Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 53 of 193
Found at i:16445811 original size:3 final size:3
Alignment explanation
Indices: 16445803--16445829 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16445793 AATTTATTTA
16445803 AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC
16445830 CACCCACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16446273 original size:24 final size:24
Alignment explanation
Indices: 16446245--16446297 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
16446235 CTGATTCATA
* *
16446245 TTTTTCTGTTGCTTTTGGATTGCT
1 TTTTTCTGTTGATTTTGGACTGCT
16446269 TTTTTCTGTTGATTTTGGACTGCT
1 TTTTTCTGTTGATTTTGGACTGCT
16446293 TTTTT
1 TTTTT
16446298 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.06, C:0.11, G:0.19, T:0.64
Consensus pattern (24 bp):
TTTTTCTGTTGATTTTGGACTGCT
Found at i:16447214 original size:18 final size:20
Alignment explanation
Indices: 16447178--16447217 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16447168 GGATTTCTTT
*
16447178 TATTTTTTGTGGTTATATTC
1 TATTTTTGGTGGTTATATTC
16447198 TATTTTTGGT-GTT-TATTC
1 TATTTTTGGTGGTTATATTC
16447216 TA
1 TA
16447218 GCAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (20 bp):
TATTTTTGGTGGTTATATTC
Found at i:16449375 original size:18 final size:18
Alignment explanation
Indices: 16449352--16449397 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
16449342 CGATCTAGTA
*
16449352 ATGCTCTTACGAGCC-AGT
1 ATGCTCTAACGAGCCGA-T
*
16449370 ATGCTCAAACGAGCCGAT
1 ATGCTCTAACGAGCCGAT
16449388 ATGCTCTAAC
1 ATGCTCTAAC
16449398 TTACGCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (18 bp):
ATGCTCTAACGAGCCGAT
Found at i:16456309 original size:18 final size:18
Alignment explanation
Indices: 16456281--16456349 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
16456271 AATGCTCTTG
*
16456281 TGAGCCAGTATACTCAAA
1 TGAGCCAGTATGCTCAAA
** *
16456299 TGAGCTTGTATGCTCTAA
1 TGAGCCAGTATGCTCAAA
*
16456317 CGAGCCAGTATGCTCAAA
1 TGAGCCAGTATGCTCAAA
* *
16456335 TGAGACGGTATGCTC
1 TGAGCCAGTATGCTC
16456350 TAACTTACGC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (18 bp):
TGAGCCAGTATGCTCAAA
Found at i:16456322 original size:36 final size:36
Alignment explanation
Indices: 16456282--16456353 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
16456272 ATGCTCTTGT
*
16456282 GAGCCAGTATACTCAAATGAG-CTTGTATGCTCTAAC
1 GAGCCAGTATACTCAAATGAGAC-GGTATGCTCTAAC
*
16456318 GAGCCAGTATGCTCAAATGAGACGGTATGCTCTAAC
1 GAGCCAGTATACTCAAATGAGACGGTATGCTCTAAC
16456354 TTACGCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (36 bp):
GAGCCAGTATACTCAAATGAGACGGTATGCTCTAAC
Found at i:16458014 original size:40 final size:40
Alignment explanation
Indices: 16457970--16458063 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
16457960 CCATAGCTTG
*
16457970 GCTTGAATTTTAACACTAG-CCCATAGCCTGCTAAGTCGTA
1 GCTTGAATTTTAACAC-AGACCCATAGCCTGCTAAGCCGTA
* * *
16458010 GCTTGAATTTTAACACCGACTCATAGCTTGCTAAGCCGTA
1 GCTTGAATTTTAACACAGACCCATAGCCTGCTAAGCCGTA
16458050 GCTTGAA-TTTAACA
1 GCTTGAATTTTAACA
16458064 TTTCATGCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 8 0.16
40 41 0.84
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (40 bp):
GCTTGAATTTTAACACAGACCCATAGCCTGCTAAGCCGTA
Found at i:16459595 original size:13 final size:13
Alignment explanation
Indices: 16459579--16459650 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
16459569 ATATAACTTA
16459579 TTCATATAACCAT
1 TTCATATAACCAT
**
16459592 TTCATATATTCAT
1 TTCATATAACCAT
*
16459605 TTTATATAACCATT
1 TTCATATAACCA-T
*
16459619 TTGA-ATAACCAT
1 TTCATATAACCAT
* *
16459631 ATCATATAAACAT
1 TTCATATAACCAT
16459644 TTCATAT
1 TTCATAT
16459651 TACAGTTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 3 0.06
13 40 0.85
14 4 0.09
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:16459949 original size:45 final size:45
Alignment explanation
Indices: 16459876--16460131 Score: 248
Period size: 45 Copynumber: 5.7 Consensus size: 45
16459866 TTTTACAAAA
* * * * *
16459876 GATGCCATAGCGTCTTTCAACCAAGGTCTTACACACTTT-CGATAT
1 GATGCCATAGTGTCTTTCAACTACGGTCTTATACA-TTTCCGACAT
* * * * **
16459921 GATGTCATAGTGTCTTTCAATTATGGTCTCATTTATTTCCGACAT
1 GATGCCATAGTGTCTTTCAACTACGGTCTTATACATTTCCGACAT
* *
16459966 GATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTTCCGACAT
1 GATGCCATAGTGTCTTTCAACTACGGTCTTATACATTTCCGACAT
* *
16460011 GATGTCATAGTGTCTTTCAACTACGGCCTTATACATTTCC-ATCAT
1 GATGCCATAGTGTCTTTCAACTACGGTCTTATACATTTCCGA-CAT
* * * * *
16460056 G-TAGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTGTCAT
1 GAT-GCCATAGTGTCTTTCAACTACGGTCTTATACATTTCCGACAT
* * * *
16460101 GTTTCCATACTGTCTTTCAACTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACTACGGTCTTA
16460132 CTCGTCTGAA
Statistics
Matches: 177, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
44 5 0.03
45 171 0.97
46 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACTACGGTCTTATACATTTCCGACAT
Found at i:16460029 original size:90 final size:90
Alignment explanation
Indices: 16459876--16460176 Score: 279
Period size: 90 Copynumber: 3.3 Consensus size: 90
16459866 TTTTACAAAA
* * ** *
16459876 GATGCCATAGCGTCTTTCAACCAAGGTCTTACACACTTT-CGATATGATGTCATAGTGTCTTTCA
1 GATGCCATAGTGTCTTTCAACTAAGGTCTTATTCA-TTTCCGACATGATGTCATAGTGTCTTTCA
* **
16459940 ATTATGGTCTCATTTATTTCCGA-CAT
65 ACTATGGTCTCATACATTTCC-ATCAT
* *
16459966 GATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTTCCGACATGATGTCATAGTGTCTTTCAA
1 GATGCCATAGTGTCTTTCAACTAAGGTCTTATTCATTTCCGACATGATGTCATAGTGTCTTTCAA
* * *
16460031 CTACGGCCTTATACATTTCCATCAT
66 CTATGGTCTCATACATTTCCATCAT
* * * * * *
16460056 G-TAGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTGTCATG-TTTCCATACTGTCTTTC
1 GAT-GCCATAGTGTCTTTCAACTAAGGTCTTATTCATTTCCGACATGATGT-CATAGTGTCTTTC
* * * **
16460119 AACTATGGTCTTACT-CGTCTGAATCAT
64 AACTATGGTCTCA-TACATTTCCATCAT
** *
16460146 GATGCCATAGCATCTTTCAACTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACTAAGGTCTTA
16460177 CTCTTAGTTG
Statistics
Matches: 176, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
89 7 0.04
90 167 0.95
91 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (90 bp):
GATGCCATAGTGTCTTTCAACTAAGGTCTTATTCATTTCCGACATGATGTCATAGTGTCTTTCAA
CTATGGTCTCATACATTTCCATCAT
Found at i:16460146 original size:45 final size:45
Alignment explanation
Indices: 16459963--16460179 Score: 149
Period size: 45 Copynumber: 4.8 Consensus size: 45
16459953 TTATTTCCGA
* * * * * * *
16459963 CATGATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTTCCGA-
1 CATGTTGCCATACTGTCTTTCAACTATGGTCTTACTCA-GTCTGAT
* * * * * * *
16460008 CATGATGTCATAGTGTCTTTCAACTACGGCCTTA-TACA-TTTCCAT
1 CATGTTGCCATACTGTCTTTCAACTATGGTCTTACT-CAGTCT-GAT
* * * *
16460053 CATGTAGCCATAATGTCTTTCAACTATGGTCTTATTCATTTCTG-T
1 CATGTTGCCATACTGTCTTTCAACTATGGTCTTACTCA-GTCTGAT
*
16460098 CATGTTTCCATACTGTCTTTCAACTATGGTCTTACTC-GTCTGAAT
1 CATGTTGCCATACTGTCTTTCAACTATGGTCTTACTCAGTCTG-AT
* *
16460143 CATGATGCCATAGC-ATCTTTCAACTATGGTCTTACTC
1 CATGTTGCCATA-CTGTCTTTCAACTATGGTCTTACTC
16460180 TTAGTTGTTA
Statistics
Matches: 141, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
43 5 0.04
44 2 0.01
45 130 0.92
46 2 0.01
47 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (45 bp):
CATGTTGCCATACTGTCTTTCAACTATGGTCTTACTCAGTCTGAT
Found at i:16460147 original size:135 final size:134
Alignment explanation
Indices: 16459876--16460168 Score: 304
Period size: 135 Copynumber: 2.2 Consensus size: 134
16459866 TTTTACAAAA
* * * * * * * *
16459876 GATGCCATAGCGTCTTTCAACCAAGGTCTTACACACTTTCGAT-ATG-ATGTCATAGTGTCTTTC
1 GATGCCATAGCATCTTTCAACTACGGCCTTATACA-TTTCCATCATGTA-GCCATAATGTCTTTC
* * * * * *
16459939 AATTATGGTCTCATTTATTTCCGACATGATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTT
64 AACTATGGTCTCATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCA-GT
16460004 CCGACAT
128 CCGACAT
* **
16460011 GATGTCATAGTGTCTTTCAACTACGGCCTTATACATTTCCATCATGTAGCCATAATGTCTTTCAA
1 GATGCCATAGCATCTTTCAACTACGGCCTTATACATTTCCATCATGTAGCCATAATGTCTTTCAA
* * * * * * *
16460076 CTATGGTCTTATTCATTTCTGTCATGTTTCCATACTGTCTTTCAACTATGGTCTTACTC-GTCTG
66 CTATGGTCTCATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCAGTCCG
16460140 AATCAT
131 -A-CAT
16460146 GATGCCATAGCATCTTTCAACTA
1 GATGCCATAGCATCTTTCAACTA
16460169 TGGTCTTACT
Statistics
Matches: 129, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
133 3 0.02
134 7 0.05
135 118 0.91
136 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (134 bp):
GATGCCATAGCATCTTTCAACTACGGCCTTATACATTTCCATCATGTAGCCATAATGTCTTTCAA
CTATGGTCTCATTCATTTCCGACATGATGCCATACTGTCTTTCAACTACGGTCTTACTCAGTCCG
ACAT
Found at i:16470959 original size:25 final size:25
Alignment explanation
Indices: 16470931--16470989 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
16470921 GAAAAAGTAA
*
16470931 AAGTGTGATCAAGTGCAAAGAATGG
1 AAGTGTGATCAAGTGCAAAAAATGG
16470956 AAGTGTGATCAAGTGCAAAAAATGG
1 AAGTGTGATCAAGTGCAAAAAATGG
16470981 -AGTG-GATCA
1 AAGTGTGATCA
16470990 CTAACTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 24 0.73
ACGTcount: A:0.41, C:0.08, G:0.31, T:0.20
Consensus pattern (25 bp):
AAGTGTGATCAAGTGCAAAAAATGG
Found at i:16473593 original size:18 final size:17
Alignment explanation
Indices: 16473570--16473611 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
16473560 TCCTTAATTC
16473570 TCTTTCTCATTTCCTTCT
1 TCTTTCTCATTT-CTTCT
16473588 TCTTTCT--TTTCTTCT
1 TCTTTCTCATTTCTTCT
*
16473603 TCTTCCTCA
1 TCTTTCTCA
16473612 GGCTTCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
18 7 0.33
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTTTCTCATTTCTTCT
Found at i:16479259 original size:33 final size:33
Alignment explanation
Indices: 16479221--16479287 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
16479211 TATGTGGCTG
*
16479221 CATTCTAGCCTGTAGTTGCATCTGGCTATGTAC
1 CATTCTAGCCTGTAGTTGCATCTAGCTATGTAC
* * *
16479254 CATTCTAGCTTGTGGTTGCGTCTAGCTATGTAC
1 CATTCTAGCCTGTAGTTGCATCTAGCTATGTAC
16479287 C
1 C
16479288 TGTATTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (33 bp):
CATTCTAGCCTGTAGTTGCATCTAGCTATGTAC
Found at i:16482076 original size:25 final size:25
Alignment explanation
Indices: 16482022--16482154 Score: 162
Period size: 25 Copynumber: 5.4 Consensus size: 25
16482012 TTACATATTA
*
16482022 ATCACATTAACAC--ATAAGCATTT
1 ATCACATTAACACATATAAGCATAT
* * *
16482045 ATAACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
*
16482070 ATCACATTAACACATATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
* *
16482095 ATCACGTTGACACATATAAGCATAT
1 ATCACATTAACACATATAAGCATAT
* * *
16482120 ACCACATTAACACATATGAGTATAT
1 ATCACATTAACACATATAAGCATAT
16482145 ATCACATTAA
1 ATCACATTAA
16482155 TCAATAGCGA
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
23 12 0.13
25 81 0.87
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.29
Consensus pattern (25 bp):
ATCACATTAACACATATAAGCATAT
Found at i:16491736 original size:28 final size:28
Alignment explanation
Indices: 16491692--16491746 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16491682 GATATCTGAT
*
16491692 TTACTCCCTGTTGACCCAAAGGCCATGC
1 TTACTCCCTATTGACCCAAAGGCCATGC
* *
16491720 TTACTCCCTATTTACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGCCATG
16491747 ATGCTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGCCATGC
Found at i:16495182 original size:7 final size:7
Alignment explanation
Indices: 16495161--16495261 Score: 53
Period size: 7 Copynumber: 14.4 Consensus size: 7
16495151 TTAATTTTAT
16495161 ACCTTAAA
1 ACCTT-AA
16495169 ACCTTAA
1 ACCTTAA
*
16495176 ACTTTAA
1 ACCTTAA
* *
16495183 ACATGAA
1 ACCTTAA
16495190 ACCTTAA
1 ACCTTAA
*
16495197 ACCCTAA
1 ACCTTAA
*
16495204 TCAC-TAA
1 AC-CTTAA
* *
16495211 ACCCT-G
1 ACCTTAA
16495217 ACCTTAA
1 ACCTTAA
*
16495224 AGCTTAA
1 ACCTTAA
*
16495231 ACCCTAA
1 ACCTTAA
* * *
16495238 GCATAAA
1 ACCTTAA
16495245 ACCTTAA
1 ACCTTAA
*
16495252 ACCCTAA
1 ACCTTAA
16495259 ACC
1 ACC
16495262 ATATGTAAAA
Statistics
Matches: 68, Mismatches: 22, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
6 5 0.07
7 57 0.84
8 6 0.09
ACGTcount: A:0.44, C:0.30, G:0.04, T:0.23
Consensus pattern (7 bp):
ACCTTAA
Found at i:16495375 original size:17 final size:18
Alignment explanation
Indices: 16495350--16495392 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
16495340 AGTAAAAACT
16495350 CATCAATAGTCAAATATA
1 CATCAATAGTCAAATATA
16495368 CA-CAATAGTCAAATATA
1 CATCAATAGTCAAATATA
16495385 CATCAATA
1 CATCAATA
16495393 AAACCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (18 bp):
CATCAATAGTCAAATATA
Found at i:16496210 original size:43 final size:43
Alignment explanation
Indices: 16496149--16496245 Score: 158
Period size: 43 Copynumber: 2.3 Consensus size: 43
16496139 AACTGCACAA
*
16496149 TTAATAACATGTCACGATATTAACAAGAGTCAAGAAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
* * *
16496192 TTAATAACATGCCACGATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
16496235 TTAATAACATG
1 TTAATAACATG
16496246 TCAAGGAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGTCAAGAAATATAAT
Found at i:16497229 original size:17 final size:17
Alignment explanation
Indices: 16497207--16497255 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
16497197 ATAACCATAC
16497207 AAAATAAAATAAATTTT
1 AAAATAAAATAAATTTT
16497224 AAAATAAAATAAATTTT
1 AAAATAAAATAAATTTT
16497241 AAAATAAAATAAATT
1 AAAATAAAATAAATT
16497256 AACTTTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAAATAAATTTT
Found at i:16497243 original size:29 final size:28
Alignment explanation
Indices: 16497172--16497248 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
16497162 CTAACAAACT
16497172 AAAT-AATTTTAAAAATAAATTTAAAATA
1 AAATAAATTTT-AAAATAAATTTAAAATA
* **
16497200 ACCATACAA-AATAAAATAAATTTTAAAATA
1 A-AATA-AATTTTAAAATAAA-TTTAAAATA
16497230 AAATAAATTTTAAAATAAA
1 AAATAAATTTTAAAATAAA
16497249 ATAAATTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.08
29 22 0.58
30 11 0.29
31 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAAATTTTAAAATAAATTTAAAATA
Found at i:16497290 original size:16 final size:16
Alignment explanation
Indices: 16497258--16497304 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
16497248 AATAAATTAA
16497258 CTTTCTTTTCCTT-TTT
1 CTTTC-TTTCCTTCTTT
*
16497274 CTTTCTTTCTTTCTTT
1 CTTTCTTTCCTTCTTT
* *
16497290 CCTTCCTTCCTTCTT
1 CTTTCTTTCCTTCTT
16497305 CTCCCTTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTTCTTTCCTTCTTT
Found at i:16498255 original size:14 final size:15
Alignment explanation
Indices: 16498233--16498274 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
16498223 TAAAAACATA
16498233 AAAATTTTAAAAATT
1 AAAATTTTAAAAATT
* *
16498248 ATAA-TTTAAAATTT
1 AAAATTTTAAAAATT
16498262 AAAATTTTAAAAA
1 AAAATTTTAAAAA
16498275 AATATATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTTAAAAATT
Found at i:16498292 original size:29 final size:29
Alignment explanation
Indices: 16498233--16498294 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
16498223 TAAAAACATA
* *
16498233 AAAATTTTAAAAATTATAATTTAAAATTT
1 AAAATTTTAAAAAATATAATTGAAAATTT
16498262 AAAATTTTAAAAAA-AT-ATATGAAAATGTT
1 AAAATTTTAAAAAATATAAT-TGAAAAT-TT
16498291 AAAA
1 AAAA
16498295 ACTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 8 0.28
29 19 0.66
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTTTAAAAAATATAATTGAAAATTT
Found at i:16499698 original size:2 final size:2
Alignment explanation
Indices: 16499691--16499719 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16499681 AAATAAATAA
16499691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16499720 ACATGATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16504180 original size:60 final size:60
Alignment explanation
Indices: 16504116--16504237 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 60
16504106 TTTTTTAATT
* *
16504116 TTGAATTCTTAAGAATTA-AGACTAAATTGACATAATGTGTAAATA-TG-AGGGTTAAATTTG
1 TTGAATT-TTAAGAATTAGAG-C-AAATTGACAGAATCTGTAAATATTGAAGGGTTAAATTTG
* * * *
16504176 TTGAATTTTTAGAGTTGGAGCAAATTGATAGAATCTGTAAATATTGAAGGGTTAAATTTG
1 TTGAATTTTAAGAATTAGAGCAAATTGACAGAATCTGTAAATATTGAAGGGTTAAATTTG
16504236 TT
1 TT
16504238 ATTATGCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 19 0.36
59 10 0.19
60 24 0.45
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (60 bp):
TTGAATTTTAAGAATTAGAGCAAATTGACAGAATCTGTAAATATTGAAGGGTTAAATTTG
Found at i:16510213 original size:10 final size:9
Alignment explanation
Indices: 16510196--16510303 Score: 73
Period size: 9 Copynumber: 11.9 Consensus size: 9
16510186 TAATATTTTC
16510196 TATT-AAAA
1 TATTAAAAA
16510204 TGATTAAAAAA
1 T-ATT-AAAAA
*
16510215 TATAAAAAA
1 TATTAAAAA
16510224 TCATTAAAAA
1 T-ATTAAAAA
*
16510234 GTA-TAAATA
1 -TATTAAAAA
*
16510243 TCATGAAAAA
1 T-ATTAAAAA
*
16510253 TATTAAAGA
1 TATTAAAAA
16510262 T-TATAAAAA
1 TAT-TAAAAA
*
16510271 TTTTAAAAA
1 TATTAAAAA
*
16510280 AATT--AAA
1 TATTAAAAA
16510287 TATTAAAAA
1 TATTAAAAA
16510296 TATTAAAA
1 TATTAAAA
16510304 TTGATATAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 47 0.60
10 16 0.21
11 6 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
TATTAAAAA
Found at i:16510220 original size:9 final size:9
Alignment explanation
Indices: 16510208--16510391 Score: 52
Period size: 9 Copynumber: 19.7 Consensus size: 9
16510198 TTAAAATGAT
16510208 TAAAAAATA
1 TAAAAAATA
16510217 TAAAAAATCA
1 TAAAAAAT-A
*
16510227 TTAAAAAGTA
1 -TAAAAAATA
*
16510237 T-AAATATCA
1 TAAAAAAT-A
*
16510246 TGAAAAATA
1 TAAAAAATA
* *
16510255 TTAAAGATTA
1 -TAAAAAATA
* *
16510265 TAAAAATTT
1 TAAAAAATA
16510274 TAAAAAA-A
1 TAAAAAATA
*
16510282 T--TAAATA
1 TAAAAAATA
*
16510289 TTAAAAATA
1 TAAAAAATA
* *
16510298 TTAAAATTGA
1 TAAAAAAT-A
**
16510308 TATAAACTTA
1 TA-AAAAATA
* **
16510318 TAATACTTA
1 TAAAAAATA
*
16510327 TAAAAACTTA
1 TAAAAA-ATA
* *
16510337 TAAATATTA
1 TAAAAAATA
16510346 TAAAAACATA
1 TAAAAA-ATA
* *
16510356 TAATAAATC
1 TAAAAAATA
16510365 TAATAAAATTA
1 TAA-AAAA-TA
16510376 TAAAAAAATA
1 T-AAAAAATA
16510386 TAAAAA
1 TAAAAA
16510392 TTAATAAACA
Statistics
Matches: 134, Mismatches: 26, Indels: 30
0.71 0.14 0.16
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 5 0.04
9 65 0.49
10 39 0.29
11 18 0.13
12 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAAATA
Found at i:16510229 original size:20 final size:20
Alignment explanation
Indices: 16510200--16510240 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16510190 ATTTTCTATT
*
16510200 AAAATGATTAAAAAATATAA
1 AAAATCATTAAAAAATATAA
*
16510220 AAAATCATTAAAAAGTATAA
1 AAAATCATTAAAAAATATAA
16510240 A
1 A
16510241 TATCATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATCATTAAAAAATATAA
Found at i:16510232 original size:19 final size:18
Alignment explanation
Indices: 16510200--16510303 Score: 63
Period size: 19 Copynumber: 5.7 Consensus size: 18
16510190 ATTTTCTATT
*
16510200 AAAATGATTAAAAAATATAA
1 AAAATCATT-AAAAATAT-A
16510220 AAAATCATTAAAAAGTATA
1 AAAATCATTAAAAA-TATA
* *
16510239 AATATCATGAAAAATATTA
1 AAAATCATTAAAAATA-TA
* * *
16510258 AAGATTA-TAAAAATTTTA
1 AAAATCATTAAAAA-TATA
* *
16510276 AAAA-AATTAAATAT-TA
1 AAAATCATTAAAAATATA
16510292 AAAAT-ATTAAAA
1 AAAATCATTAAAA
16510304 TTGATATAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.18
17 2 0.03
18 17 0.25
19 26 0.38
20 11 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
AAAATCATTAAAAATATA
Found at i:16510286 original size:27 final size:25
Alignment explanation
Indices: 16510248--16510303 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
16510238 AAATATCATG
* *
16510248 AAAAATATTAAAGATTATAAAAATTTT
1 AAAAAAATTAAAGA-T-TAAAAATATT
*
16510275 AAAAAAATTAAATATTAAAAATATT
1 AAAAAAATTAAAGATTAAAAATATT
16510300 AAAA
1 AAAA
16510304 TTGATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
26 1 0.04
27 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAAAAATTAAAGATTAAAAATATT
Found at i:16510292 original size:16 final size:16
Alignment explanation
Indices: 16510268--16510302 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16510258 AAGATTATAA
*
16510268 AAATTTTAAAAAAATT
1 AAATATTAAAAAAATT
*
16510284 AAATATTAAAAATATT
1 AAATATTAAAAAAATT
16510300 AAA
1 AAA
16510303 ATTGATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATTAAAAAAATT
Found at i:16510335 original size:19 final size:18
Alignment explanation
Indices: 16510311--16510360 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
16510301 AAATTGATAT
16510311 AAACTTATAATACTTATAA
1 AAACTTATAATA-TTATAA
16510330 AAACTTATAAATATTATAA
1 AAACTTAT-AATATTATAA
*
16510349 AAACATATAATA
1 AAACTTATAATA
16510361 AATCTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAACTTATAATATTATAA
Found at i:16510337 original size:10 final size:9
Alignment explanation
Indices: 16510208--16510623 Score: 111
Period size: 10 Copynumber: 43.7 Consensus size: 9
16510198 TTAAAATGAT
*
16510208 TAAAAAATA
1 TAAAAATTA
*
16510217 TAAAAAATCA
1 T-AAAAATTA
*
16510227 TTAAAAAGTA
1 -TAAAAATTA
* *
16510237 TAAATATCA
1 TAAAAATTA
16510246 TGAAAAA-TA
1 T-AAAAATTA
*
16510255 TTAAAGATTA
1 -TAAAAATTA
*
16510265 TAAAAATTT
1 TAAAAATTA
*
16510274 TAAAAA-AA
1 TAAAAATTA
*
16510282 T-TAAA-TA
1 TAAAAATTA
16510289 TTAAAAA-TA
1 -TAAAAATTA
*
16510298 TTAAAATTGA
1 TAAAAATT-A
*
16510308 TATAAACTTA
1 TA-AAAATTA
* *
16510318 TAATACTTA
1 TAAAAATTA
16510327 TAAAAACTTA
1 TAAAAA-TTA
*
16510337 TAAATATTA
1 TAAAAATTA
*
16510346 TAAAAACATA
1 TAAAAA-TTA
16510356 TAATAAATCTA
1 TAA-AAAT-TA
16510367 -ATAAAATTA
1 TA-AAAATTA
*
16510376 TAAAAAAATA
1 T-AAAAATTA
16510386 TAAAAATTAA
1 TAAAAATT-A
16510396 TAAACATATT-
1 TAAA-A-ATTA
*
16510406 TAAAATTTTA
1 TAAAA-ATTA
*
16510416 TAAAAACCTA
1 TAAAAA-TTA
*
16510426 TAAAAATCA
1 TAAAAATTA
16510435 TAAAAATTA
1 TAAAAATTA
**
16510444 TTAAATGTTA
1 -TAAAAATTA
*
16510454 TTAAATATTA
1 -TAAAAATTA
16510464 -AAAAA-TA
1 TAAAAATTA
* *
16510471 TTAAAATCGA
1 TAAAAAT-TA
**
16510481 TGTAAATTA
1 TAAAAATTA
*
16510490 TAAAAAAATA
1 T-AAAAATTA
*
16510500 TAATAA-TA
1 TAAAAATTA
16510508 TAAAAAATTA
1 T-AAAAATTA
16510518 TAAACAAATT-
1 T-AA-AAATTA
16510528 TACAAAATTAA
1 TA-AAAATT-A
*
16510539 TAAAATATATT
1 TAAAA-AT-TA
16510550 TAAAATATT-
1 TAAAA-ATTA
**
16510559 TAATATTTTA
1 TAA-AAATTA
*
16510569 TAAGAAGTTA
1 TAA-AAATTA
*
16510579 TAAAAAGTCA
1 TAAAAA-TTA
*
16510589 TAAAAACTTT
1 TAAAAA-TTA
16510599 TAAATAA-TA
1 TAAA-AATTA
16510608 TAATAAATTA
1 TAA-AAATTA
16510618 TAAAAA
1 TAAAAA
16510624 ATATCATTTA
Statistics
Matches: 305, Mismatches: 61, Indels: 82
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.02
8 18 0.06
9 103 0.34
10 141 0.46
11 33 0.11
12 4 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:16510376 original size:30 final size:29
Alignment explanation
Indices: 16510325--16510542 Score: 107
Period size: 29 Copynumber: 7.6 Consensus size: 29
16510315 TTATAATACT
*
16510325 TATAAAAACTT-ATAAATATTATAAAAACA
1 TATAAAAA-TTAATAAATATTATAAAAAAA
16510354 TATAATAAATCTAATAAA-ATTATAAAAAAA
1 TATAA-AAAT-TAATAAATATTATAAAAAAA
***
16510384 TATAAAAATTAATAAACATATT-TAAAATTT
1 TATAAAAATTAAT-AA-ATATTATAAAAAAA
* * * *
16510414 TATAAAAACCT-ATAAAAATCAT-AAAAAT
1 TATAAAAA-TTAATAAATATTATAAAAAAA
** *
16510442 TATTAAATGTTATTAAATA-T-T-AAAAAA
1 TA-TAAAAATTAATAAATATTATAAAAAAA
* ** *
16510469 TATTAAAATCGATGTAA-ATTATAAAAAAA
1 TATAAAAATTAAT-AAATATTATAAAAAAA
* *
16510498 TATAATAATATAA-AAA-ATTATAAACAAA
1 TATAAAAAT-TAATAAATATTATAAAAAAA
*
16510526 TTTACAAAATTAATAAA
1 TATA-AAAATTAATAAA
16510543 ATATATTTAA
Statistics
Matches: 141, Mismatches: 31, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
26 6 0.04
27 11 0.08
28 34 0.24
29 44 0.31
30 37 0.26
31 9 0.06
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (29 bp):
TATAAAAATTAATAAATATTATAAAAAAA
Found at i:16511955 original size:59 final size:59
Alignment explanation
Indices: 16511886--16512084 Score: 197
Period size: 59 Copynumber: 3.4 Consensus size: 59
16511876 TTTAAACATT
* * * *
16511886 CGAGGATAAAATGGTTATTTTTAGAAAAATCAGGACCAAAAATGGAATTTTTGGACGTC
1 CGAGGGTAAAATGGTAATTTTTAGAAAAATCAGGACAAAAAATGGAATTTTTGGAAGTC
* ** * *
16511945 CGAGGGTAAAATGGTAATTTTTGGAAAAATTGGGATAAAAAATGGAATTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTAGAAAAATCAGGACAAAAAATGGAATTTTTGGAAGTC
** * * *
16512004 CGAGGGTAAAAATGG-AATTTTTAG-AAGTTCGAGGGC-AAAAATGTAATTTTTGGAAGTTT
1 CGAGGGT-AAAATGGTAATTTTTAGAAAAATC-AGGACAAAAAATGGAATTTTTGGAAG-TC
* * *
16512063 CAAGGTTAAAATTGTAATTTTT
1 CGAGGGTAAAATGGTAATTTTT
16512085 GGAAGTTCAG
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
58 28 0.24
59 81 0.70
60 7 0.06
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTAGAAAAATCAGGACAAAAAATGGAATTTTTGGAAGTC
Found at i:16512014 original size:30 final size:29
Alignment explanation
Indices: 16511923--16512415 Score: 414
Period size: 29 Copynumber: 16.8 Consensus size: 29
16511913 AATCAGGACC
* * *
16511923 AAAAATGGAATTTTTGGACGTCCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* *
16511952 -AAAATGGTAATTTTTGGAAAAATT-G-GGAT
1 AAAAAT-GTAATTTTTGG--AAGTTCGAGGGT
*
16511981 AAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
16512011 AAAAATGGAATTTTTAGAAGTTCGAGGGC
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* *
16512040 AAAAATGTAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGTAATTTTTGGAAG-TTCGAGGGT
*
16512070 AAAATTGTAATTTTTGGAAGTTC-AGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGA-GGGT
*
16512099 AAAAATGTAATTTTTAGAAGTTTC-AGAGGT
1 AAAAATGTAATTTTTGGAAG-TTCGAG-GGT
* * *
16512129 AAAAATGTAATTTTGGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* *
16512159 TAAAATGGAATTTTTGGAAGTTC-AGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGA-GGGT
* * *
16512188 AAAAATGTAGTTTTTAGAAGTT-TAGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGA-GGGT
* *
16512217 AAAGATGTAATTTTTAGAAGTTTCGAGGGT
1 AAAAATGTAATTTTTGGAAG-TTCGAGGGT
*
16512247 AAAATTGTAA-TTTTGAAGAAGTTC-AGGGGT
1 AAAAATGTAATTTTTG--GAAGTTCGA-GGGT
* * * * *
16512277 TAAAATATAATTTTTGAAAGTCCAAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
*
16512306 -AAAATGTAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
16512334 -AAAATGTAATTTTTAGAAGTTTTGGGGGT
1 AAAAATGTAATTTTTGGAAG-TTCGAGGGT
* * *
16512363 AAAAATGTAATTTTTAGAAGTTTAGGGGGT
1 AAAAATGTAATTTTTGGAAG-TTCGAGGGT
*
16512393 AAAAATGTAATTTTGGAGAAGTT
1 AAAAATGTAATTTTTG-GAAGTT
16512416 TGGGGTCAAA
Statistics
Matches: 386, Mismatches: 53, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
28 51 0.13
29 158 0.41
30 151 0.39
31 26 0.07
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:16512090 original size:59 final size:59
Alignment explanation
Indices: 16511923--16512416 Score: 413
Period size: 59 Copynumber: 8.4 Consensus size: 59
16511913 AATCAGGACC
* * * * * *
16511923 AAAAATGGAATTTTTGGACG-TCCGAGGGT-AAAATGGTAATTTTTGGAAAAATT-G-GGAT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAAT-GTAATTTTTGG--AAGTTCGAGGGT
* * * * *
16511981 AAAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTAGAAGTTCGAGGGC
1 -AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGT
* *
16512040 AAAAATGTAATTTTTGGAAGTTTCAAGGTTAAAATTGTAATTTTTGGAAGTTC-AGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAGTTCGA-GGGT
* * * *
16512099 AAAAATGTAATTTTTAGAAGTTTC-AGAGGTAAAAATGTAATTTTGGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAG-GGTAAAAATGTAATTTTTG-GAAGTTCGAGGGT
* * * * * *
16512159 TAAAATGGAATTTTTGGAAG-TTCAGGGGTAAAAATGTAGTTTTTAGAAGTT-TAGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAGTTCGA-GGGT
* * * *
16512217 AAAGATGTAATTTTTAGAAGTTTCGAGGGTAAAATTGTAA-TTTTGAAGAAGTTC-AGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTG--GAAGTTCGA-GGGT
* * * * *
16512277 TAAAATATAATTTTTGAAAG-TCCAAGGGT-AAAATGTAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGT
* *** * * *
16512334 -AAAATGTAATTTTTAGAAGTTTTGGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAG-TTCGAGGGT
*
16512393 AAAAATGTAATTTTGGAGAAGTTT
1 AAAAATGTAATTTTTG-GAAGTTT
16512417 GGGGTCAAAA
Statistics
Matches: 356, Mismatches: 58, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
56 16 0.04
57 20 0.06
58 79 0.22
59 161 0.45
60 73 0.21
61 7 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAGTTTCAAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:16512427 original size:59 final size:60
Alignment explanation
Indices: 16511982--16512449 Score: 427
Period size: 59 Copynumber: 8.0 Consensus size: 60
16511972 AATTGGGATA
* * * * *
16511982 AAAAATGGAATTTTTG-GAAG-TTCGAGGGTAAAAATGGAATTTTTAGAAG-TTCGAGGGC
1 AAAAATGTAATTTTTGAGAAGTTTCG-GGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
* * * * *
16512040 AAAAATGTAATTTTTG-GAAGTTTCAAGGTTAAAATTGTAATTTTTGGAAGTTCA-GGGGT
1 AAAAATGTAATTTTTGAGAAGTTTC-GGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
* *
16512099 AAAAATGTAATTTTT-AGAAGTTTCAGAGGTAAAAATGTAATTTTGGAGAAGTTT-GGGGGT
1 AAAAATGTAATTTTTGAGAAGTTTC-GGGGTAAAAATGTAATTTT-TAGAAGTTTAGGGGGT
* * *
16512159 TAAAATGGAATTTTTG-GAAG-TTCAGGGGTAAAAATGTAGTTTTTAGAAGTTTA-GGGGT
1 AAAAATGTAATTTTTGAGAAGTTTC-GGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
* * * *
16512217 AAAGATGTAATTTTT-AGAAGTTTCGAGGGTAAAATTGTAATTTTGAAGAAGTTCA-GGGGT
1 AAAAATGTAATTTTTGAGAAGTTTCG-GGGTAAAAATGTAATTTT-TAGAAGTTTAGGGGGT
* * * * * *
16512277 TAAAATATAATTTTTGA-AAG-TCCAAGGGT-AAAATGTAATTTTTGGAAG-TTCGGGGGT
1 AAAAATGTAATTTTTGAGAAGTTTC-GGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
*
16512334 -AAAATGTAATTTTT-AGAAGTTTTGGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
1 AAAAATGTAATTTTTGAGAAG-TTTCGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
* * * *
16512393 AAAAATGTAATTTTGGAGAAGTTT-GGGGTCAAAATACT-ATTTTTGGATAGTTTAGGG
1 AAAAATGTAATTTTTGAGAAGTTTCGGGGTAAAAAT-GTAATTTTTAGA-AGTTTAGGG
16512450 ACCTCTAAGG
Statistics
Matches: 337, Mismatches: 49, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
55 1 0.00
56 17 0.05
57 13 0.04
58 80 0.24
59 137 0.41
60 83 0.25
61 6 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (60 bp):
AAAAATGTAATTTTTGAGAAGTTTCGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGGT
Found at i:16513659 original size:27 final size:28
Alignment explanation
Indices: 16513629--16513694 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
16513619 TAATTAAATT
* *
16513629 TAAATTCAAAA-CAAATTTAAATTTAA-A
1 TAAATTCAAAATC-AATTCAAACTTAATA
*
16513656 TAAATTTAAAATCAATTCAAACTTAATA
1 TAAATTCAAAATCAATTCAAACTTAATA
16513684 TAAATTCAAAA
1 TAAATTCAAAA
16513695 ATAAAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAATTCAAAATCAATTCAAACTTAATA
Found at i:16513667 original size:17 final size:16
Alignment explanation
Indices: 16513611--16513665 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
16513601 TTAAAACCAT
*
16513611 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
16513627 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
16513644 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
16513660 TTTAAA
1 TTTAAA
16513666 ATCAATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:16514344 original size:18 final size:18
Alignment explanation
Indices: 16514321--16514381 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
16514311 CAATTTTAAT
16514321 ATTTTAAATTTTTAATAA
1 ATTTTAAATTTTTAATAA
* *
16514339 ATTTTAGATTTTTTATGAA
1 ATTTTAAATTTTTAAT-AA
* *
16514358 TTTTTTTAATTTTTAATAA
1 -ATTTTAAATTTTTAATAA
16514377 ATTTT
1 ATTTT
16514382 TTATAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 18 0.53
19 4 0.12
20 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTAAATTTTTAATAA
Found at i:16514363 original size:20 final size:20
Alignment explanation
Indices: 16514322--16514395 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
16514312 AATTTTAATA
*
16514322 TTTTAAATTTTTAATAAA--
1 TTTTTAATTTTTAATAAATT
* *
16514340 -TTTTAGATTTTTTATGAATT
1 TTTTTA-ATTTTTAATAAATT
16514360 TTTTTAATTTTTAATAAATT
1 TTTTTAATTTTTAATAAATT
16514380 TTTTATAA-TTTTAATA
1 TTTT-TAATTTTTAATA
16514396 GAAAATATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.09
18 10 0.22
20 24 0.52
21 8 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTAATTTTTAATAAATT
Found at i:16516176 original size:59 final size:59
Alignment explanation
Indices: 16516099--16516225 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
16516089 TTGGACATTC
* * ** *
16516099 GGGGTAAAATGGTTATTTTTAGAAAAATC-AGAATCAAAAATTTAATTTTTAGACGTTCG
1 GGGGTAAAATGGTAATTTTTAGAAAAATCGAG-ATAAAAAATGGAATTTTTAGAAGTTCG
* *
16516158 GGGGTAAAATGGTAATTTTTGGAAAAATCGAGATAAAAAATGGAATTTTTTGAAGTTCG
1 GGGGTAAAATGGTAATTTTTAGAAAAATCGAGATAAAAAATGGAATTTTTAGAAGTTCG
16516217 GGGGTAAAA
1 GGGGTAAAA
16516226 ATATAATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 58 0.97
60 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTAGAAAAATCGAGATAAAAAATGGAATTTTTAGAAGTTCG
Found at i:16516236 original size:28 final size:29
Alignment explanation
Indices: 16516193--16516277 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
16516183 AATCGAGATA
* *
16516193 AAAAATGGAATTTTTTG-AAGTTCGGGGGT
1 AAAAATAGAA-TTTTTGAAAGTTAGGGGGT
*
16516222 AAAAATATAATTTTTGAAAGTTTA-GGGGT
1 AAAAATAGAATTTTTGAAAG-TTAGGGGGT
16516251 AAAAATAGAATTTTTGAAAGTTAGGGG
1 AAAAATAGAATTTTTGAAAGTTAGGGG
16516278 CATTCATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.18
29 38 0.78
30 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATAGAATTTTTGAAAGTTAGGGGGT
Found at i:16517031 original size:17 final size:17
Alignment explanation
Indices: 16517009--16517138 Score: 100
Period size: 17 Copynumber: 8.1 Consensus size: 17
16516999 ATTGGGTTTC
* *
16517009 AATTTATAATAATTTTA
1 AATTTAAAATAAATTTA
16517026 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * * *
16517043 GACTTAAATTAAATTCA
1 AATTTAAAATAAATTTA
*
16517060 AATTTAAAGT---TTT-
1 AATTTAAAATAAATTTA
16517073 AATTT----TAAATTTA
1 AATTTAAAATAAATTTA
*
16517086 AATTTAAAATAAATCTA
1 AATTTAAAATAAATTTA
16517103 AATTT-AAATCAAATTT-
1 AATTTAAAAT-AAATTTA
16517119 AATCTTAAAATAAATTTA
1 AAT-TTAAAATAAATTTA
16517137 AA
1 AA
16517139 GGGGCCCGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 23
0.72 0.10 0.19
Matches are distributed among these distances:
9 1 0.01
12 3 0.03
13 10 0.11
14 2 0.02
16 7 0.08
17 60 0.67
18 6 0.07
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:16517095 original size:7 final size:6
Alignment explanation
Indices: 16517022--16517138 Score: 84
Period size: 6 Copynumber: 20.0 Consensus size: 6
16517012 TTATAATAAT
* * * *
16517022 TTTAAA TTTAAA -ATAAA TTTAGA CTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
16517068 GTTTTAAT TTTAAA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA -TCAAA
1 --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
16517116 TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA
16517139 GGGGCCCGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
5 24 0.28
6 55 0.64
7 2 0.02
8 5 0.06
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:16517112 original size:12 final size:12
Alignment explanation
Indices: 16517022--16517138 Score: 84
Period size: 11 Copynumber: 10.0 Consensus size: 12
16517012 TTATAATAAT
16517022 TTTAAATTTAAA
1 TTTAAATTTAAA
* *
16517034 -ATAAATTTAGA
1 TTTAAATTTAAA
*
16517045 CTTAAA-TTAAA
1 TTTAAATTTAAA
*
16517056 TTCAAATTTAAA
1 TTTAAATTTAAA
*
16517068 GTTTTAATTTTAAA
1 --TTTAAATTTAAA
16517082 TTTAAATTTAAA
1 TTTAAATTTAAA
* *
16517094 -ATAAATCTAAA
1 TTTAAATTTAAA
*
16517105 TTTAAA-TCAAA
1 TTTAAATTTAAA
16517116 TTT-AATCTTAAA
1 TTTAAAT-TTAAA
*
16517128 -ATAAATTTAAA
1 TTTAAATTTAAA
16517139 GGGGCCCGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
10 2 0.02
11 38 0.47
12 31 0.38
14 10 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:16517127 original size:23 final size:24
Alignment explanation
Indices: 16517051--16517127 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 24
16517041 TAGACTTAAA
* * *
16517051 TTAAATTCAAATTTAAAGTTTTAATT
1 TTAAATTTAAATTCAAA--TTTAATC
* * *
16517077 TTAAATTTAAATTTAAAATAAATC
1 TTAAATTTAAATTCAAATTTAATC
16517101 -TAAATTTAAA-TCAAATTTAATC
1 TTAAATTTAAATTCAAATTTAATC
16517123 TTAAA
1 TTAAA
16517128 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 9 0.21
23 14 0.33
24 4 0.09
26 16 0.37
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (24 bp):
TTAAATTTAAATTCAAATTTAATC
Found at i:16518220 original size:201 final size:201
Alignment explanation
Indices: 16517461--16518295 Score: 1133
Period size: 206 Copynumber: 4.1 Consensus size: 201
16517451 ACTTGGCCTT
* * * * ** * * * *
16517461 CTTCTCAGTATTTCATCAGGAAGATGACCGCAT-AGTTTGTTTTGATCCACTTCTCTGTGTTTCA
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA-CTTGTTTCAATTCGCTTCTCTGTATCTCA
* * *
16517525 TCTGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCG
16517590 ACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCTTGGGTT
130 ACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC----G-T
* * *
16517655 TGATTTGGTCTT
190 TGAGTTGGTATA
* * * * *
16517667 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTCAAATCGCTTCTCTGTGTCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
*
16517732 CAGGAAGCCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGA
* * *
16517797 CCTGCTTCTTAGTATCTCATCAAGAAGCT-GGGTTCAAAGATTTGCTCGCATTGAGCGCTGAGTT
131 CCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAGTT
16517861 GGTATA
196 GGTATA
* * *
16517867 CTTCTCTGTATCTCATCAGGAAGATGACCTCCTCAC-TATTTCAATTCGCTTCTCTATATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
*
16517931 CAGGAAGACGAATTTGGT-CACTTCTCTGTGTCTCATCAGGAAGCTAACC-CTTTTATTGCTTCG
66 CAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCAC-TTTATTGCTTCG
* * * * *
16517994 ATCTGCTTCTTAGTGTCTAATCAGGAAGCTGGGGTTCGAAGATTTGCTCGTATTAAGCGTTGAGT
130 ACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAGT
16518059 TGGTATA
195 TGGTATA
* * * *
16518066 CTTCTCTGTATCTCATCTGGAAGATAACCGCCTCGCTTGTTTCATTTCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
* *
16518131 CAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTATCC-CTTTAATTGCTTCG
66 CAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTT-ATTGCTTCG
* * * * *
16518195 ACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGT
130 ACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAGT
*
16518260 TGGAATA
195 TGGTATA
*
16518267 CTTCTCTGTATCTTATCAGGAAGATGACC
1 CTTCTCTGTATCTCATCAGGAAGATGACC
16518296 AACTCATTGT
Statistics
Matches: 565, Mismatches: 58, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
197 1 0.00
198 68 0.12
199 110 0.19
200 87 0.15
201 129 0.23
205 26 0.05
206 143 0.25
207 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGA
CCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAGTT
GGTATA
Found at i:16518417 original size:39 final size:39
Alignment explanation
Indices: 16518358--16518580 Score: 114
Period size: 39 Copynumber: 5.7 Consensus size: 39
16518348 GTTGATGGTG
* * *
16518358 ATCTGTCCCAAGCTCAGGGTAAAAGATCAAATGGCTTTA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTTA
* * *
16518397 ATCTGCCCCAGGCTCGGGGTAAGAGAT---TTGG-TGTGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-T--TA
* * * **
16518435 ATCTGTCCTAGGCTCGGTGTAAAAGATCAAATGGCTGCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTTA
* * ** * *** * * * *
16518474 ATCTGCCTCTGGCTAAGGGTAAGAGAT-TGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCT-TTA
* * *
16518513 ATTTGCCCCAGGCTCGAGGTAAAAGATCAAATGGCTTCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTTA
** *
16518552 ATCTGCCCCTTGCTCGGGGTAAGAGATCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCA
16518581 GAATCTTTAT
Statistics
Matches: 125, Mismatches: 50, Indels: 18
0.65 0.26 0.09
Matches are distributed among these distances:
35 1 0.01
36 4 0.03
38 27 0.22
39 86 0.69
40 3 0.02
41 3 0.02
42 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTTA
Found at i:16518480 original size:77 final size:78
Alignment explanation
Indices: 16518345--16518578 Score: 312
Period size: 77 Copynumber: 3.0 Consensus size: 78
16518335 TGGAGTAATG
* * *
16518345 TTGGTTGATGGTGATCTGTCCCAAGCTCAGGGTAAAAGATCAAATGGCTTTAATCTGCCCCAGGC
1 TTGGTTGATGGTGATCTGTCCCAGGCTC-GGGTAAAAGATCAAATGGCTTCAATCTGCCCCTGGC
16518410 TCGGGGTAAGAGAT
65 TCGGGGTAAGAGAT
* * *
16518424 TTGG-TG-TGGTGATCTGTCCTAGGCTCGGTGTAAAAGATCAAATGGCTGCAATCTGCCTCTGGC
1 TTGGTTGATGGTGATCTGTCCCAGGCTCGG-GTAAAAGATCAAATGGCTTCAATCTGCCCCTGGC
**
16518487 TAAGGGTAAGAGA-
65 TCGGGGTAAGAGAT
* * * *
16518500 TTGGTTGATGATGATTTGCCCCAGGCTCGAGGTAAAAGATCAAATGGCTTCAATCTGCCCCTTGC
1 TTGGTTGATGGTGATCTGTCCCAGGCTCG-GGTAAAAGATCAAATGGCTTCAATCTGCCCCTGGC
16518565 TCGGGGTAAGAGAT
65 TCGGGGTAAGAGAT
16518579 CAGAATCTTT
Statistics
Matches: 133, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
76 6 0.05
77 61 0.46
78 61 0.46
79 5 0.04
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (78 bp):
TTGGTTGATGGTGATCTGTCCCAGGCTCGGGTAAAAGATCAAATGGCTTCAATCTGCCCCTGGCT
CGGGGTAAGAGAT
Found at i:16518993 original size:101 final size:100
Alignment explanation
Indices: 16518818--16519076 Score: 322
Period size: 101 Copynumber: 2.6 Consensus size: 100
16518808 GATAAAGACT
* *
16518818 TTTCCCTTTTATCTTTTTGC-AGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGT
1 TTTCCCTTTTATCTTTTTGCGA-TATTGGATCCG-CGTTGCGGTCTTAGATCTTTCCCATCATGT
* *
16518882 CTTCTAAGGTACACGATCCGCCGTTACGACTTAAACC
64 ATTCTAAGGTACACGATCCACCGTTACGACTTAAACC
* * * **
16518919 TTTCCCTTTTATCTTTTTACGATATTGGATCCGTCGTTACGGTCTTAAATCTTTCCCATTGTGTA
1 TTTCCCTTTTATCTTTTTGCGATATTGGATCCG-CGTTGCGGTCTTAGATCTTTCCCATCATGTA
* * * * *
16518984 TTCTGAGGTACACGGTCCATCGTTGCGACTTAGACC
65 TTCTAAGGTACACGATCCACCGTTACGACTTAAACC
* * *
16519020 TTTCTCTTTTGTCTTTTTGCGGTATTGGATCCGCTGTTGCGGTCTTAGATCTTTCCC
1 TTTCCCTTTTATCTTTTTGCGATATTGGATCCGC-GTTGCGGTCTTAGATCTTTCCC
16519077 GTCGTGTTTT
Statistics
Matches: 135, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
100 1 0.01
101 133 0.99
102 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (100 bp):
TTTCCCTTTTATCTTTTTGCGATATTGGATCCGCGTTGCGGTCTTAGATCTTTCCCATCATGTAT
TCTAAGGTACACGATCCACCGTTACGACTTAAACC
Found at i:16520250 original size:13 final size:13
Alignment explanation
Indices: 16520241--16520268 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16520231 TTTTTTTTTC
16520241 TTCTTGTTTTCTT
1 TTCTTGTTTTCTT
16520254 TTCTTGTTTTCTT
1 TTCTTGTTTTCTT
16520267 TT
1 TT
16520269 TCTTTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTGTTTTCTT
Found at i:16525618 original size:58 final size:59
Alignment explanation
Indices: 16525547--16525694 Score: 187
Period size: 58 Copynumber: 2.5 Consensus size: 59
16525537 AAAAATGATA
* * * * *
16525547 TTTTAGACATTCGGGGGTAAAAT-AGTTA-TTTTAGAAAAATCGGGATCAAAAGTGGGAT
1 TTTTGGACGTTCGGGGGTAAAATGA-TAATTTTTAGAAAAATCGGGATCAAAAATGGAAT
*
16525605 TTTTGGACGTTCGGGGG-AAAATGATAATTTTTAGAAAAATTGGGATCAAAAATGGAAT
1 TTTTGGACGTTCGGGGGTAAAATGATAATTTTTAGAAAAATCGGGATCAAAAATGGAAT
*
16525663 TTTTGGAAGTTCGGGGGTAAAAATG-TAATTTT
1 TTTTGGACGTTCGGGGGT-AAAATGATAATTTT
16525695 GGAAGTTTGG
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
57 7 0.09
58 59 0.75
59 7 0.09
60 6 0.08
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
TTTTGGACGTTCGGGGGTAAAATGATAATTTTTAGAAAAATCGGGATCAAAAATGGAAT
Found at i:16525684 original size:29 final size:29
Alignment explanation
Indices: 16525652--16526113 Score: 484
Period size: 29 Copynumber: 15.8 Consensus size: 29
16525642 AATTGGGATC
* * *
16525652 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
*
16525681 AAAAATGTAA-TTTTGGAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
*
16525709 AAAAATGTAACTTTTGGAAGTTTCG-GGGT
1 AAAAATGTAATTTTTGGAAGTTT-GAGGGT
* * * *
16525738 AAAAGTGGAATTTTTGGAAGTTCG-GGGG
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * **
16525766 CAAAATGTAATTTTTAGAAGTCTCGAGGCC
1 AAAAATGTAATTTTTGGAAGT-TTGAGGGT
*
16525796 AAAAATGTAATTTTTGGAAGTTCG-GGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
* *
16525824 AAAAATGAAATTTTGGAGAAGTTTGAGGGT
1 AAAAATGTAATTTTTG-GAAGTTTGAGGGT
* * *
16525854 CAAAATGAAATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
* *
16525883 AAAAATGTAATTTTT-GAAATTTTAGGGGT
1 AAAAATGTAATTTTTGGAAGTTTGA-GGGT
* * *
16525912 AAAAATGTAATTTTTAGAAGTTTTTAGGTT
1 AAAAATGTAATTTTTGGAAG-TTTGAGGGT
* *
16525942 AAAAATGTGATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
* *
16525971 AAAAATGTAAATTTTGGAAGTTTTGAGGTT
1 AAAAATGTAATTTTTGGAAG-TTTGAGGGT
16526001 AAAAATGTAATTTTTGGAAGTTTGAGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGT
** *
16526030 AAAAATGTAATTTTTAAAAGTTTTACGGGT
1 AAAAATGTAATTTTTGGAAGTTTGA-GGGT
* *
16526060 AAAAATGTAATTTTAGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTG-GAAGTTTGAGGGT
* *
16526090 CAAAATATAATTTTTGGACAGTTT
1 AAAAATGTAATTTTTGGA-AGTTT
16526114 ATGGACCTAC
Statistics
Matches: 368, Mismatches: 52, Indels: 25
0.83 0.12 0.06
Matches are distributed among these distances:
28 70 0.19
29 157 0.43
30 130 0.35
31 11 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTGAGGGT
Found at i:16525886 original size:59 final size:58
Alignment explanation
Indices: 16525652--16526113 Score: 484
Period size: 59 Copynumber: 7.9 Consensus size: 58
16525642 AATTGGGATC
* * * *
16525652 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAA-TTTTGGAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * * *
16525709 AAAAATGTAACTTTTGGAAGTTTCG-GGGTAAAAGTGGAATTTTTGGAAGTTCG-GGGG
1 AAAAATGTAATTTTTGGAAGTTT-GAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * ** *
16525766 CAAAATGTAATTTTTAGAAGTCTCGAGGCCAAAAATGTAATTTTTGGAAGTTCG-GGGT
1 AAAAATGTAATTTTTGGAAGT-TTGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * * *
16525824 AAAAATGAAATTTTGGAGAAGTTTGAGGGTCAAAATGAAATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTG-GAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * * *
16525883 AAAAATGTAATTTTT-GAAATTTTAGGGGTAAAAATGTAATTTTTAGAAGTTTTTAGGTT
1 AAAAATGTAATTTTTGGAAGTTTGA-GGGTAAAAATGTAATTTTTGGAAG-TTTGAGGGT
* * * *
16525942 AAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATGTAAATTTTGGAAGTTTTGAGGTT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAG-TTTGAGGGT
** *
16526001 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTTACGGGT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGA-GGGT
* * * *
16526060 AAAAATGTAATTTTAGAGAAGTTTGGGGGTCAAAATATAATTTTTGGACAGTTT
1 AAAAATGTAATTTTTG-GAAGTTTGAGGGTAAAAATGTAATTTTTGGA-AGTTT
16526114 ATGGACCTAC
Statistics
Matches: 338, Mismatches: 55, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
57 61 0.18
58 105 0.31
59 135 0.40
60 32 0.09
61 5 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
Found at i:16528011 original size:17 final size:17
Alignment explanation
Indices: 16527984--16528107 Score: 78
Period size: 17 Copynumber: 7.4 Consensus size: 17
16527974 CATTTATTTG
* *
16527984 ATTTCAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
16528001 TTTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* * *
16528018 ATTTAGACTTAAATTAA
1 ATTTAAATTTAAAATAA
* *
16528035 ATTCAAATTTAAAGT--
1 ATTTAAATTTAAAATAA
* *
16528050 -TTTAATTTTAAATTTAA
1 ATTTAAATTTAAA-ATAA
* *
16528067 ATTTAAA-ATAAATCTAA
1 ATTTAAATTTAAA-ATAA
16528084 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
16528101 ATTTAAA
1 ATTTAAA
16528108 GGGGCCCGGT
Statistics
Matches: 81, Mismatches: 19, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 57 0.70
18 11 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:16528075 original size:7 final size:6
Alignment explanation
Indices: 16528002--16528107 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
16527992 TTATAATAAT
* * * *
16528002 TTTAAA TTTAAA -ATAAA TTTAGA CTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
16528048 GTTTTAAT TTTAAA TTTAAA TTTAAA -ATAAA TCTAAA TTT-AA TCTTAAA
1 --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
*
16528097 -ATAAA TTTAAA
1 TTTAAA TTTAAA
16528108 GGGGCCCGGT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
5 20 0.26
6 51 0.65
7 2 0.03
8 5 0.06
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:16528088 original size:23 final size:23
Alignment explanation
Indices: 16528058--16528107 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16528048 GTTTTAATTT
16528058 TAAATTTAAAT-TTAAAATAAATC
1 TAAATTT-AATCTTAAAATAAATC
*
16528081 TAAATTTAATCTTAAAATAAATT
1 TAAATTTAATCTTAAAATAAATC
16528104 TAAA
1 TAAA
16528108 GGGGCCCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTTAATCTTAAAATAAATC
Found at i:16532424 original size:139 final size:139
Alignment explanation
Indices: 16532174--16532455 Score: 555
Period size: 139 Copynumber: 2.0 Consensus size: 139
16532164 AGCTCACAAG
16532174 TGTTTACAAGAAAAGGTATGAAAGAATTAAGCTCTTGGTTGTTTTGATTGATCTTTAGGCTTTGC
1 TGTTTACAAGAAAAGGTATGAAAGAATTAAGCTCTTGGTTGTTTTGATTGATCTTTAGGCTTTGC
16532239 ACATTGCTCTTATTGATGCTAGACCTTTGGAAGATGGTATTTATACCCTCTAAGTGAATTCTAAC
66 ACATTGCTCTTATTGATGCTAGACCTTTGGAAGATGGTATTTATACCCTCTAAGTGAATTCTAAC
16532304 CGTTGTGAT
131 CGTTGTGAT
*
16532313 TGTTTATAAGAAAAGGTATGAAAGAATTAAGCTCTTGGTTGTTTTGATTGATCTTTAGGCTTTGC
1 TGTTTACAAGAAAAGGTATGAAAGAATTAAGCTCTTGGTTGTTTTGATTGATCTTTAGGCTTTGC
16532378 ACATTGCTCTTATTGATGCTAGACCTTTGGAAGATGGTATTTATACCCTCTAAGTGAATTCTAAC
66 ACATTGCTCTTATTGATGCTAGACCTTTGGAAGATGGTATTTATACCCTCTAAGTGAATTCTAAC
16532443 CGTTGTGAT
131 CGTTGTGAT
16532452 TGTT
1 TGTT
16532456 GGGAAAGTAA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 142 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (139 bp):
TGTTTACAAGAAAAGGTATGAAAGAATTAAGCTCTTGGTTGTTTTGATTGATCTTTAGGCTTTGC
ACATTGCTCTTATTGATGCTAGACCTTTGGAAGATGGTATTTATACCCTCTAAGTGAATTCTAAC
CGTTGTGAT
Found at i:16532803 original size:20 final size:20
Alignment explanation
Indices: 16532778--16532831 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
16532768 AGTCTTCAAG
*
16532778 GTATCGGTAAAAGTGGAGTT
1 GTATCGATAAAAGTGGAGTT
*
16532798 GTATCGATAGAAGTGGAGTT
1 GTATCGATAAAAGTGGAGTT
* * *
16532818 TTACCGATAGAAGT
1 GTATCGATAAAAGT
16532832 CTCACTGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.30
Consensus pattern (20 bp):
GTATCGATAAAAGTGGAGTT
Found at i:16536615 original size:31 final size:29
Alignment explanation
Indices: 16536551--16536645 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
16536541 ATTTATCAAT
* ** *
16536551 TTTTAAGGGCCCAAAATTTTTTTTTTTAGC
1 TTTTAAGAG-CCAAAATTTTTTTTTCCAAC
16536581 TTTTAAGAGCCTAAAATTTTTTTTTACCAAC
1 TTTTAAGAGCC-AAAATTTTTTTTT-CCAAC
*
16536612 TTTTAACAGACCAAAATTTTTTTTCTCCAAC
1 TTTTAAGAG-CCAAAATTTTTTTT-TCCAAC
16536643 TTT
1 TTT
16536646 AATGAATCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
29 2 0.04
30 21 0.38
31 30 0.54
32 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (29 bp):
TTTTAAGAGCCAAAATTTTTTTTTCCAAC
Found at i:16536842 original size:16 final size:16
Alignment explanation
Indices: 16536817--16536868 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
16536807 TGGTTTGCTA
* * *
16536817 TAATAGAATATAGTTG
1 TAATGGAATAGAGCTG
*
16536833 TAATGTAATAGAGCTG
1 TAATGGAATAGAGCTG
*
16536849 TAATGGAATAGGGCTG
1 TAATGGAATAGAGCTG
16536865 TAAT
1 TAAT
16536869 AAGTATTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:16536942 original size:44 final size:46
Alignment explanation
Indices: 16536850--16536943 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
16536840 ATAGAGCTGT
*
16536850 AATGGAATAGGGCTGTAATAAGTATTTCAGTTGTTTAGTTGAATGG
1 AATGGAATAGAGCTGTAATAAGTATTTCAGTTGTTTAGTTGAATGG
* * *
16536896 AATGGAATAGAGTTGTAAT-AGTA-TTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAAGTATTTCAGT-TGTTTAGTTGAATGG
16536940 AATG
1 AATG
16536944 ATGCTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 4 0.09
46 17 0.40
ACGTcount: A:0.30, C:0.03, G:0.29, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATAAGTATTTCAGTTGTTTAGTTGAATGG
Found at i:16537103 original size:59 final size:59
Alignment explanation
Indices: 16537040--16537185 Score: 183
Period size: 59 Copynumber: 2.5 Consensus size: 59
16537030 TTTTCATAAG
*
16537040 ATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATTA-TATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAACT-TTTTAATATA
* * *
16537099 ATTATTGTTAAATACAATTTAAT--AAAATAATATATAATTTAATAACGTTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAAC-TTTTTAATATA
*
16537157 ATTATTATTAAAATATGAA-TGAATAAAAA
1 ATTATTATT-AAATAT-AATTTAATAAAAA
16537186 TCATAATATA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
57 20 0.27
58 18 0.24
59 31 0.42
60 2 0.03
61 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAACTTTTTAATATA
Found at i:16547364 original size:21 final size:22
Alignment explanation
Indices: 16547339--16547381 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
16547329 TAATTTCTTG
16547339 TAATTTTTAATAA-AATTTAAA
1 TAATTTTTAATAATAATTTAAA
* *
16547360 TAATTTTTTATAATTATTTAAA
1 TAATTTTTAATAATAATTTAAA
16547382 AAACCACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTTTTAATAATAATTTAAA
Found at i:16548372 original size:3 final size:3
Alignment explanation
Indices: 16548364--16548408 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
16548354 TTTTCGTGAC
16548364 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16548409 TATCCAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16550153 original size:135 final size:134
Alignment explanation
Indices: 16549912--16550180 Score: 423
Period size: 135 Copynumber: 2.0 Consensus size: 134
16549902 CTGAATTCAT
* * * *
16549912 ACATGTGTTTTCAAATAGATGGATCCTTTATCGTTTTTGGATTTAACCAAATAACCTTCTCCGTT
1 ACATGTGTTTTCAAATAAATGGATCCTTTATCGTTCTTGGATTTAACCAAATAACCTTCCCCGCT
** *
16549977 ATTCTCGTACCAAAAACTACTTTGAGTGTGGGTTCGAATGATTTAAATCAAAACACAGTACTAGA
66 ATTCTCGTACCAAAAACTACTTAAAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAGA
16550042 AATA
131 AATA
* *
16550046 ACATGTGTTTTCAAATAAATGGATCCTTTATTGTTCTTGGCTTTCAACCAAATAGA-CTTCCCCG
1 ACATGTGTTTTCAAATAAATGGATCCTTTATCGTTCTTGGATTT-AACCAAATA-ACCTTCCCCG
*
16550110 CTATTCTCGTACCAGAAACTACTTAAAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTA
64 CTATTCTCGTACCAAAAACTACTTAAAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTA
16550175 GAAATA
129 GAAATA
16550181 GTTTTCTTTG
Statistics
Matches: 123, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
134 40 0.33
135 82 0.67
136 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (134 bp):
ACATGTGTTTTCAAATAAATGGATCCTTTATCGTTCTTGGATTTAACCAAATAACCTTCCCCGCT
ATTCTCGTACCAAAAACTACTTAAAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAGA
AATA
Found at i:16550867 original size:12 final size:13
Alignment explanation
Indices: 16550845--16550874 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
16550835 ATGATTCAAT
16550845 TTTTTCATTTTCA
1 TTTTTCATTTTCA
16550858 TTTTTC-TTTTCA
1 TTTTTCATTTTCA
16550870 TTTTT
1 TTTTT
16550875 GAGAAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:16558652 original size:24 final size:24
Alignment explanation
Indices: 16558619--16558718 Score: 87
Period size: 24 Copynumber: 4.1 Consensus size: 24
16558609 CTATTGGTCA
* *
16558619 AACTCTATCTAGGCTCG-AATGAGTT
1 AACT-TATCTGGGCTCGTAA-GAGCT
16558644 AACTTATCTGGGCTCGTAAGAGCT
1 AACTTATCTGGGCTCGTAAGAGCT
* *
16558668 AACCTATCTGGGCTTGTATA-AGCT
1 AACTTATCTGGGCTCGTA-AGAGCT
* * *
16558692 AATTTTGTCTGGGCTCGTACGAGCT
1 AA-CTTATCTGGGCTCGTAAGAGCT
16558717 AA
1 AA
16558719 ATTTCTTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
24 37 0.60
25 25 0.40
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (24 bp):
AACTTATCTGGGCTCGTAAGAGCT
Found at i:16564266 original size:21 final size:21
Alignment explanation
Indices: 16564242--16564299 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
16564232 TAGAGGTAAG
*
16564242 ACTTGTATCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
16564263 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
16564284 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
16564300 ATCTGCACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:16570154 original size:45 final size:44
Alignment explanation
Indices: 16570098--16570261 Score: 166
Period size: 45 Copynumber: 3.6 Consensus size: 44
16570088 ATTACTGTAT
* *
16570098 TGGCTCGTAAGAGTGATATACGATATTAGGAGCGATATACTGAAC
1 TGGCTCGTAAGAGCGATATACG-TATTGGGAGCGATATACTGAAC
* * * * *
16570143 TGGCTCGTAAGAGCGATATAATGTACTGGGAGTGATATAATGCAC
1 TGGCTCGTAAGAGCGATAT-ACGTATTGGGAGCGATATACTGAAC
* * ** * *
16570188 TGACTCGTAAAAGTAATATACTGTATTGGGAGCGATACACTAAAC
1 TGGCTCGTAAGAGCGATATAC-GTATTGGGAGCGATATACTGAAC
*
16570233 TGGCTCATAAGAGCGATATACTGTATTGG
1 TGGCTCGTAAGAGCGATATAC-GTATTGG
16570262 CTCGAAAGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 1 0.01
45 91 0.97
46 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (44 bp):
TGGCTCGTAAGAGCGATATACGTATTGGGAGCGATATACTGAAC
Found at i:16570246 original size:26 final size:26
Alignment explanation
Indices: 16570217--16570323 Score: 99
Period size: 26 Copynumber: 4.1 Consensus size: 26
16570207 ACTGTATTGG
*
16570217 GAGCGATACACTAAACTGGCTCATAA
1 GAGCGATATACTAAACTGGCTCATAA
** *
16570243 GAGCGATATACTGTATTGGCTCGA-AA
1 GAGCGATATACTAAACTGGCTC-ATAA
* * **
16570269 GAACGATATACTAAACTAGCTTGTAA
1 GAGCGATATACTAAACTGGCTCATAA
** *
16570295 GAGCGATATACTGTACTGGCTCGTAA
1 GAGCGATATACTAAACTGGCTCATAA
16570321 GAG
1 GAG
16570324 TGATTTTTTG
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
26 62 0.98
27 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (26 bp):
GAGCGATATACTAAACTGGCTCATAA
Found at i:16570298 original size:52 final size:52
Alignment explanation
Indices: 16570220--16570322 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
16570210 GTATTGGGAG
* *
16570220 CGATACACTAAACTGGCTCATAAGAGCGATATACTGTATTGGCTCGAAAGAA
1 CGATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGAAAGAA
* ** *
16570272 CGATATACTAAACTAGCTTGTAAGAGCGATATACTGTACTGGCTCGTAAGA
1 CGATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGAAAGA
16570323 GTGATTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (52 bp):
CGATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGAAAGAA
Found at i:16583748 original size:18 final size:18
Alignment explanation
Indices: 16583733--16583775 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16583723 GGCTGCATAC
16583733 GAGCATGTGACTGCATCT
1 GAGCATGTGACTGCATCT
* *
16583751 GAGTATGTGACTACATCT
1 GAGCATGTGACTGCATCT
*
16583769 GATCATG
1 GAGCATG
16583776 ATGTGTAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (18 bp):
GAGCATGTGACTGCATCT
Found at i:16593006 original size:21 final size:21
Alignment explanation
Indices: 16592957--16593007 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
16592947 TAGTTGCATG
* *
16592957 ACAAGTATCGGTAGAAATTAT
1 ACAAGTATCGGTAGAAATAAC
** *
16592978 ACTTGTATCGGTAGAACTAAC
1 ACAAGTATCGGTAGAAATAAC
16592999 ACAAGTATC
1 ACAAGTATC
16593008 AATACAAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAAGTATCGGTAGAAATAAC
Found at i:16595123 original size:15 final size:15
Alignment explanation
Indices: 16595103--16595141 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
16595093 TAATGAGATC
16595103 TCACTACTTTCGATT
1 TCACTACTTTCGATT
16595118 TCACTACTTTCGATT
1 TCACTACTTTCGATT
*
16595133 TCCCTACTT
1 TCACTACTT
16595142 ATCAAAGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.31, G:0.05, T:0.46
Consensus pattern (15 bp):
TCACTACTTTCGATT
Found at i:16597938 original size:19 final size:18
Alignment explanation
Indices: 16597896--16597950 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
16597886 TATTTATATT
* *
16597896 ATTGAATTTTTTAATAAT
1 ATTGAATTTTATAATAAA
*
16597914 ATTGAATATTTATATTAAA
1 ATTGAAT-TTTATAATAAA
16597933 ATTGAATTATTAATAATA
1 ATTGAATT-TT-ATAATA
16597951 CCATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 8 0.27
19 17 0.57
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTGAATTTTATAATAAA
Found at i:16598334 original size:31 final size:26
Alignment explanation
Indices: 16598260--16598325 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
16598250 TCGATTCGAT
*
16598260 TCGATTCGATTTGAATTCCATTACAC
1 TCGACTCGATTTGAATTCCATTACAC
16598286 TCGACTCGATTTGAATTCCATTACAC
1 TCGACTCGATTTGAATTCCATTACAC
16598312 TCGACTCGATTTGA
1 TCGACTCGATTTGA
16598326 GAAAAATTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (26 bp):
TCGACTCGATTTGAATTCCATTACAC
Found at i:16599815 original size:28 final size:28
Alignment explanation
Indices: 16599783--16599855 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
16599773 GTGAAGGATG
16599783 AAAAACTCTTTATGGTTATAATAAAAAA
1 AAAAACTCTTTATGGTTATAATAAAAAA
16599811 AAAAACTCTTTATGGTTATAATAAAAAA
1 AAAAACTCTTTATGGTTATAATAAAAAA
16599839 AAAAACTCTTTATGGTT
1 AAAAACTCTTTATGGTT
16599856 GACATTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (28 bp):
AAAAACTCTTTATGGTTATAATAAAAAA
Found at i:16601814 original size:6 final size:6
Alignment explanation
Indices: 16601805--16601831 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16601795 TATAAATAAT
16601805 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
16601832 CCCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:16604964 original size:61 final size:61
Alignment explanation
Indices: 16604873--16604992 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
16604863 GTAAATTACT
16604873 TATATATATATATTAGGTTGAGATGATGTAAAGGTTAATGTGGGTAATTATAAAAATCTTA
1 TATATATATATATTAGGTTGAGATGATGTAAAGGTTAATGTGGGTAATTATAAAAATCTTA
16604934 TATATATATATATTAGGTTGAGATGATGTAAAGGTTAATGTGGGTAATTATAAAAATCT
1 TATATATATATATTAGGTTGAGATGATGTAAAGGTTAATGTGGGTAATTATAAAAATCT
16604993 CTGTAAGCTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (61 bp):
TATATATATATATTAGGTTGAGATGATGTAAAGGTTAATGTGGGTAATTATAAAAATCTTA
Found at i:16617557 original size:50 final size:48
Alignment explanation
Indices: 16617425--16617601 Score: 167
Period size: 50 Copynumber: 3.6 Consensus size: 48
16617415 ACAAAACAAT
* * *
16617425 GAATCTTATACCCCTAAAGTTGTAGAGGAACAGATTGAAGCCGTAATG-GC
1 GAATCTTATA-CCCTAAAGTTGTAGAGG-GCAAATTGAAGCCGCAA-GAGC
* * *
16617475 GAATCTCATACACCTAAAGCTGTAGAGAGGCAAATTAAAGCCGCAAGAGC
1 GAATCTTATAC-CCTAAAGTTGTAGAG-GGCAAATTGAAGCCGCAAGAGC
* * ** *
16617525 GAATCTTATACTCCTAAAGTTGGAAAAGGGCAAATTGAAGCTACAAGAGA
1 GAATCTTATAC-CCTAAAGTT-GTAGAGGGCAAATTGAAGCCGCAAGAGC
* *
16617575 AAATCTTATACCCTAAAGTTATAGAGG
1 GAATCTTATACCCTAAAGTTGTAGAGG
16617602 AGCGGATTAA
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
48 4 0.04
49 11 0.11
50 84 0.81
51 5 0.05
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (48 bp):
GAATCTTATACCCTAAAGTTGTAGAGGGCAAATTGAAGCCGCAAGAGC
Found at i:16618219 original size:14 final size:15
Alignment explanation
Indices: 16618200--16618229 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16618190 TTATTATTTT
16618200 ATAAATAT-AAATAA
1 ATAAATATAAAATAA
16618214 ATAAATATAAAATAA
1 ATAAATATAAAATAA
16618229 A
1 A
16618230 ATTAAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATATAAAATAA
Found at i:16627746 original size:17 final size:17
Alignment explanation
Indices: 16627724--16627757 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16627714 TATAGTTTGA
16627724 CTTCATGATTTTGTTAG
1 CTTCATGATTTTGTTAG
16627741 CTTCATGATTTTGTTAG
1 CTTCATGATTTTGTTAG
16627758 ACATGATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (17 bp):
CTTCATGATTTTGTTAG
Found at i:16627764 original size:15 final size:16
Alignment explanation
Indices: 16627727--16627765 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
16627717 AGTTTGACTT
*
16627727 CATGATTTTGTTAGCTT
1 CATGATTTTGTTAGC-A
16627744 CATGATTTTGTTAG-A
1 CATGATTTTGTTAGCA
16627759 CATGATT
1 CATGATT
16627766 AGAATTGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (16 bp):
CATGATTTTGTTAGCA
Found at i:16629675 original size:17 final size:18
Alignment explanation
Indices: 16629647--16629685 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
16629637 GAATTATTAT
16629647 TTAAGCAAATAG-TTAAA
1 TTAAGCAAATAGATTAAA
16629664 GTTAAG-AAATAGATTAAA
1 -TTAAGCAAATAGATTAAA
16629682 TTAA
1 TTAA
16629686 TTGGTCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (18 bp):
TTAAGCAAATAGATTAAA
Found at i:16629811 original size:16 final size:17
Alignment explanation
Indices: 16629784--16629819 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
16629774 TTAGAATTGG
*
16629784 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
16629801 ATTGA-AAAATTAATTA
1 ATTGAGAAAATTAATTA
16629817 ATT
1 ATT
16629820 TAGTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:16630136 original size:20 final size:21
Alignment explanation
Indices: 16630105--16630155 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
16630095 GAAAGTAGTG
16630105 TAAATT-TATTTTCTAAGAA-
1 TAAATTCTATTTTCTAAGAAT
* *
16630124 TAAATTCTATTTTTTGAGAAT
1 TAAATTCTATTTTCTAAGAAT
16630145 TACAATTCTAT
1 TA-AATTCTAT
16630156 CGGTTTCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 11 0.41
21 2 0.07
22 8 0.30
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TAAATTCTATTTTCTAAGAAT
Found at i:16630840 original size:2 final size:2
Alignment explanation
Indices: 16630833--16630875 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16630823 TAAAACTGAC
16630833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16630875 A
1 A
16630876 ACATTTTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16637205 original size:10 final size:10
Alignment explanation
Indices: 16637190--16637216 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16637180 CTACGATATA
16637190 TATGTGTGTG
1 TATGTGTGTG
16637200 TATGTGTGTG
1 TATGTGTGTG
16637210 TATGTGT
1 TATGTGT
16637217 CTAATCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.52
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:16641920 original size:19 final size:19
Alignment explanation
Indices: 16641880--16641931 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
16641870 GTTGGTATTG
* * *
16641880 TTATTTTTTAAAAAAATTA
1 TTATTTTTTATAATAATAA
16641899 TTATTTTTTATAATAATAA
1 TTATTTTTTATAATAATAA
* *
16641918 TTAATTTTAATAAT
1 TTATTTTTTATAAT
16641932 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTTTTTATAATAATAA
Found at i:16647016 original size:19 final size:20
Alignment explanation
Indices: 16646979--16647019 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
16646969 AAAAAAGAAT
16646979 TTCAAAATAATTTTCAAAAA
1 TTCAAAATAATTTTCAAAAA
16646999 TTCAAAAT-ATTTAT-AAAAA
1 TTCAAAATAATTT-TCAAAAA
16647018 TT
1 TT
16647020 TCCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
TTCAAAATAATTTTCAAAAA
Found at i:16647061 original size:19 final size:20
Alignment explanation
Indices: 16647037--16647081 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
16647027 TTTAGATATT
16647037 TTTAAAAATTATAAA-AAAA
1 TTTAAAAATTATAAAGAAAA
*
16647056 TTTAAAAATTCTAAAGAAAA
1 TTTAAAAATTATAAAGAAAA
*
16647076 TATAAA
1 TTTAAA
16647082 GAAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TTTAAAAATTATAAAGAAAA
Found at i:16660487 original size:18 final size:18
Alignment explanation
Indices: 16660461--16660520 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
16660451 TGTTCATGTT
*
16660461 CACGTCCACGTCCTCGAC
1 CACGACCACGTCCTCGAC
*
16660479 CACGACCACGACCAT-GAC
1 CACGACCACGTCC-TCGAC
* * *
16660497 CATGGCCATGTCCTCGAC
1 CACGACCACGTCCTCGAC
16660515 CACGAC
1 CACGAC
16660521 TACTAGTGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.23, C:0.45, G:0.18, T:0.13
Consensus pattern (18 bp):
CACGACCACGTCCTCGAC
Found at i:16661695 original size:24 final size:24
Alignment explanation
Indices: 16661666--16661712 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16661656 AATATGAAAG
*
16661666 GTTAAAGAAGATGAAAGGTTAAAA
1 GTTAAAGAAGATGAAAGATTAAAA
*
16661690 GTTAAAGAAGATGGAAGATTAAA
1 GTTAAAGAAGATGAAAGATTAAA
16661713 GGTCAAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (24 bp):
GTTAAAGAAGATGAAAGATTAAAA
Found at i:16662589 original size:17 final size:16
Alignment explanation
Indices: 16662569--16662617 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
16662559 TATATATGTA
16662569 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
16662586 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
* *
16662602 CAATAAA-ATTTAAAT
1 TAATAAATATTAAAAT
16662617 T
1 T
16662618 TATTGATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 7 0.26
16 11 0.41
17 9 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:16663316 original size:3 final size:3
Alignment explanation
Indices: 16663310--16663337 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16663300 AACAACAACG
16663310 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16663338 ATAGATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16664805 original size:27 final size:27
Alignment explanation
Indices: 16664767--16664914 Score: 134
Period size: 27 Copynumber: 5.7 Consensus size: 27
16664757 GGAGATATTT
*
16664767 TGATTCTTGCTCGTAAGAGCATAATTC
1 TGATTCTGGCTCGTAAGAGCATAATTC
* *
16664794 TGATTCTGGCTCGTAAGAGCGTAATTA
1 TGATTCTGGCTCGTAAGAGCATAATTC
* * *
16664821 TGATTTTGGCTCGTAGGAGCATAATTT
1 TGATTCTGGCTCGTAAGAGCATAATTC
*
16664848 TG--TCTGGCTC--AAGTG--TAATTC
1 TGATTCTGGCTCGTAAGAGCATAATTC
*
16664869 TGATTTTGGCTCGTAAGAGCA-ATATTC
1 TGATTCTGGCTCGTAAGAGCATA-ATTC
*
16664896 TG--TCTGGGCTCGAAAGAGC
1 TGATTCT-GGCTCGTAAGAGC
16664915 TAAACTCTGT
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
21 7 0.07
23 10 0.10
25 13 0.13
26 13 0.13
27 55 0.56
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (27 bp):
TGATTCTGGCTCGTAAGAGCATAATTC
Found at i:16664907 original size:26 final size:25
Alignment explanation
Indices: 16664876--16664946 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
16664866 TTCTGATTTT
*
16664876 GGCTCGTAAGAGCAATATTCTGTCTG
1 GGCTCG-AAGAGCAATATTCTGTCTA
*
16664902 GGCTCGAAAGAGCTAA-ACTCTGTCTA
1 GGCTCG-AAGAGC-AATATTCTGTCTA
*
16664928 GGCTCGAATGAGCTATATT
1 GGCTCGAA-GAGCAATATT
16664947 TCTGGAAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 3 0.08
26 32 0.86
27 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (25 bp):
GGCTCGAAGAGCAATATTCTGTCTA
Found at i:16665691 original size:21 final size:21
Alignment explanation
Indices: 16665667--16665722 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
16665657 AGTTACACTT
16665667 GTATCGATAGAAGTATCAAAA
1 GTATCGATAGAAGTATCAAAA
* *
16665688 GTATCGGTAGAAGTATCACAA
1 GTATCGATAGAAGTATCAAAA
16665709 GTATCGATAGAAGT
1 GTATCGATAGAAGT
16665723 CTGCACTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (21 bp):
GTATCGATAGAAGTATCAAAA
Found at i:16665722 original size:12 final size:12
Alignment explanation
Indices: 16665667--16665722 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
16665657 AGTTACACTT
16665667 GTATCGATAGAA
1 GTATCGATAGAA
16665679 GTATC-A-A-AA
1 GTATCGATAGAA
*
16665688 GTATCGGTAGAA
1 GTATCGATAGAA
*
16665700 GTATC---ACAA
1 GTATCGATAGAA
16665709 GTATCGATAGAA
1 GTATCGATAGAA
16665721 GT
1 GT
16665723 CTGCACTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
9 15 0.43
10 1 0.03
11 2 0.06
12 17 0.49
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (12 bp):
GTATCGATAGAA
Found at i:16678146 original size:17 final size:18
Alignment explanation
Indices: 16678115--16678151 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
16678105 TCGAACTTTA
16678115 ATTATTTAATTAGTT-AT
1 ATTATTTAATTAGTTGAT
16678132 ATTA-TTAATTAAGTTGAT
1 ATTATTTAATT-AGTTGAT
16678150 AT
1 AT
16678152 CCAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 8 0.44
18 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTATTTAATTAGTTGAT
Found at i:16690385 original size:2 final size:2
Alignment explanation
Indices: 16690378--16690405 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16690368 TCACAAAGAA
16690378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16690406 TGTAAATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16692379 original size:21 final size:21
Alignment explanation
Indices: 16692342--16692381 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16692332 ATAAAGGATT
16692342 AAATTGAAAAATAAATAAATA
1 AAATTGAAAAATAAATAAATA
*
16692363 AAATT-AAATATATAATAAA
1 AAATTGAAAAATA-AATAAA
16692382 AAATTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATTGAAAAATAAATAAATA
Found at i:16693579 original size:20 final size:19
Alignment explanation
Indices: 16693543--16693586 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
16693533 AAATAGTTTG
*
16693543 ACTTGGTAAAAGAATTTTT
1 ACTTGGTAAAAGAATTTTA
**
16693562 ACTTGGTTAAAATCATTTTA
1 ACTTGG-TAAAAGAATTTTA
16693582 ACTTG
1 ACTTG
16693587 ATTTTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (19 bp):
ACTTGGTAAAAGAATTTTA
Found at i:16693713 original size:16 final size:16
Alignment explanation
Indices: 16693692--16693729 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16693682 GGTTGTATGG
*
16693692 AATAGAGATGTAATGA
1 AATAGAGATGTAATAA
*
16693708 AATAGAGTTGTAATAA
1 AATAGAGATGTAATAA
16693724 AATAGA
1 AATAGA
16693730 ATTGTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (16 bp):
AATAGAGATGTAATAA
Found at i:16693734 original size:16 final size:16
Alignment explanation
Indices: 16693700--16693737 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16693690 GGAATAGAGA
* *
16693700 TGTAATGAAATAGAGT
1 TGTAATAAAATAGAAT
16693716 TGTAATAAAATAGAAT
1 TGTAATAAAATAGAAT
16693732 TGTAAT
1 TGTAAT
16693738 TAGTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
TGTAATAAAATAGAAT
Found at i:16694046 original size:59 final size:56
Alignment explanation
Indices: 16693906--16694043 Score: 143
Period size: 59 Copynumber: 2.4 Consensus size: 56
16693896 GTTATTAAAT
* * * *
16693906 TTTAATAAAATTATTATTAAATATATTTTAATAAAAAATAATAAATGACTTAATCATA
1 TTTAATATAATTATTATTAAATACAATTTAAT--AAAATAATAAATGAATTAATCATA
* * * *
16693964 TTGTAACATAATTAATCTTAAATACAATTTAATAAAATAATATATGAATTAATAGCAT-
1 TT-TAATATAATTATTATTAAATACAATTTAATAAAATAATAAATGAATTAAT--CATA
16694022 TCTTAATATAATTATTATTAAA
1 T-TTAATATAATTATTATTAAA
16694044 ATATGAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
57 18 0.28
58 19 0.29
59 28 0.43
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (56 bp):
TTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATGAATTAATCATA
Found at i:16694069 original size:24 final size:24
Alignment explanation
Indices: 16694040--16694085 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16694030 TAATTATTAT
16694040 TAAAATATGAAT-TAATAAAAATCA
1 TAAAATAT-AATATAATAAAAATCA
*
16694064 TAAAATATAATATTATAAAAAT
1 TAAAATATAATATAATAAAAAT
16694086 AATATATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAATATAATATAATAAAAATCA
Found at i:16698838 original size:42 final size:42
Alignment explanation
Indices: 16698752--16698840 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
16698742 TGTGCTAGTT
** *
16698752 CGTGTAACTCACTGACTTGGAACACATGGTCGTGTCTTAGAC
1 CGTGTAACTCACTGACTTGGAACACATGGTCGTGTCCCAAAC
*
16698794 CGTGTAACTCACTGACTTGGTACACATGG-CTGTGTCCCAAAC
1 CGTGTAACTCACTGACTTGGAACACATGGTC-GTGTCCCAAAC
16698836 CGTGT
1 CGTGT
16698841 GAAACCTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (42 bp):
CGTGTAACTCACTGACTTGGAACACATGGTCGTGTCCCAAAC
Found at i:16701093 original size:3 final size:3
Alignment explanation
Indices: 16701085--16701136 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
16701075 AAGGGTCCAA
* * * * *
16701085 ATT ATT ATT ATC ATT ACT ATA ATA ATA ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
16701131 ATT ATT
1 ATT ATT
16701137 TTTAGGGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:16701718 original size:51 final size:49
Alignment explanation
Indices: 16701628--16702042 Score: 153
Period size: 50 Copynumber: 8.4 Consensus size: 49
16701618 TCTTTAAAAA
***
16701628 AAAG-AAAGTTTAAATTTTT-AA-AAAATAAAAATCTGTTTTTTAGTCATTTT
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGAT-T-TTTTTTA-T-ATTTT
* * *
16701678 AAAGAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCG
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTA-TATTT-T
* ** ** * * *
16701729 AAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTA-A---A
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTATATTTT
* * * *
16701774 AAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATG-TTTTTTTAATAATTTT
1 AAAGA-AAAGTTTAAATTTTTAAACA-AAATAT-TGATTTTTTTTAT-ATTTT
** * * *
16701826 AAAGAAAAAAATTAAATTTTTAAACAAAATTTTGA-TTTTTTAACTATTTCG
1 AAAG-AAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTA-TATTT-T
* * ** * ** **
16701877 AAATAAAAATTTAAATTTTTAAGTAAAATAATGATTTTCATTA-A--AA
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTATATTTT
* * **
16701923 AAAGAAAA-ATTAGATTTTT-AA-AAAATA-AAAGTTTTTTTTAGTAATTTT
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGA-TTTTTTTTA-T-ATTTT
* * * * * *
16701971 AAAGAAAAATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTAACTATTTCG
1 AAAGAAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTA-TATTT-T
* *
16702021 AAATAAAAGTTTGAATTTTTAA
1 AAAGAAAAGTTTAAATTTTTAA
16702043 GTAAAGTAGT
Statistics
Matches: 271, Mismatches: 66, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
42 1 0.00
43 13 0.05
44 1 0.00
45 13 0.05
46 25 0.09
47 11 0.04
48 10 0.04
49 16 0.06
50 76 0.28
51 73 0.27
52 24 0.09
53 8 0.03
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (49 bp):
AAAGAAAAGTTTAAATTTTTAAACAAAATATTGATTTTTTTTATATTTT
Found at i:16701745 original size:148 final size:146
Alignment explanation
Indices: 16701564--16702139 Score: 754
Period size: 148 Copynumber: 3.9 Consensus size: 146
16701554 AGTTTTGGTT
* * *
16701564 TTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATATTCTTTAAAAAA
1 TTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTT-AAAAA
* * *
16701629 AAGAAAGTTTAAATTTTTAAAAAATAAAAATCTGTTTTTTAGTCATTTTAAAG-AAAAGTTTAAA
64 AAGAAAGTTTAGATTTTTAAAAAATAAAAATCT-TTTTTTAGTAATTTTAAAGAAAAAATTTAAA
16701693 TTTTTAAACAAAATTTTGA
128 TTTTTAAACAAAATTTTGA
16701712 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAA
1 -TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAA
* * *
16701777 GAGAAAGTTTAGATTTTT-AAAAATAAAAATATGTTTTTTTAATAATTTTAAAGAAAAAAATTAA
65 -AGAAAGTTTAGATTTTTAAAAAAT-AAAA-ATCTTTTTTTAGTAATTTTAAAGAAAAAATTTAA
16701841 ATTTTTAAACAAAATTTTGA
127 ATTTTTAAACAAAATTTTGA
* ** * *
16701861 TTTTTTAACTATTTCGAAATAAAAATTTAAATTTTTAAGTAAAATAATGATTTTCATTAAAAAAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAA
** *
16701926 GAAAAATTAGATTTTTAAAAAATAAAAGT-TTTTTTTAGTAATTTTAAAG-AAAAATTTAAATTT
66 GAAAGTTTAGATTTTTAAAAAATAAAAATCTTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTT
* *
16701989 TTAAATAAAGTTTTGA
131 TTAAACAAAATTTTGA
* *
16702005 TTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTAAGTAAAGTAGTGATTTGT-ATT-AAAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGATTT-TCTTTAAAAA
* * * *
16702067 AA-AAAGTTTAGTTTTTTTTAAAAAAAATAAAAATCTATTTTTAGTGATTTTAAAGAAAAAGTTT
64 AAGAAAGTTTAG--ATTTTT--AAAAAATAAAAATCTTTTTTTAGTAATTTTAAAGAAAAAATTT
16702131 AAATTTTTA
125 AAATTTTTA
16702140 TATCTCGAAA
Statistics
Matches: 381, Mismatches: 33, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
142 7 0.02
143 8 0.02
144 80 0.21
145 20 0.05
146 13 0.03
147 49 0.13
148 167 0.44
149 37 0.10
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (146 bp):
TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAA
GAAAGTTTAGATTTTTAAAAAATAAAAATCTTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTT
TTAAACAAAATTTTGA
Found at i:16702119 original size:292 final size:297
Alignment explanation
Indices: 16701564--16702139 Score: 794
Period size: 292 Copynumber: 2.0 Consensus size: 297
16701554 AGTTTTGGTT
* ** * *
16701564 TTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATATTCTTTAAAAAA
1 TTTTTTAAACAATTTCGAAATAAAAATTTAAATTTTTAAGAAAAATAATGATATTCATTAAAAAA
** * *
16701629 AAGAAAGTTTAAATTTTTAAAAAATAAAAATCTGTTTTTTAGTCATTTTAAAGAAAAGTTTAAAT
66 AAGAAAAATTAAATTTTTAAAAAATAAAAATCTGTTTTTTAGTAATTTTAAAGAAAAATTTAAAT
16701694 TTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATA
131 TTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATA
* * * * *
16701759 GTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAATAATT
196 GTGATTTTCATTAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAAAAATCTATTTTTAATAATT
16701824 TTAAAGAAAAAAATTAAATTTTTAAACAAAATTTTGA
261 TTAAAGAAAAAAATTAAATTTTTAAACAAAATTTTGA
* * *
16701861 TTTTTT-AACTATTTCGAAATAAAAATTTAAATTTTTAAGTAAAATAATGATTTTCATT-AAAAA
1 TTTTTTAAACAATTTCGAAATAAAAATTTAAATTTTTAAGAAAAATAATGATATTCATTAAAAAA
* *
16701924 AAGAAAAATTAGATTTTTAAAAAATAAAAGT-T-TTTTTTAGTAATTTTAAAGAAAAATTTAAAT
66 AAGAAAAATTAAATTTTTAAAAAATAAAAATCTGTTTTTTAGTAATTTTAAAGAAAAATTTAAAT
* * *
16701987 TTTTAAATAAAGTTTTGA-TTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTAAGTAAAGT
131 TTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAAT
* *
16702050 AGTGATTTGT-ATT-AAAAA-A-AAAGTTTAGTTTTTTTTAAAAAAAATAAAAATCTATTTTTAG
195 AGTGATTT-TCATTAAAAAAGAGAAAGTTTAG--ATTTTTAAAAAAAA-AAAAATCTATTTTTAA
* **
16702111 TGATTTTAAAGAAAAAGTTTAAATTTTTA
256 TAATTTTAAAGAAAAAAATTAAATTTTTA
16702140 TATCTCGAAA
Statistics
Matches: 247, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
289 9 0.04
290 1 0.00
291 21 0.09
292 87 0.35
293 46 0.19
294 1 0.00
295 32 0.13
296 44 0.18
297 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (297 bp):
TTTTTTAAACAATTTCGAAATAAAAATTTAAATTTTTAAGAAAAATAATGATATTCATTAAAAAA
AAGAAAAATTAAATTTTTAAAAAATAAAAATCTGTTTTTTAGTAATTTTAAAGAAAAATTTAAAT
TTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATA
GTGATTTTCATTAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAAAAATCTATTTTTAATAATT
TTAAAGAAAAAAATTAAATTTTTAAACAAAATTTTGA
Found at i:16705759 original size:28 final size:28
Alignment explanation
Indices: 16705719--16705785 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
16705709 AAGAGATAGC
* *
16705719 CACAAAGGCTTTCTTTAACAGAATCAGT
1 CACAAAGGCTTTCTTTAACAAAATCAAT
16705747 CACAAAGGCTTTCTTTAACAAAATCAAT
1 CACAAAGGCTTTCTTTAACAAAATCAAT
*
16705775 CATAAAGGCTT
1 CACAAAGGCTT
16705786 CTTACGAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (28 bp):
CACAAAGGCTTTCTTTAACAAAATCAAT
Found at i:16710675 original size:28 final size:29
Alignment explanation
Indices: 16710643--16710705 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
16710633 CCATAAACGC
*
16710643 TTCCTTGAACAAAATCAAGCACAAAGA-T
1 TTCCTTGAACAAAATCAACCACAAAGACT
*
16710671 TTCCTTTAACAAAATCAACCACAAAGACT
1 TTCCTTGAACAAAATCAACCACAAAGACT
16710700 TTCCTT
1 TTCCTT
16710706 ATATGCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (29 bp):
TTCCTTGAACAAAATCAACCACAAAGACT
Found at i:16723447 original size:18 final size:18
Alignment explanation
Indices: 16723407--16723451 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
16723397 ACTTAGTCTA
*
16723407 GAGACTCATGAAGCTAAC
1 GAGACTCACGAAGCTAAC
* * *
16723425 AAGACTCACGACGCTCAC
1 GAGACTCACGAAGCTAAC
16723443 GAGACTCAC
1 GAGACTCAC
16723452 CTGGCTTTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.31, G:0.20, T:0.13
Consensus pattern (18 bp):
GAGACTCACGAAGCTAAC
Done.