Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 69 of 168
Found at i:20277004 original size:20 final size:20
Alignment explanation
Indices: 20276981--20277019 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20276971 ATTTTTACAT
20276981 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
20277001 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
20277020 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:20278939 original size:31 final size:31
Alignment explanation
Indices: 20278897--20278957 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
20278887 GACAAATCAG
*
20278897 AGGGACTAACTTCTCAGATGATGTAAAATAA
1 AGGGACAAACTTCTCAGATGATGTAAAATAA
*
20278928 AGGGACAAACTTCTCAGATGCTGTAAAATA
1 AGGGACAAACTTCTCAGATGATGTAAAATA
20278958 CATACTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (31 bp):
AGGGACAAACTTCTCAGATGATGTAAAATAA
Found at i:20280909 original size:18 final size:17
Alignment explanation
Indices: 20280880--20280914 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
20280870 TTTGCAACCC
20280880 AAGGGGAGGGGAAAGGG
1 AAGGGGAGGGGAAAGGG
20280897 AAGGGGAAGGGGAAAGGG
1 AAGGGG-AGGGGAAAGGG
20280915 GAGAAGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (17 bp):
AAGGGGAGGGGAAAGGG
Found at i:20280923 original size:18 final size:18
Alignment explanation
Indices: 20280886--20280925 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20280876 ACCCAAGGGG
**
20280886 AGGGGAAAGGGAAGGGGA
1 AGGGGAAAGGGAAGAAGA
*
20280904 AGGGGAAAGGGGAGAAGA
1 AGGGGAAAGGGAAGAAGA
20280922 AGGG
1 AGGG
20280926 TAACCAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
AGGGGAAAGGGAAGAAGA
Found at i:20282500 original size:30 final size:31
Alignment explanation
Indices: 20282440--20282500 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20282430 TAATTGCACC
*
20282440 AAACCAAAATTCATATATCAAATTGCATATT
1 AAACCAAAATTCATATATCAAATTGAATATT
* * *
20282471 AAACCAAAGTTGATATAT-AAATTTAATATT
1 AAACCAAAATTCATATATCAAATTGAATATT
20282501 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (31 bp):
AAACCAAAATTCATATATCAAATTGAATATT
Found at i:20285257 original size:37 final size:38
Alignment explanation
Indices: 20285186--20285334 Score: 168
Period size: 37 Copynumber: 4.1 Consensus size: 38
20285176 AGTACACATG
** *
20285186 TAATCCAACCGA-AACAT-GCCAAACGCCCAT-AAGAGC
1 TAATCCAACCGATAACATCGCCAAGTGCTC-TGAAGAGC
20285222 TAATCCAACCGATAA-ATCGCCAAGTGCTCTGAAGAGC
1 TAATCCAACCGATAACATCGCCAAGTGCTCTGAAGAGC
* * * *
20285259 TAATACAACTGATAACAT-GTCAAATGCT-TCGAAGAGC
1 TAATCCAACCGATAACATCGCCAAGTGCTCT-GAAGAGC
20285296 TAATCCAACCGATAACA-CGCCAAGTGCTCTGAAGAGC
1 TAATCCAACCGATAACATCGCCAAGTGCTCTGAAGAGC
20285333 TA
1 TA
20285335 TATATCCTCC
Statistics
Matches: 95, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
36 16 0.17
37 76 0.80
38 3 0.03
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (38 bp):
TAATCCAACCGATAACATCGCCAAGTGCTCTGAAGAGC
Found at i:20286440 original size:13 final size:13
Alignment explanation
Indices: 20286422--20286446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20286412 TAGGTTATAT
20286422 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20286435 GTGTGAAAATTT
1 GTGTGAAAATTT
20286447 AATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20287493 original size:26 final size:26
Alignment explanation
Indices: 20287442--20287493 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
20287432 AAAAGTATGT
*
20287442 TAATTTAATAAATTTTAAGTTATGAA
1 TAATTTAATAAATTATAAGTTATGAA
20287468 TAATTT-ATATAATTATAATGTT-TGAA
1 TAATTTAATA-AATTATAA-GTTATGAA
20287494 AATACAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.13
26 17 0.74
27 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (26 bp):
TAATTTAATAAATTATAAGTTATGAA
Found at i:20288161 original size:41 final size:40
Alignment explanation
Indices: 20288104--20288212 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 40
20288094 TGATCGAATC
* * * *
20288104 TAATTCAAACTTATTGTCTAGCAGGCTTGATGCCGGTGATA
1 TAATTCAGAC-TATTGTCTAGCAGGCTTAATGCCAGTGAAA
20288145 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACT-ATTGTCTAGCAGGCTTAATGCCAGTGAAA
* * *
20288186 TTATTCGGACTATAAGTCTAGCAGGCT
1 TAATTCAGACTAT-TGTCTAGCAGGCT
20288213 AAAAGTCATT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.05
41 56 0.95
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (40 bp):
TAATTCAGACTATTGTCTAGCAGGCTTAATGCCAGTGAAA
Found at i:20290069 original size:21 final size:20
Alignment explanation
Indices: 20290012--20290069 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
20290002 AGTGGATGCC
20290012 ATTATATTGAAATTGA-ACGT
1 ATTATA-TGAAATTGATACGT
* *
20290032 ATTAT-TGATAATAGATAGGT
1 ATTATATGA-AATTGATACGT
20290052 AATTATATGAAATTGATA
1 -ATTATATGAAATTGATA
20290070 TTGAATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.10
19 5 0.16
20 8 0.26
21 12 0.39
22 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.40
Consensus pattern (20 bp):
ATTATATGAAATTGATACGT
Found at i:20297199 original size:15 final size:14
Alignment explanation
Indices: 20297172--20297204 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
20297162 ACTAATATGT
20297172 ATAATAAGATAATA
1 ATAATAAGATAATA
20297186 ATAATAATGATAATA
1 ATAATAA-GATAATA
20297201 ATAA
1 ATAA
20297205 AATCTGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (14 bp):
ATAATAAGATAATA
Found at i:20297268 original size:4 final size:4
Alignment explanation
Indices: 20297259--20297318 Score: 52
Period size: 4 Copynumber: 14.5 Consensus size: 4
20297249 ATAAAAAAGT
* *
20297259 AATA AATA AATA AATA AAT- AATA AAGGA AAAA AAGTA AA-A TAATA AATAA
1 AATA AATA AATA AATA AATA AATA AA-TA AATA AA-TA AATA -AATA AAT-A
20297309 AATA AATA AA
1 AATA AATA AA
20297319 AATGCACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
3 4 0.09
4 32 0.68
5 11 0.23
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:20297321 original size:22 final size:21
Alignment explanation
Indices: 20297249--20297319 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 21
20297239 TTTTGAAAGT
*
20297249 ATAAA-AAAGTAATAAAT-AA
1 ATAAATAAAATAATAAATAAA
*
20297268 ATAAAT-AAATAATAAAGGAAA
1 ATAAATAAAATAATAAA-TAAA
20297289 A-AAAGTAAAATAATAAATAAA
1 ATAAA-TAAAATAATAAATAAA
20297310 ATAAATAAAA
1 ATAAATAAAA
20297320 ATGCACAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 14 0.33
20 3 0.07
21 13 0.30
22 13 0.30
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (21 bp):
ATAAATAAAATAATAAATAAA
Found at i:20306078 original size:108 final size:108
Alignment explanation
Indices: 20305890--20306306 Score: 653
Period size: 108 Copynumber: 3.9 Consensus size: 108
20305880 CGGATATTTG
* * *
20305890 GCTATTTGGTTC-AACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAATTTCCAAA
1 GCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTAGCGCACGTTTTCTCGAACTTCCAAA
*
20305954 CGCAAAATATTGCCTTATTTTGAAATTTTAGAAGGATA-TTTTA
65 CGCAAAATATTGCCTTATTTTGAAATTTTAAAAGGATATTTTTA
* * *
20305997 GCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACGTTAGCGCACGCTTTCTCGAACTTTCAAA
1 GCTATTTGGTCGAACG-AAAAATCGAAACCCAGCACGTTAGCGCACGTTTTCTCGAACTTCCAAA
* *
20306062 CGTAAAATATTGCCTTATTTTGAAATTTTAAAATGATATTTTTA
65 CGCAAAATATTGCCTTATTTTGAAATTTTAAAAGGATATTTTTA
*
20306106 GCTATTTGGTCGAACGAAAAACCGAAACCCAGCACGTTA-CGGCACGTTTTCTCGAACTTCCAAA
1 GCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGC-GCACGTTTTCTCGAACTTCCAAA
* *
20306170 TGTAAAATATTGCCTTATTTTGAAATTTTAAAAGGATATTTTTA
65 CGCAAAATATTGCCTTATTTTGAAATTTTAAAAGGATATTTTTA
*
20306214 GCTATTTGGTCGAACGAAAAA-CTGAAACCCAGCACGTTAGGGCACGTTTTCTCGAACTTCCAAA
1 GCTATTTGGTCGAACGAAAAATC-GAAACCCAGCACGTTAGCGCACGTTTTCTCGAACTTCCAAA
20306278 CGCAAAATATTGCCTTATTTTGAAATTTT
65 CGCAAAATATTGCCTTATTTTGAAATTTT
20306307 TATTTGGATA
Statistics
Matches: 287, Mismatches: 17, Indels: 11
0.91 0.05 0.03
Matches are distributed among these distances:
106 2 0.01
107 15 0.05
108 250 0.87
109 20 0.07
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (108 bp):
GCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGCGCACGTTTTCTCGAACTTCCAAAC
GCAAAATATTGCCTTATTTTGAAATTTTAAAAGGATATTTTTA
Found at i:20306710 original size:9 final size:9
Alignment explanation
Indices: 20306696--20306731 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
20306686 AAATAATAAG
20306696 AAAATAAAT
1 AAAATAAAT
20306705 AAAATAAAAT
1 AAAAT-AAAT
20306715 AAAATAAAT
1 AAAATAAAT
20306724 AAAA-AAAT
1 AAAATAAAT
20306732 GTAAGCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 4 0.15
9 13 0.50
10 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:20306711 original size:5 final size:5
Alignment explanation
Indices: 20306684--20306727 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
20306674 AAATCGATAT
*
20306684 TAAAA TAATAA GAAAA T-AAA TAAAA TAAAA TAAAA T-AAA TAAAA
1 TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
20306728 AAATGTAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 8 0.24
5 22 0.65
6 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:20306720 original size:19 final size:20
Alignment explanation
Indices: 20306684--20306727 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
20306674 AAATCGATAT
20306684 TAAAATAATAAGAAAATAAA
1 TAAAATAATAAGAAAATAAA
*
20306704 TAAAATAA-AATAAAATAAA
1 TAAAATAATAAGAAAATAAA
20306723 TAAAA
1 TAAAA
20306728 AAATGTAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
TAAAATAATAAGAAAATAAA
Found at i:20306786 original size:12 final size:12
Alignment explanation
Indices: 20306769--20306795 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20306759 GTAAATAAAC
20306769 AAATATTAAATA
1 AAATATTAAATA
20306781 AAATATTAAATA
1 AAATATTAAATA
20306793 AAA
1 AAA
20306796 CCTTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATTAAATA
Found at i:20307807 original size:15 final size:16
Alignment explanation
Indices: 20307787--20307816 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20307777 TTGTTTCGAC
20307787 TTTCTTTTT-TTGTTT
1 TTTCTTTTTGTTGTTT
20307802 TTTCTTTTTGTTGTT
1 TTTCTTTTTGTTGTT
20307817 ATTTGTTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTGTTGTTT
Found at i:20311068 original size:3 final size:3
Alignment explanation
Indices: 20311062--20311111 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20311052 AATAACAATA
20311062 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20311110 AT
1 AT
20311112 AATGATGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20311943 original size:19 final size:19
Alignment explanation
Indices: 20311914--20311953 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
20311904 CCAGAATCCA
20311914 GCCATAGGCGCC-GTGACG
1 GCCATAGGCGCCAGTGACG
20311932 GCCATCAGGCGCCAGTGACG
1 GCCAT-AGGCGCCAGTGACG
20311952 GC
1 GC
20311954 TCCGCCATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 8 0.40
ACGTcount: A:0.17, C:0.35, G:0.38, T:0.10
Consensus pattern (19 bp):
GCCATAGGCGCCAGTGACG
Found at i:20318729 original size:16 final size:16
Alignment explanation
Indices: 20318704--20318741 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
20318694 AAGCATCCAA
* *
20318704 AAAACATTTCCTAAGC
1 AAAACCTTTCCTAAAC
20318720 AAAACCTTTCCTAAAC
1 AAAACCTTTCCTAAAC
20318736 AAAACC
1 AAAACC
20318742 CTAAGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAACCTTTCCTAAAC
Found at i:20327674 original size:18 final size:17
Alignment explanation
Indices: 20327651--20327685 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20327641 TTTATATTAC
*
20327651 CAATTCATATCATCATTT
1 CAATTCAAAT-ATCATTT
20327669 CAATTCAAATATCATTT
1 CAATTCAAATATCATTT
20327686 ATCAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATTCAAATATCATTT
Found at i:20329622 original size:47 final size:49
Alignment explanation
Indices: 20329539--20329638 Score: 150
Period size: 47 Copynumber: 2.1 Consensus size: 49
20329529 TAAAAAGATT
*
20329539 AAATATATAAAAGAAATCAACACATTATAATTTTTTAATTCTATTTGTG
1 AAATATATAAAAGAAATCAACACATTATAATTTTTTAACTCTATTTGTG
* * *
20329588 AAATATATAAAAGAAATGAACACA-T-TGATTTTTTAACTCTATTTTTG
1 AAATATATAAAAGAAATCAACACATTATAATTTTTTAACTCTATTTGTG
20329635 AAAT
1 AAAT
20329639 TAAGTTGACT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
47 23 0.49
48 1 0.02
49 23 0.49
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (49 bp):
AAATATATAAAAGAAATCAACACATTATAATTTTTTAACTCTATTTGTG
Found at i:20330420 original size:16 final size:16
Alignment explanation
Indices: 20330399--20330429 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20330389 ATACCCAATA
20330399 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
20330415 ATATAACATTTATAA
1 ATATAAAATTTATAA
20330430 ATAAGGTTTT
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:20334797 original size:23 final size:22
Alignment explanation
Indices: 20334771--20334833 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
20334761 TTTTAAAAGT
*
20334771 ATGTTTAGAAACTTTATTAGGGC
1 ATGTTTA-AAACTTTATTAAGGC
* *
20334794 ATGTTTTAAGACTTTATTAAGGT
1 ATG-TTTAAAACTTTATTAAGGC
*
20334817 ATGTTTTTAAACTTTAT
1 ATG-TTTAAAACTTTAT
20334834 ATTAAGGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (22 bp):
ATGTTTAAAACTTTATTAAGGC
Found at i:20334824 original size:24 final size:22
Alignment explanation
Indices: 20334779--20334833 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
20334769 GTATGTTTAG
*
20334779 AAACTTTATTAGGGCATGTTTT
1 AAACTTTATTAAGGCATGTTTT
*
20334801 AAGACTTTATTAAGGTATGTTTTT
1 AA-ACTTTATTAAGGCATG-TTTT
20334825 AAACTTTAT
1 AAACTTTAT
20334834 ATTAAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 21 0.72
24 6 0.21
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (22 bp):
AAACTTTATTAAGGCATGTTTT
Found at i:20345685 original size:15 final size:15
Alignment explanation
Indices: 20345665--20345694 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20345655 ATTTGCATAA
*
20345665 ATGAAGGTTTCTTAC
1 ATGAAGGTGTCTTAC
20345680 ATGAAGGTGTCTTAC
1 ATGAAGGTGTCTTAC
20345695 GATTGAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (15 bp):
ATGAAGGTGTCTTAC
Found at i:20351952 original size:42 final size:43
Alignment explanation
Indices: 20351868--20351986 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 43
20351858 TTTATACAAC
* * * * * *
20351868 GCCAACGTCCCAGACGTGGTCTTACATGTAATCAC-TGATCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAAACACAAG-TCGAT
** **
20351911 GCCGCTGTCCTGGACAT-GTCTTACACGAAAACACAAGTCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAAACACAAGTCGAT
*
20351953 GCCAATGTCCCAGACATGGTCTTACATGAAAACA
1 GCCAATGTCCCAGACATGGTCTTACACGAAAACA
20351987 TTTATCAGAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
42 32 0.54
43 27 0.46
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACGAAAACACAAGTCGAT
Found at i:20352705 original size:18 final size:19
Alignment explanation
Indices: 20352682--20352718 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20352672 AGCAACGATC
*
20352682 TCAAAAA-CGTAAAAATTA
1 TCAAAAACCGAAAAAATTA
20352700 TCAAAAACCGAAAAAATTA
1 TCAAAAACCGAAAAAATTA
20352719 CATACCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (19 bp):
TCAAAAACCGAAAAAATTA
Found at i:20358294 original size:18 final size:20
Alignment explanation
Indices: 20358269--20358313 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 20
20358259 AAATGTCATG
20358269 TATATTTTTTAATA-TTTAT
1 TATATTTTTTAATATTTTAT
20358288 T-TA-TTTTTAATATTTTAT
1 TATATTTTTTAATATTTTAT
20358306 TATATTTT
1 TATATTTT
20358314 ATGGGCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 3 0.13
20 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATATTTTTTAATATTTTAT
Found at i:20359525 original size:26 final size:26
Alignment explanation
Indices: 20359485--20359534 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
20359475 CTATATAAAA
*
20359485 GTGTCATTTTATTCATTATTTTTAAT
1 GTGTCAATTTATTCATTATTTTTAAT
*
20359511 GTGTCAATTTCTTCATTATTTTTA
1 GTGTCAATTTATTCATTATTTTTA
20359535 TCAAAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (26 bp):
GTGTCAATTTATTCATTATTTTTAAT
Found at i:20365170 original size:62 final size:59
Alignment explanation
Indices: 20365054--20365174 Score: 136
Period size: 62 Copynumber: 2.0 Consensus size: 59
20365044 TTGTACAAAC
* ****
20365054 TATTTTTATATTATTTTATTTAATAAAATAAAAGTTTTTTTAAATATTTTAATAGTAAAT
1 TATTTTTATATTATTTTATTTAATAAAATAAAAGTTATTTTAAATAAGGCAATAG-AAAT
* *
20365114 TATTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTATTTTGAATAAGGCAATAGAAAT
1 TATTTTTATATTATT-T--TATTTAATAAAATAAAAGTTATTTTAAATAAGGCAATAGAAAT
20365175 AATGCAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 4 0.08
62 32 0.63
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
TATTTTTATATTATTTTATTTAATAAAATAAAAGTTATTTTAAATAAGGCAATAGAAAT
Found at i:20368398 original size:124 final size:126
Alignment explanation
Indices: 20368090--20368477 Score: 448
Period size: 125 Copynumber: 3.1 Consensus size: 126
20368080 CAAACAGGAG
* *
20368090 CTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTGTTTCAGTAATTTTGCTGACAGTGCATCCTG
1 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
* *
20368155 TTTGGAA-TGTTTTTTACACTATTTTTTCAGAACCGTCTTTTCAAAATTACTTTTTTAGAAA
66 TTT-GAAGCGTTTTTTACACTATTTTTTCAGAAACGTCTTTTCAAAATTACTTTTTTAGAAA
* * *
20368216 CTATTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTT-AGTAATTTTGTTGACAGTGCATCCTG
1 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
* * * * * *
20368280 TTTGAAGCGTTTTTTATAGTATTTTTTTAGAAATGT-TTTCTC-TAATTA-TTTTTCT-GGAA
66 TTTGAAGCGTTTTTTACACTATTTTTTCAGAAACGTCTTT-TCAAAATTACTTTTT-TAGAAA
* * * * * *
20368339 CTACTGTATAAAAAGAGCGTTCATGTGGAAGCTTTTTTCAGTACTTTTGCTGACAGTGCATACTG
1 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
* * * * * * * *
20368404 CTTGAAGCGTTTTTGACATTAATTTTTCGGAATCGTCTTCTCAAAATTA-TTTTTCAGAAA
66 TTTGAAGCGTTTTTTACACTATTTTTTCAGAAACGTCTTTTCAAAATTACTTTTTTAGAAA
*
20368464 CTACTATAGAAAAA
1 CTACTGTAGAAAAA
20368478 AAAAATCTTC
Statistics
Matches: 218, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
123 40 0.18
124 64 0.29
125 80 0.37
126 34 0.16
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (126 bp):
CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
TTTGAAGCGTTTTTTACACTATTTTTTCAGAAACGTCTTTTCAAAATTACTTTTTTAGAAA
Found at i:20368612 original size:34 final size:34
Alignment explanation
Indices: 20368568--20368673 Score: 135
Period size: 34 Copynumber: 3.1 Consensus size: 34
20368558 ATTATTTTAA
* * *
20368568 AAAAAACCTAAACCCTAATTCAATTAATTTTCTT
1 AAAAACCCTAAAACCTAATTTAATTAATTTTCTT
* *
20368602 AAAAACCCTAAAACCTAATTTAATTAACTTACTT
1 AAAAACCCTAAAACCTAATTTAATTAATTTTCTT
*
20368636 --AAACCCTTAAAACCTAATTTAATTAATTTTTTT
1 AAAAACCC-TAAAACCTAATTTAATTAATTTTCTT
20368669 AAAAA
1 AAAAA
20368674 AATTTAAACC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
32 6 0.10
33 23 0.38
34 29 0.48
35 3 0.05
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (34 bp):
AAAAACCCTAAAACCTAATTTAATTAATTTTCTT
Found at i:20368671 original size:33 final size:32
Alignment explanation
Indices: 20368574--20368671 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 32
20368564 TTAAAAAAAA
* * *
20368574 CCTAAACCCTAATTCAATTAATTTTCTTAAAAAC
1 CCTAAAACCTAATTTAATTAATTTT-TT-TAAAC
* **
20368608 CCTAAAACCTAATTTAATTAACTTACTTAAAC
1 CCTAAAACCTAATTTAATTAATTTTTTTAAAC
20368640 CCTTAAAACCTAATTTAATTAATTTTTTTAAA
1 CC-TAAAACCTAATTTAATTAATTTTTTTAAA
20368672 AAAATTTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
32 6 0.11
33 27 0.50
34 21 0.39
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (32 bp):
CCTAAAACCTAATTTAATTAATTTTTTTAAAC
Found at i:20369326 original size:19 final size:20
Alignment explanation
Indices: 20369302--20369339 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
20369292 TAATCACACT
20369302 TTTAAAAATTTTA-ATTATA
1 TTTAAAAATTTTATATTATA
20369321 TTTAAAAATTTTATATTAT
1 TTTAAAAATTTTATATTAT
20369340 GTTAATAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAAAATTTTATATTATA
Found at i:20369344 original size:19 final size:19
Alignment explanation
Indices: 20369303--20369344 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20369293 AATCACACTT
*
20369303 TTAAAAATTTTAATTATAT
1 TTAAAAATTTTAATTATAG
20369322 TTAAAAATTTTATATTAT-G
1 TTAAAAATTTTA-ATTATAG
20369341 TTAA
1 TTAA
20369345 TAGTGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAAAAATTTTAATTATAG
Found at i:20370107 original size:35 final size:35
Alignment explanation
Indices: 20370057--20370123 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
20370047 TTCTCTTTTC
20370057 TTGGATTTTAATTTTGATCTGAAGTCACTTGATTT
1 TTGGATTTTAATTTTGATCTGAAGTCACTTGATTT
* *
20370092 TTGGATTTTAGTTTTGATCTGAAGTTACTTGA
1 TTGGATTTTAATTTTGATCTGAAGTCACTTGA
20370124 AAAGTAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51
Consensus pattern (35 bp):
TTGGATTTTAATTTTGATCTGAAGTCACTTGATTT
Found at i:20370428 original size:21 final size:24
Alignment explanation
Indices: 20370376--20370429 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
20370366 TGGAAGACAC
*
20370376 ATCAATTTTTTAACCGTACAAATTG
1 ATCAATTTTTTAACCG-ACAAAATG
*
20370401 ATAAATTTTTTAA-C-A-AAAATG
1 ATCAATTTTTTAACCGACAAAATG
20370422 ATCAATTT
1 ATCAATTT
20370430 GCTCTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 12 0.46
22 1 0.04
24 1 0.04
25 12 0.46
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (24 bp):
ATCAATTTTTTAACCGACAAAATG
Found at i:20376384 original size:2 final size:2
Alignment explanation
Indices: 20376377--20376417 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20376367 CATAAAAGAA
20376377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20376418 GATTATTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20376427 original size:14 final size:16
Alignment explanation
Indices: 20376377--20376433 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
20376367 CATAAAAGAA
*
20376377 ATATATATATATATAT
1 ATATATATAGATATAT
*
20376393 ATATATATATATATAT
1 ATATATATAGATATAT
20376409 ATATATATAGAT-TAT
1 ATATATATAGATATAT
*
20376424 -TATATGTAGA
1 ATATATATAGA
20376434 GTAGTGNNNN
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.23
15 3 0.08
16 27 0.69
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
ATATATATAGATATAT
Found at i:20388820 original size:29 final size:28
Alignment explanation
Indices: 20388779--20388835 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
20388769 TTTTTAAAAA
*
20388779 ATTAGAACATTATAATTTGTTT-AAAATTT
1 ATTAAAACATTATAA--TGTTTCAAAATTT
*
20388808 ATTAAAACTTTATAATGTTTCAAAATTT
1 ATTAAAACATTATAATGTTTCAAAATTT
20388836 TAAAATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 7 0.28
29 13 0.52
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
ATTAAAACATTATAATGTTTCAAAATTT
Found at i:20391054 original size:16 final size:16
Alignment explanation
Indices: 20391032--20391076 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
20391022 GTATATTTAT
20391032 CGGGCTTTGTGCCTAA
1 CGGGCTTTGTGCCTAA
* *
20391048 TGGGCTTTGTGCCTAG
1 CGGGCTTTGTGCCTAA
*
20391064 CAGGCTTTGTGCC
1 CGGGCTTTGTGCC
20391077 GGTGTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.24, G:0.33, T:0.33
Consensus pattern (16 bp):
CGGGCTTTGTGCCTAA
Found at i:20397885 original size:28 final size:29
Alignment explanation
Indices: 20397854--20397910 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
20397844 AGAACCACAA
*
20397854 AAATT-TTTCAAAAATTAAATTT-AATAAT
1 AAATTATTT-AAAAAGTAAATTTAAATAAT
*
20397882 AAATTATTTAATAAGTAAATTTAAATAAT
1 AAATTATTTAAAAAGTAAATTTAAATAAT
20397911 TTAATAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
AAATTATTTAAAAAGTAAATTTAAATAAT
Found at i:20397892 original size:15 final size:16
Alignment explanation
Indices: 20397872--20397902 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20397862 CAAAAATTAA
20397872 ATTTAATAA-TAAATT
1 ATTTAATAAGTAAATT
20397887 ATTTAATAAGTAAATT
1 ATTTAATAAGTAAATT
20397903 TAAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTAATAAGTAAATT
Found at i:20399170 original size:45 final size:44
Alignment explanation
Indices: 20399102--20399229 Score: 193
Period size: 45 Copynumber: 2.9 Consensus size: 44
20399092 ATATGTCAAT
* *
20399102 ATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATAAA
1 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATGATAAA
* *
20399146 GATGAGTAAGACCACAACTGAAAGATGCTATGGCATCAAGATAAA
1 -ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATGATAAA
* *
20399191 ATAAGTAAGACCATAACTGAAAGATGTTATGGCATCATG
1 ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATG
20399230 TGAAAGCACA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 35 0.47
45 40 0.53
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (44 bp):
ATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATGATAAA
Found at i:20401957 original size:22 final size:21
Alignment explanation
Indices: 20401926--20401968 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20401916 TAAAGGATGT
20401926 GGGATGAAAAATAAATTTTTAA
1 GGGATG-AAAATAAATTTTTAA
*
20401948 GGGATTAAAATAAATTTTTAA
1 GGGATGAAAATAAATTTTTAA
20401969 TAAAATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (21 bp):
GGGATGAAAATAAATTTTTAA
Found at i:20402431 original size:20 final size:21
Alignment explanation
Indices: 20402392--20402433 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
20402382 TAGTCAATGT
*
20402392 GGGATTAAAATTAAATTTTTAA
1 GGGATTAAAACT-AATTTTTAA
20402414 GGGATTAAAACT-ATTTTTAA
1 GGGATTAAAACTAATTTTTAA
20402434 TAAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (21 bp):
GGGATTAAAACTAATTTTTAA
Found at i:20402637 original size:93 final size:92
Alignment explanation
Indices: 20402489--20402778 Score: 311
Period size: 93 Copynumber: 3.1 Consensus size: 92
20402479 AGGTACAAAG
* * * * *
20402489 ATTAACTTTTTAATGAAATTAGTAAACAAATTGTCACTTATTTATGAGGTAAATGTCAGATATGA
1 ATTAACTTTTTAATGAAAATA-T-AAGAAATTATCACTTATTTATAAGATAAATGTCAGATATGA
* *
20402554 GAGTGTTTTCTAATTAATGTGGGATTAAA
64 GAATGTTTTCTAATTAATGTGAGATTAAA
* *
20402583 ATTAACTTTTTAATGAAAATATGAAGAAATTATCACTTATTTATAAGATAAATGTGAGATATGTG
1 ATTAACTTTTTAATGAAAATAT-AAGAAATTATCACTTATTTATAAGATAAATGTCAGATATGAG
* *
20402648 AATGTTTTATAGTTAATGTGAGATTAAA
65 AATGTTTTCTAATTAATGTGAGATTAAA
* * *
20402676 ATTAACTTTTTAATGAAAATA-AAGAAATTGA-CACTTTTTTATAGGAT-AA-G-CATGAGCATG
1 ATTAACTTTTTAATGAAAATATAAGAAATT-ATCACTTATTTATAAGATAAATGTCA-GA-TATG
* * * * * *
20402736 AGATTGTTCTCTACTCAATATGTGATTAAA
63 AGAATGTTTTCTAATTAATGTGAGATTAAA
20402766 ATTAACTTTTTAA
1 ATTAACTTTTTAA
20402779 AAGAATTAAA
Statistics
Matches: 169, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
88 1 0.01
89 3 0.02
90 40 0.24
91 22 0.13
92 1 0.01
93 82 0.49
94 20 0.12
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (92 bp):
ATTAACTTTTTAATGAAAATATAAGAAATTATCACTTATTTATAAGATAAATGTCAGATATGAGA
ATGTTTTCTAATTAATGTGAGATTAAA
Found at i:20404901 original size:172 final size:173
Alignment explanation
Indices: 20404606--20404958 Score: 656
Period size: 172 Copynumber: 2.0 Consensus size: 173
20404596 ATTAGTTTTC
*
20404606 AATAAGTATTTTTTTACTTGAATCGATTCAAAGTTTGTATCAATATTTAAGAATTTTTTATACTA
1 AATAAATATTTTTTTACTTGAATCGATTCAAAGTTTGTATCAATATTTAAGAATTTTTTATACTA
20404671 ATATGCTATATATAGATTTATAAATAAAATTAAATAAAAATATTTTAATATATAATTAATTCAAA
66 ATATGCTATATATAGATTTATAAATAAAATTAAATAAAAATATTTTAATATATAATTAATTCAAA
*
20404736 TTAAATTAAAAACTATTTATTC-ATTTTTTTTAATATTGACTG
131 TTAAATTAAAAACTATTTATTCAATTTTTTTAAATATTGACTG
20404778 AATAAATATTTTTTTTACTTGAATCGATTCAAAGTTTGTATCAATATTTAAGAA-TTTTTATACT
1 AATAAATA-TTTTTTTACTTGAATCGATTCAAAGTTTGTATCAATATTTAAGAATTTTTTATACT
*
20404842 AATATGCTATATATAGATTTATAAATAAAATTAAATAAAAATATTTTAATATGTAATTAATTCAA
65 AATATGCTATATATAGATTTATAAATAAAATTAAATAAAAATATTTTAATATATAATTAATTCAA
20404907 ATTAAATTAAAAACTATTTATTCAATTTTTTTAAATATTGACTG
130 ATTAAATTAAAAACTATTTATTCAATTTTTTTAAATATTGACTG
20404951 AATAAATA
1 AATAAATA
20404959 AATCAAACTT
Statistics
Matches: 176, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
172 104 0.59
173 72 0.41
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (173 bp):
AATAAATATTTTTTTACTTGAATCGATTCAAAGTTTGTATCAATATTTAAGAATTTTTTATACTA
ATATGCTATATATAGATTTATAAATAAAATTAAATAAAAATATTTTAATATATAATTAATTCAAA
TTAAATTAAAAACTATTTATTCAATTTTTTTAAATATTGACTG
Found at i:20406828 original size:23 final size:22
Alignment explanation
Indices: 20406757--20406827 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
20406747 ATTTAAAAAT
* *
20406757 AATTATTATTTAAATAATTTTTGA
1 AATT-TTA-TTAAATAATATTTAA
*
20406781 AATATTTATGAAA-AATACTTTAA
1 AAT-TTTATTAAATAATA-TTTAA
20406804 AATTTTATTAAATAATATTTAA
1 AATTTTATTAAATAATATTTAA
20406826 AA
1 AA
20406828 AAATATTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 18 0.45
23 15 0.38
24 6 0.15
25 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (22 bp):
AATTTTATTAAATAATATTTAA
Found at i:20407494 original size:3 final size:3
Alignment explanation
Indices: 20407486--20407511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20407476 AATTGATATT
20407486 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
20407512 AGATTGGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:20414072 original size:33 final size:33
Alignment explanation
Indices: 20414030--20414092 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
20414020 AAGGCTTGCC
20414030 TATCTGAAGTATTTGTAGATGACCTATTCAACT
1 TATCTGAAGTATTTGTAGATGACCTATTCAACT
*
20414063 TATCTGAAGTATTTGTAGATGGCCTATTCA
1 TATCTGAAGTATTTGTAGATGACCTATTCA
20414093 TATGGCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (33 bp):
TATCTGAAGTATTTGTAGATGACCTATTCAACT
Found at i:20416882 original size:16 final size:16
Alignment explanation
Indices: 20416861--20416892 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20416851 CCTGCCATGA
20416861 GTTACAATTTTTCTTT
1 GTTACAATTTTTCTTT
20416877 GTTACAATTTTTCTTT
1 GTTACAATTTTTCTTT
20416893 CTTCTGAAAC
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:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
GTTACAATTTTTCTTT
Found at i:20419350 original size:2 final size:2
Alignment explanation
Indices: 20419343--20419375 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20419333 CAAGTGTGCT
20419343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20419376 GGAAAAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20420689 original size:100 final size:99
Alignment explanation
Indices: 20420543--20420739 Score: 324
Period size: 100 Copynumber: 2.0 Consensus size: 99
20420533 AAAGACTTAT
* *
20420543 GTTAGGTTATATCCCTTTTTTATAATACATAAATTGAGTAAAAAATAGTATGAAAATTATAATAT
1 GTTAGGTTATATCCATTTTTTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATAT
20420608 ATATCATTTATAAAAAAAAACGTCTTATAAATTGAA
66 ATATCATTTATAAAAAAAAA--TCTTATAAATTGAA
* *
20420644 GTTAGGTTATAT-CATTTTTTATAATACATAAATTGATTAAAAAATAATATTAAAATTATAATAT
1 GTTAGGTTATATCCATTTTTTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATAT
*
20420708 ATATCATTTATAAAAAAATATCTTATAAATTG
66 ATATCATTTATAAAAAAAAATCTTATAAATTG
20420740 TCCAAAACTT
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
98 12 0.13
100 67 0.74
101 12 0.13
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (99 bp):
GTTAGGTTATATCCATTTTTTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATAT
ATATCATTTATAAAAAAAAATCTTATAAATTGAA
Found at i:20420766 original size:100 final size:98
Alignment explanation
Indices: 20420562--20420767 Score: 254
Period size: 100 Copynumber: 2.1 Consensus size: 98
20420552 TATCCCTTTT
*
20420562 TTATAATACATAAATTGAGTAAAAAATAGTATGAAAATTATAATATATATCATTTATAAAAAAAA
1 TTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATATATATCATTTATAAAAAAAA
* * * * *
20420627 ACGTCTTATAAATTGAAGTTAGGTTATATCATTTT
66 AC-TCTTATAAATTGAAG-AACGTTATAACACTTC
* * *
20420662 TTATAATACATAAATTGATTAAAAAATAATATTAAAATTATAATATATATCATTTATAAAAAAAT
1 TTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATATATATCATTTATAAAAAAAA
*
20420727 A-TCTTATAAATTGTCCAA-AACTTTCATAACACTTC
66 ACTCTTATAAATTG---AAGAACGTT-ATAACACTTC
20420762 TTATAA
1 TTATAA
20420768 AAATAATATA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
98 12 0.13
99 3 0.03
100 75 0.82
101 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (98 bp):
TTATAATACATAAATTGAGTAAAAAATAATATGAAAATTATAATATATATCATTTATAAAAAAAA
ACTCTTATAAATTGAAGAACGTTATAACACTTC
Found at i:20421047 original size:17 final size:18
Alignment explanation
Indices: 20421022--20421055 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20421012 TTTGTAAGAT
20421022 AAAAAAATAT-ATTTTTG
1 AAAAAAATATAATTTTTG
*
20421039 AAAATAATATAATTTTT
1 AAAAAAATATAATTTTT
20421056 ATTATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAAAAATATAATTTTTG
Found at i:20425783 original size:15 final size:15
Alignment explanation
Indices: 20425765--20425800 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20425755 ATTATAAATC
* *
20425765 ATTAAACAAATTAAA
1 ATTAAAAAAATAAAA
20425780 ATTAAAAAAATAAAA
1 ATTAAAAAAATAAAA
20425795 ATTAAA
1 ATTAAA
20425801 GAAAGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
ATTAAAAAAATAAAA
Found at i:20427700 original size:2 final size:2
Alignment explanation
Indices: 20427693--20427767 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
20427683 NNNNNNTAGG
*
20427693 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20427735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20427768 GAGATGGTAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20428640 original size:20 final size:20
Alignment explanation
Indices: 20428617--20428654 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20428607 TCCAGTATAA
* *
20428617 ATATTTTTCTTAAGGTATTG
1 ATATATTTCCTAAGGTATTG
20428637 ATATATTTCCTAAGGTAT
1 ATATATTTCCTAAGGTAT
20428655 CAATATTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
ATATATTTCCTAAGGTATTG
Found at i:20428660 original size:20 final size:20
Alignment explanation
Indices: 20428611--20428660 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
20428601 TATTGATCCA
* *
20428611 GTATAAATATTTTTCTTAAG
1 GTATAAATATATTTCCTAAG
**
20428631 GTATTGATATATTTCCTAAG
1 GTATAAATATATTTCCTAAG
*
20428651 GTATCAATAT
1 GTATAAATAT
20428661 TCCTGCTACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (20 bp):
GTATAAATATATTTCCTAAG
Found at i:20430587 original size:14 final size:15
Alignment explanation
Indices: 20430570--20430610 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
20430560 TTTTAATTTT
20430570 ATTTTAATAATAA-A
1 ATTTTAATAATAATA
*
20430584 ATTTTAA-AACAATA
1 ATTTTAATAATAATA
20430598 ATTTTAAATAATA
1 ATTTT-AATAATA
20430611 TGTTTCACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 13 0.59
15 2 0.09
16 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAATAATAATA
Found at i:20430663 original size:15 final size:15
Alignment explanation
Indices: 20430643--20430699 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
20430633 ATTCAATATT
20430643 AATATTTTAATAATA
1 AATATTTTAATAATA
*
20430658 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
20430677 AATATATTAATAATA
1 AATATTTTAATAATA
20430692 AATATTTT
1 AATATTTT
20430700 GTAGCATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:20430950 original size:26 final size:26
Alignment explanation
Indices: 20430921--20430973 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20430911 AATGATGTTG
20430921 TAATGAACCTGAATTTAACTAAATAT
1 TAATGAACCTGAATTTAACTAAATAT
20430947 TAATGAACCTGAATTTAACTAAATAT
1 TAATGAACCTGAATTTAACTAAATAT
20430973 T
1 T
20430974 TTTAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
TAATGAACCTGAATTTAACTAAATAT
Found at i:20434548 original size:30 final size:30
Alignment explanation
Indices: 20434513--20434569 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
20434503 AAAAACTCTC
* *
20434513 AAATTTCTCCCTAAATTTCTTAAAGCTATT
1 AAATTTCTCACTAAATTTCTCAAAGCTATT
*
20434543 AAATTTCTCATTAAATTTCTCAAAGCT
1 AAATTTCTCACTAAATTTCTCAAAGCT
20434570 CTCTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
AAATTTCTCACTAAATTTCTCAAAGCTATT
Found at i:20434557 original size:12 final size:12
Alignment explanation
Indices: 20434540--20434564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20434530 TCTTAAAGCT
20434540 ATTAAATTTCTC
1 ATTAAATTTCTC
20434552 ATTAAATTTCTC
1 ATTAAATTTCTC
20434564 A
1 A
20434565 AAGCTCTCTT
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:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAAATTTCTC
Found at i:20436368 original size:16 final size:18
Alignment explanation
Indices: 20436333--20436374 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
20436323 GCCAGGTGCG
20436333 TATCCTAACCCTTATATA
1 TATCCTAACCCTTATATA
20436351 TATCCTAACCCTTATATA
1 TATCCTAACCCTTATATA
*
20436369 TTTCCT
1 TATCCT
20436375 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:20436800 original size:24 final size:23
Alignment explanation
Indices: 20436773--20436895 Score: 62
Period size: 25 Copynumber: 5.3 Consensus size: 23
20436763 CATTTAATAA
*
20436773 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAA-TTATTTTTATAT-TTTT
20436797 AATAGTAAATTATTTTTATATTTTT
1 AATA--AAATTATTTTTATATTTTT
*** * *
20436822 AATAAAA-TATAAGT-TCTTTTG
1 AATAAAATTATTTTTATATTTTT
* *
20436843 CAT---ATCATTTTTA-ATATTTT
1 AATAAAATTATTTTTATAT-TTTT
20436863 AATAGTAAATTATTTTTATATTTTT
1 AATA--AAATTATTTTTATATTTTT
20436888 AATAAAAT
1 AATAAAAT
20436896 ATAAGTTCTT
Statistics
Matches: 72, Mismatches: 15, Indels: 25
0.64 0.13 0.22
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 5 0.07
21 7 0.10
22 4 0.06
23 7 0.10
24 4 0.06
25 33 0.46
26 7 0.10
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
AATAAAATTATTTTTATATTTTT
Found at i:20436823 original size:33 final size:33
Alignment explanation
Indices: 20436784--20436891 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
20436774 ATAAAAGTTG
20436784 TTTTTAATATTTTAATAGTAAATTATTTTTATA
1 TTTTTAATATTTTAATAGTAAATTATTTTTATA
* * *
20436817 TTTTTAATA---AAATA-TAAGTTCTTTTGCATATCA
1 TTTTTAATATTTTAATAGTAAATTATTTT---TAT-A
20436850 TTTTTAATATTTTAATAGTAAATTATTTTTATA
1 TTTTTAATATTTTAATAGTAAATTATTTTTATA
20436883 TTTTTAATA
1 TTTTTAATA
20436892 AAATATAAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
29 9 0.15
30 4 0.07
32 3 0.05
33 29 0.48
34 3 0.05
36 4 0.07
37 9 0.15
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (33 bp):
TTTTTAATATTTTAATAGTAAATTATTTTTATA
Found at i:20436857 original size:66 final size:66
Alignment explanation
Indices: 20436784--20436914 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
20436774 ATAAAAGTTG
20436784 TTTTTAATATTTTAATAGTAAATTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGCATATC
1 TTTTTAATATTTTAATAGTAAATTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGCATATC
20436849 A
66 A
20436850 TTTTTAATATTTTAATAGTAAATTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGCATATC
1 TTTTTAATATTTTAATAGTAAATTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGCATATC
20436915 CTTTCCCGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (66 bp):
TTTTTAATATTTTAATAGTAAATTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGCATATC
A
Found at i:20440581 original size:126 final size:126
Alignment explanation
Indices: 20440409--20440677 Score: 394
Period size: 126 Copynumber: 2.1 Consensus size: 126
20440399 GGCCAAACAT
* * * *
20440409 GAACTATTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACATGGCAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * * *
20440474 TTGCTTGAAGCATTTTTGACACTATTTTTTTAGAAACGTTTTCTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCATTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAG
* * * *
20440535 GAACTACTGTAGAAAAAGAATGTCTACATGTCAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACATGGCAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* *
20440600 CTGCTTAAAGCCTTTTTCACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCATTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAG
20440661 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
20440678 AACAAAATCC
Statistics
Matches: 127, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAACGTCCACATGGCAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTAAAGCATTTTTCACACTATTTGTTCAGAAACGTATTCTCAAAATTATTTTTTCAG
Found at i:20440813 original size:34 final size:33
Alignment explanation
Indices: 20440733--20440840 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 33
20440723 TAAACACAAT
*
20440733 ATTAA-TTTTTAAAAAAACTAAACCCTAATTTA
1 ATTAATTTTTTAAAAACACTAAACCCTAATTTA
* *
20440765 ATTAATTTTCTTAAAAACACTAAACCTTAATTTC
1 ATTAATTTT-TTAAAAACACTAAACCCTAATTTA
* * * * **
20440799 CTTAGTTTATTTAAAACCCCTAAACAATAATTTA
1 ATTAATTT-TTTAAAAACACTAAACCCTAATTTA
20440833 ATTAATTT
1 ATTAATTT
20440841 AAAAAAAGAG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
32 5 0.08
33 3 0.05
34 52 0.85
35 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTAATTTTTTAAAAACACTAAACCCTAATTTA
Found at i:20440917 original size:21 final size:21
Alignment explanation
Indices: 20440892--20440962 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
20440882 TAAAACCTAG
20440892 AACCCTAAATTATTTTAACAA
1 AACCCTAAATTATTTTAACAA
*** *** **
20440913 AACCCTAAACCCTACAAACCT
1 AACCCTAAATTATTTTAACAA
*
20440934 AAGCCTAAATTATTTTAACAA
1 AACCCTAAATTATTTTAACAA
20440955 AACCCTAA
1 AACCCTAA
20440963 CCCTAAAAAC
Statistics
Matches: 32, Mismatches: 18, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.25
Consensus pattern (21 bp):
AACCCTAAATTATTTTAACAA
Found at i:20440920 original size:36 final size:39
Alignment explanation
Indices: 20440880--20440962 Score: 100
Period size: 42 Copynumber: 2.1 Consensus size: 39
20440870 TTTTAAAATT
*
20440880 CCTAAAACCTA-GAA-C-CCTAAATTATTTTAACAAAAC
1 CCTAAAACCTACAAACCACCTAAATTATTTTAACAAAAC
*
20440916 CCTAAACCCTACAAACCTAAGCCTAAATTATTTTAACAAAAC
1 CCTAAAACCTACAAACC--A-CCTAAATTATTTTAACAAAAC
20440958 CCTAA
1 CCTAA
20440963 CCCTAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 10 0.26
37 2 0.05
38 1 0.03
42 26 0.67
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (39 bp):
CCTAAAACCTACAAACCACCTAAATTATTTTAACAAAAC
Found at i:20440973 original size:15 final size:15
Alignment explanation
Indices: 20440953--20440991 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20440943 TTATTTTAAC
* *
20440953 AAAACCCTAACCCTA
1 AAAACCCTAAACCAA
20440968 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
20440983 AAAACCCTA
1 AAAACCCTA
20440992 GGGACTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.36, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:20440977 original size:42 final size:42
Alignment explanation
Indices: 20440895--20440973 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
20440885 AACCTAGAAC
*
20440895 CCTAAATTATTTTAACAAAACCCTAAACCCTACAAACCTAAG
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
20440937 CCTAAATTATTTTAACAAAACCCT-AACCCTAAAAACC
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACC
20440974 CTAAACCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 12 0.33
42 24 0.67
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (42 bp):
CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
Found at i:20441600 original size:87 final size:89
Alignment explanation
Indices: 20441456--20441619 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 89
20441446 GTGTAAAAAT
* * *
20441456 CCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCTTGCTTTTTTTTTGTGCACTCAATTGGGTATT
1 CCCTCAAAACTTTTCAAAAAAAGCAATTAAGCCTTGCATTTTTTTTGTGCACTCAATTGGGTACT
*
20441521 TGAAACTTTCAAAATATATAAAAGA
66 TG-AACTATCAAAATATATAAAAGA
* *
20441546 CCCT-AAAACTTTTC-AAAAAAGCAATTAAGTCTCTG-ATTTTTTTT-TGCACTCAATTGGTTAC
1 CCCTCAAAACTTTTCAAAAAAAGCAATTAAGCCT-TGCATTTTTTTTGTGCACTCAATTGGGTAC
20441607 TTGAACTATCAAA
65 TTGAACTATCAAA
20441620 TGCATAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
86 9 0.13
87 18 0.27
88 25 0.37
89 11 0.16
90 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (89 bp):
CCCTCAAAACTTTTCAAAAAAAGCAATTAAGCCTTGCATTTTTTTTGTGCACTCAATTGGGTACT
TGAACTATCAAAATATATAAAAGA
Found at i:20441773 original size:9 final size:9
Alignment explanation
Indices: 20441737--20441883 Score: 66
Period size: 10 Copynumber: 15.3 Consensus size: 9
20441727 ACATGTGGCA
20441737 AAAAATTAT
1 AAAAATTAT
20441746 AAAAA--AT
1 AAAAATTAT
*
20441753 AAAAATCAAT
1 AAAAAT-TAT
20441763 AAAAATTAT
1 AAAAATTAT
*
20441772 AACAATTAT
1 AAAAATTAT
*
20441781 -TAAATTAT
1 AAAAATTAT
*
20441789 AATAAAAATAT
1 -A-AAAATTAT
*
20441800 AAAAATATTT
1 AAAAAT-TAT
*
20441810 AAAATTTATTAA
1 AAAA---ATTAT
20441822 AAATAAGTTAT
1 AAA-AA-TTAT
*
20441833 AAAAATCAT
1 AAAAATTAT
*
20441842 AAAAAAATAT
1 -AAAAATTAT
*
20441852 AAAAAATTGT
1 -AAAAATTAT
*
20441862 AAAATTTTAT
1 AAAA-ATTAT
*
20441872 AAAAATAAT
1 AAAAATTAT
20441881 AAA
1 AAA
20441884 GTGCATAAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 28
0.68 0.13 0.18
Matches are distributed among these distances:
7 7 0.07
8 6 0.06
9 32 0.31
10 40 0.38
11 12 0.12
12 4 0.04
13 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20442144 original size:29 final size:29
Alignment explanation
Indices: 20442110--20442180 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
20442100 TTCTTTATTT
20442110 TTTTATAATTTTCTTACGA-CTTTATAAAA
1 TTTTATAATTTT-TTACGATCTTTATAAAA
* * *
20442139 TTTTATAACTTTTTAGGATTTTTATAAAA
1 TTTTATAATTTTTTACGATCTTTATAAAA
* *
20442168 CTTTACAATTTTT
1 TTTTATAATTTTT
20442181 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTTATAATTTTTTACGATCTTTATAAAA
Found at i:20442163 original size:19 final size:18
Alignment explanation
Indices: 20442139--20442211 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
20442129 CTTTATAAAA
*
20442139 TTTTATAACTTTTTAGGAT
1 TTTTATAA-TTTTTACGAT
** *
20442158 TTTTATAAAACTTTACAAT
1 TTTTAT-AATTTTTACGAT
*
20442177 TTTTATAATTTTTTTATGAT
1 TTTTATAA--TTTTTACGAT
*
20442197 TTTTGTAATTTTTAC
1 TTTTATAATTTTTAC
20442212 TAATTTTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 15 0.37
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTATAATTTTTACGAT
Found at i:20442188 original size:28 final size:27
Alignment explanation
Indices: 20442130--20442278 Score: 102
Period size: 29 Copynumber: 5.2 Consensus size: 27
20442120 TTCTTACGAC
**
20442130 TTTATAAAATTTTATAACTTTTTAGGATT
1 TTTATAAAA-TTTATAA-TTTTTATAATT
*
20442159 TTTATAAAACTTTACAATTTTTATAATTTT
1 TTTATAAAA-TTTATAATTTTTATAA--TT
* ** *
20442189 TTTATGATTTTTGTAATTTTTACTAATT
1 TTTATAAAATTTATAATTTTTA-TAATT
* * *
20442217 TTAAATAAAATTTAAATATTTTTATATTT
1 TT-TATAAAATTTATA-ATTTTTATAATT
*
20442246 TTTATTAAAATTTA-ATATTTTTATAAAT
1 TTTA-TAAAATTTATA-ATTTTTATAATT
20442274 TTTAT
1 TTTAT
20442279 TAATTTTTTT
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 28 0.29
29 48 0.51
30 18 0.19
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTATAAAATTTATAATTTTTATAATT
Found at i:20442192 original size:20 final size:20
Alignment explanation
Indices: 20442169--20442209 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20442159 TTTATAAAAC
20442169 TTTACAATTTTTATAATTTT
1 TTTACAATTTTTATAATTTT
** *
20442189 TTTATGATTTTTGTAATTTT
1 TTTACAATTTTTATAATTTT
20442209 T
1 T
20442210 ACTAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTACAATTTTTATAATTTT
Found at i:20442199 original size:9 final size:9
Alignment explanation
Indices: 20442139--20442286 Score: 64
Period size: 9 Copynumber: 15.4 Consensus size: 9
20442129 CTTTATAAAA
20442139 TTTTATAACT
1 TTTTATAA-T
**
20442149 TTTTAGGAT
1 TTTTATAAT
*
20442158 TTTTATAAAA
1 TTTTAT-AAT
* *
20442168 CTTTACAAT
1 TTTTATAAT
20442177 TTTTATAATTT
1 TTTTATAA--T
*
20442188 TTTTATGAT
1 TTTTATAAT
*
20442197 TTTTGTAAT
1 TTTTATAAT
20442206 TTTTACTAAT
1 TTTTA-TAAT
* *
20442216 TTTAAATAAA
1 TTT-TATAAT
* *
20442226 ATTTAAATAT
1 TTTTATA-AT
*
20442236 TTTTATATT
1 TTTTATAAT
*
20442245 TTTTATTAAA
1 TTTTA-TAAT
*
20442255 ATTTA-ATAT
1 TTTTATA-AT
*
20442264 TTTTATAAA
1 TTTTATAAT
20442273 TTTTATTAAT
1 TTTTA-TAAT
20442283 TTTT
1 TTTT
20442287 TTGTTATCAT
Statistics
Matches: 98, Mismatches: 30, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
8 1 0.01
9 45 0.46
10 43 0.44
11 9 0.09
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:20442279 original size:28 final size:29
Alignment explanation
Indices: 20442204--20442281 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
20442194 GATTTTTGTA
*
20442204 ATTTTTACT-AATTTTAAATAAAATTTAAAT
1 ATTTTTA-TAAATTTT-ATTAAAATTTAAAT
**
20442234 ATTTTTATATTTTTTATTAAAATTT-AAT
1 ATTTTTATAAATTTTATTAAAATTTAAAT
20442262 ATTTTTATAAATTTTATTAA
1 ATTTTTATAAATTTTATTAA
20442282 TTTTTTTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 21 0.50
29 10 0.24
30 11 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTTATAAATTTTATTAAAATTTAAAT
Found at i:20450959 original size:12 final size:12
Alignment explanation
Indices: 20450942--20450968 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20450932 CACACGCCTG
20450942 TGTGCTAGGCCA
1 TGTGCTAGGCCA
20450954 TGTGCTAGGCCA
1 TGTGCTAGGCCA
20450966 TGT
1 TGT
20450969 AACTGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:20456396 original size:57 final size:57
Alignment explanation
Indices: 20456263--20456384 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
20456253 GTGGAGTAAT
* * * * * * *
20456263 TGCACATGCTACTGCTGATAGAGCAGCTGCTGTCCATTCTGCTTTTCATAAAGTAGC
1 TGCACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGC
*
20456320 TGCACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCGTAAAGCAGC
1 TGCACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGC
*
20456377 TTCACAAG
1 TGCACAAG
20456385 TTGCCTCTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (57 bp):
TGCACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGC
Found at i:20456465 original size:24 final size:24
Alignment explanation
Indices: 20456438--20456484 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20456428 TGGCATTGGT
* *
20456438 GGAGGTAGTTTAAGAGGTGGAGGA
1 GGAGGCAGTTTAAGAGGTAGAGGA
*
20456462 GGAGGCAGTTTAATAGGTAGAGG
1 GGAGGCAGTTTAAGAGGTAGAGG
20456485 TAGAAGCAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (24 bp):
GGAGGCAGTTTAAGAGGTAGAGGA
Found at i:20456493 original size:24 final size:24
Alignment explanation
Indices: 20456444--20456494 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
20456434 TGGTGGAGGT
* *
20456444 AGTTTAAGAGGTGGAGGAGGAGGC
1 AGTTTAAGAGGTAGAGGAGGAAGC
*
20456468 AGTTTAATAGGTAGAGGTA-GAAGC
1 AGTTTAAGAGGTAGAGG-AGGAAGC
20456492 AGT
1 AGT
20456495 GTTGGAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.41, T:0.22
Consensus pattern (24 bp):
AGTTTAAGAGGTAGAGGAGGAAGC
Found at i:20456563 original size:66 final size:66
Alignment explanation
Indices: 20456481--20456641 Score: 259
Period size: 66 Copynumber: 2.4 Consensus size: 66
20456471 TTAATAGGTA
* * *
20456481 GAGGTAGAAGCAGTGTTGGAGGTAGTGCTACCGGTTTCCTCGGTGGACGTGGTGCTGCCGTTGGT
1 GAGGTGGAAGCAGTGTTGGAGGTAGTGCTACCGGTTACCTCAGTGGACGTGGTGCTGCCGTTGGT
20456546 G
66 G
* *
20456547 GAGGTGGAAGCAGTGTTGGAGGTAGTGCTACCGGTTACCTTAGTGGACGTGGTGCTGCTGTTGGT
1 GAGGTGGAAGCAGTGTTGGAGGTAGTGCTACCGGTTACCTCAGTGGACGTGGTGCTGCCGTTGGT
20456612 G
66 G
* *
20456613 GAGGTGGAGGTAGTGTTGGAGGTAGTGCT
1 GAGGTGGAAGCAGTGTTGGAGGTAGTGCT
20456642 GGAGGTAGTG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 88 1.00
ACGTcount: A:0.15, C:0.13, G:0.44, T:0.28
Consensus pattern (66 bp):
GAGGTGGAAGCAGTGTTGGAGGTAGTGCTACCGGTTACCTCAGTGGACGTGGTGCTGCCGTTGGT
G
Found at i:20456634 original size:12 final size:12
Alignment explanation
Indices: 20456617--20456656 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
20456607 TTGGTGGAGG
20456617 TGGAGGTAGTGT
1 TGGAGGTAGTGT
*
20456629 TGGAGGTAGTGC
1 TGGAGGTAGTGT
20456641 TGGAGGTAGTGT
1 TGGAGGTAGTGT
20456653 TGGA
1 TGGA
20456657 AGTGGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.03, G:0.50, T:0.30
Consensus pattern (12 bp):
TGGAGGTAGTGT
Found at i:20457209 original size:43 final size:43
Alignment explanation
Indices: 20457090--20457363 Score: 286
Period size: 43 Copynumber: 6.4 Consensus size: 43
20457080 TCACATAAAC
* *
20457090 ACCTTTAGCGGCGCTTTT-CTATAAAACGCCGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTACCA-CAAACGCCGCTAAAGAACATG
* * ** * *
20457133 GCCTTTAGCGGC-ATTTTTTCACAAACACCGCTAAATG-TCATG
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAA-GAACATG
** * * ** *
20457175 TTCTTTAGCGGCTCTTGTATTACAAACGCTGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACATG
* *
20457218 ACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACATG
*
20457261 ACCTTTAGCGACGCTTTTACCACAAACGCCGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACATG
* * *
20457304 ACCTTTAGCGGCTCTTTTATCACAAACGCCGCTAAATG-TCATG
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAA-GAACATG
**
20457347 TTCTTTAGCGGCGCTTT
1 ACCTTTAGCGGCGCTTT
20457364 ACTAAAAATG
Statistics
Matches: 191, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
42 31 0.16
43 159 0.83
44 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACATG
Found at i:20457353 original size:129 final size:128
Alignment explanation
Indices: 20457090--20457380 Score: 349
Period size: 129 Copynumber: 2.3 Consensus size: 128
20457080 TCACATAAAC
* * **
20457090 ACCTTTAGCGGCGCTTTT-CTATAAAACGCCGCTAAAGAACATGGCCTTTAGCGGCATTTTTTCA
1 ACCTTTAGCGGCGCTTTTACTA-AAAACGCCGCTAAAGAACAAGACCTTTAGCGGCATTTTACCA
* ** * *
20457154 CAAACACCGCTAAATGTCATGTTCTTTAGCGGCTCTTGTATTACAAACGCTGCTAAAGAACATG
65 CAAACACCGCTAAATGACATGACCTTTAGCGGCTCTTGTATCACAAACGCCGCTAAAGAACATG
*
20457218 ACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGAACAAGACCTTTAGCGACGC-TTTTACC
1 ACCTTTAGCGGCGCTTTTACTAAAAACGCCGCTAAAGAACAAGACCTTTAGCG--GCATTTTACC
* * *
20457282 ACAAACGCCGCTAAA-GAACATGACCTTTAGCGGCTCTTTTATCACAAACGCCGCTAAATG-TCA
64 ACAAACACCGCTAAATG-ACATGACCTTTAGCGGCTCTTGTATCACAAACGCCGCTAAA-GAACA
20457345 TG
127 TG
** * *
20457347 TTCTTTAGCGGCGC-TTTACTAAAAATGCCACTAA
1 ACCTTTAGCGGCGCTTTTACTAAAAACGCCGCTAA
20457381 CTTTGGTAGA
Statistics
Matches: 140, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
128 65 0.46
129 72 0.51
130 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (128 bp):
ACCTTTAGCGGCGCTTTTACTAAAAACGCCGCTAAAGAACAAGACCTTTAGCGGCATTTTACCAC
AAACACCGCTAAATGACATGACCTTTAGCGGCTCTTGTATCACAAACGCCGCTAAAGAACATG
Found at i:20457689 original size:21 final size:21
Alignment explanation
Indices: 20457664--20457755 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
20457654 TTCTGCTCTG
20457664 CTCTGCTTCCCTAGCTGCTGC
1 CTCTGCTTCCCTAGCTGCTGC
* *
20457685 CTCTGCTTCCCTTA-CTACTAC
1 CTCTGCTTCCC-TAGCTGCTGC
* * *
20457706 CGCTGCTTCCCTCGCTGTTGC
1 CTCTGCTTCCCTAGCTGCTGC
* *
20457727 CTCTACTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTAGCTGCTGC
20457748 CTCTGCTT
1 CTCTGCTT
20457756 TAAGTTGTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 55 0.95
22 2 0.03
ACGTcount: A:0.05, C:0.43, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTAGCTGCTGC
Found at i:20466679 original size:25 final size:27
Alignment explanation
Indices: 20466655--20467043 Score: 322
Period size: 25 Copynumber: 15.6 Consensus size: 27
20466645 TATTTTTGTA
20466655 TTATGTAAATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466682 TTATGT--ATTATGAAAGGTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
*
20466707 TTGTGT--ATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
*
20466732 TTATG--ATTTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466757 TTGTGT--ATTATGAAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
**
20466782 -T-TGTGCATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
*
20466807 TTTTGT--ATTATGTAAGTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466832 TTGTGT--ATTATGTAAGTTGTGT-A-
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466855 TTATGTAAGTTATGT--TTTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* * *
20466880 TTATGTAAGTTGTG-CA-TTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466905 TTATGTAAGTTGTGT-A-TTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466930 TTATGTAAGTTATGTAAGATATGT-A-
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20466955 TTATGAAAATTATGTAAGTTGTGT-A-
1 TTATGTAAATTATGTAAGTTATGTAAG
*
20466980 TTATGTAAGTTATGT-A-TTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
* *
20467005 TTATGT-AAGT-TGTGA-TTATGTAAG
1 TTATGTAAATTATGTAAGTTATGTAAG
20467029 TTATGT--ATTATGTAA
1 TTATGTAAATTATGTAA
20467044 CTTGCGTATA
Statistics
Matches: 312, Mismatches: 31, Indels: 41
0.81 0.08 0.11
Matches are distributed among these distances:
23 23 0.07
24 27 0.09
25 245 0.79
26 3 0.01
27 14 0.04
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (27 bp):
TTATGTAAATTATGTAAGTTATGTAAG
Found at i:20466718 original size:16 final size:16
Alignment explanation
Indices: 20466651--20467067 Score: 270
Period size: 16 Copynumber: 26.2 Consensus size: 16
20466641 TATATATTTT
*
20466651 TGTATTATGTAAATTA
1 TGTATTATGTAAGTTA
20466667 TGTAAGTTATGTAAGTTA
1 TGT-A-TTATGTAAGTTA
* *
20466685 TGTATTATGAAAGGTA
1 TGTATTATGTAAGTTA
*
20466701 TGTAAGTTGTGT-A-TTA
1 TGT-A-TTATGTAAGTTA
20466717 TGTAAGTTATGTAAGTTA
1 TGT-A-TTATGTAAGTTA
20466735 TG-ATTTATGTAAGTTA
1 TGTA-TTATGTAAGTTA
*
20466751 TGTAAGTTGTGT-A-TTA
1 TGT-A-TTATGTAAGTTA
* *
20466767 TGAAAGTTATGTAAGTTG
1 TG-TA-TTATGTAAGTTA
*
20466785 TGCATTATGTAAGTTA
1 TGTATTATGTAAGTTA
*
20466801 TGTAAGTTTTGT-A-TTA
1 TGT-A-TTATGTAAGTTA
*
20466817 TGTAAGTTATGTAAGTTG
1 TGT-A-TTATGTAAGTTA
*
20466835 TGTATTATGTAAGTTG
1 TGTATTATGTAAGTTA
20466851 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
*
20466867 TGTTTTATGTAAGTTA
1 TGTATTATGTAAGTTA
* *
20466883 TGTAAGT-TGTGCA-TTA
1 TGT-ATTATGT-AAGTTA
*
20466899 TGTAAGTTATGTAAGTTG
1 TGT-A-TTATGTAAGTTA
20466917 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
*
20466933 TGTAAGTTATGTAAGATA
1 TGT-A-TTATGTAAGTTA
20466951 TGTATTATG-AA---A
1 TGTATTATGTAAGTTA
*
20466963 ---ATTATGTAAGTTG
1 TGTATTATGTAAGTTA
20466976 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
20466992 TGTATTATGT-A---A
1 TGTATTATGTAAGTTA
*
20467004 -G--TTATGTAAGTTG
1 TGTATTATGTAAGTTA
20467017 TG-ATTATGTAAGTTA
1 TGTATTATGTAAGTTA
* *
20467032 TGTATTATGTAACTTG
1 TGTATTATGTAAGTTA
* * *
20467048 CGTATAATGTAAGTTG
1 TGTATTATGTAAGTTA
20467064 TGTA
1 TGTA
20467068 AGTTGTGTAT
Statistics
Matches: 326, Mismatches: 39, Indels: 72
0.75 0.09 0.16
Matches are distributed among these distances:
9 12 0.04
10 3 0.01
11 1 0.00
12 2 0.01
14 1 0.00
15 16 0.05
16 207 0.63
17 19 0.06
18 65 0.20
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (16 bp):
TGTATTATGTAAGTTA
Found at i:20466723 original size:50 final size:50
Alignment explanation
Indices: 20466663--20467089 Score: 461
Period size: 50 Copynumber: 8.3 Consensus size: 50
20466653 TATTATGTAA
* *
20466663 ATTATGTAAGTTATGTAAGTTATGTATTATGAAAGGTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGT
20466713 ATTATGTAAGTTATGTAAGTTATG-ATTTATGTAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGTA-TTATGTAAGTTATGTAAGTTGTGT
* * * *
20466763 ATTATGAAAGTTATGTAAGTTGTGCATTATGTAAGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGT
* *
20466813 ATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTGTGTATTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAA-----G--TTATGTAAGTTGTGT
* * *
20466870 TTTATGTAAGTTATGTAAGTTGTGCATTATGTAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGT
* * * *
20466920 ATTATGTAAGTTATGTAAGTTATGTAAGATATGT-A-TTATGAAAATTATGT
1 ATTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGTGT
*
20466970 AAGTTGTGT-A-TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTG-
1 -A-TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGT
* * *
20467019 ATTATGTAAGTTATGTATTATGTAACTTGCGTATAATGTAAGTTGTGTAAGTTGTGT
1 ATTATGTAAGTTATGTA--A-GTTA--T--GTATTATGTAAGTTATGTAAGTTGTGT
*
20467076 ATAATGTAAGTTAT
1 ATTATGTAAGTTAT
20467090 ACAAGAAGTG
Statistics
Matches: 324, Mismatches: 28, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
47 5 0.02
48 7 0.02
49 10 0.03
50 197 0.61
51 6 0.02
52 14 0.04
54 1 0.00
55 1 0.00
56 24 0.07
57 59 0.18
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.46
Consensus pattern (50 bp):
ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGT
Found at i:20467013 original size:9 final size:9
Alignment explanation
Indices: 20466655--20467089 Score: 359
Period size: 9 Copynumber: 52.4 Consensus size: 9
20466645 TATTTTTGTA
*
20466655 TTATGTAAA
1 TTATGTAAG
20466664 TTATGTAAG
1 TTATGTAAG
20466673 TTATGTAAG
1 TTATGTAAG
20466682 TTATGT-A-
1 TTATGTAAG
*
20466689 TTATGAAAG
1 TTATGTAAG
*
20466698 GTATGTAAG
1 TTATGTAAG
*
20466707 TTGTGT-A-
1 TTATGTAAG
20466714 TTATGTAAG
1 TTATGTAAG
20466723 TTATGTAAG
1 TTATGTAAG
*
20466732 TTATG--AT
1 TTATGTAAG
20466739 TTATGTAAG
1 TTATGTAAG
20466748 TTATGTAAG
1 TTATGTAAG
*
20466757 TTGTGT-A-
1 TTATGTAAG
*
20466764 TTATGAAAG
1 TTATGTAAG
20466773 TTATGTAAG
1 TTATGTAAG
* *
20466782 TTGTG-CA-
1 TTATGTAAG
20466789 TTATGTAAG
1 TTATGTAAG
20466798 TTATGTAAG
1 TTATGTAAG
*
20466807 TTTTGT-A-
1 TTATGTAAG
20466814 TTATGTAAG
1 TTATGTAAG
20466823 TTATGTAAG
1 TTATGTAAG
*
20466832 TTGTGT-A-
1 TTATGTAAG
20466839 TTATGTAAG
1 TTATGTAAG
*
20466848 TTGTGT-A-
1 TTATGTAAG
20466855 TTATGTAAG
1 TTATGTAAG
*
20466864 TTATGT--T
1 TTATGTAAG
20466871 TTATGTAAG
1 TTATGTAAG
20466880 TTATGTAAG
1 TTATGTAAG
* *
20466889 TTGTG-CA-
1 TTATGTAAG
20466896 TTATGTAAG
1 TTATGTAAG
20466905 TTATGTAAG
1 TTATGTAAG
*
20466914 TTGTGT-A-
1 TTATGTAAG
20466921 TTATGTAAG
1 TTATGTAAG
20466930 TTATGTAAG
1 TTATGTAAG
20466939 TTATGTAAG
1 TTATGTAAG
*
20466948 ATATGT-A-
1 TTATGTAAG
* *
20466955 TTATGAAAA
1 TTATGTAAG
20466964 TTATGTAAG
1 TTATGTAAG
*
20466973 TTGTGT-A-
1 TTATGTAAG
20466980 TTATGTAAG
1 TTATGTAAG
20466989 TTATGT-A-
1 TTATGTAAG
20466996 TTATGTAAG
1 TTATGTAAG
20467005 TTATGTAAG
1 TTATGTAAG
*
20467014 -T-TGTGA-
1 TTATGTAAG
20467020 TTATGTAAG
1 TTATGTAAG
20467029 TTATGT-A-
1 TTATGTAAG
*
20467036 TTATGTAAC
1 TTATGTAAG
**
20467045 TTGCGT-A-
1 TTATGTAAG
*
20467052 TAATGTAAG
1 TTATGTAAG
*
20467061 TTGTGTAAG
1 TTATGTAAG
*
20467070 TTGTGT-A-
1 TTATGTAAG
*
20467077 TAATGTAAG
1 TTATGTAAG
20467086 TTAT
1 TTAT
20467090 ACAAGAAGTG
Statistics
Matches: 339, Mismatches: 50, Indels: 74
0.73 0.11 0.16
Matches are distributed among these distances:
7 87 0.26
8 35 0.10
9 217 0.64
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20467058 original size:56 final size:57
Alignment explanation
Indices: 20466905--20467089 Score: 187
Period size: 56 Copynumber: 3.2 Consensus size: 57
20466895 ATTATGTAAG
* * * * * * *
20466905 TTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTAAGATATGT-A-TTATGAAAA
1 TTATGTAAGTTATGTATTATGTAACTTACGT-A-TAATGTAAGTTATGTAAGTTGTG--TA
* * * *
20466964 TTATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTG-A
1 TTATGTAAGTTATGTATTATGTAACTTACGTATAATGTAAGTTATGTAAGTTGTGTA
* *
20467020 TTATGTAAGTTATGTATTATGTAACTTGCGTATAATGTAAGTTGTGTAAGTTGTGTA
1 TTATGTAAGTTATGTATTATGTAACTTACGTATAATGTAAGTTATGTAAGTTGTGTA
*
20467077 TAATGTAAGTTAT
1 TTATGTAAGTTAT
20467090 ACAAGAAGTG
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
56 50 0.44
57 27 0.24
58 2 0.02
59 35 0.31
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (57 bp):
TTATGTAAGTTATGTATTATGTAACTTACGTATAATGTAAGTTATGTAAGTTGTGTA
Found at i:20467068 original size:25 final size:25
Alignment explanation
Indices: 20467039--20467087 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20467029 TTATGTATTA
20467039 TGTAACTTGCGTATAATGTAAGTTG
1 TGTAACTTGCGTATAATGTAAGTTG
* *
20467064 TGTAAGTTGTGTATAATGTAAGTT
1 TGTAACTTGCGTATAATGTAAGTT
20467088 ATACAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (25 bp):
TGTAACTTGCGTATAATGTAAGTTG
Found at i:20468387 original size:26 final size:25
Alignment explanation
Indices: 20468358--20468435 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 25
20468348 TTACGCCACA
20468358 AAGGCTATTCCTTAGAGTGCGCCATG
1 AAGG-TATTCCTTAGAGTGCGCCATG
20468384 AAGGTATTCCTTTCTAGAGTGCGCCATG
1 AAGGTATTCC--T-TAGAGTGCGCCATG
* *
20468412 AAGGTATTTCTTTAGAGTGTGCCA
1 AAGGTA-TTCCTTAGAGTGCGCCA
20468436 CCAAGACGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.13
26 15 0.33
27 2 0.04
28 20 0.43
29 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (25 bp):
AAGGTATTCCTTAGAGTGCGCCATG
Found at i:20468406 original size:28 final size:28
Alignment explanation
Indices: 20468370--20468424 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
20468360 GGCTATTCCT
20468370 TAGAGTGCGCCATGAAGGTATTCCTTTC
1 TAGAGTGCGCCATGAAGGTATTCCTTTC
*
20468398 TAGAGTGCGCCATGAAGGTATTTCTTT
1 TAGAGTGCGCCATGAAGGTATTCCTTT
20468425 AGAGTGTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (28 bp):
TAGAGTGCGCCATGAAGGTATTCCTTTC
Found at i:20469123 original size:26 final size:28
Alignment explanation
Indices: 20469072--20469123 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
20469062 AGTTTATAAA
**
20469072 TTCTCTTTGAGTTTTCTTTTTTAAGAAT
1 TTCTCTTTGAGTTTTCTTTTAAAAGAAT
20469100 TTCTC-TTGAG-TTTCTTTTAAAAGA
1 TTCTCTTTGAGTTTTCTTTTAAAAGA
20469124 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 5 0.23
28 5 0.23
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (28 bp):
TTCTCTTTGAGTTTTCTTTTAAAAGAAT
Found at i:20474120 original size:29 final size:29
Alignment explanation
Indices: 20474078--20474187 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
20474068 ATCCACCATT
20474078 GGTACATAGTACCTGGAATTGTAAACACC
1 GGTACATAGTACCTGGAATTGTAAACACC
* *
20474107 GGTACATAGTACCTAGAATTGTAAACATC
1 GGTACATAGTACCTGGAATTGTAAACACC
* * * *
20474136 GGTACATAGTGCTTGGAACTGT-AACACA
1 GGTACATAGTACCTGGAATTGTAAACACC
* **
20474164 AGTACATAGTAATTGGAATTGTAA
1 GGTACATAGTACCTGGAATTGTAA
20474188 TAACCGACAA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 22 0.32
29 46 0.68
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (29 bp):
GGTACATAGTACCTGGAATTGTAAACACC
Found at i:20474183 original size:57 final size:58
Alignment explanation
Indices: 20474078--20474187 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 58
20474068 ATCCACCATT
* ** *
20474078 GGTACATAGTACCTGGAATTGTAAACACCGGTACATAGTACCTAGAATTGTAAACATC
1 GGTACATAGTACCTGGAACTGTAAACACAAGTACATAGTAACTAGAATTGTAAACATC
* * * *
20474136 GGTACATAGTGCTTGGAACTGT-AACACAAGTACATAGTAATTGGAATTGTAA
1 GGTACATAGTACCTGGAACTGTAAACACAAGTACATAGTAACTAGAATTGTAA
20474188 TAACCGACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 25 0.57
58 19 0.43
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (58 bp):
GGTACATAGTACCTGGAACTGTAAACACAAGTACATAGTAACTAGAATTGTAAACATC
Found at i:20478449 original size:14 final size:14
Alignment explanation
Indices: 20478430--20478457 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20478420 CTCGAGTGAA
20478430 CCACCCATATACAT
1 CCACCCATATACAT
20478444 CCACCCATATACAT
1 CCACCCATATACAT
20478458 TCTTCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (14 bp):
CCACCCATATACAT
Found at i:20483244 original size:127 final size:126
Alignment explanation
Indices: 20482845--20483243 Score: 611
Period size: 127 Copynumber: 3.2 Consensus size: 126
20482835 AAGGCCAAGT
* * *
20482845 AGGAACTATTGTAAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTGGCTGACAGTGC
1 AGGAACTACTGT-AGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * *
20482910 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCGTCTTAAAATTATTTTTTC
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
* * * *
20482972 AGGAACTACTGTAGAAAAAGAGCGT-CATCGTGGGAGCTTTTTTTAGTAATTTTACTGGCTGTGC
1 AGGAACTACTGTAGAAAAAGAGCGTCCA-CGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
20483036 ATCCTGCTTGAAGTGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTTA
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTA-TTTTTTC
*
20483099 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * *
20483164 TCCTGCTTGAAGCGTTTTTGTCACTATTTTTTCAGAACCGTCTTCTGAAAATTAATTTTTC
66 TCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
*
20483225 AGAAACTACTGTAGAAAAA
1 AGGAACTACTGTAGAAAAA
20483244 AATCCTTCTT
Statistics
Matches: 246, Mismatches: 23, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
125 2 0.01
126 117 0.48
127 125 0.51
128 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (126 bp):
AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC
Found at i:20485687 original size:2 final size:2
Alignment explanation
Indices: 20485680--20485706 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20485670 ATTCTCAACT
20485680 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20485707 CTAGGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20487944 original size:16 final size:16
Alignment explanation
Indices: 20487912--20487941 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20487902 TGATGTGATA
20487912 TATTATTATTTTAAAT
1 TATTATTATTTTAAAT
20487928 TATTATT-TTTTAAA
1 TATTATTATTTTAAA
20487942 ATTTATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATTATTTTAAAT
Found at i:20490217 original size:16 final size:18
Alignment explanation
Indices: 20490178--20490211 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20490168 TAAGTTTATA
20490178 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20490195 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
20490212 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:20499149 original size:322 final size:322
Alignment explanation
Indices: 20498564--20499200 Score: 1139
Period size: 322 Copynumber: 2.0 Consensus size: 322
20498554 TCCATATTAG
20498564 GCTCGATTATCATAAAATGAAGTTGTTTAAATGCTCAACCTTTAAGGAAATTGTCATTGTATTTA
1 GCTCGATTATCATAAAATGAAGTTGTTTAAATGCTCAACCTTTAAGGAAATTGTCATTGTATTTA
* ** *
20498629 AACTAAAGCCTGTGCTAGTAGTCCTTTTGTGTGTTTGCACAAACAAATAGATTTTTATGCTACGG
66 AACTAAAGCCTATGCTAGTAGTCCTTTTAAGTGTTTGCACAAACAAATAGATTGTTATGCTACGG
*
20498694 ACGATTGCAAGTTAGAAACAATCATGAATTACTATATTGATATTGTTGTGTATGCAGGGTAGGGT
131 ACGATAGCAAGTTAGAAACAATCATGAATTACTATATTGATATTGTTGTGTATGCAGGGTAGGGT
*
20498759 ATGTATATACAAGTGTGGATTTCTATAAGAGATTATGTGGAGTCTCTATTATTATGAGGTACAAC
196 ATGTACATACAAGTGTGGATTTCTATAAGAGATTATGTGGAGTCTCTATTATTATGAGGTACAAC
* *
20498824 TCCGGTCTAAAATCTTAAAACATTGTGTAAATAACTCCATCGATTGGGTGATTTAAACTAAA
261 TCCGATCTAAAATCTTAAAACATTGTGTAAATAACTCCATCGATTGCGTGATTTAAACTAAA
*
20498886 GCTCGATTATCATAAAATGAAGTTGTTTAAATGCTCAACCTTTAAGGAAGTTGTCATTGTATTTA
1 GCTCGATTATCATAAAATGAAGTTGTTTAAATGCTCAACCTTTAAGGAAATTGTCATTGTATTTA
*
20498951 AACTAAAGCCTATGCTGGTAGTCCTTTTAAGTGTTTGCACAAACAAATAGATTGTTATGCTACGG
66 AACTAAAGCCTATGCTAGTAGTCCTTTTAAGTGTTTGCACAAACAAATAGATTGTTATGCTACGG
* *
20499016 ACGATAGCAAGTTGGAAACAATCATGAATTACTATATTGATGTTGTTGTGTATGCAGGGTAGGGT
131 ACGATAGCAAGTTAGAAACAATCATGAATTACTATATTGATATTGTTGTGTATGCAGGGTAGGGT
20499081 ATGTACATACAAGTGTGGATTTCTATAAGAGATTATGTGGAGTCTCTATTATTATGAGGTACAAC
196 ATGTACATACAAGTGTGGATTTCTATAAGAGATTATGTGGAGTCTCTATTATTATGAGGTACAAC
* * *
20499146 TCCGATCTAAAATTTTAAATCATTGTGTAAATAACTCCATCGCTTGCGTGATTTA
261 TCCGATCTAAAATCTTAAAACATTGTGTAAATAACTCCATCGATTGCGTGATTTA
20499201 CAATTTTCTC
Statistics
Matches: 300, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
322 300 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (322 bp):
GCTCGATTATCATAAAATGAAGTTGTTTAAATGCTCAACCTTTAAGGAAATTGTCATTGTATTTA
AACTAAAGCCTATGCTAGTAGTCCTTTTAAGTGTTTGCACAAACAAATAGATTGTTATGCTACGG
ACGATAGCAAGTTAGAAACAATCATGAATTACTATATTGATATTGTTGTGTATGCAGGGTAGGGT
ATGTACATACAAGTGTGGATTTCTATAAGAGATTATGTGGAGTCTCTATTATTATGAGGTACAAC
TCCGATCTAAAATCTTAAAACATTGTGTAAATAACTCCATCGATTGCGTGATTTAAACTAAA
Found at i:20500643 original size:21 final size:21
Alignment explanation
Indices: 20500603--20500643 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20500593 ATTGAATTAA
*
20500603 ACCCTAAACCCTATACCTTAT
1 ACCCTAAACCCTACACCTTAT
*
20500624 ACCCTAAACCCTACATCTTA
1 ACCCTAAACCCTACACCTTA
20500644 GGGTTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCCTAAACCCTACACCTTAT
Found at i:20513531 original size:22 final size:22
Alignment explanation
Indices: 20513506--20513551 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20513496 TTAAAGTTAA
*
20513506 TCTATTTTCATTTT-TTTTATTT
1 TCTA-TTTCATTTTACTTTATTT
*
20513528 TCTATTTCCTTTTACTTTATTT
1 TCTATTTCATTTTACTTTATTT
20513550 TC
1 TC
20513552 ACGCATTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTATTTCATTTTACTTTATTT
Found at i:20514073 original size:14 final size:14
Alignment explanation
Indices: 20514054--20514083 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20514044 ATTATTGTAT
*
20514054 TTTATTATTTAAAA
1 TTTATTACTTAAAA
20514068 TTTATTACTTAAAA
1 TTTATTACTTAAAA
20514082 TT
1 TT
20514084 CGACATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTACTTAAAA
Found at i:20517212 original size:24 final size:24
Alignment explanation
Indices: 20517182--20517263 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 24
20517172 TCTGGGCTTG
20517182 TTGGGCTAAGATTCAGGTTTAGGT
1 TTGGGCTAAGATTCAGGTTTAGGT
* * * *
20517206 TTGGGCTTTA-ATT-GGGTCTGGGCTT
1 TTGGGC-TAAGATTCAGGTTTAGG--T
*
20517231 GTTGGGCTAAGAATCAGGTTTAGGT
1 -TTGGGCTAAGATTCAGGTTTAGGT
20517256 TTGGGCTA
1 TTGGGCTA
20517264 GAGTCTTCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
23 6 0.14
24 17 0.40
25 6 0.14
26 8 0.19
27 6 0.14
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (24 bp):
TTGGGCTAAGATTCAGGTTTAGGT
Found at i:20517216 original size:50 final size:50
Alignment explanation
Indices: 20517149--20517262 Score: 212
Period size: 50 Copynumber: 2.3 Consensus size: 50
20517139 GATTCGAGTC
*
20517149 GTTTA-GTTTGGGCTTTAATTGGGTCTGGGCTTGTTGGGCTAAGATTCAG
1 GTTTAGGTTTGGGCTTTAATTGGGTCTGGGCTTGTTGGGCTAAGAATCAG
20517198 GTTTAGGTTTGGGCTTTAATTGGGTCTGGGCTTGTTGGGCTAAGAATCAG
1 GTTTAGGTTTGGGCTTTAATTGGGTCTGGGCTTGTTGGGCTAAGAATCAG
20517248 GTTTAGGTTTGGGCT
1 GTTTAGGTTTGGGCT
20517263 AGAGTCTTCT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 5 0.08
50 58 0.92
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (50 bp):
GTTTAGGTTTGGGCTTTAATTGGGTCTGGGCTTGTTGGGCTAAGAATCAG
Found at i:20523067 original size:5 final size:5
Alignment explanation
Indices: 20523057--20523082 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20523047 CTCAAAAATT
20523057 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
20523083 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20523183 original size:22 final size:21
Alignment explanation
Indices: 20523131--20523191 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
20523121 AGTTTTGAGT
20523131 TTTTTTTTTATATATTTTT-G
1 TTTTTTTTTATATATTTTTAG
*** *
20523151 AAGTTTATTATATATTCTTTAG
1 TTTTTTTTTATATATT-TTTAG
*
20523173 TTTTTTTTTATAAATTTTT
1 TTTTTTTTTATATATTTTT
20523192 TAGATATATT
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 12 0.40
21 6 0.20
22 12 0.40
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTTTTTATATATTTTTAG
Found at i:20524408 original size:34 final size:34
Alignment explanation
Indices: 20524344--20524410 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
20524334 TTTTACAAAT
* *
20524344 ATCATATCAGAATGTCATATTACCATAAACATAA
1 ATCATATCAGAATATCATATTACCAGAAACATAA
**
20524378 ATCATATCAGAATATCATATTTTCAGAAACATA
1 ATCATATCAGAATATCATATTACCAGAAACATA
20524411 TCTCATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.31
Consensus pattern (34 bp):
ATCATATCAGAATATCATATTACCAGAAACATAA
Done.