Multiple sequence alignment - TraesCS2D01G402100

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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 TraesCS2D01G402100 chr2D 100.000 4530 0 0 1 4530 516923326 516927855 0.000000e+00 8366.0
1 TraesCS2D01G402100 chr2D 84.049 1235 126 26 2143 3329 517087176 517088387 0.000000e+00 1123.0
2 TraesCS2D01G402100 chr2D 82.635 1313 129 46 827 2097 517085938 517087193 0.000000e+00 1070.0
3 TraesCS2D01G402100 chr2D 81.734 1188 156 32 2171 3318 516863174 516864340 0.000000e+00 935.0
4 TraesCS2D01G402100 chr2D 85.828 755 63 16 1268 1999 517037468 517038201 0.000000e+00 761.0
5 TraesCS2D01G402100 chr2D 88.437 467 45 4 2148 2605 517038200 517038666 5.120000e-154 555.0
6 TraesCS2D01G402100 chr2D 97.980 297 6 0 4234 4530 82569847 82569551 2.420000e-142 516.0
7 TraesCS2D01G402100 chr2D 97.306 297 8 0 4234 4530 435977589 435977293 5.230000e-139 505.0
8 TraesCS2D01G402100 chr2D 90.476 273 24 2 3058 3329 517045911 517046182 4.310000e-95 359.0
9 TraesCS2D01G402100 chr2D 83.146 356 43 12 223 561 517085300 517085655 4.400000e-80 309.0
10 TraesCS2D01G402100 chr2D 87.970 266 24 4 2807 3064 517045607 517045872 1.580000e-79 307.0
11 TraesCS2D01G402100 chr2D 85.477 241 28 4 325 558 516872112 516872352 1.260000e-60 244.0
12 TraesCS2D01G402100 chr2D 89.595 173 18 0 224 396 516970227 516970399 2.120000e-53 220.0
13 TraesCS2D01G402100 chr2D 94.828 116 6 0 1026 1141 516898060 516898175 1.000000e-41 182.0
14 TraesCS2D01G402100 chr2D 91.473 129 11 0 2679 2807 517045445 517045573 1.290000e-40 178.0
15 TraesCS2D01G402100 chr2A 93.310 2616 124 27 946 3547 661151209 661153787 0.000000e+00 3814.0
16 TraesCS2D01G402100 chr2A 82.331 1330 135 54 827 2106 661446464 661447743 0.000000e+00 1062.0
17 TraesCS2D01G402100 chr2A 83.569 1132 142 21 2226 3329 661448214 661449329 0.000000e+00 1020.0
18 TraesCS2D01G402100 chr2A 80.763 1206 166 35 2165 3319 661082602 661083792 0.000000e+00 881.0
19 TraesCS2D01G402100 chr2A 84.754 833 73 21 1268 2065 661394536 661395349 0.000000e+00 785.0
20 TraesCS2D01G402100 chr2A 83.234 674 67 21 2171 2807 661395342 661396006 1.090000e-160 577.0
21 TraesCS2D01G402100 chr2A 84.055 577 67 13 1 554 661150481 661151055 2.400000e-147 532.0
22 TraesCS2D01G402100 chr2A 86.574 432 19 16 3559 3962 661153879 661154299 1.500000e-119 440.0
23 TraesCS2D01G402100 chr2A 84.527 349 37 11 224 559 661393163 661393507 3.380000e-86 329.0
24 TraesCS2D01G402100 chr2A 92.821 195 11 1 2873 3064 661396102 661396296 3.450000e-71 279.0
25 TraesCS2D01G402100 chr2A 84.615 247 31 5 223 462 661436203 661436449 5.860000e-59 239.0
26 TraesCS2D01G402100 chr2B 93.839 1477 65 9 2080 3547 608667943 608669402 0.000000e+00 2200.0
27 TraesCS2D01G402100 chr2B 93.301 1224 52 9 946 2160 608666791 608667993 0.000000e+00 1779.0
28 TraesCS2D01G402100 chr2B 81.391 1193 152 40 2171 3319 608540772 608541938 0.000000e+00 909.0
29 TraesCS2D01G402100 chr2B 89.708 719 27 20 3546 4232 608669484 608670187 0.000000e+00 874.0
30 TraesCS2D01G402100 chr2B 85.430 755 63 13 1268 1999 608801994 608802724 0.000000e+00 741.0
31 TraesCS2D01G402100 chr2B 83.668 698 68 14 2148 2807 608802723 608803412 2.320000e-172 616.0
32 TraesCS2D01G402100 chr2B 83.430 344 41 7 230 559 608800837 608801178 5.690000e-79 305.0
33 TraesCS2D01G402100 chr2B 88.800 250 27 1 3081 3329 608803767 608804016 5.690000e-79 305.0
34 TraesCS2D01G402100 chr2B 86.517 267 27 5 2807 3064 608803446 608803712 7.420000e-73 285.0
35 TraesCS2D01G402100 chr2B 84.167 120 18 1 688 806 608666652 608666771 1.030000e-21 115.0
36 TraesCS2D01G402100 chr1D 98.316 297 5 0 4234 4530 487194717 487195013 5.190000e-144 521.0
37 TraesCS2D01G402100 chr1D 99.281 139 1 0 4392 4530 273919365 273919227 7.520000e-63 252.0
38 TraesCS2D01G402100 chr1D 98.131 107 2 0 4234 4340 273919467 273919361 2.150000e-43 187.0
39 TraesCS2D01G402100 chr1D 83.871 155 18 3 394 547 474419666 474419814 1.700000e-29 141.0
40 TraesCS2D01G402100 chr7D 97.315 298 8 0 4233 4530 583986893 583987190 1.450000e-139 507.0
41 TraesCS2D01G402100 chr7D 81.041 269 31 12 3408 3658 404045653 404045919 3.580000e-46 196.0
42 TraesCS2D01G402100 chr7D 81.481 81 9 6 148 225 490897408 490897485 1.360000e-05 62.1
43 TraesCS2D01G402100 chr4B 93.603 297 19 0 4234 4530 117281006 117280710 1.160000e-120 444.0
44 TraesCS2D01G402100 chr6D 95.620 137 5 1 4234 4369 24883411 24883547 7.630000e-53 219.0
45 TraesCS2D01G402100 chr6D 100.000 36 0 0 3337 3372 412973548 412973583 2.920000e-07 67.6
46 TraesCS2D01G402100 chr7B 81.784 269 29 12 3408 3658 413559881 413560147 1.650000e-49 207.0
47 TraesCS2D01G402100 chr7B 83.439 157 17 5 395 543 488350487 488350642 2.200000e-28 137.0
48 TraesCS2D01G402100 chr7B 92.308 52 4 0 176 227 721804516 721804567 1.750000e-09 75.0
49 TraesCS2D01G402100 chr7B 76.860 121 25 3 3337 3456 423052042 423052160 1.050000e-06 65.8
50 TraesCS2D01G402100 chr4A 79.299 314 42 11 1763 2065 541336410 541336109 9.940000e-47 198.0
51 TraesCS2D01G402100 chr4A 82.051 156 21 5 395 543 37767057 37766902 4.760000e-25 126.0
52 TraesCS2D01G402100 chr4A 97.222 36 1 0 194 229 26668850 26668815 1.360000e-05 62.1
53 TraesCS2D01G402100 chr5D 85.714 133 15 3 4234 4365 72226124 72226253 2.200000e-28 137.0
54 TraesCS2D01G402100 chr5B 82.911 158 18 5 394 543 649748050 649747894 2.840000e-27 134.0
55 TraesCS2D01G402100 chr5B 81.529 157 22 6 394 543 308836183 308836339 6.150000e-24 122.0
56 TraesCS2D01G402100 chr5B 89.231 65 5 1 161 223 241893531 241893595 3.760000e-11 80.5
57 TraesCS2D01G402100 chrUn 81.529 157 22 6 394 543 292646539 292646383 6.150000e-24 122.0
58 TraesCS2D01G402100 chr1A 82.270 141 24 1 4241 4380 546025954 546026094 2.210000e-23 121.0
59 TraesCS2D01G402100 chr6B 90.909 66 6 0 158 223 544082602 544082667 6.240000e-14 89.8
60 TraesCS2D01G402100 chr7A 91.803 61 3 2 168 227 122276938 122276997 2.900000e-12 84.2
61 TraesCS2D01G402100 chr5A 93.617 47 1 2 181 226 349621550 349621595 8.130000e-08 69.4
62 TraesCS2D01G402100 chr4D 97.222 36 0 1 190 224 440823323 440823358 4.890000e-05 60.2


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 TraesCS2D01G402100 chr2D 516923326 516927855 4529 False 8366.000000 8366 100.000000 1 4530 1 chr2D.!!$F4 4529
1 TraesCS2D01G402100 chr2D 516863174 516864340 1166 False 935.000000 935 81.734000 2171 3318 1 chr2D.!!$F1 1147
2 TraesCS2D01G402100 chr2D 517085300 517088387 3087 False 834.000000 1123 83.276667 223 3329 3 chr2D.!!$F8 3106
3 TraesCS2D01G402100 chr2D 517037468 517038666 1198 False 658.000000 761 87.132500 1268 2605 2 chr2D.!!$F6 1337
4 TraesCS2D01G402100 chr2D 517045445 517046182 737 False 281.333333 359 89.973000 2679 3329 3 chr2D.!!$F7 650
5 TraesCS2D01G402100 chr2A 661150481 661154299 3818 False 1595.333333 3814 87.979667 1 3962 3 chr2A.!!$F3 3961
6 TraesCS2D01G402100 chr2A 661446464 661449329 2865 False 1041.000000 1062 82.950000 827 3329 2 chr2A.!!$F5 2502
7 TraesCS2D01G402100 chr2A 661082602 661083792 1190 False 881.000000 881 80.763000 2165 3319 1 chr2A.!!$F1 1154
8 TraesCS2D01G402100 chr2A 661393163 661396296 3133 False 492.500000 785 86.334000 224 3064 4 chr2A.!!$F4 2840
9 TraesCS2D01G402100 chr2B 608666652 608670187 3535 False 1242.000000 2200 90.253750 688 4232 4 chr2B.!!$F2 3544
10 TraesCS2D01G402100 chr2B 608540772 608541938 1166 False 909.000000 909 81.391000 2171 3319 1 chr2B.!!$F1 1148
11 TraesCS2D01G402100 chr2B 608800837 608804016 3179 False 450.400000 741 85.569000 230 3329 5 chr2B.!!$F3 3099

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
201 220 0.038166 TTTGAGAGGCCGGATTTGCT 59.962 50.000 5.05 0.0 0.0 3.91 F
1019 1732 0.595095 GAACAGAGCTTGGCACTTGG 59.405 55.000 0.00 0.0 0.0 3.61 F
2875 4244 1.001520 CGCCCCGGTGATCATATTGTA 59.998 52.381 0.00 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 2460 0.748450 TCAGGAAAGACGAACGGTGT 59.252 50.0 0.0 0.0 0.0 4.16 R
2910 4279 0.895530 TGTCGGTGAAGGAGATGGAC 59.104 55.0 0.0 0.0 0.0 4.02 R
4469 6042 0.030297 ATCCCTCTCTGCCATCCACT 60.030 55.0 0.0 0.0 0.0 4.00 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
26 27 2.224161 GCACTGTCCTCTGTTGAACTCT 60.224 50.000 0.00 0.00 0.00 3.24
48 49 6.634805 TCTGATGAACTATGTTCCTCTTGTC 58.365 40.000 13.72 3.43 0.00 3.18
52 53 2.537143 ACTATGTTCCTCTTGTCCGGT 58.463 47.619 0.00 0.00 0.00 5.28
53 54 2.233922 ACTATGTTCCTCTTGTCCGGTG 59.766 50.000 0.00 0.00 0.00 4.94
70 71 3.181497 CCGGTGATGAAATGTTGATCCAC 60.181 47.826 0.00 0.00 0.00 4.02
77 78 5.694231 TGAAATGTTGATCCACTGAACTG 57.306 39.130 0.00 0.00 0.00 3.16
80 81 1.202639 TGTTGATCCACTGAACTGCGT 60.203 47.619 0.00 0.00 0.00 5.24
81 82 1.195448 GTTGATCCACTGAACTGCGTG 59.805 52.381 0.00 0.00 0.00 5.34
92 93 2.223845 TGAACTGCGTGTTGATCATGTG 59.776 45.455 0.00 0.00 39.30 3.21
96 97 3.812609 ACTGCGTGTTGATCATGTGTTTA 59.187 39.130 0.00 0.00 35.64 2.01
97 98 4.140518 TGCGTGTTGATCATGTGTTTAC 57.859 40.909 0.00 0.00 35.64 2.01
106 107 4.325204 TGATCATGTGTTTACGTAGCGTTC 59.675 41.667 0.00 0.00 41.54 3.95
119 124 2.900122 AGCGTTCCATGATTGTTTCG 57.100 45.000 0.00 0.00 0.00 3.46
126 131 5.215160 GTTCCATGATTGTTTCGGATATGC 58.785 41.667 0.00 0.00 0.00 3.14
130 135 2.218603 GATTGTTTCGGATATGCGGGT 58.781 47.619 16.98 0.00 0.00 5.28
143 148 4.742201 CGGGTCGCAGGTGTGGAG 62.742 72.222 0.00 0.00 0.00 3.86
154 159 1.064463 AGGTGTGGAGGGCAACATATG 60.064 52.381 0.00 0.00 39.74 1.78
156 161 2.292267 GTGTGGAGGGCAACATATGAG 58.708 52.381 10.38 2.58 39.74 2.90
157 162 2.092968 GTGTGGAGGGCAACATATGAGA 60.093 50.000 10.38 0.00 39.74 3.27
158 163 2.092968 TGTGGAGGGCAACATATGAGAC 60.093 50.000 10.38 3.36 39.74 3.36
159 164 1.138859 TGGAGGGCAACATATGAGACG 59.861 52.381 10.38 0.00 39.74 4.18
160 165 1.139058 GGAGGGCAACATATGAGACGT 59.861 52.381 10.38 5.21 39.74 4.34
163 168 1.933853 GGGCAACATATGAGACGTGTC 59.066 52.381 10.38 5.61 39.74 3.67
165 170 1.588404 GCAACATATGAGACGTGTCCG 59.412 52.381 10.38 0.00 40.83 4.79
168 187 1.404391 ACATATGAGACGTGTCCGGAC 59.596 52.381 28.17 28.17 38.78 4.79
201 220 0.038166 TTTGAGAGGCCGGATTTGCT 59.962 50.000 5.05 0.00 0.00 3.91
205 224 0.912486 AGAGGCCGGATTTGCTAAGT 59.088 50.000 5.05 0.00 0.00 2.24
210 229 1.679032 GCCGGATTTGCTAAGTCTGGT 60.679 52.381 5.05 0.00 39.96 4.00
228 247 3.861840 TGGTTGTAGATGCTCTTAGTGC 58.138 45.455 0.00 0.00 0.00 4.40
243 262 7.659799 TGCTCTTAGTGCTGTATCTAAAACAAA 59.340 33.333 7.78 0.00 0.00 2.83
283 302 6.853720 TGGTGAGAGAAAACTTACGAGATAG 58.146 40.000 0.00 0.00 0.00 2.08
288 307 7.553402 TGAGAGAAAACTTACGAGATAGCTACT 59.447 37.037 0.00 0.00 0.00 2.57
292 311 7.553402 AGAAAACTTACGAGATAGCTACTCTCA 59.447 37.037 22.24 9.67 39.29 3.27
302 321 7.801315 CGAGATAGCTACTCTCAATGTTAAGAC 59.199 40.741 22.24 3.77 39.29 3.01
445 475 3.592059 ACATGCAATTTTGATGAGGTGC 58.408 40.909 0.00 0.00 0.00 5.01
453 483 2.380084 TTGATGAGGTGCCGTAGAAC 57.620 50.000 0.00 0.00 0.00 3.01
554 594 8.857098 GGCATGGCAATAAATGAGATATGATAT 58.143 33.333 15.47 0.00 0.00 1.63
609 649 8.821686 ATTTTTGAACATAGTGGGATATGACA 57.178 30.769 0.97 0.00 36.76 3.58
610 650 8.642935 TTTTTGAACATAGTGGGATATGACAA 57.357 30.769 0.97 4.60 36.76 3.18
611 651 8.821686 TTTTGAACATAGTGGGATATGACAAT 57.178 30.769 0.97 0.00 36.76 2.71
668 708 9.696917 CACACACTAGTATCATAAGCATGATAA 57.303 33.333 8.00 0.00 44.91 1.75
691 742 7.855784 AATGATACATGATACTCCCACTACA 57.144 36.000 0.00 0.00 0.00 2.74
694 745 8.262601 TGATACATGATACTCCCACTACAAAT 57.737 34.615 0.00 0.00 0.00 2.32
725 777 5.388371 GCATTAAAAGTGCACCGAAATTGTC 60.388 40.000 14.63 0.00 42.08 3.18
728 780 5.705609 AAAAGTGCACCGAAATTGTCTAT 57.294 34.783 14.63 0.00 0.00 1.98
731 783 3.863424 AGTGCACCGAAATTGTCTATACG 59.137 43.478 14.63 0.00 0.00 3.06
740 792 8.508875 ACCGAAATTGTCTATACGTTCAATTTT 58.491 29.630 18.76 9.00 44.74 1.82
762 818 5.529581 TGGACGATCAAGCATTACATCTA 57.470 39.130 0.00 0.00 0.00 1.98
809 865 2.563261 TTGTGGGGCAAACGTACATA 57.437 45.000 0.00 0.00 33.53 2.29
850 968 8.694581 TCATGATCTGGCAAAATATTATGTGA 57.305 30.769 0.00 0.00 0.00 3.58
879 1000 1.548582 CCACTTGGGCAATCTTCACCT 60.549 52.381 0.00 0.00 0.00 4.00
909 1033 1.587946 GTGCCGCTTTGTTTGTTTCAG 59.412 47.619 0.00 0.00 0.00 3.02
935 1452 9.974980 GAAAATAAATGAAGAAAAGGTACCACA 57.025 29.630 15.94 2.95 0.00 4.17
981 1693 6.723052 GGCGTACATATATATATACCCCCACT 59.277 42.308 4.54 0.00 0.00 4.00
996 1708 3.901222 CCCCCACTGGAAAACATTTTAGT 59.099 43.478 0.00 0.00 35.39 2.24
1019 1732 0.595095 GAACAGAGCTTGGCACTTGG 59.405 55.000 0.00 0.00 0.00 3.61
1069 1786 1.267365 CACAACAGTTTTGCACGTGG 58.733 50.000 18.88 0.44 0.00 4.94
1259 2010 2.032170 GCATGTGTGCCTGTGTGAA 58.968 52.632 0.00 0.00 45.76 3.18
1529 2301 5.694006 GGATGTGTGCTCATTATCTGTACTC 59.306 44.000 12.61 0.00 0.00 2.59
1530 2302 5.921962 TGTGTGCTCATTATCTGTACTCT 57.078 39.130 0.00 0.00 0.00 3.24
1688 2460 1.605971 TTACCGTCCAGGCACGCATA 61.606 55.000 6.05 0.05 46.52 3.14
1781 2571 1.961394 TGCTTTGACTGTCGTAGGTCT 59.039 47.619 2.98 0.00 34.01 3.85
1794 2584 2.223971 CGTAGGTCTTGGGCACGATTAT 60.224 50.000 0.00 0.00 34.66 1.28
2051 2853 7.739295 TCGTCTGTGAGAAAGTATTTAATTGC 58.261 34.615 0.00 0.00 39.27 3.56
2285 3554 1.352114 TGTAACCTCATTGCGTACGC 58.648 50.000 32.49 32.49 42.35 4.42
2848 4198 6.439058 ACCTTCTCTTACTAACAAGCTGATCT 59.561 38.462 0.00 0.00 0.00 2.75
2849 4199 6.756074 CCTTCTCTTACTAACAAGCTGATCTG 59.244 42.308 0.00 0.00 0.00 2.90
2851 4201 6.857956 TCTCTTACTAACAAGCTGATCTGAC 58.142 40.000 3.42 0.00 0.00 3.51
2853 4203 2.611518 ACTAACAAGCTGATCTGACGC 58.388 47.619 3.42 0.00 0.00 5.19
2875 4244 1.001520 CGCCCCGGTGATCATATTGTA 59.998 52.381 0.00 0.00 0.00 2.41
2910 4279 0.794473 GTGGGAAAGGTTACGCGAAG 59.206 55.000 15.93 0.00 0.00 3.79
2933 4302 3.967326 TCCATCTCCTTCACCGACATAAT 59.033 43.478 0.00 0.00 0.00 1.28
3178 4626 3.236003 AAGACGGCCGTGGACTTCC 62.236 63.158 39.65 19.83 0.00 3.46
3191 4639 0.108424 GACTTCCACTGCAGCGAGAT 60.108 55.000 15.27 1.51 0.00 2.75
3232 4680 1.215647 GTCAACTCCGTGGCGATCT 59.784 57.895 0.00 0.00 0.00 2.75
3234 4682 0.965866 TCAACTCCGTGGCGATCTCT 60.966 55.000 0.00 0.00 0.00 3.10
3240 4688 2.125391 GTGGCGATCTCTGCTGCA 60.125 61.111 0.88 0.88 0.00 4.41
3329 4780 6.012508 CCCAAGATCCCTTGCCTTAGATAATA 60.013 42.308 0.00 0.00 46.42 0.98
3330 4781 6.881602 CCAAGATCCCTTGCCTTAGATAATAC 59.118 42.308 0.00 0.00 46.42 1.89
3331 4782 7.256835 CCAAGATCCCTTGCCTTAGATAATACT 60.257 40.741 0.00 0.00 46.42 2.12
3354 4805 0.175989 AACTAGCAGGTAGAAGGCGC 59.824 55.000 13.77 0.00 32.41 6.53
3399 4851 2.573167 CCGCGCGTGTTTATGTGC 60.573 61.111 29.95 0.00 44.03 4.57
3405 4857 1.136584 CGCGTGTTTATGTGCGTGTAA 60.137 47.619 0.00 0.00 45.12 2.41
3455 4913 0.617820 AGTGGTATTGGGGTCGAGCT 60.618 55.000 15.18 0.00 0.00 4.09
3456 4914 0.462047 GTGGTATTGGGGTCGAGCTG 60.462 60.000 15.18 0.00 0.00 4.24
3523 4981 7.564793 TGCACACTGGTAGACTATGAAATTAT 58.435 34.615 0.00 0.00 0.00 1.28
3524 4982 8.046708 TGCACACTGGTAGACTATGAAATTATT 58.953 33.333 0.00 0.00 0.00 1.40
3573 5115 9.554395 TTTGACACTTTCAACTTATGTCTATCA 57.446 29.630 4.50 0.00 44.28 2.15
3605 5151 8.305317 TGATGCATCATTAACAGAAATTCAACA 58.695 29.630 25.42 0.00 0.00 3.33
3685 5232 9.231297 CTTACTGGGTATATTAATTCATGTGGG 57.769 37.037 0.00 0.00 0.00 4.61
3686 5233 7.161715 ACTGGGTATATTAATTCATGTGGGT 57.838 36.000 0.00 0.00 0.00 4.51
3687 5234 7.591821 ACTGGGTATATTAATTCATGTGGGTT 58.408 34.615 0.00 0.00 0.00 4.11
3690 5237 8.503573 TGGGTATATTAATTCATGTGGGTTGTA 58.496 33.333 0.00 0.00 0.00 2.41
3707 5254 7.830697 GTGGGTTGTAGTACCTTATAACCAATT 59.169 37.037 17.17 0.00 43.00 2.32
3806 5376 7.629157 TCAAGAATTTCCTACATGTATGGACA 58.371 34.615 18.19 14.35 40.72 4.02
3809 5379 7.275920 AGAATTTCCTACATGTATGGACAGTC 58.724 38.462 19.33 19.33 39.50 3.51
3847 5417 4.451379 TGCTAAAATCATATCGTGCACG 57.549 40.909 32.76 32.76 41.45 5.34
3907 5477 6.198778 GCATTTGCACCCTTTTGAAATTTTTC 59.801 34.615 0.00 0.00 41.59 2.29
3917 5487 7.307337 CCCTTTTGAAATTTTTCGAAGGACATG 60.307 37.037 24.75 13.29 45.79 3.21
3991 5561 7.721402 TCAAAGCAAAGAAGCCAAACTAATTA 58.279 30.769 0.00 0.00 34.23 1.40
4059 5630 9.478238 TGTTTATATAGTACAGTAGTTCCCACA 57.522 33.333 0.00 0.00 0.00 4.17
4070 5641 3.228188 AGTTCCCACATCAAAGAAGCA 57.772 42.857 0.00 0.00 0.00 3.91
4073 5644 4.051237 GTTCCCACATCAAAGAAGCAAAC 58.949 43.478 0.00 0.00 0.00 2.93
4079 5652 7.029563 CCCACATCAAAGAAGCAAACTATTAC 58.970 38.462 0.00 0.00 0.00 1.89
4081 5654 7.360861 CCACATCAAAGAAGCAAACTATTACGA 60.361 37.037 0.00 0.00 0.00 3.43
4114 5687 7.553881 TTAAGAAAAGAAGACTTCACAGTGG 57.446 36.000 17.34 0.00 35.05 4.00
4144 5717 8.090214 GGAAAACATCAATGGAGAATTCTGAAA 58.910 33.333 14.00 0.00 0.00 2.69
4149 5722 6.579666 TCAATGGAGAATTCTGAAACTTGG 57.420 37.500 14.00 0.00 0.00 3.61
4195 5768 6.054941 TCATGAATATCACGTGCAATTAGGT 58.945 36.000 11.67 0.40 0.00 3.08
4201 5774 7.941795 ATATCACGTGCAATTAGGTTACTAC 57.058 36.000 11.67 0.00 0.00 2.73
4205 5778 4.168014 CGTGCAATTAGGTTACTACGTGA 58.832 43.478 0.00 0.00 0.00 4.35
4234 5807 8.148351 TCCTACAATTACACTATACCAATGAGC 58.852 37.037 0.00 0.00 0.00 4.26
4235 5808 7.387948 CCTACAATTACACTATACCAATGAGCC 59.612 40.741 0.00 0.00 0.00 4.70
4236 5809 5.758296 ACAATTACACTATACCAATGAGCCG 59.242 40.000 0.00 0.00 0.00 5.52
4237 5810 2.910688 ACACTATACCAATGAGCCGG 57.089 50.000 0.00 0.00 0.00 6.13
4238 5811 1.202651 ACACTATACCAATGAGCCGGC 60.203 52.381 21.89 21.89 0.00 6.13
4239 5812 0.033504 ACTATACCAATGAGCCGGCG 59.966 55.000 23.20 8.17 0.00 6.46
4240 5813 0.670546 CTATACCAATGAGCCGGCGG 60.671 60.000 24.35 24.35 0.00 6.13
4241 5814 1.404479 TATACCAATGAGCCGGCGGT 61.404 55.000 28.82 23.76 0.00 5.68
4242 5815 2.660258 ATACCAATGAGCCGGCGGTC 62.660 60.000 28.82 22.37 37.01 4.79
4321 5894 4.530857 GCGGTGCGGTGGCTAGAT 62.531 66.667 0.00 0.00 40.82 1.98
4322 5895 2.586079 CGGTGCGGTGGCTAGATG 60.586 66.667 0.00 0.00 40.82 2.90
4323 5896 2.584608 GGTGCGGTGGCTAGATGT 59.415 61.111 0.00 0.00 40.82 3.06
4324 5897 1.815421 GGTGCGGTGGCTAGATGTG 60.815 63.158 0.00 0.00 40.82 3.21
4325 5898 2.125147 TGCGGTGGCTAGATGTGC 60.125 61.111 0.00 0.00 40.82 4.57
4326 5899 2.187946 GCGGTGGCTAGATGTGCT 59.812 61.111 0.00 0.00 35.83 4.40
4327 5900 2.176273 GCGGTGGCTAGATGTGCTG 61.176 63.158 0.00 0.00 35.83 4.41
4328 5901 2.176273 CGGTGGCTAGATGTGCTGC 61.176 63.158 0.00 0.00 0.00 5.25
4329 5902 1.821332 GGTGGCTAGATGTGCTGCC 60.821 63.158 0.00 0.00 39.65 4.85
4330 5903 1.222936 GTGGCTAGATGTGCTGCCT 59.777 57.895 0.00 0.00 39.81 4.75
4331 5904 0.393537 GTGGCTAGATGTGCTGCCTT 60.394 55.000 0.00 0.00 39.81 4.35
4332 5905 0.393402 TGGCTAGATGTGCTGCCTTG 60.393 55.000 0.00 0.00 39.81 3.61
4333 5906 1.722636 GGCTAGATGTGCTGCCTTGC 61.723 60.000 0.00 0.00 37.63 4.01
4334 5907 0.747283 GCTAGATGTGCTGCCTTGCT 60.747 55.000 0.00 0.00 0.00 3.91
4335 5908 1.297664 CTAGATGTGCTGCCTTGCTC 58.702 55.000 0.00 0.00 0.00 4.26
4336 5909 0.907486 TAGATGTGCTGCCTTGCTCT 59.093 50.000 0.00 0.00 0.00 4.09
4337 5910 0.677098 AGATGTGCTGCCTTGCTCTG 60.677 55.000 0.00 0.00 0.00 3.35
4338 5911 0.959372 GATGTGCTGCCTTGCTCTGT 60.959 55.000 0.00 0.00 0.00 3.41
4339 5912 0.538977 ATGTGCTGCCTTGCTCTGTT 60.539 50.000 0.00 0.00 0.00 3.16
4340 5913 0.752743 TGTGCTGCCTTGCTCTGTTT 60.753 50.000 0.00 0.00 0.00 2.83
4341 5914 0.318445 GTGCTGCCTTGCTCTGTTTG 60.318 55.000 0.00 0.00 0.00 2.93
4342 5915 1.288127 GCTGCCTTGCTCTGTTTGG 59.712 57.895 0.00 0.00 0.00 3.28
4343 5916 1.962144 CTGCCTTGCTCTGTTTGGG 59.038 57.895 0.00 0.00 0.00 4.12
4344 5917 2.151049 CTGCCTTGCTCTGTTTGGGC 62.151 60.000 0.00 0.00 39.93 5.36
4345 5918 2.202395 GCCTTGCTCTGTTTGGGCA 61.202 57.895 0.00 0.00 39.38 5.36
4346 5919 1.962144 CCTTGCTCTGTTTGGGCAG 59.038 57.895 0.00 0.00 37.28 4.85
4347 5920 0.538057 CCTTGCTCTGTTTGGGCAGA 60.538 55.000 0.00 0.00 42.56 4.26
4348 5921 1.542492 CTTGCTCTGTTTGGGCAGAT 58.458 50.000 0.00 0.00 43.61 2.90
4349 5922 1.471684 CTTGCTCTGTTTGGGCAGATC 59.528 52.381 0.00 0.00 43.61 2.75
4350 5923 0.322816 TGCTCTGTTTGGGCAGATCC 60.323 55.000 0.00 0.00 43.61 3.36
4351 5924 0.034670 GCTCTGTTTGGGCAGATCCT 60.035 55.000 0.00 0.00 43.61 3.24
4352 5925 2.016096 GCTCTGTTTGGGCAGATCCTC 61.016 57.143 0.00 0.00 43.61 3.71
4353 5926 1.558756 CTCTGTTTGGGCAGATCCTCT 59.441 52.381 0.00 0.00 43.61 3.69
4354 5927 1.280133 TCTGTTTGGGCAGATCCTCTG 59.720 52.381 0.00 0.00 46.90 3.35
4364 5937 2.600790 CAGATCCTCTGCTCCAGATCT 58.399 52.381 0.00 0.00 44.85 2.75
4365 5938 2.600790 AGATCCTCTGCTCCAGATCTG 58.399 52.381 16.24 16.24 42.91 2.90
4375 5948 3.491208 CCAGATCTGGCTTCTTGGG 57.509 57.895 28.45 1.94 44.73 4.12
4376 5949 0.750911 CCAGATCTGGCTTCTTGGGC 60.751 60.000 28.45 0.00 44.73 5.36
4377 5950 0.034767 CAGATCTGGCTTCTTGGGCA 60.035 55.000 15.38 0.00 39.84 5.36
4383 5956 2.985847 GCTTCTTGGGCAGCGGTT 60.986 61.111 0.00 0.00 0.00 4.44
4384 5957 2.982744 GCTTCTTGGGCAGCGGTTC 61.983 63.158 0.00 0.00 0.00 3.62
4385 5958 1.600636 CTTCTTGGGCAGCGGTTCA 60.601 57.895 0.00 0.00 0.00 3.18
4386 5959 1.856265 CTTCTTGGGCAGCGGTTCAC 61.856 60.000 0.00 0.00 0.00 3.18
4387 5960 2.594303 CTTGGGCAGCGGTTCACA 60.594 61.111 0.00 0.00 0.00 3.58
4388 5961 1.973281 CTTGGGCAGCGGTTCACAT 60.973 57.895 0.00 0.00 0.00 3.21
4389 5962 1.526575 CTTGGGCAGCGGTTCACATT 61.527 55.000 0.00 0.00 0.00 2.71
4390 5963 1.804396 TTGGGCAGCGGTTCACATTG 61.804 55.000 0.00 0.00 0.00 2.82
4391 5964 2.126346 GGCAGCGGTTCACATTGC 60.126 61.111 0.00 0.00 0.00 3.56
4392 5965 2.629656 GGCAGCGGTTCACATTGCT 61.630 57.895 0.00 0.00 38.43 3.91
4394 5967 4.481195 AGCGGTTCACATTGCTGT 57.519 50.000 0.00 0.00 36.09 4.40
4395 5968 2.719376 AGCGGTTCACATTGCTGTT 58.281 47.368 0.00 0.00 36.09 3.16
4396 5969 0.311790 AGCGGTTCACATTGCTGTTG 59.688 50.000 0.00 0.00 36.09 3.33
4397 5970 0.664166 GCGGTTCACATTGCTGTTGG 60.664 55.000 0.00 0.00 31.62 3.77
4398 5971 0.667993 CGGTTCACATTGCTGTTGGT 59.332 50.000 0.00 0.00 31.62 3.67
4399 5972 1.334960 CGGTTCACATTGCTGTTGGTC 60.335 52.381 0.00 0.00 31.62 4.02
4400 5973 1.680735 GGTTCACATTGCTGTTGGTCA 59.319 47.619 0.00 0.00 31.62 4.02
4401 5974 2.297033 GGTTCACATTGCTGTTGGTCAT 59.703 45.455 0.00 0.00 31.62 3.06
4402 5975 3.568538 GTTCACATTGCTGTTGGTCATC 58.431 45.455 0.00 0.00 31.62 2.92
4403 5976 1.805943 TCACATTGCTGTTGGTCATCG 59.194 47.619 0.00 0.00 31.62 3.84
4404 5977 1.135603 CACATTGCTGTTGGTCATCGG 60.136 52.381 0.00 0.00 31.62 4.18
4405 5978 0.452987 CATTGCTGTTGGTCATCGGG 59.547 55.000 0.00 0.00 0.00 5.14
4406 5979 0.680921 ATTGCTGTTGGTCATCGGGG 60.681 55.000 0.00 0.00 0.00 5.73
4407 5980 3.134127 GCTGTTGGTCATCGGGGC 61.134 66.667 0.00 0.00 0.00 5.80
4408 5981 2.671070 CTGTTGGTCATCGGGGCT 59.329 61.111 0.00 0.00 0.00 5.19
4409 5982 1.746615 CTGTTGGTCATCGGGGCTG 60.747 63.158 0.00 0.00 0.00 4.85
4410 5983 3.134127 GTTGGTCATCGGGGCTGC 61.134 66.667 0.00 0.00 0.00 5.25
4411 5984 4.776322 TTGGTCATCGGGGCTGCG 62.776 66.667 0.00 0.00 0.00 5.18
4457 6030 4.704833 CGGGGTCTGCTGTGGTGG 62.705 72.222 0.00 0.00 0.00 4.61
4461 6034 4.626081 GTCTGCTGTGGTGGCGGT 62.626 66.667 0.00 0.00 37.35 5.68
4462 6035 4.314440 TCTGCTGTGGTGGCGGTC 62.314 66.667 0.00 0.00 37.35 4.79
4466 6039 3.991051 CTGTGGTGGCGGTCGAGT 61.991 66.667 0.00 0.00 0.00 4.18
4467 6040 4.293648 TGTGGTGGCGGTCGAGTG 62.294 66.667 0.00 0.00 0.00 3.51
4468 6041 4.295119 GTGGTGGCGGTCGAGTGT 62.295 66.667 0.00 0.00 0.00 3.55
4469 6042 2.598099 TGGTGGCGGTCGAGTGTA 60.598 61.111 0.00 0.00 0.00 2.90
4470 6043 2.181021 GGTGGCGGTCGAGTGTAG 59.819 66.667 0.00 0.00 0.00 2.74
4471 6044 2.633509 GGTGGCGGTCGAGTGTAGT 61.634 63.158 0.00 0.00 0.00 2.73
4472 6045 1.443872 GTGGCGGTCGAGTGTAGTG 60.444 63.158 0.00 0.00 0.00 2.74
4473 6046 2.181021 GGCGGTCGAGTGTAGTGG 59.819 66.667 0.00 0.00 0.00 4.00
4474 6047 2.338015 GGCGGTCGAGTGTAGTGGA 61.338 63.158 0.00 0.00 0.00 4.02
4475 6048 1.664321 GGCGGTCGAGTGTAGTGGAT 61.664 60.000 0.00 0.00 0.00 3.41
4476 6049 0.525668 GCGGTCGAGTGTAGTGGATG 60.526 60.000 0.00 0.00 0.00 3.51
4477 6050 0.100682 CGGTCGAGTGTAGTGGATGG 59.899 60.000 0.00 0.00 0.00 3.51
4478 6051 0.179108 GGTCGAGTGTAGTGGATGGC 60.179 60.000 0.00 0.00 0.00 4.40
4479 6052 0.530744 GTCGAGTGTAGTGGATGGCA 59.469 55.000 0.00 0.00 0.00 4.92
4480 6053 0.817654 TCGAGTGTAGTGGATGGCAG 59.182 55.000 0.00 0.00 0.00 4.85
4481 6054 0.817654 CGAGTGTAGTGGATGGCAGA 59.182 55.000 0.00 0.00 0.00 4.26
4482 6055 1.202348 CGAGTGTAGTGGATGGCAGAG 60.202 57.143 0.00 0.00 0.00 3.35
4483 6056 2.103373 GAGTGTAGTGGATGGCAGAGA 58.897 52.381 0.00 0.00 0.00 3.10
4484 6057 2.100584 GAGTGTAGTGGATGGCAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
4485 6058 1.137872 GTGTAGTGGATGGCAGAGAGG 59.862 57.143 0.00 0.00 0.00 3.69
4486 6059 0.755686 GTAGTGGATGGCAGAGAGGG 59.244 60.000 0.00 0.00 0.00 4.30
4487 6060 0.636647 TAGTGGATGGCAGAGAGGGA 59.363 55.000 0.00 0.00 0.00 4.20
4488 6061 0.030297 AGTGGATGGCAGAGAGGGAT 60.030 55.000 0.00 0.00 0.00 3.85
4489 6062 0.842635 GTGGATGGCAGAGAGGGATT 59.157 55.000 0.00 0.00 0.00 3.01
4490 6063 0.841961 TGGATGGCAGAGAGGGATTG 59.158 55.000 0.00 0.00 0.00 2.67
4491 6064 0.536915 GGATGGCAGAGAGGGATTGC 60.537 60.000 0.00 0.00 37.11 3.56
4492 6065 0.883814 GATGGCAGAGAGGGATTGCG 60.884 60.000 0.00 0.00 38.69 4.85
4493 6066 1.630126 ATGGCAGAGAGGGATTGCGT 61.630 55.000 0.00 0.00 38.69 5.24
4494 6067 1.817099 GGCAGAGAGGGATTGCGTG 60.817 63.158 0.00 0.00 38.69 5.34
4495 6068 2.467826 GCAGAGAGGGATTGCGTGC 61.468 63.158 0.00 0.00 0.00 5.34
4496 6069 1.078918 CAGAGAGGGATTGCGTGCA 60.079 57.895 0.00 0.00 0.00 4.57
4497 6070 1.088340 CAGAGAGGGATTGCGTGCAG 61.088 60.000 0.00 0.00 0.00 4.41
4498 6071 1.817099 GAGAGGGATTGCGTGCAGG 60.817 63.158 1.01 1.01 0.00 4.85
4499 6072 3.512516 GAGGGATTGCGTGCAGGC 61.513 66.667 23.98 23.98 0.00 4.85
4524 6097 2.685380 AGGTCCTCCTTGGCTCCG 60.685 66.667 0.00 0.00 42.12 4.63
4525 6098 3.787001 GGTCCTCCTTGGCTCCGG 61.787 72.222 0.00 0.00 35.26 5.14
4526 6099 3.003763 GTCCTCCTTGGCTCCGGT 61.004 66.667 0.00 0.00 35.26 5.28
4527 6100 1.684734 GTCCTCCTTGGCTCCGGTA 60.685 63.158 0.00 0.00 35.26 4.02
4528 6101 1.049289 GTCCTCCTTGGCTCCGGTAT 61.049 60.000 0.00 0.00 35.26 2.73
4529 6102 1.048724 TCCTCCTTGGCTCCGGTATG 61.049 60.000 0.00 0.00 35.26 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.997655 ACATAGTTCATCAGAGTTCAACAGA 58.002 36.000 0.00 0.00 0.00 3.41
16 17 6.650807 GGAACATAGTTCATCAGAGTTCAACA 59.349 38.462 11.51 0.00 36.52 3.33
26 27 5.624509 CGGACAAGAGGAACATAGTTCATCA 60.625 44.000 21.65 0.00 32.25 3.07
48 49 3.016031 TGGATCAACATTTCATCACCGG 58.984 45.455 0.00 0.00 0.00 5.28
52 53 6.005823 AGTTCAGTGGATCAACATTTCATCA 58.994 36.000 2.34 0.00 0.00 3.07
53 54 6.320171 CAGTTCAGTGGATCAACATTTCATC 58.680 40.000 2.34 0.00 0.00 2.92
70 71 2.481568 ACATGATCAACACGCAGTTCAG 59.518 45.455 0.00 0.00 41.61 3.02
77 78 3.152983 CGTAAACACATGATCAACACGC 58.847 45.455 0.00 0.00 0.00 5.34
80 81 4.090786 CGCTACGTAAACACATGATCAACA 59.909 41.667 0.00 0.00 0.00 3.33
81 82 4.090930 ACGCTACGTAAACACATGATCAAC 59.909 41.667 0.00 0.00 38.73 3.18
92 93 4.092383 ACAATCATGGAACGCTACGTAAAC 59.908 41.667 0.00 0.00 39.99 2.01
96 97 2.380084 ACAATCATGGAACGCTACGT 57.620 45.000 0.00 0.00 43.97 3.57
97 98 3.670203 GAAACAATCATGGAACGCTACG 58.330 45.455 0.00 0.00 0.00 3.51
106 107 3.365264 CCGCATATCCGAAACAATCATGG 60.365 47.826 0.00 0.00 0.00 3.66
126 131 4.742201 CTCCACACCTGCGACCCG 62.742 72.222 0.00 0.00 0.00 5.28
134 139 1.064463 CATATGTTGCCCTCCACACCT 60.064 52.381 0.00 0.00 0.00 4.00
143 148 1.933853 GACACGTCTCATATGTTGCCC 59.066 52.381 1.90 0.00 0.00 5.36
173 192 3.121030 CCTCTCAAACGCCAGCGG 61.121 66.667 17.33 0.00 44.69 5.52
177 196 4.697756 CCGGCCTCTCAAACGCCA 62.698 66.667 0.00 0.00 43.17 5.69
243 262 6.266103 TCTCTCACCAAATGCTTCAAAAAGAT 59.734 34.615 0.00 0.00 34.14 2.40
283 302 8.934507 ACATTAGTCTTAACATTGAGAGTAGC 57.065 34.615 0.00 0.00 32.48 3.58
425 448 2.933906 GGCACCTCATCAAAATTGCATG 59.066 45.455 0.00 0.00 0.00 4.06
427 457 1.067706 CGGCACCTCATCAAAATTGCA 60.068 47.619 0.00 0.00 0.00 4.08
445 475 8.812329 CATCTCTTTCTTCATTTAGTTCTACGG 58.188 37.037 0.00 0.00 0.00 4.02
453 483 8.558973 ACTCAACCATCTCTTTCTTCATTTAG 57.441 34.615 0.00 0.00 0.00 1.85
524 564 4.476297 TCTCATTTATTGCCATGCCTGAT 58.524 39.130 0.00 0.00 0.00 2.90
528 568 6.519679 TCATATCTCATTTATTGCCATGCC 57.480 37.500 0.00 0.00 0.00 4.40
583 623 9.913310 TGTCATATCCCACTATGTTCAAAAATA 57.087 29.630 0.00 0.00 32.13 1.40
584 624 8.821686 TGTCATATCCCACTATGTTCAAAAAT 57.178 30.769 0.00 0.00 32.13 1.82
585 625 8.642935 TTGTCATATCCCACTATGTTCAAAAA 57.357 30.769 0.00 0.00 32.13 1.94
586 626 8.821686 ATTGTCATATCCCACTATGTTCAAAA 57.178 30.769 0.00 0.00 33.17 2.44
587 627 8.821686 AATTGTCATATCCCACTATGTTCAAA 57.178 30.769 0.00 0.00 33.17 2.69
588 628 8.821686 AAATTGTCATATCCCACTATGTTCAA 57.178 30.769 0.00 0.00 33.52 2.69
659 699 8.209584 GGGAGTATCATGTATCATTATCATGCT 58.790 37.037 0.00 0.00 38.82 3.79
668 708 7.855784 TTGTAGTGGGAGTATCATGTATCAT 57.144 36.000 0.00 0.00 36.25 2.45
691 742 9.677567 CGGTGCACTTTTAATGCTTATATATTT 57.322 29.630 17.98 0.00 43.77 1.40
694 745 8.439993 TTCGGTGCACTTTTAATGCTTATATA 57.560 30.769 17.98 0.00 43.77 0.86
706 757 5.705609 ATAGACAATTTCGGTGCACTTTT 57.294 34.783 17.98 0.00 0.00 2.27
725 777 7.229228 TGATCGTCCAAAATTGAACGTATAG 57.771 36.000 4.87 0.00 36.55 1.31
728 780 5.615984 GCTTGATCGTCCAAAATTGAACGTA 60.616 40.000 4.87 0.00 36.55 3.57
731 783 4.545610 TGCTTGATCGTCCAAAATTGAAC 58.454 39.130 0.00 0.00 0.00 3.18
740 792 4.406648 AGATGTAATGCTTGATCGTCCA 57.593 40.909 0.00 0.00 0.00 4.02
748 800 4.976116 TCGATCACGTAGATGTAATGCTTG 59.024 41.667 5.41 0.00 37.00 4.01
809 865 5.722263 GATCATGAAGATCGATGGAGTGAT 58.278 41.667 0.54 6.14 43.40 3.06
842 960 5.241506 CCAAGTGGTGTTGAAGTCACATAAT 59.758 40.000 0.00 0.00 37.52 1.28
843 961 4.578516 CCAAGTGGTGTTGAAGTCACATAA 59.421 41.667 0.00 0.00 37.52 1.90
850 968 0.033601 TGCCCAAGTGGTGTTGAAGT 60.034 50.000 0.00 0.00 36.04 3.01
879 1000 0.739561 AAAGCGGCACCGTTTGTTTA 59.260 45.000 12.01 0.00 41.66 2.01
909 1033 9.974980 TGTGGTACCTTTTCTTCATTTATTTTC 57.025 29.630 14.36 0.00 0.00 2.29
930 1054 1.227438 CGTCGAAACTGGGTGTGGT 60.227 57.895 0.00 0.00 0.00 4.16
935 1452 0.319641 GAGAAGCGTCGAAACTGGGT 60.320 55.000 0.00 0.00 0.00 4.51
981 1693 8.610248 TCTGTTCGATACTAAAATGTTTTCCA 57.390 30.769 0.00 0.00 0.00 3.53
996 1708 1.550524 AGTGCCAAGCTCTGTTCGATA 59.449 47.619 0.00 0.00 30.96 2.92
1019 1732 2.811317 CGCTGCAGTCTCGGGAAC 60.811 66.667 16.64 0.00 0.00 3.62
1069 1786 2.493501 GGCTCGTAAGGTCGTCCC 59.506 66.667 0.00 0.00 38.47 4.46
1183 1927 7.534723 TGGTTGTTACTAGTCTGTCAACTAT 57.465 36.000 20.66 0.00 36.46 2.12
1259 2010 5.878116 TGCCAGATTAATTAGTAAGCACGTT 59.122 36.000 0.00 0.00 30.06 3.99
1365 2119 4.657824 AACACGCCGTCCACCTCG 62.658 66.667 0.00 0.00 0.00 4.63
1366 2120 2.737376 GAACACGCCGTCCACCTC 60.737 66.667 0.00 0.00 0.00 3.85
1529 2301 0.810031 CCACGAACGCCTTCCCATAG 60.810 60.000 0.00 0.00 0.00 2.23
1530 2302 1.219664 CCACGAACGCCTTCCCATA 59.780 57.895 0.00 0.00 0.00 2.74
1610 2382 1.878656 CGACGAGGAAGGACTTGGCT 61.879 60.000 0.00 0.00 0.00 4.75
1665 2437 1.087771 CGTGCCTGGACGGTAATTCC 61.088 60.000 3.06 0.00 35.65 3.01
1688 2460 0.748450 TCAGGAAAGACGAACGGTGT 59.252 50.000 0.00 0.00 0.00 4.16
1781 2571 2.477176 GCGCCATAATCGTGCCCAA 61.477 57.895 0.00 0.00 0.00 4.12
1917 2710 2.165030 GCATAGCCTCTGCATTTGTTGT 59.835 45.455 0.00 0.00 41.13 3.32
2051 2853 6.668323 TGCTTCGTTTTAAAGGAAAGATCAG 58.332 36.000 12.77 3.12 35.17 2.90
2285 3554 2.079158 GCATGGATCGATATGGTGGTG 58.921 52.381 9.62 0.00 0.00 4.17
2823 4169 6.439058 AGATCAGCTTGTTAGTAAGAGAAGGT 59.561 38.462 0.00 0.00 0.00 3.50
2853 4203 3.589654 ATATGATCACCGGGGCGCG 62.590 63.158 17.81 17.81 0.00 6.86
2875 4244 1.376424 CACCCTGCAGTGCGAAGAT 60.376 57.895 13.81 0.00 0.00 2.40
2910 4279 0.895530 TGTCGGTGAAGGAGATGGAC 59.104 55.000 0.00 0.00 0.00 4.02
3178 4626 3.260483 GCCGATCTCGCTGCAGTG 61.260 66.667 21.43 21.43 38.18 3.66
3191 4639 3.881952 ATGTTCGTGCAGCTGCCGA 62.882 57.895 33.74 33.74 40.20 5.54
3329 4780 5.009811 CGCCTTCTACCTGCTAGTTATTAGT 59.990 44.000 0.00 0.00 0.00 2.24
3330 4781 5.462405 CGCCTTCTACCTGCTAGTTATTAG 58.538 45.833 0.00 0.00 0.00 1.73
3331 4782 4.261909 GCGCCTTCTACCTGCTAGTTATTA 60.262 45.833 0.00 0.00 0.00 0.98
3379 4831 4.530325 CATAAACACGCGCGGGCC 62.530 66.667 35.17 0.00 35.02 5.80
3455 4913 5.471797 TGTCAGAAAGATTTATTCGCAACCA 59.528 36.000 0.00 0.00 32.04 3.67
3456 4914 5.938322 TGTCAGAAAGATTTATTCGCAACC 58.062 37.500 0.00 0.00 32.04 3.77
3474 4932 7.114529 GCAATGAAAATTTCTGAAGTCTGTCAG 59.885 37.037 7.29 0.00 45.44 3.51
3571 5113 9.563748 TTCTGTTAATGATGCATCAGATATTGA 57.436 29.630 31.36 21.59 40.64 2.57
3605 5151 4.280436 TGACTTTTCACCGGACATATGT 57.720 40.909 9.46 8.43 0.00 2.29
3674 5221 5.514500 AGGTACTACAACCCACATGAATT 57.486 39.130 0.00 0.00 40.71 2.17
3677 5224 7.364939 GGTTATAAGGTACTACAACCCACATGA 60.365 40.741 0.00 0.00 38.49 3.07
3678 5225 6.764560 GGTTATAAGGTACTACAACCCACATG 59.235 42.308 0.00 0.00 38.49 3.21
3679 5226 6.444493 TGGTTATAAGGTACTACAACCCACAT 59.556 38.462 1.15 0.00 40.64 3.21
3680 5227 5.784390 TGGTTATAAGGTACTACAACCCACA 59.216 40.000 1.15 0.00 40.64 4.17
3681 5228 6.298441 TGGTTATAAGGTACTACAACCCAC 57.702 41.667 1.15 0.00 40.64 4.61
3682 5229 6.949117 TTGGTTATAAGGTACTACAACCCA 57.051 37.500 1.15 0.00 40.64 4.51
3683 5230 8.048514 TGAATTGGTTATAAGGTACTACAACCC 58.951 37.037 1.15 0.00 40.64 4.11
3684 5231 9.106070 CTGAATTGGTTATAAGGTACTACAACC 57.894 37.037 0.00 0.00 38.49 3.77
3685 5232 9.662947 ACTGAATTGGTTATAAGGTACTACAAC 57.337 33.333 0.00 0.00 38.49 3.32
3707 5254 2.294449 ACAGGAGAGTGCAGTACTGA 57.706 50.000 27.08 8.89 40.53 3.41
3749 5296 2.988010 TTGATAGCACTACCCAGCTG 57.012 50.000 6.78 6.78 41.97 4.24
3750 5297 2.840651 ACTTTGATAGCACTACCCAGCT 59.159 45.455 0.00 0.00 44.55 4.24
3751 5298 3.268023 ACTTTGATAGCACTACCCAGC 57.732 47.619 0.00 0.00 0.00 4.85
3801 5371 6.826668 TCTCTTTTATTGAACAGACTGTCCA 58.173 36.000 8.93 0.00 0.00 4.02
3806 5376 9.507329 TTTAGCATCTCTTTTATTGAACAGACT 57.493 29.630 0.00 0.00 0.00 3.24
3839 5409 0.874175 CAACTTCTGTCCGTGCACGA 60.874 55.000 39.10 22.39 43.02 4.35
3885 5455 5.643777 TCGAAAAATTTCAAAAGGGTGCAAA 59.356 32.000 6.69 0.00 37.01 3.68
3907 5477 4.395854 TGGTTGATCAAATCATGTCCTTCG 59.604 41.667 10.35 0.00 39.39 3.79
3917 5487 8.822652 ATTTCTTTTCACTGGTTGATCAAATC 57.177 30.769 10.35 6.42 32.84 2.17
4059 5630 8.784043 ACTTTCGTAATAGTTTGCTTCTTTGAT 58.216 29.630 0.00 0.00 0.00 2.57
4110 5683 3.007182 CCATTGATGTTTTCCAAGCCACT 59.993 43.478 0.00 0.00 0.00 4.00
4114 5687 4.789012 TCTCCATTGATGTTTTCCAAGC 57.211 40.909 0.00 0.00 0.00 4.01
4144 5717 3.003689 CAGACACATTTTTCGAGCCAAGT 59.996 43.478 0.00 0.00 0.00 3.16
4149 5722 4.732285 TCTTCAGACACATTTTTCGAGC 57.268 40.909 0.00 0.00 0.00 5.03
4195 5768 9.357652 GTGTAATTGTAGGATTTCACGTAGTAA 57.642 33.333 0.00 0.00 41.61 2.24
4201 5774 8.975439 GGTATAGTGTAATTGTAGGATTTCACG 58.025 37.037 0.00 0.00 40.25 4.35
4304 5877 4.530857 ATCTAGCCACCGCACCGC 62.531 66.667 0.00 0.00 37.52 5.68
4305 5878 2.586079 CATCTAGCCACCGCACCG 60.586 66.667 0.00 0.00 37.52 4.94
4306 5879 1.815421 CACATCTAGCCACCGCACC 60.815 63.158 0.00 0.00 37.52 5.01
4307 5880 2.464459 GCACATCTAGCCACCGCAC 61.464 63.158 0.00 0.00 37.52 5.34
4308 5881 2.125147 GCACATCTAGCCACCGCA 60.125 61.111 0.00 0.00 37.52 5.69
4309 5882 2.176273 CAGCACATCTAGCCACCGC 61.176 63.158 0.00 0.00 0.00 5.68
4310 5883 2.176273 GCAGCACATCTAGCCACCG 61.176 63.158 0.00 0.00 0.00 4.94
4311 5884 1.821332 GGCAGCACATCTAGCCACC 60.821 63.158 0.00 0.00 46.26 4.61
4312 5885 3.819188 GGCAGCACATCTAGCCAC 58.181 61.111 0.00 0.00 46.26 5.01
4315 5888 0.747283 AGCAAGGCAGCACATCTAGC 60.747 55.000 4.78 0.00 36.85 3.42
4316 5889 1.134461 AGAGCAAGGCAGCACATCTAG 60.134 52.381 4.78 0.00 36.85 2.43
4317 5890 0.907486 AGAGCAAGGCAGCACATCTA 59.093 50.000 4.78 0.00 36.85 1.98
4318 5891 0.677098 CAGAGCAAGGCAGCACATCT 60.677 55.000 4.78 0.00 36.85 2.90
4319 5892 0.959372 ACAGAGCAAGGCAGCACATC 60.959 55.000 4.78 0.00 36.85 3.06
4320 5893 0.538977 AACAGAGCAAGGCAGCACAT 60.539 50.000 4.78 0.00 36.85 3.21
4321 5894 0.752743 AAACAGAGCAAGGCAGCACA 60.753 50.000 4.78 0.00 36.85 4.57
4322 5895 0.318445 CAAACAGAGCAAGGCAGCAC 60.318 55.000 4.78 0.00 36.85 4.40
4323 5896 1.457823 CCAAACAGAGCAAGGCAGCA 61.458 55.000 4.78 0.00 36.85 4.41
4324 5897 1.288127 CCAAACAGAGCAAGGCAGC 59.712 57.895 0.00 0.00 0.00 5.25
4325 5898 1.962144 CCCAAACAGAGCAAGGCAG 59.038 57.895 0.00 0.00 0.00 4.85
4326 5899 2.202395 GCCCAAACAGAGCAAGGCA 61.202 57.895 0.00 0.00 40.20 4.75
4327 5900 2.151049 CTGCCCAAACAGAGCAAGGC 62.151 60.000 0.00 0.00 40.25 4.35
4328 5901 0.538057 TCTGCCCAAACAGAGCAAGG 60.538 55.000 0.00 0.00 41.72 3.61
4329 5902 3.025924 TCTGCCCAAACAGAGCAAG 57.974 52.632 0.00 0.00 41.72 4.01
4358 5931 0.034767 TGCCCAAGAAGCCAGATCTG 60.035 55.000 16.24 16.24 0.00 2.90
4359 5932 0.255318 CTGCCCAAGAAGCCAGATCT 59.745 55.000 0.00 0.00 0.00 2.75
4360 5933 1.382692 GCTGCCCAAGAAGCCAGATC 61.383 60.000 0.00 0.00 33.12 2.75
4361 5934 1.379576 GCTGCCCAAGAAGCCAGAT 60.380 57.895 0.00 0.00 33.12 2.90
4362 5935 2.034687 GCTGCCCAAGAAGCCAGA 59.965 61.111 0.00 0.00 33.12 3.86
4363 5936 3.437795 CGCTGCCCAAGAAGCCAG 61.438 66.667 0.00 0.00 35.98 4.85
4366 5939 2.982744 GAACCGCTGCCCAAGAAGC 61.983 63.158 0.00 0.00 36.03 3.86
4367 5940 1.600636 TGAACCGCTGCCCAAGAAG 60.601 57.895 0.00 0.00 0.00 2.85
4368 5941 1.896660 GTGAACCGCTGCCCAAGAA 60.897 57.895 0.00 0.00 0.00 2.52
4369 5942 2.281484 GTGAACCGCTGCCCAAGA 60.281 61.111 0.00 0.00 0.00 3.02
4370 5943 1.526575 AATGTGAACCGCTGCCCAAG 61.527 55.000 0.00 0.00 0.00 3.61
4371 5944 1.530419 AATGTGAACCGCTGCCCAA 60.530 52.632 0.00 0.00 0.00 4.12
4372 5945 2.115052 AATGTGAACCGCTGCCCA 59.885 55.556 0.00 0.00 0.00 5.36
4373 5946 2.568090 CAATGTGAACCGCTGCCC 59.432 61.111 0.00 0.00 0.00 5.36
4374 5947 2.126346 GCAATGTGAACCGCTGCC 60.126 61.111 0.00 0.00 0.00 4.85
4375 5948 1.443194 CAGCAATGTGAACCGCTGC 60.443 57.895 0.00 0.00 44.69 5.25
4376 5949 4.853507 CAGCAATGTGAACCGCTG 57.146 55.556 0.00 0.00 45.17 5.18
4377 5950 0.311790 CAACAGCAATGTGAACCGCT 59.688 50.000 0.00 0.00 34.29 5.52
4378 5951 0.664166 CCAACAGCAATGTGAACCGC 60.664 55.000 0.00 0.00 0.00 5.68
4379 5952 0.667993 ACCAACAGCAATGTGAACCG 59.332 50.000 0.00 0.00 0.00 4.44
4380 5953 1.680735 TGACCAACAGCAATGTGAACC 59.319 47.619 0.00 0.00 0.00 3.62
4381 5954 3.568538 GATGACCAACAGCAATGTGAAC 58.431 45.455 0.00 0.00 34.76 3.18
4382 5955 2.226200 CGATGACCAACAGCAATGTGAA 59.774 45.455 0.00 0.00 34.21 3.18
4383 5956 1.805943 CGATGACCAACAGCAATGTGA 59.194 47.619 0.00 0.00 34.21 3.58
4384 5957 1.135603 CCGATGACCAACAGCAATGTG 60.136 52.381 0.00 0.00 34.21 3.21
4385 5958 1.167851 CCGATGACCAACAGCAATGT 58.832 50.000 0.00 0.00 34.21 2.71
4386 5959 0.452987 CCCGATGACCAACAGCAATG 59.547 55.000 0.00 0.00 34.21 2.82
4387 5960 0.680921 CCCCGATGACCAACAGCAAT 60.681 55.000 0.00 0.00 34.21 3.56
4388 5961 1.303236 CCCCGATGACCAACAGCAA 60.303 57.895 0.00 0.00 34.21 3.91
4389 5962 2.350895 CCCCGATGACCAACAGCA 59.649 61.111 0.00 0.00 34.21 4.41
4390 5963 3.134127 GCCCCGATGACCAACAGC 61.134 66.667 0.00 0.00 0.00 4.40
4391 5964 1.746615 CAGCCCCGATGACCAACAG 60.747 63.158 0.00 0.00 0.00 3.16
4392 5965 2.350895 CAGCCCCGATGACCAACA 59.649 61.111 0.00 0.00 0.00 3.33
4393 5966 3.134127 GCAGCCCCGATGACCAAC 61.134 66.667 0.00 0.00 0.00 3.77
4394 5967 4.776322 CGCAGCCCCGATGACCAA 62.776 66.667 0.00 0.00 0.00 3.67
4440 6013 4.704833 CCACCACAGCAGACCCCG 62.705 72.222 0.00 0.00 0.00 5.73
4444 6017 4.626081 ACCGCCACCACAGCAGAC 62.626 66.667 0.00 0.00 0.00 3.51
4445 6018 4.314440 GACCGCCACCACAGCAGA 62.314 66.667 0.00 0.00 0.00 4.26
4449 6022 3.991051 ACTCGACCGCCACCACAG 61.991 66.667 0.00 0.00 0.00 3.66
4450 6023 4.293648 CACTCGACCGCCACCACA 62.294 66.667 0.00 0.00 0.00 4.17
4451 6024 2.814183 CTACACTCGACCGCCACCAC 62.814 65.000 0.00 0.00 0.00 4.16
4452 6025 2.598099 TACACTCGACCGCCACCA 60.598 61.111 0.00 0.00 0.00 4.17
4453 6026 2.181021 CTACACTCGACCGCCACC 59.819 66.667 0.00 0.00 0.00 4.61
4454 6027 1.443872 CACTACACTCGACCGCCAC 60.444 63.158 0.00 0.00 0.00 5.01
4455 6028 2.632544 CCACTACACTCGACCGCCA 61.633 63.158 0.00 0.00 0.00 5.69
4456 6029 1.664321 ATCCACTACACTCGACCGCC 61.664 60.000 0.00 0.00 0.00 6.13
4457 6030 0.525668 CATCCACTACACTCGACCGC 60.526 60.000 0.00 0.00 0.00 5.68
4458 6031 0.100682 CCATCCACTACACTCGACCG 59.899 60.000 0.00 0.00 0.00 4.79
4459 6032 0.179108 GCCATCCACTACACTCGACC 60.179 60.000 0.00 0.00 0.00 4.79
4460 6033 0.530744 TGCCATCCACTACACTCGAC 59.469 55.000 0.00 0.00 0.00 4.20
4461 6034 0.817654 CTGCCATCCACTACACTCGA 59.182 55.000 0.00 0.00 0.00 4.04
4462 6035 0.817654 TCTGCCATCCACTACACTCG 59.182 55.000 0.00 0.00 0.00 4.18
4463 6036 2.100584 CTCTCTGCCATCCACTACACTC 59.899 54.545 0.00 0.00 0.00 3.51
4464 6037 2.106566 CTCTCTGCCATCCACTACACT 58.893 52.381 0.00 0.00 0.00 3.55
4465 6038 1.137872 CCTCTCTGCCATCCACTACAC 59.862 57.143 0.00 0.00 0.00 2.90
4466 6039 1.489481 CCTCTCTGCCATCCACTACA 58.511 55.000 0.00 0.00 0.00 2.74
4467 6040 0.755686 CCCTCTCTGCCATCCACTAC 59.244 60.000 0.00 0.00 0.00 2.73
4468 6041 0.636647 TCCCTCTCTGCCATCCACTA 59.363 55.000 0.00 0.00 0.00 2.74
4469 6042 0.030297 ATCCCTCTCTGCCATCCACT 60.030 55.000 0.00 0.00 0.00 4.00
4470 6043 0.842635 AATCCCTCTCTGCCATCCAC 59.157 55.000 0.00 0.00 0.00 4.02
4471 6044 0.841961 CAATCCCTCTCTGCCATCCA 59.158 55.000 0.00 0.00 0.00 3.41
4472 6045 0.536915 GCAATCCCTCTCTGCCATCC 60.537 60.000 0.00 0.00 0.00 3.51
4473 6046 0.883814 CGCAATCCCTCTCTGCCATC 60.884 60.000 0.00 0.00 32.27 3.51
4474 6047 1.147824 CGCAATCCCTCTCTGCCAT 59.852 57.895 0.00 0.00 32.27 4.40
4475 6048 2.293318 ACGCAATCCCTCTCTGCCA 61.293 57.895 0.00 0.00 32.27 4.92
4476 6049 1.817099 CACGCAATCCCTCTCTGCC 60.817 63.158 0.00 0.00 32.27 4.85
4477 6050 2.467826 GCACGCAATCCCTCTCTGC 61.468 63.158 0.00 0.00 0.00 4.26
4478 6051 1.078918 TGCACGCAATCCCTCTCTG 60.079 57.895 0.00 0.00 0.00 3.35
4479 6052 1.220206 CTGCACGCAATCCCTCTCT 59.780 57.895 0.00 0.00 0.00 3.10
4480 6053 1.817099 CCTGCACGCAATCCCTCTC 60.817 63.158 0.00 0.00 0.00 3.20
4481 6054 2.270205 CCTGCACGCAATCCCTCT 59.730 61.111 0.00 0.00 0.00 3.69
4482 6055 3.512516 GCCTGCACGCAATCCCTC 61.513 66.667 2.56 0.00 0.00 4.30
4499 6072 3.710722 AGGAGGACCTTGCTGCCG 61.711 66.667 0.00 0.00 45.36 5.69
4508 6081 3.787001 CCGGAGCCAAGGAGGACC 61.787 72.222 0.00 0.00 41.22 4.46
4509 6082 1.049289 ATACCGGAGCCAAGGAGGAC 61.049 60.000 9.46 0.00 41.22 3.85
4510 6083 1.048724 CATACCGGAGCCAAGGAGGA 61.049 60.000 9.46 0.00 41.22 3.71
4511 6084 1.447643 CATACCGGAGCCAAGGAGG 59.552 63.158 9.46 0.00 41.84 4.30


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

AutoCloner maintained by Alex Coulton.