Multiple sequence alignment - TraesCS2A01G355600

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 TraesCS2A01G355600 chr2A 100.000 3220 0 0 1 3220 598618135 598614916 0.000000e+00 5947
1 TraesCS2A01G355600 chr2A 80.653 398 68 7 1 393 603733917 603733524 1.880000e-77 300
2 TraesCS2A01G355600 chr2A 83.806 247 39 1 407 653 191661779 191661534 1.930000e-57 233
3 TraesCS2A01G355600 chr2A 76.216 370 72 9 1 355 613071117 613071485 7.100000e-42 182
4 TraesCS2A01G355600 chr2D 89.510 2326 166 34 407 2670 450997405 450999714 0.000000e+00 2872
5 TraesCS2A01G355600 chr2D 87.160 514 31 19 2708 3220 450999712 451000191 4.690000e-153 551
6 TraesCS2A01G355600 chr2D 78.967 271 47 4 407 677 116839496 116839756 3.300000e-40 176
7 TraesCS2A01G355600 chr2B 90.952 1923 120 23 784 2670 531134947 531136851 0.000000e+00 2538
8 TraesCS2A01G355600 chr2B 85.366 451 31 16 2708 3156 531136849 531137266 4.930000e-118 435
9 TraesCS2A01G355600 chr3B 87.470 415 36 10 1938 2342 680237234 680237642 6.290000e-127 464
10 TraesCS2A01G355600 chr3B 89.627 241 24 1 407 647 223679773 223680012 4.040000e-79 305
11 TraesCS2A01G355600 chr3B 81.039 385 65 5 14 393 224165931 224166312 1.880000e-77 300
12 TraesCS2A01G355600 chr3B 84.490 245 27 6 413 655 418750765 418750530 6.950000e-57 231
13 TraesCS2A01G355600 chr3B 76.225 408 81 7 1 394 648896569 648896164 5.450000e-48 202
14 TraesCS2A01G355600 chr5D 81.704 399 59 8 1 393 550956278 550956668 1.440000e-83 320
15 TraesCS2A01G355600 chr5D 84.647 241 27 8 1 239 438091385 438091617 6.950000e-57 231
16 TraesCS2A01G355600 chr5D 81.579 190 29 5 459 647 526435268 526435084 5.560000e-33 152
17 TraesCS2A01G355600 chr4D 80.457 394 65 3 1 393 8651757 8652139 1.130000e-74 291
18 TraesCS2A01G355600 chr5A 75.976 666 93 32 1 647 598681699 598681082 6.800000e-72 281
19 TraesCS2A01G355600 chr1D 80.541 370 56 8 1 360 394482678 394483041 1.470000e-68 270
20 TraesCS2A01G355600 chr4B 88.837 215 21 3 407 620 463241846 463241634 8.860000e-66 261
21 TraesCS2A01G355600 chr3A 88.670 203 21 2 2359 2559 652825756 652825554 2.480000e-61 246
22 TraesCS2A01G355600 chr5B 80.556 324 51 3 79 393 10125355 10125035 4.150000e-59 239
23 TraesCS2A01G355600 chr7B 82.353 272 39 5 127 392 162917344 162917076 8.990000e-56 228
24 TraesCS2A01G355600 chr7B 83.258 221 32 5 407 625 741933588 741933371 7.050000e-47 198
25 TraesCS2A01G355600 chr7B 79.842 253 40 3 405 657 389015714 389015955 1.190000e-39 174
26 TraesCS2A01G355600 chr3D 90.000 180 13 1 2302 2476 517004308 517004129 8.990000e-56 228
27 TraesCS2A01G355600 chrUn 80.237 253 38 4 404 655 30896031 30895790 2.550000e-41 180
28 TraesCS2A01G355600 chrUn 76.127 377 67 19 1 360 15930372 15930742 3.300000e-40 176
29 TraesCS2A01G355600 chr7A 93.243 74 5 0 407 480 102320805 102320732 3.400000e-20 110


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 TraesCS2A01G355600 chr2A 598614916 598618135 3219 True 5947.0 5947 100.000 1 3220 1 chr2A.!!$R2 3219
1 TraesCS2A01G355600 chr2D 450997405 451000191 2786 False 1711.5 2872 88.335 407 3220 2 chr2D.!!$F2 2813
2 TraesCS2A01G355600 chr2B 531134947 531137266 2319 False 1486.5 2538 88.159 784 3156 2 chr2B.!!$F1 2372
3 TraesCS2A01G355600 chr5A 598681082 598681699 617 True 281.0 281 75.976 1 647 1 chr5A.!!$R1 646

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
342 356 0.034960 GACCAGAAGAGGAAAGGGCC 60.035 60.0 0.0 0.0 0.0 5.80 F
793 838 0.179124 GGCACGGCAGAAAACAAACA 60.179 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1566 0.817634 CGTGGCCACCAGACTTTTCA 60.818 55.0 29.95 0.0 32.34 2.69 R
2580 2688 0.179189 GCAAGGGCGTCATTCTTTCG 60.179 55.0 0.00 0.0 0.00 3.46 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
33 34 4.462417 CCGACGAGAACGAGCGCT 62.462 66.667 11.27 11.27 42.66 5.92
36 37 1.154188 GACGAGAACGAGCGCTTCT 60.154 57.895 13.26 11.25 42.66 2.85
37 38 1.129301 GACGAGAACGAGCGCTTCTC 61.129 60.000 22.26 22.26 42.66 2.87
52 53 2.202756 CTCGCTTGGGTCTACCGC 60.203 66.667 0.00 0.00 44.64 5.68
86 87 3.159984 CGGAGACAAACGCTCAGC 58.840 61.111 0.00 0.00 34.07 4.26
106 107 4.735132 CTCCGCCGGAAGAACGCA 62.735 66.667 7.50 0.00 0.00 5.24
111 112 2.561373 CCGGAAGAACGCAAAGGC 59.439 61.111 0.00 0.00 0.00 4.35
133 134 0.963856 TCTGGCTTGCCATTGAGCAG 60.964 55.000 15.21 1.75 45.13 4.24
137 138 1.798735 CTTGCCATTGAGCAGTCGG 59.201 57.895 0.00 0.00 45.13 4.79
198 208 3.058160 GCGGCAGCAAGACATGGT 61.058 61.111 3.18 0.00 44.35 3.55
199 209 1.745115 GCGGCAGCAAGACATGGTA 60.745 57.895 3.18 0.00 44.35 3.25
224 234 0.322816 GTGGCTCAAAGGGCTCATCA 60.323 55.000 0.00 0.00 0.00 3.07
232 242 1.433121 AAGGGCTCATCATCCTCTCC 58.567 55.000 0.00 0.00 0.00 3.71
240 250 2.091610 TCATCATCCTCTCCGACTCCTT 60.092 50.000 0.00 0.00 0.00 3.36
241 251 2.060050 TCATCCTCTCCGACTCCTTC 57.940 55.000 0.00 0.00 0.00 3.46
253 266 2.049802 TCCTTCGACAACGGCGAC 60.050 61.111 16.62 0.69 37.52 5.19
280 293 2.636412 CGCCTCCTCCAACGACTCA 61.636 63.158 0.00 0.00 0.00 3.41
281 294 1.216710 GCCTCCTCCAACGACTCAG 59.783 63.158 0.00 0.00 0.00 3.35
285 298 0.250597 TCCTCCAACGACTCAGACGA 60.251 55.000 2.82 0.00 34.70 4.20
289 302 0.811915 CCAACGACTCAGACGATCCT 59.188 55.000 2.82 0.00 34.70 3.24
295 308 1.032657 ACTCAGACGATCCTCCACCG 61.033 60.000 0.00 0.00 0.00 4.94
297 310 3.148279 AGACGATCCTCCACCGGC 61.148 66.667 0.00 0.00 0.00 6.13
301 314 4.222847 GATCCTCCACCGGCCGTC 62.223 72.222 26.12 8.53 0.00 4.79
316 329 2.278661 GTCGGCGCCTACAGCTAC 60.279 66.667 24.96 7.64 40.39 3.58
317 330 3.884350 TCGGCGCCTACAGCTACG 61.884 66.667 26.68 7.80 40.39 3.51
318 331 4.189188 CGGCGCCTACAGCTACGT 62.189 66.667 26.68 0.00 40.39 3.57
320 333 2.488355 GCGCCTACAGCTACGTCA 59.512 61.111 0.00 0.00 40.39 4.35
327 340 1.669265 CTACAGCTACGTCATCGACCA 59.331 52.381 0.00 0.00 40.62 4.02
328 341 0.452184 ACAGCTACGTCATCGACCAG 59.548 55.000 0.00 0.00 40.62 4.00
332 345 1.400846 GCTACGTCATCGACCAGAAGA 59.599 52.381 0.00 0.00 40.62 2.87
334 347 0.811915 ACGTCATCGACCAGAAGAGG 59.188 55.000 0.00 0.00 38.13 3.69
337 351 2.094700 CGTCATCGACCAGAAGAGGAAA 60.095 50.000 0.00 0.00 35.27 3.13
342 356 0.034960 GACCAGAAGAGGAAAGGGCC 60.035 60.000 0.00 0.00 0.00 5.80
343 357 0.772124 ACCAGAAGAGGAAAGGGCCA 60.772 55.000 6.18 0.00 0.00 5.36
346 360 1.136329 AGAAGAGGAAAGGGCCAGCA 61.136 55.000 6.18 0.00 0.00 4.41
366 380 2.884639 CAAGGAAGTGGTGAAAATCCGT 59.115 45.455 0.00 0.00 35.31 4.69
367 381 2.779506 AGGAAGTGGTGAAAATCCGTC 58.220 47.619 0.00 0.00 35.31 4.79
368 382 2.372172 AGGAAGTGGTGAAAATCCGTCT 59.628 45.455 0.00 0.00 35.31 4.18
372 386 3.665190 AGTGGTGAAAATCCGTCTTCTC 58.335 45.455 0.00 0.00 0.00 2.87
376 390 3.557264 GGTGAAAATCCGTCTTCTCCACT 60.557 47.826 0.00 0.00 35.96 4.00
377 391 4.065789 GTGAAAATCCGTCTTCTCCACTT 58.934 43.478 0.00 0.00 0.00 3.16
378 392 4.515567 GTGAAAATCCGTCTTCTCCACTTT 59.484 41.667 0.00 0.00 0.00 2.66
379 393 5.699458 GTGAAAATCCGTCTTCTCCACTTTA 59.301 40.000 0.00 0.00 0.00 1.85
380 394 6.204108 GTGAAAATCCGTCTTCTCCACTTTAA 59.796 38.462 0.00 0.00 0.00 1.52
381 395 6.940298 TGAAAATCCGTCTTCTCCACTTTAAT 59.060 34.615 0.00 0.00 0.00 1.40
382 396 7.447238 TGAAAATCCGTCTTCTCCACTTTAATT 59.553 33.333 0.00 0.00 0.00 1.40
383 397 7.761038 AAATCCGTCTTCTCCACTTTAATTT 57.239 32.000 0.00 0.00 0.00 1.82
384 398 6.986904 ATCCGTCTTCTCCACTTTAATTTC 57.013 37.500 0.00 0.00 0.00 2.17
385 399 5.860611 TCCGTCTTCTCCACTTTAATTTCA 58.139 37.500 0.00 0.00 0.00 2.69
386 400 6.292923 TCCGTCTTCTCCACTTTAATTTCAA 58.707 36.000 0.00 0.00 0.00 2.69
387 401 6.426937 TCCGTCTTCTCCACTTTAATTTCAAG 59.573 38.462 0.00 0.00 0.00 3.02
388 402 6.204882 CCGTCTTCTCCACTTTAATTTCAAGT 59.795 38.462 0.00 0.00 34.67 3.16
389 403 7.255139 CCGTCTTCTCCACTTTAATTTCAAGTT 60.255 37.037 0.95 0.00 31.83 2.66
390 404 8.129211 CGTCTTCTCCACTTTAATTTCAAGTTT 58.871 33.333 0.95 0.00 31.83 2.66
391 405 9.803315 GTCTTCTCCACTTTAATTTCAAGTTTT 57.197 29.630 0.95 0.00 31.83 2.43
442 458 9.961265 AGTTTTTAGATGTAGTTTAAACTTGGC 57.039 29.630 25.07 15.75 40.37 4.52
464 480 4.025563 GCCGTCGTTTATGTGCATTATGTA 60.026 41.667 0.00 0.00 0.00 2.29
475 491 3.857093 GTGCATTATGTAAACTTTGGCGG 59.143 43.478 0.00 0.00 0.00 6.13
482 498 7.507733 TTATGTAAACTTTGGCGGTCTTTTA 57.492 32.000 0.00 0.00 0.00 1.52
491 507 1.669265 GGCGGTCTTTTAAAGATCCGG 59.331 52.381 30.07 20.19 44.70 5.14
516 532 4.698304 GGTGATCTTTTGGTGAACGGATTA 59.302 41.667 0.00 0.00 0.00 1.75
531 547 6.992123 TGAACGGATTATGCATTTCTATGTCT 59.008 34.615 3.54 0.00 34.12 3.41
534 550 7.164122 ACGGATTATGCATTTCTATGTCTGAT 58.836 34.615 3.54 0.00 34.12 2.90
535 551 7.663081 ACGGATTATGCATTTCTATGTCTGATT 59.337 33.333 3.54 0.00 34.12 2.57
536 552 8.509690 CGGATTATGCATTTCTATGTCTGATTT 58.490 33.333 3.54 0.00 34.12 2.17
543 559 9.399797 TGCATTTCTATGTCTGATTTTATGTCT 57.600 29.630 0.00 0.00 34.12 3.41
544 560 9.875675 GCATTTCTATGTCTGATTTTATGTCTC 57.124 33.333 0.00 0.00 34.12 3.36
598 626 7.817478 CGTTGCATGGTTTAGTATGGATATAGA 59.183 37.037 0.00 0.00 0.00 1.98
647 675 2.887151 AGACCCAATTTGAGGACTGG 57.113 50.000 9.92 0.00 0.00 4.00
648 676 2.065799 AGACCCAATTTGAGGACTGGT 58.934 47.619 9.92 2.49 0.00 4.00
688 733 2.100418 GGCATTTGAGAGCCCAGATTTC 59.900 50.000 0.00 0.00 45.18 2.17
700 745 2.158755 CCCAGATTTCCGGCTGTAGATT 60.159 50.000 0.00 0.00 0.00 2.40
745 790 2.169352 TGCAAAGCCAAAGCCAAAAGTA 59.831 40.909 0.00 0.00 41.25 2.24
772 817 5.254339 AGAAATGATTTTCCATTCGAGCC 57.746 39.130 0.00 0.00 41.86 4.70
793 838 0.179124 GGCACGGCAGAAAACAAACA 60.179 50.000 0.00 0.00 0.00 2.83
797 842 0.597377 CGGCAGAAAACAAACAGGGC 60.597 55.000 0.00 0.00 0.00 5.19
903 950 6.000891 TGATGAAGATGAACCGAACAAAAG 57.999 37.500 0.00 0.00 0.00 2.27
941 988 0.386838 GCAAAACCAGAAGCAGCAGT 59.613 50.000 0.00 0.00 0.00 4.40
942 989 1.202452 GCAAAACCAGAAGCAGCAGTT 60.202 47.619 0.00 0.00 0.00 3.16
943 990 2.735823 CAAAACCAGAAGCAGCAGTTC 58.264 47.619 0.00 0.00 0.00 3.01
1022 1090 1.303970 GCAGCTTGGCCCTCTTCTT 60.304 57.895 0.00 0.00 0.00 2.52
1050 1121 1.719378 TCCTCCTCCTCTCTGTTCCTT 59.281 52.381 0.00 0.00 0.00 3.36
1061 1132 3.391296 TCTCTGTTCCTTACAAAGCAGGT 59.609 43.478 0.00 0.00 36.02 4.00
1062 1133 4.137543 CTCTGTTCCTTACAAAGCAGGTT 58.862 43.478 0.00 0.00 36.02 3.50
1105 1176 3.716006 CGGTTGTGAGGTGCAGCG 61.716 66.667 10.78 0.00 0.00 5.18
1128 1199 2.903357 CCCACCCTGTCAGGATCG 59.097 66.667 21.23 6.26 37.67 3.69
1134 1205 0.249784 CCCTGTCAGGATCGCATGAG 60.250 60.000 21.23 0.00 37.67 2.90
1140 1211 0.755079 CAGGATCGCATGAGGAGGAA 59.245 55.000 0.00 0.00 0.00 3.36
1237 1308 1.143620 GTGCTTGGTTTTGCAGGCA 59.856 52.632 0.00 0.00 40.06 4.75
1320 1391 5.500234 CCTGATCAGAATGGTTGGTTCTTA 58.500 41.667 24.62 0.00 33.82 2.10
1321 1392 5.355350 CCTGATCAGAATGGTTGGTTCTTAC 59.645 44.000 24.62 0.00 33.82 2.34
1322 1393 6.126863 TGATCAGAATGGTTGGTTCTTACT 57.873 37.500 0.00 0.00 33.82 2.24
1323 1394 6.542821 TGATCAGAATGGTTGGTTCTTACTT 58.457 36.000 0.00 0.00 33.82 2.24
1335 1406 3.127721 GGTTCTTACTTGCTGCCATCTTC 59.872 47.826 0.00 0.00 0.00 2.87
1340 1411 2.366533 ACTTGCTGCCATCTTCATCTG 58.633 47.619 0.00 0.00 0.00 2.90
1341 1412 2.290768 ACTTGCTGCCATCTTCATCTGT 60.291 45.455 0.00 0.00 0.00 3.41
1365 1454 8.685427 TGTTAATTCCATGTGATATGTTCTTGG 58.315 33.333 0.00 0.00 0.00 3.61
1373 1462 7.336679 CCATGTGATATGTTCTTGGTAGTTCAA 59.663 37.037 0.00 0.00 0.00 2.69
1374 1463 7.667043 TGTGATATGTTCTTGGTAGTTCAAC 57.333 36.000 0.00 0.00 0.00 3.18
1376 1465 7.936847 TGTGATATGTTCTTGGTAGTTCAACTT 59.063 33.333 0.00 0.00 0.00 2.66
1381 1470 5.989777 TGTTCTTGGTAGTTCAACTTAGAGC 59.010 40.000 0.00 0.00 0.00 4.09
1383 1472 5.784177 TCTTGGTAGTTCAACTTAGAGCAG 58.216 41.667 0.00 0.00 0.00 4.24
1384 1473 5.538813 TCTTGGTAGTTCAACTTAGAGCAGA 59.461 40.000 0.00 0.00 0.00 4.26
1387 1476 5.480422 TGGTAGTTCAACTTAGAGCAGATCA 59.520 40.000 0.00 0.00 0.00 2.92
1388 1477 6.039616 GGTAGTTCAACTTAGAGCAGATCAG 58.960 44.000 0.00 0.00 0.00 2.90
1389 1478 5.991933 AGTTCAACTTAGAGCAGATCAGA 57.008 39.130 0.00 0.00 0.00 3.27
1390 1479 5.719173 AGTTCAACTTAGAGCAGATCAGAC 58.281 41.667 0.00 0.00 0.00 3.51
1391 1480 5.480073 AGTTCAACTTAGAGCAGATCAGACT 59.520 40.000 0.00 0.00 0.00 3.24
1392 1481 5.991933 TCAACTTAGAGCAGATCAGACTT 57.008 39.130 0.00 0.00 0.00 3.01
1393 1482 5.960113 TCAACTTAGAGCAGATCAGACTTC 58.040 41.667 0.00 0.00 0.00 3.01
1394 1483 5.478332 TCAACTTAGAGCAGATCAGACTTCA 59.522 40.000 0.00 0.00 0.00 3.02
1395 1484 5.581126 ACTTAGAGCAGATCAGACTTCAG 57.419 43.478 0.00 0.00 0.00 3.02
1396 1485 5.260424 ACTTAGAGCAGATCAGACTTCAGA 58.740 41.667 0.00 0.00 0.00 3.27
1397 1486 5.893255 ACTTAGAGCAGATCAGACTTCAGAT 59.107 40.000 0.00 0.00 0.00 2.90
1398 1487 7.059788 ACTTAGAGCAGATCAGACTTCAGATA 58.940 38.462 0.00 0.00 0.00 1.98
1399 1488 5.772825 AGAGCAGATCAGACTTCAGATAC 57.227 43.478 0.00 0.00 0.00 2.24
1400 1489 4.275689 AGAGCAGATCAGACTTCAGATACG 59.724 45.833 0.00 0.00 0.00 3.06
1401 1490 3.049206 GCAGATCAGACTTCAGATACGC 58.951 50.000 0.00 0.00 0.00 4.42
1415 1504 5.461526 TCAGATACGCCTTTCATATTCTCG 58.538 41.667 0.00 0.00 0.00 4.04
1427 1516 1.921243 TATTCTCGTGGTGCATGTCG 58.079 50.000 0.00 0.00 0.00 4.35
1489 1578 0.322546 GGCCGGATGAAAAGTCTGGT 60.323 55.000 5.05 0.00 42.88 4.00
1575 1664 1.205893 GGTGAGAACTGGAGCTACTGG 59.794 57.143 7.84 0.00 0.00 4.00
1584 1673 3.245052 ACTGGAGCTACTGGCAGAAATTT 60.245 43.478 23.66 0.00 44.79 1.82
1593 1682 5.789643 ACTGGCAGAAATTTAGCTTTCAA 57.210 34.783 23.66 0.00 37.55 2.69
1621 1710 4.626042 AGTCAGTCACACACTTTCTGATC 58.374 43.478 0.00 0.00 37.46 2.92
1627 1716 5.297776 AGTCACACACTTTCTGATCCAAAAG 59.702 40.000 12.84 12.84 38.24 2.27
1628 1717 5.296780 GTCACACACTTTCTGATCCAAAAGA 59.703 40.000 18.63 0.88 36.27 2.52
1629 1718 6.016777 GTCACACACTTTCTGATCCAAAAGAT 60.017 38.462 18.63 7.73 36.27 2.40
1676 1765 2.110757 TTGCTGATCTCGGTGGCACA 62.111 55.000 20.82 0.00 32.47 4.57
1790 1879 6.670695 AACTGTTCTTTCCTGGCATATTTT 57.329 33.333 0.00 0.00 0.00 1.82
1811 1904 2.823747 TGTAGCGTGGTAACTGTCTCAT 59.176 45.455 0.00 0.00 37.61 2.90
1861 1954 1.061131 GATGACCTTGACGATGCAACG 59.939 52.381 15.38 15.38 39.31 4.10
1943 2036 3.767711 GAGAATGTGGAAGGGAAGGTTT 58.232 45.455 0.00 0.00 0.00 3.27
1960 2053 0.682532 TTTTGTCCACAGCCACAGCA 60.683 50.000 0.00 0.00 43.56 4.41
1966 2059 0.251354 CCACAGCCACAGCAGAGTAT 59.749 55.000 0.00 0.00 43.56 2.12
2005 2098 1.671379 GTTCGAGCTGGAACCACCC 60.671 63.158 26.10 5.43 40.28 4.61
2008 2101 2.971598 CGAGCTGGAACCACCCCAT 61.972 63.158 0.00 0.00 38.00 4.00
2059 2152 0.458716 GGCTCTACCTGTTCAGCGTC 60.459 60.000 0.00 0.00 34.51 5.19
2101 2194 6.102897 ACTGTCCTTATCACTATATGGTGC 57.897 41.667 14.01 0.00 35.39 5.01
2131 2224 6.409704 TCTATGGTCACTTTTCTCATCTTGG 58.590 40.000 0.00 0.00 0.00 3.61
2168 2262 2.300956 TTGCAGGGCTACAATGGAAA 57.699 45.000 0.00 0.00 0.00 3.13
2230 2324 2.385803 CGTAGTCTAGGGTGGTTCCAT 58.614 52.381 0.00 0.00 38.11 3.41
2381 2475 6.946583 TGTAAGCTTCCTCTTCTAGTTACAGA 59.053 38.462 0.00 0.00 0.00 3.41
2382 2476 7.616150 TGTAAGCTTCCTCTTCTAGTTACAGAT 59.384 37.037 0.00 0.00 0.00 2.90
2401 2495 6.587273 ACAGATAGAATTCAGACCTAAAGGC 58.413 40.000 8.44 0.00 39.32 4.35
2431 2526 3.202906 GGCGCATATAACAACTTCCAGA 58.797 45.455 10.83 0.00 0.00 3.86
2435 2530 4.271049 CGCATATAACAACTTCCAGACCTG 59.729 45.833 0.00 0.00 0.00 4.00
2438 2533 6.543831 GCATATAACAACTTCCAGACCTGAAT 59.456 38.462 0.00 0.00 0.00 2.57
2470 2565 3.799281 TGTTTGAAGTTTCCTTGGCTG 57.201 42.857 0.00 0.00 0.00 4.85
2489 2584 4.561105 GCTGTAGCCTACATGTCTAATCC 58.439 47.826 4.77 0.00 38.15 3.01
2500 2600 3.548745 TGTCTAATCCATGACTGGCAG 57.451 47.619 14.16 14.16 42.80 4.85
2568 2676 3.195825 CGGCCTCCATATAGGGTTCTTAG 59.804 52.174 0.00 0.00 37.11 2.18
2580 2688 7.954666 ATAGGGTTCTTAGATCTAGATCAGC 57.045 40.000 29.83 19.21 40.22 4.26
2591 2699 6.446318 AGATCTAGATCAGCGAAAGAATGAC 58.554 40.000 29.83 2.62 40.22 3.06
2614 2722 1.605710 CCTTGCCTGACTTGTGTGAAG 59.394 52.381 0.00 0.00 0.00 3.02
2617 2725 0.819259 GCCTGACTTGTGTGAAGGCA 60.819 55.000 7.11 0.00 45.21 4.75
2650 2758 9.071276 AGTATGAGTGTGATTTCAACTTTCAAT 57.929 29.630 0.00 0.00 0.00 2.57
2653 2761 4.977963 AGTGTGATTTCAACTTTCAATGCG 59.022 37.500 0.00 0.00 0.00 4.73
2670 2778 0.179150 GCGTCACTAGAGCTCCAGTG 60.179 60.000 29.66 29.66 42.88 3.66
2671 2779 0.453793 CGTCACTAGAGCTCCAGTGG 59.546 60.000 32.81 19.29 42.01 4.00
2672 2780 0.174617 GTCACTAGAGCTCCAGTGGC 59.825 60.000 32.81 30.10 42.01 5.01
2673 2781 0.972983 TCACTAGAGCTCCAGTGGCC 60.973 60.000 32.81 0.00 42.01 5.36
2675 2783 1.754621 CTAGAGCTCCAGTGGCCGA 60.755 63.158 10.93 0.00 0.00 5.54
2676 2784 1.304962 TAGAGCTCCAGTGGCCGAA 60.305 57.895 10.93 0.00 0.00 4.30
2677 2785 1.605058 TAGAGCTCCAGTGGCCGAAC 61.605 60.000 10.93 0.00 0.00 3.95
2678 2786 2.925170 AGCTCCAGTGGCCGAACT 60.925 61.111 3.51 0.00 0.00 3.01
2679 2787 2.743928 GCTCCAGTGGCCGAACTG 60.744 66.667 14.86 14.86 45.93 3.16
2685 2793 2.702847 AGTGGCCGAACTGAAACAC 58.297 52.632 0.00 0.00 0.00 3.32
2686 2794 0.818040 AGTGGCCGAACTGAAACACC 60.818 55.000 0.00 0.00 0.00 4.16
2687 2795 0.818040 GTGGCCGAACTGAAACACCT 60.818 55.000 0.00 0.00 0.00 4.00
2688 2796 0.759959 TGGCCGAACTGAAACACCTA 59.240 50.000 0.00 0.00 0.00 3.08
2689 2797 1.141254 TGGCCGAACTGAAACACCTAA 59.859 47.619 0.00 0.00 0.00 2.69
2690 2798 2.224670 TGGCCGAACTGAAACACCTAAT 60.225 45.455 0.00 0.00 0.00 1.73
2691 2799 3.008157 TGGCCGAACTGAAACACCTAATA 59.992 43.478 0.00 0.00 0.00 0.98
2692 2800 4.196971 GGCCGAACTGAAACACCTAATAT 58.803 43.478 0.00 0.00 0.00 1.28
2693 2801 5.104859 TGGCCGAACTGAAACACCTAATATA 60.105 40.000 0.00 0.00 0.00 0.86
2694 2802 5.465724 GGCCGAACTGAAACACCTAATATAG 59.534 44.000 0.00 0.00 0.00 1.31
2754 2863 8.196771 TGCAAATAAGAACAGTTCAAAGTTCAT 58.803 29.630 15.85 0.00 44.94 2.57
2796 2905 4.261801 GCTAACTTGCTAGGGTTTGATGA 58.738 43.478 0.00 0.00 0.00 2.92
2800 2909 5.649782 ACTTGCTAGGGTTTGATGAAATG 57.350 39.130 0.00 0.00 0.00 2.32
2801 2910 4.082026 ACTTGCTAGGGTTTGATGAAATGC 60.082 41.667 0.00 0.00 0.00 3.56
2822 2931 3.699067 CAGCAATACAAATGGCTACAGC 58.301 45.455 0.00 0.00 40.66 4.40
2830 2939 8.949177 CAATACAAATGGCTACAGCATGATATA 58.051 33.333 0.00 0.00 44.36 0.86
2831 2940 6.808008 ACAAATGGCTACAGCATGATATAC 57.192 37.500 0.00 0.00 44.36 1.47
2832 2941 6.298361 ACAAATGGCTACAGCATGATATACA 58.702 36.000 0.00 0.00 44.36 2.29
2833 2942 6.772233 ACAAATGGCTACAGCATGATATACAA 59.228 34.615 0.00 0.00 44.36 2.41
2834 2943 7.285172 ACAAATGGCTACAGCATGATATACAAA 59.715 33.333 0.00 0.00 44.36 2.83
2835 2944 6.808008 ATGGCTACAGCATGATATACAAAC 57.192 37.500 0.00 0.00 44.36 2.93
2836 2945 4.749598 TGGCTACAGCATGATATACAAACG 59.250 41.667 0.00 0.00 44.36 3.60
2837 2946 4.152402 GGCTACAGCATGATATACAAACGG 59.848 45.833 0.00 0.00 44.36 4.44
2838 2947 4.377431 GCTACAGCATGATATACAAACGGC 60.377 45.833 0.00 0.00 39.69 5.68
2839 2948 3.808728 ACAGCATGATATACAAACGGCT 58.191 40.909 0.00 0.00 39.69 5.52
2840 2949 4.956085 ACAGCATGATATACAAACGGCTA 58.044 39.130 0.00 0.00 39.69 3.93
2841 2950 4.991056 ACAGCATGATATACAAACGGCTAG 59.009 41.667 0.00 0.00 39.69 3.42
2842 2951 5.221441 ACAGCATGATATACAAACGGCTAGA 60.221 40.000 0.00 0.00 39.69 2.43
2843 2952 5.347093 CAGCATGATATACAAACGGCTAGAG 59.653 44.000 0.00 0.00 39.69 2.43
2844 2953 4.092091 GCATGATATACAAACGGCTAGAGC 59.908 45.833 0.00 0.00 41.14 4.09
2845 2954 4.929819 TGATATACAAACGGCTAGAGCA 57.070 40.909 3.54 0.00 44.36 4.26
2846 2955 5.468540 TGATATACAAACGGCTAGAGCAT 57.531 39.130 3.54 0.00 44.36 3.79
2847 2956 5.230182 TGATATACAAACGGCTAGAGCATG 58.770 41.667 3.54 0.00 44.36 4.06
2848 2957 3.819564 ATACAAACGGCTAGAGCATGA 57.180 42.857 3.54 0.00 44.36 3.07
2849 2958 2.698855 ACAAACGGCTAGAGCATGAT 57.301 45.000 3.54 0.00 44.36 2.45
2850 2959 3.819564 ACAAACGGCTAGAGCATGATA 57.180 42.857 3.54 0.00 44.36 2.15
2851 2960 4.342862 ACAAACGGCTAGAGCATGATAT 57.657 40.909 3.54 0.00 44.36 1.63
2852 2961 5.468540 ACAAACGGCTAGAGCATGATATA 57.531 39.130 3.54 0.00 44.36 0.86
2853 2962 5.853936 ACAAACGGCTAGAGCATGATATAA 58.146 37.500 3.54 0.00 44.36 0.98
2860 2969 5.105392 GGCTAGAGCATGATATAAGAGCAGT 60.105 44.000 3.54 0.00 44.36 4.40
2866 2975 9.253832 AGAGCATGATATAAGAGCAGTAACTAT 57.746 33.333 0.00 0.00 0.00 2.12
2980 3095 7.081526 AGCTAGAGTTGTTGAAAGCATTATG 57.918 36.000 0.00 0.00 32.42 1.90
3036 3152 8.155510 ACAAAAAGTTAACTCTAGGGTAGGAAG 58.844 37.037 8.95 0.00 0.00 3.46
3044 3161 1.860906 CTAGGGTAGGAAGGGGACTCT 59.139 57.143 0.00 0.00 42.68 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.179134 CGGTAGACCCAAGCGAGAAG 60.179 60.000 0.00 0.00 40.11 2.85
33 34 1.888018 CGGTAGACCCAAGCGAGAA 59.112 57.895 0.00 0.00 40.11 2.87
36 37 3.766691 GGCGGTAGACCCAAGCGA 61.767 66.667 0.00 0.00 40.11 4.93
38 39 4.832608 CCGGCGGTAGACCCAAGC 62.833 72.222 19.97 0.00 0.00 4.01
39 40 3.366739 GACCGGCGGTAGACCCAAG 62.367 68.421 34.29 0.36 35.25 3.61
91 92 3.308878 CTTTGCGTTCTTCCGGCGG 62.309 63.158 22.51 22.51 0.00 6.13
94 95 2.561373 GCCTTTGCGTTCTTCCGG 59.439 61.111 0.00 0.00 0.00 5.14
106 107 3.368571 GCAAGCCAGAGCGCCTTT 61.369 61.111 2.29 0.00 46.67 3.11
119 120 0.674581 TCCGACTGCTCAATGGCAAG 60.675 55.000 0.00 0.00 41.94 4.01
122 123 2.467826 GCTCCGACTGCTCAATGGC 61.468 63.158 0.00 0.00 0.00 4.40
123 124 2.169789 CGCTCCGACTGCTCAATGG 61.170 63.158 0.00 0.00 0.00 3.16
164 174 2.032528 CTTGAGCTTCGCCACCCA 59.967 61.111 0.00 0.00 0.00 4.51
195 205 1.347707 CTTTGAGCCACTGGACTACCA 59.652 52.381 0.00 0.00 44.76 3.25
197 207 1.339151 CCCTTTGAGCCACTGGACTAC 60.339 57.143 0.00 0.00 0.00 2.73
198 208 0.984230 CCCTTTGAGCCACTGGACTA 59.016 55.000 0.00 0.00 0.00 2.59
199 209 1.763770 CCCTTTGAGCCACTGGACT 59.236 57.895 0.00 0.00 0.00 3.85
204 214 0.034670 GATGAGCCCTTTGAGCCACT 60.035 55.000 0.00 0.00 0.00 4.00
206 216 0.627451 ATGATGAGCCCTTTGAGCCA 59.373 50.000 0.00 0.00 0.00 4.75
207 217 1.316651 GATGATGAGCCCTTTGAGCC 58.683 55.000 0.00 0.00 0.00 4.70
224 234 3.103637 CGAAGGAGTCGGAGAGGAT 57.896 57.895 0.00 0.00 46.45 3.24
240 250 4.688419 GGTCGTCGCCGTTGTCGA 62.688 66.667 0.00 0.00 39.71 4.20
241 251 4.986587 TGGTCGTCGCCGTTGTCG 62.987 66.667 0.00 0.00 35.01 4.35
262 275 2.182030 GAGTCGTTGGAGGAGGCG 59.818 66.667 0.00 0.00 0.00 5.52
269 282 0.809385 GGATCGTCTGAGTCGTTGGA 59.191 55.000 0.00 0.00 0.00 3.53
270 283 0.811915 AGGATCGTCTGAGTCGTTGG 59.188 55.000 0.00 0.00 0.00 3.77
271 284 1.202200 GGAGGATCGTCTGAGTCGTTG 60.202 57.143 14.65 0.00 34.37 4.10
272 285 1.096416 GGAGGATCGTCTGAGTCGTT 58.904 55.000 14.65 0.00 34.37 3.85
275 288 0.741915 GGTGGAGGATCGTCTGAGTC 59.258 60.000 14.65 0.00 34.37 3.36
280 293 3.148279 GCCGGTGGAGGATCGTCT 61.148 66.667 14.65 0.00 34.37 4.18
281 294 4.222847 GGCCGGTGGAGGATCGTC 62.223 72.222 1.90 6.88 34.37 4.20
311 324 1.402259 CTTCTGGTCGATGACGTAGCT 59.598 52.381 0.00 0.00 40.69 3.32
316 329 1.095600 TCCTCTTCTGGTCGATGACG 58.904 55.000 0.00 0.00 41.26 4.35
317 330 3.516615 CTTTCCTCTTCTGGTCGATGAC 58.483 50.000 0.00 0.00 0.00 3.06
318 331 2.497675 CCTTTCCTCTTCTGGTCGATGA 59.502 50.000 0.00 0.00 0.00 2.92
320 333 1.834263 CCCTTTCCTCTTCTGGTCGAT 59.166 52.381 0.00 0.00 0.00 3.59
327 340 1.136329 TGCTGGCCCTTTCCTCTTCT 61.136 55.000 0.00 0.00 0.00 2.85
328 341 0.251341 TTGCTGGCCCTTTCCTCTTC 60.251 55.000 0.00 0.00 0.00 2.87
332 345 1.729267 TTCCTTGCTGGCCCTTTCCT 61.729 55.000 0.00 0.00 35.26 3.36
334 347 0.540597 ACTTCCTTGCTGGCCCTTTC 60.541 55.000 0.00 0.00 35.26 2.62
337 351 2.437897 CACTTCCTTGCTGGCCCT 59.562 61.111 0.00 0.00 35.26 5.19
342 356 3.305608 GGATTTTCACCACTTCCTTGCTG 60.306 47.826 0.00 0.00 0.00 4.41
343 357 2.893489 GGATTTTCACCACTTCCTTGCT 59.107 45.455 0.00 0.00 0.00 3.91
346 360 3.146847 GACGGATTTTCACCACTTCCTT 58.853 45.455 0.00 0.00 0.00 3.36
360 374 6.940298 TGAAATTAAAGTGGAGAAGACGGATT 59.060 34.615 0.00 0.00 0.00 3.01
440 456 0.450184 AATGCACATAAACGACGGCC 59.550 50.000 0.00 0.00 0.00 6.13
442 458 4.530094 ACATAATGCACATAAACGACGG 57.470 40.909 0.00 0.00 0.00 4.79
464 480 5.585820 TCTTTAAAAGACCGCCAAAGTTT 57.414 34.783 0.00 0.00 31.20 2.66
475 491 4.320870 TCACCACCGGATCTTTAAAAGAC 58.679 43.478 9.46 0.00 41.01 3.01
491 507 2.031157 CCGTTCACCAAAAGATCACCAC 60.031 50.000 0.00 0.00 0.00 4.16
598 626 3.948473 CCGTGTATCTCATATCCGATCCT 59.052 47.826 0.00 0.00 0.00 3.24
603 631 4.415735 CACATCCGTGTATCTCATATCCG 58.584 47.826 0.00 0.00 38.41 4.18
628 656 2.040412 GACCAGTCCTCAAATTGGGTCT 59.960 50.000 8.82 3.12 40.06 3.85
632 660 1.271379 ACCGACCAGTCCTCAAATTGG 60.271 52.381 0.00 0.00 36.76 3.16
670 715 2.648059 CGGAAATCTGGGCTCTCAAAT 58.352 47.619 0.00 0.00 0.00 2.32
682 727 4.329462 GAGAATCTACAGCCGGAAATCT 57.671 45.455 5.05 0.00 0.00 2.40
722 767 0.251354 TTTGGCTTTGGCTTTGCACA 59.749 45.000 0.00 0.00 38.73 4.57
751 796 4.997565 TGGCTCGAATGGAAAATCATTTC 58.002 39.130 0.00 0.00 43.46 2.17
755 800 2.368439 CCTGGCTCGAATGGAAAATCA 58.632 47.619 0.00 0.00 0.00 2.57
756 801 1.066152 GCCTGGCTCGAATGGAAAATC 59.934 52.381 12.43 0.00 0.00 2.17
757 802 1.106285 GCCTGGCTCGAATGGAAAAT 58.894 50.000 12.43 0.00 0.00 1.82
758 803 0.251121 TGCCTGGCTCGAATGGAAAA 60.251 50.000 21.03 0.00 0.00 2.29
759 804 0.960364 GTGCCTGGCTCGAATGGAAA 60.960 55.000 21.03 0.00 0.00 3.13
760 805 1.377202 GTGCCTGGCTCGAATGGAA 60.377 57.895 21.03 0.00 0.00 3.53
772 817 0.102120 TTTGTTTTCTGCCGTGCCTG 59.898 50.000 0.00 0.00 0.00 4.85
793 838 2.242043 CAAACATCTCACCTTTGCCCT 58.758 47.619 0.00 0.00 0.00 5.19
797 842 4.136796 TGAGACCAAACATCTCACCTTTG 58.863 43.478 0.59 0.00 46.01 2.77
941 988 1.214175 TCTGCCTGTTGTTCTTGGGAA 59.786 47.619 0.00 0.00 0.00 3.97
942 989 0.843309 TCTGCCTGTTGTTCTTGGGA 59.157 50.000 0.00 0.00 0.00 4.37
943 990 1.242076 CTCTGCCTGTTGTTCTTGGG 58.758 55.000 0.00 0.00 0.00 4.12
1022 1090 1.992277 GAGGAGGAGGAGCTTGGCA 60.992 63.158 0.00 0.00 0.00 4.92
1128 1199 2.624838 CTCTCTCTCTTCCTCCTCATGC 59.375 54.545 0.00 0.00 0.00 4.06
1134 1205 0.105709 CCCCCTCTCTCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1140 1211 0.264359 CCATCACCCCCTCTCTCTCT 59.736 60.000 0.00 0.00 0.00 3.10
1290 1361 1.202782 CCATTCTGATCAGGGCCAGAG 60.203 57.143 22.42 6.15 40.13 3.35
1320 1391 2.290768 ACAGATGAAGATGGCAGCAAGT 60.291 45.455 5.19 0.00 0.00 3.16
1321 1392 2.366533 ACAGATGAAGATGGCAGCAAG 58.633 47.619 5.19 0.00 0.00 4.01
1322 1393 2.502142 ACAGATGAAGATGGCAGCAA 57.498 45.000 5.19 0.00 0.00 3.91
1323 1394 2.502142 AACAGATGAAGATGGCAGCA 57.498 45.000 5.19 0.00 0.00 4.41
1335 1406 9.888878 GAACATATCACATGGAATTAACAGATG 57.111 33.333 0.00 0.00 0.00 2.90
1340 1411 8.686334 ACCAAGAACATATCACATGGAATTAAC 58.314 33.333 0.00 0.00 34.46 2.01
1341 1412 8.821686 ACCAAGAACATATCACATGGAATTAA 57.178 30.769 0.00 0.00 34.46 1.40
1365 1454 6.750039 GTCTGATCTGCTCTAAGTTGAACTAC 59.250 42.308 0.00 0.00 0.00 2.73
1373 1462 5.260424 TCTGAAGTCTGATCTGCTCTAAGT 58.740 41.667 0.00 0.00 0.00 2.24
1374 1463 5.833406 TCTGAAGTCTGATCTGCTCTAAG 57.167 43.478 0.00 0.00 0.00 2.18
1376 1465 5.468409 CGTATCTGAAGTCTGATCTGCTCTA 59.532 44.000 4.18 0.00 36.25 2.43
1381 1470 3.317711 AGGCGTATCTGAAGTCTGATCTG 59.682 47.826 4.18 0.00 36.25 2.90
1383 1472 4.314740 AAGGCGTATCTGAAGTCTGATC 57.685 45.455 4.18 0.00 36.25 2.92
1384 1473 4.160439 TGAAAGGCGTATCTGAAGTCTGAT 59.840 41.667 6.05 6.05 38.03 2.90
1387 1476 4.744795 ATGAAAGGCGTATCTGAAGTCT 57.255 40.909 0.00 0.00 0.00 3.24
1388 1477 6.926272 AGAATATGAAAGGCGTATCTGAAGTC 59.074 38.462 0.00 0.00 0.00 3.01
1389 1478 6.821388 AGAATATGAAAGGCGTATCTGAAGT 58.179 36.000 0.00 0.00 0.00 3.01
1390 1479 6.088749 CGAGAATATGAAAGGCGTATCTGAAG 59.911 42.308 0.00 0.00 0.00 3.02
1391 1480 5.920840 CGAGAATATGAAAGGCGTATCTGAA 59.079 40.000 0.00 0.00 0.00 3.02
1392 1481 5.009710 ACGAGAATATGAAAGGCGTATCTGA 59.990 40.000 0.00 0.00 0.00 3.27
1393 1482 5.117745 CACGAGAATATGAAAGGCGTATCTG 59.882 44.000 0.00 0.00 0.00 2.90
1394 1483 5.223382 CACGAGAATATGAAAGGCGTATCT 58.777 41.667 0.00 0.00 0.00 1.98
1395 1484 4.386049 CCACGAGAATATGAAAGGCGTATC 59.614 45.833 0.00 0.00 0.00 2.24
1396 1485 4.202223 ACCACGAGAATATGAAAGGCGTAT 60.202 41.667 0.00 0.00 0.00 3.06
1397 1486 3.131577 ACCACGAGAATATGAAAGGCGTA 59.868 43.478 0.00 0.00 0.00 4.42
1398 1487 2.093658 ACCACGAGAATATGAAAGGCGT 60.094 45.455 0.00 0.00 0.00 5.68
1399 1488 2.285220 CACCACGAGAATATGAAAGGCG 59.715 50.000 0.00 0.00 0.00 5.52
1400 1489 2.032178 GCACCACGAGAATATGAAAGGC 59.968 50.000 0.00 0.00 0.00 4.35
1401 1490 3.270027 TGCACCACGAGAATATGAAAGG 58.730 45.455 0.00 0.00 0.00 3.11
1415 1504 1.665679 CATCCTTACGACATGCACCAC 59.334 52.381 0.00 0.00 0.00 4.16
1427 1516 9.614792 ACCTATCTGAACAAATTACATCCTTAC 57.385 33.333 0.00 0.00 0.00 2.34
1477 1566 0.817634 CGTGGCCACCAGACTTTTCA 60.818 55.000 29.95 0.00 32.34 2.69
1575 1664 9.196552 ACTATGTTTTGAAAGCTAAATTTCTGC 57.803 29.630 0.00 0.64 39.45 4.26
1584 1673 6.989759 TGTGACTGACTATGTTTTGAAAGCTA 59.010 34.615 0.00 0.00 0.00 3.32
1593 1682 6.258727 CAGAAAGTGTGTGACTGACTATGTTT 59.741 38.462 0.00 0.00 34.02 2.83
1621 1710 7.805071 GTGTCTAAATCAGAACACATCTTTTGG 59.195 37.037 0.00 0.00 35.73 3.28
1627 1716 5.934625 ACTGGTGTCTAAATCAGAACACATC 59.065 40.000 6.79 0.00 37.19 3.06
1628 1717 5.702670 CACTGGTGTCTAAATCAGAACACAT 59.297 40.000 6.79 0.00 37.19 3.21
1629 1718 5.056480 CACTGGTGTCTAAATCAGAACACA 58.944 41.667 6.79 0.00 37.19 3.72
1716 1805 1.401670 GGGCGCTACGATGACAGATAG 60.402 57.143 7.64 0.00 0.00 2.08
1765 1854 5.649782 ATATGCCAGGAAAGAACAGTTTG 57.350 39.130 0.00 0.00 0.00 2.93
1790 1879 2.232399 TGAGACAGTTACCACGCTACA 58.768 47.619 0.00 0.00 0.00 2.74
1943 2036 1.526686 CTGCTGTGGCTGTGGACAA 60.527 57.895 0.00 0.00 39.59 3.18
1960 2053 6.320926 GGTAGTAAGTTCTTCCGGAATACTCT 59.679 42.308 23.98 20.32 33.96 3.24
1966 2059 4.154942 ACTGGTAGTAAGTTCTTCCGGAA 58.845 43.478 17.73 17.73 35.65 4.30
2005 2098 4.240888 CCGTAGCTGTGATGAAGATATGG 58.759 47.826 0.00 0.00 36.61 2.74
2008 2101 3.371102 GCCGTAGCTGTGATGAAGATA 57.629 47.619 0.00 0.00 35.50 1.98
2059 2152 3.974401 CAGTTATTTCACCGTTTGCAGTG 59.026 43.478 0.00 0.00 35.24 3.66
2101 2194 7.912056 TGAGAAAAGTGACCATAGAAATCAG 57.088 36.000 0.00 0.00 0.00 2.90
2131 2224 7.011389 GCCCTGCAAAAATACATAATTCCTTTC 59.989 37.037 0.00 0.00 0.00 2.62
2168 2262 3.950395 GCTTCAGATCCTTGTAATGCCTT 59.050 43.478 0.00 0.00 0.00 4.35
2258 2352 7.147828 CGGCATCCCTCATCTTCTCTAATAATA 60.148 40.741 0.00 0.00 0.00 0.98
2271 2365 2.550830 ACATAACGGCATCCCTCATC 57.449 50.000 0.00 0.00 0.00 2.92
2331 2425 9.499585 CATACAATGTTCAATTTCTTCAGCTAG 57.500 33.333 0.00 0.00 0.00 3.42
2381 2475 4.381411 GCGCCTTTAGGTCTGAATTCTAT 58.619 43.478 7.05 0.00 37.57 1.98
2382 2476 3.431766 GGCGCCTTTAGGTCTGAATTCTA 60.432 47.826 22.15 0.00 37.57 2.10
2470 2565 6.015010 AGTCATGGATTAGACATGTAGGCTAC 60.015 42.308 17.76 17.76 44.57 3.58
2489 2584 2.174363 TCAGTTCACTGCCAGTCATG 57.826 50.000 0.00 0.00 43.46 3.07
2500 2600 8.841300 TCTACATGTATCAGTCTATCAGTTCAC 58.159 37.037 5.91 0.00 0.00 3.18
2568 2676 5.341993 CGTCATTCTTTCGCTGATCTAGATC 59.658 44.000 23.47 23.47 38.29 2.75
2580 2688 0.179189 GCAAGGGCGTCATTCTTTCG 60.179 55.000 0.00 0.00 0.00 3.46
2591 2699 2.281761 ACAAGTCAGGCAAGGGCG 60.282 61.111 0.00 0.00 42.47 6.13
2614 2722 3.136763 CACACTCATACTCCATGATGCC 58.863 50.000 0.00 0.00 42.82 4.40
2617 2725 6.892485 TGAAATCACACTCATACTCCATGAT 58.108 36.000 0.00 0.00 42.82 2.45
2650 2758 0.609406 ACTGGAGCTCTAGTGACGCA 60.609 55.000 29.64 8.30 36.28 5.24
2670 2778 1.886886 TTAGGTGTTTCAGTTCGGCC 58.113 50.000 0.00 0.00 0.00 6.13
2671 2779 5.465724 CCTATATTAGGTGTTTCAGTTCGGC 59.534 44.000 0.00 0.00 41.18 5.54
2696 2804 4.202090 TGTCACATATACTCAGCTGCTCAG 60.202 45.833 9.47 0.00 0.00 3.35
2697 2805 3.701040 TGTCACATATACTCAGCTGCTCA 59.299 43.478 9.47 0.00 0.00 4.26
2698 2806 4.297510 CTGTCACATATACTCAGCTGCTC 58.702 47.826 9.47 0.00 0.00 4.26
2699 2807 3.492309 GCTGTCACATATACTCAGCTGCT 60.492 47.826 9.47 0.00 45.14 4.24
2700 2808 2.799412 GCTGTCACATATACTCAGCTGC 59.201 50.000 9.47 0.00 45.14 5.25
2704 2812 6.640092 CACTACATGCTGTCACATATACTCAG 59.360 42.308 0.00 0.00 0.00 3.35
2705 2813 6.507023 CACTACATGCTGTCACATATACTCA 58.493 40.000 0.00 0.00 0.00 3.41
2706 2814 6.999956 CACTACATGCTGTCACATATACTC 57.000 41.667 0.00 0.00 0.00 2.59
2721 2829 7.584108 TGAACTGTTCTTATTTGCACTACATG 58.416 34.615 20.18 0.00 0.00 3.21
2761 2870 9.717942 CCTAGCAAGTTAGCATATCTTAGAATT 57.282 33.333 0.00 0.00 36.85 2.17
2762 2871 8.317679 CCCTAGCAAGTTAGCATATCTTAGAAT 58.682 37.037 0.00 0.00 36.85 2.40
2779 2888 4.082081 TGCATTTCATCAAACCCTAGCAAG 60.082 41.667 0.00 0.00 0.00 4.01
2780 2889 3.831333 TGCATTTCATCAAACCCTAGCAA 59.169 39.130 0.00 0.00 0.00 3.91
2781 2890 3.429492 TGCATTTCATCAAACCCTAGCA 58.571 40.909 0.00 0.00 0.00 3.49
2782 2891 3.736126 GCTGCATTTCATCAAACCCTAGC 60.736 47.826 0.00 0.00 0.00 3.42
2783 2892 3.444742 TGCTGCATTTCATCAAACCCTAG 59.555 43.478 0.00 0.00 0.00 3.02
2784 2893 3.429492 TGCTGCATTTCATCAAACCCTA 58.571 40.909 0.00 0.00 0.00 3.53
2785 2894 2.250031 TGCTGCATTTCATCAAACCCT 58.750 42.857 0.00 0.00 0.00 4.34
2786 2895 2.747396 TGCTGCATTTCATCAAACCC 57.253 45.000 0.00 0.00 0.00 4.11
2796 2905 4.210724 AGCCATTTGTATTGCTGCATTT 57.789 36.364 1.84 0.00 31.98 2.32
2800 2909 3.699067 CTGTAGCCATTTGTATTGCTGC 58.301 45.455 0.00 0.00 36.22 5.25
2801 2910 3.129113 TGCTGTAGCCATTTGTATTGCTG 59.871 43.478 0.80 0.00 41.18 4.41
2822 2931 5.230182 TGCTCTAGCCGTTTGTATATCATG 58.770 41.667 0.00 0.00 41.18 3.07
2830 2939 2.698855 ATCATGCTCTAGCCGTTTGT 57.301 45.000 0.00 0.00 41.18 2.83
2831 2940 6.159293 TCTTATATCATGCTCTAGCCGTTTG 58.841 40.000 0.00 0.00 41.18 2.93
2832 2941 6.346477 TCTTATATCATGCTCTAGCCGTTT 57.654 37.500 0.00 0.00 41.18 3.60
2833 2942 5.623368 GCTCTTATATCATGCTCTAGCCGTT 60.623 44.000 0.00 0.00 41.18 4.44
2834 2943 4.142271 GCTCTTATATCATGCTCTAGCCGT 60.142 45.833 0.00 0.00 41.18 5.68
2835 2944 4.142293 TGCTCTTATATCATGCTCTAGCCG 60.142 45.833 0.00 0.00 41.18 5.52
2836 2945 5.105392 ACTGCTCTTATATCATGCTCTAGCC 60.105 44.000 0.00 0.00 41.18 3.93
2837 2946 5.964758 ACTGCTCTTATATCATGCTCTAGC 58.035 41.667 0.00 0.00 42.50 3.42
2838 2947 8.739039 AGTTACTGCTCTTATATCATGCTCTAG 58.261 37.037 0.00 0.00 0.00 2.43
2839 2948 8.642935 AGTTACTGCTCTTATATCATGCTCTA 57.357 34.615 0.00 0.00 0.00 2.43
2840 2949 7.537596 AGTTACTGCTCTTATATCATGCTCT 57.462 36.000 0.00 0.00 0.00 4.09
2933 3048 8.383318 GCTTAATGCTGGTTCTTCTATGATTA 57.617 34.615 0.00 0.00 38.95 1.75
2935 3050 6.874288 GCTTAATGCTGGTTCTTCTATGAT 57.126 37.500 0.00 0.00 38.95 2.45
2956 3071 6.881065 TCATAATGCTTTCAACAACTCTAGCT 59.119 34.615 0.00 0.00 0.00 3.32
2980 3095 8.139989 AGCTTGCCTGTGAATATTGATTTAATC 58.860 33.333 0.00 0.00 0.00 1.75
2989 3104 5.500234 TGTTCTAGCTTGCCTGTGAATATT 58.500 37.500 0.00 0.00 0.00 1.28
3044 3161 8.061304 AGAGCAATTTTTAAGATATTGGGAGGA 58.939 33.333 0.00 0.00 31.54 3.71


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

AutoCloner maintained by Alex Coulton.