Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 87 of 335
Found at i:28669241 original size:15 final size:14
Alignment explanation
Indices: 28669205--28669237 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28669195 CTCTGAGGTA
28669205 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
28669219 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
28669233 TTTTC
1 TTTTC
28669238 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:28669363 original size:182 final size:177
Alignment explanation
Indices: 28669061--28669393 Score: 427
Period size: 182 Copynumber: 1.8 Consensus size: 177
28669051 TGTCTTTCAA
* * * * * * *
28669061 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCATTTCT
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
* * * *
28669126 GTTCTTCAATTTTTATGTTTCAAAAAAATCAACTTATATTGCGAGTGGTGAGTTGAGCCT-TGAC
66 GTTCTTCAA-TTTTATGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGA-
* *
28669190 TCACACTCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
129 TCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
*
28669239 AAAAAATCAACTCATATTACGAGAGGTGAGTTCAGCCTCAGGACACGCTGAGATATTTTCAATTT
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTCAACCTCA--ACACGCTGAGATATTTTCAATTT
* *
28669304 CTTTTTTTTTCAA-TTTATGTTTGTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
64 C--TGTTCTTCAATTTTATG-TT-TCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
*
28669368 CAGATCATACGCCGAGGTATTTTCAA
125 CAGATCACACGCCGAGGTATTTTCAA
28669394 TTGATTTTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
178 36 0.27
180 26 0.20
181 2 0.02
182 65 0.50
183 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (177 bp):
AAAAAATCAACTCATATTACGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
GTTCTTCAATTTTATGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGATC
ACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
Found at i:28669402 original size:91 final size:88
Alignment explanation
Indices: 28669040--28669630 Score: 359
Period size: 91 Copynumber: 6.5 Consensus size: 88
28669030 CGTTGAGGTA
* * * * *
28669040 TTTTAAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA-A-G
1 TTTTCAATTTATGT-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACA
* *
28669103 ACGCTGAGGTGTTTTCCATTTCTGT
64 ACGCTGAGGTATTTTCAATTTCTGT
* * * *
28669128 TCTTCAATTTTTATG-TTTCAAAAAAATCAACTTATATTGCGAGTGGTGAGTTGAGCCT-TGACT
1 TTTTCAA--TTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA--
* *
28669191 CACACTCTGAGGTATTTTCAAATTCTGT
62 CA-ACGCTGAGGTATTTTCAATTTCTGT
* * *
28669219 TTTTCAAATTT-TGTTTTTCCAAAAAATCAACTCATATTACGAGAGGTGAGTTCAGCCTCAGGAC
1 TTTTC-AATTTATG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GAC
* *
28669283 -ACGCTGAGATATTTTCAATTTCTTTTT
63 AACGCTGAGGTATTTTCAATTTC--TGT
*
28669310 TTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGATCA
1 TTTTCAATTTATGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-CA
* * *
28669375 TACGCCGAGGTATTTTCAATTGATTTTT
64 -ACGCTGAGGTATTTTCAATT--TCTGT
* * * *** *
28669403 ATTTTTATTTTTTTTCAATTTATGCTTTGCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
1 -TTTTCA----ATTT--ATGT-T--TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* **
28669468 CTCGGGTCACATAC-C-GAGGTATTTTCAAAATCTGT
56 CTC-AG--ACA-ACGCTGAGGTATTTTCAATTTCTGT
* * * ** * *
28669503 TTTACAAATTT-TGTTTT---AAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTTGGCCCA
1 TTTTC-AATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAA
*
28669564 CGTGCTGAGCTATTTTCAATTTCTGT
65 C--GCTGAGGTATTTTCAATTTCTGT
* * *
28669590 TTTT-AATGTT-TAGTTTT--GAAAAGTCAATTCATATTGCGAGA
1 TTTTCAAT-TTAT-GTTTTCAAAAAAATCAACTCATATTGCGAGA
28669631 AATAAGTTAA
Statistics
Matches: 400, Mismatches: 61, Indels: 84
0.73 0.11 0.15
Matches are distributed among these distances:
83 2 0.00
84 1 0.00
85 3 0.01
86 6 0.01
87 95 0.24
88 29 0.07
89 21 0.05
90 20 0.05
91 113 0.28
92 3 0.01
93 25 0.06
94 5 0.01
95 1 0.00
96 3 0.01
98 3 0.01
99 3 0.01
100 7 0.02
101 1 0.00
102 50 0.12
103 3 0.01
104 5 0.01
105 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (88 bp):
TTTTCAATTTATGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAAC
GCTGAGGTATTTTCAATTTCTGT
Found at i:28669485 original size:102 final size:103
Alignment explanation
Indices: 28669306--28669495 Score: 285
Period size: 102 Copynumber: 1.8 Consensus size: 103
28669296 TTCAATTTCT
*
28669306 TTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAG
1 TTTTTTTTCAATTTATGTTTGTC-AAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAG
* *
28669371 ATCATACGCCGAGGTATTTTCAATTGATTTTTATTTTTA
65 ATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
* *
28669410 TTTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGG
1 TTTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAG
* *
28669473 GTCACATACCGAGGTATTTTCAA
65 ATCACACACCGAGGTATTTTCAA
28669496 AATCTGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 56 0.72
104 18 0.23
105 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (103 bp):
TTTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGA
TCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
Found at i:28669579 original size:87 final size:88
Alignment explanation
Indices: 28669428--28669631 Score: 225
Period size: 87 Copynumber: 2.3 Consensus size: 88
28669418 CAATTTATGC
* * ** *
28669428 TTTGCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTT
1 TTTG-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCCCACATACCGAGCTATTTT
28669493 CAAAATCTGTTTTACAAAT-TTT-GT
65 CAAAATCTGTTTT--AAATGTTTAGT
* * * * *
28669517 TTT-AAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTTGGCCCACGTGCTGAGCTATTTTC
1 TTTGAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCCCACATACCGAGCTATTTTC
** *
28669581 AATTTCTGTTTTTAATGTTTAGT
66 AAAATCTGTTTTAAATGTTTAGT
* *
28669604 TTTGAAAAGTCAATTCATATTGCGAGAA
1 TTTGAAAAATCAACTCATATTGCGAGAA
28669632 ATAAGTTAAG
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
85 3 0.03
86 3 0.03
87 66 0.69
88 21 0.22
89 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (88 bp):
TTTGAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCCCACATACCGAGCTATTTTC
AAAATCTGTTTTAAATGTTTAGT
Found at i:28670310 original size:18 final size:18
Alignment explanation
Indices: 28670287--28670340 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28670277 CTACTACCAA
28670287 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
28670305 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
28670317 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
28670335 CTCCAC
1 CTCCAC
28670341 CACCAACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:28670316 original size:30 final size:30
Alignment explanation
Indices: 28670282--28670375 Score: 179
Period size: 30 Copynumber: 3.1 Consensus size: 30
28670272 CTTTGCTACT
28670282 ACCAACTCCACTAGCCACACTTGCTCCACC
1 ACCAACTCCACTAGCCACACTTGCTCCACC
28670312 ACCAACTCCACTAGCCACACTTGCTCCACC
1 ACCAACTCCACTAGCCACACTTGCTCCACC
*
28670342 ACCAACTCCACTAGCCACACTTGTTCCACC
1 ACCAACTCCACTAGCCACACTTGCTCCACC
28670372 ACCA
1 ACCA
28670376 CTTATACCTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.28, C:0.49, G:0.06, T:0.17
Consensus pattern (30 bp):
ACCAACTCCACTAGCCACACTTGCTCCACC
Found at i:28671066 original size:25 final size:25
Alignment explanation
Indices: 28670928--28671078 Score: 92
Period size: 25 Copynumber: 5.9 Consensus size: 25
28670918 ATTCTAAATT
* * *
28670928 CTATATTACGTATATATATATATTATA
1 CTATATTATGTATATAT-T-TTTTACA
* * * *
28670955 CTATTTTATGTATATATCTTTAAAA
1 CTATATTATGTATATATTTTTTACA
* *
28670980 CTATATTATTTATATTTTTTTTTCTACA
1 CTATATTATGTATA--TATTTTT-TACA
* *
28671008 TGTTATCTTATGTATATA--TTTTA-A
1 --CTATATTATGTATATATTTTTTACA
* *
28671032 TTATATTATGTATGTATTTTTTACA
1 CTATATTATGTATATATTTTTTACA
*
28671057 CTATATTATGTACATATTTTTT
1 CTATATTATGTATATATTTTTT
28671079 TTATATCTAT
Statistics
Matches: 95, Mismatches: 21, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
22 14 0.15
24 6 0.06
25 38 0.40
26 3 0.03
27 20 0.21
28 3 0.03
30 11 0.12
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (25 bp):
CTATATTATGTATATATTTTTTACA
Found at i:28671114 original size:77 final size:73
Alignment explanation
Indices: 28670939--28671114 Score: 163
Period size: 77 Copynumber: 2.3 Consensus size: 73
28670929 TATATTACGT
* * * *
28670939 ATATATATATATTATACTATTTTATGTATATATCTTTAAAACTATATTATTTATATTTTTTTTTC
1 ATATGTATATATTATA-TA--TTATGTATATATCTTTAAAACTATATTATGTACATTTTTTTTTA
28671004 TACATGTTATC
63 TACATGTTATC
* * * * *
28671015 TTATGTATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTT
1 ATATGTATATA--TT-A-TATATTATGTATATATCTTTAAAACTATATTATGTACAT-TTTTTTT
*
28671080 TATATCTATTTTATAC
61 TATA-C-ATGTTAT-C
28671096 ATATGTATATATTATATAT
1 ATATGTATATATTATATAT
28671115 ATCTTAACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
76 9 0.11
77 34 0.42
78 13 0.16
79 6 0.07
80 8 0.10
81 11 0.14
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (73 bp):
ATATGTATATATTATATATTATGTATATATCTTTAAAACTATATTATGTACATTTTTTTTTATAC
ATGTTATC
Found at i:28671168 original size:25 final size:24
Alignment explanation
Indices: 28671140--28671195 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28671130 GTTATATTTT
*
28671140 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
28671165 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
28671188 CACTATTA
1 CACTATTA
28671196 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:28676796 original size:7 final size:7
Alignment explanation
Indices: 28676786--28676891 Score: 76
Period size: 7 Copynumber: 14.9 Consensus size: 7
28676776 TTTCTTAATT
28676786 TTTATTA
1 TTTATTA
28676793 TTTATTA
1 TTTATTA
28676800 TTTATTA
1 TTTATTA
*
28676807 TTTTTTA
1 TTTATTA
*
28676814 TTTTATTT
1 -TTTATTA
*
28676822 TATTAGTA
1 T-TTATTA
28676830 TTTATTA
1 TTTATTA
28676837 -TT-TTA
1 TTTATTA
*
28676842 TTTCATTT
1 TTT-ATTA
*
28676850 TATTAGTA
1 T-TTATTA
28676858 TTTATTA
1 TTTATTA
28676865 -TT-TTA
1 TTTATTA
*
28676870 TTTTGTTA
1 -TTTATTA
28676878 TTTATTA
1 TTTATTA
28676885 CTTTATT
1 -TTTATT
28676892 TTTGGATATT
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
5 6 0.08
6 6 0.08
7 39 0.50
8 25 0.32
9 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:28676800 original size:10 final size:10
Alignment explanation
Indices: 28676794--28676884 Score: 66
Period size: 10 Copynumber: 9.3 Consensus size: 10
28676784 TTTTTATTAT
28676794 TTATTATTTA
1 TTATTATTTA
*
28676804 TTATTTTTTA
1 TTATTATTTA
28676814 TT-TTATTTTA
1 TTATTA-TTTA
*
28676824 TTAGTATTTA
1 TTATTATTTA
28676834 TTA-T-TTTA
1 TTATTATTTA
*
28676842 TT-TCATTTTA
1 TTATTA-TTTA
*
28676852 TTAGTATTTA
1 TTATTATTTA
*
28676862 TTATT-TTATT
1 TTATTATT-TA
*
28676872 TTGTTATTTA
1 TTATTATTTA
28676882 TTA
1 TTA
28676885 CTTTATTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.10
9 5 0.08
10 46 0.74
11 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:28676840 original size:23 final size:20
Alignment explanation
Indices: 28676797--28676893 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
28676787 TTATTATTTA
28676797 TTATTTATTATTTT-TTATT-
1 TTATTTATTATTTTATT-TTG
28676816 TTATTTTATTAGTATTTATTATT-
1 TTA-TTTATTA-T-TTTATT-TTG
* *
28676839 TTA-TT-TCATTTTA-TTAG
1 TTATTTATTATTTTATTTTG
28676856 -TATTTATTATTTTATTTTG
1 TTATTTATTATTTTATTTTG
*
28676875 TTATTTATTACTTTATTTT
1 TTATTTATTATTTTATTTT
28676894 TGGATATTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.05
17 3 0.05
18 11 0.17
19 7 0.11
20 26 0.41
21 3 0.05
22 3 0.05
23 8 0.12
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (20 bp):
TTATTTATTATTTTATTTTG
Found at i:28676849 original size:28 final size:28
Alignment explanation
Indices: 28676798--28676872 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
28676788 TATTATTTAT
*
28676798 TATTTATTATTTTTTATTTTATTTTATTAG
1 TATTTATTA--TTTTATTTCATTTTATTAG
28676828 TATTTATTATTTTATTTCATTTTATTAG
1 TATTTATTATTTTATTTCATTTTATTAG
28676856 TATTTATTATTTTATTT
1 TATTTATTATTTTATTT
28676873 TGTTATTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 35 0.80
30 9 0.20
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (28 bp):
TATTTATTATTTTATTTCATTTTATTAG
Found at i:28676889 original size:28 final size:26
Alignment explanation
Indices: 28676763--28676891 Score: 97
Period size: 28 Copynumber: 4.9 Consensus size: 26
28676753 CAACCCAACC
* * * *
28676763 TTTATTTTTTACTT-TTCTTAATTTT
1 TTTATTTTTTATTTATTATTTATTAT
* *
28676788 TATTATTTATTATTTATTATTTTTTAT
1 T-TTATTTTTTATTTATTATTTATTAT
*
28676815 TTTA--TTTTA-TTAGTATTTATTAT
1 TTTATTTTTTATTTATTATTTATTAT
*
28676838 TTTATTTCATTT-TATTAGTATTTATTAT
1 TTTATTT--TTTAT-TTATTATTTATTAT
28676866 TTTATTTTGTTATTTATTACTTTATT
1 TTTATTTT-TTATTTATTA-TTTATT
28676892 TTTGGATATT
Statistics
Matches: 83, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
23 16 0.19
24 4 0.05
25 2 0.02
26 15 0.18
27 18 0.22
28 28 0.34
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTATTTTTTATTTATTATTTATTAT
Found at i:28677123 original size:9 final size:10
Alignment explanation
Indices: 28677100--28677126 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28677090 ACCTTAATTT
28677100 TTTTTTACCC
1 TTTTTTACCC
28677110 TTTTTTACCC
1 TTTTTTACCC
28677120 TTTTTTA
1 TTTTTTA
28677127 GATAGTGAAT
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:0.22, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTACCC
Found at i:28677905 original size:21 final size:20
Alignment explanation
Indices: 28677874--28677913 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
28677864 TAAAAACAAA
28677874 TAAAAGAAAAAAAGTAAAAG
1 TAAAAGAAAAAAAGTAAAAG
*
28677894 TAAAATGAAAAAAATTAAAA
1 TAAAA-GAAAAAAAGTAAAA
28677914 AAAAAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (20 bp):
TAAAAGAAAAAAAGTAAAAG
Found at i:28678572 original size:10 final size:10
Alignment explanation
Indices: 28678557--28678606 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
28678547 TTAATTTAAG
28678557 ATTTAT-TTT
1 ATTTATCTTT
28678566 CATTTATCTTT
1 -ATTTATCTTT
*
28678577 AATTATCTTT
1 ATTTATCTTT
28678587 ATTTAT-TTGT
1 ATTTATCTT-T
28678597 ATTTATCTTT
1 ATTTATCTTT
28678607 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28678960 original size:37 final size:35
Alignment explanation
Indices: 28678891--28679014 Score: 99
Period size: 35 Copynumber: 3.5 Consensus size: 35
28678881 TCATGAGATT
* *
28678891 TTTTTTAAATTTTAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTTTAAAAATTAATTTCAAAAATACA
* *
28678926 TTTTTAAAATTTATAAATAATTAATTTCACAAATATA
1 TTTTTAAAATTT-TAAA-AATTAATTTCAAAAATACA
* * * * * *
28678963 TATATATAAA-GTTAAAAAATATTTTTAAAAATA-A
1 TTTTTA-AAATTTTAAAAATTAATTTCAAAAATACA
**
28678997 TAATTAAAATTTTAAAAA
1 TTTTTAAAATTTTAAAAA
28679015 AATATTATAA
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
33 3 0.04
34 12 0.17
35 24 0.34
36 8 0.11
37 21 0.30
38 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (35 bp):
TTTTTAAAATTTTAAAAATTAATTTCAAAAATACA
Found at i:28679010 original size:21 final size:21
Alignment explanation
Indices: 28678985--28679071 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
28678975 TAAAAAATAT
28678985 TTTTAAAAATAATAATTAAAA
1 TTTTAAAAATAATAATTAAAA
*
28679006 TTTTAAAAA-AATATTATAAAACA
1 TTTTAAAAATAATA--ATTAAA-A
*
28679029 TTTTAAATAT-AT-ATTACAAA
1 TTTTAAAAATAATAATTA-AAA
*
28679049 TTTTTTAAAATTAATAATATAAA
1 --TTTTAAAAATAATAAT-TAAA
28679072 TTAAATAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
20 8 0.16
21 11 0.22
22 13 0.25
23 13 0.25
24 4 0.08
25 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAATAATAATTAAAA
Found at i:28679072 original size:23 final size:22
Alignment explanation
Indices: 28678983--28679073 Score: 62
Period size: 23 Copynumber: 4.1 Consensus size: 22
28678973 GTTAAAAAAT
*
28678983 ATTTTTAAAAATAATAAT-TAA
1 ATTTTTTAAAATAATAATATAA
* * *
28679004 A-ATTTTAAAAAAATATTATAAA
1 ATTTTTTAAAATAATAATAT-AA
** * *
28679026 ACATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATAATATAA
28679048 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATAATATAA
28679071 ATT
1 ATT
28679074 AAATAAGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
20 12 0.22
21 2 0.04
22 14 0.26
23 24 0.44
24 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTTAAAATAATAATATAA
Found at i:28679106 original size:18 final size:18
Alignment explanation
Indices: 28679056--28679107 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
28679046 AAATTTTTTA
*
28679056 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
28679074 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
28679092 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
28679108 ACTTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:28685284 original size:29 final size:29
Alignment explanation
Indices: 28685249--28685319 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
28685239 TCCTTATTTT
28685249 GTCATTTTGGCTCCAATTCTCTTTTTTGA
1 GTCATTTTGGCTCCAATTCTCTTTTTTGA
28685278 GTCATTTTGGCTCCAATTCTCTTTTTTGA
1 GTCATTTTGGCTCCAATTCTCTTTTTTGA
28685307 GTCATTTTGGCTC
1 GTCATTTTGGCTC
28685320 TCAACCTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (29 bp):
GTCATTTTGGCTCCAATTCTCTTTTTTGA
Found at i:28688746 original size:19 final size:18
Alignment explanation
Indices: 28688724--28688799 Score: 52
Period size: 19 Copynumber: 4.2 Consensus size: 18
28688714 ATATTTTTTC
28688724 ATTTATGTAATTTTAATTA
1 ATTTATGTAATTTT-ATTA
*
28688743 A-TT-T-TAATTTT-TGA
1 ATTTATGTAATTTTATTA
* * *
28688757 ATATTATTTAATATTTTTTC
1 AT-TTATGTAAT-TTTATTA
28688777 ATTTATGTAATTTTAATTA
1 ATTTATGTAATTTT-ATTA
28688796 ATTT
1 ATTT
28688800 GTATTTTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 3 0.07
16 9 0.20
17 2 0.05
18 9 0.20
19 18 0.41
20 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTTATGTAATTTTATTA
Found at i:28688806 original size:53 final size:52
Alignment explanation
Indices: 28688691--28688799 Score: 191
Period size: 53 Copynumber: 2.1 Consensus size: 52
28688681 GTAACGATTT
**
28688691 ATTTTAAACTTTGAATATTTTTAATATTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTTTTAATATTTTTTCATTTATGTAATTTTAATTA
28688743 ATTTTAATTTTTGAATATTATTTAATATTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATT-TTTAATATTTTTTCATTTATGTAATTTTAATTA
28688796 ATTT
1 ATTT
28688800 GTATTTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 17 0.31
53 37 0.69
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (52 bp):
ATTTTAATTTTTGAATATTTTTAATATTTTTTCATTTATGTAATTTTAATTA
Found at i:28690360 original size:18 final size:18
Alignment explanation
Indices: 28690337--28690379 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28690327 TGTCAGGTGC
*
28690337 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
28690355 GTATCCTAACCTTTATAT
1 GTATCCTAACCCTTATAT
*
28690373 GTTTCCT
1 GTATCCT
28690380 TTTCTCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:28693967 original size:46 final size:44
Alignment explanation
Indices: 28693863--28693970 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
28693853 TGTCTTTGAC
** * * *
28693863 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
28693907 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
28693953 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
28693971 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:28695675 original size:13 final size:13
Alignment explanation
Indices: 28695657--28695685 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28695647 GGTCACGCAT
28695657 TCTGTGTGGTAGA
1 TCTGTGTGGTAGA
28695670 TCTGTGTGGTAGA
1 TCTGTGTGGTAGA
28695683 TCT
1 TCT
28695686 AACGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.41
Consensus pattern (13 bp):
TCTGTGTGGTAGA
Found at i:28698484 original size:39 final size:39
Alignment explanation
Indices: 28698441--28698632 Score: 289
Period size: 39 Copynumber: 4.9 Consensus size: 39
28698431 ATATATAATG
* *
28698441 CCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACA
* *
28698480 CCAGCACGAATGCCTTCGGGGCTTAACCCGGATATAACA
1 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACA
*
28698519 CCAACACGAATGCCTTCGGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACA
* *
28698558 CCAGTACGAATGCCTTCAGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACA
*
28698597 CCAGCACGAATG-CTTCAGGACTTAGCCCGGATATAA
1 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
28698633 TTCTCCATTA
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 24 0.17
39 106 0.75
40 11 0.08
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (39 bp):
CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACA
Found at i:28705191 original size:77 final size:76
Alignment explanation
Indices: 28705033--28705222 Score: 292
Period size: 77 Copynumber: 2.5 Consensus size: 76
28705023 CCGTATAATG
* * * *
28705033 CCAGCAC-AAAGCCTACGGGACTTTAGCCGGATATAACACCAGCACGAATGCCTTCGGGCTTAAC
1 CCAGCACGAATGCCTTCGGGAC-TTAGCCCGATATAACACCAGCACGAATGCCTTCGGACTTAAC
28705097 CCGGATATAACA
65 CCGGATATAACA
*
28705109 CCAGCACGAATGCCTTCGGGACTTAGCCCGATATAACACCAGCACGAATGCCTTCAGGACTTAGC
1 CCAGCACGAATGCCTTCGGGACTTAGCCCGATATAACACCAGCACGAATGCCTTC-GGACTTAAC
28705174 CCGGATATAACA
65 CCGGATATAACA
*
28705186 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAA
1 CCAGCACGAATGCCTTCGGGACTTAGCCC-GATATAA
28705223 TTCTCCATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
76 39 0.37
77 59 0.56
78 7 0.07
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (76 bp):
CCAGCACGAATGCCTTCGGGACTTAGCCCGATATAACACCAGCACGAATGCCTTCGGACTTAACC
CGGATATAACA
Found at i:28705192 original size:39 final size:39
Alignment explanation
Indices: 28705033--28705222 Score: 289
Period size: 38 Copynumber: 4.9 Consensus size: 39
28705023 CCGTATAATG
* * *
28705033 CCAGCAC-AAAGCCTACGGGACTTTAG-CCGGATATAACA
1 CCAGCACGAATGCCTTCAGGAC-TTAGCCCGGATATAACA
* *
28705071 CCAGCACGAATGCCTTC-GGGCTTAACCCGGATATAACA
1 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACA
*
28705109 CCAGCACGAATGCCTTCGGGACTTAGCCC-GATATAACA
1 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACA
28705147 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACA
28705186 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAA
1 CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAA
28705223 TTCTCCATTA
Statistics
Matches: 141, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
37 3 0.02
38 76 0.54
39 62 0.44
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (39 bp):
CCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACA
Found at i:28705248 original size:2 final size:2
Alignment explanation
Indices: 28705241--28705268 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28705231 TATCATGCAC
28705241 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
28705269 CATAACACAT
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:28707321 original size:28 final size:29
Alignment explanation
Indices: 28707288--28707353 Score: 116
Period size: 28 Copynumber: 2.3 Consensus size: 29
28707278 TTATTTTAAA
28707288 AAACCCTAAACCATAATTTAATTTATTTT
1 AAACCCTAAACCATAATTTAATTTATTTT
*
28707317 -AACCCTAAACCCTAATTTAATTTATTTT
1 AAACCCTAAACCATAATTTAATTTATTTT
28707345 AAACCCTAA
1 AAACCCTAA
28707354 CTTAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (29 bp):
AAACCCTAAACCATAATTTAATTTATTTT
Found at i:28707350 original size:22 final size:22
Alignment explanation
Indices: 28707322--28707499 Score: 103
Period size: 22 Copynumber: 8.1 Consensus size: 22
28707312 ATTTTAACCC
*
28707322 TAAACCCTAATTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
28707344 TAAACCCTAACTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
* *
28707366 AAAACCCTAGAACCTTAATTTA-AT
1 TAAACCCT--AA-CTTAATTTATTT
*** * * * *
28707390 TAATTTC-AACCT-A-TAAATA
1 TAAACCCTAACTTAATTTATTT
* ** ***
28707409 TAAACCCTAATTTAATAAACCC
1 TAAACCCTAACTTAATTTATTT
* *
28707431 AAAACCCTAATTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
*
28707453 TAAAACCTAACTTAATTTATTT
1 TAAACCCTAACTTAATTTATTT
* * *
28707475 AAAACCCTAATTTAATTAATTT
1 TAAACCCTAACTTAATTTATTT
28707497 TAA
1 TAA
28707500 CCAAAAAATA
Statistics
Matches: 115, Mismatches: 34, Indels: 14
0.71 0.21 0.09
Matches are distributed among these distances:
18 2 0.02
19 5 0.04
20 5 0.04
21 3 0.03
22 85 0.74
24 6 0.05
25 9 0.08
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAACCCTAACTTAATTTATTT
Found at i:28707493 original size:101 final size:101
Alignment explanation
Indices: 28707376--28707557 Score: 240
Period size: 101 Copynumber: 1.8 Consensus size: 101
28707366 AAAACCCTAG
* * *
28707376 AACCTTAATTTAATTAATTTCAACCTATAAATATAAAC-CCTAATTTAATAAACCCAAAACCCTA
1 AACCCTAATTTAATTAATTTCAACCAAAAAATAT-AACTCCTAATTTAATAAACCCAAAACCCTA
*
28707440 ATTTAATTTATTTTAAAACCTAACTTAATTTATTTAA
65 ACTTAATTTATTTTAAAACCTAACTTAATTTATTTAA
* * ** *** *
28707477 AACCCTAATTTAATTAATTTTAACCAAAAAATATAACTGCTAATTTAATTTATTTAAAACCCTCA
1 AACCCTAATTTAATTAATTTCAACCAAAAAATATAACTCCTAATTTAATAAACCCAAAACCCTAA
28707542 CTTAATTTATTTTAAA
66 CTTAATTTATTTTAAA
28707558 CCTTAAAACC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
100 3 0.04
101 65 0.96
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.40
Consensus pattern (101 bp):
AACCCTAATTTAATTAATTTCAACCAAAAAATATAACTCCTAATTTAATAAACCCAAAACCCTAA
CTTAATTTATTTTAAAACCTAACTTAATTTATTTAA
Found at i:28707622 original size:22 final size:21
Alignment explanation
Indices: 28707584--28707632 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
28707574 TACTTAATCT
28707584 ATTTAA-AAACATAAATCCTA
1 ATTTAATAAACATAAATCCTA
28707604 ATTTAATAAACACTAAATCCTA
1 ATTTAATAAACA-TAAATCCTA
28707626 ATTTAAT
1 ATTTAAT
28707633 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.22
21 5 0.19
22 16 0.59
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAATAAACATAAATCCTA
Found at i:28707642 original size:22 final size:22
Alignment explanation
Indices: 28707617--28707669 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
28707607 TAATAAACAC
*
28707617 TAAATCCTAATTTAATTTATTT
1 TAAATCCTAACTTAATTTATTT
28707639 TAAA-CACTAACTTAATTTATTT
1 TAAATC-CTAACTTAATTTATTT
*
28707661 AAAATCCTA
1 TAAATCCTA
28707670 GAACCCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATCCTAACTTAATTTATTT
Found at i:28707661 original size:186 final size:187
Alignment explanation
Indices: 28707328--28707669 Score: 499
Period size: 186 Copynumber: 1.8 Consensus size: 187
28707318 ACCCTAAACC
* * *
28707328 CTAATTTAATTTATTTTAAACCCTAACTTAATTTATTTAAAACCCTAGAACCTTAATTTAATTAA
1 CTAATTTAATTTATTTAAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCTAATTTAATTAA
* * *
28707393 TTTCAACCTATAAATATAAACCCTAATTTAATAAACCCAAAACCCTAATTTAATTTATTTTAAAA
66 -TTCAACCTAAAAACATAAACCCTAATTTAATAAACACAAAACCCTAATTTAATTTATTTTAAAA
28707458 CCTAACTTAATTTATTTAAAACCCTAATTTAATTAATTTTAACCAAAAAATATAACTG
130 CCTAACTTAATTTATTTAAAACCCTAATTTAATTAATTTTAACCAAAAAATATAACTG
* * * *
28707516 CTAATTTAATTTATTTAAAACCCTCACTTAATTTATTTTAAACCTTAAAACCCTAATTTACTTAA
1 CTAATTTAATTTATTTAAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCTAATTTAATTAA
* ** * * *
28707581 -TCTATTTAAAAACATAAATCCTAATTTAATAAACACTAAATCCTAATTTAATTTATTTT-AAAC
66 TTCAACCTAAAAACATAAACCCTAATTTAATAAACACAAAACCCTAATTTAATTTATTTTAAAAC
*
28707644 ACTAACTTAATTTATTTAAAATCCTA
131 -CTAACTTAATTTATTTAAAACCCTA
28707670 GAACCCTAAT
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
185 4 0.03
186 74 0.54
188 58 0.43
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.40
Consensus pattern (187 bp):
CTAATTTAATTTATTTAAAACCCTAACTTAATTTATTTAAAACCCTAAAACCCTAATTTAATTAA
TTCAACCTAAAAACATAAACCCTAATTTAATAAACACAAAACCCTAATTTAATTTATTTTAAAAC
CTAACTTAATTTATTTAAAACCCTAATTTAATTAATTTTAACCAAAAAATATAACTG
Found at i:28710294 original size:2 final size:2
Alignment explanation
Indices: 28710287--28710330 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
28710277 TCTTCATAAT
*
28710287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28710329 TA
1 TA
28710331 ACACTTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28719568 original size:17 final size:16
Alignment explanation
Indices: 28719533--28719582 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
28719523 TGAACTAAAA
*
28719533 AAAAATTTAAAAGTAGC
1 AAAAA-TTAAAAGTTGC
28719550 AAAAATTAAATAGTTGC
1 AAAAATTAAA-AGTTGC
*
28719567 AAGTAATTAAAAGTTG
1 AA-AAATTAAAAGTTG
28719583 TCATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.28
Consensus pattern (16 bp):
AAAAATTAAAAGTTGC
Found at i:28725969 original size:2 final size:2
Alignment explanation
Indices: 28725962--28726003 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28725952 TGTAAATTAG
28725962 CT CT CT CT CT CT 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 CT CT CT CT CT CT
28726004 GGAAACAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28732964 original size:16 final size:16
Alignment explanation
Indices: 28732943--28732974 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28732933 AAATATGATT
28732943 TTGAACCGATTAGATA
1 TTGAACCGATTAGATA
28732959 TTGAACCGATTAGATA
1 TTGAACCGATTAGATA
28732975 AGGAACCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
TTGAACCGATTAGATA
Found at i:28732980 original size:16 final size:16
Alignment explanation
Indices: 28732945--28732981 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28732935 ATATGATTTT
**
28732945 GAACCGATTAGATATT
1 GAACCGATTAGATAAG
28732961 GAACCGATTAGATAAG
1 GAACCGATTAGATAAG
28732977 GAACC
1 GAACC
28732982 AATGCGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (16 bp):
GAACCGATTAGATAAG
Found at i:28734657 original size:32 final size:31
Alignment explanation
Indices: 28734596--28734659 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
28734586 AAAACGAAAT
*
28734596 TTTAAATTTGTTTATTTTCAACTAATTTAAA
1 TTTAAATTTGTTTATTTTCAAATAATTTAAA
* *
28734627 TTTAAAGTTT-TTTATTTTTTAAATATTTTAAA
1 TTTAAA-TTTGTTTA-TTTTCAAATAATTTAAA
28734659 T
1 T
28734660 GAATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAAATTTGTTTATTTTCAAATAATTTAAA
Found at i:28736701 original size:24 final size:23
Alignment explanation
Indices: 28736647--28736701 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
28736637 ACAAAGCTAA
*
28736647 AGATGGAGATGAAGATAAAGACG
1 AGATGGAAATGAAGATAAAGACG
* * *
28736670 ACAGTGGAAATGAATATAAAGATG
1 AGA-TGGAAATGAAGATAAAGACG
28736694 ATGATGGA
1 A-GATGGA
28736702 GGTAAAGACG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.31, T:0.18
Consensus pattern (23 bp):
AGATGGAAATGAAGATAAAGACG
Found at i:28742696 original size:21 final size:21
Alignment explanation
Indices: 28742672--28742728 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
28742662 TCTTTATTAA
*
28742672 CTAATTATTATTTTATTTTTT
1 CTAATTATTATTTAATTTTTT
*
28742693 CTAATTAGT-TTTAATTTTTT
1 CTAATTATTATTTAATTTTTT
*
28742713 -TAATTATTATTAAATT
1 CTAATTATTATTTAATT
28742729 AAATTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 7 0.23
20 16 0.52
21 8 0.26
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
CTAATTATTATTTAATTTTTT
Found at i:28742704 original size:19 final size:18
Alignment explanation
Indices: 28742678--28742725 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
28742668 TTAACTAATT
28742678 ATTATTTT-ATTTTTTCTA
1 ATTATTTTAATTTTTT-TA
28742696 ATTAGTTTTAATTTTTTTA
1 ATTA-TTTTAATTTTTTTA
28742715 ATTATTATTAA
1 ATTATT-TTAA
28742726 ATTAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTATTTTAATTTTTTTA
Found at i:28746465 original size:39 final size:39
Alignment explanation
Indices: 28746411--28746486 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
28746401 TCTAGTTAAA
28746411 AAATTATACTAAGGGTACTCTAGTCATTTCAAATTTTTG
1 AAATTATACTAAGGGTACTCTAGTCATTTCAAATTTTTG
28746450 AAATTATACTAAGGGTACTCTAGTCATTTCAAATTTT
1 AAATTATACTAAGGGTACTCTAGTCATTTCAAATTTT
28746487 AATAAGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
AAATTATACTAAGGGTACTCTAGTCATTTCAAATTTTTG
Found at i:28754848 original size:20 final size:20
Alignment explanation
Indices: 28754823--28754868 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
28754813 ATAGTAAATG
28754823 TTAATTCTATTCT-AATTT-TT
1 TTAATTCT-TT-TAAATTTATT
28754843 TTAATTCTTTTAAATTTATT
1 TTAATTCTTTTAAATTTATT
28754863 TTAATT
1 TTAATT
28754869 AATTCTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 7 0.29
20 16 0.67
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAATTCTTTTAAATTTATT
Found at i:28759808 original size:12 final size:12
Alignment explanation
Indices: 28759791--28759817 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28759781 GAAAATAGGG
28759791 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28759803 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28759815 TTT
1 TTT
28759818 ATCAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:28759997 original size:41 final size:41
Alignment explanation
Indices: 28759853--28760132 Score: 307
Period size: 41 Copynumber: 6.9 Consensus size: 41
28759843 AAACACAGAT
* * * * *
28759853 CAATAGCGGCGTTTTTGGTAAAACGCCACTAAAA-ACAGAG
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
* * * * *
28759893 CAATA--GGCACTTTTTGTTAAAACGCCGCTAAAA-ACAGAG
1 CAATAGCGGCGC-TTTCGGTAAAACGCCGCTAAAAGTCGGAG
* * * * *
28759932 CAATAGCGGCGTTTTTGGTCAAACGACGTTAAAAGTCGGAG
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
** *
28759973 CAATAGCGATGCTTCCGGTAAAACGCCGCTAAAAGTCGGAG
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
**
28760014 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTTAGAG
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
*
28760055 CAATAGCGGCGCTTTCGGTAAAACGTCGCTAAAAGTCGGAG
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
* * *
28760096 CATTAGCGGCGCTTTTGATAAAACGCCGCTAAAAGTC
1 CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTC
28760133 ATATAACCCC
Statistics
Matches: 204, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
38 3 0.01
39 31 0.15
40 23 0.11
41 147 0.72
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (41 bp):
CAATAGCGGCGCTTTCGGTAAAACGCCGCTAAAAGTCGGAG
Found at i:28760366 original size:7 final size:7
Alignment explanation
Indices: 28760354--28760417 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
28760344 TTTATTTTTT
*
28760354 GGTTTAC
1 GGTTTAA
28760361 GGTTTAA
1 GGTTTAA
**
28760368 TATTTAA
1 GGTTTAA
28760375 GGTTTAA
1 GGTTTAA
* *
28760382 GGTCTAT
1 GGTTTAA
*
28760389 GGTTTAG
1 GGTTTAA
*
28760396 GGTTTTAT
1 GG-TTTAA
28760404 GGTTTAA
1 GGTTTAA
28760411 GGTTTAA
1 GGTTTAA
28760418 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:28760406 original size:15 final size:15
Alignment explanation
Indices: 28760370--28760420 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
28760360 CGGTTTAATA
*
28760370 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
28760384 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
28760399 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
28760414 TTAATGG
1 TTTATGG
28760421 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:28760981 original size:8 final size:8
Alignment explanation
Indices: 28760970--28761054 Score: 113
Period size: 8 Copynumber: 11.0 Consensus size: 8
28760960 ACTCAAAAAA
28760970 TAAAAATT
1 TAAAAATT
28760978 TAAAAATT
1 TAAAAATT
28760986 TAAAAATT
1 TAAAAATT
28760994 TAAAAATT
1 TAAAAATT
28761002 TAAAAA-T
1 TAAAAATT
28761009 T-AAAATT
1 TAAAAATT
28761016 TAAAAA-T
1 TAAAAATT
*
28761023 AAAAAATT
1 TAAAAATT
* *
28761031 AAAAAACT
1 TAAAAATT
*
28761039 TAAAAACT
1 TAAAAATT
28761047 TAAAAATT
1 TAAAAATT
28761055 AATATTTTAG
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
6 4 0.06
7 10 0.14
8 56 0.80
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
TAAAAATT
Found at i:28760982 original size:14 final size:14
Alignment explanation
Indices: 28760978--28761035 Score: 80
Period size: 14 Copynumber: 4.0 Consensus size: 14
28760968 AATAAAAATT
28760978 TAAAAATTTAAAAA
1 TAAAAATTTAAAAA
28760992 TTTAAAAATTTAAAAA
1 --TAAAAATTTAAAAA
*
28761008 TTAAAATTTAAAAA
1 TAAAAATTTAAAAA
*
28761022 TAAAAAATTAAAAA
1 TAAAAATTTAAAAA
28761036 ACTTAAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
14 25 0.64
16 14 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAATTTAAAAA
Found at i:28761043 original size:45 final size:46
Alignment explanation
Indices: 28760970--28761061 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
28760960 ACTCAAAAAA
* * * *
28760970 TAAAAATTTAAAAATTTAAAAATTTAAAAATTTAAAAATTAAAATT
1 TAAAAATTAAAAAATTAAAAAACTTAAAAACTTAAAAATTAAAATT
*
28761016 TAAAAA-TAAAAAATTAAAAAACTTAAAAACTTAAAAATTAATATT
1 TAAAAATTAAAAAATTAAAAAACTTAAAAACTTAAAAATTAAAATT
28761061 T
1 T
28761062 TAGTCCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 35 0.85
46 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (46 bp):
TAAAAATTAAAAAATTAAAAAACTTAAAAACTTAAAAATTAAAATT
Found at i:28763778 original size:17 final size:18
Alignment explanation
Indices: 28763758--28763795 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28763748 CATTGATATC
28763758 TTTA-TATTTAATTTAAT
1 TTTATTATTTAATTTAAT
* *
28763775 TTTATTATTTATTTTAGT
1 TTTATTATTTAATTTAAT
28763793 TTT
1 TTT
28763796 GATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTATTTAATTTAAT
Found at i:28763814 original size:19 final size:21
Alignment explanation
Indices: 28763786--28763833 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
28763776 TTATTATTTA
28763786 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
28763806 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
28763826 TTTTAGTT
1 TTTTAGTT
28763834 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:28763932 original size:27 final size:28
Alignment explanation
Indices: 28763897--28763950 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
28763887 TATTTTGATA
*
28763897 ATGAATTTTA-AATTTTTTATATTTTTC
1 ATGAATTTTATAATATTTTATATTTTTC
* *
28763924 ATGACTTTTATAATATTTTATTTTTTT
1 ATGAATTTTATAATATTTTATATTTTT
28763951 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
ATGAATTTTATAATATTTTATATTTTTC
Found at i:28770331 original size:29 final size:29
Alignment explanation
Indices: 28770273--28770331 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
28770263 AAATAAAGAA
**
28770273 ATTAAATTCATAAAAATAAAAGTGTACAG
1 ATTAAATTCATAAAAATAAAAAAGTACAG
* *
28770302 ATTAAATTC-TAAAATTGAAAAAAGTGCAG
1 ATTAAATTCATAAAAAT-AAAAAAGTACAG
28770331 A
1 A
28770332 AACTTGGACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (29 bp):
ATTAAATTCATAAAAATAAAAAAGTACAG
Found at i:28770838 original size:2 final size:2
Alignment explanation
Indices: 28770831--28770856 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28770821 ATGACATGAG
28770831 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
28770857 GCAAGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28772027 original size:31 final size:31
Alignment explanation
Indices: 28771992--28772052 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
28771982 ACTCGGTGAT
*
28771992 TTAAATAAAAACTTTT-GAATAGTTCAATGAC
1 TTAAATAAAAA-TTTTCGAATAATTCAATGAC
28772023 TTAAATAAAAATTTTCGAATAATTCAATGA
1 TTAAATAAAAATTTTCGAATAATTCAATGA
28772053 TCAAATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (31 bp):
TTAAATAAAAATTTTCGAATAATTCAATGAC
Found at i:28773863 original size:30 final size:30
Alignment explanation
Indices: 28773827--28773913 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
28773817 CCTAAACTTT
28773827 TCCACCACCAACTCCACTAGCCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
* * *
28773857 TCCACCACTAACTCTACTAGGCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
* *
28773887 TCCACTACCTACTCCACTAGCCACACT
1 TCCACCACCAACTCCACTAGCCACACT
28773914 CCACCACCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.26, C:0.46, G:0.07, T:0.21
Consensus pattern (30 bp):
TCCACCACCAACTCCACTAGCCACACTTGC
Found at i:28774451 original size:24 final size:23
Alignment explanation
Indices: 28774403--28774454 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
28774393 CTTTTTTTGT
*
28774403 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
28774426 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
28774450 TATTA
1 TATTA
28774455 GGTATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:28774512 original size:27 final size:26
Alignment explanation
Indices: 28774484--28774545 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
28774474 ATTACGTATA
*
28774484 TATATATATATT-ATACTATTTTATG
1 TATATATATATTAATACTATATTATG
* *
28774509 TATATATCT-TTAATACTATATTATT
1 TATATATATATTAATACTATATTATG
28774534 TATATATATATT
1 TATATATATATT
28774546 TTTTCTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 27 0.87
26 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (26 bp):
TATATATATATTAATACTATATTATG
Found at i:28774543 original size:52 final size:50
Alignment explanation
Indices: 28774420--28774544 Score: 124
Period size: 52 Copynumber: 2.4 Consensus size: 50
28774410 ATATTTCTTA
* * *
28774420 ATATTATATTATATATATATTCTTTTAATATATTAGGTATATTCTAAATTCT
1 ATATTAT-TTATATATATA-TATTATAATATATTAGGTATATTCTAAATACT
* * * * *
28774472 ATATTACGTATATATATATATATTATACTATTTTATGTATATATCTTTAATACT
1 ATATTA--TTTATATATATATATTATAATATATTAGGTATAT-TC-TAAATACT
28774526 ATATTATTTATATATATAT
1 ATATTATTTATATATATAT
28774545 TTTTTCTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
52 35 0.58
53 12 0.20
54 13 0.22
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (50 bp):
ATATTATTTATATATATATATTATAATATATTAGGTATATTCTAAATACT
Found at i:28774582 original size:22 final size:22
Alignment explanation
Indices: 28774557--28774664 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
28774547 TTTCTATATG
*
28774557 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
28774579 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
28774604 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
28774627 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
28774647 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
28774665 ATGTAATATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:28774583 original size:29 final size:28
Alignment explanation
Indices: 28774503--28774584 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
28774493 ATTATACTAT
28774503 TTTATGTATATATCTTTAA-TACTATATTA
1 TTTATGTATATAT-TTTAATTA-TATATTA
* * *
28774532 TTTATATATATATTTT-TTCTATATGTTA
1 TTTATGTATATATTTTAAT-TATATATTA
28774560 TCTTATGTATATATTTTAATTATAT
1 T-TTATGTATATATTTTAATTATAT
28774585 TATGTATGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 10 0.23
29 33 0.75
30 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTATGTATATATTTTAATTATATATTA
Found at i:28774613 original size:25 final size:24
Alignment explanation
Indices: 28774563--28774649 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
28774553 TATGTTATCT
*
28774563 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
28774589 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
** * *
28774614 TACATA-TTTTTAA-TATTATCACG
1 TATGTATTTTTTAACTA-TATTATG
*
28774637 TATTTATTTTTTA
1 TATGTATTTTTTA
28774650 TATATGTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 10 0.20
24 17 0.33
25 15 0.29
26 7 0.14
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:28774805 original size:16 final size:15
Alignment explanation
Indices: 28774781--28774828 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
28774771 TAATTATTAT
*
28774781 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
28774797 TATTTTAATATTTTA
1 TATTTTAATATTTTA
*
28774812 TATTTTATATACTTTA
1 TATTTTA-ATATTTTA
28774828 T
1 T
28774829 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:28774816 original size:7 final size:8
Alignment explanation
Indices: 28774781--28774832 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
28774771 TAATTATTAT
*
28774781 TATTCTAA
1 TATTTTAA
*
28774789 TATTTTGA
1 TATTTTAA
28774797 TATTTTAA
1 TATTTTAA
28774805 TATTTT-A
1 TATTTTAA
28774812 TATTTTATA
1 TATTTTA-A
* *
28774821 TACTTTAT
1 TATTTTAA
28774829 TATT
1 TATT
28774833 CACATCACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:28775965 original size:32 final size:32
Alignment explanation
Indices: 28775928--28775992 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28775918 GATGAGAACT
28775928 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
1 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
28775960 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
1 TATTAAAGAAAACCTTTTCAAATTTTCATAGA
28775992 T
1 T
28775993 CTAATGTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (32 bp):
TATTAAAGAAAACCTTTTCAAATTTTCATAGA
Found at i:28778529 original size:22 final size:22
Alignment explanation
Indices: 28778486--28778531 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28778476 AAAATTTATC
*
28778486 TTAATTTAGAACAAATATTCAA
1 TTAATTTAAAACAAATATTCAA
*
28778508 TTAATTTATAAACATATA-TCAA
1 TTAATTTA-AAACAAATATTCAA
28778530 TT
1 TT
28778532 CATAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAATTTAAAACAAATATTCAA
Found at i:28779458 original size:23 final size:23
Alignment explanation
Indices: 28779432--28779480 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
28779422 CAGAGTGTAA
28779432 AATCTACTTGACTTGCTTTAAGT
1 AATCTACTTGACTTGCTTTAAGT
28779455 AATCTACTTGACTTGCTTTAAGT
1 AATCTACTTGACTTGCTTTAAGT
28779478 AAT
1 AAT
28779481 GCAATCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (23 bp):
AATCTACTTGACTTGCTTTAAGT
Found at i:28780991 original size:20 final size:20
Alignment explanation
Indices: 28780936--28781003 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
28780926 GATGCAAAAC
* * *
28780936 AGGGGCACCAAAGTGTAATC
1 AGGGGCACCAGAGTGCAATT
* * * *
28780956 AAGAGCACGAGTGTGCAATT
1 AGGGGCACCAGAGTGCAATT
*
28780976 AGGGGCACCAGAGTGCATTT
1 AGGGGCACCAGAGTGCAATT
28780996 AGGGGCAC
1 AGGGGCAC
28781004 GAATGTGCTG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.34, T:0.16
Consensus pattern (20 bp):
AGGGGCACCAGAGTGCAATT
Found at i:28781011 original size:20 final size:20
Alignment explanation
Indices: 28780960--28781011 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28780950 GTAATCAAGA
*
28780960 GCACGAGTGTGCAATTAGGG
1 GCACGAATGTGCAATTAGGG
* *
28780980 GCACCAGA-GTGCATTTAGGG
1 GCACGA-ATGTGCAATTAGGG
28781000 GCACGAATGTGC
1 GCACGAATGTGC
28781012 TGCTAGGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.25, C:0.19, G:0.37, T:0.19
Consensus pattern (20 bp):
GCACGAATGTGCAATTAGGG
Found at i:28781091 original size:40 final size:40
Alignment explanation
Indices: 28781015--28781130 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
28781005 AATGTGCTGC
* * *
28781015 TAGGGGAAAAATTGTGCAAATAGGGACACCAAAGTGTTTA
1 TAGGGGCAAAATTGTGCAAATAGGAACACCGAAGTGTTTA
*
28781055 TAGGGGCACAATTGTGCAAATAGGAACACCGAAGTGTTTA
1 TAGGGGCAAAATTGTGCAAATAGGAACACCGAAGTGTTTA
* * * * *
28781095 CAGTGGCATAGTTGTGCAAATAGGAACATCGAAGTG
1 TAGGGGCAAAATTGTGCAAATAGGAACACCGAAGTG
28781131 CAATCAAGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (40 bp):
TAGGGGCAAAATTGTGCAAATAGGAACACCGAAGTGTTTA
Found at i:28787219 original size:12 final size:12
Alignment explanation
Indices: 28787202--28787232 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28787192 TCTTTTGGAT
*
28787202 TTATTTATTTAA
1 TTATTTATGTAA
28787214 TTATTTATGTAA
1 TTATTTATGTAA
28787226 TTATTTA
1 TTATTTA
28787233 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TTATTTATGTAA
Found at i:28787284 original size:12 final size:14
Alignment explanation
Indices: 28787248--28787285 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
28787238 TTTTTAAAAT
28787248 CTATTATTTT-AAC
1 CTATTATTTTGAAC
28787261 CTATTATTTTGAA-
1 CTATTATTTTGAAC
28787274 CTATT-TTTTGAA
1 CTATTATTTTGAA
28787286 TTCCATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 15 0.62
14 2 0.08
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (14 bp):
CTATTATTTTGAAC
Found at i:28791821 original size:7 final size:7
Alignment explanation
Indices: 28791809--28791849 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
28791799 GGAGTTAAAA
28791809 ATAAATT
1 ATAAATT
28791816 ATAAATT
1 ATAAATT
28791823 ATAAATT
1 ATAAATT
*
28791830 AAAAACTT
1 ATAAA-TT
28791838 A-AAA-T
1 ATAAATT
28791843 ATAAATT
1 ATAAATT
28791850 TACCAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 2 0.07
6 3 0.10
7 22 0.73
8 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAAATT
Found at i:28797866 original size:22 final size:21
Alignment explanation
Indices: 28797837--28797877 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28797827 GTCATTGTAT
28797837 TTTCATTTTAAAAATTTAATC
1 TTTCATTTTAAAAATTTAATC
**
28797858 TTTCTATTTTTTAAATTTAA
1 TTTC-ATTTTAAAAATTTAA
28797878 AATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTCATTTTAAAAATTTAATC
Found at i:28798184 original size:3 final size:3
Alignment explanation
Indices: 28798176--28798233 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
28798166 TTTAAAGCAT
28798176 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28798224 TAA TAA TAA T
1 TAA TAA TAA T
28798234 TGATTTATGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28802218 original size:17 final size:17
Alignment explanation
Indices: 28802164--28802218 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
28802154 TTAAAAATAA
*
28802164 ATATAATATAATAGTA-
1 ATATAAAATAATAGTAT
28802180 ATATTAAAATAA-AGT-T
1 ATA-TAAAATAATAGTAT
*
28802196 AT-TAAAATAATACTAT
1 ATATAAAATAATAGTAT
28802212 ATATAAA
1 ATATAAA
28802219 TGTACGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 11 0.34
17 11 0.34
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (17 bp):
ATATAAAATAATAGTAT
Found at i:28802239 original size:8 final size:7
Alignment explanation
Indices: 28802225--28802293 Score: 62
Period size: 6 Copynumber: 10.6 Consensus size: 7
28802215 TAAATGTACG
28802225 AATATAT
1 AATATAT
28802232 ACATATAT
1 A-ATATAT
28802240 AATATA-
1 AATATAT
*
28802246 CATATATT
1 AATATA-T
28802254 AATAT-T
1 AATATAT
28802260 AATA-AT
1 AATATAT
28802266 AATA-AT
1 AATATAT
28802272 AATA-AT
1 AATATAT
28802278 AATA-AT
1 AATATAT
28802284 AATA-AT
1 AATATAT
28802290 AATA
1 AATA
28802294 ATTATTGGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
6 39 0.70
7 6 0.11
8 11 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:28802245 original size:15 final size:13
Alignment explanation
Indices: 28802225--28802293 Score: 72
Period size: 12 Copynumber: 5.3 Consensus size: 13
28802215 TAAATGTACG
28802225 AATATATACATATAT
1 AATATATA-ATA-AT
* *
28802240 AATATACATATATT
1 AATATATA-ATAAT
28802254 AATAT-TAATAAT
1 AATATATAATAAT
28802266 AATA-ATAATAAT
1 AATATATAATAAT
28802278 AATA-ATAATAAT
1 AATATATAATAAT
28802290 AATA
1 AATA
28802294 ATTATTGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
12 31 0.65
13 1 0.02
14 6 0.12
15 10 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATAATAAT
Found at i:28802267 original size:3 final size:3
Alignment explanation
Indices: 28802253--28802422 Score: 111
Period size: 3 Copynumber: 56.7 Consensus size: 3
28802243 ATACATATAT
* *
28802253 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
** * ** * *
28802299 TGG TAA TAA TAA TACT TTT TAA AAA TAA TTAA TAA -AT TAA TAA -AA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* *
28802344 TAA CAA TAA TGAA -AA TAA TAA TAA CT-G TAA TAA TAA -AGA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TA-A TAA TAA
* *
28802389 TAGA -AA TAA -AA TAA TAG TAA TAA TAT TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28802423 TGTAAAAAGA
Statistics
Matches: 130, Mismatches: 23, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
2 10 0.08
3 109 0.84
4 11 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28803062 original size:22 final size:22
Alignment explanation
Indices: 28803020--28803063 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28803010 AAAAATTCAA
* *
28803020 ATTTTTTTTATTTTCTAATATT
1 ATTTTATTTATTTTATAATATT
28803042 ATTTTATTTATATTTAT-ATATT
1 ATTTTATTTAT-TTTATAATATT
28803064 TAGATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTATTTATTTTATAATATT
Found at i:28809647 original size:4 final size:4
Alignment explanation
Indices: 28809640--28809677 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
28809630 TATTTTTATT
*
28809640 TTTA TTTA TTT- TTTT TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
28809678 TTCTTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTA
Found at i:28809659 original size:27 final size:27
Alignment explanation
Indices: 28809623--28809699 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
28809613 CAACCCAATC
28809623 TTTTTTTTATTTTTATTTTTATTTATT
1 TTTTTTTTATTTTTATTTTTATTTATT
*
28809650 TTTTTTTTATTTATT-TATTTATTTATT
1 TTTTTTTTATTT-TTATTTTTATTTATT
*
28809677 TTTCTTTTATTTTTA-TTTTATTT
1 TTTTTTTTATTTTTATTTTTATTT
28809700 TATTATTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.20
27 34 0.76
28 2 0.04
ACGTcount: A:0.16, C:0.01, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTTTTATTTTTATTTTTATTTATT
Found at i:28809892 original size:43 final size:42
Alignment explanation
Indices: 28809809--28809899 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
28809799 TCCATGCTGT
* * * *
28809809 CAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCAGC
1 CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
*
28809851 CAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCAGC
1 CAAACAGTCCTATTCCAGCC-CAGAAT-CCCAAAACTCTGCAGC
28809894 CAAACA
1 CAAACA
28809900 CCCCTTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 19 0.45
43 18 0.43
44 5 0.12
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (42 bp):
CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
Found at i:28810865 original size:118 final size:118
Alignment explanation
Indices: 28810657--28810887 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
28810647 TGTTTTCCAT
* *
28810657 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
28810722 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
28810775 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
28810840 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
28810888 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:28811030 original size:21 final size:21
Alignment explanation
Indices: 28810991--28811030 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28810981 TATTCCTAAG
* * *
28810991 TAAATAAATAATAATAAAATT
1 TAAAAAAATAAAAAAAAAATT
28811012 TAAAAAAATAAAAAAAAAA
1 TAAAAAAATAAAAAAAAAA
28811031 AAGGAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAAAATAAAAAAAAAATT
Found at i:28811031 original size:13 final size:13
Alignment explanation
Indices: 28811013--28811054 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
28811003 AATAAAATTT
*
28811013 AAAAAAATAAAAA
1 AAAAAAAGAAAAA
28811026 AAAAAAAGGAAAAA
1 AAAAAAA-GAAAAA
*
28811040 AAAAGAAGAAAAA
1 AAAAAAAGAAAAA
28811053 AA
1 AA
28811055 TAAGTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:28811032 original size:14 final size:14
Alignment explanation
Indices: 28811021--28811054 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28811011 TTAAAAAAAT
*
28811021 AAAAAAAAAAAAGG
1 AAAAAAAAAAAAGA
*
28811035 AAAAAAAAAGAAGA
1 AAAAAAAAAAAAGA
28811049 AAAAAA
1 AAAAAA
28811055 TAAGTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:28818998 original size:2 final size:2
Alignment explanation
Indices: 28818991--28819050 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
28818981 TTCAGTTTTA
28818991 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
28819033 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
28819051 GAACAAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28820745 original size:29 final size:30
Alignment explanation
Indices: 28820682--28820748 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
28820672 ATCTCAAAAC
*
28820682 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTATGATTT-ATGTGAAATTG
* *
28820713 TATACATGAACTTTGATTT-TGTGAAATTT
1 TATACATGAACTATGATTTATGTGAAATTG
28820742 TATACAT
1 TATACAT
28820749 AAAATTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.45
31 18 0.55
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGAAATTG
Found at i:28820978 original size:29 final size:30
Alignment explanation
Indices: 28820903--28821013 Score: 109
Period size: 31 Copynumber: 3.7 Consensus size: 30
28820893 GATTAAATCA
* * * *
28820903 AAATTAAAGTTTCAAGCATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* *
28820933 ACAATTAGAGTTTCATGTATATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
*
28820964 AAATTAAAG-TTCATGTATACAATTGCACATT
1 AAATTAAAGTTTCATGTATACAATTGCAC--C
*
28820995 AAATCAAAG-TTCATGTATA
1 AAATTAAAGTTTCATGTATA
28821014 ATTTTGAGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.26
30 8 0.12
31 42 0.62
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:28821007 original size:31 final size:29
Alignment explanation
Indices: 28820944--28821013 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
28820934 CAATTAGAGT
* *
28820944 TTCATGTATATAATTGCACCAAATTAAAG
1 TTCATGTATACAATTGCACCAAATCAAAG
*
28820973 TTCATGTATACAATTGCACATTAAATCAAAG
1 TTCATGTATACAATTGCAC--CAAATCAAAG
28821004 TTCATGTATA
1 TTCATGTATA
28821014 ATTTTGAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (29 bp):
TTCATGTATACAATTGCACCAAATCAAAG
Found at i:28821945 original size:23 final size:23
Alignment explanation
Indices: 28821919--28821988 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
28821909 TTTGTTTCTT
*
28821919 AAAACCCAAGCTATTATGTTATA
1 AAAACCCATGCTATTATGTTATA
* * *
28821942 AAAA---ATGATATT-TGTTTCTT
1 AAAACCCATGCTATTATG-TTATA
28821962 AAAACCCATGCTATTATGTTATA
1 AAAACCCATGCTATTATGTTATA
28821985 AAAA
1 AAAA
28821989 ATTACCATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
23 18 0.51
24 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAACCCATGCTATTATGTTATA
Found at i:28821959 original size:43 final size:43
Alignment explanation
Indices: 28821899--28821990 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
28821889 AAATGAAAAC
28821899 AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
1 AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
*
28821942 AAAAATGATATTTGTTTCTTAAAACCCATGCTATTATGTTATA
1 AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
28821985 AAAAAT
1 AAAAAT
28821991 TACCATGTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (43 bp):
AAAAATGATATTTGTTTCTTAAAACCCAAGCTATTATGTTATA
Found at i:28821965 original size:20 final size:20
Alignment explanation
Indices: 28821899--28821965 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
28821889 AAATGAAAAC
28821899 AAAAATGATATTTGTTTCTT
1 AAAAATGATATTTGTTTCTT
* * * *
28821919 AAAACCCAAGCTATTATG-TTATA
1 AAAA---ATGATATT-TGTTTCTT
28821942 AAAAATGATATTTGTTTCTT
1 AAAAATGATATTTGTTTCTT
28821962 AAAA
1 AAAA
28821966 CCCATGCTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
23 13 0.38
24 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAAATGATATTTGTTTCTT
Found at i:28830635 original size:46 final size:46
Alignment explanation
Indices: 28830568--28830879 Score: 493
Period size: 46 Copynumber: 6.8 Consensus size: 46
28830558 AGTGTGCTCT
*
28830568 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28830614 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28830660 GTGATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28830705 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
28830751 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
28830797 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
28830843 ATGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
28830880 TATGACATCA
Statistics
Matches: 250, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
45 45 0.18
46 205 0.82
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28845956 original size:31 final size:31
Alignment explanation
Indices: 28845920--28845979 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
28845910 TTAAACAACA
28845920 TATTTAGACAACAAATACATTATGTTCTTTG
1 TATTTAGACAACAAATACATTATGTTCTTTG
* *
28845951 TATTTAGACAGCAGATACATTATGTTCTT
1 TATTTAGACAACAAATACATTATGTTCTT
28845980 CAATTGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (31 bp):
TATTTAGACAACAAATACATTATGTTCTTTG
Found at i:28846003 original size:16 final size:16
Alignment explanation
Indices: 28845982--28846013 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28845972 ATGTTCTTCA
28845982 ATTGGAATCCTTCTTT
1 ATTGGAATCCTTCTTT
*
28845998 ATTGGAATCTTTCTTT
1 ATTGGAATCCTTCTTT
28846014 TGACACCATA
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:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTGGAATCCTTCTTT
Found at i:28846966 original size:35 final size:35
Alignment explanation
Indices: 28846920--28847003 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
28846910 TCTTTGTGTT
*
28846920 TAAATTTTAATGCAACTTCAAGATAATCAATGTAC
1 TAAATTTTAATGCAACTTCAAAATAATCAATGTAC
*
28846955 TAAATTTTAATGCAACTTCAAAATAATTAATGTAC
1 TAAATTTTAATGCAACTTCAAAATAATCAATGTAC
28846990 TAAATTTTAATGCA
1 TAAATTTTAATGCA
28847004 GATCGTTTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (35 bp):
TAAATTTTAATGCAACTTCAAAATAATCAATGTAC
Found at i:28850515 original size:22 final size:22
Alignment explanation
Indices: 28850490--28850560 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
28850480 GATAACAACG
28850490 AAAATACTGACCACAAACTTAT
1 AAAATACTGACCACAAACTTAT
* ** **
28850512 AAAAT--GGAAAACAAAGGGTAT
1 AAAATACTGACCACAAA-CTTAT
*
28850533 AGTAATACTGACCACAAACTTAT
1 A-AAATACTGACCACAAACTTAT
28850556 AAAAT
1 AAAAT
28850561 GGAAAACAAA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 7 0.21
21 4 0.12
22 11 0.33
23 4 0.12
24 7 0.21
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.21
Consensus pattern (22 bp):
AAAATACTGACCACAAACTTAT
Found at i:28850542 original size:44 final size:44
Alignment explanation
Indices: 28850492--28850579 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
28850482 TAACAACGAA
28850492 AATACTGACCACAAACTTATAAAATGGAAAACAAAGGGTATAGT
1 AATACTGACCACAAACTTATAAAATGGAAAACAAAGGGTATAGT
28850536 AATACTGACCACAAACTTATAAAATGGAAAACAAAGGGTATAGT
1 AATACTGACCACAAACTTATAAAATGGAAAACAAAGGGTATAGT
28850580 TTAGATAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (44 bp):
AATACTGACCACAAACTTATAAAATGGAAAACAAAGGGTATAGT
Found at i:28860874 original size:34 final size:34
Alignment explanation
Indices: 28860830--28860906 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
28860820 GGTTGCATTT
* * *
28860830 CTGATACTGTTACT-ATAATGGGTTAAGGCCCACA
1 CTGATACTGTTACTCA-AATGAGCTAAAGCCCACA
*
28860864 TTGATACTGTTACTCAAATGAGCTAAAGCCCACA
1 CTGATACTGTTACTCAAATGAGCTAAAGCCCACA
28860898 CTGATACTG
1 CTGATACTG
28860907 GACTGTCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (34 bp):
CTGATACTGTTACTCAAATGAGCTAAAGCCCACA
Found at i:28867279 original size:34 final size:34
Alignment explanation
Indices: 28867234--28867310 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
28867224 GTTTGCATTT
*
28867234 CTGATACTGTTACT-ATAATGGGTTAAGACCCACA
1 CTGATACTGTTACTGA-AATGGGCTAAGACCCACA
* * *
28867268 TTGATATTGTTACTGAAATGGGCTAAGGCCCACA
1 CTGATACTGTTACTGAAATGGGCTAAGACCCACA
28867302 CTGATACTG
1 CTGATACTG
28867311 GATTGTCACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (34 bp):
CTGATACTGTTACTGAAATGGGCTAAGACCCACA
Found at i:28871510 original size:17 final size:18
Alignment explanation
Indices: 28871488--28871528 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
28871478 GGTTAAAGTA
*
28871488 TAATTTTATTATTGTA-T
1 TAATTTTATAATTGTATT
*
28871505 TAA-TTTATAATTTTATT
1 TAATTTTATAATTGTATT
28871522 TAATTTT
1 TAATTTT
28871529 TAAGATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 10 0.50
17 7 0.35
18 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TAATTTTATAATTGTATT
Found at i:28874176 original size:2 final size:2
Alignment explanation
Indices: 28874169--28874195 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28874159 GAAAGCCGGG
28874169 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 A
28874196 AAACATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28874734 original size:26 final size:27
Alignment explanation
Indices: 28874689--28874743 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
28874679 CAAGTGAAAG
28874689 AATAATTTAGTGCTTTAAAAA-AAAAC
1 AATAATTTAGTGCTTTAAAAACAAAAC
*
28874715 AATAATTTAG-GTTTTCAAAAACAAAAC
1 AATAATTTAGTGCTTT-AAAAACAAAAC
28874742 AA
1 AA
28874744 AACAATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
27 7 0.27
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (27 bp):
AATAATTTAGTGCTTTAAAAACAAAAC
Found at i:28876457 original size:4 final size:4
Alignment explanation
Indices: 28876448--28876521 Score: 148
Period size: 4 Copynumber: 18.5 Consensus size: 4
28876438 AAGTAAATAC
28876448 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
28876496 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
28876522 ATATAACAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:28878591 original size:17 final size:18
Alignment explanation
Indices: 28878566--28878603 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
28878556 TTTAAATTTA
28878566 ATTACATAAAT-ATAAAT
1 ATTACATAAATAATAAAT
*
28878583 ATTAGATAAATAATAAAT
1 ATTACATAAATAATAAAT
28878601 ATT
1 ATT
28878604 TACTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATTACATAAATAATAAAT
Found at i:28880584 original size:10 final size:9
Alignment explanation
Indices: 28880562--28880627 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
28880552 ATTTTAGTTG
28880562 TTTTATATA
1 TTTTATATA
28880571 -TTTATATA
1 TTTTATATA
28880579 TTTT-TATAA
1 TTTTATAT-A
* *
28880588 CTTTATAAA
1 TTTTATATA
28880597 TTTTAGT-TA
1 TTTTA-TATA
* *
28880606 GTTTACATA
1 TTTTATATA
28880615 TTTTATATA
1 TTTTATATA
28880624 TTTT
1 TTTT
28880628 TAAAATAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 11 0.25
9 30 0.68
10 3 0.07
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTATATA
Found at i:28880665 original size:17 final size:16
Alignment explanation
Indices: 28880621--28880668 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
28880611 CATATTTTAT
28880621 ATATTTTTAAAATAATA
1 ATATTTTTAAAA-AATA
**
28880638 ATATCCTTAAAAAATA
1 ATATTTTTAAAAAATA
28880654 ATATTTTATAAAAAA
1 ATATTTT-TAAAAAA
28880669 AGATTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTTTTAAAAAATA
Found at i:28880666 original size:16 final size:15
Alignment explanation
Indices: 28880625--28880667 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
28880615 TTTTATATAT
28880625 TTTTAAAATAATAATA
1 TTTTAAAA-AATAATA
*
28880641 TCCTTAAAAAATAATA
1 T-TTTAAAAAATAATA
28880657 TTTTATAAAAA
1 TTTTA-AAAAA
28880668 AAGATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTAAAAAATAATA
Found at i:28884150 original size:43 final size:43
Alignment explanation
Indices: 28884088--28884169 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
28884078 TGCAACGCCG
*
28884088 CTAAAGAACAGGACTTTTAGCGGCGCTCTTTTAAAAAACACCA
1 CTAAAGAACAGGACCTTTAGCGGCGCTCTTTTAAAAAACACCA
* * * *
28884131 CTAAAGACCGGGACCTTTAGCGGTGCTTTTTTAAAAAAC
1 CTAAAGAACAGGACCTTTAGCGGCGCTCTTTTAAAAAAC
28884170 GCCGCTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (43 bp):
CTAAAGAACAGGACCTTTAGCGGCGCTCTTTTAAAAAACACCA
Found at i:28884494 original size:21 final size:21
Alignment explanation
Indices: 28884470--28884517 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
28884460 TTCTGTTCTG
* *
28884470 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCGCACTGCTGC
28884491 CTCCGCCTCCCGCACTGCTGC
1 CTCCGCCTCCCGCACTGCTGC
28884512 CTCCGC
1 CTCCGC
28884518 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.58, G:0.19, T:0.21
Consensus pattern (21 bp):
CTCCGCCTCCCGCACTGCTGC
Found at i:28889099 original size:31 final size:31
Alignment explanation
Indices: 28889061--28889131 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
28889051 CTGTGGCCCA
*
28889061 TATTCATCCTCATTAGCATCTTCTGTATCTC
1 TATTCATCCTCATTAACATCTTCTGTATCTC
28889092 TATTCATCCTCATTAACATCTTCTGTATCTC
1 TATTCATCCTCATTAACATCTTCTGTATCTC
28889123 TATTCATCC
1 TATTCATCC
28889132 AACGAGATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.30, G:0.04, T:0.45
Consensus pattern (31 bp):
TATTCATCCTCATTAACATCTTCTGTATCTC
Done.