Multiple sequence alignment - TraesCS6A01G043900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G043900 chr6A 100.000 3805 0 0 690 4494 22952632 22956436 0.000000e+00 7027.0
1 TraesCS6A01G043900 chr6A 100.000 491 0 0 1 491 22951943 22952433 0.000000e+00 907.0
2 TraesCS6A01G043900 chr6A 89.899 594 33 9 697 1278 22930728 22931306 0.000000e+00 739.0
3 TraesCS6A01G043900 chr6A 86.592 179 17 6 4074 4247 48707558 48707734 1.650000e-44 191.0
4 TraesCS6A01G043900 chr6A 89.516 124 12 1 4372 4494 22975995 22976118 6.020000e-34 156.0
5 TraesCS6A01G043900 chr6D 96.161 2683 89 6 997 3671 24377989 24375313 0.000000e+00 4372.0
6 TraesCS6A01G043900 chr6D 80.892 2444 376 68 1106 3499 27056853 27059255 0.000000e+00 1842.0
7 TraesCS6A01G043900 chr6D 88.889 1386 135 10 2218 3589 24293781 24292401 0.000000e+00 1688.0
8 TraesCS6A01G043900 chr6D 92.680 724 33 1 1245 1968 24294982 24294279 0.000000e+00 1026.0
9 TraesCS6A01G043900 chr6D 90.580 276 26 0 1104 1379 24384160 24383885 2.550000e-97 366.0
10 TraesCS6A01G043900 chr6D 88.968 281 21 5 1 272 169166263 169165984 5.570000e-89 339.0
11 TraesCS6A01G043900 chr6D 89.494 257 20 3 730 980 24378231 24377976 7.250000e-83 318.0
12 TraesCS6A01G043900 chr6D 90.708 226 19 1 1964 2189 24294007 24293784 2.630000e-77 300.0
13 TraesCS6A01G043900 chr6D 92.453 159 3 1 1433 1591 24383424 24383275 7.570000e-53 219.0
14 TraesCS6A01G043900 chr6D 94.245 139 7 1 3936 4073 24368957 24368819 1.270000e-50 211.0
15 TraesCS6A01G043900 chr6D 85.405 185 21 6 4068 4247 471006978 471006795 2.130000e-43 187.0
16 TraesCS6A01G043900 chr6D 82.278 158 8 11 253 408 24378465 24378326 7.900000e-23 119.0
17 TraesCS6A01G043900 chr6B 92.287 1465 92 10 2101 3544 39368108 39369572 0.000000e+00 2060.0
18 TraesCS6A01G043900 chr6B 79.731 2452 397 68 1106 3499 49733993 49736402 0.000000e+00 1683.0
19 TraesCS6A01G043900 chr6B 93.716 1098 49 7 999 2080 39367027 39368120 0.000000e+00 1628.0
20 TraesCS6A01G043900 chr6B 88.769 650 53 10 3847 4494 39370113 39370744 0.000000e+00 778.0
21 TraesCS6A01G043900 chr6B 94.248 226 6 2 3688 3912 39369910 39370129 5.570000e-89 339.0
22 TraesCS6A01G043900 chr6B 100.000 31 0 0 3819 3849 39370188 39370218 1.750000e-04 58.4
23 TraesCS6A01G043900 chr5D 81.296 2454 367 54 1111 3510 447194061 447191646 0.000000e+00 1905.0
24 TraesCS6A01G043900 chr5D 84.834 1233 174 12 2287 3510 447142111 447140883 0.000000e+00 1229.0
25 TraesCS6A01G043900 chr5D 77.321 1045 172 39 1199 2206 447143248 447142232 1.410000e-154 556.0
26 TraesCS6A01G043900 chr5A 79.898 2358 370 75 1199 3501 565488446 565490754 0.000000e+00 1633.0
27 TraesCS6A01G043900 chr5A 81.094 2084 332 41 1441 3501 565416049 565418093 0.000000e+00 1609.0
28 TraesCS6A01G043900 chr2D 79.005 2453 439 61 1106 3526 17011036 17013444 0.000000e+00 1607.0
29 TraesCS6A01G043900 chr2D 87.571 177 19 3 4069 4242 553758806 553758982 7.620000e-48 202.0
30 TraesCS6A01G043900 chr2B 78.958 2457 436 60 1106 3526 28883110 28885521 0.000000e+00 1598.0
31 TraesCS6A01G043900 chr2B 88.321 274 24 3 1 267 427574877 427575149 5.610000e-84 322.0
32 TraesCS6A01G043900 chr2A 78.115 2536 466 68 1106 3615 18424976 18422504 0.000000e+00 1526.0
33 TraesCS6A01G043900 chr2A 89.139 267 25 3 1 267 657347573 657347311 3.350000e-86 329.0
34 TraesCS6A01G043900 chr2A 86.517 178 18 5 4075 4247 653037387 653037563 1.650000e-44 191.0
35 TraesCS6A01G043900 chr5B 84.132 1273 184 14 2236 3501 545576260 545577521 0.000000e+00 1216.0
36 TraesCS6A01G043900 chr5B 77.575 1039 171 42 1199 2203 545575185 545576195 5.040000e-159 571.0
37 TraesCS6A01G043900 chr5B 88.278 273 26 3 1 267 618295490 618295218 5.610000e-84 322.0
38 TraesCS6A01G043900 chr5B 88.485 165 15 4 4075 4236 660152204 660152041 3.550000e-46 196.0
39 TraesCS6A01G043900 chrUn 78.592 1023 186 23 1195 2206 35132788 35133788 0.000000e+00 645.0
40 TraesCS6A01G043900 chr1D 89.377 273 23 2 1 267 356362760 356362488 5.570000e-89 339.0
41 TraesCS6A01G043900 chr1D 86.559 186 21 4 4065 4247 297540102 297539918 7.620000e-48 202.0
42 TraesCS6A01G043900 chr3A 89.051 274 22 3 1 267 233550098 233550370 2.590000e-87 333.0
43 TraesCS6A01G043900 chr3A 88.603 272 28 2 1 269 130349095 130348824 1.210000e-85 327.0
44 TraesCS6A01G043900 chr3A 88.068 176 16 4 4075 4247 621234093 621234266 2.120000e-48 204.0
45 TraesCS6A01G043900 chr1B 88.603 272 26 4 1 267 211094088 211094359 4.340000e-85 326.0
46 TraesCS6A01G043900 chr7D 87.681 276 29 4 1 271 160131264 160131539 2.610000e-82 316.0
47 TraesCS6A01G043900 chr7B 87.151 179 19 4 4073 4247 717027588 717027766 2.740000e-47 200.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G043900 chr6A 22951943 22956436 4493 False 3967.000000 7027 100.0000 1 4494 2 chr6A.!!$F4 4493
1 TraesCS6A01G043900 chr6A 22930728 22931306 578 False 739.000000 739 89.8990 697 1278 1 chr6A.!!$F1 581
2 TraesCS6A01G043900 chr6D 27056853 27059255 2402 False 1842.000000 1842 80.8920 1106 3499 1 chr6D.!!$F1 2393
3 TraesCS6A01G043900 chr6D 24375313 24378465 3152 True 1603.000000 4372 89.3110 253 3671 3 chr6D.!!$R5 3418
4 TraesCS6A01G043900 chr6D 24292401 24294982 2581 True 1004.666667 1688 90.7590 1245 3589 3 chr6D.!!$R4 2344
5 TraesCS6A01G043900 chr6D 24383275 24384160 885 True 292.500000 366 91.5165 1104 1591 2 chr6D.!!$R6 487
6 TraesCS6A01G043900 chr6B 49733993 49736402 2409 False 1683.000000 1683 79.7310 1106 3499 1 chr6B.!!$F1 2393
7 TraesCS6A01G043900 chr6B 39367027 39370744 3717 False 972.680000 2060 93.8040 999 4494 5 chr6B.!!$F2 3495
8 TraesCS6A01G043900 chr5D 447191646 447194061 2415 True 1905.000000 1905 81.2960 1111 3510 1 chr5D.!!$R1 2399
9 TraesCS6A01G043900 chr5D 447140883 447143248 2365 True 892.500000 1229 81.0775 1199 3510 2 chr5D.!!$R2 2311
10 TraesCS6A01G043900 chr5A 565488446 565490754 2308 False 1633.000000 1633 79.8980 1199 3501 1 chr5A.!!$F2 2302
11 TraesCS6A01G043900 chr5A 565416049 565418093 2044 False 1609.000000 1609 81.0940 1441 3501 1 chr5A.!!$F1 2060
12 TraesCS6A01G043900 chr2D 17011036 17013444 2408 False 1607.000000 1607 79.0050 1106 3526 1 chr2D.!!$F1 2420
13 TraesCS6A01G043900 chr2B 28883110 28885521 2411 False 1598.000000 1598 78.9580 1106 3526 1 chr2B.!!$F1 2420
14 TraesCS6A01G043900 chr2A 18422504 18424976 2472 True 1526.000000 1526 78.1150 1106 3615 1 chr2A.!!$R1 2509
15 TraesCS6A01G043900 chr5B 545575185 545577521 2336 False 893.500000 1216 80.8535 1199 3501 2 chr5B.!!$F1 2302
16 TraesCS6A01G043900 chrUn 35132788 35133788 1000 False 645.000000 645 78.5920 1195 2206 1 chrUn.!!$F1 1011

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
292 293 0.994247 ACCCATCACAATCTGCAGGA 59.006 50.000 15.13 2.6 0.00 3.86 F
972 1010 1.142060 TCCACGCGGGGAATATCAATT 59.858 47.619 31.73 0.0 37.22 2.32 F
2375 3370 0.328258 ACTCATGGTACTTGGTGCCC 59.672 55.000 2.63 0.0 37.51 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 2276 1.227823 CCACTTGAACTCCACGCCA 60.228 57.895 0.00 0.00 0.0 5.69 R
2603 3599 0.895100 ATCGCCACAACATGCAGGTT 60.895 50.000 11.64 11.64 0.0 3.50 R
3644 4801 0.105039 GCATCTACCCTTCCACCTCG 59.895 60.000 0.00 0.00 0.0 4.63 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.432403 AAGGCTCAATTTGGTTATTTTCCA 57.568 33.333 0.00 0.00 0.00 3.53
29 30 6.625532 AGGCTCAATTTGGTTATTTTCCAT 57.374 33.333 0.00 0.00 34.75 3.41
30 31 6.643388 AGGCTCAATTTGGTTATTTTCCATC 58.357 36.000 0.00 0.00 34.75 3.51
31 32 6.213195 AGGCTCAATTTGGTTATTTTCCATCA 59.787 34.615 0.00 0.00 34.75 3.07
32 33 6.313658 GGCTCAATTTGGTTATTTTCCATCAC 59.686 38.462 0.00 0.00 34.75 3.06
33 34 6.873076 GCTCAATTTGGTTATTTTCCATCACA 59.127 34.615 0.00 0.00 34.75 3.58
34 35 7.387397 GCTCAATTTGGTTATTTTCCATCACAA 59.613 33.333 0.00 0.00 34.75 3.33
35 36 8.830201 TCAATTTGGTTATTTTCCATCACAAG 57.170 30.769 0.00 0.00 34.75 3.16
36 37 8.428063 TCAATTTGGTTATTTTCCATCACAAGT 58.572 29.630 0.00 0.00 34.75 3.16
37 38 9.054922 CAATTTGGTTATTTTCCATCACAAGTT 57.945 29.630 0.00 0.00 34.75 2.66
38 39 8.831715 ATTTGGTTATTTTCCATCACAAGTTC 57.168 30.769 0.00 0.00 34.75 3.01
39 40 6.968263 TGGTTATTTTCCATCACAAGTTCA 57.032 33.333 0.00 0.00 0.00 3.18
40 41 6.980593 TGGTTATTTTCCATCACAAGTTCAG 58.019 36.000 0.00 0.00 0.00 3.02
41 42 6.775142 TGGTTATTTTCCATCACAAGTTCAGA 59.225 34.615 0.00 0.00 0.00 3.27
42 43 7.451255 TGGTTATTTTCCATCACAAGTTCAGAT 59.549 33.333 0.00 0.00 0.00 2.90
43 44 8.306761 GGTTATTTTCCATCACAAGTTCAGATT 58.693 33.333 0.00 0.00 0.00 2.40
50 51 9.739276 TTCCATCACAAGTTCAGATTATAAAGT 57.261 29.630 0.00 0.00 0.00 2.66
51 52 9.166173 TCCATCACAAGTTCAGATTATAAAGTG 57.834 33.333 0.00 0.00 0.00 3.16
52 53 7.912250 CCATCACAAGTTCAGATTATAAAGTGC 59.088 37.037 0.00 0.00 0.00 4.40
53 54 7.977789 TCACAAGTTCAGATTATAAAGTGCA 57.022 32.000 0.00 0.00 0.00 4.57
54 55 8.565896 TCACAAGTTCAGATTATAAAGTGCAT 57.434 30.769 0.00 0.00 0.00 3.96
55 56 9.013229 TCACAAGTTCAGATTATAAAGTGCATT 57.987 29.630 0.00 0.00 0.00 3.56
69 70 5.728351 AAGTGCATTAAATCATTGCATGC 57.272 34.783 11.82 11.82 46.90 4.06
70 71 4.760878 AGTGCATTAAATCATTGCATGCA 58.239 34.783 18.46 18.46 46.90 3.96
71 72 5.179533 AGTGCATTAAATCATTGCATGCAA 58.820 33.333 33.57 33.57 46.90 4.08
72 73 5.293324 AGTGCATTAAATCATTGCATGCAAG 59.707 36.000 34.15 25.40 46.90 4.01
73 74 5.064198 GTGCATTAAATCATTGCATGCAAGT 59.936 36.000 34.15 21.32 46.90 3.16
74 75 6.256104 GTGCATTAAATCATTGCATGCAAGTA 59.744 34.615 34.15 25.25 46.90 2.24
75 76 6.987404 TGCATTAAATCATTGCATGCAAGTAT 59.013 30.769 34.15 26.18 40.64 2.12
76 77 7.496263 TGCATTAAATCATTGCATGCAAGTATT 59.504 29.630 34.15 29.40 40.64 1.89
77 78 8.980610 GCATTAAATCATTGCATGCAAGTATTA 58.019 29.630 34.15 25.22 39.47 0.98
81 82 8.812147 AAATCATTGCATGCAAGTATTATGAG 57.188 30.769 34.15 16.39 39.47 2.90
82 83 7.754851 ATCATTGCATGCAAGTATTATGAGA 57.245 32.000 34.15 20.12 39.47 3.27
83 84 7.571080 TCATTGCATGCAAGTATTATGAGAA 57.429 32.000 34.15 10.64 39.47 2.87
84 85 7.998580 TCATTGCATGCAAGTATTATGAGAAA 58.001 30.769 34.15 10.19 39.47 2.52
85 86 8.468399 TCATTGCATGCAAGTATTATGAGAAAA 58.532 29.630 34.15 9.52 39.47 2.29
86 87 9.256477 CATTGCATGCAAGTATTATGAGAAAAT 57.744 29.630 34.15 12.14 39.47 1.82
87 88 9.826574 ATTGCATGCAAGTATTATGAGAAAATT 57.173 25.926 34.15 11.77 39.47 1.82
88 89 8.637281 TGCATGCAAGTATTATGAGAAAATTG 57.363 30.769 20.30 0.00 0.00 2.32
89 90 8.468399 TGCATGCAAGTATTATGAGAAAATTGA 58.532 29.630 20.30 0.00 0.00 2.57
90 91 8.749499 GCATGCAAGTATTATGAGAAAATTGAC 58.251 33.333 14.21 0.00 0.00 3.18
91 92 9.241317 CATGCAAGTATTATGAGAAAATTGACC 57.759 33.333 0.00 0.00 0.00 4.02
92 93 8.347004 TGCAAGTATTATGAGAAAATTGACCA 57.653 30.769 0.00 0.00 0.00 4.02
93 94 8.801299 TGCAAGTATTATGAGAAAATTGACCAA 58.199 29.630 0.00 0.00 0.00 3.67
94 95 9.807649 GCAAGTATTATGAGAAAATTGACCAAT 57.192 29.630 0.00 0.00 0.00 3.16
96 97 9.807649 AAGTATTATGAGAAAATTGACCAATGC 57.192 29.630 0.00 0.00 0.00 3.56
97 98 8.970020 AGTATTATGAGAAAATTGACCAATGCA 58.030 29.630 0.00 0.00 0.00 3.96
98 99 9.754382 GTATTATGAGAAAATTGACCAATGCAT 57.246 29.630 0.00 0.00 0.00 3.96
99 100 8.657074 ATTATGAGAAAATTGACCAATGCATG 57.343 30.769 0.00 0.00 0.00 4.06
100 101 5.471556 TGAGAAAATTGACCAATGCATGT 57.528 34.783 0.00 0.00 0.00 3.21
101 102 6.587206 TGAGAAAATTGACCAATGCATGTA 57.413 33.333 0.00 0.00 0.00 2.29
102 103 6.389091 TGAGAAAATTGACCAATGCATGTAC 58.611 36.000 0.00 0.00 0.00 2.90
103 104 6.209192 TGAGAAAATTGACCAATGCATGTACT 59.791 34.615 0.00 0.00 0.00 2.73
104 105 6.996509 AGAAAATTGACCAATGCATGTACTT 58.003 32.000 0.00 0.00 0.00 2.24
105 106 7.444299 AGAAAATTGACCAATGCATGTACTTT 58.556 30.769 0.00 0.00 0.00 2.66
106 107 8.584157 AGAAAATTGACCAATGCATGTACTTTA 58.416 29.630 0.00 0.00 0.00 1.85
107 108 9.369904 GAAAATTGACCAATGCATGTACTTTAT 57.630 29.630 0.00 0.00 0.00 1.40
108 109 8.706492 AAATTGACCAATGCATGTACTTTATG 57.294 30.769 0.00 0.00 0.00 1.90
136 137 9.984190 ATGCATGCATTGTAATTAATACATTGA 57.016 25.926 27.46 0.00 43.64 2.57
137 138 9.984190 TGCATGCATTGTAATTAATACATTGAT 57.016 25.926 18.46 3.76 43.64 2.57
171 172 7.826260 TTTTTAAAGAAAACAAGAGCTGGTG 57.174 32.000 0.00 0.00 34.24 4.17
172 173 3.443099 AAAGAAAACAAGAGCTGGTGC 57.557 42.857 0.00 0.00 40.05 5.01
173 174 6.350949 TTTTAAAGAAAACAAGAGCTGGTGCT 60.351 34.615 0.00 0.00 39.84 4.40
174 175 7.793648 TTTTAAAGAAAACAAGAGCTGGTGCTT 60.794 33.333 0.00 0.00 38.43 3.91
208 209 7.648039 ACAAAAAGTATTTAACCACTCACCA 57.352 32.000 0.00 0.00 37.28 4.17
209 210 8.245195 ACAAAAAGTATTTAACCACTCACCAT 57.755 30.769 0.00 0.00 37.28 3.55
210 211 8.357402 ACAAAAAGTATTTAACCACTCACCATC 58.643 33.333 0.00 0.00 37.28 3.51
211 212 8.576442 CAAAAAGTATTTAACCACTCACCATCT 58.424 33.333 0.00 0.00 37.28 2.90
212 213 9.802039 AAAAAGTATTTAACCACTCACCATCTA 57.198 29.630 0.00 0.00 37.28 1.98
213 214 9.975218 AAAAGTATTTAACCACTCACCATCTAT 57.025 29.630 0.00 0.00 37.28 1.98
214 215 9.614792 AAAGTATTTAACCACTCACCATCTATC 57.385 33.333 0.00 0.00 35.86 2.08
215 216 8.554490 AGTATTTAACCACTCACCATCTATCT 57.446 34.615 0.00 0.00 0.00 1.98
216 217 8.993424 AGTATTTAACCACTCACCATCTATCTT 58.007 33.333 0.00 0.00 0.00 2.40
217 218 9.046296 GTATTTAACCACTCACCATCTATCTTG 57.954 37.037 0.00 0.00 0.00 3.02
218 219 6.620877 TTAACCACTCACCATCTATCTTGT 57.379 37.500 0.00 0.00 0.00 3.16
219 220 5.505181 AACCACTCACCATCTATCTTGTT 57.495 39.130 0.00 0.00 0.00 2.83
220 221 5.505181 ACCACTCACCATCTATCTTGTTT 57.495 39.130 0.00 0.00 0.00 2.83
221 222 5.248640 ACCACTCACCATCTATCTTGTTTG 58.751 41.667 0.00 0.00 0.00 2.93
222 223 5.013079 ACCACTCACCATCTATCTTGTTTGA 59.987 40.000 0.00 0.00 0.00 2.69
223 224 6.118170 CCACTCACCATCTATCTTGTTTGAT 58.882 40.000 0.00 0.00 0.00 2.57
224 225 6.037940 CCACTCACCATCTATCTTGTTTGATG 59.962 42.308 0.00 0.00 36.87 3.07
225 226 6.820152 CACTCACCATCTATCTTGTTTGATGA 59.180 38.462 0.00 0.00 38.72 2.92
226 227 7.011202 CACTCACCATCTATCTTGTTTGATGAG 59.989 40.741 0.00 0.00 38.72 2.90
227 228 7.093156 ACTCACCATCTATCTTGTTTGATGAGA 60.093 37.037 0.00 0.00 38.72 3.27
228 229 7.799081 TCACCATCTATCTTGTTTGATGAGAT 58.201 34.615 0.00 0.00 38.72 2.75
229 230 8.270030 TCACCATCTATCTTGTTTGATGAGATT 58.730 33.333 0.00 0.00 38.72 2.40
230 231 8.900781 CACCATCTATCTTGTTTGATGAGATTT 58.099 33.333 0.00 0.00 38.72 2.17
231 232 9.471702 ACCATCTATCTTGTTTGATGAGATTTT 57.528 29.630 0.00 0.00 38.72 1.82
242 243 9.206870 TGTTTGATGAGATTTTTAAATTGAGCC 57.793 29.630 0.00 0.00 0.00 4.70
243 244 8.659491 GTTTGATGAGATTTTTAAATTGAGCCC 58.341 33.333 0.00 0.00 0.00 5.19
244 245 7.722949 TGATGAGATTTTTAAATTGAGCCCT 57.277 32.000 0.00 0.00 0.00 5.19
245 246 8.821686 TGATGAGATTTTTAAATTGAGCCCTA 57.178 30.769 0.00 0.00 0.00 3.53
246 247 9.425248 TGATGAGATTTTTAAATTGAGCCCTAT 57.575 29.630 0.00 0.00 0.00 2.57
254 255 8.887264 TTTTAAATTGAGCCCTATAAACCAGA 57.113 30.769 0.00 0.00 0.00 3.86
255 256 8.887264 TTTAAATTGAGCCCTATAAACCAGAA 57.113 30.769 0.00 0.00 0.00 3.02
256 257 8.887264 TTAAATTGAGCCCTATAAACCAGAAA 57.113 30.769 0.00 0.00 0.00 2.52
257 258 7.410120 AAATTGAGCCCTATAAACCAGAAAG 57.590 36.000 0.00 0.00 0.00 2.62
258 259 4.503714 TGAGCCCTATAAACCAGAAAGG 57.496 45.455 0.00 0.00 45.67 3.11
259 260 4.108570 TGAGCCCTATAAACCAGAAAGGA 58.891 43.478 0.00 0.00 41.22 3.36
260 261 4.164221 TGAGCCCTATAAACCAGAAAGGAG 59.836 45.833 0.00 0.00 41.22 3.69
261 262 3.459969 AGCCCTATAAACCAGAAAGGAGG 59.540 47.826 0.00 0.00 41.22 4.30
262 263 3.435169 GCCCTATAAACCAGAAAGGAGGG 60.435 52.174 0.00 0.00 45.37 4.30
263 264 4.045022 CCCTATAAACCAGAAAGGAGGGA 58.955 47.826 0.00 0.00 45.41 4.20
264 265 4.103311 CCCTATAAACCAGAAAGGAGGGAG 59.897 50.000 0.00 0.00 45.41 4.30
265 266 4.722279 CCTATAAACCAGAAAGGAGGGAGT 59.278 45.833 0.00 0.00 41.22 3.85
273 274 8.401955 AACCAGAAAGGAGGGAGTAATATAAA 57.598 34.615 0.00 0.00 41.22 1.40
276 277 7.225011 CAGAAAGGAGGGAGTAATATAAACCC 58.775 42.308 0.00 0.00 40.71 4.11
277 278 6.912561 AGAAAGGAGGGAGTAATATAAACCCA 59.087 38.462 0.00 0.00 42.62 4.51
290 291 6.889301 ATATAAACCCATCACAATCTGCAG 57.111 37.500 7.63 7.63 0.00 4.41
292 293 0.994247 ACCCATCACAATCTGCAGGA 59.006 50.000 15.13 2.60 0.00 3.86
337 338 7.701809 CATGCATGCATGTTTCATACATAAA 57.298 32.000 40.30 8.56 45.71 1.40
338 339 7.560700 CATGCATGCATGTTTCATACATAAAC 58.439 34.615 40.30 6.41 45.71 2.01
339 340 6.628185 TGCATGCATGTTTCATACATAAACA 58.372 32.000 26.79 8.91 45.71 2.83
340 341 7.095270 TGCATGCATGTTTCATACATAAACAA 58.905 30.769 26.79 0.00 46.59 2.83
341 342 7.601508 TGCATGCATGTTTCATACATAAACAAA 59.398 29.630 26.79 0.00 46.59 2.83
373 374 7.513371 TCAACCAACAATAATCTAAACGGTT 57.487 32.000 0.00 0.00 34.64 4.44
374 375 8.618702 TCAACCAACAATAATCTAAACGGTTA 57.381 30.769 0.00 0.00 33.09 2.85
404 405 4.023193 CACCCTGAAACAAAGCGAGTATTT 60.023 41.667 0.00 0.00 0.00 1.40
405 406 4.023193 ACCCTGAAACAAAGCGAGTATTTG 60.023 41.667 0.00 0.00 42.17 2.32
462 487 5.839063 TGAGAGTGTCTTCTTTTCTAGGGAA 59.161 40.000 0.00 0.00 0.00 3.97
715 740 5.492895 TCGCTCCTACACCATTTTTGAATA 58.507 37.500 0.00 0.00 0.00 1.75
726 751 8.264347 ACACCATTTTTGAATAAAGAGTTTGGT 58.736 29.630 0.00 0.00 0.00 3.67
729 754 9.492973 CCATTTTTGAATAAAGAGTTTGGTCAT 57.507 29.630 0.00 0.00 0.00 3.06
786 818 9.284968 ACTATACCCTATGTCAATGTAAATTGC 57.715 33.333 0.22 0.00 0.00 3.56
794 826 6.503616 TGTCAATGTAAATTGCGTCAAAAC 57.496 33.333 0.22 0.00 0.00 2.43
803 835 1.310904 TGCGTCAAAACCCCACTTAC 58.689 50.000 0.00 0.00 0.00 2.34
960 998 2.738521 CAAGGTCAGTCCACGCGG 60.739 66.667 12.47 0.00 39.02 6.46
961 999 4.003788 AAGGTCAGTCCACGCGGG 62.004 66.667 12.47 6.05 39.02 6.13
972 1010 1.142060 TCCACGCGGGGAATATCAATT 59.858 47.619 31.73 0.00 37.22 2.32
1021 1059 2.104859 CATGGGCTGACTCACTGCG 61.105 63.158 0.00 0.00 42.94 5.18
1034 1072 2.512286 CTGCGTGCATGGACCGAT 60.512 61.111 12.15 0.00 0.00 4.18
1035 1073 1.227234 CTGCGTGCATGGACCGATA 60.227 57.895 12.15 0.30 0.00 2.92
1036 1074 1.490693 CTGCGTGCATGGACCGATAC 61.491 60.000 12.15 0.00 0.00 2.24
1419 1477 2.742372 GGCGCGGTGAACATCACT 60.742 61.111 8.83 0.00 46.19 3.41
1824 2402 1.211969 GCTCCTCAACACGTCGCTA 59.788 57.895 0.00 0.00 0.00 4.26
2375 3370 0.328258 ACTCATGGTACTTGGTGCCC 59.672 55.000 2.63 0.00 37.51 5.36
2530 3525 2.297129 GGTGGAGCTGGAGAAGGCT 61.297 63.158 0.00 0.00 41.88 4.58
2603 3599 4.331968 GGTGTACAAAGGGATCATGTCAA 58.668 43.478 0.00 0.00 0.00 3.18
2858 3857 1.347707 TGAGAATTGCAACGGAGACCT 59.652 47.619 0.00 0.00 0.00 3.85
2870 3869 0.107410 GGAGACCTCGAGAGCTCTCA 60.107 60.000 36.27 24.18 40.33 3.27
3037 4036 0.546122 CCATCCAAGGGACATTCGGA 59.454 55.000 0.00 0.00 32.98 4.55
3216 4215 1.433534 GCAACAGGCAGTCTAGTCAC 58.566 55.000 0.00 0.00 43.97 3.67
3281 4280 3.455910 TGAAGAGGTAGCTATGTTGGCAT 59.544 43.478 0.00 0.00 39.03 4.40
3416 4415 4.035558 CGCCTAGTTATACAGTGGTTACGA 59.964 45.833 0.00 0.00 0.00 3.43
3619 4776 2.943036 TAAGGAAACAACGAGGCCTT 57.057 45.000 6.77 0.00 41.51 4.35
3642 4799 4.059511 TGTTAACCAAGTCATACACACCG 58.940 43.478 2.48 0.00 0.00 4.94
3643 4800 4.202233 TGTTAACCAAGTCATACACACCGA 60.202 41.667 2.48 0.00 0.00 4.69
3644 4801 2.450609 ACCAAGTCATACACACCGAC 57.549 50.000 0.00 0.00 0.00 4.79
3671 4828 0.983378 AAGGGTAGATGCGCCTCCTT 60.983 55.000 4.18 6.09 0.00 3.36
3673 4830 0.756903 GGGTAGATGCGCCTCCTTTA 59.243 55.000 4.18 0.00 0.00 1.85
3674 4831 1.140252 GGGTAGATGCGCCTCCTTTAA 59.860 52.381 4.18 0.00 0.00 1.52
3675 4832 2.420967 GGGTAGATGCGCCTCCTTTAAA 60.421 50.000 4.18 0.00 0.00 1.52
3677 4834 3.883489 GGTAGATGCGCCTCCTTTAAATT 59.117 43.478 4.18 0.00 0.00 1.82
3679 4836 5.529800 GGTAGATGCGCCTCCTTTAAATTTA 59.470 40.000 4.18 0.00 0.00 1.40
3680 4837 6.038936 GGTAGATGCGCCTCCTTTAAATTTAA 59.961 38.462 4.18 6.54 0.00 1.52
3681 4838 6.136541 AGATGCGCCTCCTTTAAATTTAAG 57.863 37.500 4.18 5.79 0.00 1.85
3683 4840 6.547510 AGATGCGCCTCCTTTAAATTTAAGAT 59.452 34.615 4.18 0.00 0.00 2.40
3684 4841 5.890334 TGCGCCTCCTTTAAATTTAAGATG 58.110 37.500 4.18 4.90 0.00 2.90
3685 4842 5.163561 TGCGCCTCCTTTAAATTTAAGATGG 60.164 40.000 4.18 13.17 0.00 3.51
3771 4982 9.832445 ACACATATGAATAGTTAACCTTAGGTG 57.168 33.333 10.38 9.54 35.34 4.00
3842 5053 2.972348 TGGGTCTCTTTGACTAGGTGT 58.028 47.619 0.00 0.00 44.74 4.16
3843 5054 2.632996 TGGGTCTCTTTGACTAGGTGTG 59.367 50.000 0.00 0.00 44.74 3.82
3849 5060 6.295688 GGTCTCTTTGACTAGGTGTGGAATTA 60.296 42.308 0.00 0.00 44.74 1.40
3933 5192 2.616842 GTTGACGTGTTTGATGGGTCTT 59.383 45.455 0.00 0.00 0.00 3.01
3934 5193 2.489971 TGACGTGTTTGATGGGTCTTC 58.510 47.619 0.00 0.00 0.00 2.87
3966 5225 7.220030 AGGTGTGGAATTTATGCTAGTAGATG 58.780 38.462 0.00 0.00 0.00 2.90
3969 5228 8.930760 GTGTGGAATTTATGCTAGTAGATGATC 58.069 37.037 0.00 0.00 0.00 2.92
3970 5229 8.874156 TGTGGAATTTATGCTAGTAGATGATCT 58.126 33.333 0.00 0.00 0.00 2.75
3999 5258 0.036732 GTGACAGCTGTGGAATGGGA 59.963 55.000 27.27 0.00 0.00 4.37
4027 5286 8.837099 TTGGGGATGACACAAAGAAATTATAT 57.163 30.769 0.00 0.00 0.00 0.86
4101 5360 6.742999 TTTAATACAGTATAGACGCAAGCG 57.257 37.500 13.50 13.50 46.03 4.68
4113 5372 3.057526 AGACGCAAGCGCTCATATATACA 60.058 43.478 12.06 0.00 44.19 2.29
4128 5387 7.480810 TCATATATACACGCATACACTCATCC 58.519 38.462 0.00 0.00 0.00 3.51
4129 5388 5.984695 ATATACACGCATACACTCATCCT 57.015 39.130 0.00 0.00 0.00 3.24
4135 5395 4.445718 CACGCATACACTCATCCTATGAAC 59.554 45.833 0.00 0.00 39.11 3.18
4143 5403 5.037385 CACTCATCCTATGAACGTACACAG 58.963 45.833 0.00 0.00 39.11 3.66
4147 5407 2.094390 TCCTATGAACGTACACAGGCAC 60.094 50.000 0.00 0.00 34.78 5.01
4154 5414 0.535335 CGTACACAGGCACACCCTAT 59.465 55.000 0.00 0.00 44.09 2.57
4166 5426 4.263506 GGCACACCCTATCCTATTAGCATT 60.264 45.833 0.00 0.00 0.00 3.56
4169 5429 6.072452 GCACACCCTATCCTATTAGCATTTTC 60.072 42.308 0.00 0.00 0.00 2.29
4172 5432 7.106239 CACCCTATCCTATTAGCATTTTCGAT 58.894 38.462 0.00 0.00 0.00 3.59
4224 5484 0.595310 GAAGTCATCGTAGGCGCCTC 60.595 60.000 36.73 23.04 38.14 4.70
4254 5514 1.939980 GGACTGTCCCTCTAACCACT 58.060 55.000 16.14 0.00 0.00 4.00
4258 5518 2.900546 ACTGTCCCTCTAACCACTCAAG 59.099 50.000 0.00 0.00 0.00 3.02
4261 5521 1.623811 TCCCTCTAACCACTCAAGCAC 59.376 52.381 0.00 0.00 0.00 4.40
4264 5524 2.300152 CCTCTAACCACTCAAGCACAGA 59.700 50.000 0.00 0.00 0.00 3.41
4280 5540 3.804325 GCACAGATTGCTTCGCTATCTAA 59.196 43.478 11.33 0.00 45.88 2.10
4358 5618 9.739786 CACAACAAACAAAGAAACAAGAAATAC 57.260 29.630 0.00 0.00 0.00 1.89
4368 5628 7.373778 AGAAACAAGAAATACCCGTGATAAC 57.626 36.000 0.00 0.00 0.00 1.89
4375 5635 5.987347 AGAAATACCCGTGATAACGTATTGG 59.013 40.000 1.04 0.00 32.99 3.16
4405 5665 7.295952 AGCTATTGTCTTTGTCATTCTTACG 57.704 36.000 0.00 0.00 0.00 3.18
4409 5669 6.525121 TTGTCTTTGTCATTCTTACGACTG 57.475 37.500 0.00 0.00 33.18 3.51
4441 5702 3.509575 TGTTTTATGGTCACATTCCAGCC 59.490 43.478 0.00 0.00 38.42 4.85
4453 5714 2.024176 TTCCAGCCGAGCTTATGAAC 57.976 50.000 0.00 0.00 36.40 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.261035 TGGAAAATAACCAAATTGAGCCTTATA 57.739 29.630 0.00 0.00 34.25 0.98
4 5 7.546250 TGGAAAATAACCAAATTGAGCCTTA 57.454 32.000 0.00 0.00 34.25 2.69
5 6 6.432403 TGGAAAATAACCAAATTGAGCCTT 57.568 33.333 0.00 0.00 34.25 4.35
6 7 6.213195 TGATGGAAAATAACCAAATTGAGCCT 59.787 34.615 0.00 0.00 40.93 4.58
8 9 6.873076 TGTGATGGAAAATAACCAAATTGAGC 59.127 34.615 0.00 0.00 40.93 4.26
9 10 8.830201 TTGTGATGGAAAATAACCAAATTGAG 57.170 30.769 0.00 0.00 40.93 3.02
10 11 8.428063 ACTTGTGATGGAAAATAACCAAATTGA 58.572 29.630 0.00 0.00 40.93 2.57
11 12 8.606040 ACTTGTGATGGAAAATAACCAAATTG 57.394 30.769 0.00 0.00 40.93 2.32
12 13 9.271828 GAACTTGTGATGGAAAATAACCAAATT 57.728 29.630 0.00 0.00 40.93 1.82
13 14 8.428063 TGAACTTGTGATGGAAAATAACCAAAT 58.572 29.630 0.00 0.00 40.93 2.32
14 15 7.786030 TGAACTTGTGATGGAAAATAACCAAA 58.214 30.769 0.00 0.00 40.93 3.28
15 16 7.286546 TCTGAACTTGTGATGGAAAATAACCAA 59.713 33.333 0.00 0.00 40.93 3.67
16 17 6.775142 TCTGAACTTGTGATGGAAAATAACCA 59.225 34.615 0.00 0.00 41.83 3.67
17 18 7.214467 TCTGAACTTGTGATGGAAAATAACC 57.786 36.000 0.00 0.00 0.00 2.85
24 25 9.739276 ACTTTATAATCTGAACTTGTGATGGAA 57.261 29.630 0.00 0.00 0.00 3.53
25 26 9.166173 CACTTTATAATCTGAACTTGTGATGGA 57.834 33.333 0.00 0.00 0.00 3.41
26 27 7.912250 GCACTTTATAATCTGAACTTGTGATGG 59.088 37.037 0.00 0.00 0.00 3.51
27 28 8.453320 TGCACTTTATAATCTGAACTTGTGATG 58.547 33.333 0.00 0.00 0.00 3.07
28 29 8.565896 TGCACTTTATAATCTGAACTTGTGAT 57.434 30.769 0.00 0.00 0.00 3.06
29 30 7.977789 TGCACTTTATAATCTGAACTTGTGA 57.022 32.000 0.00 0.00 0.00 3.58
61 62 9.826574 AATTTTCTCATAATACTTGCATGCAAT 57.173 25.926 31.96 22.79 35.20 3.56
62 63 9.089601 CAATTTTCTCATAATACTTGCATGCAA 57.910 29.630 30.12 30.12 0.00 4.08
63 64 8.468399 TCAATTTTCTCATAATACTTGCATGCA 58.532 29.630 18.46 18.46 0.00 3.96
64 65 8.749499 GTCAATTTTCTCATAATACTTGCATGC 58.251 33.333 11.82 11.82 0.00 4.06
65 66 9.241317 GGTCAATTTTCTCATAATACTTGCATG 57.759 33.333 0.00 0.00 0.00 4.06
66 67 8.970020 TGGTCAATTTTCTCATAATACTTGCAT 58.030 29.630 0.00 0.00 0.00 3.96
67 68 8.347004 TGGTCAATTTTCTCATAATACTTGCA 57.653 30.769 0.00 0.00 0.00 4.08
68 69 9.807649 ATTGGTCAATTTTCTCATAATACTTGC 57.192 29.630 0.00 0.00 0.00 4.01
70 71 9.807649 GCATTGGTCAATTTTCTCATAATACTT 57.192 29.630 0.00 0.00 0.00 2.24
71 72 8.970020 TGCATTGGTCAATTTTCTCATAATACT 58.030 29.630 0.00 0.00 0.00 2.12
72 73 9.754382 ATGCATTGGTCAATTTTCTCATAATAC 57.246 29.630 0.00 0.00 0.00 1.89
73 74 9.752961 CATGCATTGGTCAATTTTCTCATAATA 57.247 29.630 0.00 0.00 0.00 0.98
74 75 8.262227 ACATGCATTGGTCAATTTTCTCATAAT 58.738 29.630 0.00 0.00 0.00 1.28
75 76 7.613585 ACATGCATTGGTCAATTTTCTCATAA 58.386 30.769 0.00 0.00 0.00 1.90
76 77 7.172868 ACATGCATTGGTCAATTTTCTCATA 57.827 32.000 0.00 0.00 0.00 2.15
77 78 6.045072 ACATGCATTGGTCAATTTTCTCAT 57.955 33.333 0.00 0.00 0.00 2.90
78 79 5.471556 ACATGCATTGGTCAATTTTCTCA 57.528 34.783 0.00 0.00 0.00 3.27
79 80 6.624423 AGTACATGCATTGGTCAATTTTCTC 58.376 36.000 0.00 0.00 0.00 2.87
80 81 6.594788 AGTACATGCATTGGTCAATTTTCT 57.405 33.333 0.00 0.00 0.00 2.52
81 82 7.656707 AAAGTACATGCATTGGTCAATTTTC 57.343 32.000 0.00 0.00 0.00 2.29
82 83 9.153721 CATAAAGTACATGCATTGGTCAATTTT 57.846 29.630 0.00 0.00 0.00 1.82
83 84 7.278424 GCATAAAGTACATGCATTGGTCAATTT 59.722 33.333 10.82 0.00 46.47 1.82
84 85 6.757947 GCATAAAGTACATGCATTGGTCAATT 59.242 34.615 10.82 0.00 46.47 2.32
85 86 6.275335 GCATAAAGTACATGCATTGGTCAAT 58.725 36.000 10.82 0.00 46.47 2.57
86 87 5.649557 GCATAAAGTACATGCATTGGTCAA 58.350 37.500 10.82 0.00 46.47 3.18
87 88 5.247507 GCATAAAGTACATGCATTGGTCA 57.752 39.130 10.82 0.00 46.47 4.02
108 109 7.640616 TGTATTAATTACAATGCATGCATGC 57.359 32.000 38.71 38.71 44.50 4.06
110 111 9.984190 TCAATGTATTAATTACAATGCATGCAT 57.016 25.926 27.46 27.46 43.84 3.96
111 112 9.984190 ATCAATGTATTAATTACAATGCATGCA 57.016 25.926 25.04 25.04 43.84 3.96
147 148 6.312672 GCACCAGCTCTTGTTTTCTTTAAAAA 59.687 34.615 0.00 0.00 35.62 1.94
148 149 5.810074 GCACCAGCTCTTGTTTTCTTTAAAA 59.190 36.000 0.00 0.00 37.91 1.52
149 150 5.348164 GCACCAGCTCTTGTTTTCTTTAAA 58.652 37.500 0.00 0.00 37.91 1.52
150 151 4.932146 GCACCAGCTCTTGTTTTCTTTAA 58.068 39.130 0.00 0.00 37.91 1.52
151 152 4.568152 GCACCAGCTCTTGTTTTCTTTA 57.432 40.909 0.00 0.00 37.91 1.85
152 153 3.443099 GCACCAGCTCTTGTTTTCTTT 57.557 42.857 0.00 0.00 37.91 2.52
165 166 3.129871 TGTAATTTGCAAAAGCACCAGC 58.870 40.909 17.19 2.02 42.56 4.85
166 167 5.731599 TTTGTAATTTGCAAAAGCACCAG 57.268 34.783 17.19 0.00 33.51 4.00
167 168 6.150140 ACTTTTTGTAATTTGCAAAAGCACCA 59.850 30.769 17.19 6.16 43.70 4.17
168 169 6.550843 ACTTTTTGTAATTTGCAAAAGCACC 58.449 32.000 17.19 3.59 43.70 5.01
169 170 9.715123 AATACTTTTTGTAATTTGCAAAAGCAC 57.285 25.926 17.19 13.97 43.70 4.40
182 183 9.186837 TGGTGAGTGGTTAAATACTTTTTGTAA 57.813 29.630 0.00 0.00 34.45 2.41
183 184 8.749026 TGGTGAGTGGTTAAATACTTTTTGTA 57.251 30.769 0.00 0.00 35.37 2.41
184 185 7.648039 TGGTGAGTGGTTAAATACTTTTTGT 57.352 32.000 0.00 0.00 0.00 2.83
185 186 8.576442 AGATGGTGAGTGGTTAAATACTTTTTG 58.424 33.333 0.00 0.00 0.00 2.44
186 187 8.706322 AGATGGTGAGTGGTTAAATACTTTTT 57.294 30.769 0.00 0.00 0.00 1.94
187 188 9.975218 ATAGATGGTGAGTGGTTAAATACTTTT 57.025 29.630 0.00 0.00 0.00 2.27
188 189 9.614792 GATAGATGGTGAGTGGTTAAATACTTT 57.385 33.333 0.00 0.00 0.00 2.66
189 190 8.993424 AGATAGATGGTGAGTGGTTAAATACTT 58.007 33.333 0.00 0.00 0.00 2.24
190 191 8.554490 AGATAGATGGTGAGTGGTTAAATACT 57.446 34.615 0.00 0.00 0.00 2.12
191 192 9.046296 CAAGATAGATGGTGAGTGGTTAAATAC 57.954 37.037 0.00 0.00 0.00 1.89
192 193 8.768397 ACAAGATAGATGGTGAGTGGTTAAATA 58.232 33.333 0.00 0.00 0.00 1.40
193 194 7.633789 ACAAGATAGATGGTGAGTGGTTAAAT 58.366 34.615 0.00 0.00 0.00 1.40
194 195 7.016153 ACAAGATAGATGGTGAGTGGTTAAA 57.984 36.000 0.00 0.00 0.00 1.52
195 196 6.620877 ACAAGATAGATGGTGAGTGGTTAA 57.379 37.500 0.00 0.00 0.00 2.01
196 197 6.620877 AACAAGATAGATGGTGAGTGGTTA 57.379 37.500 0.00 0.00 0.00 2.85
197 198 5.505181 AACAAGATAGATGGTGAGTGGTT 57.495 39.130 0.00 0.00 0.00 3.67
198 199 5.013079 TCAAACAAGATAGATGGTGAGTGGT 59.987 40.000 0.00 0.00 0.00 4.16
199 200 5.491070 TCAAACAAGATAGATGGTGAGTGG 58.509 41.667 0.00 0.00 0.00 4.00
200 201 6.820152 TCATCAAACAAGATAGATGGTGAGTG 59.180 38.462 0.00 0.00 38.64 3.51
201 202 6.950842 TCATCAAACAAGATAGATGGTGAGT 58.049 36.000 0.00 0.00 38.64 3.41
202 203 7.270779 TCTCATCAAACAAGATAGATGGTGAG 58.729 38.462 7.79 7.79 45.97 3.51
203 204 7.186570 TCTCATCAAACAAGATAGATGGTGA 57.813 36.000 0.00 0.00 38.64 4.02
204 205 8.447924 AATCTCATCAAACAAGATAGATGGTG 57.552 34.615 0.00 0.00 38.64 4.17
205 206 9.471702 AAAATCTCATCAAACAAGATAGATGGT 57.528 29.630 0.00 0.00 38.64 3.55
216 217 9.206870 GGCTCAATTTAAAAATCTCATCAAACA 57.793 29.630 0.00 0.00 0.00 2.83
217 218 8.659491 GGGCTCAATTTAAAAATCTCATCAAAC 58.341 33.333 0.00 0.00 0.00 2.93
218 219 8.596293 AGGGCTCAATTTAAAAATCTCATCAAA 58.404 29.630 0.00 0.00 0.00 2.69
219 220 8.137745 AGGGCTCAATTTAAAAATCTCATCAA 57.862 30.769 0.00 0.00 0.00 2.57
220 221 7.722949 AGGGCTCAATTTAAAAATCTCATCA 57.277 32.000 0.00 0.00 0.00 3.07
228 229 9.315363 TCTGGTTTATAGGGCTCAATTTAAAAA 57.685 29.630 0.00 0.00 0.00 1.94
229 230 8.887264 TCTGGTTTATAGGGCTCAATTTAAAA 57.113 30.769 0.00 0.00 0.00 1.52
230 231 8.887264 TTCTGGTTTATAGGGCTCAATTTAAA 57.113 30.769 0.00 0.00 0.00 1.52
231 232 8.887264 TTTCTGGTTTATAGGGCTCAATTTAA 57.113 30.769 0.00 0.00 0.00 1.52
232 233 7.559897 CCTTTCTGGTTTATAGGGCTCAATTTA 59.440 37.037 0.00 0.00 0.00 1.40
233 234 6.381133 CCTTTCTGGTTTATAGGGCTCAATTT 59.619 38.462 0.00 0.00 0.00 1.82
234 235 5.893824 CCTTTCTGGTTTATAGGGCTCAATT 59.106 40.000 0.00 0.00 0.00 2.32
235 236 5.193728 TCCTTTCTGGTTTATAGGGCTCAAT 59.806 40.000 0.00 0.00 37.07 2.57
236 237 4.538490 TCCTTTCTGGTTTATAGGGCTCAA 59.462 41.667 0.00 0.00 37.07 3.02
237 238 4.108570 TCCTTTCTGGTTTATAGGGCTCA 58.891 43.478 0.00 0.00 37.07 4.26
238 239 4.445019 CCTCCTTTCTGGTTTATAGGGCTC 60.445 50.000 0.00 0.00 37.07 4.70
239 240 3.459969 CCTCCTTTCTGGTTTATAGGGCT 59.540 47.826 0.00 0.00 37.07 5.19
240 241 3.435169 CCCTCCTTTCTGGTTTATAGGGC 60.435 52.174 0.00 0.00 37.92 5.19
241 242 4.045022 TCCCTCCTTTCTGGTTTATAGGG 58.955 47.826 0.00 0.00 43.08 3.53
242 243 4.722279 ACTCCCTCCTTTCTGGTTTATAGG 59.278 45.833 0.00 0.00 37.07 2.57
243 244 5.959583 ACTCCCTCCTTTCTGGTTTATAG 57.040 43.478 0.00 0.00 37.07 1.31
244 245 9.684702 ATATTACTCCCTCCTTTCTGGTTTATA 57.315 33.333 0.00 0.00 37.07 0.98
245 246 6.910259 ATTACTCCCTCCTTTCTGGTTTAT 57.090 37.500 0.00 0.00 37.07 1.40
246 247 9.510062 TTATATTACTCCCTCCTTTCTGGTTTA 57.490 33.333 0.00 0.00 37.07 2.01
247 248 6.910259 ATATTACTCCCTCCTTTCTGGTTT 57.090 37.500 0.00 0.00 37.07 3.27
248 249 8.272889 GTTTATATTACTCCCTCCTTTCTGGTT 58.727 37.037 0.00 0.00 37.07 3.67
249 250 7.147355 GGTTTATATTACTCCCTCCTTTCTGGT 60.147 40.741 0.00 0.00 37.07 4.00
250 251 7.225011 GGTTTATATTACTCCCTCCTTTCTGG 58.775 42.308 0.00 0.00 37.10 3.86
251 252 7.147373 TGGGTTTATATTACTCCCTCCTTTCTG 60.147 40.741 0.00 0.00 38.95 3.02
252 253 6.912561 TGGGTTTATATTACTCCCTCCTTTCT 59.087 38.462 0.00 0.00 38.95 2.52
253 254 7.145474 TGGGTTTATATTACTCCCTCCTTTC 57.855 40.000 0.00 0.00 38.95 2.62
254 255 7.352522 TGATGGGTTTATATTACTCCCTCCTTT 59.647 37.037 0.00 0.00 38.95 3.11
255 256 6.855061 TGATGGGTTTATATTACTCCCTCCTT 59.145 38.462 0.00 0.00 38.95 3.36
256 257 6.272558 GTGATGGGTTTATATTACTCCCTCCT 59.727 42.308 0.00 0.00 38.95 3.69
257 258 6.043938 TGTGATGGGTTTATATTACTCCCTCC 59.956 42.308 0.00 0.00 38.95 4.30
258 259 7.074653 TGTGATGGGTTTATATTACTCCCTC 57.925 40.000 0.00 0.00 38.95 4.30
259 260 7.460214 TTGTGATGGGTTTATATTACTCCCT 57.540 36.000 0.00 0.00 38.95 4.20
260 261 8.164070 AGATTGTGATGGGTTTATATTACTCCC 58.836 37.037 0.00 0.00 38.68 4.30
261 262 9.003658 CAGATTGTGATGGGTTTATATTACTCC 57.996 37.037 0.00 0.00 0.00 3.85
262 263 8.507249 GCAGATTGTGATGGGTTTATATTACTC 58.493 37.037 0.00 0.00 0.00 2.59
263 264 7.998383 TGCAGATTGTGATGGGTTTATATTACT 59.002 33.333 0.00 0.00 0.00 2.24
264 265 8.165239 TGCAGATTGTGATGGGTTTATATTAC 57.835 34.615 0.00 0.00 0.00 1.89
265 266 7.448161 CCTGCAGATTGTGATGGGTTTATATTA 59.552 37.037 17.39 0.00 0.00 0.98
273 274 0.994247 TCCTGCAGATTGTGATGGGT 59.006 50.000 17.39 0.00 0.00 4.51
276 277 2.776312 GCATCCTGCAGATTGTGATG 57.224 50.000 17.39 18.85 44.26 3.07
290 291 1.930908 GCAGCTGACTGGTTGCATCC 61.931 60.000 20.43 6.88 44.63 3.51
292 293 2.330372 CGCAGCTGACTGGTTGCAT 61.330 57.895 20.43 0.00 44.63 3.96
347 348 8.117813 ACCGTTTAGATTATTGTTGGTTGATT 57.882 30.769 0.00 0.00 0.00 2.57
369 370 4.457603 TGTTTCAGGGTGATTGATTAACCG 59.542 41.667 0.00 0.00 34.62 4.44
373 374 5.335583 CGCTTTGTTTCAGGGTGATTGATTA 60.336 40.000 0.00 0.00 0.00 1.75
374 375 4.559300 CGCTTTGTTTCAGGGTGATTGATT 60.559 41.667 0.00 0.00 0.00 2.57
416 417 9.920133 TCTCAATATCAGTATATCTCTTTGCAC 57.080 33.333 0.00 0.00 0.00 4.57
435 460 7.674348 TCCCTAGAAAAGAAGACACTCTCAATA 59.326 37.037 0.00 0.00 0.00 1.90
438 463 5.394738 TCCCTAGAAAAGAAGACACTCTCA 58.605 41.667 0.00 0.00 0.00 3.27
689 714 5.492895 TCAAAAATGGTGTAGGAGCGATAA 58.507 37.500 0.00 0.00 0.00 1.75
690 715 5.092554 TCAAAAATGGTGTAGGAGCGATA 57.907 39.130 0.00 0.00 0.00 2.92
691 716 3.950397 TCAAAAATGGTGTAGGAGCGAT 58.050 40.909 0.00 0.00 0.00 4.58
692 717 3.410631 TCAAAAATGGTGTAGGAGCGA 57.589 42.857 0.00 0.00 0.00 4.93
693 718 4.701956 ATTCAAAAATGGTGTAGGAGCG 57.298 40.909 0.00 0.00 0.00 5.03
694 719 7.826690 TCTTTATTCAAAAATGGTGTAGGAGC 58.173 34.615 0.00 0.00 0.00 4.70
695 720 9.014297 ACTCTTTATTCAAAAATGGTGTAGGAG 57.986 33.333 0.00 0.00 0.00 3.69
763 790 6.770785 ACGCAATTTACATTGACATAGGGTAT 59.229 34.615 5.78 0.00 42.35 2.73
786 818 4.577834 AATTGTAAGTGGGGTTTTGACG 57.422 40.909 0.00 0.00 0.00 4.35
876 911 7.338710 ACAGAACCAATAATAGCACTGTATGT 58.661 34.615 0.00 0.00 35.95 2.29
877 912 7.792374 ACAGAACCAATAATAGCACTGTATG 57.208 36.000 0.00 0.00 35.95 2.39
895 933 5.108517 TGTTCATTTTCCTTGCAACAGAAC 58.891 37.500 0.00 3.40 34.89 3.01
960 998 3.057315 CACGCCCATGAATTGATATTCCC 60.057 47.826 0.00 0.00 39.56 3.97
961 999 3.569701 ACACGCCCATGAATTGATATTCC 59.430 43.478 0.00 0.00 39.56 3.01
993 1031 2.835764 AGTCAGCCCATGCATTGATTTT 59.164 40.909 0.00 0.00 41.13 1.82
1021 1059 1.068588 TGCTAGTATCGGTCCATGCAC 59.931 52.381 0.00 0.00 0.00 4.57
1034 1072 4.644954 CGTGCGACGAATATATGCTAGTA 58.355 43.478 0.00 0.00 46.05 1.82
1035 1073 3.489444 CGTGCGACGAATATATGCTAGT 58.511 45.455 0.00 0.00 46.05 2.57
1036 1074 2.276540 GCGTGCGACGAATATATGCTAG 59.723 50.000 11.94 0.00 46.05 3.42
1701 2276 1.227823 CCACTTGAACTCCACGCCA 60.228 57.895 0.00 0.00 0.00 5.69
2375 3370 3.674997 TCATCTTCCGGGTCAAAAAGAG 58.325 45.455 0.00 0.00 31.75 2.85
2530 3525 4.654015 GTGCTTTGTCGAAACTGTTTGTA 58.346 39.130 11.03 0.00 0.00 2.41
2603 3599 0.895100 ATCGCCACAACATGCAGGTT 60.895 50.000 11.64 11.64 0.00 3.50
2746 3742 3.257375 TGAACTCGTACACTAGCAATGGT 59.743 43.478 0.00 0.00 0.00 3.55
2816 3815 2.044053 ATCCACCCATGGCAACGG 60.044 61.111 6.09 3.32 46.80 4.44
2858 3857 2.719531 AGGTATGTGAGAGCTCTCGA 57.280 50.000 32.86 24.20 45.72 4.04
2870 3869 1.255667 ACGGCCGAGTGAAGGTATGT 61.256 55.000 35.90 0.00 0.00 2.29
3216 4215 4.750598 CCACAATCTGATGATCTAGCACAG 59.249 45.833 0.00 0.00 31.51 3.66
3281 4280 2.202919 CATCCTCACGCATGCCGA 60.203 61.111 13.15 8.24 41.02 5.54
3416 4415 2.122167 CCTCCTCCGCGCTCTTACT 61.122 63.158 5.56 0.00 0.00 2.24
3619 4776 4.512198 CGGTGTGTATGACTTGGTTAACAA 59.488 41.667 8.10 0.00 37.55 2.83
3642 4799 1.409427 CATCTACCCTTCCACCTCGTC 59.591 57.143 0.00 0.00 0.00 4.20
3643 4800 1.486211 CATCTACCCTTCCACCTCGT 58.514 55.000 0.00 0.00 0.00 4.18
3644 4801 0.105039 GCATCTACCCTTCCACCTCG 59.895 60.000 0.00 0.00 0.00 4.63
3709 4919 7.012515 CAGTAAGGACGATTGATAGTCACTACT 59.987 40.741 6.58 8.31 39.01 2.57
3710 4920 7.133513 CAGTAAGGACGATTGATAGTCACTAC 58.866 42.308 6.58 6.68 39.01 2.73
3711 4921 6.262496 CCAGTAAGGACGATTGATAGTCACTA 59.738 42.308 6.58 0.00 41.22 2.74
3712 4922 5.067936 CCAGTAAGGACGATTGATAGTCACT 59.932 44.000 6.58 0.00 41.22 3.41
3713 4923 5.282510 CCAGTAAGGACGATTGATAGTCAC 58.717 45.833 6.58 0.00 41.22 3.67
3714 4924 4.341235 CCCAGTAAGGACGATTGATAGTCA 59.659 45.833 6.58 0.00 41.22 3.41
3724 4934 1.202964 TGACTGACCCAGTAAGGACGA 60.203 52.381 0.00 0.00 45.44 4.20
3771 4982 1.867233 CACACTAGTCACAACCTGCAC 59.133 52.381 0.00 0.00 0.00 4.57
3913 5136 2.631160 AGACCCATCAAACACGTCAA 57.369 45.000 0.00 0.00 0.00 3.18
3918 5177 4.489679 GTCAAGAAGACCCATCAAACAC 57.510 45.455 0.00 0.00 41.56 3.32
3933 5192 5.880332 GCATAAATTCCACACCTAGTCAAGA 59.120 40.000 0.00 0.00 0.00 3.02
3934 5193 5.882557 AGCATAAATTCCACACCTAGTCAAG 59.117 40.000 0.00 0.00 0.00 3.02
3966 5225 2.544686 GCTGTCACAGATGCATGAGATC 59.455 50.000 9.70 0.00 32.44 2.75
3969 5228 1.666189 CAGCTGTCACAGATGCATGAG 59.334 52.381 10.74 0.00 40.91 2.90
3970 5229 1.734163 CAGCTGTCACAGATGCATGA 58.266 50.000 10.74 0.00 40.91 3.07
3999 5258 5.885449 TTTCTTTGTGTCATCCCCAAATT 57.115 34.783 0.00 0.00 0.00 1.82
4027 5286 5.914635 CGAAGCAAGCAATTGAACTCTTTTA 59.085 36.000 10.34 0.00 0.00 1.52
4080 5339 4.023450 AGCGCTTGCGTCTATACTGTATTA 60.023 41.667 16.38 0.00 45.69 0.98
4081 5340 3.050619 GCGCTTGCGTCTATACTGTATT 58.949 45.455 16.38 0.00 0.00 1.89
4083 5342 1.674441 AGCGCTTGCGTCTATACTGTA 59.326 47.619 16.38 0.00 45.69 2.74
4084 5343 0.456221 AGCGCTTGCGTCTATACTGT 59.544 50.000 16.38 0.00 45.69 3.55
4085 5344 1.124462 GAGCGCTTGCGTCTATACTG 58.876 55.000 13.26 0.00 45.69 2.74
4086 5345 0.738975 TGAGCGCTTGCGTCTATACT 59.261 50.000 13.26 3.73 45.69 2.12
4087 5346 1.772182 ATGAGCGCTTGCGTCTATAC 58.228 50.000 13.26 0.00 45.69 1.47
4088 5347 3.850122 ATATGAGCGCTTGCGTCTATA 57.150 42.857 13.26 11.75 45.69 1.31
4089 5348 2.732412 ATATGAGCGCTTGCGTCTAT 57.268 45.000 13.26 10.15 45.69 1.98
4090 5349 3.850122 ATATATGAGCGCTTGCGTCTA 57.150 42.857 13.26 0.00 45.69 2.59
4091 5350 2.732412 ATATATGAGCGCTTGCGTCT 57.268 45.000 13.26 13.17 45.69 4.18
4092 5351 3.059570 GTGTATATATGAGCGCTTGCGTC 59.940 47.826 13.26 12.36 45.69 5.19
4093 5352 2.987149 GTGTATATATGAGCGCTTGCGT 59.013 45.455 13.26 3.24 45.69 5.24
4094 5353 2.026860 CGTGTATATATGAGCGCTTGCG 59.973 50.000 13.26 10.90 45.69 4.85
4095 5354 2.222596 GCGTGTATATATGAGCGCTTGC 60.223 50.000 13.26 0.00 41.37 4.01
4096 5355 2.986479 TGCGTGTATATATGAGCGCTTG 59.014 45.455 13.26 0.00 44.34 4.01
4097 5356 3.297830 TGCGTGTATATATGAGCGCTT 57.702 42.857 13.26 0.00 44.34 4.68
4098 5357 3.510388 ATGCGTGTATATATGAGCGCT 57.490 42.857 11.27 11.27 44.34 5.92
4099 5358 4.027621 GTGTATGCGTGTATATATGAGCGC 60.028 45.833 16.99 16.99 44.29 5.92
4100 5359 5.332707 AGTGTATGCGTGTATATATGAGCG 58.667 41.667 0.00 0.00 0.00 5.03
4101 5360 6.322491 TGAGTGTATGCGTGTATATATGAGC 58.678 40.000 0.00 0.00 0.00 4.26
4113 5372 4.621991 GTTCATAGGATGAGTGTATGCGT 58.378 43.478 0.00 0.00 40.94 5.24
4128 5387 2.666508 GTGTGCCTGTGTACGTTCATAG 59.333 50.000 11.22 11.22 0.00 2.23
4129 5388 2.610976 GGTGTGCCTGTGTACGTTCATA 60.611 50.000 0.00 0.00 0.00 2.15
4135 5395 0.535335 ATAGGGTGTGCCTGTGTACG 59.465 55.000 0.00 0.00 34.45 3.67
4143 5403 2.637872 TGCTAATAGGATAGGGTGTGCC 59.362 50.000 0.00 0.00 0.00 5.01
4147 5407 6.464222 TCGAAAATGCTAATAGGATAGGGTG 58.536 40.000 0.00 0.00 0.00 4.61
4154 5414 8.178313 TCAGTCTATCGAAAATGCTAATAGGA 57.822 34.615 0.00 0.00 0.00 2.94
4166 5426 6.663523 TGATATATGGGCTCAGTCTATCGAAA 59.336 38.462 0.00 0.00 0.00 3.46
4169 5429 6.489700 AGATGATATATGGGCTCAGTCTATCG 59.510 42.308 0.00 0.00 0.00 2.92
4172 5432 7.184862 TCAAGATGATATATGGGCTCAGTCTA 58.815 38.462 0.00 0.00 0.00 2.59
4224 5484 1.226323 GACAGTCCCATCGACGACG 60.226 63.158 0.00 0.00 46.92 5.12
4368 5628 5.794894 AGACAATAGCTTATCCCCAATACG 58.205 41.667 0.00 0.00 0.00 3.06
4375 5635 7.500559 AGAATGACAAAGACAATAGCTTATCCC 59.499 37.037 0.00 0.00 0.00 3.85
4405 5665 7.865706 ACCATAAAACATATTGGTCTCAGTC 57.134 36.000 0.00 0.00 38.00 3.51
4441 5702 4.872691 AGATGAACAAGGTTCATAAGCTCG 59.127 41.667 20.84 0.00 39.08 5.03
4453 5714 7.555554 AGGTCTCAATATTGAAGATGAACAAGG 59.444 37.037 18.47 3.54 36.64 3.61


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.