Multiple sequence alignment - TraesCS3A01G446600

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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 TraesCS3A01G446600 chr3A 100.000 6591 0 0 1 6591 686833695 686840285 0.000000e+00 12172.0
1 TraesCS3A01G446600 chr3A 85.254 1926 195 40 4191 6102 686853526 686855376 0.000000e+00 1901.0
2 TraesCS3A01G446600 chr3A 85.637 738 91 11 3439 4173 686852746 686853471 0.000000e+00 761.0
3 TraesCS3A01G446600 chr3A 83.418 591 86 8 2545 3130 686851925 686852508 7.520000e-149 538.0
4 TraesCS3A01G446600 chr3A 84.547 453 56 10 1919 2361 686850589 686851037 2.820000e-118 436.0
5 TraesCS3A01G446600 chr3A 85.269 353 41 6 1559 1904 686850069 686850417 2.920000e-93 353.0
6 TraesCS3A01G446600 chr3D 95.105 3698 145 19 2410 6099 549624950 549628619 0.000000e+00 5794.0
7 TraesCS3A01G446600 chr3D 88.006 1976 122 56 1 1916 549622430 549624350 0.000000e+00 2230.0
8 TraesCS3A01G446600 chr3D 84.693 2084 218 47 4191 6233 549639709 549641732 0.000000e+00 1988.0
9 TraesCS3A01G446600 chr3D 84.844 739 95 11 3439 4173 549638933 549639658 0.000000e+00 728.0
10 TraesCS3A01G446600 chr3D 92.274 453 20 8 1923 2362 549624499 549624949 4.340000e-176 628.0
11 TraesCS3A01G446600 chr3D 83.986 587 83 8 2545 3128 549638119 549638697 2.690000e-153 553.0
12 TraesCS3A01G446600 chr3D 85.207 507 48 11 6104 6591 549628666 549629164 4.590000e-136 496.0
13 TraesCS3A01G446600 chr3D 83.260 454 61 13 1919 2361 549636778 549637227 2.860000e-108 403.0
14 TraesCS3A01G446600 chr3D 88.699 292 33 0 1613 1904 549636310 549636601 2.260000e-94 357.0
15 TraesCS3A01G446600 chr3B 94.331 3422 169 13 2410 5822 729206331 729209736 0.000000e+00 5221.0
16 TraesCS3A01G446600 chr3B 86.704 1948 137 63 1 1916 729203787 729205644 0.000000e+00 2050.0
17 TraesCS3A01G446600 chr3B 87.016 1602 157 26 4191 5778 729385929 729387493 0.000000e+00 1759.0
18 TraesCS3A01G446600 chr3B 87.398 738 79 10 3439 4173 729385151 729385877 0.000000e+00 835.0
19 TraesCS3A01G446600 chr3B 84.076 628 72 19 2507 3130 729384315 729384918 1.230000e-161 580.0
20 TraesCS3A01G446600 chr3B 95.225 356 15 1 2007 2362 729205976 729206329 4.460000e-156 562.0
21 TraesCS3A01G446600 chr3B 85.902 532 42 6 5807 6307 729209926 729210455 2.700000e-148 536.0
22 TraesCS3A01G446600 chr3B 83.850 452 57 13 1919 2360 729382722 729383167 3.680000e-112 416.0
23 TraesCS3A01G446600 chr3B 85.552 353 44 4 1559 1904 729382193 729382545 4.860000e-96 363.0
24 TraesCS3A01G446600 chr3B 87.732 269 14 8 6336 6591 729210454 729210716 5.000000e-76 296.0
25 TraesCS3A01G446600 chr3B 86.026 229 27 5 5777 6001 729387587 729387814 2.370000e-59 241.0
26 TraesCS3A01G446600 chr7D 83.213 417 38 15 6016 6404 113585902 113586314 2.920000e-93 353.0
27 TraesCS3A01G446600 chr7D 100.000 49 0 0 2363 2411 6946568 6946616 2.530000e-14 91.6
28 TraesCS3A01G446600 chr7D 100.000 49 0 0 2363 2411 44737507 44737555 2.530000e-14 91.6
29 TraesCS3A01G446600 chr7A 81.102 381 34 15 6016 6374 619308039 619308403 3.030000e-68 270.0
30 TraesCS3A01G446600 chr7B 100.000 49 0 0 2363 2411 460330464 460330512 2.530000e-14 91.6
31 TraesCS3A01G446600 chr6D 100.000 49 0 0 2363 2411 108495700 108495748 2.530000e-14 91.6
32 TraesCS3A01G446600 chr6D 100.000 49 0 0 2363 2411 458913852 458913804 2.530000e-14 91.6
33 TraesCS3A01G446600 chr6A 100.000 49 0 0 2363 2411 52030697 52030649 2.530000e-14 91.6
34 TraesCS3A01G446600 chr4B 100.000 49 0 0 2363 2411 209120939 209120987 2.530000e-14 91.6
35 TraesCS3A01G446600 chr2D 100.000 49 0 0 2363 2411 18026308 18026356 2.530000e-14 91.6
36 TraesCS3A01G446600 chr2D 100.000 49 0 0 2363 2411 648539948 648539900 2.530000e-14 91.6


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 TraesCS3A01G446600 chr3A 686833695 686840285 6590 False 12172.0 12172 100.0000 1 6591 1 chr3A.!!$F1 6590
1 TraesCS3A01G446600 chr3A 686850069 686855376 5307 False 797.8 1901 84.8250 1559 6102 5 chr3A.!!$F2 4543
2 TraesCS3A01G446600 chr3D 549622430 549629164 6734 False 2287.0 5794 90.1480 1 6591 4 chr3D.!!$F1 6590
3 TraesCS3A01G446600 chr3D 549636310 549641732 5422 False 805.8 1988 85.0964 1613 6233 5 chr3D.!!$F2 4620
4 TraesCS3A01G446600 chr3B 729203787 729210716 6929 False 1733.0 5221 89.9788 1 6591 5 chr3B.!!$F1 6590
5 TraesCS3A01G446600 chr3B 729382193 729387814 5621 False 699.0 1759 85.6530 1559 6001 6 chr3B.!!$F2 4442

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
825 868 0.036765 TGGTTGCACGAGGATACCAC 60.037 55.0 0.00 0.00 34.13 4.16 F
826 869 0.036765 GGTTGCACGAGGATACCACA 60.037 55.0 0.00 0.00 37.17 4.17 F
1380 1450 0.320421 TTGTCAAGGACGGCTGCTAC 60.320 55.0 0.00 0.00 34.95 3.58 F
2376 2728 1.378531 TCTCCCGAATTTCATTGCGG 58.621 50.0 0.00 0.00 43.20 5.69 F
2980 4362 1.110442 TCTTAATTGCCGGCATTGGG 58.890 50.0 33.25 18.98 0.00 4.12 F
3402 4790 0.751643 GTGTGCACAGAAAGGGTGGT 60.752 55.0 22.40 0.00 36.76 4.16 F
4287 5720 2.414559 GGCAAGTAGTACGTTACTCGCA 60.415 50.0 11.38 0.00 44.19 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2743 0.178801 ACCCCCTTTTCCTCCCTCAT 60.179 55.000 0.00 0.00 0.0 2.90 R
2392 2744 0.845102 GACCCCCTTTTCCTCCCTCA 60.845 60.000 0.00 0.00 0.0 3.86 R
2393 2745 0.845102 TGACCCCCTTTTCCTCCCTC 60.845 60.000 0.00 0.00 0.0 4.30 R
3384 4772 0.033601 AACCACCCTTTCTGTGCACA 60.034 50.000 20.37 20.37 32.3 4.57 R
4460 5898 1.218450 TGGGTCATGATGCCATTGGAT 59.782 47.619 6.95 0.00 0.0 3.41 R
4894 6332 1.781025 TTCGCCTTGTTGCCAACTCG 61.781 55.000 9.30 7.32 0.0 4.18 R
5672 7115 0.034337 ACTGTTTACGCGGTCACCAT 59.966 50.000 12.47 0.00 0.0 3.55 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 3.928779 TCCGCCATGGAGGATCGC 61.929 66.667 31.29 5.43 43.74 4.58
34 35 4.240103 CCGCCATGGAGGATCGCA 62.240 66.667 29.31 0.00 42.00 5.10
35 36 2.031616 CGCCATGGAGGATCGCAT 59.968 61.111 18.40 0.00 41.22 4.73
36 37 2.031516 CGCCATGGAGGATCGCATC 61.032 63.158 18.40 0.00 41.22 3.91
71 79 0.675837 GGAGTTGAAACTACCGGGCC 60.676 60.000 6.32 0.00 39.88 5.80
72 80 0.323957 GAGTTGAAACTACCGGGCCT 59.676 55.000 6.32 0.00 39.88 5.19
210 230 0.103208 GTCCGATGGCGAGATGACTT 59.897 55.000 0.00 0.00 40.82 3.01
233 253 3.429141 CGTGGCTGGCTTCTGCTG 61.429 66.667 2.00 0.00 39.59 4.41
234 254 2.033141 GTGGCTGGCTTCTGCTGA 59.967 61.111 2.00 0.00 39.59 4.26
235 255 2.039405 GTGGCTGGCTTCTGCTGAG 61.039 63.158 2.00 0.00 39.59 3.35
236 256 2.219164 TGGCTGGCTTCTGCTGAGA 61.219 57.895 2.00 0.00 39.59 3.27
237 257 1.744741 GGCTGGCTTCTGCTGAGAC 60.745 63.158 0.00 0.00 39.59 3.36
238 258 2.099431 GCTGGCTTCTGCTGAGACG 61.099 63.158 0.00 0.00 39.59 4.18
239 259 1.291588 CTGGCTTCTGCTGAGACGT 59.708 57.895 0.00 0.00 39.59 4.34
240 260 0.735632 CTGGCTTCTGCTGAGACGTC 60.736 60.000 7.70 7.70 39.59 4.34
241 261 1.803519 GGCTTCTGCTGAGACGTCG 60.804 63.158 10.46 0.00 39.59 5.12
242 262 2.440569 GCTTCTGCTGAGACGTCGC 61.441 63.158 12.80 12.80 36.03 5.19
243 263 1.081175 CTTCTGCTGAGACGTCGCA 60.081 57.895 20.95 20.95 33.27 5.10
244 264 1.069924 CTTCTGCTGAGACGTCGCAG 61.070 60.000 35.85 35.85 44.65 5.18
248 268 4.803426 CTGAGACGTCGCAGCCCC 62.803 72.222 31.55 8.05 37.00 5.80
273 299 2.358898 CTCCTAAATGGGTCGCCAAATG 59.641 50.000 0.00 0.00 36.20 2.32
324 351 0.856641 GCAGTGCAAGCATGTTGTTG 59.143 50.000 11.09 0.00 0.00 3.33
329 356 1.479730 TGCAAGCATGTTGTTGGAACA 59.520 42.857 0.00 0.00 37.08 3.18
330 357 2.129607 GCAAGCATGTTGTTGGAACAG 58.870 47.619 0.00 0.00 42.39 3.16
332 359 3.553508 GCAAGCATGTTGTTGGAACAGAT 60.554 43.478 0.00 0.00 42.39 2.90
333 360 3.928727 AGCATGTTGTTGGAACAGATG 57.071 42.857 0.00 8.32 42.39 2.90
334 361 2.029649 AGCATGTTGTTGGAACAGATGC 60.030 45.455 20.56 20.56 46.37 3.91
335 362 2.029649 GCATGTTGTTGGAACAGATGCT 60.030 45.455 20.71 0.00 44.64 3.79
336 363 3.553508 GCATGTTGTTGGAACAGATGCTT 60.554 43.478 20.71 0.00 44.64 3.91
337 364 3.988379 TGTTGTTGGAACAGATGCTTC 57.012 42.857 0.00 0.00 42.39 3.86
338 365 3.554934 TGTTGTTGGAACAGATGCTTCT 58.445 40.909 0.00 0.00 42.39 2.85
341 368 4.836125 TGTTGGAACAGATGCTTCTTTC 57.164 40.909 0.00 7.46 42.39 2.62
342 369 4.464008 TGTTGGAACAGATGCTTCTTTCT 58.536 39.130 16.53 1.58 42.39 2.52
343 370 4.889409 TGTTGGAACAGATGCTTCTTTCTT 59.111 37.500 16.53 4.90 42.39 2.52
406 439 6.161855 TCAGTACAGAGTTCAATGAACAGT 57.838 37.500 25.63 21.21 44.11 3.55
407 440 6.582636 TCAGTACAGAGTTCAATGAACAGTT 58.417 36.000 25.63 7.44 44.11 3.16
408 441 7.722363 TCAGTACAGAGTTCAATGAACAGTTA 58.278 34.615 25.63 9.96 44.11 2.24
409 442 8.201464 TCAGTACAGAGTTCAATGAACAGTTAA 58.799 33.333 25.63 7.49 44.11 2.01
410 443 8.826710 CAGTACAGAGTTCAATGAACAGTTAAA 58.173 33.333 25.63 6.04 44.11 1.52
411 444 9.561069 AGTACAGAGTTCAATGAACAGTTAAAT 57.439 29.630 25.63 5.27 44.11 1.40
474 507 6.541278 AGACATGGTGATTACTTCATGATGTG 59.459 38.462 21.20 6.87 38.32 3.21
478 511 6.355747 TGGTGATTACTTCATGATGTGCATA 58.644 36.000 21.20 7.15 36.54 3.14
480 513 7.503230 TGGTGATTACTTCATGATGTGCATATT 59.497 33.333 21.20 1.52 36.54 1.28
481 514 8.019669 GGTGATTACTTCATGATGTGCATATTC 58.980 37.037 21.20 9.65 36.54 1.75
482 515 8.562052 GTGATTACTTCATGATGTGCATATTCA 58.438 33.333 21.20 11.59 36.54 2.57
483 516 9.122779 TGATTACTTCATGATGTGCATATTCAA 57.877 29.630 21.20 7.83 34.82 2.69
484 517 9.390795 GATTACTTCATGATGTGCATATTCAAC 57.609 33.333 21.20 1.26 34.82 3.18
492 525 1.093972 TGCATATTCAACAGTGCCCG 58.906 50.000 0.00 0.00 36.79 6.13
541 574 6.355397 ACATTGAGATGATGCTAGAAAACG 57.645 37.500 0.00 0.00 36.73 3.60
543 576 6.765036 ACATTGAGATGATGCTAGAAAACGAT 59.235 34.615 0.00 0.00 36.73 3.73
544 577 6.834959 TTGAGATGATGCTAGAAAACGATC 57.165 37.500 0.00 0.00 0.00 3.69
546 579 6.577103 TGAGATGATGCTAGAAAACGATCTT 58.423 36.000 0.00 0.00 0.00 2.40
547 580 6.699204 TGAGATGATGCTAGAAAACGATCTTC 59.301 38.462 0.00 0.00 0.00 2.87
549 582 7.271511 AGATGATGCTAGAAAACGATCTTCTT 58.728 34.615 0.00 0.00 34.90 2.52
550 583 7.768120 AGATGATGCTAGAAAACGATCTTCTTT 59.232 33.333 0.00 0.00 34.90 2.52
553 586 6.712241 TGCTAGAAAACGATCTTCTTTCAG 57.288 37.500 0.00 4.57 34.90 3.02
560 593 6.677781 AAACGATCTTCTTTCAGTTGTCAA 57.322 33.333 0.00 0.00 0.00 3.18
592 625 5.470098 GCAGAGATAAACTGGAACTGAAACA 59.530 40.000 0.00 0.00 36.09 2.83
619 659 0.790814 GCACTTACGCTCACAAGTCC 59.209 55.000 0.00 0.00 32.72 3.85
633 673 0.398318 AAGTCCCAGGTGACAAGAGC 59.602 55.000 9.90 0.00 37.73 4.09
634 674 0.472734 AGTCCCAGGTGACAAGAGCT 60.473 55.000 9.90 0.00 37.73 4.09
692 732 2.092914 CCACCTTCCCTGGTTAGCTTAG 60.093 54.545 0.00 0.00 38.45 2.18
693 733 1.560146 ACCTTCCCTGGTTAGCTTAGC 59.440 52.381 0.00 0.00 36.89 3.09
694 734 1.134068 CCTTCCCTGGTTAGCTTAGCC 60.134 57.143 0.00 0.00 0.00 3.93
717 757 4.093998 CGTTCAAGATCACAAGATTCCCAG 59.906 45.833 0.00 0.00 33.72 4.45
749 789 3.063084 GACGGCTCCGGTGAGACT 61.063 66.667 13.31 0.00 45.19 3.24
821 864 1.338674 CCTGTTGGTTGCACGAGGATA 60.339 52.381 0.00 0.00 0.00 2.59
825 868 0.036765 TGGTTGCACGAGGATACCAC 60.037 55.000 0.00 0.00 34.13 4.16
826 869 0.036765 GGTTGCACGAGGATACCACA 60.037 55.000 0.00 0.00 37.17 4.17
827 870 1.406887 GGTTGCACGAGGATACCACAT 60.407 52.381 0.00 0.00 37.17 3.21
828 871 2.356135 GTTGCACGAGGATACCACATT 58.644 47.619 0.00 0.00 37.17 2.71
832 875 3.386402 TGCACGAGGATACCACATTCATA 59.614 43.478 0.00 0.00 37.17 2.15
842 885 6.297010 GGATACCACATTCATACATACCCCAT 60.297 42.308 0.00 0.00 0.00 4.00
892 947 7.307042 GGTTTACAGAGAAAAGTAACGAACCTC 60.307 40.741 0.00 0.00 31.02 3.85
908 964 1.277580 CCTCTTGTCATCCTGGGCCT 61.278 60.000 4.53 0.00 0.00 5.19
946 1002 9.586435 GCCTATAAAAGCAAGTCATTGTTAAAT 57.414 29.630 0.00 0.00 38.76 1.40
952 1008 9.476202 AAAAGCAAGTCATTGTTAAATAAGACC 57.524 29.630 0.00 0.00 38.76 3.85
956 1012 7.060633 GCAAGTCATTGTTAAATAAGACCAACG 59.939 37.037 0.00 0.00 38.76 4.10
998 1058 4.078537 AGAGATCATCATCGTACCTCCAG 58.921 47.826 0.00 0.00 33.75 3.86
1020 1080 1.069935 GGCCGAGCCTCTGATAACC 59.930 63.158 7.58 0.00 46.69 2.85
1224 1284 6.017440 TCGGTTCGACAGAAATCTTCATTTTT 60.017 34.615 0.00 0.00 38.23 1.94
1254 1316 1.999648 AGCAAGGGAACTGCATCAAA 58.000 45.000 0.00 0.00 42.68 2.69
1256 1318 2.699846 AGCAAGGGAACTGCATCAAAAA 59.300 40.909 0.00 0.00 42.68 1.94
1282 1344 3.326588 CCGATTCCTGTTATGATGGGGTA 59.673 47.826 0.00 0.00 0.00 3.69
1294 1364 4.487714 TGATGGGGTACTTTCTCATGAC 57.512 45.455 0.00 0.00 0.00 3.06
1295 1365 4.104086 TGATGGGGTACTTTCTCATGACT 58.896 43.478 0.00 0.00 0.00 3.41
1296 1366 3.981071 TGGGGTACTTTCTCATGACTG 57.019 47.619 0.00 0.00 0.00 3.51
1297 1367 2.027192 TGGGGTACTTTCTCATGACTGC 60.027 50.000 0.00 0.00 0.00 4.40
1298 1368 2.027192 GGGGTACTTTCTCATGACTGCA 60.027 50.000 0.00 0.00 0.00 4.41
1303 1373 4.574599 ACTTTCTCATGACTGCAAAACC 57.425 40.909 0.00 0.00 0.00 3.27
1306 1376 2.507484 TCTCATGACTGCAAAACCAGG 58.493 47.619 0.00 0.00 37.16 4.45
1310 1380 3.896888 TCATGACTGCAAAACCAGGAATT 59.103 39.130 0.00 0.00 37.16 2.17
1311 1381 4.344679 TCATGACTGCAAAACCAGGAATTT 59.655 37.500 0.00 0.00 37.16 1.82
1371 1441 2.423538 ACAGCACAGTTTTGTCAAGGAC 59.576 45.455 0.00 0.00 34.62 3.85
1380 1450 0.320421 TTGTCAAGGACGGCTGCTAC 60.320 55.000 0.00 0.00 34.95 3.58
1424 1494 5.430886 TGTCAATCCATCATGGTAGACTTG 58.569 41.667 19.50 11.02 39.03 3.16
1509 1583 9.086336 CAAACAACCCAACATATTAATTAGCTG 57.914 33.333 0.00 0.00 0.00 4.24
1601 1677 9.229784 GTGAATGTAATATTTGCAATCTGACTG 57.770 33.333 0.00 0.00 0.00 3.51
1610 1686 3.904571 TGCAATCTGACTGTGATTTTGC 58.095 40.909 7.14 7.14 32.47 3.68
1818 1900 6.319658 TGCTTCTCCTTCCATTGATGAAATAC 59.680 38.462 0.00 0.00 0.00 1.89
1821 1903 5.824624 TCTCCTTCCATTGATGAAATACTGC 59.175 40.000 0.00 0.00 0.00 4.40
1869 1951 3.062042 CGGCGATGGTAAGTAAATACCC 58.938 50.000 0.00 0.00 43.97 3.69
1884 1966 8.024145 AGTAAATACCCTCCACTTATCTTCTG 57.976 38.462 0.00 0.00 0.00 3.02
1889 1971 3.519510 CCCTCCACTTATCTTCTGGACAA 59.480 47.826 0.00 0.00 30.61 3.18
1904 1986 9.349713 TCTTCTGGACAAAACTTGTATGTTTAT 57.650 29.630 0.00 0.00 45.52 1.40
1939 2188 8.583810 TTGTATGTTTACAGAGTACTGACAAC 57.416 34.615 0.00 0.00 46.03 3.32
1950 2199 7.450634 ACAGAGTACTGACAACCATTAGAAGTA 59.549 37.037 0.00 0.00 46.03 2.24
1987 2237 8.980143 GCATTAAGCACTTAGTTCCATAAAAA 57.020 30.769 0.00 0.00 44.79 1.94
2014 2363 8.472413 AGAAAATCCAAAATATGTGAGACCATG 58.528 33.333 0.00 0.00 0.00 3.66
2016 2365 8.821686 AAATCCAAAATATGTGAGACCATGTA 57.178 30.769 0.00 0.00 0.00 2.29
2017 2366 8.821686 AATCCAAAATATGTGAGACCATGTAA 57.178 30.769 0.00 0.00 0.00 2.41
2055 2407 7.857734 TTTGTTCAAGTGAGAGTTTGTCATA 57.142 32.000 0.00 0.00 0.00 2.15
2313 2665 1.463444 GTTATTGGTGACGGTGTGCTC 59.537 52.381 0.00 0.00 0.00 4.26
2363 2715 4.392921 TCTTTCTTAAGCTCATCTCCCG 57.607 45.455 0.00 0.00 0.00 5.14
2364 2716 4.023980 TCTTTCTTAAGCTCATCTCCCGA 58.976 43.478 0.00 0.00 0.00 5.14
2365 2717 4.466370 TCTTTCTTAAGCTCATCTCCCGAA 59.534 41.667 0.00 0.00 0.00 4.30
2366 2718 5.129485 TCTTTCTTAAGCTCATCTCCCGAAT 59.871 40.000 0.00 0.00 0.00 3.34
2367 2719 5.359194 TTCTTAAGCTCATCTCCCGAATT 57.641 39.130 0.00 0.00 0.00 2.17
2369 2721 5.360591 TCTTAAGCTCATCTCCCGAATTTC 58.639 41.667 0.00 0.00 0.00 2.17
2370 2722 3.634397 AAGCTCATCTCCCGAATTTCA 57.366 42.857 0.00 0.00 0.00 2.69
2371 2723 3.853355 AGCTCATCTCCCGAATTTCAT 57.147 42.857 0.00 0.00 0.00 2.57
2373 2725 3.881688 AGCTCATCTCCCGAATTTCATTG 59.118 43.478 0.00 0.00 0.00 2.82
2375 2727 2.613595 TCATCTCCCGAATTTCATTGCG 59.386 45.455 0.00 0.00 0.00 4.85
2376 2728 1.378531 TCTCCCGAATTTCATTGCGG 58.621 50.000 0.00 0.00 43.20 5.69
2380 2732 2.645730 CCGAATTTCATTGCGGGAAA 57.354 45.000 0.00 0.61 40.08 3.13
2381 2733 3.163630 CCGAATTTCATTGCGGGAAAT 57.836 42.857 0.00 4.72 44.52 2.17
2390 2742 5.514274 TCATTGCGGGAAATTAGGATTTC 57.486 39.130 3.83 3.83 46.75 2.17
2400 2752 6.890979 GAAATTAGGATTTCATGAGGGAGG 57.109 41.667 0.00 0.00 46.71 4.30
2405 2974 4.864726 AGGATTTCATGAGGGAGGAAAAG 58.135 43.478 0.00 0.00 37.85 2.27
2408 2977 1.298953 TCATGAGGGAGGAAAAGGGG 58.701 55.000 0.00 0.00 0.00 4.79
2634 4007 8.413229 ACACCCAATTTGCAGTGTAATATATTC 58.587 33.333 17.04 0.00 41.48 1.75
2666 4045 5.473162 TGATTGCTTTCAGCTTAGCTAACAA 59.527 36.000 6.35 7.61 42.97 2.83
2752 4133 5.588958 AGTCGTTAACTCAAGGTATACCC 57.411 43.478 18.65 0.73 30.02 3.69
2829 4211 7.775053 TCTTAGGTTGCCAGTTTTATTTGAT 57.225 32.000 0.00 0.00 0.00 2.57
2980 4362 1.110442 TCTTAATTGCCGGCATTGGG 58.890 50.000 33.25 18.98 0.00 4.12
3213 4595 4.387862 GGTGCTGCATTGATCTTGAAAAAG 59.612 41.667 5.27 0.00 0.00 2.27
3244 4630 5.003804 TGCTCCTTGTTTATTCAGAAGTCC 58.996 41.667 0.00 0.00 0.00 3.85
3324 4710 2.740981 GGTCACTTCAATGTGAGAGCAG 59.259 50.000 0.00 0.00 46.09 4.24
3384 4772 8.992073 GCCTTTTCATTATTTTGATTTGAGTGT 58.008 29.630 0.00 0.00 0.00 3.55
3402 4790 0.751643 GTGTGCACAGAAAGGGTGGT 60.752 55.000 22.40 0.00 36.76 4.16
3510 4900 8.682128 TTACTTTCCACGATCAATAAATTTGC 57.318 30.769 0.00 0.00 0.00 3.68
3631 5022 3.696051 CAGTATTGCTTGCTTACATGGGT 59.304 43.478 0.00 0.00 0.00 4.51
4052 5445 6.515531 CGGCAATGCATATGGTAAGAAAATCT 60.516 38.462 7.79 0.00 0.00 2.40
4121 5515 9.709495 AGATCATTTCTGCTATAAGATTGAGAC 57.291 33.333 0.00 0.00 31.79 3.36
4157 5551 8.786826 TCTATTATTCCCTTACACAACTGTTG 57.213 34.615 18.44 18.44 0.00 3.33
4162 5556 2.622942 CCCTTACACAACTGTTGCATGT 59.377 45.455 19.82 18.41 0.00 3.21
4163 5557 3.068024 CCCTTACACAACTGTTGCATGTT 59.932 43.478 19.82 6.10 0.00 2.71
4175 5569 9.121517 CAACTGTTGCATGTTATTTCTCTTAAG 57.878 33.333 7.70 0.00 0.00 1.85
4242 5675 6.317088 AGTTGCTCATAACATGATGTTTTCG 58.683 36.000 16.75 5.64 41.45 3.46
4287 5720 2.414559 GGCAAGTAGTACGTTACTCGCA 60.415 50.000 11.38 0.00 44.19 5.10
4316 5749 4.919754 GCTATATTGCCATTGCTGCTTAAC 59.080 41.667 0.00 0.00 38.71 2.01
4351 5784 7.228108 TCCAGAAAGAGTGAAATCATCATATGC 59.772 37.037 0.00 0.00 40.97 3.14
4415 5848 5.243981 AGATGTGATAATGTCTGCATAGCC 58.756 41.667 0.00 0.00 34.39 3.93
4460 5898 4.527816 CCAGATTGGTCCATTCTTCCAAAA 59.472 41.667 12.69 0.00 43.11 2.44
4724 6162 6.154192 TGCACTCTTTCCAATAATATTTGGCA 59.846 34.615 1.77 0.00 44.85 4.92
4894 6332 2.884639 AGTGTCAAACAACTATGTGGCC 59.115 45.455 0.00 0.00 40.46 5.36
5314 6752 3.879892 AGCCTTCTGTTGAAGTTCAAGAC 59.120 43.478 18.56 9.47 46.07 3.01
5645 7088 3.654414 AGCTTCAGTTTTCTCAGTACCG 58.346 45.455 0.00 0.00 0.00 4.02
5672 7115 4.444022 GCAGAAAGGATATGCAGAGGAAGA 60.444 45.833 0.00 0.00 39.75 2.87
5691 7139 0.034337 ATGGTGACCGCGTAAACAGT 59.966 50.000 4.92 0.00 0.00 3.55
5723 7171 1.193323 ACAGCAGAGGATGGACAGAG 58.807 55.000 0.00 0.00 33.84 3.35
5727 7175 2.235898 AGCAGAGGATGGACAGAGTTTC 59.764 50.000 0.00 0.00 0.00 2.78
5874 7650 1.688735 GGCCAACTCTTTGCCTTCTTT 59.311 47.619 0.00 0.00 0.00 2.52
5924 7700 6.632834 GTGCAGTTGTACACAAAGATTGTAAG 59.367 38.462 0.00 0.00 43.23 2.34
5947 7723 3.343380 ACCGGCAAAAGTTAAACGAAG 57.657 42.857 0.00 0.00 0.00 3.79
6046 7827 3.546271 GCACTTCAGACGTTTTTGTTTCC 59.454 43.478 0.00 0.00 0.00 3.13
6055 7836 2.478879 CGTTTTTGTTTCCGAGGCAAGT 60.479 45.455 0.00 0.00 0.00 3.16
6116 7947 2.515057 TGCCACCAACCGTGTGAC 60.515 61.111 0.00 0.00 41.26 3.67
6211 8051 9.519905 CTCAGCAAACAAATCAAAAATTTATCG 57.480 29.630 0.00 0.00 0.00 2.92
6247 8087 0.035439 GTCCGAAATCAGCAGGGGAA 60.035 55.000 0.00 0.00 0.00 3.97
6307 8148 3.610242 GCACAGAACTAGTTCGACATGAG 59.390 47.826 25.92 18.51 43.97 2.90
6334 8175 1.021202 CAAACAGCCCACGAAGTTGA 58.979 50.000 0.00 0.00 41.61 3.18
6336 8177 0.468226 AACAGCCCACGAAGTTGAGA 59.532 50.000 0.00 0.00 41.61 3.27
6337 8178 0.468226 ACAGCCCACGAAGTTGAGAA 59.532 50.000 0.00 0.00 41.61 2.87
6338 8179 1.072331 ACAGCCCACGAAGTTGAGAAT 59.928 47.619 0.00 0.00 41.61 2.40
6370 8211 2.546778 GCAGGCATTCCATCAAACATG 58.453 47.619 0.00 0.00 33.74 3.21
6415 8256 2.682952 AATACTGCGAGGTCGTATCG 57.317 50.000 0.69 3.02 43.00 2.92
6416 8257 1.590932 ATACTGCGAGGTCGTATCGT 58.409 50.000 0.69 0.00 42.13 3.73
6417 8258 2.223537 TACTGCGAGGTCGTATCGTA 57.776 50.000 0.69 3.73 42.13 3.43
6418 8259 1.590932 ACTGCGAGGTCGTATCGTAT 58.409 50.000 0.69 0.00 42.13 3.06
6419 8260 1.530293 ACTGCGAGGTCGTATCGTATC 59.470 52.381 0.69 0.00 42.13 2.24
6420 8261 0.870393 TGCGAGGTCGTATCGTATCC 59.130 55.000 0.69 0.00 42.13 2.59
6421 8262 1.155042 GCGAGGTCGTATCGTATCCT 58.845 55.000 0.69 0.00 42.13 3.24
6444 8285 1.477558 CCTATGCACTCCATTCCACCC 60.478 57.143 0.00 0.00 35.34 4.61
6458 8299 4.404098 ACCCGGGCGAATCCACAC 62.404 66.667 24.08 0.00 36.21 3.82
6485 8326 2.586357 GACCGATCGCTGCTTCCC 60.586 66.667 10.32 0.00 0.00 3.97
6486 8327 3.077556 ACCGATCGCTGCTTCCCT 61.078 61.111 10.32 0.00 0.00 4.20
6498 8339 0.251165 GCTTCCCTTTGCCACCAGTA 60.251 55.000 0.00 0.00 0.00 2.74
6500 8341 1.073923 CTTCCCTTTGCCACCAGTACT 59.926 52.381 0.00 0.00 0.00 2.73
6501 8342 0.400213 TCCCTTTGCCACCAGTACTG 59.600 55.000 16.34 16.34 0.00 2.74
6563 8423 6.790232 TGGAAGTTGGAACAGAAGAAAAAT 57.210 33.333 0.00 0.00 42.39 1.82
6580 8440 3.611766 AAATGGAAACGAGTCGAGGAT 57.388 42.857 21.50 1.46 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.483106 GGTAGTTTCAACTCCCTTTCGC 59.517 50.000 0.00 0.00 40.37 4.70
63 71 2.687200 ATGACAGCAGGCCCGGTA 60.687 61.111 0.00 0.00 0.00 4.02
71 79 1.144565 CGAGCGGAAGATGACAGCAG 61.145 60.000 0.00 0.00 0.00 4.24
72 80 1.153765 CGAGCGGAAGATGACAGCA 60.154 57.895 0.00 0.00 0.00 4.41
194 214 0.807275 TGCAAGTCATCTCGCCATCG 60.807 55.000 0.00 0.00 0.00 3.84
231 251 4.803426 GGGGCTGCGACGTCTCAG 62.803 72.222 27.15 27.15 0.00 3.35
233 253 4.500116 GAGGGGCTGCGACGTCTC 62.500 72.222 14.70 6.24 0.00 3.36
235 255 4.500116 GAGAGGGGCTGCGACGTC 62.500 72.222 5.18 5.18 0.00 4.34
237 257 4.200283 GAGAGAGGGGCTGCGACG 62.200 72.222 0.00 0.00 0.00 5.12
238 258 2.912987 TAGGAGAGAGGGGCTGCGAC 62.913 65.000 0.00 0.00 0.00 5.19
239 259 2.224805 TTAGGAGAGAGGGGCTGCGA 62.225 60.000 0.00 0.00 0.00 5.10
240 260 1.330655 TTTAGGAGAGAGGGGCTGCG 61.331 60.000 0.00 0.00 0.00 5.18
241 261 1.135960 ATTTAGGAGAGAGGGGCTGC 58.864 55.000 0.00 0.00 0.00 5.25
242 262 1.419387 CCATTTAGGAGAGAGGGGCTG 59.581 57.143 0.00 0.00 41.22 4.85
243 263 1.697291 CCCATTTAGGAGAGAGGGGCT 60.697 57.143 0.00 0.00 41.22 5.19
244 264 0.767998 CCCATTTAGGAGAGAGGGGC 59.232 60.000 0.00 0.00 41.22 5.80
245 265 2.050918 GACCCATTTAGGAGAGAGGGG 58.949 57.143 0.00 0.00 40.64 4.79
246 266 1.689273 CGACCCATTTAGGAGAGAGGG 59.311 57.143 0.00 0.00 41.22 4.30
247 267 1.069358 GCGACCCATTTAGGAGAGAGG 59.931 57.143 0.00 0.00 41.22 3.69
248 268 1.069358 GGCGACCCATTTAGGAGAGAG 59.931 57.143 0.00 0.00 41.22 3.20
273 299 8.447053 CAAATGTTTACTCTTCTTCTAAGCCTC 58.553 37.037 0.00 0.00 0.00 4.70
368 395 7.976734 ACTCTGTACTGAATTATCTGCTGTAAC 59.023 37.037 3.89 0.00 0.00 2.50
474 507 3.924238 CGGGCACTGTTGAATATGC 57.076 52.632 0.00 0.00 37.35 3.14
484 517 4.504858 AGAAAGTTAGAATACGGGCACTG 58.495 43.478 0.00 0.00 42.99 3.66
546 579 4.201950 GCTTGCTTCTTGACAACTGAAAGA 60.202 41.667 3.50 0.00 37.43 2.52
547 580 4.040376 GCTTGCTTCTTGACAACTGAAAG 58.960 43.478 0.00 0.00 42.29 2.62
549 582 3.016031 TGCTTGCTTCTTGACAACTGAA 58.984 40.909 0.00 0.00 0.00 3.02
550 583 2.615447 CTGCTTGCTTCTTGACAACTGA 59.385 45.455 0.00 0.00 0.00 3.41
553 586 2.874701 TCTCTGCTTGCTTCTTGACAAC 59.125 45.455 0.00 0.00 0.00 3.32
560 593 4.019860 TCCAGTTTATCTCTGCTTGCTTCT 60.020 41.667 0.00 0.00 0.00 2.85
565 598 5.240891 TCAGTTCCAGTTTATCTCTGCTTG 58.759 41.667 0.00 0.00 0.00 4.01
592 625 1.226746 GAGCGTAAGTGCCAACTTGT 58.773 50.000 1.42 0.00 46.30 3.16
619 659 0.673022 GAGCAGCTCTTGTCACCTGG 60.673 60.000 15.78 0.00 0.00 4.45
692 732 3.181506 GGAATCTTGTGATCTTGAACGGC 60.182 47.826 0.00 0.00 31.51 5.68
693 733 3.375299 GGGAATCTTGTGATCTTGAACGG 59.625 47.826 0.00 0.00 31.51 4.44
694 734 4.002982 TGGGAATCTTGTGATCTTGAACG 58.997 43.478 0.00 0.00 31.51 3.95
717 757 2.789203 CGTCTTTCTACGCCGCAGC 61.789 63.158 0.00 0.00 35.87 5.25
749 789 7.997107 ATATTGTTATCGTTCGCTTTAGTCA 57.003 32.000 0.00 0.00 0.00 3.41
821 864 4.415179 TGATGGGGTATGTATGAATGTGGT 59.585 41.667 0.00 0.00 0.00 4.16
825 868 4.761739 GTGGTGATGGGGTATGTATGAATG 59.238 45.833 0.00 0.00 0.00 2.67
826 869 4.415179 TGTGGTGATGGGGTATGTATGAAT 59.585 41.667 0.00 0.00 0.00 2.57
827 870 3.783082 TGTGGTGATGGGGTATGTATGAA 59.217 43.478 0.00 0.00 0.00 2.57
828 871 3.388913 TGTGGTGATGGGGTATGTATGA 58.611 45.455 0.00 0.00 0.00 2.15
832 875 0.918983 CCTGTGGTGATGGGGTATGT 59.081 55.000 0.00 0.00 0.00 2.29
842 885 2.046292 TGTGATCTGAACCTGTGGTGA 58.954 47.619 0.00 0.00 35.34 4.02
892 947 0.181350 GGTAGGCCCAGGATGACAAG 59.819 60.000 0.00 0.00 39.69 3.16
908 964 1.487300 TTATAGGCACGCACTGGGTA 58.513 50.000 0.00 0.00 0.00 3.69
913 969 2.107950 TGCTTTTATAGGCACGCACT 57.892 45.000 0.00 0.00 33.23 4.40
917 973 4.882671 ATGACTTGCTTTTATAGGCACG 57.117 40.909 0.00 0.00 38.23 5.34
946 1002 0.321298 GGCCTTCTGCGTTGGTCTTA 60.321 55.000 0.00 0.00 42.61 2.10
949 1005 3.423154 CGGCCTTCTGCGTTGGTC 61.423 66.667 0.00 0.00 42.61 4.02
956 1012 3.130160 CTCTTGCCGGCCTTCTGC 61.130 66.667 26.77 0.00 40.16 4.26
968 1024 5.185668 ACGATGATGATCTCTCACTCTTG 57.814 43.478 0.00 0.00 33.22 3.02
1005 1065 1.560923 CGTTGGTTATCAGAGGCTCG 58.439 55.000 9.22 4.43 0.00 5.03
1016 1076 0.037590 AGCTCCATTGCCGTTGGTTA 59.962 50.000 0.00 0.00 35.64 2.85
1020 1080 2.180017 GCAGCTCCATTGCCGTTG 59.820 61.111 0.00 0.00 35.54 4.10
1167 1227 0.609406 GGGAAGAACAGACCTTGGCC 60.609 60.000 0.00 0.00 0.00 5.36
1224 1284 5.278758 GCAGTTCCCTTGCTTGTATTGTAAA 60.279 40.000 0.00 0.00 38.51 2.01
1254 1316 6.040842 CCCATCATAACAGGAATCGGAAATTT 59.959 38.462 0.00 0.00 0.00 1.82
1256 1318 5.072741 CCCATCATAACAGGAATCGGAAAT 58.927 41.667 0.00 0.00 0.00 2.17
1282 1344 3.953612 TGGTTTTGCAGTCATGAGAAAGT 59.046 39.130 0.00 0.00 0.00 2.66
1294 1364 5.816777 TCTTTGAAAATTCCTGGTTTTGCAG 59.183 36.000 0.27 0.00 0.00 4.41
1295 1365 5.738909 TCTTTGAAAATTCCTGGTTTTGCA 58.261 33.333 0.27 1.57 0.00 4.08
1296 1366 6.676237 TTCTTTGAAAATTCCTGGTTTTGC 57.324 33.333 0.27 0.00 0.00 3.68
1297 1367 8.491331 TCTTTCTTTGAAAATTCCTGGTTTTG 57.509 30.769 0.27 0.00 0.00 2.44
1303 1373 9.971922 ACTGTTATCTTTCTTTGAAAATTCCTG 57.028 29.630 0.00 0.00 0.00 3.86
1310 1380 7.283127 AGTGCAGACTGTTATCTTTCTTTGAAA 59.717 33.333 3.99 0.00 0.00 2.69
1311 1381 6.767902 AGTGCAGACTGTTATCTTTCTTTGAA 59.232 34.615 3.99 0.00 0.00 2.69
1371 1441 4.181578 ACATTAGTTACTTGTAGCAGCCG 58.818 43.478 0.00 0.00 0.00 5.52
1406 1476 4.718774 AGTGACAAGTCTACCATGATGGAT 59.281 41.667 20.11 5.13 40.96 3.41
1407 1477 4.096681 AGTGACAAGTCTACCATGATGGA 58.903 43.478 20.11 0.76 40.96 3.41
1509 1583 6.064846 TGCAAGCTTATAAGATGCTAAAGC 57.935 37.500 28.74 18.99 42.21 3.51
1601 1677 5.622378 CGGTAAGAAAGAGAGCAAAATCAC 58.378 41.667 0.00 0.00 0.00 3.06
1610 1686 3.067106 TGCTTTGCGGTAAGAAAGAGAG 58.933 45.455 0.00 0.00 31.89 3.20
1818 1900 3.336468 AGCTCTCAAGACAATGAAGCAG 58.664 45.455 11.29 0.00 36.64 4.24
1821 1903 6.592994 TGTCATTAGCTCTCAAGACAATGAAG 59.407 38.462 5.98 0.00 36.65 3.02
1869 1951 6.234177 AGTTTTGTCCAGAAGATAAGTGGAG 58.766 40.000 0.00 0.00 41.11 3.86
1904 1986 9.298250 ACTCTGTAAACATACAAGTCTTCTCTA 57.702 33.333 0.00 0.00 0.00 2.43
1919 2002 5.601583 TGGTTGTCAGTACTCTGTAAACA 57.398 39.130 0.00 0.00 41.91 2.83
1920 2003 8.086522 TCTAATGGTTGTCAGTACTCTGTAAAC 58.913 37.037 0.00 0.00 41.91 2.01
1921 2004 8.185506 TCTAATGGTTGTCAGTACTCTGTAAA 57.814 34.615 0.00 0.00 41.91 2.01
1939 2188 5.010213 GCTCAGACCCTAGTACTTCTAATGG 59.990 48.000 0.00 0.00 0.00 3.16
1950 2199 3.107601 TGCTTAATGCTCAGACCCTAGT 58.892 45.455 0.00 0.00 43.37 2.57
1987 2237 8.421249 TGGTCTCACATATTTTGGATTTTCTT 57.579 30.769 0.00 0.00 0.00 2.52
1988 2238 8.472413 CATGGTCTCACATATTTTGGATTTTCT 58.528 33.333 0.00 0.00 0.00 2.52
2055 2407 8.636213 CCTGCAAAGGTTATGAATTCATAAGAT 58.364 33.333 31.82 22.91 46.05 2.40
2069 2421 0.179015 TGTTCCGCCTGCAAAGGTTA 60.179 50.000 0.00 0.00 0.00 2.85
2313 2665 3.624861 GCTCACCTGAAATACATGGAGTG 59.375 47.826 0.00 0.00 0.00 3.51
2363 2715 5.901552 TCCTAATTTCCCGCAATGAAATTC 58.098 37.500 16.51 0.00 44.84 2.17
2365 2717 6.484364 AATCCTAATTTCCCGCAATGAAAT 57.516 33.333 0.00 0.00 42.63 2.17
2366 2718 5.930837 AATCCTAATTTCCCGCAATGAAA 57.069 34.783 0.00 0.00 36.26 2.69
2367 2719 5.420421 TGAAATCCTAATTTCCCGCAATGAA 59.580 36.000 8.07 0.00 46.84 2.57
2369 2721 5.261209 TGAAATCCTAATTTCCCGCAATG 57.739 39.130 8.07 0.00 46.84 2.82
2370 2722 5.598005 TCATGAAATCCTAATTTCCCGCAAT 59.402 36.000 0.00 0.00 46.84 3.56
2371 2723 4.952957 TCATGAAATCCTAATTTCCCGCAA 59.047 37.500 0.00 0.00 46.84 4.85
2373 2725 4.022849 CCTCATGAAATCCTAATTTCCCGC 60.023 45.833 0.00 0.00 46.84 6.13
2375 2727 5.705400 TCCCTCATGAAATCCTAATTTCCC 58.295 41.667 0.00 0.00 46.84 3.97
2376 2728 5.772169 CCTCCCTCATGAAATCCTAATTTCC 59.228 44.000 0.00 0.00 46.84 3.13
2378 2730 6.596869 TCCTCCCTCATGAAATCCTAATTT 57.403 37.500 0.00 0.00 37.80 1.82
2379 2731 6.596869 TTCCTCCCTCATGAAATCCTAATT 57.403 37.500 0.00 0.00 0.00 1.40
2380 2732 6.596869 TTTCCTCCCTCATGAAATCCTAAT 57.403 37.500 0.00 0.00 0.00 1.73
2381 2733 6.401537 TTTTCCTCCCTCATGAAATCCTAA 57.598 37.500 0.00 0.00 0.00 2.69
2382 2734 5.103940 CCTTTTCCTCCCTCATGAAATCCTA 60.104 44.000 0.00 0.00 0.00 2.94
2383 2735 4.325658 CCTTTTCCTCCCTCATGAAATCCT 60.326 45.833 0.00 0.00 0.00 3.24
2384 2736 3.956848 CCTTTTCCTCCCTCATGAAATCC 59.043 47.826 0.00 0.00 0.00 3.01
2385 2737 3.956848 CCCTTTTCCTCCCTCATGAAATC 59.043 47.826 0.00 0.00 0.00 2.17
2386 2738 3.310141 CCCCTTTTCCTCCCTCATGAAAT 60.310 47.826 0.00 0.00 0.00 2.17
2390 2742 0.259938 CCCCCTTTTCCTCCCTCATG 59.740 60.000 0.00 0.00 0.00 3.07
2391 2743 0.178801 ACCCCCTTTTCCTCCCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2392 2744 0.845102 GACCCCCTTTTCCTCCCTCA 60.845 60.000 0.00 0.00 0.00 3.86
2393 2745 0.845102 TGACCCCCTTTTCCTCCCTC 60.845 60.000 0.00 0.00 0.00 4.30
2394 2746 0.846870 CTGACCCCCTTTTCCTCCCT 60.847 60.000 0.00 0.00 0.00 4.20
2395 2747 1.140772 ACTGACCCCCTTTTCCTCCC 61.141 60.000 0.00 0.00 0.00 4.30
2396 2748 1.665137 TACTGACCCCCTTTTCCTCC 58.335 55.000 0.00 0.00 0.00 4.30
2398 2750 5.871324 TTTTATACTGACCCCCTTTTCCT 57.129 39.130 0.00 0.00 0.00 3.36
2400 2752 7.069085 GGGTTATTTTATACTGACCCCCTTTTC 59.931 40.741 0.00 0.00 40.64 2.29
2405 2974 4.392047 CGGGTTATTTTATACTGACCCCC 58.608 47.826 3.93 0.00 42.97 5.40
2408 2977 6.293790 GGATTGCGGGTTATTTTATACTGACC 60.294 42.308 0.00 0.00 0.00 4.02
2562 3932 7.976135 AAGCTGCTTCAATACTATAATCTGG 57.024 36.000 9.53 0.00 0.00 3.86
2610 3983 8.532186 TGAATATATTACACTGCAAATTGGGT 57.468 30.769 0.00 0.00 0.00 4.51
3143 4525 4.460382 ACATCTTAGGGTGAACAATTGCAG 59.540 41.667 5.05 0.00 0.00 4.41
3213 4595 8.686334 TCTGAATAAACAAGGAGCATTTATTCC 58.314 33.333 18.79 2.86 45.89 3.01
3223 4605 6.734104 CAGGACTTCTGAATAAACAAGGAG 57.266 41.667 0.00 0.00 46.18 3.69
3244 4630 8.918658 CACAAAAGACACAATATCCATTTTCAG 58.081 33.333 0.00 0.00 0.00 3.02
3324 4710 5.645497 AGATGAGTTGCTTGATTACCTGAAC 59.355 40.000 0.00 0.00 0.00 3.18
3384 4772 0.033601 AACCACCCTTTCTGTGCACA 60.034 50.000 20.37 20.37 32.30 4.57
3402 4790 4.565652 GCACAGAGTTTATTCCCTCTCCAA 60.566 45.833 0.00 0.00 35.90 3.53
3484 4874 9.301153 GCAAATTTATTGATCGTGGAAAGTAAT 57.699 29.630 0.00 0.00 0.00 1.89
3485 4875 8.300286 TGCAAATTTATTGATCGTGGAAAGTAA 58.700 29.630 0.00 0.00 0.00 2.24
3565 4955 3.258872 AGCCAATCTGCAGTGCAATAAAA 59.741 39.130 20.22 2.87 38.41 1.52
3631 5022 0.465287 TGCGAAGATATGCAGCCTGA 59.535 50.000 0.00 0.00 35.90 3.86
4121 5515 9.160496 GTAAGGGAATAATAGAAGCATGAGATG 57.840 37.037 0.00 0.00 0.00 2.90
4163 5557 9.529823 TCAGGTGAAGACTACTTAAGAGAAATA 57.470 33.333 10.09 0.00 36.39 1.40
4215 5648 5.475273 ACATCATGTTATGAGCAACTTCG 57.525 39.130 1.62 0.00 43.53 3.79
4242 5675 2.246719 ATCTGGGCAAATAGACGAGC 57.753 50.000 0.00 0.00 29.80 5.03
4287 5720 6.070995 AGCAGCAATGGCAATATAGCATATTT 60.071 34.615 0.00 0.00 44.61 1.40
4316 5749 2.490903 CACTCTTTCTGGATTTGGCAGG 59.509 50.000 0.00 0.00 0.00 4.85
4460 5898 1.218450 TGGGTCATGATGCCATTGGAT 59.782 47.619 6.95 0.00 0.00 3.41
4894 6332 1.781025 TTCGCCTTGTTGCCAACTCG 61.781 55.000 9.30 7.32 0.00 4.18
5043 6481 9.679661 TTGTTTCTATATTGCTGATTGGTAAGA 57.320 29.630 0.00 0.00 0.00 2.10
5456 6894 1.243902 TTCTTCACCAAACCGGCATC 58.756 50.000 0.00 0.00 39.03 3.91
5645 7088 3.801698 TCTGCATATCCTTTCTGCACTC 58.198 45.455 0.00 0.00 40.75 3.51
5672 7115 0.034337 ACTGTTTACGCGGTCACCAT 59.966 50.000 12.47 0.00 0.00 3.55
5691 7139 0.972134 CTGCTGTTCTGTCAGGGAGA 59.028 55.000 0.00 0.00 36.12 3.71
5701 7149 1.554160 CTGTCCATCCTCTGCTGTTCT 59.446 52.381 0.00 0.00 0.00 3.01
5723 7171 0.233848 CACCACTTGTACGCGGAAAC 59.766 55.000 12.47 6.29 0.00 2.78
5727 7175 0.233848 GTTTCACCACTTGTACGCGG 59.766 55.000 12.47 0.00 0.00 6.46
5924 7700 2.223845 TCGTTTAACTTTTGCCGGTAGC 59.776 45.455 1.90 0.00 44.14 3.58
5958 7735 8.143193 ACAATTTGAGATGAATGTACAAAAGCA 58.857 29.630 0.00 0.00 34.86 3.91
5959 7736 8.430063 CACAATTTGAGATGAATGTACAAAAGC 58.570 33.333 0.00 0.00 34.86 3.51
6055 7836 5.668471 TGTCATGTTTGGCAAATCTTTTGA 58.332 33.333 16.74 11.47 33.65 2.69
6116 7947 3.085952 TGGCCCTTCCATTTCTTACAG 57.914 47.619 0.00 0.00 40.72 2.74
6142 7973 5.401550 ACTGATGCACATTTGTTTAATCCG 58.598 37.500 0.00 0.00 0.00 4.18
6211 8051 1.078143 ACCTCAAATCGAGCAGGGC 60.078 57.895 0.00 0.00 40.78 5.19
6307 8148 1.002624 TGGGCTGTTTGGGATCGAC 60.003 57.895 0.00 0.00 0.00 4.20
6310 8151 0.608035 TTCGTGGGCTGTTTGGGATC 60.608 55.000 0.00 0.00 0.00 3.36
6319 8160 1.813513 ATTCTCAACTTCGTGGGCTG 58.186 50.000 0.00 0.00 0.00 4.85
6334 8175 1.123928 CTGCCGGGACCTCTTATTCT 58.876 55.000 2.18 0.00 0.00 2.40
6336 8177 1.984288 GCCTGCCGGGACCTCTTATT 61.984 60.000 2.18 0.00 37.23 1.40
6337 8178 2.444256 GCCTGCCGGGACCTCTTAT 61.444 63.158 2.18 0.00 37.23 1.73
6338 8179 3.081409 GCCTGCCGGGACCTCTTA 61.081 66.667 2.18 0.00 37.23 2.10
6370 8211 1.195448 CTCGTGACAAATGCCTGTGAC 59.805 52.381 0.00 0.00 30.95 3.67
6415 8256 5.746990 ATGGAGTGCATAGGTAAGGATAC 57.253 43.478 0.00 0.00 0.00 2.24
6416 8257 5.248477 GGAATGGAGTGCATAGGTAAGGATA 59.752 44.000 0.00 0.00 0.00 2.59
6417 8258 4.042187 GGAATGGAGTGCATAGGTAAGGAT 59.958 45.833 0.00 0.00 0.00 3.24
6418 8259 3.391296 GGAATGGAGTGCATAGGTAAGGA 59.609 47.826 0.00 0.00 0.00 3.36
6419 8260 3.136443 TGGAATGGAGTGCATAGGTAAGG 59.864 47.826 0.00 0.00 0.00 2.69
6420 8261 4.130118 GTGGAATGGAGTGCATAGGTAAG 58.870 47.826 0.00 0.00 0.00 2.34
6421 8262 3.118038 GGTGGAATGGAGTGCATAGGTAA 60.118 47.826 0.00 0.00 0.00 2.85
6458 8299 1.398739 AGCGATCGGTCTCTATATGCG 59.601 52.381 15.21 0.00 0.00 4.73
6485 8326 0.593128 GCACAGTACTGGTGGCAAAG 59.407 55.000 26.12 7.05 36.76 2.77
6486 8327 1.163420 CGCACAGTACTGGTGGCAAA 61.163 55.000 26.12 0.00 36.76 3.68
6563 8423 0.530744 CCATCCTCGACTCGTTTCCA 59.469 55.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.