Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_pilon, whole genome shotgun sequence
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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 26
Found at i:199789 original size:42 final size:42
Alignment explanation
Indices: 199742--199906 Score: 118
Period size: 41 Copynumber: 4.1 Consensus size: 42
199732 TTTTATACGT
199742 TTTATATATATTTTCTTAATATTATATTTTTATTTTTATTTA
1 TTTATATATATTTTCTTAATATTATATTTTTATTTTTATTTA
* *
199784 TTTATATATATATATATATT-AT-TTTTA-TTTTA-TTTTATTTA
1 TTTATATATAT-T-T-TCTTAATATTATATTTTTATTTTTATTTA
* * * *
199825 TTT-TATTATTATTTTCTTAATA-T-CATGTATATCTTTATTT-
1 TTTATA-TA-TATTTTCTTAATATTATATTTTTATTTTTATTTA
* * * *
199865 TTTAT-T-TATTTACTTAGTATTATATATTTATTATT-TTTA
1 TTTATATATATTTTCTTAATATTATATTTTTATTTTTATTTA
199904 TTT
1 TTT
199907 GTTTTAGTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
37 11 0.11
38 4 0.04
39 16 0.17
40 12 0.12
41 23 0.24
42 19 0.20
43 5 0.05
44 3 0.03
45 3 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (42 bp):
TTTATATATATTTTCTTAATATTATATTTTTATTTTTATTTA
Found at i:199816 original size:5 final size:5
Alignment explanation
Indices: 199806--199839 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
199796 TATATATTAT
199806 TTTTA TTTTA TTTTA -TTTA TTTTA TTATTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTT
199840 CTTAATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:199818 original size:48 final size:47
Alignment explanation
Indices: 199744--199906 Score: 115
Period size: 47 Copynumber: 3.4 Consensus size: 47
199734 TTATACGTTT
*
199744 TATATATATT-TTCTTAATATTATATTTTTATTTTTATTTATTTATATATA
1 TATATATATTATT-TT--TATTTTATTTTTATTTTTATTTA-TTATATATA
*
199794 TATATATATTATTTTTATTTTA-TTTTATTTAT-TTTATTAT-TAT-
1 TATATATATTATTTTTATTTTATTTTTATTTTTATTTATTATATATA
* * * * * *
199837 TTTCTTAATATCATGTATATCTTTATTTTT-TATTTATTTACTTAGTAT-TA
1 TAT-AT-ATATTATTTTTAT-TTTATTTTTATTTTTATTTA-TTA-TATATA
*
199887 TATATTTATTATTTTTATTT
1 TATATATATTATTTTTATTT
199907 GTTTTAGTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
43 2 0.02
44 4 0.05
45 14 0.16
46 11 0.12
47 19 0.22
48 18 0.20
49 3 0.03
50 15 0.17
51 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (47 bp):
TATATATATTATTTTTATTTTATTTTTATTTTTATTTATTATATATA
Found at i:199856 original size:56 final size:57
Alignment explanation
Indices: 199769--199875 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
199759 AATATTATAT
*
199769 TTTTATTTTTATTTATTTATATATATATATAT-ATTA-TTTTTATTTTATTTTATTTA
1 TTTTATTATTATTTATTTATATATATATATATCATTATTTTTTA-TTTATTTTATTTA
* *
199825 TTTTATTATTATTT-TCTTA-ATATCATGTATATCTTTATTTTTTATTTATTT
1 TTTTATTATTATTTAT-TTATATAT-ATATATATCATTATTTTTTATTTATTT
199876 ACTTAGTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
55 5 0.11
56 23 0.52
57 10 0.23
58 6 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (57 bp):
TTTTATTATTATTTATTTATATATATATATATCATTATTTTTTATTTATTTTATTTA
Found at i:199897 original size:93 final size:84
Alignment explanation
Indices: 199741--199906 Score: 217
Period size: 93 Copynumber: 1.9 Consensus size: 84
199731 ATTTTATACG
*
199741 TTTTATATATATTTTCTTAATATTATATTTTTATTTTTATTTATTTATATATATATATATATTAT
1 TTTTATATATATTTTCTTAATATTATATCTTTATTTTTATTTATTTATATATATATATATATTAT
199806 TTTTATTTTATTTTATTTA
66 TTTTATTTTATTTTATTTA
199825 TTTTAT-TATTATTTTCTTAATATCATGTATATCTTTATTTTTTATTTATTTACTTAGTATTATA
1 TTTTATATA-TATTTTCTT-A-AT-AT-TATATCTTTA-TTTTTATTTATTTA--TA-TA-TATA
*
199889 TATTTATTATTTTTATTT
56 TATATATTATTTTTATTT
199907 GTTTTAGTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
83 2 0.03
84 15 0.21
85 1 0.01
86 2 0.03
87 2 0.03
88 9 0.13
89 14 0.20
91 2 0.03
92 2 0.03
93 21 0.30
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (84 bp):
TTTTATATATATTTTCTTAATATTATATCTTTATTTTTATTTATTTATATATATATATATATTAT
TTTTATTTTATTTTATTTA
Found at i:200115 original size:26 final size:25
Alignment explanation
Indices: 200059--200119 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
200049 ATTTTTATTA
200059 TTTTATTATTATTTTTTACATGTTT
1 TTTTATTATTATTTTTTACATGTTT
* * *
200084 TGTTATTTTCTATTTTTT-CTTGTTT
1 TTTTATTAT-TATTTTTTACATGTTT
200109 TATTTATTATT
1 T-TTTATTATT
200120 CACACATTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTTATTATTATTTTTTACATGTTT
Found at i:200119 original size:22 final size:22
Alignment explanation
Indices: 200050--200119 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
200040 ATTTTGTTTA
*
200050 TTTTTATTATTTTA-TTATTAT
1 TTTTTCTTATTTTATTTATTAT
*
200071 TTTTTACATGTTTTGTTATTT-TCTAT
1 TTTTT-C-T-TATT-TTATTTAT-TAT
*
200097 TTTTTCTTGTTTTATTTATTAT
1 TTTTTCTTATTTTATTTATTAT
200119 T
1 T
200120 CACACATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
21 5 0.13
22 10 0.26
23 5 0.13
24 4 0.10
25 5 0.13
26 10 0.26
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTCTTATTTTATTTATTAT
Found at i:203197 original size:9 final size:9
Alignment explanation
Indices: 203183--203233 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
203173 CAATCAGAAC
203183 AAAAAGAGA
1 AAAAAGAGA
203192 AAAAAGAGA
1 AAAAAGAGA
203201 AAAAA-AGTA
1 AAAAAGAG-A
*
203210 AAGAAA-AAA
1 AA-AAAGAGA
203219 TAAAAAGAGA
1 -AAAAAGAGA
203229 AAAAA
1 AAAAA
203234 CAAAGGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 2 0.06
9 26 0.72
10 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:203229 original size:15 final size:14
Alignment explanation
Indices: 203191--203233 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
203181 ACAAAAAGAG
203191 AAAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
*
203205 AAGTAAAGA-AAAAA
1 AA-AAAAGAGAAAAA
*
203219 TAAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
203233 A
1 A
203234 CAAAGGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAAGAGAAAAA
Found at i:203238 original size:13 final size:13
Alignment explanation
Indices: 203191--203243 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
203181 ACAAAAAGAG
203191 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
203204 AAAGTAAAGA-AAAA
1 AAA--AAAGAGAAAA
203218 ATAAAAAGAGAAAA
1 A-AAAAAGAGAAAA
*
203232 AACAAAG-GAAAA
1 AAAAAAGAGAAAA
203244 TTGAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.14
13 13 0.37
14 10 0.29
15 7 0.20
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:204956 original size:37 final size:38
Alignment explanation
Indices: 204901--204975 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
204891 GAAGATTTTA
* * *
204901 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
*
204938 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
204976 AAAGCATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
Found at i:205040 original size:37 final size:36
Alignment explanation
Indices: 204982--205067 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 36
204972 ATTGAAAGCA
* * *
204982 TTTCCCTTAAAAAGAATTTTGTCACTCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTGTCACCCTTGAGATAG
*
205018 TTTCCCTTGAAACGAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACG-AATTTTGTCACCCTTGAGATAG
*
205055 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
205068 ATAAACATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTGTCACCCTTGAGATAG
Found at i:205071 original size:102 final size:101
Alignment explanation
Indices: 204906--205271 Score: 430
Period size: 102 Copynumber: 3.6 Consensus size: 101
204896 TTTTATCTCG
*
204906 CTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
* *
204971 CATTGAAAGCATTTCCCTT-AAAAAGAATTTTGTCACT
65 CATTGAAAACATTTCCCTTGAAAAA-AATTTCGTCACT
*
205008 CTTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
* *
205073 CATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCT
65 CATTGAAAACATTTCCCTTGAAAAAAATTTCGTCACT
* * * * **
205110 CTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATT
1 CTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
* ** *** * * *
205174 ATTTGAATATGTTTTATTTGAAACAAATTTCGTCTCC
66 A-TTGAAAACATTTCCCTTGAAAAAAATTTCGTCACT
* ** * * *
205211 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
205272 AATTTCGTAT
Statistics
Matches: 233, Mismatches: 28, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
100 3 0.01
101 80 0.34
102 146 0.63
103 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (101 bp):
CTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
ATTGAAAACATTTCCCTTGAAAAAAATTTCGTCACT
Found at i:205137 original size:36 final size:36
Alignment explanation
Indices: 205084--205309 Score: 216
Period size: 36 Copynumber: 6.4 Consensus size: 36
205074 ATTGAAAACA
*
205084 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
205120 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
205156 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** *
205185 TTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
205221 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
205258 TTTCTCTTGAAACAAATTTCGTATCTCTTGACACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
205294 TTTCTCTTGAAACAAA
1 TTTCCCTTGAAACAAA
205310 ATCTTTGAAT
Statistics
Matches: 156, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
30 2 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 98 0.63
37 33 0.21
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:205246 original size:138 final size:138
Alignment explanation
Indices: 205104--205363 Score: 376
Period size: 138 Copynumber: 1.9 Consensus size: 138
205094 AATAAATTTC
* * *
205104 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTATCTCTTGACACAGTTTCCCTTGAAAC
* * * ** *
205169 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
205234 TAAGTTTT
131 TAAGTTTT
* * *
205242 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTATCTCTTGACACAGTTTCTCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTATCTCTTGACACAGTTTCCCTTGAAAC
* * * *
205307 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
205364 CTTGAAACAA
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTATCTCTTGACACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:205262 original size:203 final size:203
Alignment explanation
Indices: 204901--205271 Score: 462
Period size: 203 Copynumber: 1.8 Consensus size: 203
204891 GAAGATTTTA
* * *
204901 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * *
204966 ATAAACATTGAAAGCATTTCCCTTAAAAAGAATTTTGTCACTCTTGAGATAGTTTCCCTTGAAAC
66 ATAAACATTGAAAG-ATTTCACTTAAAAAGAATTTCGTCACCCTTGAGACAGTTTCCCTTGAAAC
*
205031 GAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
130 GAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
205096 TAAATTTCG
195 TAAATTTCG
* * *
205105 TCTCTCTTGAGACAGTTTCCCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
** * * * * ** *
205169 A-AATTATTTGAATATG-TTTTATTTGAAACA-AATTTCGTCTCCCTTGAGACAGTTTCTTTTGG
66 ATAAACA-TTGAA-A-GATTTCACTT-AAAAAGAATTTCGTCACCCTTGAGACAGTTTCCCTTGA
* * *
205231 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
127 AACGAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
205272 AATTTCGTAT
Statistics
Matches: 140, Mismatches: 23, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
202 3 0.02
203 106 0.76
204 30 0.21
205 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (203 bp):
TCTCGCTTGAGACAGTTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
ATAAACATTGAAAGATTTCACTTAAAAAGAATTTCGTCACCCTTGAGACAGTTTCCCTTGAAACG
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
AAATTTCG
Found at i:205406 original size:68 final size:67
Alignment explanation
Indices: 205258--205441 Score: 203
Period size: 65 Copynumber: 2.8 Consensus size: 67
205248 CTTGAGACAG
* * * * * **
205258 TTTCTCTTGAAACAAATTTCGTATCTCTTGACACAGTTTCTCTTGAAAC--AAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTATCCCTTGAGACAGTTTCTCTTGAAACAAAAAATCTTCAAATT
205321 TA
66 TA
* *
205323 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAAAATCTTCAAAT
1 TTTCCCTTAAAACAAATTTTGTATCCCTTGAGACAGTTTCTCTTGAAAC-AAAAAATCTTCAAAT
205388 TTA
65 TTA
* * * * *
205391 TTTCCCTTTAAACAAAATTTTATTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTAAAAC-AAATTTTGTATCCCTTGAGACAGTTTCTCTTGAAACAA
205442 CATATATCTT
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 42 0.42
67 2 0.02
68 33 0.33
69 23 0.23
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.39
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTATCCCTTGAGACAGTTTCTCTTGAAACAAAAAATCTTCAAATT
TA
Found at i:206231 original size:63 final size:63
Alignment explanation
Indices: 206121--206275 Score: 211
Period size: 63 Copynumber: 2.4 Consensus size: 63
206111 GCCACTCGAG
* * * * * *
206121 ATAACACAAGTTCAACTTAACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTC
1 ATAAC-CAATTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTC
*
206185 ATAACCAATTTCAACTTCACAACGAAGGGACGACTGGTTGTTAACAAACAACTTCCCAATTTC
1 ATAACCAATTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
206248 AGAGCCAATTTCAACTTCACAGCGAAGG
1 ATAACCAATTTCAACTTCACAACGAAGG
206276 ATATTGGACT
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 76 0.94
64 5 0.06
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (63 bp):
ATAACCAATTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:206380 original size:106 final size:106
Alignment explanation
Indices: 206195--206590 Score: 433
Period size: 106 Copynumber: 3.9 Consensus size: 106
206185 ATAACCAATT
* * ** * *
206195 TCAACTTCACAACGAAGGGACGACTGGTTGTTAACAAACAACTTCCCAATTTCAGAGCCAATTTC
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTTC
* *
206260 AACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGC
66 AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
* * *
206301 TCAACTTCACAGGGAAGGGGCGGCTGACTGTCAACAAACAACTTCCCAATTTCAGGGTCAATTTC
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTTC
* * *
206366 AACTTCCCAACGAAGGATATTGGACCCAAGACAACACAAGT
66 AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
* * * *
206407 TCAACTTCAC-GACGAATGGGAGACTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTCAATTT
1 TCAACTTCACAG-CGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTT
* * * *
206465 CAACTTCACAATGAAGGATATTAGACTCGAGACAGCACAAGC
65 CAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
* * * *
206507 TCAACTTCACAGTGAAGGGGCGGCTGACTGTCAACAAACAA--T-----TTCCAGAGCCAATTTC
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTTC
* *
206565 AACTTCACGACGGAGGATATTGGACT
66 AACTTCACAACGAAGGATATTGGACT
206591 TGGATTTCAA
Statistics
Matches: 246, Mismatches: 39, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
99 35 0.14
100 76 0.31
101 5 0.02
102 3 0.01
103 2 0.01
104 2 0.01
105 3 0.01
106 120 0.49
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTTCAGAGTCAATTTC
AACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
Found at i:206929 original size:85 final size:85
Alignment explanation
Indices: 206827--207056 Score: 338
Period size: 85 Copynumber: 2.7 Consensus size: 85
206817 TGTAGAATAT
* * *
206827 CTCAAGGTAAGAAGGGTTATCTATCATC-AAAGACCT-TCGAGTTCGATTACATTCAACTCAGAG
1 CTCAAGGCAAGAAGGGTTATATATCAACGAAA-A-CTATCGAGTTCGATTACATTCAACTCAGAG
206890 ATAAATCAAATTTACAGCATAG
64 ATAAATCAAATTTACAGCATAG
* * *
206912 CTCAAGGCAAGAAGGGTTATATGTCAACGAAAATTATCGAGTTCGATTACATTCAACTCAGAGGT
1 CTCAAGGCAAGAAGGGTTATATATCAACGAAAACTATCGAGTTCGATTACATTCAACTCAGAGAT
206977 AAATCAAATTTACAGCATAG
66 AAATCAAATTTACAGCATAG
* * * *
206997 CTCAAGGCAAGAAGGGTTATATGTCAACGAAAATTATCGAGTTCGATTCCATTCATCTCA
1 CTCAAGGCAAGAAGGGTTATATATCAACGAAAACTATCGAGTTCGATTACATTCAACTCA
207057 ATCACACTAT
Statistics
Matches: 135, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
84 1 0.01
85 131 0.97
86 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (85 bp):
CTCAAGGCAAGAAGGGTTATATATCAACGAAAACTATCGAGTTCGATTACATTCAACTCAGAGAT
AAATCAAATTTACAGCATAG
Found at i:208925 original size:44 final size:44
Alignment explanation
Indices: 208856--209244 Score: 366
Period size: 44 Copynumber: 9.0 Consensus size: 44
208846 AAAAAATAGA
* *
208856 GGCCTTAATTATAAAGGTAGAAATTGAGATCGAAAAAAACTTAGG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTG-AAAAAACTTAGG
* *
208901 GGCATCAATTATAAAGGTA-TAATTGAGATTGAAAAAACTTAGG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
* * * *
208944 GGCCTCAATTATAAAGGTAGAAAGTGAGACTGAAAACACTTAAG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
* * * *
208988 GGCCTTAATTATAAAGTTAAAAAAGTGAGATT-AAAAAA-TTAGG
1 GGCCTCAATTATAAAGGT-AGAAATTGAGATTGAAAAAACTTAGG
** * *
209031 GGATTCAATTATAAGGGTAGAGATTGAGATTGAAAAAACTTAGG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
* * * *
209075 GGCCTCAATTGTAAAGGTAGAAAATGAGATTGGAAAAACTTAAG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
* * * * *
209119 GGCCTCAATTATAAAGTTAAAAAGTGGGGTT--AAAAA-TTAGG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
* * * *
209160 GGACTCAATTATAAAGGTAAAAATATG-TATTG-AAAAA-TTAGA
1 GGCCTCAATTATAAAGGTAGAAAT-TGAGATTGAAAAAACTTAGG
* * * * *
209202 GACTTCAATTATAAAGATAAAAAGTGAGATTGAATAAAA-TTAG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTGAA-AAAACTTAG
209245 AACATCAATT
Statistics
Matches: 284, Mismatches: 51, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
41 29 0.10
42 49 0.17
43 54 0.19
44 124 0.44
45 28 0.10
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (44 bp):
GGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAGG
Found at i:209040 original size:87 final size:87
Alignment explanation
Indices: 208862--209269 Score: 386
Period size: 87 Copynumber: 4.7 Consensus size: 87
208852 TAGAGGCCTT
* * * * *
208862 AATTATAAAGGTAGAAATTGAGATCGAAAAAAACTTAGGGGCATCAATTATAAAGGT-ATAATTG
1 AATTATAAAGGTAGAAAGTGAGATTG-AAAAAACTTAGGGGCCTCAATTATAAAGGTAAAAAATG
*
208926 AGATTGAAAAAACTTAGGGGCCTC
65 AGATTGAAAAAA-TTAGGGGACTC
* * * * *
208950 AATTATAAAGGTAGAAAGTGAGACTGAAAACACTTAAGGGCCTTAATTATAAAGTTAAAAAAGTG
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAAAAAA-TG
*
209015 AGATT-AAAAAATTAGGGGATTC
65 AGATTGAAAAAATTAGGGGACTC
* * * * *
209037 AATTATAAGGGTAGAGATTGAGATTGAAAAAACTTAGGGGCCTCAATTGTAAAGGTAGAAAATGA
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAAAAAATGA
* * *
209102 GATTGGAAAAACTTAAGGGCCTC
66 GATT-GAAAAAATTAGGGGACTC
* * * * *
209125 AATTATAAAGTTAAAAAGTGGGGTT--AAAAA-TTAGGGGACTCAATTATAAAGGTAAAAATATG
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAAAAA-ATG
* *
209187 -TATTG-AAAAATTA-GAGACTTC
65 AGATTGAAAAAATTAGGGGAC-TC
* * ** * *
209208 AATTATAAAGATAAAAAGTGAGATTGAATAAAA-TTA-GAACATCAATTATGAAGGTAAAAAAT
1 AATTATAAAGGTAGAAAGTGAGATTGAA-AAAACTTAGGGGCCTCAATTATAAAGGTAAAAAAT
209270 AATAAAATTA
Statistics
Matches: 263, Mismatches: 48, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
82 3 0.01
83 31 0.12
84 3 0.01
85 48 0.18
86 22 0.08
87 86 0.33
88 63 0.24
89 7 0.03
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (87 bp):
AATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAAAAAATGA
GATTGAAAAAATTAGGGGACTC
Found at i:209062 original size:131 final size:127
Alignment explanation
Indices: 208856--209235 Score: 453
Period size: 131 Copynumber: 2.9 Consensus size: 127
208846 AAAAAATAGA
* * * * *
208856 GGCCTTAATTATAAAGGTAGAAATTGAGATCGAAAAAAACTTAGGGGCATCAATTATAAAGGTAT
1 GGCCTTAATTATAAAGTTAAAAAGTGAGAT--TAAAAAA-TTAGGGG-ATCAATTATAAAGGTAA
*
208921 AATTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGACTGAAAACACTTA
62 AATTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAA-ACTTA
208986 AG
126 AG
* *
208988 GGCCTTAATTATAAAGTTAAAAAAGTGAGATTAAAAAATTAGGGGATTCAATTATAAGGGTAGAG
1 GGCCTTAATTATAAAGTT-AAAAAGTGAGATTAAAAAATTAGGGGA-TCAATTATAAAGGTA-AA
* *
209053 ATTGAGATTGAAAAAACTTAGGGGCCTCAATTGTAAAGGTAGAAAATGAGATTGGAAAAACTTAA
63 ATTGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATT-GAAAAACTTAA
209118 G
127 G
* * *
209119 GGCCTCAATTATAAAGTTAAAAAGTGGGGTT-AAAAATTAGGGGACTCAATTATAAAGGTAAAAA
1 GGCCTTAATTATAAAGTTAAAAAGTGAGATTAAAAAATTAGGGGA-TCAATTATAAAGGT-AAAA
* * * * * *
209183 TATG-TATTG-AAAAA-TTAGAGACTTCAATTATAAAGATAAAAAGTGAGATTGAA
64 T-TGAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAA
209236 TAAAATTAGA
Statistics
Matches: 218, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
126 3 0.01
127 29 0.13
128 5 0.02
129 34 0.16
130 35 0.16
131 80 0.37
132 22 0.10
133 10 0.05
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (127 bp):
GGCCTTAATTATAAAGTTAAAAAGTGAGATTAAAAAATTAGGGGATCAATTATAAAGGTAAAATT
GAGATTGAAAAAACTTAGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAACTTAAG
Found at i:209266 original size:43 final size:42
Alignment explanation
Indices: 209150--209267 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
209140 AAGTGGGGTT
*
209150 AAAAATTAGGGGAC-TCAATTATAAAGGTAAAAATATGTATTG
1 AAAAATTA-GAGACATCAATTATAAAGGTAAAAATATGTATTG
* *
209192 AAAAATTAGAGACTTCAATTATAAAGATAAAAAGTGA-G-ATTG
1 AAAAATTAGAGACATCAATTATAAAGGTAAAAA-T-ATGTATTG
*
209234 AATAAAATTAGA-ACATCAATTATGAAGGTAAAAA
1 -A-AAAATTAGAGACATCAATTATAAAGGTAAAAA
209268 ATAATAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
41 4 0.06
42 30 0.45
43 22 0.33
44 10 0.15
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAAATTAGAGACATCAATTATAAAGGTAAAAATATGTATTG
Found at i:209541 original size:66 final size:64
Alignment explanation
Indices: 209396--209519 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
209386 TGATGTATTG
*
209396 AACTTTGAATATTAAAATATAATTATATCCTTTTTAATATTTTAAATTAAAATAATATCTATAT
1 AACTTTGAATATTAAAAGATAATTATATCCTTTTTAATATTTTAAATTAAAATAATATCTATAT
* *
209460 AAATTTGAATATTAAAAGATATATATATATCTTTTTTGAATATTTTAAATTAAAA-AATAT
1 AACTTTGAATATTAAAAGATA-AT-TATATCCTTTTT-AATATTTTAAATTAAAATAATAT
209520 TTATTATCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
64 19 0.35
65 2 0.04
66 16 0.30
67 17 0.31
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (64 bp):
AACTTTGAATATTAAAAGATAATTATATCCTTTTTAATATTTTAAATTAAAATAATATCTATAT
Found at i:209898 original size:23 final size:20
Alignment explanation
Indices: 209843--209904 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 20
209833 TTAGGAACAC
209843 ATAATTTTATTAATTTAAAAA
1 ATAA-TTTATTAATTTAAAAA
* *
209864 ATTATTAATTAATTGATAAAATA
1 ATAATTTATTAATT--TAAAA-A
209887 ATAATTTATTAATTTAAA
1 ATAATTTATTAATTTAAA
209905 GATATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.26
21 7 0.21
22 5 0.15
23 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAATTTATTAATTTAAAAA
Found at i:212098 original size:21 final size:21
Alignment explanation
Indices: 212074--212115 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
212064 GTCCATACAA
212074 GTATTTTTGTAGTCTCCACAC
1 GTATTTTTGTAGTCTCCACAC
212095 GTATTTTTGTAGTCTCCACAC
1 GTATTTTTGTAGTCTCCACAC
212116 CCTGGTCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (21 bp):
GTATTTTTGTAGTCTCCACAC
Found at i:235307 original size:2 final size:2
Alignment explanation
Indices: 235261--235291 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
235251 GTCTAGTATT
235261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
235292 GAAATATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:235341 original size:22 final size:22
Alignment explanation
Indices: 235313--235374 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
235303 ATATACTCCA
235313 ATCAGTGCTTAGGCACTTTAGT
1 ATCAGTGCTTAGGCACTTTAGT
*
235335 ATCAGTGCTTAGGCATTTTAGT
1 ATCAGTGCTTAGGCACTTTAGT
* *
235357 A-CTAATGCTGAGGCACTT
1 ATC-AGTGCTTAGGCACTT
235375 CAGTTATTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (22 bp):
ATCAGTGCTTAGGCACTTTAGT
Found at i:245542 original size:20 final size:20
Alignment explanation
Indices: 245514--245551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
245504 CTCATCAAAT
245514 TATAAATACAACTTTAATAA
1 TATAAATACAACTTTAATAA
* *
245534 TATATATACAATTTTAAT
1 TATAAATACAACTTTAAT
245552 TTCATGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAATACAACTTTAATAA
Found at i:254630 original size:12 final size:12
Alignment explanation
Indices: 254613--254689 Score: 50
Period size: 14 Copynumber: 6.0 Consensus size: 12
254603 TATATTATAG
254613 ATATTAATTTTA
1 ATATTAATTTTA
254625 ATATTAAATTTTTA
1 ATATT-AA-TTTTA
* *
254639 A-A-TAAATTAA
1 ATATTAATTTTA
254649 ATATTAATTTTTTA
1 ATATTAA--TTTTA
*
254663 ATATTATATTATA
1 ATATTA-ATTTTA
254676 TATATTTAATTTTA
1 -ATA-TTAATTTTA
254690 TATCATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 9 0.18
13 7 0.14
14 23 0.46
15 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTAATTTTA
Found at i:254683 original size:21 final size:21
Alignment explanation
Indices: 254659--254711 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
254649 ATATTAATTT
*
254659 TTTAATATTATATTATATATA
1 TTTAATTTTATATTATATATA
*
254680 TTTAATTTTATATCATATA-A
1 TTTAATTTTATATTATATATA
*
254700 ATT-ATTTTATAT
1 TTTAATTTTATAT
254712 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 17 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATTTTATATTATATATA
Found at i:254691 original size:14 final size:15
Alignment explanation
Indices: 254649--254715 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 15
254639 AATAAATTAA
*
254649 ATATTAATTTTTTA-
1 ATATTAATTTTATAT
*
254663 ATATT-ATATTATAT
1 ATATTAATTTTATAT
254677 ATATTTAATTTTATAT
1 ATA-TTAATTTTATAT
* *
254693 CATATAAATTATTTTAT
1 -ATATTAATT-TTATAT
254710 ATATTA
1 ATATTA
254716 TTAAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.14
14 8 0.19
15 2 0.05
16 18 0.43
17 8 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTAATTTTATAT
Found at i:258208 original size:63 final size:64
Alignment explanation
Indices: 258122--258257 Score: 177
Period size: 63 Copynumber: 2.1 Consensus size: 64
258112 TATATATACG
** * * * *
258122 GTGACTAAATTATAAATAAAATAAAATTCGAATACT-GAATTAAAATATATGAAAATTTATTGTA
1 GTGACTAAATTATAAATAAAATAAAATTAAAAGA-TAGAATTAAAACATATAAAAATTGATTGTA
*
258186 GTGACTAAATTAT-AATAAAATAAAATTAAAAGATAGAATTAAAACATATAAAAATTGATTTTA
1 GTGACTAAATTATAAATAAAATAAAATTAAAAGATAGAATTAAAACATATAAAAATTGATTGTA
*
258249 GTGGCTAAA
1 GTGACTAAA
258258 ATAGAAGTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
62 1 0.02
63 49 0.78
64 13 0.21
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.32
Consensus pattern (64 bp):
GTGACTAAATTATAAATAAAATAAAATTAAAAGATAGAATTAAAACATATAAAAATTGATTGTA
Found at i:258993 original size:45 final size:45
Alignment explanation
Indices: 258925--259022 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
258915 TGGAACGGGG
* * *
258925 ACGTGGAGAGACTGTTGGTAGTGCTGGAAGCT-ACTGGAATTTACA
1 ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGA-TGGAATTTACA
* * **
258970 ACGTGGAGTGGCTGCTGGCAGTGCTGGAAACTGATGGAATTTGTA
1 ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGATGGAATTTACA
259015 ACGTGGAG
1 ACGTGGAG
259023 CTGCTGGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (45 bp):
ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGATGGAATTTACA
Found at i:259495 original size:39 final size:39
Alignment explanation
Indices: 259440--259738 Score: 404
Period size: 39 Copynumber: 7.7 Consensus size: 39
259430 AGGTTGAATA
* *
259440 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * * * *
259479 AGTTCTTCAGATTATGAACTCCTTC-TCTTCTTCATATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
259517 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* *
259556 AGTTCTTCAGATTATGAAC-TCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTC-TTCTTCCTCTTCAGACG
*
259595 AGTTCTTCAGACTATGAACTTCTTCTTTCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * * *
259634 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAAATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* *
259673 AGTTCTTTAGACTATGAATTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * *
259712 AGTTTTTCAGATTATGAACTCCTTCTT
1 AGTTCTTCAGACTATGAACTTCTTCTT
259739 GAAATGTTTT
Statistics
Matches: 226, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
38 35 0.15
39 189 0.84
40 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
Found at i:259733 original size:78 final size:78
Alignment explanation
Indices: 259440--259738 Score: 483
Period size: 78 Copynumber: 3.8 Consensus size: 78
259430 AGGTTGAATA
* *
259440 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGATGAGTTCTTCAGATTATGAACTCCTTC-
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
* *
259504 TCTTCTTCATATG
66 TCCTCTTCAAATG
* *
259517 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
* *
259582 TCCTCTTCAGACG
66 TCCTCTTCAAATG
*
259595 AGTTCTTCAGACTATGAACTTCTTCTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
259660 TCCTCTTCAAATG
66 TCCTCTTCAAATG
* * *
259673 AGTTCTTTAGACTATGAATTTCTTCTTCCTCTTCAGACGAGTTTTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
259738 T
66 T
259739 GAAATGTTTT
Statistics
Matches: 205, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
77 60 0.29
78 145 0.71
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (78 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
TCCTCTTCAAATG
Found at i:259864 original size:73 final size:73
Alignment explanation
Indices: 259743--260003 Score: 425
Period size: 73 Copynumber: 3.6 Consensus size: 73
259733 CTTCTTGAAA
* ** *
259743 TGTTTTAAGAAAAACAATCTTAAGTGAGATAAATTGCTATTTTGAGTGAAACTTTCTTCAACGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
*
259808 AAACAGTT
66 AAACAATT
* *
259816 TGTTTTAAGAAAAACAATGTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC-TCTAGCGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTC-AGCGA
259880 GAAACAATT
65 GAAACAATT
*
259889 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
259954 AAACAATT
66 AAACAATT
*
259962 GGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
260004 GAAAACATCC
Statistics
Matches: 175, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
72 2 0.01
73 172 0.98
74 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
AAACAATT
Found at i:260711 original size:22 final size:22
Alignment explanation
Indices: 260686--260740 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
260676 AATAAAGCTT
260686 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAAAAAGAATCTA
* *
260708 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAAAGAATCTA
260730 TCATCTTTGAA
1 TCATCTTTGAA
260741 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAAAGAATCTA
Found at i:261203 original size:54 final size:54
Alignment explanation
Indices: 261109--261257 Score: 226
Period size: 54 Copynumber: 2.8 Consensus size: 54
261099 ATAATCAATG
* *
261109 GTTCATAAAATATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
* * *
261163 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
* * *
261217 GGTCGTAAAACATTTAACAACACATTCATCATTTCTTGTGG
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGG
261258 CTTTTGCTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
Found at i:263460 original size:14 final size:13
Alignment explanation
Indices: 263437--263474 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
263427 AATTTCTTTT
263437 TTTTCTTCTTTCC
1 TTTTCTTCTTTCC
*
263450 TTTTCTCTCTTTCT
1 TTTTCT-TCTTTCC
263464 TTTTCTTCTTT
1 TTTTCTTCTTT
263475 TTCATATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTTCTTTCC
Found at i:265902 original size:16 final size:16
Alignment explanation
Indices: 265881--265911 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
265871 GAAATCCTTA
265881 TTTTAATGAATGATTG
1 TTTTAATGAATGATTG
*
265897 TTTTAATGCATGATT
1 TTTTAATGAATGATT
265912 TGGAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTTAATGAATGATTG
Found at i:268435 original size:45 final size:45
Alignment explanation
Indices: 268371--268468 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
268361 TGGAACGGGG
268371 ACGTGGAGGGACTACTGGCAGTGCTGGAAGCT-ACTGGAATTTGCA
1 ACGTGGAGGGACTACTGGCAGTGCTGGAAGCTGA-TGGAATTTGCA
* * * *
268416 ACGTGGTGGGGCTGCTGGCAGTGCTGGAAGCTGATGGAATTTGTA
1 ACGTGGAGGGACTACTGGCAGTGCTGGAAGCTGATGGAATTTGCA
268461 ACGTGGAG
1 ACGTGGAG
268469 CTGCTGGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.23
Consensus pattern (45 bp):
ACGTGGAGGGACTACTGGCAGTGCTGGAAGCTGATGGAATTTGCA
Found at i:272904 original size:55 final size:55
Alignment explanation
Indices: 272842--273264 Score: 448
Period size: 55 Copynumber: 7.9 Consensus size: 55
272832 TGACGAGTCT
* * * *
272842 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * * *
272897 GCTCCCTATTCATTCAGGGAGTAT-AGAACTCGAACAATCTTCATA-AAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA-ACAAACGTGTCC
*
272952 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* * ** * *
273007 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAATAATCTTCATGAAATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* *
273062 GCTCTCC-ATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACTTGTCC
1 GCTC-CCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * * *
273117 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * *
273168 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* *
273219 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
273265 AATTTGCTTC
Statistics
Matches: 333, Mismatches: 29, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
51 112 0.34
54 5 0.02
55 214 0.64
56 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
Found at i:272986 original size:110 final size:110
Alignment explanation
Indices: 272838--273249 Score: 513
Period size: 110 Copynumber: 3.8 Consensus size: 110
272828 CAAATGACGA
* * * *
272838 GTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCTGCTCC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTCCGCTCC
* *
272902 CTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
65 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
* *
272948 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCTC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCCC
* * *
273013 TATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATGAAATGG
66 TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
* * *
273058 GTCCGCTCTCC-ATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACTTGTCCGCTCC
1 GTCTGCTC-CCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCC
* * **
273122 CTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTT
65 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGG
* * *
273164 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCCC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCCC
* *
273225 TATTCTTTCAGAGAGTATAGGACTC
66 TATTCCTTCAGAGAGTATAGAACTC
273250 AATCTTCAAC
Statistics
Matches: 269, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
102 49 0.18
105 2 0.01
106 38 0.14
110 178 0.66
111 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (110 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCCGCTCCC
TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
Found at i:274561 original size:22 final size:20
Alignment explanation
Indices: 274536--274605 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
274526 TGAACCCTCC
274536 TTTTATTTCTCTTTTTTTTCAT
1 TTTTATTT-T-TTTTTTTTCAT
*
274558 TTTTCTTTTTTTCATTTTTCAT
1 TTTTATTTTTTT--TTTTTCAT
*
274580 TTTTCATTTTTTCATTTTTCAT
1 TTTT-ATTTTTT-TTTTTTCAT
274602 TTTT
1 TTTT
274606 TCTTCCCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 31 0.76
23 6 0.15
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTTTTTTTTCAT
Found at i:274562 original size:7 final size:7
Alignment explanation
Indices: 274550--274675 Score: 107
Period size: 7 Copynumber: 17.9 Consensus size: 7
274540 ATTTCTCTTT
274550 TTTTTCA
1 TTTTTCA
*
274557 TTTTTCTT
1 TTTTTC-A
274565 TTTTTCA
1 TTTTTCA
274572 TTTTTCA
1 TTTTTCA
274579 TTTTTCA
1 TTTTTCA
274586 TTTTTTCA
1 -TTTTTCA
274594 TTTTTCA
1 TTTTTCA
274601 TTTTT--
1 TTTTTCA
* * *
274606 TCTTCCC
1 TTTTTCA
*
274613 TTTTCCA
1 TTTTTCA
274620 TTTTT--
1 TTTTTCA
***
274625 TCCCATCA
1 T-TTTTCA
274633 TTTTTCA
1 TTTTTCA
274640 TTTTTCA
1 TTTTTCA
274647 TTTTTCA
1 TTTTTCA
274654 TTTTTCTCA
1 -TTTT-TCA
274663 TTTTTCA
1 TTTTTCA
274670 TTTTTC
1 TTTTTC
274676 TCTTTTATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
5 4 0.04
6 1 0.01
7 67 0.69
8 22 0.23
9 3 0.03
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:274564 original size:16 final size:16
Alignment explanation
Indices: 274536--274676 Score: 107
Period size: 16 Copynumber: 8.8 Consensus size: 16
274526 TGAACCCTCC
* *
274536 TTTT-ATTTCTCTTTT
1 TTTTCATTTTTCTTAT
274551 TTTTCATTTTTCTT-T
1 TTTTCATTTTTCTTAT
274566 TTTTCATTTTTC--AT
1 TTTTCATTTTTCTTAT
*
274580 TTTTCATTTTT-TCAT
1 TTTTCATTTTTCTTAT
*
274595 TTTTCATTTTTTCTTCCCT
1 TTTTCA-TTTTTCTT--AT
* *
274614 TTTCCATTTTTTCCCATCAT
1 TTTTCA-TTTTT--C-TTAT
274634 TTTTCATTTTTC--AT
1 TTTTCATTTTTCTTAT
*
274648 TTTTCATTTTTCTCAT
1 TTTTCATTTTTCTTAT
274664 TTTTCATTTTTCT
1 TTTTCATTTTTCT
274677 CTTTTATTTC
Statistics
Matches: 106, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
14 26 0.25
15 25 0.24
16 28 0.26
17 2 0.02
19 17 0.16
20 6 0.06
21 1 0.01
22 1 0.01
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCATTTTTCTTAT
Found at i:274566 original size:14 final size:14
Alignment explanation
Indices: 274549--274691 Score: 99
Period size: 15 Copynumber: 9.1 Consensus size: 14
274539 TATTTCTCTT
274549 TTTTTTCATTTTTC
1 TTTTTTCATTTTTC
274563 TTTTTTTCATTTTTC
1 -TTTTTTCATTTTTC
*
274578 ATTTTTCATTTTTTC
1 TTTTTTCA-TTTTTC
*
274593 ATTTTTCATTTTTTC
1 TTTTTTCA-TTTTTC
274608 TTCCCTTTTCCATTTTTTCCC
1 TT---TTTT-CA-TTTTT--C
274629 ATCATTTTTCATTTTTC
1 -T--TTTTTCATTTTTC
*
274646 ATTTTTCATTTTTC
1 TTTTTTCATTTTTC
274660 TCATTTTTCATTTTTC
1 T--TTTTTCATTTTTC
*
274676 TCTTTT-ATTTCTTC
1 TTTTTTCATTT-TTC
274690 TT
1 TT
274692 CAAGCAAAAT
Statistics
Matches: 109, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
13 4 0.04
14 28 0.26
15 36 0.33
16 14 0.13
17 1 0.01
18 4 0.04
19 13 0.12
20 2 0.02
21 5 0.05
22 1 0.01
24 1 0.01
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTCATTTTTC
Found at i:278137 original size:8 final size:8
Alignment explanation
Indices: 278124--278151 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
278114 AAGAGAAGAT
278124 ATATATAC
1 ATATATAC
278132 ATATATAC
1 ATATATAC
278140 ATATATAC
1 ATATATAC
278148 ATAT
1 ATAT
278152 GGGAAGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:284356 original size:45 final size:47
Alignment explanation
Indices: 284299--284387 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
284289 AAAAAGAAAT
*
284299 CCTAACCTCATGATATCTAATTCGCATGC-TTATTC-AAAAAATGAA
1 CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAAATGAA
*
284344 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGAAAAAA
1 CCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGAAAAAA
284388 ACGAACATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
45 27 0.69
47 6 0.15
48 6 0.15
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.30
Consensus pattern (47 bp):
CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAAATGAA
Found at i:295135 original size:19 final size:19
Alignment explanation
Indices: 295104--295160 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
295094 TTTCATACAT
*
295104 TAAAA-ATTGAAATATTCAA
1 TAAAATATT-AAATATTAAA
295123 TAAAATATTAAATATTTAAA
1 TAAAATATTAAATA-TTAAA
295143 TAAACATAATTAAATATT
1 TAAA-AT-ATTAAATATT
295161 TTTACCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.30
20 11 0.33
21 4 0.12
22 8 0.24
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAATATTAAATATTAAA
Found at i:295305 original size:14 final size:14
Alignment explanation
Indices: 295257--295305 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
295247 AAAATTAGTA
295257 ATTAAAATAAACTA-
1 ATTAAAATAAA-TAT
*
295271 A-TAAAATAAAAAAT
1 ATTAAAAT-AAATAT
295285 ATT-AAATAAATAT
1 ATTAAAATAAATAT
295298 ATTAAAAT
1 ATTAAAAT
295306 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 15 0.52
14 13 0.45
15 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAATAT
Found at i:295613 original size:30 final size:30
Alignment explanation
Indices: 295557--295613 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
295547 CATATTGTCA
*
295557 TAAAGGATACTATTTTGATATATATTAGAC
1 TAAAGGATACTATTTTGATACATATTAGAC
* *
295587 TAAAGG-TTCTATTTTGGTACATTATTA
1 TAAAGGATACTATTTTGATACA-TATTA
295614 TTTTTTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
TAAAGGATACTATTTTGATACATATTAGAC
Found at i:295997 original size:31 final size:31
Alignment explanation
Indices: 295962--296028 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
295952 AACAAATCAA
*
295962 TCACTAACAATATCGATTTATAACAAAATGG
1 TCACTAACAATATCAATTTATAACAAAATGG
** *
295993 TCACTAACGTTATCAATTTGTAACAAAATGG
1 TCACTAACAATATCAATTTATAACAAAATGG
296024 TCACT
1 TCACT
296029 CAACCGTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (31 bp):
TCACTAACAATATCAATTTATAACAAAATGG
Found at i:302110 original size:28 final size:28
Alignment explanation
Indices: 302070--302135 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
302060 ATAATAATAG
302070 ATGCCAATATCTGGCCTCGGATAGGTTC
1 ATGCCAATATCTGGCCTCGGATAGGTTC
302098 ATGCCAATATCTGGCCTCGGATAGGTTC
1 ATGCCAATATCTGGCCTCGGATAGGTTC
302126 ATGCCAATAT
1 ATGCCAATAT
302136 TGACCAGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (28 bp):
ATGCCAATATCTGGCCTCGGATAGGTTC
Found at i:304910 original size:11 final size:11
Alignment explanation
Indices: 304894--304925 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
304884 CGACCGCACT
304894 TGCATCAAACA
1 TGCATCAAACA
304905 TGCATCAAACA
1 TGCATCAAACA
304916 TGCATCAAAC
1 TGCATCAAAC
304926 CAAGAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (11 bp):
TGCATCAAACA
Found at i:318526 original size:13 final size:13
Alignment explanation
Indices: 318508--318533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318498 TTGCTAGTGA
318508 CCAAAATGTAAGT
1 CCAAAATGTAAGT
318521 CCAAAATGTAAGT
1 CCAAAATGTAAGT
318534 TTTGAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CCAAAATGTAAGT
Found at i:321587 original size:64 final size:64
Alignment explanation
Indices: 321506--321662 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 64
321496 GAAGGTGTAT
** ***
321506 CGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATGCA
1 CGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATGCA
*
321569 T
64 C
* * * *
321570 TGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGCAC
1 CGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGCAC
* *
321634 CGATGCATCAGTAGTGCATCGATGTATAC
1 CGATGCATAAGTAGTGCATCGATGCATAC
321663 TTTCATTGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 74 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
CGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGCAC
Found at i:322368 original size:31 final size:31
Alignment explanation
Indices: 322315--322402 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
322305 GGGTCGAGGG
322315 TTACCTATGTTCTTC-GGACATAT-GAACTGT
1 TTACCTATGTTCTTCGGGACATATGGAA-TGT
322345 TTACCTATGTTCTTCGGGACATATGGAATGT
1 TTACCTATGTTCTTCGGGACATATGGAATGT
*
322376 TTACCTAGGTTCTTCGGGATC-TATGGA
1 TTACCTATGTTCTTCGGGA-CATATGGA
322403 CTGGTCCTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
30 15 0.28
31 35 0.65
32 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGAATGT
Found at i:325385 original size:31 final size:31
Alignment explanation
Indices: 325343--325404 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
325333 GACATATAGA
*
325343 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTAGGTTCTAAGGAACATATGGACAGTT
** *
325374 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTAGGTTCTAAGGAACATATGGACAGTT
325405 ACCGAGGATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTAGGTTCTAAGGAACATATGGACAGTT
Found at i:328384 original size:3 final size:3
Alignment explanation
Indices: 328378--328407 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
328368 CATCATCATC
328378 TCT TCT TCT TCTT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TC-T TCT TCT TCT TCT TCT TC
328408 ATGTACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:328544 original size:19 final size:20
Alignment explanation
Indices: 328511--328548 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
328501 ATACTTAAGC
*
328511 TTATGGAAAGCTTAAAGAAG
1 TTATGGAAAGATTAAAGAAG
328531 TTAT-GAAAGATTAAAGAA
1 TTATGGAAAGATTAAAGAA
328549 AATGAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (20 bp):
TTATGGAAAGATTAAAGAAG
Found at i:329028 original size:64 final size:60
Alignment explanation
Indices: 328917--329071 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 60
328907 TTGAAGGTGT
** ***
328917 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAAAATAAAAACATCGAATGCAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAAAATAAAAACATCGAAT----TTCATGC
* *
328981 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAAT-ACAACATCGAATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAA-AATAAAAACATCGAATTTCATGC
* *
329041 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
329072 TTTCATTGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
60 35 0.44
63 1 0.01
64 41 0.51
65 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (60 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAAAATAAAAACATCGAATTTCATGC
Found at i:329751 original size:30 final size:31
Alignment explanation
Indices: 329715--329795 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 31
329705 AGGGTCGAGG
329715 GTTTACCTATGTTCTTCGGGACATAT-GACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
329745 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
329776 GTTTACCTA-GTTCTTTGGGA
1 GTTTACCTATGTTCTTCGGGA
329796 TCTATCGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 36 0.73
31 13 0.27
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:337357 original size:11 final size:11
Alignment explanation
Indices: 337341--337365 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
337331 ATAAAAAATA
337341 CCCCTTAGCAG
1 CCCCTTAGCAG
337352 CCCCTTAGCAG
1 CCCCTTAGCAG
337363 CCC
1 CCC
337366 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:340620 original size:15 final size:16
Alignment explanation
Indices: 340592--340623 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
340582 GGTATCTTTC
340592 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
340608 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
340623 T
1 T
340624 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:341398 original size:16 final size:16
Alignment explanation
Indices: 341374--341407 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
341364 TATCGCCGAC
*
341374 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
341390 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
341406 CG
1 CG
341408 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:341779 original size:11 final size:11
Alignment explanation
Indices: 341763--341787 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
341753 ATAAAAAATA
341763 CCCCTTAGCAG
1 CCCCTTAGCAG
341774 CCCCTTAGCAG
1 CCCCTTAGCAG
341785 CCC
1 CCC
341788 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:345799 original size:15 final size:16
Alignment explanation
Indices: 345779--345808 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
345769 ATAAAAAATT
345779 AAATAAT-TTTATTAA
1 AAATAATGTTTATTAA
345794 AAATAATGTTTATTA
1 AAATAATGTTTATTA
345809 TTTTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAATAATGTTTATTAA
Found at i:346244 original size:23 final size:23
Alignment explanation
Indices: 346218--346261 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
346208 ATTAATAATC
346218 TTCTAATAAGA-TGATGACATGTG
1 TTCTAATAAGAGTG-TGACATGTG
346241 TTCTAATAAGAGTGTGACATG
1 TTCTAATAAGAGTGTGACATG
346262 CATTGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTAATAAGAGTGTGACATGTG
Found at i:350391 original size:21 final size:21
Alignment explanation
Indices: 350365--350442 Score: 156
Period size: 21 Copynumber: 3.7 Consensus size: 21
350355 TTCTGGGCAG
350365 AGTGCATCGATGCATATTCAT
1 AGTGCATCGATGCATATTCAT
350386 AGTGCATCGATGCATATTCAT
1 AGTGCATCGATGCATATTCAT
350407 AGTGCATCGATGCATATTCAT
1 AGTGCATCGATGCATATTCAT
350428 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
350443 CAAGGTTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
AGTGCATCGATGCATATTCAT
Found at i:350612 original size:64 final size:64
Alignment explanation
Indices: 350509--350632 Score: 148
Period size: 64 Copynumber: 1.9 Consensus size: 64
350499 ATGCACTCTT
* *
350509 TTAAAATAAAAAGATCGAATGCAATTAGTGCATCCATGCATAAGGCA-TGCATCGATGCATCCCA
1 TTAAAATAAAAACATCGAATGCAATTAGTGCATCCATGCACAA-GCAGTGCATCGATGCATCCCA
* *
350573 TTAATAAT-AAAACATCGAATGCATTTTA-TGCA-CCGATGCACAAGTAGTGCATCGATGCAT
1 TTAA-AATAAAAACATCGAATGCA-ATTAGTGCATCC-ATGCACAAGCAGTGCATCGATGCAT
350633 ACCTTCATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
63 4 0.08
64 42 0.81
65 6 0.12
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (64 bp):
TTAAAATAAAAACATCGAATGCAATTAGTGCATCCATGCACAAGCAGTGCATCGATGCATCCCA
Found at i:351029 original size:12 final size:12
Alignment explanation
Indices: 350994--351029 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
350984 TTCAAATACC
*
350994 TATGTGATATAA
1 TATGTGATATGA
351006 TATGTGATATGA
1 TATGTGATATGA
*
351018 TATGTGACATGA
1 TATGTGATATGA
351030 GAACATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (12 bp):
TATGTGATATGA
Found at i:351071 original size:29 final size:29
Alignment explanation
Indices: 351028--351108 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
351018 TATGTGACAT
351028 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
351058 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
351087 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
351109 ACAAATGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:356056 original size:15 final size:15
Alignment explanation
Indices: 356036--356069 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
356026 TTTAGTTGGA
*
356036 CGGGCGGATGTGGGG
1 CGGGCGGATGCGGGG
356051 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
356066 CGGG
1 CGGG
356070 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.68, T:0.09
Consensus pattern (15 bp):
CGGGCGGATGCGGGG
Found at i:357146 original size:14 final size:14
Alignment explanation
Indices: 357113--357151 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
357103 GAACATATAA
* *
357113 TGTGTGGGGCCCTT
1 TGTGTGGGTCCCTC
*
357127 TATGTGGGTCCCTC
1 TGTGTGGGTCCCTC
357141 TGTGTGGGTCC
1 TGTGTGGGTCC
357152 TGATTTCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.38, T:0.36
Consensus pattern (14 bp):
TGTGTGGGTCCCTC
Found at i:359253 original size:2 final size:2
Alignment explanation
Indices: 359246--359271 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
359236 TCAAAAACGA
359246 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
359272 TGAAAATATA
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:362565 original size:21 final size:21
Alignment explanation
Indices: 362541--362580 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
362531 ATGTTTAATG
362541 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
362562 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
362581 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:362937 original size:20 final size:20
Alignment explanation
Indices: 362908--362945 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
362898 ACTTTATGCA
*
362908 ATACCAATTGTTGAAATTTG
1 ATACCAATTGTTAAAATTTG
*
362928 ATACCGATTGTTAAAATT
1 ATACCAATTGTTAAAATT
362946 AAATGCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
ATACCAATTGTTAAAATTTG
Found at i:363759 original size:19 final size:19
Alignment explanation
Indices: 363737--363773 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
363727 AAAATTTCAT
*
363737 TTTGATTTTCAAAATCAAC
1 TTTGACTTTCAAAATCAAC
*
363756 TTTGGCTTTCAAAATCAA
1 TTTGACTTTCAAAATCAA
363774 ATCATTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (19 bp):
TTTGACTTTCAAAATCAAC
Found at i:365045 original size:20 final size:20
Alignment explanation
Indices: 365020--365074 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
365010 TTGCAATCTT
365020 GGTGCATGGATGCACAGCAG
1 GGTGCATGGATGCACAGCAG
*
365040 GGTGCATGGATGCAAAGCAG
1 GGTGCATGGATGCACAGCAG
*
365060 GGTGCATCGATGCAC
1 GGTGCATGGATGCAC
365075 TAATTGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.16
Consensus pattern (20 bp):
GGTGCATGGATGCACAGCAG
Found at i:365705 original size:20 final size:19
Alignment explanation
Indices: 365678--365732 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
365668 ATTAAGCTCT
365678 TTAGTATCGATACTGACAC
1 TTAGTATCGATACTGACAC
* *
365697 TTGAGTATCGATACTCACCC
1 TT-AGTATCGATACTGACAC
*
365717 TTTGTATCGATACTGA
1 TTAGTATCGATACTGA
365733 AAATGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (19 bp):
TTAGTATCGATACTGACAC
Found at i:367110 original size:20 final size:23
Alignment explanation
Indices: 367085--367138 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 23
367075 CCTTGAAGTT
367085 CATCGATGCATTC-TAT-A-GTG
1 CATCGATGCATTCTTATCATGTG
367105 CATCGATGCATTCTTTATCATGTG
1 CATCGATGCATTC-TTATCATGTG
367129 CATCGATGCA
1 CATCGATGCA
367139 CTACCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.43
22 3 0.10
23 1 0.03
24 13 0.43
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
CATCGATGCATTCTTATCATGTG
Found at i:367197 original size:64 final size:64
Alignment explanation
Indices: 367126--367268 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
367116 TCTTTATCAT
* * *
367126 GTGCATCGATGCACTAC-CCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CTCCATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAA-GG
367189 G
64 G
** * * ** *
367190 GTGCATCGATGCACTCTTTATGCATCGATGCACTAATTGCATTCAATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCTCCATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGG
367254 GTGCATCGATGCACT
1 GTGCATCGATGCACT
367269 TCTTGTGCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 60 0.90
65 6 0.09
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTCTCCATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGG
Found at i:368903 original size:21 final size:21
Alignment explanation
Indices: 368879--368923 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
368869 CAAAGAATCA
*
368879 ATCTATCAATGAAAATGATTG
1 ATCTATCAATGAAAATGATCG
* *
368900 ATCTCTCGATGAAAATGATCG
1 ATCTATCAATGAAAATGATCG
368921 ATC
1 ATC
368924 CCTTCTCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
ATCTATCAATGAAAATGATCG
Found at i:368982 original size:205 final size:205
Alignment explanation
Indices: 368630--369013 Score: 619
Period size: 205 Copynumber: 1.9 Consensus size: 205
368620 CCTTGTGTAA
* * *
368630 TGGATTCTAGTAAGTTTTGGATTAATCATTTCATAAACTAATCAATCTATCAATGAAAATGTTTG
1 TGGATTCTAGTAAGTTTTGGATTAATCATTTCACAAACGAATCAATCTATCAATGAAAATGATTG
* * * * *
368695 ATCCCTCGGTGAAAAAGATCGACTCATTCTCCTAAAATATCAATCCCTTTCTTGTAACGGTCGAA
66 ATCCCTCGATGAAAAAGATCGACTCATTCTCCTAAAAGATCAATCACTTTATTGTAACGATCGAA
368760 TTATTTGAAAAATAATCAATCCCTTTCACAAAAGAATTGATCCCTTGTGATTGTTTGCTCAAATG
131 TTATTTGAAAAATAATCAATCCCTTTCACAAAAGAATTGATCCCTTGTGATTGTTTGCTCAAATG
368825 ATCGATCCCT
196 ATCGATCCCT
368835 TGGATTCTAGTAAGTTTTGGATTAATCATTTCACCAAA-GAATCAATCTATCAATGAAAATGATT
1 TGGATTCTAGTAAGTTTTGGATTAATCATTTCA-CAAACGAATCAATCTATCAATGAAAATGATT
* * * *
368899 GATCTCTCGATGAAAATGATCGA-TCCCTTCTCCTAAAGGATCAATCACTTTATTGTAACGATCG
65 GATCCCTCGATGAAAAAGATCGACT-CATTCTCCTAAAAGATCAATCACTTTATTGTAACGATCG
*
368963 AATTATTTGAAAAATAATCAATCCCTTTCACAAAAGGATTGATCCCTTGTG
129 AATTATTTGAAAAATAATCAATCCCTTTCACAAAAGAATTGATCCCTTGTG
369014 TATTAAATGT
Statistics
Matches: 164, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
204 1 0.01
205 160 0.98
206 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (205 bp):
TGGATTCTAGTAAGTTTTGGATTAATCATTTCACAAACGAATCAATCTATCAATGAAAATGATTG
ATCCCTCGATGAAAAAGATCGACTCATTCTCCTAAAAGATCAATCACTTTATTGTAACGATCGAA
TTATTTGAAAAATAATCAATCCCTTTCACAAAAGAATTGATCCCTTGTGATTGTTTGCTCAAATG
ATCGATCCCT
Found at i:376849 original size:25 final size:25
Alignment explanation
Indices: 376804--376852 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
376794 GTGCTTTTCC
376804 CATATTAAGACAATCATAATTATTA
1 CATATTAAGACAATCATAATTATTA
376829 CATATTAA-ACTAA-CATGAATTATT
1 CATATTAAGAC-AATCAT-AATTATT
376853 GGGTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (25 bp):
CATATTAAGACAATCATAATTATTA
Found at i:380017 original size:21 final size:21
Alignment explanation
Indices: 379993--380034 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
379983 GCTTGCGTGT
379993 CCTCCCCTTGAACTTGAGGCC
1 CCTCCCCTTGAACTTGAGGCC
380014 CCTCCCCTTGAACTTGAGGCC
1 CCTCCCCTTGAACTTGAGGCC
380035 ATTGTATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTCCCCTTGAACTTGAGGCC
Found at i:380700 original size:8 final size:8
Alignment explanation
Indices: 380687--380727 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
380677 CTCATTTTCA
380687 GAGAATTT
1 GAGAATTT
380695 GAGAATTT
1 GAGAATTT
*
380703 -AGAGTTT
1 GAGAATTT
380710 GAGAATTT
1 GAGAATTT
380718 GAGAATTT
1 GAGAATTT
380726 GA
1 GA
380728 AAGCTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:380712 original size:15 final size:16
Alignment explanation
Indices: 380687--380727 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
380677 CTCATTTTCA
380687 GAGAATTTGAGAATTT
1 GAGAATTTGAGAATTT
*
380703 -AGAGTTTGAGAATTT
1 GAGAATTTGAGAATTT
380718 GAGAATTTGA
1 GAGAATTTGA
380728 AAGCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (16 bp):
GAGAATTTGAGAATTT
Found at i:381401 original size:128 final size:128
Alignment explanation
Indices: 380808--381681 Score: 1416
Period size: 128 Copynumber: 6.8 Consensus size: 128
380798 ACTATTCACG
* * *
380808 TGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTTTTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *** *
380873 TTATATCACTCAAGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACT
*
380936 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
381001 TAATGTCACTCATGTCCCTC-GGG-CACTAGATATATTAGTACCTATTATTTCTCAAGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
*
381062 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
381127 TTATGTTACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
**
381190 TGAAGGCGCGTTCTAAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTC-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
381255 ATTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
65 ATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
**
381319 TGAAGGCGCGTTCCCATGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
381384 TTATGTCTCTCATGTCCCTCGGGGACACTAGATATATCAGCACCTATTATTTATCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
*
381447 TGAAGGCGCGGTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
381512 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
*
381575 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
381640 TTATGTCACTCATGTCCCTCGGGGACTCTAGATATATCAGTA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
381682 AATCAAGTAA
Statistics
Matches: 695, Mismatches: 43, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
125 1 0.00
126 111 0.16
127 7 0.01
128 454 0.65
129 122 0.18
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:382073 original size:34 final size:34
Alignment explanation
Indices: 382034--382140 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
382024 TAAGTTGAAA
* *
382034 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
382068 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
382102 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
382136 TTTAA
1 TTTAA
382141 AAACATTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:382692 original size:21 final size:20
Alignment explanation
Indices: 382668--382733 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 20
382658 TAAAACCCTA
*
382668 CGGGCTAGGCATGTAACCTGG
1 CGGGCTAGGAATGTAACCT-G
382689 CGGGCTAGGAATGTAACCCTG
1 CGGGCTAGGAATGTAA-CCTG
*
382710 CGGGCTCGGAATGTAACCCTG
1 CGGGCTAGGAATGTAA-CCTG
382731 CGG
1 CGG
382734 AGATGGCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 39 0.93
22 3 0.07
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.18
Consensus pattern (20 bp):
CGGGCTAGGAATGTAACCTG
Found at i:382777 original size:21 final size:21
Alignment explanation
Indices: 382737--382778 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
382727 CCTGCGGAGA
*
382737 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
382758 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
382779 GTGCATGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:384545 original size:34 final size:30
Alignment explanation
Indices: 384522--384595 Score: 67
Period size: 31 Copynumber: 2.3 Consensus size: 30
384512 TAAATAATAA
*
384522 TTATATAAATATTATTTTAATAAAAAAATAATAT
1 TTATATAAATA-TA--TTAAT-AAAAAATAATAA
*
384556 TTACATAAATATATTAATAAAAATATAATAA
1 TTATATAAATATATTAATAAAAA-ATAATAA
* *
384587 CTATTTAAA
1 TTATATAAA
384596 AAAATACTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.15
31 17 0.50
33 2 0.06
34 10 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
TTATATAAATATATTAATAAAAAATAATAA
Found at i:384598 original size:21 final size:23
Alignment explanation
Indices: 384560--384601 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
384550 TAATATTTAC
384560 ATAAATATATTAATAAAAATATA
1 ATAAATATATTAATAAAAATATA
*
384583 ATAACTAT-TTAA-AAAAATA
1 ATAAATATATTAATAAAAATA
384602 CTAACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATATATTAATAAAAATATA
Found at i:401599 original size:14 final size:14
Alignment explanation
Indices: 401580--401607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
401570 TCGATTATAT
401580 GTTCATTTATGTTC
1 GTTCATTTATGTTC
401594 GTTCATTTATGTTC
1 GTTCATTTATGTTC
401608 ATTTATGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:401609 original size:24 final size:26
Alignment explanation
Indices: 401567--401618 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 26
401557 CGTTCGTGAA
401567 CGTTCGATTATATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
401593 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
401617 CG
1 CG
401619 AACAGAGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.69
25 3 0.12
26 5 0.19
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:401895 original size:10 final size:10
Alignment explanation
Indices: 401880--401928 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
401870 GTTTGTCTTA
401880 TTCGTTTATG
1 TTCGTTTATG
401890 TTCGTTTATG
1 TTCGTTTATG
401900 TTCGTTTATTGTG
1 TTCGTTTA---TG
*
401913 TTTGTTTATG
1 TTCGTTTATG
401923 TTCGTT
1 TTCGTT
401929 CGCTTGTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 25 0.74
13 9 0.26
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.63
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:401914 original size:23 final size:23
Alignment explanation
Indices: 401888--401955 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
401878 TATTCGTTTA
401888 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
* **
401911 TGTTTGTTTATGTTCGTTCGCTTG
1 TGTTCGTTTATGTTCGTT-TATTG
* *
401935 TGTTCGTTTACGATCGTTTAT
1 TGTTCGTTTATGTTCGTTTAT
401956 CATTTAAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:404124 original size:21 final size:21
Alignment explanation
Indices: 404099--404159 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
404089 GAAAGTATTA
404099 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
404120 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
404134 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
404155 AAATG
1 AAATG
404160 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:404205 original size:36 final size:36
Alignment explanation
Indices: 404098--404210 Score: 176
Period size: 35 Copynumber: 3.2 Consensus size: 36
404088 TGAAAGTATT
404098 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
404133 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
404169 AAAATAGTTTTTCAAAGTTTGGTAATTGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
404205 AAAATG
1 AAAATG
404211 ATAATGGGAT
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 36 0.49
36 14 0.19
37 23 0.32
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.44
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:408708 original size:21 final size:20
Alignment explanation
Indices: 408684--408744 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
408674 AACTTTGAAA
408684 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTT-GT
*
408705 AAAT-G-TTTC----TTTGA
1 AAATGGTTTTCAAAGTTTGT
408719 AAATGGTTTTCAAAGTTTAGT
1 AAATGGTTTTCAAAGTTT-GT
408740 AAATG
1 AAATG
408745 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (20 bp):
AAATGGTTTTCAAAGTTTGT
Found at i:408790 original size:36 final size:36
Alignment explanation
Indices: 408676--408795 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
408666 TGGTAACCAA
408676 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
408713 CTTTG-AAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
408748 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
408785 -GTTGAAAAATG
1 CTTTGAAAAATG
408796 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:412118 original size:23 final size:23
Alignment explanation
Indices: 412087--412171 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
412077 ACAGGTAAAA
*
412087 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
412110 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
412133 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
**
412156 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
412172 TAATTACTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:412781 original size:87 final size:87
Alignment explanation
Indices: 412630--412884 Score: 325
Period size: 87 Copynumber: 2.9 Consensus size: 87
412620 ATTAAATAAT
* * *
412630 TAACATATTTTATTATATAAACACTAAT-TATTACGTTATATAAGCGCTACATAATATATTATTG
1 TAACCTATTTTATTATATAAACACT-ATCTATTACATTATATAAGCGATACATAATATATTATTG
412694 TGCTTGATAATATTTCCAGTAAG
65 TGCTTGATAATATTTCCAGTAAG
** * *** *
412717 TAACCTATTTTATTATATAAATGCTATCTATTACTTTATATAAGTTTTACCTAATATATTATTGT
1 TAACCTATTTTATTATATAAACACTATCTATTACATTATATAAGCGATACATAATATATTATTGT
** * *
412782 GCTTGATAATGGTTGCAGTAAT
66 GCTTGATAATATTTCCAGTAAG
* *
412804 TAACCTATTTTATTATATAAGCACTA-CATATTACATTATATAAACGATACATAATATATTATTG
1 TAACCTATTTTATTATATAAACACTATC-TATTACATTATATAAGCGATACATAATATATTATTG
*
412868 TGTTTGATAATATTTCC
65 TGCTTGATAATATTTCC
412885 GATTAACTTC
Statistics
Matches: 141, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
86 3 0.02
87 138 0.98
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (87 bp):
TAACCTATTTTATTATATAAACACTATCTATTACATTATATAAGCGATACATAATATATTATTGT
GCTTGATAATATTTCCAGTAAG
Found at i:412854 original size:23 final size:23
Alignment explanation
Indices: 412815--412865 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
412805 AACCTATTTT
* *
412815 ATTATATAAGCACTACATATTAC
1 ATTATATAAACACTACATAATAC
*
412838 ATTATATAAACGA-TACATAATAT
1 ATTATATAAAC-ACTACATAATAC
412861 ATTAT
1 ATTAT
412866 TGTGTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (23 bp):
ATTATATAAACACTACATAATAC
Found at i:413361 original size:25 final size:25
Alignment explanation
Indices: 413332--413385 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
413322 TAATCCCTTG
413332 TTTTCTTTTCCTTTACCTTGTTAGT
1 TTTTCTTTTCCTTTACCTTGTTAGT
413357 TTTTCTTTTCCTTTACCTTGTTAGT
1 TTTTCTTTTCCTTTACCTTGTTAGT
413382 TTTT
1 TTTT
413386 GTACTTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.07, C:0.19, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTCTTTTCCTTTACCTTGTTAGT
Found at i:417412 original size:22 final size:22
Alignment explanation
Indices: 417384--417439 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
417374 AATTCTGACT
417384 ATCGCATTGCGATTTTCCGACC
1 ATCGCATTGCGATTTTCCGACC
*
417406 ATCGCATTGCGATTTTCCGACT
1 ATCGCATTGCGATTTTCCGACC
*
417428 ATCGCAATGCGA
1 ATCGCATTGCGA
417440 ATATGTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (22 bp):
ATCGCATTGCGATTTTCCGACC
Found at i:417504 original size:20 final size:20
Alignment explanation
Indices: 417428--417541 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
417418 TTTTCCGACT
*
417428 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATTATGTAA
* * *
417448 ATCGAAATACGAGTATGTAA
1 ATCGCAATGCGATTATGTAA
* *
417468 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGATTATGTAA
*
417488 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGATTATGTA-A
* *
417508 ATCGCAATGCGATTCTG-ACT
1 ATCGCAATGCGATTATGTA-A
417528 ATCGCAATGCGATT
1 ATCGCAATGCGATT
417542 CTGACTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 83 0.99
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGATTATGTAA
Found at i:417512 original size:40 final size:40
Alignment explanation
Indices: 417406--417554 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
417396 TTTTCCGACC
* *
417406 ATCGCATTGCGATTTTCCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATTAT--GACTATCGCAATGCGAATATGTAA
* * * * *
417448 ATCGAAATACGAGTATGTA-AATCGCAATACGAATATGTAA
1 ATCGCAATGCGATTATG-ACTATCGCAATGCGAATATGTAA
* * *
417488 ATCGCAATGCGATTATGACTATCGCAATGCGATTCTG-ACT
1 ATCGCAATGCGATTATGACTATCGCAATGCGAATATGTA-A
*
417528 ATCGCAATGCGATTCTGACTATCGCAA
1 ATCGCAATGCGATTATGACTATCGCAA
417555 CGTGATTCTG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.02
40 74 0.84
41 1 0.01
42 11 0.12
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (40 bp):
ATCGCAATGCGATTATGACTATCGCAATGCGAATATGTAA
Found at i:417542 original size:20 final size:20
Alignment explanation
Indices: 417488--417574 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
417478 GAATATGTAA
*
417488 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTCTGACT
417508 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
417528 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
* *
417548 ATCGCAACGTGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
417568 GTCGCAA
1 ATCGCAA
417575 CACTGAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:418424 original size:24 final size:24
Alignment explanation
Indices: 418392--418445 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
418382 GTATTCGAAA
418392 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
418416 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
418440 TTTGAT
1 TTTGAT
418446 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:418664 original size:14 final size:14
Alignment explanation
Indices: 418635--418671 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
418625 AGAAAAAGAA
418635 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
418650 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
418664 GAAGAAAA
1 GAAGAAAA
418672 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:420731 original size:18 final size:18
Alignment explanation
Indices: 420708--420742 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
420698 AGAAAAAGGC
420708 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
420726 AATCAAAATCGCAATCA
1 AATCAAAATCGCAATCA
420743 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.23, G:0.06, T:0.17
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:421054 original size:140 final size:140
Alignment explanation
Indices: 420802--421071 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
420792 AAACGTTGTA
*
420802 TTATGTGTAAATTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
*
420867 TGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
420932 TATGTGTATT
131 TATGTGTATT
*
420942 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
*
421007 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
421072 CGCAACGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGATA
TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:421067 original size:20 final size:20
Alignment explanation
Indices: 421042--421260 Score: 152
Period size: 20 Copynumber: 11.8 Consensus size: 20
421032 TTACACATTC
421042 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
421062 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
421082 ATTTGAATATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
421101 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
421116 ATTTGACTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* * *
421136 ATATGACTATCACAACGC-A
1 ATTTGAATATCGCAACGCGA
*
421155 A----AA-ATCGTAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
421170 ATTTGACTATCACAACG-GCT
1 ATTTGAATATCGCAACGCG-A
* *
421190 ATTTGACTATCGCAA--TG-
1 ATTTGAATATCGCAACGCGA
*
421207 A---GAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
421224 ATTTGAGTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
421244 ATTTGATTATCGCAACG
1 ATTTGAATATCGCAACG
421261 AGAAAATCGC
Statistics
Matches: 156, Mismatches: 23, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
14 26 0.17
15 7 0.04
16 1 0.01
17 2 0.01
19 8 0.05
20 112 0.72
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:421137 original size:54 final size:55
Alignment explanation
Indices: 421050--421309 Score: 325
Period size: 54 Copynumber: 4.8 Consensus size: 55
421040 TCATTTGAAT
*
421050 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAATATCGCAACTCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAGAAA
* * * *
421104 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCACAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAGAAA
* * * *
421158 ATCGTAACGCGAATTTGACTATCACAACG-GCTATTTGACTATCGCAA-TGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCG-AATTTGACTATCGCAACTCAGAAA
* * *
421212 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAAC-GAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAGAAA
* * * *
421266 ATCGCAAAGCGTATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
421310 GTTGCGATTT
Statistics
Matches: 178, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
53 11 0.06
54 166 0.93
55 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (55 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAGAAA
Found at i:422998 original size:42 final size:42
Alignment explanation
Indices: 422919--423011 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
422909 CCTCTTCAAC
* * *
422919 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
422961 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
423003 GATGACAGG
1 GATGACAGG
423012 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Done.