Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001563.1 Hibiscus syriacus cultivar Beakdansim tig00003096_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: 849978
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:110073 original size:10 final size:10
Alignment explanation
Indices: 110060--110120 Score: 88
Period size: 10 Copynumber: 6.1 Consensus size: 10
110050 TGTTTTATAT
*
110060 TGTTTTCTTC
1 TGTTTGCTTC
110070 TGTTTGCTTC
1 TGTTTGCTTC
110080 TGTTTGCTTC
1 TGTTTGCTTC
110090 TGTTTGCTTC
1 TGTTTGCTTC
*
110100 TGTTTGATAT-
1 TGTTTGCT-TC
110110 TGTTTGCTTC
1 TGTTTGCTTC
110120 T
1 T
110121 ACTTGATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 1 0.02
10 44 0.96
11 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.18, T:0.62
Consensus pattern (10 bp):
TGTTTGCTTC
Found at i:110126 original size:20 final size:20
Alignment explanation
Indices: 110090--110130 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
110080 TGTTTGCTTC
**
110090 TGTTTGCTTCTGTTTGATAT
1 TGTTTGCTTCTACTTGATAT
110110 TGTTTGCTTCTACTTGATAT
1 TGTTTGCTTCTACTTGATAT
110130 T
1 T
110131 TGTAAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (20 bp):
TGTTTGCTTCTACTTGATAT
Found at i:110937 original size:18 final size:17
Alignment explanation
Indices: 110891--110949 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
110881 CATGAATTGG
* *
110891 AATTAACATAAAAACTA
1 AATTAATATAAAAATTA
*
110908 AATTTATAATATACAAATTA
1 AA--T-TAATATAAAAATTA
110928 TAATTAATATAAAAATTA
1 -AATTAATATAAAAATTA
110946 AATT
1 AATT
110950 TCAAAAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.18
18 13 0.38
19 2 0.06
20 11 0.32
21 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAATATAAAAATTA
Found at i:114844 original size:21 final size:21
Alignment explanation
Indices: 114820--114860 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
114810 ATTATCCAAT
*
114820 AAACATGACATCCATAACAAC
1 AAACATGAAATCCATAACAAC
* *
114841 AAACTTTAAATCCATAACAA
1 AAACATGAAATCCATAACAA
114861 TCAACTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACATGAAATCCATAACAAC
Found at i:114866 original size:21 final size:21
Alignment explanation
Indices: 114829--114876 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
114819 TAAACATGAC
114829 ATCCATAACAACAAACTTTAA
1 ATCCATAACAACAAACTTTAA
114850 ATCCATAACAATC-AACTTTAA
1 ATCCATAACAA-CAAACTTTAA
114871 ATCCAT
1 ATCCAT
114877 TATAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
ATCCATAACAACAAACTTTAA
Found at i:118056 original size:95 final size:95
Alignment explanation
Indices: 117919--118109 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 95
117909 TACTGAAGAG
* * *
117919 GTAGTATCAATACCATGGTAAGGGTATCGATACTAGTAAACATCAAATATAATTTTGGTATCGAT
1 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGAAACATCAAATATAATTTCGGTATCGAT
*
117984 ACTAGAAAGGGGTATCAATACCATAATATA
66 ACCAGAAAGGGGTATCAATACCATAATATA
* *
118014 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGCAACATCGAATATAATTTCGGTATCGAT
1 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGAAACATCAAATATAATTTCGGTATCGAT
* * *
118079 ACCGGAAGGGGGTATCAGTACCATAATATA
66 ACCAGAAAGGGGTATCAATACCATAATATA
118109 G
1 G
118110 AATTATCAGT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (95 bp):
GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGAAACATCAAATATAATTTCGGTATCGAT
ACCAGAAAGGGGTATCAATACCATAATATA
Found at i:118139 original size:95 final size:95
Alignment explanation
Indices: 117921--118141 Score: 264
Period size: 95 Copynumber: 2.3 Consensus size: 95
117911 CTGAAGAGGT
* * * ** *
117921 AGTATCAATACCATGGTAAGGGTATCGATACTAGTAAACATCAAATATAATTTTGGTATCGATAC
1 AGTATCAATACCAGGGTAAGAGTATCGATACCAGGCAACATCAAATATAATTTCGGTATCGATAC
* *
117986 TAGAAAGGGGTATCAATACCATAATATAGT
66 CAGAAAGGGGTATCAATACCATAATATAGA
* * *
118016 AGTATCAATACCATGGTAAGGGTATCGATACCAGGCAACATCGAATATAATTTCGGTATCGATAC
1 AGTATCAATACCAGGGTAAGAGTATCGATACCAGGCAACATCAAATATAATTTCGGTATCGATAC
* * *
118081 CGGAAGGGGGTATCAGTACCATAATATAGA
66 CAGAAAGGGGTATCAATACCATAATATAGA
* * * *
118111 ATTATCAGTACTAGGGT-AGTAGTCTCGATAC
1 AGTATCAATACCAGGGTAAG-AGTATCGATAC
118142 TATGGACCCT
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
94 2 0.02
95 107 0.98
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (95 bp):
AGTATCAATACCAGGGTAAGAGTATCGATACCAGGCAACATCAAATATAATTTCGGTATCGATAC
CAGAAAGGGGTATCAATACCATAATATAGA
Found at i:118573 original size:20 final size:20
Alignment explanation
Indices: 118548--118644 Score: 113
Period size: 20 Copynumber: 4.5 Consensus size: 20
118538 TGAAAATGCT
118548 TGAAAGGATGCATTAAGGCA
1 TGAAAGGATGCATTAAGGCA
*
118568 TGAAAGGATGCCATAATTGAAAATGCA
1 TGAAAGGATG-C---ATT---AAGGCA
118595 TGAAAGGATGCATTAAGGCA
1 TGAAAGGATGCATTAAGGCA
*
118615 TGAAAGGATACATTAAGGCA
1 TGAAAGGATGCATTAAGGCA
118635 TGAAAGGATG
1 TGAAAGGATG
118645 ACATATATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
20 43 0.65
21 1 0.02
23 3 0.05
24 3 0.05
26 1 0.02
27 15 0.23
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (20 bp):
TGAAAGGATGCATTAAGGCA
Found at i:118602 original size:47 final size:47
Alignment explanation
Indices: 118533--118623 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
118523 AATCGAATCT
*
118533 ATAATTGAAAATGCTTGAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
118580 ATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 ATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
118624 ACATTAAGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (47 bp):
ATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
Found at i:125189 original size:95 final size:94
Alignment explanation
Indices: 125064--125253 Score: 247
Period size: 94 Copynumber: 2.0 Consensus size: 94
125054 TACCGAAGAG
* * * *
125064 GTAGTATCGATACCATAGTAAGGGTATCGATACTAGTAAACATCGAATATAATATT-GGTATCGA
1 GTAGTATCAATACCATAGTAAGGGTATCGATACCAGGAAACATC-AAGATAAT-TTCGGTATCGA
*
125128 TACCAGAAAGGAGTATCAATACCATAGTATA
64 TACCAGAAAGGAGTATCAATACCATAATATA
* * *
125159 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGCAACATCAAGCTAATTTCGGTATCGATA
1 GTAGTATCAATACCATAGTAAGGGTATCGATACCAGGAAACATCAAGATAATTTCGGTATCGATA
* * * *
125224 CCGGAAGGGGGTATCAGTACCATAATATA
66 CCAGAAAGGAGTATCAATACCATAATATA
125253 G
1 G
125254 AATTATCGGT
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 2 0.02
94 41 0.50
95 39 0.48
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (94 bp):
GTAGTATCAATACCATAGTAAGGGTATCGATACCAGGAAACATCAAGATAATTTCGGTATCGATA
CCAGAAAGGAGTATCAATACCATAATATA
Found at i:125717 original size:20 final size:20
Alignment explanation
Indices: 125689--125930 Score: 142
Period size: 20 Copynumber: 10.7 Consensus size: 20
125679 AGTTGAAAAT
* *
125689 GCATAAAAGGGTGCATTAAG
1 GCATGAAAGGATGCATTAAG
125709 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
125729 GCATGAAAGTATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
125756 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
125776 GCATGAAAGGATGCCATAATTGAGAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
125803 GCATGAAAGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
125823 GCATGAAAGGATGCCACAATTTAAAAT
1 GCATGAAAGGATG---C-A-TT--AAG
125850 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
125870 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
125897 TCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
125917 GCATGAAAGGATGC
1 GCATGAAAGGATGC
125931 CATATATATT
Statistics
Matches: 176, Mismatches: 18, Indels: 56
0.70 0.07 0.22
Matches are distributed among these distances:
20 88 0.50
21 3 0.02
22 2 0.01
23 11 0.06
24 11 0.06
25 2 0.01
26 3 0.02
27 56 0.32
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:125763 original size:47 final size:47
Alignment explanation
Indices: 125709--125958 Score: 394
Period size: 47 Copynumber: 5.3 Consensus size: 47
125699 GTGCATTAAG
*
125709 GCATGAAAGGATGCATTAAGGCATGAAAGTATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
* *
125756 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTGAGAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
* * *
125803 GCATGAAAGAATGCATTAAGGCATGAAAGGATGCCACAATTTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
125850 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
* *
125897 TCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATATATATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA-AT-TGAAAAT
125946 GCAT-AAATGGATG
1 GCATGAAA-GGATG
125959 TGTTAATACG
Statistics
Matches: 186, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 167 0.90
48 5 0.03
49 14 0.08
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
Found at i:129943 original size:5 final size:5
Alignment explanation
Indices: 129935--129960 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
129925 AAAAGGGGAA
129935 AAGAG AAGAG AAGAG AAGAG AAGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG A
129961 GGGCTTACTT
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:131396 original size:18 final size:17
Alignment explanation
Indices: 131369--131414 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
131359 TTTCTTTCAA
131369 ATTTTTTATTACTTATT
1 ATTTTTTATTACTTATT
* *
131386 ATTTTTATATTATTTTTT
1 ATTTTT-TATTACTTATT
131404 ATTTATTTATT
1 ATTT-TTTATT
131415 TTATTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 17 0.68
19 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTACTTATT
Found at i:133452 original size:13 final size:13
Alignment explanation
Indices: 133424--133466 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
133414 GAGTAACACC
*
133424 TTTTCATATATGCA
1 TTTTCAT-TTTGCA
133438 TTTTCATTTTGCA
1 TTTTCATTTTGCA
133451 TTTTTCATTTTGCA
1 -TTTTCATTTTGCA
133465 TT
1 TT
133467 CATACTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTTCATTTTGCA
Found at i:133454 original size:7 final size:7
Alignment explanation
Indices: 133434--133466 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
133424 TTTTCATATA
133434 TGCATTT
1 TGCATTT
133441 T-CATTT
1 TGCATTT
133447 TGCATTT
1 TGCATTT
*
133454 TTCATTT
1 TGCATTT
133461 TGCATT
1 TGCATT
133467 CATACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (7 bp):
TGCATTT
Found at i:137771 original size:114 final size:114
Alignment explanation
Indices: 137571--138024 Score: 818
Period size: 114 Copynumber: 4.0 Consensus size: 114
137561 GTGCCATGTT
137571 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
137636 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
137685 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
137750 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
*
137799 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
137864 GTTTGGTATAAACCACAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
* *
137913 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATAATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * *
137978 GTTCGGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAATT
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
138025 GCATGATTGT
Statistics
Matches: 327, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 327 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:139220 original size:18 final size:18
Alignment explanation
Indices: 139197--139234 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
139187 GAATATTTGT
139197 ATTAGCAAATGCTGGGGC
1 ATTAGCAAATGCTGGGGC
139215 ATTAGCAAATGCTGGGGC
1 ATTAGCAAATGCTGGGGC
139233 AT
1 AT
139235 GCTAAAGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (18 bp):
ATTAGCAAATGCTGGGGC
Found at i:140032 original size:54 final size:54
Alignment explanation
Indices: 139947--140104 Score: 157
Period size: 54 Copynumber: 3.0 Consensus size: 54
139937 TAATTGAGAA
*
139947 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGAAGAATGTGTTGTCAAATGCTTTACGAAC
* * * *
140001 ATCTGAGCAGAAGCTACA-AGAAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAGA-AAAGGAAGAATGTGTTGTCAAATGCTTTACGAAC
* * * * * *
140054 -TC-GA-TAGAAACCACAGGTAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-GAAAAGGAAGAATGTGTTGTCAAATGCTTTACGAAC
140105 CAGTGATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
50 31 0.36
51 7 0.08
52 2 0.02
53 3 0.03
54 44 0.51
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAGAAAAGGAAGAATGTGTTGTCAAATGCTTTACGAAC
Found at i:141835 original size:76 final size:76
Alignment explanation
Indices: 141346--142317 Score: 1753
Period size: 75 Copynumber: 12.9 Consensus size: 76
141336 CTATTTCCCG
*
141346 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141410 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
141421 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCTTTCAGGAGTTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141485 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
141496 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
141561 A-CCTTCGAGT
66 AGCCTTCGGGT
*
141571 CATCTGTATGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141635 AGCCTTCGGGT
66 AGCCTTCGGGT
141646 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141710 AGCCTTCGGGT
66 AGCCTTCGGGT
*
141721 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141786 AGCCTTCGGGT
66 AGCCTTCGGGT
141797 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141861 AGCCTTCGGGT
66 AGCCTTCGGGT
141872 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141937 AGCCTTCGGGT
66 AGCCTTCGGGT
141948 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
142012 AGCCTTCGGGT
66 AGCCTTCGGGT
142023 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
142088 AAAGCCTTC-GGT
64 AAAGCCTTCGGGT
142100 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
142165 AGCCTTAGGGT
66 AGCCTTCGGGT
*
142176 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
142241 AGCCTTAGGGT
66 AGCCTTCGGGT
*
142252 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
142317 A
66 A
142318 ACCCTTCAGT
Statistics
Matches: 868, Mismatches: 21, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
74 2 0.00
75 499 0.57
76 293 0.34
77 66 0.08
78 8 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:141860 original size:151 final size:151
Alignment explanation
Indices: 141346--142316 Score: 1768
Period size: 151 Copynumber: 6.4 Consensus size: 151
141336 CTATTTCCCG
*
141346 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
141411 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCTTTCAGGAGTTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
141476 ATGTTTTC-AAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
* *
141496 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
141561 ACCTTCGAGTCATCTGTATGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
141626 ATGTTTTC-AAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
141646 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
141711 GCCTTCGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
141776 ATGTTTTCAAAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
141797 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
141862 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
141927 ATGTTTTCAAAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
141948 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
142013 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTT
66 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTT
142078 TGATGTTTTCAAAGCCTTC-GGT
129 TGATGTTTTCAAAGCCTTCGGGT
142100 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
142165 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
65 AGCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
142230 GATGTTTTCAAAGCCTTAGGGT
130 GATGTTTTCAAAGCCTTCGGGT
*
142252 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
142317 AACCCTTCAG
Statistics
Matches: 796, Mismatches: 20, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
150 273 0.34
151 309 0.39
152 131 0.16
153 83 0.10
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (151 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGT
Found at i:143146 original size:5 final size:5
Alignment explanation
Indices: 143136--143161 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
143126 AAAAGGGGAA
143136 AAGAG AAGAG AAGAG AAGAG AAGAG A
1 AAGAG AAGAG AAGAG AAGAG AAGAG A
143162 GAGCTTACTT
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:145597 original size:41 final size:41
Alignment explanation
Indices: 145540--145662 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
145530 GATGTGTTTC
* *
145540 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
1 CTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAAACACCA
* * * *
145581 CTAAATTATGAGTCTATAGCAGCGTTTTTATAAAAACACTA
1 CTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAAACACCA
* * * *
145622 CTAAAGTACGAGTTTATAGCTGCATTTGTATACAAACACCA
1 CTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAAACACCA
145663 AGAATGTATG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (41 bp):
CTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAAACACCA
Found at i:145892 original size:40 final size:40
Alignment explanation
Indices: 145821--145979 Score: 128
Period size: 40 Copynumber: 4.0 Consensus size: 40
145811 TGCTTAAAAA
* * * *
145821 CCACTAAAGAACTAGTATTT-GACGTCGTTTGTATCAAACG
1 CCACTAAAGTACGAGTATTTAG-CGGCATTTGTATCAAACG
*
145861 CCACTAAAGTACGAGTCTTTAGCGGCATTTGTA-CAAAAACG
1 CCACTAAAGTACGAGTATTTAGCGGCATTTGTATC--AAACG
* * * * *
145902 CCACTAAAGTA-TAGTATTTAGTGGCATTTATATAAAAAAAG
1 CCACTAAAGTACGAGTATTTAGCGGCATTTGTAT--CAAACG
* * *
145943 CCACTAAAATACGAGTATTTACCGGCGTTTGT-TCAAA
1 CCACTAAAGTACGAGTATTTAGCGGCATTTGTATCAAA
145980 AAAGTCACTA
Statistics
Matches: 94, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
39 4 0.04
40 43 0.46
41 32 0.34
42 15 0.16
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (40 bp):
CCACTAAAGTACGAGTATTTAGCGGCATTTGTATCAAACG
Found at i:145981 original size:42 final size:41
Alignment explanation
Indices: 145860--145993 Score: 153
Period size: 41 Copynumber: 3.3 Consensus size: 41
145850 TGTATCAAAC
* * *
145860 GCCACTAAAGTACGAGTCTTTAGCGGCATTTGTACAAAAAC
1 GCCACTAAAGTACGAGTATTTAGCGGCATTTGTTCAAAAAA
* * * *
145901 GCCACTAAAGTA-TAGTATTTAGTGGCATTTATATAAAAAAA
1 GCCACTAAAGTACGAGTATTTAGCGGCATTTGT-TCAAAAAA
* * *
145942 GCCACTAAAATACGAGTATTTACCGGCGTTTGTTCAAAAAA
1 GCCACTAAAGTACGAGTATTTAGCGGCATTTGTTCAAAAAA
*
145983 GTCACTAAAGT
1 GCCACTAAAGT
145994 GCAATATTTA
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 16 0.21
41 44 0.59
42 15 0.20
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTATTTAGCGGCATTTGTTCAAAAAA
Found at i:150412 original size:4 final size:4
Alignment explanation
Indices: 150391--150431 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
150381 TTTATGATAT
* * *
150391 TCTA TCTA TATC TATA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
150432 ATAAAAGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:151481 original size:18 final size:19
Alignment explanation
Indices: 151443--151481 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
151433 AGACCAAATC
*
151443 CAAGTGCATAACTTTGGGTT
1 CAAGTGCATAAC-TAGGGTT
151463 CAAGTGCATAA-TAGGGTT
1 CAAGTGCATAACTAGGGTT
151481 C
1 C
151482 CTTGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (19 bp):
CAAGTGCATAACTAGGGTT
Found at i:154525 original size:2 final size:2
Alignment explanation
Indices: 154518--154567 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
154508 TGTAAAAATT
154518 TA TA TA TA TA TA TA TA TA 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
154560 TA TA TA TA
1 TA TA TA TA
154568 ACCCAAACGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155771 original size:45 final size:45
Alignment explanation
Indices: 155699--156789 Score: 605
Period size: 45 Copynumber: 24.3 Consensus size: 45
155689 TCATTTCTGT
* * * * * * **
155699 GAGAAAGTCCAGAATAACACCATTAAAAGGTTGGCTCTTTTTCGT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * *
155744 GAGAAAGTCAAGAAGAACAACACTAAAAGATCGACTCCTATTCAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
*
155789 GAGAAAGTCAAGAATAA-AATCACTAAAAGGTTGACT-TCTCTTCAC
1 GAGAAAGTCAAGAAGAACAA-CACTAAAAGGTTGACTCT-TCTTCAC
* * *
155834 GAGAAAGTCAAGAACAACACCACTAAAAGTTTGACT-TCTCTTCAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * * *
155879 CAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTCTACGA-
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTC-AC
* ** * *
155924 GAGAAAGTCAAGGAAG-ACAACATTAAAATATTGACTCCTCTTCCC
1 GAGAAAGTCAA-GAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * * *
155969 GAGAAAGTCAAGAATAACATCACTAAAAGGTTAAAT-TCTATTCAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * *
156014 GAGAAAGTCAAGAACAACACCACTAAAAGGTTAACT-TCTCTTCAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * *** * **
156059 AACAAAGTCAAGTAGGACAACACTAAAATAATGACTATTCTTCGT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * *
156104 GAAAAAGTTAAGGAAG-ACAACACTAAAAGATTGACTCCTT-TTCAT
1 GAGAAAGTCAA-GAAGAACAACACTAAAAGGTTGACT-CTTCTTCAC
* * * *
156149 GAGAAAGTCAAGAATAACATCACTAAAAGGTTGAGT-TCTCTTCAT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* *
156194 GAGAAAGTCAAGAATG-ACACCACTAAAAGGTTGACT-TCTCTTCAT
1 GAGAAAGTCAAGAA-GAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * ** * **
156239 GAGAAAGTCAAGTAGGAA-AACACT-AAAGATCAACTCCTCTTCGT
1 GAGAAAGTCAAG-AAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * *
156283 GA-AACATTCAAGGAAG-GCAACACTAAAAGATTGA-TTTCTCTTCAC
1 GAGAA-AGTCAA-GAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * * * *
156328 AAGAAAGTCAATAATAACACCACTAAAAGGTTGAGT-TATCTTAAT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * * * * *
156373 GAGAAAGTGAAGTAGGACAACACTAAAAGATCGGCTCATCTGCGA-
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTC-AC
* * ** *
156418 GAAAAATTCAAGGAAG-ACAACACTAAAATATTGACTCCTCTTCAC
1 GAGAAAGTCAA-GAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * ** **
156463 AAGAAAGTTAGGAATTACTTCACTAAAAGGTTGACT-TCTCTTCAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * *
156508 GAGAAAGTCAAGAACAACACCAATAAAATGTTGACT-TCTCTACAC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * ** * * *
156553 GAGAAAGACAAGTAGGACAACACTAAAAGATCAACTCCTATTCGC
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * ** * *
156598 GAGAAAGTCAAGAATAACATCACTAAAATATTGACTTTTCTTCAT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
* * * * *
156643 GAGAAAGTCAAGAATAACAATACTGAAAGATTGACT-TCTCTTCAT
1 GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * * * * *
156688 GAGAAAGTCAAGAATG-ATAATACTGAAAGATTGGCT-TCTCTTAAT
1 GAGAAAGTCAAGAA-GAACAACACTAAAAGGTTGACTCT-TCTTCAC
* * * *
156733 GAGAAAGTCAAGAATG-ACAATACTGAAAGATTGACTCCTCTTCAC
1 GAGAAAGTCAAGAA-GAACAACACTAAAAGGTTGACTCTTCTTCAC
*
156778 GAGAGAGTCAAG
1 GAGAAAGTCAAG
156790 TTGAAGCTTC
Statistics
Matches: 822, Mismatches: 187, Indels: 74
0.76 0.17 0.07
Matches are distributed among these distances:
43 3 0.00
44 46 0.06
45 753 0.92
46 20 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
GAGAAAGTCAAGAAGAACAACACTAAAAGGTTGACTCTTCTTCAC
Found at i:155839 original size:90 final size:89
Alignment explanation
Indices: 155699--156789 Score: 802
Period size: 90 Copynumber: 12.1 Consensus size: 89
155689 TCATTTCTGT
* * * * * * * *
155699 GAGAAAGTCCAGAATAACACCATTAAAAGGTTGGC-TCTTTTTCGTGAGAAAGTCAAGAAGAACA
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAAG-ACA
* *
155763 ACACTAAAAGATCGACTCCTATTCAC
64 ACACTAAAAGATTGACTCCTCTTCAC
* * * *
155789 GAGAAAGTCAAGAATAAAATCACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGAACAACAC
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAA
* *
155854 CACTAAAAGTTTGACTTCTCTTCAC
65 CACTAAAAGATTGACTCCTCTTCAC
* ** * * *
155879 CAGAAAGTCAAGTAGGACAA-CACTAAAAGATTGACTCCTCTACGA-GAGAAAGTCAAGGAAGAC
1 GAGAAAGTCAAG-AATAAAATCACTAAAAGATTGACTTCTCTTC-ATGAGAAAGTCAA-GAAGAC
* * *
155942 AACATTAAAATATTGACTCCTCTTCCC
63 AACACTAAAAGATTGACTCCTCTTCAC
* * * * * * * *
155969 GAGAAAGTCAAGAATAACATCACTAAAAGGTTAAATTCTATTCACGAGAAAGTCAAGAACAACAC
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAA
* * *
156034 CACTAAAAGGTTAACTTCTCTTCAC
65 CACTAAAAGATTGACTCCTCTTCAC
* * ** * * * * * *
156059 AACAAAGTCAAGTAGGACAA-CACTAAAATAATGACTAT-TCTTCGTGAAAAAGTTAAGGAAGAC
1 GAGAAAGTCAAG-AATAAAATCACTAAAAGATTGACT-TCTCTTCATGAGAAAGTCAA-GAAGAC
* *
156122 AACACTAAAAGATTGACTCCTTTTCAT
63 AACACTAAAAGATTGACTCCTCTTCAC
* * * *
156149 GAGAAAGTCAAGAATAACATCACTAAAAGGTTGAGTTCTCTTCATGAGAAAGTCAAGAATGACAC
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAA
* * *
156214 CACTAAAAGGTTGACTTCTCTTCAT
65 CACTAAAAGATTGACTCCTCTTCAC
** ** * * * *
156239 GAGAAAGTCAAGTAGGAAAA-CACT-AAAGATCAACTCCTCTTCGTGA-AACATTCAAGGAAGGC
1 GAGAAAGTCAAG-AATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAA-AGTCAA-GAAGAC
* *
156301 AACACTAAAAGATTGATTTCTCTTCAC
63 AACACTAAAAGATTGACTCCTCTTCAC
* * * * * * * * * *
156328 AAGAAAGTCAATAATAACACCACTAAAAGGTTGAGTTATCTTAATGAGAAAGTGAAGTAGGACAA
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAG-AAGACAA
* * * *
156393 CACTAAAAGATCGGCTCATCTGCGA-
65 CACTAAAAGATTGACTCCTCTTC-AC
* * * * * * ** * * * *
156418 GAAAAATTCAAGGAAGACAA-CACTAAAATATTGACTCCTCTTCACAAGAAAGTTAGGAATTACT
1 GAGAAAGTCAA-GAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACA
* * *
156482 TCACTAAAAGGTTGACTTCTCTTCAC
64 ACACTAAAAGATTGACTCCTCTTCAC
* * * * * * * *
156508 GAGAAAGTCAAGAACAACACCAATAAAATG-TTGACTTCTCTACACGAGAAAGACAAGTAGGACA
1 GAGAAAGTCAAGAATAAAATCACTAAAA-GATTGACTTCTCTTCATGAGAAAGTCAAG-AAGACA
** * *
156572 ACACTAAAAGATCAACTCCTATTCGC
64 ACACTAAAAGATTGACTCCTCTTCAC
* * * *
156598 GAGAAAGTCAAGAATAACATCACTAAAATATTGACTTTTCTTCATGAGAAAGTCAAGAATAACAA
1 GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAA
* * * *
156663 TACTGAAAGATTGACTTCTCTTCAT
65 CACTAAAAGATTGACTCCTCTTCAC
* * * *
156688 GAGAAAGTCAAGAATGATAAT-ACTGAAAGATTGGCTTCTCTTAATGAGAAAGTCAAGAATGACA
1 GAGAAAGTCAAGAAT-AAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACA
* *
156752 ATACTGAAAGATTGACTCCTCTTCAC
64 ACACTAAAAGATTGACTCCTCTTCAC
*
156778 GAGAGAGTCAAG
1 GAGAAAGTCAAG
156790 TTGAAGCTTC
Statistics
Matches: 766, Mismatches: 204, Indels: 62
0.74 0.20 0.06
Matches are distributed among these distances:
88 6 0.01
89 83 0.11
90 645 0.84
91 32 0.04
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (89 bp):
GAGAAAGTCAAGAATAAAATCACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGACAAC
ACTAAAAGATTGACTCCTCTTCAC
Found at i:155884 original size:135 final size:134
Alignment explanation
Indices: 155744--156789 Score: 793
Period size: 135 Copynumber: 7.8 Consensus size: 134
155734 TCTTTTTCGT
* *
155744 GAGAAAGTCAAGAAGAACAACACTAAAAGATCGACTCCTATTCACGAGAAAGTCAAGAATAAAAT
1 GAGAAAGTCAAGAAG-ACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAAT
* * *
155809 CACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGTTTGACTTCTC
65 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAAGATTGACTTCTC
155874 TTCAC
130 TTCAC
* * * * *
155879 CAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTCTACGA-GAGAAAGTCAAGGAAGACA
1 GAGAAAGTCAAG-AAGACAACACTAAAAGATTGACTCCTCTTC-ACGAGAAAGTCAA-GAATAAA
* * * * * * * * *
155943 A-CATTAAAATATTGACTCCTCTTCCCGAGAAAGTCAAGAATAACATCACTAAAAGGTTAAATTC
63 ATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAAGATTGACTTC
*
156007 TATTCAC
128 TCTTCAC
* * * * * * * ** *
156014 GAGAAAGTCAAGAACAACACCACTAAAAGGTTAACTTCTCTTCACAACAAAGTCAAGTAGGACAA
1 GAGAAAGTCAAGAA-GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAG-AATAAAA
* * ** * * * *
156079 -CACTAAAATAATGACTAT-TCTTCGTGAAAAAGTTAAGGAA-GACAACACTAAAAGATTGACTC
64 TCACTAAAAGATTGACT-TCTCTTCACGAGAAAGTCAA-GAACAACAACACTAAAAGATTGACTT
* *
156141 CTTTTCAT
127 CTCTTCAC
* * * * * * * * *
156149 GAGAAAGTCAAGAATAACATCACTAAAAGGTTGAGTTCTCTTCATGAGAAAGTCAAGAATGACAC
1 GAGAAAGTCAAGAA-GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAAT
* * ** ** *
156214 CACTAAAAGGTTGACTTCTCTTCATGAGAAAGTCAAGTAGGAA-AACACT-AAAGATCAACTCCT
65 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAG-AACAACAACACTAAAAGATTGACTTCT
**
156277 CTTCGT
129 CTTCAC
* * * * * * *
156283 GA-AACATTCAAGGAAGGCAACACTAAAAGATTGATTTCTCTTCACAAGAAAGTCAATAATAACA
1 GAGAA-AGTCAA-GAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAA
* * * * * * * * ** * *
156347 CCACTAAAAGGTTGAGTTATCTTAATGAGAAAGTGAAGTAGGACAACACTAAAAGATCGGC-TCA
64 TCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAAGATTGACTTC-
*
156411 TCTGCGA-
128 TCTTC-AC
* * * * * * * **
156418 GAAAAATTCAAGGAAGACAACACTAAAATATTGACTCCTCTTCACAAGAAAGTTAGGAATTACTT
1 GAGAAAGTCAA-GAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAAT
* * *
156483 CACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGAACAACACCAATAAAATG-TTGACTTCT
65 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAA-GATTGACTTCT
*
156547 CTACAC
129 CTTCAC
* * ** * * *
156553 GAGAAAGACAAGTAGGACAACACTAAAAGATCAACTCCTATTCGCGAGAAAGTCAAGAATAACAT
1 GAGAAAGTCAAG-AAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAAT
* * * * * *
156618 CACTAAAATATTGACTTTTCTTCATGAGAAAGTCAAGAATAACAATACTGAAAGATTGACTTCTC
65 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAAGATTGACTTCTC
*
156683 TTCAT
130 TTCAC
* * * * * * * *
156688 GAGAAAGTCAAGAATGATAATACTGAAAGATTGGCTTCTCTTAATGAGAAAGTCAAGAATGACAA
1 GAGAAAGTCAAGAA-GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT-AAAA
* * *
156753 T-ACTGAAAGATTGACTCCTCTTCACGAGAGAGTCAAG
64 TCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAG
156790 TTGAAGCTTC
Statistics
Matches: 726, Mismatches: 159, Indels: 52
0.77 0.17 0.06
Matches are distributed among these distances:
133 4 0.01
134 115 0.16
135 586 0.81
136 21 0.03
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (134 bp):
GAGAAAGTCAAGAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAAATC
ACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAACAACAACACTAAAAGATTGACTTCTCT
TCAC
Found at i:156015 original size:180 final size:180
Alignment explanation
Indices: 155739--156790 Score: 961
Period size: 180 Copynumber: 5.8 Consensus size: 180
155729 TTGGCTCTTT
* *
155739 TTCGTGAGAAAGTCAA-GAAGAACAACACTAAAAGATCGACTCCTATTCACGAGAAAGTCAAGAA
1 TTCGTGAGAAAGTCAAGGAAG-ACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * *
155803 TAAAATCACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGTTTGA
65 TAACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGA
*
155868 CTTCTCTTCACCAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
130 CTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
* * * * *
155919 TACGAGAGAAAGTCAAGGAAGACAACATTAAAATATTGACTCCTCTTCCCGAGAAAGTCAAGAAT
1 TTCGTGAGAAAGTCAAGGAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT
* * *
155984 AACATCACTAAAAGGTTAAATTCTATTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTAAC
66 AACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGAC
* * * **
156049 TTCTCTTCACAACAAAGTCAAGTAGGACAACACTAAAATAATGACTATTC
131 TTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
* * * *
156099 TTCGTGAAAAAGTTAAGGAAGACAACACTAAAAGATTGACTCCTTTTCATGAGAAAGTCAAGAAT
1 TTCGTGAGAAAGTCAAGGAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT
* * **
156164 AACATCACTAAAAGGTTGAGTTCTCTTCATGAGAAAGTCAAGAATGACACCACTAAAAGGTTGAC
66 AACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGAC
** * **
156229 TTCTCTTCATGAGAAAGTCAAGTAGGAAAACACT-AAAGATCAACTCCTC
131 TTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
* * * * * *
156278 TTCGTGA-AACATTCAAGGAAGGCAACACTAAAAGATTGATTTCTCTTCACAAGAAAGTCAATAA
1 TTCGTGAGAA-AGTCAAGGAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * * * * ** * * * *
156342 TAACACCACTAAAAGGTTGAGTTATCTTAATGAGAAAGTGAAGTAGGACAACACTAAAAGATCGG
65 TAACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGA
* * * * * *
156407 C-TCATCTGCGAGAA-AAATTCAAGGAAGACAACACTAAAATATTGACTCCTC
130 CTTC-TCTTC-ACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
*** * * ** * *
156458 TTCACAAGAAAGT-TAGGAATTACTTCACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGAA
1 TTCGTGAGAAAGTCAAGGAA-GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * * * * * ** * * **
156522 CAACACCAATAAAATGTTGACTTCTCTACACGAGAAAGACAAGTAGGACAACACTAAAAGATCAA
65 TAACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGA
* * * * * ** * * **
156587 CTCCTATTCGCGAGAAAGTCAAGAATAACATCACTAAAATATTGACTTTTC
130 CTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
* * * * * *
156638 TTCATGAGAAAGTCAA-GAATAACAATACTGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA
1 TTCGTGAGAAAGTCAAGGAA-GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * ** * * ** ** * *
156702 TGATA-AT-ACTGAAAGATTGGCTTCTCTTAATGAGAAAGTCAAGAATGACAATACTGAAAGATT
65 T-A-ACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTT
* * *
156765 GACTCCTCTTCACGAGAGAGTCAAGT
128 GACTTCTCTTCACAAGAAAGTCAAGT
156791 TGAAGCTTCA
Statistics
Matches: 717, Mismatches: 143, Indels: 24
0.81 0.16 0.03
Matches are distributed among these distances:
178 4 0.01
179 144 0.20
180 558 0.78
181 10 0.01
182 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (180 bp):
TTCGTGAGAAAGTCAAGGAAGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT
AACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTCAAGAACAACACCACTAAAAGGTTGAC
TTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATTGACTCCTC
Found at i:158297 original size:44 final size:44
Alignment explanation
Indices: 158234--158318 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
158224 TGCATTCATG
158234 GATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
1 GATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
*
158278 GATGATATGAGCCTTTAAAAATGTCCCAACATTTATCATTT
1 GATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTT
158319 CTTTCTCCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (44 bp):
GATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
Found at i:158547 original size:255 final size:255
Alignment explanation
Indices: 158090--158599 Score: 1002
Period size: 255 Copynumber: 2.0 Consensus size: 255
158080 GCAATGGAAA
158090 CCAAAGAACAAAGCTCATTGGGAATATAAGTGGGATGCTTTGGCTTGCCAACATTAATGCATGAG
1 CCAAAGAACAAAGCTCATTGGGAATATAAGTGGGATGCTTTGGCTTGCCAACATTAATGCATGAG
158155 AAATCACCATTTTCATTCTTCGCACCTTTTATCTCATTGAAAATAAATGGTTTCTCAATTCAATG
66 AAATCACCATTTTCATTCTTCGCACCTTTTATCTCATTGAAAATAAATGGTTTCTCAATTCAATG
158220 ATCTTGCATTCATGGATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTTGATGATA
131 ATCTTGCATTCATGGATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTTGATGATA
*
158285 TGAGCCTTTAAAAATGTCCCAACATTTATCATTTCTTTCTCCAGCTCTGATTCTAAGCAT
196 CGAGCCTTTAAAAATGTCCCAACATTTATCATTTCTTTCTCCAGCTCTGATTCTAAGCAT
158345 CCAAAGAACAAAGCTCATTGGGAATATAAGTGGGATGCTTTGGCTTGCCAACATTAATGCATGAG
1 CCAAAGAACAAAGCTCATTGGGAATATAAGTGGGATGCTTTGGCTTGCCAACATTAATGCATGAG
*
158410 AAATCACCATTTTTATTCTTCGCACCTTTTATCTCATTGAAAATAAATGGTTTCTCAATTCAATG
66 AAATCACCATTTTCATTCTTCGCACCTTTTATCTCATTGAAAATAAATGGTTTCTCAATTCAATG
158475 ATCTTGCATTCATGGATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTTGATGATA
131 ATCTTGCATTCATGGATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTTGATGATA
158540 CGAGCCTTTAAAAATGTCCCAACATTTATCATTTCTTTCTCCAGCTCTGATTCTAAGCAT
196 CGAGCCTTTAAAAATGTCCCAACATTTATCATTTCTTTCTCCAGCTCTGATTCTAAGCAT
158600 GAGCTCTATG
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 253 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (255 bp):
CCAAAGAACAAAGCTCATTGGGAATATAAGTGGGATGCTTTGGCTTGCCAACATTAATGCATGAG
AAATCACCATTTTCATTCTTCGCACCTTTTATCTCATTGAAAATAAATGGTTTCTCAATTCAATG
ATCTTGCATTCATGGATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTTGATGATA
CGAGCCTTTAAAAATGTCCCAACATTTATCATTTCTTTCTCCAGCTCTGATTCTAAGCAT
Found at i:158552 original size:44 final size:44
Alignment explanation
Indices: 158489--158573 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
158479 TGCATTCATG
*
158489 GATGATATGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
1 GATGATACGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
*
158533 GATGATACGAGCCTTTAAAAATGTCCCAACATTTATCATTT
1 GATGATACGAGCCTTTAAAAATGCCCCAACATTTATCATTT
158574 CTTTCTCCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (44 bp):
GATGATACGAGCCTTTAAAAATGCCCCAACATTTATCATTTTTT
Found at i:161075 original size:4 final size:4
Alignment explanation
Indices: 161066--161090 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
161056 GTTTTTTGCA
161066 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
161091 TGAGGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:162500 original size:2 final size:2
Alignment explanation
Indices: 162493--162537 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
162483 ACATGCATTC
162493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
162535 AT A
1 AT A
162538 AAGTACGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:164721 original size:42 final size:42
Alignment explanation
Indices: 164645--164726 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
164635 TCTTGATTTG
* *
164645 TAAATCCTTCGGGTCAATAGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCAATAGTAAGCCTTTCGAGCAAGATGCT
* * *
164687 TAAATCCTTTGGGTCATCTA-TAAGCCTTTTGAGCAAGATG
1 TAAATCCTTCGGGTCA-ATAGTAAGCCTTTCGAGCAAGATG
164727 ATAAGTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (42 bp):
TAAATCCTTCGGGTCAATAGTAAGCCTTTCGAGCAAGATGCT
Found at i:165188 original size:3 final size:3
Alignment explanation
Indices: 165160--165224 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
165150 TTGTCCCATT
* *
165160 TTA TT- TTA ATA TTA ATA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
165206 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
165225 AGGCCCGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:167267 original size:42 final size:43
Alignment explanation
Indices: 167200--167282 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
167190 TCGATTACGA
167200 CAAACGCCACTAAAGTAGAACTCTATAGCGGCGTTT-TAAAAC
1 CAAACGCCACTAAAGTAGAACTCTATAGCGGCGTTTGTAAAAC
*
167242 CAAACGCCACTAAAGTATG-AGTCTATAGCGGCGTTTGTAAA
1 CAAACGCCACTAAAGTA-GAACTCTATAGCGGCGTTTGTAAA
167283 CTAACAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 33 0.87
43 5 0.13
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (43 bp):
CAAACGCCACTAAAGTAGAACTCTATAGCGGCGTTTGTAAAAC
Found at i:172916 original size:2 final size:2
Alignment explanation
Indices: 172904--172949 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
172894 CTGTATTAAT
*
172904 TA TA GA TA TA TA TA TA TA 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
172946 TA TA
1 TA TA
172950 CAATTTTAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:174467 original size:2 final size:2
Alignment explanation
Indices: 174460--174525 Score: 71
Period size: 2 Copynumber: 33.5 Consensus size: 2
174450 TCATTATAAT
* * * * *
174460 TC TC TC TC TC TC TC TC CC CC TC TC TC CC CC TC TC -C CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
174501 TC TC TC CC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
174526 ATATATATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (2 bp):
TC
Found at i:175181 original size:21 final size:19
Alignment explanation
Indices: 175155--175197 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
175145 CATGTTTATA
175155 AAATTTTAAAAAGACAAATAT
1 AAATTTTAAAAAGA-AAAT-T
*
175176 AAATTTTAAACAGAAAATT
1 AAATTTTAAAAAGAAAATT
175195 AAA
1 AAA
175198 AAAAATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTTTAAAAAGAAAATT
Found at i:175473 original size:17 final size:16
Alignment explanation
Indices: 175451--175487 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
175441 TTTTATATTA
175451 TTAATATATATTCACCT
1 TTAA-ATATATTCACCT
175468 TT-AATATATTCACCT
1 TTAAATATATTCACCT
175483 TTAAA
1 TTAAA
175488 ATTATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.74
16 3 0.16
17 2 0.11
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATATATTCACCT
Found at i:175476 original size:15 final size:15
Alignment explanation
Indices: 175456--175486 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
175446 TATTATTAAT
175456 ATATATTCACCTTTA
1 ATATATTCACCTTTA
175471 ATATATTCACCTTTA
1 ATATATTCACCTTTA
175486 A
1 A
175487 AATTATTTAT
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:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATTCACCTTTA
Found at i:177354 original size:18 final size:18
Alignment explanation
Indices: 177331--177395 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
177321 ATGATAAACA
177331 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
* * **
177349 ATATCAAAACCATGATAAAC
1 ATATC-ATA-CATAATAGTC
177369 AATATCATACATAATAGTC
1 -ATATCATACATAATAGTC
177388 ATATCATA
1 ATATCATA
177396 TTCTTTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 13 0.36
19 9 0.25
20 9 0.25
21 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:177365 original size:39 final size:39
Alignment explanation
Indices: 177311--177393 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
177301 CTCATGATTT
177311 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
177350 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
177389 TATCA
1 TATCA
177394 TATTCTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.27
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:177461 original size:19 final size:19
Alignment explanation
Indices: 177434--177480 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
177424 CTTTCATAAC
177434 TCATTTTCACCTTTCAC-TT
1 TCATTTTCA-CTTTCACATT
*
177453 TCATATTCACTTTCACATT
1 TCATTTTCACTTTCACATT
177472 TCATTTTCA
1 TCATTTTCA
177481 TAATTCGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (19 bp):
TCATTTTCACTTTCACATT
Found at i:177463 original size:12 final size:13
Alignment explanation
Indices: 177445--177530 Score: 57
Period size: 13 Copynumber: 6.4 Consensus size: 13
177435 CATTTTCACC
177445 TTTCACTTTCATA
1 TTTCACTTTCATA
*
177458 -TTCACTTTCACA
1 TTTCACTTTCATA
*
177470 TTTCATTTTCATA
1 TTTCACTTTCATA
* * *
177483 ATTCGTTCTTTCACA
1 TTTC--ACTTTCATA
*
177498 TTTCATTTTCATA
1 TTTCACTTTCATA
* *
177511 ATTCGTACTTTCACA
1 TTTC--ACTTTCATA
177526 TTTCA
1 TTTCA
177531 AAACTCATTC
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
12 11 0.21
13 23 0.43
15 19 0.36
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTCACTTTCATA
Found at i:177499 original size:28 final size:28
Alignment explanation
Indices: 177438--177530 Score: 138
Period size: 28 Copynumber: 3.4 Consensus size: 28
177428 CATAACTCAT
* *
177438 TTTCACCTTTCACTTTCAT-ATTC--AC
1 TTTCACATTTCATTTTCATAATTCGTAC
*
177463 TTTCACATTTCATTTTCATAATTCGTTC
1 TTTCACATTTCATTTTCATAATTCGTAC
177491 TTTCACATTTCATTTTCATAATTCGTAC
1 TTTCACATTTCATTTTCATAATTCGTAC
177519 TTTCACATTTCA
1 TTTCACATTTCA
177531 AAACTCATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
25 17 0.28
26 4 0.07
28 40 0.66
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTCACATTTCATTTTCATAATTCGTAC
Found at i:177587 original size:18 final size:18
Alignment explanation
Indices: 177561--177615 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
177551 AACTTGTTTC
*
177561 CAGACTCATAAATTATTT
1 CAGATTCATAAATTATTT
*
177579 CAGATTCATAATTTAATTT
1 CAGATTCATAAATT-ATTT
* *
177598 CATATTCATAACTTATTT
1 CAGATTCATAAATTATTT
177616 TCAAGATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (18 bp):
CAGATTCATAAATTATTT
Found at i:177597 original size:19 final size:19
Alignment explanation
Indices: 177561--177627 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
177551 AACTTGTTTC
*
177561 CAGACTCATAAATT-ATTT
1 CAGATTCATAAATTAATTT
*
177579 CAGATTCATAATTTAATTT
1 CAGATTCATAAATTAATTT
* * *
177598 CATATTCATAACTTATTTT
1 CAGATTCATAAATTAATTT
177617 CAAGA-TCATAA
1 C-AGATTCATAA
177628 CCCAATGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.29
19 27 0.66
20 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (19 bp):
CAGATTCATAAATTAATTT
Found at i:178246 original size:23 final size:22
Alignment explanation
Indices: 178220--178263 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
178210 TTTCCAAGGT
* *
178220 TCTTTTTTTTTCTTTATTTTTAA
1 TCTTTTGTTTTCCTT-TTTTTAA
178243 TCTTTTGTTTTCCTTTTTTTA
1 TCTTTTGTTTTCCTTTTTTTA
178264 CTTTTGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (22 bp):
TCTTTTGTTTTCCTTTTTTTAA
Found at i:179188 original size:14 final size:14
Alignment explanation
Indices: 179169--179198 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
179159 GTTCATTATC
179169 TTTCAGTACTTTAA
1 TTTCAGTACTTTAA
*
179183 TTTCAGTCCTTTAA
1 TTTCAGTACTTTAA
179197 TT
1 TT
179199 ATAGCACCTT
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:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTCAGTACTTTAA
Found at i:179305 original size:16 final size:16
Alignment explanation
Indices: 179281--179347 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
179271 TTTTAGGAAC
*
179281 TTTAATTTATTATTCT
1 TTTATTTTATTATTCT
* *
179297 TTTATTTTATTAACACTAACA
1 TTTATTTTATT---A-T-TCT
*
179318 TTTATTTTATTATTAT
1 TTTATTTTATTATTCT
179334 TTTATTTTATTATT
1 TTTATTTTATTATT
179348 TAATTTTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 24 0.60
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 12 0.30
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTTATTATTCT
Found at i:179345 original size:13 final size:13
Alignment explanation
Indices: 179319--179356 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
179309 ACACTAACAT
179319 TTATTTTA--TTA
1 TTATTTTATTTTA
179330 TTATTTTATTTTA
1 TTATTTTATTTTA
*
179343 TTATTTAATTTTA
1 TTATTTTATTTTA
179356 T
1 T
179357 GCATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:179631 original size:286 final size:280
Alignment explanation
Indices: 179026--179636 Score: 881
Period size: 286 Copynumber: 2.2 Consensus size: 280
179016 TTTTTTTAAT
** * * **
179026 TAACACTAACATTTATTTTATTATTCTTTTATTTTTATTATTTAATTTTATGCATATTTAAATTT
1 TAACACTAACATTTATTGCAATATTATTACA-TTTTATTATTTAATTTTATGCATATTTAAATTT
*
179091 CTAACCTTTACTTTTTATTTATTTAATTTCAGTCTTTAAGTTTCATTGTTTTATTTTTTTTTATT
65 CTAACCTTTACTTTTTATTTATTTAATTTCAGTCCTTAAGTTTCATTGTTTTATTTTTTTTTATT
179156 TCGGTTCATTATCTTTCAGTACTTTAATTTCAGTCCTTTAATTATAGCACCTTACATTCTGTTTA
130 TCGGTTCATTATCTTTCAGTACTTTAATTTCAGTCCTTTAATTATAGCACCTTACATTCTGTTTA
179221 TTTTATTTTGTTCCTTTTTTTGTCTTGCTATAACATTTTTGTTGTTTGGATTTTAGGAACTTTAA
195 TTTTATTTTGTTCCTTTTTTTGTCTTGCTATAACATTTTTGTTGTTTGGATTTTAGGAACTTTAA
* * * *
179286 TTTATTATTCTTTTATTTTAT
260 TTTATTATTATTTCATTTGAA
** * **
179307 TAACACTAACATTTATTTTATTATTATTTTATTTTATTATTTAATTTTATGCATATTTAAATTTC
1 TAACACTAACATTTATTGCAATATTATTACATTTTATTATTTAATTTTATGCATATTTAAATTTC
179372 TAACCTTTACTTTTTATTTATTTAATTTCAGTCCTTAAGTTTCATTGTTTTAATTTTCTGTTTTT
66 TAACCTTTACTTTTTATTTATTTAATTTCAGTCCTTAAGTTTCATTGTTTT-A---T-T-TTTTT
* *
179437 TTATTTCGGTTCATTATCTTTTAGTACTTTAATTTCAGTCCTTTAATTATAGTACCTTACATTCT
125 TTATTTCGGTTCATTATCTTTCAGTACTTTAATTTCAGTCCTTTAATTATAGCACCTTACATTCT
*
179502 GTTTATTTTATTTTGTTCC-TTTTTTGTCTTGCTATAACATTTTTTTTGTTTGGATTTTAGGAAC
190 GTTTATTTTATTTTGTTCCTTTTTTTGTCTTGCTATAACATTTTTGTTGTTTGGATTTTAGGAAC
179566 TTTAATTTATT-TTATTTACATTTGAA
255 TTTAATTTATTATTATTT-CATTTGAA
* **
179592 T-AC-TTTTCATTTATTGCAAT-TTACTTACATCCCTTTATTATTTAA
1 TAACACTAACATTTATTGCAATATTA-TTACAT---TTTATTATTTAA
179637 GCTTTACTAT
Statistics
Matches: 302, Mismatches: 17, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
280 84 0.28
281 31 0.10
282 3 0.01
283 15 0.05
284 8 0.03
285 62 0.21
286 99 0.33
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.59
Consensus pattern (280 bp):
TAACACTAACATTTATTGCAATATTATTACATTTTATTATTTAATTTTATGCATATTTAAATTTC
TAACCTTTACTTTTTATTTATTTAATTTCAGTCCTTAAGTTTCATTGTTTTATTTTTTTTTATTT
CGGTTCATTATCTTTCAGTACTTTAATTTCAGTCCTTTAATTATAGCACCTTACATTCTGTTTAT
TTTATTTTGTTCCTTTTTTTGTCTTGCTATAACATTTTTGTTGTTTGGATTTTAGGAACTTTAAT
TTATTATTATTTCATTTGAA
Found at i:183444 original size:14 final size:14
Alignment explanation
Indices: 183351--183457 Score: 74
Period size: 15 Copynumber: 7.2 Consensus size: 14
183341 TATATAGCAT
183351 AAAAAAGAAAAA-A
1 AAAAAAGAAAAAGA
* *
183364 AAAGAA-AAAAACA
1 AAAAAAGAAAAAGA
* *
183377 TAAAAAAGAGAGAGA
1 -AAAAAAGAAAAAGA
183392 AAAGAAAGATAAAAGA
1 AAA-AAAGA-AAAAGA
* *
183408 AATATAGATAAAAGA
1 AAAAAAGA-AAAAGA
183423 AAGCAAAAGAGGAAAAGA
1 AA--AAAAGA--AAAAGA
183441 AAAAAAGAAAAAGA
1 AAAAAAGAAAAAGA
183455 AAA
1 AAA
183458 CATATCAACC
Statistics
Matches: 74, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
12 5 0.07
13 6 0.08
14 17 0.23
15 22 0.30
16 12 0.16
17 4 0.05
18 8 0.11
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:185580 original size:54 final size:54
Alignment explanation
Indices: 185407--186629 Score: 567
Period size: 53 Copynumber: 22.7 Consensus size: 54
185397 TGTGTTTTTT
* *
185407 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGAAATGCTATTTTTTAAA-GAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTG--ATG--A--TTTTAAATGAGTTTTTAA
* * * *
185466 AGTAACT-A---TGATTTTTATAAGTTTCTTGATGATTTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * *
185517 AGACACTAAGTCCGATTTTCGGAAGTTT-TCTGATGATTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCT-TGATGATTTTAAATGAGTTTTTAA
* * * **
185571 AGAAACTAAGTGTAATTTTCATAAGTTTCTTGACAATTTTCAAATGAGTTTTTTTTAAAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAG---TTTTT--AA
* * * * * *
185631 AAAAACTAAGTCCGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTTAA
* * * * *
185686 AGAAACTAAGTATGATTTTCAGAAGTTTCTAGACAGTTTTTAAATGA-TATTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TGATTTTAAATGAGTTTTTAA
* * * * * * *
185740 A-AAACTAATTTTGATTTTCATAAGTTTCTTTATTATTTTTAAATGAG-CTTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTTAA
* * *
185793 AGAAACCAAGTCTGATTTTTAGAAGTTTCTTGATGATTTT-AACGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTAAATGAGTTTTTAA
* * * * *
185846 AGAAACTAAGTCTGATTTTCGGTAGTTCCTTGATGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTTAA
* * * * * *
185901 TGAAATTAAGCCTGATTTTCA-AAGGTTTCTTGATG-TTTTCAAGTGAATTTATAA
1 AGAAACTAAGTCTGATTTTCAGAA-GTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * * * ** * *
185955 A-AATGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAA-ACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
** * * ** *
186008 AGAAGTTAAGCCTGATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * * ** * * *
186061 AGAAGCTAAGCCTGATTTTTAGGGGCTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * * ** *
186114 AGAAGCTAAGCCTGATTTTCA-AGGGTTTCTTGATG-TTTTCAAAT-AAATTTGAA
1 AGAAACTAAGTCTGATTTTCAGA-AGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* ** * *
186167 AGAAGCTAAGTCTGATTTT-AGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * ** * * *
186219 AGAAGCTAAG-CTTGATTTTTAGGGGTTTCTTGATG-TTTCAAATGA-ATTTGAA
1 AGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTAAATGAGTTTTTAA
* * ** ** *
186271 AGTAGCTAAG-CATGATTTTCAGGGGTTTCTTGATG-TTTTCAAAT-AAATTTGAA
1 AGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * * * ** * *
186324 AGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* *
186377 AGAAACTAAGCCTGATTTTCATG-AGTTTCTTGATG-TGTTCAAATGA-TTTTTAA
1 AGAAACTAAGTCTGATTTTCA-GAAGTTTCTTGATGAT-TTTAAATGAGTTTTTAA
** * * * ** * * *
186430 AGATGCTAAGCCTAATAATT-AGGGGTTTTTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGAT-TTTCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * ** *
186483 GGAAGCTAAG-CTTGATTTAT-AGGGGTTTCTTGATG-TTTTCAAATGAATTTTTAA
1 AGAAACTAAGTC-TGATTT-TCAGAAGTTTCTTGATGATTTT-AAATGAGTTTTTAA
* * * ** * * *
186537 AGAAGCTAA-TCCTAATTTTTAGGGGTTTCTTGATGATAACTGTAAACGAAATTTTT-A
1 AGAAACTAAGT-CTGATTTTCAGAAGTTTCTTGATGAT---TTTAAATG-AGTTTTTAA
*
186594 AGAAACTAAG-CTTGATTTTCA-AGGGTTTCTTGATGA
1 AGAAACTAAGTC-TGATTTTCAGA-AGTTTCTTGATGA
186630 GTAAGACCTT
Statistics
Matches: 968, Mismatches: 140, Indels: 114
0.79 0.11 0.09
Matches are distributed among these distances:
49 4 0.00
50 3 0.00
51 17 0.02
52 107 0.11
53 446 0.46
54 166 0.17
55 126 0.13
56 1 0.00
57 36 0.04
58 15 0.02
59 6 0.01
60 37 0.04
61 4 0.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41
Consensus pattern (54 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTAAATGAGTTTTTAA
Found at i:185779 original size:53 final size:54
Alignment explanation
Indices: 185409--185934 Score: 300
Period size: 55 Copynumber: 9.6 Consensus size: 54
185399 TGTTTTTTAG
* * *
185409 AAACTAAGTCTGATTTTCAGAGGTTTCTTGAAATGCTATTTTTTAAA-GAGTTTTC---
1 AAACTAAGTATGATTTTCAGAAGTTTCTTG--AT--TA-TTTTTAAATGAGATTTCAAA
* * * * * * *
185464 AAAGTAACTATGATTTTTATAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAA
1 AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAA
* ** * * * *
185518 GACACTAAGTCCGATTTTCGGAAGTTT-TCTGATGA-TTTTAAATGAGTTTTTAAA
1 -AAACTAAGTATGATTTTCAGAAGTTTCT-TGATTATTTTTAAATGAGATTTCAAA
* * * ** * * *
185572 GAAACTAAGTGTAATTTTCATAAGTTTCTTGACAATTTTCAAATGAGTTTTTTTTAAAAAA
1 -AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAG----ATTT--CAAA
** * *
185633 AAACTAAGTCCGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAA
1 AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAA
* * *
185687 GAAACTAAGTATGATTTTCAGAAGTTTCTAGA-CAGTTTTTAAATGATATTT-AAA
1 -AAACTAAGTATGATTTTCAGAAGTTTCTTGATTA-TTTTTAAATGAGATTTCAAA
* * * * * * *
185741 AAACTAATTTTGATTTTCATAAGTTTCTTTATTATTTTTAAATGAGCTTTGAAG
1 AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAA
* * * * * * *
185795 AAACCAAGTCTGATTTTTAGAAGTTTCTTGATGA-TTTT-AACGAGTTTTTAAA
1 AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAA
* * * * * * *
185847 GAAACTAAGTCTGATTTTCGGTAGTTCCTTGATGATTTTTAAATGAGCTTTCAATG
1 -AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAA-A
* **
185903 AAATTAAGCCTGATTTTCA-AAGGTTTCTTGAT
1 AAACTAAGTATGATTTTCAGAA-GTTTCTTGAT
185935 GTTTTCAAGT
Statistics
Matches: 369, Mismatches: 79, Indels: 46
0.75 0.16 0.09
Matches are distributed among these distances:
50 7 0.02
51 9 0.02
52 10 0.03
53 75 0.20
54 85 0.23
55 135 0.37
56 3 0.01
59 4 0.01
60 38 0.10
61 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (54 bp):
AAACTAAGTATGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAA
Found at i:186041 original size:53 final size:53
Alignment explanation
Indices: 185907--186571 Score: 949
Period size: 53 Copynumber: 12.5 Consensus size: 53
185897 TCAATGAAAT
* ** * *
185907 TAAGCCTGATTTTCAAAGGTTTCTTGATGTTTTCAAGTGAATTT-ATAAAAATGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGA-AAGAA-GC
* *
185961 TAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGT
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
*
186014 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
*
186067 TAAGCCTGATTTTTAGGGGCTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* * *
186120 TAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
*
186173 TAAGTCTGA-TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* *
186225 TAAGCTTGATTTTTAGGGGTTTCTTGATG-TTTCAAATGAATTTGAAAGTAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* * *
186277 TAAGCATGATTTTCAGGGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* *
186330 TAAGCCTCATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAAC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* * * * * * *
186383 TAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATGATTTTTAAAGATGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* ** * *
186436 TAAGCCTAATAATTAGGGGTTTTTTGATGTTTTCAAATGAATTTGAAGGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
* * *
186489 TAAGCTTGATTTATAGGGGTTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA-TTTGAAAGAAGC
* *
186543 TAATCCTAATTTTTAGGGGTTTCTTGATG
1 TAAGCCTGATTTTTAGGGGTTTCTTGATG
186572 ATAACTGTAA
Statistics
Matches: 542, Mismatches: 65, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
52 96 0.18
53 367 0.68
54 78 0.14
55 1 0.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (53 bp):
TAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGC
Found at i:186388 original size:316 final size:318
Alignment explanation
Indices: 185844--186571 Score: 971
Period size: 316 Copynumber: 2.3 Consensus size: 318
185834 ACGAGTTTTT
* * * * * * * **
185844 AAAGAAACTAAGTCTGATTTTCGGTAGTTCCTTGATGATTTTTAAATGAGCTTTCAATGAAATTA
1 AAAGAAGCTAAGTCTGATTTTAGG-GGTTTCTTGATG-TTTTCAAATGA-ATTTCAAAGAAGCTA
* ** * *
185909 AGCCTGATTTTCAAAGGTTTCTTGATGTTTTCAAGTGAATTTATAAAAATGCTAAGCCTAATTTT
63 AGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTATAAAAATGCTAAGCATAATTTT
* * * *
185974 TAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGTTAAGCCTGATTTTTAGGGGTTTCTT
128 CAGGGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTT
* * * * *
186039 GATGTTTTCAAATGAATTTTAAAGAAGCTAAGCCTGATTTTTAGGGGCTTCTTGATGTTTTCAAA
193 GATGTTTTCAAATGAATTTGAAAGAAACTAAGCCTGATTTTCAGGAGCTTCTTGATGTGTTCAAA
* *
186104 TGAATTTGAAAGAAGCTAAGCCTGAT-TTTCAAGGGTTTCTTGATGTTTTCAAATAAATTTG
258 TGAATTTGAAAGAAGCTAAGCCTAATAATT-AAGGGTTTCTTGATGTTTTCAAATAAATTTG
*
186165 AAAGAAGCTAAGTCTGATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGC
1 AAAGAAGCTAAGTCTGATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAGCTAAGC
* * * *
186230 TTGATTTTTAGGGGTTTCTTGATG-TTTCAAATGAA-TT-TGAAAGTAGCTAAGCATGATTTTCA
66 CTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTATAAAAAT-GCTAAGCATAATTTTCA
186292 GGGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGA
130 GGGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGA
* *
186357 TGTTTTCAAATGAATTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATG
195 TGTTTTCAAATGAATTTGAAAGAAACTAAGCCTGATTTTCAGGAGCTTCTTGATGTGTTCAAATG
* * * * * *
186422 ATTTTTAAAGATGCTAAGCCTAATAATTAGGGGTTTTTTGATGTTTTCAAATGAATTTG
260 AATTTGAAAGAAGCTAAGCCTAATAATTAAGGGTTTCTTGATGTTTTCAAATAAATTTG
* *
186481 AAGGAAGCTAAG-CTTGATTTATAGGGGTTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTA
1 AAAGAAGCTAAGTC-TGATTT-TAGGGGTTTCTTGATGTTTTCAAATGAA-TTTCAAAGAAGCTA
* *
186545 ATCCTAATTTTTAGGGGTTTCTTGATG
63 AGCCTGATTTTTAGGGGTTTCTTGATG
186572 ATAACTGTAA
Statistics
Matches: 359, Mismatches: 43, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
315 6 0.02
316 201 0.56
317 40 0.11
318 70 0.19
319 10 0.03
320 10 0.03
321 22 0.06
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (318 bp):
AAAGAAGCTAAGTCTGATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAGCTAAGC
CTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTATAAAAATGCTAAGCATAATTTTCAG
GGGTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGAT
GTTTTCAAATGAATTTGAAAGAAACTAAGCCTGATTTTCAGGAGCTTCTTGATGTGTTCAAATGA
ATTTGAAAGAAGCTAAGCCTAATAATTAAGGGTTTCTTGATGTTTTCAAATAAATTTG
Found at i:187109 original size:238 final size:239
Alignment explanation
Indices: 186665--187111 Score: 707
Period size: 240 Copynumber: 1.9 Consensus size: 239
186655 TCTTTCGAGC
* * * * * * *
186665 ATGATGTTTAAATTCTTTGGGCCATCTATAAGTCTTTCGAGCAAGATGAAAAGTCTTTCGGGCCA
1 ATGATGATTAAATCCTTCGGGCCATCTATAAGTATTTCAAACAAGATGAAAACTCTTTCGGGCCA
* *
186730 TCCATAAGACCTTCGGGTAGGATGTTTTCATATGATTTTCGTAAAATGAGAAAGAGATTTCCAAA
66 TCCATAAGACCTTCGGGCAGGATGTTTTCATATGATTTTCGAAAAATGAG-AAGAGATTTCCAAA
* *
186795 GTTTCTCATTAAATCCTTTCTAAAAGTTGATTTTTCTTGAAAAGTAAGAAAATGATTTCCAAAGT
130 GTTTCTCATTAAATACTTTCTAAAAGTTGATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGT
186860 TTCTTACTTAGTAAGTCCTTTCTGCCATAAGTAATTGTTTTGAGT
195 TTCTTACTTAGTAAGTCCTTTCTGCCATAAGTAATTGTTTTGAGT
* *
186905 ATGATGATTAAATCCTTCGGGTCATCTATAAGTATTTCAAACAAGATGATAACTCTTTCGGGCCA
1 ATGATGATTAAATCCTTCGGGCCATCTATAAGTATTTCAAACAAGATGAAAACTCTTTCGGGCCA
* * *
186970 TCTATAAGACCTTTGGGCAGGATGTTTTCATATGATTTTCGAAAAATGAG-AGCGATTTCCAAAG
66 TCCATAAGACCTTCGGGCAGGATGTTTTCATATGATTTTCGAAAAATGAGAAGAGATTTCCAAAG
* * *
187034 TTTCTCATTAAATATTTTCTGAACGTTGATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTT
131 TTTCTCATTAAATACTTTCTAAAAGTTGATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTT
187099 TCTTACTTAGTAA
196 TCTTACTTAGTAA
187112 ATCCCTTGGG
Statistics
Matches: 188, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
238 86 0.46
240 102 0.54
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (239 bp):
ATGATGATTAAATCCTTCGGGCCATCTATAAGTATTTCAAACAAGATGAAAACTCTTTCGGGCCA
TCCATAAGACCTTCGGGCAGGATGTTTTCATATGATTTTCGAAAAATGAGAAGAGATTTCCAAAG
TTTCTCATTAAATACTTTCTAAAAGTTGATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTT
TCTTACTTAGTAAGTCCTTTCTGCCATAAGTAATTGTTTTGAGT
Found at i:187153 original size:238 final size:239
Alignment explanation
Indices: 186636--187174 Score: 749
Period size: 238 Copynumber: 2.3 Consensus size: 239
186626 ATGAGTAAGA
* * * *
186636 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATTCTTTGGGCCATCTATAAGTCTT
1 CCTTC-GGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGCCATCTATAAGTATT
* * * *
186701 TCGAGCAAGATGAAAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCATATGAT
65 TCAAACAAGATGAAAACTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCATATGAT
* *
186766 TTTCGTAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTAAATCCTTTCTAAAAGTTGATTTTTC
130 TTTCGAAAAATGAG-AAGAGATTTCCAAAGTTTCTCATTAAATACTTTCTAAAAGTTGATTTTTC
* *
186831 TTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTC
194 TTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAATC
* * * * * * * *
186877 CTTTCTGCCATAAGTAATTGTTTTGAGTATGATGATTAAATCCTTCGGGTCATCTATAAGTATTT
1 CCTTCGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGCCATCTATAAGTATTT
* * *
186942 CAAACAAGATGATAACTCTTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCATATGATT
66 CAAACAAGATGAAAACTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCATATGATT
* * * *
187007 TTCGAAAAATGAG-AGCGATTTCCAAAGTTTCTCATTAAATATTTTCTGAACGTTGATTTTTCTT
131 TTCGAAAAATGAGAAGAGATTTCCAAAGTTTCTCATTAAATACTTTCTAAAAGTTGATTTTTCTT
187071 GAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAATC
196 GAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAATC
* * * * *
187115 CCTTGGGTCACT-AGTAAGTCTTTCGAGCATGGTGATTAAGTTCTTCGGGCCATCCATAAG
1 CCTTCGGCCA-TAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGCCATCTATAAG
187175 ACTATCAAGC
Statistics
Matches: 257, Mismatches: 40, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
238 133 0.52
239 1 0.00
240 119 0.46
241 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (239 bp):
CCTTCGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGCCATCTATAAGTATTT
CAAACAAGATGAAAACTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCATATGATT
TTCGAAAAATGAGAAGAGATTTCCAAAGTTTCTCATTAAATACTTTCTAAAAGTTGATTTTTCTT
GAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAATC
Found at i:192358 original size:14 final size:14
Alignment explanation
Indices: 192341--192371 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
192331 TTAAAACCTT
192341 TACAAGCAAACCCC
1 TACAAGCAAACCCC
*
192355 TACAATCAAACCCC
1 TACAAGCAAACCCC
192369 TAC
1 TAC
192372 CTCAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.42, G:0.03, T:0.13
Consensus pattern (14 bp):
TACAAGCAAACCCC
Found at i:196235 original size:21 final size:21
Alignment explanation
Indices: 196209--196256 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
196199 AAACTTGGGA
196209 AAGCTCTATATGGTCTTAAGC
1 AAGCTCTATATGGTCTTAAGC
196230 AAGCTCTATATGGTCTTAAGC
1 AAGCTCTATATGGTCTTAAGC
196251 AAGCTC
1 AAGCTC
196257 CTTGCAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGCTCTATATGGTCTTAAGC
Found at i:206928 original size:3 final size:3
Alignment explanation
Indices: 206916--206948 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
206906 TTTGAATTTG
206916 TCT TCTT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TC
206949 CATATTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:210982 original size:16 final size:16
Alignment explanation
Indices: 210958--210990 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
210948 ATTGACTCCT
210958 TGTTCTTGACTTGGTG
1 TGTTCTTGACTTGGTG
*
210974 TGTTGTTGACTTGGTG
1 TGTTCTTGACTTGGTG
210990 T
1 T
210991 AATGGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.33, T:0.52
Consensus pattern (16 bp):
TGTTCTTGACTTGGTG
Found at i:211919 original size:53 final size:53
Alignment explanation
Indices: 211861--211962 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
211851 GGGTAACTAC
* * * *
211861 AAGATAGTACATGTTCATAGATAATTCTTAATCTTTTAACATTGAACGCGTAT
1 AAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGCGTAT
211914 AAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGC
1 AAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGC
211963 TCACATTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (53 bp):
AAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGCGTAT
Found at i:220521 original size:19 final size:19
Alignment explanation
Indices: 220497--220533 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
220487 ATTATAATTG
220497 ATGAAATTGTGAGATTTTA
1 ATGAAATTGTGAGATTTTA
220516 ATGAAATTGTGAGATTTT
1 ATGAAATTGTGAGATTTT
220534 GAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
ATGAAATTGTGAGATTTTA
Found at i:220816 original size:24 final size:24
Alignment explanation
Indices: 220756--220816 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
220746 TTTATGTTTT
* *
220756 ATGTAATAATTAATTAATAATTTAA
1 ATGTAAT-ATAAATTAACAATTTAA
*
220781 ATGTAATTTAAATTAACAATTTAA
1 ATGTAATATAAATTAACAATTTAA
220805 A-GTATATATAAA
1 ATGTA-ATATAAA
220817 AGATGAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 3 0.10
24 21 0.68
25 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
ATGTAATATAAATTAACAATTTAA
Found at i:222843 original size:42 final size:42
Alignment explanation
Indices: 222742--222835 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
222732 CGAAAATCAG
* *
222742 AAGAATCAATAAACTTAACAATTTCATGAAATTTAATAATAA
1 AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
* *
222784 AAGAATCAATAAACTTAACTATTTCACGCAATTTAATAACAA
1 AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
222826 AAGAATCAAT
1 AAGAATCAAT
222836 TACCTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (42 bp):
AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
Found at i:224169 original size:43 final size:43
Alignment explanation
Indices: 224036--224154 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 43
224026 AAAGTCTCAG
* * * *
224036 TTAGAGAAGAGGAACATAAGAAGAAGAAGGGGAAGAATCTAAA
1 TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCTAGA
* * *
224079 TTAGAGAATA--ACT-GAAGAATAAGAAGGGGAAGAATCTTGA
1 TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCTAGA
224119 TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGA
1 TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGA
224155 GACTCGGTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.50
41 1 0.02
42 2 0.03
43 29 0.45
ACGTcount: A:0.51, C:0.03, G:0.31, T:0.14
Consensus pattern (43 bp):
TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCTAGA
Found at i:224177 original size:43 final size:43
Alignment explanation
Indices: 224036--224179 Score: 143
Period size: 43 Copynumber: 3.4 Consensus size: 43
224026 AAAGTCTCAG
* * * * **
224036 TTAGAGAAGAGGAACATAAGAAGAAGAAGGGGAAGAATCTAAA
1 TTAGAGAACAGGAATAGAAGAATAAGAAGGGGAAGAATCTCGA
* * *
224079 TTAGAGAATA--ACT-GAAGAATAAGAAGGGGAAGAATCTTGA
1 TTAGAGAACAGGAATAGAAGAATAAGAAGGGGAAGAATCTCGA
* *
224119 TTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAGA-CTCGG
1 TTAGAGAACAGGAATAGAAGAATAAGAAGGGGAAGA-ATCTCGA
*
224162 TTAGAGAACATGAATAGA
1 TTAGAGAACAGGAATAGA
224180 GATAGAAGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 32 0.38
41 1 0.01
42 2 0.02
43 48 0.57
44 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.31, T:0.15
Consensus pattern (43 bp):
TTAGAGAACAGGAATAGAAGAATAAGAAGGGGAAGAATCTCGA
Found at i:226406 original size:26 final size:26
Alignment explanation
Indices: 226372--226422 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
226362 TACATTTGTA
* * *
226372 CATATATATATTCATACTTCATACAT
1 CATACATATATACATACATCATACAT
*
226398 CATACATATGTACATACATCATACA
1 CATACATATATACATACATCATACA
226423 CTTATGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (26 bp):
CATACATATATACATACATCATACAT
Found at i:228089 original size:26 final size:26
Alignment explanation
Indices: 228053--228112 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
228043 ATCGAAGTGC
228053 TAATACACATAAGGACATGCCCACCA
1 TAATACACATAAGGACATGCCCACCA
* ***
228079 TAATACACATATGGTTGTGCCCACCA
1 TAATACACATAAGGACATGCCCACCA
228105 TAATACAC
1 TAATACAC
228113 TTAGTGCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGACATGCCCACCA
Found at i:229044 original size:30 final size:30
Alignment explanation
Indices: 228987--229056 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
228977 CAACCATTCA
* *
228987 CAACTTTTCCAAAATTATTGATTTGGTCCCC
1 CAACTTTT-CAAAATTATAGATATGGTCCCC
229018 CAACTTTTCAAAATATATAGA-ATGGTCCCC
1 CAACTTTTCAAAAT-TATAGATATGGTCCCC
* *
229048 AAATTTTTC
1 CAACTTTTC
229057 TAAGGCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (30 bp):
CAACTTTTCAAAATTATAGATATGGTCCCC
Found at i:241566 original size:23 final size:23
Alignment explanation
Indices: 241529--241634 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
241519 GTCGAAGGTT
*
241529 CTATGTGGTCCTTTGGGACAAAA
1 CTATGTGGTCATTTGGGACAAAA
* *
241552 CTACGTGGTCATTTGAGACAAAA
1 CTATGTGGTCATTTGGGACAAAA
* * *
241575 TTATTTGGTCCTTTGGGACAAAA
1 CTATGTGGTCATTTGGGACAAAA
* *
241598 CTATATGGTCATTCGGGAC-AAA
1 CTATGTGGTCATTTGGGACAAAA
241620 -TATGTGG-CACTTTGG
1 CTATGTGGTCA-TTTGG
241635 TGCAAATTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.03
21 10 0.15
22 3 0.04
23 53 0.78
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (23 bp):
CTATGTGGTCATTTGGGACAAAA
Found at i:248487 original size:22 final size:23
Alignment explanation
Indices: 248438--248520 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
248428 GTCGAGGGTT
*
248438 CTATGTGGTCCTTAGGGAAAAAA
1 CTATGTGGTCCTTCGGGAAAAAA
*
248461 CTATGTGGTCCTTCGGG-GAAAA
1 CTATGTGGTCCTTCGGGAAAAAA
* *
248483 TTATGTGGTCCTTCGGGATAAAA
1 CTATGTGGTCCTTCGGGAAAAAA
*
248506 CTATGTAGTCCTTCG
1 CTATGTGGTCCTTCG
248521 AGACAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
22 20 0.38
23 33 0.62
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGAAAAAA
Found at i:249202 original size:23 final size:24
Alignment explanation
Indices: 249150--249204 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
249140 ATAAATTACA
* *
249150 CCGAAGTG-CCACGTAGAATTTTTC
1 CCGAAG-GACCACGTAGAATATGTC
249174 CCGAAGGACCACGTAGAA-ATGTC
1 CCGAAGGACCACGTAGAATATGTC
249197 CCGAAGGA
1 CCGAAGGA
249205 TCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (24 bp):
CCGAAGGACCACGTAGAATATGTC
Found at i:251080 original size:26 final size:26
Alignment explanation
Indices: 251051--251110 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
251041 ACCGAAGTGC
* *
251051 TAATACACGTAAATTCGTGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
*
251077 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
251103 TAATACAC
1 TAATACAC
251111 TTATTGCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.22
Consensus pattern (26 bp):
TAATACACATAAAGTCGTGCCCACCA
Found at i:254482 original size:31 final size:31
Alignment explanation
Indices: 254447--254519 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
254437 TGGGACTCCA
*
254447 AATCAAGCAAAGAAAAGGTGACATCTTCATC
1 AATCAAGCAAAGAAAAGATGACATCTTCATC
*
254478 AATCAAGCAAAGAAAAGATGACATCTTCATT
1 AATCAAGCAAAGAAAAGATGACATCTTCATC
254509 AATCAAGCAAA
1 AATCAAGCAAA
254520 ATACGTCAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (31 bp):
AATCAAGCAAAGAAAAGATGACATCTTCATC
Found at i:255162 original size:15 final size:15
Alignment explanation
Indices: 255142--255172 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
255132 GGACATTGAA
255142 ATTAGACATCATTTC
1 ATTAGACATCATTTC
*
255157 ATTAGAGATCATTTC
1 ATTAGACATCATTTC
255172 A
1 A
255173 CAAAAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (15 bp):
ATTAGACATCATTTC
Found at i:255622 original size:23 final size:22
Alignment explanation
Indices: 255591--255664 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
255581 GAAAGTGTAC
255591 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * *
255614 CGATACAT-CATGAA-GATGCAC
1 CGATGCATCCTTGAATG-TGCAT
255635 CGATGCATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
255658 CGATGCA
1 CGATGCA
255665 CTATGCTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 15 0.37
22 1 0.02
23 23 0.56
24 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:256127 original size:13 final size:13
Alignment explanation
Indices: 256109--256142 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
256099 TTCATATTGA
*
256109 TTTTCAAACATCG
1 TTTTCAAACATAG
256122 TTTTCAAACATAG
1 TTTTCAAACATAG
*
256135 CTTTCAAA
1 TTTTCAAA
256143 ATTGCCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:258558 original size:34 final size:33
Alignment explanation
Indices: 258519--258589 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
258509 TTTTGTAAAG
*
258519 GGGAAAGGTTATAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTAAGCCCGTG-AAAAACTA
* * * *
258553 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
258586 GGGA
1 GGGA
258590 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
Found at i:260523 original size:21 final size:20
Alignment explanation
Indices: 260476--260530 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
260466 AGTACTCAAG
260476 GGAGTATCGATACCTAGGGTA
1 GGAGTATCGATACCTA-GGTA
260497 -GAGTATCGATACTCTCA-GTA
1 GGAGTATCGATAC-CT-AGGTA
*
260517 GGAGTATTGATACC
1 GGAGTATCGATACC
260531 GAGCTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 16 0.53
21 13 0.43
22 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (20 bp):
GGAGTATCGATACCTAGGTA
Found at i:261818 original size:79 final size:79
Alignment explanation
Indices: 261658--261818 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 79
261648 TACGATTTCC
* * * ** ** *
261658 TTTTTCAAAATAGGAAAATAAAATCAACGATTTATTTTCTTTTATGAACCAGGAAAATAAATTAA
1 TTTTTCAAAATAAGAAAATAAAATCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTAA
*
261723 ACGATTTATTTTAT
66 ACGATTTATTTCAT
* * **
261737 TTTTTCAAAATAAGAAAATAAATTCAACAATTCATTACCTTTTACAAAACATGAAAATAAATTCG
1 TTTTTCAAAATAAGAAAATAAAATCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTAA
* *
261802 ACGGTTTGTTTCAT
66 ACGATTTATTTCAT
261816 TTT
1 TTT
261819 ACAAGATAGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (79 bp):
TTTTTCAAAATAAGAAAATAAAATCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTAA
ACGATTTATTTCAT
Found at i:262008 original size:58 final size:58
Alignment explanation
Indices: 261923--262331 Score: 465
Period size: 58 Copynumber: 7.1 Consensus size: 58
261913 CCTTTTATAA
* * * * * *
261923 AATCATTTAAAATTATCAAGAAAATAAATTTAACAATTTCTTTCTT-TCTA-AAAGATAG
1 AATCATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTT-TTCT-TACAAAGTTAG
* * * * * *
261981 AATCATCCACGATTCTTAAGAAAATAAATTCAACGATTTATTTTTCATACAAATTTAG
1 AATCATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* *
262039 AATCATTCAAGATTCTCAAGAAAATAAATTAAACAATTTATTTTTCTTACAAAGTTAC
1 AATCATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* * *
262097 AATCATTCAAGATTCTCAAGGAAAT-AATTCAAACTATTTA-TTTTCATTATAAAGTTAG
1 AATCATTCAAGATTCTCAAGAAAATAAATTC-AACAATTTATTTTTC-TTACAAAGTTAG
* * * **
262155 AATCATTTAAGATTCTCAAGGAAATAAA-TCTAACTATACATTTTTCTTACAAAGTTAG
1 AATCATTCAAGATTCTCAAGAAAATAAATTC-AACAATTTATTTTTCTTACAAAGTTAG
* *
262213 AATCATTCAAGATTCTAAATG-AAATAAATTCAACAATTT-TTTTTCTTACAAAATTAG
1 AATCATTCAAGATTCTCAA-GAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* * *
262270 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTAATTTTCCTTACAAAGTTA-
1 AATCATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
262327 AATCA
1 AATCA
262332 ACACAAGATT
Statistics
Matches: 301, Mismatches: 40, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
56 1 0.00
57 70 0.23
58 220 0.73
59 10 0.03
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (58 bp):
AATCATTCAAGATTCTCAAGAAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
Found at i:262571 original size:44 final size:47
Alignment explanation
Indices: 262483--262646 Score: 141
Period size: 45 Copynumber: 3.6 Consensus size: 47
262473 AAATTAATAA
*
262483 TTTAA-TTTTAGCAACTCAATAATCAGAATGAACTAATTCTTTGA-T
1 TTTAATTTTTAGCAACTCAATAATCAAAATGAACTAATTCTTTGATT
*
262528 TTTAATTTTTA-CAA-TCCAATAAT-AAAATGAGCTAA-TCATTTGATT
1 TTTAATTTTTAGCAACT-CAATAATCAAAATGAACTAATTC-TTTGATT
* ** * *
262573 TTTAATTTTCA-CTTCCCAATAATCGAAAA-GAATTAA-TCTTTTGATT
1 TTTAATTTTTAGCAACTCAATAATC-AAAATGAACTAATTC-TTTGATT
**
262619 TTTAA-TTTCCGCAACTCAATAATCAAAA
1 TTTAATTTTTAGCAACTCAATAATCAAAA
262647 GTTTTGGATT
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
43 2 0.02
44 16 0.16
45 42 0.43
46 34 0.35
47 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (47 bp):
TTTAATTTTTAGCAACTCAATAATCAAAATGAACTAATTCTTTGATT
Found at i:263264 original size:41 final size:41
Alignment explanation
Indices: 263175--263292 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 41
263165 TTCCATGAAA
*
263175 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCC-GAAAATGTTT
263217 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
*
263258 TCCCGTGTTTGTTTCACGTAATTCATTTTTCCGAA
1 TCCCGTGTTTGTTTCACGTAATTC-GTTTTCCGAA
263293 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
41 34 0.47
42 39 0.53
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (41 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
Found at i:263506 original size:21 final size:23
Alignment explanation
Indices: 263463--263513 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
263453 CATTTTCATC
263463 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
263487 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
263508 ATAATA
1 AAAATA
263514 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:263533 original size:21 final size:23
Alignment explanation
Indices: 263465--263541 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
263455 TTTTCATCAA
* *
263465 AATATTATTTATTAAAATATTTAA-
1 AATA-TATATATTAATAT-TTTAAT
*
263489 AATATATTTATTAATATTTATAAT
1 AATATATATATTAATATTT-TAAT
263513 AATATA-ATATT-ATATTTTAAT
1 AATATATATATTAATATTTTAAT
*
263534 ATTATATA
1 AATATATA
263542 AAATAATCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.19
22 9 0.19
23 19 0.40
24 10 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATATATATTAATATTTTAAT
Found at i:263535 original size:30 final size:30
Alignment explanation
Indices: 263499--263656 Score: 96
Period size: 30 Copynumber: 5.6 Consensus size: 30
263489 AATATATTTA
263499 TTAATATTTATAATAATATAATATTATATT
1 TTAATATTTATAATAATATAATATTATATT
* *
263529 TTAATA-TTAT-ATAAAAT-A-ATCA-A--
1 TTAATATTTATAATAATATAATATTATATT
263552 TT-ATA-TTATAATAATATAAGATATTATATT
1 TTAATATTTATAATAATAT-A-ATATTATATT
* * *
263582 TTTAT-TTTAATAAT-ATATAATA-AATTTT
1 TTAATATTT-ATAATAATATAATATTATATT
*
263610 TTATATATTTAATAATGA-ATAATATTAT-TT
1 TTA-ATATTT-ATAATAATATAATATTATATT
*
263640 AT-ATATTTA-AATAATAT
1 TTAATATTTATAATAATAT
263657 TTTAGTAAAG
Statistics
Matches: 102, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
22 7 0.07
23 8 0.08
25 1 0.01
26 8 0.08
27 7 0.07
28 19 0.19
29 9 0.09
30 27 0.26
31 11 0.11
32 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTAATATTTATAATAATATAATATTATATT
Found at i:263646 original size:28 final size:29
Alignment explanation
Indices: 263490--263656 Score: 112
Period size: 29 Copynumber: 5.6 Consensus size: 29
263480 AATATTTAAA
*
263490 ATATATTTATTAATATTTATAATAATATAATATT
1 ATATATTTAATAATA--TATAATAAT-T-AT-TT
* * *
263524 ATAT-TTTAATATTATATAAAATAATCAATT
1 ATATATTTAATA--ATATATAATAATTATTT
* *
263554 ATAT-TATAATAATATA-AGATATTATATTT
1 ATATATTTAATAATATATA-ATAAT-TATTT
* *
263583 TTAT-TTTAATAATATATAATAAATTTTTT
1 ATATATTTAATAATATATAAT-AATTATTT
263612 ATATATTTAATAATGA-ATAAT-ATTATTT
1 ATATATTTAATAAT-ATATAATAATTATTT
263640 ATATATTTAAATAATAT
1 ATATATTT-AATAATAT
263657 TTTAGTAAAG
Statistics
Matches: 109, Mismatches: 14, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 24 0.22
29 32 0.29
30 29 0.27
31 2 0.02
33 14 0.13
34 4 0.04
35 3 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATATTTAATAATATATAATAATTATTT
Found at i:264102 original size:20 final size:20
Alignment explanation
Indices: 263984--264093 Score: 202
Period size: 20 Copynumber: 5.5 Consensus size: 20
263974 TTTCCAGATG
263984 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
264004 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
264024 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
264044 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
264064 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
264084 TTTTCCAGAA
1 TTTTCCAGAA
264094 TTCAAATTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:264109 original size:29 final size:30
Alignment explanation
Indices: 264076--264148 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
264066 TTCCAAAAAT
264076 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
264105 GTAATTTATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
264135 GTAATTCATTTTCC
1 GTAATTCATTTTCC
264149 GGAAAATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:264118 original size:15 final size:15
Alignment explanation
Indices: 264076--264148 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
264066 TTCCAAAAAT
264076 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
264091 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
264105 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
** *
264120 GTAATTCAAATTCTA
1 GTAATTCATTTTCCA
264135 GTAATTCATTTTCC
1 GTAATTCATTTTCC
264149 GGAAAATCAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:266111 original size:23 final size:23
Alignment explanation
Indices: 266085--266145 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
266075 AATTAAATAA
* *
266085 TTATTTATATATATTTATAAAAT
1 TTATTTATATATATTCAAAAAAT
*
266108 TTATATTAAAT-TATTCAAAAAAT
1 TTAT-TTATATATATTCAAAAAAT
266131 TATATTTATA-ATATT
1 T-TATTTATATATATT
266146 ATTTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTATATATATTCAAAAAAT
Found at i:266165 original size:20 final size:22
Alignment explanation
Indices: 266130--266170 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
266120 ATTCAAAAAA
*
266130 TTATATTTATAATA-TTATTTT
1 TTATATTTAAAATATTTATTTT
266151 TTATA-TTAAAATATTTATTT
1 TTATATTTAAAATATTTATTT
266171 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATATTTAAAATATTTATTTT
Found at i:267115 original size:69 final size:70
Alignment explanation
Indices: 266955--267197 Score: 210
Period size: 69 Copynumber: 3.5 Consensus size: 70
266945 ATAGAGAATT
* * * * * *** *
266955 ATGATTAGGCGCTCCCGTGAGAG--ACTTTAATCCTTCG-AGGCTCCCGCGCGAGACACCCGAAA
1 ATGATTAGGCGCTCCCATGCGAGTCGCTCTAACCCTTCGAAGGCTCCCATACGAGACACCCAAAA
*
267017 TACAT
66 TACAC
* ** * * *
267022 ATGATTAGGCGCTCTCATATGAGTCGCTCTAATCCTTCGGA-TCTCCCATACGAGACACCCAAAA
1 ATGATTAGGCGCTCCCATGCGAGTCGCTCTAACCCTTCGAAGGCTCCCATACGAGACACCCAAAA
*
267086 TTA-AT
66 -TACAC
* * ** * * *
267091 ATGATTAGGTGTTCCTGTGCGAGTCTCTCTAACCCTT-GAAGGCTCCCATACGAGACACTCAGAA
1 ATGATTAGGCGCTCCCATGCGAGTCGCTCTAACCCTTCGAAGGCTCCCATACGAGACACCCAAAA
267155 TACAC
66 TACAC
*
267160 ATGATTAGGCGCTCCCATGCGAGTCGTTCTAACCCTTC
1 ATGATTAGGCGCTCCCATGCGAGTCGCTCTAACCCTTC
267198 AGAACTTCTG
Statistics
Matches: 138, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
67 19 0.14
68 4 0.03
69 112 0.81
70 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (70 bp):
ATGATTAGGCGCTCCCATGCGAGTCGCTCTAACCCTTCGAAGGCTCCCATACGAGACACCCAAAA
TACAC
Found at i:267259 original size:2 final size:2
Alignment explanation
Indices: 267252--267301 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
267242 CTGATTCGTG
267252 TA TA TA TA TA TA TA TA TA 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
267294 TA TA TA TA
1 TA TA TA TA
267302 AACTTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:267415 original size:20 final size:20
Alignment explanation
Indices: 267377--267415 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
267367 TCAGCCCAAT
* * *
267377 AGTATCGGTACTCCCATAGG
1 AGTATCGATACTACAATAGG
267397 AGTATCGATACTACAATAG
1 AGTATCGATACTACAATAG
267416 CTTGGTATCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTACAATAGG
Found at i:269309 original size:19 final size:22
Alignment explanation
Indices: 269285--269337 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
269275 GTAAAAATGA
*
269285 TATCGATACCGTA-T-TAG-AG
1 TATCGATACCATAGTATAGTAG
*
269304 TATCGATATCATAGTATAGTAG
1 TATCGATACCATAGTATAGTAG
269326 TATCGATACCAT
1 TATCGATACCAT
269338 GGTAGGGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 1 0.04
21 3 0.11
22 13 0.46
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (22 bp):
TATCGATACCATAGTATAGTAG
Found at i:269350 original size:20 final size:20
Alignment explanation
Indices: 269325--269373 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
269315 TAGTATAGTA
269325 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
269345 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
269365 GTATCGATA
1 GTATCGATA
269374 ATATTGAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATGGTAGGG
Found at i:269789 original size:55 final size:55
Alignment explanation
Indices: 269698--269970 Score: 366
Period size: 55 Copynumber: 4.9 Consensus size: 55
269688 CTAAGTGTAC
* *
269698 TACAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
269753 TACATGTACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATTAATAACCG
1 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * * * * * * *
269808 TACAAGCACTATGTATGCAAGTCCATGAAATTCATCATGAGTTGATAAATAATCA
1 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
269863 TACAGGCACTATGTGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAACTAACTG
1 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAAC---C-G
* *
269922 TACATGCACCATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAA
1 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA
269971 CTACCATATA
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
55 143 0.76
58 1 0.01
59 45 0.24
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (55 bp):
TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:276213 original size:19 final size:22
Alignment explanation
Indices: 276189--276242 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
276179 TGCAAAAATG
*
276189 GTATCGATACCGT-AT-TAG-A
1 GTATCGATACCATAATATAGTA
*
276208 GTATCGGTACCATAATATAGTA
1 GTATCGATACCATAATATAGTA
276230 GTATCGATACCAT
1 GTATCGATACCAT
276243 GGTAGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 3 0.10
22 13 0.45
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAATATAGTA
Found at i:276675 original size:55 final size:55
Alignment explanation
Indices: 276591--276874 Score: 403
Period size: 55 Copynumber: 5.2 Consensus size: 55
276581 TGTACTATAA
* * *
276591 GCACTATGTGTGCAAATCCATGGAATTCATCATGAATTGATGAATAACCGTACAT
1 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAG
* *
276646 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACAA
1 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAG
* **
276701 GCA-TATGTGT-AAAATCCACATAATTCATCATGAGTTGATGAATAACCGTACAG
1 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAG
* ** *
276754 GCACTATGTGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAATTGTACAT
1 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAG
* * *
276809 GCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTAATGAACT-ACCGTATAG
1 GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAG
276864 GCACTATGTGT
1 GCACTATGTGT
276875 ACATCTTAAT
Statistics
Matches: 203, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
53 41 0.20
54 14 0.07
55 147 0.72
56 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAG
Found at i:276793 original size:108 final size:110
Alignment explanation
Indices: 276589--276874 Score: 416
Period size: 108 Copynumber: 2.6 Consensus size: 110
276579 AGTGTACTAT
* ** * *
276589 AAGCACTATGTGTGCAAATCCATGGAATTCATCATGAATTGATGAATAACCGTACATGCACTATG
1 AAGCACTATGTGTGAAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATG
*
276654 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATAC
66 TGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAACCATAC
*
276699 AAGCA-TATGTGT-AAAATCCACATAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATG
1 AAGCACTATGTGTGAAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATG
***
276762 TGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAATTGTAC
66 TGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAACCATAC
* * * *
276807 ATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTAATGAACT-ACCGTATAGGCACTAT
1 AAGCACTATGTGTGAAAATCCACAGAATTCATCATGAGTTGATGAA-TAACCGTACAGGCACTAT
276871 GTGT
65 GTGT
276875 ACATCTTAAT
Statistics
Matches: 158, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
108 90 0.57
109 14 0.09
110 53 0.34
111 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (110 bp):
AAGCACTATGTGTGAAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATG
TGTGCAAATCCAAGGAATTCATCATGAGTTGATGAATAACCATAC
Found at i:283629 original size:134 final size:135
Alignment explanation
Indices: 283444--284032 Score: 728
Period size: 134 Copynumber: 4.4 Consensus size: 135
283434 CAGATCTCAA
* * * ** * * * *
283444 AAAATTTTGATTCACTTCGCTACTCTTCAGGCTAGAATGAATC-AAATGTGATTTACTTAATTGC
1 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTTACTTCACTGC
* *
283508 TCTTTAGGAAGATCAAAT-TGAAAGAAAGAGAATCAGCTCCACTACTCTTTAGGGGAGGTCAGAC
66 TCTTCAGGAAGATCAAATCTGAAAGAAAGAGAATCTGCTCCACTACTCTTTAGGGGAGGTCAGAC
283572 TCGAGG
131 TCGA-G
* * * * * *
283578 AAAACTTTGATCCACTTCTCTACTCTTTAGGGAAGATTGGATC-GAATGTGATTTGCTTCACTGC
1 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTTACTTCACTGC
* * *
283642 TCTTCAGAAAGATCAAATCTGAAAGAAAGAAAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGAC
66 TCTTCAGGAAGATCAAATCTGAAAGAAAGAGAATCTGCTCCACTACTCTTTAGGGGAGGTCAGAC
283707 TCGAG
131 TCGAG
* * * * * *
283712 GAAACTTTGATTCATTTCACTGCTCTTCA--GAAGATTGAATCGGACTTTGATTTCCTTCACTAC
1 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTTACTTCACTGC
*
283775 TCTTCAGGAAGATCAAATCTGAAAGAAAAAGAATCTGCT-CATCTACTCTTTAGGGGAGGTCAGA
66 TCTTCAGGAAGATCAAATCTGAAAGAAAGAGAATCTGCTCCA-CTACTCTTTAGGGGAGGTCAGA
283839 CTCGAG
130 CTCGAG
* * *
283845 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTAAATCGGACTATGATTTACTTCACTGC
1 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTTACTTCACTGC
* ** * *
283910 ACTTCA-GAAGATCAAATCTGAAAG-AAGAAGAATCTGCTCTGCTACTCCTTAGGGGAGGTCATA
66 TCTTCAGGAAGATCAAATCTGAAAGAAAG-AGAATCTGCTCCACTACTCTTTAGGGGAGGTCAGA
*
283973 CTTGAG
130 CTCGAG
* * * *
283979 AAAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAAGCAG-ATGTGATTT
1 AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTT
284033 GTTTCAAAAA
Statistics
Matches: 396, Mismatches: 52, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
132 12 0.03
133 117 0.30
134 185 0.47
135 82 0.21
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (135 bp):
AAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGAATGTGATTTACTTCACTGC
TCTTCAGGAAGATCAAATCTGAAAGAAAGAGAATCTGCTCCACTACTCTTTAGGGGAGGTCAGAC
TCGAG
Found at i:283964 original size:267 final size:268
Alignment explanation
Indices: 283507--284019 Score: 757
Period size: 267 Copynumber: 1.9 Consensus size: 268
283497 TACTTAATTG
* *
283507 CTCTTTAGGAAGATCAAATTGAAAGAAAGAGAATCAGCTCCACTACTCTTTAGGGGAGGTCAGAC
1 CTCTTCAGGAAGATCAAATTGAAAGAAAAAGAATCAGCTCCACTACTCTTTAGGGGAGGTCAGAC
* * ** * *
283572 TCGAGGAAAACTTTGATCCACTTCTCTACTCTTTAGGGAAGATTGGATCGAATGTGATTTGCTTC
66 TCGAGGAAAACTTTGATCCACTTCACTACTCTTCAGGGAAGATTAAATCGAATATGATTTACTTC
* *
283637 ACTGCTCTTCAGAAAGATCAAATCTGAAAGAAAGAAAATCTGCTCCGCTACTCTTTAGGGGAGGT
131 ACTGCACTTCAGAAAGATCAAATCTGAAAGAAAGAAAATCTGCTCCGCTACTCCTTAGGGGAGGT
* * *
283702 CAGACTCGAGGAAACTTTGATTCATTTCACTGCTCTTCA-GAAGATTGAATCGGACTTTGATTTC
196 CAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGAAGATTGAATCGGACTTTGATTTC
283766 CTTCACTA
261 CTTCACTA
*
283774 CTCTTCAGGAAGATCAAATCTGAAAGAAAAAGAATCTGCT-CATCTACTCTTTAGGGGAGGTCAG
1 CTCTTCAGGAAGATCAAAT-TGAAAGAAAAAGAATCAGCTCCA-CTACTCTTTAGGGGAGGTCAG
* * *
283838 ACTCGA-GAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTAAATCGGACTATGATTTAC
64 ACTCGAGGAAAACTTTGATCCACTTCACTACTCTTCAGGGAAGATTAAATC-GAATATGATTTAC
*
283902 TTCACTGCACTTCAG-AAGATCAAATCTGAAAG-AAGAAGAATCTGCTCTGCTACTCCTTAGGGG
128 TTCACTGCACTTCAGAAAGATCAAATCTGAAAGAAAGAA-AATCTGCTCCGCTACTCCTTAGGGG
* * *
283965 AGGTCATACTTGAGAAAACTTTGATCCACTTCTCTGCTCTTCAGGGAAGATTGAA
192 AGGTCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCA-GGAAGATTGAA
284020 GCAGATGTGA
Statistics
Matches: 219, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
266 5 0.02
267 135 0.62
268 69 0.32
269 10 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (268 bp):
CTCTTCAGGAAGATCAAATTGAAAGAAAAAGAATCAGCTCCACTACTCTTTAGGGGAGGTCAGAC
TCGAGGAAAACTTTGATCCACTTCACTACTCTTCAGGGAAGATTAAATCGAATATGATTTACTTC
ACTGCACTTCAGAAAGATCAAATCTGAAAGAAAGAAAATCTGCTCCGCTACTCCTTAGGGGAGGT
CAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGAAGATTGAATCGGACTTTGATTTC
CTTCACTA
Found at i:285326 original size:7 final size:7
Alignment explanation
Indices: 285310--285421 Score: 99
Period size: 7 Copynumber: 16.3 Consensus size: 7
285300 ACCCCATTTA
285310 TTTT-TT
1 TTTTATT
285316 TTTTATT
1 TTTTATT
285323 TTTTATT
1 TTTTATT
285330 TTTTATT
1 TTTTATT
285337 TTTTATT
1 TTTTATT
285344 TTTTATT
1 TTTTATT
*
285351 TTTT-CT
1 TTTTATT
285357 TTTT-TT
1 TTTTATT
**
285363 TTTCCTT
1 TTTTATT
*
285370 TTTTCTT
1 TTTTATT
**
285377 TTTT-CC
1 TTTTATT
285383 TTTTATT
1 TTTTATT
285390 TTTTATT
1 TTTTATT
285397 TGTTT-TT
1 T-TTTATT
*
285404 CTTCTTCTT
1 -TT-TTATT
285413 TTTTATT
1 TTTTATT
285420 TT
1 TT
285422 ATCCTCGGGC
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
6 17 0.19
7 63 0.70
8 8 0.09
9 2 0.02
ACGTcount: A:0.07, C:0.08, G:0.01, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:285350 original size:39 final size:38
Alignment explanation
Indices: 285311--285404 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
285301 CCCCATTTAT
* **
285311 TTTTTTTTTATTTTTT-ATTTTTTATTTTTTATTTTTTA
1 TTTTTTTTTTTTTTTTCATTTTTTATTTTTT-CCTTTTA
* *
285349 TTTTTTCTTTTTTTTTTCCTTTTTTCTTTTTTCCTTTTA
1 TTTTTT-TTTTTTTTTTCATTTTTTATTTTTTCCTTTTA
* *
285388 TTTTTTATTTGTTTTTC
1 TTTTTTTTTTTTTTTTC
285405 TTCTTCTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 15 0.32
39 20 0.43
40 12 0.26
ACGTcount: A:0.07, C:0.07, G:0.01, T:0.84
Consensus pattern (38 bp):
TTTTTTTTTTTTTTTTCATTTTTTATTTTTTCCTTTTA
Found at i:285372 original size:46 final size:46
Alignment explanation
Indices: 285310--285397 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
285300 ACCCCATTTA
* **
285310 TTTTTTTTTTA-TTTTTTATTTTTTATTTTTTATTTTTTATTTTTTC
1 TTTTTTTTTTACTTTTTTCTTTTTT-CCTTTTATTTTTTATTTTTTC
*
285356 TTTTTTTTTTCCTTTTTTCTTTTTTCCTTTTATTTTTTATTT
1 TTTTTTTTTTACTTTTTTCTTTTTTCCTTTTATTTTTTATTT
285398 GTTTTTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 25 0.68
47 12 0.32
ACGTcount: A:0.08, C:0.07, G:0.00, T:0.85
Consensus pattern (46 bp):
TTTTTTTTTTACTTTTTTCTTTTTTCCTTTTATTTTTTATTTTTTC
Found at i:285416 original size:1 final size:1
Alignment explanation
Indices: 285310--285403 Score: 62
Period size: 1 Copynumber: 94.0 Consensus size: 1
285300 ACCCCATTTA
* * * * * * ** *
285310 TTTTTTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTCTTTTTTTTTTCCTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * *
285375 TTTTTTCCTTTTATTTTTTATTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
285404 CTTCTTCTTT
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.07, C:0.06, G:0.01, T:0.85
Consensus pattern (1 bp):
T
Found at i:286367 original size:46 final size:46
Alignment explanation
Indices: 286308--286664 Score: 387
Period size: 46 Copynumber: 7.8 Consensus size: 46
286298 TAATATATCA
* ** * * *
286308 TTATGTATTTTCATTGGTGACATCCTTTCATGCCAATTATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
*
286354 TTAAT-CATTTTCATTTATGGCATCCTTTCATGCCTATAATGTACCG
1 TT-ATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
* *
286400 TTATGCATTTTCATTTATGCCATCCTTTCATGCCGATAATGTACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
* * *
286446 TTATGCATTTTCATTTATGGCATCCTTTTATGTCGATAATGTACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
* * * * *
286492 TTATACATTTTCATTTATGGCAT-ATTTTATGCCTATAATGAACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
* * * * *
286537 TTATACATTTTCATTTATGACATCCTTTCATG-TATATAATGCACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCA-ATAATGTACCG
* ** **
286583 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATACACTA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
* * * * *
286629 TTACGCATTTTTATTTATGTCCTCATTTCATGCCAA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAA
286665 AGGCATTTAA
Statistics
Matches: 270, Mismatches: 36, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
45 42 0.16
46 226 0.84
47 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.43
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGTACCG
Found at i:286576 original size:137 final size:138
Alignment explanation
Indices: 286306--286662 Score: 448
Period size: 137 Copynumber: 2.6 Consensus size: 138
286296 GTTAATATAT
* ** * * *
286306 CATTATGTATTTTCATTGGTGACATCCTTTCATGCCAATTATGCACCGTTAATCATTTTCATTTA
1 CATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAATCATTTTCATTTA
* * * * *
286371 TGGCATCCTTTCATGCCTATAATGTACCGTTATGCATTTTCATTTATGCCATCCTTTCATGCCGA
66 TGGCATCATTTCATGCCTATAATGAACCGTTATACATTTTCATTTATGACATCCTTTCATGCAGA
*
286436 TAATGTAC
131 TAATGCAC
* * * *
286444 CGTTATGCATTTTCATTTATGGCATCCTTTTATGTCGATAATGTACCGTT-ATACATTTTCATTT
1 CATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAT-CATTTTCATTT
* * *
286508 ATGGCAT-ATTTTATGCCTATAATGAACCGTTATACATTTTCATTTATGACATCCTTTCATGTAT
65 ATGGCATCATTTCATGCCTATAATGAACCGTTATACATTTTCATTTATGACATCCTTTCATGCAG
286572 ATAATGCAC
130 ATAATGCAC
* ** ** *
286581 CATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATACACTATTACGCATTTTTATTTA
1 CATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAATCATTTTCATTTA
* *
286646 TGTCCTCATTTCATGCC
66 TGGCATCATTTCATGCC
286663 AAAGGCATTT
Statistics
Matches: 184, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
137 117 0.64
138 67 0.36
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (138 bp):
CATTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAATCATTTTCATTTA
TGGCATCATTTCATGCCTATAATGAACCGTTATACATTTTCATTTATGACATCCTTTCATGCAGA
TAATGCAC
Found at i:286791 original size:70 final size:70
Alignment explanation
Indices: 286671--286810 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 70
286661 CCAAAGGCAT
* * * * * *
286671 TTAACCTTTCATCTAACTTGCATTATTGGAATCTTTTTGCCAAATGCACAGCTAGGCAAATAATC
1 TTAACCTCTCATCTAACTGGCATGATTGGAACCTTTCTGCCAAATACACAGCTAGGCAAATAATC
286736 TTTTA
66 TTTTA
* *
286741 TTAACCTCTCATCTAACTGGCATGATT-GATACCTTTCTGTCAAATACACAGCTAGGCAATTAAT
1 TTAACCTCTCATCTAACTGGCATGATTGGA-ACCTTTCTGCCAAATACACAGCTAGGCAAATAAT
286805 CTTTTA
65 CTTTTA
286811 CTCAAAGGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 2 0.03
70 59 0.97
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (70 bp):
TTAACCTCTCATCTAACTGGCATGATTGGAACCTTTCTGCCAAATACACAGCTAGGCAAATAATC
TTTTA
Found at i:286876 original size:81 final size:82
Alignment explanation
Indices: 286741--286908 Score: 266
Period size: 81 Copynumber: 2.1 Consensus size: 82
286731 TAATCTTTTA
* *
286741 TTAACCTCTCATCTAACTGGCATGATTGATACCTTTCTGTCAAATACACAGCTAGGCAATTAATC
1 TTAACCTCTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACACAGCTAGGCAATTAATC
286806 -TTTTACTCAAAGGTAT
66 TTTTTACTCAAAGGTAT
* * * *
286822 TTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAATTGCATAGCTAGGCAATTAATC
1 TTAACCTCTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACACAGCTAGGCAATTAATC
*
286887 TTTTTACTCATAGGTAT
66 TTTTTACTCAAAGGTAT
286904 TTAAC
1 TTAAC
286909 ACAAATTATA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 59 0.75
82 20 0.25
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (82 bp):
TTAACCTCTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACACAGCTAGGCAATTAATC
TTTTTACTCAAAGGTAT
Found at i:288094 original size:13 final size:13
Alignment explanation
Indices: 288076--288100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
288066 TGTTATAATT
288076 TAATCTAAATCAC
1 TAATCTAAATCAC
288089 TAATCTAAATCA
1 TAATCTAAATCA
288101 TTTCTCATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATCTAAATCAC
Done.