC TTG TTC TT- TTC TTTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
20899413 TT- TTCC TTC TTC TTC
1 TTC TT-C TTC TTC TTC
20899428 CTCTACCTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 6 0.13
3 33 0.70
4 8 0.17
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20899407 original size:15 final size:15
Alignment explanation
Indices: 20899371--20899427 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
20899361 CAACATTTTC
*
20899371 TTCTTT-TTCTTC-C
1 TTCTTTCTTCTTCTT
*
20899384 TTCTCTTCTTGTTCTT
1 TTCT-TTCTTCTTCTT
20899400 TTCTTTCTTCTTCTT
1 TTCTTTCTTCTTCTT
*
20899415 TTCCTTCTTCTTC
1 TTCTTTCTTCTTC
20899428 CTCTACCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 4 0.11
14 2 0.05
15 27 0.73
16 4 0.11
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (15 bp):
TTCTTTCTTCTTCTT
Found at i:20903939 original size:195 final size:191
Alignment explanation
Indices: 20903580--20903941 Score: 426
Period size: 195 Copynumber: 1.9 Consensus size: 191
20903570 AAGAAAAGAA
*
20903580 ATATGGATCCTAAATGGATTACAGGACCTACAATGGCTGAGATTTATGCATAAGTGCATATTCTC
1 ATATGGATCCTAAATGGATTACAGGACCTACAATGGCTGAGATTTATGCATAAGTGCATACTCTC
* * * * * * *
20903645 GATAGCTTGTATGAGCAGCATCGTTAGGGAATAGTTATATGCACATAACGTATCGATGGTTGAGG
66 GACAGCTCGTATGAGCAGCATCGTTAGGGAACAGTTATATACACACAACGTACCGATGGCTGAGG
* *
20903710 TACCGCATATGTTGCGAGTCCTCGAAAGCTCATGTGAAAAGCATAGTGACTCTGAAAACAG
131 TACCGCAAACGTTGCGAGTCCTCGAAAGCTCATGTGAAAAGCATAGTGACTCTGAAAACAG
* * * * *
20903771 ATATGGATCCTAAATGGATTACAGGCCCTACGATGGTTG-G-TTGTATGC-TTATTGCATACTCT
1 ATATGGATCCTAAATGGATTACAGGACCTACAATGGCTGAGATT-TATGCATAAGTGCATACTCT
* * * * *
20903833 TGACAGCTCGTCTGAGTAGCATCGTTAGGGAACGGTTTATAGTACAGACAGGCACCGTACCGATG
65 CGACAGCTCGTATGAGCAGCATCGTTAGGGAACAG-TTATA-TAC--ACA--CAACGTACCGATG
* *
20903898 GCTGAGGTACTGGAAACGTTGCGAGTCCTCGATAA-CTCATGTGA
124 GCTGAGGTACCGCAAACGTTGCGAGTCCTCGA-AAGCTCATGTGA
20903942 GCAGTATCGT
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
189 41 0.29
190 11 0.08
191 38 0.27
193 3 0.02
195 46 0.33
196 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (191 bp):
ATATGGATCCTAAATGGATTACAGGACCTACAATGGCTGAGATTTATGCATAAGTGCATACTCTC
GACAGCTCGTATGAGCAGCATCGTTAGGGAACAGTTATATACACACAACGTACCGATGGCTGAGG
TACCGCAAACGTTGCGAGTCCTCGAAAGCTCATGTGAAAAGCATAGTGACTCTGAAAACAG
Found at i:20904732 original size:21 final size:21
Alignment explanation
Indices: 20904703--20904754 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20904693 GGAGTTTTTA
20904703 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
20904724 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
20904745 GTATCGGTAG
1 GTATCGGTAG
20904755 TATTGTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:20910498 original size:114 final size:114
Alignment explanation
Indices: 20910298--20910526 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
20910288 AGCAAATCTA
*
20910298 ACATTAAAAGACACTTCTGTGTTCATTCAATTGTCAATAGTATTCATCGACATTTAAGAGGGATT
1 ACATTAAAAGACACTTCTGTGTTCATTCAATTGTAAATAGTATTCATCGACATTTAAGAGGGATT
*
20910363 AACAAATGAATTGAAATATCCTATTCCTAGTCTATTAGAATTCTCCCTT
66 AACAAATGAATTAAAATATCCTATTCCTAGTCTATTAGAATTCTCCCTT
20910412 ACATTAAAAGACACTTCTGTGTTCATTCAATTGTAAATAGTATTCATCGACATTTAAGAGGGATT
1 ACATTAAAAGACACTTCTGTGTTCATTCAATTGTAAATAGTATTCATCGACATTTAAGAGGGATT
20910477 AACAAATGAATTAAAATATCCTATTCCTAGTCTATTAGAATTCTCCCTT
66 AACAAATGAATTAAAATATCCTATTCCTAGTCTATTAGAATTCTCCCTT
20910526 A
1 A
20910527 ACCGCTCCTC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (114 bp):
ACATTAAAAGACACTTCTGTGTTCATTCAATTGTAAATAGTATTCATCGACATTTAAGAGGGATT
AACAAATGAATTAAAATATCCTATTCCTAGTCTATTAGAATTCTCCCTT
Found at i:20915949 original size:17 final size:17
Alignment explanation
Indices: 20915927--20915959 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20915917 ATTAACATTA
*
20915927 AAATGCAATGACAATAG
1 AAATGCAACGACAATAG
20915944 AAATGCAACGACAATA
1 AAATGCAACGACAATA
20915960 TGCACTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (17 bp):
AAATGCAACGACAATAG
Found at i:20927693 original size:17 final size:17
Alignment explanation
Indices: 20927671--20927703 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20927661 ACTAACACTA
20927671 AAATGCAATGACAATGG
1 AAATGCAATGACAATGG
20927688 AAATGCAATGACAATG
1 AAATGCAATGACAATG
20927704 TGCACTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATGG
Found at i:20928043 original size:59 final size:59
Alignment explanation
Indices: 20927943--20928060 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
20927933 GGCATCATCT
* *
20927943 GCTGCGTCTTGTGTCGGATGGATCACCTTACGTGGTTTAGTGTAGACTACGATTACCAA
1 GCTGCGTCTTGTGTCGGATGGATCACCTTACGTGGTCTAGTGTAGACCACGATTACCAA
* *
20928002 GCTGTGTCTTGTGTCGGATGGATCACCTTACGTGGTCTAGTGTAGACCATGATTACCAA
1 GCTGCGTCTTGTGTCGGATGGATCACCTTACGTGGTCTAGTGTAGACCACGATTACCAA
20928061 AGGATTGTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (59 bp):
GCTGCGTCTTGTGTCGGATGGATCACCTTACGTGGTCTAGTGTAGACCACGATTACCAA
Found at i:20934348 original size:21 final size:22
Alignment explanation
Indices: 20934300--20934358 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
20934290 CATTGAAGAG
*
20934300 TGTTGTGGCTACATCT-GATTC
1 TGTTGTGGCTGCATCTGGATTC
* *
20934321 TGGTGTGGCTGCATCTGGCTT-
1 TGTTGTGGCTGCATCTGGATTC
*
20934342 TGTTGTGGATGCATCTG
1 TGTTGTGGCTGCATCTG
20934359 AGTATCTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (22 bp):
TGTTGTGGCTGCATCTGGATTC
Found at i:20938654 original size:6 final size:6
Alignment explanation
Indices: 20938644--20938690 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
20938634 GCAAATGAAT
* * * *
20938644 CATTTT CATTTT CATTTC CATTTC CATTTC CATTTC AAATTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
20938691 TGGAAACCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:20944866 original size:17 final size:18
Alignment explanation
Indices: 20944844--20944877 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20944834 TAAATGAGTT
20944844 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
20944861 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
20944878 AATAGAAATT
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:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:20946351 original size:17 final size:17
Alignment explanation
Indices: 20946329--20946361 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20946319 TAAGAGGTGT
*
20946329 TACATTACATGAAAACA
1 TACATTAAATGAAAACA
20946346 TACATTAAATGAAAAC
1 TACATTAAATGAAAAC
20946362 GACTAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
TACATTAAATGAAAACA
Found at i:20958948 original size:12 final size:14
Alignment explanation
Indices: 20958913--20958957 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
20958903 AAGAAGAGAA
20958913 AAGAGAAGAAGAAGG
1 AAGAGAAGAA-AAGG
20958928 AAGAGAAGAAAAGG
1 AAGAGAAGAAAAGG
*
20958942 AA-A-AAGAAAATG
1 AAGAGAAGAAAAGG
20958954 AAGA
1 AAGA
20958958 TTTTGTGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 6 0.21
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAGAGAAGAAAAGG
Found at i:20958949 original size:15 final size:16
Alignment explanation
Indices: 20958897--20958949 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
20958887 GTGGGTGTTG
*
20958897 AAGAGGAAGAAGAGAAA
1 AAGAAGAAGAAG-GAAA
20958914 AGAGAAGAAGAAGG-AA
1 A-AGAAGAAGAAGGAAA
*
20958930 GAGAAGAA-AAGGAAA
1 AAGAAGAAGAAGGAAA
20958945 AAGAA
1 AAGAA
20958950 AATGAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.13
15 13 0.42
16 2 0.06
17 2 0.06
18 10 0.32
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAGGAAA
Found at i:20959387 original size:17 final size:17
Alignment explanation
Indices: 20959361--20959398 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20959351 TTTCATATAG
20959361 TTGTCACTGCATTTTAC
1 TTGTCACTGCATTTTAC
* *
20959378 TTGTCTCTGCATTTTAT
1 TTGTCACTGCATTTTAC
20959395 TTGT
1 TTGT
20959399 TAACGCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.55
Consensus pattern (17 bp):
TTGTCACTGCATTTTAC
Found at i:20963823 original size:17 final size:17
Alignment explanation
Indices: 20963801--20963858 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
20963791 ATATATATGG
*
20963801 AAATGCAATGACAATGA
1 AAATGCAATGACAATAA
* *
20963818 AAATGC-ATCAATAATAA
1 AAATGCAAT-GACAATAA
*
20963835 AAATGTAATGACAATAA
1 AAATGCAATGACAATAA
20963852 AAATGCA
1 AAATGCA
20963859 GGGACAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:20963864 original size:17 final size:17
Alignment explanation
Indices: 20963801--20963866 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 17
20963791 ATATATATGG
* *
20963801 AAATGCAATGACAATGA
1 AAATGCAAGGACAATAA
*** *
20963818 AAATGCATCAATAATAA
1 AAATGCAAGGACAATAA
* *
20963835 AAATGTAATGACAATAA
1 AAATGCAAGGACAATAA
*
20963852 AAATGCAGGGACAAT
1 AAATGCAAGGACAAT
20963867 TATACTACAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.20
Consensus pattern (17 bp):
AAATGCAAGGACAATAA
Found at i:20984455 original size:22 final size:22
Alignment explanation
Indices: 20984427--20984485 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
20984417 TTATACTAAA
20984427 TTTTAATTCAATAATTAAAATT
1 TTTTAATTCAATAATTAAAATT
20984449 TTTTAATTCAATAATTAAAATT
1 TTTTAATTCAATAATTAAAATT
*
20984471 CTTTAATTCAA-AATT
1 TTTTAATTCAATAATT
20984486 CCATATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATTCAATAATTAAAATT
Found at i:20998614 original size:26 final size:26
Alignment explanation
Indices: 20998580--20998732 Score: 177
Period size: 26 Copynumber: 5.9 Consensus size: 26
20998570 AGTAAATTTA
* * *
20998580 GCTCATACGAGCCCCGT-CAGTAAATC
1 GCTCTTACGAG-CCAGTACAGTATATC
20998606 GCTCTTACGAGCCAGTACAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
*
20998632 GCTCTTACGAGCCAGTGCAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
*
20998658 GCTCTTTCGAGCCAGTACAGTATA-C
1 GCTCTTACGAGCCAGTACAGTATATC
* * *
20998683 AACTCTTCCGAGCCAGTACAATATATC
1 -GCTCTTACGAGCCAGTACAGTATATC
*
20998710 GCTCCTT-CGAGCCAGTATAGTAT
1 GCT-CTTACGAGCCAGTACAGTAT
20998733 CTTCAAGTCT
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.05
26 102 0.92
27 4 0.04
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (26 bp):
GCTCTTACGAGCCAGTACAGTATATC
Found at i:21003282 original size:6 final size:6
Alignment explanation
Indices: 21003271--21003305 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
21003261 ACCGATTTAA
* *
21003271 CCACCG CCACCG CCACCG CCACTG CCACTG CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACC
21003306 TTCACCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.63, G:0.14, T:0.06
Consensus pattern (6 bp):
CCACCG
Found at i:21006455 original size:18 final size:17
Alignment explanation
Indices: 21006432--21006475 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
21006422 ATTATTTCTC
**
21006432 AAAAGTATTTTTGGCAT
1 AAAAGTATTTTTGAAAT
*
21006449 AAAAAGTACTTTTGAAAT
1 -AAAAGTATTTTTGAAAT
21006467 AAAAGTATT
1 AAAAGTATT
21006476 ATTAAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (17 bp):
AAAAGTATTTTTGAAAT
Found at i:21006913 original size:15 final size:16
Alignment explanation
Indices: 21006888--21006921 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21006878 AAAATGTAAT
21006888 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
21006904 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
21006919 TTT
1 TTT
21006922 TTAAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:21007854 original size:21 final size:21
Alignment explanation
Indices: 21007816--21007855 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21007806 AAACTTCTAA
*
21007816 AATATATAAAAATTTATATTG
1 AATATATAAAAATATATATTG
* *
21007837 AATATATATACATATATAT
1 AATATATAAAAATATATAT
21007856 GCTCACTCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
AATATATAAAAATATATATTG
Found at i:21015285 original size:5 final size:5
Alignment explanation
Indices: 21015275--21015299 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21015265 TGGAAAGATT
21015275 GAATC GAATC GAATC GAATC GAATC
1 GAATC GAATC GAATC GAATC GAATC
21015300 TGTGACAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
GAATC
Found at i:21018433 original size:6 final size:6
Alignment explanation
Indices: 21018419--21018449 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
21018409 TTTCTTTCCA
*
21018419 TTGTTT TTGTCT TTGTTT TTGTTT TTGTTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT T
21018450 CTTGAGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (6 bp):
TTGTTT
Found at i:21027021 original size:21 final size:21
Alignment explanation
Indices: 21026995--21027040 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
21026985 GGTTGGTTTG
* *
21026995 AAGGACAAGAAGAGGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
21027016 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
21027037 AAGG
1 AAGG
21027041 GGGAAGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.30, T:0.00
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCAC
Found at i:21027174 original size:18 final size:16
Alignment explanation
Indices: 21027142--21027183 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
21027132 GGTAGTTGCA
21027142 TGCATTTTATTGTCAT
1 TGCATTTTATTGTCAT
21027158 TGCATTGTTATTTGTCAT
1 TGCATT-TTA-TTGTCAT
*
21027176 TTCATTTT
1 TGCATTTT
21027184 TCATATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 12 0.52
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (16 bp):
TGCATTTTATTGTCAT
Found at i:21027808 original size:21 final size:20
Alignment explanation
Indices: 21027784--21027822 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21027774 AATTTTGAAT
21027784 GAAAAAAAGAAAAGAAAAAGA
1 GAAAAAAAG-AAAGAAAAAGA
*
21027805 GAAAAAGAGAAAGAAAAA
1 GAAAAAAAGAAAGAAAAA
21027823 AAAGAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
GAAAAAAAGAAAGAAAAAGA
Found at i:21027823 original size:21 final size:19
Alignment explanation
Indices: 21027787--21027829 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
21027777 TTTGAATGAA
*
21027787 AAAAAGAAAAGAAAAAGAG
1 AAAAAGAAAAGAAAAAAAG
21027806 AAAAAGAGAAAGAAAAAAAAG
1 AAAAAGA-AAAG-AAAAAAAG
21027827 AAA
1 AAA
21027830 TATTACTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAAAG
Found at i:21028889 original size:42 final size:42
Alignment explanation
Indices: 21028820--21028906 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
21028810 GTAGTCTAGA
* *
21028820 GATAGTGAGCTTCAATATATTTTTTAACCCCTCTTTTATGCT
1 GATAGTGAGCTTCAATATATATGTTAACCCCTCTTTTATGCT
* *
21028862 GATAGTGAGCTTCGATGTATATGTTAACCCCTCTTTTATGCT
1 GATAGTGAGCTTCAATATATATGTTAACCCCTCTTTTATGCT
21028904 GAT
1 GAT
21028907 GAATTACTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (42 bp):
GATAGTGAGCTTCAATATATATGTTAACCCCTCTTTTATGCT
Found at i:21035058 original size:25 final size:27
Alignment explanation
Indices: 21035021--21035070 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
21035011 TCTTCTTTTG
* *
21035021 TTTCTACTCATTCTTTTCTTTTTGGTT
1 TTTCTACTCATTCGTCTCTTTTTGGTT
21035048 TTTC-ACT-ATTCGTCTCTTTTTGG
1 TTTCTACTCATTCGTCTCTTTTTGG
21035071 CTAAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 3 0.14
27 4 0.19
ACGTcount: A:0.08, C:0.20, G:0.10, T:0.62
Consensus pattern (27 bp):
TTTCTACTCATTCGTCTCTTTTTGGTT
Found at i:21039204 original size:17 final size:18
Alignment explanation
Indices: 21039166--21039204 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21039156 AGATGCAACA
*
21039166 ACAATAAAAATGTAATGG
1 ACAATAAAAATGTAAGGG
21039184 -CAATAAAAATGT-AGGG
1 ACAATAAAAATGTAAGGG
21039200 ACAAT
1 ACAAT
21039205 TATACTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.21
Consensus pattern (18 bp):
ACAATAAAAATGTAAGGG
Found at i:21041444 original size:19 final size:19
Alignment explanation
Indices: 21041409--21041450 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
21041399 CTACAAAAAA
*
21041409 AAAACTAAGAAAGATAACT
1 AAAACTAAGAAAAATAACT
21041428 AAAACATAA-AAAAATAACT
1 AAAAC-TAAGAAAAATAACT
21041447 AAAA
1 AAAA
21041451 GTAAAGGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAACTAAGAAAAATAACT
Found at i:21049909 original size:53 final size:53
Alignment explanation
Indices: 21049836--21049973 Score: 168
Period size: 53 Copynumber: 2.6 Consensus size: 53
21049826 CACCTTTGAT
* * **
21049836 AACTCACGATGACACGGAGTCATCAGACCTTTAATCCGTAATAGGATTCATAA
1 AACTCACGATGACACAGAGTCATCGGACCTTTAATCCACAATAGGATTCATAA
* * * * ** *
21049889 AACTCATGATAACACAGAGTCACCGGATCTTTAATTTACAATAGGATTCATAT
1 AACTCACGATGACACAGAGTCATCGGACCTTTAATCCACAATAGGATTCATAA
*
21049942 AACTCACGATGATACAGAGTCATCGGACCTTT
1 AACTCACGATGACACAGAGTCATCGGACCTTT
21049974 TTGCATTTAC
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 69 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (53 bp):
AACTCACGATGACACAGAGTCATCGGACCTTTAATCCACAATAGGATTCATAA
Found at i:21053212 original size:16 final size:17
Alignment explanation
Indices: 21053191--21053232 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
21053181 CAATTAAAAT
*
21053191 TAATAAAAT-AAACAAG
1 TAATAAAATAAAACAAA
21053207 TAATAAAATAAAACAAA
1 TAATAAAATAAAACAAA
21053224 TAATTAAAA
1 TAA-TAAAA
21053233 ATAATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
TAATAAAATAAAACAAA
Found at i:21053217 original size:21 final size:22
Alignment explanation
Indices: 21053185--21053242 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
21053175 TAAACTCAAT
*
21053185 TAAAATTAATAAAATAAACAAG
1 TAAAAATAATAAAATAAACAAG
* * * *
21053207 TAATAA-AATAAAACAAATAAT
1 TAAAAATAATAAAATAAACAAG
21053228 TAAAAATAATAAAAT
1 TAAAAATAATAAAAT
21053243 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAATAATAAAATAAACAAG
Found at i:21053238 original size:13 final size:14
Alignment explanation
Indices: 21053185--21053242 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 14
21053175 TAAACTCAAT
*
21053185 TAAAATTAATAAAA
1 TAAAAATAATAAAA
21053199 TAAACAAGTAATAAAA
1 TAAA-AA-TAATAAAA
*
21053215 TAAAACA-AAT-AAT
1 TAAAA-ATAATAAAA
21053228 TAAAAATAATAAAA
1 TAAAAATAATAAAA
21053242 T
1 T
21053243 TTAATTTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 10 0.28
14 10 0.28
15 2 0.06
16 13 0.36
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:21054490 original size:26 final size:26
Alignment explanation
Indices: 21054454--21054508 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
21054444 AATTTTGGGC
*
21054454 ACAATTCTGGACACGTTCATGTAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
*
21054480 ACAATTCTGGACATGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
21054506 ACA
1 ACA
21054509 TTCCTATGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATGCAGCG
Found at i:21059046 original size:12 final size:12
Alignment explanation
Indices: 21059028--21059064 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
21059018 AGTTGCGACG
*
21059028 ACAATTCTGGGC
1 ACAATTCTGGAC
*
21059040 GCAATTCTGGAC
1 ACAATTCTGGAC
21059052 ACAATTCTGGAC
1 ACAATTCTGGAC
21059064 A
1 A
21059065 TGTTCATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (12 bp):
ACAATTCTGGAC
Found at i:21059087 original size:26 final size:26
Alignment explanation
Indices: 21059052--21059110 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
21059042 AATTCTGGAC
21059052 ACAATTCTGGACATGTTCATGCAGCG
1 ACAATTCTGGACATGTTCATGCAGCG
21059078 ACAATTCTGGACATGTTCATGCAGCG
1 ACAATTCTGGACATGTTCATGCAGCG
21059104 AC-ATTCT
1 ACAATTCT
21059111 TGGGTGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (26 bp):
ACAATTCTGGACATGTTCATGCAGCG
Found at i:21059137 original size:37 final size:37
Alignment explanation
Indices: 21059096--21059192 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
21059086 GGACATGTTC
* *
21059096 ATGCAGCGACATTCTTGGGTGCAATTGAAGAATACTT
1 ATGCAGCAACAGTCTTGGGTGCAATTGAAGAATACTT
* * * *
21059133 ATGCAGCAATAGTCCTGGATGCAATTGAAGAATATTT
1 ATGCAGCAACAGTCTTGGGTGCAATTGAAGAATACTT
*
21059170 ATGCAGTAACAGTCTTGGGTGCA
1 ATGCAGCAACAGTCTTGGGTGCA
21059193 TTCCGGAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (37 bp):
ATGCAGCAACAGTCTTGGGTGCAATTGAAGAATACTT
Found at i:21063714 original size:36 final size:37
Alignment explanation
Indices: 21063655--21063763 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 37
21063645 TGACATGTTC
* *
21063655 ATGCAGCGGCATTCCTAGG-TGCAATTAAAGAATATTT
1 ATGCAGCGACAGTCCT-GGATGCAATTAAAGAATATTT
* *
21063692 ATGCA-CGATAGTCCTGGATGCAATTGAAGAATATTT
1 ATGCAGCGACAGTCCTGGATGCAATTAAAGAATATTT
* * *
21063728 ATGCAGCGACAGTCTTGGGTGCATTTCAAA-AATATT
1 ATGCAGCGACAGTCCTGGATGCAATT-AAAGAATATT
21063764 CACACAGTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
35 2 0.03
36 29 0.48
37 27 0.45
38 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (37 bp):
ATGCAGCGACAGTCCTGGATGCAATTAAAGAATATTT
Found at i:21071250 original size:21 final size:21
Alignment explanation
Indices: 21071226--21071277 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
21071216 TGAGATAATA
21071226 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
21071247 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
21071268 CTACCGATAC
1 CTACCGATAC
21071278 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:21075478 original size:26 final size:26
Alignment explanation
Indices: 21075440--21075494 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
21075430 AATTCTGGGC
21075440 ACAATTCTAGACATGTTCATGCAGCG
1 ACAATTCTAGACATGTTCATGCAGCG
*
21075466 ACAATTCTGGACATGTTCATGCAGCG
1 ACAATTCTAGACATGTTCATGCAGCG
21075492 ACA
1 ACA
21075495 TTCCTAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (26 bp):
ACAATTCTAGACATGTTCATGCAGCG
Found at i:21075529 original size:37 final size:37
Alignment explanation
Indices: 21075488--21075580 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
21075478 ATGTTCATGC
*
21075488 AGCGACATTCCTAGG-TGCAATTGAAGAAT-TCTTATGT
1 AGCGACAGTCCT-GGATGCAATTGAAGAATAT-TTATGT
*
21075525 AGCGATAGTCCTGGATGCAATTGAAGAATATTTATGT
1 AGCGACAGTCCTGGATGCAATTGAAGAATATTTATGT
* * *
21075562 AGTGACAGTCTTGGGTGCA
1 AGCGACAGTCCTGGATGCA
21075581 TTGCGAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 2 0.04
37 45 0.94
38 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (37 bp):
AGCGACAGTCCTGGATGCAATTGAAGAATATTTATGT
Found at i:21077229 original size:3 final size:3
Alignment explanation
Indices: 21077216--21077253 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
21077206 ACTATAGCCT
21077216 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
21077254 GAAAATAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21093472 original size:13 final size:13
Alignment explanation
Indices: 21093454--21093478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21093444 TAAGTTAAAA
21093454 ATGCTAAAAATGC
1 ATGCTAAAAATGC
21093467 ATGCTAAAAATG
1 ATGCTAAAAATG
21093479 ATAACATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:21113518 original size:17 final size:17
Alignment explanation
Indices: 21113498--21113545 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
21113488 CATATTTCCT
**
21113498 TTGTCATTGCATTTTTA
1 TTGTCATTGCATTTACA
* *
21113515 TTGTCACTGCATCTACA
1 TTGTCATTGCATTTACA
21113532 TTGTCATTGCATTT
1 TTGTCATTGCATTT
21113546 CCATATATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTACA
Found at i:21122465 original size:18 final size:18
Alignment explanation
Indices: 21122444--21122487 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
21122434 TGGCTACATA
21122444 TGAGCATGTGA-TTGCATC
1 TGAGCATGTGACTT-CATC
21122462 TGAGCATGTGACTTCATC
1 TGAGCATGTGACTTCATC
*
21122480 TGATCATG
1 TGAGCATG
21122488 ATGTGCTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (18 bp):
TGAGCATGTGACTTCATC
Found at i:21127686 original size:171 final size:171
Alignment explanation
Indices: 21127401--21127746 Score: 674
Period size: 171 Copynumber: 2.0 Consensus size: 171
21127391 CACTGGAAAG
*
21127401 TGCAGCGACAGTTCAAGCTAACAAGCATAACAACGGAAGTTGCTTGAGGATTAAAGGGATTTATT
1 TGCAGCGACAGTTCAAGCTAACAAGCATAACAACGGAAGTTGCTTGAGGATTAAAGGGATTTAAT
21127466 CCACTTGTTCTTAATTGTGTTCCATTGCCATCATCGAAAGGTGTGGTTAATGTGCATGTTTAAGT
66 CCACTTGTTCTTAATTGTGTTCCATTGCCATCATCGAAAGGTGTGGTTAATGTGCATGTTTAAGT
21127531 CTTAGATCAAATATAGAAGTTAAGCTTGGTAAGATATTCAT
131 CTTAGATCAAATATAGAAGTTAAGCTTGGTAAGATATTCAT
*
21127572 TGCAGCGACAGTTCAAGCTAACAAGCATAACAACGGAAGTTTCTTGAGGATTAAAGGGATTTAAT
1 TGCAGCGACAGTTCAAGCTAACAAGCATAACAACGGAAGTTGCTTGAGGATTAAAGGGATTTAAT
21127637 CCACTTGTTCTTAATTGTGTTCCATTGCCATCATCGAAAGGTGTGGTTAATGTGCATGTTTAAGT
66 CCACTTGTTCTTAATTGTGTTCCATTGCCATCATCGAAAGGTGTGGTTAATGTGCATGTTTAAGT
21127702 CTTAGATCAAATATAGAAGTTAAGCTTGGTAAGATATTCAT
131 CTTAGATCAAATATAGAAGTTAAGCTTGGTAAGATATTCAT
21127743 TGCA
1 TGCA
21127747 AATTATTGCA
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 173 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (171 bp):
TGCAGCGACAGTTCAAGCTAACAAGCATAACAACGGAAGTTGCTTGAGGATTAAAGGGATTTAAT
CCACTTGTTCTTAATTGTGTTCCATTGCCATCATCGAAAGGTGTGGTTAATGTGCATGTTTAAGT
CTTAGATCAAATATAGAAGTTAAGCTTGGTAAGATATTCAT
Found at i:21129334 original size:12 final size:12
Alignment explanation
Indices: 21129317--21129341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21129307 TGTTATGATG
21129317 ATGAATTCTATT
1 ATGAATTCTATT
21129329 ATGAATTCTATT
1 ATGAATTCTATT
21129341 A
1 A
21129342 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
ATGAATTCTATT
Found at i:21143012 original size:19 final size:20
Alignment explanation
Indices: 21142976--21143020 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
21142966 AGAGTCGAAA
21142976 TTAAACCAAATGGGAACATC
1 TTAAACCAAATGGGAACATC
21142996 TTAAACCAAAT-GGAACATC
1 TTAAACCAAATGGGAACATC
21143015 TTAAAC
1 TTAAAC
21143021 AAAAAGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (20 bp):
TTAAACCAAATGGGAACATC
Found at i:21157056 original size:30 final size:30
Alignment explanation
Indices: 21157015--21157075 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
21157005 ACCAACTGAC
* * *
21157015 TAGGGGAAAATTTTCGCTGTAAAATGATAT
1 TAGGAGAAAATTGTCGCCGTAAAATGATAT
21157045 TAGGAGAAAATTGTCGCCGTAAAATGATAT
1 TAGGAGAAAATTGTCGCCGTAAAATGATAT
21157075 T
1 T
21157076 TTTGTGCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGAGAAAATTGTCGCCGTAAAATGATAT
Found at i:21165495 original size:20 final size:21
Alignment explanation
Indices: 21165458--21165496 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21165448 AAACCGAGCA
*
21165458 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
21165479 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
21165497 TAAAAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:21167013 original size:80 final size:80
Alignment explanation
Indices: 21166880--21167042 Score: 254
Period size: 80 Copynumber: 2.0 Consensus size: 80
21166870 TTCACTTATA
* **
21166880 AATAGGGGTTGAAGTAGTGGAGAGCCTTAAGATGGGTTTGGATGGATGATGTGTTTATTTATGAT
1 AATAGGGGTTGAAGTAGTGGAGAGCCTTAAGATGGGTTTGGATGGATGATGTGTTTATCTACAAT
*
21166945 TAGTATAAAAATAAT
66 TAGTATAAAAACAAT
** * *
21166960 AATAGGGGTTGAAGTAGTGGAGAGTTTTAGGGTGGGTTTGGATGGATGATGTGTTTATCTACAAT
1 AATAGGGGTTGAAGTAGTGGAGAGCCTTAAGATGGGTTTGGATGGATGATGTGTTTATCTACAAT
21167025 TAGTATAAAAACAAT
66 TAGTATAAAAACAAT
21167040 AAT
1 AAT
21167043 GATCCCCCTA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (80 bp):
AATAGGGGTTGAAGTAGTGGAGAGCCTTAAGATGGGTTTGGATGGATGATGTGTTTATCTACAAT
TAGTATAAAAACAAT
Found at i:21167710 original size:28 final size:28
Alignment explanation
Indices: 21167667--21167741 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
21167657 TTTAGATTCA
* *
21167667 TTAAAAGTTGA-AAAAAAAATTAAATCTT
1 TTAAAAGTTGATAAAAAAATTTAAA-CAT
*
21167695 TTAAAAATTGATAAAAAAAATTTAAACAT
1 TTAAAAGTTGAT-AAAAAAATTTAAACAT
21167724 TTAAAAGTTGATAAAAAA
1 TTAAAAGTTGATAAAAAA
21167742 TAATTTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.39
29 13 0.32
30 12 0.29
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.31
Consensus pattern (28 bp):
TTAAAAGTTGATAAAAAAATTTAAACAT
Found at i:21167747 original size:30 final size:30
Alignment explanation
Indices: 21167667--21167747 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 30
21167657 TTTAGATTCA
*
21167667 TTAAAAGTTGA-AAAAAAAA-TTAAATCTT
1 TTAAAAGTTGATAAAAAAAATTTAAATCAT
*
21167695 TTAAAAATTGATAAAAAAAATTTAAA-CAT
1 TTAAAAGTTGATAAAAAAAATTTAAATCAT
21167724 TTAAAAGTTGATAAAAAATAATTT
1 TTAAAAGTTGATAAAAAA-AATTT
21167748 TTGACCTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
28 10 0.21
29 27 0.57
30 10 0.21
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (30 bp):
TTAAAAGTTGATAAAAAAAATTTAAATCAT
Found at i:21174420 original size:149 final size:146
Alignment explanation
Indices: 21174196--21174668 Score: 508
Period size: 148 Copynumber: 3.2 Consensus size: 146
21174186 ATAAATATTT
* * * *
21174196 TTTTAAAGAAAAATAGCTT-GA-TTTTAAGA-AAAAATTTGATTTTTTTAAATAATTTCGAAATA
1 TTTTAAAGAAAAAT-GTTTAAATTTTTAA-ACAAAATTTTGATTTTTTTAACT-ATTTCGAAATA
21174258 AAAGTTTTG-ATTTTTAAGAAAAATAGTGATTTTCTTTTAAAAAGAGAAAGTTTAGATTTTTAAA
63 AAAG-TTTGAATTTTTAAGAAAAATAGTGATTTTC-TTTAAAAAGAGAAAGTTTAGATTTTTAAA
*
21174322 TAAAAATCTGTTTTTTAGTTA
126 TAAAAATCTGTTTTTTAGTCA
21174343 TTTTAAAGAAAAATGTTTAAATTTTTAAACAAAGA-TTTGATTTTTTTTTAACTATTTCGAAATA
1 TTTTAAAGAAAAATGTTTAAATTTTTAAACAAA-ATTTTGA--TTTTTTTAACTATTTCGAAATA
* *
21174407 AAAGTTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAATAAAGAGAAAGTTTAGATTTGTAAAA
63 AAAGTTTGAATTTTTAAGAAAAATAGTGATTTTCTTTAA-AAAGAGAAAGTTTAGATTT-T-TAA
* *
21174472 ATAAAAATATG-TTTTTAGGCA
125 ATAAAAATCTGTTTTTTAGTCA
* *
21174493 TTTTAAAAGAAAAA-GTTTAAATTTTTAATCAAAATTTTGATTTTTTTAACTATTTTGAAATAAA
1 TTTT-AAAGAAAAATGTTTAAATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAA
* *
21174557 AGTTT-AGATTTTTAA-ATAAAATAGTAATTTTCATT--AAA-A-AAA-TTTAGATTTTTTAAAA
65 AGTTTGA-ATTTTTAAGA-AAAATAGTGATTTTCTTTAAAAAGAGAAAGTTTAGA-TTTTT---A
* *
21174615 AATAAAAAACTGATTTTTTTAGTGA
124 AATAAAAATCTG--TTTTTTAGTCA
* *
21174640 TTTTAAAGAAAGAT-TTTAAAATTTTAAAC
1 TTTTAAAGAAAAATGTTTAAATTTTTAAAC
21174669 CGTTGGGCTC
Statistics
Matches: 283, Mismatches: 21, Indels: 45
0.81 0.06 0.13
Matches are distributed among these distances:
142 7 0.02
143 6 0.02
144 12 0.04
145 3 0.01
146 24 0.08
147 29 0.10
148 75 0.27
149 60 0.21
150 46 0.16
151 21 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (146 bp):
TTTTAAAGAAAAATGTTTAAATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAA
GTTTGAATTTTTAAGAAAAATAGTGATTTTCTTTAAAAAGAGAAAGTTTAGATTTTTAAATAAAA
ATCTGTTTTTTAGTCA
Found at i:21174587 original size:51 final size:48
Alignment explanation
Indices: 21174304--21174579 Score: 140
Period size: 51 Copynumber: 5.5 Consensus size: 48
21174294 TTAAAAAGAG
* **
21174304 AAAGTTTAGATTTTTAAATAAAA-ATCTGTTTTTTAGTTATTTTAAAGAA
1 AAAGTTTAGATTTTTAAATAAAATATAT-TTTTTTAACTATTTTAAA-AA
* * * * *
21174353 AAATGTTTAAATTTTTAAACAAAGATTTGATTTTTTTTTAACTATTTCGAAATA
1 AAA-GTTTAGATTTTTAAATAAA-A--T-ATATTTTTTTAACTATTT-TAAAAA
* * *
21174407 AAAGTTT-GAATTTTTAAGTAAAATAGTGATTTTCTTTAA-TA----AAGAG
1 AAAGTTTAG-ATTTTTAAATAAAATA-T-ATTTT-TTTAACTATTTTAAAAA
* * *
21174453 AAAGTTTAGATTTGTAAAAATAAAA-ATATGTTTTTAGGC-ATTTTAAAAGAA
1 AAAGTTTAGATTT-T-TAAATAAAATATATTTTTTTA-ACTATTTT-AAA-AA
* * *
21174504 AAAGTTTAAATTTTT-AATCAAAATTTTGATTTTTTTAACTATTTTGAAATA
1 AAAGTTTAGATTTTTAAAT-AAAA-TAT-ATTTTTTTAACTATTTT-AAAAA
21174555 AAAGTTTAGATTTTTAAATAAAATA
1 AAAGTTTAGATTTTTAAATAAAATA
21174580 GTAATTTTCA
Statistics
Matches: 170, Mismatches: 29, Indels: 55
0.67 0.11 0.22
Matches are distributed among these distances:
44 4 0.02
45 5 0.03
46 14 0.08
47 3 0.02
48 10 0.06
49 8 0.05
50 23 0.14
51 41 0.24
52 25 0.15
53 15 0.09
54 16 0.09
55 6 0.04
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (48 bp):
AAAGTTTAGATTTTTAAATAAAATATATTTTTTTAACTATTTTAAAAA
Found at i:21174612 original size:19 final size:19
Alignment explanation
Indices: 21174554--21174616 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
21174544 ATTTTGAAAT
*
21174554 AAAAGTTTAGA-TTTTTAA
1 AAAAATTTAGATTTTTTAA
*
21174572 ATAAAATAGTA-ATTTTCATTAA
1 A-AAAAT-TTAGATTTT--TTAA
21174594 AAAAATTTAGATTTTTTAA
1 AAAAATTTAGATTTTTTAA
21174613 AAAA
1 AAAA
21174617 TAAAAAACTG
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
18 1 0.03
19 13 0.36
20 7 0.19
21 10 0.28
22 5 0.14
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (19 bp):
AAAAATTTAGATTTTTTAA
Found at i:21183128 original size:21 final size:21
Alignment explanation
Indices: 21183104--21183158 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
21183094 TTCAGACTCC
*
21183104 TACCAATACAAGTGA-TAGTTT
1 TACCAATACAAGTGACT-CTTT
*
21183125 TACCAATACTAGTGACTCTTT
1 TACCAATACAAGTGACTCTTT
*
21183146 TACCGATACAAGT
1 TACCAATACAAGT
21183159 CTTACTTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (21 bp):
TACCAATACAAGTGACTCTTT
Found at i:21188314 original size:16 final size:15
Alignment explanation
Indices: 21188295--21188324 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21188285 AACTTGAACA
21188295 AAAACAAAAACAAAAC
1 AAAACAAAAA-AAAAC
21188311 AAAACAAAAAAAAA
1 AAAACAAAAAAAAA
21188325 TTACATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAAAAC
Found at i:21195063 original size:30 final size:30
Alignment explanation
Indices: 21195024--21195095 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
21195014 CTGATTGTGT
* *
21195024 GTGTCCGCAACAGGAGTGTTCACAGCTCCTA
1 GTGTTCGCAACAGGAGTGTTCACAACTCC-A
* *
21195055 -TGTTCGCAACATGAGTGTTTACAACTCCA
1 GTGTTCGCAACAGGAGTGTTCACAACTCCA
21195084 GTGTTCGCAACA
1 GTGTTCGCAACA
21195096 CTAATGCTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (30 bp):
GTGTTCGCAACAGGAGTGTTCACAACTCCA
Found at i:21200512 original size:16 final size:16
Alignment explanation
Indices: 21200491--21200522 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21200481 AGTAATTTTT
*
21200491 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
21200507 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
21200523 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:21201424 original size:41 final size:41
Alignment explanation
Indices: 21201379--21201642 Score: 293
Period size: 41 Copynumber: 6.4 Consensus size: 41
21201369 CGAATCACTT
** *
21201379 GATTATATTAAAGGAAGACTCATTTCTCAGGGTGAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTCAGGATGAGCATGA
* * *
21201420 GATTATATTAAAGGAAGACTCGTGACT-TGAAATGAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTCAG-GATGAGCATGA
** *
21201461 GATTATATTAAAGGAAGACTCATGACTCAAAACGAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTCAGGATGAGCATGA
* * * * *
21201502 GATTATATTAAAGGAAGACTCATGTCTTAGGGTGAACACGA
1 GATTATATTAAAGGAAGACTCATGACTCAGGATGAGCATGA
* *
21201543 GATTATATTAAAGAAAGACTCATGACTCAGGATAAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTCAGGATGAGCATGA
* *
21201584 GATTATATTTAAAGGAAGACTTATGACTC-GG-TAGAGCATAA
1 GATTATA-TTAAAGGAAGACTCATGACTCAGGAT-GAGCATGA
*
21201625 GATTGT-TTAGAAGGAAGA
1 GATTATATTA-AAGGAAGA
21201643 TCTACGACTC
Statistics
Matches: 188, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 10 0.05
41 156 0.83
42 19 0.10
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (41 bp):
GATTATATTAAAGGAAGACTCATGACTCAGGATGAGCATGA
Found at i:21201621 original size:123 final size:123
Alignment explanation
Indices: 21201379--21201642 Score: 345
Period size: 123 Copynumber: 2.1 Consensus size: 123
21201369 CGAATCACTT
* * * * *
21201379 GATTATATTAAAGGAAGACTCATTTCTCAGGGTGAGCATGAGATTATATTAAAGGAAGACTCGTG
1 GATTATATTAAAGGAAGACTCATGTCTCAGGGTGAACACGAGATTATATTAAAGAAAGACTCATG
* * *
21201444 ACTTGAAATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAAACGAGCATGA
66 ACTAGAAATAAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAAACGAGCATAA
*
21201502 GATTATATTAAAGGAAGACTCATGTCTTAGGGTGAACACGAGATTATATTAAAGAAAGACTCATG
1 GATTATATTAAAGGAAGACTCATGTCTCAGGGTGAACACGAGATTATATTAAAGAAAGACTCATG
* * ***
21201567 ACTCAG-GATAAGCATGAGATTATATTTAAAGGAAGACTTATGACTCGGTA-GAGCATAA
66 ACT-AGAAATAAGCATGAGATTATA-TTAAAGGAAGACTCATGACTCAAAACGAGCATAA
*
21201625 GATTGT-TTAGAAGGAAGA
1 GATTATATTA-AAGGAAGA
21201643 TCTACGACTC
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
122 3 0.02
123 98 0.80
124 22 0.18
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (123 bp):
GATTATATTAAAGGAAGACTCATGTCTCAGGGTGAACACGAGATTATATTAAAGAAAGACTCATG
ACTAGAAATAAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAAACGAGCATAA
Found at i:21204777 original size:30 final size:30
Alignment explanation
Indices: 21204707--21204868 Score: 159
Period size: 30 Copynumber: 5.4 Consensus size: 30
21204697 TCATAACACG
* *
21204707 AGTGTTCGCAACATCAGTGCTCGCATTG-T-G
1 AGTGTTCGCAACATGAGTGCTCGCA--GCTCC
* * * * *
21204737 TGTGTCCGCAACATGAGTGTTTGTAGCTCC
1 AGTGTTCGCAACATGAGTGCTCGCAGCTCC
* *
21204767 AGTGTTCGCAA-ATGAGTGCTCACAGCTCT
1 AGTGTTCGCAACATGAGTGCTCGCAGCTCC
*
21204796 AGTGTTCGCAACATGAGTACTCGCAGCTCC
1 AGTGTTCGCAACATGAGTGCTCGCAGCTCC
** * *
21204826 AGTGTTCGCAACACCAATGCTCGCAGCTCT
1 AGTGTTCGCAACATGAGTGCTCGCAGCTCC
21204856 AGTGTTCGCAACA
1 AGTGTTCGCAACA
21204869 CTAATGCTCG
Statistics
Matches: 107, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
28 1 0.01
29 25 0.23
30 81 0.76
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (30 bp):
AGTGTTCGCAACATGAGTGCTCGCAGCTCC
Found at i:21204806 original size:59 final size:60
Alignment explanation
Indices: 21204738--21204868 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 60
21204728 CGCATTGTGT
* ** * * ** *
21204738 GTGTCCGCAACATGAGTGTTTGTAGCTCCAGTGTTCGCAA-ATGAGTGCTCACAGCTCTA
1 GTGTTCGCAACATGAGTACTCGCAGCTCCAGTGTTCGCAACACCAATGCTCACAGCTCTA
*
21204797 GTGTTCGCAACATGAGTACTCGCAGCTCCAGTGTTCGCAACACCAATGCTCGCAGCTCTA
1 GTGTTCGCAACATGAGTACTCGCAGCTCCAGTGTTCGCAACACCAATGCTCACAGCTCTA
21204857 GTGTTCGCAACA
1 GTGTTCGCAACA
21204869 CTAATGCTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 35 0.56
60 27 0.44
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (60 bp):
GTGTTCGCAACATGAGTACTCGCAGCTCCAGTGTTCGCAACACCAATGCTCACAGCTCTA
Found at i:21204879 original size:15 final size:15
Alignment explanation
Indices: 21204831--21204880 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
21204821 GCTCCAGTGT
*
21204831 TCGCAACACCAATGC
1 TCGCAACACTAATGC
* * * *
21204846 TCGCAGCTCTAGTGT
1 TCGCAACACTAATGC
21204861 TCGCAACACTAATGC
1 TCGCAACACTAATGC
21204876 TCGCA
1 TCGCA
21204881 TCTTCTAAGT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (15 bp):
TCGCAACACTAATGC
Found at i:21209252 original size:17 final size:16
Alignment explanation
Indices: 21209226--21209266 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
21209216 TTGTTTAAAT
21209226 AAAAAAAACAAAACAA-
1 AAAAAAAACAAAA-AAG
21209242 AAAAAAGAACAAAAAAG
1 AAAAAA-AACAAAAAAG
21209259 AAAAAAAA
1 AAAAAAAA
21209267 TAAAGAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAG
Found at i:21209266 original size:23 final size:24
Alignment explanation
Indices: 21209228--21209272 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21209218 GTTTAAATAA
21209228 AAAAAACAAAACAAAAAAAAGAAC
1 AAAAAACAAAACAAAAAAAAGAAC
* *
21209252 AAAAAAGAAAA-AAAATAAAGA
1 AAAAAACAAAACAAAAAAAAGA
21209273 GAGTAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (24 bp):
AAAAAACAAAACAAAAAAAAGAAC
Found at i:21209728 original size:42 final size:42
Alignment explanation
Indices: 21209668--21210181 Score: 693
Period size: 42 Copynumber: 12.4 Consensus size: 42
21209658 AAGGAAAGGA
*
21209668 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
21209710 TTCATCGCATTTAAAGGCCAAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21209752 TTCATCT-CATTTAGAGGCCCA-G-GT----GCCCATTTACTT
1 TTCAT-TGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21209788 TTCATTACATTTAGAGGCCCAGGTGTAGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
21209830 TTCATTACATTTAAAGGCCCAAGTGTGTAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21209872 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
21209914 TTCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21209956 TTCATTGCATTTTGAGGCCCAGGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
21209998 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
21210040 TTCATCGTATTTAGAGGCCTAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21210082 TTCATCGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21210124 TTCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
21210166 TTCATTGCATTTAGAG
1 TTCATTGCATTTAGAG
21210182 TCCTAAGTGT
Statistics
Matches: 418, Mismatches: 44, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.00
36 31 0.07
37 1 0.00
38 2 0.00
40 2 0.00
41 2 0.00
42 378 0.90
43 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:21211012 original size:19 final size:19
Alignment explanation
Indices: 21210979--21211015 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21210969 ATAATTTTGA
**
21210979 AAGAAAAATTTTGATTTTT
1 AAGAAAAATAGTGATTTTT
21210998 AAGAAAAATAGTGATTTT
1 AAGAAAAATAGTGATTTT
21211016 CTTTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
AAGAAAAATAGTGATTTTT
Found at i:21211249 original size:9 final size:9
Alignment explanation
Indices: 21211235--21211259 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21211225 AAAGTTTAAA
21211235 TTTTTAATT
1 TTTTTAATT
21211244 TTTTTAATT
1 TTTTTAATT
21211253 TTTTTAA
1 TTTTTAA
21211260 CTATTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:21211288 original size:143 final size:143
Alignment explanation
Indices: 21210972--21211373 Score: 502
Period size: 146 Copynumber: 2.8 Consensus size: 143
21210962 TTTTAAAATA
* * * * *
21210972 ATTTTGAAAGAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTTAAAAAAGTGAAAGTTTA
1 ATTTTGAAA-TAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTA
* *
21211037 GA-TTTT-AAAATAAAAATATGTTTTTTAGTTATTTT-AAAGAAAAATTATAAATTTTTAAATAA
65 GATTTTTAAAAAT-AAAATATGTTTTTTAGTCATTTTAAAAG-AAAGTT-TAAATTTTTAAAT--
21211099 ATTTTTTATTTTTTTAACT
125 ATTTTTTATTTTTTTAACT
* *
21211118 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAATGATTTT-TTTAAAAAAAAGAGAAAGTT
1 ATTTTGAAAT-AAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTT--AAAAAAGAGAAAGTT
21211182 TAGATTTTTAAAAATAAAATATGTTTTTTAGTCATTTTAAAAGAAAGTTTAAATTTTT-AAT-TT
63 TAGATTTTTAAAAATAAAATATGTTTTTTAGTCATTTTAAAAGAAAGTTTAAATTTTTAAATATT
21211245 TTTTAATTTTTTTAACT
128 TTTT-ATTTTTTTAACT
* *
21211262 ATTTTGAAATAAAGTTTGGATTTTTAAATAAAATAGTGATTTTCATTAAAAAA-AGAAAGTTTAG
1 ATTTTGAAATAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAG
* *
21211326 ATTTTTAAAAA-AATAAT-T-TTTTTT-GTGATTTTAAACAAAAAGTTTAAA
66 ATTTTTAAAAATAA-AATATGTTTTTTAGTCATTTTAAA-AGAAAGTTTAAA
21211374 ATTGTAAACA
Statistics
Matches: 231, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
138 10 0.04
139 17 0.07
140 3 0.01
141 25 0.11
142 6 0.03
143 37 0.16
144 23 0.10
145 3 0.01
146 40 0.17
147 27 0.12
148 31 0.13
149 9 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (143 bp):
ATTTTGAAATAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAG
ATTTTTAAAAATAAAATATGTTTTTTAGTCATTTTAAAAGAAAGTTTAAATTTTTAAATATTTTT
TATTTTTTTAACT
Found at i:21220780 original size:26 final size:26
Alignment explanation
Indices: 21220745--21220803 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
21220735 ATTTCACCCA
*
21220745 AGAA-TGTCGCTGCATGAATATGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
*
21220770 AGAATTGTCGCTGCATGAACGTGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
21220796 AGAATTGT
1 AGAATTGT
21220804 GCCTAGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (26 bp):
AGAATTGTCGCTGCATGAACATGTCC
Found at i:21222731 original size:15 final size:15
Alignment explanation
Indices: 21222713--21222751 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
21222703 AATTTCCCAC
21222713 TCTTCGTAATACCCG
1 TCTTCGTAATACCCG
21222728 TCTTCGTAATACCCG
1 TCTTCGTAATACCCG
21222743 TCTTCGTAA
1 TCTTCGTAA
21222752 ATTTCAGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (15 bp):
TCTTCGTAATACCCG
Found at i:21226288 original size:20 final size:22
Alignment explanation
Indices: 21226248--21226288 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
21226238 TGATCTTCTG
*
21226248 ACAGCAAAATGAAATCTACAAA
1 ACAGCAAAATGAAATCCACAAA
21226270 ACAGC-AAATG-AATCCACAA
1 ACAGCAAAATGAAATCCACAA
21226289 GTAAGCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.12
Consensus pattern (22 bp):
ACAGCAAAATGAAATCCACAAA
Found at i:21226521 original size:28 final size:28
Alignment explanation
Indices: 21226490--21226600 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
21226480 GCTCGAGCCA
* * *
21226490 TAAATAGATCAAATCTCTACCTGACCTG
1 TAAATAGATCAAAGCTCTACCCGAGCTG
21226518 TAAAT-GAATCAAAGCTCTACCCGAGCTG
1 TAAATAG-ATCAAAGCTCTACCCGAGCTG
* * *
21226546 TTAACAAATCAAAGCTCTACCCGAGCTG
1 TAAATAGATCAAAGCTCTACCCGAGCTG
* *
21226574 TAAATAGATCAAAACTCTACCCAAGCT
1 TAAATAGATCAAAGCTCTACCCGAGCT
21226601 AAAATTAAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.01
28 69 0.99
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (28 bp):
TAAATAGATCAAAGCTCTACCCGAGCTG
Found at i:21228749 original size:14 final size:15
Alignment explanation
Indices: 21228718--21228751 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21228708 TTTTTATATG
21228718 GAATTTTGAATTAAT
1 GAATTTTGAATTAAT
*
21228733 GAATTTT-AATTATT
1 GAATTTTGAATTAAT
21228747 GAATT
1 GAATT
21228752 AAAAGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
GAATTTTGAATTAAT
Found at i:21230408 original size:27 final size:27
Alignment explanation
Indices: 21230370--21230469 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
21230360 AAGGTTTGAG
* *
21230370 GAGTAATT-TGATTCTAGTTCGAAAGA
1 GAGTTATTCTGATTCTAGCTCGAAAGA
21230396 GAGTTATTCTGATTCTAGCTCGAAAGA
1 GAGTTATTCTGATTCTAGCTCGAAAGA
* *
21230423 GCGTTATTCTGATTCTAACTCGAAAGA
1 GAGTTATTCTGATTCTAGCTCGAAAGA
*
21230450 GTGTTATTCTGATTCTAGCT
1 GAGTTATTCTGATTCTAGCT
21230470 TAGAGGAGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
26 7 0.10
27 60 0.90
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (27 bp):
GAGTTATTCTGATTCTAGCTCGAAAGA
Found at i:21230526 original size:26 final size:26
Alignment explanation
Indices: 21230482--21230564 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 26
21230472 GAGGAGAAAT
*
21230482 ACTCTGTCTGGGCTCGTATGAGCTAA
1 ACTCTGTTTGGGCTCGTATGAGCTAA
* *
21230508 ACTTTGTTTGGGCTCGTATAAGCTAA
1 ACTCTGTTTGGGCTCGTATGAGCTAA
* *
21230534 ACTCTGTTTAGGCTCGTAAGAGCTAA
1 ACTCTGTTTGGGCTCGTATGAGCTAA
*
21230560 TCTCT
1 ACTCT
21230565 ATTTCGGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (26 bp):
ACTCTGTTTGGGCTCGTATGAGCTAA
Found at i:21234422 original size:18 final size:18
Alignment explanation
Indices: 21234401--21234456 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
21234391 TTTTTAATAC
21234401 TCAATTTTTTTTCTTCTT
1 TCAATTTTTTTTCTTCTT
* **
21234419 TCAATTCTTTTTTTTTAAT
1 TCAATT-TTTTTTCTTCTT
21234438 TCGAA-TTTTTTTCTTCTT
1 TC-AATTTTTTTTCTTCTT
21234456 T
1 T
21234457 TTTCAAACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 16 0.53
19 12 0.40
20 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (18 bp):
TCAATTTTTTTTCTTCTT
Found at i:21234471 original size:28 final size:27
Alignment explanation
Indices: 21234423--21234520 Score: 85
Period size: 28 Copynumber: 3.6 Consensus size: 27
21234413 CTTCTTTCAA
* *
21234423 TTCTTTTTTTT-TAA-TTCGAATTTTT
1 TTCTTTTTTTTCAAACTTTGAATTTTT
21234448 TTCTTCTTTTTTCAAACTTTGAATTTTCT
1 TTCTT-TTTTTTCAAACTTTGAATTTT-T
** *
21234477 TT-TATTTTTTTCAATTTTTCAATTTTT
1 TTCT-TTTTTTTCAAACTTTGAATTTTT
*
21234504 TTCCTTTTTTTCGAAAC
1 TTCTTTTTTTTC-AAAC
21234521 ACGAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
25 5 0.09
26 6 0.10
27 13 0.22
28 30 0.52
29 4 0.07
ACGTcount: A:0.17, C:0.13, G:0.03, T:0.66
Consensus pattern (27 bp):
TTCTTTTTTTTCAAACTTTGAATTTTT
Found at i:21235835 original size:50 final size:49
Alignment explanation
Indices: 21235710--21235858 Score: 140
Period size: 50 Copynumber: 2.9 Consensus size: 49
21235700 AAATAATGGA
* *
21235710 TTACTAAATGCATG-ACTTGATTTAATGATGCAAACTTTAACTAACATGGGAG
1 TTACTTAATGCATGCA-TT-ATTT-ATGATGCAAA-TTTAACTAACATGGAAG
* * * * *
21235762 TTACATAATGCATG-ATGGGATTTATTATGCATATTTAACTAACATGTAAG
1 TTACTTAATGCATGCAT--TATTTATGATGCAAATTTAACTAACATGGAAG
*
21235812 TTACTTAATGCATGTCATTATTTATGATGCAAACTTAACTAATCATG
1 TTACTTAATGCATG-CATTATTTATGATGCAAATTTAACTAA-CATG
21235859 AGAGTAAATG
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
50 48 0.60
51 13 0.16
52 19 0.24
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (49 bp):
TTACTTAATGCATGCATTATTTATGATGCAAATTTAACTAACATGGAAG
Found at i:21236091 original size:17 final size:17
Alignment explanation
Indices: 21236060--21236092 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21236050 CAAACACTTA
21236060 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
21236077 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
21236093 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:21249995 original size:22 final size:22
Alignment explanation
Indices: 21249969--21250021 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
21249959 AGTGCTGGTT
21249969 TGTCGCAACGTAGCTCCCTTTG
1 TGTCGCAACGTAGCTCCCTTTG
21249991 TGTCGCAACGTAGCTCCCTTTG
1 TGTCGCAACGTAGCTCCCTTTG
*
21250013 TGTCCCAAC
1 TGTCGCAAC
21250022 AAACCCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.34, G:0.21, T:0.30
Consensus pattern (22 bp):
TGTCGCAACGTAGCTCCCTTTG
Found at i:21250742 original size:26 final size:26
Alignment explanation
Indices: 21250713--21250766 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
21250703 CACCCAGGAA
*
21250713 TGTCGCTGTATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
* *
21250739 TGTCGCTGCATGAACGTGTCTAGAAT
1 TGTCGCTGCATGAACATGTCCAGAAT
21250765 TG
1 TG
21250767 CACCCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAGAAT
Found at i:21251587 original size:16 final size:16
Alignment explanation
Indices: 21251566--21251596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21251556 TTGTGGATCC
21251566 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
21251582 CATTTTATCTTTATT
1 CATTTTACCTTTATT
21251597 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Done.