Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009169.1 Hibiscus syriacus cultivar Beakdansim tig00112717_pilon, whole genome shotgun sequence
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: 345057
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3662 original size:2 final size:2
Alignment explanation
Indices: 3657--3696 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
3647 TTTTTCATTC
3657 AT AT AT AT AT AT CAT 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 A
3697 CTTTAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6783 original size:21 final size:21
Alignment explanation
Indices: 6759--6800 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6749 AAATCTAATT
*
6759 ATTTTTTCTTT-TCCAAATATC
1 ATTTTTTATTTAT-CAAATATC
6780 ATTTTTTATTTATCAAATATC
1 ATTTTTTATTTATCAAATATC
6801 CTTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTTATCAAATATC
Found at i:13097 original size:15 final size:15
Alignment explanation
Indices: 13079--13129 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
13069 TTAGGGACCA
13079 AAAAGTGTAAATTTC
1 AAAAGTGTAAATTTC
****
13094 AAAAGT-TCAAGGACC
1 AAAAGTGT-AAATTTC
13109 AAAAGTGTAAATTTC
1 AAAAGTGTAAATTTC
13124 AAAAGT
1 AAAAGT
13130 ATGTATTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (15 bp):
AAAAGTGTAAATTTC
Found at i:13115 original size:30 final size:31
Alignment explanation
Indices: 13063--13129 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
13053 TAAAGTTTGG
* *
13063 AAAAGTTTAGGGACCAAAAAGTGTAAATTTC
1 AAAAGTTCAAGGACCAAAAAGTGTAAATTTC
13094 AAAAGTTCAAGGACC-AAAAGTGTAAATTTC
1 AAAAGTTCAAGGACCAAAAAGTGTAAATTTC
13124 AAAAGT
1 AAAAGT
13130 ATGTATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (31 bp):
AAAAGTTCAAGGACCAAAAAGTGTAAATTTC
Found at i:15945 original size:177 final size:177
Alignment explanation
Indices: 15638--15987 Score: 520
Period size: 177 Copynumber: 2.0 Consensus size: 177
15628 AGTATGATGA
* * * * * *
15638 TTATCGATCGATTTGGTTTGATTCATTATTTCGTTCTTGTAGTAGTACATTTGTTTTACTATGGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
* * * *
15703 ACTATGTGTGCTAGGATGGTGTTCATAATGAATTACCACTCTGTAATTGTTAGTATAGTGTCGTT
66 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATAGAGTCGTT
* * * *
15768 GTGTACTACAATTCCTATATGTCATTGTAGCACTTAAGTACTACATG
131 GTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
* * * *
15815 TTATCTATCGATTTTGTTTAATGCATTATTGCGTTTTTGTAGTAGTATATTTGTTGTACCATAGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
*
15880 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCATTATGGAATTGTTAGTATAGAGTCGTT
66 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATAGAGTCGTT
*
15945 GTGGACTAAAATACCTATACGTCATTGTAGCACTTAGGTACTA
131 GTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTA
15988 ATTGTGTACC
Statistics
Matches: 153, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
177 153 1.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (177 bp):
TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCACTATGGAATTGTTAGTATAGAGTCGTT
GTGGACTAAAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
Found at i:18832 original size:79 final size:79
Alignment explanation
Indices: 18701--19094 Score: 550
Period size: 79 Copynumber: 5.1 Consensus size: 79
18691 AAAACAAATG
*
18701 AAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
18766 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* *
18780 AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATTCAATAGCTGAAATGTATATGGG
1 AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
18845 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* *
18859 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
18924 TAAATTGTCAGCAT
66 TACATTGTCAGCAT
* * *
18938 --AATGAATAATTCATATGGGTGAATTATTGGCATGAATGGATGCCATAACTGAAATGTATATGG
1 AAAAT-AATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
19001 GTACATTGTCAGTAT
65 GTACATTGTCAGCAT
* * * * ** *
19016 AAAAGAATAAAT-CATAT---TG-GTTATTGGCATGAAAAGATGCCATCGCTGAAATACATATGA
1 AAAATAAT-AATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
* *
19076 GTGCATTATCAGCAT
65 GTACATTGTCAGCAT
19091 AAAA
1 AAAA
19095 GTATATTTTA
Statistics
Matches: 284, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
75 49 0.17
76 2 0.01
77 2 0.01
78 68 0.24
79 158 0.56
80 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (79 bp):
AAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TACATTGTCAGCAT
Found at i:19032 original size:157 final size:157
Alignment explanation
Indices: 18701--19067 Score: 566
Period size: 157 Copynumber: 2.4 Consensus size: 157
18691 AAAACAAATG
*
18701 AAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* * *
18766 TACATTGTCAGCATAAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATTCAATAGCT
66 TAAATTGTCAGCAT-AAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCAATAACT
18831 GAAATGTATATGGGTACATTGTCAGCAT
130 GAAATGTATATGGGTACATTGTCAGCAT
18859 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* * *
18924 TAAATTGTCAGCAT-AATGAATAATTCATATGGGTGAATTATTGGCATGAATGGATGCCATAACT
66 TAAATTGTCAGCATAAAT-AATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCAATAACT
*
18988 GAAATGTATATGGGTACATTGTCAGTAT
130 GAAATGTATATGGGTACATTGTCAGCAT
* * *
19016 AAAAGAATAAAT-CATAT---TG-GTTATTGGCATGAAAAGATGCCATCGCTGAAAT
1 AAAAGAAT-AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAAT
19068 ACATATGAGT
Statistics
Matches: 196, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
153 30 0.15
154 2 0.01
156 3 0.02
157 81 0.41
158 80 0.41
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (157 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TAAATTGTCAGCATAAATAATAATGCATATGGGTGAATTATTGGCATGAAAGGATGCAATAACTG
AAATGTATATGGGTACATTGTCAGCAT
Found at i:23080 original size:30 final size:30
Alignment explanation
Indices: 23044--23106 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
23034 GAAATCAAAG
23044 ACTTTGAAATAAAAGTGGATGGATGTCTAT
1 ACTTTGAAATAAAAGTGGATGGATGTCTAT
23074 ACTTTGAAATAAAAGTGGATGGATGTCTAT
1 ACTTTGAAATAAAAGTGGATGGATGTCTAT
23104 ACT
1 ACT
23107 ATAAGGGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (30 bp):
ACTTTGAAATAAAAGTGGATGGATGTCTAT
Found at i:23798 original size:15 final size:15
Alignment explanation
Indices: 23778--23808 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23768 TCAAGTATTC
23778 TAATAGGGCGAGCCA
1 TAATAGGGCGAGCCA
23793 TAATAGGGCGAGCCA
1 TAATAGGGCGAGCCA
23808 T
1 T
23809 TCAGAGCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (15 bp):
TAATAGGGCGAGCCA
Found at i:26054 original size:79 final size:79
Alignment explanation
Indices: 25918--26317 Score: 622
Period size: 79 Copynumber: 5.1 Consensus size: 79
25908 AAAACGAATG
* * *
25918 AAAATAATAATGCATATGGGGGTATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
25983 TACATTGTCAGTAT
66 TACATTGTCAGCAT
*
25997 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
26062 TACATTGTCAACAT
66 TACATTGTCAGCAT
* *
26076 AAAAGACTAATGCATATGGGTCCATTATTGGCATGAAAGGACT-CCATAGCTGAAATGTATATGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGA-TGCCATAGCTGAAATGTATATGG
* *
26140 GTACATTATCAACAT
65 GTACATTGTCAGCAT
* * *
26155 AAAAGAATAATGCATACGGGTGAATTATTGGCATGAAAGGATGCCATAGTTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
26220 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* * *
26234 AAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCATCGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* *
26299 TGCATTATCAGCAT
66 TACATTGTCAGCAT
26313 AAAAG
1 AAAAG
26318 TATATATTTT
Statistics
Matches: 294, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 292 0.99
80 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TACATTGTCAGCAT
Found at i:27540 original size:62 final size:62
Alignment explanation
Indices: 27439--27566 Score: 202
Period size: 62 Copynumber: 2.1 Consensus size: 62
27429 GAAGTATCAG
*
27439 TACTCTCTACAAGGGTATCGATACTCGTGGTCCAATATCAATACTCAAAGGGTCAATATCGA
1 TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
* * * * *
27501 TACTCTCTATAAGGGTATCTATACTCGTGATCCAGTATCAATACTCAGAGGGTCAGTATCGA
1 TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
27563 TACT
1 TACT
27567 GAGGAATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (62 bp):
TACTCTCTACAAGGGTATCGATACTCGTGATCCAATATCAATACTCAAAGGGTCAATATCGA
Found at i:29539 original size:59 final size:59
Alignment explanation
Indices: 29461--29919 Score: 656
Period size: 59 Copynumber: 7.8 Consensus size: 59
29451 ATTATTCCCC
*
29461 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AATGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAA-GTGCCCT
* * * **
29520 ATAAGGAAATTCATACACTTAATATGAATTTCTTATCATTTTAGCACATG-AGCACCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
* *
29578 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGACCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
*
29637 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTACCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
* **
29696 ATATGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGTTCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
* * * * *
29755 ATATGGAAATTCATACACTTTGTATGCATTTCTTATCATTTTAGCACACAAATTGCCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
* * * * *
29814 ATATGAAAATTCATACATTTAGTATGAATTTCTTATCATTTTTGCACACGATGTGCCC-
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
* * *
29872 -TACGGAAATTTATACACTTAATATGAATTTCTTATCATTTTAGTACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
29920 TTATTGCCAT
Statistics
Matches: 357, Mismatches: 41, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
57 41 0.11
58 50 0.14
59 266 0.75
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
Found at i:30297 original size:22 final size:20
Alignment explanation
Indices: 30252--30303 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
30242 TTGTTCCTCA
*
30252 GTATCGATACTGCCACCATG
1 GTATCGATACTACCACCATG
*
30272 GTATCGATACTACTCTACTATG
1 GTATCGATACTAC-C-ACCATG
*
30294 GTATCAATAC
1 GTATCGATAC
30304 CCCCTTCTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACCACCATG
Found at i:30397 original size:95 final size:95
Alignment explanation
Indices: 30250--30474 Score: 256
Period size: 95 Copynumber: 2.4 Consensus size: 95
30240 TCTTGTTCCT
* * * *
30250 CAGTATCGATACTGCC--ACCATGGTATCGATACTACTCTACTATGGTATCAATACCCCCTTCTG
1 CAGTATCGATAC--CCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATG
* * * *
30313 GTATGGTTACCAAAATTAGATTCGATATGGCC
64 GTATCGATACCAAAATTAGATTCAATATGACC
* **
30345 CAGTATCGATACCCTTACCATGGTATCGATATTACTATACTATGATACCAATACCCTTTTATGGT
1 CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATGGT
* * * *
30410 ATCGATACCAAAATTAGGTTTAATGTTACC
66 ATCGATACCAAAATTAGATTCAATATGACC
** *
30440 TGGTATCGATACCCTTACTATGGTATCGATACTAC
1 CAGTATCGATACCCTTACCATGGTATCGATACTAC
30475 CTCGTCGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
93 2 0.02
95 107 0.98
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (95 bp):
CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGATACCAATACCCCCTTATGGT
ATCGATACCAAAATTAGATTCAATATGACC
Found at i:33997 original size:10 final size:10
Alignment explanation
Indices: 33982--34011 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
33972 TAGTTTGAAT
33982 ATGGAATTGA
1 ATGGAATTGA
33992 ATGGAATTGA
1 ATGGAATTGA
34002 ATGGAATTGA
1 ATGGAATTGA
34012 TGTTAGGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (10 bp):
ATGGAATTGA
Found at i:38290 original size:27 final size:26
Alignment explanation
Indices: 38252--38309 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
38242 AGAACATATA
*
38252 TAAAACTGCCTAAACACTGCCTAATT
1 TAAAACTACCTAAACACTGCCTAATT
38278 TAAAGACTACCTAAACACTGCCTAATT
1 TAAA-ACTACCTAAACACTGCCTAATT
38305 TAAAA
1 TAAAA
38310 ACCAATTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (26 bp):
TAAAACTACCTAAACACTGCCTAATT
Found at i:40867 original size:29 final size:29
Alignment explanation
Indices: 40799--40871 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
40789 AAAACTATAT
* * *
40799 TTTTGGTCCCTAAATTTTCAAAAGTTTATA
1 TTTTGGTCACT-AACTTTCAAAAGTTTACA
* *
40829 CTTT-GACACTGAACTTTCAAAA-TTTACA
1 TTTTGGTCACT-AACTTTCAAAAGTTTACA
40857 TTTTGGTCACTAACT
1 TTTTGGTCACTAACT
40872 AAAATTTGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 12 0.35
29 19 0.56
30 3 0.09
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTGGTCACTAACTTTCAAAAGTTTACA
Found at i:44968 original size:15 final size:15
Alignment explanation
Indices: 44948--44996 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
44938 AAGAAAACCT
44948 ATTAAAAATGGATAA
1 ATTAAAAATGGATAA
44963 ATT-AAAAT-GACT--
1 ATTAAAAATGGA-TAA
44975 ATTAAAAATGGATAA
1 ATTAAAAATGGATAA
44990 ATTAAAA
1 ATTAAAA
44997 TATTATCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 3 0.10
13 8 0.28
14 8 0.28
15 10 0.34
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (15 bp):
ATTAAAAATGGATAA
Found at i:44971 original size:14 final size:14
Alignment explanation
Indices: 44952--44997 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
44942 AAACCTATTA
44952 AAAATGGATAAATT
1 AAAATGGATAAATT
44966 AAAAT-GACT--ATT
1 AAAATGGA-TAAATT
44978 AAAAATGGATAAATT
1 -AAAATGGATAAATT
44993 AAAAT
1 AAAAT
44998 ATTATCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 13 0.48
15 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (14 bp):
AAAATGGATAAATT
Found at i:44977 original size:27 final size:27
Alignment explanation
Indices: 44946--44997 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
44936 GGAAGAAAAC
44946 CTATTAAAAATGGATAAATTAAAATGA
1 CTATTAAAAATGGATAAATTAAAATGA
44973 CTATTAAAAATGGATAAATTAAAAT
1 CTATTAAAAATGGATAAATTAAAAT
44998 ATTATCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.31
Consensus pattern (27 bp):
CTATTAAAAATGGATAAATTAAAATGA
Found at i:54774 original size:20 final size:20
Alignment explanation
Indices: 54749--54789 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
54739 ACTCAAAAAT
54749 AAGAAAATAAAAAG-AAGAAA
1 AAGAAAA-AAAAAGCAAGAAA
*
54769 AAGAAAAGAAAAGCAAGAAA
1 AAGAAAAAAAAAGCAAGAAA
54789 A
1 A
54790 GTTTAAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAAAGCAAGAAA
Found at i:79952 original size:25 final size:25
Alignment explanation
Indices: 79872--79952 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
79862 ATAAGTGTGT
*
79872 GTGTATTTTTTTTATTATGCAGTAA
1 GTGTGTTTTTTTTATTATGCAGTAA
** *
79897 GTGTGGGTTTTTAATATATATTCA-T--
1 GTGT--GTTTTTTTTAT-TATGCAGTAA
79922 GTGTGTTTTTTTTATTATGCAGTAA
1 GTGTGTTTTTTTTATTATGCAGTAA
79947 GTGTGT
1 GTGTGT
79953 GTGTATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
22 5 0.12
23 10 0.23
25 14 0.33
27 9 0.21
28 5 0.12
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (25 bp):
GTGTGTTTTTTTTATTATGCAGTAA
Found at i:80058 original size:25 final size:26
Alignment explanation
Indices: 79986--80062 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 26
79976 GTGTATGCTT
* *
79986 TTTTTATTATGCAGTACGTGTGTGTG
1 TTTTTATTATGCAATACGTGTGTGTC
* *
80012 TTTAATATATATG---TATGTGTGTGTTC
1 TTT-TTAT-TATGCAATACGTGTGTG-TC
80038 TTTTTATTATGCAATACGTGTGTGT
1 TTTTTATTATGCAATACGTGTGTGT
80063 GTTTAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
24 4 0.10
25 12 0.30
26 8 0.20
27 12 0.30
28 4 0.10
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.52
Consensus pattern (26 bp):
TTTTTATTATGCAATACGTGTGTGTC
Found at i:80068 original size:106 final size:103
Alignment explanation
Indices: 79869--80075 Score: 292
Period size: 106 Copynumber: 2.0 Consensus size: 103
79859 GCAATAAGTG
*
79869 TGTGTGTATTTTTTTTATTATGCAGTAAGTGTGGGTTTTTAATATATATTCATGTGTGTTTTTTT
1 TGTGTGTATTTTTTTTATTATGCAGTAAGTGTGGGTGTTTAATATATATTCATGTGTGTTTTTTT
*
79934 TATTATGCAGTAAGTGTGTGTGTATTTAATATATATTTA
66 TATTATGCAATAAGTGTGTGTG-ATTTAATATATATTTA
* *
79973 TGTGTGTATGCTTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGT-ATGTGTGTGTT
1 TGTGTGTAT--TTTTTTTATTATGCAGTAAGTGTGGGTGTTTAATATATAT-TCATGTGTGT-TT
* *
80037 CTTTTTATTATGCAATACGTGTGTGTG-TTTAATGTATAT
62 -TTTTTATTATGCAATAAGTGTGTGTGATTTAATATATAT
80076 ATGAAATGTG
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
104 9 0.10
106 56 0.61
107 3 0.03
108 24 0.26
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (103 bp):
TGTGTGTATTTTTTTTATTATGCAGTAAGTGTGGGTGTTTAATATATATTCATGTGTGTTTTTTT
TATTATGCAATAAGTGTGTGTGATTTAATATATATTTA
Found at i:80076 original size:54 final size:51
Alignment explanation
Indices: 79869--80090 Score: 259
Period size: 52 Copynumber: 4.2 Consensus size: 51
79859 GCAATAAGTG
* * *
79869 TGTGTGTATTTTTTTTATTATGCAGTAAGTGTGGGTTTTTAATATATAT-TCA
1 TGTGTGT-GTTTTTTTATTATGCAGTAAGTGTGTGTGTTTAATATATATGT-A
*
79921 TGTGTGT-TTTTTTTATTATGCAGTAAGTGTGTGTGTATTTAATATATATTTA
1 TGTGTGTGTTTTTTTATTATGCAGTAAGTGTGTGTG--TTTAATATATATGTA
*
79973 TGTGTGTATGCTTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGTA
1 TGTGTG--TG-TTTTTTTATTATGCAGTAAGTGTGTGTGTTTAATATATATGTA
* * *
80027 TGTGTGTGTTCTTTTTATTATGCAATACGTGTGTGTGTTTAATGTATATATGAAA
1 TGTGTGTGTT-TTTTTATTATGCAGTAAGTGTGTGTGTTTAA--TATATATG-TA
80082 TGTGTGTGT
1 TGTGTGTGT
80091 GACTTATTAT
Statistics
Matches: 153, Mismatches: 6, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
50 26 0.17
51 2 0.01
52 58 0.38
53 1 0.01
54 29 0.19
55 10 0.07
56 27 0.18
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.53
Consensus pattern (51 bp):
TGTGTGTGTTTTTTTATTATGCAGTAAGTGTGTGTGTTTAATATATATGTA
Found at i:80127 original size:24 final size:26
Alignment explanation
Indices: 80085--80164 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
80075 TATGAAATGT
80085 GTGTGTGACTTATTATAATATAAAGG
1 GTGTGTGACTTATTATAATATAAAGG
* *
80111 GTGTGTG-CTCATT-TAATATGAAA-T
1 GTGTGTGACTTATTATAATAT-AAAGG
* *
80135 GTGTGTGAGTTTTTATAATATAAAGG
1 GTGTGTGACTTATTATAATATAAAGG
80161 GTGT
1 GTGT
80165 ATGTTGTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
24 13 0.30
25 14 0.32
26 17 0.39
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (26 bp):
GTGTGTGACTTATTATAATATAAAGG
Found at i:80178 original size:48 final size:49
Alignment explanation
Indices: 80074--80200 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 49
80064 TTTAATGTAT
* * *
80074 ATATGAAATGTGTGTGTGACTTATTATAATATAAAGGGTGTGTGCTCATTTA
1 ATATGAAA--TGTGTGTGAGTTTTTATAATATAAAGGGTGTATGCT-ATTTA
80126 ATATGAAATGTGTGTGAGTTTTTATAATATAAAGGGTGTATG-T-TGTTA
1 ATATGAAATGTGTGTGAGTTTTTATAATATAAAGGGTGTATGCTAT-TTA
80174 ATATGAAA--TGT-TGAGTTTTTATAATAT
1 ATATGAAATGTGTGTGAGTTTTTATAATAT
80201 GAGGCGTGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
45 16 0.23
46 3 0.04
47 1 0.01
48 11 0.15
49 1 0.01
50 31 0.44
52 8 0.11
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.43
Consensus pattern (49 bp):
ATATGAAATGTGTGTGAGTTTTTATAATATAAAGGGTGTATGCTATTTA
Found at i:83853 original size:20 final size:20
Alignment explanation
Indices: 83830--83899 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
83820 AAAAAGAAAG
* *
83830 AAAGGAGGAGGGAACACCGT
1 AAAGGAGGAGGGAACACTGC
83850 AAAGGAGGAGGGAACACTGC
1 AAAGGAGGAGGGAACACTGC
83870 AAAGGAGGAGGGAACACTGC
1 AAAGGAGGAGGGAACACTGC
83890 AAAGGAGGAG
1 AAAGGAGGAG
83900 AACGAGAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.41, T:0.04
Consensus pattern (20 bp):
AAAGGAGGAGGGAACACTGC
Found at i:85527 original size:13 final size:13
Alignment explanation
Indices: 85509--85550 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
85499 AATGACACGC
85509 AATGTAAGTCATA
1 AATGTAAGTCATA
85522 AATGTAAGTCATA
1 AATGTAAGTCATA
*
85535 AATGCAAGTCATA
1 AATGTAAGTCATA
85548 AAT
1 AAT
85551 TTATGGCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:87821 original size:8 final size:8
Alignment explanation
Indices: 87798--87828 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
87788 CTCTTTAAAC
87798 TTTTTATT
1 TTTTTATT
87806 TCTTTTATT
1 T-TTTTATT
87815 TTTTTATT
1 TTTTTATT
87823 TTTTTA
1 TTTTTA
87829 CTAACCCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:89070 original size:17 final size:17
Alignment explanation
Indices: 89038--89080 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
89028 TAAGAGTTAA
* *
89038 TTTAATAAACGAACTAG
1 TTTAATGAATGAACTAG
*
89055 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
89072 TTTAATGAA
1 TTTAATGAA
89081 CTACTTCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:97278 original size:90 final size:90
Alignment explanation
Indices: 97172--97338 Score: 284
Period size: 90 Copynumber: 1.9 Consensus size: 90
97162 ATTTAATCTC
* *
97172 AATTAATTAAATATAGATTTATTTAATTTGAAATAGT-AAAATCCTTAATATGATTAGGGTAACT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCC-TAATATGATTAGGGTAACT
97236 TGGA-TATAAAAGGATTGTTAAATTCT
65 T-GACTATAAAAGGATTGTTAAATTCT
97262 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGGGTAACTT
97327 GACTATAAAAGG
66 GACTATAAAAGG
97339 GTGTGTTAGG
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
89 2 0.03
90 64 0.88
91 7 0.10
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.38
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAGGGTAACTT
GACTATAAAAGGATTGTTAAATTCT
Found at i:106722 original size:34 final size:35
Alignment explanation
Indices: 106651--106747 Score: 115
Period size: 34 Copynumber: 2.7 Consensus size: 35
106641 GTGCTTGTGG
* * * *
106651 ATCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCTAT-TTTAGGAGTTTGAATCCTAGCAAAAGTCT
*
106687 ATCTATTTTAGGAG-TTGAATCCTAGCAGAAGTCT
1 ATCTATTTTAGGAGTTTGAATCCTAGCAAAAGTCT
*
106721 ATCTATTTTTGAGAGTTTGAATCCTAG
1 ATCTATTTTAG-GAGTTTGAATCCTAG
106748 TAGGACGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 25 0.47
35 11 0.21
36 17 0.32
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (35 bp):
ATCTATTTTAGGAGTTTGAATCCTAGCAAAAGTCT
Found at i:114216 original size:21 final size:22
Alignment explanation
Indices: 114168--114216 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
114158 ACAACTCTAA
*
114168 AACATCAACAACATCAAAATCT
1 AACATCAACAACATCAAAACCT
*
114190 ATCATCAA-AACAT-AAAACCCT
1 AACATCAACAACATCAAAA-CCT
114211 AACATC
1 AACATC
114217 CCCTTCATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (22 bp):
AACATCAACAACATCAAAACCT
Found at i:121878 original size:29 final size:30
Alignment explanation
Indices: 121810--121879 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
121800 AAAATAATAA
*
121810 TTTGGTC-CTTAAACTTTCCAAACTTTATAT
1 TTTGGTCAC-TAAACTTTCCAAACTTTACAT
* *
121840 TTTAGACACTAAACTTT-CAAACTTTACAT
1 TTTGGTCACTAAACTTTCCAAACTTTACAT
121869 TTTGGTCACTA
1 TTTGGTCACTA
121880 TAAAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 20 0.59
30 13 0.38
31 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTGGTCACTAAACTTTCCAAACTTTACAT
Found at i:126116 original size:50 final size:50
Alignment explanation
Indices: 126020--126116 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 50
126010 CTCTAAAGGG
* *
126020 TGTGTTTGATAGTTGAAAAATATTTACATAAAAAGTTTTCCTTGTTTTCT
1 TGTGTTTGATAGATGAAAAATATTTACATAAAAAGTTTTCCGTGTTTTCT
* *
126070 TGTGTTTGATAGATG-AAAATATTTTCCA-AAAATGTTTTCCAGTGTTT
1 TGTGTTTGATAGATGAAAAATA-TTTACATAAAAAGTTTTCC-GTGTTT
126117 GATAATTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 17 0.41
50 24 0.59
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (50 bp):
TGTGTTTGATAGATGAAAAATATTTACATAAAAAGTTTTCCGTGTTTTCT
Found at i:126321 original size:11 final size:11
Alignment explanation
Indices: 126302--126332 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
126292 TATATTATTT
*
126302 TATTTATTTAA
1 TATTAATTTAA
126313 TATTAATTTAA
1 TATTAATTTAA
126324 TATTAATTT
1 TATTAATTT
126333 CATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:126436 original size:23 final size:22
Alignment explanation
Indices: 126387--126439 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
126377 ATATTTTTAG
126387 TATTATA-TTAATATGTACTCA
1 TATTATATTTAATATGTACTCA
*
126408 TA-TATATTATAATAATGTA-TGA
1 TATTATATT-TAAT-ATGTACTCA
126430 TATTATATTT
1 TATTATATTT
126440 TGAATTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.15
21 3 0.11
22 9 0.33
23 11 0.41
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (22 bp):
TATTATATTTAATATGTACTCA
Found at i:126870 original size:15 final size:15
Alignment explanation
Indices: 126852--126902 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
126842 AAAACATATT
*
126852 AATTTTACGTAAAAC
1 AATTTTACATAAAAC
*
126867 AATTTT-CATATAATTC
1 AATTTTACATA-AA-AC
126883 -ATTTTACATAAAAC
1 AATTTTACATAAAAC
126897 AATTTT
1 AATTTT
126903 CAAGTAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 4 0.14
15 20 0.69
16 5 0.17
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (15 bp):
AATTTTACATAAAAC
Found at i:126887 original size:30 final size:30
Alignment explanation
Indices: 126853--126921 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
126843 AAACATATTA
126853 ATTTTACGTAAAACAATTTTCATA-TAAT-T
1 ATTTTACGTAAAACAATTTTCA-AGTAATCT
*
126882 CATTTTACATAAAACAATTTTCAAGTAATCT
1 -ATTTTACGTAAAACAATTTTCAAGTAATCT
126913 ATTTTACGT
1 ATTTTACGT
126922 TTATTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTTTACGTAAAACAATTTTCAAGTAATCT
Found at i:128158 original size:49 final size:49
Alignment explanation
Indices: 128104--128202 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 49
128094 TTTAAGATAG
* * *
128104 AATATATA-TATTAATAACATAAAATAA-TGA-TAAATATAAAATTTGAA
1 AATATATATTATTAATAAAAT-AAATAACTAATTAAAAATAAAATTTGAA
*
128151 AATATATATTATTAATAAAATAAATAACTAATTAAAAATAAAATTTTAA
1 AATATATATTATTAATAAAATAAATAACTAATTAAAAATAAAATTTGAA
128200 AAT
1 AAT
128203 CAGCACGCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
47 14 0.31
48 13 0.29
49 18 0.40
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (49 bp):
AATATATATTATTAATAAAATAAATAACTAATTAAAAATAAAATTTGAA
Found at i:132475 original size:17 final size:17
Alignment explanation
Indices: 132427--132475 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
132417 GCAATATTGC
*
132427 TCTTATCGCAGTGTCAT
1 TCTTCTCGCAGTGTCAT
* *
132444 TCTCCTCGTAGTGTCAT
1 TCTTCTCGCAGTGTCAT
*
132461 TCTTCTCGCAATGTC
1 TCTTCTCGCAGTGTC
132476 GCTCCCATCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (17 bp):
TCTTCTCGCAGTGTCAT
Found at i:132624 original size:3 final size:3
Alignment explanation
Indices: 132605--132646 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
132595 AGGTAATTTC
* * *
132605 ATT ATT A-T ATA AAT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
132647 GAAATCCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:135205 original size:91 final size:91
Alignment explanation
Indices: 135050--135232 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
135040 GCTAGAACAC
* * *
135050 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAACCCCCATATGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
135115 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
** * * *
135141 CCATGTGTTTTGCATGTGATCAACCCCCATATGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAACCCCCATATGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
135206 AAGAGTTCTCTCCCTATTCGACCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
135232 C
1 C
135233 ATCAACTACC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAACCCCCATATGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGACCAAG
Found at i:138921 original size:22 final size:22
Alignment explanation
Indices: 138866--138927 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
138856 AATTTTTTCA
* * *
138866 CCGAAGTGCCACATAGGTTTTTC
1 CCGAAGTACCACATA-GATTATC
* *
138889 TCGAAGGACCACATAGATTATC
1 CCGAAGTACCACATAGATTATC
138911 CCGAAGTACCACATAGA
1 CCGAAGTACCACATAGA
138928 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (22 bp):
CCGAAGTACCACATAGATTATC
Found at i:139822 original size:20 final size:20
Alignment explanation
Indices: 139797--139848 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
139787 TACTTAATAA
*
139797 CAGTATCGATACCTTACTCTT
1 CAGTATCGATACCTCACT-TT
* *
139818 -GGTATTGATACCTCACTTT
1 CAGTATCGATACCTCACTTT
139837 CAGTATCGATAC
1 CAGTATCGATAC
139849 TAATTCAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (20 bp):
CAGTATCGATACCTCACTTT
Found at i:144636 original size:23 final size:23
Alignment explanation
Indices: 144584--144638 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
144574 CAGCTCATAT
* *
144584 AAATTCACCGAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACGTAG
** *
144607 ATTTGCACCAAAGTGCCGCGTAG
1 AAATGCACCAAAGTGCCACGTAG
144630 AAATGCACC
1 AAATGCACC
144639 GTAGTTCCGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACGTAG
Found at i:151346 original size:23 final size:23
Alignment explanation
Indices: 151313--151376 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
151303 TAGCTGATAT
151313 AAATACACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
** *
151336 ATTTACACCGAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
151359 AAATACACCGTAGTGCCA
1 AAATACACCGAAGTGCCA
151377 TATATAATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:152531 original size:15 final size:15
Alignment explanation
Indices: 152511--152563 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
152501 TTTCCTAGTC
152511 CATTTTTCCTTCCAT
1 CATTTTTCCTTCCAT
152526 CATTTTTCCTTCCAT
1 CATTTTTCCTTCCAT
152541 --TTTTTCCTTCCAT
1 CATTTTTCCTTCCAT
152554 CATTTTTCCT
1 CATTTTTCCT
152564 AAAGCTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.36
15 23 0.64
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.57
Consensus pattern (15 bp):
CATTTTTCCTTCCAT
Found at i:152550 original size:28 final size:27
Alignment explanation
Indices: 152509--152563 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 27
152499 AGTTTCCTAG
152509 TCCATTTTTCCTTCCATCATTTTTCCT
1 TCCATTTTTCCTTCCATCATTTTTCCT
152536 TCCATTTTTTCCTTCCATCATTTTTCCT
1 TCCA-TTTTTCCTTCCATCATTTTTCCT
152564 AAAGCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (27 bp):
TCCATTTTTCCTTCCATCATTTTTCCT
Found at i:157537 original size:21 final size:22
Alignment explanation
Indices: 157513--157558 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
157503 ACAGCTGATA
157513 TAAA-TGCACCGAAGAGCAGCG
1 TAAATTGCACCGAAGAGCAGCG
* *
157534 TAAATTTGCACCGAAGTGCCGCG
1 TAAA-TTGCACCGAAGAGCAGCG
157557 TA
1 TA
157559 GAAATACACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (22 bp):
TAAATTGCACCGAAGAGCAGCG
Found at i:159744 original size:23 final size:23
Alignment explanation
Indices: 159661--159778 Score: 72
Period size: 23 Copynumber: 5.3 Consensus size: 23
159651 CACCACAGCT
*
159661 CATA-ATTTGCATCGAAGTG-CA
1 CATAGATTTGCACCGAAGTGCCA
* *
159682 TATA-A-TTGTC-CCGAAGGGCCA
1 CATAGATTTG-CACCGAAGTGCCA
* *
159703 CATAAGTTTTGTACCGAAGTGCCA
1 CAT-AGATTTGCACCGAAGTGCCA
*
159727 CATAGATTTGCACTGAAGTGCCA
1 CATAGATTTGCACCGAAGTGCCA
*
159750 TATAGGATTAT-C-CCGAAG-GACCA
1 CATA-GATT-TGCACCGAAGTG-CCA
159773 CATAGA
1 CATAGA
159779 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
20 9 0.12
21 9 0.12
22 4 0.05
23 31 0.41
24 21 0.28
25 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (23 bp):
CATAGATTTGCACCGAAGTGCCA
Found at i:164050 original size:7 final size:7
Alignment explanation
Indices: 164005--164053 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
163995 TTCTACTAAA
*
164005 ATTTTAA
1 ATTTTAT
164012 ATTTTGAT
1 ATTTT-AT
164020 ATATTTCAAT
1 AT-TTT--AT
164030 ATTTTAT
1 ATTTTAT
164037 ATTTTAT
1 ATTTTAT
164044 ATTTTAT
1 ATTTTAT
164051 ATT
1 ATT
164054 AAAACTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 24 0.65
8 3 0.08
9 6 0.16
10 4 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (7 bp):
ATTTTAT
Found at i:167088 original size:3 final size:3
Alignment explanation
Indices: 167082--167126 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
167072 AAAAGACACA
**
167082 AAT AAT AAT AAT AAT AAT AAT AAT AATT GTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA
167127 CAAGCTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.97
4 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:167238 original size:27 final size:25
Alignment explanation
Indices: 167199--167249 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
167189 TCTTTAAAAA
167199 ATATATTACATGTTTTTTGAAAACTAT
1 ATATATTACATG-TTTTT-AAAACTAT
* *
167226 ATATGTTATATGTTTTTAAAACTA
1 ATATATTACATGTTTTTAAAACTA
167250 CAAATATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 5 0.23
27 10 0.45
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (25 bp):
ATATATTACATGTTTTTAAAACTAT
Found at i:167321 original size:27 final size:24
Alignment explanation
Indices: 167253--167397 Score: 112
Period size: 22 Copynumber: 6.3 Consensus size: 24
167243 AAAACTACAA
*
167253 ATATGTTTTAAAAAAC--TATATT
1 ATATATTTTAAAAAACTATATATT
167275 ATATATTTTAAAAAACTATATATT
1 ATATATTTTAAAAAACTATATATT
**
167299 ATATTATTTTTTAAAACTATATA--
1 ATA-TATTTTAAAAAACTATATATT
* *
167322 ATATGTTTTCAAAAACTATACTA-T
1 ATATATTTTAAAAAACTATA-TATT
* *
167346 ATAT-TTTT-AAAACCCATATA-T
1 ATATATTTTAAAAAACTATATATT
*
167367 -TAT-TTTTAGACAAAGCTATATATT
1 ATATATTTTA-A-AAAACTATATATT
167391 ATATATT
1 ATATATT
167398 ATCATATATT
Statistics
Matches: 102, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.07
21 3 0.03
22 38 0.37
23 18 0.18
24 14 0.14
25 20 0.20
26 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (24 bp):
ATATATTTTAAAAAACTATATATT
Found at i:167365 original size:69 final size:68
Alignment explanation
Indices: 167149--167369 Score: 236
Period size: 69 Copynumber: 3.2 Consensus size: 68
167139 ATATTTAAAA
* * * * * * *
167149 AAAACTATATAATATATTATATTTTCAAAACCATATAATAT-CTTTAAAAAATATATTACATGTT
1 AAAACTATATATTATATTATATTTTTAAAACTATATAATATGTTTTAAAAACTATATTATAT-AT
167213 TTTT
65 TTTT
* *
167217 GAAAACTATATATGT-TA-TATGTTTTTAAAACTACA-AATATGTTTTAAAAAACTATATTATAT
1 -AAAACTATATAT-TATATTATATTTTTAAAACTATATAATATGTTTT-AAAAACTATATTATAT
*
167279 ATTTTAA
63 ATTTT-T
*
167286 AAAACTATATATTATATTAT-TTTTTAAAACTATATAATATGTTTTCAAAAACTATACTATATAT
1 AAAACTATATATTATATTATATTTTTAAAACTATATAATATGTTTT-AAAAACTATATTATATAT
167350 TTTT
65 TTTT
*
167354 AAAACCCATATATTAT
1 AAAA-CTATATATTAT
167370 TTTTAGACAA
Statistics
Matches: 129, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
67 6 0.05
68 52 0.40
69 70 0.54
70 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (68 bp):
AAAACTATATATTATATTATATTTTTAAAACTATATAATATGTTTTAAAAACTATATTATATATT
TTT
Found at i:167372 original size:20 final size:19
Alignment explanation
Indices: 167298--167374 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 19
167288 AACTATATAT
167298 TATATTATTTTTTAAAACTA
1 TATATTA-TTTTTAAAACTA
*
167318 TATAATATGTTTTCAAAAACTA
1 TATATTAT-TTTT--AAAACTA
*
167340 TACTATATATTTTTAAAACCCA
1 TA-TAT-TATTTTTAAAA-CTA
167362 TATATTATTTTTA
1 TATATTATTTTTA
167375 GACAAAGCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.02
20 18 0.38
21 7 0.15
22 13 0.27
23 6 0.12
24 3 0.06
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (19 bp):
TATATTATTTTTAAAACTA
Found at i:167389 original size:69 final size:69
Alignment explanation
Indices: 167243--167388 Score: 172
Period size: 69 Copynumber: 2.2 Consensus size: 69
167233 ATATGTTTTT
* * *
167243 AAAACTACA-AATATGTTTTAAAAAACTATATTATATATTTTAAAAAACTATATATTATATTATT
1 AAAACTATATAATATGTTTTAAAAAACTATACTATATATTTTAAAAAACCATATATTATATTATT
****
167307 TTTT
66 AGAC
* * *
167311 AAAACTATATAATATGTTTTCAAAAACTATACTATATATTTTTAAAACCCATATATTAT-TT-TT
1 AAAACTATATAATATGTTTTAAAAAACTATACTATATATTTTAAAAAACCATATATTATATTATT
167374 AGAC
66 AGAC
*
167378 AAAGCTATATA
1 AAAACTATATA
167389 TTATATATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
67 12 0.18
68 10 0.15
69 44 0.67
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (69 bp):
AAAACTATATAATATGTTTTAAAAAACTATACTATATATTTTAAAAAACCATATATTATATTATT
AGAC
Found at i:168075 original size:223 final size:225
Alignment explanation
Indices: 167740--168271 Score: 628
Period size: 223 Copynumber: 2.4 Consensus size: 225
167730 GTTTCGGAAT
* * * * * *
167740 AAGAATCCTCCATTATGAAGTTGAAATTTGGC-TTGAAAAC-TGACTGAAAACTAGCTCATCGCC
1 AAGAATCCTCCGTTGTGAAGTTGAGACTTGGCATAGAAACCTTGACTGAAAACTAGCTCATCGCC
* *** * ** *
167803 GTTGAGTTAAGCTAGAATGCAGTGGATTCTGGAATGGTTTTTGAACCCAAAATCCGCCCTCGTGG
66 GCTGAGTTAAGCTAGAATGCAGCCAATTCTGGAATGATTTTCAAACCCAAAATCCGCCCTCATGG
* * *
167868 AGTTGAGATTGACTTCGAAGAGATTTGATTGGAAGATGGATCATCG-CAACTGAGTTAAACCAAA
131 AGTTGAGATTGAATTCGAAGAGATTTGACTGGAAAATGGATCATCGTC-ACTGAGTTAAACCAAA
* *
167932 ATACAG-CCATTTTGGATGCGTTTCTGGGTC
195 ATACAGTCCATTATGGATACGTTTCTGGGTC
* * * *
167962 AAGAATCCT-CTTTCGTGAAGTTGAGACTTGGCCA-A-AAACTTTGACTGGAAACTAGATCATCG
1 AAGAATCCTCCGTT-GTGAAGTTGAGACTTGG-CATAGAAACCTTGACTGAAAACTAGCTCATCG
* * **
168024 CCGCTGAGTTAAGCTAGAATGCAGCCAATTTTGGAATGATTTTCAAACCCAAAATCCTCTTTCAT
64 CCGCTGAGTTAAGCTAGAATGCAGCCAATTCTGGAATGATTTTCAAACCCAAAATCCGCCCTCAT
* * * *
168089 TGAGTTGAGATTGAATTCGAAGAGATTTGACTGGAAAATGGCTCCTCGTCGCTGAGTTAAACCAA
129 GGAGTTGAGATTGAATTCGAAGAGATTTGACTGGAAAATGGATCATCGTCACTGAGTTAAACCAA
* ***
168154 AATGCAGTTGGTTATGGATACGTTTCTGGGTC
194 AATACAGTCCATTATGGATACGTTTCTGGGTC
* *
168186 AAGAATCCTCCGTTGTGAAGTTGAGACTTGGCATAGAAACCTTGACTGTAAACTAGCTCCTCGCC
1 AAGAATCCTCCGTTGTGAAGTTGAGACTTGGCATAGAAACCTTGACTGAAAACTAGCTCATCGCC
* * *
168251 GCTAAGTTAAGATAAAATGCA
66 GCTGAGTTAAGCTAGAATGCA
168272 ATCTATTTTG
Statistics
Matches: 259, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
221 3 0.01
222 26 0.10
223 137 0.53
224 47 0.18
225 46 0.18
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (225 bp):
AAGAATCCTCCGTTGTGAAGTTGAGACTTGGCATAGAAACCTTGACTGAAAACTAGCTCATCGCC
GCTGAGTTAAGCTAGAATGCAGCCAATTCTGGAATGATTTTCAAACCCAAAATCCGCCCTCATGG
AGTTGAGATTGAATTCGAAGAGATTTGACTGGAAAATGGATCATCGTCACTGAGTTAAACCAAAA
TACAGTCCATTATGGATACGTTTCTGGGTC
Found at i:168158 original size:113 final size:109
Alignment explanation
Indices: 167862--168160 Score: 264
Period size: 113 Copynumber: 2.7 Consensus size: 109
167852 AAATCCGCCC
* * *
167862 TCGTGGAGTTGAGATTGACTTCGAAGAGATTTGATTGGAAGATGGATCATCGCAACTGAGTTAAA
1 TCGT-GAGTTGAGATTGA-TTCGAAGAGATTTGACTGGAAAATGGATCATCGC-GCTGAGTTAAA
* * *****
167927 CCAAAATACAGCCATTTTGGATGCGTTTCTGGGTCAAGAATCCTCTT
63 CCAAAATGCAGCCATTTTGGATGAGTTTCAAACCCAAGAATCCTCTT
* * * * *
167974 TCGTGAAGTTGAGACTTG--GCCAA-AAACTTTGACTGGAAACTAGATCATCGCCGCTGAGTTAA
1 TCGTG-AGTTGAGA-TTGATTCGAAGAGA-TTTGACTGGAAAATGGATCATCG-CGCTGAGTTAA
* * * *
168036 GCTAGAATGCAGCCAATTTTGGAATGATTTTCAAACCCAA-AATCCTCTT
62 ACCAAAATGCAGCC-ATTTTGG-ATGAGTTTCAAACCCAAGAATCCTCTT
* * *
168085 TCATTGAGTTGAGATTGAATTCGAAGAGATTTGACTGGAAAATGGCTCCTCGTCGCTGAGTTAAA
1 TC-GTGAGTTGAGATTG-ATTCGAAGAGATTTGACTGGAAAATGGATCATCG-CGCTGAGTTAAA
168150 CCAAAATGCAG
63 CCAAAATGCAG
168161 TTGGTTATGG
Statistics
Matches: 145, Mismatches: 31, Indels: 21
0.74 0.16 0.11
Matches are distributed among these distances:
109 2 0.01
110 44 0.30
111 28 0.19
112 24 0.17
113 45 0.31
114 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (109 bp):
TCGTGAGTTGAGATTGATTCGAAGAGATTTGACTGGAAAATGGATCATCGCGCTGAGTTAAACCA
AAATGCAGCCATTTTGGATGAGTTTCAAACCCAAGAATCCTCTT
Found at i:175482 original size:314 final size:314
Alignment explanation
Indices: 174913--175540 Score: 1229
Period size: 314 Copynumber: 2.0 Consensus size: 314
174903 AATAATTGGT
174913 TACTTCTAATTTTTAAGGATGACAATATTTCATTATTTCAATTAAAACATAAAAAATAATCACCT
1 TACTTCTAATTTTTAAGGATGACAATATTTCATTATTTCAATTAAAACATAAAAAATAATCACCT
174978 TAATTCCGATTAGGGGATTAGTTCCTTTTTTTAATTGGAAACAGACAAATATTGTACGTCTCACT
66 TAATTCCGATTAGGGGATTAGTTCCTTTTTTTAATTGGAAACAGACAAATATTGTACGTCTCACT
*
175043 AAAATTTTAAAGTATTCTTTTTAAGAAAGGAAAAGATCATTAATTAAATATATATTCGAATTTCT
131 AAAATTTTAAAGTATTCTTTTTAAGAAAAGAAAAGATCATTAATTAAATATATATTCGAATTTCT
175108 TAATTTTTAATACAGAGACAAATTTATAATCGTAGGTACCAATTTTTCGTCATTGTGGGGGTGCA
196 TAATTTTTAATACAGAGACAAATTTATAATCGTAGGTACCAATTTTTCGTCATTGTGGGGGTGCA
175173 AATCCTTCCCCAAGCGTAATCGAATCCTGAACCCAAAATATCTGAATCGCAGAC
261 AATCCTTCCCCAAGCGTAATCGAATCCTGAACCCAAAATATCTGAATCGCAGAC
175227 TACTTCTAATTTTTAAGGATGACAATATTTCATTATTTCAATTAAAACATAAAAAATAATCACCT
1 TACTTCTAATTTTTAAGGATGACAATATTTCATTATTTCAATTAAAACATAAAAAATAATCACCT
*
175292 TAATTCCGATTAGGGGATTAGTTCCTTTTTTTAATTGGAAACAGACAAATATTGTGCGTCTCACT
66 TAATTCCGATTAGGGGATTAGTTCCTTTTTTTAATTGGAAACAGACAAATATTGTACGTCTCACT
*
175357 AAAATTTTAAAGTATTCTTTTTAGGAAAAGAAAAGATCATTAATTAAATATATATTCGAATTTCT
131 AAAATTTTAAAGTATTCTTTTTAAGAAAAGAAAAGATCATTAATTAAATATATATTCGAATTTCT
175422 TAATTTTTAATACAGAGACAAATTTATAATCGTAGGTACCAATTTTTCGTCATTGTGGGGGTGCA
196 TAATTTTTAATACAGAGACAAATTTATAATCGTAGGTACCAATTTTTCGTCATTGTGGGGGTGCA
175487 AATCCTTCCCCAAGCGTAATCGAATCCTGAACCCAAAATATCTGAATCGCAGAC
261 AATCCTTCCCCAAGCGTAATCGAATCCTGAACCCAAAATATCTGAATCGCAGAC
175541 CAAAACGTGT
Statistics
Matches: 311, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 311 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (314 bp):
TACTTCTAATTTTTAAGGATGACAATATTTCATTATTTCAATTAAAACATAAAAAATAATCACCT
TAATTCCGATTAGGGGATTAGTTCCTTTTTTTAATTGGAAACAGACAAATATTGTACGTCTCACT
AAAATTTTAAAGTATTCTTTTTAAGAAAAGAAAAGATCATTAATTAAATATATATTCGAATTTCT
TAATTTTTAATACAGAGACAAATTTATAATCGTAGGTACCAATTTTTCGTCATTGTGGGGGTGCA
AATCCTTCCCCAAGCGTAATCGAATCCTGAACCCAAAATATCTGAATCGCAGAC
Found at i:177755 original size:18 final size:17
Alignment explanation
Indices: 177732--177769 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
177722 TCAATTTTTA
177732 TCATTTTATTGTTAATAT
1 TCATTTTA-TGTTAATAT
*
177750 TCA-TTTATGTTTATAT
1 TCATTTTATGTTAATAT
177766 TCAT
1 TCAT
177770 ATCCATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 11 0.61
17 4 0.22
18 3 0.17
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (17 bp):
TCATTTTATGTTAATAT
Found at i:177765 original size:16 final size:17
Alignment explanation
Indices: 177736--177769 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
177726 TTTTTATCAT
177736 TTTATTGTTAATATTCA
1 TTTATTGTTAATATTCA
*
177753 TTTA-TGTTTATATTCA
1 TTTATTGTTAATATTCA
177769 T
1 T
177770 ATCCATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTATTGTTAATATTCA
Found at i:178917 original size:19 final size:20
Alignment explanation
Indices: 178893--178941 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
178883 TTTATGTTTG
178893 TCACATATACACA-TTCATA
1 TCACATATACACATTTCATA
*
178912 TCACATAGT-CATATTTTCATA
1 TCACATA-TACACA-TTTCATA
178933 TCACATATA
1 TCACATATA
178942 TCTTGTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (20 bp):
TCACATATACACATTTCATA
Found at i:189824 original size:59 final size:57
Alignment explanation
Indices: 189648--189935 Score: 197
Period size: 59 Copynumber: 4.9 Consensus size: 57
189638 ACATTCCATA
* ** * *
189648 GGAAATTCATACCATTAGTATGATTTTGTTACCATTTTAGCACATGAAATGCCCTATGT
1 GGAAATCCATA-CATTAGTATGATTTCCTTATCATTTTAGCACAT-AAATGCCCTATCT
* * * * * **
189707 GAAAATCCATTCCATTAGTATGATTTCCTTATC-TTTGTAGCACCCTTAGTGCTTTATCT
1 GGAAATCCA-TACATTAGTATGATTTCCTTATCATTT-TAGCA-CATAAATGCCCTATCT
*
189766 GGAAATCCATACATTCAGTATGATTCCCTTA-CGATTTTAGCACATAAAATGCCCTATCT
1 GGAAATCCATACATT-AGTATGATTTCCTTATC-ATTTTAGCACAT-AAATGCCCTATCT
** * * * *
189825 GGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACTCAGTGCTCC-ATAT
1 GGAAATCCATACATT-AGTATGATTTCCTTATCATTTTAGCACA-TAAATGC-CCTATCT
* * * * * * *
189883 GAAAATCTATACACTCAATATGATTTTCTTATCTTTTTAGCACACAAAGTGCC
1 GGAAATCCATACA-TTAGTATGATTTCCTTATCATTTTAGCACATAAA-TGCC
189936 ATTCGGTAAT
Statistics
Matches: 179, Mismatches: 37, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
58 54 0.30
59 118 0.66
60 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (57 bp):
GGAAATCCATACATTAGTATGATTTCCTTATCATTTTAGCACATAAATGCCCTATCT
Found at i:189856 original size:118 final size:116
Alignment explanation
Indices: 189648--189876 Score: 282
Period size: 118 Copynumber: 1.9 Consensus size: 116
189638 ACATTCCATA
* *** * *
189648 GGAAATTCATACCATTAGTATGATTTTGTTACCATTTTAGCACATGAAATGCCCTATGTGAAAAT
1 GGAAATCCATACCATTAGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAAT
* * * *
189713 CCATTCCATTAGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCT
66 CCATT-CATTAATATGATTTCCTTATCATT-TAGCACACTCAGTGCTTTATCT
* *
189766 GGAAATCCATA-CATTCAGTATGATTCCCTTACGATTTTAGCACATAAAATGCCCTATCTGGAAA
1 GGAAATCCATACCATT-AGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAA
*
189830 TCCATAT-TTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCT
65 TCCAT-TCATT-AATATGATTTCCTTATCATTTAGCACACTCAGTGCT
189877 CCATATGAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
117 20 0.21
118 74 0.78
119 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (116 bp):
GGAAATCCATACCATTAGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAAT
CCATTCATTAATATGATTTCCTTATCATTTAGCACACTCAGTGCTTTATCT
Found at i:201914 original size:262 final size:267
Alignment explanation
Indices: 201401--201935 Score: 883
Period size: 261 Copynumber: 2.0 Consensus size: 267
201391 TCAGAGCTTT
*
201401 GGTGGAAGAAGTAAGTGCACAACAACAAAAATACAAAAAAAAAAAAAATTGCAAGTGAAAAGAAT
1 GGTGGAAGAAGTAAGTG-ACAACAACAAAAATACAAAAAAAAAAAAAAGTGCAAGTG--AAGAA-
201466 CAAGAAAATCAGCAAAGAAATTGCAAGCACCAAAAAGATAAAAAATAAAAAGAAGAAAAGAAAAA
62 CAAGAAAATCAGCAAAGAAATTGCAAGCACCAAAAAGATAAAAAATAAAAAGAAGAAAAG-AAAA
201531 AAAAAATAAAAAGTTGAAAAGCACACAACAACAACAAGTCTCATCTCAAGCCATTAAAGCCTTGA
126 AAAAAATAAAAAGTTGAAAAGCACACAACAACAACAAGTCTCATCTCAAGCCATTAAAGCCTTGA
201596 AAATTGATGTGGTGATAGAAGGGTTGTGAATTAACTTTGTGTAAGTAACCCATTTATT-TC-TAT
191 AAATTGATGTGGTGATAGAAGGGTTGTGAATTAACTTTGTGTAAGTAACCCATTTATTCTCTTAT
201659 TT-TA-TTCTAA
256 TTCTATTTCTAA
201669 GGTGGAAGAAGTAACGTG-CAACAACAAAAATACAAAAAAAAAAAAAAGTGCAAGTG-A-AA-AA
1 GGTGGAAGAAGTAA-GTGACAACAACAAAAATACAAAAAAAAAAAAAAGTGCAAGTGAAGAACAA
201730 GAAAATCAGCAAAGAAATTGCAAGCACTCAAAAAGAT-AAAAATAAAAAGAAGAAGAAG-AAAAA
65 GAAAATCAGCAAAGAAATTGCAAGCAC-CAAAAAGATAAAAAATAAAAAGAAGAA-AAGAAAAAA
* *
201793 GAAATAAAAAGTTGAAAAGCACACAACAACAACAAGTCTCATCATCAAGCCATTCAAGCCTTGAA
128 AAAATAAAAAGTTGAAAAGCACACAACAACAACAAGTCTCATC-TCAAGCCATTAAAGCCTTGAA
201858 AATTGATTGTGGTGATAGAAGGGTTGTGAATTAACTTTGTGTAAGTAACCCATTTATTCTCTTAT
192 AATTGA-TGTGGTGATAGAAGGGTTGTGAATTAACTTTGTGTAAGTAACCCATTTATTCTCTTAT
201923 TTCTATTTCTAA
256 TTCTATTTCTAA
201935 G
1 G
201936 CCACCCTTTC
Statistics
Matches: 255, Mismatches: 3, Indels: 20
0.92 0.01 0.07
Matches are distributed among these distances:
260 47 0.18
261 72 0.28
262 63 0.25
263 4 0.02
264 6 0.02
265 2 0.01
266 7 0.03
267 37 0.15
268 14 0.05
269 3 0.01
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (267 bp):
GGTGGAAGAAGTAAGTGACAACAACAAAAATACAAAAAAAAAAAAAAGTGCAAGTGAAGAACAAG
AAAATCAGCAAAGAAATTGCAAGCACCAAAAAGATAAAAAATAAAAAGAAGAAAAGAAAAAAAAA
ATAAAAAGTTGAAAAGCACACAACAACAACAAGTCTCATCTCAAGCCATTAAAGCCTTGAAAATT
GATGTGGTGATAGAAGGGTTGTGAATTAACTTTGTGTAAGTAACCCATTTATTCTCTTATTTCTA
TTTCTAA
Found at i:242550 original size:24 final size:26
Alignment explanation
Indices: 242502--242556 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
242492 CAATATTAAG
*
242502 CATAAAAAAACTTCTTCATTCAAAAA
1 CATAAAAAAACATCTTCATTCAAAAA
* *
242528 CATAAAATAACAT-TTCATT-AAAAC
1 CATAAAAAAACATCTTCATTCAAAAA
242552 CATAA
1 CATAA
242557 CCAACACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 6 0.23
26 11 0.42
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (26 bp):
CATAAAAAAACATCTTCATTCAAAAA
Found at i:248340 original size:17 final size:16
Alignment explanation
Indices: 248309--248342 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
248299 CACGTGAGGA
248309 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
248325 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
248342 T
1 T
248343 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:259222 original size:1 final size:1
Alignment explanation
Indices: 259218--259260 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
259208 AATCAAAATC
* * * *
259218 AAAAAAATAAAAAAAAATAAAAAAAAAAAGAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
259261 GTTTAAAGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.00, G:0.05, T:0.05
Consensus pattern (1 bp):
A
Found at i:259230 original size:9 final size:9
Alignment explanation
Indices: 259212--259260 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
259202 TCAAAAAATC
*
259212 AAAATCAAA
1 AAAATAAAA
259221 AAAATAAAAA
1 AAAAT-AAAA
259231 AAAATAAAA
1 AAAATAAAA
*
259240 AAAA-AAAG
1 AAAATAAAA
*
259248 AAAAGAAAA
1 AAAATAAAA
259257 AAAA
1 AAAA
259261 GTTTAAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.20
9 20 0.57
10 8 0.23
ACGTcount: A:0.88, C:0.02, G:0.04, T:0.06
Consensus pattern (9 bp):
AAAATAAAA
Found at i:259239 original size:17 final size:17
Alignment explanation
Indices: 259218--259260 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
259208 AATCAAAATC
* *
259218 AAAAAAATAAAAAAAAAT
1 AAAAAAA-AAAAGAAAAG
259236 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
259253 AAAAAAAA
1 AAAAAAAA
259261 GTTTAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.91, C:0.00, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:269202 original size:27 final size:28
Alignment explanation
Indices: 269151--269203 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
269141 AACCTAAGGG
*
269151 AGTACCTTAGGGCCTTATAGCCTACCTA
1 AGTACCTTAGGGCCTTAAAGCCTACCTA
* *
269179 AGTACC-TCGGGCCTTAAAGTCTACC
1 AGTACCTTAGGGCCTTAAAGCCTACC
269204 CAAAGGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (28 bp):
AGTACCTTAGGGCCTTAAAGCCTACCTA
Found at i:276752 original size:16 final size:16
Alignment explanation
Indices: 276731--276794 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
276721 TACTAATGAG
276731 GCATCAGGTGAGTGCA
1 GCATCAGGTGAGTGCA
276747 GCATCAGGTGAGTGCA
1 GCATCAGGTGAGTGCA
*
276763 GCATCAGGTGAGTACA
1 GCATCAGGTGAGTGCA
*
276779 GCATCATGTGAGTGCA
1 GCATCAGGTGAGTGCA
276795 TCTTACTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (16 bp):
GCATCAGGTGAGTGCA
Found at i:282021 original size:13 final size:13
Alignment explanation
Indices: 281994--282033 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
281984 TTGGTTATGT
*
281994 AAATGAATG-TGA
1 AAATGAAAGATGA
282006 AAATGAAAGATGA
1 AAATGAAAGATGA
*
282019 AAATGAAATATGA
1 AAATGAAAGATGA
282032 AA
1 AA
282034 GTTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (13 bp):
AAATGAAAGATGA
Found at i:284345 original size:16 final size:17
Alignment explanation
Indices: 284307--284352 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
284297 TGTTTATGAG
284307 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
284325 GGAATTAGAATCTGT-A
1 GGAATTGGAATCTGTAA
284341 GGAATTGGAATC
1 GGAATTGGAATC
284353 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:285392 original size:257 final size:253
Alignment explanation
Indices: 284956--285505 Score: 870
Period size: 257 Copynumber: 2.2 Consensus size: 253
284946 GACCTGACCT
* *
284956 GACCCGAATATCACACTTAAAAAATCCGACTCGACCTGAACAAAATAAAGTTTCATCCGACCCGA
1 GACCCGAATATCACACTTAAAAAACCCGACTCGACCCGAACAAAATAAAGTTTCATCCGACCCGA
** *
285021 ATATATGAATTAGAAATCTGACCCGACCCTACCCGAAATAATAAAAAATTATTTTTATTTAATAA
66 ATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAA
*
285086 AAACAGTGACTTAATCTGATCCGACCCGAATTATATATATTTTCGGGTCGGTCC-GGTTTATTCA
131 AAACAGTGACTTAATCCGATCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGGTTTATTCA
* *
285150 CCCTAAACCAGACCCGATCCGACCCGAATATCGCACTTAAAAAAACCCGACCCAACTC
196 CCCTAAACCAGACCCGATCCGACCCGAATATCACACTTAAAAAAAACCGACCCAACTC
* *
285208 GAGCCGAATATCACACTTAAAAAACCCGACTTGACCCGAACAAAATAAAGTTTCATCCGACCCGA
1 GACCCGAATATCACACTTAAAAAACCCGACTCGACCCGAACAAAATAAAGTTTCATCCGA-CC--
**
285273 CTAGAATATATGAATTAGAAATCCAACCCGACCCGACTTGAAATAATAAAAAATTATTTTTATTT
63 C--GAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTT
*
285338 AATAAAAACAGTGACTTAATCCGA-CTCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTT
126 AATAAAAACAGTGACTTAATCCGATC-CGACCCGAATTATATATATTTTCGGGTCGGTCCAGGTT
* * * *
285402 TTTTCACCCTAAACCCGACCCGATCCGACCCGAATATCACACTTAAAAAAAATCGACCCGACTC
190 TATTCACCCTAAACCAGACCCGATCCGACCCGAATATCACACTTAAAAAAAACCGACCCAACTC
*
285466 GACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAA
1 GACCCGAATATCACACTTAAAAAACCCGACTCGACCCGAA
285506 TATATGAATT
Statistics
Matches: 271, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
252 56 0.21
253 2 0.01
255 1 0.00
256 1 0.00
257 113 0.42
258 98 0.36
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (253 bp):
GACCCGAATATCACACTTAAAAAACCCGACTCGACCCGAACAAAATAAAGTTTCATCCGACCCGA
ATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAA
AAACAGTGACTTAATCCGATCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGGTTTATTCA
CCCTAAACCAGACCCGATCCGACCCGAATATCACACTTAAAAAAAACCGACCCAACTC
Found at i:285497 original size:37 final size:39
Alignment explanation
Indices: 285412--285504 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 39
285402 TTTTCACCCT
285412 AAACCCGACCCGA-TCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACTCCGACCCGAATATCACACTTAAAA
**
285450 AAAATCGACCCGACT-CGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACTCCGACCCGAATATCACACTTAAAA
285487 AAACCCGACCCGAC-CCGA
1 AAACCCGACCCGACTCCGA
285505 ATATATGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 18 0.37
38 30 0.61
39 1 0.02
ACGTcount: A:0.39, C:0.38, G:0.12, T:0.12
Consensus pattern (39 bp):
AAACCCGACCCGACTCCGACCCGAATATCACACTTAAAA
Found at i:287610 original size:24 final size:24
Alignment explanation
Indices: 287580--287652 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
287570 ATACATTACC
* * *
287580 TGAATTCTGTTCTAATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* * *
287604 TGGATTCTATTATGATATCTGATA
1 TGAATTCTGTTATGATTTCTGATA
*
287628 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
287652 T
1 T
287653 CTTTGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:290018 original size:2 final size:2
Alignment explanation
Indices: 290011--290039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
290001 AGTTATGCCG
290011 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 T
290040 TTTTTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:290978 original size:29 final size:30
Alignment explanation
Indices: 290946--291014 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
290936 CATTTTACAG
* *
290946 AAATAACACCCT-TTTTAAATTAATTACTA
1 AAATAGCACCCTATTTCAAATTAATTACTA
*
290975 AAATAGCA-CCTATTTCGAATTAATTACTA
1 AAATAGCACCCTATTTCAAATTAATTACTA
291004 AAATAGCACCC
1 AAATAGCACCC
291015 GGTTAACGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 3 0.09
29 30 0.86
30 2 0.06
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATAGCACCCTATTTCAAATTAATTACTA
Found at i:300949 original size:29 final size:30
Alignment explanation
Indices: 300907--300981 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
300897 GTCAACCATT
*
300907 TTACAAAAATAGCACCCT-TTTTAAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
*
300936 TTACTAAAATAGCA-CCTATTTTGAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
*
300965 TTACTAAAATAACACCC
1 TTACTAAAATAGCACCC
300982 GGTCAACGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.88
30 2 0.05
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (30 bp):
TTACTAAAATAGCACCCTATTTTAAATTAA
Found at i:301011 original size:25 final size:24
Alignment explanation
Indices: 300982--301034 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
300972 AATAACACCC
* * *
300982 GGTCAACGGTTGGGTTAACAGTTCG
1 GGTCAACGGTCGGGTCAAC-GGTCG
301007 GGTCAACGGTCGGGTCAACGGTCG
1 GGTCAACGGTCGGGTCAACGGTCG
301031 GGTC
1 GGTC
301035 GGGTCAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.23
Consensus pattern (24 bp):
GGTCAACGGTCGGGTCAACGGTCG
Found at i:301021 original size:12 final size:12
Alignment explanation
Indices: 300982--301034 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
300972 AATAACACCC
*
300982 GGTCAACGGTTG
1 GGTCAACGGTCG
* *
300994 GGTTAACAGTTCG
1 GGTCAAC-GGTCG
301007 GGTCAACGGTCG
1 GGTCAACGGTCG
301019 GGTCAACGGTCG
1 GGTCAACGGTCG
301031 GGTC
1 GGTC
301035 GGGTCAGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 26 0.74
13 9 0.26
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.23
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:307052 original size:5 final size:5
Alignment explanation
Indices: 307039--307081 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
307029 GCTTCTCTTC
*
307039 TTTCTT TTTCT TTTC- TTTCT TTTTT TTTCT TTTCT GTTTCT TT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TT
307082 GCTGCGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
4 4 0.12
5 20 0.61
6 9 0.27
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:307054 original size:15 final size:15
Alignment explanation
Indices: 307031--307081 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
307021 CTCGGTAAGC
*
307031 TTCTCTTCTTTCTTT
1 TTCTTTTCTTTCTTT
307046 TTCTTTTCTTTCTTT
1 TTCTTTTCTTTCTTT
*
307061 TT-TTTTCTTTTCTGT
1 TTCTTTTC-TTTCTTT
307076 TTCTTT
1 TTCTTT
307082 GCTGCGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 5 0.16
15 24 0.75
16 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTCTTT
Found at i:307060 original size:19 final size:20
Alignment explanation
Indices: 307031--307073 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
307021 CTCGGTAAGC
307031 TTCTCTTCTTTCTTTTTCTT
1 TTCTCTTCTTTCTTTTTCTT
*
307051 TTCT-TTCTTTTTTTTTCTT
1 TTCTCTTCTTTCTTTTTCTT
307070 TTCT
1 TTCT
307074 GTTTCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTCTTCTTTCTTTTTCTT
Found at i:307567 original size:3 final size:3
Alignment explanation
Indices: 307549--307625 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
307539 TGTAATATTA
* * * * * * *
307549 AAT AAT ATAT ATT AAT AAT AAT AAT AAT TAT TAT TAT TAT ATT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
307595 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
307626 TAAATAACAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:307631 original size:9 final size:10
Alignment explanation
Indices: 307550--307641 Score: 65
Period size: 9 Copynumber: 9.7 Consensus size: 10
307540 GTAATATTAA
307550 ATAAT-ATAT
1 ATAATAATAT
307559 ATTAATAATA-
1 A-TAATAATAT
307569 ATAATAAT-T
1 ATAATAATAT
* *
307578 ATTATTATTAT
1 A-TAATAATAT
*
307589 ATTTATAATA-
1 A-TAATAATAT
307599 ATAATAAT-T
1 ATAATAATAT
307608 ATAATAATA-
1 ATAATAATAT
307617 ATAATAATAT
1 ATAATAATAT
*
307627 A-AATAACAT
1 ATAATAATAT
307636 -TAATAA
1 ATAATAA
307642 GAAAAAAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
9 44 0.66
10 12 0.18
11 11 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAATAATAT
Found at i:308066 original size:113 final size:113
Alignment explanation
Indices: 307870--308635 Score: 1164
Period size: 113 Copynumber: 6.8 Consensus size: 113
307860 GTTGATAAGC
*
307870 TCTTCTCATTATGAACTTCTTCTT--TTC--CTGATGAGTTCTTCTCATTATGAACTT-CTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * * *
307930 AAAAACTGACCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* * *
307978 TCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * *
308043 AAAAGTTCATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* *
308091 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* *
308156 AAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* * * * **
308204 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAAGGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
*
308269 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* **
308317 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* *
308382 AAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* * **
308430 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * *
308495 AAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
* *
308543 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
*
308608 AAAAGCTGATCCATCAAGTGATGGATTT
66 AAAAGCTAATCCATCAAGTGATGGATTT
308636 AAATCTTTGC
Statistics
Matches: 617, Mismatches: 36, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
108 23 0.04
110 3 0.00
112 26 0.04
113 565 0.92
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
Found at i:308466 original size:24 final size:23
Alignment explanation
Indices: 308431--308475 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
308421 TGAACAAATT
308431 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
308455 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
308476 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:312294 original size:13 final size:13
Alignment explanation
Indices: 312278--312302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312268 TTTTCATGTT
312278 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
312291 TTTTTTCTTTTT
1 TTTTTTCTTTTT
312303 TTTAACAACA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:322624 original size:19 final size:20
Alignment explanation
Indices: 322600--322645 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
322590 CCAAAATGGC
*
322600 TCAATTTC-ACATTATAACA
1 TCAATTTCAACACTATAACA
322619 TCAATTTCAACACTATAACA
1 TCAATTTCAACACTATAACA
*
322639 TTAATTT
1 TCAATTT
322646 ATATCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAATTTCAACACTATAACA
Found at i:327272 original size:117 final size:117
Alignment explanation
Indices: 327059--327311 Score: 316
Period size: 117 Copynumber: 2.2 Consensus size: 117
327049 AATACAAGAT
* * * * *
327059 ACCCAATAAGCACCTAAGTGCTACACAGAAGTATAGGTATTGTAGTATACAACGACACTATGCTA
1 ACCCAATAAGCACATAAGTACCACACAGAAGTATAGGTACTGTAGTATACAACGACACCATGCTA
* *
327124 ACAATTTCGATGTGGTATTTATTTATTAATAT-ATTCCTTGAACACAAAGTGC
66 ACAATTTCGATGTGGTATTCATTTATGAATATCA-TCCTTGAACACAAAGTGC
* * * *
327176 ACCCAATAAGCACGTAAGTACCACA-ATGACGTGTATGTACTGTAGTATACAACGACACCATGCT
1 ACCCAATAAGCACATAAGTACCACACA-GAAGTATAGGTACTGTAGTATACAACGACACCATGCT
* * *
327240 AATAATTCTGGA-GTGGTACTTCA-TTATGAATATCATCCTTGCACACAAAGTGC
65 AACAATT-TCGATGTGGTA-TTCATTTATGAATATCATCCTTGAACACAAAGTGC
327293 ACCCAATAAGCACATAAGT
1 ACCCAATAAGCACATAAGT
327312 GTCACAGTAC
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
116 1 0.01
117 110 0.93
118 7 0.06
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (117 bp):
ACCCAATAAGCACATAAGTACCACACAGAAGTATAGGTACTGTAGTATACAACGACACCATGCTA
ACAATTTCGATGTGGTATTCATTTATGAATATCATCCTTGAACACAAAGTGC
Found at i:327368 original size:45 final size:45
Alignment explanation
Indices: 327302--327402 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 45
327292 CACCCAATAA
* *
327302 GCACATA-AGTGTCACAGTACAAAAAATGTAATACTACCATATTT
1 GCACATATAGTGCCACAGTACAAAAAATATAATACTACCATATTT
* * * * *
327346 GTACATATAGTGCCATAGTACAACAAATATACTACTACCATCTTT
1 GCACATATAGTGCCACAGTACAAAAAATATAATACTACCATATTT
*
327391 GCACACATAGTG
1 GCACATATAGTG
327403 TCATTTGTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 6 0.13
45 41 0.87
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (45 bp):
GCACATATAGTGCCACAGTACAAAAAATATAATACTACCATATTT
Done.