Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 25
Found at i:3149732 original size:18 final size:19
Alignment explanation
Indices: 3149695--3149741 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
3149685 TTTCTTCACT
3149695 TTTCTTTTTCTTTGAATTTTTC
1 TTTCTTTTTC-TT--ATTTTTC
3149717 -TTCTTTTTCTT-TTTTTC
1 TTTCTTTTTCTTATTTTTC
3149734 TTTCTTTT
1 TTTCTTTT
3149742 GCACTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
20 2 0.08
21 9 0.38
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTCTTATTTTTC
Found at i:3151853 original size:21 final size:19
Alignment explanation
Indices: 3151808--3151858 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
3151798 GTCTACCTAT
*
3151808 ATTTTAGGTTTAATCCTTA
1 ATTTTAGGTTTAAGCCTTA
* *
3151827 AATTTAGGTCTTAAAGCCTTC
1 ATTTTAGGT-TT-AAGCCTTA
3151848 ATTTTAGGTTT
1 ATTTTAGGTTT
3151859 CATATCACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.31
20 4 0.15
21 14 0.54
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (19 bp):
ATTTTAGGTTTAAGCCTTA
Found at i:3156315 original size:19 final size:19
Alignment explanation
Indices: 3156291--3156335 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3156281 AAACCTAGTG
3156291 TATGTGTTTGGCACGACCT
1 TATGTGTTTGGCACGACCT
3156310 TATGTGTTTGGCACGACCT
1 TATGTGTTTGGCACGACCT
3156329 TATGTGT
1 TATGTGT
3156336 CATATCCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (19 bp):
TATGTGTTTGGCACGACCT
Found at i:3164047 original size:21 final size:21
Alignment explanation
Indices: 3163993--3164055 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3163983 GATACCCCTG
3163993 TGGGGGGAATCGGTTCCCTTCA
1 TGGGGGGAATCGGTTCCC-TCA
**
3164015 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
3164036 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
3164056 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.24
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:3172463 original size:58 final size:58
Alignment explanation
Indices: 3172353--3172465 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
3172343 AGTGCAAGTG
* ** * *
3172353 GTGGGTACAACCTTATGTGTCATATTCGGATTAGCAATAGAGTGTGAACCTAGTGTAA
1 GTGGGCACAACCTTATGTGTCATAACCGGATTAGCAATAAAGCGTGAACCTAGTGTAA
*
3172411 GTGGGCACAACCTTATGTGTCATAACCGGATTAGCACTAAAGCGT-AAGCCTAGTG
1 GTGGGCACAACCTTATGTGTCATAACCGGATTAGCAATAAAGCGTGAA-CCTAGTG
3172466 CAACTTTAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 2 0.04
58 46 0.96
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (58 bp):
GTGGGCACAACCTTATGTGTCATAACCGGATTAGCAATAAAGCGTGAACCTAGTGTAA
Found at i:3191399 original size:81 final size:81
Alignment explanation
Indices: 3191305--3191552 Score: 300
Period size: 81 Copynumber: 3.1 Consensus size: 81
3191295 AAGCATTTAG
* * * * * *
3191305 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACCATTT-TGCCAAATG
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACC-TTTCTGTCAAATG
* **
3191369 CATAACTAGGCTTTTAA
65 CACAACTAGGCAATTAA
* * * *
3191386 TCTTTAACTCAAAGGGATTTATCCTTTCAGCTAACTGGCATAATTGTCACCTTTCTGTCAAATGC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
3191451 ACATCTAGGCAATTAA
66 ACAACTAGGCAATTAA
* * * * *
3191467 TCTTTAACTCAAATGTATTTAATCTTTCATCTAACTGGCAAAATTGACACTTTTCTGTCAAATGC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
3191532 ACAGCTAGGCAATTAA
66 ACAACTAGGCAATTAA
3191548 TCTTT
1 TCTTT
3191553 TATTTAAAAT
Statistics
Matches: 144, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 3 0.02
81 141 0.98
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAACTAGGCAATTAA
Found at i:3192114 original size:94 final size:94
Alignment explanation
Indices: 3191963--3192137 Score: 255
Period size: 94 Copynumber: 1.9 Consensus size: 94
3191953 CATGGAATCA
* *
3191963 ATACTTCTATACTGTGGTACCGATACTCCCTTTCAGTATTGATACCATTTCTACATTCTAG-ATC
1 ATACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTAGAATC
* *
3192027 TATGGTATTGATACTTTCCTTCTAGTACCG
66 CATGG-ATCGATACTTTCCTTCTAGTACCG
* * *
3192057 ATACTTCTATACTATGTTACCGATACTCCCTTTCAGTATCGATACCATTT-TGGCATTCTGGAAT
1 ATACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCT-ACATTCTAGAAT
3192121 CCATGGATCGATACTTT
65 CCATGGATCGATACTTT
3192138 ATTGGTATCG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
93 1 0.01
94 64 0.89
95 7 0.10
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (94 bp):
ATACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTAGAATC
CATGGATCGATACTTTCCTTCTAGTACCG
Found at i:3198346 original size:81 final size:81
Alignment explanation
Indices: 3198171--3198414 Score: 269
Period size: 81 Copynumber: 3.0 Consensus size: 81
3198161 AAGCATTTAG
* * * * * * * *
3198171 TCTTTTACCCAAAGGCATTTATCCTTTCATCTAACTTGCATGAA-TGGCAC-TTTCT-TCCAAAT
1 TCTTTAACTCAAAGGAATTTAACCTTTCATCTAACTAGCAT-AACTGACACATTTATGT-AAAAT
* *
3198233 GCACAACTAGCCATTTAA
64 GCACAACTAGGCAATTAA
* * * * * *
3198251 TCTTTAACTCAAAGGCATTTAGCCTTTTATCTAACTAGCATAATTGACATATTTATGTGAAATGC
1 TCTTTAACTCAAAGGAATTTAACCTTTCATCTAACTAGCATAACTGACACATTTATGTAAAATGC
*
3198316 ACAGCTAGGCAATTAA
66 ACAACTAGGCAATTAA
* * *
3198332 TCTTTAACTGAAAGGAATTTAACCTTTCATCTAACTTGCATAACTGACACATTTCTGTAAAATGC
1 TCTTTAACTCAAAGGAATTTAACCTTTCATCTAACTAGCATAACTGACACATTTATGTAAAATGC
3198397 ACAACTAGGCAATTAA
66 ACAACTAGGCAATTAA
3198413 TC
1 TC
3198415 ATTCATAATA
Statistics
Matches: 139, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.01
80 40 0.29
81 96 0.69
82 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (81 bp):
TCTTTAACTCAAAGGAATTTAACCTTTCATCTAACTAGCATAACTGACACATTTATGTAAAATGC
ACAACTAGGCAATTAA
Found at i:3198937 original size:94 final size:95
Alignment explanation
Indices: 3198793--3198976 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 95
3198783 CTACCATGGA
* * *
3198793 ATTGATACTTCAATATTGTGGTACCGATACTCCCGTTCAGTATCGGTACCATTTCT-ACATTATG
1 ATTGATACTTCAATACTATGGTACCGATACTCCCGTTCAGTATCGATACCATTT-TGACATTATG
*
3198857 G-ATCCATTGTATCAATACTTTCCTTCAAGT
65 GAATCCATGGTATCAATACTTTCCTTCAAGT
* * * * * * *
3198887 ATTGATAGTTCTATACTATGGTACTGGTACTCCCTTTCAGTATCGATACCATTTTGGCATTCTGG
1 ATTGATACTTCAATACTATGGTACCGATACTCCCGTTCAGTATCGATACCATTTTGACATTATGG
*
3198952 AATCCATGGTATCGATACTTTCCTT
66 AATCCATGGTATCAATACTTTCCTT
3198977 TTTAGTATCG
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
93 1 0.01
94 53 0.70
95 22 0.29
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (95 bp):
ATTGATACTTCAATACTATGGTACCGATACTCCCGTTCAGTATCGATACCATTTTGACATTATGG
AATCCATGGTATCAATACTTTCCTTCAAGT
Found at i:3199596 original size:5 final size:5
Alignment explanation
Indices: 3199586--3199610 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3199576 CCCTTTTCCT
3199586 CTTTA CTTTA CTTTA CTTTA CTTTA
1 CTTTA CTTTA CTTTA CTTTA CTTTA
3199611 ATACCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTTA
Found at i:3200068 original size:38 final size:38
Alignment explanation
Indices: 3200023--3200097 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
3200013 ATGAAAGAAC
*
3200023 AACATATTTCA-TTCTTTTAGGTTGGACATGAATGTATT
1 AACATATTCCATTTC-TTTAGGTTGGACATGAATGTATT
*
3200061 AACATATTCCATTTCTTTAGGTTGGAGATGAATGTAT
1 AACATATTCCATTTCTTTAGGTTGGACATGAATGTAT
3200098 GTTGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 31 0.91
39 3 0.09
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (38 bp):
AACATATTCCATTTCTTTAGGTTGGACATGAATGTATT
Found at i:3214069 original size:26 final size:26
Alignment explanation
Indices: 3214033--3214084 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3214023 GCCTTTCCTG
3214033 ATTGTAATCAATAAGCACATCATCAT
1 ATTGTAATCAATAAGCACATCATCAT
*
3214059 ATTGTAATCAATAAGCACGTCATCAT
1 ATTGTAATCAATAAGCACATCATCAT
3214085 TTTATAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (26 bp):
ATTGTAATCAATAAGCACATCATCAT
Found at i:3214096 original size:26 final size:26
Alignment explanation
Indices: 3214041--3214097 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3214031 TGATTGTAAT
* *
3214041 CAATAAGCACATCATCATATTGTAAT
1 CAATAAGCACATCATCATATTATAAA
* *
3214067 CAATAAGCACGTCATCATTTTATAAA
1 CAATAAGCACATCATCATATTATAAA
3214093 CAATA
1 CAATA
3214098 TAATCTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (26 bp):
CAATAAGCACATCATCATATTATAAA
Found at i:3217773 original size:24 final size:26
Alignment explanation
Indices: 3217720--3217773 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
3217710 TAATTCTATT
*
3217720 GGATCACCAAATGAACATACATGTTT
1 GGATCACCAAATGAACATACATGTTA
*
3217746 GGATCA-CAAA-GCACATAACAT-TTA
1 GGATCACCAAATGAACAT-ACATGTTA
3217770 GGAT
1 GGAT
3217774 TCACTTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.44
25 8 0.32
26 6 0.24
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (26 bp):
GGATCACCAAATGAACATACATGTTA
Found at i:3218454 original size:33 final size:33
Alignment explanation
Indices: 3218417--3218483 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3218407 TTAATATAAT
3218417 ATTAAAAATTATTAAAAATT-ATATTATAAGTAA
1 ATTAAAAATT-TTAAAAATTAATATTATAAGTAA
* * * *
3218450 ATTAAATATTTTAATAATTAATATTTTAATTAA
1 ATTAAAAATTTTAAAAATTAATATTATAAGTAA
3218483 A
1 A
3218484 ATGGTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATTAAAAATTTTAAAAATTAATATTATAAGTAA
Found at i:3218474 original size:15 final size:16
Alignment explanation
Indices: 3218449--3218479 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3218439 ATTATAAGTA
3218449 AATTAAATATTTTAAT
1 AATTAAATATTTTAAT
3218465 AATT-AATATTTTAAT
1 AATTAAATATTTTAAT
3218480 TAAAATGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAATATTTTAAT
Found at i:3225567 original size:36 final size:35
Alignment explanation
Indices: 3225507--3225620 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 35
3225497 AATTCTCTGC
* *
3225507 AGGTTCAACTTTGATCTAGCTGGTAATTCCTTATAT
1 AGGTTCAACTCTGATC-AGTTGGTAATTCCTTATAT
*
3225543 AGGTTCAACTCTGATCACGTTGGTAA-TCCTT-TAGC
1 AGGTTCAACTCTGATCA-GTTGGTAATTCCTTATA-T
* * * ** *
3225578 AGGTTCACCACCGATCAGTTCATAGTTCCTTATAT
1 AGGTTCAACTCTGATCAGTTGGTAATTCCTTATAT
3225613 AGGTTCAA
1 AGGTTCAA
3225621 TATTGATCAG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
34 7 0.11
35 32 0.51
36 24 0.38
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (35 bp):
AGGTTCAACTCTGATCAGTTGGTAATTCCTTATAT
Found at i:3225582 original size:35 final size:37
Alignment explanation
Indices: 3225505--3225584 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
3225495 TGAATTCTCT
*
3225505 GCAGGTTCAACTTTGATCTAGCTGGTAATTCCTTATA
1 GCAGGTTCAACTCTGATCTAGCTGGTAATTCCTTATA
* *
3225542 -TAGGTTCAACTCTGATC-ACGTTGGTAA-TCCTT-TA
1 GCAGGTTCAACTCTGATCTA-GCTGGTAATTCCTTATA
3225576 GCAGGTTCA
1 GCAGGTTCA
3225585 CCACCGATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
34 2 0.05
35 13 0.35
36 22 0.59
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (37 bp):
GCAGGTTCAACTCTGATCTAGCTGGTAATTCCTTATA
Found at i:3229966 original size:35 final size:35
Alignment explanation
Indices: 3229864--3229982 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 35
3229854 CTTATCAAGC
* *
3229864 TGGTGATTCCTTATATAGGTTAAACATTGATCACGT
1 TGGTAATTCCTTATATAGGTTCAACATTGATCA-GT
* ** * **
3229900 TGGTAATCCCTTA-GCAGGTTCAGCACCGATCAGT
1 TGGTAATTCCTTATATAGGTTCAACATTGATCAGT
* * *
3229934 TGGTAGTTCCTTATATAGGTTCAATATTGATCAGC
1 TGGTAATTCCTTATATAGGTTCAACATTGATCAGT
* *
3229969 TAGTAATTCGTTAT
1 TGGTAATTCCTTAT
3229983 GGATCTTAGG
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
34 13 0.21
35 38 0.61
36 11 0.18
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (35 bp):
TGGTAATTCCTTATATAGGTTCAACATTGATCAGT
Found at i:3232508 original size:19 final size:19
Alignment explanation
Indices: 3232484--3232531 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3232474 GAGTCAACGC
3232484 GACCCAACCCGTTAACTTT
1 GACCCAACCCGTTAACTTT
* *
3232503 GACCCAACCTGTTGACTTT
1 GACCCAACCCGTTAACTTT
3232522 GACCCAACCC
1 GACCCAACCC
3232532 TGGACTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (19 bp):
GACCCAACCCGTTAACTTT
Found at i:3232539 original size:18 final size:18
Alignment explanation
Indices: 3232484--3232543 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
3232474 GAGTCAACGC
**
3232484 GACCCAACCCGTTAACTTT
1 GACCCAACCC-TGGACTTT
3232503 GACCCAA-CCTGTTGACTTT
1 GACCCAACCCTG--GACTTT
3232522 GACCCAACCCTGGACTTT
1 GACCCAACCCTGGACTTT
3232540 GACC
1 GACC
3232544 AAAAACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.33
19 19 0.53
20 4 0.11
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.25
Consensus pattern (18 bp):
GACCCAACCCTGGACTTT
Found at i:3236367 original size:16 final size:16
Alignment explanation
Indices: 3236348--3236380 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3236338 CCATCGGTGG
*
3236348 CTATCATCGTCGGCAC
1 CTATCACCGTCGGCAC
3236364 CTATCACCGTCGGCAC
1 CTATCACCGTCGGCAC
3236380 C
1 C
3236381 ATTGGTAGCA
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:0.18, C:0.42, G:0.18, T:0.21
Consensus pattern (16 bp):
CTATCACCGTCGGCAC
Found at i:3243913 original size:2 final size:2
Alignment explanation
Indices: 3243908--3243934 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3243898 TGTGTGTGTG
3243908 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3243935 TAACATGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3272724 original size:19 final size:18
Alignment explanation
Indices: 3272684--3272725 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3272674 TTAAAGTTTA
*
3272684 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
3272701 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
3272720 TAAATT
1 TAAATT
3272726 GACTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:3273002 original size:19 final size:18
Alignment explanation
Indices: 3272962--3273003 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3272952 TAAAAGTTTA
*
3272962 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
3272979 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
3272998 TAAATT
1 TAAATT
3273004 GACTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:3276479 original size:17 final size:18
Alignment explanation
Indices: 3276452--3276499 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3276442 ATAAATAAAC
3276452 ATCGAATGCACTG-AGTGT
1 ATCG-ATGCACTGAAGTGT
*
3276470 ATCGATGCACAGATAGTGT
1 ATCGATGCACTGA-AGTGT
*
3276489 ATTGATGCACT
1 ATCGATGCACT
3276500 CCCTTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 7 0.28
18 4 0.16
19 14 0.56
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (18 bp):
ATCGATGCACTGAAGTGT
Found at i:3281826 original size:18 final size:18
Alignment explanation
Indices: 3281793--3281827 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3281783 CCCGTAAGAC
**
3281793 CACTATGTCCTGAAGGAA
1 CACTATGTCCCAAAGGAA
3281811 CACTATGTCCCAAAGGA
1 CACTATGTCCCAAAGGA
3281828 CCAGATAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (18 bp):
CACTATGTCCCAAAGGAA
Found at i:3286734 original size:20 final size:20
Alignment explanation
Indices: 3286709--3286746 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3286699 TTCCCATTGA
*
3286709 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
3286729 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
3286747 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3287788 original size:59 final size:58
Alignment explanation
Indices: 3287724--3287948 Score: 177
Period size: 58 Copynumber: 3.9 Consensus size: 58
3287714 ATGACACTTT
* * *
3287724 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATAGAGCACTGA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
* ** * *
3287783 GTGTGCTAAATGATAAGGAAATCATATTGA-AATATGGATTTCCAAATAG-GTCATTTTA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAG-CA-CTAA
* * * * * * *
3287841 -TATGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCAGTAA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
* * * * * *** *
3287899 GGGTTCTAGATGATAAGGAAATAATATTGAAAATATGGATTTCCAGATAG
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAG
3287949 GGCATATTAT
Statistics
Matches: 129, Mismatches: 31, Indels: 13
0.75 0.18 0.08
Matches are distributed among these distances:
56 1 0.01
57 22 0.17
58 79 0.61
59 26 0.20
60 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (58 bp):
GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
Found at i:3287806 original size:58 final size:59
Alignment explanation
Indices: 3287724--3288072 Score: 198
Period size: 59 Copynumber: 6.0 Consensus size: 59
3287714 ATGACACTTT
* * *
3287724 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATAGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
* ** * *
3287783 GTGTGCT-AAATGATAAGGAAATCATATTGA-AATATGGATTTCCAAATAG-GTCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAG-CA-CTAA
* * * * * * *
3287841 -TATGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCAGTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
* * * * * *** * *
3287899 GGGTTCT-AGATGATAAGGAAATAATATTGAAAATATGGATTTCCAGATAGGGCA-TATTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTA--A
* ** * * * * * **
3287958 -TGTGCTAAAATGGTAATAAAAGCATACT-AATGGTATGGATTTTCGAATAGGGCACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCAAATAGAGCACTAA
* * * *
3288016 GTGTGCTAAAATGAAAAAGGAAGA--ATACTAAGTGTAT-GATTTTCCAGATGGAGCACT
1 GTGTGCTAAAATG-ATAAGGAA-ATCATACTGAGTGTATGGA-TTTCCAAATAGAGCACT
3288073 GATAGTGCTA
Statistics
Matches: 216, Mismatches: 58, Indels: 32
0.71 0.19 0.10
Matches are distributed among these distances:
56 1 0.00
57 24 0.11
58 90 0.42
59 92 0.43
60 8 0.04
61 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAAATAGAGCACTAA
Found at i:3288215 original size:17 final size:18
Alignment explanation
Indices: 3288190--3288223 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3288180 ATTATAGTAT
3288190 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
3288207 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
3288224 TATCGAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:3289599 original size:36 final size:36
Alignment explanation
Indices: 3289552--3289622 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
3289542 ATTCTTGAGT
*
3289552 ATGTAGGTTCAGCTCCGATCAAACTAGTAATTCCTC
1 ATGTAGGTTCAGCACCGATCAAACTAGTAATTCCTC
* *
3289588 ATGTAGGTTCAGCACCGATCAAATTGGTAATTCCT
1 ATGTAGGTTCAGCACCGATCAAACTAGTAATTCCT
3289623 TATGGATCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (36 bp):
ATGTAGGTTCAGCACCGATCAAACTAGTAATTCCTC
Found at i:3301109 original size:36 final size:36
Alignment explanation
Indices: 3301052--3301122 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
3301042 ATTTTGGAGT
* *
3301052 ATGTAGGTTCAACTCCGATCAAGCTGGTAATTCCTC
1 ATGTAGGTTCAACACCAATCAAGCTGGTAATTCCTC
*
3301088 ATGTAGGTTCAGCACCAATCAAGCTGGTAATTCCT
1 ATGTAGGTTCAACACCAATCAAGCTGGTAATTCCT
3301123 TATGGACCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (36 bp):
ATGTAGGTTCAACACCAATCAAGCTGGTAATTCCTC
Found at i:3305075 original size:44 final size:44
Alignment explanation
Indices: 3305027--3305177 Score: 248
Period size: 44 Copynumber: 3.4 Consensus size: 44
3305017 TAAAATGAAT
3305027 CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATG
*
3305071 CCATAAATGAAATGCATAATGGTGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATG
* * * * *
3305115 TCATAAATGAAATGTATAACGATGCATTAAGGCATGAAAAGATT
1 CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATG
3305159 CCATAAATGAAATGCATAA
1 CCATAAATGAAATGCATAA
3305178 CAGTGCATTA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 98 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (44 bp):
CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATG
Found at i:3305178 original size:44 final size:44
Alignment explanation
Indices: 3305026--3305211 Score: 232
Period size: 44 Copynumber: 4.2 Consensus size: 44
3305016 CTAAAATGAA
* *
3305026 TCCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATAACGATGCATTAAGGCATGAAAAGAT
* * * *
3305070 GCCATAAATGAAATGCATAATGGTGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATAACGATGCATTAAGGCATGAAAAGAT
*
3305114 GT-CATAAATGAAATGTATAACGATGCATTAAGGCATGAAAAGAT
1 -TCCATAAATGAAATGCATAACGATGCATTAAGGCATGAAAAGAT
** *
3305158 TCCATAAATGAAATGCATAAC-AGTGCATTAGAGGTTTGAAAAAAT
1 TCCATAAATGAAATGCATAACGA-TGCATTA-AGGCATGAAAAGAT
*
3305203 GCCATAAAT
1 TCCATAAAT
3305212 TAAAATATTG
Statistics
Matches: 126, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
43 2 0.02
44 105 0.83
45 19 0.15
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (44 bp):
TCCATAAATGAAATGCATAACGATGCATTAAGGCATGAAAAGAT
Found at i:3308153 original size:54 final size:53
Alignment explanation
Indices: 3308089--3308299 Score: 269
Period size: 54 Copynumber: 3.9 Consensus size: 53
3308079 ACCAAATAGG
*
3308089 CACTAAGTGTGCAATCCACATAATTCATCATATGTTGATGAATAACCATTTCGA
1 CACTAAGTGTGCAATCCACA-AATTCATCATATGTTGATGAATAACCGTTTCGA
* *
3308143 CACTATGTGTGCAATCCACGAAATTCATCATATGTTGATGAATAACTGTTTCGA
1 CACTAAGTGTGCAATCCAC-AAATTCATCATATGTTGATGAATAACCGTTTCGA
* * * *
3308197 CACTAAGTGTGCATTTCACAAAATTCATCATATGTTGATGAATAACCGTTTTGC
1 CACTAAGTGTGCAATCCAC-AAATTCATCATATGTTGATGAATAACCGTTTCGA
* * ** * *
3308251 CACTAAGTGTGCATTTCATGGAATTTATCATATGTTGGTGAATAACCGT
1 CACTAAGTGTGCAATCCA-CAAATTCATCATATGTTGATGAATAACCGT
3308300 ACAAACACTA
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
54 140 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (53 bp):
CACTAAGTGTGCAATCCACAAATTCATCATATGTTGATGAATAACCGTTTCGA
Found at i:3308376 original size:55 final size:55
Alignment explanation
Indices: 3308143--3308671 Score: 553
Period size: 55 Copynumber: 9.7 Consensus size: 55
3308133 ACCATTTCGA
* * * *
3308143 CACTATGTGTGC-AATCCACGAAATTCATCAT-ATGTTGATGAATAACTGT--TTCG
1 CACTATGTGTGCAAATCCATGAAATTCATCATGA-GTTGGTGAATAACCGTACAT-G
* ** * **
3308196 ACACTAAGTGTGCATTTCACA--AAATTCATCAT-ATGTTGATGAATAACCGT-TTTG
1 -CACTATGTGTGCAAATC-CATGAAATTCATCATGA-GTTGGTGAATAACCGTACATG
* * * * * **
3308250 CCACTAAGTGTGC-ATTTCATGGAATTTATCAT-ATGTTGGTGAATAACCGTACAAA
1 -CACTATGTGTGCAAATCCATGAAATTCATCATGA-GTTGGTGAATAACCGTACATG
* * * *
3308305 CACTATGTGAT-CAAATCCATGAAATTGATCCTGAGTTGATGGATAACCGTACATG
1 CACTATGTG-TGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
*
3308360 CACTATGTGTGCAAATCCATGAAATTCACCATGAGTTGGTGAATAACCGTACATG
1 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
* * * *
3308415 CACTATGTGTACTAATCCACGAAATTCATCATGAGTTGGTGAATAACCGTACAAG
1 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
* *
3308470 CACTATGTGTGCAAATCCATGAAAATCATCATGAGTTGGTGAATAACTGTACATG
1 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
* * * *
3308525 CACTATGTGTCCAAATCCACGGAATTCATCATGAGTTGGTGAATAACCATACATG
1 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
* * * *
3308580 AACTATGTGTGCAAATCCACGAAATTCATCATTAGTTGGTAAATAACCGTACA-G
1 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
3308634 ACACTATGTGTGCAAATCCACTG-AATTCATCATGAGTT
1 -CACTATGTGTGCAAATCCA-TGAAATTCATCATGAGTT
3308672 CATGAACTAC
Statistics
Matches: 408, Mismatches: 55, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.00
53 2 0.00
54 89 0.22
55 311 0.76
56 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGGTGAATAACCGTACATG
Found at i:3309007 original size:46 final size:46
Alignment explanation
Indices: 3308957--3309092 Score: 139
Period size: 46 Copynumber: 2.9 Consensus size: 46
3308947 ACATAATGTT
* * * *
3308957 GTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGTATAATAGC
1 GTATAAAAAGGAAAGAAAGAATGCCATAAATGAAATGTATAATAGC
* *
3309003 GTATAAAAAGGAAAGAAATAATGCCATAAATGAAATGTATATTAGC
1 GTATAAAAAGGAAAGAAAGAATGCCATAAATGAAATGTATAATAGC
* * * * * *
3309049 TTATAAAAAAAGAAGGAAATG-ATGTCATAATTGAAATGCATAAT
1 GTAT-AAAAAGGAAAGAAA-GAATGCCATAAATGAAATGTATAAT
3309093 GGTGCATTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
46 43 0.58
47 31 0.42
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (46 bp):
GTATAAAAAGGAAAGAAAGAATGCCATAAATGAAATGTATAATAGC
Found at i:3309078 original size:47 final size:46
Alignment explanation
Indices: 3308971--3309092 Score: 154
Period size: 46 Copynumber: 2.6 Consensus size: 46
3308961 AAAAGGGCAT
* *
3308971 GAAAGGATGCCATAAATGAAATGTATAATAGCGTATAAAAAGGAAA
1 GAAATGATGCCATAAATGAAATGTATAATAGCGTATAAAAAAGAAA
* * * *
3309017 GAAATAATGCCATAAATGAAATGTATATTAGCTTATAAAAAAAGAAG
1 GAAATGATGCCATAAATGAAATGTATAATAGCGTAT-AAAAAAGAAA
* * *
3309064 GAAATGATGTCATAATTGAAATGCATAAT
1 GAAATGATGCCATAAATGAAATGTATAAT
3309093 GGTGCATTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
46 32 0.50
47 32 0.50
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (46 bp):
GAAATGATGCCATAAATGAAATGTATAATAGCGTATAAAAAAGAAA
Found at i:3314902 original size:44 final size:44
Alignment explanation
Indices: 3314838--3315114 Score: 437
Period size: 44 Copynumber: 6.3 Consensus size: 44
3314828 TAAAATGAAT
* * *
3314838 CCATAAATAAAATCCATAACGGTGCCTTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* * *
3314882 TCATAAATGAAATCCATAACGGTGCATTAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
3314926 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* *
3314970 CCATAAACGAAATGCATAACAGTGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* *
3315014 CCATAAATGAAATGCATAACAGTGCATTAAGGCATGAAAGGGTG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
**
3315058 CCATAAATGAAATGTGTAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATT-AAGGCATGAAAGGATG
3315103 CCATAAATGAAA
1 CCATAAATGAAA
3315115 ATAATGAATA
Statistics
Matches: 217, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
44 190 0.88
45 27 0.12
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (44 bp):
CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
Found at i:3318972 original size:13 final size:13
Alignment explanation
Indices: 3318954--3319022 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
3318944 TTGGCATGAA
**
3318954 GGTGATGGACTAT
1 GGTGATGGAAGAT
3318967 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
3318980 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
3318992 GGCG-T-GAAAAT
1 GGTGATGGAAGAT
3319003 GGTGATGGAAGAT
1 GGTGATGGAAGAT
3319016 GGTGATG
1 GGTGATG
3319023 TTTAGGTAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:3324676 original size:13 final size:13
Alignment explanation
Indices: 3324658--3324726 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
3324648 TTGGCGTGAA
**
3324658 GGTGATGGACTAT
1 GGTGATGGAAGAT
3324671 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
3324684 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
3324696 GGCG-T-GAAAAT
1 GGTGATGGAAGAT
3324707 GGTGATGGAAGAT
1 GGTGATGGAAGAT
3324720 GGTGATG
1 GGTGATG
3324727 TTTAGGTAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:3327814 original size:58 final size:57
Alignment explanation
Indices: 3327728--3328132 Score: 530
Period size: 58 Copynumber: 7.0 Consensus size: 57
3327718 CATATTTCCC
* * * *
3327728 ATACAGAAGTTCATACACTTACTGTGAATCTCTTAACTTTTTGCACACAAAGTGTCCA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG-CCA
* *
3327786 ATAC-GAAAATTCATGCACTTAGTATGAATTTCTTAACTTTTTTTCACACAAAGTGCCCA
1 ATACAG-AAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACACAAAGTG-CCA
* * *
3327845 ATA-TGAAAATTCATACACTTAGTATGAATTTCTTACCTTTTTGCACTCAAAGTGCCTA
1 ATACAG-AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCC-A
* * *
3327903 ATAC-GAAAATTTATACACTTAGTATGAATTTCATAACTCTTTGCACACAAAGTGCCCA
1 ATACAG-AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG-CCA
* *
3327961 ATACACAAATTCATACACTTAGTATGAATTTCTTAACTATTTGCACACAAAGTGTCCA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG-CCA
*
3328019 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTGCCTA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCC-A
* **
3328077 ATACAGAAATTCATACAATTAGTATGAATTTCTTAAC-TTTTGCACACTTAGTGCCA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCA
3328133 TTTGGTAATC
Statistics
Matches: 312, Mismatches: 27, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
56 1 0.00
57 21 0.07
58 235 0.75
59 55 0.18
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (57 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCA
Found at i:3328530 original size:19 final size:19
Alignment explanation
Indices: 3328491--3328530 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3328481 ACTACCATAC
*
3328491 TTATGGTACCGATACCCTT
1 TTATGGTACCGATACCATT
* *
3328510 TTATGGTATCGATACTATT
1 TTATGGTACCGATACCATT
3328529 TT
1 TT
3328531 TTCACTCTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (19 bp):
TTATGGTACCGATACCATT
Found at i:3328572 original size:20 final size:20
Alignment explanation
Indices: 3328547--3328599 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
3328537 CTGTTTTGAA
3328547 TGGTATCGATACCTTCC-CTC
1 TGGTATCGATA-CTTCCACTC
*
3328567 TGGTATCGATA-TTCCACTT
1 TGGTATCGATACTTCCACTC
3328586 TCGGTATCGATACT
1 T-GGTATCGATACT
3328600 GATCGAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 3 0.10
20 21 0.72
21 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACTTCCACTC
Found at i:3329766 original size:21 final size:21
Alignment explanation
Indices: 3329742--3329783 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3329732 TAAGGCTTCG
3329742 ATCGATATTGTGTGGGCTTTT
1 ATCGATATTGTGTGGGCTTTT
3329763 ATCGATATTGTGTGGGCTTTT
1 ATCGATATTGTGTGGGCTTTT
3329784 CCAAAGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.29, T:0.48
Consensus pattern (21 bp):
ATCGATATTGTGTGGGCTTTT
Found at i:3332547 original size:45 final size:45
Alignment explanation
Indices: 3332456--3332853 Score: 467
Period size: 45 Copynumber: 9.0 Consensus size: 45
3332446 GTAAGTATGC
* * * * *
3332456 AAATAAGCTTACGAGCTTATGGAAT-AATTGCAAGTGTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
3332500 AAATAATG-TTACAAGCTTATGGGATAAATGGAAAGTGTATTGGTA
1 AAATAA-GCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
3332545 AAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTTTATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * **
3332590 AAATAAGCTTATGAGCTTATGGGATAAATGGCAAGCGTATTGGT-
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
3332634 -AA-AA-C-T---AGCTTAT-GGAGTAAATGCTAACTTTATTGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATATTGGTA
*
3332672 AAATAATCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
3332717 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTC
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
3332762 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTAGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
*
3332807 AAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATATTGGTA
3332853 A
1 A
3332854 GAAATGTTAT
Statistics
Matches: 306, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
36 3 0.01
37 22 0.07
39 2 0.01
40 3 0.01
41 2 0.01
42 3 0.01
43 2 0.01
44 22 0.07
45 225 0.74
46 22 0.07
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:3332669 original size:127 final size:132
Alignment explanation
Indices: 3332456--3332853 Score: 459
Period size: 127 Copynumber: 3.0 Consensus size: 132
3332446 GTAAGTATGC
* ** *
3332456 AAATAAGCTTACGAGCTTATGGAAT-AATTGCAAGTGTTTTGGTAAAATAATG-TTACAAGCTTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGCATATTGGT-AAATAA-GCTT--AAGCTTA
* ** * * * *
3332519 TGGGATAAATGGAAAGTGTATTGGTAAAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTTTA
62 TGGAATAAATGCTAACTTTATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATA
3332584 TTGGTA
127 TTGGTA
* * *
3332590 AAATAAGCTTATGAGCTTATGGGATAAATGGCAAGCGTATTGGT-AA-AA-C-T-AGCTTATGGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGCATATTGGTAAATAAGCTTAAGCTTATGGA
* * *
3332650 GTAAATGCTAACTTTATTGGTAAAATAATCTTACGAGCTTATGGGATAAATGGTAAGTATATTGG
66 ATAAATGCTAACTTTATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
3332715 TA
131 TA
* *
3332717 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTCAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGCATATTGGT-AAATAAGCTTA--AGCTTAT
* * * * *
3332782 GGAATAAATGGTAAGTTTATTAGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATA
63 GGAATAAATGCTAACTTTATTGGTAAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATA
3332847 TTGGTA
127 TTGGTA
3332853 A
1 A
3332854 GAAATGTTAT
Statistics
Matches: 225, Mismatches: 28, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
127 106 0.47
129 2 0.01
130 3 0.01
131 1 0.00
132 3 0.01
133 2 0.01
134 23 0.10
135 62 0.28
136 23 0.10
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (132 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGCATATTGGTAAATAAGCTTAAGCTTATGGA
ATAAATGCTAACTTTATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
TA
Found at i:3332693 original size:172 final size:171
Alignment explanation
Indices: 3332469--3332792 Score: 515
Period size: 172 Copynumber: 1.9 Consensus size: 171
3332459 TAAGCTTACG
* * *
3332469 AGCTTATGGAATAATTGCAAGTGTTTTGGTAAAATAATGTTACAAGCTTATGGGATAAATGGAAA
1 AGCTTATGGAATAAATGCAACTGTTTTGGTAAAATAATCTTACAAGCTTATGGGATAAATGGAAA
* *
3332534 GTGTATTGGTAAAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTTTATTGGTAAAATAAGCT
66 GTATATTGGTAAAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCT
* *
3332599 TATGAGCTTATGGGATAAATGGCAAGCGTATTGGTAAAACT
131 TACGAGCTTATGGAATAAATGGCAAGCGTATTGGTAAAACT
* * *
3332640 AGCTTATGGAGTAAATGCTAACT-TTATTGGTAAAATAATCTTACGAGCTTATGGGATAAATGGT
1 AGCTTATGGAATAAATGC-AACTGTT-TTGGTAAAATAATCTTACAAGCTTATGGGATAAATGGA
* *
3332704 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTCAAATAAG
64 AAGTATATTGGTAAAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAG
3332769 CTTACGAGCTTATGGAATAAATGG
129 CTTACGAGCTTATGGAATAAATGG
3332793 TAAGTTTATT
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
171 18 0.13
172 121 0.87
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (171 bp):
AGCTTATGGAATAAATGCAACTGTTTTGGTAAAATAATCTTACAAGCTTATGGGATAAATGGAAA
GTATATTGGTAAAATAAGCTCACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCT
TACGAGCTTATGGAATAAATGGCAAGCGTATTGGTAAAACT
Found at i:3346894 original size:21 final size:22
Alignment explanation
Indices: 3346836--3346900 Score: 105
Period size: 23 Copynumber: 3.0 Consensus size: 22
3346826 GGAATCAATA
3346836 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
3346858 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
*
3346881 CCCCC-TGTAGGGGAACCGAT
1 CCCCCTTGAAGGGGAACCGAT
3346901 ACACACCTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 14 0.34
22 5 0.12
23 22 0.54
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.18
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:3349208 original size:11 final size:12
Alignment explanation
Indices: 3349192--3349224 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3349182 TAAGGGGGAG
3349192 TAATTTCAAAC-
1 TAATTTCAAACT
3349203 TAATTTCAAACT
1 TAATTTCAAACT
*
3349215 TGATTTCAAA
1 TAATTTCAAA
3349225 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTTCAAACT
Found at i:3351275 original size:53 final size:53
Alignment explanation
Indices: 3351209--3351635 Score: 500
Period size: 53 Copynumber: 8.0 Consensus size: 53
3351199 AAAGTTAAAT
* * * *
3351209 GCCTAACTGTGCATATTAGTAGAAAAGTGTTAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * * *
3351262 GCCTAACTGTGCATATTAGCATAAAGGTGTCATTAATGCAAATTAGATGATCAATTAAAT
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG-------AAAG
*
3351322 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTATATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
3351375 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* ** * * * * *
3351428 GGCTAACTACGCATATTGGTATAAAGGTTTTAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
3351481 GCCTAATTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * *
3351533 GCCTAACTCTGCAT-TTGGCATAAAAGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
3351585 GCTTAACTGTGCAT-TTGGAAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
3351636 AATTAAATGC
Statistics
Matches: 325, Mismatches: 42, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
52 125 0.38
53 153 0.47
60 47 0.14
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:3351401 original size:113 final size:107
Alignment explanation
Indices: 3351202--3351695 Score: 498
Period size: 113 Copynumber: 4.6 Consensus size: 107
3351192 ATGAAGAAAA
* * *
3351202 GTTAAATGCCTAACTGTGCATATTAGTAGAAAAGTGTTAATAATGCAAGTTAGATGAAAGGCCTA
1 GTTAAATGCCTAACTGTGCATATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAAAGGCCTA
* * * * *
3351267 ACTGTGCATATTAGCATAAAGGTGTCATTAATGCAAATTAGAT
66 ACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGAT
* *
3351310 GATCAATTAAATGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTATATGAAAG
1 G-----TTAAATGCCTAACTGTGCATATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAAAG
* * *
3351375 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGAT
61 GCCTAACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGAT
* * ** * * * * * *
3351423 G--AAAGGGCTAACTACGCATATTGGTATAAAGGTTTTAATAATGTAAGTTAGATGAAAGGCCTA
1 GTTAAATGCCTAACTGTGCATATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAAAGGCCTA
* *
3351486 ATTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGAT
66 ACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAT
* * * * *
3351528 G--AAAGGCCTAACTCTGCAT-TTGGCATAAAAGTGCCAATAATGCAAGTTAGATGAAAGGCTTA
1 GTTAAATGCCTAACTGTGCATATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAAAGGCCTA
*
3351590 ACTGTGCATTTGGAAGAAAGGTGCCAATAATGCAAGTTAGAT
66 ACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAT
* * * *
3351632 GAAAAATTAAATGCCTAA-TGATGCATTTTTGGCAGAAATGTGCCACTAATG-AAGTTAGATGAA
1 G-----TTAAATGCCTAACTG-TGCA-TATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAA
3351695 A
59 A
3351696 AGTTAAATTC
Statistics
Matches: 327, Mismatches: 44, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
104 76 0.23
105 46 0.14
106 59 0.18
108 1 0.00
110 1 0.00
111 13 0.04
112 14 0.04
113 117 0.36
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (107 bp):
GTTAAATGCCTAACTGTGCATATTGGCAGAAAAGTGTCAATAATGCAAGTTAGATGAAAGGCCTA
ACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAT
Found at i:3351537 original size:52 final size:53
Alignment explanation
Indices: 3351322--3351635 Score: 418
Period size: 52 Copynumber: 6.0 Consensus size: 53
3351312 TCAATTAAAT
* *
3351322 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTATATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * *
3351375 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* ** * * *** *
3351428 GGCTAACTACGCATATTGGTATAAAGGTTTTAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* *
3351481 GCCTAATTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * *
3351533 GCCTAACTCTGCAT-TTGGCATAAAAGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* *
3351585 GCTTAACTGTGCAT-TTGGAAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
3351636 AATTAAATGC
Statistics
Matches: 232, Mismatches: 29, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
52 125 0.54
53 107 0.46
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
Found at i:3351545 original size:26 final size:26
Alignment explanation
Indices: 3351357--3351635 Score: 68
Period size: 26 Copynumber: 10.7 Consensus size: 26
3351347 GGTGTCAATA
*
3351357 ATGCAAGTTATATGAAAGGCCTAACT
1 ATGCAAGTTAGATGAAAGGCCTAACT
* **
3351383 ATGCATA-TTGGCA-GAAAGGTGTCAA-T
1 ATGCA-AGTTAG-ATGAAAGGCCT-AACT
* *
3351409 AATGTAAGTTAGATGAAAGGGCTAACT
1 -ATGCAAGTTAGATGAAAGGCCTAACT
* * **
3351436 ACGCATA-TTGGTAT-AAAGGTTTTAA-T
1 ATGCA-AGTTAG-ATGAAAGG-CCTAACT
* *
3351462 AATGTAAGTTAGATGAAAGGCCTAATT
1 -ATGCAAGTTAGATGAAAGGCCTAACT
* * *
3351489 GTGC-ATTTGGCA-GAAATGTGCC-AA-T
1 ATGCAAGTTAG-ATGAAA-G-GCCTAACT
3351514 AATGCAAGTTAGATGAAAGGCCTAACT
1 -ATGCAAGTTAGATGAAAGGCCTAACT
* * * *
3351541 CTGC-ATTTGGCATAAAAGTGCC-AA-T
1 ATGCAAGTTAG-ATGAAAG-GCCTAACT
*
3351566 AATGCAAGTTAGATGAAAGGCTTAACT
1 -ATGCAAGTTAGATGAAAGGCCTAACT
* * * *
3351593 GTGC-ATTTGGAAGAAAGGTGCC-AA-T
1 ATGCAAGTTAGATGAAA-G-GCCTAACT
3351618 AATGCAAGTTAGATGAAA
1 -ATGCAAGTTAGATGAAA
3351636 AATTAAATGC
Statistics
Matches: 178, Mismatches: 43, Indels: 63
0.63 0.15 0.22
Matches are distributed among these distances:
25 29 0.16
26 81 0.46
27 68 0.38
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (26 bp):
ATGCAAGTTAGATGAAAGGCCTAACT
Found at i:3351709 original size:60 final size:60
Alignment explanation
Indices: 3351594--3351753 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
3351584 GGCTTAACTG
* * *
3351594 TGCA-TTTGGAAGAAAGGTGCCAATAATGCAAGTTAGATGAAAAATTAAATGCCTAATGA
1 TGCATTTTGGCAGAAAGGTGCCACTAATGAAAGTTAGATGAAAAATTAAATGCCTAATGA
* * * *
3351653 TGCATTTTTGGCAGAAATGTGCCACTAATG-AAGTTAGATGAAAAGTTAAATTCCTAATGG
1 TGCA-TTTTGGCAGAAAGGTGCCACTAATGAAAGTTAGATGAAAAATTAAATGCCTAATGA
*
3351713 TGCATTTCGGCAGAAAGGTGCCACTAATGAAAGTTAGATGA
1 TGCATTTTGGCAGAAAGGTGCCACTAATGAAAGTTAGATGA
3351754 CAAACGGTGC
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
59 27 0.30
60 42 0.47
61 21 0.23
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (60 bp):
TGCATTTTGGCAGAAAGGTGCCACTAATGAAAGTTAGATGAAAAATTAAATGCCTAATGA
Found at i:3356990 original size:53 final size:53
Alignment explanation
Indices: 3356924--3357245 Score: 262
Period size: 53 Copynumber: 6.0 Consensus size: 53
3356914 AAAGTTAAAT
* *
3356924 GCCTAACTGTGCATATTCGCATAAAGGTGTCAATAATGCAAGTTAGATGAAAT
1 GCCTAACTGTGCATATTCGCATAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * * * *
3356977 GCATAACTGTGCATA-TCGGCATAAAAGTGCCATTAATTCAAGTTAGATGATCAGTTAAAT
1 GCCTAACTGTGCATATTC-GCATAAAGGTGCCAATAATGCAAGTT--A-GAT--G--AAAG
** ** * *
3357037 GCCTAACTGTGCATATT-GGTTGAAAGGTATCAATAATGCAAGATATATGAAAG
1 GCCTAACTGTGCATATTCGCAT-AAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * * * * * *
3357090 GTCTAACTATACATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTCGCATAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * *
3357143 GCCTAATTGTGCAT-TT-GACAAAAAGGTGCCTATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTCG-CATAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* *
3357195 GTCTAATTGTGC--ATTCGGCA-AAGAGGTGCCAATAATGCAAGTTAGATGAAA
1 GCCTAACTGTGCATATTC-GCATAA-AGGTGCCAATAATGCAAGTTAGATGAAA
3357246 AGTTAAATGC
Statistics
Matches: 217, Mismatches: 36, Indels: 33
0.76 0.13 0.12
Matches are distributed among these distances:
51 5 0.02
52 74 0.34
53 91 0.42
54 1 0.00
55 2 0.01
56 3 0.01
57 2 0.01
58 2 0.01
59 2 0.01
60 34 0.16
61 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (53 bp):
GCCTAACTGTGCATATTCGCATAAAGGTGCCAATAATGCAAGTTAGATGAAAG
Found at i:3357133 original size:113 final size:113
Alignment explanation
Indices: 3356916--3357263 Score: 294
Period size: 113 Copynumber: 3.2 Consensus size: 113
3356906 AATGAAGAAA
* * *
3356916 AGTTAAATGCCTAACTGTGCATATTCGCATAAAGGTGTCAATAATGCAAGTTAGATGAAATGCAT
1 AGTTAAATGCCTAACTGTGCATATTCGCATAAAGGTATCAATAATGCAAGATAGATGAAAGGCAT
* * * *
3356981 AACTGTGCATATCGGCATAAAAGTGCCATTAATTCAAGTTAGATGATC
66 AACTATACATATCGGCAGAAAAGTGCCAATAATTCAAGTTAGATGATC
** *
3357029 AGTTAAATGCCTAACTGTGCATATT-GGTTGAAAGGTATCAATAATGCAAGATATATGAAAGGTC
1 AGTTAAATGCCTAACTGTGCATATTCGCAT-AAAGGTATCAATAATGCAAGATAGATGAAAGG-C
* * *
3357093 -TAACTATACATATTGGCAGAAAGGTGTCAATAATGT-AAGTT--A-GAT-
64 ATAACTATACATATCGGCAGAAAAGTGCCAATAAT-TCAAGTTAGATGATC
* * * ** * *
3357138 -G--AAAGGCCTAATTGTGCAT-TT-GACAAAAAGGTGCCTATAATGCAAGTTAGATGAAAGGTC
1 AGTTAAATGCCTAACTGTGCATATTCG-CATAAAGGTATCAATAATGCAAGATAGATGAAAGG-C
* * * * * **
3357198 -TAATTGTGCAT-TCGGCA-AAGAGGTGCCAATAATGCAAGTTAGATGAAA
64 ATAACTATACATATCGGCAGAA-AAGTGCCAATAATTCAAGTTAGATGATC
3357246 AGTTAAATGCCTAACTGT
1 AGTTAAATGCCTAACTGT
3357264 AACACTCATA
Statistics
Matches: 190, Mismatches: 32, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
103 2 0.01
104 22 0.12
105 40 0.21
106 17 0.09
107 2 0.01
108 1 0.01
109 1 0.01
110 3 0.02
111 13 0.07
112 2 0.01
113 85 0.45
114 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (113 bp):
AGTTAAATGCCTAACTGTGCATATTCGCATAAAGGTATCAATAATGCAAGATAGATGAAAGGCAT
AACTATACATATCGGCAGAAAAGTGCCAATAATTCAAGTTAGATGATC
Found at i:3357185 original size:52 final size:52
Alignment explanation
Indices: 3357067--3357245 Score: 232
Period size: 52 Copynumber: 3.4 Consensus size: 52
3357057 TGAAAGGTAT
* * * * * * *
3357067 CAATAATGCAAGATATATGAAAGGTCTAACTATACATATTGGCAGAAAGGTGT
1 CAATAATGCAAGTTAGATGAAAGGTCTAATTGTGCAT-TTGGCAAAAAGGTGC
* * *
3357120 CAATAATGTAAGTTAGATGAAAGGCCTAATTGTGCATTTGACAAAAAGGTGC
1 CAATAATGCAAGTTAGATGAAAGGTCTAATTGTGCATTTGGCAAAAAGGTGC
* * *
3357172 CTATAATGCAAGTTAGATGAAAGGTCTAATTGTGCATTCGGCAAAGAGGTGC
1 CAATAATGCAAGTTAGATGAAAGGTCTAATTGTGCATTTGGCAAAAAGGTGC
3357224 CAATAATGCAAGTTAGATGAAA
1 CAATAATGCAAGTTAGATGAAA
3357246 AGTTAAATGC
Statistics
Matches: 109, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 79 0.72
53 30 0.28
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (52 bp):
CAATAATGCAAGTTAGATGAAAGGTCTAATTGTGCATTTGGCAAAAAGGTGC
Found at i:3357819 original size:54 final size:54
Alignment explanation
Indices: 3357761--3358248 Score: 401
Period size: 54 Copynumber: 9.1 Consensus size: 54
3357751 CATGTAGTGG
* * *
3357761 CTATACGGTTATTCATAAATATATTATGAATTTCAT-GGTTCGCACA-TATAATGC
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATGGGTT-GCACACT-TAATGC
* * *
3357815 CTATACGGTTGTTCATCAACATATGATGAATTTCATGGGTTGCACACTTAGTTC
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATGGGTTGCACACTTAATGC
* * ** *
3357869 CTATACGGTTGTTCATCAACATATGA--AATATT-TTGTGGTT--TTACTTAGTGC
1 CTATACGGTTGTTCATAAACATATGATGAAT-TTCATG-GGTTGCACACTTAATGC
* * * * * * * *
3357920 CTATATGGTTGTTCATCAACATAAGATGAATTTCATAGTTTACACACTTAGTGT
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATGGGTTGCACACTTAATGC
* *
3357974 CTATACGATTGTTCATCAACATATGATGAA-TT-ATGTGGCTTGCACACTTAATGC
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATG-GG-TTGCACACTTAATGC
* * * **
3358028 ATATACGGTTTTTCATCAAA-ATATGATGAA-TTCTGTGGGTTGCACACTTAGCGC
1 CTATACGGTTGTTCAT-AAACATATGATGAATTTC-ATGGGTTGCACACTTAATGC
* * * *
3358082 CTATACGGTTGTTCATCAACATATGATGAATTCCATGAGTTGCACACTTAGTGC
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATGGGTTGCACACTTAATGC
* * * * * * *
3358136 CTATACAGTTGTTTATCAATATATGATGAA-TT-ATGTGGTTTACATACTTAGTGC
1 CTATACGGTTGTTCATAAACATATGATGAATTTCATG-GG-TTGCACACTTAATGC
* * * * *
3358190 CTATACGGTTGTTCATCAACATATGATGAA-TTCTGTGGGCTGCACACTTAGTTC
1 CTATACGGTTGTTCATAAACATATGATGAATTTC-ATGGGTTGCACACTTAATGC
3358244 CTATA
1 CTATA
3358249 GTACACATAG
Statistics
Matches: 359, Mismatches: 55, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
51 32 0.09
52 15 0.04
53 17 0.05
54 278 0.77
55 13 0.04
56 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (54 bp):
CTATACGGTTGTTCATAAACATATGATGAATTTCATGGGTTGCACACTTAATGC
Found at i:3358076 original size:108 final size:107
Alignment explanation
Indices: 3357755--3358248 Score: 511
Period size: 108 Copynumber: 4.6 Consensus size: 107
3357745 GATGCGCATG
* * * * * *
3357755 TAGTGGCTATACGGTTATTCATAAATATATTATGAATT-TCATGGTTCGCACA-TATAATGCCTA
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTAT-GTGGTT-GCACACT-TAATGCCTA
*
3357818 TACGGTTGTTCATCAACATATGATGAATTTCATGGGTTGCACACT
63 TACGGTTGTTCATCAACATATGATGAATTTCATGGGTTACACACT
* * * ** *
3357863 TAGTTCCTATACGGTTGTTCATCAACATATGA-AATATTTTGTGGTT--TTACTTAGTGCCTATA
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGA-ATTATGTGGTTGCACACTTAATGCCTATA
* * * *
3357925 TGGTTGTTCATCAACATAAGATGAATTTCATAGTTTACACACT
65 CGGTTGTTCATCAACATATGATGAATTTCATGGGTTACACACT
* * *
3357968 TAGTGTCTATACGATTGTTCATCAACATATGATGAATTATGTGGCTTGCACACTTAATGCATATA
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGG-TTGCACACTTAATGCCTATA
* * * *
3358033 CGGTTTTTCATCAAAATATGATGAA-TTCTGTGGGTTGCACACT
65 CGGTTGTTCATCAACATATGATGAATTTC-ATGGGTTACACACT
* * *
3358076 TAGCGCCTATACGGTTGTTCATCAACATATGATGAATTCCATG-AGTTGCACACTTAGTGCCTAT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATT--ATGTGGTTGCACACTTAATGCCTAT
* * * *
3358140 ACAGTTGTTTATCAATATATGATGAA-TT-ATGTGGTTTACATACT
64 ACGGTTGTTCATCAACATATGATGAATTTCATG-GG-TTACACACT
* * * *
3358184 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGCTGCACACTTAGTTCCTATA
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGT-GGTTGCACACTTAATGCCTATA
3358249 GTACACATAG
Statistics
Matches: 321, Mismatches: 51, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
105 86 0.27
106 8 0.02
107 6 0.02
108 216 0.67
109 2 0.01
110 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (107 bp):
TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGTTGCACACTTAATGCCTATAC
GGTTGTTCATCAACATATGATGAATTTCATGGGTTACACACT
Found at i:3358164 original size:162 final size:160
Alignment explanation
Indices: 3357761--3358240 Score: 580
Period size: 162 Copynumber: 3.0 Consensus size: 160
3357751 CATGTAGTGG
* * * * *
3357761 CTATACGGTTATTCATAAATATATTATGAATTTCATG-GTTCGCACA-TATAATGCCTATACGGT
1 CTATACGGTTGTTCATCAACATATGATGAATTTCATGAGTT-GCACACT-TAGTGCCTATAC-GT
*
3357824 TGTTCATCAACATATGATGAATTTCATG-GGTTGCACACTTAGTTCCTATACGGTTGTTCATCAA
63 TGTTCATCAACATATGATGAA-TT-ATGTGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAA
* * ** *
3357888 CATATGA-AATATTTTGT-GGTT--TTACTTAGTGC
126 CATATGATGA-ATTCTGTGGGTTGCACACTTAGCGC
* * * *
3357920 CTATATGGTTGTTCATCAACATAAGATGAATTTCAT-AGTTTACACACTTAGTGTCTATACGATT
1 CTATACGGTTGTTCATCAACATATGATGAATTTCATGAG-TTGCACACTTAGTGCCTATACG-TT
* * * *
3357984 GTTCATCAACATATGATGAATTATGTGGCTTGCACACTTAATGCATATACGGTTTTTCATCAAAA
64 GTTCATCAACATATGATGAATTATGTGG-TTGCACACTTAGTGCCTATACGGTTGTTCATCAACA
3358049 TATGATGAATTCTGTGGGTTGCACACTTAGCGC
128 TATGATGAATTCTGTGGGTTGCACACTTAGCGC
*
3358082 CTATACGGTTGTTCATCAACATATGATGAATTCCATGAGTTGCACACTTAGTGCCTATACAGTTG
1 CTATACGGTTGTTCATCAACATATGATGAATTTCATGAGTTGCACACTTAGTGCCTATAC-GTTG
* * * *
3358147 TTTATCAATATATGATGAATTATGTGGTTTACATACTTAGTGCCTATACGGTTGTTCATCAACAT
65 TTCATCAACATATGATGAATTATGTGG-TTGCACACTTAGTGCCTATACGGTTGTTCATCAACAT
*
3358212 ATGATGAATTCTGTGGGCTGCACACTTAG
129 ATGATGAATTCTGTGGGTTGCACACTTAG
3358241 TTCCTATAGT
Statistics
Matches: 275, Mismatches: 34, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
157 3 0.01
158 5 0.02
159 109 0.40
160 8 0.03
162 147 0.53
163 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (160 bp):
CTATACGGTTGTTCATCAACATATGATGAATTTCATGAGTTGCACACTTAGTGCCTATACGTTGT
TCATCAACATATGATGAATTATGTGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATAT
GATGAATTCTGTGGGTTGCACACTTAGCGC
Found at i:3363509 original size:54 final size:54
Alignment explanation
Indices: 3363444--3363886 Score: 541
Period size: 54 Copynumber: 8.2 Consensus size: 54
3363434 GATGCACATG
* ** * * *
3363444 TAGTGCATATACGGTCATTCATAAACATATTATGAATTCTGT-AGTTCGTACA-T
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTT-GTACACT
* * * *
3363497 ATAATGCCTATACGGTTGTTCATCAACATATAATGAATTCCGTGGATTGTACACT
1 -TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
*
3363552 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCT-TGGGTTGCACACT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAA-TTCTGTGGGTTGTACACT
* * *
3363606 TAGTGCCTGTACGGTTATTCATCAACATATGATGAATTCAGTGGGTTGTACACT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
** * *
3363660 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACGCT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
* * * * *
3363714 TAGTGTCTATACAGTTGTTCATCAACATATGATGAATTTTGTGGGTTGCAAACT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
* * * *
3363768 TAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTTGTGGGTTGCAAACT
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
* ** * *
3363822 TAGTGCCTATACAGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACG
1 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
*
3363876 TAATGCCTATA
1 TAGTGCCTATA
3363887 GTACACATAA
Statistics
Matches: 347, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
53 3 0.01
54 338 0.97
55 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (54 bp):
TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGTTGTACACT
Found at i:3363734 original size:162 final size:162
Alignment explanation
Indices: 3363436--3363886 Score: 622
Period size: 162 Copynumber: 2.8 Consensus size: 162
3363426 TTCATTAAGA
* * * * *
3363436 TGCACA-TGTAGTGCATATACGGTCATTCATAAACATATTATGAATTCTGT-AGTTCGTACA-TA
1 TGCACACT-TAGTGCCTATACGGTTATTCATCAACATATGATGAATTCTGTGGGTT-GTACACT-
* * * * *
3363498 TAATGCCTATACGGTTGTTCATCAACATATAATGAATTCCGTGGATTGTACACTTAGTGCCTATA
63 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCCTATA
*
3363563 CGGTTGTTCATCAACATATGATGAATTTCT-TGGGT
128 CAGTTGTTCATCAACATATGATGAATTT-TGTGGGT
* *
3363598 TGCACACTTAGTGCCTGTACGGTTATTCATCAACATATGATGAATTCAGTGGGTTGTACACTTAG
1 TGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAATTCTGTGGGTTGTACACTTAG
* *
3363663 TGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACGCTTAGTGTCTATACAG
66 TGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCCTATACAG
3363728 TTGTTCATCAACATATGATGAATTTTGTGGGT
131 TTGTTCATCAACATATGATGAATTTTGTGGGT
* * * * * *
3363760 TGCAAACTTAGTGCCTATACAGTTGTTCATCAACATATGATGAATTTTGTGGGTTGCAAACTTAG
1 TGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAATTCTGTGGGTTGTACACTTAG
* * *
3363825 TGCCTATACAGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACGTAATGCCTATA
66 TGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCCTATA
3363887 GTACACATAA
Statistics
Matches: 257, Mismatches: 28, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
161 1 0.00
162 251 0.98
163 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (162 bp):
TGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAATTCTGTGGGTTGTACACTTAG
TGCCTATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCCTATACAG
TTGTTCATCAACATATGATGAATTTTGTGGGT
Found at i:3367376 original size:30 final size:31
Alignment explanation
Indices: 3367340--3367399 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3367330 ATAAAAATTT
* *
3367340 GGGGACC-ATTCTATAATTTTTGAAAAGTTG
1 GGGGACCAAATCTATAATTTTGGAAAAGTTG
3367370 GGGGACCAAATCTATAATTTTGGAAAAGTT
1 GGGGACCAAATCTATAATTTTGGAAAAGTT
3367400 CTGAATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (31 bp):
GGGGACCAAATCTATAATTTTGGAAAAGTTG
Found at i:3370615 original size:15 final size:14
Alignment explanation
Indices: 3370593--3370628 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
3370583 ATTTTCAAAT
3370593 TTTATTTTCTTTAA
1 TTTATTTTCTTTAA
*
3370607 TTTACTTTTCTTTAT
1 TTTA-TTTTCTTTAA
3370622 TTTATTT
1 TTTATTT
3370629 AATTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTTCTTTAA
Found at i:3370621 original size:24 final size:22
Alignment explanation
Indices: 3370593--3370640 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
3370583 ATTTTCAAAT
*
3370593 TTTATTTTCTTTAATTTACTTTTC
1 TTTATTTTATTTAA-TTA-TTTTC
3370617 TTTATTTTATTTAATTATTTTC
1 TTTATTTTATTTAATTATTTTC
3370639 TT
1 TT
3370641 CTTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 3 0.13
24 13 0.57
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATTTTATTTAATTATTTTC
Found at i:3370955 original size:31 final size:31
Alignment explanation
Indices: 3370920--3371005 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
3370910 TTAGACTCGC
* * *
3370920 GAGTTTTTGAGACAAATTGAGCTCTAGTTTT
1 GAGTTTTCGAGACAAATCGAACTCTAGTTTT
* *
3370951 GAGTTTTCGAGTCAAGTCGAACTCTAGTTTT
1 GAGTTTTCGAGACAAATCGAACTCTAGTTTT
* *
3370982 GAGTTTTCGAGTCAAGTCGAACTC
1 GAGTTTTCGAGACAAATCGAACTC
3371006 AACAATACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (31 bp):
GAGTTTTCGAGACAAATCGAACTCTAGTTTT
Found at i:3375968 original size:21 final size:21
Alignment explanation
Indices: 3375919--3375969 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
3375909 TTTGAGAAGA
* **
3375919 GGAGTATTGGTACTCATGAAG
1 GGAGTATCGGTACTCACCAAG
*
3375940 GAGAGTATCGGTAGTCACCAAG
1 G-GAGTATCGGTACTCACCAAG
3375962 GGAGTATC
1 GGAGTATC
3375970 AATACTCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (21 bp):
GGAGTATCGGTACTCACCAAG
Found at i:3377248 original size:24 final size:25
Alignment explanation
Indices: 3377216--3377267 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
3377206 CCTACTCGAA
*
3377216 ATATCATTCATGATAAATATCATAT
1 ATATCATTCATGATAAACATCATAT
*
3377241 ATAT-ATTCATGATAACCATCATAT
1 ATATCATTCATGATAAACATCATAT
3377265 ATA
1 ATA
3377268 AACAGTGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (25 bp):
ATATCATTCATGATAAACATCATAT
Found at i:3379284 original size:23 final size:25
Alignment explanation
Indices: 3379238--3379284 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
3379228 TTTATCCTTT
*
3379238 ATTTAAGCTTAAATAATTAAAATTC
1 ATTTAAGCTTAAATAATGAAAATTC
*
3379263 ATTTAA-CTTAGA-AATGAAAATT
1 ATTTAAGCTTAAATAATGAAAATT
3379285 TTGCCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTTAAGCTTAAATAATGAAAATTC
Found at i:3382695 original size:21 final size:22
Alignment explanation
Indices: 3382671--3382729 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
3382661 CCTTTGAATA
3382671 TGCATCGAT-ACACCATGAAGG
1 TGCATCGATCACACCATGAAGG
* * * *
3382692 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT-CACACCATGAAGG
3382715 TGCATCGATGCACAC
1 TGCATCGAT-CACAC
3382730 TGCCATTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 8 0.27
23 22 0.73
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (22 bp):
TGCATCGATCACACCATGAAGG
Found at i:3385195 original size:20 final size:20
Alignment explanation
Indices: 3385166--3385203 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3385156 TTTCAAAGGG
3385166 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
3385186 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
3385204 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:3385283 original size:65 final size:64
Alignment explanation
Indices: 3385214--3385372 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 64
3385204 GAATAAATTG
* * * * *
3385214 AACATCGAATGCAATTAATGCACCGATGCAC-TCTCCATGCATCGATGCACTCGGG-TTTTAATG
1 AACATCGAATGCATTTTATGCATCGATGCACAT-ACCATGCATCGATGCACTCGGGATTTT--TC
3385277 AA
63 AA
* *
3385279 AACATCGAATGCATTTTATGCATCGATGCGCATACCATGCATCGATGCACTTGGGATTTTTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCGGGATTTTTCAA
*
3385343 AACATTGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTTATGCATCGATGCA
3385373 TGCTTAGTGC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 31 0.37
65 47 0.57
66 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCGGGATTTTTCAA
Found at i:3393833 original size:24 final size:24
Alignment explanation
Indices: 3393780--3393834 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3393770 AGCCATTAAA
* *
3393780 AAAGATGATCAAGGAATAAATATT
1 AAAGATGATCAAGGAAGAAAAATT
** *
3393804 TTAGATGATCAGGGAAGAAAAATT
1 AAAGATGATCAAGGAAGAAAAATT
3393828 AAAGATG
1 AAAGATG
3393835 GAGCCGCAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (24 bp):
AAAGATGATCAAGGAAGAAAAATT
Found at i:3395566 original size:17 final size:16
Alignment explanation
Indices: 3395516--3395568 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
3395506 GGAATTACAA
3395516 AAAAGAGAAATTATAAT
1 AAAAGAGAAA-TATAAT
* *
3395533 AAAAAATAAATCA-AAT
1 AAAAGAGAAAT-ATAAT
3395549 AAAAGACGAAATATAAT
1 AAAAGA-GAAATATAAT
3395566 AAA
1 AAA
3395569 CTATATGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.70, C:0.04, G:0.08, T:0.19
Consensus pattern (16 bp):
AAAAGAGAAATATAAT
Found at i:3400193 original size:226 final size:225
Alignment explanation
Indices: 3399531--3400199 Score: 955
Period size: 226 Copynumber: 3.0 Consensus size: 225
3399521 GATATTATCG
* * * * *
3399531 ATCATAATAACATAAAAAGTAGTGTTTATTTAATGTAATAGGTAGCGCCTGTTTTAAGTTGATGG
1 ATCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAGGTAGCACCTATTTAAAGTTGATGG
* *
3399596 GGCCTTGGAAATCCGACGATAACAAAATAGGTTAATTATTTAATTTGTTATCAGTATTATCAACA
66 GGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACA
* *
3399661 TATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAA
131 TATTAGGTAGCGCCTAAAATGTTACTAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAA
* *
3399726 CAAAATAGATTAATTACTGGAAATATTATTA
196 CAAAATAG-TTAATTACTTGAAACATTATTA
* * * *
3399757 ACCATAATAACATAACAAGTAGCGTTTATTTAATATAATAGGTAGCACTTATTTAAAGCTGATGG
1 ATCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAGGTAGCACCTATTTAAAGTTGATGG
* * * * * *
3399822 GGCCTTAAAAATCCAACGAAAACAAATTAGGTTAATTACTTAATTTTTTTATCAATATTATCAAC
66 GGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAA-TTTGTTATCAGTATTATCAAC
* * * *
3399887 ATATGAGGTAGCGCCTAAAATGTTACTAAAGTTTAAGCTGATGGAGCCCTAGATATCCAACGATA
130 ATATTAGGTAGCGCCTAAAATGTTACTAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATA
* *
3399952 ACAAAATAGGTTAATTATTTGAAGCATTATTA
195 ACAAAATA-GTTAATTACTTGAAACATTATTA
* * *
3399984 ATCATAATAACATAACAAGTAGCAG-TT-TTTAATGTAATAGGTAACACCTATTAAAAGTTGATA
1 ATCATAATAACATAACAAGTAGC-GTTTATTTAATGTAATAGGTAGCACCTATTTAAAGTTGATG
** *
3400047 GACCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAAC
65 GGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAAC
* *
3400112 ATATTAGGTAGCGCCTAAAATGTTACTAAAGTTTAATGATGATGGAGCCTTAGAAATCCGACTAT
130 ATATTAGGTAGCGCCTAAAATGTTACTAAAGTTTAA-GCTGATGGAGCCTTAGAAATCCGACGAT
3400177 AACAAAATATGTTAATTACTTGA
194 AACAAAATA-GTTAATTACTTGA
3400200 TTTGTTATCA
Statistics
Matches: 388, Mismatches: 51, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
225 53 0.14
226 205 0.53
227 128 0.33
228 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (225 bp):
ATCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAGGTAGCACCTATTTAAAGTTGATGG
GGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACA
TATTAGGTAGCGCCTAAAATGTTACTAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAA
CAAAATAGTTAATTACTTGAAACATTATTA
Found at i:3400737 original size:201 final size:199
Alignment explanation
Indices: 3400380--3400833 Score: 572
Period size: 201 Copynumber: 2.3 Consensus size: 199
3400370 ATTGAGATGG
* * * **
3400380 AAAGTATCAATACCTATACAAAAAGTATTGATACTTTATGTTTATGCCTATTATCATTAAACCGG
1 AAAGTATCGATACCTATACAAAAAGTATCGATACTTTATGTTTAAGCCTATTATCATTAAACCAA
* * * * * * * *
3400445 TATATTTTTACTGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTACG
66 TAGATTTATACCGTTTACATTGTAAATTTACCAATAAATGTAAAGTAATAGGTTTCAAAATTACA
* * * * *
3400510 AGTATCGATACTTCTGATACATGTATCGATACTTTCTGTGTGCAAGTTGTTTGAGAAGCATATTG
131 AGTATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTG-TTAAAAAACATATTG
3400575 GACTAA
195 GACT-A
* *
3400581 AAAGTATCGATACCTATACAAAGATTATCGATACTTTATGTTTAAGCCTATTATCATTAAACCAA
1 AAAGTATCGATACCTATACAAAAAGTATCGATACTTTATGTTTAAGCCTATTATCATTAAACCAA
*
3400646 TAGATTTATACCGTTTACATTGTAAATTTACCAATAAATGTAAAGTAATCA-GTTTC-GAATGTA
66 TAGATTTATACCGTTTACATTGTAAATTTACCAATAAATGTAAAGTAAT-AGGTTTCAAAAT-TA
* * * * * * *
3400709 TAAGTATTGATACTTGTTATATATGTATCGATACTTTGTGCGTTCAAATTGTTAAAAAACATATT
129 CAAGTATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTGTTAAAAAACATATT
3400774 GGACTA
194 GGACTA
* *
3400780 AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTACA-CCTATTAT
1 AAAGTATCGATACCTATACAAAAAGTATCGATACTTTATGTTTA-AGCCTATTAT
3400834 TAGGTACCAA
Statistics
Matches: 219, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
199 50 0.23
200 20 0.09
201 148 0.68
202 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (199 bp):
AAAGTATCGATACCTATACAAAAAGTATCGATACTTTATGTTTAAGCCTATTATCATTAAACCAA
TAGATTTATACCGTTTACATTGTAAATTTACCAATAAATGTAAAGTAATAGGTTTCAAAATTACA
AGTATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTGTTAAAAAACATATTGG
ACTA
Found at i:3400922 original size:199 final size:198
Alignment explanation
Indices: 3400380--3400922 Score: 526
Period size: 201 Copynumber: 2.7 Consensus size: 198
3400370 ATTGAGATGG
* * ** * * **
3400380 AAAGTATCAATACCTATACAAAAAGTATTGATACTTTATGTTTATGCCTATTATCATTAAACCGG
1 AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTAAGCCTATTATCAGT-AACCAA
* * * * * * * **
3400445 TATATTTTTACTGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTACG
65 TACATATATACCGTGTACATTGTAAATTTACCTATTACATTAAAGTAATA-G-TTCGAAATTATA
* * * * *
3400510 AGTATCGATACTTCTGATACATGTATCGATACTTTCTGTGTGCAAGTTGTTTGAGAAGCATATTG
128 AGTATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTGTTTAAAAAACATATTG
3400575 GACTAA
193 GACTAA
* * * *
3400581 AAAGTATCGATACCTATACAAAGATTATCGATACTTTATGTTTAAGCCTATTATCATTAAACCAA
1 AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTAAGCCTATTATCAGT-AACCAA
* * * * *
3400646 TAGATTTATACCGTTTACATTGTAAATTTACC-AATAAATGTAAAGTAATCAGTTTCG-AATGTA
65 TACATATATACCGTGTACATTGTAAATTTACCTATTACAT-TAAAGTAAT-AG-TTCGAAAT-TA
* * * * * *
3400709 TAAGTATTGATACTTGTTATATATGTATCGATACTTTGTGCGTTCAAATTG-TTAAAAAACATAT
126 TAAGTATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTGTTTAAAAAACATAT
3400773 TGGACT-A
191 TGGACTAA
*
3400780 AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTACA-CCTATTATTAGGT-ACCA
1 AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTA-AGCCTATTATCA-GTAACCA
* *
3400843 AGGTTCAACATAT-TACCGTGTACATTGTTAATTTACCTATTACATTAAAGTAATA-TTGGAAAT
64 A---T--ACATATATACCGTGTACATTGTAAATTTACCTATTACATTAAAGTAATAGTTCGAAAT
*
3400906 TATAAGAATCGATACTT
124 TATAAGTATCGATACTT
3400923 ATATGACAGT
Statistics
Matches: 289, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
198 5 0.02
199 69 0.24
200 28 0.10
201 146 0.51
202 32 0.11
203 9 0.03
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (198 bp):
AAAGTATCGATACCTATACAAACAGTATCAATACTTTATGTTTAAGCCTATTATCAGTAACCAAT
ACATATATACCGTGTACATTGTAAATTTACCTATTACATTAAAGTAATAGTTCGAAATTATAAGT
ATCGATACTTCTGATACATGTATCGATACTTTCTGCGTGCAAATTGTTTAAAAAACATATTGGAC
TAA
Found at i:3401292 original size:22 final size:23
Alignment explanation
Indices: 3401238--3401292 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
3401228 ACTGGAGTTA
3401238 AAAGTATCGAGACCGATATAACATTT
1 AAAGTATCGAGACCGATATAAC---T
*
3401264 AAAGTATCGAGATCGATATAAC-
1 AAAGTATCGAGACCGATATAACT
3401286 AAAGTAT
1 AAAGTAT
3401293 TGGTACGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 7 0.25
26 21 0.75
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (23 bp):
AAAGTATCGAGACCGATATAACT
Found at i:3404114 original size:20 final size:21
Alignment explanation
Indices: 3404089--3404132 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3404079 TTTAAGATGC
3404089 ATACTGGAATAA-AAATATCG
1 ATACTGGAATAATAAATATCG
*
3404109 ATACTGGAATAATAAGTATCG
1 ATACTGGAATAATAAATATCG
3404130 ATA
1 ATA
3404133 GTTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (21 bp):
ATACTGGAATAATAAATATCG
Found at i:3404193 original size:201 final size:199
Alignment explanation
Indices: 3403783--3404224 Score: 550
Period size: 201 Copynumber: 2.2 Consensus size: 199
3403773 TACGCCTATT
* * * **
3403783 ATTGTAAATTGACCTCTAACTTTAAAGTAATAGGTTTCAAAATTTCGCGTATTGATACTTTATAC
1 ATTGTAAATTTACCTATAACTTTAAAGTAATAGATTTCAAAATTTCGCGTATCAATACTTTATAC
* * * * *
3403848 ATGTGTATCGATACTTTTTCCGTGCAAATTGTTGATAATCATATTGGACTAAAAATTTTGATACC
66 ATGTGTATCGATACTTTTTCCATGCAAATTGTTGATAATCATACTGGAATAAAAATATCGATACC
* * *
3403913 TATACAAAATGTATTGATACTTGATGTTTACGCCTATTATCATTAAACCGGTAGACTTTTACCGT
131 TATACAAAATGTATCGATACTTGATATTTACACCTATTATCATTAAACCGGTAGACTTTTACCGT
3403978 TTAC
196 TTAC
* * ** *
3403982 ATTATAAATTTACCTATAACTTTAAAGTAATCGATTTTGAAATTTCGTGTATCAATACTTTATAC
1 ATTGTAAATTTACCTATAACTTTAAAGTAATAGATTTCAAAATTTCGCGTATCAATACTTTATAC
* * *
3404047 ATGTGTATCGATACTTTTTTGCATGTAAATTGTTTA-AGATGCATACTGGAATAAAAATATCGAT
66 ATGTGTATCGATAC-TTTTTCCATGCAAATTGTTGATA-AT-CATACTGGAATAAAAATATCGAT
* * * *
3404111 A-CTGGAATA-ATAA-GTATCGATAGTTTATATTTACACCTATTATCATTAAACCGGTAGATTTT
128 ACCT---ATACAAAATGTATCGATACTTGATATTTACACCTATTATCATTAAACCGGTAGACTTT
3404173 TACCGTTTAC
190 TACCGTTTAC
* * *
3404183 ATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAA
1 ATTGTAAATTTACCTATAACTTTAAAGTAATAGATTTCAAAA
3404225 CTCTAAGTAT
Statistics
Matches: 205, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
199 70 0.34
200 21 0.10
201 108 0.53
202 3 0.01
203 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (199 bp):
ATTGTAAATTTACCTATAACTTTAAAGTAATAGATTTCAAAATTTCGCGTATCAATACTTTATAC
ATGTGTATCGATACTTTTTCCATGCAAATTGTTGATAATCATACTGGAATAAAAATATCGATACC
TATACAAAATGTATCGATACTTGATATTTACACCTATTATCATTAAACCGGTAGACTTTTACCGT
TTAC
Found at i:3404257 original size:201 final size:200
Alignment explanation
Indices: 3403787--3404313 Score: 493
Period size: 201 Copynumber: 2.6 Consensus size: 200
3403777 CCTATTATTG
* * * * * **
3403787 TAAATTGACCTCTAACTTTAAAGTAATAG-GTTTCAAAATTTCGCGTATTGATACTTTATACATG
1 TAAATTTACCTATAACTTTAAAGAAATAGAGTTTCAAAA-CTCGTGTATCAATACTTTATACA-G
* * * * * * * * *
3403851 TGTATCGATACTTTTTCCGTGCAAATTGTTGATA-AT-CATATTGGACTAA-AAATTTTGATACC
64 TGTATCGATACTTTGTGCATGCAAACTGTTTA-AGATGCATACTGGAATAATAAATATCGATA-C
* * * * * *
3403913 T---ATACAAAATGTATTGATACTTGATGTTTACGCCTATTATCATTAAACCGGTAGACTTTTAC
127 TGGAATA-ATAA-GTATCGATAGTTTATATTTACACCTATTATCATTAAACCGGTAGACTTTTAC
3403975 CGTTTACATTA
190 CGTTTACATTA
* * * * **
3403986 TAAATTTACCTATAACTTTAAAGTAATCGATTTTGAAATTTCGTGTATCAATACTTTATACATGT
1 TAAATTTACCTATAACTTTAAAGAAATAGAGTTTCAAAACTCGTGTATCAATACTTTATACA-GT
* * *
3404051 GTATCGATACTTTTTTGCATGTAAATTGTTTAAGATGCATACTGGAATAA-AAATATCGATACTG
65 GTATCGATAC-TTTGTGCATGCAAACTGTTTAAGATGCATACTGGAATAATAAATATCGATACTG
*
3404115 GAATAATAAGTATCGATAGTTTATATTTACACCTATTATCATTAAACCGGTAGATTTTTACCGTT
129 GAATAATAAGTATCGATAGTTTATATTTACACCTATTATCATTAAACCGGTAGACTTTTACCGTT
*
3404180 TACATTG
194 TACATTA
* *
3404187 TAAATTTACCTATTACTTTAAAGAAATAG-GTTTCAAAACTC-TAAGTATCGATACATGTTATGA
1 TAAATTTACCTATAACTTTAAAGAAATAGAGTTTCAAAACTCGT--GTATCAATAC-T-TTAT-A
* * * * *
3404250 -A-TGTATCGATACTTTGTGCGTGCAAACTGTTTGAGATGCATATTGGAGTAATAAGTATCGATA
61 CAGTGTATCGATACTTTGTGCATGCAAACTGTTTAAGATGCATACTGGAATAATAAATATCGATA
3404313 C
126 C
3404314 ATTATGGTTA
Statistics
Matches: 274, Mismatches: 41, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
199 61 0.22
200 67 0.24
201 133 0.49
202 4 0.01
203 8 0.03
204 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (200 bp):
TAAATTTACCTATAACTTTAAAGAAATAGAGTTTCAAAACTCGTGTATCAATACTTTATACAGTG
TATCGATACTTTGTGCATGCAAACTGTTTAAGATGCATACTGGAATAATAAATATCGATACTGGA
ATAATAAGTATCGATAGTTTATATTTACACCTATTATCATTAAACCGGTAGACTTTTACCGTTTA
CATTA
Found at i:3416628 original size:18 final size:17
Alignment explanation
Indices: 3416595--3416628 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3416585 GCAAATACAT
*
3416595 TTTAGAACATATTAATA
1 TTTAGAACATAATAATA
3416612 TTTAGAACATAAATAAT
1 TTTAGAACAT-AATAAT
3416629 GAATTACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (17 bp):
TTTAGAACATAATAATA
Found at i:3417714 original size:18 final size:18
Alignment explanation
Indices: 3417693--3417732 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3417683 GGTCAGAATC
3417693 CCTTACTTGAGAAGAAGA
1 CCTTACTTGAGAAGAAGA
** *
3417711 CCTTGGTTGAGAAGATGA
1 CCTTACTTGAGAAGAAGA
3417729 CCTT
1 CCTT
3417733 GGTTGAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (18 bp):
CCTTACTTGAGAAGAAGA
Found at i:3417733 original size:18 final size:18
Alignment explanation
Indices: 3417699--3417741 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3417689 AATCCCTTAC
3417699 TTGAGAAGAAGACCTTGG
1 TTGAGAAGAAGACCTTGG
*
3417717 TTGAGAAGATGACCTTGG
1 TTGAGAAGAAGACCTTGG
3417735 TTGAGAA
1 TTGAGAA
3417742 TAAGGTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (18 bp):
TTGAGAAGAAGACCTTGG
Found at i:3418359 original size:21 final size:21
Alignment explanation
Indices: 3418333--3418372 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3418323 CTAAATTATA
3418333 AGTATCGATACTTGTGATATG
1 AGTATCGATACTTGTGATATG
*
3418354 AGTATCGATACTTTTGATA
1 AGTATCGATACTTGTGATA
3418373 CGTGTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
AGTATCGATACTTGTGATATG
Found at i:3418379 original size:21 final size:21
Alignment explanation
Indices: 3418333--3418389 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3418323 CTAAATTATA
* *
3418333 AGTATCGATACTTGTGATATG
1 AGTATCGATACTTTTGATACG
3418354 AGTATCGATACTTTTGATACG
1 AGTATCGATACTTTTGATACG
* * *
3418375 TGTATTGATATTTTT
1 AGTATCGATACTTTT
3418390 TCCGTGCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (21 bp):
AGTATCGATACTTTTGATACG
Found at i:3418860 original size:178 final size:178
Alignment explanation
Indices: 3418402--3419304 Score: 927
Period size: 179 Copynumber: 4.9 Consensus size: 178
3418392 CGTGCATGTT
*
3418402 GTTTGAGAAGCATACTGGACTAAAAGTATCGATACCTATACAAAGAGTATCGATTCTTTATGTTT
1 GTTTGAGAAGCATACT-GACTAAAAGTATCGATACATATACAAAGAGTATCGATTCTTTATGTTT
* * ** * * * *
3418467 ACGCCTATTATCATTAAATTGATAGATTTTTACCGCCTAAATTGTAAATTTACCTATTACTTTAA
65 ATGCCTATTATCAGTAAACAGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTAA
* * * * *
3418532 GGTAATAGGTTTCGAAATTATAAGTATTGATACTTTCTGCATGCATATT
130 AGTAATAGGTTTCGAAATTATAAGTATAGATACTTTCTACATACATATA
* **
3418581 GATTGAGAAGCATACTGAACTAAAAGTATCGATACATATACAAAGAGTATTTATTCTTTATGTTT
1 GTTTGAGAAGCATACTG-ACTAAAAGTATCGATACATATACAAAGAGTATCGATTCTTTATGTTT
*
3418646 ATGCCTATTATC-GTTAAACAAGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTA
65 ATGCCTATTATCAG-TAAACAGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTA
* * *
3418710 AAGTAATACGTTTCGAAATTATAAGTATAGATACTTTCTACGTACATCTA
129 AAGTAATAGGTTTCGAAATTATAAGTATAGATACTTTCTACATACATATA
* * * * **
3418760 GTTTGAGAATCATACTAGAC-CAAAGTATCGATACATATACAAAAATTATCGAAACTTTATGTTT
1 GTTTGAGAAGCATACT-GACTAAAAGTATCGATACATATACAAAGAGTATCGATTCTTTATGTTT
*
3418824 ATGCCTATTATCAGTAAACCGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTAA
65 ATGCCTATTATCAGTAAACAGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTAA
* * *
3418889 AGTAATAGGTTTC-AGAATTATAAGTATCGATACTTGTTATACTTGTATTGATACTTTATGTGTG
130 AGTAATAGGTTTCGA-AATTATAAGTATAGATAC---TT-T-C---TA--CATAC---A--TAT-
3418953 CA
178 -A
* **
3418955 TGTTGTTTGAGAAGCATACTGGACCAAAAGTATCGATACATATACAAA-ATGTATCGAAACTTTA
1 ----GTTTGAGAAGCATACT-GACTAAAAGTATCGATACATATACAAAGA-GTATCGATTCTTTA
* * * *
3419019 TGTTTATGCCTATTATCATTAAACTGGTAGATTTTTGCCGCTTACATTGTAAATTTACCTATTAC
60 TGTTTATGCCTATTATCAGTAAACAGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAG
* * * * * * * *
3419084 TTTAAAGTAATTGGTTTCGAAGTTATAACAAGTATCGATACTTTCTGCGTGCATGTT
125 TTTAAAGTAATAGGTTTCGAAATTAT---AAGTATAGATACTTTCTACATACATATA
* * *
3419141 GTTTGAGAAGCATACTGGACTAAAAGTATTGATACCTATACAAAGAGTATCGATACTTTATGTTT
1 GTTTGAGAAGCATACT-GACTAAAAGTATCGATACATATACAAAGAGTATCGATTCTTTATGTTT
* * * * * * * *
3419206 ACGCCTATTATCATTAAACA-GTAGACTTTTACCG-TTGATATTATAAATTTACTTATAACTTTA
65 ATGCCTATTATCAGTAAACAGGTAGATTTTTACCGCTT-ACATTGTAAATTTACCTATTAGTTTA
* * *
3419269 AAGTAATATGTTTCGAAAATATAAGTATCGATACTT
129 AAGTAATAGGTTTCGAAATTATAAGTATAGATACTT
3419305 GATATACATG
Statistics
Matches: 622, Mismatches: 68, Indels: 69
0.82 0.09 0.09
Matches are distributed among these distances:
177 1 0.00
178 142 0.23
179 172 0.28
180 3 0.00
181 54 0.09
182 78 0.13
183 2 0.00
186 2 0.00
188 6 0.01
190 1 0.00
191 1 0.00
193 4 0.01
195 2 0.00
198 1 0.00
199 20 0.03
200 120 0.19
201 1 0.00
203 12 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (178 bp):
GTTTGAGAAGCATACTGACTAAAAGTATCGATACATATACAAAGAGTATCGATTCTTTATGTTTA
TGCCTATTATCAGTAAACAGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTAAA
GTAATAGGTTTCGAAATTATAAGTATAGATACTTTCTACATACATATA
Found at i:3419081 original size:200 final size:200
Alignment explanation
Indices: 3418760--3419126 Score: 605
Period size: 200 Copynumber: 1.8 Consensus size: 200
3418750 CGTACATCTA
*
3418760 GTTTGAGAATCATACTAGACCAAAGTATCGATACATATACAAAAATTATCGAAACTTTATGTTTA
1 GTTTGAGAAGCATACTAGACCAAAGTATCGATACATATACAAAAATTATCGAAACTTTATGTTTA
*
3418825 TGCCTATTATCAGTAAACCGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTAGTTTAAA
66 TGCCTATTATCAGTAAACCGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAA
3418890 GTAATAGGTTTCAGAA-TTAT-AAGTATCGATACTTGTTATACTTGTATTGATACTTTATGTGTG
131 GTAATAGGTTTC-GAAGTTATAAAGTATCGATACTTGTTATACTTGTATTGATACTTTATGTGTG
3418953 CATGTT
195 CATGTT
*
3418959 GTTTGAGAAGCATACTGGACCAAAAGTATCGATACATATAC-AAAATGTATCGAAACTTTATGTT
1 GTTTGAGAAGCATACTAGACC-AAAGTATCGATACATATACAAAAAT-TATCGAAACTTTATGTT
* * *
3419023 TATGCCTATTATCATTAAACTGGTAGATTTTTGCCGCTTACATTGTAAATTTACCTATTACTTTA
64 TATGCCTATTATCAGTAAACCGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTA
*
3419088 AAGTAATTGGTTTCGAAGTTATAACAAGTATCGATACTT
129 AAGTAATAGGTTTCGAAGTTAT-A-AAGTATCGATACTT
3419127 TCTGCGTGCA
Statistics
Matches: 155, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
199 27 0.17
200 114 0.74
203 14 0.09
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (200 bp):
GTTTGAGAAGCATACTAGACCAAAGTATCGATACATATACAAAAATTATCGAAACTTTATGTTTA
TGCCTATTATCAGTAAACCGGTAGATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAA
GTAATAGGTTTCGAAGTTATAAAGTATCGATACTTGTTATACTTGTATTGATACTTTATGTGTGC
ATGTT
Found at i:3422183 original size:18 final size:18
Alignment explanation
Indices: 3422152--3422202 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
3422142 ACTTTGCTCA
*
3422152 TCACATACATAATTTTAT
1 TCACATACATAATTTCAT
* *
3422170 TCAGATACAAAATTTCAT
1 TCACATACATAATTTCAT
3422188 TCACATACATAATTT
1 TCACATACATAATTT
3422203 GGCTTACATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (18 bp):
TCACATACATAATTTCAT
Found at i:3424108 original size:12 final size:12
Alignment explanation
Indices: 3424073--3424111 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3424063 TCCCCTACTA
* *
3424073 CCTTTTCTTCTA
1 CCTTATCTTCTT
*
3424085 CCTTCTCTTCTT
1 CCTTATCTTCTT
3424097 CCTTATCTTCTT
1 CCTTATCTTCTT
3424109 CCT
1 CCT
3424112 CCTCTACCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (12 bp):
CCTTATCTTCTT
Found at i:3425762 original size:229 final size:228
Alignment explanation
Indices: 3425359--3425822 Score: 696
Period size: 229 Copynumber: 2.0 Consensus size: 228
3425349 TATAGTAATT
* **
3425359 GGGTTTCCTTCAAAGGAATGGGAATACTCTCTACTACAAGTATCGGTACCTTTATACAACATACA
1 GGGTTTCCTTCAAAGGAATAGGAATACTCTCTACTACAAGTATCAATACCTTTATACAACATACA
*
3425424 ATATCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTAGAATATCAC
66 ATATCATTTTCTACCTATAATATTACATAAAAGTATCAATATTTATTTTCTACCTAGAATATCAC
* * * * *
3425489 TTTCTAACTGTAATCGGTCCCAAATTCTTCTTTACTTCGAAAACCCCATACCCATAAACCTAATC
131 TTTCTAAATGTAATCCGTCCCAAATGCTTCTTTACTTCGAAAACCCCAAACCCATAAAACTAATC
*
3425554 CCTATTT-TTGAATACTATAATACTAAAAAAACTA
196 CCTATTTCCT-AATACTATAATACT-AAAAAACTA
* * *
3425588 GGGTTTCCTTCAAAGGAATAGGAATACTCTCTACTACAAGTATCAATAGCTTTATACAACCTATA
1 GGGTTTCCTTCAAAGGAATAGGAATACTCTCTACTACAAGTATCAATACCTTTATACAACATACA
*
3425653 ATATCATTTTCTACCTATAATATTACATAAAAGTATCGATATTTATTTTCTACCTAGAATATCAC
66 ATATCATTTTCTACCTATAATATTACATAAAAGTATCAATATTTATTTTCTACCTAGAATATCAC
* * * * * *
3425718 TTTCTAAATGTAATCCGTCTCAAATGCTTTTTTACTTTGAAAACCCTAAACTCATAAAACTATTC
131 TTTCTAAATGTAATCCGTCCCAAATGCTTCTTTACTTCGAAAACCCCAAACCCATAAAACTAATC
* * *
3425783 CCTATTTCCTATTATTGTAATACTAAAAAACTA
196 CCTATTTCCTAATACTATAATACTAAAAAACTA
3425816 GGGTTTC
1 GGGTTTC
3425823 GACAACATAC
Statistics
Matches: 211, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
228 16 0.08
229 194 0.92
230 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.36
Consensus pattern (228 bp):
GGGTTTCCTTCAAAGGAATAGGAATACTCTCTACTACAAGTATCAATACCTTTATACAACATACA
ATATCATTTTCTACCTATAATATTACATAAAAGTATCAATATTTATTTTCTACCTAGAATATCAC
TTTCTAAATGTAATCCGTCCCAAATGCTTCTTTACTTCGAAAACCCCAAACCCATAAAACTAATC
CCTATTTCCTAATACTATAATACTAAAAAACTA
Found at i:3426436 original size:197 final size:194
Alignment explanation
Indices: 3426071--3426442 Score: 487
Period size: 197 Copynumber: 1.9 Consensus size: 194
3426061 ACATTTTCAT
* *
3426071 TTCTTTTCAATTCCTAAAGAATCGATACTATGATACATATGCTTATAAAAGTATCGATACCTTCA
1 TTCTTTTAAATCCCTAAAGAATCGATACTATGATACATATGCTTATAAAAGTATCGATACCTTCA
* * * * * *
3426136 ACATATCCAGTAGCGCTTTACATGTTTTGTTATATTGAAACCGGTTTTATCAAATTTTAACATGT
66 ACATATCCAGTAGCGCTTTACAGGTTTTGTTAAACTGAAACAGGTTTTATCAAACTTCAACATGT
3426201 TATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGGCGCTATTATTGCAA
131 TATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGGCGCTATTATTGCAA
* * * *
3426265 TTCTTTTAAATCCCTAAAGTAA-CGATACTTTGGTGCATATGCTTATAAAAGTATCGATACAAAT
1 TTCTTTTAAATCCCTAAAG-AATCGATACTATGATACATATGCTTATAAAAGTATCGATAC---C
* ** * * * *
3426329 TTTAACCAT-TCTGGTATCTCTTTACCGGTTTTGTTAAACTGAAACAGGTTTTGTCAAACTTCAA
62 TTCAA-CATATCCAGTAGCGCTTTACAGGTTTTGTTAAACTGAAACAGGTTTTATCAAACTTCAA
* * *
3426393 CATGTTATATTGTCATGTATCGATACATGTGTGTCATGTATCGATACTTT
126 CATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTT
3426443 CGAGACATTT
Statistics
Matches: 151, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
194 52 0.34
195 2 0.01
197 94 0.62
198 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (194 bp):
TTCTTTTAAATCCCTAAAGAATCGATACTATGATACATATGCTTATAAAAGTATCGATACCTTCA
ACATATCCAGTAGCGCTTTACAGGTTTTGTTAAACTGAAACAGGTTTTATCAAACTTCAACATGT
TATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGGCGCTATTATTGCAA
Found at i:3428326 original size:171 final size:172
Alignment explanation
Indices: 3428133--3428476 Score: 620
Period size: 171 Copynumber: 2.0 Consensus size: 172
3428123 AAATTACATC
* *
3428133 ATTCATCACTCAACTCTCTTCTCACTCATATTTTGGTCACTAAAGTTTAAAATTTTCAATTTAAC
1 ATTCATCACTCAACTATCTTCTCACTCATATTTTGGTCACTAAAGTTTAAAATTTACAATTT-AC
*
3428198 -TACTCAACCTTCAAATTTCTCATGTTTTAATCACTTTAATTATTTTATTAATAA-CTTTCGTGA
65 TTACTCAACCTTCAAATTTCTCATGTTTTAATCACTTTAATTATTTCATTAATAATCTTTCGTGA
*
3428261 CATAACATTTATTATTATCATTATTTTATTAATATATTATGAA
130 CATAACATTTATTATTATCATTATTTTATTAATATATAATGAA
3428304 ATTCATCACTCAACTATCTTCTCACTCATATTTTGGTCACTAAAGTTTAAAATTTACAATTTACT
1 ATTCATCACTCAACTATCTTCTCACTCATATTTTGGTCACTAAAGTTTAAAATTTACAATTTACT
*
3428369 TACTCAACCTTCAAATTTCTCATGTTTTAATCACTTTAATTATTTCATTAATAATTTTTCGTGAC
66 TACTCAACCTTCAAATTTCTCATGTTTTAATCACTTTAATTATTTCATTAATAATCTTTCGTGAC
3428434 ATAACATTTATTATTATCATTATTTTATTAATATATAATGAA
131 ATAACATTTATTATTATCATTATTTTATTAATATATAATGAA
3428476 A
1 A
3428477 ATAAAATAAT
Statistics
Matches: 166, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
170 2 0.01
171 113 0.68
172 51 0.31
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (172 bp):
ATTCATCACTCAACTATCTTCTCACTCATATTTTGGTCACTAAAGTTTAAAATTTACAATTTACT
TACTCAACCTTCAAATTTCTCATGTTTTAATCACTTTAATTATTTCATTAATAATCTTTCGTGAC
ATAACATTTATTATTATCATTATTTTATTAATATATAATGAA
Found at i:3428859 original size:18 final size:18
Alignment explanation
Indices: 3428836--3428877 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3428826 GACAGTGGAA
*
3428836 ATTTTTCAATT-ATCATAT
1 ATTTTT-AATTGATAATAT
*
3428854 ATTTTTTATTGATAATAT
1 ATTTTTAATTGATAATAT
3428872 ATTTTT
1 ATTTTT
3428878 GTTCCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTAATTGATAATAT
Found at i:3438272 original size:2 final size:2
Alignment explanation
Indices: 3438267--3438295 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3438257 GGTTCATACG
3438267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3438296 GAAAACTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3445279 original size:41 final size:42
Alignment explanation
Indices: 3445214--3445316 Score: 102
Period size: 44 Copynumber: 2.4 Consensus size: 42
3445204 AAATGGTTAA
* *
3445214 GATATTTAGCGACGCTTTTCGG-ATAAACG-CGCAAAAAGTCT
1 GATATATAGCGACG-TTTTAGGAATAAACGTCGCAAAAAGTCT
* * * *
3445255 GTTATATAGCGACGTTTTAAGGATATAAATGTCGCAAAAGGTGT
1 GATATATAGCGACGTTTT-AGGA-ATAAACGTCGCAAAAAGTCT
*
3445299 GATATATAGCGGCGTTTT
1 GATATATAGCGACGTTTT
3445317 TCATACAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.08
41 14 0.28
43 6 0.12
44 26 0.52
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (42 bp):
GATATATAGCGACGTTTTAGGAATAAACGTCGCAAAAAGTCT
Found at i:3445334 original size:42 final size:43
Alignment explanation
Indices: 3445243--3445403 Score: 128
Period size: 44 Copynumber: 3.7 Consensus size: 43
3445233 CGGATAAACG
* * * * * * *
3445243 CGCAAAAAGTCTGTTATATAGCGACG-TTTTAAGGATATAAATGT
1 CGCAAAAGGTCTGGTATATAGCGGCGTTTTTCA--ATACAAAAGC
* * *
3445287 CGCAAAAGGTGTGATATATAGCGGCGTTTTTC-ATACAAACGC
1 CGCAAAAGGTCTGGTATATAGCGGCGTTTTTCAATACAAAAGC
* * * * *
3445329 CGCAAAAGATTTGGTATATATCAGCGTTTTTCGAATACAAAATC
1 CGCAAAAGGTCTGGTATATAGCGGCGTTTTTC-AATACAAAAGC
* *
3445373 TGCAAAAGGTCTGGTATATAGCGTCGTTTTT
1 CGCAAAAGGTCTGGTATATAGCGGCGTTTTT
3445404 TTGTAACAAG
Statistics
Matches: 93, Mismatches: 21, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
42 34 0.37
44 55 0.59
45 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (43 bp):
CGCAAAAGGTCTGGTATATAGCGGCGTTTTTCAATACAAAAGC
Found at i:3450683 original size:15 final size:15
Alignment explanation
Indices: 3450663--3450696 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3450653 CCACGCCATT
3450663 ACACTTTCAAGCTCA
1 ACACTTTCAAGCTCA
3450678 ACACTTTCAAGCTCA
1 ACACTTTCAAGCTCA
3450693 ACAC
1 ACAC
3450697 AGACTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.24
Consensus pattern (15 bp):
ACACTTTCAAGCTCA
Found at i:3454581 original size:21 final size:22
Alignment explanation
Indices: 3454526--3454581 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3454516 TTCGGTAGAA
*
3454526 CGCTACCTAAAATGTTATTTTT
1 CGCTACCTAAAATGTTATATTT
**
3454548 TTCTACC-ATAAATGTTA-ATTT
1 CGCTACCTA-AAATGTTATATTT
3454569 CGCTACCTAAAAT
1 CGCTACCTAAAAT
3454582 AAATATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
CGCTACCTAAAATGTTATATTT
Found at i:3468430 original size:21 final size:22
Alignment explanation
Indices: 3468404--3468444 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3468394 AGGACAAGTG
3468404 GTATCAGTAC-TCCTTTAATGA
1 GTATCAGTACTTCCTTTAATGA
3468425 GTATCAGTACTTCCTTTAAT
1 GTATCAGTACTTCCTTTAAT
3468445 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (22 bp):
GTATCAGTACTTCCTTTAATGA
Found at i:3476615 original size:3 final size:3
Alignment explanation
Indices: 3476609--3476638 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3476599 TAAAAAAATT
3476609 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3476639 GTTGATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3482623 original size:40 final size:37
Alignment explanation
Indices: 3482579--3482701 Score: 131
Period size: 40 Copynumber: 3.1 Consensus size: 37
3482569 AAAAATATAT
*
3482579 AAAAAGAGAAAAAGAAAGAAGACATAGAAAAAGAAGAAGG
1 AAAAA-AGAAAAAGAAA-AAGAGA-AGAAAAAGAAGAAGG
* *
3482619 AAAAAAGAGAAAAGAAAAAGAGAAAGAGAAAAGAAAAAAG
1 AAAAAAGA-AAAAGAAAAAGAG-AAGA-AAAAGAAGAAGG
3482659 AAAAAAGAAAAAAGAAAAAGAGAAGAAAAA-AAGAGAGAG
1 AAAAAAG-AAAAAGAAAAAGAGAAGAAAAAGAAGA-AG-G
3482698 AAAA
1 AAAA
3482702 TAAATCAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
37 3 0.04
38 5 0.07
39 19 0.26
40 44 0.61
41 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.01
Consensus pattern (37 bp):
AAAAAAGAAAAAGAAAAAGAGAAGAAAAAGAAGAAGG
Found at i:3482625 original size:14 final size:14
Alignment explanation
Indices: 3482579--3482700 Score: 96
Period size: 14 Copynumber: 8.9 Consensus size: 14
3482569 AAAAATATAT
3482579 AAAAAG-AGAAA-A
1 AAAAAGAAGAAAGA
*
3482591 AGAAAGAAGACATAG-
1 AAAAAGAAGA-A-AGA
*
3482606 AAAAAGAAGAAGGA
1 AAAAAGAAGAAAGA
3482620 AAAAAG-AGAAA-A
1 AAAAAGAAGAAAGA
3482632 GAAAAAG-AGAAAGA
1 -AAAAAGAAGAAAGA
* *
3482646 GAAAAGAAAAAAGA
1 AAAAAGAAGAAAGA
*
3482660 AAAAAGAAAAAAGA
1 AAAAAGAAGAAAGA
3482674 AAAAGAGAAGAAA-A
1 AAAA-AGAAGAAAGA
*
3482688 AAAGAGAGAGAAA
1 AAAAAGA-AGAAA
3482701 ATAAATCAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.07
13 27 0.30
14 41 0.45
15 17 0.19
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.01
Consensus pattern (14 bp):
AAAAAGAAGAAAGA
Found at i:3482625 original size:33 final size:32
Alignment explanation
Indices: 3482587--3482701 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 32
3482577 ATAAAAAGAG
* *
3482587 AAAAAGAAAGAAGACATAGAAAAAGAAGAAGGA
1 AAAAAGAAA-AAGAAAAAGAAAAAGAAGAAGGA
3482620 AAAAAGAGAAAAGAAAAAGAGAAAGAGAA-AA-GA
1 AAAAAGA-AAAAGAAAAAGA-AAA-AGAAGAAGGA
*
3482653 AAAAAGAAAAAAGAAAAAAGAAAAAG-AGAAGAA
1 AAAAAG-AAAAAG-AAAAAGAAAAAGAAGAAGGA
* *
3482686 AAAAAGAGAGAGAAAA
1 AAAAAGAAAAAGAAAA
3482702 TAAATCAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
31 5 0.07
32 8 0.11
33 38 0.54
34 15 0.21
35 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.01
Consensus pattern (32 bp):
AAAAAGAAAAAGAAAAAGAAAAAGAAGAAGGA
Found at i:3482693 original size:13 final size:13
Alignment explanation
Indices: 3482579--3482701 Score: 76
Period size: 13 Copynumber: 9.2 Consensus size: 13
3482569 AAAAATATAT
3482579 AAAAAGAGAA-AA
1 AAAAAGAGAAGAA
* * *
3482591 AGAAAGAAGACATAG
1 AAAAAG-AGA-AGAA
*
3482606 AAAAAGAAGAAGGA
1 AAAAAG-AGAAGAA
3482620 AAAAAGAGAA-AA
1 AAAAAGAGAAGAA
3482632 GAAAAAGAGAAAGAGA
1 -AAAAAGAG-AAGA-A
*
3482648 AAAGAA-AAAAG-A
1 AAA-AAGAGAAGAA
*
3482660 AAAAAGA-AAAAA
1 AAAAAGAGAAGAA
3482672 GAAAAAGAGAAGAA
1 -AAAAAGAGAAGAA
3482686 AAAAAGAGAGAGAA
1 AAAAAGAGA-AGAA
3482700 AA
1 AA
3482702 TAAATCAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
11 4 0.05
12 12 0.14
13 31 0.35
14 23 0.26
15 15 0.17
16 3 0.03
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.01
Consensus pattern (13 bp):
AAAAAGAGAAGAA
Found at i:3484894 original size:257 final size:257
Alignment explanation
Indices: 3484438--3485468 Score: 1379
Period size: 257 Copynumber: 4.0 Consensus size: 257
3484428 AGTTTCTTAC
* * * * *
3484438 TTGGTAAGT-ACTTCGTGCCATCAATAAGTCTTTTGAGCATGATAATTAAATCCTTTGGGTCATC
1 TTGGTAAGTCA-TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
* * * *
3484502 TGTAAGTCTTTCGAGCAACATGGTAAGTCCTTCGGGCCATCCGTAAGACCTTCGATTAGGATGTT
65 TGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGAGTAGGATGTT
*
3484567 TTCACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTGTTTTTAGAAAAT
130 TTCACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAAT
* *
3484632 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAG-TTCTTTACCTAATAAATTATTTCCCAAA
195 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTC-TTACCTAATAAACTATTTCCAAAA
* *
3484695 TTGGTAAGTCATTCGGACCATCAGTAAGTCTTTCGAGCAAGATGATTAAAT-CTTCCGGGTCATC
1 TTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT-CGGGTCATC
* * * * * * * *
3484759 TTTAAGTCTTTCGAGCGAGATTATAAGTCCTTCGTGCCATTTGTAAGACCTTTGGGTATGATGTT
65 TGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGAGTAGGATGTT
* * * *
3484824 TTCATAAGAATTTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAGTATTTTGAGAAAAT
130 TTCACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAAT
*
3484889 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAAT-AACTATTTCCAAAA
195 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAA
* * * * *
3484951 TTGATAAGTCCTTCGGGCCATTAGTAAGTCTCTCGAGCATGATGATTAAATCCTTCGGGTCACCT
1 TTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
* * * * * *
3485016 GTAAGTCTTTCGAGCCAGATGATAAGTCCTTCGGGCCATCTGTAGGTCCTTCGAATAAGATATTT
66 GTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGAGTAGGATGTTT
* * *
3485081 TCATATGAATTTGAAAAATGAGAAAGCAATTTCCATAGTTTCTCATTTAGTATTTTTAGAAAATG
131 TCACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATG
** *
3485146 AAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTATTAAACTATTTCCAAAA
196 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAA
* * * *
3485208 TTAGTTAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCT
1 TTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
** * * * * * * *
3485273 GTCTGTCTTTCGAGTAAGATGTTAAGTCCTTCGAGACATCTATAAGACCTTCAAGAAGGATGTTT
66 GTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGAGTAGGATGTTT
* * * * * *
3485338 TCACATGATTTTTTAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAA
131 TCACATGA--ATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAA
* * *
3485403 TGAAATGTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTATAC-AATAAACTATTTCCAAAA
194 TGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA-CCTAATAAACTATTTCCAAAA
3485467 TT
1 TT
3485469 ATACTTTTAG
Statistics
Matches: 674, Mismatches: 92, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
256 225 0.33
257 339 0.50
258 4 0.01
259 105 0.16
260 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (257 bp):
TTGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
GTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGAGTAGGATGTTT
TCACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATG
AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAA
Found at i:3485059 original size:41 final size:41
Alignment explanation
Indices: 3484952--3485069 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 41
3484942 TTTCCAAAAT
*
3484952 TGATAAGTCCTTCGGGCCAT-TAGTAAGTCTCTCGAGCATGA
1 TGATAAGTCCTTCGGGCCATCT-GTAAGTCTTTCGAGCATGA
* * *
3484993 TGATTAAATCCTTCGGGTCACCTGTAAGTCTTTCGAGCCA-GA
1 TGA-TAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAG-CATGA
* *
3485035 TGATAAGTCCTTCGGGCCATCTGTAGGTCCTTCGA
1 TGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGA
3485070 ATAAGATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 30 0.46
42 32 0.49
43 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (41 bp):
TGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGA
Found at i:3485281 original size:42 final size:41
Alignment explanation
Indices: 3485216--3485305 Score: 99
Period size: 42 Copynumber: 2.2 Consensus size: 41
3485206 AATTAGTTAG
*
3485216 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATG-TTAAA
* * ** * * *
3485258 TCCTTCGGGTCATCTGTCTGTCTTTCGAGTAAGATGTTAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGTTAAA
3485299 TCCTTCG
1 TCCTTCG
3485306 AGACATCTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 11 0.28
42 29 0.73
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGTTAAA
Found at i:3486016 original size:38 final size:38
Alignment explanation
Indices: 3485905--3486468 Score: 574
Period size: 38 Copynumber: 14.7 Consensus size: 38
3485895 GAAGCTTCAA
* *
3485905 CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
3485947 CTTGACTTCCTCGTG-A-AG-AGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
3485982 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
3486020 CCTAAC-TCCTTCGTGACA-AGGAGTCAATCTTTGTTATT
1 CTTGACTTCC-TCGTGA-AGAGAAGTCAATCTTTGTTATT
* * * * *
3486058 CCTGACTCCCTCGCGAAGAGGAGTCAATCTTTTTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
3486096 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA-T
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
** * * * *
3486133 CCCGACTCCCTCACGGGAAG-G-AGGCAGTCTTTGTTATT
1 CTTGACTTCCT--CGTGAAGAGAAGTCAATCTTTGTTATT
* * *
3486171 CTTGACTTCCCCATGAAGAGAAGTCAATCTTTATTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * ****
3486209 ATTGACTCCCTTACAAAGATGAA-TCAATCTTTCAATGTTATT
1 CTTGACTTCCTCGTGAAGA-GAAGTCAATC-TT---TGTTATT
3486251 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
3486289 CTTGACTTCCTCATTAAGATAAGTCAATCTTTGCTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
3486327 ATTGACTTCCTCGTGAAGAGAAGCCAATCTTT-TTCTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
3486364 CCTTGACTTTCGCGTGAAGAGAAGTCAATCTTTGTTATT
1 -CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
3486403 CTTGACTTCCTCGTTAAGAGAAGTCAATCTTTG-TCTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
3486440 CATTGACTTCCTCGTGAAGAGGAGTCAAT
1 C-TTGACTTCCTCGTGAAGAGAAGTCAAT
3486469 TTTTCAGTGT
Statistics
Matches: 436, Mismatches: 65, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
35 21 0.05
36 6 0.01
37 35 0.08
38 301 0.69
39 26 0.06
40 2 0.00
41 6 0.01
42 39 0.09
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (38 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:3486499 original size:45 final size:44
Alignment explanation
Indices: 3486433--3486900 Score: 427
Period size: 45 Copynumber: 10.4 Consensus size: 44
3486423 AAGTCAATCT
*
3486433 TTGTCTTCATTGACTTCCTCGTGAAGAGGAGTCAAT-TTTTCAGTG
1 TTGTCTTC-TTGACTTTCTCGTGAAGAGGAGTCAATCTTTT-AGTG
3486478 TTGTCTTCCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
1 TTGTCTT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
3486523 TTATCTTCCTTGAATTTCTCGTGAAGATGAGTCAATCTCTTAATG
1 TTGTCTT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * **
3486568 TTTTCCTTCTTGTCTTTTTCACGAAGAGGAGTCAATCTTTTAGTG
1 TTGT-CTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
3486613 TTGTCCTTTTTGACTTTCTCATGAAGATGACTTAATCTTTTAGTG
1 TTGT-CTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* ** * *
3486658 TTGTCCTTCTTGATTTTCTCACGAAAATGAGTCAATCTTTTAGTG
1 TTGT-CTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
** * * *
3486703 CAGTACTTCTTGACTTTCTCGTGAAGAGAAGTTAATCTTTTGGTG
1 TTGT-CTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * * *
3486748 TTGACCTTGTTAACTTTCTTGCGAAGAGGGGTAAATCTTTTTGT-
1 TTG-TCTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * *
3486792 TTTTCTTCCTTGACTTTCTCGTGAAGAGGAGTCAATCGTTTAGTC
1 TTGTCTT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* ** *
3486837 TTGCCTTCCTTGACTTTCTCACGAAGAGGAGTCAATCTTTTAATG
1 TTGTCTT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* *
3486882 TTGTCCTTTTTTACTTTCT
1 TTGT-CTTCTTGACTTTCT
3486901 TGCGGAGATG
Statistics
Matches: 345, Mismatches: 71, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
43 3 0.01
44 30 0.09
45 301 0.87
46 11 0.03
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.44
Consensus pattern (44 bp):
TTGTCTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
Found at i:3488057 original size:231 final size:231
Alignment explanation
Indices: 3487464--3488147 Score: 763
Period size: 231 Copynumber: 3.0 Consensus size: 231
3487454 AATGTTTGAT
* * * * * *
3487464 TTTCATATTCAATCTTCCTTGAAGAGCAACAAAGTGGATCAAAGTTTTCTCGTGTATGATCTCCC
1 TTTCAGATTCAATCTTCC-TGAAGAGTAGCGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCC
* * *
3487529 CTAAAGAGTAATAGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGTGAAGCAA
65 CTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAA
* * *
3487594 ATCAATTCTGATTCAATCTTCCCTGAAGAGCAGT-AGAGTGAATC--AATTTTCTTTGAAAGGTC
130 ATCAATTCTGATTCAATCTTCCCTGAAAAACAGTGA-AGTGGATCAAAATTTTC-TT--AA-GTC
* * * * * *
3487656 TGGTATTCACTAAAGAGTAGTGGAGCA-AATCCCCTTTTTTC
190 TGATCTCCACTAAAGAGTAGTGGAGCATATTCCCCTTCTATC
*** * * *
3487697 TTTCAGATTTGGTCTTCCTGAAGAGTAGCGAAGTCGATCAAAGTTTTCTCGAGTCTGGTCTCCTC
1 TTTCAGATTCAATCTTCCTGAAGAGTAGCGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
* * * **
3487762 TAAAGAGTAGTGGAGCAGATTATTCTTCTTTCAGATTTGGTCTTCCTGGAGAGCAGCAAAGCAAA
66 TAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAA
* * *
3487827 TCATGTTC-GATTTAATCTTCCTTGAAAAACAGTGAAGTGGATCAAAATTTTCTTAAGTCTGATC
131 TCA-ATTCTGATTCAATCTTCCCTGAAAAACAGTGAAGTGGATCAAAATTTTCTTAAGTCTGATC
* **
3487891 TCCTCTAAAGAGTAGTGGAGCATATTCTTCTTCTAT-
195 TCCACTAAAGAGTAGTGGAGCATATTCCCCTTCTATC
* * *
3487927 TTTCTGATTCAATCTTCCCT-AGAGAAG-AGTGAAGTGGACCAAAGTTTTCTCGAGTCTGATCTC
1 TTTCAGATTCAATCTT-CCTGA-AG-AGTAGCGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTC
* * * * * *
3487990 CCCTAAAGAGTAGTGGAGTATATTCTTCTTATTTCAAATTTGGTATTTCTGAAGAGTAGTGAAGC
63 CCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGC
* * *
3488055 AAATCAATTCTGATTCAATTTTCCCTGAAAAACAGTGAAGTGGATCAAAGTTTTCTCAAGTCTGA
128 AAATCAATTCTGATTCAATCTTCCCTGAAAAACAGTGAAGTGGATCAAAATTTTCTTAAGTCTGA
* * * *
3488120 TCTCCCCTAAAGAATAATAGAGCATATT
193 TCTCCACTAAAGAGTAGTGGAGCATATT
3488148 TTTTTTTCTT
Statistics
Matches: 377, Mismatches: 65, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
230 42 0.11
231 179 0.47
232 129 0.34
233 20 0.05
234 7 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (231 bp):
TTTCAGATTCAATCTTCCTGAAGAGTAGCGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
TAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAA
TCAATTCTGATTCAATCTTCCCTGAAAAACAGTGAAGTGGATCAAAATTTTCTTAAGTCTGATCT
CCACTAAAGAGTAGTGGAGCATATTCCCCTTCTATC
Found at i:3491595 original size:20 final size:22
Alignment explanation
Indices: 3491550--3491607 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
3491540 GAATCGGTAG
3491550 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
3491574 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
3491594 TGTATCGATGCACT
1 TGCATCGATGCACT
3491608 TCAAGGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:3492495 original size:39 final size:39
Alignment explanation
Indices: 3492441--3492536 Score: 183
Period size: 39 Copynumber: 2.5 Consensus size: 39
3492431 TGAATTTCAA
3492441 ATGACGCGCATTTATGACACACATTTATGACGCACATTT
1 ATGACGCGCATTTATGACACACATTTATGACGCACATTT
*
3492480 ATGACGCGCATTTATGATACACATTTATGACGCACATTT
1 ATGACGCGCATTTATGACACACATTTATGACGCACATTT
3492519 ATGACGCGCATTTATGAC
1 ATGACGCGCATTTATGAC
3492537 GTTCATTAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (39 bp):
ATGACGCGCATTTATGACACACATTTATGACGCACATTT
Found at i:3492543 original size:13 final size:13
Alignment explanation
Indices: 3492441--3492537 Score: 140
Period size: 13 Copynumber: 7.5 Consensus size: 13
3492431 TGAATTTCAA
*
3492441 ATGACGCGCATTT
1 ATGACGCACATTT
*
3492454 ATGACACACATTT
1 ATGACGCACATTT
3492467 ATGACGCACATTT
1 ATGACGCACATTT
*
3492480 ATGACGCGCATTT
1 ATGACGCACATTT
**
3492493 ATGATACACATTT
1 ATGACGCACATTT
3492506 ATGACGCACATTT
1 ATGACGCACATTT
*
3492519 ATGACGCGCATTT
1 ATGACGCACATTT
3492532 ATGACG
1 ATGACG
3492538 TTCATTAAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 74 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (13 bp):
ATGACGCACATTT
Found at i:3495210 original size:59 final size:60
Alignment explanation
Indices: 3495107--3495229 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 60
3495097 CCATAATATA
3495107 GAATTCACCCTAGCATTACAGAAATCACGCAATATTAACCACCAAAGTTCGAAGTGCAAG
1 GAATTCACCCTAGCATTACAGAAATCACGCAATATTAACCACCAAAGTTCGAAGTGCAAG
3495167 GAATTCACCCTAGCATTACAG-AATCACGCAATATTAACCACCAAAGTTCGAAGTGCAAG
1 GAATTCACCCTAGCATTACAGAAATCACGCAATATTAACCACCAAAGTTCGAAGTGCAAG
3495226 GAAT
1 GAAT
3495230 GACTTTCTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 42 0.67
60 21 0.33
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.20
Consensus pattern (60 bp):
GAATTCACCCTAGCATTACAGAAATCACGCAATATTAACCACCAAAGTTCGAAGTGCAAG
Found at i:3498367 original size:2 final size:2
Alignment explanation
Indices: 3498355--3498452 Score: 166
Period size: 2 Copynumber: 50.5 Consensus size: 2
3498345 ATGAATGTGA
*
3498355 AT AT CT AT AT AT AT AT AT AT AT AT A- 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
3498396 AT AT A- AT AT AT AT AT AT -T 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
3498436 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3498453 AGACATAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
1 3 0.03
2 88 0.97
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3498907 original size:23 final size:23
Alignment explanation
Indices: 3498839--3498907 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3498829 CAACCTTATA
*
3498839 TGGCACTTCGGTACATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
3498862 CGGGACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
3498885 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
3498908 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:3500837 original size:31 final size:30
Alignment explanation
Indices: 3500802--3500862 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3500792 TTTTATGCTA
* * *
3500802 AAGGGACAAACTTTGATTTTTAAAATTTCAG
1 AAGGGACAAAC-TTAACTTATAAAATTTCAG
*
3500833 AAGGGACGAACTTAACTTATAAAATTTCAG
1 AAGGGACAAACTTAACTTATAAAATTTCAG
3500863 GAGAGGCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (30 bp):
AAGGGACAAACTTAACTTATAAAATTTCAG
Done.