Multiple sequence alignment - TraesCS1B01G387100

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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 TraesCS1B01G387100 chr1B 100.000 2201 0 0 1 2201 621272922 621270722 0.000000e+00 4065
1 TraesCS1B01G387100 chr1B 89.496 1390 92 27 563 1928 620785975 620787334 0.000000e+00 1709
2 TraesCS1B01G387100 chr1B 96.481 682 23 1 526 1206 620899895 620900576 0.000000e+00 1125
3 TraesCS1B01G387100 chr1B 89.356 808 71 14 560 1361 610558243 610559041 0.000000e+00 1002
4 TraesCS1B01G387100 chr1B 89.507 791 50 22 563 1337 621059167 621059940 0.000000e+00 970
5 TraesCS1B01G387100 chr1B 85.567 291 42 0 1 291 620785555 620785845 2.750000e-79 305
6 TraesCS1B01G387100 chr1B 85.560 277 40 0 1 277 621058753 621059029 7.690000e-75 291
7 TraesCS1B01G387100 chr1B 92.308 91 6 1 345 435 621059032 621059121 6.380000e-26 128
8 TraesCS1B01G387100 chr1B 90.000 90 8 1 346 435 620785844 620785932 4.970000e-22 115
9 TraesCS1B01G387100 chr1A 91.234 867 46 11 563 1405 546216297 546217157 0.000000e+00 1153
10 TraesCS1B01G387100 chr1A 87.677 779 45 27 632 1364 542167879 542168652 0.000000e+00 859
11 TraesCS1B01G387100 chr1A 83.587 329 26 13 1435 1758 546217152 546217457 1.290000e-72 283
12 TraesCS1B01G387100 chr1A 84.314 255 30 5 1942 2196 546217577 546217821 7.850000e-60 241
13 TraesCS1B01G387100 chr1A 79.125 297 40 15 1171 1459 557098441 557098159 3.730000e-43 185
14 TraesCS1B01G387100 chr1D 90.595 840 42 14 563 1372 451624990 451625822 0.000000e+00 1079
15 TraesCS1B01G387100 chr1D 88.489 834 63 23 560 1364 446434635 446435464 0.000000e+00 977
16 TraesCS1B01G387100 chr1D 90.750 627 29 20 730 1336 451524632 451525249 0.000000e+00 809
17 TraesCS1B01G387100 chr1D 85.159 283 40 2 1 282 451624578 451624859 2.760000e-74 289
18 TraesCS1B01G387100 chr1D 85.496 262 30 7 1941 2198 451626507 451626764 1.300000e-67 267
19 TraesCS1B01G387100 chr1D 81.402 328 29 12 1406 1728 451625814 451626114 2.820000e-59 239
20 TraesCS1B01G387100 chr1D 84.462 251 27 9 1120 1361 202283329 202283082 1.020000e-58 237
21 TraesCS1B01G387100 chr5B 85.714 252 23 10 1120 1361 436562604 436562852 1.010000e-63 254
22 TraesCS1B01G387100 chr4A 85.600 250 23 10 1120 1359 666809644 666809398 1.300000e-62 250
23 TraesCS1B01G387100 chr3D 86.192 239 21 9 1120 1351 118253860 118254093 4.690000e-62 248
24 TraesCS1B01G387100 chr3D 86.875 160 15 6 1171 1327 118436176 118436332 8.080000e-40 174
25 TraesCS1B01G387100 chr2B 84.000 250 27 10 1122 1361 439691732 439691978 6.110000e-56 228


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 TraesCS1B01G387100 chr1B 621270722 621272922 2200 True 4065.000000 4065 100.000000 1 2201 1 chr1B.!!$R1 2200
1 TraesCS1B01G387100 chr1B 620899895 620900576 681 False 1125.000000 1125 96.481000 526 1206 1 chr1B.!!$F2 680
2 TraesCS1B01G387100 chr1B 610558243 610559041 798 False 1002.000000 1002 89.356000 560 1361 1 chr1B.!!$F1 801
3 TraesCS1B01G387100 chr1B 620785555 620787334 1779 False 709.666667 1709 88.354333 1 1928 3 chr1B.!!$F3 1927
4 TraesCS1B01G387100 chr1B 621058753 621059940 1187 False 463.000000 970 89.125000 1 1337 3 chr1B.!!$F4 1336
5 TraesCS1B01G387100 chr1A 542167879 542168652 773 False 859.000000 859 87.677000 632 1364 1 chr1A.!!$F1 732
6 TraesCS1B01G387100 chr1A 546216297 546217821 1524 False 559.000000 1153 86.378333 563 2196 3 chr1A.!!$F2 1633
7 TraesCS1B01G387100 chr1D 446434635 446435464 829 False 977.000000 977 88.489000 560 1364 1 chr1D.!!$F1 804
8 TraesCS1B01G387100 chr1D 451524632 451525249 617 False 809.000000 809 90.750000 730 1336 1 chr1D.!!$F2 606
9 TraesCS1B01G387100 chr1D 451624578 451626764 2186 False 468.500000 1079 85.663000 1 2198 4 chr1D.!!$F3 2197

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
453 455 0.177604 TGCCTTTGCAACAGTTTGGG 59.822 50.0 0.0 0.0 46.66 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2554 0.109086 AGTTCCGACTGCATCACTCG 60.109 55.0 0.0 0.0 33.99 4.18 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
24 25 5.008316 ACCAAAGGTTCGAGAATTGTTGTAC 59.992 40.000 0.00 0.00 27.29 2.90
79 80 1.543607 TTCAATTTGCATCCGCTCCA 58.456 45.000 0.00 0.00 39.64 3.86
101 102 5.860182 CCATTTTCAATAGCGCTATTCATGG 59.140 40.000 34.13 31.67 33.79 3.66
107 108 1.895707 GCGCTATTCATGGGCAGCT 60.896 57.895 0.00 0.00 41.97 4.24
143 144 4.794648 CCGAAAGCCCGGCATCCA 62.795 66.667 13.15 0.00 43.25 3.41
149 150 4.195334 GCCCGGCATCCAGTCCAT 62.195 66.667 3.91 0.00 0.00 3.41
163 164 2.124612 CCATGCATGGGCTCGACA 60.125 61.111 34.31 0.00 44.31 4.35
168 169 1.255882 TGCATGGGCTCGACATTTTT 58.744 45.000 0.00 0.00 41.91 1.94
173 174 1.243902 GGGCTCGACATTTTTGTCCA 58.756 50.000 0.83 0.00 35.52 4.02
177 178 3.243401 GGCTCGACATTTTTGTCCAAAGT 60.243 43.478 0.83 0.00 35.52 2.66
183 184 5.528870 GACATTTTTGTCCAAAGTCCGAAT 58.471 37.500 0.00 0.00 32.97 3.34
187 188 7.982354 ACATTTTTGTCCAAAGTCCGAATAAAA 59.018 29.630 0.00 0.00 0.00 1.52
188 189 8.821894 CATTTTTGTCCAAAGTCCGAATAAAAA 58.178 29.630 0.00 0.00 0.00 1.94
422 423 1.040339 TTGTCAAGCAAAGGCCCGTT 61.040 50.000 0.00 0.00 42.56 4.44
435 437 2.109431 CCCGTTCAAGGGCATGATG 58.891 57.895 0.00 0.00 45.72 3.07
436 438 1.434696 CCGTTCAAGGGCATGATGC 59.565 57.895 9.33 9.33 44.08 3.91
452 454 3.756739 TGCCTTTGCAACAGTTTGG 57.243 47.368 0.00 0.00 46.66 3.28
453 455 0.177604 TGCCTTTGCAACAGTTTGGG 59.822 50.000 0.00 0.00 46.66 4.12
454 456 0.463620 GCCTTTGCAACAGTTTGGGA 59.536 50.000 0.00 0.00 37.47 4.37
455 457 1.538849 GCCTTTGCAACAGTTTGGGAG 60.539 52.381 0.00 0.00 37.47 4.30
456 458 1.756538 CCTTTGCAACAGTTTGGGAGT 59.243 47.619 0.00 0.00 32.81 3.85
457 459 2.481795 CCTTTGCAACAGTTTGGGAGTG 60.482 50.000 0.00 0.00 32.81 3.51
458 460 1.846007 TTGCAACAGTTTGGGAGTGT 58.154 45.000 0.00 0.00 43.79 3.55
459 461 1.102154 TGCAACAGTTTGGGAGTGTG 58.898 50.000 0.00 0.00 41.06 3.82
460 462 1.102978 GCAACAGTTTGGGAGTGTGT 58.897 50.000 0.00 0.00 41.06 3.72
461 463 1.065551 GCAACAGTTTGGGAGTGTGTC 59.934 52.381 0.00 0.00 41.06 3.67
462 464 1.676006 CAACAGTTTGGGAGTGTGTCC 59.324 52.381 0.00 0.00 41.06 4.02
469 471 4.655527 GGAGTGTGTCCACGTCAG 57.344 61.111 0.00 0.00 46.10 3.51
470 472 1.664965 GGAGTGTGTCCACGTCAGC 60.665 63.158 0.00 0.00 46.10 4.26
471 473 2.016704 GAGTGTGTCCACGTCAGCG 61.017 63.158 0.00 0.00 46.56 5.18
472 474 2.027024 GTGTGTCCACGTCAGCGA 59.973 61.111 0.00 0.00 42.00 4.93
473 475 1.372997 GTGTGTCCACGTCAGCGAT 60.373 57.895 0.00 0.00 42.00 4.58
474 476 1.080772 TGTGTCCACGTCAGCGATC 60.081 57.895 0.00 0.00 42.00 3.69
475 477 1.805945 GTGTCCACGTCAGCGATCC 60.806 63.158 0.00 0.00 42.00 3.36
476 478 2.579787 GTCCACGTCAGCGATCCG 60.580 66.667 0.00 0.00 42.00 4.18
486 488 4.891727 GCGATCCGCGGTGTCCAT 62.892 66.667 27.15 11.04 44.55 3.41
487 489 2.961721 CGATCCGCGGTGTCCATG 60.962 66.667 27.15 8.44 36.03 3.66
488 490 2.186903 GATCCGCGGTGTCCATGT 59.813 61.111 27.15 1.90 0.00 3.21
489 491 1.449601 GATCCGCGGTGTCCATGTT 60.450 57.895 27.15 0.00 0.00 2.71
490 492 1.002624 ATCCGCGGTGTCCATGTTT 60.003 52.632 27.15 0.00 0.00 2.83
491 493 0.250793 ATCCGCGGTGTCCATGTTTA 59.749 50.000 27.15 0.03 0.00 2.01
492 494 0.390603 TCCGCGGTGTCCATGTTTAG 60.391 55.000 27.15 0.00 0.00 1.85
493 495 0.672401 CCGCGGTGTCCATGTTTAGT 60.672 55.000 19.50 0.00 0.00 2.24
494 496 1.153353 CGCGGTGTCCATGTTTAGTT 58.847 50.000 0.00 0.00 0.00 2.24
495 497 1.533731 CGCGGTGTCCATGTTTAGTTT 59.466 47.619 0.00 0.00 0.00 2.66
496 498 2.031508 CGCGGTGTCCATGTTTAGTTTT 60.032 45.455 0.00 0.00 0.00 2.43
497 499 3.561503 GCGGTGTCCATGTTTAGTTTTC 58.438 45.455 0.00 0.00 0.00 2.29
498 500 3.003897 GCGGTGTCCATGTTTAGTTTTCA 59.996 43.478 0.00 0.00 0.00 2.69
499 501 4.533222 CGGTGTCCATGTTTAGTTTTCAC 58.467 43.478 0.00 0.00 0.00 3.18
500 502 4.555906 CGGTGTCCATGTTTAGTTTTCACC 60.556 45.833 0.00 0.00 39.24 4.02
501 503 4.261867 GGTGTCCATGTTTAGTTTTCACCC 60.262 45.833 0.00 0.00 37.44 4.61
510 512 0.187606 AGTTTTCACCCCTGGTTCCC 59.812 55.000 0.00 0.00 31.02 3.97
511 513 0.187606 GTTTTCACCCCTGGTTCCCT 59.812 55.000 0.00 0.00 31.02 4.20
512 514 0.938192 TTTTCACCCCTGGTTCCCTT 59.062 50.000 0.00 0.00 31.02 3.95
513 515 0.481128 TTTCACCCCTGGTTCCCTTC 59.519 55.000 0.00 0.00 31.02 3.46
515 517 0.699577 TCACCCCTGGTTCCCTTCAA 60.700 55.000 0.00 0.00 31.02 2.69
516 518 0.187361 CACCCCTGGTTCCCTTCAAA 59.813 55.000 0.00 0.00 31.02 2.69
518 520 0.893727 CCCCTGGTTCCCTTCAAACG 60.894 60.000 0.00 0.00 0.00 3.60
520 522 1.271926 CCCTGGTTCCCTTCAAACGAT 60.272 52.381 0.00 0.00 0.00 3.73
521 523 1.812571 CCTGGTTCCCTTCAAACGATG 59.187 52.381 0.00 0.00 0.00 3.84
522 524 1.200020 CTGGTTCCCTTCAAACGATGC 59.800 52.381 0.00 0.00 0.00 3.91
523 525 1.202879 TGGTTCCCTTCAAACGATGCT 60.203 47.619 0.00 0.00 0.00 3.79
528 530 1.330306 CCTTCAAACGATGCTTTGCG 58.670 50.000 0.00 0.00 32.10 4.85
542 544 2.587473 TGCGTTGCAGCAGTTCGA 60.587 55.556 16.91 0.00 42.92 3.71
556 558 0.179081 GTTCGAGAGTGGGCCATACC 60.179 60.000 10.70 1.57 37.93 2.73
591 593 3.432051 GATCCGAGGCACTGACCCG 62.432 68.421 0.00 0.00 41.55 5.28
610 612 4.170062 CCACCAATCAGCGCGCAG 62.170 66.667 35.10 26.96 0.00 5.18
719 731 2.610859 ACCACCGGAGCTCCCAAT 60.611 61.111 27.20 9.75 34.14 3.16
763 775 0.401738 CCCCAAGGCAGACAAGAAGA 59.598 55.000 0.00 0.00 0.00 2.87
801 813 2.264794 GAGAAGGCGGCGGAGAAA 59.735 61.111 9.78 0.00 0.00 2.52
922 934 4.085876 GCAGCAAGGCCAAGAAGA 57.914 55.556 5.01 0.00 0.00 2.87
927 939 1.916697 GCAAGGCCAAGAAGAGCGTC 61.917 60.000 5.01 0.00 0.00 5.19
1226 1286 1.589803 GGCGTGTAGTTGGTTTCTGT 58.410 50.000 0.00 0.00 0.00 3.41
1262 1339 7.542890 TGCTTATCTATCTATCTGCAAGTAGC 58.457 38.462 0.00 0.00 45.96 3.58
1327 1420 4.385146 GCTCGTTGGTTGTAGTAAGAACTC 59.615 45.833 0.00 0.00 37.15 3.01
1366 1463 7.766278 TGGCAAACTGAAATCTATCTAGAACTC 59.234 37.037 0.00 0.00 35.69 3.01
1375 1472 9.646427 GAAATCTATCTAGAACTCAAGTTGTGT 57.354 33.333 4.75 4.75 38.56 3.72
1389 1486 8.251721 ACTCAAGTTGTGTTCCTATATCTGTAC 58.748 37.037 4.75 0.00 0.00 2.90
1401 1498 8.568676 TCCTATATCTGTACTAGTGATCTTGC 57.431 38.462 5.39 0.00 0.00 4.01
1402 1499 7.612244 TCCTATATCTGTACTAGTGATCTTGCC 59.388 40.741 5.39 0.00 0.00 4.52
1403 1500 7.613801 CCTATATCTGTACTAGTGATCTTGCCT 59.386 40.741 5.39 0.00 0.00 4.75
1404 1501 4.991153 TCTGTACTAGTGATCTTGCCTG 57.009 45.455 5.39 0.00 0.00 4.85
1405 1502 4.600062 TCTGTACTAGTGATCTTGCCTGA 58.400 43.478 5.39 0.00 0.00 3.86
1414 1511 4.223700 AGTGATCTTGCCTGACTGATGTTA 59.776 41.667 0.00 0.00 0.00 2.41
1421 1518 3.503363 TGCCTGACTGATGTTAGCTTTTG 59.497 43.478 0.00 0.00 0.00 2.44
1452 1551 5.964758 TGAAATGTCTGGCCATTTGTATTC 58.035 37.500 5.51 8.07 43.28 1.75
1486 1585 3.411446 TCTGGTTATCTGCAAACAGTGG 58.589 45.455 1.28 0.00 42.68 4.00
1489 1588 4.720046 TGGTTATCTGCAAACAGTGGTAA 58.280 39.130 2.40 0.00 44.77 2.85
1492 1591 6.943146 TGGTTATCTGCAAACAGTGGTAATAA 59.057 34.615 2.40 0.00 44.77 1.40
1493 1592 7.448777 TGGTTATCTGCAAACAGTGGTAATAAA 59.551 33.333 2.40 0.00 44.77 1.40
1494 1593 8.301002 GGTTATCTGCAAACAGTGGTAATAAAA 58.699 33.333 2.40 0.00 44.77 1.52
1496 1595 9.685828 TTATCTGCAAACAGTGGTAATAAAAAC 57.314 29.630 0.00 0.00 44.77 2.43
1497 1596 6.508777 TCTGCAAACAGTGGTAATAAAAACC 58.491 36.000 0.00 0.00 44.77 3.27
1498 1597 5.282510 TGCAAACAGTGGTAATAAAAACCG 58.717 37.500 0.00 0.00 40.08 4.44
1499 1598 5.067413 TGCAAACAGTGGTAATAAAAACCGA 59.933 36.000 0.00 0.00 40.08 4.69
1501 1600 6.513720 GCAAACAGTGGTAATAAAAACCGAGA 60.514 38.462 0.00 0.00 40.08 4.04
1502 1601 7.590279 CAAACAGTGGTAATAAAAACCGAGAT 58.410 34.615 0.00 0.00 40.08 2.75
1503 1602 7.754851 AACAGTGGTAATAAAAACCGAGATT 57.245 32.000 0.00 0.00 40.08 2.40
1504 1603 7.373778 ACAGTGGTAATAAAAACCGAGATTC 57.626 36.000 0.00 0.00 40.08 2.52
1505 1604 6.091713 ACAGTGGTAATAAAAACCGAGATTCG 59.908 38.462 0.00 0.00 40.08 3.34
1506 1605 6.091713 CAGTGGTAATAAAAACCGAGATTCGT 59.908 38.462 0.00 0.00 40.08 3.85
1507 1606 6.652062 AGTGGTAATAAAAACCGAGATTCGTT 59.348 34.615 0.00 0.00 40.08 3.85
1508 1607 7.173735 AGTGGTAATAAAAACCGAGATTCGTTT 59.826 33.333 0.00 0.00 40.08 3.60
1509 1608 8.442384 GTGGTAATAAAAACCGAGATTCGTTTA 58.558 33.333 0.00 0.00 40.08 2.01
1510 1609 9.165035 TGGTAATAAAAACCGAGATTCGTTTAT 57.835 29.630 0.00 0.13 40.08 1.40
1511 1610 9.429600 GGTAATAAAAACCGAGATTCGTTTATG 57.570 33.333 6.42 0.00 38.40 1.90
1512 1611 9.429600 GTAATAAAAACCGAGATTCGTTTATGG 57.570 33.333 6.42 0.00 38.40 2.74
1513 1612 7.852971 ATAAAAACCGAGATTCGTTTATGGA 57.147 32.000 0.00 0.00 38.40 3.41
1514 1613 6.563222 AAAAACCGAGATTCGTTTATGGAA 57.437 33.333 0.00 0.00 38.40 3.53
1515 1614 6.753107 AAAACCGAGATTCGTTTATGGAAT 57.247 33.333 0.00 0.00 38.40 3.01
1535 1637 8.893563 TGGAATTTGGAATTTGGTAGTAAGAT 57.106 30.769 0.00 0.00 0.00 2.40
1561 1663 0.531974 TCACTGGTGCAAACCGAGAC 60.532 55.000 0.00 0.00 0.00 3.36
1571 1673 4.092091 GTGCAAACCGAGACTGAGAAATAG 59.908 45.833 0.00 0.00 0.00 1.73
1602 1704 8.416329 ACATTTATGCAGTAGGGATTTGATTTC 58.584 33.333 0.00 0.00 0.00 2.17
1648 1751 3.419943 TGCCATGTCTGTGCTTTCATAA 58.580 40.909 0.00 0.00 0.00 1.90
1649 1752 4.018490 TGCCATGTCTGTGCTTTCATAAT 58.982 39.130 0.00 0.00 0.00 1.28
1688 1797 5.710513 TTTGTGTTTCCAGATTCCTGATG 57.289 39.130 0.00 0.00 43.02 3.07
1690 1799 2.424956 GTGTTTCCAGATTCCTGATGCC 59.575 50.000 0.00 0.00 43.02 4.40
1741 1853 4.136796 CAGAACCCAGTCTTGTTCAATCA 58.863 43.478 12.36 0.00 42.57 2.57
1772 1884 3.939740 ATTTCCTGCTGCTATTGAGGA 57.060 42.857 0.00 0.89 32.56 3.71
1774 1886 3.482156 TTCCTGCTGCTATTGAGGATC 57.518 47.619 6.51 0.00 34.53 3.36
1794 1906 2.746904 TCATGGTCATTTAACGTGGCAG 59.253 45.455 0.00 0.00 0.00 4.85
1796 1908 1.072489 TGGTCATTTAACGTGGCAGGA 59.928 47.619 14.98 0.00 0.00 3.86
1825 1937 1.529152 CCCAACGGTTTGCCTTACCC 61.529 60.000 0.00 0.00 31.75 3.69
1837 1949 1.066071 GCCTTACCCTGTCCTGTTCTC 60.066 57.143 0.00 0.00 0.00 2.87
1856 1968 8.015185 TGTTCTCAAGGTACAGTAGTTTACTT 57.985 34.615 0.00 0.00 36.76 2.24
1863 1975 7.294017 AGGTACAGTAGTTTACTTTGCAGTA 57.706 36.000 0.00 0.00 36.76 2.74
1893 2005 0.467106 TTGGCAGCAGCAGTTTGGTA 60.467 50.000 2.65 0.00 44.61 3.25
1907 2019 6.995091 AGCAGTTTGGTATTATCCTCTGAATC 59.005 38.462 0.00 0.00 0.00 2.52
1928 2040 2.997986 CCTGAAAATGGCAAATGTGAGC 59.002 45.455 0.00 0.00 0.00 4.26
1931 2043 2.088950 AAATGGCAAATGTGAGCTGC 57.911 45.000 0.00 0.00 35.28 5.25
1933 2045 0.815734 ATGGCAAATGTGAGCTGCTC 59.184 50.000 22.38 22.38 36.32 4.26
1935 2047 0.170561 GGCAAATGTGAGCTGCTCTG 59.829 55.000 28.04 18.86 36.32 3.35
1936 2048 0.879765 GCAAATGTGAGCTGCTCTGT 59.120 50.000 28.04 12.67 33.20 3.41
1937 2049 1.401148 GCAAATGTGAGCTGCTCTGTG 60.401 52.381 28.04 15.58 33.20 3.66
1938 2050 2.148768 CAAATGTGAGCTGCTCTGTGA 58.851 47.619 28.04 7.25 0.00 3.58
1940 2052 1.805869 ATGTGAGCTGCTCTGTGAAC 58.194 50.000 28.04 18.32 0.00 3.18
1948 2323 2.292267 CTGCTCTGTGAACAACCTTGT 58.708 47.619 0.00 0.00 44.72 3.16
1969 2344 1.134946 GCAGTTTGCAACCAGAGTGTT 59.865 47.619 0.00 0.00 44.26 3.32
2016 2391 4.736631 GCGGCGCAAAGGACGTTC 62.737 66.667 29.21 0.00 0.00 3.95
2024 2399 1.737793 GCAAAGGACGTTCGGATGAAT 59.262 47.619 0.00 0.00 36.29 2.57
2034 2410 3.429085 GTTCGGATGAATTGCACATGAC 58.571 45.455 0.00 0.00 36.29 3.06
2038 2414 4.158209 TCGGATGAATTGCACATGACAAAT 59.842 37.500 0.00 0.00 0.00 2.32
2044 2420 3.763097 TTGCACATGACAAATCCGATC 57.237 42.857 0.00 0.00 0.00 3.69
2067 2443 9.768662 GATCCAGAATATTTTGCATTACCAAAT 57.231 29.630 0.41 0.00 34.92 2.32
2069 2445 8.203485 TCCAGAATATTTTGCATTACCAAATCC 58.797 33.333 0.41 0.00 34.92 3.01
2073 2449 3.971245 TTTGCATTACCAAATCCACCC 57.029 42.857 0.00 0.00 30.28 4.61
2080 2456 4.637387 TTACCAAATCCACCCGTCTTTA 57.363 40.909 0.00 0.00 0.00 1.85
2083 2459 3.583966 ACCAAATCCACCCGTCTTTACTA 59.416 43.478 0.00 0.00 0.00 1.82
2084 2460 3.937079 CCAAATCCACCCGTCTTTACTAC 59.063 47.826 0.00 0.00 0.00 2.73
2111 2487 6.690530 TCTTGGATTGCACTTATTTTCCTTG 58.309 36.000 0.00 0.00 0.00 3.61
2125 2501 9.143631 CTTATTTTCCTTGCATTAAACCTTCAG 57.856 33.333 0.00 0.00 0.00 3.02
2126 2502 4.519540 TTCCTTGCATTAAACCTTCAGC 57.480 40.909 0.00 0.00 0.00 4.26
2135 2511 6.040391 TGCATTAAACCTTCAGCTAAACACTT 59.960 34.615 0.00 0.00 0.00 3.16
2138 2514 7.817418 TTAAACCTTCAGCTAAACACTTCAT 57.183 32.000 0.00 0.00 0.00 2.57
2162 2538 3.831323 CCAATACAGGGCATGTGGATAA 58.169 45.455 16.06 0.00 43.80 1.75
2166 2542 3.386932 ACAGGGCATGTGGATAAATGT 57.613 42.857 3.00 0.00 41.91 2.71
2172 2548 3.548014 GGCATGTGGATAAATGTACGCAC 60.548 47.826 0.00 0.00 0.00 5.34
2178 2554 4.849383 GTGGATAAATGTACGCACAAACAC 59.151 41.667 0.00 0.00 38.42 3.32
2197 2573 3.822607 GAGTGATGCAGTCGGAACT 57.177 52.632 0.00 0.00 35.60 3.01
2198 2574 1.634702 GAGTGATGCAGTCGGAACTC 58.365 55.000 0.00 0.00 31.71 3.01
2199 2575 0.109086 AGTGATGCAGTCGGAACTCG 60.109 55.000 0.00 0.00 40.90 4.18
2200 2576 0.109272 GTGATGCAGTCGGAACTCGA 60.109 55.000 0.00 0.00 46.77 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.565439 GCCCATGAATAGCGCTATTGAAAAT 60.565 40.000 39.62 25.28 36.02 1.82
91 92 0.533755 ACGAGCTGCCCATGAATAGC 60.534 55.000 0.00 0.23 36.45 2.97
149 150 1.067706 CAAAAATGTCGAGCCCATGCA 60.068 47.619 0.00 0.00 41.13 3.96
163 164 8.822855 GTTTTTATTCGGACTTTGGACAAAAAT 58.177 29.630 0.00 0.00 0.00 1.82
168 169 4.023878 CGGTTTTTATTCGGACTTTGGACA 60.024 41.667 0.00 0.00 0.00 4.02
173 174 6.206048 ACTCATTCGGTTTTTATTCGGACTTT 59.794 34.615 0.00 0.00 0.00 2.66
177 178 6.563222 AAACTCATTCGGTTTTTATTCGGA 57.437 33.333 0.00 0.00 33.76 4.55
337 338 9.139174 CAGAAACATTTGAACAGTACAGTTTTT 57.861 29.630 5.03 1.11 0.00 1.94
338 339 7.759433 CCAGAAACATTTGAACAGTACAGTTTT 59.241 33.333 5.03 0.00 0.00 2.43
339 340 7.257722 CCAGAAACATTTGAACAGTACAGTTT 58.742 34.615 5.03 0.00 0.00 2.66
340 341 6.680378 GCCAGAAACATTTGAACAGTACAGTT 60.680 38.462 2.94 2.94 0.00 3.16
341 342 5.221048 GCCAGAAACATTTGAACAGTACAGT 60.221 40.000 0.00 0.00 0.00 3.55
342 343 5.215160 GCCAGAAACATTTGAACAGTACAG 58.785 41.667 0.00 0.00 0.00 2.74
383 384 2.014594 GCCCGAAGCAAGAATACCG 58.985 57.895 0.00 0.00 42.97 4.02
435 437 0.463620 TCCCAAACTGTTGCAAAGGC 59.536 50.000 0.00 0.00 41.68 4.35
436 438 1.756538 ACTCCCAAACTGTTGCAAAGG 59.243 47.619 0.00 0.00 33.01 3.11
437 439 2.166254 ACACTCCCAAACTGTTGCAAAG 59.834 45.455 0.00 3.85 33.01 2.77
438 440 2.094286 CACACTCCCAAACTGTTGCAAA 60.094 45.455 0.00 0.00 33.01 3.68
439 441 1.476085 CACACTCCCAAACTGTTGCAA 59.524 47.619 0.00 0.00 33.01 4.08
440 442 1.102154 CACACTCCCAAACTGTTGCA 58.898 50.000 0.00 0.00 33.01 4.08
441 443 1.065551 GACACACTCCCAAACTGTTGC 59.934 52.381 0.00 0.00 33.01 4.17
442 444 1.676006 GGACACACTCCCAAACTGTTG 59.324 52.381 0.00 0.00 31.83 3.33
443 445 1.283613 TGGACACACTCCCAAACTGTT 59.716 47.619 0.00 0.00 38.49 3.16
444 446 0.916086 TGGACACACTCCCAAACTGT 59.084 50.000 0.00 0.00 38.49 3.55
445 447 1.308998 GTGGACACACTCCCAAACTG 58.691 55.000 0.00 0.00 44.29 3.16
446 448 0.179056 CGTGGACACACTCCCAAACT 60.179 55.000 3.12 0.00 45.50 2.66
447 449 0.463116 ACGTGGACACACTCCCAAAC 60.463 55.000 3.12 0.00 45.50 2.93
448 450 0.179067 GACGTGGACACACTCCCAAA 60.179 55.000 0.00 0.00 45.50 3.28
449 451 1.331399 TGACGTGGACACACTCCCAA 61.331 55.000 0.00 0.00 45.50 4.12
450 452 1.744320 CTGACGTGGACACACTCCCA 61.744 60.000 0.00 0.00 45.50 4.37
451 453 1.006102 CTGACGTGGACACACTCCC 60.006 63.158 0.00 0.00 45.50 4.30
452 454 1.664965 GCTGACGTGGACACACTCC 60.665 63.158 0.00 0.00 45.50 3.85
453 455 2.016704 CGCTGACGTGGACACACTC 61.017 63.158 0.00 0.00 45.50 3.51
454 456 1.806461 ATCGCTGACGTGGACACACT 61.806 55.000 0.00 0.00 45.50 3.55
455 457 1.344942 GATCGCTGACGTGGACACAC 61.345 60.000 0.00 0.00 44.23 3.82
456 458 1.080772 GATCGCTGACGTGGACACA 60.081 57.895 0.00 0.00 41.18 3.72
457 459 1.805945 GGATCGCTGACGTGGACAC 60.806 63.158 0.00 0.00 41.18 3.67
458 460 2.571757 GGATCGCTGACGTGGACA 59.428 61.111 0.00 0.00 41.18 4.02
459 461 2.579787 CGGATCGCTGACGTGGAC 60.580 66.667 0.00 0.00 41.18 4.02
470 472 2.961721 CATGGACACCGCGGATCG 60.962 66.667 35.90 21.75 38.08 3.69
471 473 1.024579 AAACATGGACACCGCGGATC 61.025 55.000 35.90 27.08 0.00 3.36
472 474 0.250793 TAAACATGGACACCGCGGAT 59.749 50.000 35.90 20.33 0.00 4.18
473 475 0.390603 CTAAACATGGACACCGCGGA 60.391 55.000 35.90 9.64 0.00 5.54
474 476 0.672401 ACTAAACATGGACACCGCGG 60.672 55.000 26.86 26.86 0.00 6.46
475 477 1.153353 AACTAAACATGGACACCGCG 58.847 50.000 0.00 0.00 0.00 6.46
476 478 3.003897 TGAAAACTAAACATGGACACCGC 59.996 43.478 0.00 0.00 0.00 5.68
477 479 4.533222 GTGAAAACTAAACATGGACACCG 58.467 43.478 0.00 0.00 0.00 4.94
478 480 4.261867 GGGTGAAAACTAAACATGGACACC 60.262 45.833 0.00 0.00 42.73 4.16
479 481 4.261867 GGGGTGAAAACTAAACATGGACAC 60.262 45.833 0.00 0.00 0.00 3.67
480 482 3.892588 GGGGTGAAAACTAAACATGGACA 59.107 43.478 0.00 0.00 0.00 4.02
481 483 4.022329 CAGGGGTGAAAACTAAACATGGAC 60.022 45.833 0.00 0.00 0.00 4.02
482 484 4.148838 CAGGGGTGAAAACTAAACATGGA 58.851 43.478 0.00 0.00 0.00 3.41
483 485 3.258123 CCAGGGGTGAAAACTAAACATGG 59.742 47.826 0.00 0.00 0.00 3.66
484 486 3.895041 ACCAGGGGTGAAAACTAAACATG 59.105 43.478 0.00 0.00 32.98 3.21
485 487 4.193240 ACCAGGGGTGAAAACTAAACAT 57.807 40.909 0.00 0.00 32.98 2.71
486 488 3.673543 ACCAGGGGTGAAAACTAAACA 57.326 42.857 0.00 0.00 32.98 2.83
487 489 3.319972 GGAACCAGGGGTGAAAACTAAAC 59.680 47.826 0.00 0.00 35.34 2.01
488 490 3.568443 GGAACCAGGGGTGAAAACTAAA 58.432 45.455 0.00 0.00 35.34 1.85
489 491 3.232720 GGAACCAGGGGTGAAAACTAA 57.767 47.619 0.00 0.00 35.34 2.24
490 492 2.963599 GGAACCAGGGGTGAAAACTA 57.036 50.000 0.00 0.00 35.34 2.24
491 493 3.842069 GGAACCAGGGGTGAAAACT 57.158 52.632 0.00 0.00 35.34 2.66
510 512 2.036556 ACGCAAAGCATCGTTTGAAG 57.963 45.000 0.67 0.00 39.40 3.02
511 513 2.115595 CAACGCAAAGCATCGTTTGAA 58.884 42.857 0.67 0.00 45.25 2.69
512 514 1.752753 CAACGCAAAGCATCGTTTGA 58.247 45.000 0.67 0.00 45.25 2.69
513 515 0.159345 GCAACGCAAAGCATCGTTTG 59.841 50.000 0.00 0.00 45.25 2.93
516 518 1.081906 CTGCAACGCAAAGCATCGT 60.082 52.632 0.00 0.00 40.42 3.73
518 520 1.342082 CTGCTGCAACGCAAAGCATC 61.342 55.000 3.02 0.00 38.62 3.91
520 522 2.026445 CTGCTGCAACGCAAAGCA 59.974 55.556 3.02 3.34 39.80 3.91
521 523 1.543106 GAACTGCTGCAACGCAAAGC 61.543 55.000 3.02 0.00 39.80 3.51
522 524 1.264141 CGAACTGCTGCAACGCAAAG 61.264 55.000 3.02 0.00 39.80 2.77
523 525 1.298264 CGAACTGCTGCAACGCAAA 60.298 52.632 3.02 0.00 39.80 3.68
528 530 0.510359 CACTCTCGAACTGCTGCAAC 59.490 55.000 3.02 0.00 0.00 4.17
542 544 2.423898 CGACGGTATGGCCCACTCT 61.424 63.158 0.00 0.00 0.00 3.24
591 593 4.166011 GCGCGCTGATTGGTGGAC 62.166 66.667 26.67 0.00 0.00 4.02
610 612 4.564613 GCTGGATTTTATAGGGGAGAGAGC 60.565 50.000 0.00 0.00 0.00 4.09
927 939 5.660629 AGATGTAGATCTTGTACGTCTCG 57.339 43.478 11.52 0.00 41.07 4.04
1366 1463 9.737427 CTAGTACAGATATAGGAACACAACTTG 57.263 37.037 0.00 0.00 0.00 3.16
1375 1472 9.015367 GCAAGATCACTAGTACAGATATAGGAA 57.985 37.037 0.00 0.00 0.00 3.36
1389 1486 4.141981 ACATCAGTCAGGCAAGATCACTAG 60.142 45.833 0.00 0.00 0.00 2.57
1399 1496 3.423539 AAAGCTAACATCAGTCAGGCA 57.576 42.857 0.00 0.00 0.00 4.75
1400 1497 3.753272 TCAAAAGCTAACATCAGTCAGGC 59.247 43.478 0.00 0.00 0.00 4.85
1401 1498 4.154918 GGTCAAAAGCTAACATCAGTCAGG 59.845 45.833 0.00 0.00 0.00 3.86
1402 1499 4.154918 GGGTCAAAAGCTAACATCAGTCAG 59.845 45.833 0.00 0.00 0.00 3.51
1403 1500 4.072131 GGGTCAAAAGCTAACATCAGTCA 58.928 43.478 0.00 0.00 0.00 3.41
1404 1501 4.327680 AGGGTCAAAAGCTAACATCAGTC 58.672 43.478 0.00 0.00 0.00 3.51
1405 1502 4.373156 AGGGTCAAAAGCTAACATCAGT 57.627 40.909 0.00 0.00 0.00 3.41
1414 1511 4.218312 ACATTTCAGAAGGGTCAAAAGCT 58.782 39.130 0.00 0.00 0.00 3.74
1421 1518 2.087646 GCCAGACATTTCAGAAGGGTC 58.912 52.381 7.78 7.78 0.00 4.46
1452 1551 1.972872 AACCAGAGTTCAGCAACCAG 58.027 50.000 0.00 0.00 32.22 4.00
1496 1595 5.295787 TCCAAATTCCATAAACGAATCTCGG 59.704 40.000 0.67 0.00 45.59 4.63
1497 1596 6.358118 TCCAAATTCCATAAACGAATCTCG 57.642 37.500 0.00 0.00 46.93 4.04
1498 1597 9.586435 AAATTCCAAATTCCATAAACGAATCTC 57.414 29.630 0.00 0.00 0.00 2.75
1499 1598 9.369904 CAAATTCCAAATTCCATAAACGAATCT 57.630 29.630 0.00 0.00 0.00 2.40
1501 1600 8.100164 ACCAAATTCCAAATTCCATAAACGAAT 58.900 29.630 0.00 0.00 0.00 3.34
1502 1601 7.445945 ACCAAATTCCAAATTCCATAAACGAA 58.554 30.769 0.00 0.00 0.00 3.85
1503 1602 6.998802 ACCAAATTCCAAATTCCATAAACGA 58.001 32.000 0.00 0.00 0.00 3.85
1504 1603 8.032451 ACTACCAAATTCCAAATTCCATAAACG 58.968 33.333 0.00 0.00 0.00 3.60
1508 1607 9.983024 TCTTACTACCAAATTCCAAATTCCATA 57.017 29.630 0.00 0.00 0.00 2.74
1509 1608 8.893563 TCTTACTACCAAATTCCAAATTCCAT 57.106 30.769 0.00 0.00 0.00 3.41
1510 1609 8.893563 ATCTTACTACCAAATTCCAAATTCCA 57.106 30.769 0.00 0.00 0.00 3.53
1511 1610 9.190317 AGATCTTACTACCAAATTCCAAATTCC 57.810 33.333 0.00 0.00 0.00 3.01
1513 1612 9.753674 TCAGATCTTACTACCAAATTCCAAATT 57.246 29.630 0.00 0.00 0.00 1.82
1514 1613 9.753674 TTCAGATCTTACTACCAAATTCCAAAT 57.246 29.630 0.00 0.00 0.00 2.32
1515 1614 9.753674 ATTCAGATCTTACTACCAAATTCCAAA 57.246 29.630 0.00 0.00 0.00 3.28
1535 1637 2.622942 GGTTTGCACCAGTGAATTCAGA 59.377 45.455 8.80 0.00 43.61 3.27
1545 1647 0.249868 TCAGTCTCGGTTTGCACCAG 60.250 55.000 0.00 0.00 44.53 4.00
1571 1673 7.986085 AATCCCTACTGCATAAATGTATCAC 57.014 36.000 0.00 0.00 0.00 3.06
1602 1704 4.429108 GACTAGCTCAAGAACCTAGCAAG 58.571 47.826 0.00 0.00 38.75 4.01
1649 1752 9.549509 GAAACACAAATTACATTGCTACGATAA 57.450 29.630 0.00 0.00 33.52 1.75
1688 1797 1.351350 AGAAACAGAACCTACTGGGGC 59.649 52.381 0.00 0.00 41.59 5.80
1690 1799 2.224523 TGCAGAAACAGAACCTACTGGG 60.225 50.000 0.00 0.00 41.59 4.45
1741 1853 1.282157 AGCAGGAAATTAAGCCCGACT 59.718 47.619 0.00 0.00 0.00 4.18
1772 1884 3.351740 TGCCACGTTAAATGACCATGAT 58.648 40.909 0.00 0.00 0.00 2.45
1774 1886 2.159393 CCTGCCACGTTAAATGACCATG 60.159 50.000 0.00 0.00 0.00 3.66
1777 1889 1.816074 TCCTGCCACGTTAAATGACC 58.184 50.000 0.00 0.00 0.00 4.02
1778 1890 4.873827 TCTTATCCTGCCACGTTAAATGAC 59.126 41.667 0.00 0.00 0.00 3.06
1787 1899 1.737793 GGTTGTTCTTATCCTGCCACG 59.262 52.381 0.00 0.00 0.00 4.94
1825 1937 3.322254 ACTGTACCTTGAGAACAGGACAG 59.678 47.826 14.06 12.93 43.91 3.51
1837 1949 6.482308 ACTGCAAAGTAAACTACTGTACCTTG 59.518 38.462 0.00 0.00 39.39 3.61
1856 1968 5.679601 TGCCAACTGATATACATACTGCAA 58.320 37.500 0.00 0.00 0.00 4.08
1863 1975 3.144506 GCTGCTGCCAACTGATATACAT 58.855 45.455 3.85 0.00 0.00 2.29
1874 1986 0.467106 TACCAAACTGCTGCTGCCAA 60.467 50.000 13.47 0.00 38.71 4.52
1893 2005 6.492772 GCCATTTTCAGGATTCAGAGGATAAT 59.507 38.462 0.00 0.00 0.00 1.28
1907 2019 2.997986 GCTCACATTTGCCATTTTCAGG 59.002 45.455 0.00 0.00 0.00 3.86
1928 2040 2.032550 CACAAGGTTGTTCACAGAGCAG 59.967 50.000 0.00 0.00 39.91 4.24
1931 2043 2.016318 TGCACAAGGTTGTTCACAGAG 58.984 47.619 0.00 0.00 39.91 3.35
1933 2045 1.745087 ACTGCACAAGGTTGTTCACAG 59.255 47.619 12.50 12.50 39.91 3.66
1935 2047 2.923020 CAAACTGCACAAGGTTGTTCAC 59.077 45.455 0.00 0.00 46.80 3.18
1936 2048 3.229276 CAAACTGCACAAGGTTGTTCA 57.771 42.857 0.00 0.00 46.80 3.18
1961 2336 6.349115 CCAGATTTGAATCCAAGAACACTCTG 60.349 42.308 0.27 0.00 36.04 3.35
1969 2344 4.996793 TGGAACCAGATTTGAATCCAAGA 58.003 39.130 7.29 0.00 36.53 3.02
2016 2391 3.490800 TTGTCATGTGCAATTCATCCG 57.509 42.857 0.00 0.00 0.00 4.18
2024 2399 2.423185 GGATCGGATTTGTCATGTGCAA 59.577 45.455 0.00 0.00 0.00 4.08
2034 2410 6.506147 TGCAAAATATTCTGGATCGGATTTG 58.494 36.000 0.00 0.00 0.00 2.32
2038 2414 6.206634 GGTAATGCAAAATATTCTGGATCGGA 59.793 38.462 0.00 0.00 0.00 4.55
2044 2420 7.986320 TGGATTTGGTAATGCAAAATATTCTGG 59.014 33.333 0.00 0.00 38.88 3.86
2067 2443 4.091549 AGAATGTAGTAAAGACGGGTGGA 58.908 43.478 0.00 0.00 0.00 4.02
2069 2445 4.630069 CCAAGAATGTAGTAAAGACGGGTG 59.370 45.833 0.00 0.00 0.00 4.61
2073 2449 6.092122 TGCAATCCAAGAATGTAGTAAAGACG 59.908 38.462 0.00 0.00 0.00 4.18
2080 2456 7.944729 AATAAGTGCAATCCAAGAATGTAGT 57.055 32.000 0.00 0.00 0.00 2.73
2083 2459 7.038799 AGGAAAATAAGTGCAATCCAAGAATGT 60.039 33.333 0.00 0.00 0.00 2.71
2084 2460 7.325694 AGGAAAATAAGTGCAATCCAAGAATG 58.674 34.615 0.00 0.00 0.00 2.67
2111 2487 6.013842 AGTGTTTAGCTGAAGGTTTAATGC 57.986 37.500 0.00 0.00 0.00 3.56
2125 2501 3.874392 ATTGGCCATGAAGTGTTTAGC 57.126 42.857 6.09 0.00 0.00 3.09
2126 2502 5.163622 CCTGTATTGGCCATGAAGTGTTTAG 60.164 44.000 6.09 0.00 0.00 1.85
2162 2538 2.033236 CACTCGTGTTTGTGCGTACATT 60.033 45.455 7.30 0.00 36.53 2.71
2166 2542 1.790043 CATCACTCGTGTTTGTGCGTA 59.210 47.619 0.00 0.00 34.49 4.42
2172 2548 1.136529 CGACTGCATCACTCGTGTTTG 60.137 52.381 0.00 0.00 0.00 2.93
2178 2554 0.109086 AGTTCCGACTGCATCACTCG 60.109 55.000 0.00 0.00 33.99 4.18


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

AutoCloner maintained by Alex Coulton.