Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 27 of 28
Found at i:4155891 original size:20 final size:21
Alignment explanation
Indices: 4155844--4155900 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
4155834 TTTATCGATA
*
4155844 CATTGTATCGATACATACTTG
1 CATTGTATCGATACATACGTG
* *
4155865 AATTGTATCAATACATA-GTG
1 CATTGTATCGATACATACGTG
4155885 CATTGTATCGATACAT
1 CATTGTATCGATACAT
4155901 TGAGCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
CATTGTATCGATACATACGTG
Found at i:4157552 original size:17 final size:17
Alignment explanation
Indices: 4157530--4157562 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4157520 GCTATGAACT
4157530 CATATATTATAGTGGAC
1 CATATATTATAGTGGAC
4157547 CATATATTATAGTGGA
1 CATATATTATAGTGGA
4157563 TCTAGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (17 bp):
CATATATTATAGTGGAC
Found at i:4158605 original size:19 final size:20
Alignment explanation
Indices: 4158561--4158653 Score: 118
Period size: 19 Copynumber: 4.8 Consensus size: 20
4158551 CTGCCAGTTT
**
4158561 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
4158581 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
**
4158600 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
4158620 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
4158639 CATGTATTGATACAA
1 CATGTATCGATACAA
4158654 AGCATAATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 34 0.52
20 31 0.48
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:4158614 original size:39 final size:39
Alignment explanation
Indices: 4158561--4158653 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
4158551 CTGCCAGTTT
4158561 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
*
4158600 CATGTATCGATACAATTGTGCATGTATTGATACAATGAA
1 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
*
4158639 CATGTATTGATACAA
1 CATGTATCGATACAA
4158654 AGCATAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (39 bp):
CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
Found at i:4158664 original size:39 final size:39
Alignment explanation
Indices: 4158561--4158670 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
4158551 CTGCCAGTTT
* * *
4158561 CATGTATCGATACAATTGTGCATGTATCGATACAATGAA
1 CATGTATCGATACAATAGTGAATGTATTGATACAATGAA
* *
4158600 CATGTATCGATACAATTGTGCATGTATTGATACAATGAA
1 CATGTATCGATACAATAGTGAATGTATTGATACAATGAA
*
4158639 CATGTATTGATACAA-AGCAT-AATGTATTGATA
1 CATGTATCGATACAATAG--TGAATGTATTGATA
4158671 TATCTGGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.02
39 63 0.97
40 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (39 bp):
CATGTATCGATACAATAGTGAATGTATTGATACAATGAA
Found at i:4158665 original size:20 final size:19
Alignment explanation
Indices: 4158581--4158670 Score: 83
Period size: 19 Copynumber: 4.6 Consensus size: 19
4158571 TACAATTGTG
* *
4158581 CATGTATCGATACAATGAA
1 CATGTATTGATACAAAGAA
* * **
4158600 CATGTATCGATACAATTGTG
1 CATGTATTGATACAA-AGAA
*
4158620 CATGTATTGATACAATGAA
1 CATGTATTGATACAAAGAA
4158639 CATGTATTGATACAAAGCATA
1 CATGTATTGATACAAAG-A-A
4158660 -ATGTATTGATA
1 CATGTATTGATA
4158671 TATCTGGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
19 33 0.53
20 28 0.45
21 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (19 bp):
CATGTATTGATACAAAGAA
Found at i:4159254 original size:21 final size:21
Alignment explanation
Indices: 4159230--4159274 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4159220 AGCTCTCGTT
**
4159230 TAAAAAATTTCTCCCTTTTGA
1 TAAAAAATTTCTCCCCCTTGA
*
4159251 TAAAAATTTTCTCCCCCTTGA
1 TAAAAAATTTCTCCCCCTTGA
4159272 TAA
1 TAA
4159275 TCGTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAAAATTTCTCCCCCTTGA
Found at i:4162131 original size:20 final size:20
Alignment explanation
Indices: 4162094--4162186 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
4162084 TTTCACAATA
*
4162094 TGTATTGATACA-TGTTCAT
1 TGTATCGATACATTGTTCAT
*
4162113 TATATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
*
4162133 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGTTCAT
*
4162153 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGTT-CAT
4162173 TGTATCGATACATT
1 TGTATCGATACATT
4162187 CAGGCATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.17
20 55 0.83
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:4164625 original size:79 final size:78
Alignment explanation
Indices: 4164487--4164986 Score: 331
Period size: 79 Copynumber: 6.3 Consensus size: 78
4164477 ATTTCATCTT
* * * * * *
4164487 GGGGATACTCCAACCCCGGTTTTATTTCCAAAATATCAATTTTTCATAATCGAGAATACTCCAAC
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
4164552 CCCGTTATTTCCGA
65 CCCGTTATTTCCGA
* *
4164566 GGGGATACTCCAAACCCGATTTTATTTCTAAAACACCCATTTTCCATAATCGGGGATACTCCAAC
1 GGGGATACTCC-AACCCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
**
4164631 TCCAATTTTATTTCC-A
65 -CC--CGTTATTTCCGA
** * * *** * ** ** *
4164647 --AAATA--CCAATTTTTCACAATCGGGGA-TACTCCAAC-CCCGTTATTTCAT--T-GGAGATA
1 GGGGATACTCCAA-----CCCGAT--TTTATTTCTAAAACACCAATT-TTTCATAATCGGGGATA
4164703 CTCCAACCCCGTTATTTCCGA
58 CTCCAACCCCGTTATTTCCGA
* ** * ** * *
4164724 AGGGATACTCCAACTCCGGCTTTATTTCTAAAATATTAATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAAC-CCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
** *
4164789 CCCGTTATTTTTGC
65 CCCGTTATTTCCGA
** * * ** *
4164803 GGGGATACTCCAACCCTGGCTTTATTTCTAAAGCATCAATTTTTCATAATCGGGGATACTTTAAT
1 GGGGATACTCCAACCC-GATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
4164868 CCCGTTATTTTCGA
65 CCCGTTATTTCCGA
* * * *
4164882 GGGGATACTCCAACCTCGATTTTATTT-TCAAAACACCGATTTTTCACAATTGGGGATACTCTAA
1 GGGGATACTCCAACC-CGATTTTATTTCT-AAAACACCAATTTTTCATAATCGGGGATACTCCAA
4164946 CCCCGTTATTAT-CGA
64 CCCCGTTATT-TCCGA
4164961 GGGGATACTCCAACCCTGATTTTATT
1 GGGGATACTCCAACCC-GATTTTATT
4164987 CTCAAAATGT
Statistics
Matches: 325, Mismatches: 68, Indels: 56
0.72 0.15 0.12
Matches are distributed among these distances:
75 1 0.00
76 20 0.06
77 6 0.02
78 7 0.02
79 250 0.77
80 7 0.02
81 14 0.04
82 19 0.06
83 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTCCGA
Found at i:4164639 original size:51 final size:50
Alignment explanation
Indices: 4164566--4164683 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 50
4164556 TTATTTCCGA
* * * *
4164566 GGGGATACTCCAAACCCGATTTTATTTCTAAAACACCCATTTTCCATAATC
1 GGGGATACTCC-AACCCAATTTTATTTCCAAAACACCAATTTTCCACAATC
* *
4164617 GGGGATACTCCAACTCCAATTTTATTTCCAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCAATTTTATTTCCAAAACACCAATTTTCCACAATC
4164668 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
4164684 CGTTATTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 5 0.08
51 55 0.92
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (50 bp):
GGGGATACTCCAACCCAATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:4164730 original size:28 final size:27
Alignment explanation
Indices: 4164669--4164737 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
4164659 TTCACAATCG
*
4164669 GGGATACTCCAACCCCGTTATTTCATT
1 GGGATACTCCAACCCCGTTATTTCATA
4164696 GGAGATACTCCAACCCCGTTATTTCCGA-A
1 GG-GATACTCCAACCCCGTTATTT-C-ATA
4164725 GGGATACTCCAAC
1 GGGATACTCCAAC
4164738 TCCGGCTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 2 0.05
28 32 0.84
29 3 0.08
30 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTCATA
Found at i:4164810 original size:107 final size:106
Alignment explanation
Indices: 4164618--4164818 Score: 296
Period size: 107 Copynumber: 1.9 Consensus size: 106
4164608 TCCATAATCG
* *
4164618 GGGATACTCCAACTCCAATTTTATTTCCAAAATACCAATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACTCCAACTTTATTTCCAAAATACCAATTTCTCACAATCGGGGATACTCCAACC
4164683 CCGTTATTTCATTGGAGATACTCCAACCCCGTTATTTCCGAA
66 CCGTTATTT-ATTGGAGATACTCCAACCCCGTTATTTCCGAA
** * **
4164725 GGGATACTCCAACTCCGGCTTTATTTCTAAAATATTAATTTCTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACTCCAACTTTATTTCCAAAATACCAATTTCTCACAATCGGGGATACTCCAACC
*
4164790 CCGTTATTT-TTGCGGGGATACTCCAACCC
66 CCGTTATTTATT--GGAGATACTCCAACCC
4164819 TGGCTTTATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 2 0.02
107 82 0.98
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (106 bp):
GGGATACTCCAACTCCAACTTTATTTCCAAAATACCAATTTCTCACAATCGGGGATACTCCAACC
CCGTTATTTATTGGAGATACTCCAACCCCGTTATTTCCGAA
Found at i:4164993 original size:79 final size:79
Alignment explanation
Indices: 4164699--4164986 Score: 339
Period size: 79 Copynumber: 3.6 Consensus size: 79
4164689 TTTCATTGGA
* * * * *
4164699 GATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACTCC-GGCTTTATTTCTAAAATATTAA
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC-CCTGACTTTATTTCTAAAACATCAA
*
4164763 TTTCTCACAATCGGG
65 TTTTTCACAATCGGG
* * * *
4164778 GATACTCCAACCCCGTTATTTTTGCGGGGATACTCCAACCCTGGCTTTATTTCTAAAGCATCAAT
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGACTTTATTTCTAAAACATCAAT
*
4164843 TTTTCATAATCGGG
66 TTTTCACAATCGGG
** * * * *
4164857 GATACTTTAATCCCGTTATTTTCGAGGGGATACTCCAA-CCTCGATTTTATTT-TCAAAACACCG
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCT-GACTTTATTTCT-AAAACATCA
*
4164920 ATTTTTCACAATTGGG
64 ATTTTTCACAATCGGG
* * *
4164936 GATACTCTAACCCCGTTATTATCGAGGGGATACTCCAACCCTGATTTTATT
1 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGACTTTATT
4164987 CTCAAAATGT
Statistics
Matches: 181, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
78 6 0.03
79 172 0.95
80 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGACTTTATTTCTAAAACATCAAT
TTTTCACAATCGGG
Found at i:4165010 original size:158 final size:158
Alignment explanation
Indices: 4164710--4165021 Score: 355
Period size: 158 Copynumber: 2.0 Consensus size: 158
4164700 ATACTCCAAC
* * **
4164710 CCCGTTATTTCCGAAGGGATACTCCAACTCCGGCTTTATTTCTAAAATATTAATTTCTCACAATC
1 CCCGTTATTTCCGAAGGGATACTCCAACTCCGACTTTATTTCTAAAACACCAATTTCTCACAATC
* * * * *
4164775 GGGGATACTCCAACCCCGTTATTTTTGCGGGGATACTCCAACCCTGGCTTTATTTCTAAAGCATC
66 GGGGATACTCCAACCCCGTTATTATCGAGGGGATACTCCAACCCTGACTTTATTTCAAAAG-ATC
* *
4164840 AATTTTTCATAA-TCGGGGATACTTTAAT
130 AATTTCTCATAATTAGGGGATACTTTAAT
* * * * *
4164868 CCCGTTATTTTCGAGGGGATACTCCAAC-CTCGATTTTATTT-TCAAAACACCGATTTTTCACAA
1 CCCGTTATTTCCGAAGGGATACTCCAACTC-CGACTTTATTTCT-AAAACACCAATTTCTCACAA
* * *
4164931 TTGGGGATACTCTAACCCCGTTATTATCGAGGGGATACTCCAACCCTGATTTTATTCTCAAAATG
64 TCGGGGATACTCCAACCCCGTTATTATCGAGGGGATACTCCAACCCTGACTTTATT-TCAAAA-G
*
4164996 -TCGATTTC-CTATAATTAGGGGATACT
127 ATCAATTTCTC-ATAATTAGGGGATACT
4165022 ACAGCCCCGT
Statistics
Matches: 128, Mismatches: 20, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
157 3 0.02
158 109 0.85
159 15 0.12
160 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (158 bp):
CCCGTTATTTCCGAAGGGATACTCCAACTCCGACTTTATTTCTAAAACACCAATTTCTCACAATC
GGGGATACTCCAACCCCGTTATTATCGAGGGGATACTCCAACCCTGACTTTATTTCAAAAGATCA
ATTTCTCATAATTAGGGGATACTTTAAT
Found at i:4171439 original size:13 final size:13
Alignment explanation
Indices: 4171421--4171445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4171411 CAATTCATCA
4171421 TGTATCGATACAT
1 TGTATCGATACAT
4171434 TGTATCGATACA
1 TGTATCGATACA
4171446 ATATCCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4171543 original size:19 final size:19
Alignment explanation
Indices: 4171495--4171550 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
4171485 CTGCCAGTTT
* **
4171495 CATGTATCGATATAATTGTG
1 CATGTATCGATACAA-TGAA
*
4171515 CATTTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
4171534 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
4171551 TATCGATGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:4171553 original size:13 final size:13
Alignment explanation
Indices: 4171535--4171561 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4171525 TACAATGAAC
4171535 ATGTATCGATGCA
1 ATGTATCGATGCA
4171548 ATGTATCGATGCA
1 ATGTATCGATGCA
4171561 A
1 A
4171562 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (13 bp):
ATGTATCGATGCA
Found at i:4175725 original size:17 final size:17
Alignment explanation
Indices: 4175698--4175738 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4175688 TTGGGATTAC
* *
4175698 TAAAAAATAAAACTATT
1 TAAAAATTAAAACAATT
*
4175715 TTAAAATTAAAACAATT
1 TAAAAATTAAAACAATT
4175732 TAAAAAT
1 TAAAAAT
4175739 CAAGAAATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATTAAAACAATT
Found at i:4177620 original size:16 final size:16
Alignment explanation
Indices: 4177599--4177632 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4177589 GTTAAACTTG
*
4177599 AAATAACTCAAATTCA
1 AAATAACTCAAACTCA
*
4177615 AAATAACTTAAACTCA
1 AAATAACTCAAACTCA
4177631 AA
1 AA
4177633 TTGACCGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAACTCAAACTCA
Found at i:4181901 original size:3 final size:3
Alignment explanation
Indices: 4181893--4181924 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4181883 TACCTAGTCA
*
4181893 AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4181925 AGCCTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4184228 original size:15 final size:14
Alignment explanation
Indices: 4184204--4184254 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
4184194 TGAAATAAAT
4184204 TTAT-TTATTGAATA
1 TTATATTATTGAA-A
4184218 TTATATTATTGAAA
1 TTATATTATTGAAA
*
4184232 TT-TATT-TTTAAA
1 TTATATTATTGAAA
4184244 TTATTATTATT
1 TTA-TATTATT
4184255 TACAAATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 7 0.22
13 4 0.12
14 11 0.34
15 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (14 bp):
TTATATTATTGAAA
Found at i:4184232 original size:29 final size:27
Alignment explanation
Indices: 4184200--4184254 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
4184190 ATTCTGAAAT
4184200 AAATTTATTTATTGAATATTA-TATTATTG
1 AAATTTATTT-TT-AA-ATTATTATTATTG
4184229 AAATTTATTTTTAAATTATTATTATT
1 AAATTTATTTTTAAATTATTATTATT
4184255 TACAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.16
27 9 0.36
28 2 0.08
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
AAATTTATTTTTAAATTATTATTATTG
Found at i:4184261 original size:29 final size:29
Alignment explanation
Indices: 4184200--4184263 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
4184190 ATTCTGAAAT
*
4184200 AAATTTATTTATTGAATATTATATTATTG
1 AAATTTATTTATTGAATATTATATTATTC
4184229 AAATTTATTT-TT-AA-ATTATTATTATTTAC
1 AAATTTATTTATTGAATATTA-TATTA-TT-C
4184258 AAATTT
1 AAATTT
4184264 GGCTTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 7 0.23
28 4 0.13
29 16 0.52
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
AAATTTATTTATTGAATATTATATTATTC
Found at i:4184721 original size:64 final size:64
Alignment explanation
Indices: 4184620--4184749 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
4184610 TTTACATGCT
4184620 TATGAGATTCATTTAATAAGTATATGACACTGTTATATCTTATATCCATGAATTTGGAGTATGA
1 TATGAGATTCATTTAATAAGTATATGACACTGTTATATCTTATATCCATGAATTTGGAGTATGA
4184684 TATGAGATTCATTTAATAAGTATATGACACTGTTATATCTTATATCCATGAATTTGGAGTATGA
1 TATGAGATTCATTTAATAAGTATATGACACTGTTATATCTTATATCCATGAATTTGGAGTATGA
4184748 TA
1 TA
4184750 AATAATGATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (64 bp):
TATGAGATTCATTTAATAAGTATATGACACTGTTATATCTTATATCCATGAATTTGGAGTATGA
Found at i:4196619 original size:6 final size:6
Alignment explanation
Indices: 4196608--4196785 Score: 75
Period size: 6 Copynumber: 29.5 Consensus size: 6
4196598 AAAATCCAAA
* * ***
4196608 AAAAAG AAAAAG AAAAA- AAGAGG AAGAAAG GCGAA- AAAAAG ACAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG A-AAAAG
* * * * * **
4196656 AAAAAAG AGAAAG -AAAGG AGAAAT AAAAAG AAAATAA AAAAAG -AAGGG
1 -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG
* *
4196704 AAAAATT AAAAA- AAAAAG AAAAAAG AAAACAAA AAAAAG AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAAG -AAAAAG -AAA-AAG AAAAAG AAAAAG AAAAAG
**
4196755 -AAAAG GGAAAG AGAAAAG -AAAAG -AAAAG AAA
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAA
4196786 GGAAAAAAAG
Statistics
Matches: 127, Mismatches: 30, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
5 31 0.24
6 54 0.43
7 39 0.31
8 3 0.02
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:4196660 original size:35 final size:34
Alignment explanation
Indices: 4196606--4196758 Score: 120
Period size: 35 Copynumber: 4.5 Consensus size: 34
4196596 AAAAAATCCA
* *
4196606 AAAAAAAGAAAAAGAAAAAAAGAGGAAGAAAGGCG
1 AAAAAAAGAAAAAG-AAAAAAGAGAAAGAAAGGAG
4196641 AAAAAAAGACAAAAGAAAAAAGAGAAAGAAAGGAG
1 AAAAAAAGA-AAAAGAAAAAAGAGAAAGAAAGGAG
* * * * *
4196676 AAATAAA-AAGAA-AATAAA-A-AAAGAAGGGAA
1 AAAAAAAGAAAAAGAAAAAAGAGAAAGAAAGGAG
* * * *
4196706 AAATTAAAAAAAAAAGAAAAAAGA-AAACAAA-AAA
1 AAA--AAAAGAAAAAGAAAAAAGAGAAAGAAAGGAG
4196740 AAGAAAAAGAAAAAGAAAA
1 AA-AAAAAGAAAAAGAAAA
4196759 GGGAAAGAGA
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
30 12 0.12
31 1 0.01
32 8 0.08
33 21 0.22
34 10 0.10
35 40 0.41
36 5 0.05
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.03
Consensus pattern (34 bp):
AAAAAAAGAAAAAGAAAAAAGAGAAAGAAAGGAG
Found at i:4196687 original size:30 final size:30
Alignment explanation
Indices: 4196651--4196788 Score: 116
Period size: 30 Copynumber: 4.8 Consensus size: 30
4196641 AAAAAAAGAC
*
4196651 AAAAGAAAAAAGAGAAAGAAAGGAGAAATA
1 AAAAGAAAAAAGAAAAAGAAAGGAGAAATA
* * *
4196681 AAAAGAAAATAA-AAAAAGAAGGGAAAAATT
1 AAAAGAAAA-AAGAAAAAGAAAGGAGAAATA
*
4196711 AAAA-AAAAAAGAAAAAAGAAA--ACAAA-A
1 AAAAGAAAAAAG-AAAAAGAAAGGAGAAATA
*
4196738 AAAAG-AAAAAGAAAAAGAAAAGG-GAAAGA
1 AAAAGAAAAAAGAAAAAG-AAAGGAGAAATA
4196767 GAAAAG--AAAAG-AAAAGAAAGGA
1 -AAAAGAAAAAAGAAAAAGAAAGGA
4196789 AAAAAAGGGA
Statistics
Matches: 90, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
26 6 0.07
27 18 0.20
28 14 0.16
29 10 0.11
30 40 0.44
31 2 0.02
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.03
Consensus pattern (30 bp):
AAAAGAAAAAAGAAAAAGAAAGGAGAAATA
Found at i:4196725 original size:5 final size:5
Alignment explanation
Indices: 4196724--4196791 Score: 66
Period size: 5 Copynumber: 12.8 Consensus size: 5
4196714 AAAAAAAGAA
*
4196724 AAAAG AAAAC AAAA- AAAAG AAAAAG AAAAAG AAAAGGG AAAGAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG -AAAAG -AAAAG AAAA--G AAA-AG AAAAG
*
4196773 AAAAG AAAAG AAAGG AAAA
1 AAAAG AAAAG AAAAG AAAA
4196792 AAAGGGAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.07
5 31 0.56
6 15 0.27
7 4 0.07
8 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4196773 original size:7 final size:7
Alignment explanation
Indices: 4196642--4196758 Score: 61
Period size: 7 Copynumber: 16.6 Consensus size: 7
4196632 AGAAAGGCGA
4196642 AAAAAAG
1 AAAAAAG
*
4196649 ACAAAAG
1 AAAAAAG
4196656 AAAAAAG
1 AAAAAAG
*
4196663 -AGAAAG
1 AAAAAAG
4196669 AAAGGAGAA-
1 AAA--A-AAG
4196678 ATAAAAAG
1 A-AAAAAG
*
4196686 AAAATA-
1 AAAAAAG
4196692 AAAAAAG
1 AAAAAAG
4196699 AAGGGAAAA-
1 AA---AAAAG
*
4196708 ATTAAAA-
1 A-AAAAAG
4196715 AAAAAAG
1 AAAAAAG
4196722 AAAAAAG
1 AAAAAAG
4196729 AAAACAA-
1 AAAA-AAG
4196736 AAAAAAG
1 AAAAAAG
4196743 -AAAAAG
1 AAAAAAG
4196749 -AAAAAG
1 AAAAAAG
4196755 AAAA
1 AAAA
4196759 GGGAAAGAGA
Statistics
Matches: 87, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
6 28 0.32
7 44 0.51
8 4 0.05
9 3 0.03
10 8 0.09
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:4205980 original size:13 final size:12
Alignment explanation
Indices: 4205931--4205981 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
4205921 ACCTTCACTG
4205931 TTTCAAATTGAA
1 TTTCAAATTGAA
*
4205943 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
4205958 TTTCAAATTGAA
1 TTTCAAATTGAA
4205970 TTTCAAAATTGA
1 TTTC-AAATTGA
4205982 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:4206001 original size:12 final size:12
Alignment explanation
Indices: 4205984--4206009 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4205974 AAAATTGACG
4205984 GCACAGTTGGCA
1 GCACAGTTGGCA
4205996 GCACAGTTGGCA
1 GCACAGTTGGCA
4206008 GC
1 GC
4206010 CTTTGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (12 bp):
GCACAGTTGGCA
Found at i:4210517 original size:21 final size:21
Alignment explanation
Indices: 4210475--4210517 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4210465 ATTAATTTTA
* **
4210475 ATTTTCTTTTAATTTTGGATT
1 ATTTTATTTTAATTTTAAATT
*
4210496 ATTTTATTTTATTTTTAAATT
1 ATTTTATTTTAATTTTAAATT
4210517 A
1 A
4210518 GTTTCATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTAATTTTAAATT
Found at i:4212240 original size:157 final size:153
Alignment explanation
Indices: 4211956--4212506 Score: 551
Period size: 157 Copynumber: 3.5 Consensus size: 153
4211946 AATTGAATTT
* * ** * * *
4211956 GATGTAGTTACTGGGATGCTTTTATGATAAAGGTGTTCATTTATGATAGGTTCACC-TTTTTGGA
1 GATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCTTTTTTTGA
* * * *
4212020 TCATTTTCGAGTATTTTAGGGTAACTGGGATACTTTCATG-CTAAAGTTATACCCTAAGGGCATT
66 TCATTTTCGAGTCTTTTAGGGTAACTGAGATACTTTAATGTC-AAAGGTATA-CCTAAGGGCATT
*
4212084 TTGATAATTTTCCTAGAACCAAGTCC
129 TTGATAATTTT-TTAGAACCAAGTCC
* * *
4212110 AATGTAGTCACTGAGATGCTTTTATGCCAAAGATGTGCATTTAGGATAGGTTTTTACCTTTTTTT
1 GATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGG--TTCACCTTTTTTT
* *
4212175 GATCATTTTTGAGTCTTTTAGGGTAACTGAGATACTTTAATGTCAAAGGTATATCCTAAAGGCAT
64 GATCATTTTCGAGTCTTTTAGGGTAACTGAGATACTTTAATGTCAAAGGTATA-CCTAAGGGCAT
* *
4212240 TTTGGTAATTTTTTTAAAACCAAGTCC
128 TTTGATAA-TTTTTTAGAACCAAGTCC
* * * * *
4212267 GTTGTAGTCATTGAGATGCATTTATGCCAAAGGTGTACATTAAGGATAGGTTCACCCCCTTTTTT
1 GATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCA---CCTTTTTT
* * * * * * *
4212332 TGATCATTTTCAAGTCCTTTAGGTTAA-TCAAGATATTTTCATAT-TGAAA-GTATACTTTAAGG
63 TGATCATTTTCGAGTCTTTTAGGGTAACT-GAGATACTTT-A-ATGTCAAAGGTATAC-CTAAGG
*** *
4212394 GCATTTTGATAATTCTTTTAGAATTGAGTCT
124 GCATTTTGATAATT-TTTTAGAACCAAGTCC
* *
4212425 GATGTAGTCA-TCGGGATGCTTTTATGCCAAAGGTTTGCATTTAGGATAGAG-TCA-CTTTTTTT
1 GATGTAGTCACT-GAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAG-GTTCACCTTTTTTT
*
4212487 GATCATTTTTGAGTCTTTTA
64 GATCATTTTCGAGTCTTTTA
4212507 AGGTTACTAG
Statistics
Matches: 330, Mismatches: 52, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
154 67 0.20
155 3 0.01
156 5 0.02
157 128 0.39
158 119 0.36
159 6 0.02
160 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (153 bp):
GATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCTTTTTTTGA
TCATTTTCGAGTCTTTTAGGGTAACTGAGATACTTTAATGTCAAAGGTATACCTAAGGGCATTTT
GATAATTTTTTAGAACCAAGTCC
Found at i:4212431 original size:158 final size:154
Alignment explanation
Indices: 4211866--4212515 Score: 545
Period size: 157 Copynumber: 4.2 Consensus size: 154
4211856 ACCATTATTT
* *
4211866 ATCATTTTCAAGTCTTTT-GAGGTTACTGAA-ATACTTTTATGTTGAAAG-ATAT-CTGAAAGGC
1 ATCATTTTCAAGTCTTTTAG-GGTAACT-AAGATAC-TTTATATTGAAAGTATATCCT-AAAGGC
* ** ** * * **
4211927 ATTTTGGTAATTTTCTTAGAATTGAA-TTTGATGTAGTTACTGGGATGCTTTTATGATAAAGGTG
62 ATTTTGATAATTTTCTTAGAA-CCAAGTCCGATGTAGTCACTGAGATGCTTTTATGCCAAAGGTG
* * *
4211991 TTCATTTATGATAGGTTCACC-TTTTTGG
126 TGCATTTAGGATAGGTTCACCTTTTTTTG
* * ** ** * *
4212019 ATCATTTTCGAGTATTTTAGGGTAACTGGGATACTTTCATGCT-AAAGTTATACCCTAAGGGCAT
1 ATCATTTTCAAGTCTTTTAGGGTAACTAAGATACTTT-ATATTGAAAG-TATATCCTAAAGGCAT
* * *
4212083 TTTGATAATTTTCCTAGAACCAAGTCCAATGTAGTCACTGAGATGCTTTTATGCCAAAGATGTGC
64 TTTGATAATTTTCTTAGAACCAAGTCCGATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGC
*
4212148 ATTTAGGATAGGTTTTTACCTTTTTTTG
129 ATTTAGGATAGG--TTCACCTTTTTTTG
** * *
4212176 ATCATTTTTGAGTCTTTTAGGGTAACTGAGATACTTTA-ATGTCAAAGGTATATCCTAAAGGCAT
1 ATCATTTTCAAGTCTTTTAGGGTAACTAAGATACTTTATAT-TGAAA-GTATATCCTAAAGGCAT
* * * * * * *
4212240 TTTGGTAATTTTTTTAAAACCAAGTCCGTTGTAGTCATTGAGATGCATTTATGCCAAAGGTGTAC
64 TTTGATAATTTTCTTAGAACCAAGTCCGATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGC
*
4212305 ATTAAGGATAGGTTCACCCCCTTTTTTTG
129 ATTTAGGATAGGTTCA---CCTTTTTTTG
* * * * *
4212334 ATCATTTTCAAGTCCTTTAGGTTAA-TCAAGATATTTTCATATTGAAAGTATA-CTTTAAGGGCA
1 ATCATTTTCAAGTCTTTTAGGGTAACT-AAGATACTTT-ATATTGAAAGTATATC-CTAAAGGCA
*** * * *
4212397 TTTTGATAATTCTT-TTAGAATTGAGTCTGATGTAGTCA-TCGGGATGCTTTTATGCCAAAGGTT
63 TTTTGATAATT-TTCTTAGAACCAAGTCCGATGTAGTCACT-GAGATGCTTTTATGCCAAAGGTG
4212460 TGCATTTAGGATAGAG-TCA-CTTTTTTTG
126 TGCATTTAGGATAG-GTTCACCTTTTTTTG
** * *
4212488 ATCATTTTTGAGTCTTTTAAGGTTACTA
1 ATCATTTTCAAGTCTTTTAGGGTAACTA
4212516 GAATATTTTC
Statistics
Matches: 403, Mismatches: 70, Indels: 47
0.77 0.13 0.09
Matches are distributed among these distances:
152 7 0.02
153 32 0.08
154 100 0.25
155 6 0.01
156 7 0.02
157 126 0.31
158 115 0.29
159 8 0.02
160 2 0.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (154 bp):
ATCATTTTCAAGTCTTTTAGGGTAACTAAGATACTTTATATTGAAAGTATATCCTAAAGGCATTT
TGATAATTTTCTTAGAACCAAGTCCGATGTAGTCACTGAGATGCTTTTATGCCAAAGGTGTGCAT
TTAGGATAGGTTCACCTTTTTTTG
Found at i:4216733 original size:20 final size:20
Alignment explanation
Indices: 4216708--4216882 Score: 98
Period size: 20 Copynumber: 7.7 Consensus size: 20
4216698 TTTTACCCAG
*
4216708 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
4216728 ATGTATCGATACATTCTGTTTTTTACCCA
1 ATGTATCGATACA------TTTTT---CA
*
4216757 GATGTATCGTTACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * * *
4216778 ATGTATCAATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
4216798 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
4216818 ATGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
4216848 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
4216869 ATGTATCGATACAT
1 ATGTATCGATACAT
4216883 CTAGTTAAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
20 69 0.57
21 4 0.03
24 10 0.08
26 5 0.04
27 4 0.03
29 2 0.02
30 14 0.12
31 13 0.11
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4216875 original size:91 final size:90
Alignment explanation
Indices: 4216708--4216882 Score: 305
Period size: 91 Copynumber: 1.9 Consensus size: 90
4216698 TTTTACCCAG
* *
4216708 ATGTATCAATACATTTTTCAATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGTTACATT
1 ATGTATCAATACATTCTTCAATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGATACATT
4216773 TTTCAATGTATCAATACATGTATGA
66 TTTCAATGTATCAATACATGTATGA
*
4216798 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCAATACATTCTTCAATGTATCGATACATTCTGT-TTTTTACCCAGATGTATCGATACAT
*
4216863 TTTTCAATGTATCGATACAT
65 TTTTCAATGTATCAATACAT
4216883 CTAGTTAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 37 0.46
91 43 0.54
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (90 bp):
ATGTATCAATACATTCTTCAATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGATACATT
TTTCAATGTATCAATACATGTATGA
Found at i:4217307 original size:61 final size:61
Alignment explanation
Indices: 4217232--4217351 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
4217222 GGCTATAAAT
* * *
4217232 AGGCCAATGTAATCCTAGCAAATG-ATCCCCTTTTGTAATCACATTTTCTAGCCTCATTATC
1 AGGCCAATGCAATCCTAGCAAA-GAATCCCCTTTTGCAACCACATTTTCTAGCCTCATTATC
4217293 AGGCCAATGCAATCCTAGCAAAGAATCCCCTTTTGCAACCACATTTTCTAGCCTCATTA
1 AGGCCAATGCAATCCTAGCAAAGAATCCCCTTTTGCAACCACATTTTCTAGCCTCATTA
4217352 CCATCCATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 1 0.02
61 54 0.98
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (61 bp):
AGGCCAATGCAATCCTAGCAAAGAATCCCCTTTTGCAACCACATTTTCTAGCCTCATTATC
Found at i:4222870 original size:79 final size:76
Alignment explanation
Indices: 4222734--4222919 Score: 284
Period size: 79 Copynumber: 2.4 Consensus size: 76
4222724 AGGAAACATG
* *
4222734 TTAGAAAATAAAGCCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTA
1 TTAG-AAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTAT-CCC--TGA
4222799 TGAAAAATTGATGTT
62 TGAAAAATTGATGTT
*
4222814 TTAGAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTGATGAA
1 TTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTGATGAA
4222879 AAATTGATGTT
66 AAATTGATGTT
**
4222890 TT-GAAATGGAACCGGGGTTGGAGTATCCCC
1 TTAGAAATAAAACCGGGGTTGGAGTATCCCC
4222920 GAGATGAAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
75 25 0.25
76 19 0.19
78 3 0.03
79 49 0.49
80 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (76 bp):
TTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTGATGAA
AAATTGATGTT
Found at i:4225319 original size:13 final size:13
Alignment explanation
Indices: 4225301--4225326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4225291 ATAAAGATCG
4225301 ATGTATCGATACA
1 ATGTATCGATACA
4225314 ATGTATCGATACA
1 ATGTATCGATACA
4225327 TTGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4225386 original size:13 final size:13
Alignment explanation
Indices: 4225364--4225421 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
4225354 GGCAGTAGCT
*
4225364 TTGTAGCGATACA
1 TTGTATCGATACA
4225377 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
4225393 CTTATGTATCGATACA
1 --T-TGTATCGATACA
4225409 TTGTATCGATACA
1 TTGTATCGATACA
4225422 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4225402 original size:19 final size:19
Alignment explanation
Indices: 4225378--4225482 Score: 105
Period size: 19 Copynumber: 5.7 Consensus size: 19
4225368 AGCGATACAT
4225378 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
4225397 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
4225410 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
4225429 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
4225448 TGTATCGATACAGTTACTATC
1 TGTATCGATACA-AAACT-TA
4225469 TGTATCGATACAAA
1 TGTATCGATACAAA
4225483 TTGTTTGAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
16 2 0.03
18 1 0.01
19 42 0.58
20 3 0.04
21 13 0.18
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:4225411 original size:32 final size:32
Alignment explanation
Indices: 4225365--4225440 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
4225355 GCAGTAGCTT
*
4225365 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
4225397 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
4225429 TGTATCGATACA
1 TGTATCGATACA
4225441 ACACTTATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:4232181 original size:13 final size:13
Alignment explanation
Indices: 4232163--4232188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4232153 CTAATCTTGG
4232163 TAAAAATAAAAAA
1 TAAAAATAAAAAA
4232176 TAAAAATAAAAAA
1 TAAAAATAAAAAA
4232189 GAGAAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:4233545 original size:30 final size:30
Alignment explanation
Indices: 4233114--4233537 Score: 490
Period size: 30 Copynumber: 13.7 Consensus size: 30
4233104 TCTTCAAATT
* *
4233114 TCTCTTCTTAAAGTCTACGACTCAGTGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGC-A
*
4233145 TCTCTTCTCAAAGTCCACGACTCAGTAGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
4233175 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
4233205 TCTTTTTTTCTTCAAAGTCCACGACTCAGTGGCA
1 TC---TCTTC-TCAAAGTCCACGACTCAGTGGCA
* *
4233239 TCTTTTCTTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
* * *
4233270 TCTCTTTTCTAAGTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* *
4233300 TCCTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 T-CTCTTC-TCAAAGTCCACGACTCAGTGGCA
* * * *
4233332 TTTTTTTCTTCAAAGTCCACAACTTAGTGGCA
1 -TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
* *
4233364 TCTCTTCTCAAAGTCCATGACTTAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* *
4233394 -CTTTTCTTCAAAGTCGACGACTCAGTGGCAA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGC-A
*
4233425 TCTCTTCTCAAAGTCCATGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
4233455 TCTCTTCCCAAAGTCCATGTCTCAGTGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGC-A
* *
4233486 TCTCTTCTCAAAGTCCACAACTCGGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
4233516 TCTCTTCCCAAAGTCCACGACT
1 TCTCTTCTCAAAGTCCACGACT
4233538 TTGTGGCACT
Statistics
Matches: 343, Mismatches: 39, Indels: 23
0.85 0.10 0.06
Matches are distributed among these distances:
29 5 0.01
30 142 0.41
31 114 0.33
32 52 0.15
33 5 0.01
34 25 0.07
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (30 bp):
TCTCTTCTCAAAGTCCACGACTCAGTGGCA
Found at i:4233545 original size:61 final size:60
Alignment explanation
Indices: 4233114--4233537 Score: 490
Period size: 61 Copynumber: 6.9 Consensus size: 60
4233104 TCTTCAAATT
* * *
4233114 TCTCTTCTTAAAGTCTACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTAGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
4233175 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATC---TCTTC-TCAAAGTCCACGACTCAGTGGCA
* * * * *
4233239 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATGACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * * * * *
4233300 TCCTTTTCTTCCAAGTCCACGACTCAGTGGCATTTTTTTCTTCAAAGTCCACAACTTAGTGGCA
1 T-CTCTTC-TCAAAGTCCACGACTCAGTGGCA-TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
* * * *
4233364 TCTCTTCTCAAAGTCCATGACTTAGTGGCA-CTTTTCTTCAAAGTCGACGACTCAGTGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTC-TCAAAGTCCACGACTCAGTGGC-A
* * * *
4233425 TCTCTTCTCAAAGTCCATGACTCAGTGGCATCTCTTCCCAAAGTCCATGTCTCAGTGGCAA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGC-A
* * *
4233486 TCTCTTCTCAAAGTCCACAACTCGGTGGCATCTCTTCCCAAAGTCCACGACT
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACT
4233538 TTGTGGCACT
Statistics
Matches: 315, Mismatches: 38, Indels: 20
0.84 0.10 0.05
Matches are distributed among these distances:
60 28 0.09
61 146 0.46
62 56 0.18
63 13 0.04
64 48 0.15
65 24 0.08
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (60 bp):
TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCA
Found at i:4233577 original size:34 final size:33
Alignment explanation
Indices: 4233526--4234027 Score: 392
Period size: 34 Copynumber: 15.6 Consensus size: 33
4233516 TCTCTTCCCA
* ** *
4233526 AAGTCCACGACTTTGTGGCACTTTTTTCCTTTCA
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTT-T
* *
4233560 AAGTCCATAACTCTGTGGCAC------CCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
4233587 AAGT-CATAACTCCGTGGCA-TCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
*
4233619 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
*
4233654 AAGTCCACAACTTCGTGGCAC------CCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
4233681 AAGTCTACAACTCCATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
**
4233715 AAGTCCACAACTTTGTGGCAAC---TTTCCTTTT
1 AAGTCCACAACTCCGTGGC-ACTTTTTTCCTTTT
* * *
4233746 AAGTCCACAACTCCGTGGTACCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
4233779 AAAGCCCACAACTTCGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
* * *
4233814 AAGTTCATAACTCCGTGGCAC------CCTTTG
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
4233841 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
*
4233874 AAGTCCACAACTCCGTGGCACCTTGTTT-CTTTT
1 AAGTCCACAACTCCGTGGCA-CTTTTTTCCTTTT
* *
4233907 AAGTCCACAACTCCGTGGCAC-CTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* * *
4233939 AAGTCCACGACTCCGTAGCACATTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCAC-TTTTTTCCTTTT
* * * *
4233973 AAGCCCACACCTCTGTGGCATCCCTTTTTCC-TTT
1 AAGTCCACAACTCCGTGGCA--CTTTTTTCCTTTT
* *
4234007 AAGTCCATAACTCCATGGCAC
1 AAGTCCACAACTCCGTGGCAC
4234028 CTTTAAGTCC
Statistics
Matches: 375, Mismatches: 56, Indels: 76
0.74 0.11 0.15
Matches are distributed among these distances:
26 14 0.04
27 51 0.14
28 5 0.01
30 2 0.01
31 28 0.07
32 30 0.08
33 61 0.16
34 152 0.41
35 31 0.08
36 1 0.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
Found at i:4233674 original size:280 final size:276
Alignment explanation
Indices: 4233118--4233644 Score: 624
Period size: 280 Copynumber: 1.9 Consensus size: 276
4233108 CAAATTTCTC
* *
4233118 TTCTTAAAGTCTACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTAGCATCTCTTCT
1 TTCTTAAAGTCGACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTAGCATCTCTTCC
* * * *
4233183 CAAAGTCCACGACTCAGTGGCATCTTTTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTT
66 CAAAGTCCACGACTCAGTGGCATC--TTCTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTCTC
* *
4233248 CAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATGACTCAGTGGCATCCTTTTCTTCCA
129 CAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATAACTCAGTGGCATCCTCTTCTT-CA
* * *
4233313 AGTCCACGACTCAGTGGCATTTTTTTCTTCAAAGTCCACAACTTAGTGGCATCTCTTCTCAAAGT
193 AGTCCACAACTCAGTGGCATTTTTTTCTTCAAAGCCCACAACTCAGTGGCATCTCTTCTCAAAGT
**
4233378 CCATGACTTAGTGGCACTT
258 CCACAACTTAGTGGCACTT
* *
4233397 TTCTTCAAAGTCGACGACTCAGTGGCAATCTCTTCTCAAAGTCCATGACTCAGTGGCATCTCTTC
1 TTCTT-AAAGTCGACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTAGCATCTCTTC
* * *
4233462 CCAAAGTCCATGTCTCAGTGGCAATC-TCTTC-TCAAAGTCCACAACTCGGTGGCATCTCTTC-C
65 CCAAAGTCCACGACTCAGTGGC-ATCTTCTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTCTC
* ** * *
4233524 CAAAGTCCACGACTTTGTGGCA-CTTTTTTCCTTTCAAAGTCCATAACTCTGTGGCA-CC-CTT-
129 CAAAGTCCACAACTCAGTGGCATCTCTTTT-C--T--AAGTCCATAACTCAGTGGCATCCTCTTC
* * * * *
4233585 TT-AAGT-CATAACTCCGTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CTCTT
189 TTCAAGTCCACAACTCAGTGGCAT-TTTTT-TCTTCAAAGCCCACAACTCAGTGGCATCTCTT
4233645 TTTCCTTTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
274 13 0.06
275 20 0.09
276 41 0.19
277 29 0.14
278 7 0.03
279 7 0.03
280 93 0.44
281 3 0.01
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (276 bp):
TTCTTAAAGTCGACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTAGCATCTCTTCC
CAAAGTCCACGACTCAGTGGCATCTTCTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTCTCCA
AAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATAACTCAGTGGCATCCTCTTCTTCAAGT
CCACAACTCAGTGGCATTTTTTTCTTCAAAGCCCACAACTCAGTGGCATCTCTTCTCAAAGTCCA
CAACTTAGTGGCACTT
Found at i:4233690 original size:27 final size:27
Alignment explanation
Indices: 4233648--4233707 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
4233638 CACTCTTTTT
* *
4233648 CCTTTTAAGTCCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCAC
*
4233675 CCTTTTAAGTCTACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCAC
*
4233702 TCTTTT
1 CCTTTT
4233708 TCCTTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.35
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCATGGCAC
Found at i:4233700 original size:61 final size:61
Alignment explanation
Indices: 4233615--4234000 Score: 283
Period size: 65 Copynumber: 6.1 Consensus size: 61
4233605 ATCTTTTTCT
*
4233615 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCC
* * *
4233677 TTTTAAGTCTACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCAACTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGC-AC---CC
* * *
4233742 TTTTAAGTCCACAACTCCGTGGTAC-CTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACTCTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAGTCCACAACTTCGTGGCA--C---
4233806 TTCC
60 --CC
* * * *
4233810 TTTTAAGTTCATAACTCCGTGGCA--C-----CCTTTGAAGTCCACAACTCCGTGGCATCTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCA-C-----
4233868 CC
60 CC
*
4233870 TTTTAAGTCCACAACTCCGTGGCAC-CTTGTTT-CTTTTAAGTCCACAACTCCGTGGCACCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTT-TTTCCTTTTAAGTCCACAACTTCGTGGCACC----
4233933 C
61 C
* * * * *
4233934 TTTTTAAGTCCACGACTCCGTAGCACAT-TTTTCCCTTTTAAGCCCAC-ACCTCTGTGGCATCCC
1 -TTTTAAGTCCACAACTCCGTGGCAC-TCTTTTTCCTTTTAAGTCCACAACTTC-GTGGCA-CCC
4233997 TTTT
1 TTTT
4234001 TCCTTTAAGT
Statistics
Matches: 272, Mismatches: 26, Indels: 52
0.78 0.07 0.15
Matches are distributed among these distances:
60 32 0.12
61 68 0.25
62 14 0.05
63 1 0.00
64 13 0.05
65 70 0.26
66 45 0.17
67 3 0.01
68 26 0.10
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.37
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCC
Found at i:4233788 original size:160 final size:160
Alignment explanation
Indices: 4233541--4234000 Score: 591
Period size: 160 Copynumber: 2.9 Consensus size: 160
4233531 CACGACTTTG
* * *
4233541 TGGCACT-TTTTTCCTTTCAAAGTCCATAACTCTGTGGC-AC---CCTTTTAAGT-CATAACTCC
1 TGGCACTCTTTTTCCTTT-TAAGTCCACAACTCTGTGGCAACTTTCCTTTTAAGTCCACAACTCC
*
4233600 GTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAAC
65 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAAC
*
4233665 TTCGTGGCACCCTTTTAAGTCTACAACTCCA
130 TTCGTGGCACCCTTTTAAGTCCACAACTCCA
*
4233696 TGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCAACTTTCCTTTTAAGTCCACAACTCCG
1 TGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAACTTTCCTTTTAAGTCCACAACTCCG
* * * *
4233761 TGGTACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTTCATAACT
66 TGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACT
* * *
4233826 CCGTGGCACCCTTTGAAGTCCACAACTCCG
131 TCGTGGCACCCTTTTAAGTCCACAACTCCA
* * *
4233856 TGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTTCTTTTAAGTCCACAACTC
1 TGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAAC-T-TTCCTTTTAAGTCCACAACTC
* * * * *
4233920 CGTGGCACC-TTTTCTTTTT-AAGTCCACGACTCCGTAGCACAT-TTTTCCCTTTTAAGCCCAC-
64 CGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-TCTTTTTCCTTTTAAGTCCACA
*
4233981 ACCTCTGTGGCATCCCTTTT
128 ACTTC-GTGGCA-CCCTTTT
4234001 TCCTTTAAGT
Statistics
Matches: 265, Mismatches: 29, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
155 24 0.09
156 12 0.05
158 3 0.01
159 80 0.30
160 118 0.45
161 28 0.11
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (160 bp):
TGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAACTTTCCTTTTAAGTCCACAACTCCG
TGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACT
TCGTGGCACCCTTTTAAGTCCACAACTCCA
Found at i:4233792 original size:126 final size:118
Alignment explanation
Indices: 4233575--4233932 Score: 355
Period size: 126 Copynumber: 2.9 Consensus size: 118
4233565 CATAACTCTG
* * * * *
4233575 TGGCACCCTTTTAAGT-CATAACTCCGTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGC
1 TGGCACCCTTTGAAGTCCACAACTCCGTGGCAAC-TTTTCCTTTT-AAGTCCACAACTCCGTGGC
4233639 ACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAG-TCTACAACTCCA
64 AC-CTTTTT-CTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTTC-ACAACTCCA
* **
4233696 TGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCAAC-TTTCCTTTTAAGTCCACAACTCC
1 TGGCA--C-----CCTTTGAAGTCCACAACTCCGTGGCAACTTTTCCTTTTAAGTCCACAACTCC
* * *
4233760 GTGGTACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTTCATAAC
59 GTGGCACCTTTTTC-TTTT-AAGTCCACAACTTCGTGGCA--C-----CCTTTTAAGTTCACAAC
*
4233825 TCCG
115 TCCA
*
4233829 TGGCACCCTTTGAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 TGGCACCCTTTGAAGTCCACAACTCCGTGGCAAC-TTTTCCTTTTAAGTCCACAACTCCGTGGCA
*
4233894 CCTTGTTTCTTTTAAGTCCACAACTCCGTGGCA-CCTTTT
65 CCTT-TTTCTTTTAAGTCCACAACTTCGTGGCACCCTTTT
4233933 CTTTTTAAGT
Statistics
Matches: 199, Mismatches: 17, Indels: 44
0.77 0.07 0.17
Matches are distributed among these distances:
119 6 0.03
121 5 0.03
123 1 0.01
124 1 0.01
125 10 0.05
126 62 0.31
127 26 0.13
128 47 0.24
129 17 0.09
131 1 0.01
133 21 0.11
134 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (118 bp):
TGGCACCCTTTGAAGTCCACAACTCCGTGGCAACTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
CTTTTTCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTTCACAACTCCA
Found at i:4233838 original size:27 final size:27
Alignment explanation
Indices: 4233808--4233928 Score: 89
Period size: 33 Copynumber: 4.0 Consensus size: 27
4233798 CACTCTTTTT
* * *
4233808 CCTTTTAAGTTCATAACTCCGTGGCAC
1 CCTTTGAAGTCCACAACTCCGTGGCAC
4233835 CCTTTGAAGTCCACAACTCCGTGGCATC
1 CCTTTGAAGTCCACAACTCCGTGGCA-C
*
4233863 TTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
1 -----CCTTTGAAGTCCACAACTCCGTGGCAC
*
4233895 CTTGTTTCTTTTAAGTCCACAACTCCGTGGCAC
1 C------CTTTGAAGTCCACAACTCCGTGGCAC
4233928 C
1 C
4233929 TTTTCTTTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
27 24 0.31
28 1 0.01
32 1 0.01
33 52 0.67
ACGTcount: A:0.20, C:0.32, G:0.15, T:0.33
Consensus pattern (27 bp):
CCTTTGAAGTCCACAACTCCGTGGCAC
Found at i:4233941 original size:193 final size:191
Alignment explanation
Indices: 4233675--4234038 Score: 495
Period size: 193 Copynumber: 1.9 Consensus size: 191
4233665 TTCGTGGCAC
* **
4233675 CCTTTTAAGTCTACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCAACTTT
1 CCTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAACTTT
* * * * * *
4233740 CCTTTTAAGTCCACAACTCCGTGGTACCTTTTT-CTTTTTAAAGCCCACAACT-TCGTGGCA-CT
66 CCTTTTAAGTCCACAACTCCGTAGCACATTTTTCCCTTTT-AAGCCCACACCTCT-GTGGCATCC
* *
4233802 CTTTTTCCTTTTAAGTTCATAACTCCGTGGCACCCTTTGAAGTCCACAACTCCGTGGCATCTTTT
129 CTTTTTCC-TTTAAGTCCATAACTCCATGGCA-CCTTT-AAGTCCACAACTCCGTGGCATCTTTT
4233867 T
191 T
* *
4233868 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTGTTT-CTTTTAAGTCCACAACTCCGTGGCACCTT
1 CCTTTTAAGTCCACAACTCCATGGCACTCTT-TTTCCTTTTAAGTCCACAACTCCGTGGCAAC-T
* *
4233931 TTCTTTTTAAGTCCACGACTCCGTAGCACATTTTTCCCTTTTAAGCCCACACCTCTGTGGCATCC
64 TTCCTTTTAAGTCCACAACTCCGTAGCACATTTTTCCCTTTTAAGCCCACACCTCTGTGGCATCC
4233996 CTTTTTCCTTTAAGTCCATAACTCCATGGCACCTTTAAGTCCA
129 CTTTTTCCTTTAAGTCCATAACTCCATGGCACCTTTAAGTCCA
4234039 ATATCGCTTG
Statistics
Matches: 151, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
191 7 0.05
192 32 0.21
193 97 0.64
194 15 0.10
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (191 bp):
CCTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAACTTT
CCTTTTAAGTCCACAACTCCGTAGCACATTTTTCCCTTTTAAGCCCACACCTCTGTGGCATCCCT
TTTTCCTTTAAGTCCATAACTCCATGGCACCTTTAAGTCCACAACTCCGTGGCATCTTTTT
Found at i:4234070 original size:43 final size:43
Alignment explanation
Indices: 4234022--4234431 Score: 268
Period size: 43 Copynumber: 9.2 Consensus size: 43
4234012 CATAACTCCA
* *
4234022 TGGCACCTTTAAGTCCAATATCGCTTGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGACCAATATCGCTTGCCTTGAATCAGCACAT
* * *
4234065 TGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATTAGCACAT
1 TGGCA-C-----CTTTAAGACCAATATCGCTTGCCTTGAATCAGCACAT
* * * * *
4234114 TGGCACCTTTAAGTCCAATATCCCTGGCCTTGAATCAACATAT
1 TGGCACCTTTAAGACCAATATCGCTTGCCTTGAATCAGCACAT
*
4234157 TGGCACCTTTATCTTTAAGACCAATGTCGC-TGACCTTGAATCAGCACAT
1 TGGCA-C-----CTTTAAGACCAATATCGCTTG-CCTTGAATCAGCACAT
* * * *
4234206 TGGCACCTTTAAGTCTAATATCG-TTGGCCTTGAATCAACATAT
1 TGGCACCTTTAAGACCAATATCGCTT-GCCTTGAATCAGCACAT
* * * *
4234249 TGGCACCTTGTCTCTAAGACCCATGTCGCTAGACTTGAATCAGCACAT
1 TGGCACC---T-T-TAAGACCAATATCGCTTGCCTTGAATCAGCACAT
* *
4234297 TGGCA----TAAGCCCAATATCG-TTGGCCTTGAATCAGCATAT
1 TGGCACCTTTAAGACCAATATCGCTT-GCCTTGAATCAGCACAT
**
4234336 TGGCACCATGTCTTTAAGACCAATGCCG-TTGGCCTTGAATCAGCACAT
1 TGGCA-C----CTTTAAGACCAATATCGCTT-GCCTTGAATCAGCACAT
* *
4234384 TGGCA-C---AAGCCCAATATCGCTAGCCTTGAATCAGCACAT
1 TGGCACCTTTAAGACCAATATCGCTTGCCTTGAATCAGCACAT
*
4234423 TGGTACCTT
1 TGGCACCTT
4234432 CATCTTTAAG
Statistics
Matches: 286, Mismatches: 46, Indels: 71
0.71 0.11 0.18
Matches are distributed among these distances:
38 1 0.00
39 62 0.22
40 2 0.01
42 1 0.00
43 76 0.27
44 3 0.01
46 1 0.00
47 1 0.00
48 67 0.23
49 72 0.25
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
TGGCACCTTTAAGACCAATATCGCTTGCCTTGAATCAGCACAT
Found at i:4234101 original size:49 final size:49
Alignment explanation
Indices: 4234028--4234727 Score: 480
Period size: 49 Copynumber: 14.9 Consensus size: 49
4234018 TCCATGGCAC
* * * *
4234028 CTTTAAGTCCAATATCGCTTGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* *
4234077 CTTTAAGACCAATGTCGCTAGCCTTGAATTAGCACATTGGCA-C-----
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * * *
4234120 CTTTAAGTCCAATATCCCTGGCCTTGAATCAACATATTGGCACCTTTAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
*
4234169 CTTTAAGACCAATGTCGCTGACCTTGAATCAGCACATTGGCA-C-----
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * * * * *
4234212 CTTTAAGTCTAATATCGTTGGCCTTGAATCAACATATTGGCACC-TTGT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * *
4234260 CTCTAAGACCCATGTCGCTAGACTTGAATCAGCACATTGG---C---A-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * * * *
4234302 ---TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-ATGT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* *
4234347 CTTTAAGACCAATGCCGTTGGCCTTGAATCAGCACATTGG---C---A-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * * *
4234389 C---AAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGTACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * *
4234435 CTTTAAGACCGATGCCGTTGGCCTTGAATCAGCACATTGGCA-CTTTAACCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT----AT
* * * * * *
4234487 CTTTAAGTCTAATGTCGCCGGCCTTGAATCAGCACATTGGTATCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * * * * * *
4234536 CTTTAAGTCCGATATCGTTGGCCATGAATCAGCATATTGGTACCTTTAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* *
4234585 CTTTAGGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* ** * * * * * * *
4234634 CTTTAAGTCTGATATCGTTGGCCTTAAATCATCATATTGGCATCTTTAA
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
* * **
4234683 CATTCCTAAGCCCAATGTTGCTGGCCTTGTCTCAGCACATTGGCA
1 C-TT--TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
4234728 TTCTTCTTCA
Statistics
Matches: 502, Mismatches: 111, Indels: 73
0.73 0.16 0.11
Matches are distributed among these distances:
39 61 0.12
42 3 0.01
43 70 0.14
44 2 0.00
45 3 0.01
46 1 0.00
48 68 0.14
49 224 0.45
50 2 0.00
52 65 0.13
53 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
Found at i:4234179 original size:92 final size:91
Alignment explanation
Indices: 4234022--4234482 Score: 580
Period size: 92 Copynumber: 5.1 Consensus size: 91
4234012 CATAACTCCA
*
4234022 TGGCACCTTTAAGTCCAATATCGCTTGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
1 TGGCA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
*
4234087 AATGTCGCTAGCCTTGAATTAGCACAT
65 AATGTCGCTAGCCTTGAATCAGCACAT
* *
4234114 TGGCACCTTTAAGTCCAATATCCCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACC
1 TGGCA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
4234179 AATGTCGCT-GACCTTGAATCAGCACAT
65 AATGTCGCTAG-CCTTGAATCAGCACAT
* * * * *
4234206 TGGCACCTTTAAGTCTAATATCGTTGGCCTTGAATCAACATATTGGCACC-TTGTCTCTAAGACC
1 TGGCA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
* *
4234270 CATGTCGCTAGACTTGAATCAGCACAT
65 AATGTCGCTAGCCTTGAATCAGCACAT
* * * *
4234297 TGGCA---TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-ATGTCTTTAAGACCA
1 TGGCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCA
* * *
4234358 ATGCCGTTGGCCTTGAATCAGCACAT
66 ATGTCGCTAGCCTTGAATCAGCACAT
* * * * * *
4234384 TGGCAC---AAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAGACCG
1 TGGCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCA
* * *
4234446 ATGCCGTTGGCCTTGAATCAGCACAT
66 ATGTCGCTAGCCTTGAATCAGCACAT
4234472 TGGCACTTTAA
1 TGGCACTTTAA
4234483 CCATCTTTAA
Statistics
Matches: 333, Mismatches: 29, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
87 113 0.34
88 43 0.13
91 43 0.13
92 134 0.40
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (91 bp):
TGGCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCA
ATGTCGCTAGCCTTGAATCAGCACAT
Found at i:4234258 original size:21 final size:21
Alignment explanation
Indices: 4234189--4234258 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
4234179 AATGTCGCTG
* *
4234189 ACCTTGAATCAGCACATTGGC
1 ACCTTGAATCAACATATTGGC
* * *
4234210 ACCTTTAAGTCTAATATCGTTGG-
1 ACCTTGAA-TC-AACAT-ATTGGC
4234233 -CCTTGAATCAACATATTGGC
1 ACCTTGAATCAACATATTGGC
4234253 ACCTTG
1 ACCTTG
4234259 TCTCTAAGAC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 14 0.39
22 8 0.22
23 2 0.06
24 4 0.11
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
ACCTTGAATCAACATATTGGC
Found at i:4234338 original size:39 final size:39
Alignment explanation
Indices: 4234282--4234425 Score: 144
Period size: 39 Copynumber: 3.5 Consensus size: 39
4234272 TGTCGCTAGA
4234282 CTTGAATCAGCACATTGGCATAAGCCCAATATCGTTGGC
1 CTTGAATCAGCACATTGGCATAAGCCCAATATCGTTGGC
* * **
4234321 CTTGAATCAGCATATTGGCACCATGTCTTTAAGACCAATGCCGTTGGC
1 CTTGAATCAGCACATTGG---CA------TAAGCCCAATATCGTTGGC
* * *
4234369 CTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGC
1 CTTGAATCAGCACATTGGCATAAGCCCAATATCGTTGGC
4234408 CTTGAATCAGCACATTGG
1 CTTGAATCAGCACATTGG
4234426 TACCTTCATC
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
39 48 0.56
42 2 0.02
45 2 0.02
48 33 0.39
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (39 bp):
CTTGAATCAGCACATTGGCATAAGCCCAATATCGTTGGC
Found at i:4234708 original size:150 final size:148
Alignment explanation
Indices: 4234390--4234725 Score: 377
Period size: 150 Copynumber: 2.2 Consensus size: 148
4234380 ACATTGGCAC
* * * *
4234390 AAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAGACCGATGCCGTTG
1 AAGCCCAATATCGCTGGCCATGAATCAGCACATTGGTACCTTCATCTTTAAGACCAATGCCGCTG
* * *
4234455 GCCTTGAATCAGCACATTGGCACTTTAACCATCTTTAAGTCTAATGTCGCCGGCCTTGAATCAGC
66 GCCTTGAATCAGCACATTGGCACCTT-A-CATCTTTAAGTCTAATATCGCCGGCCTTAAATCAGC
* *
4234520 ACATTGGTATCTTCATCTTT
129 ACATTGGCATCTTCAACTTT
* * * * * * *
4234540 AAGTCCGATATCGTTGGCCATGAATCAGCATATTGGTACCTTTATCTTTAGGACCAATGTCGCTG
1 AAGCCCAATATCGCTGGCCATGAATCAGCACATTGGTACCTTCATCTTTAAGACCAATGCCGCTG
* ** * *
4234605 GCCTTGAATCAGCACATTGGCACCTT-CATCTTTAAGTCTGATATCGTTGGCCTTAAATCATCAT
66 GCCTTGAATCAGCACATTGGCACCTTACATCTTTAAGTCTAATATCGCCGGCCTTAAATCAGCAC
*
4234669 ATTGGCATCTTTAACATTCCT
131 ATTGGCATCTTCAAC-TT--T
* * * **
4234690 AAGCCCAATGTTGCTGGCCTTGTCTCAGCACATTGG
1 AAGCCCAATATCGCTGGCCATGAATCAGCACATTGG
4234726 CATTCTTCTT
Statistics
Matches: 152, Mismatches: 31, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
147 43 0.28
148 2 0.01
150 107 0.70
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (148 bp):
AAGCCCAATATCGCTGGCCATGAATCAGCACATTGGTACCTTCATCTTTAAGACCAATGCCGCTG
GCCTTGAATCAGCACATTGGCACCTTACATCTTTAAGTCTAATATCGCCGGCCTTAAATCAGCAC
ATTGGCATCTTCAACTTT
Found at i:4235804 original size:21 final size:21
Alignment explanation
Indices: 4235759--4235804 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4235749 TTTTTGCCAA
* *
4235759 AATGTATCGATACATGCCCTT
1 AATGTATCGATACAGGCCCTC
4235780 AATGTATCGATACAAGGCCC-C
1 AATGTATCGATAC-AGGCCCTC
4235801 AATG
1 AATG
4235805 GTCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
AATGTATCGATACAGGCCCTC
Found at i:4235855 original size:20 final size:21
Alignment explanation
Indices: 4235830--4235884 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
4235820 TTTTCACAAT
*
4235830 TTGTATCGATATATTGTT-CA
1 TTGTATCGATACATTGTTACA
4235850 TTGTATCGATACATTGTT-CA
1 TTGTATCGATACATTGTTACA
4235870 TTGTATCGATACATT
1 TTGTATCGATACATT
4235885 CTGGGTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (21 bp):
TTGTATCGATACATTGTTACA
Found at i:4235925 original size:20 final size:19
Alignment explanation
Indices: 4235900--4235974 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 19
4235890 TTTACCCAGA
4235900 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
4235920 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
4235940 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
4235960 TGTATCGATACATTT
1 TGTATCGATACATTT
4235975 AGGCATTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:4238429 original size:51 final size:51
Alignment explanation
Indices: 4238319--4238434 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
4238309 AATTTTTCTT
* * * * * *
4238319 AATTGGGGATACTCTAACTCCGATTTTATTTCTAAAGCATCGATTTACCGC
1 AATTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTACCAC
* *
4238370 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATGTT-TCAC
1 AATTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAAT-TTACCAC
4238421 AATTGGGGATACTC
1 AATTGGGGATACTC
4238435 TAACCCCGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 53 0.96
52 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (51 bp):
AATTGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTACCAC
Found at i:4238459 original size:28 final size:27
Alignment explanation
Indices: 4238426--4238498 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
4238416 TTCACAATTG
4238426 GGGATACTCTAACCCCGTTATTTCATCGA
1 GGGATACTCTAACCCCGTTATTT--TCGA
* *
4238455 -GGATACTCCAAACCCGTTATTTTCGA
1 GGGATACTCTAACCCCGTTATTTTCGA
4238481 GGGGATACTCTAACCCCG
1 -GGGATACTCTAACCCCG
4238499 GCTTTATATC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
28 34 0.89
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (27 bp):
GGGATACTCTAACCCCGTTATTTTCGA
Found at i:4238622 original size:109 final size:109
Alignment explanation
Indices: 4238415--4238614 Score: 274
Period size: 109 Copynumber: 1.8 Consensus size: 109
4238405 AACACCAATG
* *
4238415 TTTCACAATTGGGGATACTCTAACCCCGTTATTTCATCGAGGATACTCCAAACCCGTTATTTTCG
1 TTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCGAGGATACTCCAAACCCGTTATTTTCG
* *
4238480 AGGGGATACTCTAACCCCGGCTTTATATCTAAAAATATTGTTTT
66 AGGGGATACTCCAACCCCGACTTTATATCTAAAAATATTGTTTT
* * * * * * * *
4238524 TTTCATAATCGGGGGTACTCCAACCCCGTTATTTCGTCGGGGATATTCTAATCCTGTTATTTTCG
1 TTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCGAGGATACTCCAAACCCGTTATTTTCG
* *
4238589 AGGGGATACTCCAACCTCGATTTTAT
66 AGGGGATACTCCAACCCCGACTTTAT
4238615 TTTTAAAATA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
109 77 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCGAGGATACTCCAAACCCGTTATTTTCG
AGGGGATACTCCAACCCCGACTTTATATCTAAAAATATTGTTTT
Found at i:4238660 original size:51 final size:51
Alignment explanation
Indices: 4238590--4238706 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
4238580 TTATTTTCGA
** *
4238590 GGGGATACTCCAACCTCGATTTTATTTTTAAAATACCAATTTTCCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* * * *
4238641 TGGGATACTTCAACTTCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCACAATC
4238692 GGGGATACTCCAACC
1 GGGGATACTCCAACC
4238707 CCGTTATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:4238746 original size:79 final size:79
Alignment explanation
Indices: 4238657--4238860 Score: 248
Period size: 79 Copynumber: 2.6 Consensus size: 79
4238647 ACTTCAACTT
* * * *
4238657 CGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGCGA
1 CGATTTTATTTCCAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGA
4238722 AAATACTCCAACCC
66 AAATACTCCAACCC
* * * *
4238736 CGATTTTATTTTCAAAATACCGA-TTTTCTATAATCAGGGATACTCCAACCCTATTATTTTCGAG
1 CGATTTTATTTCCAAAACACCGATTTTTC-ATAATCGGGGATACTCCAACCCCATTATTTTCGAG
***
4238800 GGGATACTCCAACCC
65 AAAATACTCCAACCC
* * * *
4238815 TGATTTTTATTTCTAGAACACCGATTTTCCATAATCGGGGATACTC
1 CGA-TTTTATTTCCAAAACACCGATTTTTCATAATCGGGGATACTC
4238861 TAGTCCCGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 5 0.05
79 64 0.62
80 31 0.30
81 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (79 bp):
CGATTTTATTTCCAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGA
AAATACTCCAACCC
Found at i:4251220 original size:1 final size:1
Alignment explanation
Indices: 4251216--4251304 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
4251206 ATTCTTTTTC
* * * * * * * *
4251216 AAAAAACAAAAAAACAACAAAAAAAATAAAAAAACAAAAAAACAAAAAAAAAATAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
4251281 AAACAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
4251305 GAGAGAAAAG
Statistics
Matches: 64, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (1 bp):
A
Found at i:4251255 original size:28 final size:28
Alignment explanation
Indices: 4251216--4251304 Score: 135
Period size: 27 Copynumber: 3.2 Consensus size: 28
4251206 ATTCTTTTTC
4251216 AAAAAACAAAAAAACAACAAAAAAAATA
1 AAAAAACAAAAAAACAACAAAAAAAATA
4251244 AAAAAACAAAAAAACAA-AAAAAAAATA
1 AAAAAACAAAAAAACAACAAAAAAAATA
* * *
4251271 AAAAAACAAAAAACAAAACAAAACAAAGA
1 AAAAAACAAAAAA-ACAACAAAAAAAATA
4251300 AAAAA
1 AAAAA
4251305 GAGAGAAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 23 0.41
28 20 0.36
29 13 0.23
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (28 bp):
AAAAAACAAAAAAACAACAAAAAAAATA
Found at i:4251261 original size:36 final size:35
Alignment explanation
Indices: 4251216--4251304 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 35
4251206 ATTCTTTTTC
4251216 AAAAAACAAAAAAACAACA-AAAAAAATAAAAAAAC-A
1 AAAAAACAAAAAAA-AA-ATAAAAAAA-AAAAAAACAA
*
4251252 AAAAAACAAAAAAAAAATAAAAAAACAAAAAACAA
1 AAAAAACAAAAAAAAAATAAAAAAAAAAAAAACAA
*
4251287 AACAAAACAAAGAAAAAA
1 AA-AAAACAAAAAAAAAA
4251305 GAGAGAAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
34 8 0.17
35 12 0.25
36 28 0.58
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (35 bp):
AAAAAACAAAAAAAAAATAAAAAAAAAAAAAACAA
Found at i:4251302 original size:26 final size:25
Alignment explanation
Indices: 4251216--4251303 Score: 97
Period size: 26 Copynumber: 3.2 Consensus size: 25
4251206 ATTCTTTTTC
4251216 AAAAAACAAAAAAACAACAAAAAAAATA
1 AAAAAACAAAAAAAC-A-AAAAAAAA-A
4251244 AAAAAACAAAAAAACAAAAAAAAAA
1 AAAAAACAAAAAAACAAAAAAAAAA
4251269 TAAAAAA-ACAAAAAACAAAACAAAACAA
1 -AAAAAACA-AAAAAACAAAA-AAAA-AA
4251297 AGAAAAA
1 A-AAAAA
4251304 AGAGAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.04
26 25 0.45
27 6 0.11
28 22 0.40
ACGTcount: A:0.86, C:0.10, G:0.01, T:0.02
Consensus pattern (25 bp):
AAAAAACAAAAAAACAAAAAAAAAA
Found at i:4252556 original size:156 final size:155
Alignment explanation
Indices: 4252306--4252731 Score: 630
Period size: 156 Copynumber: 2.8 Consensus size: 155
4252296 GACGCCTTTT
* *
4252306 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGCAGGACG------CC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC
*
4252365 TTTTAAAGCCCATACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
65 TTTTAAAGCCCACACAAGTTGGTGGCACTT-CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
4252430 ACCCTTTAGTCCTCAAAAAGCAAGACG
129 ACCCTTTAGTCCTCAAAAAGCAAGACG
* * *
4252457 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGTAGGACGCCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
*
4252522 TTTAAAGCCTACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCA
66 TTTAAAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCA
* * *
4252587 CCCTTTAGTCCTTAAAGAGCAGGACG
130 CCCTTTAGTCCTCAAAAAGCAAGACG
* *
4252613 TCTTTCAAAGCCCACACAAGTTGGTAGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
* * *
4252678 TTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGACGC
66 TTTAAAGCCCACACAAGTTGGTGGCA--CTTCTAGTCCTCAAAGAGCAGGACGC
4252732 CTTTTAAAGC
Statistics
Matches: 247, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
150 23 0.09
151 28 0.11
156 169 0.68
157 27 0.11
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (155 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
TTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCAC
CCTTTAGTCCTCAAAAAGCAAGACG
Found at i:4252584 original size:61 final size:62
Alignment explanation
Indices: 4252457--4252584 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 62
4252447 AAGCAAGACG
* * * *
4252457 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
*
4252519 CCTTTTAAAGCCTACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGACG-CTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCTAGTCCTCAAAGAGCAGGACGCCT-TCT
4252580 CCTTT
1 CCTTT
4252585 CACCCTTTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
60 2 0.03
61 29 0.48
62 29 0.48
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
Found at i:4252714 original size:62 final size:61
Alignment explanation
Indices: 4252592--4252974 Score: 472
Period size: 62 Copynumber: 6.4 Consensus size: 61
4252582 TTTCACCCTT
* *
4252592 TAGTCCTTAAAGAGCAGGACG----T-CTTTCAAAGCCCACACAAGTTGGTAGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
4252648 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTT
1 TAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
4252710 TAGTCCTCAAAGAGCAGGACGCC--T--TTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
4252766 TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCTACACAAGTTGGTGGCA-TTTT-
1 TAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
4252826 TCGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTC-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * *
4252887 CAGTCCTTAAAGAGCAGGACGACTTTCTTTTACAAAGCCCACACGAGTTGGTGGCACTTTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTCCTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
*
4252948 TTGTCCTCAAAGAGCAGGACGCACTTT
1 TAGTCCTCAAAGAGCAGGACGC-CTTT
4252975 ATTTTCCTTT
Statistics
Matches: 285, Mismatches: 23, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
56 69 0.24
57 3 0.01
58 4 0.01
59 7 0.02
60 45 0.16
61 70 0.25
62 87 0.31
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (61 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:4252798 original size:118 final size:118
Alignment explanation
Indices: 4252590--4252974 Score: 530
Period size: 118 Copynumber: 3.2 Consensus size: 118
4252580 CCTTTCACCC
* * *
4252590 TTTAGTCCTTAAAGAGCAGGACG-TCTTTCAAAGCCCACACAAGTTGGTAGCACTTTTCTAGTCC
1 TTTAGTCCTCAAAGAGCAGGACGCTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
4252654 TCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
66 TCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTT
4252708 TTTAGTCCTCAAAGAGCAGGACGC-CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
1 TTTAGTCCTCAAAGAGCAGGACGCTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
* *
4252772 TCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCTACACAAGTTGGTGGCA-TT
66 TCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
* * * *
4252824 TTTCGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCC
1 TTTAGTCCTCAAAGAGCAGGACGC--TCT-TTT--AAAGCCCACACAAGTTGGTGGCACTTTTCT
* * * *
4252888 AGTCCTTAAAGAGCAGGACGAC-TTTCTTTTACAAAGCCCACACGAGTTGGTGGCACTTT
61 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTT-CAAAGCCCACACAAGTTGGTGGCA-TTT
*
4252947 TTT-GTCCTCAAAGAGCAGGACGCACTTT
1 TTTAGTCCTCAAAGAGCAGGACGCTCTTT
4252975 ATTTTCCTTT
Statistics
Matches: 240, Mismatches: 17, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
116 24 0.10
118 108 0.45
119 4 0.02
120 12 0.05
121 44 0.18
122 43 0.18
123 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (118 bp):
TTTAGTCCTCAAAGAGCAGGACGCTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
TCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
Found at i:4253006 original size:42 final size:42
Alignment explanation
Indices: 4252947--4253137 Score: 206
Period size: 42 Copynumber: 4.5 Consensus size: 42
4252937 GTGGCACTTT
4252947 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTCTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTCTCC
* * * ** *
4252989 TTTGTCCTCAAAAAGCAGGACACACTTCATTCCCTTATTTTCTCT
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATT---TTCCTTTCTCC
* *
4253034 TTTGTCCTCAAAGAGCAAGACGCACTTTATTTTCCTCTT-TCT
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCT-TTCTCC
* * *
4253076 TTTGTCCTCAAAGAGCAGGACGCATTTTGTTTTCCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TTTCTCC
*
4253119 TTTATCCTCGAAA-AGCAGG
1 TTTGTCCTC-AAAGAGCAGG
4253138 GCATACTCTT
Statistics
Matches: 125, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
42 68 0.54
43 19 0.15
44 3 0.02
45 35 0.28
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (42 bp):
TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTCTCC
Found at i:4253272 original size:41 final size:39
Alignment explanation
Indices: 4253147--4253272 Score: 112
Period size: 41 Copynumber: 3.1 Consensus size: 39
4253137 GGCATACTCT
* *
4253147 TTTTCACTTTGCCCTCAAGAAGCAGGACA-CTTTCCTTTTCC
1 TTTTC-CTTTGTCCTCAAGAAGC-GGACACCTTTCCATTT-C
* * *
4253188 TTTTTCCTTTGTCCTCAAGGAGC-GAGACCTATTTCATTCTC
1 -TTTTCCTTTGTCCTCAAGAAGCGGACACCT-TTCCATT-TC
*
4253229 TTTTCCTTTGTCCTCAAAAAGTCGGACACCTCTTCCATTTC
1 TTTTCCTTTGTCCTCAAGAAG-CGGACACCT-TTCCATTTC
4253270 TTT
1 TTT
4253273 CCCCTCCTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
39 3 0.04
40 21 0.30
41 27 0.39
42 18 0.26
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.40
Consensus pattern (39 bp):
TTTTCCTTTGTCCTCAAGAAGCGGACACCTTTCCATTTC
Found at i:4253274 original size:40 final size:40
Alignment explanation
Indices: 4253189--4253272 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
4253179 TCCTTTTCCT
** * *
4253189 TTTTCCTTTGTCCTCAAGGAGCGAGACCTATTTCATTCTC
1 TTTTCCTTTGTCCTCAAAAAGCGACACCTATTCCATTCTC
*
4253229 TTTTCCTTTGTCCTCAAAAAGTCGGACACCTCTTCCATT-TC
1 TTTTCCTTTGTCCTCAAAAAG-C-GACACCTATTCCATTCTC
4253270 TTT
1 TTT
4253273 CCCCTCCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 19 0.51
41 6 0.16
42 12 0.32
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.42
Consensus pattern (40 bp):
TTTTCCTTTGTCCTCAAAAAGCGACACCTATTCCATTCTC
Found at i:4253816 original size:21 final size:21
Alignment explanation
Indices: 4253771--4253816 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4253761 TTTTTGCCAA
* *
4253771 AATGTATCGATACATGCCCTT
1 AATGTATCGATACAGGCCCTC
4253792 AATGTATCGATACAAGGCCC-C
1 AATGTATCGATAC-AGGCCCTC
4253813 AATG
1 AATG
4253817 GTCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
AATGTATCGATACAGGCCCTC
Found at i:4253876 original size:13 final size:13
Alignment explanation
Indices: 4253860--4253889 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4253850 ATACATTGTT
4253860 CATTGTATCGATA
1 CATTGTATCGATA
4253873 CATTGTATCGATA
1 CATTGTATCGATA
4253886 CATT
1 CATT
4253890 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4253884 original size:33 final size:34
Alignment explanation
Indices: 4253842--4253991 Score: 108
Period size: 33 Copynumber: 4.1 Consensus size: 34
4253832 TTTTCACAAT
*
4253842 TTGTATCGATACATTGTT-CATTGTATCGATACA
1 TTGTATCGATACATTGTTACAATGTATCGATACA
4253875 TTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATACATTTTGCA
1 TTGTATCGATACA-T-T--G-TTA--CA-ATGTATCGAT--A-----CA
* * *
4253924 TTGTAACGATACATTGCT-CATTGTATCGATACA
1 TTGTATCGATACATTGTTACAATGTATCGATACA
4253957 TTGTATCGATACATT-TTACAATGTATCGATACA
1 TTGTATCGATACATTGTTACAATGTATCGATACA
4253990 TT
1 TT
4253992 TAGGCATTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 34
0.69 0.05 0.25
Matches are distributed among these distances:
32 1 0.01
33 45 0.48
34 1 0.01
35 1 0.01
37 1 0.01
38 3 0.03
40 9 0.10
41 4 0.04
42 9 0.10
44 2 0.02
45 1 0.01
47 1 0.01
48 1 0.01
49 14 0.15
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (34 bp):
TTGTATCGATACATTGTTACAATGTATCGATACA
Found at i:4253933 original size:20 final size:20
Alignment explanation
Indices: 4253905--4253959 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4253895 TTTACCCAGA
*
4253905 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
4253925 TGTAACGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
4253945 TGTATCGATACATTG
1 TGTATCGATACATTG
4253960 TATCGATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:4253976 original size:20 final size:20
Alignment explanation
Indices: 4253905--4253992 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
4253895 TTTACCCAGA
*
4253905 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTACAT
* *
4253925 TGTAACGATACATTGCT-CAT
1 TGTATCGATACATT-TTACAT
4253945 TGTATCG----A---TACAT
1 TGTATCGATACATTTTACAT
*
4253958 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTTACAT
4253978 TGTATCGATACATTT
1 TGTATCGATACATTT
4253993 AGGCATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
12 1 0.02
13 10 0.18
16 1 0.02
17 1 0.02
20 41 0.75
21 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTACAT
Found at i:4253989 original size:13 final size:13
Alignment explanation
Indices: 4253942--4253971 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4253932 ATACATTGCT
4253942 CATTGTATCGATA
1 CATTGTATCGATA
4253955 CATTGTATCGATA
1 CATTGTATCGATA
4253968 CATT
1 CATT
4253972 TTACAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4256358 original size:51 final size:51
Alignment explanation
Indices: 4256293--4256461 Score: 205
Period size: 51 Copynumber: 3.3 Consensus size: 51
4256283 ATTTTTCATC
* * **
4256293 TCGGGGATACTCCAA-TCCCGATTTCATTTCCAAAACGTCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTTCACAA
* * * * * *
4256344 TCGGGGATACTCCAACTCCGTTTTTATTTCTAAAGCATCGATTTATCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAA
* *
4256395 TCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAA
*
4256446 TTGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
4256462 CCCATTATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
51 97 0.99
52 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAA
Found at i:4256480 original size:28 final size:28
Alignment explanation
Indices: 4256448--4256520 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
4256438 TTTCACAATT
*
4256448 GGGGATACTCCAACCCCATTATTTCAT-C
1 GGGGATACTCCAACCCCATTATTTC-TGA
* *
4256476 GGGGATACTCCAACCTCGTTATTTCTGA
1 GGGGATACTCCAACCCCATTATTTCTGA
*
4256504 GGGGATACTCTAACCCC
1 GGGGATACTCCAACCCC
4256521 GGCTTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTCTGA
Found at i:4256656 original size:109 final size:109
Alignment explanation
Indices: 4256399--4256677 Score: 297
Period size: 109 Copynumber: 2.6 Consensus size: 109
4256389 TCGCAATCGA
* *
4256399 GGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAA--TTTTTCACAATTGGGGATACTCCAA
1 GGATACTCCAACCT-CGATTTTATTTCTAAAATACCAATTTTTTTCACAATTGGGGATACTCCAA
* *
4256461 CCCCATTATTTCATCGGGGATACTCCAACCTCGTTATTTCTGAGG
65 CCCCATTATTTCATCGGAGATACTCCAACCTCATTATTTCTGAGG
* * ** * *** *
4256506 GGATACTCTAACCCCGGCTTTATATCTAAAAATA-TTGTTTTTTTCATAATTGAGGG-TACTCCA
1 GGATACTCCAACCTCGATTTTATTTCT-AAAATACCAATTTTTTTCACAATTG-GGGATACTCCA
* * *
4256569 TCCCCGTTATTTCATCGGAGATTCTCCAATCC-CATTATTTCTGAGG
64 ACCCCATTATTTCATCGGAGATACTCCAA-CCTCATTATTTCTGAGG
*
4256615 GGATACTCCAACCTCAATTTTATTTCTAAAATACCAA--TTTTTCACAATCT-GGGATACTCCAA
1 GGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTTTTCACAAT-TGGGGATACTCCAA
4256677 C
65 C
4256678 TCTGACTTTA
Statistics
Matches: 136, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
106 3 0.02
107 37 0.27
108 13 0.10
109 78 0.57
110 5 0.04
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (109 bp):
GGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTTTTCACAATTGGGGATACTCCAAC
CCCATTATTTCATCGGAGATACTCCAACCTCATTATTTCTGAGG
Found at i:4256781 original size:51 final size:52
Alignment explanation
Indices: 4256614--4256781 Score: 209
Period size: 51 Copynumber: 3.3 Consensus size: 52
4256604 TATTTCTGAG
* * *
4256614 GGGATACTCCAACCTCAATTTTA-TTTCTAAAATACCAATTTT-TCACAATCT
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTCTCACAATCA
* * * * * *
4256665 GGGATACTCCAACTCTGACTTTATTTCCAAAACACCAA-TTTCTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCTCACAATCA
*
4256716 GGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCT-ATAATCA
1 GGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCTCACAATCA
4256767 GGGATACTCCAACCC
1 GGGATACTCCAACCC
4256782 TATTATTTTC
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
50 3 0.03
51 88 0.89
52 8 0.08
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (52 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCTCACAATCA
Found at i:4265689 original size:28 final size:29
Alignment explanation
Indices: 4265650--4266379 Score: 823
Period size: 28 Copynumber: 25.5 Consensus size: 29
4265640 ATACGACACT
4265650 TTTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
4265678 TTTTCAAAGCCCACAAGTCAATTGTA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
4265706 CTTTCAAAGCCCACAAGTTAGTGGCA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
4265734 CTTTCAGAGCCCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4265763 -TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4265791 -TTTCAAAGCCCACGAGTCAGTGGCATCCC
1 TTTTCAAAGCCCACAAGTCAGTGGCAT-CC
* * *
4265820 TTTCCAAAGCCCACGAGTTAGTGGCATCTC
1 TTTTCAAAGCCCACAAGTCAGTGGCATC-C
* * *
4265850 TTTCCAAGGCCCACGAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4265879 TTTTCTAAAGCCCACAAGTCAATGGCATCC
1 TTTTC-AAAGCCCACAAGTCAGTGGCATCC
4265909 -TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
** *
4265937 -TTTCTGAGCCCACAAGTTAGTGGCAATCC
1 TTTTCAAAGCCCACAAGTCAGTGGC-ATCC
4265966 TTTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4265994 TTTTCAAAGCTCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4266023 -TTTCAAAGCCCACAAGTTAGTGGCA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4266050 CTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4266079 -TTTCAGAGCCCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
4266107 TTTT-AGAGCCCACAAGTCAGGGGCAACCC
1 TTTTCAAAGCCCACAAGTCAGTGGC-ATCC
* *
4266136 TTTTCAAAGCCCACAATTCAATGGCA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
4266164 TTTTCAAAGCTCACAAGTCAGTGGCA-CT
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
4266192 TTTTTAAAGCCCATAAGTCAGTGGCAT-C
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
*
4266220 ATTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* **
4266249 -TTTCAAAGCCTACAAGTCAGTAACA-CC
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
4266276 TTTTCAAAACCCGCAAGTTAGTGGCAT-C
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
4266304 TTTTCAAAGCGCACAAGTCAATGGCAACA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
4266333 TCTTCTAAAGCCCACACAGGTCGGTGGCAACC
1 TTTTC-AAAGCCCACA-A-GTCAGTGGCATCC
*
4266365 -CTTCTAAAGCCCACA
1 TTTTC-AAAGCCCACA
4266380 CAAGTTGATA
Statistics
Matches: 609, Mismatches: 72, Indels: 39
0.85 0.10 0.05
Matches are distributed among these distances:
27 4 0.01
28 422 0.69
29 39 0.06
30 118 0.19
31 16 0.03
32 10 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (29 bp):
TTTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:4266118 original size:170 final size:168
Alignment explanation
Indices: 4265650--4266379 Score: 874
Period size: 170 Copynumber: 4.2 Consensus size: 168
4265640 ATACGACACT
* * *
4265650 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAATTGTACCCTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
4265715 CCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGT
65 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGT
* *
4265780 TAGTGGCATCC-TTTCAAAGCCCACGAGTCAGTGGCATCCC
130 TAGTGGCATCCTTTTCAAAGCCCACAAGTCAATGGCA--CC
* * * * * *
4265820 TTTCCAAAGCCCACGAGTTAGTGGCATCTCTTTCCAAGGCCCACGAGTCAGTGGCATCCTTTTCT
1 TTTTCAAAGCCCACAAGTCAGTGGCA-C-CTTT-CAAAGCCCACAAGTCAGTGGCA-CCCTTTC-
* *
4265885 AAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCT-GAGCCCA
61 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTT-TAAAGCCCA
*
4265949 CAAGTTAGTGGCAATCCTTTTCAAAGCCCACAAGTCAGTGGCACC
125 CAAGTTAGTGGC-ATCCTTTTCAAAGCCCACAAGTCAATGGCACC
* *
4265994 TTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
4266059 CCCACAAGTCAGTGGCATCCTTTCAGAGCCCACAAGTCAGTGGCATCCTTTTAGAGCCCACAAGT
65 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGT
* * * *
4266124 CAGGGGCAACCCTTTTCAAAGCCCACAATTCAATGGCACC
130 TAGTGGC-ATCCTTTTCAAAGCCCACAAGTCAATGGCACC
* * * * * *
4266164 TTTTCAAAGCTCACAAGTCAGTGGCACTTTTTTAAAGCCCATAAGTCAGTGGCATCATTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* ** * *
4266229 CCCACAAGTCAGTGGCATCCTTTCAAAGCCTACAAGTCAGTAACA-CCTTTTCAAAACCCGCAAG
65 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAG
* *
4266293 TTAGTGGCAT-CTTTTCAAAGCGCACAAGTCAATGGCAACA
129 TTAGTGGCATCCTTTTCAAAGCCCACAAGTCAATGGC-ACC
* * *
4266333 TCTTCTAAAGCCCACACAGGTCGGTGGCAACCCTTCTAAAGCCCACA
1 TTTTC-AAAGCCCACA-A-GTCAGTGGC-ACCTTTC-AAAGCCCACA
4266380 CAAGTTGATA
Statistics
Matches: 486, Mismatches: 57, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
168 24 0.05
169 15 0.03
170 245 0.50
171 11 0.02
172 47 0.10
173 21 0.04
174 95 0.20
175 4 0.01
176 24 0.05
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (168 bp):
TTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTT
AGTGGCATCCTTTTCAAAGCCCACAAGTCAATGGCACC
Found at i:4266362 original size:32 final size:31
Alignment explanation
Indices: 4266315--4266412 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 31
4266305 TTTCAAAGCG
*
4266315 CACAAGTCAATGGCAACATCTTCTAAAGCCCA
1 CACAAGTCGATGGCAAC-TCTTCTAAAGCCCA
* * *
4266347 CACAGGTCGGTGGCAACCCTTCTAAAGCCCA
1 CACAAGTCGATGGCAACTCTTCTAAAGCCCA
* * *
4266378 CACAAGTTGATAGCAACCTTTTCTAAAGCCCA
1 CACAAGTCGATGGCAA-CTCTTCTAAAGCCCA
4266410 CAC
1 CAC
4266413 GAGTTGGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (31 bp):
CACAAGTCGATGGCAACTCTTCTAAAGCCCA
Found at i:4266371 original size:31 final size:31
Alignment explanation
Indices: 4266325--4266435 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
4266315 CACAAGTCAA
* *
4266325 TGGCAACATCTTCTAAAGCCCACACAGGTCGG
1 TGGCAAC-CCTTCTAAAGCCCACACAGGTTGG
* *
4266357 TGGCAACCCTTCTAAAGCCCACACAAGTTGA
1 TGGCAACCCTTCTAAAGCCCACACAGGTTGG
* *
4266388 TAGCAACCTTTTCTAAAGCCCACAC-GAGTTGG
1 TGGCAACC-CTTCTAAAGCCCACACAG-GTTGG
* *
4266420 TGACAACCCTTTTAAA
1 TGGCAACCCTTCTAAA
4266436 CCTAATGTCG
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
31 33 0.51
32 32 0.49
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (31 bp):
TGGCAACCCTTCTAAAGCCCACACAGGTTGG
Found at i:4267451 original size:31 final size:32
Alignment explanation
Indices: 4267372--4267457 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
4267362 GAAAGTCACA
4267372 TTTTTACCCAGATGTATCGATACATTATCGATAC
1 TTTTTA-CCAGATGTATCGATACA-TATCGATAC
* *
4267406 ATTTT--CA-ATGTATCGATACA-ATCTAT-C
1 TTTTTACCAGATGTATCGATACATATCGATAC
4267433 TTTTTACCTAGATGTATCGATACAT
1 TTTTTACC-AGATGTATCGATACAT
4267458 TTTGCAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 5 0.11
28 5 0.11
29 1 0.02
30 14 0.32
31 15 0.34
34 4 0.09
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (32 bp):
TTTTTACCAGATGTATCGATACATATCGATAC
Found at i:4272931 original size:50 final size:50
Alignment explanation
Indices: 4272868--4272967 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
4272858 TCTTTTGCAA
*
4272868 CCTGAAACTGAAAGTAAGATTTGCCCCTAGATCTGTAATCTTTTAGTTTT
1 CCTGAAACTGAAAGTAAGATTGGCCCCTAGATCTGTAATCTTTTAGTTTT
4272918 CCTGAAACTGAAAGTAAGATTGGCCCCTAGATCTGTAATCTTTTAGTTTT
1 CCTGAAACTGAAAGTAAGATTGGCCCCTAGATCTGTAATCTTTTAGTTTT
4272968 AGTTTAGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (50 bp):
CCTGAAACTGAAAGTAAGATTGGCCCCTAGATCTGTAATCTTTTAGTTTT
Found at i:4275505 original size:164 final size:163
Alignment explanation
Indices: 4275116--4276091 Score: 963
Period size: 165 Copynumber: 6.0 Consensus size: 163
4275106 CTCCATGAAT
* *** * * ** *
4275116 TTTTTTAGGAGGATTTTTCTCAATTTTTAATTTTTAAAATTCATTAAATATTATTATTTAACTCG
1 TTTTTTAGG-GGATTTTTTTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTTCA
* * * *
4275181 CATTAAATCAGTTTTCAAAAATTTATTCATCTT-CATAAAATTTTGAATTTTTTCCTTGAAGTTT
65 TATTAATTCAGTTTTCAAAAATTCATTCAT-TTCCAT-AAATTTTGAATTTTTTCCTTGAA---A
* * *
4275245 TCCTCTTTTTCTGAAATACGGAGTTTTTTGCTCCGTAAA
125 TCTTCTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
* * * * *
4275284 TTTTTTAAGAAGGATTTTTCATGGTTTTAT-ATTTTTAAAATTCATCAAATCTTATTATTTATTT
1 TTTTTT-AG-GGGATTTTT-TTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTT
* *
4275348 CTTATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTCGAAATCT
63 CATATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATCT
* *
4275413 TATTTTTCTGAAATACGGAGTTTTCTACTTCGTAAA
128 TCTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
4275449 TTCTTTTAGGGGATTTTTTTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTTCA
1 TT-TTTTAGGGGATTTTTTTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTTCA
* * * * *
4275514 TATTAATTTATTTTTTAAAAATTAATTCATTTCTATAAATTTTGAATTTTTTCCTTGAAATCCTT
65 TATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAAT-CTT
* * **
4275579 -TTTTTCTAAAATATGGAGTTTTCTACTCTATAAA
129 CTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
* *
4275613 TTCTTTT-GGAGGATTTTTTTTGTTTTTTTTATTTTTAAAATTTATCAAATATTATTATTTATTT
1 TT-TTTTAGG-GGATTTTTTTTG-TTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTT
* * * *
4275677 TATATTATTTCAGTTTTCAAAAATTCACTT-ATTTCCTTAAATTTTGGATTTTTTTCCTTGAAAT
63 CATATTAATTCAGTTTTCAAAAATTCA-TTCATTTCCATAAATTTT-GAATTTTTTCCTTGAAAT
* * **
4275741 CTCCTTTTT-TGAAATATGGAGTTTTCTACTATGTAAA
126 CTTCTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
* * *
4275778 TTCTTTCAGGGGGATTTTTCTTT-TTTTTTTATTTCTAAAA-TCTATCAAATATTATTATTTATT
1 TT-TTTTA-GGGGATTTTT-TTTGTTTTTTGATTTTTAAAATTC-ATCAAATATTATTATTTATT
* ** * *
4275841 TCATATTCATTCA--TTTC-------CATAAATTT---TGAA---T---TTT-TTCCTTGAATTC
62 TCATATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATC
* *
4275887 -CCTTTTTCTGAAATACTG-GTTTTCTACTCCGTAAA
127 TTCTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
* * *
4275922 TTTTTTCAAGAGGGATTTTTCTTGGTTTTTGA-TTTTAAAATTAATCAAATATTATTATTTATTT
1 TTTTTT--AG-GGGATTTTTTTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTT
* *
4275986 CATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTTT-CTTGAAATTC
63 CATATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAA-TC
* *
4276050 TTTTTTTTC-AAAATACGGAGTTTTCTACTCCGTAAA
127 TTCTTTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
4276086 TTTTTT
1 TTTTTT
4276092 CAGAGAGATT
Statistics
Matches: 683, Mismatches: 80, Indels: 94
0.80 0.09 0.11
Matches are distributed among these distances:
143 3 0.00
144 66 0.10
145 36 0.05
146 7 0.01
150 1 0.00
153 10 0.01
155 1 0.00
156 10 0.01
159 1 0.00
162 9 0.01
163 24 0.04
164 175 0.26
165 193 0.28
166 36 0.05
167 5 0.01
168 30 0.04
169 71 0.10
170 5 0.01
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (163 bp):
TTTTTTAGGGGATTTTTTTTGTTTTTTGATTTTTAAAATTCATCAAATATTATTATTTATTTCAT
ATTAATTCAGTTTTCAAAAATTCATTCATTTCCATAAATTTTGAATTTTTTCCTTGAAATCTTCT
TTTTCTGAAATACGGAGTTTTCTACTCCGTAAA
Found at i:4275921 original size:144 final size:146
Alignment explanation
Indices: 4275699--4275997 Score: 405
Period size: 144 Copynumber: 2.1 Consensus size: 146
4275689 GTTTTCAAAA
* *
4275699 ATTCACTT-ATTTCCTTAAATTTTGGATTTTTTTCCTTGAAATCTCCTTTTTTGAAATATGGAGT
1 ATTCA-TTCATTTCCATAAATTTTGGAATTTTTTCCTTGAAATCTCCTTTTTTGAAATATGGAGT
* * ** *
4275763 TTTCTACTATGTAAATTCTTTC-AGGGGGATTTTTCTTTTTTTTTTATTTCTAAAATCT-ATCAA
65 TTTCTACTACGTAAATTCTTTCAAGAGGGATTTTTCTTGGTTTTTGATTT-TAAAAT-TAATCAA
4275826 ATATTATTATTTATTTCAT
128 ATATTATTATTTATTTCAT
*
4275845 ATTCATTCATTTCCATAAATTTT-GAATTTTTTCCTTGAATTC-CCTTTTTCTGAAATACT-G-G
1 ATTCATTCATTTCCATAAATTTTGGAATTTTTTCCTTGAAATCTCCTTTTT-TGAAATA-TGGAG
* *
4275906 TTTTCTACTCCGTAAATTTTTTCAAGAGGGATTTTTCTTGGTTTTTGATTTTAAAATTAATCAAA
64 TTTTCTACTACGTAAATTCTTTCAAGAGGGATTTTTCTTGGTTTTTGATTTTAAAATTAATCAAA
4275971 TATTATTATTTATTTCAT
129 TATTATTATTTATTTCAT
*
4275989 ATTAATTCA
1 ATTCATTCA
4275998 ATTTTCAAAA
Statistics
Matches: 137, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
143 1 0.01
144 66 0.48
145 50 0.36
146 20 0.15
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (146 bp):
ATTCATTCATTTCCATAAATTTTGGAATTTTTTCCTTGAAATCTCCTTTTTTGAAATATGGAGTT
TTCTACTACGTAAATTCTTTCAAGAGGGATTTTTCTTGGTTTTTGATTTTAAAATTAATCAAATA
TTATTATTTATTTCAT
Found at i:4276195 original size:164 final size:163
Alignment explanation
Indices: 4275849--4276203 Score: 387
Period size: 164 Copynumber: 2.2 Consensus size: 163
4275839 TTTCATATTC
* *
4275849 ATTCATTTCCATAAATTTTGAATTTTTTCCTTGAATTCCCTTTTTCTGAAATACTGGTTTTCTAC
1 ATTCATTTCCATAAATTTTGAATTTTTTCCTTGAATTCCCTTTTTCTAAAATACGGGTTTTCTAC
* * *** *
4275914 TCCGTAAATTTTTTCAAGAGGGATTTTTCTTGGTTTTTGATTTTAAAATTAATCAAATATTATTA
66 TCCGTAAATTTTTTCAAGAGAGATTTTTCTTGATTTAAAATTTTAAAATTAATCAAATATTATCA
* ** * *
4275979 TTTATTTCATATTAATTCAATTTTCAAAAATTC
131 TTGAACTCACATTAATTCAATTTTCAAAAATTA
* * *
4276012 ATTCATTTCCATGAATTTTGAATTTTTT-CTTGAAATT-CTTTTTTTTCAAAATACGGAGTTTTC
1 ATTCATTTCCATAAATTTTGAATTTTTTCCTTG-AATTCCCTTTTTCT-AAAATACGG-GTTTTC
* *
4276075 TACTCCGTAAATTTTTTC-AGAGAGATTTTTCTTGATTTAAAATTTTTTAAATTCAT-ATAATAT
63 TACTCCGTAAATTTTTTCAAGAGAGATTTTTCTTGATTTAAAA-TTTTAAAATTAATCA-AATAT
* * * * * *
4276138 TGTCATTGAACTCCCATTAATTTAGTTTTGAAAATTTTA
126 TATCATTGAACTCACATTAATTCAATTTTCAAAA-ATTA
* *
4276177 ATTTATTT-CATTAATTTTGAATTTTTT
1 ATTCATTTCCATAAATTTTGAATTTTTT
4276204 TGTATATAGT
Statistics
Matches: 160, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
162 11 0.07
163 58 0.36
164 82 0.51
165 9 0.06
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (163 bp):
ATTCATTTCCATAAATTTTGAATTTTTTCCTTGAATTCCCTTTTTCTAAAATACGGGTTTTCTAC
TCCGTAAATTTTTTCAAGAGAGATTTTTCTTGATTTAAAATTTTAAAATTAATCAAATATTATCA
TTGAACTCACATTAATTCAATTTTCAAAAATTA
Found at i:4276694 original size:10 final size:10
Alignment explanation
Indices: 4276676--4276711 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4276666 AAAGGGAGAA
4276676 AGAAAAAAAT
1 AGAAAAAAAT
*
4276686 AGAAGAAAAT
1 AGAAAAAAAT
*
4276696 ATAAAAAAAT
1 AGAAAAAAAT
4276706 AGAAAA
1 AGAAAA
4276712 GCTAGGCCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:4278201 original size:159 final size:160
Alignment explanation
Indices: 4277799--4278423 Score: 877
Period size: 159 Copynumber: 3.9 Consensus size: 160
4277789 TAAAATTAAA
* * * * *
4277799 TAATATTTATTTTTTCTAATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAAGGTTTAAA
1 TAATATTTATTTTTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAA
* *
4277864 AAACTTTTCGTATTCTTTC-GAGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAGTAAA
66 AAACCTTTCGTATTCTTTCAG-GCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAA--ATA
* *
4277928 ATTAAATTAAATTGATATTATCGGGATAAATTT
128 ATTAAATTAAATTGATATTATTGGGATAAATTC
*
4277961 TAATATTTATTTTTTCTAATCTGTTTATATTCCTAT-GGATATCCGTAGAGGTATAAAAGATTTC
1 TAATATTTATTTTTTCTAATCT-TTTATATTCCTATAGG-CATCCGTAGAGGTATAAAAGATTTC
* * * *
4278025 AAAAATCTTTCGTATTCTTTCAGGCTTCCATTAGGGTATGAACTAGTATTTTCAAAAATAAATAA
64 AAAAACCTTTCGTATTCTTTCAGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAA
* * *
4278090 TTAAATAAAATTGATATTATTAGGATGAATTC
129 TTAAATTAAATTGATATTATTGGGATAAATTC
* * * *
4278122 TAATATTTATTTTTT-TAATTTTTTATATTCTTATAGGCATCCGTAGGGGTGTAAAAGATTTCAA
1 TAATATTTATTTTTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAA
** * *
4278186 AAACCTTTCGTATTCTTTCAAACTTCCAGTAGGATACGAAATGGTATTTTCAAAAATAAATAATT
66 AAACCTTTCGTATTCTTTCAGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAATT
*
4278251 AAATTAAATTGGTATTATTGGGATAAATTC
131 AAATTAAATTGATATTATTGGGATAAATTC
* *
4278281 TAATATCTATTTTTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTTAA
1 TAATATTTATTTTTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAA
* * *
4278346 AAACCTTTCGCATTCTTTCGGGCTTCCATTAGAGTACGAAATGGTATTTTCAAAAATAAAT-A--
66 AAACCTTTCGTATTCTTTCAGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAATT
4278408 AAATTAAATTGA-ATTA
131 AAATTAAATTGATATTA
4278424 ATACTTTCGA
Statistics
Matches: 411, Mismatches: 47, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
156 4 0.01
157 11 0.03
159 134 0.33
160 105 0.26
161 45 0.11
162 24 0.06
163 87 0.21
164 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (160 bp):
TAATATTTATTTTTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAA
AAACCTTTCGTATTCTTTCAGGCTTCCATTAGGGTACGAAATGGTATTTTCAAAAATAAATAATT
AAATTAAATTGATATTATTGGGATAAATTC
Found at i:4278561 original size:145 final size:145
Alignment explanation
Indices: 4278134--4278529 Score: 363
Period size: 160 Copynumber: 2.6 Consensus size: 145
4278124 ATATTTATTT
* * * * * *
4278134 TTTTAATTTTTTATATTCTTATAGGCATCCGTAGGGGTGTAAAAGATTTCAAAAACCTTTCGTAT
1 TTTTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTTAAAAACCTTTCGCAT
** *
4278199 TCTTTCAAACTTCCAGTAGGA-TACGAAATGGTATTTTCAAAAATAAATAATTAAATTAAATTGG
66 TCTTTCAGGCTTCCA-TAAGAGTACGAAATGGTATTTTCAAAAATAAAT-A--AAATTAAATT-G
* ** * *
4278263 TATTATTGGGATAAATTCTA-ATATCTATTT
126 -A--ATT--AATACTTTCGAGA-A---A--A
4278293 TTTCTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTTAAAAACCTTTCGCA
1 TTT-TAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTTAAAAACCTTTCGCA
* *
4278358 TTCTTTCGGGCTTCCATTAGAGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTGAATT
65 TTCTTTCAGGCTTCCATAAGAGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTGAATT
4278423 AATACTTTCGAGAAAA
130 AATACTTTCGAGAAAA
* * * * *
4278439 TTTTAATCTTTTATATTTCTATGGGCGTCCGTTAG-GGTATAAACGATTTTAAAAA-CTTT-TCA
1 TTTTAATCTTTTATATTCCTATAGGCATCCG-TAGAGGTATAAAAGATTTTAAAAACCTTTCGCA
*
4278501 TATCTTTTCAGGCTTCTGATAAG-GTACGA
65 T-TC-TTTCAGGCTTC-CATAAGAGTACGA
4278530 TATGATTTAT
Statistics
Matches: 206, Mismatches: 24, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
143 3 0.01
144 6 0.03
145 60 0.29
146 10 0.05
148 1 0.00
151 8 0.04
152 1 0.00
153 3 0.01
155 1 0.00
156 1 0.00
157 10 0.05
159 7 0.03
160 95 0.46
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (145 bp):
TTTTAATCTTTTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTTAAAAACCTTTCGCAT
TCTTTCAGGCTTCCATAAGAGTACGAAATGGTATTTTCAAAAATAAATAAAATTAAATTGAATTA
ATACTTTCGAGAAAA
Found at i:4279006 original size:154 final size:155
Alignment explanation
Indices: 4278726--4279026 Score: 374
Period size: 154 Copynumber: 1.9 Consensus size: 155
4278716 TATCGAGTAC
* *
4278726 TTTTACGTCGAAAGAATCTCATAGGGGCATTTTCGTAATTTTTTAAAATCGAGTCCTAGGTTGTC
1 TTTTACGTCGAAAGAATCTCATAGGGGCACTTTCGTAATTTCTTAAAATCGAGTCCTAGGTTGTC
* * ** * **
4278791 ATCGGGTCTGCTTTTGTGCCAATGGTAGATATTTAGGATAGGTTCATCTCATATATTATCCTCTT
66 ATCGAGTATGCTTTCATGCCAATGGTAGATATTTAGGATAGGTTCATCCCATATAAAATCCTCTT
4278856 TAAGTCCTTTAG-GGTACCAGGCAT
131 TAAGTCCTTTAGAGGTACCAGGCAT
* * * * * *
4278880 TTTTACGTCGAAGGTATCTCTTAGGGGTACTTTGGTAATTTCTTAAAATCGAGTTCTAGGTTGTC
1 TTTTACGTCGAAAGAATCTCATAGGGGCACTTTCGTAATTTCTTAAAATCGAGTCCTAGGTTGTC
* * * * * *
4278945 A-CTGAGTATGCTTTCATGCTGAA-GGTGGGTATTTAGGATAGGTTCATCCCTTTTAAAATCCTT
66 ATC-GAGTATGCTTTCATGC-CAATGGTAGATATTTAGGATAGGTTCATCCCATATAAAATCCTC
4279008 TTTAAGTCCTTTAGAGGTA
129 TTTAAGTCCTTTAGAGGTA
4279027 TTGGTTACTT
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
153 1 0.01
154 116 0.94
155 6 0.05
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (155 bp):
TTTTACGTCGAAAGAATCTCATAGGGGCACTTTCGTAATTTCTTAAAATCGAGTCCTAGGTTGTC
ATCGAGTATGCTTTCATGCCAATGGTAGATATTTAGGATAGGTTCATCCCATATAAAATCCTCTT
TAAGTCCTTTAGAGGTACCAGGCAT
Found at i:4281543 original size:28 final size:28
Alignment explanation
Indices: 4281503--4281576 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
4281493 GAAAAAAAAT
* ** *
4281503 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4281531 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4281559 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
4281577 AATTAAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:4281628 original size:52 final size:52
Alignment explanation
Indices: 4281564--4281680 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 52
4281554 AATAACGAGG
*
4281564 TTGGAGTATCCCCAATTAAAGG-AAAATTGGTGTTTT-GAAAATAAAACCGGGA
1 TTGGAGTATCCCCAATT-AAGGAAAAATTAGTGTTTTAG-AAATAAAACCGGGA
* ** ** *
4281616 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAACCGGGG
1 TTGGAGTATCCCCAATTAAGGAAAAATTAGTGTTTTAGAAATAAAACCGGGA
4281668 TTGGAGTATCCCC
1 TTGGAGTATCCCC
4281681 TCAAAAATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 2 0.04
52 53 0.95
53 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (52 bp):
TTGGAGTATCCCCAATTAAGGAAAAATTAGTGTTTTAGAAATAAAACCGGGA
Found at i:4281700 original size:160 final size:160
Alignment explanation
Indices: 4281498--4281811 Score: 404
Period size: 160 Copynumber: 2.0 Consensus size: 160
4281488 CAGAAGAAAA
* ** * *
4281498 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATG-AATAACGAG
*
4281563 GTTGGAGTATCCCC-AAT-TAAAGGAAAATT-G-GTGTTTTGAAAATAAAACCGG-GATTGGAGT
65 GTTGGAGTATCCCCGAATGTAAA-G-AAATTAGTGTGTTTTGAAAATAAAACCGGAG-TTAGAGT
* *
4281623 ATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGAT
127 ATCCCCGATTATAG-AAAATTAGTGTTTTAGCGAT
* * *
4281658 AAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATGATTAACGGGG
1 AAAACCGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATGAATAACGAGG
* * * * *
4281723 TTGGAGTATCCCCGATTGTGAAGAAATTAGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCC
66 TTGGAGTATCCCCGAATGTAAAGAAATTAGTGTGTTTTGAAAATAAAACCGGAGTTAGAGTATCC
4281788 CCGATTATAGAAAATTAGTGTTTT
131 CCGATTATAGAAAATTAGTGTTTT
4281812 GAAAATAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
159 26 0.20
160 67 0.50
161 39 0.29
162 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (160 bp):
AAAACCGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCGATGAATAACGAGG
TTGGAGTATCCCCGAATGTAAAGAAATTAGTGTGTTTTGAAAATAAAACCGGAGTTAGAGTATCC
CCGATTATAGAAAATTAGTGTTTTAGCGAT
Found at i:4281726 original size:27 final size:27
Alignment explanation
Indices: 4281654--4281738 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
4281644 AGTGTTTTAG
*
4281654 CGATAAA-ACCGGGGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
* * *
4281680 CTCAAAAATAACGAGGTTGGAGTATCCC
1 C-GATAAATAACGGGGTTGGAGTATCCC
* *
4281708 CGATGATTAACGGGGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
4281735 CGAT
1 CGAT
4281739 TGTGAAGAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (27 bp):
CGATAAATAACGGGGTTGGAGTATCCC
Found at i:4281822 original size:51 final size:53
Alignment explanation
Indices: 4281726--4281844 Score: 163
Period size: 51 Copynumber: 2.3 Consensus size: 53
4281716 AACGGGGTTG
* *
4281726 GAGTATCCCCGATTGTGAAGAAATTAGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
4281780 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
4281831 GAATATCCCCGATT
1 GAGTATCCCCGATT
4281845 GTGGAGAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
51 34 0.57
52 2 0.03
53 9 0.15
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:4284289 original size:19 final size:18
Alignment explanation
Indices: 4284265--4284332 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4284255 CAGTAGCTAA
4284265 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4284284 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4284299 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4284316 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4284333 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4284305 original size:13 final size:13
Alignment explanation
Indices: 4284287--4284311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4284277 ACAATACTTA
4284287 TGTATCGATACAT
1 TGTATCGATACAT
4284300 TGTATCGATACA
1 TGTATCGATACA
4284312 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4284309 original size:32 final size:32
Alignment explanation
Indices: 4284268--4284330 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4284258 TAGCTAATTA
*
4284268 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4284300 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4284331 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4284412 original size:21 final size:21
Alignment explanation
Indices: 4284388--4284444 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
4284378 CATTTGTAGG
4284388 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
4284409 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
4284430 ATGTATCGATACATT
1 ATGTATCGATACATT
4284445 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:4285249 original size:55 final size:55
Alignment explanation
Indices: 4285165--4285852 Score: 872
Period size: 55 Copynumber: 12.3 Consensus size: 55
4285155 AAGTGTATCT
* * * * * *
4285165 TGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
4285220 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCC
* *
4285275 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
* * *
4285330 TGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
* **
4285385 TGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCC
* *
4285446 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCC
* *
4285505 CGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCC
*
4285564 CGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCC
* *
4285618 TGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
*
4285673 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
* ** *
4285728 TGCTCTTTGAGGACCGAAAAATGCCGCCAACTTGTGTGGGCTTTGAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
*
4285783 TGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
4285838 TGCTCTTTGAGGACT
1 TGCTCTTTGAGGACT
4285853 AAAAAGCGGA
Statistics
Matches: 581, Mismatches: 31, Indels: 42
0.89 0.05 0.06
Matches are distributed among these distances:
53 2 0.00
54 30 0.05
55 378 0.65
56 18 0.03
59 102 0.18
60 27 0.05
61 18 0.03
64 6 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (55 bp):
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
Found at i:4285349 original size:26 final size:26
Alignment explanation
Indices: 4285320--4285407 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
4285310 GTGGGCTTTA
4285320 AAAGGTGTCCTGCTCTTTGGGGAATG
1 AAAGGTGTCCTGCTCTTTGGGGAATG
** * **
4285346 AAAGGTG-CCACCAACTTGTGTGGGCTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGG-AATG
* *
4285375 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGAATG
4285401 AAAGGTG
1 AAAGGTG
4285408 CCACCAACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 5 0.11
28 5 0.11
29 11 0.24
30 3 0.07
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGAATG
Found at i:4286851 original size:5 final size:5
Alignment explanation
Indices: 4286843--4286891 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
4286833 TCTCTTTTTC
*
4286843 TTTGT TTTGT TTT-T TTTGT TTTGT TTT-T TTT-T TTTGC TTT-T TTT-T
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT
4286888 TTTG
1 TTTG
4286892 CTCTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 19 0.49
5 20 0.51
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (5 bp):
TTTGT
Found at i:4286855 original size:14 final size:13
Alignment explanation
Indices: 4286838--4286905 Score: 68
Period size: 14 Copynumber: 5.0 Consensus size: 13
4286828 TTTTCTCTCT
4286838 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
4286852 TTTTTTTTGTTTTG
1 -TTTTTTTGTTTTG
*
4286866 TTTTTTTTTTTTG
1 TTTTTTTGTTTTG
4286879 CTTTTTTT-TTTTG
1 -TTTTTTTGTTTTG
4286892 CTCTTTTTT-TTTTG
1 -T-TTTTTTGTTTTG
4286906 AAGAGAAGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
13 19 0.38
14 27 0.54
15 4 0.08
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:4286859 original size:19 final size:18
Alignment explanation
Indices: 4286837--4286890 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
4286827 CTTTTCTCTC
4286837 TTTTTCTTTGTTTTGTTTT
1 TTTTTCTTTGTTTT-TTTT
4286856 TTTTGT-TTTGTTTTTTTT
1 TTTT-TCTTTGTTTTTTTT
*
4286874 TTTTGCTTT-TTTTTTTT
1 TTTTTCTTTGTTTTTTTT
4286891 GCTCTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 12 0.38
20 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTGTTTTTTTT
Found at i:4286871 original size:13 final size:13
Alignment explanation
Indices: 4286847--4286905 Score: 82
Period size: 14 Copynumber: 4.4 Consensus size: 13
4286837 TTTTTCTTTG
*
4286847 TTTTGTTTTTTTT
1 TTTTGCTTTTTTT
*
4286860 GTTTTGTTTTTTTT
1 -TTTTGCTTTTTTT
4286874 TTTTGCTTTTTTT
1 TTTTGCTTTTTTT
4286887 TTTTGCTCTTTTTT
1 TTTTGCT-TTTTTT
4286901 TTTTG
1 TTTTG
4286906 AAGAGAAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
13 19 0.44
14 24 0.56
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (13 bp):
TTTTGCTTTTTTT
Found at i:4286885 original size:15 final size:15
Alignment explanation
Indices: 4286836--4286904 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 15
4286826 TCTTTTCTCT
*
4286836 CTTTTTCTTTGTTTTG
1 CTTTTT-TTTTTTTTG
*
4286852 -TTTTTTTTGTTTTG
1 CTTTTTTTTTTTTTG
4286866 --TTTTTTTTTTTTG
1 CTTTTTTTTTTTTTG
4286879 C--TTTTTTTTTTTG
1 CTTTTTTTTTTTTTG
4286892 CTCTTTTTTTTTT
1 CT-TTTTTTTTTT
4286905 GAAGAGAAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
13 25 0.52
14 9 0.19
15 5 0.10
16 9 0.19
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (15 bp):
CTTTTTTTTTTTTTG
Found at i:4286904 original size:19 final size:18
Alignment explanation
Indices: 4286843--4286890 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
4286833 TCTCTTTTTC
4286843 TTTGTTTTGTTTTTTTTGT
1 TTTGTTTT-TTTTTTTTGT
*
4286862 TTTGTTTTTTTTTTTTGC
1 TTTGTTTTTTTTTTTTGT
4286880 TTT-TTTTTTTT
1 TTTGTTTTTTTT
4286891 GCTCTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 8 0.29
18 12 0.43
19 8 0.29
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (18 bp):
TTTGTTTTTTTTTTTTGT
Found at i:4299424 original size:28 final size:28
Alignment explanation
Indices: 4299384--4299457 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
4299374 GAAAAAAAAT
* ** *
4299384 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4299412 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4299440 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
4299458 AATTAAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:4299672 original size:51 final size:53
Alignment explanation
Indices: 4299580--4299698 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
4299570 AACGGGGTTG
* * *
4299580 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
4299634 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
4299685 GAATATCCCCGATT
1 GAGTATCCCCGATT
4299699 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Done.