Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 82 of 144
Found at i:18458130 original size:8 final size:8
Alignment explanation
Indices: 18458117--18458142 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
18458107 AATAAATAGC
18458117 TAATTAAA
1 TAATTAAA
18458125 TAATTAAA
1 TAATTAAA
18458133 TAATTAAA
1 TAATTAAA
18458141 TA
1 TA
18458143 TTTGGGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:18458163 original size:42 final size:41
Alignment explanation
Indices: 18458117--18458223 Score: 129
Period size: 34 Copynumber: 2.7 Consensus size: 41
18458107 AATAAATAGC
18458117 TAATTAAATAATTAAATAATTAAATATTTGGGCTGCTTTTAT
1 TAATTAAATAATTAAATAATTAAATATTT-GGCTGCTTTTAT
*
18458159 TAATTAAATAATTAAAT-ATT---TA---GGTTGCTTTTAT
1 TAATTAAATAATTAAATAATTAAATATTTGGCTGCTTTTAT
18458193 TAATTAAATAATTAAATATAATTAAATATTT
1 TAATTAAATAATT-AA-ATAATTAAATATTT
18458224 AATTAACTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
34 24 0.44
35 2 0.04
36 2 0.04
37 3 0.05
38 2 0.04
40 2 0.04
41 3 0.05
42 17 0.31
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (41 bp):
TAATTAAATAATTAAATAATTAAATATTTGGCTGCTTTTAT
Found at i:18458166 original size:34 final size:34
Alignment explanation
Indices: 18458125--18458211 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
18458115 GCTAATTAAA
*
18458125 TAATTAAATAATTAAATATTTGGGCTGCTTTTAT
1 TAATTAAATAATTAAATATTTAGGCTGCTTTTAT
*
18458159 TAATTAAATAATTAAATATTTAGGTTGCTTTTAT
1 TAATTAAATAATTAAATATTTAGGCTGCTTTTAT
18458193 TAATTAAATAATTAAATAT
1 TAATTAAATAATTAAATAT
18458212 AATTAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (34 bp):
TAATTAAATAATTAAATATTTAGGCTGCTTTTAT
Found at i:18458215 original size:10 final size:10
Alignment explanation
Indices: 18458200--18458271 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 10
18458190 TATTAATTAA
18458200 ATAATTAAAT
1 ATAATTAAAT
18458210 ATAATTAAAT
1 ATAATTAAAT
*
18458220 ATTTAATTAACT
1 A--TAATTAAAT
***
18458232 A-ATATTGTTT
1 ATA-ATTAAAT
18458242 ATAATTAAAT
1 ATAATTAAAT
18458252 ATTTAATTAAAT
1 A--TAATTAAAT
18458264 ATAATTAA
1 ATAATTAA
18458272 TTATTTTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
9 1 0.02
10 28 0.57
11 1 0.02
12 19 0.39
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:18458226 original size:22 final size:22
Alignment explanation
Indices: 18458201--18458297 Score: 60
Period size: 22 Copynumber: 4.3 Consensus size: 22
18458191 ATTAATTAAA
18458201 TAATTAAATATAATTAAATATT
1 TAATTAAATATAATTAAATATT
* *
18458223 TAATTAACTA-ATATT--GT-TT
1 TAATTAAATATA-ATTAAATATT
18458242 ATAATTAAATATTTAATTAAATATAAT
1 -TAATTAAATA--TAATTAAATAT--T
* *
18458269 TAATT-ATTTTAAATTAAATATT
1 TAATTAAATAT-AATTAAATATT
18458291 TAATTAA
1 TAATTAA
18458298 CTAATACTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 23
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.04
20 10 0.18
21 1 0.02
22 21 0.37
23 3 0.05
24 11 0.19
25 3 0.05
26 5 0.09
27 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATTAAATATAATTAAATATT
Found at i:18458229 original size:148 final size:146
Alignment explanation
Indices: 18457910--18458221 Score: 348
Period size: 148 Copynumber: 2.1 Consensus size: 146
18457900 TAGTTGCAAA
** * * *
18457910 TAAATAACTAATT-AA-ATAACCAAATAATTAAATATTTGGGTTATTTTTTAATAAATAACAAAC
1 TAAAT-ACTAATTAAATATAATTAAATAATTAAATATTTCGATTAGTTTTTAATAAATAACAAAC
* * * * *
18457973 TGAATAATTAAATAATTAAATATTTGAGTTGTTTTTAATAATTAACTAATTAAATAATTAAATAT
65 TAAATAATTAAATAATTAAATATTTGAGCTGCTTTTAATAATTAAATAATTAAATAATT--ATAG
*
18458038 TTTGGTTTATTTTAATAAT
128 GTTGGTTTATTTTAATAAT
* * * *
18458057 TAAATACTTAATTAAATATAATTAAATAATTAAATATTTCTATT-GTTTTTAATAAATAGCTAAT
1 TAAATAC-TAATTAAATATAATTAAATAATTAAATATTTCGATTAGTTTTTAATAAATAACAAAC
* *
18458121 TAAATAATTAAATAATTAAATATTTGGGCTGCTTTTATTAATTAAATAATTAAAT-ATT-TAGGT
65 TAAATAATTAAATAATTAAATATTTGAGCTGCTTTTAATAATTAAATAATTAAATAATTATAGGT
*
18458184 TGCTTTTATTAATTAAATAAT
130 TG-GTTTATT--TT-AATAAT
18458205 TAAATA-TAATTAAATAT
1 TAAATACTAATTAAATAT
18458222 TTAATTAACT
Statistics
Matches: 140, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
144 5 0.04
145 6 0.04
146 13 0.09
147 15 0.11
148 79 0.56
149 22 0.16
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (146 bp):
TAAATACTAATTAAATATAATTAAATAATTAAATATTTCGATTAGTTTTTAATAAATAACAAACT
AAATAATTAAATAATTAAATATTTGAGCTGCTTTTAATAATTAAATAATTAAATAATTATAGGTT
GGTTTATTTTAATAAT
Found at i:18458248 original size:32 final size:32
Alignment explanation
Indices: 18458209--18458312 Score: 129
Period size: 32 Copynumber: 3.1 Consensus size: 32
18458199 AATAATTAAA
18458209 TATAATTAAATATTTAATTAACTAATATTGTT
1 TATAATTAAATATTTAATTAACTAATATTGTT
* *
18458241 TATAATTAAATATTTAATTAAATATAATTAATTATT
1 TATAATTAAATATTTAATT-AA-CTAA-T-ATTGTT
*
18458277 T-TAAATTAAATATTTAATTAACTAATACTGTT
1 TAT-AATTAAATATTTAATTAACTAATATTGTT
18458309 TATA
1 TATA
18458313 TATATATGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
32 25 0.41
33 4 0.07
34 6 0.10
35 4 0.07
36 22 0.36
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (32 bp):
TATAATTAAATATTTAATTAACTAATATTGTT
Found at i:18461529 original size:20 final size:21
Alignment explanation
Indices: 18461490--18461537 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18461480 GATAAGACTG
18461490 AAGAAGAGAAGGGCGAGCGTC
1 AAGAAGAGAAGGGCGAGCGTC
* * *
18461511 AAGAAGGGAA-GGCGTGCGTG
1 AAGAAGAGAAGGGCGAGCGTC
18461531 AAGAAGA
1 AAGAAGA
18461538 AGGTAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.40, C:0.10, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGAAGAGAAGGGCGAGCGTC
Found at i:18461959 original size:29 final size:30
Alignment explanation
Indices: 18461926--18461998 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
18461916 CAATTATTAT
*
18461926 TAATTTATATTATTTTTATTAA-T-ATTAA
1 TAATTTATATTATTTATATTAAGTAATTAA
* *
18461954 GTAATTAATAATATTTATATTAAGTAATTAA
1 -TAATTTATATTATTTATATTAAGTAATTAA
18461985 TAATATTTATATTA
1 T-A-ATTTATATTA
18461999 ATAATTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 19 0.54
30 2 0.06
31 6 0.17
32 8 0.23
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATTTATATTATTTATATTAAGTAATTAA
Found at i:18461960 original size:23 final size:23
Alignment explanation
Indices: 18461942--18462035 Score: 124
Period size: 23 Copynumber: 4.2 Consensus size: 23
18461932 ATATTATTTT
*
18461942 TATTAATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
18461965 TATTTATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
18461988 TATTTATATTAA-TAATTAATATA
1 TATTTATATTAAGTAATTAATA-A
* *
18462011 TTTTTATATTTA-T-ATTAAT-A
1 TATTTATATTAAGTAATTAATAA
18462031 TATTT
1 TATTT
18462036 CGATTTAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
20 5 0.08
22 15 0.23
23 46 0.70
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTATATTAAGTAATTAATAA
Found at i:18461998 original size:52 final size:52
Alignment explanation
Indices: 18461926--18462028 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
18461916 CAATTATTAT
* * *
18461926 TAATTTATATTATTTTTATTAAT-ATTAAGTA-ATTAATAATATTTATATTAAG
1 TAATTAATAATATTTATATTAATAATTAA-TATATT-ATAATATTTATATTAAG
* *
18461978 TAATTAATAATATTTATATTAATAATTAATATATTTTTATATTTATATTAA
1 TAATTAATAATATTTATATTAATAATTAATATATTATAATATTTATATTAA
18462029 TATATTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
52 36 0.82
53 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (52 bp):
TAATTAATAATATTTATATTAATAATTAATATATTATAATATTTATATTAAG
Found at i:18462076 original size:12 final size:12
Alignment explanation
Indices: 18462059--18462110 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
18462049 TATATTTCTA
18462059 TATTATTTATTT
1 TATTATTTATTT
18462071 TATTATTCTATCTAT
1 TATTATT-TAT-T-T
* *
18462086 TATTATATATAT
1 TATTATTTATTT
18462098 TATTATTTTATTT
1 TATTA-TTTATTT
18462111 AAATAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 13 0.41
13 8 0.25
14 4 0.12
15 7 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:18462481 original size:170 final size:168
Alignment explanation
Indices: 18462195--18462528 Score: 517
Period size: 170 Copynumber: 2.0 Consensus size: 168
18462185 AGCCCGGCAA
* * *
18462195 ATAGACATCCACAGGAATTAGCTTATCTACCCCCCAAACAGTACTATAAGAATTAGTGCTGAACA
1 ATAGACATCCACAGGAATTAGCTTATCGACCCCCCAAACAGTACTATAAGAATCAGTACTGAACA
* * *
18462260 TCCCTCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTACGTTCAGGCTTTTGCTCATAT
66 TCCCTCCTGTAATTATACACGCGCCCATAACAATAACATATTTACGTTCAGGCATTTGCTC--AT
18462325 ATAATCTCACTAAAGAGGGCGCCATTTTCATTGTTACTAT
129 ATAATCTCACTAAAGAGGGCGCCATTTTCATTGTTACTAT
* * *
18462365 ATAGACATCCAC-GAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCATTATTGAAC
1 ATAGACATCCACAG-GAATTAGCTTATCGACCCCCCAAACAGTACTATAAGAATCAGTACTGAAC
* * *
18462429 ATTCCTCCTGTAATTATACACGCGCCCATAACAATAACATATTTAGGTTCAGGCATTTGTTCATA
65 ATCCCTCCTGTAATTATACACGCGCCCATAACAATAACATATTTACGTTCAGGCATTTGCTCATA
*
18462494 TAATCTCGCTAAAGAGGGCGCCATTTTCATTGTTA
130 TAATCTCACTAAAGAGGGCGCCATTTTCATTGTTA
18462529 ATGTTCCAAC
Statistics
Matches: 150, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
168 37 0.25
169 1 0.01
170 112 0.75
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (168 bp):
ATAGACATCCACAGGAATTAGCTTATCGACCCCCCAAACAGTACTATAAGAATCAGTACTGAACA
TCCCTCCTGTAATTATACACGCGCCCATAACAATAACATATTTACGTTCAGGCATTTGCTCATAT
AATCTCACTAAAGAGGGCGCCATTTTCATTGTTACTAT
Found at i:18463103 original size:41 final size:41
Alignment explanation
Indices: 18463058--18463145 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
18463048 TTTAAATAAA
* ** * *
18463058 TTAGCGGCGCTTATGGGAAAGCGCCGCCAATACTCTGACCT
1 TTAGCGGCACTTAAAGGAAAGCGCCACCAATACCCTGACCT
* *
18463099 TTAGCGGCACTTAAAGGAAAGCGTCACTAATACCCTGACCT
1 TTAGCGGCACTTAAAGGAAAGCGCCACCAATACCCTGACCT
18463140 TTAGCG
1 TTAGCG
18463146 ACGTTTTTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (41 bp):
TTAGCGGCACTTAAAGGAAAGCGCCACCAATACCCTGACCT
Found at i:18463214 original size:41 final size:41
Alignment explanation
Indices: 18463157--18463245 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
18463147 CGTTTTTGGG
*
18463157 AATGCCCTGAACTTTAGCGGCACTTATGGGAAAGCGCGGCT
1 AATGCCCTGAACTTTAGCGGCACTTATAGGAAAGCGCGGCT
* *
18463198 AATGCCCT-AACCTTTAGCGGCGCTTATAGGAAAGTGCGGCT
1 AATGCCCTGAA-CTTTAGCGGCACTTATAGGAAAGCGCGGCT
18463239 AATGCCC
1 AATGCCC
18463246 AGACATAAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.05
41 42 0.95
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (41 bp):
AATGCCCTGAACTTTAGCGGCACTTATAGGAAAGCGCGGCT
Found at i:18463295 original size:64 final size:62
Alignment explanation
Indices: 18463188--18463307 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 62
18463178 ACTTATGGGA
* * *
18463188 AAGCGCGGCTAATGCCCTAACCTTTAGCGGCGCTTATAGGAAAGTGCGGCTAATGCCCAGACAT
1 AAGCGCCGCTAATGCCCTAACCTTTAGCGACGCTTATAGGAAA--GCCGCTAATGCCCAGACAT
*
18463252 AAGCGCCGCTAATGCCCTGACCTTTAGCGACGCTTAT-GAGAAAGCCGCTAATGCCC
1 AAGCGCCGCTAATGCCCTAACCTTTAGCGACGCTTATAG-GAAAGCCGCTAATGCCC
18463308 TGACCTTTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 12 0.24
63 1 0.02
64 38 0.75
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.20
Consensus pattern (62 bp):
AAGCGCCGCTAATGCCCTAACCTTTAGCGACGCTTATAGGAAAGCCGCTAATGCCCAGACAT
Found at i:18463343 original size:103 final size:105
Alignment explanation
Indices: 18463157--18463348 Score: 273
Period size: 103 Copynumber: 1.8 Consensus size: 105
18463147 CGTTTTTGGG
* *
18463157 AATGCCCTGAACTTTAGCGGCACTTATGGGAAAGCGCGGCTAATGCCCTAACCTTTAGCGGCGCT
1 AATGCCCTGAACTTTAGCGACACTTATGAGAAAGCGCGGCTAATGCCCTAACCTTTAGCGGCGCT
** *
18463222 TATAGGAAAGTGCGGCTAATGCCCAGACATAAGCGCCGCT
66 TATAGGAAAGCACCGCTAATGCCCAGACATAAGCGCCGCT
* * * *
18463262 AATGCCCTGACCTTTAGCGACGCTTATGAGAAAGC-C-GCTAATGCCCTGACCTTTAGCGGTGCT
1 AATGCCCTGAACTTTAGCGACACTTATGAGAAAGCGCGGCTAATGCCCTAACCTTTAGCGGCGCT
18463325 TAT-GGTAAAGCACCGCTAATGCCC
66 TATAGG-AAAGCACCGCTAATGCCC
18463349 TGACCTTTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
102 2 0.03
103 43 0.56
104 1 0.01
105 31 0.40
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (105 bp):
AATGCCCTGAACTTTAGCGACACTTATGAGAAAGCGCGGCTAATGCCCTAACCTTTAGCGGCGCT
TATAGGAAAGCACCGCTAATGCCCAGACATAAGCGCCGCT
Found at i:18463353 original size:41 final size:40
Alignment explanation
Indices: 18463252--18463366 Score: 171
Period size: 39 Copynumber: 2.9 Consensus size: 40
18463242 GCCCAGACAT
*
18463252 AAGCGCCGCTAATGCCCTGACCTTTAGCGACGCTTATGAGA
1 AAGC-CCGCTAATGCCCTGACCTTTAGCGGCGCTTATGAGA
*
18463293 AAG-CCGCTAATGCCCTGACCTTTAGCGGTGCTTATG-GTA
1 AAGCCCGCTAATGCCCTGACCTTTAGCGGCGCTTATGAG-A
18463332 AAGCACCGCTAATGCCCTGACCTTTAGCGGCGCTT
1 AAGC-CCGCTAATGCCCTGACCTTTAGCGGCGCTT
18463367 TCTCTATAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
38 1 0.01
39 35 0.51
41 32 0.47
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (40 bp):
AAGCCCGCTAATGCCCTGACCTTTAGCGGCGCTTATGAGA
Found at i:18463396 original size:41 final size:40
Alignment explanation
Indices: 18463351--18463490 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
18463341 TAATGCCCTG
* * *
18463351 ACCTTTAGCGGCGCTTTCTCTATAAACGCCGCTATTGCTTT
1 ACCTTTTGCGGCGCTTTCT-GAAAAACGCCGCTATTGCTTT
* * *
18463392 ACCTTTTGCGGCGCCTACTGAAAAACGTCGCTATTGCTTT
1 ACCTTTTGCGGCGCTTTCTGAAAAACGCCGCTATTGCTTT
** *
18463432 ACCTTTTGTAGCG-TTTATGGAAAAACGCCGCTATTGCTTT
1 ACCTTTTGCGGCGCTTTCT-GAAAAACGCCGCTATTGCTTT
*
18463472 ACCTTTTGCGGCGTTTTCT
1 ACCTTTTGCGGCGCTTTCT
18463491 TTCCAAACGC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 60 0.73
41 20 0.24
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (40 bp):
ACCTTTTGCGGCGCTTTCTGAAAAACGCCGCTATTGCTTT
Found at i:18463486 original size:40 final size:40
Alignment explanation
Indices: 18463374--18463487 Score: 167
Period size: 40 Copynumber: 2.9 Consensus size: 40
18463364 CTTTCTCTAT
**
18463374 AAACGCCGCTATTGCTTTACCTTTTGCGGCGCCTACTGAA
1 AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTACTGAA
* **
18463414 AAACGTCGCTATTGCTTTACCTTTTGTAGCGTTTA-TGGAA
1 AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTACT-GAA
18463454 AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTT
1 AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTT
18463488 TCTTTCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 64 0.98
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (40 bp):
AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTACTGAA
Found at i:18464752 original size:14 final size:14
Alignment explanation
Indices: 18464723--18464774 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
18464713 CACAAACAAT
18464723 TATACGAATGAATAAA
1 TATACGAA--AATAAA
18464739 TATACGAAAATAAA
1 TATACGAAAATAAA
*
18464753 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
18464768 -ATACGAA
1 TATACGAA
18464775 TCATGAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 2 0.06
14 15 0.45
15 8 0.24
16 8 0.24
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:18465106 original size:58 final size:58
Alignment explanation
Indices: 18464925--18465165 Score: 265
Period size: 58 Copynumber: 4.2 Consensus size: 58
18464915 GAAAATTTAG
* * * * *
18464925 GGGTAAAAATGTAATTTTGGAAAAGTTTA-GGGTAAAAATGTGATTTTTGGAAGTTTGG
1 GGGTAAAAATGTAATTTTTG-AAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTCGA
* * * * *
18464983 GGGTAAAAATATAATTTTTGGAAGTTTAGGGG-CAAAATGTAATTATTGGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTCGA
* * * *
18465040 GTGCAAAAATGTCATTTTTGAAAGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTCGA
* * * *
18465098 GGGTAAAAATGTGATTTTTGAGAAGTTCAAGGGT-AAAATATAATTTTTGAGAAGTTCG-
1 GGGTAAAAATGTAATTTTTGA-AAGTTTAGGGGTAAAAATGTAATTTTTGA-AAGTTCGA
18465156 GGGTAAAAAT
1 GGGTAAAAAT
18465166 ATGATTTTAA
Statistics
Matches: 155, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
57 54 0.35
58 84 0.54
59 17 0.11
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTCGA
Found at i:18465173 original size:29 final size:29
Alignment explanation
Indices: 18464889--18465165 Score: 226
Period size: 29 Copynumber: 9.6 Consensus size: 29
18464879 AAGTTTCAAA
* * * * *
18464889 AAGTTCGAGGTTAAAACGTAATTTTGGAA
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * * *
18464918 AATTTAGGGGTAAAAATGTAATTTTGGAA
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
** *
18464947 AAGTTTAGGGTAAAAATGTGATTTTTG-G
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* *
18464975 AAGTTTGGGGGTAAAAATATAATTTTTG-G
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
* * *
18465004 AAGTTTAGGGG-CAAAATGTAATTATTG-G
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
* * *
18465032 AAGTTCGAGTGCAAAAATGTCATTTTTGA-
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
* *
18465061 AAGTTTAGGGGTAAAAATGTGATTTTTGA-
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
*
18465090 AAGTTCGAGGGTAAAAATGTGATTTTTGAG
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
* *
18465120 AAGTTCAAGGGT-AAAATATAATTTTTGAG
1 AAGTTC-GGGGTAAAAATGTAATTTTTGAG
18465149 AAGTTCGGGGTAAAAAT
1 AAGTTCGGGGTAAAAAT
18465166 ATGATTTTAA
Statistics
Matches: 206, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
27 3 0.01
28 29 0.14
29 161 0.78
30 13 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
AAGTTCGGGGTAAAAATGTAATTTTTGAG
Found at i:18466639 original size:17 final size:17
Alignment explanation
Indices: 18466617--18466668 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
18466607 CCTTTTTAAT
18466617 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
18466634 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
18466651 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
18466669 ATTGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:18466667 original size:7 final size:6
Alignment explanation
Indices: 18466616--18466663 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
18466606 ACCTTTTTAA
* * *
18466616 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TCAAA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
18466662 TT
1 TT
18466664 TAAAAATTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:18469787 original size:29 final size:29
Alignment explanation
Indices: 18469745--18469803 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
18469735 TGGACTCTAG
18469745 TGCTCAAATATAGGACACTCTTGCAAATA
1 TGCTCAAATATAGGACACTCTTGCAAATA
18469774 TGCTCAAATATAGGACACTCTTGCAAATA
1 TGCTCAAATATAGGACACTCTTGCAAATA
18469803 T
1 T
18469804 ATATGGTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (29 bp):
TGCTCAAATATAGGACACTCTTGCAAATA
Found at i:18477345 original size:13 final size:14
Alignment explanation
Indices: 18477327--18477355 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18477317 ATTGTAATCA
18477327 TTGTT-GAATTTGG
1 TTGTTGGAATTTGG
18477340 TTGTTGGAATTTGG
1 TTGTTGGAATTTGG
18477354 TT
1 TT
18477356 TAGGTTAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.55
Consensus pattern (14 bp):
TTGTTGGAATTTGG
Found at i:18478844 original size:34 final size:35
Alignment explanation
Indices: 18478806--18478881 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
18478796 ACATCACGAG
*
18478806 TTTAGTAGCA-GATTTTCTTAAAA-A-ATTAGGATAA
1 TTTAGTAG-AGGA-TTTCTCAAAAGACATTAGGATAA
*
18478840 TTTAGTTGAGGATTTCTCAAAAGATCATTAGGATAA
1 TTTAGTAGAGGATTTCTCAAAAGA-CATTAGGATAA
18478876 TTTAGT
1 TTTAGT
18478882 TATGGATTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 10 0.28
34 10 0.28
36 16 0.44
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (35 bp):
TTTAGTAGAGGATTTCTCAAAAGACATTAGGATAA
Found at i:18480089 original size:16 final size:17
Alignment explanation
Indices: 18480062--18480096 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18480052 ATAGTTAAAT
18480062 AACTCAATTTTCTATAA
1 AACTCAATTTTCTATAA
*
18480079 AACTC-ATTTTCTTTAA
1 AACTCAATTTTCTATAA
18480095 AA
1 AA
18480097 TATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (17 bp):
AACTCAATTTTCTATAA
Found at i:18480114 original size:19 final size:20
Alignment explanation
Indices: 18480092--18480145 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
18480082 TCATTTTCTT
18480092 TAAAATATAAAATTTATT-A
1 TAAAATATAAAATTTATTGA
*
18480111 TAAAA-ATGAAAA-TGATTGA
1 TAAAATAT-AAAATTTATTGA
18480130 TGAAAATA-AAAATTTA
1 T-AAAATATAAAATTTA
18480146 CTAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 6 0.21
21 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
TAAAATATAAAATTTATTGA
Found at i:18481186 original size:21 final size:21
Alignment explanation
Indices: 18481162--18481205 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18481152 GTACTTGAAC
18481162 TTTCAAAATGCATAAAAAAAA
1 TTTCAAAATGCATAAAAAAAA
* **
18481183 TTTCAAACTTTATAAAAAAAA
1 TTTCAAAATGCATAAAAAAAA
18481204 TT
1 TT
18481206 AAGTCTCTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (21 bp):
TTTCAAAATGCATAAAAAAAA
Found at i:18481323 original size:21 final size:21
Alignment explanation
Indices: 18481288--18481330 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
18481278 TAAAATTTAA
18481288 TAAAAAATCAAATATTAAAAAT
1 TAAAAAATCAAATA-TAAAAAT
*
18481310 TAAAAAAT-ATATATAAAAAT
1 TAAAAAATCAAATATAAAAAT
18481330 T
1 T
18481331 GTAAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAAATCAAATATAAAAAT
Found at i:18481335 original size:9 final size:9
Alignment explanation
Indices: 18481323--18481375 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
18481313 AAAATATATA
18481323 TAAAAATTG
1 TAAAAATTG
* *
18481332 TAAAAAGTA
1 TAAAAATTG
18481341 TAAAGAATTG
1 TAAA-AATTG
* *
18481351 TAAAATTTTA
1 TAAAA-ATTG
18481361 TAAAAATTG
1 TAAAAATTG
18481370 TAAAAA
1 TAAAAA
18481376 ATTATAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (9 bp):
TAAAAATTG
Found at i:18481375 original size:10 final size:10
Alignment explanation
Indices: 18481310--18481410 Score: 59
Period size: 10 Copynumber: 10.3 Consensus size: 10
18481300 TATTAAAAAT
18481310 TAAAAAATATA
1 TAAAAAAT-TA
*
18481321 TATAAAAATTG
1 TA-AAAAATTA
*
18481332 T-AAAAAGTA
1 TAAAAAATTA
* *
18481341 TAAAGAATTG
1 TAAAAAATTA
**
18481351 TAAAATTTTA
1 TAAAAAATTA
*
18481361 T-AAAAATTG
1 TAAAAAATTA
18481370 TAAAAAATTA
1 TAAAAAATTA
*
18481380 TAAAATA-TA
1 TAAAAAATTA
*
18481389 T-AGAAA-TA
1 TAAAAAATTA
18481397 TAAAAAAATTA
1 T-AAAAAATTA
18481408 TAA
1 TAA
18481411 TGTTTTATAA
Statistics
Matches: 66, Mismatches: 18, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
8 6 0.09
9 16 0.24
10 31 0.47
11 7 0.11
12 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:18481380 original size:19 final size:19
Alignment explanation
Indices: 18481303--18481384 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
18481293 AATCAAATAT
*
18481303 TAAAAATT-AAAAAATATATA
1 TAAAAATTGTAAAAA-AT-TA
*
18481323 TAAAAATTGT-AAAAAGTA
1 TAAAAATTGTAAAAAATTA
**
18481341 TAAAGAATTGTAAAATTTTA
1 TAAA-AATTGTAAAAAATTA
18481361 TAAAAATTGTAAAAAATTA
1 TAAAAATTGTAAAAAATTA
18481380 TAAAA
1 TAAAA
18481385 TATATAGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.12
19 25 0.48
20 21 0.40
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
TAAAAATTGTAAAAAATTA
Found at i:18486598 original size:9 final size:10
Alignment explanation
Indices: 18486573--18486607 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
18486563 AATAATAATT
*
18486573 AATTTTTTCA
1 AATTTTTTAA
*
18486583 ATTTTTTTAA
1 AATTTTTTAA
18486593 AATTTTTTAA
1 AATTTTTTAA
18486603 AATTT
1 AATTT
18486608 AATTTATTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:18487136 original size:2 final size:2
Alignment explanation
Indices: 18487129--18487158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18487119 TCCTGTGCTC
18487129 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18487159 ACCTCTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18505696 original size:30 final size:30
Alignment explanation
Indices: 18505657--18505791 Score: 138
Period size: 29 Copynumber: 4.6 Consensus size: 30
18505647 TATTTTTTAA
18505657 CCTCTAAACTTTCCAAAAATTT-AGATTTGAC
1 CCTC-AAACTTTCCAAAAATTTGA-ATTTGAC
* *
18505688 CCTCAAACTTTCCAAATATTATG-TTTTGAC
1 CCTCAAACTTTCCAAAAATT-TGAATTTGAC
* * *
18505718 CCCCGAAC-TTCCTAAAATTTGAATTTGAC
1 CCTCAAACTTTCCAAAAATTTGAATTTGAC
18505747 CCT-AAACTTTCCAAAAATTTGAATTT-AGC
1 CCTCAAACTTTCCAAAAATTTGAATTTGA-C
*
18505776 CC-CTAACTTTCCAAAA
1 CCTCAAACTTTCCAAAA
18505792 TTTCATTTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
28 6 0.07
29 49 0.56
30 27 0.31
31 5 0.06
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (30 bp):
CCTCAAACTTTCCAAAAATTTGAATTTGAC
Found at i:18505803 original size:58 final size:59
Alignment explanation
Indices: 18505663--18505799 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 59
18505653 TTAACCTCTA
* *
18505663 AACTTTCCAAAAATTTAGATTTGACCCTCAAACTTTCCAAATATTATGTTTTGACCCCCG
1 AACTTTCCAAAAATTTA-ATTTGACCCTCAAACTTTCCAAAAATTATGATTTGACCCCCG
* * *
18505723 AAC-TTCCTAAAATTTGAATTTGACCCT-AAACTTTCCAAAAATT-TGAATTT-AGCCCCT
1 AACTTTCCAAAAATTT-AATTTGACCCTCAAACTTTCCAAAAATTATG-ATTTGACCCCCG
*
18505780 AACTTTCC-AAAATTTCATTT
1 AACTTTCCAAAAATTTAATTT
18505800 TTGATCCCGT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
56 4 0.06
57 17 0.25
58 22 0.32
59 21 0.31
60 4 0.06
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (59 bp):
AACTTTCCAAAAATTTAATTTGACCCTCAAACTTTCCAAAAATTATGATTTGACCCCCG
Found at i:18509733 original size:15 final size:17
Alignment explanation
Indices: 18509694--18509736 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
18509684 GAGGTCAAAA
*
18509694 AAAGAGGAAAAAGAAAG
1 AAAGAAGAAAAAGAAAG
*
18509711 AAAGAAGAAAAA-AAGG
1 AAAGAAGAAAAAGAAAG
18509727 AAA-AAGAAAA
1 AAAGAAGAAAA
18509737 GGGTCGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAG
Found at i:18509806 original size:5 final size:5
Alignment explanation
Indices: 18509782--18509829 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
18509772 ATTAAAACCC
*
18509782 AAGAA AAGGAAA AAGAAA AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AA-G-AA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
18509830 GGAAAAGTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 27 0.69
6 8 0.21
7 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:18509814 original size:10 final size:9
Alignment explanation
Indices: 18509782--18509836 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 9
18509772 ATTAAAACCC
18509782 AAGAAAAGGA
1 AAGAAAA-GA
18509792 AA-AAGAA-A
1 AAGAA-AAGA
18509800 AAGAAAAGCA
1 AAGAAAAG-A
18509810 AAGAAAAGAA
1 AAGAAAAG-A
18509820 AAGAAAAGA
1 AAGAAAAGA
*
18509829 AGGAAAAG
1 AAGAAAAG
18509837 TCGAGATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 5 0.13
9 12 0.31
10 22 0.56
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:18510715 original size:16 final size:14
Alignment explanation
Indices: 18510702--18510749 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
18510692 ATGAAAAAGG
18510702 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
*
18510716 GAAAAAAAG--GAA
1 GAAAAAAAGAAAAA
18510728 GAAGAAAAAGAAAAA
1 GAA-AAAAAGAAAAA
18510743 GAAAAAA
1 GAAAAAA
18510750 GGAGAGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 5 0.17
13 6 0.21
14 13 0.45
15 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAAAAA
Found at i:18510716 original size:6 final size:6
Alignment explanation
Indices: 18510705--18510748 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
18510695 AAAAAGGGAA
*
18510705 AAAAAG AAAAAG AAAAAAAGG AAGAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG --AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA
18510749 AGGAGAGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 23 0.70
7 4 0.12
8 5 0.15
9 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:18510762 original size:27 final size:26
Alignment explanation
Indices: 18510695--18510749 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
18510685 AGAAGAAATG
18510695 AAAAAGG--GAAAAAAAGAAAAAGAA
1 AAAAAGGAAGAAAAAAAGAAAAAGAA
18510719 AAAAAGGAAGAAGAAAAAGAAAAAGAA
1 AAAAAGGAAGAA-AAAAAGAAAAAGAA
18510746 AAAA
1 AAAA
18510750 GGAGAGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.25
26 3 0.11
27 18 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (26 bp):
AAAAAGGAAGAAAAAAAGAAAAAGAA
Found at i:18511702 original size:49 final size:49
Alignment explanation
Indices: 18511585--18511876 Score: 243
Period size: 49 Copynumber: 6.0 Consensus size: 49
18511575 TCTAAAGACT
* * *
18511585 TGAAGAGAAAGATTGAGGTCGCAACGACGAATCTTGTACCTTAG-GAATG
1 TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAG-ATG
* * * *
18511634 TGAAGGGAAAAATTAAGGCCGTAACGATGAATCTTGTACCCTAGAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAGATG
* * * * * * * *
18511683 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCATATACCTTAGAAATAA
1 TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAGAT-G
* ** * * *
18511733 T-AAAGTCAA-ATTGAAGCCGCAACGACGAATCTTGAACCCTAAAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAGATG
* * * * * * *
18511780 TGAAGGAAAAGGTTAAGGCCGCAATGACGAACCTTATACTCTAGAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAGATG
* * *
18511829 TGAAGGGAAAGATTGAGGCCGTAACTG-CGAATCATATACCCTA-AGATG
1 TGAAGGGAAAGATTGAGGCCGCAAC-GACGAATCTTGTACCCTAGAGATG
18511877 AAGTAGACTG
Statistics
Matches: 185, Mismatches: 53, Indels: 11
0.74 0.21 0.04
Matches are distributed among these distances:
47 1 0.01
48 37 0.20
49 144 0.78
50 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
TGAAGGGAAAGATTGAGGCCGCAACGACGAATCTTGTACCCTAGAGATG
Found at i:18511865 original size:146 final size:146
Alignment explanation
Indices: 18511604--18511868 Score: 372
Period size: 146 Copynumber: 1.8 Consensus size: 146
18511594 AGATTGAGGT
* * * * * *
18511604 CGCAACGACGAATCTTGTACCTTAGGAATGTGAAGGGAAAAATTAAGGCCGTAACGATGAATCTT
1 CGCAACGACGAATCTTGAACCTAAAGAATGTGAAGGGAAAAATTAAGGCCGCAACGACGAACCTT
* *
18511669 GTACCCTAGAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCATATACCTTAGAAATAAT
66 ATACCCTAGAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCATATACCTTAGAAATAAT
18511734 AAAGTCAAATTGAAGC
131 AAAGTCAAATTGAAGC
* *
18511750 CGCAACGACGAATCTTGAACCCTAAAG-ATGTGAA-GGAAAAGGTTAAGGCCGCAATGACGAACC
1 CGCAACGACGAATCTTGAA-CCTAAAGAATGTGAAGGGAAAA-ATTAAGGCCGCAACGACGAACC
* * * *
18511813 TTATACTCTAGAGATGTGAAGGGAAAGATTGAGGCCGTAACTGCGAATCATATACC
64 TTATACCCTAGAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCATATACC
18511869 CTAAGATGAA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
145 6 0.06
146 92 0.89
147 5 0.05
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (146 bp):
CGCAACGACGAATCTTGAACCTAAAGAATGTGAAGGGAAAAATTAAGGCCGCAACGACGAACCTT
ATACCCTAGAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCATATACCTTAGAAATAAT
AAAGTCAAATTGAAGC
Found at i:18511875 original size:97 final size:96
Alignment explanation
Indices: 18511604--18511876 Score: 266
Period size: 97 Copynumber: 2.8 Consensus size: 96
18511594 AGATTGAGGT
* * * * * *
18511604 CGCAACGACGAATCTTGTACCTTAGGAATGTGAAGGGAAAAATTAAGGCCGTAACGATGAATCTT
1 CGCAACGACGAACCATATACCTTAGAAATGTGAAGGG-AAAATTGAGGCCGTAACGACGAATCTT
* * *
18511669 GTACCCTAGAGATGTGAAGGGAAAGGTTGAGGC
65 ATACCCTA-AGATGTGAAGGAAAAGGTTAAGGC
* * * ** * *
18511702 CGCAACGGCGAACCATATACCTTAGAAATAAT-AAAGTCAAATTGAAGCCGCAACGACGAATCTT
1 CGCAACGACGAACCATATACCTTAGAAAT-GTGAAGGGAAAATTGAGGCCGTAACGACGAATCTT
18511766 GA-ACCCTAAAGATGTGAAGGAAAAGGTTAAGGC
65 -ATACCCT-AAGATGTGAAGGAAAAGGTTAAGGC
* * *
18511799 CGCAATGACGAACCTTATA-CTCTAGAGATGTGAAGGGAAAGATTGAGGCCGTAACTG-CGAATC
1 CGCAACGACGAACCATATACCT-TAGAAATGTGAAGGGAAA-ATTGAGGCCGTAAC-GACGAATC
*
18511862 ATATACCCTAAGATG
63 TTATACCCTAAGATG
18511877 AAGTAGACTG
Statistics
Matches: 140, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
96 3 0.02
97 83 0.59
98 52 0.37
99 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (96 bp):
CGCAACGACGAACCATATACCTTAGAAATGTGAAGGGAAAATTGAGGCCGTAACGACGAATCTTA
TACCCTAAGATGTGAAGGAAAAGGTTAAGGC
Found at i:18512286 original size:48 final size:48
Alignment explanation
Indices: 18512194--18512286 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
18512184 CTTCAAACCC
** *
18512194 CATCTTCCTGATGAGAGACAGAAAAATGGGTCAAAACAATGAAGCAGT
1 CATCTTCCTGATGAGAGACAGAAAAATGGACCAAAACAACGAAGCAGT
* * * * *
18512242 CATCTTCCTGATTAGATACAGAGAAGTGGACCAAATCAACGAAGC
1 CATCTTCCTGATGAGAGACAGAAAAATGGACCAAAACAACGAAGC
18512287 GAAGCGAAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (48 bp):
CATCTTCCTGATGAGAGACAGAAAAATGGACCAAAACAACGAAGCAGT
Found at i:18512333 original size:133 final size:133
Alignment explanation
Indices: 18512159--18512403 Score: 373
Period size: 133 Copynumber: 1.8 Consensus size: 133
18512149 CCAAATCAAT
*
18512159 GAAGCGAAGCTCAATGCAAGTGAAACTTCAAACCCCATCTTCCTGATGAGAGACAGAAAAATGGG
1 GAAGCGAAGCTCAATACAAGTGAAACTTCAAACCCCATCTTCCTGATGAGAGACAGAAAAATGGG
*
18512224 TCAAAACAATGAAGCAGTCATCTTCCTGATTAGATACAGAGAAGTGGACCAAATCAACGAAGCGA
66 TCAAAACAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAACGAAGCGA
18512289 AGC
131 AGC
** * * * *
18512292 GAAGCGAAGCTCAATATGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACATATAAATGGT
1 GAAGCGAAGCTCAATACAAGTGAAACTTCAAACCCCATCTTCCTGATGAGAGACAGAAAAATGGG
* * ** *
18512357 TCAAAACCATGAGGTGGTCATCTTCCTGATGAGATATAGAGAAGTGG
66 TCAAAACAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTGG
18512404 GTCAAAACAA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 99 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (133 bp):
GAAGCGAAGCTCAATACAAGTGAAACTTCAAACCCCATCTTCCTGATGAGAGACAGAAAAATGGG
TCAAAACAATGAAGCAGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAACGAAGCGA
AGC
Found at i:18512409 original size:48 final size:48
Alignment explanation
Indices: 18512326--18512449 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 48
18512316 ACTTCAAACC
* * * * * * *
18512326 CCATCTTCCTGATGAGATACATATAAATGGTTCAAAACCATGAGGTGG
1 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGG
* *
18512374 TCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAACAATAAAGTGG
1 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGG
*
18512422 CCATCTTCCTAATGAGATACAGAGAAGT
1 CCATCTTCCTGATGAGATACAGAGAAGT
18512450 AGACCAAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (48 bp):
CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGG
Found at i:18512458 original size:48 final size:48
Alignment explanation
Indices: 18512370--18512462 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
18512360 AAACCATGAG
* * * * **
18512370 GTGGTCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAACAATAAA
1 GTGGCCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATAAA
18512418 GTGGCCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAAT
1 GTGGCCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAAT
18512463 GAAGCGAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (48 bp):
GTGGCCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATAAA
Found at i:18514397 original size:29 final size:28
Alignment explanation
Indices: 18514342--18514430 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
18514332 GTATTTTAAC
*
18514342 CCCTAAACTTCCCCAAAA-TTCAGATTTGA
1 CCCTAAACTT-TCCAAAATTTCA-ATTTGA
* *
18514371 CCCTAAACTTTCCAAAAATTTGAATTTGGC
1 CCCTAAACTTTCC-AAAATTTCAATTT-GA
* * *
18514401 CCCTAAATTTTCCAAAATTTTATTTTGA
1 CCCTAAACTTTCCAAAATTTCAATTTGA
18514429 CC
1 CC
18514431 TCAAAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.10
29 29 0.58
30 16 0.32
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTTCAATTTGA
Found at i:18514407 original size:30 final size:29
Alignment explanation
Indices: 18514341--18514417 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
18514331 TGTATTTTAA
* *
18514341 CCCCTAAACTTCCCCAAAATTCAGATTTG
1 CCCCTAAACTTTCCAAAAATTCAGATTTG
* *
18514370 ACCCTAAACTTTCCAAAAATT-TGAATTTGG
1 CCCCTAAACTTTCCAAAAATTCAG-ATTT-G
*
18514400 CCCCTAAATTTTCCAAAA
1 CCCCTAAACTTTCCAAAA
18514418 TTTTATTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.03
29 22 0.55
30 17 0.43
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.30
Consensus pattern (29 bp):
CCCCTAAACTTTCCAAAAATTCAGATTTG
Found at i:18522705 original size:440 final size:440
Alignment explanation
Indices: 18521884--18522764 Score: 1334
Period size: 440 Copynumber: 2.0 Consensus size: 440
18521874 ATAATTGTGT
* * *
18521884 GGCGCAAGGTCGTGTGGAATATGTTCATCGTGGGTGGTCAACCAAACCTCGTGCTTGAGTGTTCC
1 GGCGCAAGGTCGTGTGGAATATGCTCATCATGGGTGGTCAACCAAACCTCGTGCTCGAGTGTTCC
18521949 AAGAGCCAAATTTTGATGCCAGGGTGGGTCCGTTTATTCCTAGGCCGATTATAGAATGGGCGAGT
66 AAGAGCCAAATTTTGATGCCAGGGTGGGTCCGTTTATTCCTAGGCCGATTATAGAATGGGCGAGT
* * * *
18522014 CGTCCTCGGGTTACGGATGTCTCGGGTTCTAAATTTTTGATAGGCAGTGCCTCTGATGCTATATC
131 CATCCTCGGGTTACGGATGTCTCGGGTTCTAAATTTTCGACAGGCAGTGCCTCTGATGCTACATC
* * *
18522079 ACCGTTGTATGAGGTTGGTTCGTGTTCTAACACAATTAATACGGATTCACAGTATGTTCCTGAGC
196 ACCGGTGTATGAGGTTAGCTCGTGTTCTAACACAATTAATACGGATTCACAGTATGTTCCTGAGC
18522144 CGGTGGGTAATGATGGTAATGGTGCGTGGTATCCTGACTCGGGTGTAACCCACCATGTATGCAAA
261 CGGTGGGTAATGATGGTAATGGTGCGTGGTATCCTGACTCGGGTGTAACCCACCATGTATGCAAA
* * * * *
18522209 CAGGCAATCGAGCTAAATACGTTCACTTCATATCCAGGTAAGGTATCGCTTTTGATGGGTGATGG
326 CAGGCAACCGAGCTAAACACGTCCACTTCATATCCAAGTAAGGCATCGCTTTTGATGGGTGATGG
* * *
18522274 TGCATGTGCTAGAATTGTAGGTGTTGGTGCGTCTACATTAACTACGAAGA
391 TACATGTGCTAGAATTATAGGTGTTGGTGCATCTACATTAACTACGAAGA
* * *
18522324 GGCGCAAGGTTGTGTGGAATATGCTCATTATGGGTGGTCAACCAAACCTCGTGCTCGAGTGTTTC
1 GGCGCAAGGTCGTGTGGAATATGCTCATCATGGGTGGTCAACCAAACCTCGTGCTCGAGTGTTCC
* *** * * * *
18522389 AAGGGTTGAATTTTGATGTC-GTGGTGGGTCCGTTTATTCCTAGGTCGATTATGGAATGGGCGGG
66 AAGAGCCAAATTTTGATGCCAG-GGTGGGTCCGTTTATTCCTAGGCCGATTATAGAATGGGCGAG
* * *
18522453 TCATCCTCGGGTTACGGATGTCTCGGGTTCTGAATTTTCGACGGGCAGTGCCTTTGATGCTACAT
130 TCATCCTCGGGTTACGGATGTCTCGGGTTCTAAATTTTCGACAGGCAGTGCCTCTGATGCTACAT
* * *
18522518 CGCTGGTGTATGAGGTTAGCTCGTGTTCTAACATAATTAATACGGATTCACAGTATGTTCCTGAG
195 CACCGGTGTATGAGGTTAGCTCGTGTTCTAACACAATTAATACGGATTCACAGTATGTTCCTGAG
* * *
18522583 CCGGTGGTTAATGATGGTAATGGTGCGTGGTATCCTGACTTGGGTGTAACTCACCATGTATGCAA
260 CCGGTGGGTAATGATGGTAATGGTGCGTGGTATCCTGACTCGGGTGTAACCCACCATGTATGCAA
** * *
18522648 GGAGGCAACCGGGCTAAACACGTCCAC-TCTATATCCAAGTAAGGCATCGTTTTTGATGGGTGAT
325 ACAGGCAACCGAGCTAAACACGTCCACTTC-ATATCCAAGTAAGGCATCGCTTTTGATGGGTGAT
* *
18522712 GGTACATGTGCTAGAATTATAGGTGTTGGTGTATCTACGTTAACTACGAAGA
389 GGTACATGTGCTAGAATTATAGGTGTTGGTGCATCTACATTAACTACGAAGA
18522764 G
1 G
18522765 TAGAGTCTTA
Statistics
Matches: 395, Mismatches: 44, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
439 3 0.01
440 392 0.99
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (440 bp):
GGCGCAAGGTCGTGTGGAATATGCTCATCATGGGTGGTCAACCAAACCTCGTGCTCGAGTGTTCC
AAGAGCCAAATTTTGATGCCAGGGTGGGTCCGTTTATTCCTAGGCCGATTATAGAATGGGCGAGT
CATCCTCGGGTTACGGATGTCTCGGGTTCTAAATTTTCGACAGGCAGTGCCTCTGATGCTACATC
ACCGGTGTATGAGGTTAGCTCGTGTTCTAACACAATTAATACGGATTCACAGTATGTTCCTGAGC
CGGTGGGTAATGATGGTAATGGTGCGTGGTATCCTGACTCGGGTGTAACCCACCATGTATGCAAA
CAGGCAACCGAGCTAAACACGTCCACTTCATATCCAAGTAAGGCATCGCTTTTGATGGGTGATGG
TACATGTGCTAGAATTATAGGTGTTGGTGCATCTACATTAACTACGAAGA
Found at i:18528156 original size:16 final size:17
Alignment explanation
Indices: 18528135--18528169 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18528125 ATAATTTTTT
*
18528135 TTATAAATTTTAT-ATA
1 TTATAAACTTTATAATA
18528151 TTATAAACTTTATAATA
1 TTATAAACTTTATAATA
18528168 TT
1 TT
18528170 TTAGACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAAACTTTATAATA
Found at i:18537710 original size:15 final size:15
Alignment explanation
Indices: 18537690--18537721 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
18537680 TAACGATTGA
18537690 AAGAAAAATCAAGTT
1 AAGAAAAATCAAGTT
18537705 AAGAAAAATCAAGTT
1 AAGAAAAATCAAGTT
18537720 AA
1 AA
18537722 TAGAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (15 bp):
AAGAAAAATCAAGTT
Found at i:18538014 original size:18 final size:19
Alignment explanation
Indices: 18537983--18538032 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
18537973 AAAAATATAA
*
18537983 ATTTTAAATTTTTTATAAA-T
1 ATTTTAAA--TTTTAAAAATT
*
18538003 ATTTTGAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
18538022 ATTTTAAATTT
1 ATTTTAAATTT
18538033 ACTGGCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:18538755 original size:361 final size:362
Alignment explanation
Indices: 18538288--18539010 Score: 1146
Period size: 361 Copynumber: 2.0 Consensus size: 362
18538278 ATTTTTTCAC
*
18538288 AAATCGTGTGTTTGTTCACCCCTAATAATAACCACGAGTTGAACCAAGTATACTATTCAACCTAA
1 AAATCGTGTGTTTGCTCACCCCTAATAATAACCACGAGTTGAACCAAGTATACTATTCAACCTAA
* *
18538353 TTAAATCAAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTTAAAATTTTAA
66 TTAAATCAAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTAAAAATTCTAA
*
18538418 TTTAGACTTTAATACTCAAAAATACCGAAATTTTTTTAAATTTATCGAATTAGGCCGATTTTTGG
131 TTTAGACTTTAATACCCAAAAATACCGAAATTTTTTTAAATTTATCGAATTAGGCCGATTTTTGG
** * * * *
18538483 AATAATTACT-GGAATTGGTTGATTTAAGGAAAATACTTCCAACTGAAAACGTTTTCAAGTGATA
196 AATAATTA-TAGGAATAAGCTGATTTAAGAAAAACACTTCCAACTGAAAACATTTTCAAGTGATA
* * * * ** *
18538547 TGCAGAAAAACGCTTTCAGCTAGAAGCACTTTTCGCGTGTC-ACTAGTAAAACGTTTCCAGTTGG
260 AGCAGAAAAACGCTTTCAGCTAGAAGCACTTTCCGCATGTCAAC-AGTAAAACGTGTCCAACTAG
*
18538611 AAGCATTTTTAGGTAATCGCATGTAAATGCTTCCAACTG
324 AAGCATTTTTAGGTAATCGCATGTAAACGCTTCCAACTG
* * * *
18538650 AAATCGTGT-TTTGCTCACCCCTAATAATAGCCATGAGTTGAACCAAGTATACTATTTAGCCTAA
1 AAATCGTGTGTTTGCTCACCCCTAATAATAACCACGAGTTGAACCAAGTATACTATTCAACCTAA
* *
18538714 TTAAATCGAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTGTTAAAATTTAAAAATTCTAA
66 TTAAATCAAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTAAAAATTCTAA
18538779 TTTAGACTTTAATACCCAAAAATACCGAAATTTTTTTAAATTTATCGAATTAGGCCGATTTTTGG
131 TTTAGACTTTAATACCCAAAAATACCGAAATTTTTTTAAATTTATCGAATTAGGCCGATTTTTGG
*
18538844 AATAATTATAGGAATAAGCTGATTTAAGAAAAACACTTCCAACTGAAAATATTTTCAAGTGATAA
196 AATAATTATAGGAATAAGCTGATTTAAGAAAAACACTTCCAACTGAAAACATTTTCAAGTGATAA
*
18538909 GCAGAAAAACGCTTTCAGCTGGAAGCACTTTCCGCATGTCAACAGTAAAACGTGTCCAACTAGAA
261 GCAGAAAAACGCTTTCAGCTAGAAGCACTTTCCGCATGTCAACAGTAAAACGTGTCCAACTAGAA
* * *
18538974 GCATTTTTAGGTAGTTGCATGTAAACGCTTCCTACTG
326 GCATTTTTAGGTAATCGCATGTAAACGCTTCCAACTG
18539011 GAAGCGTTTT
Statistics
Matches: 330, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
360 1 0.00
361 318 0.96
362 11 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (362 bp):
AAATCGTGTGTTTGCTCACCCCTAATAATAACCACGAGTTGAACCAAGTATACTATTCAACCTAA
TTAAATCAAGTTATTTTATTAAAATAGGTTGTCCTTATACTTTTATTAAAATTTAAAAATTCTAA
TTTAGACTTTAATACCCAAAAATACCGAAATTTTTTTAAATTTATCGAATTAGGCCGATTTTTGG
AATAATTATAGGAATAAGCTGATTTAAGAAAAACACTTCCAACTGAAAACATTTTCAAGTGATAA
GCAGAAAAACGCTTTCAGCTAGAAGCACTTTCCGCATGTCAACAGTAAAACGTGTCCAACTAGAA
GCATTTTTAGGTAATCGCATGTAAACGCTTCCAACTG
Found at i:18540494 original size:46 final size:44
Alignment explanation
Indices: 18540444--18540550 Score: 108
Period size: 46 Copynumber: 2.3 Consensus size: 44
18540434 GGACTCAAGA
* *
18540444 ATGTGTTGAGGTTCCTAGTTACTGCAT-ATGTTGCAAATTGATGAAT
1 ATGTGTT-AGGTTCC-AGCTACTGCATGA-GTTGCAAACTGATGAAT
* * *
18540490 ATGTGTATAGGTTCACAGCTCCTGCATGAGTTGCAGACTGGTGAAT
1 ATGTGT-TAGGTTC-CAGCTACTGCATGAGTTGCAAACTGATGAAT
18540536 ATGTGTTTAGGTTCC
1 ATGTG-TTAGGTTCC
18540551 CAATTTTTGC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
45 1 0.02
46 47 0.90
47 4 0.08
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (44 bp):
ATGTGTTAGGTTCCAGCTACTGCATGAGTTGCAAACTGATGAAT
Found at i:18540562 original size:46 final size:46
Alignment explanation
Indices: 18540465--18540586 Score: 136
Period size: 46 Copynumber: 2.7 Consensus size: 46
18540455 TTCCTAGTTA
* * * * *
18540465 CTGCATATGTTGCAAATTGATGAATATGTGTATAGGTTCACAGCTC
1 CTGCATAAGTTGCAGACTGGTGAATATGTGTATAGGTTCACAACTC
* * * * *
18540511 CTGCATGAGTTGCAGACTGGTGAATATGTGTTTAGGTTCCCAATTT
1 CTGCATAAGTTGCAGACTGGTGAATATGTGTATAGGTTCACAACTC
* *
18540557 TTGCATAAGTTGTAGACTGGTGAATATGTG
1 CTGCATAAGTTGCAGACTGGTGAATATGTG
18540587 GATGATAAGC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (46 bp):
CTGCATAAGTTGCAGACTGGTGAATATGTGTATAGGTTCACAACTC
Found at i:18542219 original size:25 final size:25
Alignment explanation
Indices: 18542188--18542239 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
18542178 AGTTTGACTC
* *
18542188 AAACAAATAAACAGAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAACTGA
18542213 AAACAAATAAACAAAGTTTAACTGA
1 AAACAAATAAACAAAGTTTAACTGA
18542238 AA
1 AA
18542240 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (25 bp):
AAACAAATAAACAAAGTTTAACTGA
Found at i:18543911 original size:29 final size:31
Alignment explanation
Indices: 18543869--18543941 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
18543859 ATAATCTATA
*
18543869 TTTTTATAATTTTTAAAAAATT-AAAT-TAAT
1 TTTTTATTA-TTTTAAAAAATTAAAATATAAT
* *
18543899 TTTTTATTATTTTAAGAGATTAAAATATAAT
1 TTTTTATTATTTTAAAAAATTAAAATATAAT
*
18543930 TTTATTTTTATT
1 TTT-TTATTATT
18543942 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.28
30 12 0.33
31 7 0.19
32 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTTATTATTTTAAAAAATTAAAATATAAT
Found at i:18550565 original size:107 final size:107
Alignment explanation
Indices: 18550379--18550595 Score: 425
Period size: 107 Copynumber: 2.0 Consensus size: 107
18550369 ACATGCTTGA
18550379 TATTAAACCAAGACAATACTAGCAAAGTAGACATGTCAAATCTAGTTCAAAACAACCAAATTAGG
1 TATTAAACCAAGACAATACTAGCAAAGTAGACATGTCAAATCTAGTTCAAAACAACCAAATTAGG
18550444 GTTCATAAAAAATTTAAATCAAAATATACATACCTAAGTTGT
66 GTTCATAAAAAATTTAAATCAAAATATACATACCTAAGTTGT
*
18550486 TATTAAACCAAGACAATACTAGCAAAGTAGACATGTCAAATCTAGTTCAAAACGACCAAATTAGG
1 TATTAAACCAAGACAATACTAGCAAAGTAGACATGTCAAATCTAGTTCAAAACAACCAAATTAGG
18550551 GTTCATAAAAAATTTAAATCAAAATATACATACCTAAGTTGT
66 GTTCATAAAAAATTTAAATCAAAATATACATACCTAAGTTGT
18550593 TAT
1 TAT
18550596 AGTCTGCTTT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 109 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (107 bp):
TATTAAACCAAGACAATACTAGCAAAGTAGACATGTCAAATCTAGTTCAAAACAACCAAATTAGG
GTTCATAAAAAATTTAAATCAAAATATACATACCTAAGTTGT
Found at i:18551161 original size:16 final size:16
Alignment explanation
Indices: 18551140--18551171 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18551130 TCAAGCAATC
*
18551140 TAATTAACCTAAAAAT
1 TAATTAAACTAAAAAT
18551156 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
18551172 CAATCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATTAAACTAAAAAT
Found at i:18554336 original size:30 final size:30
Alignment explanation
Indices: 18554300--18554388 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
18554290 AATTATTAAG
*
18554300 GACTAAATTGGAATTTTTGAAAAAATTAGA
1 GACTAAATTGGAATTTTAGAAAAAATTAGA
* ** *
18554330 GACTAAATTATG-ATTTTAGTGAAACTTAGA
1 GACTAAATT-GGAATTTTAGAAAAAATTAGA
* * *
18554360 GACCAAATTGGAATTTTAGAGAAATTTAG
1 GACTAAATTGGAATTTTAGAAAAAATTAG
18554389 GGATTAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 46 0.96
31 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (30 bp):
GACTAAATTGGAATTTTAGAAAAAATTAGA
Found at i:18562997 original size:43 final size:43
Alignment explanation
Indices: 18562941--18563025 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
18562931 TCCCTATGAT
18562941 AAGACGTATCAGCAAAGGAAGAAGTTCCTTCATGATGCTAAGA
1 AAGACGTATCAGCAAAGGAAGAAGTTCCTTCATGATGCTAAGA
18562984 AAGACGTATCAGCAAAGGAAGAAGTTCCTTCATGATGCTAAG
1 AAGACGTATCAGCAAAGGAAGAAGTTCCTTCATGATGCTAAG
18563026 TATACTTCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (43 bp):
AAGACGTATCAGCAAAGGAAGAAGTTCCTTCATGATGCTAAGA
Found at i:18563613 original size:28 final size:28
Alignment explanation
Indices: 18563573--18563657 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
18563563 AAACACGGAG
18563573 TAAGACACAAGATTGCTACAACTTACCA
1 TAAGACACAAGATTGCTACAACTTACCA
* *
18563601 TAAGACACAAGATTGCTATAGCTTACCA
1 TAAGACACAAGATTGCTACAACTTACCA
* ** * *
18563629 TACGATGCAAAATTGTTACAACTTACCA
1 TAAGACACAAGATTGCTACAACTTACCA
18563657 T
1 T
18563658 CCACAGACGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (28 bp):
TAAGACACAAGATTGCTACAACTTACCA
Found at i:18563851 original size:17 final size:17
Alignment explanation
Indices: 18563811--18563843 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18563801 CTATAGATTG
18563811 GTATTTGGAAAAGCCTA
1 GTATTTGGAAAAGCCTA
*
18563828 GTATTTGGGAAAGCCT
1 GTATTTGGAAAAGCCT
18563844 GTCATTTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (17 bp):
GTATTTGGAAAAGCCTA
Found at i:18565988 original size:18 final size:18
Alignment explanation
Indices: 18565965--18566005 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
18565955 TGGTCTTAAT
18565965 GAAGAAGAAGATCCTGAA
1 GAAGAAGAAGATCCTGAA
*
18565983 GAAGAAGAAGATCCTGAG
1 GAAGAAGAAGATCCTGAA
18566001 GAAGA
1 GAAGA
18566006 TACTGTGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.32, T:0.10
Consensus pattern (18 bp):
GAAGAAGAAGATCCTGAA
Found at i:18570979 original size:19 final size:19
Alignment explanation
Indices: 18570955--18571011 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
18570945 GAAGGAATCT
*
18570955 GCAATACTGGCTTGGAAGA
1 GCAATACTGGCTCGGAAGA
*
18570974 GCAATACTGGCTCGTAAGA
1 GCAATACTGGCTCGGAAGA
* * *
18570993 GCGATACTAGCTCGTAAGA
1 GCAATACTGGCTCGGAAGA
18571012 CCAGTATACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (19 bp):
GCAATACTGGCTCGGAAGA
Found at i:18577168 original size:36 final size:36
Alignment explanation
Indices: 18577121--18577221 Score: 184
Period size: 36 Copynumber: 2.8 Consensus size: 36
18577111 CGATATTCAA
18577121 TTTACTCCCTGTTAACACAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTAACACAAAGGTCATGATGCTCAT
*
18577157 TTTACTCCCTGTTGACACAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTAACACAAAGGTCATGATGCTCAT
*
18577193 TTTACTCCCTGTTAACCCAAAGGTCATGA
1 TTTACTCCCTGTTAACACAAAGGTCATGA
18577222 CTGTTACCAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (36 bp):
TTTACTCCCTGTTAACACAAAGGTCATGATGCTCAT
Found at i:18579296 original size:19 final size:19
Alignment explanation
Indices: 18579282--18579386 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
18579272 ATTGGCTAAG
* *
18579282 AAGAGCAATAATGGCTTGA
1 AAGAGCAATACTGGCTCGA
*
18579301 AAGAGCAATACTAGCTCGA
1 AAGAGCAATACTGGCTCGA
18579320 AAGAGCAATACTGGCTCGA
1 AAGAGCAATACTGGCTCGA
* *
18579339 AAGAACAATACTGGCTCGT
1 AAGAGCAATACTGGCTCGA
* *
18579358 AAGAGCAATAATGGCTCGT
1 AAGAGCAATACTGGCTCGA
*
18579377 AAGAGAAATA
1 AAGAGCAATA
18579387 TACTGTACTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 77 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGAGCAATACTGGCTCGA
Found at i:18598264 original size:4 final size:4
Alignment explanation
Indices: 18598257--18598284 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
18598247 TGCTTATTAT
18598257 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
18598285 ATTGAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:18599788 original size:39 final size:40
Alignment explanation
Indices: 18599719--18599801 Score: 150
Period size: 39 Copynumber: 2.1 Consensus size: 40
18599709 GAATGAGACC
18599719 AAAATCTTTAAATAAAAAAAATATAATAGCTTAATTTCTCA
1 AAAATCTTTAAAT-AAAAAAATATAATAGCTTAATTTCTCA
18599760 AAAATCTTTAAAT-AAAAAATATAATAGCTTAATTTCTCA
1 AAAATCTTTAAATAAAAAAATATAATAGCTTAATTTCTCA
18599799 AAA
1 AAA
18599802 TTGAAGTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 29 0.69
41 13 0.31
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (40 bp):
AAAATCTTTAAATAAAAAAATATAATAGCTTAATTTCTCA
Found at i:18600577 original size:16 final size:16
Alignment explanation
Indices: 18600558--18600600 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
18600548 TTTTTATTAA
*
18600558 ATTAAATTATAATCAT
1 ATTATATTATAATCAT
*
18600574 ATTATATTCTAATCAT
1 ATTATATTATAATCAT
18600590 A-TATATTATAA
1 ATTATATTATAA
18600601 GGTTTAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTATAATCAT
Found at i:18602092 original size:69 final size:70
Alignment explanation
Indices: 18601981--18602146 Score: 196
Period size: 69 Copynumber: 2.4 Consensus size: 70
18601971 TAATTTATTA
* * * * * ** *
18601981 ACTATGTTCATTAAAAAGTTGATTTTAGTTCCATGTTGACTAGTGAATACTCTTATAGT-TCACT
1 ACTATTTTCATTAAAAAGTTAATTTTAATTCCACGTTAACTAGAAAATACTCTCATA-TCTCACT
18602045 T-TTTC
65 TCTTTC
18602050 ACTATTTTCATTAAAAAGTTAATTTTAA-TCTCACGTTAACTAGAAAATACTCTCATATCTCACT
1 ACTATTTTCATTAAAAAGTTAATTTTAATTC-CACGTTAACTAGAAAATACTCTCATATCTCACT
18602114 TCTTTC
65 TCTTTC
* *
18602120 ACTATTTTCACTAAAAA-ATAATTTTAA
1 ACTATTTTCATTAAAAAGTTAATTTTAA
18602147 ACCCTTAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 3 0.04
69 61 0.73
70 20 0.24
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (70 bp):
ACTATTTTCATTAAAAAGTTAATTTTAATTCCACGTTAACTAGAAAATACTCTCATATCTCACTT
CTTTC
Found at i:18602231 original size:349 final size:348
Alignment explanation
Indices: 18601593--18602234 Score: 880
Period size: 349 Copynumber: 1.8 Consensus size: 348
18601583 GGAACACCCC
* * * * * *
18601593 ATATCTCACATTTACCTTATAAATAAGTGGTTATTTCTTCACTATTTTTATTAAAAAATTAATTT
1 ATATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTATGTTCATTAAAAAATTAATTT
*
18601658 TAACTCCAGATTAACTATAGAACACTTTTATAGCTCACTTTCTCACTTTTTCATTAAAAAGTTAA
66 TAACTCCAGATTAACTATAGAACACTCTTATAGCTCACTTTCTCACTTTTTCATTAAAAAGTTAA
* * * ** * *
18601723 TTTTAATCCCCATTAACTAGAAAATACTCACATGGCCTATTTCTTTTTCTATTTTCATTAAAAAT
131 TTTTAATCCACATTAACTAGAAAATACTCACATAGCCTACTTCTTTCACTATTTTCACTAAAAAA
* * *
18601788 TAATTTTTAATCCCTTAAAATGTTAATTTTAAAATTAATTTTAATCCTATACTAGCTAGAGATCA
196 TAATTTTTAAACCCTTAAAAAGTTAATTTTAAAATTAATTTTAATCCTATACTAGCTAGAGAACA
18601853 CTCCCATGCTCACACTTATCCTATAAATAAGTGGCAATTTCTTGAATACTCTCAAGTTAATTTTA
261 CTCCCATGCTCACACTTATCCTATAAATAAGTGGCAATTTCTTGAATACTCTCAAGTTAATTTTA
18601918 ATCCCACTTTAACTAGAGAACAT
326 ATCCCACTTTAACTAGAGAACAT
* * * *
18601941 ATATCTCACATTTACTTTATAAGTAAGTGATAATTTATTAACTATGTTCATTAAAAAGTTGATTT
1 ATATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTATGTTCATTAAAAAATTAATTT
** * * * *
18602006 TAGTTCCATG-TTGACTAGT-GAATACTCTTATAGTTCACTTTTTCACTATTTTCATTAAAAAGT
66 TAACTCCA-GATTAACTA-TAGAACACTCTTATAGCTCACTTTCTCACT-TTTTCATTAAAAAGT
* * *
18602069 TAATTTTAATCTCACGTTAACTAGAAAATACTCTCATA-TCTCACTTCTTTCACTATTTTCACTA
128 TAATTTTAATC-CACATTAACTAGAAAATACTCACATAGCCT-ACTTCTTTCACTATTTTCACTA
** * *
18602133 AAAAATAA-TTTTAAACCCTTAAAAAGTTAATTTTAAAATTAATTTTAATTTTATATTAGTTAGA
191 AAAAATAATTTTTAAACCCTTAAAAAGTTAATTTTAAAATTAATTTTAATCCTATACTAGCTAGA
*
18602197 GAACACTCTCATGCTCACACTTA-CCTTATAAATAAGTG
256 GAACACTCCCATGCTCACACTTATCC-TATAAATAAGTG
18602235 TTTTTTTCTT
Statistics
Matches: 253, Mismatches: 35, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
348 93 0.37
349 113 0.45
350 47 0.19
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (348 bp):
ATATCTCACATTTACCTTATAAATAAGTGATAATTTATTAACTATGTTCATTAAAAAATTAATTT
TAACTCCAGATTAACTATAGAACACTCTTATAGCTCACTTTCTCACTTTTTCATTAAAAAGTTAA
TTTTAATCCACATTAACTAGAAAATACTCACATAGCCTACTTCTTTCACTATTTTCACTAAAAAA
TAATTTTTAAACCCTTAAAAAGTTAATTTTAAAATTAATTTTAATCCTATACTAGCTAGAGAACA
CTCCCATGCTCACACTTATCCTATAAATAAGTGGCAATTTCTTGAATACTCTCAAGTTAATTTTA
ATCCCACTTTAACTAGAGAACAT
Found at i:18607162 original size:16 final size:17
Alignment explanation
Indices: 18607123--18607163 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
18607113 ATAGTAAAAA
18607123 TATAATTTTATCATTTT
1 TATAATTTTATCATTTT
*
18607140 AAT-ATTTTAT-ATTTT
1 TATAATTTTATCATTTT
18607155 TATAATTTT
1 TATAATTTT
18607164 TAAAGGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TATAATTTTATCATTTT
Found at i:18611515 original size:21 final size:21
Alignment explanation
Indices: 18611489--18611537 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
18611479 TGTCATCGAA
18611489 GCCTCTATCTCCCAAGTGGCT
1 GCCTCTATCTCCCAAGTGGCT
18611510 GCCTCTATCTCCCAAGTGGCT
1 GCCTCTATCTCCCAAGTGGCT
*
18611531 TCCTCTA
1 GCCTCTA
18611538 ACCCGTGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.39, G:0.16, T:0.31
Consensus pattern (21 bp):
GCCTCTATCTCCCAAGTGGCT
Found at i:18633011 original size:18 final size:18
Alignment explanation
Indices: 18632988--18633036 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
18632978 TTGATATAAA
*
18632988 TAAAAAAATAAAATATTT
1 TAAAAAAATAAAATAGTT
* *
18633006 TAAAAATATAAATTAGTT
1 TAAAAAAATAAAATAGTT
*
18633024 TAAAAAAGTAAAA
1 TAAAAAAATAAAA
18633037 AAATTCAGCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
TAAAAAAATAAAATAGTT
Found at i:18634527 original size:188 final size:187
Alignment explanation
Indices: 18634183--18634541 Score: 501
Period size: 188 Copynumber: 1.9 Consensus size: 187
18634173 TGCAATCAAG
* * * *
18634183 TCACCTATTGTCAATTATGCAAACAACTATAATCCCAAATTAATTTATAATACTTTTGATTAAAT
1 TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAATACCTTTCATTAAAT
*
18634248 TACCCATATTTCATTGTCATCATCCAGTATGCCTATATCAAACATATATTGACACTTCAACGCAT
66 TACCCATATTTCATTGTCATCATCCAGTATGCCTATATCAAACATATA-TGACACTTCAACACAT
18634313 GCATGATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
130 GCATGATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
* * *
18634371 TCACCTTTTGCCAAGTATGCAAACAACTATAATCCCAGATTAATTTATAA-CCCTTTCATTAAAT
1 TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAATACCTTTCATTAAAT
* * * *
18634435 TACCTATATTTCATTGTCATCAT-CTGCTTTGTCTGTATATCAAACATATA-GACACTTCAAGCA
66 TACCCATATTTCATTGTCATCATCCAG-TATG-C-CTATATCAAACATATATGACACTTCAA-CA
* * *
18634498 CATGCAT-ATGTAGCAAATAGCCCAATTTTATAATACTGCACTAC
127 CATGCATGAT-TAGAAAACAGCCAAATTTTATAATACTGCACTAC
18634542 TAAAAAATGT
Statistics
Matches: 151, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
186 2 0.01
187 48 0.32
188 86 0.57
189 15 0.10
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (187 bp):
TCACCTATTGCCAAGTATGCAAACAACTATAATCCCAAATTAATTTATAATACCTTTCATTAAAT
TACCCATATTTCATTGTCATCATCCAGTATGCCTATATCAAACATATATGACACTTCAACACATG
CATGATTAGAAAACAGCCAAATTTTATAATACTGCACTACCAAACCAGCCAATCATT
Found at i:18637169 original size:1 final size:1
Alignment explanation
Indices: 18637165--18637193 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18637155 CTGCATTTTT
18637165 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
18637194 TGGTTTGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:18639344 original size:146 final size:145
Alignment explanation
Indices: 18639052--18639331 Score: 323
Period size: 146 Copynumber: 1.9 Consensus size: 145
18639042 CTCCGAGATG
* *
18639052 ATTGTGATGTTGTTATTGTTGTTATATTTTTTGAATATGTTCTACGCATTATATAAGAAAGTTAT
1 ATTGTGATGTTGTTA-T-TTGTTATATTTGTTGAATATGTTCTACGCATGATATAAGAAAGTTAT
* * *
18639117 GTTATTTTGTATGGTTTAGGTTGTAATAAATTAGTTTTAATGTTGTTGGAATCGTTGTTAGTAAA
64 GTTACTGTGTATGGTTTA-GTTGTAATAAATTAATTTT-ATGTTGTTGGAATCGTTGTTAGTAAA
18639182 AATTATTGAAATTGTTAGA
127 AATTATTGAAATTGTTAGA
* * * * *
18639201 ATTGTGATGTTGTTA-TTGTTATATTTGTTGAATATGTTCTATGTATGGTATAAGGAAGTTGTGT
1 ATTGTGATGTTGTTATTTGTTATATTTGTTGAATATGTTCTACGCATGATATAAGAAAGTTATG-
* * * * * *
18639265 TTACTGTGTATGGTTGTCA-TTGTAGTAAGTTAAATTTT-TTTTTTTGGAATCGTTGTTATTAAT
65 TTACTGTGTATGGTT-T-AGTTGTAATAAATT-AATTTTATGTTGTTGGAATCGTTGTTAGTAAA
18639328 AATT
127 AATT
18639332 TTTTAATTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
146 66 0.59
147 23 0.21
148 6 0.05
149 16 0.14
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.50
Consensus pattern (145 bp):
ATTGTGATGTTGTTATTTGTTATATTTGTTGAATATGTTCTACGCATGATATAAGAAAGTTATGT
TACTGTGTATGGTTTAGTTGTAATAAATTAATTTTATGTTGTTGGAATCGTTGTTAGTAAAAATT
ATTGAAATTGTTAGA
Found at i:18647174 original size:21 final size:22
Alignment explanation
Indices: 18647141--18647181 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18647131 ATCTCGTGCT
* *
18647141 CAGGAGTCGATGTTACGACACA
1 CAGGAGTCCATGTCACGACACA
18647163 CAGG-GTCCATGTCACGACA
1 CAGGAGTCCATGTCACGACA
18647182 TGGCCGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (22 bp):
CAGGAGTCCATGTCACGACACA
Found at i:18653586 original size:26 final size:26
Alignment explanation
Indices: 18653557--18653682 Score: 148
Period size: 26 Copynumber: 4.8 Consensus size: 26
18653547 ATAAGAGTGT
*
18653557 AACTCTGTCTGGTCTCGAATGAACTA
1 AACTCTGTCTGGGCTCGAATGAACTA
*
18653583 AACTCTGTCTGGGCTCGAA-CAAGCTA
1 AACTCTGTCTGGGCTCGAATGAA-CTA
* * *
18653609 AACTCTATCTGAGCTCG-ATGAGCTA
1 AACTCTGTCTGGGCTCGAATGAACTA
* * *
18653634 AACTCTGTCTGGGCTTGAACGAGCTA
1 AACTCTGTCTGGGCTCGAATGAACTA
18653660 AACTCTGTTCTGGGCTCGAATGA
1 AACTCTG-TCTGGGCTCGAATGA
18653683 GATGTATTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
25 20 0.24
26 51 0.61
27 13 0.15
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (26 bp):
AACTCTGTCTGGGCTCGAATGAACTA
Found at i:18653646 original size:51 final size:51
Alignment explanation
Indices: 18653557--18653683 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 51
18653547 ATAAGAGTGT
* *
18653557 AACTCTGTCTGGTCTCGAATGAACTAAACTCTGTCTGGGCTCGAACAAGCTA
1 AACTCTATCTGG-CTCGAATGAGCTAAACTCTGTCTGGGCTCGAACAAGCTA
* *
18653609 AACTCTATCTGAGCTCG-ATGAGCTAAACTCTGTCTGGGCTTGAACGAGCTA
1 AACTCTATCTG-GCTCGAATGAGCTAAACTCTGTCTGGGCTCGAACAAGCTA
*
18653660 AACTCTGTTCTGGGCTCGAATGAG
1 AACTCT-ATCT-GGCTCGAATGAG
18653684 ATGTATTTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
51 37 0.56
52 22 0.33
53 7 0.11
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (51 bp):
AACTCTATCTGGCTCGAATGAGCTAAACTCTGTCTGGGCTCGAACAAGCTA
Found at i:18664268 original size:15 final size:17
Alignment explanation
Indices: 18664248--18664279 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
18664238 AAATTCCTAT
18664248 ACTTTT-CTC-ACTCTG
1 ACTTTTCCTCGACTCTG
18664263 ACTTTTCCTCGACTCTG
1 ACTTTTCCTCGACTCTG
18664280 TATCCTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.12, C:0.34, G:0.09, T:0.44
Consensus pattern (17 bp):
ACTTTTCCTCGACTCTG
Found at i:18664575 original size:15 final size:15
Alignment explanation
Indices: 18664555--18664584 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18664545 CACTTTGAAA
18664555 TAATCTAAGTTTGGC
1 TAATCTAAGTTTGGC
18664570 TAATCTAAGTTTGGC
1 TAATCTAAGTTTGGC
18664585 ATCAGACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TAATCTAAGTTTGGC
Found at i:18669998 original size:24 final size:24
Alignment explanation
Indices: 18669936--18669998 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 24
18669926 CAGACAATAT
** *
18669936 TTAGCTCACACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAAAATGG
18669960 TTAGCT-TTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAAAATGG
18669983 TTAGCTCTTACGAGCC
1 TTAGCTCTTACGAGCC
18669999 TAAATAGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAAATGG
Found at i:18674398 original size:23 final size:24
Alignment explanation
Indices: 18674370--18674423 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
18674360 TTTAACTCAC
18674370 ACGAGCCCAGAATGGTTAGCT-TT
1 ACGAGCCCAGAATGGTTAGCTCTT
18674393 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
18674417 ACGAGCC
1 ACGAGCC
18674424 TAAATAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:18677917 original size:19 final size:20
Alignment explanation
Indices: 18677895--18677942 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
18677885 AAAATTCTAA
18677895 AAAATATATAAAATTTTT-T
1 AAAATATATAAAATTTTTCT
*
18677914 AAAAT-TTTAAAATTTTTCT
1 AAAATATATAAAATTTTTCT
18677933 AAAATA-ATAA
1 AAAATATATAA
18677943 TTTTGGGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATATATAAAATTTTTCT
Found at i:18679390 original size:6 final size:6
Alignment explanation
Indices: 18679375--18679436 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
18679365 CTTTAGCCTT
* * * *
18679375 TTTTTA TTTTTG TTTTAATA TTTGTA TTTGTA TTTTTA TTTTAA TTTTTA
1 TTTTTA TTTTTA TTTT--TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
18679425 TATTTTA ATTTT
1 T-TTTTA TTTTT
18679437 CCCTCTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 37 0.80
7 5 0.11
8 4 0.09
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:18679430 original size:14 final size:13
Alignment explanation
Indices: 18679381--18679436 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
18679371 CCTTTTTTTA
*
18679381 TTTTTGTTTTAAT
1 TTTTTATTTTAAT
*
18679394 ATTTGTATTTGT-A-
1 -TTTTTATTT-TAAT
18679407 TTTTTATTTTAAT
1 TTTTTATTTTAAT
18679420 TTTTATATTTTAAT
1 TTTT-TATTTTAAT
18679434 TTT
1 TTT
18679437 CCCTCTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
11 1 0.03
12 9 0.26
13 4 0.11
14 20 0.57
15 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:18679435 original size:26 final size:25
Alignment explanation
Indices: 18679376--18679436 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
18679366 TTTAGCCTTT
* *
18679376 TTTTATTTTTGTTTTAATATTTGTA
1 TTTTATTTTTATTTTAATATTTATA
*
18679401 TTTGTATTTTTATTTTAATTTTTATA
1 TTT-TATTTTTATTTTAATATTTATA
*
18679427 TTTTAATTTT
1 TTTTATTTTT
18679437 CCCTCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTTATTTTTATTTTAATATTTATA
Found at i:18684903 original size:8 final size:8
Alignment explanation
Indices: 18684879--18684912 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
18684869 TTTATCACTT
18684879 AAAAAATA
1 AAAAAATA
18684887 AAAATAATA
1 AAAA-AATA
*
18684896 AGAAAATA
1 AAAAAATA
18684904 AAAAAATA
1 AAAAAATA
18684912 A
1 A
18684913 TTCACACACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:18684903 original size:17 final size:16
Alignment explanation
Indices: 18684881--18684912 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
18684871 TATCACTTAA
18684881 AAAATAAAAATAATAAG
1 AAAATAAAAA-AATAAG
18684898 AAAATAAAAAAATAA
1 AAAATAAAAAAATAA
18684913 TTCACACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAAATAAG
Found at i:18685802 original size:5 final size:5
Alignment explanation
Indices: 18685792--18685864 Score: 73
Period size: 5 Copynumber: 14.4 Consensus size: 5
18685782 GTATTTTCAC
18685792 TTTAT TTTA- TTTAT TTTA- -TTAT TTTAT TTTAT TTTCAT TTTCAT TTCTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTT-AT TT-TAT
18685842 TTTCA- TTTAT TATTAT TTTAT TT
1 TTT-AT TTTAT T-TTAT TTTAT TT
18685865 ATTATTTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
3 3 0.05
4 5 0.08
5 31 0.52
6 20 0.33
7 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:18685808 original size:28 final size:26
Alignment explanation
Indices: 18685777--18685872 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 26
18685767 AATCTTTTTT
18685777 TTTTCGTATTTTCACTTTATTTTATTTA
1 TTTTC-TATTTTCA-TTTATTTTATTTA
*
18685805 TTTTATTATTTT-ATTTTATTTTCATTT-
1 TTTT-CTATTTTCA-TTTATTTT-ATTTA
18685832 TCATTTCTATTTTCATTTATTATTATTTTA
1 T--TTTCTATTTTCATTTATT-TTA-TTTA
18685862 TTTAT-TATTTT
1 TTT-TCTATTTT
18685873 TAATTTAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
27 10 0.18
28 35 0.62
29 10 0.18
30 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (26 bp):
TTTTCTATTTTCATTTATTTTATTTA
Found at i:18685815 original size:12 final size:11
Alignment explanation
Indices: 18685792--18685872 Score: 62
Period size: 12 Copynumber: 7.3 Consensus size: 11
18685782 GTATTTTCAC
18685792 TTTA-TTTTA-
1 TTTATTTTTAT
18685801 TTTATTTTATTAT
1 TTTA-TTT-TTAT
18685814 TTTA-TTTTAT
1 TTTATTTTTAT
*
18685824 TTTCATTTTCAT
1 TTT-ATTTTTAT
*
18685836 TTCTATTTTCA-
1 TT-TATTTTTAT
*
18685847 TTTATTATTAT
1 TTTATTTTTAT
18685858 TTTATTTATTAT
1 TTTATTT-TTAT
18685870 TTT
1 TTT
18685873 TAATTTAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.07
10 13 0.22
11 13 0.22
12 24 0.41
13 5 0.08
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:18685879 original size:18 final size:18
Alignment explanation
Indices: 18685796--18685907 Score: 52
Period size: 18 Copynumber: 6.1 Consensus size: 18
18685786 TTTCACTTTA
18685796 TTTT-ATTTATTTTATTA-
1 TTTTAATTTA-TTTATTAT
* *
18685813 TTTTATTTTATTT-TCAT
1 TTTTAATTTATTTATTAT
* *
18685830 TTTCATTTCTATTTTCATTTAT
1 TTTTAATT-TA-TTT-A-TTAT
* *
18685852 TATTATTTTATTTATTAT
1 TTTTAATTTATTTATTAT
*
18685870 TTTTAATTTAATTATT-T
1 TTTTAATTTATTTATTAT
* *
18685887 TGTGTAACTTAATTTATTAT
1 T-TTTAA-TTTATTTATTAT
18685907 T
1 T
18685908 CTTCGGGTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
16 2 0.03
17 16 0.22
18 27 0.37
19 12 0.16
20 5 0.07
21 2 0.03
22 9 0.12
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTAATTTATTTATTAT
Found at i:18685886 original size:15 final size:14
Alignment explanation
Indices: 18685841--18685887 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
18685831 TTCATTTCTA
*
18685841 TTTTCATTTATTAT
1 TTTTAATTTATTAT
*
18685855 TATTTTATTTATTAT
1 T-TTTAATTTATTAT
18685870 TTTTAATTTAATTAT
1 TTTTAATTT-ATTAT
18685885 TTT
1 TTT
18685888 GTGTAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTAATTTATTAT
Found at i:18687110 original size:25 final size:24
Alignment explanation
Indices: 18687066--18687113 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
18687056 GATCTCCTTT
18687066 TATTTTAGTTTATTTCTTTATTTC
1 TATTTTAGTTTATTTCTTTATTTC
18687090 TATTTTAAGTTTTATTT-TTTATTT
1 TATTTT-AG-TTTATTTCTTTATTT
18687114 TTGGTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 7 0.32
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (24 bp):
TATTTTAGTTTATTTCTTTATTTC
Found at i:18688136 original size:13 final size:13
Alignment explanation
Indices: 18688113--18688145 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
18688103 GATTGAATTG
18688113 GAAAGAAAAAAAGA
1 GAAA-AAAAAAAGA
18688127 GAAAAAAAAAAGA
1 GAAAAAAAAAAGA
18688140 -AAAAAA
1 GAAAAAA
18688146 TATTTGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 9 0.47
14 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAGA
Found at i:18688403 original size:19 final size:19
Alignment explanation
Indices: 18688379--18688417 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18688369 TTTCATTCTA
18688379 TAGTGGTGGATATTTGATT
1 TAGTGGTGGATATTTGATT
18688398 TAGTGGTGGATATTTGATT
1 TAGTGGTGGATATTTGATT
18688417 T
1 T
18688418 TCAAGCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.49
Consensus pattern (19 bp):
TAGTGGTGGATATTTGATT
Found at i:18696379 original size:80 final size:80
Alignment explanation
Indices: 18696234--18696547 Score: 378
Period size: 80 Copynumber: 3.9 Consensus size: 80
18696224 TAATCATTTT
* * * * * * * * *
18696234 CGTCAAATCATGGCACCCAATGCCCAACAGATAAATC-GCGATAAATGAGCTCAGCACTAGTTGG
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAA-CAGCAATGAATGAGCCCAGCTCTAGTTGG
18696298 ATTAACCAACGAAATC
65 ATTAACCAACGAAATC
* * * * * * *
18696314 TGTCAATTCATGGCATCCAGTGCCTAGCGGATAAACCGTAATGAATGAGTCCAACTCTAGCTGGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACAGCAATGAATGAGCCCAGCTCTAGTTGGA
18696379 TTAACCAACGAAATC
66 TTAACCAACGAAATC
* * * * ** *
18696394 CATCAATTCATGACACCCAGTGCTTAGTGGATAAAGTGCAATGAATGAGCCCAGTTCTAGTTGGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACAGCAATGAATGAGCCCAGCTCTAGTTGGA
*
18696459 TTAACCAATGAAATC
66 TTAACCAACGAAATC
* *
18696474 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACAACAATGAATGAGCCCAGCTCTAGTTCGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACAGCAATGAATGAGCCCAGCTCTAGTTGGA
18696539 TTAACCAAC
66 TTAACCAAC
18696548 AGTTTGCGCC
Statistics
Matches: 194, Mismatches: 39, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
79 1 0.01
80 193 0.99
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (80 bp):
CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACAGCAATGAATGAGCCCAGCTCTAGTTGGA
TTAACCAACGAAATC
Found at i:18699336 original size:24 final size:20
Alignment explanation
Indices: 18699307--18699358 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
18699297 ATATATCAAG
18699307 ATAAATATTAGATTAAAATTAAT
1 ATAAATATT--ATTAAAA-TAAT
*
18699330 ATTAAATCTTATTAAAATAAT
1 A-TAAATATTATTAAAATAAT
18699351 A-AAATATT
1 ATAAATATT
18699359 TATCTACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 6 0.23
21 5 0.19
22 7 0.27
23 1 0.04
24 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAATATTATTAAAATAAT
Found at i:18699435 original size:25 final size:25
Alignment explanation
Indices: 18699381--18699435 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
18699371 AAAATTTTAA
*
18699381 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
18699406 TTTAATTTTAA-ATTAATAAAAT-AC
1 TTTAA-TTTAATATTAAGAAAATCAC
18699430 TATTAA
1 T-TTAA
18699436 AATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:18699459 original size:37 final size:35
Alignment explanation
Indices: 18699389--18699482 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 35
18699379 AATTTAATTT
* *
18699389 AATATTAAGATAATCACTTTAATTTTAAATTAATA-AA
1 AATATTAAAATAAT-A--TTAAATTTAAATTAATATAA
*
18699426 ATACTATTAAAATAAGTATTAAATTTAATTTAATATTAA
1 A-A-TATTAAAATAA-TATTAAATTTAAATTAATA-TAA
18699465 AATATTAAAATAATATTA
1 AATATTAAAATAATATTA
18699483 TTTTTGGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
36 5 0.10
37 27 0.55
38 2 0.04
39 14 0.29
40 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (35 bp):
AATATTAAAATAATATTAAATTTAAATTAATATAA
Found at i:18699947 original size:9 final size:9
Alignment explanation
Indices: 18699933--18699974 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
18699923 ACACCCAAAA
18699933 ACCTTCATC
1 ACCTTCATC
18699942 ACCTTCATC
1 ACCTTCATC
18699951 ACCTTCATC
1 ACCTTCATC
**
18699960 TTCTTCATC
1 ACCTTCATC
*
18699969 ATCTTC
1 ACCTTC
18699975 TCCAAATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.19, C:0.40, G:0.00, T:0.40
Consensus pattern (9 bp):
ACCTTCATC
Found at i:18714231 original size:11 final size:11
Alignment explanation
Indices: 18714215--18714400 Score: 68
Period size: 11 Copynumber: 17.8 Consensus size: 11
18714205 CTTAATCACT
18714215 TTAATATTAAA
1 TTAATATTAAA
18714226 TTAATA-T-AA
1 TTAATATTAAA
*
18714235 -T-AT-TTAAT
1 TTAATATTAAA
18714243 TTAATATTAAA
1 TTAATATTAAA
*
18714254 -TATTATTAAA
1 TTAATATTAAA
*
18714264 ATAATA--AAA
1 TTAATATTAAA
**
18714273 -T-AT-TTATC
1 TTAATATTAAA
*
18714281 TGTAATATAAAAA
1 T-TAATAT-TAAA
18714294 TTAA-ATTAAA
1 TTAATATTAAA
18714304 TTTAATATTAAGA
1 -TTAATATTAA-A
**
18714317 -T-A-ATTACT
1 TTAATATTAAA
18714325 TTAATATTAAA
1 TTAATATTAAA
18714336 TTAATA--AAA
1 TTAATATTAAA
18714345 -TAATATTAAA
1 TTAATATTAAA
*
18714355 ATAAGTATTAAA
1 TTAA-TATTAAA
18714367 TTTAAT-TTAATA
1 -TTAATATTAA-A
18714379 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
18714392 ATAATATTA
1 TTAATATTA
18714401 TTTTTAGAAC
Statistics
Matches: 131, Mismatches: 16, Indels: 56
0.65 0.08 0.28
Matches are distributed among these distances:
7 5 0.04
8 9 0.07
9 14 0.11
10 21 0.16
11 47 0.36
12 22 0.17
13 9 0.07
14 4 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:18714246 original size:17 final size:16
Alignment explanation
Indices: 18714216--18714383 Score: 65
Period size: 17 Copynumber: 9.6 Consensus size: 16
18714206 TTAATCACTT
18714216 TAATATTAAATTAATA
1 TAATATTAAATTAATA
*
18714232 TAATATTTAATTTAATA
1 TAATA-TTAAATTAATA
*
18714249 TTAAATATTATTAAAATAATA
1 -T--A-A-TATTAAATTAATA
* **
18714270 AAATATTTATCTGTAATA
1 TAATA-TTAAAT-TAATA
* *
18714288 TAAAAATTAAATTAAATT
1 T-AATATTAAATT-AATA
18714306 TAATATTAAGA-TAATTA
1 TAATATTAA-ATTAA-TA
18714323 CTTTAATATTAAATTAATA
1 ---TAATATTAAATTAATA
*
18714342 -AA-A-TAATATTAAAA
1 TAATATTAA-ATTAATA
*
18714356 TAAGTATTAAATTTAATT
1 TAA-TATTAAA-TTAATA
18714374 TAATATTAAA
1 TAATATTAAA
18714384 CTATTAAAAT
Statistics
Matches: 113, Mismatches: 17, Indels: 43
0.65 0.10 0.25
Matches are distributed among these distances:
13 3 0.03
14 7 0.06
15 4 0.04
16 9 0.08
17 33 0.29
18 26 0.23
19 6 0.05
20 13 0.12
21 10 0.09
22 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:18714263 original size:38 final size:38
Alignment explanation
Indices: 18714219--18714336 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 38
18714209 ATCACTTTAA
18714219 TATTAAATTAATATAATATTTAATTTAATATTAAATAT
1 TATTAAATTAATATAATATTTAATTTAATATTAAATAT
* * *
18714257 TATTAAAATAATAAAATATTT-ATCTGTAATA-TAAAAAT
1 TATTAAATTAATATAATATTTAAT-T-TAATATTAAATAT
* *
18714295 TAAATTAAATTTAATATTAAGATAATTACTTTAATATTAAAT
1 T--ATTAAA-TTAATA-T-A-ATATTTAATTTAATATTAAAT
18714337 TAATAAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
37 2 0.03
38 27 0.44
39 5 0.08
40 6 0.10
41 5 0.08
43 6 0.10
44 10 0.16
45 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (38 bp):
TATTAAATTAATATAATATTTAATTTAATATTAAATAT
Found at i:18721147 original size:54 final size:54
Alignment explanation
Indices: 18721084--18721193 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
18721074 ATCAACCTTA
18721084 TGCCACTATCAACATTCCGAAAAGTGGGAATTGGTAACATGAAGTCCACTGCAG
1 TGCCACTATCAACATTCCGAAAAGTGGGAATTGGTAACATGAAGTCCACTGCAG
*
18721138 TGCCACTATCAACATTCCGAAAATTGGGAATTGGTAACATGAAGTCCACTGCAG
1 TGCCACTATCAACATTCCGAAAAGTGGGAATTGGTAACATGAAGTCCACTGCAG
18721192 TG
1 TG
18721194 ACATTGCAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (54 bp):
TGCCACTATCAACATTCCGAAAAGTGGGAATTGGTAACATGAAGTCCACTGCAG
Found at i:18726425 original size:12 final size:12
Alignment explanation
Indices: 18726408--18726482 Score: 75
Period size: 12 Copynumber: 6.2 Consensus size: 12
18726398 GGGTATTAAG
18726408 GAAGAGAAAGAA
1 GAAGAGAAAGAA
18726420 GAAGAGAAAGAA
1 GAAGAGAAAGAA
* *
18726432 GAAGAGAAGGAG
1 GAAGAGAAAGAA
*
18726444 GAGGA-AAAGGAA
1 GAAGAGAAA-GAA
18726456 GAAG-GAAAAGAA
1 GAAGAG-AAAGAA
18726468 TG-AGAGAAAGAA
1 -GAAGAGAAAGAA
18726480 GAA
1 GAA
18726483 ATTTTTATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.06
12 43 0.84
13 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.01
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:18741213 original size:24 final size:24
Alignment explanation
Indices: 18741180--18741278 Score: 135
Period size: 24 Copynumber: 4.1 Consensus size: 24
18741170 GTATACTGGT
*
18741180 TAACCATTCTGGGCTTGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* * *
18741204 TAACCGTTCTGGTCTCATAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
18741228 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* **
18741252 TAACCATTCTAGGCTCGTGTGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
18741276 TAA
1 TAA
18741279 AGTTGTTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:18749458 original size:59 final size:61
Alignment explanation
Indices: 18749381--18749497 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
18749371 ATCACTTTAA
* * * *
18749381 TATTAAATTAATATAATATTTA-T-CAAGATAAATAATAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTCCAAGATAAACAATAAATTAAATTTAATATTAAATCT
*
18749440 TATTAAAATAATAAAATATTTATCTCCAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTA-CTCCAAGATAAACAATAAATTAAATTTAATATTAA
18749498 TATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTCCAAGATAAACAATAAATTAAATTTAATATTAAATCT
Found at i:18749521 original size:5 final size:6
Alignment explanation
Indices: 18749476--18749565 Score: 55
Period size: 6 Copynumber: 14.8 Consensus size: 6
18749466 CAAGATAAAC
18749476 ATTAA- ATTAA- ATTTAAT ATTAAT A-TAAT CACTTTAAT ATTAA- ATTAAT
1 ATTAAT ATTAAT A-TTAAT ATTAAT ATTAAT -A--TTAAT ATTAAT ATTAAT
* * * *
18749524 AAAATACT ATTAAA ATTAAT ATTAAA ATTAAT -TTAAT ATTAA
1 --ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
18749566 ACTATTAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
5 20 0.30
6 37 0.55
7 1 0.01
8 5 0.07
9 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTAAT
Found at i:18749523 original size:20 final size:18
Alignment explanation
Indices: 18749476--18749574 Score: 69
Period size: 20 Copynumber: 5.3 Consensus size: 18
18749466 CAAGATAAAC
18749476 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
18749493 ATT-AATATAATCACTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
** *
18749513 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
18749532 ATTAAAATTAATA-TTAAA
1 ATT-AAATTAATATTTAAT
* *
18749550 ATTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
18749569 ATTAAA
1 ATTAAA
18749575 ATATTATTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 3 0.05
17 14 0.22
18 8 0.13
19 13 0.21
20 22 0.35
21 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:18749536 original size:25 final size:25
Alignment explanation
Indices: 18749488--18749565 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
18749478 TAAATTAAAT
*
18749488 TTAATATTAATATAATCACTTTAATA
1 TTAATATTAATAAAAT-ACTTTAATA
*
18749514 TTAA-ATTAATAAAATACTATTAAAA
1 TTAATATTAATAAAATACT-TTAATA
* *
18749539 TTAATATT-A-AAATTAATTTAATA
1 TTAATATTAATAAAATACTTTAATA
18749562 TTAA
1 TTAA
18749566 ACTATTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.20
24 9 0.20
25 20 0.44
26 7 0.16
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAATATTAATAAAATACTTTAATA
Done.