Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 14 of 85
Found at i:4545744 original size:27 final size:26
Alignment explanation
Indices: 4545714--4545789 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
4545704 AGAGATGGAA
4545714 GCCTTTATGGCAAATCTTGTAAAGAA-G
1 GCCTTTATGGCAAA-CTT-TAAAGAATG
* **
4545741 GCCTTTGTGGCGCACTTTAAAGAATG
1 GCCTTTATGGCAAACTTTAAAGAATG
* *
4545767 ACCTTTATGGCAACCTTCTAAAG
1 GCCTTTATGGCAAACTT-TAAAG
4545790 GAAACGCCTC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 7 0.18
26 16 0.41
27 16 0.41
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (26 bp):
GCCTTTATGGCAAACTTTAAAGAATG
Found at i:4549176 original size:18 final size:19
Alignment explanation
Indices: 4549133--4549177 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
4549123 AAATCAAAAT
4549133 ATTGTGAG-AGTTAAAAGC
1 ATTGTGAGTAGTTAAAAGC
4549151 A-TGATGAGTA-TTAAAAGC
1 ATTG-TGAGTAGTTAAAAGC
4549169 ATTGTGAGT
1 ATTGTGAGT
4549178 GAAAGAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (19 bp):
ATTGTGAGTAGTTAAAAGC
Found at i:4556269 original size:31 final size:30
Alignment explanation
Indices: 4556198--4556287 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
4556188 GTGACCAATT
4556198 AAAAAAA--ATAGTTAAGTGACCAAAAAAG
1 AAAAAAATCATAGTTAAGTGACCAAAAAAG
* *
4556226 AAACAAATTCATAGTTAAGTGGCCAAATTAAA-
1 AAA-AAAATCATAGTTAAGTGACCAAA--AAAG
* * *
4556258 AAAAAAATCATAATTGAGAGACCAGAAAAA
1 AAAAAAATCATAGTTAAGTGACCA-AAAAA
4556288 AATTTAACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.06
29 3 0.06
30 3 0.06
31 32 0.65
32 5 0.10
33 3 0.06
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (30 bp):
AAAAAAATCATAGTTAAGTGACCAAAAAAG
Found at i:4557638 original size:27 final size:27
Alignment explanation
Indices: 4557601--4557661 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
4557591 TTGGTGCAGA
**
4557601 ATCATCATCATTTTCAACAACAGCAAC
1 ATCATCATCATCATCAACAACAGCAAC
**
4557628 ATCATCATCATCATCTGCAACAGCAAC
1 ATCATCATCATCATCAACAACAGCAAC
*
4557655 AACATCA
1 ATCATCA
4557662 ACAGCAGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (27 bp):
ATCATCATCATCATCAACAACAGCAAC
Found at i:4562339 original size:20 final size:20
Alignment explanation
Indices: 4562314--4562364 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4562304 AAATTATAAA
*
4562314 AATAAAAATTATTAAACTTT
1 AATAAAAATTATTAAAATTT
4562334 AATAAAAAGTT-TTAAAATTT
1 AATAAAAA-TTATTAAAATTT
*
4562354 ACTAAAAATTA
1 AATAAAAATTA
4562365 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AATAAAAATTATTAAAATTT
Found at i:4562387 original size:18 final size:18
Alignment explanation
Indices: 4562366--4562409 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4562356 TAAAAATTAG
4562366 AAAAAATATAAAATTGTA
1 AAAAAATATAAAATTGTA
*
4562384 AAAAAATATAAAATTTTA
1 AAAAAATATAAAATTGTA
*
4562402 TAAAAATA
1 AAAAAATA
4562410 ATTAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAAATATAAAATTGTA
Found at i:4570270 original size:195 final size:195
Alignment explanation
Indices: 4569938--4570331 Score: 754
Period size: 195 Copynumber: 2.0 Consensus size: 195
4569928 AACCACATAC
4569938 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
*
4570003 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCGGAATAACCAC
66 TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC
*
4570068 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCATAACCATATTATAA
131 AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA
4570133 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAG-TCGCACCGCTCACATCGAAAACACTAC
1 TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCT-GCACCGCTCACATCGAAAACACTAC
4570197 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA
65 TTATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCA
4570262 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA
130 CAAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATA
4570327 A
195 A
4570328 TCAA
1 TCAA
4570332 GCAAAATAAC
Statistics
Matches: 196, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
194 1 0.01
195 195 0.99
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (195 bp):
TCAAAAGTTTATTGCCTTTCTAGGATCACTTCCTTAGCTGCACCGCTCACATCGAAAACACTACT
TATCTGCAAGATTAAGTAAGGAGTTTGTGAGCTTAAACAAGTTCAGTGAATGTCAGAATAACCAC
AAAGCATACACAACATCAAAAGTTAAGCAAGAGCATACTACAACACATTCACAACCATATTATAA
Found at i:4571092 original size:31 final size:31
Alignment explanation
Indices: 4571056--4571119 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
4571046 TTCACTTACT
*
4571056 TTACTTGTCACATCAATATCACATTCCACAA
1 TTACTTGTCACATCAACATCACATTCCACAA
4571087 TTACTTGTCACATCAACATCACATTCCACAA
1 TTACTTGTCACATCAACATCACATTCCACAA
4571118 TT
1 TT
4571120 CGACAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (31 bp):
TTACTTGTCACATCAACATCACATTCCACAA
Found at i:4580476 original size:30 final size:29
Alignment explanation
Indices: 4580422--4580489 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
4580412 AGATTAGGAT
*
4580422 TAATTTAATTTTTCTTAAAATAAATAAAG
1 TAATTTAATTTTTATTAAAATAAATAAAG
* * *
4580451 TAATTTAGTTTTTATATAGAATAAATGAAG
1 TAATTTAATTTTTAT-TAAAATAAATAAAG
*
4580481 TAATATAAT
1 TAATTTAAT
4580490 ATTAAGATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (29 bp):
TAATTTAATTTTTATTAAAATAAATAAAG
Found at i:4584608 original size:72 final size:72
Alignment explanation
Indices: 4584416--4584582 Score: 230
Period size: 72 Copynumber: 2.3 Consensus size: 72
4584406 AAAATCATAT
* * * *
4584416 ATAAACAACTATTGATAAAACTA-ATTTA-ATAAAAATAAGTAGAACATAAATTCAATATTTAAA
1 ATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATTCAAA
*
4584479 GACCAAAC
65 AACCAAAC
* *
4584487 ATAAACAACTATTAATAGAAGTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
1 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
4584552 ACCAAAC
66 ACCAAAC
* *
4584559 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTAATAAAACTAG
4584583 TTTAGCATTG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 23 0.28
72 60 0.72
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
ACCAAAC
Found at i:4585028 original size:18 final size:18
Alignment explanation
Indices: 4585007--4585041 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4584997 TCCATCAATT
4585007 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
4585025 TGAACATCATTTGAAAT
1 TGAACATCATTTGAAAT
4585042 TTTCTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:4590982 original size:59 final size:60
Alignment explanation
Indices: 4590902--4591022 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 60
4590892 TGTATGAATA
* * * * *
4590902 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATT-TTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
4590961 TTGTAATTA-TTTAAAATTTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
4591021 TT
1 TT
4591023 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 6 0.11
59 41 0.75
60 8 0.15
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:4591164 original size:16 final size:15
Alignment explanation
Indices: 4591140--4591174 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
4591130 CTCATTTAAT
*
4591140 TTTTCTATAATGTAA
1 TTTTATATAATGTAA
4591155 CTTTTATATAATGTAA
1 -TTTTATATAATGTAA
4591171 TTTT
1 TTTT
4591175 GTTTGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:4592502 original size:27 final size:27
Alignment explanation
Indices: 4592451--4592560 Score: 150
Period size: 27 Copynumber: 4.1 Consensus size: 27
4592441 GAAAAATAAG
* * *
4592451 ACCATTAGCGCCTCTCA-ATATGGCACA
1 ACCATTGGCGCCTGTCAGATA-GGCACC
* *
4592478 ACTAATGGCGCCTGTCAGATAGGCACC
1 ACCATTGGCGCCTGTCAGATAGGCACC
4592505 ACCATTGGCGCCTGTCAGATAGGCACC
1 ACCATTGGCGCCTGTCAGATAGGCACC
*
4592532 ACCATTGGCGCCTGTCAGATAGGCGCC
1 ACCATTGGCGCCTGTCAGATAGGCACC
4592559 AC
1 AC
4592561 TATTTTGTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 71 0.96
28 3 0.04
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.19
Consensus pattern (27 bp):
ACCATTGGCGCCTGTCAGATAGGCACC
Found at i:4592982 original size:14 final size:15
Alignment explanation
Indices: 4592957--4592985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4592947 ATTTTATTTT
4592957 ATAATAAATTTTAAA
1 ATAATAAATTTTAAA
4592972 ATAAT-AATTTTAAA
1 ATAATAAATTTTAAA
4592986 GTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATTTTAAA
Found at i:4593028 original size:18 final size:19
Alignment explanation
Indices: 4593005--4593042 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4592995 ATATTCTTCA
*
4593005 TATATTATTAA-AAATATT
1 TATATTAGTAATAAATATT
4593023 TATATTAGTAATAAATATT
1 TATATTAGTAATAAATATT
4593042 T
1 T
4593043 TATAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATTAGTAATAAATATT
Found at i:4601047 original size:2 final size:2
Alignment explanation
Indices: 4600994--4601028 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4600984 TATACTTGTG
4600994 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 A
4601029 NNNNTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4602018 original size:19 final size:19
Alignment explanation
Indices: 4601996--4602044 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4601986 CTATCTTTTT
**
4601996 TTTTTTGTATTTTCTTTGA
1 TTTTTTGTATCATCTTTGA
*
4602015 TTTTTCTCT-TCATCTTTGA
1 TTTTT-TGTATCATCTTTGA
4602034 TTTTTTGTATC
1 TTTTTTGTATC
4602045 GGCACCCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.10, C:0.12, G:0.08, T:0.69
Consensus pattern (19 bp):
TTTTTTGTATCATCTTTGA
Found at i:4604732 original size:44 final size:45
Alignment explanation
Indices: 4604682--4604771 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
4604672 ACATCGTTCT
4604682 ATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGAATTACTATTACGCCTCTATTCCATTAC
*
4604726 ATTCAACCAAACAATTGAATTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
4604771 A
1 A
4604772 CCTCTATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (45 bp):
ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
Found at i:4604775 original size:16 final size:16
Alignment explanation
Indices: 4604750--4604787 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
4604740 TTGAATTACT
*
4604750 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
4604766 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
4604782 ATTACA
1 ATTACA
4604788 ACGAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:4616959 original size:22 final size:21
Alignment explanation
Indices: 4616912--4616964 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
4616902 TTTAGTTTTT
*
4616912 TTAATGTTTTAACCTTTAATA
1 TTAATATTTTAACCTTTAATA
* * *
4616933 ATAATATTTTAACATTTTATTA
1 TTAATATTTTAAC-CTTTAATA
4616955 TTAATTATTT
1 TTAA-TATTT
4616965 AATTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 9 0.36
23 5 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATATTTTAACCTTTAATA
Found at i:4620965 original size:26 final size:26
Alignment explanation
Indices: 4620927--4620987 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
4620917 TATTTAAGCA
*
4620927 TATATCACTACACATATAAATCCTAT
1 TATATCACAACACATATAAATCCTAT
4620953 TATATCACAACACATATAAATCCTAT
1 TATATCACAACACATATAAATCCTAT
4620979 T-TAATCACA
1 TAT-ATCACA
4620988 TTTAGTCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (26 bp):
TATATCACAACACATATAAATCCTAT
Found at i:4621438 original size:35 final size:36
Alignment explanation
Indices: 4621390--4621471 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
4621380 TACATTATAA
*
4621390 TCACTATTACATGG-TATGAA-AACATACCCACATAT
1 TCACTATCACATGGCT-TGAATAACATACCCACATAT
*
4621425 TTACTATCACATGGCTTGAATAACATACCCACATAT
1 TCACTATCACATGGCTTGAATAACATACCCACATAT
*
4621461 TCACTTTCACA
1 TCACTATCACA
4621472 ACAATCATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 16 0.39
36 25 0.61
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (36 bp):
TCACTATCACATGGCTTGAATAACATACCCACATAT
Found at i:4625547 original size:17 final size:17
Alignment explanation
Indices: 4625527--4625564 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4625517 TGAAACATTA
4625527 AAGTTAATTGAACATAG
1 AAGTTAATTGAACATAG
*
4625544 AAGTTAATTGGACATAG
1 AAGTTAATTGAACATAG
4625561 AAGT
1 AAGT
4625565 ATGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (17 bp):
AAGTTAATTGAACATAG
Found at i:4631458 original size:131 final size:131
Alignment explanation
Indices: 4631219--4631807 Score: 919
Period size: 131 Copynumber: 4.5 Consensus size: 131
4631209 AAATCAGTAA
* *
4631219 AAATTGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATTGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
* * *
4631284 CCAGGAGTAGGGAAATAGATTTAAGTCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
4631349 G
131 G
** *
4631350 AAATGGCAGATCTTATCTCCCTAAGCAGTAGAAGAGTAGATCGAAGATGGCGAATCTTATCGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
*
4631415 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTA
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
4631480 G
131 G
* * *
4631481 AAATGGCAGATCTTATCTCCCTAAGAAGTAGCGGAGCAAATCGAAGATGGTGAATCTTATCGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
4631546 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
4631611 G
131 G
* * * *
4631612 AAATGGCAGATCTTACCTCCCTGAGCAGTAGCGAAGCAGATCGAAGATGGCGAATCTTATCTTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
* * * *
4631677 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTGTGACCCTGACCAGTAGTGGGATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
4631742 G
131 G
* * * * * * * *
4631743 AAATTGTAGATCTTGTCTCCTTAAGCAGTAGCGGAGTAGATCGAATACGGCGAATCTGATC-TCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
4631807 C
66 C
4631808 TGAGATTACA
Statistics
Matches: 420, Mismatches: 38, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
130 4 0.01
131 416 0.99
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (131 bp):
AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
G
Found at i:4632512 original size:301 final size:302
Alignment explanation
Indices: 4631970--4632574 Score: 1194
Period size: 301 Copynumber: 2.0 Consensus size: 302
4631960 CGGGCAAAAT
4631970 TGGCCAATGTTTTAGTCTTTGCCTCATTCCCGTTACACGACAAATGAGCAAAGAGGGGCAGCTGT
1 TGGCCAATGTTTTAGTCTTTGCCTCATTCCCGTTACACGACAAATGAGCAAAGAGGGGCAGCTGT
*
4632035 AATAGCCCAAATTTACCCGGCCCAAATCAGAGATAAATAAGCAATAAATATAAAACTAAAATTAA
66 AATAGCCCAAATTTACCCGGCCCAAATCAGAGATAAATAAGCAATAAATATAAAACCAAAATTAA
4632100 GTGTCCAAAATAGTCCTTTTACATTAGGCCCAAACTAAACACAACCCACTACCCAAAATCAAACC
131 GTGTCCAAAATAGTCCTTTTACATTAGGCCCAAACTAAACACAACCCACTACCCAAAATCAAACC
4632165 CGAATTACCCAATACATCCCAGCCCAATAACCAATGCCCTAAACTTAAACCCTAGCAGCCTCCAC
196 CGAATTACCCAATACATCCCAGCCCAATAACCAATGCCCTAAACTTAAACCCTAGCAGCCTCCAC
4632230 GCCGTAACCGCCCAGGGCCTTCGTCCCCACGTG-CGAGCCTC
261 GCCGTAACCGCCCAGGGCCTTCGTCCCCACGTGCCGAGCCTC
4632271 TGGCCAATGTTTTAGTCTTTGCCTCATTCCCGTTACACGACAAATGAGCAAAGAGGGGCAGCTGT
1 TGGCCAATGTTTTAGTCTTTGCCTCATTCCCGTTACACGACAAATGAGCAAAGAGGGGCAGCTGT
4632336 AATAGCCCAAATTTACCCGGCCCAAATCAGAGATAAATAAGCAATAAATATAAAACCAAAATTAA
66 AATAGCCCAAATTTACCCGGCCCAAATCAGAGATAAATAAGCAATAAATATAAAACCAAAATTAA
4632401 GTGTCCAAAATAGTCCTTTTACATTAGGCCCAAACTAAACACAACCCACTACCCAAAATCAAACC
131 GTGTCCAAAATAGTCCTTTTACATTAGGCCCAAACTAAACACAACCCACTACCCAAAATCAAACC
4632466 CGAATTACCCAATACATCCCAGCCCAATAACCAATGCCCTAAACTTAAACCCTAGCAGCCTCCAC
196 CGAATTACCCAATACATCCCAGCCCAATAACCAATGCCCTAAACTTAAACCCTAGCAGCCTCCAC
4632531 GCCGTAACCGCCCAGGGCCTTCGTCCCCACGTGCCGAGCCTC
261 GCCGTAACCGCCCAGGGCCTTCGTCCCCACGTGCCGAGCCTC
4632573 TG
1 TG
4632575 CCAGCATGCG
Statistics
Matches: 302, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
301 292 0.97
302 10 0.03
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (302 bp):
TGGCCAATGTTTTAGTCTTTGCCTCATTCCCGTTACACGACAAATGAGCAAAGAGGGGCAGCTGT
AATAGCCCAAATTTACCCGGCCCAAATCAGAGATAAATAAGCAATAAATATAAAACCAAAATTAA
GTGTCCAAAATAGTCCTTTTACATTAGGCCCAAACTAAACACAACCCACTACCCAAAATCAAACC
CGAATTACCCAATACATCCCAGCCCAATAACCAATGCCCTAAACTTAAACCCTAGCAGCCTCCAC
GCCGTAACCGCCCAGGGCCTTCGTCCCCACGTGCCGAGCCTC
Found at i:4636150 original size:22 final size:21
Alignment explanation
Indices: 4636104--4636150 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
4636094 ATGACATTCT
*
4636104 AAATTATACTTTTAAAAGAAT
1 AAATTATACTTTTAAAAGAAA
*
4636125 AAATTATTCTTATTAAATA-AAA
1 AAATTATACTT-TTAAA-AGAAA
4636147 AAAT
1 AAAT
4636151 GTCTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 11 0.50
23 1 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTATACTTTTAAAAGAAA
Found at i:4636655 original size:18 final size:17
Alignment explanation
Indices: 4636634--4636667 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4636624 AATAAAAAAA
4636634 TTATTATAGAAATTTAAT
1 TTATTA-AGAAATTTAAT
*
4636652 TTATTAATAAATTTAA
1 TTATTAAGAAATTTAA
4636668 AATAAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATTAAGAAATTTAAT
Found at i:4638658 original size:81 final size:82
Alignment explanation
Indices: 4638563--4638725 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
4638553 AATTTACATG
4638563 TTATAATATATATTTATAAAAAGCTATGATCAAGAAGTATGAACATAACTTATTTATATGTCCAT
1 TTATAATATATATTTATAAAAAGCTATGATCAAGAAGTATGAACATAACTTATTTATATGTCCAT
4638628 GCTATA-ATTATAAAAA
66 GCTATATATTATAAAAA
4638644 TTATAATATATATTTATAAAAAGCTATGATCAAGAAGTATGAACATAACTTATTTATATGTCCAT
1 TTATAATATATATTTATAAAAAGCTATGATCAAGAAGTATGAACATAACTTATTTATATGTCCAT
4638709 GCTATATATTATAAAAA
66 GCTATATATTATAAAAA
4638726 CAATATACTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.88
82 10 0.12
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (82 bp):
TTATAATATATATTTATAAAAAGCTATGATCAAGAAGTATGAACATAACTTATTTATATGTCCAT
GCTATATATTATAAAAA
Found at i:4639604 original size:49 final size:50
Alignment explanation
Indices: 4639512--4639609 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 50
4639502 ATTTATTTAT
* * * *
4639512 AGGTTGAAAAAACCTTATTCTAATCAATGTCAAATAGATGAAGTGTAGTC
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTC
4639562 AGGTTG-AAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
4639610 TCTATATGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (50 bp):
AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTC
Found at i:4653854 original size:3 final size:3
Alignment explanation
Indices: 4653846--4653871 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4653836 TTATGTAAAA
4653846 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4653872 AGAAAGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4655095 original size:18 final size:19
Alignment explanation
Indices: 4655060--4655096 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
4655050 GTTAAAAGGT
4655060 TTTTTTGATGCATTTTATA
1 TTTTTTGATGCATTTTATA
4655079 TTTTTT-ATG-ATTATTATA
1 TTTTTTGATGCATT-TTATA
4655097 AAATTCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 8 0.47
19 6 0.35
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTGATGCATTTTATA
Found at i:4655151 original size:20 final size:21
Alignment explanation
Indices: 4655105--4655160 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 21
4655095 TAAAATTCTA
4655105 CAATATTTTATAAATTTTTTTT
1 CAAT-TTTTATAAATTTTTTTT
4655127 CAATTTTTAT-AA-TTTTTTT
1 CAATTTTTATAAATTTTTTTT
4655146 CTAATTTTTAATAAA
1 C-AATTTTT-ATAAA
4655161 ACTTAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.26
20 9 0.29
21 8 0.26
22 6 0.19
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
CAATTTTTATAAATTTTTTTT
Found at i:4655197 original size:28 final size:29
Alignment explanation
Indices: 4655136--4655212 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
4655126 TCAATTTTTA
* * *
4655136 TAATTTTTTTCTAATTTTTAATAAAACTT
1 TAATATTTTTATATTTTTTAATAAAACTT
* *
4655165 AAATATTTTTATATTTTTTATTAAAA-TT
1 TAATATTTTTATATTTTTTAATAAAACTT
*
4655193 TAATAATTTATATGATTTTT
1 TAAT-ATTTTTAT-ATTTTT
4655213 ATTTTTTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.13
29 28 0.72
30 6 0.15
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (29 bp):
TAATATTTTTATATTTTTTAATAAAACTT
Found at i:4655968 original size:3 final size:3
Alignment explanation
Indices: 4655960--4655991 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4655950 TTGACCAAGT
4655960 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
4655992 TAATTTTGAA
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:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:4656684 original size:16 final size:16
Alignment explanation
Indices: 4656663--4656696 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4656653 TCATAACGGT
4656663 TACCCCTCCCAACAGC
1 TACCCCTCCCAACAGC
*
4656679 TACCCCTCCCAACGGC
1 TACCCCTCCCAACAGC
4656695 TA
1 TA
4656697 TTTAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.53, G:0.09, T:0.15
Consensus pattern (16 bp):
TACCCCTCCCAACAGC
Found at i:4658416 original size:17 final size:16
Alignment explanation
Indices: 4658396--4658444 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
4658386 AAAAAAAAAA
4658396 CTAAACCCTATAAAACC
1 CTAAA-CCTATAAAACC
*
4658413 CTAAA-CTATAAAACA
1 CTAAACCTATAAAACC
4658428 CTAAAACCTATAAAACC
1 CT-AAACCTATAAAACC
4658445 TTAATCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 14 0.50
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (16 bp):
CTAAACCTATAAAACC
Found at i:4659333 original size:26 final size:23
Alignment explanation
Indices: 4659291--4659350 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
4659281 TTTGGTTCTC
*
4659291 GATTTTTATATTGATTTTGGAATAT
1 GATTTTTAGATTGATTTT--AATAT
4659316 AGATTTTTAGACTT-ATTTTAATAT
1 -GATTTTTAGA-TTGATTTTAATAT
*
4659340 GACTTTTAGAT
1 GATTTTTAGAT
4659351 ATTATTTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 5 0.16
26 14 0.45
27 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (23 bp):
GATTTTTAGATTGATTTTAATAT
Found at i:4659355 original size:24 final size:24
Alignment explanation
Indices: 4659311--4659357 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4659301 TTGATTTTGG
* *
4659311 AATATAGATTTTTAGACTTATTTT
1 AATATAGACTTTTAGAATTATTTT
4659335 AATAT-GACTTTTAGATATTATTT
1 AATATAGACTTTTAGA-ATTATTT
4659358 GGTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
AATATAGACTTTTAGAATTATTTT
Found at i:4660504 original size:20 final size:22
Alignment explanation
Indices: 4660467--4660506 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
4660457 ATATAAACAC
*
4660467 ATATAATATAATTTTTATAAAT
1 ATATAATATAATTATTATAAAT
4660489 ATATAA-ATAA-TATTATAA
1 ATATAATATAATTATTATAA
4660507 TGTGTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATATAATTATTATAAAT
Found at i:4662235 original size:19 final size:18
Alignment explanation
Indices: 4662213--4662250 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
4662203 TATAATAATG
*
4662213 ATAACAATAATAAATAGTA
1 ATAAAAATAAT-AATAGTA
4662232 ATAAAAATAATAATAGTA
1 ATAAAAATAATAATAGTA
4662250 A
1 A
4662251 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAAATAATAATAGTA
Found at i:4664646 original size:44 final size:44
Alignment explanation
Indices: 4664574--4665011 Score: 217
Period size: 44 Copynumber: 9.5 Consensus size: 44
4664564 TATCTCCGTG
* * *
4664574 AAGTTGCAGTGGAGCAAGA-TGAACCTACAAATCCTATATCCCTG
1 AAGTTGCAGTGGATC-AGATTGAAGCTACAAATCCTATATCCCTA
* * *
4664618 AAGTTGCAGTGGATC-GTATTGAAGCTACAATTCCTATACCCCAA
1 AAGTTGCAGTGGATCAG-ATTGAAGCTACAAATCCTATATCCCTA
* * * * *
4664662 AAGTTGTAGTGGGTCAGAATGAAACTACAATGACAAATCCTATATCCTTA
1 AAGTTGCAGTGGATCAGATTG-AA--GC--T-ACAAATCCTATATCCCTA
* * * * *
4664712 AAGTTACAGTGGATC-GAATTAAAGCTACAAATCTTATACCCCTG
1 AAGTTGCAGTGGATCAG-ATTGAAGCTACAAATCCTATATCCCTA
* * * *
4664756 AAGTTGCAGTAGG-TCGGATTGAATCTACCATAGCAAGTCTTATCTCCCTA
1 AAGTTGCAGT-GGATCAGATTGAAGCTA-C--A--AA-TCCTATATCCCTA
* * * * * *
4664806 AACTTGCAGTCGAACAAGA-TGAAGCTACAAATCTTATA-CCATTG
1 AAGTTGCAGTGGATC-AGATTGAAGCTACAAATCCTATATCC-CTA
* * * *
4664850 AATTTGCAGTGGGTCAGATTGAAGTTACCATAA-CGAACTTTATCTCTCTA
1 AAGTTGCAGTGGATCAGATTGAAGCTA-CA-AATC---CTATATC-C-CTA
* * * * * *
4664900 AAGTTTCAGCGGAGCA-AGGTGAACCTACAAATCTTATATCCCTA
1 AAGTTGCAGTGGATCAGA-TTGAAGCTACAAATCCTATATCCCTA
* * *
4664944 AAGTTGTAGTGGATCAGATTGAAGCTACAAATCCTATACCCCTG
1 AAGTTGCAGTGGATCAGATTGAAGCTACAAATCCTATATCCCTA
* *
4664988 AAGTTGCAGTGGGTCGGATTGAAG
1 AAGTTGCAGTGGATCAGATTGAAG
4665012 TTACCATAGC
Statistics
Matches: 292, Mismatches: 70, Indels: 64
0.69 0.16 0.15
Matches are distributed among these distances:
42 1 0.00
43 6 0.02
44 165 0.57
45 15 0.05
46 7 0.02
47 4 0.01
48 5 0.02
49 13 0.04
50 74 0.25
51 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGTTGCAGTGGATCAGATTGAAGCTACAAATCCTATATCCCTA
Found at i:4664760 original size:94 final size:93
Alignment explanation
Indices: 4664599--4664973 Score: 308
Period size: 94 Copynumber: 4.0 Consensus size: 93
4664589 AAGATGAACC
* * * * *
4664599 TACAAATCCTATATCCCTGAAGTTGCAGTGGATCGTA-TTGAAGCTACAATTCCTATACCCCAAA
1 TACAAATCCTATATCCCTAAAGTTGCAGTGGATC-AAGTTGAAGCTACAAATCTTATACCCCTAA
* * *
4664663 AGTTGTAGTGGGTCAGAATGAAACTACAA
65 AGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * *
4664692 TGACAAATCCTATATCCTTAAAGTTACAGTGGATCGAA-TTAAAGCTACAAATCTTATACCCCTG
1 T-ACAAATCCTATATCCCTAAAGTTGCAGTGGATC-AAGTTGAAGCTACAAATCTTATACCCCTA
* * * *
4664756 AAGTTGCAGTAGGTCGGATTGAATCTACCA
64 AAGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * * * * * ** *
4664786 TAGCAAGTCTTATCTCCCTAAACTTGCAGTCGAACAAGATGAAGCTACAAATCTTATACCATTGA
1 TA-CAAATCCTATATCCCTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCTAA
* * *
4664851 ATTTGCAGTGGGTCAGATTGAAGTTACCA
65 AGTTGCAGTGGGTCAGATTGAAGCTACAA
* * * * * * * *
4664880 TAACGAA--CTTTATCTCTCTAAAGTTTCAGCGGAGCAAGGTGAACCTACAAATCTTATATCCCT
1 T-ACAAATCCTATATC-C-CTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCT
* *
4664943 AAAGTTGTAGTGGATCAGATTGAAGCTACAA
63 AAAGTTGCAGTGGGTCAGATTGAAGCTACAA
4664974 ATCCTATACC
Statistics
Matches: 223, Mismatches: 53, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
92 4 0.02
93 5 0.02
94 213 0.96
95 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (93 bp):
TACAAATCCTATATCCCTAAAGTTGCAGTGGATCAAGTTGAAGCTACAAATCTTATACCCCTAAA
GTTGCAGTGGGTCAGATTGAAGCTACAA
Found at i:4665029 original size:94 final size:94
Alignment explanation
Indices: 4664931--4665105 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 94
4664921 AACCTACAAA
* *
4664931 TCTTATATCCCTAAAGTTGTAGT-GGATC-AGATTGAAGCTACAAATCCTATACCCCTGAAGTTG
1 TCTTATATCCCTAAAGTTGTAGTAGG-GCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTA
* *
4664994 CAGTGGGTCGGATTGAAGTTACCATAGCGAG
64 AAGTGGATCGGATTGAAGTTACCATAGCGAG
* * * * *
4665025 TCTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTGCAAATCCTATATCTCTGTAGTTAAA
1 TCTTATATCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTAAA
4665090 GTGGATCGGATTGAAG
66 GTGGATCGGATTGAAG
4665106 AGACAATTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 65 0.93
95 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (94 bp):
TCTTATATCCCTAAAGTTGTAGTAGGGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTAAA
GTGGATCGGATTGAAGTTACCATAGCGAG
Found at i:4665041 original size:138 final size:138
Alignment explanation
Indices: 4664793--4665141 Score: 364
Period size: 138 Copynumber: 2.5 Consensus size: 138
4664783 CCATAGCAAG
* * * * * * * *
4664793 TCTTATCTCCCTAAACTTGCAGTCGAACAAGA-TGAAGCTACAAATCTTATACCATTGAATTTGC
1 TCTTATATCCCTAAAGTTGAAGTGGATC-AGATTGAAGCTACAAATCCTATACCACTGAAGTTGC
* * * *
4664857 AGTGGGTCAGATTGAAGTTACCATAACGAACTTTATCTCTCTAAAGTT-TCAG-CGGAGCAAGGT
65 AGTGGGTCGGATTGAAGTTACCATAACGAACTTTATCTCCCTAAAGTTGT-AGTAGG-GCAAGAT
4664920 GAACCTACAAA
128 GAACCTACAAA
* *
4664931 TCTTATATCCCTAAAGTTGTAGTGGATCAGATTGAAGCTACAAATCCTATACCCCTGAAGTTGCA
1 TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
* *
4664996 GTGGGTCGGATTGAAGTTACCATAGCG-AGTCTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGA
66 GTGGGTCGGATTGAAGTTACCATAACGAACT-TTATCTCCCTAAAGTTGTAGTAGGGCAAGATGA
* *
4665060 AGCTGCAAA
130 ACCTACAAA
* * ** * * ** * * *
4665069 TCCTATATCTCTGTAGTTAAAGTGGATCGGATTGAAGAGACAATTCCTATACCTCTGAAGTTACA
1 TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
*
4665134 GTAGGTCG
66 GTGGGTCG
4665142 TAATGAAATT
Statistics
Matches: 177, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
137 5 0.03
138 169 0.95
139 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (138 bp):
TCTTATATCCCTAAAGTTGAAGTGGATCAGATTGAAGCTACAAATCCTATACCACTGAAGTTGCA
GTGGGTCGGATTGAAGTTACCATAACGAACTTTATCTCCCTAAAGTTGTAGTAGGGCAAGATGAA
CCTACAAA
Found at i:4665189 original size:232 final size:228
Alignment explanation
Indices: 4664511--4665191 Score: 583
Period size: 232 Copynumber: 2.9 Consensus size: 228
4664501 ACATCTTAAC
* * * * * * * * *
4664511 TCCTATACCCCTAAAATAGCAGTGGGTCGGATTGAAGCTA-AAGTGGCGAATCTTATCTCCGTGA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCA-TAGCGAGTCTTATCTCCCTAA
* * *
4664575 AGTTGCAGTGGAGCAAGATGAACCTACAAATCCTATATCCCTGAAGTTGCAGTGGATCGTATTGA
65 AGTTGCAGTGG-GCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGA
* * * ** * * *
4664640 AGCTACAATTCCTATACCCCAAAAGTTGTAGTGGGTCAGAATGAAACTACAATGACAAATCCTAT
129 AGATACAATTCCTATACCTCTAAAGTTACAGTAGGTC-GAATGAAA-TATAATG-CAAATCTTAT
*
4664705 AT-CCTTAAAGTTACAGTGGATCGAATTAAAGCTACAAA
191 ATCCCTT-AAGTTGCAGTGGATCGAATTAAAGCTACAAA
* * *
4664743 TCTTATACCCCTGAAGTTGCAGTAGGTCGGATTGAA-TCTACCATAGCAAGTCTTATCTCCCTAA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGT-TACCATAGCGAGTCTTATCTCCCTAA
* ** * * * * *
4664807 ACTTGCAGTCGAACAAGATGAAGCTACAAATCTTATACCAT-TGAATTTGCAGTGGGTCAGATTG
65 AGTTGCAGT-GGGCAAGATGAAGCTACAAATCCTATATC-TCTGAAGTTGCAGTGGATCGGATTG
* * * * * * * **
4664871 AAGTTACCATAACGAACTTTATCTCTCTAAAGTTTCAG-CGG-AGCAAGGTG-AACCT-A--CAA
128 AAGATACAAT-TC---CTATA-C-CTCTAAAGTTACAGTAGGTCG-AA--TGAAATATAATGCAA
* * *
4664930 ATCTTATATCCCTAAAGTTGTAGTGGATC-AGATTGAAGCTACAAA
184 ATCTTATATCCCTTAAGTTGCAGTGGATCGA-ATTAAAGCTACAAA
4664975 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
1 TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
* * * **
4665040 GTTGTAGTAGGGCAAGATGAAGCTGCAAATCCTATATCTCTGTAGTTAAAGTGGATCGGATTGAA
66 GTTGCAGT-GGGCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGAA
* * * * *
4665105 GAGACAATTCCTATACCTCTGAAGTTACAGTAGGTCGTAATGAAATTATAATGGCGAATCTTTTT
130 GATACAATTCCTATACCTCTAAAGTTACAGTAGGTCG-AATGAAA-TATAAT-GCAAATCTTATA
*
4665170 TCCCTTAATTTGCAGTGGATCG
192 TCCCTTAAGTTGCAGTGGATCG
4665192 GAATGAAATT
Statistics
Matches: 347, Mismatches: 76, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
226 14 0.04
227 5 0.01
228 8 0.02
229 1 0.00
231 3 0.01
232 284 0.82
233 7 0.02
235 2 0.01
236 6 0.02
237 5 0.01
238 12 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (228 bp):
TCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGTTACCATAGCGAGTCTTATCTCCCTAAA
GTTGCAGTGGGCAAGATGAAGCTACAAATCCTATATCTCTGAAGTTGCAGTGGATCGGATTGAAG
ATACAATTCCTATACCTCTAAAGTTACAGTAGGTCGAATGAAATATAATGCAAATCTTATATCCC
TTAAGTTGCAGTGGATCGAATTAAAGCTACAAA
Found at i:4665222 original size:50 final size:50
Alignment explanation
Indices: 4665126--4665238 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
4665116 TATACCTCTG
* * * *
4665126 AAGTTACAGTAGG-TCGTAATGAAATTATAATGGCGAATCTTTTTTCCCTT
1 AAGTTGCAGT-GGATCGGAATGAAATTACAATGGCGAATCTTTTTTCCCTA
*
4665176 AATTTGCAGTGGATCGGAATGAAATTACAATGGCGAAT-TTTATTTCCCTA
1 AAGTTGCAGTGGATCGGAATGAAATTACAATGGCGAATCTTT-TTTCCCTA
4665226 AAGTTGCAGTGGA
1 AAGTTGCAGTGGA
4665239 GCAAGATGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 5 0.09
50 50 0.91
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (50 bp):
AAGTTGCAGTGGATCGGAATGAAATTACAATGGCGAATCTTTTTTCCCTA
Found at i:4665255 original size:50 final size:50
Alignment explanation
Indices: 4665143--4665255 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
4665133 AGTAGGTCGT
* * * * * *
4665143 AATGAAATTATAATGGCGAATCTTTTTTCCCTTAATTTGCAGTGGATCGG
1 AATGAAACTACAATGGCGAATCTTTTTTCCCTAAAGTTGCAGTGGAGCAG
*
4665193 AATGAAATTACAATGGCGAAT-TTTATTTCCCTAAAGTTGCAGTGGAGCA-
1 AATGAAACTACAATGGCGAATCTTT-TTTCCCTAAAGTTGCAGTGGAGCAG
*
4665242 AGATGAAGCTACAA
1 A-ATGAAACTACAA
4665256 ATATTATATC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (50 bp):
AATGAAACTACAATGGCGAATCTTTTTTCCCTAAAGTTGCAGTGGAGCAG
Found at i:4666521 original size:21 final size:21
Alignment explanation
Indices: 4666492--4666531 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4666482 TTTTATTGTA
*
4666492 GTTTCAATTTAGTCTCCTGTTC
1 GTTTCAATTGAGTC-CCTGTTC
4666514 GTTT-AATTGAGTCCCTGT
1 GTTTCAATTGAGTCCCTGT
4666532 ACTTGCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (21 bp):
GTTTCAATTGAGTCCCTGTTC
Found at i:4666710 original size:16 final size:17
Alignment explanation
Indices: 4666691--4666731 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4666681 TATGTAATTA
4666691 TTTTATTATCAT-ACAT
1 TTTTATTATCATGACAT
*
4666707 TTTTA-TATCATGCCAT
1 TTTTATTATCATGACAT
*
4666723 TATTATTAT
1 TTTTATTAT
4666732 TATTATCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTATTATCATGACAT
Found at i:4674990 original size:16 final size:16
Alignment explanation
Indices: 4674966--4675003 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4674956 AGTGATTTTG
4674966 ATAAACTCAAAAACTC
1 ATAAACTCAAAAACTC
*
4674982 ATAACCTCAAAAACTC
1 ATAAACTCAAAAACTC
4674998 AGTAAA
1 A-TAAA
4675004 TTTGTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (16 bp):
ATAAACTCAAAAACTC
Found at i:4680127 original size:49 final size:49
Alignment explanation
Indices: 4680018--4680127 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
4680008 GAAACCATTG
* *
4680018 TTGTCGGACAACCCAGGGTGGTAGAATGTACATATGCTAGTAGTCATCA
1 TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
** * * * * *
4680067 TTACCGAGCAACCCAGGGTGATAGTATGTACATGTTCTATTAGTCATCA
1 TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
4680116 TTGTCGGGCAAC
1 TTGTCGGGCAAC
4680128 TTGGGATGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (49 bp):
TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
Found at i:4685568 original size:136 final size:136
Alignment explanation
Indices: 4685324--4685579 Score: 476
Period size: 136 Copynumber: 1.9 Consensus size: 136
4685314 TGAGTGATAA
*
4685324 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATGTTATTCAAATGCAAATAATCAATTCA
1 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
* *
4685389 AATATATTTTTCAACTGATTAGTGCACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
66 AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
4685454 TATTTC
131 TATTTC
4685460 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
1 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
*
4685525 AATATATTTTTCAACTAATTAGTATACCAAATTTTAACATAGACTTAGTAATCAA
66 AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAA
4685580 CACCTACCTA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 116 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (136 bp):
AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
TATTTC
Found at i:4686279 original size:86 final size:86
Alignment explanation
Indices: 4686134--4686294 Score: 232
Period size: 86 Copynumber: 1.9 Consensus size: 86
4686124 AGCACTATAA
* * * *
4686134 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAA
1 TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
4686199 CAATTGTACTGGCACGCGTAG
66 CAATTATACTGGCACGCGTAG
* * * *
4686220 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAA
1 TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
4686285 TAATTATACT
66 CAATTATACT
4686295 AACACACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (86 bp):
TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
CAATTATACTGGCACGCGTAG
Found at i:4686307 original size:86 final size:86
Alignment explanation
Indices: 4686134--4686315 Score: 229
Period size: 86 Copynumber: 2.1 Consensus size: 86
4686124 AGCACTATAA
* * * * *
4686134 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAA
1 TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
* ** * *
4686199 CAATTGTACTGGCACGCGTAG
66 CAATTATACTAACACACATAG
* * *
4686220 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAA
1 TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
4686285 TAATTATACTAACACACATAG
66 CAATTATACTAACACACATAG
*
4686306 TGCATTATCG
1 TGCATCATCG
4686316 AAAAAATTGA
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (86 bp):
TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
CAATTATACTAACACACATAG
Found at i:4686336 original size:86 final size:86
Alignment explanation
Indices: 4686157--4686380 Score: 223
Period size: 86 Copynumber: 2.6 Consensus size: 86
4686147 AAATCGAAGG
* * * * ** * *
4686157 AAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAACAATTGTACTGGCACGCGTAGTG
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
* *
4686222 CATCATCGGATAAACCAAAGA
66 CATCATCGAAAAAACCAAAGA
* *
4686243 AAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
* *** **
4686308 CATTATCGAAAAAATTGAATT
66 CATCATCGAAAAAACCAAAGA
* * ** * * *
4686329 AATTATACTAGCACCCACAGTGCATCATCGAACAAGTCGAAGTAATTATACT
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACT
4686381 GGCACACAGA
Statistics
Matches: 111, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (86 bp):
AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
CATCATCGAAAAAACCAAAGA
Found at i:4686413 original size:43 final size:43
Alignment explanation
Indices: 4686134--4686415 Score: 186
Period size: 43 Copynumber: 6.6 Consensus size: 43
4686124 AGCACTATAA
* * * * * * *
4686134 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * ** * * **
4686177 TTCATCATCGGACAAGCCGAAACAATTGTACTGGCACGCGTAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * * * * * *
4686220 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * ** *
4686263 TGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * * ** * * *
4686306 TGCATTATCGAAAAAATTGAATTAATTATACTAGCACCCACAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* ** * *
4686349 TGCATCATCGAACAAGTCGAAGTAATTATACTGGCACACAGAC
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* *
4686392 TACATCATCGGATAAACCGAAGTA
1 TGCATCATCGGACAAACCGAAGTA
4686416 TAACATGTAC
Statistics
Matches: 179, Mismatches: 60, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
43 179 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (43 bp):
TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
Found at i:4695799 original size:44 final size:43
Alignment explanation
Indices: 4695714--4695800 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
4695704 ATTTAAACTA
* * *
4695714 GTAAACTTCTAGTTTACTATGCATGTGATTCAGCATTACTAAT
1 GTAAACTTCTAGTTTACCATGCATGTGATTAACCATTACTAAT
* *
4695757 GTAAACTTCTGGTTTACCATCGTATGTGATTTAACCA-TACTAAT
1 GTAAACTTCTAGTTTACCAT-GCATGTGA-TTAACCATTACTAAT
4695801 ATATGATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 18 0.49
44 14 0.38
45 5 0.14
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (43 bp):
GTAAACTTCTAGTTTACCATGCATGTGATTAACCATTACTAAT
Found at i:4696679 original size:13 final size:13
Alignment explanation
Indices: 4696661--4696693 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4696651 CAAAATAAAT
4696661 ATTAATTA-ATTAA
1 ATTAATTAGA-TAA
4696674 ATTAATTAGATAA
1 ATTAATTAGATAA
4696687 ATTAATT
1 ATTAATT
4696694 TTTCAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTAATTAGATAA
Found at i:4696710 original size:16 final size:18
Alignment explanation
Indices: 4696684--4696716 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4696674 ATTAATTAGA
4696684 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
4696701 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
4696717 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:4699602 original size:54 final size:54
Alignment explanation
Indices: 4699517--4699924 Score: 450
Period size: 54 Copynumber: 7.6 Consensus size: 54
4699507 TGGGGTCAAT
*
4699517 AAATGACTGAATTA-CCCCATAGGGTAAAATGAACGAATTACCCTCACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * *
4699570 AAATGACTAAATTACCCCCACAGGGTAAAATG-ACAGTATTACCCCTACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAAC-GAATTACCCCCACAGGGTA
* * * * **
4699624 AAATGACCGTATTACCCCCATAGGGTAAAAT-AATCGTATTGCCTTCACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAA-CGAATTACCCCCACAGGGTA
* * * ** * *
4699678 AAATGACCGTATTACTCCCATAGCCTAAAATGATCGAATTACCCCCATAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * * * *
4699732 AAATGATTGAATTACCCTCACAGGGTAAAATGATCAAATTACCCCCACAAGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * *
4699786 AAATGACCGAATTACCCCTATAGGGTAAAATGACCGAATTACCCCCACAGGATA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * * *
4699840 AAATGACTGAATTA-ACCTATAGGGTAAAATGACCGAATTACCCCTATAGGGT-
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
4699892 AAATGA-TCGAATTACCCCCATAGGGTAAAATGA
1 AAATGACT-GAATTACCCCCATAGGGTAAAATGA
4699925 CTATTTTACC
Statistics
Matches: 299, Mismatches: 49, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
51 1 0.00
52 12 0.04
53 65 0.22
54 219 0.73
55 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (54 bp):
AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
Found at i:4699638 original size:81 final size:80
Alignment explanation
Indices: 4699517--4699925 Score: 445
Period size: 81 Copynumber: 5.1 Consensus size: 80
4699507 TGGGGTCAAT
* * * *
4699517 AAATGACTGAATTACCCC-ATAGGGTAAAATGAACGAATTACCCTCACAGGGTAAAATGACTAAA
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCC-CATAGGGTAAAATGACTGAA
4699581 TTACCCCCACAGGGTA
65 TTACCCCCACAGGGTA
* * * * *
4699597 AAATGACAGTATTACCCCTACAGGGTAAAATGACCGTATTACCCCCATAGGGTAAAAT-AATCGT
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTA-CCCCATAGGGTAAAATGACT-GA
* **
4699661 ATTGCCTTCACAGGGTA
64 ATTACCCCCACAGGGTA
* * ** * *
4699678 AAATGACCGTATTACTCCC-ATAGCCTAAAATGATCGAATTACCCCCATAGGGTAAAATGATTGA
1 AAATGACAGAATTAC-CCCTATAGGGTAAAATGACCGAATTA-CCCCATAGGGTAAAATGACTGA
*
4699742 ATTACCCTCACAGGGTA
64 ATTACCCCCACAGGGTA
* * * *
4699759 AAATGATCA-AATTACCCCCACAAGGTAAAATGACCGAATTACCCCTATAGGGTAAAATGACCGA
1 AAATGA-CAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCC-ATAGGGTAAAATGACTGA
*
4699823 ATTACCCCCACAGGATA
64 ATTACCCCCACAGGGTA
* *
4699840 AAATGACTGAATTA-ACCTATAGGGTAAAATGACCGAATTACCCCTATAGGGT-AAATGA-TCGA
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCC-ATAGGGTAAAATGACT-GA
*
4699902 ATTACCCCCATAGGGTA
64 ATTACCCCCACAGGGTA
4699919 AAATGAC
1 AAATGAC
4699926 TATTTTACCC
Statistics
Matches: 278, Mismatches: 41, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
79 30 0.11
80 60 0.22
81 179 0.64
82 9 0.03
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (80 bp):
AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCCATAGGGTAAAATGACTGAAT
TACCCCCACAGGGTA
Found at i:4699936 original size:27 final size:26
Alignment explanation
Indices: 4699517--4699925 Score: 392
Period size: 27 Copynumber: 15.3 Consensus size: 26
4699507 TGGGGTCAAT
4699517 AAATGACTGAATTA-CCCCATAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
* *
4699543 AAATGAACGAATTACCCTCACAGGGTA
1 AAATG-ACGAATTACCCCCATAGGGTA
* *
4699570 AAATGACTAAATTACCCCCACAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
* * *
4699597 AAATGACAGTATTACCCCTACAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
*
4699624 AAATGACCGTATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * * ** *
4699651 AAATAATCGTATTGCCTTCACAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * **
4699678 AAATGACCGTATTACTCCCATAGCCTA
1 AAATGA-CGAATTACCCCCATAGGGTA
4699705 AAATGATCGAATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * *
4699732 AAATGATTGAATTACCCTCACAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * *
4699759 AAATGATCAAATTACCCCCACAAGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
*
4699786 AAATGACCGAATTACCCCTATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* *
4699813 AAATGACCGAATTACCCCCACAGGATA
1 AAATGA-CGAATTACCCCCATAGGGTA
* *
4699840 AAATGACTGAATTA-ACCTATAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
*
4699866 AAATGACCGAATTACCCCTATAGGGT-
1 AAATGA-CGAATTACCCCCATAGGGTA
4699892 AAATGATCGAATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
4699919 AAATGAC
1 AAATGAC
4699926 TATTTTACCC
Statistics
Matches: 323, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
26 59 0.18
27 263 0.81
28 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATGACGAATTACCCCCATAGGGTA
Found at i:4700114 original size:26 final size:26
Alignment explanation
Indices: 4700084--4700138 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
4700074 TGGAGGAAGT
* *
4700084 ATACTGTTACTGACAGCTTTGTTGCG
1 ATACTGTTACTGACAACTTTGCTGCG
*
4700110 ATACTGTTACTGGCAACTTTGCTGCG
1 ATACTGTTACTGACAACTTTGCTGCG
4700136 ATA
1 ATA
4700139 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGACAACTTTGCTGCG
Found at i:4700289 original size:28 final size:27
Alignment explanation
Indices: 4700246--4700306 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 27
4700236 ACTGTATCGA
*
4700246 TACTGTATTGGACTAAGGCCCACATTG
1 TACTGTATTGGACTAAGGCCCACACTG
*
4700273 TTACTGTATTGGGCTAAGGCCCACACTG
1 -TACTGTATTGGACTAAGGCCCACACTG
4700301 TACTGT
1 TACTGT
4700307 TACTGAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
TACTGTATTGGACTAAGGCCCACACTG
Found at i:4700320 original size:33 final size:34
Alignment explanation
Indices: 4700271--4700339 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
4700261 AGGCCCACAT
* *
4700271 TGTTACTGTATTGGGCTAAGGCCCACACTG-TAC
1 TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
* *
4700304 TGTTACTGAATAGGGCTCAGGCCCAGACTGTTAC
1 TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
4700338 TG
1 TG
4700340 CATGTTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (34 bp):
TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
Found at i:4711682 original size:20 final size:20
Alignment explanation
Indices: 4711659--4711703 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
4711649 CCAGCATGTC
4711659 ATAAAATATAAGAAAAAGGA
1 ATAAAATATAAGAAAAAGGA
4711679 ATAAAATATAAGAAAAAGGA
1 ATAAAATATAAGAAAAAGGA
4711699 ATAAA
1 ATAAA
4711704 CTTTAGGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (20 bp):
ATAAAATATAAGAAAAAGGA
Found at i:4713367 original size:31 final size:31
Alignment explanation
Indices: 4713326--4713387 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
4713316 AATGTGTTAG
4713326 TGAATGACATATTTGTAAATTAACATTCGAA
1 TGAATGACATATTTGTAAATTAACATTCGAA
*
4713357 TGAATTACATATTTGTAAATTAACATTCGAA
1 TGAATGACATATTTGTAAATTAACATTCGAA
4713388 GTTCAGTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (31 bp):
TGAATGACATATTTGTAAATTAACATTCGAA
Found at i:4718362 original size:22 final size:22
Alignment explanation
Indices: 4718334--4718509 Score: 160
Period size: 22 Copynumber: 7.6 Consensus size: 22
4718324 AGCAATATTG
4718334 ATGCTGTCCATTTTAATGTATA
1 ATGCTGTCCATTTTAATGTATA
*
4718356 ATGCTGTCCAATCTTAA-GTATA
1 ATGCTGTCC-ATTTTAATGTATA
4718378 TTGATGCTGTCCATTTTAATGTATA
1 ---ATGCTGTCCATTTTAATGTATA
4718403 ATGCTGTCCAATTTTAA-GTATA
1 ATGCTGTCC-ATTTTAATGTATA
4718425 TTGATGCTGTCCATTTTAATGTATA
1 ---ATGCTGTCCATTTTAATGTATA
*
4718450 ATGCTGTCCAATTTTGA-GTATA
1 ATGCTGTCC-ATTTTAATGTATA
* * * **
4718472 TTTAAGCTGTCTAATTCGATGTATA
1 ---ATGCTGTCCATTTTAATGTATA
4718497 ATGCTGTCCATTT
1 ATGCTGTCCATTT
4718510 AGAGCATATT
Statistics
Matches: 129, Mismatches: 10, Indels: 30
0.76 0.06 0.18
Matches are distributed among these distances:
22 52 0.40
23 19 0.15
24 18 0.14
25 40 0.31
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (22 bp):
ATGCTGTCCATTTTAATGTATA
Found at i:4718379 original size:47 final size:46
Alignment explanation
Indices: 4718302--4718554 Score: 294
Period size: 47 Copynumber: 5.4 Consensus size: 46
4718292 TTATAATTTG
* * *
4718302 ATGTATAATGCTATCCAATTAAAGCAATATTGATGCTGTCCATTTTA
1 ATGTATAATGCTGTCCAATTTAAG-TATATTGATGCTGTCCATTTTA
4718349 ATGTATAATGCTGTCCAATCTTAAGTATATTGATGCTGTCCATTTTA
1 ATGTATAATGCTGTCCAAT-TTAAGTATATTGATGCTGTCCATTTTA
4718396 ATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTA
1 ATGTATAATGCTGTCCAA-TTTAAGTATATTGATGCTGTCCATTTTA
* * * * * **
4718443 ATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTCG
1 ATGTATAATGCTGTCCAA-TTTAAGTATATTGATGCTGTCCATTTTA
* * *
4718490 ATGTATAATGCTGTCC-ATTTAGAGCATATT-ATTGCTGTCCAATTTC
1 ATGTATAATGCTGTCCAATTTA-AGTATATTGA-TGCTGTCCATTTTA
* *
4718536 ATGAATAATTGTTGTCCAA
1 ATGTATAA-TGCTGTCCAA
4718555 AATAGGGTTG
Statistics
Matches: 182, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
45 4 0.02
46 25 0.14
47 147 0.81
48 6 0.03
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (46 bp):
ATGTATAATGCTGTCCAATTTAAGTATATTGATGCTGTCCATTTTA
Found at i:4724416 original size:22 final size:22
Alignment explanation
Indices: 4724338--4724417 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
4724328 GTGTTATAAA
*
4724338 TTTAATGTATAATGCTGTCAAAT
1 TTTAA-GTATAATGCTGTCCAAT
4724361 TTTAAGTATATTGATGCTGTCC-AT
1 TTTAAGTATA---ATGCTGTCCAAT
4724385 TTTAATGTATAATGCTGTCCAAT
1 TTTAA-GTATAATGCTGTCCAAT
*
4724408 TTTGAGTATA
1 TTTAAGTATA
4724418 TTATATATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
22 19 0.38
23 11 0.22
24 7 0.14
25 13 0.26
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (22 bp):
TTTAAGTATAATGCTGTCCAAT
Found at i:4724427 original size:31 final size:31
Alignment explanation
Indices: 4724392--4724450 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
4724382 CATTTTAATG
*
4724392 TATAATGCTGTCCAATTTTGAGTATATTATA
1 TATAATGCTGTCCAATTTTAAGTATATTATA
4724423 TATAATGCTGTCCAATTTTAAGTATATT
1 TATAATGCTGTCCAATTTTAAGTATATT
4724451 GATGTTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (31 bp):
TATAATGCTGTCCAATTTTAAGTATATTATA
Found at i:4724474 original size:78 final size:78
Alignment explanation
Indices: 4724345--4724497 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
4724335 AAATTTAATG
4724345 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
1 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
4724410 TGAGTATATTATA
66 TGAGTATATTATA
* * *
4724423 TATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCTATTTTAATGTATAATGCTGTCCAATTT
1 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
4724488 TGAGTATATT
66 TGAGTATATT
4724498 TAAGCTGTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (78 bp):
TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
TGAGTATATTATA
Found at i:4724494 original size:22 final size:22
Alignment explanation
Indices: 4724423--4724558 Score: 71
Period size: 25 Copynumber: 5.8 Consensus size: 22
4724413 GTATATTATA
*
4724423 TATAATGCTGTCCAATTTTAAG
1 TATAATGCTGTCCAATTTTGAG
* * *
4724445 TATATTGATGTTGT-CTATTTTAATG
1 TATA---ATGCTGTCCAATTTTGA-G
4724470 TATAATGCTGTCCAATTTTGAG
1 TATAATGCTGTCCAATTTTGAG
* * *
4724492 TATATTTAAGCTGTCTAA-TTCGATG
1 TATA---ATGCTGTCCAATTTTGA-G
*
4724517 TATAATGCTGTCC-ATTTAGAG
1 TATAATGCTGTCCAATTTTGAG
*
4724538 CATATTATTGCTGTCCAATTT
1 --TA-TAATGCTGTCCAATTT
4724559 GATGAATAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
21 2 0.02
22 26 0.30
23 9 0.10
24 22 0.25
25 29 0.33
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (22 bp):
TATAATGCTGTCCAATTTTGAG
Found at i:4724494 original size:47 final size:47
Alignment explanation
Indices: 4724423--4724543 Score: 154
Period size: 47 Copynumber: 2.6 Consensus size: 47
4724413 GTATATTATA
* * * * *
4724423 TATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCTATTTTAATG
1 TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
* *
4724470 TATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTCGATG
1 TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
* *
4724517 TATAATGCTGTCC-ATTTAGAGCATATT
1 TATAATGCTGTCCAATTTTGAGTATATT
4724544 ATTGCTGTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 12 0.18
47 53 0.82
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (47 bp):
TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
Found at i:4724568 original size:46 final size:46
Alignment explanation
Indices: 4724471--4724577 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 46
4724461 ATTTTAATGT
* * * *
4724471 ATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTCGATGT
1 ATAATGCTGTCC-ATTTAGAGCATATTTAAGCTGTCCAATTCGATGA
* *
4724518 ATAATGCTGTCCATTTAGAGCATA-TTATTGCTGTCCAATTTGATGA
1 ATAATGCTGTCCATTTAGAGCATATTTA-AGCTGTCCAATTCGATGA
*
4724564 ATAATTACTGTCCA
1 ATAA-TGCTGTCCA
4724578 AAATAGGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 3 0.06
46 28 0.55
47 20 0.39
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (46 bp):
ATAATGCTGTCCATTTAGAGCATATTTAAGCTGTCCAATTCGATGA
Found at i:4728044 original size:3 final size:3
Alignment explanation
Indices: 4728036--4728066 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4728026 ATGGCAAATC
*
4728036 ACA ACA ACA ACA ACA ACA ACA ACA CCA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
4728067 GGTGAGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:4736406 original size:2 final size:2
Alignment explanation
Indices: 4736399--4736445 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
4736389 AAATCCTACC
*
4736399 AT AT AT AT AT AT AT AT A- AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4736440 AT AT AT
1 AT AT AT
4736446 CAAACTTACC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4737374 original size:44 final size:44
Alignment explanation
Indices: 4737199--4737363 Score: 126
Period size: 43 Copynumber: 3.8 Consensus size: 44
4737189 AATGCAAAAC
* * *
4737199 GTCCCAGACGTGGTCTTACATG-AAATCA-AATATCAATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAATCACAA-ATCAATGCCAAT
* * ** * * **
4737242 GTCCCCA-ACAGGGTCTTACACG-AACTCGTATAT-GATGCGGAT
1 GT-CCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* * *
4737284 GTCCTAGACATGGTCTTACACGTAAATTACAAATCGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* *
4737328 GTCCCAGACGTGGTCTTACACGT-AATCACATATCAA
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAA
4737364 AATCCTATGT
Statistics
Matches: 93, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 3 0.03
42 21 0.23
43 36 0.39
44 33 0.35
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
Found at i:4746546 original size:2 final size:2
Alignment explanation
Indices: 4746539--4746568 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4746529 NNNNNNNNNN
*
4746539 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4746569 CAAACTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4747497 original size:44 final size:44
Alignment explanation
Indices: 4747322--4747486 Score: 126
Period size: 43 Copynumber: 3.8 Consensus size: 44
4747312 AATGCAAAAC
* * *
4747322 GTCCCAGACGTGGTCTTACATG-AAATCA-AATATCAATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAATCACAA-ATCAATGCCAAT
* * ** * * **
4747365 GTCCCCA-ACAGGGTCTTACACG-AACTCGTATAT-GATGCGGAT
1 GT-CCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* * *
4747407 GTCCTAGACATGGTCTTACACGTAAATTACAAATCGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* *
4747451 GTCCCAGACGTGGTCTTACACGT-AATCACATATCAA
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAA
4747487 AATCCTATGT
Statistics
Matches: 93, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 3 0.03
42 21 0.23
43 36 0.39
44 33 0.35
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
Found at i:4749540 original size:21 final size:21
Alignment explanation
Indices: 4749499--4749550 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
4749489 TATAGATACA
4749499 AATTTTATTTTTAGTCATATT
1 AATTTTATTTTTAGTCATATT
*
4749520 -ATTTTATTTTTTG-CACTTATT
1 AATTTTATTTTTAGTCA--TATT
4749541 AATTTTATTT
1 AATTTTATTT
4749551 CCACTACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 4 0.15
22 9 0.33
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (21 bp):
AATTTTATTTTTAGTCATATT
Found at i:4759060 original size:14 final size:14
Alignment explanation
Indices: 4759017--4759062 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
4759007 CCCATTTACC
4759017 CCTCCTCTCCCTTT
1 CCTCCTCTCCCTTT
*
4759031 CTTCTCC-CTCCATTT
1 C--CTCCTCTCCCTTT
4759046 CCTCCTCTCCCTTT
1 CCTCCTCTCCCTTT
4759060 CCT
1 CCT
4759063 TGTTGGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 8 0.30
16 4 0.15
ACGTcount: A:0.02, C:0.54, G:0.00, T:0.43
Consensus pattern (14 bp):
CCTCCTCTCCCTTT
Found at i:4766369 original size:23 final size:23
Alignment explanation
Indices: 4766328--4766420 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
4766318 ACCTGATTAG
** *
4766328 TATACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
4766351 AATATGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
4766374 TATACAACACATAAAGTACCTGA
1 TATACGACACATAAAGTGCCTGA
4766397 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
4766420 T
1 T
4766421 CAGCAAGGCA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:4767066 original size:19 final size:19
Alignment explanation
Indices: 4767042--4767079 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4767032 TTTTAGTCCC
4767042 TAAAACATAAAACTTATAG
1 TAAAACATAAAACTTATAG
4767061 TAAAACATAAAACTTATAG
1 TAAAACATAAAACTTATAG
4767080 CTTACTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAAACATAAAACTTATAG
Found at i:4767402 original size:27 final size:25
Alignment explanation
Indices: 4767355--4767406 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
4767345 GTTCGAATGG
4767355 CTTCTTGTTCTTTTTGTTTCTTTTA
1 CTTCTTGTTCTTTTTGTTTCTTTTA
4767380 CTTCTT-TTCTTTCTTTAGTTTCTTTTA
1 CTTCTTGTTC-TT-TTT-GTTTCTTTTA
4767407 TTTACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.12
25 8 0.33
26 3 0.12
27 10 0.42
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (25 bp):
CTTCTTGTTCTTTTTGTTTCTTTTA
Found at i:4767425 original size:14 final size:14
Alignment explanation
Indices: 4767405--4767431 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4767395 TAGTTTCTTT
4767405 TATTTACTTTATTC
1 TATTTACTTTATTC
4767419 TATTTACTTTATT
1 TATTTACTTTATT
4767432 GTTTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTACTTTATTC
Found at i:4771477 original size:16 final size:16
Alignment explanation
Indices: 4771442--4771495 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
4771432 TCCATCCTTG
4771442 CCCTCCTTTCTTCCTTCC
1 CCCT-CTTT-TTCCTTCC
*
4771460 CCCTCTTTTTCATTCC
1 CCCTCTTTTTCCTTCC
4771476 CCCTCTTTTTCCTTCC
1 CCCTCTTTTTCCTTCC
4771492 CCCT
1 CCCT
4771496 TACCGAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 26 0.76
17 4 0.12
18 4 0.12
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (16 bp):
CCCTCTTTTTCCTTCC
Found at i:4773345 original size:6 final size:6
Alignment explanation
Indices: 4773334--4773379 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
4773324 TTTGTCTTTT
*
4773334 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAT TTTTATG TTT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTA-G TTT
4773380 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 34 0.92
7 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (6 bp):
TTTTAG
Found at i:4773380 original size:6 final size:5
Alignment explanation
Indices: 4773315--4773389 Score: 62
Period size: 6 Copynumber: 13.6 Consensus size: 5
4773305 ATGAAGATCG
*
4773315 TTTAT TTTAT TTGTCT TTT-T TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
1 TTTAT TTTAT TT-TAT TTTAT TTTA-T TTTA-T TTTA-T TTTA-T TTTA-T
4773365 TTTATT TTTAT GTTTAT TTTAT TTT
1 TTTA-T TTTAT -TTTAT TTTAT TTT
4773390 CTTAGACTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.06
5 17 0.27
6 43 0.67
ACGTcount: A:0.15, C:0.01, G:0.09, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:4773380 original size:18 final size:18
Alignment explanation
Indices: 4773333--4773389 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
4773323 ATTTGTCTTT
4773333 TTTTTAGTTTTAGTTTTA
1 TTTTTAGTTTTAGTTTTA
*
4773351 GTTTTAGTTTTAGTTTTA
1 TTTTTAGTTTTAGTTTTA
4773369 TTTTTA-TGTTTA-TTTTA
1 TTTTTAGT-TTTAGTTTTA
4773386 TTTT
1 TTTT
4773390 CTTAGACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 10 0.28
18 26 0.72
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTTAGTTTTAGTTTTA
Found at i:4774702 original size:24 final size:24
Alignment explanation
Indices: 4774674--4774721 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4774664 GTTTGAGCAG
4774674 TTTCATCATCAAGCTGAGCGTATA
1 TTTCATCATCAAGCTGAGCGTATA
4774698 TTTCATCATCAAGCTGAGCGTATA
1 TTTCATCATCAAGCTGAGCGTATA
4774722 CTTAGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTCATCATCAAGCTGAGCGTATA
Found at i:4776386 original size:18 final size:19
Alignment explanation
Indices: 4776365--4776433 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
4776355 TAGAAATTCT
*
4776365 AAAATTTAT-ATTTTTTAA
1 AAAATTTATAAATTTTTAA
*
4776383 AAAAATTATAAATTTTTAA
1 AAAATTTATAAATTTTTAA
* * *
4776402 AAAATCTA-AAATATATATA
1 AAAATTTATAAATTTTTA-A
4776421 AAAATTTAATAAA
1 AAAATTT-ATAAA
4776434 ATAATAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
18 15 0.38
19 21 0.52
20 1 0.03
21 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTATAAATTTTTAA
Found at i:4776757 original size:21 final size:21
Alignment explanation
Indices: 4776733--4776773 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4776723 CCTTTTTCTA
*
4776733 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGACAAAACTATC
4776754 AAGTTAAAAGACAAAACTAT
1 AAGTTAAAAGACAAAACTAT
4776774 ATTGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (21 bp):
AAGTTAAAAGACAAAACTATC
Found at i:4779425 original size:19 final size:18
Alignment explanation
Indices: 4779403--4779453 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
4779393 TTTTTTATAT
4779403 TTTTTAAATTTTAAATAAC
1 TTTTTAAATTTTAAAT-AC
*
4779422 TTTTTAGAATTTTTACATAC
1 TTTTTA-AA-TTTTAAATAC
*
4779442 TTTTTGAATTTT
1 TTTTTAAATTTT
4779454 GAAAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 9 0.32
21 7 0.25
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTAAATAC
Found at i:4779432 original size:20 final size:19
Alignment explanation
Indices: 4779403--4779453 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4779393 TTTTTTATAT
4779403 TTTTTA-AATTTTAAATAAC
1 TTTTTAGAATTTTAAAT-AC
*
4779422 TTTTTAGAATTTTTACATAC
1 TTTTTAGAA-TTTTAAATAC
4779442 TTTTT-GAATTTT
1 TTTTTAGAATTTT
4779454 GAAAAATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 9 0.31
21 7 0.24
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTAGAATTTTAAATAC
Found at i:4779500 original size:10 final size:10
Alignment explanation
Indices: 4779486--4779542 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
4779476 ATGTTTTTTC
*
4779486 ATTTTCATA-
1 ATTTTTATAT
4779495 ATTTTTATAT
1 ATTTTTATAT
4779505 ATTTTTATAT
1 ATTTTTATAT
* *
4779515 ATTTATAATTT
1 ATTT-TTATAT
*
4779526 GTTTTTATAT
1 ATTTTTATAT
*
4779536 GTTTTTA
1 ATTTTTA
4779543 CATTTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.20
10 25 0.62
11 7 0.17
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:4779642 original size:19 final size:19
Alignment explanation
Indices: 4779598--4779644 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
4779588 ATATATATTT
*
4779598 ATGATTTTTACATTTTTAAA
1 ATGATTTTTACAATTTT-AA
4779618 AT-ATTTTCTACAATTTT-A
1 ATGATTTT-TACAATTTTAA
4779636 ATGATTTTT
1 ATGATTTTT
4779645 TTGGTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (19 bp):
ATGATTTTTACAATTTTAA
Found at i:4786945 original size:96 final size:96
Alignment explanation
Indices: 4786781--4786973 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 96
4786771 AACTCAGTTA
* *
4786781 TGAATTTTATTAATAATATAGATAATATATACAATTAATGGAGGTAATCAAGTGTGCATAGTAAA
1 TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAGTAAA
* *
4786846 ATTAAAATGTATAAAAATGTTAAAATGAAAC
66 ATTAAAATGTATAAAAATATTAAAATAAAAC
* *
4786877 TGAATTTTATTAATAGTATAGATAAAATATACAATTGATGGAGGTAATCAAGTGTACAT-GATAA
1 TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAG-TAA
*
4786941 AATTAAAATGTATCAAAATATTAAAATAAAAC
65 AATTAAAATGTATAAAAATATTAAAATAAAAC
4786973 T
1 T
4786974 TTAATTGAGT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 1 0.01
96 88 0.99
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (96 bp):
TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAGTAAA
ATTAAAATGTATAAAAATATTAAAATAAAAC
Found at i:4799754 original size:33 final size:33
Alignment explanation
Indices: 4799717--4799783 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4799707 AATTTGAAAG
4799717 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
1 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
*
4799750 TTCTCTCTCGAAAATTACCTTGAAAGTAACGTC
1 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
4799783 T
1 T
4799784 CAGTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (33 bp):
TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
Found at i:4827572 original size:30 final size:31
Alignment explanation
Indices: 4827516--4827597 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
4827506 AATCTCAAAA
* * *
4827516 TTACACATGAAA-TTTGGTTTCATGTGCAATT
1 TTACACATAAAATTTTGATTT-TTGTGCAATT
4827547 TTACACA-AAAATTTTGATTTTTGTGCAATT
1 TTACACATAAAATTTTGATTTTTGTGCAATT
*
4827577 TTATACATAAAATTTTGATTT
1 TTACACATAAAATTTTGATTT
4827598 GATTTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TTACACATAAAATTTTGATTTTTGTGCAATT
Found at i:4827954 original size:23 final size:24
Alignment explanation
Indices: 4827919--4827971 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
4827909 AACTAATTTT
* *
4827919 TAAAATTTCATAAAATAAAA-AAA
1 TAAATTTTAATAAAATAAAATAAA
*
4827942 TAAATTTTAATAAATTAAAATAAA
1 TAAATTTTAATAAAATAAAATAAA
*
4827966 TGAATT
1 TAAATT
4827972 AACTCTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAATTTTAATAAAATAAAATAAA
Found at i:4855010 original size:21 final size:22
Alignment explanation
Indices: 4854981--4855027 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
4854971 CAGAAGGAGT
4854981 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTTCACAGCAGGTG
*
4855003 GAGT-GTACTTCGCAGCAGGTG
1 GAGTAGTACTTCACAGCAGGTG
4855024 GAGT
1 GAGT
4855028 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTTCACAGCAGGTG
Found at i:4857900 original size:16 final size:16
Alignment explanation
Indices: 4857879--4857915 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
4857869 TTGGTTCGCT
4857879 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
4857895 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
4857911 GTAAT
1 GTAAT
4857916 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:4857984 original size:44 final size:46
Alignment explanation
Indices: 4857895--4857992 Score: 164
Period size: 44 Copynumber: 2.2 Consensus size: 46
4857885 GAATAGAGGC
*
4857895 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
4857941 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
*
4857985 GGAATGGA
1 GTAATGGA
4857993 TGTGTAATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 26 0.52
45 3 0.06
46 21 0.42
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.37
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:4858164 original size:15 final size:15
Alignment explanation
Indices: 4858144--4858182 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
4858134 CATAATTGTT
4858144 ATAAAATATAATTTA
1 ATAAAATATAATTTA
4858159 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
4858176 ATAAAAT
1 ATAAAAT
4858183 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:4858189 original size:17 final size:17
Alignment explanation
Indices: 4858149--4858182 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4858139 TTGTTATAAA
4858149 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4858166 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4858183 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:4858254 original size:20 final size:21
Alignment explanation
Indices: 4858215--4858254 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4858205 AATTTACTAA
*
4858215 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
4858236 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
4858255 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:4861729 original size:25 final size:25
Alignment explanation
Indices: 4861695--4861756 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
4861685 CAATTTACTG
4861695 GAATTGCAACTATAAAAAACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
*
4861720 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
4861745 GAATTGCAACTA
1 GAATTGCAACTA
4861757 GAGCTTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (25 bp):
GAATTGCAACTATAAAAAACCTCTT
Found at i:4862015 original size:12 final size:12
Alignment explanation
Indices: 4861998--4862031 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4861988 CCGCATTTTA
4861998 AGCAAAAGAACG
1 AGCAAAAGAACG
4862010 AGCAAAAGAACG
1 AGCAAAAGAACG
4862022 AGCAAAAGAA
1 AGCAAAAGAA
4862032 AAGAAAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.15, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:4863864 original size:45 final size:45
Alignment explanation
Indices: 4863813--4863906 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
4863803 GAAACGGGAG
*
4863813 CGGCGATTTCAGGAGGGAGTGAGAGGGAGAGGGTGGAGGG-GATTT
1 CGGCGATTTCAGGAGGGAGGGAGAGGGA-AGGGTGGAGGGCGATTT
* * *
4863858 CGGCGATTTCGGGAGGGAGGGAGGGGGAAGGGTGGGGGGTCGATTT
1 CGGCGATTTCAGGAGGGAGGGAGAGGGAAGGGTGGAGGG-CGATTT
4863904 CGG
1 CGG
4863907 TGAGGGTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 10 0.23
45 25 0.58
46 8 0.19
ACGTcount: A:0.18, C:0.09, G:0.56, T:0.17
Consensus pattern (45 bp):
CGGCGATTTCAGGAGGGAGGGAGAGGGAAGGGTGGAGGGCGATTT
Found at i:4880834 original size:20 final size:20
Alignment explanation
Indices: 4880809--4880846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4880799 AACTATCATG
*
4880809 TTTTCTTCATTTTTTTAACC
1 TTTTCTTCATTTTATTAACC
*
4880829 TTTTCTTTATTTTATTAA
1 TTTTCTTCATTTTATTAA
4880847 TAAAATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTTCATTTTATTAACC
Found at i:4884056 original size:14 final size:14
Alignment explanation
Indices: 4884011--4884058 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
4884001 TTTAAGTAAC
*
4884011 TTAAAATAAATATAT
1 TTAAATTAAATAT-T
*
4884026 TATAAATTATATA-T
1 T-TAAATTAAATATT
4884040 TTAAATTAAATATT
1 TTAAATTAAATATT
4884054 TTAAA
1 TTAAA
4884059 ATAATGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 8 0.29
15 1 0.04
16 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATTAAATATT
Found at i:4884509 original size:10 final size:10
Alignment explanation
Indices: 4884490--4884539 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
4884480 TTAGAAATAT
*
4884490 ATTTTTTAAA
1 ATTTTATAAA
4884500 ATTTTATAAA
1 ATTTTATAAA
4884510 ATTTTA-AAA
1 ATTTTATAAA
**
4884519 ACATTATAAA
1 ATTTTATAAA
4884529 CA-TTTATAAA
1 -ATTTTATAAA
4884539 A
1 A
4884540 GTATCAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.24
10 25 0.74
11 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:4884514 original size:19 final size:20
Alignment explanation
Indices: 4884492--4884539 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
4884482 AGAAATATAT
**
4884492 TTTTTAAAATTTTATAAA-A
1 TTTTTAAAACATTATAAACA
*
4884511 TTTTAAAAACATTATAAACA
1 TTTTTAAAACATTATAAACA
*
4884531 TTTATAAAA
1 TTTTTAAAA
4884540 GTATCAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAACATTATAAACA
Found at i:4885742 original size:40 final size:40
Alignment explanation
Indices: 4885669--4885761 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
4885659 TTTGGACCGA
* * *
4885669 AAATGCCGCAAAAGGTAAAGCAGTAGCGGCGTTTTTCTCAT
1 AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTT-TCAT
4885710 AAATGCCACAAAAGGT-AAGCAATAGCGACGTTTTTTCAT
1 AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTTTCAT
*
4885749 AAACGCCACAAAA
1 AAATGCCACAAAA
4885762 TATCCTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 16 0.33
40 17 0.35
41 15 0.31
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTTTCAT
Found at i:4885859 original size:32 final size:33
Alignment explanation
Indices: 4885823--4885887 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
4885813 TCCCCAAATC
* *
4885823 AATTTCCTAAAATTCCTTATT-TTTCCCCTAAA
1 AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
* *
4885855 AATTTCCCCAAATCCCTTATTATTTTCCCTAAA
1 AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
4885888 TCAAAATCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
Found at i:4887002 original size:21 final size:18
Alignment explanation
Indices: 4886978--4887023 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
4886968 TAAATTGAGA
4886978 AAATTATTTAATTGGGAAATT
1 AAATTATTT-ATT--GAAATT
*
4886999 AAATTATTTATTTAAATT
1 AAATTATTTATTGAAATT
4887017 AAATTAT
1 AAATTAT
4887024 GATGTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
20 3 0.12
21 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
AAATTATTTATTGAAATT
Found at i:4903046 original size:100 final size:100
Alignment explanation
Indices: 4902855--4903212 Score: 555
Period size: 100 Copynumber: 3.6 Consensus size: 100
4902845 ATCATATAGC
*
4902855 CTTACTTCCTTGAGCA--ACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
1 CTTACTTCCTT-AGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
4902918 ATTGTAATTAAAAAGATT-AAAGCCACAACGGCGGAT
65 ATTGTAATTAAAAAGATTGAAA-CCACAACGGCGGAT
* * **
4902954 CTTACTTCCTTAGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCAGATCTAATTTCCCTGATA
1 CTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
4903019 TTGTAATTAAAAAGATTGAAACCACAACGGCGGAT
66 TTGTAATTAAAAAGATTGAAACCACAACGGCGGAT
*
4903054 CTTACTTCCTTAGCAGTGCAGTGGAACAAATTGAAGCTACGAC-GCGGATCTGGTTTCCCTGATA
1 CTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
* * *
4903118 TTGCAATTAAGAAGATTGAAGCCACAACGGCGGAT
66 TTGTAATTAAAAAGATTGAAACCACAACGGCGGAT
* *
4903153 CTTACTTACCTGA-CGGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
1 CTTACTT-CCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
4903213 CAACATTGCA
Statistics
Matches: 238, Mismatches: 16, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
98 4 0.02
99 96 0.40
100 135 0.57
101 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (100 bp):
CTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
TTGTAATTAAAAAGATTGAAACCACAACGGCGGAT
Found at i:4903223 original size:50 final size:50
Alignment explanation
Indices: 4902872--4903233 Score: 246
Period size: 50 Copynumber: 7.3 Consensus size: 50
4902862 CCTTGAGCAA
* *
4902872 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
* * ** * * * * * * * *
4902922 TAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGA-CATTG
* * * *
4902972 TAGTGGAACAGATTGAAGCTACGACGGCAGATCTAATTTCCCTGATATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
* * ** * * * * * * * *
4903022 TAATTAAAAAGATTGAAACCACAACGGCGGATCTTACTT-CCTTAGCAGTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGA-CATTG
* * *
4903072 CAGTGGAACAAATTGAAGCTACGAC-GCGGATCTGGTTTCCCTGATATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
* * * * * * * * **
4903121 CAAT-TAAGAAGATTGAAGCCACAACGGCGGATCTTACTTACCTGACGGTG
1 CAGTGGAA-CAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
* **
4903171 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATTG
1 CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
*
4903221 CAGTTGAACAGAT
1 CAGTGGAACAGAT
4903234 CGAATATTAC
Statistics
Matches: 223, Mismatches: 82, Indels: 14
0.70 0.26 0.04
Matches are distributed among these distances:
48 2 0.01
49 37 0.17
50 178 0.80
51 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCTGACATTG
Done.