Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 26
Found at i:3517547 original size:23 final size:23
Alignment explanation
Indices: 3517477--3517549 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
3517467 ATAGGTAAAC
* * **
3517477 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
3517500 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
3517523 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
3517546 ATAT
1 ATAT
3517550 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:3517957 original size:21 final size:23
Alignment explanation
Indices: 3517907--3517967 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
3517897 ATAGGTAAAC
*
3517907 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
3517930 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
3517952 -TATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
3517968 ATGGTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 16 0.46
22 3 0.09
23 16 0.46
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:3517975 original size:21 final size:21
Alignment explanation
Indices: 3517931--3517982 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3517921 GTAGCCCTTA
*
3517931 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
3517952 TATAATGTAATAGGTAAT-GGT
1 TATAATGTAATAGGT-ATCGGT
*
3517973 TATATTGTAA
1 TATAATGTAA
3517983 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:3518307 original size:428 final size:431
Alignment explanation
Indices: 3517378--3518397 Score: 1994
Period size: 428 Copynumber: 2.4 Consensus size: 431
3517368 AATTCGCAGT
3517378 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
3517443 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
3517508 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCATTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCATTTTTAT
3517573 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
3517638 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
3517703 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
3517768 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
3517809 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
3517873 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
3517938 TAATAGGTATCG-TT-TATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCATTTTTAT
3518001 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
3518066 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
3518131 ATTAAATTTAAAATTCTAAATAATA-TTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
3518195 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
3518236 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
3518301 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
3518366 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
3518398 TCTATCTCGC
Statistics
Matches: 584, Mismatches: 2, Indels: 7
0.98 0.00 0.01
Matches are distributed among these distances:
427 144 0.25
428 279 0.48
429 4 0.01
430 93 0.16
431 64 0.11
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCATTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:3518398 original size:23 final size:23
Alignment explanation
Indices: 3518335--3518399 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
3518325 ATAGGTAAAC
* *
3518335 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
3518358 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
3518381 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
3518400 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:3518624 original size:18 final size:18
Alignment explanation
Indices: 3518603--3518639 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3518593 GTAATTGGAG
3518603 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3518621 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3518639 T
1 T
3518640 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3518647 original size:24 final size:24
Alignment explanation
Indices: 3518595--3518641 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3518585 TTTCATATGT
* *
3518595 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
3518619 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
3518642 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:3521407 original size:3 final size:3
Alignment explanation
Indices: 3521399--3521430 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3521389 ACTTCGCTCA
3521399 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3521431 ATTAGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3521753 original size:56 final size:55
Alignment explanation
Indices: 3521668--3521773 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 55
3521658 TTAAAAATTG
*
3521668 TTATGTGATAAAAATGAGTGTTAAATCGATAATTAATCACTTATAGTGTTTCTTA
1 TTATGTGATAAAAATGAGTATTAAATCGATAATTAATCACTTATAGTGTTTCTTA
3521723 TTATGTGATAAAAAATGAGTATTAAATCGATAATTAATCACTTATAGTGTT
1 TTATGTGAT-AAAAATGAGTATTAAATCGATAATTAATCACTTATAGTGTT
3521774 AATTTGGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 9 0.18
56 40 0.82
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (55 bp):
TTATGTGATAAAAATGAGTATTAAATCGATAATTAATCACTTATAGTGTTTCTTA
Found at i:3522962 original size:2 final size:2
Alignment explanation
Indices: 3522955--3522999 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3522945 AATAATTCTA
3522955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3522996 AT AT
1 AT AT
3523000 TACAACGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3535083 original size:17 final size:18
Alignment explanation
Indices: 3535050--3535090 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
3535040 ATATTATGTA
*
3535050 TTTAATTTATTTAAATAT
1 TTTACTTTATTTAAATAT
3535068 TTTACTTTATTT-AATAT
1 TTTACTTTATTTAAATAT
3535085 TTTACT
1 TTTACT
3535091 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAATAT
Found at i:3537408 original size:35 final size:32
Alignment explanation
Indices: 3537373--3537453 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
3537363 TTCAGTTAAT
3537373 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAAT-TC--TTATTGTAA
3537407 TTTGATTATCATTTACCATTTAATTCTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATTCTTATTGTAA
*
3537442 GTTTGTTGTATT
1 -TTTGTTATATT
3537454 TAAATACCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 3 0.07
38 12 0.29
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATTCTTATTGTAA
Found at i:3541916 original size:10 final size:10
Alignment explanation
Indices: 3541901--3541953 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
3541891 CATTTAATAA
3541901 ATAAACGAAC
1 ATAAACGAAC
3541911 ATAAACGAAC
1 ATAAACGAAC
3541921 AT----GAAC
1 ATAAACGAAC
3541927 ATAAACGAAC
1 ATAAACGAAC
3541937 ----ACGAAC
1 ATAAACGAAC
3541943 ATAAACGAAC
1 ATAAACGAAC
3541953 A
1 A
3541954 CGAACATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3541981 original size:16 final size:16
Alignment explanation
Indices: 3541905--3541979 Score: 132
Period size: 16 Copynumber: 4.7 Consensus size: 16
3541895 TAATAAATAA
3541905 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
3541921 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
3541937 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
3541953 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3541969 ACGAACATAAA
1 ACGAACATAAA
3541980 TGTTGGAGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3542251 original size:11 final size:11
Alignment explanation
Indices: 3542190--3542277 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
3542180 AAATTTCATC
* *
3542190 AGCTCGAATAA
1 AGCTCGATTCA
*
3542201 AGCTCGACTCA
1 AGCTCGATTCA
* *
3542212 AGCTTGATTGA
1 AGCTCGATTCA
* **
3542223 AGCTCAATTTTG
1 AGCTCGA-TTCA
3542235 AGCTCGATTCA
1 AGCTCGATTCA
**
3542246 AGCTCGATTTTG
1 AGCTCGA-TTCA
3542258 AGCTCGATTCA
1 AGCTCGATTCA
3542269 AGCTCGATT
1 AGCTCGATT
3542278 GATCCAGTCC
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
11 42 0.71
12 17 0.29
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:3542263 original size:12 final size:12
Alignment explanation
Indices: 3542223--3542266 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3542213 GCTTGATTGA
*
3542223 AGCTCAATTTTG
1 AGCTCGATTTTG
**
3542235 AGCTCGA-TTCA
1 AGCTCGATTTTG
3542246 AGCTCGATTTTG
1 AGCTCGATTTTG
3542258 AGCTCGATT
1 AGCTCGATT
3542267 CAAGCTCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:3542274 original size:23 final size:23
Alignment explanation
Indices: 3542212--3542277 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
3542202 GCTCGACTCA
* * *
3542212 AGCTTGATTGAAGCTCAATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
3542235 AGCTCGATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
3542258 AGCTCGATTCAAGCTCGATT
1 AGCTCGATTCAAGCTCGATT
3542278 GATCCAGTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTTTG
Found at i:3543518 original size:21 final size:21
Alignment explanation
Indices: 3543475--3543542 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
3543465 GGGTTAGGGG
* **
3543475 TTAGGTTTTATGGTTTAAAAT
1 TTAGGGTTTATGGTTTAGGAT
3543496 TTAGGGTTTATGGTTTAGGAT
1 TTAGGGTTTATGGTTTAGGAT
*
3543517 TTAGAGTTTA-GGTTTTAGGAT
1 TTAGGGTTTATGG-TTTAGGAT
3543538 TTAGG
1 TTAGG
3543543 ATTTTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 2 0.05
21 39 0.95
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAGGAT
Found at i:3543519 original size:7 final size:7
Alignment explanation
Indices: 3543494--3543546 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
3543484 ATGGTTTAAA
3543494 ATTTAGG
1 ATTTAGG
*
3543501 GTTTATGG
1 ATTTA-GG
3543509 -TTTAGG
1 ATTTAGG
3543515 ATTTA-G
1 ATTTAGG
3543521 AGTTTAGG
1 A-TTTAGG
*
3543529 TTTTAGG
1 ATTTAGG
3543536 ATTTAGG
1 ATTTAGG
3543543 ATTT
1 ATTT
3543547 TTAATAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 4 0.10
7 32 0.82
8 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (7 bp):
ATTTAGG
Found at i:3543585 original size:21 final size:22
Alignment explanation
Indices: 3543559--3543604 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3543549 AATAATTAGA
*
3543559 TTAAGGGTTTAGGGTTTA-GGT
1 TTAAGGGTTTAAGGTTTAGGGT
* *
3543580 TTAAGGTTTTAAGTTTTAGGGT
1 TTAAGGGTTTAAGGTTTAGGGT
3543602 TTA
1 TTA
3543605 GGATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (22 bp):
TTAAGGGTTTAAGGTTTAGGGT
Found at i:3543604 original size:14 final size:14
Alignment explanation
Indices: 3543566--3543604 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3543556 AGATTAAGGG
*
3543566 TTTAGGGTTTAGGT
1 TTTAGGGTTTAAGT
* *
3543580 TTAAGGTTTTAAGT
1 TTTAGGGTTTAAGT
3543594 TTTAGGGTTTA
1 TTTAGGGTTTA
3543605 GGATTTTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTAAGT
Found at i:3543750 original size:14 final size:14
Alignment explanation
Indices: 3543733--3543762 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3543723 AATGACCATA
*
3543733 AACGAACATAATCG
1 AACGAACATAAACG
3543747 AACGAACATAAACG
1 AACGAACATAAACG
3543761 AA
1 AA
3543763 TATAACCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:3543756 original size:24 final size:24
Alignment explanation
Indices: 3543729--3543774 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3543719 AATGAATGAC
*
3543729 CATAAACGAACATAATCGAACGAA
1 CATAAACGAACATAACCGAACGAA
*
3543753 CATAAACGAATATAACCGAACG
1 CATAAACGAACATAACCGAACG
3543775 TTCACGAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.22, G:0.13, T:0.13
Consensus pattern (24 bp):
CATAAACGAACATAACCGAACGAA
Found at i:3543934 original size:27 final size:27
Alignment explanation
Indices: 3543904--3543989 Score: 172
Period size: 27 Copynumber: 3.2 Consensus size: 27
3543894 CGCCACACAA
3543904 TTCATAAACGGTTCGCTGAACGTTCAG
1 TTCATAAACGGTTCGCTGAACGTTCAG
3543931 TTCATAAACGGTTCGCTGAACGTTCAG
1 TTCATAAACGGTTCGCTGAACGTTCAG
3543958 TTCATAAACGGTTCGCTGAACGTTCAG
1 TTCATAAACGGTTCGCTGAACGTTCAG
3543985 TTCAT
1 TTCAT
3543990 TTACAGGCCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (27 bp):
TTCATAAACGGTTCGCTGAACGTTCAG
Found at i:3543944 original size:16 final size:16
Alignment explanation
Indices: 3543925--3543971 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3543915 TTCGCTGAAC
3543925 GTTCAGTTCATAAACG
1 GTTCAGTTCATAAACG
*
3543941 GTTC-G--C-TGAAC-
1 GTTCAGTTCATAAACG
3543952 GTTCAGTTCATAAACG
1 GTTCAGTTCATAAACG
3543968 GTTC
1 GTTC
3543972 GCTGAACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
11 4 0.17
12 5 0.21
13 1 0.04
14 1 0.04
15 5 0.21
16 8 0.33
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (16 bp):
GTTCAGTTCATAAACG
Found at i:3544873 original size:2 final size:2
Alignment explanation
Indices: 3544866--3544890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3544856 TGATCAAAAT
3544866 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 T
3544891 GTTTGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3544909 original size:8 final size:8
Alignment explanation
Indices: 3544868--3544921 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
3544858 ATCAAAATTA
*
3544868 TATATATA
1 TATATATG
*
3544876 TATATATA
1 TATATATG
3544884 TATATATG
1 TATATATG
*
3544892 TTTGTATATG
1 --TATATATG
*
3544902 TATGTATG
1 TATATATG
3544910 TATATATG
1 TATATATG
3544918 TATA
1 TATA
3544922 ATACCGGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 32 0.82
10 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATATATG
Found at i:3554837 original size:14 final size:14
Alignment explanation
Indices: 3554812--3555059 Score: 159
Period size: 14 Copynumber: 17.1 Consensus size: 14
3554802 TTTAATGCTT
*
3554812 TAATGATGTAATAA
1 TAATGATTTAATAA
*
3554826 TAATAATTTAATAA
1 TAATGATTTAATAA
*
3554840 TAATGATTTAACT-T
1 TAATGATTTAA-TAA
*
3554854 TAATAATTTAATAA
1 TAATGATTTAATAA
* *
3554868 TAATTATTTAACT-T
1 TAATGATTTAA-TAA
3554882 TAATGATTTAATAA
1 TAATGATTTAATAA
*
3554896 TAATTATTTAACTTTAA
1 TAATGATTTAA---TAA
3554913 TAATTTGATGATTTAATAA
1 T-A----ATGATTTAATAA
* *
3554932 TAATTATTTAACT-T
1 TAATGATTTAA-TAA
3554946 TAATGATTTAATAA
1 TAATGATTTAATAA
* *
3554960 TAATAATTTAACT-T
1 TAATGATTTAA-TAA
* *
3554974 TAATTATTTAACT-T
1 TAATGATTTAA-TAA
3554988 TAATGATTTAATAA
1 TAATGATTTAATAA
*
3555002 TAATGATTTAACT-T
1 TAATGATTTAA-TAA
*
3555016 TAATGATTTACTAA
1 TAATGATTTAATAA
* *
3555030 TAATAATTTAACT-T
1 TAATGATTTAA-TAA
3555044 TAATGATTTAATAA
1 TAATGATTTAATAA
3555058 TA
1 TA
3555060 GTAATGAAAT
Statistics
Matches: 185, Mismatches: 29, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
13 6 0.03
14 155 0.84
15 6 0.03
17 4 0.02
18 2 0.01
19 4 0.02
22 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:3554857 original size:28 final size:28
Alignment explanation
Indices: 3554826--3555054 Score: 189
Period size: 28 Copynumber: 7.9 Consensus size: 28
3554816 GATGTAATAA
3554826 TAATAATTTAATAATAATGATTTAACTT
1 TAATAATTTAATAATAATGATTTAACTT
*
3554854 TAATAATTTAATAATAATTATTTAACTT
1 TAATAATTTAATAATAATGATTTAACTT
* *
3554882 TAATGATTTAATAATAATTATTTAACTTT
1 TAATAATTTAATAATAATGATTTAAC-TT
*
3554911 AATAATTTGATGATTTAATAATAATTATTTAACTT
1 --TAA--T-A--ATTTAATAATAATGATTTAACTT
* *
3554946 TAATGATTTAATAATAATAATTTAACTT
1 TAATAATTTAATAATAATGATTTAACTT
* * *
3554974 TAATTATTTAACT-TTAATGATTTAA-TAA
1 TAATAATTTAA-TAATAATGATTTAACT-T
* * *
3555002 TAATGATTTAACT-TTAATGATTT-ACTAA
1 TAATAATTTAA-TAATAATGATTTAACT-T
*
3555030 TAATAATTTAACT-TTAATGATTTAA
1 TAATAATTTAA-TAATAATGATTTAA
3555055 TAATAGTAAT
Statistics
Matches: 178, Mismatches: 11, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.01
28 141 0.79
29 4 0.02
31 4 0.02
33 4 0.02
35 2 0.01
36 21 0.12
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (28 bp):
TAATAATTTAATAATAATGATTTAACTT
Found at i:3554866 original size:42 final size:42
Alignment explanation
Indices: 3554799--3555025 Score: 217
Period size: 42 Copynumber: 5.2 Consensus size: 42
3554789 ACTAATGATT
*
3554799 TGATTTAATGCTTTAATGATGTAATAATAATAATTTAA-TAATAA
1 TGATTTAA--CTTTAATGATTTAATAATAATAATTTAACT-ATAA
* * *
3554843 TGATTTAACTTTAATAATTTAATAATAATTATTTAACTTTAA
1 TGATTTAACTTTAATGATTTAATAATAATAATTTAACTATAA
* *
3554885 TGATTTAA-TAATAATTATTTAACTTTAATAATTTGATGATTTAA-TAATAA
1 TGATTTAACT-TTAATGATTTAA---TAATAA--T-A--ATTTAACT-ATAA
* *
3554935 TTATTTAACTTTAATGATTTAATAATAATAATTTAACTTTAA
1 TGATTTAACTTTAATGATTTAATAATAATAATTTAACTATAA
* * *
3554977 TTATTTAACTTTAATGATTTAATAATAATGATTTAACTTTAA
1 TGATTTAACTTTAATGATTTAATAATAATAATTTAACTATAA
3555019 TGATTTA
1 TGATTTA
3555026 CTAATAATAA
Statistics
Matches: 156, Mismatches: 14, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 102 0.65
43 2 0.01
44 9 0.06
45 7 0.04
47 7 0.04
49 1 0.01
50 26 0.17
51 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (42 bp):
TGATTTAACTTTAATGATTTAATAATAATAATTTAACTATAA
Found at i:3555059 original size:28 final size:28
Alignment explanation
Indices: 3554826--3554984 Score: 201
Period size: 28 Copynumber: 5.4 Consensus size: 28
3554816 GATGTAATAA
* *
3554826 TAATAATTTAATAATAATGATTTAACTT
1 TAATGATTTAATAATAATTATTTAACTT
*
3554854 TAATAATTTAATAATAATTATTTAACTT
1 TAATGATTTAATAATAATTATTTAACTT
3554882 TAATGATTTAATAATAATTATTTAACTTT
1 TAATGATTTAATAATAATTATTTAAC-TT
3554911 AATAATTTGATGATTTAATAATAATTATTTAACTT
1 --T-A----ATGATTTAATAATAATTATTTAACTT
*
3554946 TAATGATTTAATAATAATAATTTAACTT
1 TAATGATTTAATAATAATTATTTAACTT
*
3554974 TAATTATTTAA
1 TAATGATTTAA
3554985 CTTTAATGAT
Statistics
Matches: 119, Mismatches: 4, Indels: 16
0.86 0.03 0.12
Matches are distributed among these distances:
28 87 0.73
29 2 0.02
31 1 0.01
32 2 0.02
33 1 0.01
35 2 0.02
36 24 0.20
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATGATTTAATAATAATTATTTAACTT
Found at i:3555083 original size:56 final size:56
Alignment explanation
Indices: 3554974--3555083 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 56
3554964 AATTTAACTT
* * * * * *
3554974 TAATTATTTAACTTTAATGATTTAATAATAATGATTTAACTTTAATGATTTACTAA
1 TAATAATTTAACTTTAATGATTTAATAATAATGAATGAAATTTAATCAATTACTAA
* *
3555030 TAATAATTTAACTTTAATGATTTAATAATAGT-AATGAAATTCTATTCAATTACT
1 TAATAATTTAACTTTAATGATTTAATAATAATGAATGAAATT-TAATCAATTACT
3555084 TCAATTTGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 6 0.13
56 39 0.87
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (56 bp):
TAATAATTTAACTTTAATGATTTAATAATAATGAATGAAATTTAATCAATTACTAA
Found at i:3557972 original size:32 final size:33
Alignment explanation
Indices: 3557931--3558018 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
3557921 TTGGTGGACC
*
3557931 TATGAAGAAGACGCTGAG-ACATCC-CCCTCCC-A
1 TATGAAGAAGACGCCGAGTA-ATCCACCC-CCCAA
3557963 TATGAAGAAGACGCCGAGTAATCCACCCCCCAA
1 TATGAAGAAGACGCCGAGTAATCCACCCCCCAA
* *
3557996 TATGAAGAAGATGCCGAGAAATC
1 TATGAAGAAGACGCCGAGTAATC
3558019 TTCTAATGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 24 0.48
33 26 0.52
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.15
Consensus pattern (33 bp):
TATGAAGAAGACGCCGAGTAATCCACCCCCCAA
Found at i:3558004 original size:33 final size:31
Alignment explanation
Indices: 3557931--3558015 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 31
3557921 TTGGTGGACC
*
3557931 TATGAAGAAGACGCTGAGACATCCCCCTCCCA
1 TATGAAGAAGACGCCGAGA-ATCCCCCTCCCA
3557963 TATGAAGAAGACGCCGAGTAATCCACCC-CCCAA
1 TATGAAGAAGACGCCGAG-AATCC-CCCTCCC-A
*
3557996 TATGAAGAAGATGCCGAGAA
1 TATGAAGAAGACGCCGAGAA
3558016 ATCTTCTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
32 26 0.54
33 22 0.46
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.14
Consensus pattern (31 bp):
TATGAAGAAGACGCCGAGAATCCCCCTCCCA
Found at i:3560434 original size:15 final size:15
Alignment explanation
Indices: 3560409--3560457 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
3560399 CTAAATAGTC
3560409 ACTTCAATAATTTGTT
1 ACTT-AATAATTTGTT
*
3560425 ACTTAATAATTTAG-A
1 ACTTAATAATTT-GTT
3560440 ACATTAATAATTTGTT
1 AC-TTAATAATTTGTT
3560456 AC
1 AC
3560458 ACATATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
ACTTAATAATTTGTT
Found at i:3564019 original size:9 final size:9
Alignment explanation
Indices: 3563995--3564038 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
3563985 CCTGCAAAAA
*
3563995 AATAAAATT
1 AATAATATT
*
3564004 AAAAATATT
1 AATAATATT
*
3564013 AATAATAAT
1 AATAATATT
3564022 AATAATAATT
1 AATAAT-ATT
3564032 AATAATA
1 AATAATA
3564039 ACAATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAATATT
Found at i:3564020 original size:3 final size:3
Alignment explanation
Indices: 3564007--3564050 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
3563997 TAAAATTAAA
* *
3564007 AAT ATT AAT AAT AAT AAT AAT AATT AAT AAT AAC AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT
3564051 GTATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3564036 original size:16 final size:16
Alignment explanation
Indices: 3564013--3564050 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3564003 TAAAAATATT
*
3564013 AATAATAATAATAATA
1 AATAATAATAACAATA
*
3564029 ATTAATAATAACAATA
1 AATAATAATAACAATA
3564045 AATAAT
1 AATAAT
3564051 GTATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAATAATAACAATA
Found at i:3564501 original size:106 final size:104
Alignment explanation
Indices: 3564295--3565510 Score: 623
Period size: 94 Copynumber: 12.6 Consensus size: 104
3564285 ATTATGAGGT
* * * * * * **
3564295 CAATATCTTTCGAC-GTGAAGTTGAAGTTGACTCTGAAACTGGAAAATTTGTTTATTGACAACCA
1 CAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAA-TTGTTTGTTGACAGTCA
* * *
3564359 GCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTC
63 GCCG-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
3564402 CAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAGTCAGC
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTGTTGACAGTCAGC
* *
3564467 CGCCCTTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTC
65 CGCCC-TTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
3564508 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA------GTTGACAGTCAGTC
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3564567 GCCCCTTCTTCGTGAAGTTGAGCTTGAGTTGTCTTTAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3564607 CAATATCCTTCGCTGTGAAGTTG-AA----CT-TG----GGA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3564661 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3564701 CAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * * *
3564755 GTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3564795 CAATATCCTTCGTTGTGAAGTTG-AATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3564848 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * * * *
3564888 TAATATCCTTCGTTGTGAAATTGAAATT-G----G--A---A-AATTGTTTATTGACA-ACAAGC
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTC-AGC
* ** * *
3564941 AGTCCCTTCGTCGTGAAGTTGAAATTGTGTTGTCTGGAATC
65 CG-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
** * ** *
3564982 CAATATCCTTCATTGTGAAGTTGAAATTGG--C--------A-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * **
3565036 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3565076 CAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3565130 GTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * * ** *
3565170 CAATATCCTTCGTTGCGAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3565224 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3565264 CAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3565318 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * ** *
3565358 CAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
* * *
3565412 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
66 G-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
3565452 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAG
3565511 ACAACTTTTC
Statistics
Matches: 1006, Mismatches: 71, Indels: 66
0.88 0.06 0.06
Matches are distributed among these distances:
88 2 0.00
89 1 0.00
93 94 0.09
94 685 0.68
95 6 0.01
98 2 0.00
99 68 0.07
100 3 0.00
104 2 0.00
105 16 0.02
106 95 0.09
107 32 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (104 bp):
CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTGTTGACAGTCAGCC
GCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
Found at i:3564701 original size:94 final size:94
Alignment explanation
Indices: 3564435--3565481 Score: 1632
Period size: 94 Copynumber: 11.1 Consensus size: 94
3564425 AAATTGGCTC
* * * ** * * * * *
3564435 TGAAATTGAGAAGTTGTTTGTTGACAGTCAGCCG-CCCTTTCGCCGTGAAGTTGAGCTTGTGCTG
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTG
* *
3564499 TCTTGAGTCCAATATCCTTCGCTGTGAAGT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGT
*** ** * * *
3564529 TGAAATTGGCTCTGAAATTGGGAAGTTGACAGTCAGTC-GCCCCTTCTTCGTGAAGTTGAGCTTG
1 TGAAATTGG----GAAATTGTTTA-TTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTG
* ** *
3564593 AGTTGTCTTTAGTCCAATATCCTTCGCTGTGAAGT
60 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
3564628 TGAACTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
3564693 CTAGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*
3564722 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3564787 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3564816 TG-AATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
3564880 CTGGAGTCTAATATCCTTCGTTGTGAAAT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * * *
3564909 TGAAATTGGAAAATTGTTTATTGACAACAAGCAGTCCCTTCGTCGTGAAGTTGAAATTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
3564974 CTGGAATCCAATATCCTTCATTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*
3565003 TGAAATTGGCAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
**
3565068 CTCAAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
3565097 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
3565162 CTGGAGTCCAATATCCTTCGTTGCGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3565191 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3565256 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3565285 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3565350 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3565379 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3565444 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
3565473 TGAAATTGG
1 TGAAATTGG
3565482 CTCTGAAATT
Statistics
Matches: 887, Mismatches: 57, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
93 91 0.10
94 707 0.80
95 8 0.01
98 6 0.01
99 71 0.08
100 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:3570777 original size:3 final size:3
Alignment explanation
Indices: 3570764--3570810 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
3570754 TAAAATTAAA
* *
3570764 AAT ATT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAC AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT
3570811 GTATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3573303 original size:35 final size:35
Alignment explanation
Indices: 3573263--3573332 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3573253 AAAAATTTCA
3573263 ATTTTTATCTTTGATTGTTATAGAAATATAAATTT
1 ATTTTTATCTTTGATTGTTATAGAAATATAAATTT
3573298 ATTTTTATCTTTGATTGTTATAGAAATATAAATTT
1 ATTTTTATCTTTGATTGTTATAGAAATATAAATTT
3573333 TAAATATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (35 bp):
ATTTTTATCTTTGATTGTTATAGAAATATAAATTT
Found at i:3573324 original size:29 final size:30
Alignment explanation
Indices: 3573254--3573323 Score: 77
Period size: 35 Copynumber: 2.1 Consensus size: 30
3573244 AGTGCAACTA
3573254 AAAATTTCAATTTTTATCTTTGATTGTTATAG
1 AAAATTT--ATTTTTATCTTTGATTGTTATAG
3573286 AAATATAAATTTATTTTTATCTTTGATTGTTATAG
1 ----A-AAATTTATTTTTATCTTTGATTGTTATAG
3573321 AAA
1 AAA
3573324 TATAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
30 2 0.06
31 1 0.03
35 23 0.70
36 1 0.03
37 6 0.18
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (30 bp):
AAAATTTATTTTTATCTTTGATTGTTATAG
Found at i:3573343 original size:31 final size:34
Alignment explanation
Indices: 3573273--3573343 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
3573263 ATTTTTATCT
** *
3573273 TTGATTGTTATAGAAATATAAATTTATTTTTATCT
1 TTGATTGTTATAGAAATATAAA-TTATTTAAATCA
3573308 TTGATTGTTATAGAAATATAAA-T-TTTAAAT-A
1 TTGATTGTTATAGAAATATAAATTATTTAAATCA
3573339 TTGAT
1 TTGAT
3573344 ATTTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 5 0.15
32 5 0.15
33 1 0.03
35 22 0.67
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (34 bp):
TTGATTGTTATAGAAATATAAATTATTTAAATCA
Found at i:3589166 original size:18 final size:20
Alignment explanation
Indices: 3589139--3589181 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3589129 ACTAATATTA
3589139 TAATCATAT-ATTCT-TTTT
1 TAATCATATAATTCTGTTTT
* *
3589157 TAATCCTATAATTGTGTTTT
1 TAATCATATAATTCTGTTTT
3589177 TAATC
1 TAATC
3589182 TTAGAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 9 0.43
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (20 bp):
TAATCATATAATTCTGTTTT
Found at i:3591088 original size:17 final size:17
Alignment explanation
Indices: 3591066--3591129 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
3591056 GGAATCCATT
*
3591066 AGATTCTAATTCCTGAC
1 AGATTCCAATTCCTGAC
3591083 AGATTCCAATTCCTGAC
1 AGATTCCAATTCCTGAC
* *
3591100 ATATTCCAATTCCTTCAC
1 AGATTCCAATTCC-TGAC
3591118 AGATTCCAATTC
1 AGATTCCAATTC
3591130 TCTCAGAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (17 bp):
AGATTCCAATTCCTGAC
Found at i:3601321 original size:24 final size:24
Alignment explanation
Indices: 3601292--3601415 Score: 149
Period size: 24 Copynumber: 5.2 Consensus size: 24
3601282 AACATATTTA
* * *
3601292 AGGTCAAATAGCATATCAGAATCC
1 AGGTCAAGTATCATATCAAAATCC
* *
3601316 ATGTCAAGTATCATATAAAAATCC
1 AGGTCAAGTATCATATCAAAATCC
3601340 AGGTCAAGTATCATATCAAAATCC
1 AGGTCAAGTATCATATCAAAATCC
* * * *
3601364 AGGTCAAGTATTATATTATAATTC
1 AGGTCAAGTATCATATCAAAATCC
* *
3601388 AGGTCAAATATCATACCAAAATCC
1 AGGTCAAGTATCATATCAAAATCC
3601412 AGGT
1 AGGT
3601416 TAAAAATCAA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
AGGTCAAGTATCATATCAAAATCC
Found at i:3601355 original size:48 final size:48
Alignment explanation
Indices: 3601292--3601415 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 48
3601282 AACATATTTA
* * *
3601292 AGGTCAAATAGCATATCAGAATCCATGTCAAGTATCATATAAAAATCC
1 AGGTCAAATATCATATCAAAATCCAGGTCAAGTATCATATAAAAATCC
* * * * *
3601340 AGGTCAAGTATCATATCAAAATCCAGGTCAAGTATTATATTATAATTC
1 AGGTCAAATATCATATCAAAATCCAGGTCAAGTATCATATAAAAATCC
*
3601388 AGGTCAAATATCATACCAAAATCCAGGT
1 AGGTCAAATATCATATCAAAATCCAGGT
3601416 TAAAAATCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (48 bp):
AGGTCAAATATCATATCAAAATCCAGGTCAAGTATCATATAAAAATCC
Found at i:3602130 original size:29 final size:28
Alignment explanation
Indices: 3602094--3602271 Score: 134
Period size: 29 Copynumber: 6.3 Consensus size: 28
3602084 TTTACACATT
3602094 TATCACCCTTTTTAAAAAATTTTAC-AAAA
1 TATCACCCTTTTTAAAAAA--TTACTAAAA
*
3602123 TATCACCCTTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTTAAAA-AATTACTAAAA
*
3602152 TATCA--CTTTTTAAAAAAATTA-TGAAAT
1 TATCACCCTTTTT-AAAAAATTACT-AAAA
** *
3602179 TATCA-TTTTTTTAAAAAATTACAAAAA
1 TATCACCCTTTTTAAAAAATTACTAAAA
* * * *
3602206 TAGCA-CATTTTCAAAAATAATTACCAAAA
1 TATCACCCTTTT-TAAAA-AATTACTAAAA
* * *
3602235 TATCATCATTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTTAAAA-AATTACTAAAA
3602264 TATCACCC
1 TATCACCC
3602272 GGTCAACGAT
Statistics
Matches: 124, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
26 1 0.01
27 38 0.31
28 17 0.14
29 60 0.48
30 8 0.06
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (28 bp):
TATCACCCTTTTTAAAAAATTACTAAAA
Found at i:3602160 original size:27 final size:28
Alignment explanation
Indices: 3602115--3602270 Score: 149
Period size: 29 Copynumber: 5.6 Consensus size: 28
3602105 TTAAAAAATT
3602115 TTAC-AAAATATCACCCTTTTCAAAATAA
1 TTACTAAAATATCA-CCTTTTCAAAATAA
* *
3602143 TTACTAAAATATCA-CTTTTTAAAAAAA
1 TTACTAAAATATCACCTTTTCAAAATAA
* ** *
3602170 TTA-TGAAATTATCATTTTTTTAAAA-AA
1 TTACT-AAAATATCACCTTTTCAAAATAA
* * *
3602197 TTACAAAAATAGCACATTTTCAAAAATAA
1 TTACTAAAATATCACCTTTTC-AAAATAA
* *
3602226 TTACCAAAATATCATCATTTTCAAAATAA
1 TTACTAAAATATCA-CCTTTTCAAAATAA
3602255 TTACTAAAATATCACC
1 TTACTAAAATATCACC
3602271 CGGTCAACGA
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 38 0.36
28 18 0.17
29 43 0.40
30 7 0.07
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (28 bp):
TTACTAAAATATCACCTTTTCAAAATAA
Found at i:3602183 original size:56 final size:55
Alignment explanation
Indices: 3602101--3602269 Score: 180
Period size: 56 Copynumber: 3.0 Consensus size: 55
3602091 ATTTATCACC
* *
3602101 CTTTTT-AAAAAATTTTACAAAATATCACCCTTTTCAAAATAATTACTAAAATATCA
1 CTTTTTAAAAAAATTAT-CAAAATATCA-CATTTTCAAAATAATTACTAAAATATCA
* * ** * * *
3602157 CTTTTTAAAAAAATTATGAAATTATCATTTTTTTAAAA-AATTACAAAAATAGCA
1 CTTTTTAAAAAAATTATCAAAATATCACATTTTCAAAATAATTACTAAAATATCA
* *
3602211 CATTTTCAAAAATAATTACCAAAATATCATCATTTTCAAAATAATTACTAAAATATCA
1 C-TTTTTAAAAA-AATTATCAAAATATCA-CATTTTCAAAATAATTACTAAAATATCA
3602269 C
1 C
3602270 CCGGTCAACG
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
54 15 0.16
55 17 0.19
56 27 0.30
57 17 0.19
58 15 0.16
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.37
Consensus pattern (55 bp):
CTTTTTAAAAAAATTATCAAAATATCACATTTTCAAAATAATTACTAAAATATCA
Found at i:3603976 original size:23 final size:23
Alignment explanation
Indices: 3603950--3604010 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3603940 CACCACAGCT
*
3603950 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
3603973 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3603996 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
3604011 TAGTTCCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3604205 original size:103 final size:103
Alignment explanation
Indices: 3604034--3604251 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
3604024 TAATGTCCAT
* *
3604034 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
3604099 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
*
3604137 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3604202 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
*
3604240 AAGGACTACATA
1 AAGGACCACATA
3604252 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:3609325 original size:23 final size:23
Alignment explanation
Indices: 3609299--3609367 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3609289 CACCACAGCT
*
3609299 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
3609322 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
3609345 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3609368 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3609554 original size:103 final size:103
Alignment explanation
Indices: 3609383--3609600 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
3609373 TAATGTCCAT
* * *
3609383 AAGGACCATATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3609448 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3609486 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3609551 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3609589 AAGGACCACATA
1 AAGGACCACATA
3609601 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3611006 original size:20 final size:21
Alignment explanation
Indices: 3610965--3611025 Score: 97
Period size: 20 Copynumber: 2.9 Consensus size: 21
3610955 TTCGCTTGAG
3610965 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
*
3610987 GGGTACCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
3611007 GGGTATCGATTCCCCTTGA
1 GGGTATCGATTCCCCTTGA
3611026 CCAGAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 16 0.44
21 10 0.28
22 10 0.28
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:3617211 original size:24 final size:24
Alignment explanation
Indices: 3617181--3617290 Score: 157
Period size: 24 Copynumber: 4.6 Consensus size: 24
3617171 CAACTAGTAG
* *
3617181 ATCAAAATTCATGTCAAGTATTAT
1 ATCAAAATTCAGGTCAAGTATCAT
* *
3617205 ATAAAAATCCAGGTCAAGTATCAT
1 ATCAAAATTCAGGTCAAGTATCAT
3617229 ATCAAAATTCAGGTCAAGTATCAT
1 ATCAAAATTCAGGTCAAGTATCAT
* * *
3617253 ATTAAAATCCAGGTCAAATATCAT
1 ATCAAAATTCAGGTCAAGTATCAT
3617277 ATCAAAATTCAGGT
1 ATCAAAATTCAGGT
3617291 TAAAAATCAG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (24 bp):
ATCAAAATTCAGGTCAAGTATCAT
Found at i:3617238 original size:48 final size:48
Alignment explanation
Indices: 3617181--3617290 Score: 184
Period size: 48 Copynumber: 2.3 Consensus size: 48
3617171 CAACTAGTAG
* * *
3617181 ATCAAAATTCATGTCAAGTATTATATAAAAATCCAGGTCAAGTATCAT
1 ATCAAAATTCAGGTCAAGTATCATATAAAAATCCAGGTCAAATATCAT
*
3617229 ATCAAAATTCAGGTCAAGTATCATATTAAAATCCAGGTCAAATATCAT
1 ATCAAAATTCAGGTCAAGTATCATATAAAAATCCAGGTCAAATATCAT
3617277 ATCAAAATTCAGGT
1 ATCAAAATTCAGGT
3617291 TAAAAATCAG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (48 bp):
ATCAAAATTCAGGTCAAGTATCATATAAAAATCCAGGTCAAATATCAT
Found at i:3618031 original size:29 final size:29
Alignment explanation
Indices: 3617992--3618152 Score: 138
Period size: 29 Copynumber: 5.8 Consensus size: 29
3617982 CCTCTTTTAA
* * * *
3617992 AAAAAAATTACAAAAATATAACCCTTTTC
1 AAAATAATTACTAAAATATCACCATTTTC
* *
3618021 AAAATAATTACTAAAATATCA--TTTTTT
1 AAAATAATTACTAAAATATCACCATTTTC
* * *
3618048 AAAA-AATTAC-GAAAT-T-ATCATTTTT
1 AAAATAATTACTAAAATATCACCATTTTC
*** * *
3618073 TTTA-AATTACGAAAATAGCACCATTTTC
1 AAAATAATTACTAAAATATCACCATTTTC
*
3618101 AAAATAATTACCAAAATATCACCATTTTC
1 AAAATAATTACTAAAATATCACCATTTTC
3618130 AAAATAATTACTAAAATATCACC
1 AAAATAATTACTAAAATATCACC
3618153 CGATCAACGG
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 16 0.15
26 10 0.09
27 8 0.08
28 8 0.08
29 62 0.58
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATAATTACTAAAATATCACCATTTTC
Found at i:3618184 original size:18 final size:18
Alignment explanation
Indices: 3618161--3618195 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3618151 CCCGATCAAC
3618161 GGTCAACCGGTCGGGTCG
1 GGTCAACCGGTCGGGTCG
*
3618179 GGTCAACGGGTCGGGTC
1 GGTCAACCGGTCGGGTC
3618196 AGGTTGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACCGGTCGGGTCG
Found at i:3618188 original size:13 final size:13
Alignment explanation
Indices: 3618172--3618196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3618162 GTCAACCGGT
3618172 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
3618185 CGGGTCGGGTCA
1 CGGGTCGGGTCA
3618197 GGTTGGAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:3620140 original size:32 final size:32
Alignment explanation
Indices: 3620097--3620260 Score: 104
Period size: 32 Copynumber: 5.1 Consensus size: 32
3620087 TTCGTCCTAG
*
3620097 TATT-TTT-TCAAAATAAAAAATTGTGACAAA
1 TATTATTTATCAAAATAAAAAATTGTAACAAA
* * *
3620127 T-TTATTTAATCAAAATAACAATTTATAACAAA
1 TATTATTT-ATCAAAATAAAAAATTGTAACAAA
* ** **
3620159 TATTAATTTCTCATTATAAAAAATTGGGACAAA
1 TATT-ATTTATCAAAATAAAAAATTGTAACAAA
* *
3620192 TGA-TATTCTTTCACAATAAAAAATTGTAA-AAA
1 T-ATTATT-TATCAAAATAAAAAATTGTAACAAA
* * * * *
3620224 AATTATTTAGTCACAATAAAAAGTTATAAAAAA
1 TATTATTTA-TCAAAATAAAAAATTGTAACAAA
3620257 TATT
1 TATT
3620261 TAGTAACGAA
Statistics
Matches: 102, Mismatches: 22, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
29 2 0.02
30 4 0.04
31 2 0.02
32 47 0.46
33 42 0.41
34 5 0.05
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (32 bp):
TATTATTTATCAAAATAAAAAATTGTAACAAA
Found at i:3620206 original size:197 final size:198
Alignment explanation
Indices: 3619838--3620240 Score: 551
Period size: 197 Copynumber: 2.0 Consensus size: 198
3619828 GGTTCTTTTT
* * * * * *
3619838 GTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGCCAAATTTATTTTGTCACAATAT
1 GTCACAATTACACATTAAATTTAGTCAAAATAAAAAGTTATGCAAAATTTATTTCGTCACAATAT
* * * * *
3619903 TTTGTCAAAATAAAAATTTTTGATAAATTTATTTAATCAAAATAATATTTTATAACAAATATTAA
66 TTTGTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAA
* * * *
3619968 TTTCTCATCATAAAAATTGTGATAAGTAATATTCTTTTCACAATAATAAATCGTAAAAAAATGA-
131 TTTCTCATCATAAAAATTGGGACAAATAATATTCTTTTCACAATAAAAAATCGTAAAAAAATGAT
3620032 TTA
196 TTA
* * * *
3620035 GTTACAATTACACATTAAATTTAGTCAAAGTAAAAAGTTATGTAAAATTTATTTCGTC-CTAGTA
1 GTCACAATTACACATTAAATTTAGTCAAAATAAAAAGTTATGCAAAATTTATTTCGTCAC-AATA
*
3620099 TTTTTTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTA
65 TTTTGTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTA
* * * *
3620164 ATTTCTCATTATAAAAAATTGGGACAAATGATATTC-TTTCACAATAAAAAATTGTAAAAAAATT
130 ATTTCTCATCAT-AAAAATTGGGACAAATAATATTCTTTTCACAATAAAAAATCGTAAAAAAATG
3620228 ATTTA
194 ATTTA
3620233 GTCACAAT
1 GTCACAAT
3620241 AAAAAGTTAT
Statistics
Matches: 178, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
196 1 0.01
197 148 0.83
198 29 0.16
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (198 bp):
GTCACAATTACACATTAAATTTAGTCAAAATAAAAAGTTATGCAAAATTTATTTCGTCACAATAT
TTTGTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAA
TTTCTCATCATAAAAATTGGGACAAATAATATTCTTTTCACAATAAAAAATCGTAAAAAAATGAT
TTA
Found at i:3620255 original size:30 final size:32
Alignment explanation
Indices: 3620202--3620264 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
3620192 TGATATTCTT
* *
3620202 TCACAATAAAAAATTGTAAAAAAATTATTTAG
1 TCACAATAAAAAAGTGTAAAAAAAATATTTAG
*
3620234 TCACAAT-AAAAAGT-TATAAAAAATATTTAG
1 TCACAATAAAAAAGTGTAAAAAAAATATTTAG
3620264 T
1 T
3620265 AACGAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 6 0.21
32 7 0.25
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (32 bp):
TCACAATAAAAAAGTGTAAAAAAAATATTTAG
Found at i:3620274 original size:32 final size:32
Alignment explanation
Indices: 3620204--3620276 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
3620194 ATATTCTTTC
* *
3620204 ACAATAAAAAATTGTAAAAAAATTATTTAGTC
1 ACAATAAAAAATTATAAAAAAATTATTTAGTA
*
3620236 ACAATAAAAAGTTAT-AAAAAA-TATTTAGTA
1 ACAATAAAAAATTATAAAAAAATTATTTAGTA
3620266 ACGAAATAAAA
1 AC--AATAAAA
3620277 GTAATGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 10 0.28
31 6 0.17
32 20 0.56
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (32 bp):
ACAATAAAAAATTATAAAAAAATTATTTAGTA
Found at i:3625356 original size:21 final size:20
Alignment explanation
Indices: 3625335--3625373 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3625325 TAAACTTTTA
3625335 AAAATTA-CAAAATAATTATT
1 AAAATTATC-AAATAATTATT
*
3625355 AAATTTATCAAATAATTAT
1 AAAATTATCAAATAATTAT
3625374 AAACCTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTATCAAATAATTATT
Found at i:3631710 original size:14 final size:14
Alignment explanation
Indices: 3631691--3631718 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3631681 ACCTGGATGT
3631691 AAAACATTTTCCAG
1 AAAACATTTTCCAG
3631705 AAAACATTTTCCAG
1 AAAACATTTTCCAG
3631719 TACTTGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:3637519 original size:21 final size:20
Alignment explanation
Indices: 3637487--3637530 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3637477 TATGAGAAAT
*
3637487 TGATTTTTAAAATAT-AAAAA
1 TGATTTTCAAAAT-TGAAAAA
3637507 TGATATTTCAAAATTGAAAAA
1 TGAT-TTTCAAAATTGAAAAA
3637528 TGA
1 TGA
3637531 AAATAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (20 bp):
TGATTTTCAAAATTGAAAAA
Found at i:3641410 original size:23 final size:22
Alignment explanation
Indices: 3641340--3641420 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
3641330 TTGTGCTTAA
3641340 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCA-CCC-TTGAATG
* * *
3641364 TGCATCGATACA-CCATGAAGG
1 TGCATCGATGCACCCTTGAATG
*
3641385 TGCAGCGATGCACGCCTTGAATG
1 TGCATCGATGCAC-CCTTGAATG
3641408 TGCATCGATGCAC
1 TGCATCGATGCAC
3641421 AAGGCCATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 19 0.40
24 11 0.23
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACCCTTGAATG
Found at i:3642610 original size:21 final size:21
Alignment explanation
Indices: 3642568--3642610 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3642558 ACTCTGGGAG
* *
3642568 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3642589 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3642610 C
1 C
3642611 GGCACCAGCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.40, G:0.16, T:0.35
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3643765 original size:90 final size:91
Alignment explanation
Indices: 3643611--3643782 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 91
3643601 TTTTTAAAGG
*
3643611 GATGCACCGATGCACCAATCCATGCATCGATGCACCATTGAATATATTGAACATCAAATGCATTT
1 GATGCACCGATGCACCAAGCCATGCATCGATGCACCATTGAATATATTGAACATCAAATGCATTT
*
3643676 TATGCATTGATGCACTCAGTGCATTT
66 TATGCATCGATGCACTCAGTGCATTT
* * * ** * *
3643702 GATGCATCGATGCA-CAAGCCATGCATCTATGCA-CTTTGGCTATTTTGAAACATCGAATGCATT
1 GATGCACCGATGCACCAAGCCATGCATCGATGCACCATTGAATATATTG-AACATCAAATGCATT
3643765 TTATGCATCGATGCACTC
65 TTATGCATCGATGCACTC
3643783 TTAGTGCACC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
89 10 0.14
90 48 0.68
91 13 0.18
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (91 bp):
GATGCACCGATGCACCAAGCCATGCATCGATGCACCATTGAATATATTGAACATCAAATGCATTT
TATGCATCGATGCACTCAGTGCATTT
Found at i:3648588 original size:18 final size:18
Alignment explanation
Indices: 3648565--3648604 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3648555 ATCCTTAAGG
*
3648565 AGTGGTCTTTCGGGAA-AT
1 AGTGGTCCTTC-GGAACAT
3648583 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAT
3648601 AGTG
1 AGTG
3648605 TTCAGTGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:3653815 original size:15 final size:15
Alignment explanation
Indices: 3653795--3653837 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3653785 TTGAACCAAC
*
3653795 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTA
*
3653810 TTTTCTATTTTTTTA
1 TTTTCTTTTTTTTTA
*
3653825 GTTTCATTTTTTT
1 TTTTC-TTTTTTT
3653838 GAATTTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTTTTA
Found at i:3658501 original size:21 final size:21
Alignment explanation
Indices: 3658477--3658568 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
3658467 TTGAGAAAAT
*
3658477 TAAAATTTTTATAAACTTAAA
1 TAAAATTATTATAAACTTAAA
* * *
3658498 TAAACTTGTTATATACTTGGACAAA
1 TAAAATTATTATAAACTT----AAA
* *
3658523 TTAAAATTATCATAAATTTAAA
1 -TAAAATTATTATAAACTTAAA
* *
3658545 TAAACTTATTATAAACCTAAA
1 TAAAATTATTATAAACTTAAA
3658566 TAA
1 TAA
3658569 TCTTGTTACG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
21 35 0.65
22 3 0.06
25 3 0.06
26 13 0.24
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAAATTATTATAAACTTAAA
Found at i:3665467 original size:17 final size:19
Alignment explanation
Indices: 3665431--3665472 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3665421 TTATTGCTTA
*
3665431 AAATAAATATTTATTCATT
1 AAATAAATATTAATTCATT
3665450 AAATAAAT-TTAATT-ATT
1 AAATAAATATTAATTCATT
3665467 AAATAA
1 AAATAA
3665473 TCTTTAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 5 0.23
19 8 0.36
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAAATATTAATTCATT
Found at i:3669882 original size:3 final size:3
Alignment explanation
Indices: 3669874--3669925 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
3669864 TTTTTTGTTT
** *
3669874 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
3669920 -TA TTA T
1 TTA TTA T
3669926 AATTTACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3669897 original size:18 final size:18
Alignment explanation
Indices: 3669874--3669929 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
3669864 TTTTTTGTTT
3669874 TTATTATTATTATTAAAA
1 TTATTATTATTATTAAAA
3669892 TTATTATTATTATTAAATA
1 TTATTATTATTATTAAA-A
*
3669911 TTATTATTA-TATTATAA
1 TTATTATTATTATTAAAA
3669928 TT
1 TT
3669930 TACAAACAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
17 3 0.08
18 23 0.64
19 10 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTATTATTAAAA
Found at i:3669972 original size:26 final size:26
Alignment explanation
Indices: 3669936--3669990 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3669926 AATTTACAAA
* *
3669936 CAGTTACAAACAAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3669962 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3669988 CAG
1 CAG
3669991 ACCAACTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.31, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:3670203 original size:17 final size:17
Alignment explanation
Indices: 3670179--3670215 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
3670169 AGCTGCAAAA
3670179 CAAAAAAAAGAGAGAGAG
1 CAAAAAAAAG-GAGAGAG
3670197 CAAAAAAAAGGAGAGAG
1 CAAAAAAAAGGAGAGAG
3670214 CA
1 CA
3670216 CGAACAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.08, G:0.27, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAGGAGAGAG
Found at i:3671946 original size:20 final size:21
Alignment explanation
Indices: 3671923--3671974 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3671913 AGAAATTAAA
3671923 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
3671943 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
3671965 -ATT-ATTTATT
1 AATTCATTTATT
3671975 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:3678468 original size:114 final size:114
Alignment explanation
Indices: 3678267--3678490 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
3678257 GTGCCACGTT
*
3678267 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGATATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGATATCTGATCTG
* * *
3678332 ATTTGGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTCGGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
* *
3678381 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGATATCTGATCTG
* * *
3678446 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 ATTCGGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
3678491 CTGCATGATC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGATATCTGATCTG
ATTCGGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
Found at i:3679516 original size:76 final size:75
Alignment explanation
Indices: 3679435--3679606 Score: 202
Period size: 76 Copynumber: 2.3 Consensus size: 75
3679425 TAACAAGAAA
* *
3679435 CAAATGTTGGGGCATGCTGAAA-ACCCTTGTCAATCAGAATCAGGAATGTTGATGAATCCTGAAT
1 CAAATGTTGGGGCATGCTGAAAGACCCTT-TCAATCAGAATCAAGAATGTTGATGAATCCTGAAC
* *
3679499 GTTTATATCAG
65 GCTCATATCAG
* * * * * * **
3679510 CAAAATGCTAGGGCATGCTGAAAGCCCCTTTCAATCAGAATGAATAATGTTGATGTATTTTGAAC
1 C-AAATGTTGGGGCATGCTGAAAGACCCTTTCAATCAGAATCAAGAATGTTGATGAATCCTGAAC
3679575 GCTCATATCAG
65 GCTCATATCAG
*
3679586 CAAATATTGGGGCATGCTGAA
1 CAAATGTTGGGGCATGCTGAA
3679607 GGCCCATAAC
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
75 18 0.22
76 57 0.71
77 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (75 bp):
CAAATGTTGGGGCATGCTGAAAGACCCTTTCAATCAGAATCAAGAATGTTGATGAATCCTGAACG
CTCATATCAG
Found at i:3680984 original size:22 final size:22
Alignment explanation
Indices: 3680955--3681009 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3680945 ATCTACACTC
3680955 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
3680977 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3680999 TTCAAAGATGA
1 TTCAAAGATGA
3681010 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3681780 original size:76 final size:76
Alignment explanation
Indices: 3681684--3682243 Score: 917
Period size: 76 Copynumber: 7.4 Consensus size: 76
3681674 CTATTTCCCA
*
3681684 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3681749 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3681760 CATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3681825 A-CCTTCGGGT
66 AGCCTTAGGGT
*
3681835 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3681900 AGCCTTAGGCT
66 AGCCTTAGGGT
3681911 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3681976 AACCTTAGGGT
66 AGCCTTAGGGT
* * * *
3681987 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3682052 AGCCTTCGGGT
66 AGCCTTAGGGT
* * * * *
3682063 CATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3682128 A-CCTTCGGGT
66 AGCCTTAGGGT
*
3682138 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3682203 AACCTTAGGGT
66 AGCCTTAGGGT
*
3682214 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
3682244 TTAAGACCTC
Statistics
Matches: 450, Mismatches: 32, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
75 140 0.31
76 310 0.69
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3681932 original size:151 final size:151
Alignment explanation
Indices: 3681684--3682243 Score: 958
Period size: 151 Copynumber: 3.7 Consensus size: 151
3681674 CTATTTCCCA
*
3681684 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3681749 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
3681814 GATGTTTTCAAACCTTCGGGT
131 GATGTTTTCAAACCTTCGGGT
*
3681835 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
3681900 AGCCTTAGGCTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
3681965 GATGTTTTCAAAACCTTAGGGT
131 GATGTTTTC-AAACCTTCGGGT
* * * *
3681987 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * *
3682052 AGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
3682117 GATGTTTTCAAACCTTCGGGT
131 GATGTTTTCAAACCTTCGGGT
*
3682138 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
3682203 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTT
3682244 TTAAGACCTC
Statistics
Matches: 380, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
151 242 0.64
152 138 0.36
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (151 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAACCTTCGGGT
Found at i:3682143 original size:227 final size:227
Alignment explanation
Indices: 3681684--3682244 Score: 962
Period size: 227 Copynumber: 2.5 Consensus size: 227
3681674 CTATTTCCCA
*
3681684 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * *
3681749 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTT
* * *
3681814 GATGTTTTCAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCG
131 GATGTTTTCAAACCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTCG
*
3681879 GGAGGTTTTTGATGTTTTCAAAGCCTTAGGCT
196 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGCT
3681911 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
3681976 AACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTT
* *
3682041 GATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTCCAAAAAGCCTTT
131 GATGTTTTCAAA-CCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTC
* *
3682106 GGGAGCTTTTTGATGTTTTCAAA-CCTTCGGGT
195 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGCT
*
3682138 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3682203 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTT
3682245 TAAGACCTCT
Statistics
Matches: 315, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
227 246 0.78
228 69 0.22
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (227 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCATTCGGGAGCTTTTT
GATGTTTTCAAACCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTTCG
GGAGCTTTTTGATGTTTTCAAAGCCTTAGGCT
Found at i:3682412 original size:3 final size:3
Alignment explanation
Indices: 3682404--3682458 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
3682394 TTTTTTGTTT
** *
3682404 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
3682450 TTA -TA TTA T
1 TTA TTA TTA T
3682459 AATTTACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3682430 original size:21 final size:22
Alignment explanation
Indices: 3682404--3682458 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
3682394 TTTTTTGTTT
3682404 TTATTATTATTATTAAA-ATTA
1 TTATTATTATTATTAAATATTA
3682425 TTATTATTATTATTAAATATTA
1 TTATTATTATTATTAAATATTA
3682447 TTATTA-TATTAT
1 TTATTATTATTAT
3682459 AATTTACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTATTATTATTAAATATTA
Found at i:3682520 original size:26 final size:26
Alignment explanation
Indices: 3682469--3682523 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3682459 AATTTACAAA
** * *
3682469 CAGTTACAAACAAAATTGGACTGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3682495 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3682521 CAG
1 CAG
3682524 ACCAACCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.13
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:3685496 original size:24 final size:24
Alignment explanation
Indices: 3685456--3685541 Score: 97
Period size: 24 Copynumber: 3.6 Consensus size: 24
3685446 CATAGGTCTC
* *
3685456 GTTCGTTCAT-TTACGTTCGTGAAT
1 GTTCGTTTATGTT-CGTTCGTGTAT
*
3685480 GTTCGGTTATGTTCGTTCG-GTTAT
1 GTTCGTTTATGTTCGTTCGTG-TAT
3685504 GTTCGTTTATGTTCGTTCGAT-TAT
1 GTTCGTTTATGTTCGTTCG-TGTAT
3685528 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
3685542 ATTTGTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 51 0.94
25 2 0.04
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.51
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGTGTAT
Found at i:3685499 original size:14 final size:14
Alignment explanation
Indices: 3685480--3685534 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
3685470 GTTCGTGAAT
3685480 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
3685494 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
3685508 G-T---TTATGTTC
1 GTTCGGTTATGTTC
*
3685518 GTTCGATTATGTTC
1 GTTCGGTTATGTTC
3685532 GTT
1 GTT
3685535 TATGTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.09, C:0.13, G:0.25, T:0.53
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:3685554 original size:24 final size:24
Alignment explanation
Indices: 3685478--3685541 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
3685468 ACGTTCGTGA
* *
3685478 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCGATT
3685502 ATGTTCGTTTATGTTCGTTCGATT
1 ATGTTCGTTTATGTTCGTTCGATT
3685526 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
3685542 ATTTGTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.53
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCGTTCGATT
Found at i:3686294 original size:10 final size:10
Alignment explanation
Indices: 3686279--3686352 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
3686269 GGTCTCCAAT
3686279 GTTTATGTTC
1 GTTTATGTTC
3686289 GTTTATGTTC
1 GTTTATGTTC
*
3686299 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
* *
3686311 GTTCATGTCC
1 GTTTATGTTC
3686321 GTTTATGTTC
1 GTTTATGTTC
3686331 G----TGTTC
1 GTTTATGTTC
3686337 GTTTATGTTC
1 GTTTATGTTC
3686347 GTTTAT
1 GTTTAT
3686353 TTATTAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.68
11 6 0.12
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:3686303 original size:16 final size:16
Alignment explanation
Indices: 3686284--3686348 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
3686274 CCAATGTTTA
3686284 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
3686300 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
*
3686316 TGTCCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3686332 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3686348 T
1 T
3686349 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.09, C:0.14, G:0.22, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3686439 original size:16 final size:16
Alignment explanation
Indices: 3686418--3686450 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3686408 CACAAAAAAT
3686418 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3686434 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3686450 T
1 T
3686451 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3687042 original size:20 final size:19
Alignment explanation
Indices: 3687005--3687043 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3686995 GGACCGGCTG
*
3687005 AAAACCGAAAAAATCGGGA
1 AAAACCGAAAAAACCGGGA
*
3687024 AAAACCGGAGAAAACCGGGA
1 AAAACC-GAAAAAACCGGGA
3687044 TTTTGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.18, G:0.26, T:0.03
Consensus pattern (19 bp):
AAAACCGAAAAAACCGGGA
Found at i:3687270 original size:24 final size:25
Alignment explanation
Indices: 3687233--3687279 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3687223 GAACTCAAAA
3687233 AAAAATTAGAAGCTCGATTGAAGCC
1 AAAAATTAGAAGCTCGATTGAAGCC
* *
3687258 AAAAATTCG-AGCTTGATTGAAG
1 AAAAATTAGAAGCTCGATTGAAG
3687280 TGAACGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (25 bp):
AAAAATTAGAAGCTCGATTGAAGCC
Found at i:3687721 original size:22 final size:21
Alignment explanation
Indices: 3687696--3687736 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3687686 TATAAAAAAT
3687696 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
3687718 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
3687737 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:3692241 original size:65 final size:65
Alignment explanation
Indices: 3692137--3692267 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
3692127 ACTGTGCGTT
* *
3692137 ACACCTTCAACCTGAGCACGAAATAATCGTAATTCAAAATAAAAGCATCGAAACTACATGTAAAC
1 ACACCTTCAACCTGAGCACGAAATAATCGTAATTCAAAATAAAAGCACCAAAACTACATGTAAAC
*
3692202 ACACCTTCAACCTGAGCACGAAATAATCGT-ATGTTAAAATAAAAGCACCAAAACTACATGTAAA
1 ACACCTTCAACCTGAGCACGAAATAATCGTAAT-TCAAAATAAAAGCACCAAAACTACATGTAAA
3692266 C
65 C
3692267 A
1 A
3692268 TAGCTGTTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 2 0.03
65 60 0.97
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.20
Consensus pattern (65 bp):
ACACCTTCAACCTGAGCACGAAATAATCGTAATTCAAAATAAAAGCACCAAAACTACATGTAAAC
Found at i:3703863 original size:64 final size:64
Alignment explanation
Indices: 3703779--3704004 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 64
3703769 TTGAAGGTGT
* *
3703779 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTAGTGC
** * * * *
3703843 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTGATAATAC-AACATCGAATGTAATTCGAG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATTAGTG
3703906 C
64 C
* *
3703907 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTA-T
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTAGT
3703969 GC
63 GC
* *
3703971 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
3704005 CATTAAAAGA
Statistics
Matches: 136, Mismatches: 18, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
63 3 0.02
64 121 0.89
65 11 0.08
66 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTAGTGC
Found at i:3704676 original size:15 final size:15
Alignment explanation
Indices: 3704658--3704765 Score: 198
Period size: 15 Copynumber: 7.2 Consensus size: 15
3704648 GAGGGTATAA
*
3704658 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
3704673 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
3704688 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
3704703 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
3704718 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
3704733 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
3704748 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
3704763 TAG
1 TAG
3704766 GAGTCCTACG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 91 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:3708798 original size:64 final size:64
Alignment explanation
Indices: 3708714--3708939 Score: 257
Period size: 64 Copynumber: 3.5 Consensus size: 64
3708704 TTGAAGGTGT
* *
3708714 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTT-AAATACAAACATCGAATGCAATTAGTGC
** * * *
3708778 ATCGATGCATAAGTCA-TGCATCGATGCATCCCAGTGATAATAC-AACATCGAATGTAATTCGTG
1 ATCGATGCATAAGT-AGTGCATCGATGCATCCCTTTTA-AATACAAACATCGAATGCAATTAGTG
3708841 C
64 C
* *
3708842 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-GAAACATCGAATGCATTTTA-T
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATACAAACATCGAATGCA-ATTAGT
3708904 GC
63 GC
* *
3708906 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
3708940 CATTAAAAGA
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.02
64 123 0.89
65 11 0.08
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATACAAACATCGAATGCAATTAGTGC
Found at i:3709611 original size:15 final size:15
Alignment explanation
Indices: 3709593--3709685 Score: 168
Period size: 15 Copynumber: 6.2 Consensus size: 15
3709583 GAGGGTATAA
3709593 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
3709608 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
3709623 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
3709638 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
3709653 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3709668 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
3709683 TAG
1 TAG
3709686 GAGTCCTACG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 74 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:3716848 original size:18 final size:20
Alignment explanation
Indices: 3716817--3716855 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3716807 AATCATTTAT
3716817 AAAATAAAATATTAAT-TAA
1 AAAATAAAATATTAATATAA
*
3716836 AAAATGAAA-ATTAATATAA
1 AAAATAAAATATTAATATAA
3716855 A
1 A
3716856 GAATTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATAAAATATTAATATAA
Found at i:3723873 original size:22 final size:22
Alignment explanation
Indices: 3723848--3723890 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3723838 ATTTTTTTTA
* *
3723848 TAAATAATATAACATTTTAAGC
1 TAAATAAAATAACATCTTAAGC
*
3723870 TAAATAAAATAATATCTTAAG
1 TAAATAAAATAACATCTTAAG
3723891 TTGACAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (22 bp):
TAAATAAAATAACATCTTAAGC
Found at i:3724402 original size:16 final size:17
Alignment explanation
Indices: 3724381--3724418 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3724371 TGTGCAAATC
* *
3724381 CGGGTACCCGG-ATTTT
1 CGGGTACACGGAACTTT
3724397 CGGGTACACGGAACTTT
1 CGGGTACACGGAACTTT
3724414 CGGGT
1 CGGGT
3724419 CGACGATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.26
Consensus pattern (17 bp):
CGGGTACACGGAACTTT
Found at i:3724466 original size:17 final size:17
Alignment explanation
Indices: 3724444--3724483 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3724434 CCGTGTCTCG
*
3724444 ATCCGGATGTTACGGGT
1 ATCCGGATGTTACAGGT
* *
3724461 ATCCGGATTTTGCAGGT
1 ATCCGGATGTTACAGGT
3724478 ATCCGG
1 ATCCGG
3724484 TAATCGGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (17 bp):
ATCCGGATGTTACAGGT
Found at i:3724653 original size:16 final size:15
Alignment explanation
Indices: 3724627--3724662 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3724617 CAAAATACAA
3724627 AATATAATAATTCAT
1 AATATAATAATTCAT
3724642 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
3724658 TATAT
1 AATAT
3724663 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:3725903 original size:18 final size:19
Alignment explanation
Indices: 3725872--3725909 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3725862 ATTAAATTAC
3725872 GAGTCAAATCAAAATAAATT
1 GAGTCAAA-CAAAATAAATT
*
3725892 GAGTCAAA-AAAATTAATT
1 GAGTCAAACAAAATAAATT
3725910 TTTTGAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (19 bp):
GAGTCAAACAAAATAAATT
Found at i:3734635 original size:14 final size:14
Alignment explanation
Indices: 3734616--3734645 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3734606 ACAAATGTTT
3734616 AATGCGTTAAGTCA
1 AATGCGTTAAGTCA
3734630 AATGCGTTAAGTCA
1 AATGCGTTAAGTCA
3734644 AA
1 AA
3734646 GGTTTATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (14 bp):
AATGCGTTAAGTCA
Found at i:3740422 original size:88 final size:83
Alignment explanation
Indices: 3740276--3740435 Score: 230
Period size: 88 Copynumber: 1.9 Consensus size: 83
3740266 TTTTTATCTT
** *
3740276 ATAAGCTCATAAGCTTATTTTATTTTACATTTACTTACCATAAGCTCGTAAGCTTATTTTACCAA
1 ATAAGCTCATAAGCTTATTTTATAATACACTTACTTACCATAAGCTCGTAAGCTTATTTTACCAA
3740341 TACACTTACCAATATTTC
66 TACACTTACCAATATTTC
*
3740359 ATAAGCTCCTAAGCTTATTTTATCAATACACTTACCATTATTCCATAAGCTCGTAAGCTTATTTT
1 ATAAGCTCATAAGCTTATTTTAT-AATACACTTA-C-TTA--CCATAAGCTCGTAAGCTTATTTT
*
3740424 ACCCATACACTT
61 ACCAATACACTT
3740436 GCCATTTATC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
83 22 0.33
84 7 0.10
85 1 0.01
86 3 0.04
88 34 0.51
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (83 bp):
ATAAGCTCATAAGCTTATTTTATAATACACTTACTTACCATAAGCTCGTAAGCTTATTTTACCAA
TACACTTACCAATATTTC
Found at i:3740441 original size:44 final size:44
Alignment explanation
Indices: 3740313--3740441 Score: 204
Period size: 44 Copynumber: 2.9 Consensus size: 44
3740303 CATTTACTTA
*
3740313 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCAATATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTATT
* * *
3740357 TCATAAGCTCCTAAGCTTATTTTATCAATACACTTACCATTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTATT
* *
3740401 CCATAAGCTCGTAAGCTTATTTTACCCATACACTTGCCATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATT
3740442 TATCCAATAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (44 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTATT
Found at i:3740606 original size:60 final size:61
Alignment explanation
Indices: 3740533--3740646 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 61
3740523 GTAGTGCTAA
* *
3740533 ACCTGCACTAAGCTTATGCCATAGTGCTAATCC-GACAAT-ACACATAAGGTCGTGCCCACC
1 ACCTGCACTAAGCTTACGCCATAGTACTAATCCGGAC-ATGACACATAAGGTCGTGCCCACC
* *
3740593 ACCTGCACTAAGCTTACGCTATAGTACTAATCCGGACATGATACATAAGGTCGT
1 ACCTGCACTAAGCTTACGCCATAGTACTAATCCGGACATGACACATAAGGTCGT
3740647 ATCCACCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
60 32 0.67
61 16 0.33
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (61 bp):
ACCTGCACTAAGCTTACGCCATAGTACTAATCCGGACATGACACATAAGGTCGTGCCCACC
Found at i:3745380 original size:191 final size:191
Alignment explanation
Indices: 3745056--3745438 Score: 766
Period size: 191 Copynumber: 2.0 Consensus size: 191
3745046 TAGGTGTTGA
3745056 GCCACTGATGCCCCTTCCGCCATCCGCAAATTGAATAATCGCCTCATCAAGTGAACTTTGTTTGA
1 GCCACTGATGCCCCTTCCGCCATCCGCAAATTGAATAATCGCCTCATCAAGTGAACTTTGTTTGA
3745121 TGTCGATGGCTTCTCATACATACTGGAGAGAGCTGCCATAAGACCCGCCATGGTCTTTTCCTTTG
66 TGTCGATGGCTTCTCATACATACTGGAGAGAGCTGCCATAAGACCCGCCATGGTCTTTTCCTTTG
3745186 CTATGTTGAAAGCAACATTGTGGGATAACGTTAGTCGAATAACTCCGAGGGTTTGTCTGTC
131 CTATGTTGAAAGCAACATTGTGGGATAACGTTAGTCGAATAACTCCGAGGGTTTGTCTGTC
3745247 GCCACTGATGCCCCTTCCGCCATCCGCAAATTGAATAATCGCCTCATCAAGTGAACTTTGTTTGA
1 GCCACTGATGCCCCTTCCGCCATCCGCAAATTGAATAATCGCCTCATCAAGTGAACTTTGTTTGA
3745312 TGTCGATGGCTTCTCATACATACTGGAGAGAGCTGCCATAAGACCCGCCATGGTCTTTTCCTTTG
66 TGTCGATGGCTTCTCATACATACTGGAGAGAGCTGCCATAAGACCCGCCATGGTCTTTTCCTTTG
3745377 CTATGTTGAAAGCAACATTGTGGGATAACGTTAGTCGAATAACTCCGAGGGTTTGTCTGTC
131 CTATGTTGAAAGCAACATTGTGGGATAACGTTAGTCGAATAACTCCGAGGGTTTGTCTGTC
3745438 G
1 G
3745439 ATAAGAGCTC
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 192 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (191 bp):
GCCACTGATGCCCCTTCCGCCATCCGCAAATTGAATAATCGCCTCATCAAGTGAACTTTGTTTGA
TGTCGATGGCTTCTCATACATACTGGAGAGAGCTGCCATAAGACCCGCCATGGTCTTTTCCTTTG
CTATGTTGAAAGCAACATTGTGGGATAACGTTAGTCGAATAACTCCGAGGGTTTGTCTGTC
Found at i:3749288 original size:17 final size:17
Alignment explanation
Indices: 3749266--3749309 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3749256 ATGTAAAAAT
*
3749266 AAATATTTAAGTTTAAA
1 AAATATTTAAATTTAAA
* **
3749283 AAATATTAAAATTTATT
1 AAATATTTAAATTTAAA
3749300 AAATATTTAA
1 AAATATTTAA
3749310 TTAAGTAGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:3754122 original size:31 final size:31
Alignment explanation
Indices: 3754052--3754129 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
3754042 ACTTTTAAAA
**
3754052 TTGCAATACAGTCCCCAAACATTTAGTCCAT
1 TTGCAATATGGTCCCCAAACATTTAGTCCAT
* * *
3754083 TTGCAATATGGTCCCCTAACATTTAGTTCGT
1 TTGCAATATGGTCCCCAAACATTTAGTCCAT
3754114 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
3754130 GATGTAACCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (31 bp):
TTGCAATATGGTCCCCAAACATTTAGTCCAT
Found at i:3756290 original size:21 final size:21
Alignment explanation
Indices: 3756266--3756307 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3756256 AGAGAAGTTG
3756266 TAATTCCTATTTTCTCATAGT
1 TAATTCCTATTTTCTCATAGT
*
3756287 TAATTCCTATTTTCTTATAGT
1 TAATTCCTATTTTCTCATAGT
3756308 GAAATTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATTCCTATTTTCTCATAGT
Found at i:3767648 original size:87 final size:87
Alignment explanation
Indices: 3767502--3767664 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
3767492 TATGTTATAT
3767502 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
3767567 AGCGCTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
*
3767589 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
3767654 AGCACTTATAT
66 AGCACTTATAT
3767665 TGACCTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCACTTATATAATAAAATAGG
Found at i:3768551 original size:181 final size:182
Alignment explanation
Indices: 3767800--3769543 Score: 2990
Period size: 182 Copynumber: 9.6 Consensus size: 182
3767790 TGCGTTCACC
** * *
3767800 TTTTGTCATTTATAAACCGGTTTTATCATATTTTTACATGTTATATTAG-TATGGATCGATACAT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATT-GTTATGGATCGATACAT
*
3767864 TTTTATAAAGTATCGACACTTTATTGGTGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTC
65 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTC
* **
3767928 GATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTATATG
129 GATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3767982 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3768047 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCACTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3768112 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTATCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3768164 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3768229 TTTCTAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3768294 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACTTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3768346 TTTTGTCATTTCGAGACC-GTTTTGTCATATTTTTACATGTTATATTTTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3768410 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCCAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3768474 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3768526 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
3768591 TTTATAAAATATCGACACTTTATTGGCTCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
3768655 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3768707 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
3768772 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3768837 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
3768889 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
3768954 TTTATAAAATATCGGCACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3769019 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTATCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
3769071 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACA-T
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
3769135 TTTATAAAGTATCGACACGTTATTGACGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
3769197 ATACTTATAATAAATTATCGACACTTTCAACATAACCGATAGCGCTTTACATG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3769250 TTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3769315 TTTATAAAGTATCGATACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
3769379 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* **
3769431 TTTTGTCATTTCGAGATCGG--TTGTCATATTTTTACATGTTATATTGTTATAAATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
3769494 TTTATAAAGTATTGACACTTTATTGACGATATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
3769544 AAAGGTAAAA
Statistics
Matches: 1488, Mismatches: 64, Indels: 22
0.95 0.04 0.01
Matches are distributed among these distances:
178 2 0.00
179 207 0.14
180 143 0.10
181 457 0.31
182 679 0.46
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:3769049 original size:725 final size:724
Alignment explanation
Indices: 3767800--3769543 Score: 3016
Period size: 725 Copynumber: 2.4 Consensus size: 724
3767790 TGCGTTCACC
* * * *
3767800 TTTTGTCATTTATAAACCGGTTTTATCATATTTTTACATGTTATATTAGTATGGATCGATACATT
1 TTTTGTCATTTAGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
3767865 TTTATAAAGTATCGACACTTTATTGG-TGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTC
66 TTTATAAAGTATCGACACTTTATTGGCT-CTATAAC-TCTTCTCTT-TTAAATTCCAAAAGTGTC
* * *
3767928 GATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTATATGTTTTGTCATTT
128 GATACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTT
3767993 CGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTA
193 CGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTA
*
3768058 TCGACACTTTATTGGCGCTATAACTTCTTCACTTTTAAATTCCAAAAGTGTCGATACTTATAATA
258 TCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATA
*
3768123 AATTATCGACACTTTCAACATAACCGGTAGCGCTTTATCTGTTTTGTCATTTCGAGACCGGTTTT
323 AATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTT
* * *
3768188 GTCATATTATTACATGTTATATTGTTATGGATCGATACATTTTTCTAAAGTATCGACACTTTATT
388 GTCATATTATTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACACTTTATT
3768253 GGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACT
453 GGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACT
*
3768318 TTCAACATAACCGGTAGCGCTTTACTTGTTTTGTCATTTCGAGACC-GTTTTGTCATATTTTTAC
518 TTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTAC
* * *
3768382 ATGTTATATTTTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAAC-T
583 ATGTTATATTGTTATGGATCGATACA-TTTTATAAAGTATCGACACGTTATTGACGCTATAACTT
*
3768446 CTTCTCTT-TTAAATTCCCAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAACC
647 CTTCTCTTATT-AATT-CCAAA-AGTCGATACGTATAATAAATTATCGACACTTTCAACATAACC
* *
3768510 GGTAGCGCTTTACCTG
709 GATAGCGCTTTACATG
*
3768526 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTAGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* *
3768591 TTTATAAAATATCGACACTTTATTGGCTCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCAAT
66 TTTATAAAGTATCGACACTTTATTGGCTCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
3768656 ACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGA
131 ACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGA
3768721 GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
196 GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
3768786 ACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAT
261 ACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAT
*
3768851 TATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTC
326 TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTC
* * *
3768916 ATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAATATCGGCACTTTATTGGC
391 ATATTATTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGC
3768981 GCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTC
456 GCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTC
*
3769046 AACATAACCGGTATCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATG
521 AACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATG
3769111 TTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACGTTATTGACGCTATAACTTCTTC
586 TTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACGTTATTGACGCTATAACTTCTTC
*
3769176 TCTTATTAATTCCAAAAGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGATAGCG
651 TCTTATTAATTCCAAAAGTCGATACGTATAATAAATTATCGACACTTTCAACATAACCGATAGCG
3769241 CTTTACATG
716 CTTTACATG
* *
3769250 TTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTAGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* *
3769315 TTTATAAAGTATCGATACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
66 TTTATAAAGTATCGACACTTTATTGGCTCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
*
3769380 ACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGA
131 ACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGA
* * ** *
3769445 GATCGG--TTGTCATATTTTTACATGTTATATTGTTATAAATCGATACATTTTTATAAAGTATTG
196 GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
* *
3769508 ACACTTTATTGACGATATAACTTCTTCTCTTTTAAA
261 ACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
3769544 AAAGGTAAAA
Statistics
Matches: 971, Mismatches: 42, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
722 87 0.09
724 249 0.26
725 484 0.50
726 148 0.15
727 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (724 bp):
TTTTGTCATTTAGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCTCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
ACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGA
GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
ACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAT
TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTC
ATATTATTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGC
GCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTC
AACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATG
TTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACGTTATTGACGCTATAACTTCTTC
TCTTATTAATTCCAAAAGTCGATACGTATAATAAATTATCGACACTTTCAACATAACCGATAGCG
CTTTACATG
Done.