Multiple sequence alignment - TraesCS1B01G337200

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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 TraesCS1B01G337200 chr1B 100.000 4786 0 0 1 4786 564166506 564161721 0.000000e+00 8839
1 TraesCS1B01G337200 chr1A 92.064 4423 169 71 461 4786 514554402 514550065 0.000000e+00 6056
2 TraesCS1B01G337200 chr1A 79.531 469 60 22 4272 4730 566590114 566590556 7.780000e-78 302
3 TraesCS1B01G337200 chr1A 87.500 88 11 0 1015 1102 521331968 521332055 8.470000e-18 102
4 TraesCS1B01G337200 chr1D 90.832 2585 88 45 465 2992 417577357 417574865 0.000000e+00 3323
5 TraesCS1B01G337200 chr1D 94.615 1207 36 8 3033 4224 417574866 417573674 0.000000e+00 1842
6 TraesCS1B01G337200 chr1D 97.885 520 11 0 4267 4786 417573667 417573148 0.000000e+00 900
7 TraesCS1B01G337200 chr1D 86.432 199 13 7 189 375 417577557 417577361 6.280000e-49 206
8 TraesCS1B01G337200 chr1D 91.667 120 10 0 1 120 417577718 417577599 2.960000e-37 167
9 TraesCS1B01G337200 chrUn 97.093 344 9 1 3907 4249 240128728 240128385 3.210000e-161 579
10 TraesCS1B01G337200 chrUn 97.353 340 9 0 3910 4249 435744926 435744587 3.210000e-161 579
11 TraesCS1B01G337200 chrUn 88.182 110 9 4 356 462 37289273 37289165 1.400000e-25 128
12 TraesCS1B01G337200 chr2B 97.093 344 9 1 3907 4249 77877104 77876761 3.210000e-161 579
13 TraesCS1B01G337200 chr2B 78.107 845 124 28 2968 3775 581584960 581584140 3.350000e-131 479
14 TraesCS1B01G337200 chr2B 93.617 94 5 1 375 467 357917645 357917552 6.460000e-29 139
15 TraesCS1B01G337200 chr2B 90.588 85 6 2 4416 4498 331027275 331027359 1.410000e-20 111
16 TraesCS1B01G337200 chr6B 96.512 344 11 1 3907 4249 418246684 418246341 6.950000e-158 568
17 TraesCS1B01G337200 chr6B 91.262 103 9 0 1000 1102 71148075 71148177 1.800000e-29 141
18 TraesCS1B01G337200 chr4B 96.512 344 11 1 3907 4249 517726313 517726656 6.950000e-158 568
19 TraesCS1B01G337200 chr3B 96.512 344 11 1 3907 4249 170507271 170507614 6.950000e-158 568
20 TraesCS1B01G337200 chr5B 96.221 344 12 1 3907 4249 140517300 140516957 3.230000e-156 562
21 TraesCS1B01G337200 chr5A 96.221 344 12 1 3907 4249 88286341 88285998 3.230000e-156 562
22 TraesCS1B01G337200 chr5A 87.255 102 13 0 4421 4522 66049294 66049193 3.030000e-22 117
23 TraesCS1B01G337200 chr2D 78.343 845 123 29 2968 3775 493195450 493194629 4.300000e-135 492
24 TraesCS1B01G337200 chr2D 80.851 376 44 11 2968 3340 87414390 87414040 2.200000e-68 270
25 TraesCS1B01G337200 chr2A 80.702 285 35 9 2968 3249 733429734 733430001 2.260000e-48 204
26 TraesCS1B01G337200 chr2A 91.919 99 7 1 378 475 715989490 715989392 2.320000e-28 137
27 TraesCS1B01G337200 chr2A 86.555 119 9 5 351 465 101846796 101846911 1.810000e-24 124
28 TraesCS1B01G337200 chr4D 95.556 90 3 1 375 463 467435667 467435756 4.990000e-30 143
29 TraesCS1B01G337200 chr3D 92.233 103 5 3 374 474 491624176 491624277 4.990000e-30 143
30 TraesCS1B01G337200 chr6D 91.262 103 9 0 1000 1102 34394980 34395082 1.800000e-29 141
31 TraesCS1B01G337200 chr6A 91.262 103 9 0 1000 1102 38550579 38550681 1.800000e-29 141
32 TraesCS1B01G337200 chr4A 92.708 96 5 2 369 463 473777168 473777262 2.320000e-28 137
33 TraesCS1B01G337200 chr4A 89.815 108 7 3 356 462 524911579 524911683 8.350000e-28 135
34 TraesCS1B01G337200 chr7A 90.385 104 8 2 371 472 824956 825059 8.350000e-28 135
35 TraesCS1B01G337200 chr7D 91.139 79 7 0 4421 4499 326034705 326034627 1.820000e-19 108


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 TraesCS1B01G337200 chr1B 564161721 564166506 4785 True 8839.0 8839 100.0000 1 4786 1 chr1B.!!$R1 4785
1 TraesCS1B01G337200 chr1A 514550065 514554402 4337 True 6056.0 6056 92.0640 461 4786 1 chr1A.!!$R1 4325
2 TraesCS1B01G337200 chr1D 417573148 417577718 4570 True 1287.6 3323 92.2862 1 4786 5 chr1D.!!$R1 4785
3 TraesCS1B01G337200 chr2B 581584140 581584960 820 True 479.0 479 78.1070 2968 3775 1 chr2B.!!$R3 807
4 TraesCS1B01G337200 chr2D 493194629 493195450 821 True 492.0 492 78.3430 2968 3775 1 chr2D.!!$R2 807

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
173 174 0.032316 TATGGGTGGCGTAGTGGGTA 60.032 55.0 0.00 0.0 0.00 3.69 F
680 700 0.249911 GGAACAGTGAGCGAGTGGTT 60.250 55.0 0.00 0.0 0.00 3.67 F
1475 1551 0.033011 GTCCCTGCTAGTCTCCTCCA 60.033 60.0 0.00 0.0 0.00 3.86 F
1583 1673 0.036388 CTCCCTGTTTCTAGGCGCAA 60.036 55.0 10.83 0.0 36.47 4.85 F
2513 2630 0.458370 TGTCACTGATGATGGTCGCG 60.458 55.0 0.00 0.0 37.14 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1529 0.033011 TGGAGGAGACTAGCAGGGAC 60.033 60.0 0.00 0.00 44.43 4.46 R
2570 2688 0.383949 TGCTTTCCGTTCAACCAAGC 59.616 50.0 6.76 6.76 40.29 4.01 R
3419 3549 0.323908 AGCTTCCGAGTACCTGAGCT 60.324 55.0 0.00 0.00 0.00 4.09 R
3530 3672 2.166459 TCAGCTCTTCACCCTACAATCG 59.834 50.0 0.00 0.00 0.00 3.34 R
3816 3971 0.179078 TGCAAAACAAAGGGCTGCTG 60.179 50.0 0.00 0.00 34.10 4.41 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
63 64 2.253758 GCAACAAGCGGCAGTCTCA 61.254 57.895 1.45 0.00 0.00 3.27
74 75 2.612972 CGGCAGTCTCACCAAATAGTGT 60.613 50.000 0.00 0.00 38.91 3.55
75 76 3.412386 GGCAGTCTCACCAAATAGTGTT 58.588 45.455 0.00 0.00 38.91 3.32
76 77 3.189287 GGCAGTCTCACCAAATAGTGTTG 59.811 47.826 0.00 0.00 38.91 3.33
94 95 6.227522 AGTGTTGGTGCACTTTTAAGTTTTT 58.772 32.000 17.98 0.00 46.45 1.94
98 99 6.777213 TGGTGCACTTTTAAGTTTTTAGGA 57.223 33.333 17.98 0.00 37.08 2.94
100 101 6.378848 TGGTGCACTTTTAAGTTTTTAGGACT 59.621 34.615 17.98 0.00 37.08 3.85
101 102 7.556996 TGGTGCACTTTTAAGTTTTTAGGACTA 59.443 33.333 17.98 0.00 37.08 2.59
130 131 5.859205 ACCCAAAGAAAATGATCTATGCC 57.141 39.130 0.00 0.00 0.00 4.40
136 137 6.757897 AAGAAAATGATCTATGCCGTGAAA 57.242 33.333 0.00 0.00 0.00 2.69
156 157 8.742554 GTGAAACGAATCATTTTTCCACTTAT 57.257 30.769 0.00 0.00 0.00 1.73
169 170 1.651987 CACTTATGGGTGGCGTAGTG 58.348 55.000 0.00 0.00 33.95 2.74
170 171 0.539986 ACTTATGGGTGGCGTAGTGG 59.460 55.000 0.00 0.00 0.00 4.00
171 172 0.179056 CTTATGGGTGGCGTAGTGGG 60.179 60.000 0.00 0.00 0.00 4.61
172 173 0.910566 TTATGGGTGGCGTAGTGGGT 60.911 55.000 0.00 0.00 0.00 4.51
173 174 0.032316 TATGGGTGGCGTAGTGGGTA 60.032 55.000 0.00 0.00 0.00 3.69
174 175 0.910566 ATGGGTGGCGTAGTGGGTAA 60.911 55.000 0.00 0.00 0.00 2.85
175 176 0.910566 TGGGTGGCGTAGTGGGTAAT 60.911 55.000 0.00 0.00 0.00 1.89
176 177 0.253894 GGGTGGCGTAGTGGGTAATT 59.746 55.000 0.00 0.00 0.00 1.40
177 178 1.485895 GGGTGGCGTAGTGGGTAATTA 59.514 52.381 0.00 0.00 0.00 1.40
178 179 2.105306 GGGTGGCGTAGTGGGTAATTAT 59.895 50.000 0.00 0.00 0.00 1.28
179 180 3.434024 GGGTGGCGTAGTGGGTAATTATT 60.434 47.826 0.00 0.00 0.00 1.40
180 181 3.562557 GGTGGCGTAGTGGGTAATTATTG 59.437 47.826 0.00 0.00 0.00 1.90
181 182 4.444536 GTGGCGTAGTGGGTAATTATTGA 58.555 43.478 0.00 0.00 0.00 2.57
182 183 4.271776 GTGGCGTAGTGGGTAATTATTGAC 59.728 45.833 0.00 0.00 0.00 3.18
183 184 4.081031 TGGCGTAGTGGGTAATTATTGACA 60.081 41.667 0.00 0.00 0.00 3.58
184 185 4.877251 GGCGTAGTGGGTAATTATTGACAA 59.123 41.667 0.00 0.00 0.00 3.18
185 186 5.220719 GGCGTAGTGGGTAATTATTGACAAC 60.221 44.000 0.00 0.00 0.00 3.32
186 187 5.583457 GCGTAGTGGGTAATTATTGACAACT 59.417 40.000 0.00 0.00 0.00 3.16
187 188 6.093082 GCGTAGTGGGTAATTATTGACAACTT 59.907 38.462 0.00 0.00 0.00 2.66
193 194 9.444600 GTGGGTAATTATTGACAACTTTAGAGA 57.555 33.333 0.00 0.00 0.00 3.10
208 209 9.173939 CAACTTTAGAGACAATTTTGATGACAC 57.826 33.333 0.00 0.00 0.00 3.67
211 212 5.695851 AGAGACAATTTTGATGACACACC 57.304 39.130 0.00 0.00 0.00 4.16
214 215 2.360483 ACAATTTTGATGACACACCGCA 59.640 40.909 0.00 0.00 0.00 5.69
391 404 7.519927 AGATATAGATATACTCCCTCCGTTCC 58.480 42.308 0.00 0.00 0.00 3.62
392 405 3.897657 AGATATACTCCCTCCGTTCCA 57.102 47.619 0.00 0.00 0.00 3.53
393 406 4.194678 AGATATACTCCCTCCGTTCCAA 57.805 45.455 0.00 0.00 0.00 3.53
394 407 4.553678 AGATATACTCCCTCCGTTCCAAA 58.446 43.478 0.00 0.00 0.00 3.28
395 408 4.966805 AGATATACTCCCTCCGTTCCAAAA 59.033 41.667 0.00 0.00 0.00 2.44
396 409 5.607171 AGATATACTCCCTCCGTTCCAAAAT 59.393 40.000 0.00 0.00 0.00 1.82
397 410 6.785963 AGATATACTCCCTCCGTTCCAAAATA 59.214 38.462 0.00 0.00 0.00 1.40
398 411 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
399 412 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
400 413 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
401 414 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
402 415 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
403 416 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
404 417 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
405 418 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
406 419 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
407 420 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
408 421 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
409 422 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
410 423 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
411 424 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
412 425 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
455 468 9.868277 AGTTGAGTCATCTATTTTAGAACAGAG 57.132 33.333 1.70 0.00 38.50 3.35
456 469 9.092876 GTTGAGTCATCTATTTTAGAACAGAGG 57.907 37.037 0.00 0.00 38.50 3.69
457 470 8.595362 TGAGTCATCTATTTTAGAACAGAGGA 57.405 34.615 0.00 0.00 38.50 3.71
458 471 9.035890 TGAGTCATCTATTTTAGAACAGAGGAA 57.964 33.333 0.00 0.00 38.50 3.36
459 472 9.528018 GAGTCATCTATTTTAGAACAGAGGAAG 57.472 37.037 0.00 0.00 38.50 3.46
460 473 9.041354 AGTCATCTATTTTAGAACAGAGGAAGT 57.959 33.333 0.00 0.00 38.50 3.01
496 509 3.949132 AGGGTCAAATGAAAGAGAGAGC 58.051 45.455 0.00 0.00 0.00 4.09
537 550 6.036300 CGTTGTAGAAGTGACACCAAAAGTAA 59.964 38.462 0.84 0.00 0.00 2.24
538 551 7.413219 CGTTGTAGAAGTGACACCAAAAGTAAA 60.413 37.037 0.84 0.00 0.00 2.01
539 552 7.548196 TGTAGAAGTGACACCAAAAGTAAAG 57.452 36.000 0.84 0.00 0.00 1.85
540 553 7.332557 TGTAGAAGTGACACCAAAAGTAAAGA 58.667 34.615 0.84 0.00 0.00 2.52
541 554 7.825270 TGTAGAAGTGACACCAAAAGTAAAGAA 59.175 33.333 0.84 0.00 0.00 2.52
542 555 7.696992 AGAAGTGACACCAAAAGTAAAGAAA 57.303 32.000 0.84 0.00 0.00 2.52
543 556 7.762382 AGAAGTGACACCAAAAGTAAAGAAAG 58.238 34.615 0.84 0.00 0.00 2.62
544 557 7.610305 AGAAGTGACACCAAAAGTAAAGAAAGA 59.390 33.333 0.84 0.00 0.00 2.52
653 673 1.278699 GCCATCTCCATCTCCATCTCC 59.721 57.143 0.00 0.00 0.00 3.71
654 674 2.617658 CCATCTCCATCTCCATCTCCA 58.382 52.381 0.00 0.00 0.00 3.86
656 676 3.198200 CCATCTCCATCTCCATCTCCATC 59.802 52.174 0.00 0.00 0.00 3.51
657 677 2.523245 TCTCCATCTCCATCTCCATCG 58.477 52.381 0.00 0.00 0.00 3.84
660 680 0.975135 CATCTCCATCTCCATCGGCT 59.025 55.000 0.00 0.00 0.00 5.52
661 681 0.975135 ATCTCCATCTCCATCGGCTG 59.025 55.000 0.00 0.00 0.00 4.85
678 698 1.367471 TGGAACAGTGAGCGAGTGG 59.633 57.895 0.00 0.00 0.00 4.00
679 699 1.367840 GGAACAGTGAGCGAGTGGT 59.632 57.895 0.00 0.00 0.00 4.16
680 700 0.249911 GGAACAGTGAGCGAGTGGTT 60.250 55.000 0.00 0.00 0.00 3.67
715 735 1.243230 ATAGTGGGGGAAGGGAGGGA 61.243 60.000 0.00 0.00 0.00 4.20
722 742 0.253020 GGGAAGGGAGGGACCTAACA 60.253 60.000 0.00 0.00 40.87 2.41
779 814 1.740043 GCTGAGCTGAGCTTCTTCCTC 60.740 57.143 18.71 0.00 39.88 3.71
877 928 0.686441 TTGGTCCCGGATCGATCTGT 60.686 55.000 28.08 0.00 0.00 3.41
924 975 4.354943 ACCCAGGACCAGGAGGGG 62.355 72.222 4.06 4.18 45.83 4.79
963 1014 9.716531 ATTGAATTCAAGAAAGAAAGAAATCCC 57.283 29.630 24.17 0.00 39.47 3.85
964 1015 7.370383 TGAATTCAAGAAAGAAAGAAATCCCG 58.630 34.615 5.45 0.00 0.00 5.14
1109 1160 2.125106 CCCCACCGTAAGCTGCTC 60.125 66.667 1.00 0.00 0.00 4.26
1116 1167 1.519455 CGTAAGCTGCTCCCTTCCG 60.519 63.158 1.00 0.00 0.00 4.30
1121 1172 2.269241 CTGCTCCCTTCCGTTCCC 59.731 66.667 0.00 0.00 0.00 3.97
1122 1173 2.203938 TGCTCCCTTCCGTTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
1123 1174 1.842381 CTGCTCCCTTCCGTTCCCTT 61.842 60.000 0.00 0.00 0.00 3.95
1124 1175 1.078356 GCTCCCTTCCGTTCCCTTC 60.078 63.158 0.00 0.00 0.00 3.46
1125 1176 1.602771 CTCCCTTCCGTTCCCTTCC 59.397 63.158 0.00 0.00 0.00 3.46
1126 1177 0.910088 CTCCCTTCCGTTCCCTTCCT 60.910 60.000 0.00 0.00 0.00 3.36
1127 1178 0.908180 TCCCTTCCGTTCCCTTCCTC 60.908 60.000 0.00 0.00 0.00 3.71
1128 1179 1.602771 CCTTCCGTTCCCTTCCTCC 59.397 63.158 0.00 0.00 0.00 4.30
1129 1180 1.602771 CTTCCGTTCCCTTCCTCCC 59.397 63.158 0.00 0.00 0.00 4.30
1144 1196 4.405756 TCCTCCCTTCTTCAACTACTCT 57.594 45.455 0.00 0.00 0.00 3.24
1168 1230 8.395605 TCTACCCTACATACATGTACATGGATA 58.604 37.037 33.32 20.88 40.28 2.59
1200 1262 9.713684 ATAGATAGATAGATCCCCTTCTTCTTG 57.286 37.037 0.00 0.00 0.00 3.02
1246 1316 6.310941 TCCCCACTTTTACAAGATGAATCAA 58.689 36.000 0.00 0.00 33.72 2.57
1249 1319 7.308435 CCCACTTTTACAAGATGAATCAAGAC 58.692 38.462 0.00 0.00 33.72 3.01
1320 1390 9.539194 ACTAGGGAAAAAGAAGATTGATTGATT 57.461 29.630 0.00 0.00 0.00 2.57
1475 1551 0.033011 GTCCCTGCTAGTCTCCTCCA 60.033 60.000 0.00 0.00 0.00 3.86
1534 1624 6.985059 TCAAATCAATTGCTGTCACATGAAAA 59.015 30.769 0.00 0.00 38.98 2.29
1542 1632 6.691754 TGCTGTCACATGAAAACTCTTAAA 57.308 33.333 0.00 0.00 0.00 1.52
1582 1672 1.596934 CTCCCTGTTTCTAGGCGCA 59.403 57.895 10.83 0.00 36.47 6.09
1583 1673 0.036388 CTCCCTGTTTCTAGGCGCAA 60.036 55.000 10.83 0.00 36.47 4.85
1610 1716 7.306167 GCACACACACAAAATGACTTTTAGATG 60.306 37.037 0.00 0.00 32.81 2.90
1642 1751 2.923655 GCGTTCGTTCATCTTCATCTGA 59.076 45.455 0.00 0.00 0.00 3.27
1643 1752 3.241804 GCGTTCGTTCATCTTCATCTGAC 60.242 47.826 0.00 0.00 0.00 3.51
1644 1753 4.169508 CGTTCGTTCATCTTCATCTGACT 58.830 43.478 0.00 0.00 0.00 3.41
1645 1754 4.031089 CGTTCGTTCATCTTCATCTGACTG 59.969 45.833 0.00 0.00 0.00 3.51
1646 1755 4.115401 TCGTTCATCTTCATCTGACTGG 57.885 45.455 0.00 0.00 0.00 4.00
1647 1756 3.511540 TCGTTCATCTTCATCTGACTGGT 59.488 43.478 0.00 0.00 0.00 4.00
1648 1757 3.615937 CGTTCATCTTCATCTGACTGGTG 59.384 47.826 0.00 0.00 0.00 4.17
1668 1777 5.018809 GGTGCCACCCAATATGATGAATAT 58.981 41.667 1.17 0.00 29.81 1.28
1703 1812 5.645929 TGCGTTTTCATATCCAATGTACAGT 59.354 36.000 0.33 0.00 0.00 3.55
1754 1864 2.622064 ACGTGCCTTATCCTCCATTC 57.378 50.000 0.00 0.00 0.00 2.67
1757 1867 2.548920 CGTGCCTTATCCTCCATTCCTC 60.549 54.545 0.00 0.00 0.00 3.71
1972 2088 6.414694 GTGTGTGTGTGTTCAATAAATCACAG 59.585 38.462 0.00 0.00 40.63 3.66
2243 2360 9.793252 GAGATATGACATGTGCTTGTAATTTTT 57.207 29.630 1.15 0.00 0.00 1.94
2270 2387 1.035932 TCCCTGAGCTACGGCACTAC 61.036 60.000 0.00 0.00 41.70 2.73
2369 2486 7.076842 GCTTCTGCAAAGTATCACATTTCTA 57.923 36.000 9.40 0.00 39.41 2.10
2398 2515 1.748879 GCCGGAACTATGCTTGGCA 60.749 57.895 5.05 0.00 44.86 4.92
2511 2628 2.662006 ACTGTCACTGATGATGGTCG 57.338 50.000 0.00 0.00 37.14 4.79
2512 2629 1.284657 CTGTCACTGATGATGGTCGC 58.715 55.000 0.00 0.00 37.14 5.19
2513 2630 0.458370 TGTCACTGATGATGGTCGCG 60.458 55.000 0.00 0.00 37.14 5.87
2514 2631 1.141665 TCACTGATGATGGTCGCGG 59.858 57.895 6.13 0.00 0.00 6.46
2515 2632 1.153568 CACTGATGATGGTCGCGGT 60.154 57.895 6.13 0.00 0.00 5.68
2703 2821 7.964604 TTTTTCTTCTACTAAGAACCAGCTC 57.035 36.000 0.00 0.00 36.80 4.09
2705 2823 6.859112 TTCTTCTACTAAGAACCAGCTCAT 57.141 37.500 0.00 0.00 36.80 2.90
2706 2824 6.214191 TCTTCTACTAAGAACCAGCTCATG 57.786 41.667 0.00 0.00 36.80 3.07
2722 2840 5.573337 GCTCATGGTTTAGCTGAGAAATT 57.427 39.130 0.00 0.00 38.96 1.82
2833 2951 8.856103 CCTTATAATTAATGTTGAATTCCCCGT 58.144 33.333 2.27 0.00 0.00 5.28
2851 2969 4.277423 CCCCGTTGTGAAATTAAGACTTGT 59.723 41.667 0.00 0.00 0.00 3.16
2867 2985 5.734720 AGACTTGTTGTGATGATATTCGGT 58.265 37.500 0.00 0.00 0.00 4.69
2899 3017 6.273071 TGATAAAGGTGTGATGATACTCGTG 58.727 40.000 0.00 0.00 0.00 4.35
2976 3094 5.406780 CAGTGACTAGACATCAGTTTGAACC 59.593 44.000 0.00 0.00 0.00 3.62
3022 3140 6.480763 TGTAGTCCATATTCTTTGGCTCAAA 58.519 36.000 1.27 1.27 34.06 2.69
3028 3146 6.612456 TCCATATTCTTTGGCTCAAATCCAAT 59.388 34.615 1.56 4.07 42.57 3.16
3029 3147 7.784073 TCCATATTCTTTGGCTCAAATCCAATA 59.216 33.333 1.56 5.59 42.57 1.90
3112 3230 8.540507 TCTTGATGTTATTACCTCTTAGAGCT 57.459 34.615 3.26 0.00 0.00 4.09
3127 3245 1.202580 AGAGCTCTGCACACGTTCTTT 60.203 47.619 17.42 0.00 0.00 2.52
3162 3281 6.347402 CGACGGTTTAGTCAATTTGAGAACAT 60.347 38.462 15.99 8.19 40.98 2.71
3419 3549 1.005450 GGGGCTGTTCCTATTTCCACA 59.995 52.381 0.00 0.00 34.39 4.17
3530 3672 4.099266 AGTGATCTCATCTCTGTGGCTAAC 59.901 45.833 0.00 0.00 32.37 2.34
3608 3750 2.618709 AGCTCAAAAACACAGCAGGTAC 59.381 45.455 0.00 0.00 35.46 3.34
3625 3767 3.118482 AGGTACAATGAGTGCATCTCCTG 60.118 47.826 11.99 11.38 42.12 3.86
3637 3779 3.582647 TGCATCTCCTGGTAGTGAAGAAA 59.417 43.478 0.00 0.00 0.00 2.52
3647 3792 6.295688 CCTGGTAGTGAAGAAAAAGGCTAGTA 60.296 42.308 0.00 0.00 0.00 1.82
3675 3830 3.237268 TGGGTTAGTGATTTGGTTGCT 57.763 42.857 0.00 0.00 0.00 3.91
3816 3971 2.977772 AATGGTAGAGTGAGCTGAGC 57.022 50.000 0.00 0.00 0.00 4.26
3842 3997 2.418609 GCCCTTTGTTTTGCAGTGTCTT 60.419 45.455 0.00 0.00 0.00 3.01
3892 4071 0.035458 CCTCGCCTCTCCTTGTTGTT 59.965 55.000 0.00 0.00 0.00 2.83
3893 4072 1.151668 CTCGCCTCTCCTTGTTGTTG 58.848 55.000 0.00 0.00 0.00 3.33
3894 4073 0.468226 TCGCCTCTCCTTGTTGTTGT 59.532 50.000 0.00 0.00 0.00 3.32
3895 4074 1.134220 TCGCCTCTCCTTGTTGTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
3896 4075 1.002468 CGCCTCTCCTTGTTGTTGTTG 60.002 52.381 0.00 0.00 0.00 3.33
3897 4076 2.024414 GCCTCTCCTTGTTGTTGTTGT 58.976 47.619 0.00 0.00 0.00 3.32
3898 4077 2.427095 GCCTCTCCTTGTTGTTGTTGTT 59.573 45.455 0.00 0.00 0.00 2.83
3899 4078 3.734902 GCCTCTCCTTGTTGTTGTTGTTG 60.735 47.826 0.00 0.00 0.00 3.33
3900 4079 3.443681 CCTCTCCTTGTTGTTGTTGTTGT 59.556 43.478 0.00 0.00 0.00 3.32
3987 4169 2.490903 GCAGCTCATGATGAACTTGGTT 59.509 45.455 0.00 0.00 0.00 3.67
3992 4174 5.182001 AGCTCATGATGAACTTGGTTTGTAC 59.818 40.000 0.00 0.00 0.00 2.90
4244 4440 6.017440 GCTTAACAATTCAGTTGGTACAGACA 60.017 38.462 0.00 0.00 39.64 3.41
4245 4441 7.490962 TTAACAATTCAGTTGGTACAGACAG 57.509 36.000 0.00 0.00 39.64 3.51
4246 4442 5.036117 ACAATTCAGTTGGTACAGACAGT 57.964 39.130 0.00 0.00 42.39 3.55
4247 4443 5.437060 ACAATTCAGTTGGTACAGACAGTT 58.563 37.500 0.00 0.00 42.39 3.16
4248 4444 5.885912 ACAATTCAGTTGGTACAGACAGTTT 59.114 36.000 0.00 0.00 42.39 2.66
4249 4445 7.051623 ACAATTCAGTTGGTACAGACAGTTTA 58.948 34.615 0.00 0.00 42.39 2.01
4250 4446 7.719633 ACAATTCAGTTGGTACAGACAGTTTAT 59.280 33.333 0.00 0.00 42.39 1.40
4251 4447 8.567948 CAATTCAGTTGGTACAGACAGTTTATT 58.432 33.333 0.00 0.00 42.39 1.40
4252 4448 7.724305 TTCAGTTGGTACAGACAGTTTATTC 57.276 36.000 0.00 0.00 42.39 1.75
4253 4449 6.822442 TCAGTTGGTACAGACAGTTTATTCA 58.178 36.000 0.00 0.00 42.39 2.57
4255 4451 7.936847 TCAGTTGGTACAGACAGTTTATTCATT 59.063 33.333 0.00 0.00 42.39 2.57
4356 4553 1.896660 CGTCTGGTTTGGTGGTGGG 60.897 63.158 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.298859 CCACTAGCGCCAGGTGTTTC 61.299 60.000 18.76 0.00 0.00 2.78
74 75 7.036829 GTCCTAAAAACTTAAAAGTGCACCAA 58.963 34.615 14.63 1.89 39.66 3.67
75 76 6.378848 AGTCCTAAAAACTTAAAAGTGCACCA 59.621 34.615 14.63 0.00 39.66 4.17
76 77 6.802608 AGTCCTAAAAACTTAAAAGTGCACC 58.197 36.000 14.63 0.00 39.66 5.01
120 121 2.951457 TCGTTTCACGGCATAGATCA 57.049 45.000 0.00 0.00 42.81 2.92
122 123 3.792401 TGATTCGTTTCACGGCATAGAT 58.208 40.909 0.00 0.00 42.81 1.98
124 125 4.536364 AATGATTCGTTTCACGGCATAG 57.464 40.909 0.00 0.00 42.81 2.23
127 128 3.634568 AAAATGATTCGTTTCACGGCA 57.365 38.095 4.38 0.00 42.81 5.69
128 129 3.363724 GGAAAAATGATTCGTTTCACGGC 59.636 43.478 4.38 0.00 42.81 5.68
129 130 4.381566 GTGGAAAAATGATTCGTTTCACGG 59.618 41.667 4.38 0.00 42.81 4.94
130 131 5.212194 AGTGGAAAAATGATTCGTTTCACG 58.788 37.500 4.38 0.00 44.19 4.35
150 151 1.651987 CACTACGCCACCCATAAGTG 58.348 55.000 0.00 0.00 37.51 3.16
151 152 0.539986 CCACTACGCCACCCATAAGT 59.460 55.000 0.00 0.00 0.00 2.24
153 154 0.910566 ACCCACTACGCCACCCATAA 60.911 55.000 0.00 0.00 0.00 1.90
154 155 0.032316 TACCCACTACGCCACCCATA 60.032 55.000 0.00 0.00 0.00 2.74
156 157 0.910566 ATTACCCACTACGCCACCCA 60.911 55.000 0.00 0.00 0.00 4.51
158 159 2.985957 TAATTACCCACTACGCCACC 57.014 50.000 0.00 0.00 0.00 4.61
159 160 4.271776 GTCAATAATTACCCACTACGCCAC 59.728 45.833 0.00 0.00 0.00 5.01
160 161 4.081031 TGTCAATAATTACCCACTACGCCA 60.081 41.667 0.00 0.00 0.00 5.69
161 162 4.444536 TGTCAATAATTACCCACTACGCC 58.555 43.478 0.00 0.00 0.00 5.68
162 163 5.583457 AGTTGTCAATAATTACCCACTACGC 59.417 40.000 0.00 0.00 0.00 4.42
163 164 7.605410 AAGTTGTCAATAATTACCCACTACG 57.395 36.000 0.00 0.00 0.00 3.51
166 167 9.449719 CTCTAAAGTTGTCAATAATTACCCACT 57.550 33.333 0.00 0.00 0.00 4.00
167 168 9.444600 TCTCTAAAGTTGTCAATAATTACCCAC 57.555 33.333 0.00 0.00 0.00 4.61
168 169 9.444600 GTCTCTAAAGTTGTCAATAATTACCCA 57.555 33.333 0.00 0.00 0.00 4.51
169 170 9.444600 TGTCTCTAAAGTTGTCAATAATTACCC 57.555 33.333 0.00 0.00 0.00 3.69
178 179 9.734620 CATCAAAATTGTCTCTAAAGTTGTCAA 57.265 29.630 0.00 0.00 0.00 3.18
179 180 9.119418 TCATCAAAATTGTCTCTAAAGTTGTCA 57.881 29.630 0.00 0.00 0.00 3.58
180 181 9.387123 GTCATCAAAATTGTCTCTAAAGTTGTC 57.613 33.333 0.00 0.00 0.00 3.18
181 182 8.902806 TGTCATCAAAATTGTCTCTAAAGTTGT 58.097 29.630 0.00 0.00 0.00 3.32
182 183 9.173939 GTGTCATCAAAATTGTCTCTAAAGTTG 57.826 33.333 0.00 0.00 0.00 3.16
183 184 8.902806 TGTGTCATCAAAATTGTCTCTAAAGTT 58.097 29.630 0.00 0.00 0.00 2.66
184 185 8.345565 GTGTGTCATCAAAATTGTCTCTAAAGT 58.654 33.333 0.00 0.00 0.00 2.66
185 186 7.805071 GGTGTGTCATCAAAATTGTCTCTAAAG 59.195 37.037 0.00 0.00 0.00 1.85
186 187 7.519809 CGGTGTGTCATCAAAATTGTCTCTAAA 60.520 37.037 0.00 0.00 0.00 1.85
187 188 6.073276 CGGTGTGTCATCAAAATTGTCTCTAA 60.073 38.462 0.00 0.00 0.00 2.10
193 194 2.360483 TGCGGTGTGTCATCAAAATTGT 59.640 40.909 0.00 0.00 0.00 2.71
200 201 1.511850 CTTCTTGCGGTGTGTCATCA 58.488 50.000 0.00 0.00 0.00 3.07
208 209 3.611433 GCTATTGCTTCTTGCGGTG 57.389 52.632 0.00 0.00 46.63 4.94
368 381 7.222180 TGGAACGGAGGGAGTATATCTATAT 57.778 40.000 0.00 0.00 0.00 0.86
379 392 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
380 393 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
381 394 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
382 395 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
383 396 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
384 397 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
385 398 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
386 399 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
429 442 9.868277 CTCTGTTCTAAAATAGATGACTCAACT 57.132 33.333 0.00 0.00 32.88 3.16
430 443 9.092876 CCTCTGTTCTAAAATAGATGACTCAAC 57.907 37.037 0.00 0.00 32.88 3.18
431 444 9.035890 TCCTCTGTTCTAAAATAGATGACTCAA 57.964 33.333 0.00 0.00 32.88 3.02
432 445 8.595362 TCCTCTGTTCTAAAATAGATGACTCA 57.405 34.615 0.00 0.00 32.88 3.41
433 446 9.528018 CTTCCTCTGTTCTAAAATAGATGACTC 57.472 37.037 0.00 0.00 32.88 3.36
434 447 9.041354 ACTTCCTCTGTTCTAAAATAGATGACT 57.959 33.333 0.00 0.00 32.88 3.41
447 460 9.930158 AATCTATACTTCTACTTCCTCTGTTCT 57.070 33.333 0.00 0.00 0.00 3.01
452 465 9.816787 CCCTTAATCTATACTTCTACTTCCTCT 57.183 37.037 0.00 0.00 0.00 3.69
453 466 9.590828 ACCCTTAATCTATACTTCTACTTCCTC 57.409 37.037 0.00 0.00 0.00 3.71
454 467 9.590828 GACCCTTAATCTATACTTCTACTTCCT 57.409 37.037 0.00 0.00 0.00 3.36
455 468 9.364653 TGACCCTTAATCTATACTTCTACTTCC 57.635 37.037 0.00 0.00 0.00 3.46
496 509 1.069022 CAACGTCAGCACAAATCCAGG 60.069 52.381 0.00 0.00 0.00 4.45
538 551 9.460019 CCATCCTATCTTTCTTTCTTTCTTTCT 57.540 33.333 0.00 0.00 0.00 2.52
539 552 9.454859 TCCATCCTATCTTTCTTTCTTTCTTTC 57.545 33.333 0.00 0.00 0.00 2.62
540 553 9.987726 ATCCATCCTATCTTTCTTTCTTTCTTT 57.012 29.630 0.00 0.00 0.00 2.52
541 554 9.406113 CATCCATCCTATCTTTCTTTCTTTCTT 57.594 33.333 0.00 0.00 0.00 2.52
542 555 7.501892 GCATCCATCCTATCTTTCTTTCTTTCT 59.498 37.037 0.00 0.00 0.00 2.52
543 556 7.519649 CGCATCCATCCTATCTTTCTTTCTTTC 60.520 40.741 0.00 0.00 0.00 2.62
544 557 6.261826 CGCATCCATCCTATCTTTCTTTCTTT 59.738 38.462 0.00 0.00 0.00 2.52
653 673 1.364626 GCTCACTGTTCCAGCCGATG 61.365 60.000 0.00 0.00 34.37 3.84
654 674 1.078848 GCTCACTGTTCCAGCCGAT 60.079 57.895 0.00 0.00 34.37 4.18
656 676 3.114616 CGCTCACTGTTCCAGCCG 61.115 66.667 0.00 0.00 34.37 5.52
657 677 1.739562 CTCGCTCACTGTTCCAGCC 60.740 63.158 0.00 0.00 34.37 4.85
660 680 1.367471 CCACTCGCTCACTGTTCCA 59.633 57.895 0.00 0.00 0.00 3.53
661 681 0.249911 AACCACTCGCTCACTGTTCC 60.250 55.000 0.00 0.00 0.00 3.62
662 682 0.861837 CAACCACTCGCTCACTGTTC 59.138 55.000 0.00 0.00 0.00 3.18
663 683 0.178068 ACAACCACTCGCTCACTGTT 59.822 50.000 0.00 0.00 0.00 3.16
664 684 0.530650 CACAACCACTCGCTCACTGT 60.531 55.000 0.00 0.00 0.00 3.55
665 685 1.224069 CCACAACCACTCGCTCACTG 61.224 60.000 0.00 0.00 0.00 3.66
666 686 1.069765 CCACAACCACTCGCTCACT 59.930 57.895 0.00 0.00 0.00 3.41
667 687 0.032952 TACCACAACCACTCGCTCAC 59.967 55.000 0.00 0.00 0.00 3.51
668 688 0.317160 CTACCACAACCACTCGCTCA 59.683 55.000 0.00 0.00 0.00 4.26
669 689 0.317479 ACTACCACAACCACTCGCTC 59.683 55.000 0.00 0.00 0.00 5.03
670 690 0.033504 CACTACCACAACCACTCGCT 59.966 55.000 0.00 0.00 0.00 4.93
671 691 0.949105 CCACTACCACAACCACTCGC 60.949 60.000 0.00 0.00 0.00 5.03
672 692 0.391597 ACCACTACCACAACCACTCG 59.608 55.000 0.00 0.00 0.00 4.18
673 693 2.631545 ACTACCACTACCACAACCACTC 59.368 50.000 0.00 0.00 0.00 3.51
674 694 2.367567 CACTACCACTACCACAACCACT 59.632 50.000 0.00 0.00 0.00 4.00
675 695 2.366266 TCACTACCACTACCACAACCAC 59.634 50.000 0.00 0.00 0.00 4.16
676 696 2.680251 TCACTACCACTACCACAACCA 58.320 47.619 0.00 0.00 0.00 3.67
677 697 3.975168 ATCACTACCACTACCACAACC 57.025 47.619 0.00 0.00 0.00 3.77
678 698 5.408356 CACTATCACTACCACTACCACAAC 58.592 45.833 0.00 0.00 0.00 3.32
679 699 4.464951 CCACTATCACTACCACTACCACAA 59.535 45.833 0.00 0.00 0.00 3.33
680 700 4.021229 CCACTATCACTACCACTACCACA 58.979 47.826 0.00 0.00 0.00 4.17
715 735 3.054802 CAGAGGAGGATTTGCTGTTAGGT 60.055 47.826 0.00 0.00 0.00 3.08
843 884 1.857348 CCAAAGGAAGGGGAGGGGT 60.857 63.158 0.00 0.00 0.00 4.95
849 900 2.355115 CGGGACCAAAGGAAGGGG 59.645 66.667 0.00 0.00 0.00 4.79
893 944 2.355956 GGGTCGATCGATTCCCGC 60.356 66.667 23.55 14.57 38.37 6.13
962 1013 3.567579 TTGGCCTGCCCTTTCTCGG 62.568 63.158 3.32 0.00 34.56 4.63
963 1014 2.034066 TTGGCCTGCCCTTTCTCG 59.966 61.111 3.32 0.00 34.56 4.04
964 1015 2.346541 GCTTGGCCTGCCCTTTCTC 61.347 63.158 3.32 0.00 34.56 2.87
1109 1160 1.602771 GAGGAAGGGAACGGAAGGG 59.397 63.158 0.00 0.00 0.00 3.95
1116 1167 1.985895 TGAAGAAGGGAGGAAGGGAAC 59.014 52.381 0.00 0.00 0.00 3.62
1121 1172 4.775253 AGAGTAGTTGAAGAAGGGAGGAAG 59.225 45.833 0.00 0.00 0.00 3.46
1122 1173 4.753186 AGAGTAGTTGAAGAAGGGAGGAA 58.247 43.478 0.00 0.00 0.00 3.36
1123 1174 4.405756 AGAGTAGTTGAAGAAGGGAGGA 57.594 45.455 0.00 0.00 0.00 3.71
1124 1175 4.403113 GGTAGAGTAGTTGAAGAAGGGAGG 59.597 50.000 0.00 0.00 0.00 4.30
1125 1176 4.403113 GGGTAGAGTAGTTGAAGAAGGGAG 59.597 50.000 0.00 0.00 0.00 4.30
1126 1177 4.045590 AGGGTAGAGTAGTTGAAGAAGGGA 59.954 45.833 0.00 0.00 0.00 4.20
1127 1178 4.354662 AGGGTAGAGTAGTTGAAGAAGGG 58.645 47.826 0.00 0.00 0.00 3.95
1128 1179 5.950549 TGTAGGGTAGAGTAGTTGAAGAAGG 59.049 44.000 0.00 0.00 0.00 3.46
1129 1180 7.648039 ATGTAGGGTAGAGTAGTTGAAGAAG 57.352 40.000 0.00 0.00 0.00 2.85
1144 1196 8.395605 TCTATCCATGTACATGTATGTAGGGTA 58.604 37.037 29.25 14.78 43.32 3.69
1200 1262 3.634397 TCCATCCATCTGTCTTGTTCC 57.366 47.619 0.00 0.00 0.00 3.62
1246 1316 7.110155 TGAACTGAAAACAAAGGAAGTAGTCT 58.890 34.615 0.00 0.00 0.00 3.24
1249 1319 6.972901 GGTTGAACTGAAAACAAAGGAAGTAG 59.027 38.462 0.00 0.00 0.00 2.57
1320 1390 3.156293 CAACCTCCAACACAATCCATGA 58.844 45.455 0.00 0.00 0.00 3.07
1456 1529 0.033011 TGGAGGAGACTAGCAGGGAC 60.033 60.000 0.00 0.00 44.43 4.46
1457 1530 0.710588 TTGGAGGAGACTAGCAGGGA 59.289 55.000 0.00 0.00 44.43 4.20
1458 1531 0.827368 GTTGGAGGAGACTAGCAGGG 59.173 60.000 0.00 0.00 44.43 4.45
1459 1532 1.754226 GAGTTGGAGGAGACTAGCAGG 59.246 57.143 0.00 0.00 44.43 4.85
1534 1624 4.856182 AGGGAGGGGTTAACATTTAAGAGT 59.144 41.667 8.10 0.00 0.00 3.24
1542 1632 0.426022 AGGGAGGGAGGGGTTAACAT 59.574 55.000 8.10 0.00 0.00 2.71
1582 1672 4.454728 AAGTCATTTTGTGTGTGTGCTT 57.545 36.364 0.00 0.00 0.00 3.91
1583 1673 4.454728 AAAGTCATTTTGTGTGTGTGCT 57.545 36.364 0.00 0.00 0.00 4.40
1616 1725 3.644823 TGAAGATGAACGAACGCAGTAA 58.355 40.909 0.00 0.00 45.00 2.24
1642 1751 0.998928 TCATATTGGGTGGCACCAGT 59.001 50.000 35.69 22.80 42.47 4.00
1643 1752 1.958579 CATCATATTGGGTGGCACCAG 59.041 52.381 35.69 18.08 42.47 4.00
1644 1753 1.568123 TCATCATATTGGGTGGCACCA 59.432 47.619 35.69 18.91 41.02 4.17
1645 1754 2.363306 TCATCATATTGGGTGGCACC 57.637 50.000 28.69 28.69 37.60 5.01
1646 1755 5.948162 AGATATTCATCATATTGGGTGGCAC 59.052 40.000 9.70 9.70 33.21 5.01
1647 1756 5.947566 CAGATATTCATCATATTGGGTGGCA 59.052 40.000 0.00 0.00 33.21 4.92
1648 1757 6.182627 TCAGATATTCATCATATTGGGTGGC 58.817 40.000 0.00 0.00 33.21 5.01
1725 1834 6.015603 GGAGGATAAGGCACGTTTAGTAGTAT 60.016 42.308 0.00 0.00 0.00 2.12
1735 1844 1.141053 GGAATGGAGGATAAGGCACGT 59.859 52.381 0.00 0.00 0.00 4.49
1754 1864 7.067496 ACATAGTCCTGTAATGTAATGGAGG 57.933 40.000 0.00 0.00 32.21 4.30
1972 2088 6.478512 TTTCCCATTAATTATTCTGGTGGC 57.521 37.500 5.96 0.00 0.00 5.01
2243 2360 1.781786 GTAGCTCAGGGATCCACTGA 58.218 55.000 23.54 23.54 42.31 3.41
2369 2486 4.275936 GCATAGTTCCGGCAAGAATTACAT 59.724 41.667 0.00 0.00 0.00 2.29
2398 2515 4.545678 TGCAATAGGACATAAAAGGGCAT 58.454 39.130 0.00 0.00 0.00 4.40
2570 2688 0.383949 TGCTTTCCGTTCAACCAAGC 59.616 50.000 6.76 6.76 40.29 4.01
2703 2821 7.095523 CCAACAAAATTTCTCAGCTAAACCATG 60.096 37.037 0.00 0.00 0.00 3.66
2705 2823 6.127196 ACCAACAAAATTTCTCAGCTAAACCA 60.127 34.615 0.00 0.00 0.00 3.67
2706 2824 6.280643 ACCAACAAAATTTCTCAGCTAAACC 58.719 36.000 0.00 0.00 0.00 3.27
2708 2826 6.323739 AGGACCAACAAAATTTCTCAGCTAAA 59.676 34.615 0.00 0.00 0.00 1.85
2711 2829 4.218312 AGGACCAACAAAATTTCTCAGCT 58.782 39.130 0.00 0.00 0.00 4.24
2712 2830 4.590850 AGGACCAACAAAATTTCTCAGC 57.409 40.909 0.00 0.00 0.00 4.26
2713 2831 7.978975 TGTTTAAGGACCAACAAAATTTCTCAG 59.021 33.333 0.00 0.00 29.81 3.35
2714 2832 7.841956 TGTTTAAGGACCAACAAAATTTCTCA 58.158 30.769 0.00 0.00 29.81 3.27
2715 2833 8.710835 TTGTTTAAGGACCAACAAAATTTCTC 57.289 30.769 6.22 0.00 39.40 2.87
2716 2834 8.536175 TCTTGTTTAAGGACCAACAAAATTTCT 58.464 29.630 9.24 0.00 41.26 2.52
2717 2835 8.710835 TCTTGTTTAAGGACCAACAAAATTTC 57.289 30.769 9.24 0.00 41.26 2.17
2718 2836 9.508642 TTTCTTGTTTAAGGACCAACAAAATTT 57.491 25.926 9.24 0.00 41.26 1.82
2719 2837 9.508642 TTTTCTTGTTTAAGGACCAACAAAATT 57.491 25.926 9.24 0.00 41.26 1.82
2720 2838 9.679661 ATTTTCTTGTTTAAGGACCAACAAAAT 57.320 25.926 9.24 4.97 41.26 1.82
2721 2839 8.940952 CATTTTCTTGTTTAAGGACCAACAAAA 58.059 29.630 9.24 3.25 41.26 2.44
2722 2840 7.550906 CCATTTTCTTGTTTAAGGACCAACAAA 59.449 33.333 9.24 0.00 41.26 2.83
2831 2949 6.964370 TCACAACAAGTCTTAATTTCACAACG 59.036 34.615 0.00 0.00 0.00 4.10
2833 2951 8.681806 TCATCACAACAAGTCTTAATTTCACAA 58.318 29.630 0.00 0.00 0.00 3.33
2851 2969 8.421002 TCAGAGATAAACCGAATATCATCACAA 58.579 33.333 0.00 0.00 33.17 3.33
2899 3017 8.243426 TCTCTGCAACATTCATTAATTTGGTAC 58.757 33.333 0.00 0.00 0.00 3.34
3022 3140 7.554959 AAACAGACCTCGGTATATATTGGAT 57.445 36.000 0.00 0.00 0.00 3.41
3028 3146 8.416329 GGTAAAGAAAACAGACCTCGGTATATA 58.584 37.037 0.00 0.00 0.00 0.86
3029 3147 7.125356 AGGTAAAGAAAACAGACCTCGGTATAT 59.875 37.037 0.00 0.00 35.57 0.86
3112 3230 4.630894 ATTTGAAAAGAACGTGTGCAGA 57.369 36.364 0.00 0.00 0.00 4.26
3127 3245 4.809958 TGACTAAACCGTCGTGAATTTGAA 59.190 37.500 0.00 0.00 36.71 2.69
3162 3281 1.093972 CAACAGCACTGTGTTCCACA 58.906 50.000 9.86 0.00 44.13 4.17
3249 3369 9.477484 GGAATAATGTCACATCTTATTAGACGT 57.523 33.333 0.00 0.00 31.99 4.34
3250 3370 8.639428 CGGAATAATGTCACATCTTATTAGACG 58.361 37.037 0.00 0.00 31.99 4.18
3262 3382 4.436718 CGAAACATGCGGAATAATGTCACA 60.437 41.667 0.00 0.00 35.99 3.58
3419 3549 0.323908 AGCTTCCGAGTACCTGAGCT 60.324 55.000 0.00 0.00 0.00 4.09
3453 3587 7.332926 ACGCATATGCTATTTATCTTCTCAAGG 59.667 37.037 24.56 5.67 39.32 3.61
3462 3596 7.010183 ACGGAACATACGCATATGCTATTTATC 59.990 37.037 24.56 15.18 41.83 1.75
3530 3672 2.166459 TCAGCTCTTCACCCTACAATCG 59.834 50.000 0.00 0.00 0.00 3.34
3608 3750 2.414994 ACCAGGAGATGCACTCATTG 57.585 50.000 15.22 12.53 46.54 2.82
3625 3767 5.581479 GCTACTAGCCTTTTTCTTCACTACC 59.419 44.000 0.00 0.00 34.48 3.18
3637 3779 2.290323 CCCAACACTGCTACTAGCCTTT 60.290 50.000 5.58 0.00 41.51 3.11
3647 3792 3.508845 AATCACTAACCCAACACTGCT 57.491 42.857 0.00 0.00 0.00 4.24
3675 3830 2.016318 CGCCTTGATATTCTGCACCAA 58.984 47.619 0.00 0.00 0.00 3.67
3816 3971 0.179078 TGCAAAACAAAGGGCTGCTG 60.179 50.000 0.00 0.00 34.10 4.41
3892 4071 9.469807 CAAGCCAAACTAAATTATACAACAACA 57.530 29.630 0.00 0.00 0.00 3.33
3893 4072 9.685828 TCAAGCCAAACTAAATTATACAACAAC 57.314 29.630 0.00 0.00 0.00 3.32
3987 4169 8.251026 GCAGTCCATATATATAGCACAGTACAA 58.749 37.037 0.00 0.00 0.00 2.41
3992 4174 7.105241 TGAGCAGTCCATATATATAGCACAG 57.895 40.000 0.00 0.00 0.00 3.66
4065 4259 3.871485 TCCAAAATGCAAAGCACAAACT 58.129 36.364 0.00 0.00 43.04 2.66
4106 4302 5.665381 TTTTCAAAACATTTGGGATTCGC 57.335 34.783 3.25 0.00 0.00 4.70
4255 4451 8.501904 TCCAGTCTAGTCTAGTCTAGTCTAGTA 58.498 40.741 26.77 17.32 41.87 1.82
4443 4640 2.045926 CCCCAACTCCAGCTTCCG 60.046 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.