Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 98 of 311
Found at i:32420284 original size:30 final size:28
Alignment explanation
Indices: 32420248--32420304 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
32420238 AAGCGAAAAA
* *
32420248 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
32420278 GAAAAAGAGAGTGAGCAAAAAGAAAGT
1 GAAAAAGAGAGTGAGCAAAAAGAAAGT
32420305 GTGGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 16 0.64
ACGTcount: A:0.53, C:0.04, G:0.30, T:0.14
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:32422318 original size:29 final size:29
Alignment explanation
Indices: 32422285--32422344 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
32422275 ATAACCAAAC
* *
32422285 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
32422314 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
32422343 CT
1 CT
32422345 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:32422337 original size:15 final size:15
Alignment explanation
Indices: 32422291--32422338 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
32422281 AAACCTACAA
*
32422291 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
32422306 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
32422320 AAACTTCATATCCAT
1 AAACTTCATATCCAT
32422335 AAAC
1 AAAC
32422339 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:32422982 original size:14 final size:14
Alignment explanation
Indices: 32422960--32423004 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
32422950 ACCTAAACCG
* *
32422960 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
32422974 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
32422988 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
32423002 ACC
1 ACC
32423005 TTTCCATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.18, C:0.33, G:0.07, T:0.42
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:32423885 original size:20 final size:20
Alignment explanation
Indices: 32423862--32423907 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
32423852 TAAGCTCGGT
32423862 TGAGCTCAAACGAGCTGAAC
1 TGAGCTCAAACGAGCTGAAC
* *
32423882 TGAGCTCAAATGAGCTGAAT
1 TGAGCTCAAACGAGCTGAAC
32423902 TGAGCT
1 TGAGCT
32423908 AGACGGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (20 bp):
TGAGCTCAAACGAGCTGAAC
Found at i:32425307 original size:20 final size:21
Alignment explanation
Indices: 32425269--32425308 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
32425259 TGAGCTAGAT
*
32425269 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAATTCGAGCTCAAA
32425290 CGAGCTGAA-TCGAGCTCAA
1 CGAGCTGAATTCGAGCTCAA
32425309 GTGAGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
CGAGCTGAATTCGAGCTCAAA
Found at i:32432752 original size:10 final size:10
Alignment explanation
Indices: 32432725--32432755 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
32432715 TTTTTCAATT
32432725 TTTTTTTCTGA
1 TTTTTTT-TGA
32432736 TTTTTTTTGA
1 TTTTTTTTGA
32432746 TTTTTTTTGA
1 TTTTTTTTGA
32432756 ATCTACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:32432753 original size:12 final size:12
Alignment explanation
Indices: 32432697--32432743 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
32432687 ACCGTATGCA
32432697 AATTTTTTTTTC
1 AATTTTTTTTTC
32432709 AATTTTTTTTTC
1 AATTTTTTTTTC
32432721 AATTTTTTTTTC
1 AATTTTTTTTTC
*
32432733 TGATTTTTTTT
1 -AATTTTTTTT
32432744 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:32434557 original size:18 final size:17
Alignment explanation
Indices: 32434521--32434560 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
32434511 TTTATCTCAA
*
32434521 TTTCTTTTTCCACTCTT
1 TTTCTTGTTCCACTCTT
*
32434538 TTTCTTGTTCACATTCTT
1 TTTCTTGTTC-CACTCTT
32434556 TTTCT
1 TTTCT
32434561 CTCTCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTCTTGTTCCACTCTT
Found at i:32436809 original size:12 final size:12
Alignment explanation
Indices: 32436792--32436836 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
32436782 CTCTCTGAAA
32436792 CTCTTTTTCATT
1 CTCTTTTTCATT
*
32436804 CTCTTTTTCAAT
1 CTCTTTTTCATT
* *
32436816 CTCATTTTCTTT
1 CTCTTTTTCATT
*
32436828 TTCTTTTTC
1 CTCTTTTTC
32436837 TTTTTGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:32436858 original size:12 final size:12
Alignment explanation
Indices: 32436843--32436873 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
32436833 TTTCTTTTTG
32436843 TTTTT-AAAGGC
1 TTTTTCAAAGGC
32436854 TTTTTCAAAGGC
1 TTTTTCAAAGGC
32436866 TTTTTCAA
1 TTTTTCAA
32436874 GGTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTTTCAAAGGC
Found at i:32436931 original size:5 final size:5
Alignment explanation
Indices: 32436921--32436977 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
32436911 CTTTTGCCTC
*
32436921 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTTT TCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
32436968 TCTTT TCTTT
1 TCTTT TCTTT
32436978 GTTTTATCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 26 0.58
6 14 0.31
7 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:32436942 original size:16 final size:14
Alignment explanation
Indices: 32436921--32436982 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 14
32436911 CTTTTGCCTC
32436921 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
32436936 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
32436951 TCTTTTTCTTTTTCTTT
1 TC-TTTTC-TTTT-TTT
32436968 TCTTTTCTTTGTTTT
1 TCTTTTCTTT-TTTT
32436983 ATCGTTACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 16 0.40
16 20 0.50
17 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:32439462 original size:20 final size:21
Alignment explanation
Indices: 32439424--32439472 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
32439414 TGAGCTAGAT
*
32439424 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAATTCGAGCTCAAA
*
32439445 CGAGCTGAA-TCGAGCTCAAG
1 CGAGCTGAATTCGAGCTCAAA
*
32439465 TGAGCTGA
1 CGAGCTGA
32439473 TGGGAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
CGAGCTGAATTCGAGCTCAAA
Found at i:32440345 original size:197 final size:197
Alignment explanation
Indices: 32440010--32440405 Score: 792
Period size: 197 Copynumber: 2.0 Consensus size: 197
32440000 AATATCTGTG
32440010 GTTTCGAGTGAACGAGTTACGTGGGATTTCTTTCAATCTGAATTTCAGAAGAAATATATCAGTTA
1 GTTTCGAGTGAACGAGTTACGTGGGATTTCTTTCAATCTGAATTTCAGAAGAAATATATCAGTTA
32440075 GAGATTCATTGATTAGAAACGTAAAGAGTTTCTCGAGCTTAAACAAGGTTGTATGTCTGTTACAG
66 GAGATTCATTGATTAGAAACGTAAAGAGTTTCTCGAGCTTAAACAAGGTTGTATGTCTGTTACAG
32440140 AATACGAGTGGGAATTTGTAAGGTTGAGTCAGTATGCCTATGAATGTGTATCTTCAGAAGCAATA
131 AATACGAGTGGGAATTTGTAAGGTTGAGTCAGTATGCCTATGAATGTGTATCTTCAGAAGCAATA
32440205 AT
196 AT
32440207 GTTTCGAGTGAACGAGTTACGTGGGATTTCTTTCAATCTGAATTTCAGAAGAAATATATCAGTTA
1 GTTTCGAGTGAACGAGTTACGTGGGATTTCTTTCAATCTGAATTTCAGAAGAAATATATCAGTTA
32440272 GAGATTCATTGATTAGAAACGTAAAGAGTTTCTCGAGCTTAAACAAGGTTGTATGTCTGTTACAG
66 GAGATTCATTGATTAGAAACGTAAAGAGTTTCTCGAGCTTAAACAAGGTTGTATGTCTGTTACAG
32440337 AATACGAGTGGGAATTTGTAAGGTTGAGTCAGTATGCCTATGAATGTGTATCTTCAGAAGCAATA
131 AATACGAGTGGGAATTTGTAAGGTTGAGTCAGTATGCCTATGAATGTGTATCTTCAGAAGCAATA
32440402 AT
196 AT
32440404 GT
1 GT
32440406 GTAAGAGATT
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 199 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (197 bp):
GTTTCGAGTGAACGAGTTACGTGGGATTTCTTTCAATCTGAATTTCAGAAGAAATATATCAGTTA
GAGATTCATTGATTAGAAACGTAAAGAGTTTCTCGAGCTTAAACAAGGTTGTATGTCTGTTACAG
AATACGAGTGGGAATTTGTAAGGTTGAGTCAGTATGCCTATGAATGTGTATCTTCAGAAGCAATA
AT
Found at i:32441362 original size:4 final size:4
Alignment explanation
Indices: 32441353--32441380 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
32441343 TTAAACTAAG
32441353 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
32441381 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:32449055 original size:15 final size:14
Alignment explanation
Indices: 32449037--32449079 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
32449027 GAAGAAAAAT
32449037 AAAAAGCAAAAGAAG
1 AAAAAG-AAAAGAAG
*
32449052 AAAAAGAAAATGAAAT
1 AAAAAGAAAA-G-AAG
32449068 AAAAAGAAAAGA
1 AAAAAGAAAAGA
32449080 GAGGCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 12 0.48
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (14 bp):
AAAAAGAAAAGAAG
Found at i:32449071 original size:16 final size:15
Alignment explanation
Indices: 32449024--32449079 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
32449014 AAGAGAAAAT
32449024 AAAGAAGAA-AAATAA
1 AAAGAA-AAGAAATAA
*
32449039 AAAGCAAAAG-AAGAA
1 AAAG-AAAAGAAATAA
32449054 AAAGAAAATGAAATAA
1 AAAGAAAA-GAAATAA
32449070 AAAGAAAAGA
1 AAAGAAAAGA
32449080 GAGGCAAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 4 0.11
15 17 0.49
16 14 0.40
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAGAAAAGAAATAA
Found at i:32449156 original size:12 final size:12
Alignment explanation
Indices: 32449148--32449172 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32449138 TTTGAAAAGC
32449148 AAAAAGAAAATG
1 AAAAAGAAAATG
32449160 AAAAAGAAAATG
1 AAAAAGAAAATG
32449172 A
1 A
32449173 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:32449169 original size:18 final size:18
Alignment explanation
Indices: 32449142--32449197 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
32449132 AAAGCCTTTG
32449142 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
32449161 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
32449179 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
32449196 AA
1 AA
32449198 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:32449182 original size:30 final size:31
Alignment explanation
Indices: 32449148--32449229 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
32449138 TTTGAAAAGC
*
32449148 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
32449178 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
32449208 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
32449230 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:32451440 original size:30 final size:30
Alignment explanation
Indices: 32451406--32451503 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
32451396 AGCTCACTCC
32451406 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
32451436 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
32451466 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
32451496 TAGCTCAT
1 TAGCTCAT
32451504 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:32453040 original size:20 final size:21
Alignment explanation
Indices: 32453002--32453050 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
32452992 TGAGCTAGAT
*
32453002 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAATTCGAGCTCAAA
*
32453023 CGAGCTGAA-TCGAGCTCAAG
1 CGAGCTGAATTCGAGCTCAAA
*
32453043 TGAGCTGA
1 CGAGCTGA
32453051 TGGGAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
CGAGCTGAATTCGAGCTCAAA
Found at i:32453724 original size:29 final size:29
Alignment explanation
Indices: 32453658--32453714 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
32453648 GATTCAAAGA
*
32453658 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
32453687 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
32453715 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:32456833 original size:30 final size:30
Alignment explanation
Indices: 32456748--32456844 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32456738 TAAACTAAAA
* *
32456748 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
32456778 TGAGCTGAGGGTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
32456808 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
32456837 ATGAGCTA
1 -TGAGCTA
32456845 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:32459662 original size:20 final size:20
Alignment explanation
Indices: 32459616--32459662 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32459606 AGCTCGTTTC
*
32459616 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
32459636 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32459656 CAGCTCA
1 CAGCTCA
32459663 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32461196 original size:12 final size:12
Alignment explanation
Indices: 32461179--32461215 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
32461169 AAAAGAGAAG
32461179 AAATTCAAAAAA
1 AAATTCAAAAAA
32461191 AAATTCAAAAAA
1 AAATTCAAAAAA
32461203 AAA-TCAAAAAA
1 AAATTCAAAAAA
32461214 AA
1 AA
32461216 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:32461202 original size:11 final size:11
Alignment explanation
Indices: 32461179--32461215 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
32461169 AAAAGAGAAG
32461179 AAATTCAAAAAA
1 AAATTC-AAAAA
32461191 AAATTCAAAAA
1 AAATTCAAAAA
*
32461202 AAAATCAAAAA
1 AAATTCAAAAA
32461213 AAA
1 AAA
32461216 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:32464145 original size:20 final size:20
Alignment explanation
Indices: 32464099--32464145 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32464089 AGCTCGTTTC
*
32464099 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
32464119 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32464139 CAGCTCA
1 CAGCTCA
32464146 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32466132 original size:70 final size:68
Alignment explanation
Indices: 32465927--32466116 Score: 236
Period size: 70 Copynumber: 2.7 Consensus size: 68
32465917 TTTTGGAGAG
* * * *
32465927 CACATTAAGCATTTAAAATGGACGTAAATGAACACATTTTCAAGACAACAAATCAGCCCTTTACA
1 CACATTAAGCATTT-AAATGAACGTAAATGAACACATTTTTAAGATAACAAATCAGCACTTTACA
*
32465992 GCAG
65 GCAA
* * * * *
32465996 CACATTAAGCATCTAAAATTAACGTGAGTGAACACATTTTTTAAGATAACAAATTAGCACTTTAC
1 CACATTAAGCAT-TTAAATGAACGTAAATGAACACA-TTTTTAAGATAACAAATCAGCACTTTAC
32466061 AGCAA
64 AGCAA
* *
32466066 CACATTAAGCATTTAAATCGAACGTAAATGAAGACATTTTTAATATAACAA
1 CACATTAAGCATTTAAAT-GAACGTAAATGAACACATTTTTAAGATAACAA
32466117 CTCATCAATT
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
69 48 0.47
70 54 0.53
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.27
Consensus pattern (68 bp):
CACATTAAGCATTTAAATGAACGTAAATGAACACATTTTTAAGATAACAAATCAGCACTTTACAG
CAA
Found at i:32470442 original size:29 final size:29
Alignment explanation
Indices: 32470409--32470465 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
32470399 ATAACCAAAC
*
32470409 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
32470438 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
32470466 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:32471627 original size:12 final size:12
Alignment explanation
Indices: 32471609--32471642 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32471599 TCCCTCGTTT
32471609 CTTTTCACTCAC
1 CTTTTCACTCAC
* *
32471621 TTTTTCACACAC
1 CTTTTCACTCAC
32471633 CTTTTCACTC
1 CTTTTCACTC
32471643 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTTTCACTCAC
Found at i:32473114 original size:20 final size:20
Alignment explanation
Indices: 32473091--32473138 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
32473081 AGCTTCGTCC
32473091 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
**** *
32473111 AGCTTGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
32473131 AGCTCAAC
1 AGCTCAAC
32473139 CGAGCTTACT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:32476161 original size:21 final size:22
Alignment explanation
Indices: 32476122--32476165 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
32476112 ATGCATACTC
32476122 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
32476144 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
32476165 C
1 C
32476166 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:32485510 original size:21 final size:22
Alignment explanation
Indices: 32485471--32485514 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
32485461 ATGCATACTC
32485471 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
32485493 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
32485514 C
1 C
32485515 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:32490648 original size:30 final size:30
Alignment explanation
Indices: 32490614--32490711 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
32490604 AGCTCACTCC
32490614 TAGCTCATATTCAGCTTACGAGCTAAACCT
1 TAGCTCATATTCAGCTTACGAGCTAAACCT
** * * * *
32490644 TAGCTCAGCTTCAACTTA-GAAGTTTAATCT
1 TAGCTCATATTCAGCTTACG-AGCTAAACCT
* * * *
32490674 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTTACGAGCTAAACCT
32490704 TAGCTCAT
1 TAGCTCAT
32490712 TTTAATTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 1 0.02
30 47 0.96
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTTACGAGCTAAACCT
Found at i:32493459 original size:18 final size:18
Alignment explanation
Indices: 32493374--32493461 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
32493364 TTCTTTTGTT
** *
32493374 TCTTTTTCTAATTCATTT
1 TCTTTTTCTTTTTCATTC
*
32493392 TC-TCTTCTTTCTTCATT-
1 TCTTTTTCTTT-TTCATTC
** * *
32493409 TCTTTTTCACTCTCAATC
1 TCTTTTTCTTTTTCATTC
32493427 TCTTTTTGCTCTTTTTCATTC
1 TC-TTTT--TCTTTTTCATTC
32493448 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
32493462 CGCACTTGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 11 0.21
18 23 0.44
19 4 0.08
20 4 0.08
21 10 0.19
ACGTcount: A:0.09, C:0.25, G:0.01, T:0.65
Consensus pattern (18 bp):
TCTTTTTCTTTTTCATTC
Found at i:32496808 original size:20 final size:20
Alignment explanation
Indices: 32496761--32496808 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
32496751 AGTAAGCTCG
32496761 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
32496781 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
32496801 GTTGAGCT
1 GTTGAGCT
32496809 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:32499103 original size:14 final size:13
Alignment explanation
Indices: 32499076--32499144 Score: 88
Period size: 13 Copynumber: 5.4 Consensus size: 13
32499066 ATACAAGTAT
32499076 AAAAAAATTC--A
1 AAAAAAATTCAAA
32499087 AAAAAAATTCGAAA
1 AAAAAAATTC-AAA
*
32499101 AAAAAAATTCGAA
1 AAAAAAATTCAAA
32499114 AAAAAAATTCAAA
1 AAAAAAATTCAAA
**
32499127 AAAAAGTTTCAAA
1 AAAAAAATTCAAA
32499140 AAAAA
1 AAAAA
32499145 TGATTTGTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.20
13 30 0.59
14 11 0.22
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:32500068 original size:9 final size:10
Alignment explanation
Indices: 32500061--32500117 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
32500051 AAGAGAAAAT
32500061 AAAGAAAAGA
1 AAAGAAAAGA
32500071 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
32500083 AAAGAAGA-A
1 AAAGAAAAGA
32500092 AAAGAAAATGA
1 AAAGAAAA-GA
32500103 AATA-AAAAGA
1 AA-AGAAAAGA
32500113 AAAGA
1 AAAGA
32500118 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:32500085 original size:6 final size:5
Alignment explanation
Indices: 32500061--32500117 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
32500051 AAGAGAAAAT
*
32500061 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
32500108 AAAGA AAAGA
1 AAAGA AAAGA
32500118 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:32500092 original size:15 final size:14
Alignment explanation
Indices: 32500061--32500117 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
32500051 AAGAGAAAAT
32500061 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
32500077 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
32500092 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
32500108 AAAGAAAAGA
1 AAAGAAAAGA
32500118 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:32500197 original size:11 final size:12
Alignment explanation
Indices: 32500165--32500195 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
32500155 TTGAGAGAAC
32500165 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32500177 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32500189 TTGAAAA
1 TTGAAAA
32500196 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:32500266 original size:31 final size:31
Alignment explanation
Indices: 32500198--32500268 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
32500188 TTTGAAAAGC
* *
32500198 AAAAAGAAA-ATGAGATTGAAAAAAAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAAAGAACG
*
32500228 -AAAAGAAATTTGAGAGTGAAAAAGAAG-ATG
1 AAAAAGAAATTTGAGAGTGAAAAA-AAGAACG
32500258 AAAAAGAAATT
1 AAAAAGAAATT
32500269 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 14 0.40
31 13 0.37
ACGTcount: A:0.63, C:0.01, G:0.21, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAAAGAACG
Found at i:32500768 original size:14 final size:14
Alignment explanation
Indices: 32500734--32500781 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
32500724 GTACGAATGG
* *
32500734 AATGGTAGGGACGA
1 AATGGTAGGAACAA
*
32500748 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
32500762 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
32500776 ATTGGT
1 AATGGT
32500782 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:32503611 original size:21 final size:22
Alignment explanation
Indices: 32503572--32503615 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
32503562 ATGCATACTC
32503572 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
32503594 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
32503615 C
1 C
32503616 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:32505773 original size:19 final size:19
Alignment explanation
Indices: 32505728--32505773 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
32505718 ATTAACACAG
*
32505728 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
32505747 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
32505765 AATTAATAA
1 AATTAATAA
32505774 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:32506000 original size:10 final size:10
Alignment explanation
Indices: 32505987--32506021 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
32505977 AAGCTCAGTT
32505987 GAGCTCAAAC
1 GAGCTCAAAC
*
32505997 GAGCTGAAAC
1 GAGCTCAAAC
*
32506007 GAGCTCAAAT
1 GAGCTCAAAC
32506017 GAGCT
1 GAGCT
32506022 AAGTTAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:32507404 original size:30 final size:30
Alignment explanation
Indices: 32507318--32507405 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
32507308 CTATCTCATA
*
32507318 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTTAGCTCACGAGCTAAAGCTTAGCTCAAC
* * * ** *
32507348 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTTAGCTCACGAGCTAAAG-CTTAGCTCAAC
32507378 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTTAGCTCACGAGCTAAAGCTTAGCTCA
32507406 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (30 bp):
TTTAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:32509313 original size:18 final size:19
Alignment explanation
Indices: 32509290--32509328 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
32509280 TTTATCTCAA
*
32509290 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
32509308 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
32509327 TT
1 TT
32509329 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:32509384 original size:24 final size:22
Alignment explanation
Indices: 32509321--32509400 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 22
32509311 CTTGTTCACA
*
32509321 TTCTTTTTCTCTCTCAAACTTTTT
1 TTCTTTTTC-CTCTCAATC-TTTT
* * * *
32509345 TTCATTCTCTTTTCAATCTTATT
1 TTCTTTTTCCTCTCAATCTT-TT
32509368 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTC-CTCTCAATCT-TTT
32509392 TTCTTTTTC
1 TTCTTTTTC
32509401 TTTCATTTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.05
23 15 0.34
24 26 0.59
25 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (22 bp):
TTCTTTTTCCTCTCAATCTTTT
Found at i:32511940 original size:20 final size:20
Alignment explanation
Indices: 32511894--32511941 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
32511884 GGTAAGCTAG
*
32511894 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACAAGCTGA
*** *
32511914 AACGAGCTCAAATAAGCTGA
1 GTTGAGCTCAAACAAGCTGA
32511934 GTTGAGCT
1 GTTGAGCT
32511942 GGACGAAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACAAGCTGA
Found at i:32513252 original size:30 final size:30
Alignment explanation
Indices: 32513209--32513305 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
32513199 AGCTCACTCC
*
32513209 TAGCTCATA-TTCAGCACACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * * *
32513239 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
32513269 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
32513299 TAGCTCA
1 TAGCTCA
32513306 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:32514949 original size:12 final size:11
Alignment explanation
Indices: 32514924--32514991 Score: 66
Period size: 13 Copynumber: 5.7 Consensus size: 11
32514914 ATACAAGTAT
32514924 AAAAAAATTC-
1 AAAAAAATTCA
32514934 AAAAAAATTCGAA
1 AAAAAAATTC--A
32514947 AAAAAAATTCGAA
1 AAAAAAATTC--A
*
32514960 AAAAAAATTTA
1 AAAAAAATTCA
32514971 AAAAAAAGTTTCA
1 AAAAAAA--TTCA
32514984 AAAAAAAT
1 AAAAAAAT
32514992 GATTTGTGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.20
11 9 0.18
13 32 0.63
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:32514950 original size:13 final size:13
Alignment explanation
Indices: 32514934--32514990 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
32514924 AAAAAAATTC
32514934 AAAAAAATTCGAA
1 AAAAAAATTCGAA
32514947 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
32514960 AAAAAAATT-TAA
1 AAAAAAATTCGAA
*
32514972 AAAAAAGTTTC-AA
1 AAAAAA-ATTCGAA
32514985 AAAAAA
1 AAAAAA
32514991 TGATTTGTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.20
13 32 0.80
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:32522124 original size:30 final size:29
Alignment explanation
Indices: 32522090--32522157 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
32522080 ATGAATCGGA
32522090 AGCTTTGGCACTAAGTGTGCAATTTAAACT
1 AGCTTTGGCACTAAGTGTGCAATTT-AACT
*
32522120 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTGTGCAATTTAACT
32522149 AGCTTTGGC
1 AGCTTTGGC
32522158 TACTTGAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCAATTTAACT
Found at i:32526450 original size:12 final size:11
Alignment explanation
Indices: 32526412--32526468 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 11
32526402 GTAGCTTTGA
32526412 AAAAAAAAGTT-
1 AAAAAAAA-TTG
32526423 AAAAAAAAGTTTTG
1 AAAAAAAA---TTG
32526437 AAAAAAAATCTG
1 AAAAAAAAT-TG
32526449 AAAAAAAATTG
1 AAAAAAAATTG
32526460 CAAAAAAAA
1 -AAAAAAAA
32526469 ATTGCATACG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 11 0.28
12 19 0.47
13 2 0.05
14 8 0.20
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:32526452 original size:26 final size:26
Alignment explanation
Indices: 32526407--32526456 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
32526397 TAAATGTAGC
* *
32526407 TTTGAAAAAAAAAGTTAAAAAAAAGT
1 TTTGAAAAAAAAACTGAAAAAAAAGT
*
32526433 TTTGAAAAAAAATCTGAAAAAAAA
1 TTTGAAAAAAAAACTGAAAAAAAA
32526457 TTGCAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (26 bp):
TTTGAAAAAAAAACTGAAAAAAAAGT
Found at i:32526453 original size:13 final size:12
Alignment explanation
Indices: 32526437--32526474 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
32526427 AAAAGTTTTG
32526437 AAAAAAAATCTG-
1 AAAAAAAAT-TGC
32526449 AAAAAAAATTGC
1 AAAAAAAATTGC
32526461 AAAAAAAAATTGC
1 -AAAAAAAATTGC
32526474 A
1 A
32526475 TACGGTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.42
13 12 0.50
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGC
Found at i:32526880 original size:29 final size:29
Alignment explanation
Indices: 32526795--32526889 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
32526785 TAAACTAAAA
* *
32526795 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTC-TGAGCTGAAGT
* * * *
32526825 TGAGCTAAGGCTAAACTCTTAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCTGAGCTGAAGT
32526854 TGAGCTAAGGTTTAGCTCATGAG-TGAAAG-
1 TGAGCTAAGGTTTAGCTC-TGAGCTG-AAGT
32526883 TGAGCTA
1 TGAGCTA
32526890 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 33 0.62
30 20 0.38
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (29 bp):
TGAGCTAAGGTTTAGCTCTGAGCTGAAGT
Found at i:32527420 original size:30 final size:29
Alignment explanation
Indices: 32527386--32527453 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
32527376 ATGAATCGGA
32527386 AGCTTTGGCACTAAGTGTGCAATTTAAACT
1 AGCTTTGGCACTAAGTGTGCAATTT-AACT
*
32527416 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTGTGCAATTTAACT
32527445 AGCTTTGGC
1 AGCTTTGGC
32527454 TACTGAGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCAATTTAACT
Found at i:32529610 original size:14 final size:14
Alignment explanation
Indices: 32529591--32529617 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32529581 GTAAAGTTTT
32529591 TTTTTATTTATTTA
1 TTTTTATTTATTTA
32529605 TTTTTATTTATTT
1 TTTTTATTTATTT
32529618 TTACTTAGTT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:32533392 original size:9 final size:9
Alignment explanation
Indices: 32533373--32533408 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
32533363 AGTTGTAAAG
32533373 TTTTATTT-
1 TTTTATTTA
32533381 TTTT-TTTA
1 TTTTATTTA
32533389 TTTTATTTA
1 TTTTATTTA
32533398 -TTTATTTA
1 TTTTATTTA
32533406 TTT
1 TTT
32533409 ACTTAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 3 0.12
8 16 0.64
9 6 0.24
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTTA
Found at i:32533394 original size:16 final size:17
Alignment explanation
Indices: 32533373--32533408 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
32533363 AGTTGTAAAG
*
32533373 TTTTATTT-TTTTTTTA
1 TTTTATTTATTTATTTA
32533389 TTTTATTTATTTATTTA
1 TTTTATTTATTTATTTA
32533406 TTT
1 TTT
32533409 ACTTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:32534862 original size:12 final size:12
Alignment explanation
Indices: 32534847--32534877 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
32534837 TTCTTTTTGC
32534847 TTTTCAAAGGCT
1 TTTTCAAAGGCT
32534859 TTTTCAAAGGCT
1 TTTTCAAAGGCT
32534871 TTTTCAA
1 TTTTCAA
32534878 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:32534954 original size:6 final size:6
Alignment explanation
Indices: 32534938--32534987 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
32534928 TTTCTTTTTA
*
32534938 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
32534987 T
1 T
32534988 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:32534970 original size:37 final size:37
Alignment explanation
Indices: 32534927--32534997 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
32534917 CTTGCCTCTC
32534927 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
32534964 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
32534998 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:32534998 original size:16 final size:16
Alignment explanation
Indices: 32534923--32534983 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
32534913 GCCTCTTGCC
*
32534923 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
32534939 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
32534955 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
32534971 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
32534984 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:32535945 original size:12 final size:13
Alignment explanation
Indices: 32535930--32535968 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
32535920 TTTTTTTTCC
32535930 TTTTTTTCG-ATT
1 TTTTTTTCGAATT
32535942 TTTTTTT-GAATT
1 TTTTTTTCGAATT
32535954 TTTTTTTCTGAATT
1 TTTTTTTC-GAATT
32535968 T
1 T
32535969 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 17 0.71
14 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:32535957 original size:14 final size:14
Alignment explanation
Indices: 32535940--32535978 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
32535930 TTTTTTTCGA
32535940 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
*
32535954 TTTTTTTCTGAATT
1 TTTTTTTTTGAATT
32535968 TCTTCTTTTTT
1 T-TT-TTTTTT
32535979 TTTAAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 2 0.10
16 5 0.24
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:32537721 original size:30 final size:30
Alignment explanation
Indices: 32537687--32537783 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
32537677 AAAACTAAAA
32537687 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
32537717 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
32537747 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
32537776 ATGAGCTA
1 -TGAGCTA
32537784 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:32538641 original size:21 final size:21
Alignment explanation
Indices: 32538612--32538654 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
32538602 TTGGTATTTG
32538612 GGAAGTGGTACGAAATGGTAT
1 GGAAGTGGTACGAAATGGTAT
* *
32538633 GGAATTGGTATGAAATGGTAT
1 GGAAGTGGTACGAAATGGTAT
32538654 G
1 G
32538655 TGATGTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.28
Consensus pattern (21 bp):
GGAAGTGGTACGAAATGGTAT
Found at i:32541130 original size:20 final size:21
Alignment explanation
Indices: 32541107--32541152 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
32541097 AGCTCCAACC
32541107 AGCTCACTTGAGCTTG-TTTT
1 AGCTCACTTGAGCTTGATTTT
**
32541127 AGCTCGTTTGAGCTTGATTTT
1 AGCTCACTTGAGCTTGATTTT
32541148 AGCTC
1 AGCTC
32541153 GTTTCAGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (21 bp):
AGCTCACTTGAGCTTGATTTT
Found at i:32541149 original size:21 final size:20
Alignment explanation
Indices: 32541114--32541161 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
32541104 ACCAGCTCAC
32541114 TTGAGCTTGTTTTAGCTCGT
1 TTGAGCTTGTTTTAGCTCGT
32541134 TTGAGCTTGATTTTAGCTCGT
1 TTGAGCTTG-TTTTAGCTCGT
*
32541155 TTCAGCT
1 TTGAGCT
32541162 CATTTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TTGAGCTTGTTTTAGCTCGT
Found at i:32543593 original size:15 final size:15
Alignment explanation
Indices: 32543573--32543604 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32543563 CAAAAATAGT
*
32543573 AAAAGAATAAAAAGA
1 AAAAGAAGAAAAAGA
32543588 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
32543603 AA
1 AA
32543605 GTAAAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:32543608 original size:34 final size:35
Alignment explanation
Indices: 32543528--32543616 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 35
32543518 GAATGGATGT
* *
32543528 GAAAAAGAAAG-AAAAGAAAAATGAGAAAAAGCAT
1 GAAAAAGAAAGTAAAAGAAAAATAAGAAAAAGCAA
* *
32543562 GCAAAA-ATAGTAAAAGAATAAA-AAGAAAAAG-AA
1 GAAAAAGAAAGTAAAAGAA-AAATAAGAAAAAGCAA
32543595 GAAAAAGAAAGTAAAAAGAAAA
1 GAAAAAGAAAGT-AAAAGAAAA
32543617 GTTTGTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
33 9 0.20
34 26 0.58
35 10 0.22
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (35 bp):
GAAAAAGAAAGTAAAAGAAAAATAAGAAAAAGCAA
Found at i:32543611 original size:43 final size:43
Alignment explanation
Indices: 32543530--32543611 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
32543520 ATGGATGTGA
* *
32543530 AAAAGAAAGAAAAGAAAAATGAGAAAAAGCATGCAAAAATAGT
1 AAAAGAAAGAAAAGAAAAATGAGAAAAAGAAAGCAAAAATAGT
*
32543573 AAAAGAATA-AAAAGAAAAA-GAAGAAAAAGAAAGTAAAAA
1 AAAAGAA-AGAAAAGAAAAATG-AGAAAAAGAAAGCAAAAA
32543612 GAAAAGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.94
44 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (43 bp):
AAAAGAAAGAAAAGAAAAATGAGAAAAAGAAAGCAAAAATAGT
Found at i:32545248 original size:22 final size:22
Alignment explanation
Indices: 32545220--32545266 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
32545210 CCTTTTTGAA
32545220 CCCTTACCATTTCGTACCAAAT
1 CCCTTACCATTTCGTACCAAAT
*
32545242 CCCTTACCATTTCGTACCAATT
1 CCCTTACCATTTCGTACCAAAT
32545264 CCC
1 CCC
32545267 AAATACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.32
Consensus pattern (22 bp):
CCCTTACCATTTCGTACCAAAT
Found at i:32547242 original size:10 final size:10
Alignment explanation
Indices: 32547209--32547257 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
32547199 AAAAAGGAAT
*
32547209 GAGCTGAAAC
1 GAGCTCAAAC
32547219 GAGCT-AAATTC
1 GAGCTCAAA--C
32547230 GAGCTCAAAC
1 GAGCTCAAAC
*
32547240 GAGCTAAAAC
1 GAGCTCAAAC
32547250 GAGCTCAA
1 GAGCTCAA
32547258 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:32547264 original size:20 final size:21
Alignment explanation
Indices: 32547209--32547257 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
32547199 AAAAAGGAAT
* *
32547209 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
32547230 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
32547250 GAGCTCAA
1 GAGCTCAA
32547258 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:32548112 original size:17 final size:18
Alignment explanation
Indices: 32548090--32548126 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32548080 TGGAATAAAC
32548090 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
32548107 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
32548125 TT
1 TT
32548127 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:32551158 original size:30 final size:29
Alignment explanation
Indices: 32551103--32551166 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
32551093 TTTTTCAATT
*
32551103 TCTTTTTCACTCTCAAACTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAACTTCTTTTC-TTC
* *
32551133 TCTTTTTCAATCTCAATC-TCATTTTCTTT
1 TCTTTTTCAATCTCAAACTTC-TTTTCTTC
32551162 TCTTT
1 TCTTT
32551167 GTTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.14, C:0.27, G:0.02, T:0.58
Consensus pattern (29 bp):
TCTTTTTCAATCTCAAACTTCTTTTCTTC
Found at i:32551181 original size:19 final size:20
Alignment explanation
Indices: 32551157--32551197 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
32551147 AATCTCATTT
32551157 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
32551176 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
32551196 TC
1 TC
32551198 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:32554072 original size:30 final size:30
Alignment explanation
Indices: 32554038--32554134 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
32554028 TAAACTAAAA
32554038 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
32554068 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
32554098 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
32554127 ATGAGCTA
1 -TGAGCTA
32554135 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:32555293 original size:14 final size:14
Alignment explanation
Indices: 32555274--32555318 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
32555264 AACTCATCTT
*
32555274 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
32555288 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
32555301 AATTTAATTTAATG
1 AGTTTAATTTAATG
32555315 AGTT
1 AGTT
32555319 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:32557628 original size:29 final size:29
Alignment explanation
Indices: 32557595--32557654 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
32557585 ATAACCAAAC
*
32557595 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
32557624 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
32557653 CT
1 CT
32557655 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:32557647 original size:15 final size:15
Alignment explanation
Indices: 32557601--32557648 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
32557591 AAACCTACAA
*
32557601 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
32557616 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
32557630 AAACTTCATATCCAT
1 AAACTTCATATCCAT
32557645 AAAC
1 AAAC
32557649 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:32560439 original size:20 final size:21
Alignment explanation
Indices: 32560416--32560461 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
32560406 AGCTCCAACC
32560416 AGCTCACTTGAGCTTG-TTTT
1 AGCTCACTTGAGCTTGATTTT
**
32560436 AGCTCGTTTGAGCTTGATTTT
1 AGCTCACTTGAGCTTGATTTT
*
32560457 TGCTC
1 AGCTC
32560462 GTTTTAGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (21 bp):
AGCTCACTTGAGCTTGATTTT
Found at i:32560461 original size:21 final size:20
Alignment explanation
Indices: 32560423--32560470 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
32560413 ACCAGCTCAC
32560423 TTGAGCTTGTTTTAGCTCGT
1 TTGAGCTTGTTTTAGCTCGT
*
32560443 TTGAGCTTGATTTTTGCTCGT
1 TTGAGCTTG-TTTTAGCTCGT
*
32560464 TTTAGCT
1 TTGAGCT
32560471 CATTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.52
Consensus pattern (20 bp):
TTGAGCTTGTTTTAGCTCGT
Found at i:32568010 original size:27 final size:27
Alignment explanation
Indices: 32567972--32568025 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
32567962 TCTAGAAAAA
32567972 AATCAAGAAGCTTCATGGGAGTTTCCT
1 AATCAAGAAGCTTCATGGGAGTTTCCT
*
32567999 AATCAAGAAGCTTCGTGGGAGTTTCCT
1 AATCAAGAAGCTTCATGGGAGTTTCCT
32568026 CCTTGCTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (27 bp):
AATCAAGAAGCTTCATGGGAGTTTCCT
Found at i:32568825 original size:119 final size:118
Alignment explanation
Indices: 32568609--32568845 Score: 384
Period size: 119 Copynumber: 2.0 Consensus size: 118
32568599 CACTAAGAAG
* * *
32568609 TGATACGAACTATCTCGGGAAGAGTCGAGTTGTATGTAGATTGCCCGATCGTCTACGAGAAGTTA
1 TGATACGAACCATCTCGAGAAGAGTCGAGTCGTATGTAGATTGCCCGATCGTCTACGAGAAGTTA
* *
32568674 CGTTAGGTTTAGTTGAGTTAAAGGTATGGTCGAAGTAGAAAGAGGGATACGAAT
66 CGTTAGGATTAGTTGAGTTAAAGGTATAGTCG-AGTAGAAAGAGGGATACGAAT
*
32568728 TGATACGAACCGTCTCGAGAAGAGTCGAGTCGTATGTAGATTGCCCGATCGTCTACGAGAAGTTA
1 TGATACGAACCATCTCGAGAAGAGTCGAGTCGTATGTAGATTGCCCGATCGTCTACGAGAAGTTA
** *
32568793 CGTTAGGATTAGTTGAGTTGTAGGTATAGTCGAGTAGAAAGAGGGGTACGAAT
66 CGTTAGGATTAGTTGAGTTAAAGGTATAGTCGAGTAGAAAGAGGGATACGAAT
32568846 GGAATGGTAG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
118 20 0.18
119 89 0.82
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.27
Consensus pattern (118 bp):
TGATACGAACCATCTCGAGAAGAGTCGAGTCGTATGTAGATTGCCCGATCGTCTACGAGAAGTTA
CGTTAGGATTAGTTGAGTTAAAGGTATAGTCGAGTAGAAAGAGGGATACGAAT
Found at i:32569542 original size:22 final size:22
Alignment explanation
Indices: 32569512--32569555 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32569502 TTTGGTATTT
32569512 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
32569534 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
32569556 TGATTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:32571972 original size:14 final size:14
Alignment explanation
Indices: 32571953--32571992 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
32571943 CGAATGGAAT
*
32571953 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
32571967 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
32571981 GATATGAACAAA
1 GGTAGGAACAAA
32571993 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:32573367 original size:20 final size:20
Alignment explanation
Indices: 32573344--32573389 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
32573334 CCAGCTCGAA
*
32573344 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
32573364 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
32573384 TTAGCT
1 TTAGCT
32573390 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:32573371 original size:30 final size:30
Alignment explanation
Indices: 32573336--32573409 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
32573326 AGTTTTTCCC
32573336 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
32573366 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
32573396 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
32573410 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:32575216 original size:32 final size:32
Alignment explanation
Indices: 32575180--32575242 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
32575170 TTGGAAAGTG
32575180 AAAAGAAACTCCCAAAAAGGCCCTTGCTGTTT
1 AAAAGAAACTCCCAAAAAGGCCCTTGCTGTTT
32575212 AAAAGAAACTCCCAAAAAGGCCCTTGCTGTT
1 AAAAGAAACTCCCAAAAAGGCCCTTGCTGTT
32575243 CATGAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (32 bp):
AAAAGAAACTCCCAAAAAGGCCCTTGCTGTTT
Found at i:32581975 original size:23 final size:22
Alignment explanation
Indices: 32581924--32581975 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32581914 CCTCGTCTTT
*
32581924 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32581946 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32581969 TTCTTTT
1 TTCTTTT
32581976 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:32582518 original size:20 final size:21
Alignment explanation
Indices: 32582472--32582518 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
32582462 AGCTCGTTTC
*
32582472 CAGCTCACTCGAGCTCAAGTT
1 CAGCTCACTCAAGCTCAAGTT
*
32582493 -AACTCACTCAAGCTCAA-TT
1 CAGCTCACTCAAGCTCAAGTT
32582512 CAGCTCA
1 CAGCTCA
32582519 ATCATTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (21 bp):
CAGCTCACTCAAGCTCAAGTT
Found at i:32583883 original size:20 final size:20
Alignment explanation
Indices: 32583837--32583883 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32583827 AGCTCGTTTC
*
32583837 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
32583857 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32583877 CAGCTCA
1 CAGCTCA
32583884 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32593072 original size:12 final size:12
Alignment explanation
Indices: 32593046--32593099 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
32593036 CCGTATGCAA
32593046 TTTTTTTTCAAAAT
1 TTTTTTTTC--AAT
32593060 TTTTTTTTCAA-
1 TTTTTTTTCAAT
32593071 TTTTTTTT--AT
1 TTTTTTTTCAAT
*
32593081 TTTTTTTTCGAT
1 TTTTTTTTCAAT
32593093 TTTTTTT
1 TTTTTTT
32593100 AATCTACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.03
10 8 0.22
11 8 0.22
12 11 0.30
14 9 0.24
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:32593074 original size:11 final size:11
Alignment explanation
Indices: 32593043--32593099 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
32593033 AGACCGTATG
32593043 CAATTTTTTTT
1 CAATTTTTTTT
32593054 CAAAATTTTTTTTT
1 C--AA-TTTTTTTT
32593068 CAATTTTTTTT
1 CAATTTTTTTT
*
32593079 -ATTTTTTTTT
1 CAATTTTTTTT
*
32593089 CGATTTTTTTT
1 CAATTTTTTTT
32593100 AATCTACAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 9 0.23
11 17 0.44
12 2 0.05
13 2 0.05
14 9 0.23
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:32593082 original size:21 final size:21
Alignment explanation
Indices: 32593058--32593100 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
32593048 TTTTTTCAAA
32593058 ATTTTTTTTTCAATTTTTTTT
1 ATTTTTTTTTCAATTTTTTTT
*
32593079 ATTTTTTTTTCGATTTTTTTT
1 ATTTTTTTTTCAATTTTTTTT
32593100 A
1 A
32593101 ATCTACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
ATTTTTTTTTCAATTTTTTTT
Found at i:32597329 original size:20 final size:20
Alignment explanation
Indices: 32597304--32597358 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
32597294 TGTGGTTCAA
*
32597304 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
32597324 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
32597344 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
32597359 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:32599170 original size:12 final size:12
Alignment explanation
Indices: 32599155--32599194 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
32599145 AAAAAGAAGG
32599155 AAAAAATTCAAA
1 AAAAAATTCAAA
32599167 AAAAAATTCAAA
1 AAAAAATTCAAA
32599179 AAAAAATTCAAA
1 AAAAAATTCAAA
32599191 AAAA
1 AAAA
32599195 TTTATATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:32599284 original size:19 final size:19
Alignment explanation
Indices: 32599246--32599284 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32599236 TCAATATTGG
*
32599246 AAAAAAAAGAGAAATTAAA
1 AAAAAAAAGAGAAATAAAA
32599265 AAAAAAAAGAAGAAA-AAAA
1 AAAAAAAAG-AGAAATAAAA
32599284 A
1 A
32599285 TGTTTCAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAAAAAGAGAAATAAAA
Found at i:32600221 original size:17 final size:15
Alignment explanation
Indices: 32600201--32600239 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
32600191 GCGAGCGAGA
32600201 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
32600218 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
32600233 AAGATGA
1 AA-ATGA
32600240 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:32601746 original size:20 final size:20
Alignment explanation
Indices: 32601721--32601775 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
32601711 TGTGGTTCAA
*
32601721 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
32601741 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
32601761 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
32601776 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:32604114 original size:30 final size:30
Alignment explanation
Indices: 32604080--32604176 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32604070 AGCTCACTCC
32604080 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
32604110 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
32604140 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
32604170 TAGCTCA
1 TAGCTCA
32604177 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32610632 original size:30 final size:30
Alignment explanation
Indices: 32610551--32610633 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
32610541 ATTTAGCTCA
*
32610551 CTCACGAGCTAAACCTTAGCTCAACTTCAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTCAG
* * ** * *
32610581 CTTAGGAG-TTTAGCCTCAGCTCAACTTTAG
1 CTCACGAGCTAAAG-CTTAGCTCAACTTCAG
32610611 CTCACGAGCTAAAGCTTAGCTCA
1 CTCACGAGCTAAAGCTTAGCTCA
32610634 TTTTAGTTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
CTCACGAGCTAAAGCTTAGCTCAACTTCAG
Found at i:32612335 original size:11 final size:11
Alignment explanation
Indices: 32612319--32612359 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
32612309 GAGAAATTCG
32612319 AAAAAAAATTA
1 AAAAAAAATTA
*
32612330 AAAAAAAATCGA
1 AAAAAAAAT-TA
32612342 AAAAAAAATTA
1 AAAAAAAATTA
32612353 AAAAAAA
1 AAAAAAA
32612360 TCGAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:32612372 original size:23 final size:23
Alignment explanation
Indices: 32612319--32612364 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
32612309 GAGAAATTCG
32612319 AAAAAAAATTAAAAAAAAATCGA
1 AAAAAAAATTAAAAAAAAATCGA
32612342 AAAAAAAATT-AAAAAAAATCGA
1 AAAAAAAATTAAAAAAAAATCGA
32612364 A
1 A
32612365 GTATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAAAATTAAAAAAAAATCGA
Found at i:32613317 original size:37 final size:37
Alignment explanation
Indices: 32613266--32613336 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
32613256 CATTCTTGTA
32613266 AAGAGAAAACAAAG-AAAAGAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAAAG-AAAGAAAAAGAAAAAGC
*
32613303 AAGAGAAGAA-AAAGAAAAAGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAAAGAAAGAAAAAGAAAA
32613337 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.01
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAAAGAAAGAAAAAGAAAAAGC
Found at i:32613324 original size:15 final size:16
Alignment explanation
Indices: 32613265--32613336 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
32613255 ACATTCTTGT
*
32613265 AAAGAGAAAACAAAG-A
1 AAAGA-AAAAGAAAGAA
*
32613281 AAAGAAAAGAAAAAGAA
1 AAAGAAAA-AGAAAGAA
* *
32613298 AAAGCAAGAG-AAGAA
1 AAAGAAAAAGAAAGAA
*
32613313 AAAGAAAAAGAAATAA
1 AAAGAAAAAGAAAGAA
32613329 AAAGAAAA
1 AAAGAAAA
32613337 GAGAGGCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 16 0.35
16 23 0.50
17 7 0.15
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:32613336 original size:6 final size:6
Alignment explanation
Indices: 32613276--32613325 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
32613266 AAGAGAAAAC
32613276 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
32613325 A
1 A
32613326 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.22
6 23 0.56
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:32613338 original size:21 final size:21
Alignment explanation
Indices: 32613276--32613336 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
32613266 AAGAGAAAAC
32613276 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
* * *
32613298 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
32613319 AAAGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
32613337 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:32613418 original size:11 final size:12
Alignment explanation
Indices: 32613386--32613416 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
32613376 TTGAGAGAAC
32613386 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32613398 TTGAAAAAGCCT
1 TTGAAAAAGCCT
32613410 TTGAAAA
1 TTGAAAA
32613417 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:32613443 original size:30 final size:32
Alignment explanation
Indices: 32613409--32613475 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
32613399 TGAAAAAGCC
32613409 TTTGAAAAG-CAAAAAGAAAATG-AAAAGAAA
1 TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
* * *
32613439 TTTG-AGAGTGAAAAAGAAGATGAAAAAGAAA
1 TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
32613470 -TTGAAA
1 TTTGAAA
32613476 CAAAAGAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
29 3 0.10
30 18 0.60
31 9 0.30
ACGTcount: A:0.61, C:0.01, G:0.21, T:0.16
Consensus pattern (32 bp):
TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
Found at i:32615577 original size:30 final size:30
Alignment explanation
Indices: 32615543--32615639 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32615533 AGCTCACTCC
32615543 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
32615573 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
32615603 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
32615633 TAGCTCA
1 TAGCTCA
32615640 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32617525 original size:20 final size:20
Alignment explanation
Indices: 32617479--32617525 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32617469 AGCTTGTTTC
*
32617479 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
32617499 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
32617519 CAGCTCA
1 CAGCTCA
32617526 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:32620139 original size:48 final size:47
Alignment explanation
Indices: 32620060--32620165 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
32620050 GAGTGTCATG
*
32620060 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
32620108 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
32620156 GAAAAAGAAA
1 GAAAAAGAAA
32620166 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Done.