Multiple sequence alignment - TraesCS1D01G424000

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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 TraesCS1D01G424000 chr1D 100.000 2474 0 0 1 2474 478691989 478694462 0.000000e+00 4569.0
1 TraesCS1D01G424000 chr1D 97.311 1525 36 3 1 1525 478507768 478509287 0.000000e+00 2584.0
2 TraesCS1D01G424000 chr1D 93.827 891 21 9 637 1525 478452372 478453230 0.000000e+00 1310.0
3 TraesCS1D01G424000 chr1D 95.546 696 30 1 828 1522 478579867 478580562 0.000000e+00 1112.0
4 TraesCS1D01G424000 chr1D 92.147 624 42 7 1 620 478451445 478452065 0.000000e+00 874.0
5 TraesCS1D01G424000 chr1D 91.640 622 46 6 1 619 478517520 478518138 0.000000e+00 856.0
6 TraesCS1D01G424000 chr1D 97.252 473 12 1 1030 1501 478518398 478518870 0.000000e+00 800.0
7 TraesCS1D01G424000 chr1D 94.406 429 23 1 828 1255 478501483 478501911 0.000000e+00 658.0
8 TraesCS1D01G424000 chr1D 85.202 223 14 4 695 898 478701016 478701238 6.930000e-51 211.0
9 TraesCS1D01G424000 chr1D 98.077 104 2 0 1419 1522 478501910 478502013 5.440000e-42 182.0
10 TraesCS1D01G424000 chr1D 94.624 93 4 1 529 620 478451827 478451919 2.560000e-30 143.0
11 TraesCS1D01G424000 chr1D 94.565 92 5 0 529 620 478508150 478508241 2.560000e-30 143.0
12 TraesCS1D01G424000 chr1D 94.565 92 5 0 383 474 478508296 478508387 2.560000e-30 143.0
13 TraesCS1D01G424000 chr1D 94.565 92 5 0 529 620 478692371 478692462 2.560000e-30 143.0
14 TraesCS1D01G424000 chr1D 94.565 92 5 0 383 474 478692517 478692608 2.560000e-30 143.0
15 TraesCS1D01G424000 chr1D 93.548 93 5 1 529 620 478517902 478517994 1.190000e-28 137.0
16 TraesCS1D01G424000 chr1D 82.738 168 14 1 653 805 478499847 478500014 4.290000e-28 135.0
17 TraesCS1D01G424000 chr1D 82.143 168 15 1 653 805 478578234 478578401 2.000000e-26 130.0
18 TraesCS1D01G424000 chr1D 100.000 28 0 0 813 840 478500043 478500070 4.000000e-03 52.8
19 TraesCS1D01G424000 chr1D 100.000 28 0 0 813 840 478578430 478578457 4.000000e-03 52.8
20 TraesCS1D01G424000 chr1A 90.982 876 49 9 676 1522 574727343 574728217 0.000000e+00 1153.0
21 TraesCS1D01G424000 chr1A 86.703 549 52 10 1592 2122 60360028 60359483 7.620000e-165 590.0
22 TraesCS1D01G424000 chr1A 81.373 714 88 21 813 1517 574682206 574681529 7.780000e-150 540.0
23 TraesCS1D01G424000 chr1A 96.226 53 1 1 1474 1525 574728443 574728495 4.380000e-13 86.1
24 TraesCS1D01G424000 chr1A 97.143 35 1 0 497 531 537048051 537048017 2.660000e-05 60.2
25 TraesCS1D01G424000 chr1B 83.571 560 74 11 963 1517 666572086 666571540 2.200000e-140 508.0
26 TraesCS1D01G424000 chr6D 87.675 357 37 7 2122 2474 387880285 387880638 2.290000e-110 409.0
27 TraesCS1D01G424000 chr6D 89.161 286 27 3 2191 2474 446536761 446536478 1.090000e-93 353.0
28 TraesCS1D01G424000 chr6D 81.724 290 43 9 2118 2402 387880220 387880504 1.480000e-57 233.0
29 TraesCS1D01G424000 chr3B 86.389 360 43 5 2119 2474 494225762 494226119 2.980000e-104 388.0
30 TraesCS1D01G424000 chr5B 78.300 553 91 19 1588 2122 537901154 537901695 1.830000e-86 329.0
31 TraesCS1D01G424000 chr3A 85.759 316 34 4 1591 1895 714519489 714519174 8.530000e-85 324.0
32 TraesCS1D01G424000 chr3A 90.948 232 19 1 1893 2122 714512377 714512146 6.640000e-81 311.0
33 TraesCS1D01G424000 chr5D 82.451 359 49 11 2122 2474 21008007 21008357 4.000000e-78 302.0
34 TraesCS1D01G424000 chr5D 86.547 223 24 4 2182 2402 21007944 21008162 8.840000e-60 241.0
35 TraesCS1D01G424000 chr5D 81.973 294 41 10 2114 2402 21007938 21008224 3.180000e-59 239.0
36 TraesCS1D01G424000 chr5D 80.405 296 41 14 2122 2409 21007977 21008263 2.490000e-50 209.0
37 TraesCS1D01G424000 chr2D 82.016 367 51 12 2114 2474 608510824 608511181 5.170000e-77 298.0
38 TraesCS1D01G424000 chr7B 86.869 198 22 3 1929 2122 566619074 566618877 4.140000e-53 219.0
39 TraesCS1D01G424000 chr7B 89.381 113 9 2 2013 2122 48778361 48778473 3.320000e-29 139.0
40 TraesCS1D01G424000 chr3D 76.216 185 34 7 1 180 189463601 189463422 3.390000e-14 89.8
41 TraesCS1D01G424000 chr7A 94.737 38 2 0 494 531 559194527 559194490 2.660000e-05 60.2
42 TraesCS1D01G424000 chr2A 97.222 36 0 1 496 531 455480944 455480910 2.660000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G424000 chr1D 478691989 478694462 2473 False 1618.333333 4569 96.376667 1 2474 3 chr1D.!!$F7 2473
1 TraesCS1D01G424000 chr1D 478507768 478509287 1519 False 956.666667 2584 95.480333 1 1525 3 chr1D.!!$F4 1524
2 TraesCS1D01G424000 chr1D 478451445 478453230 1785 False 775.666667 1310 93.532667 1 1525 3 chr1D.!!$F2 1524
3 TraesCS1D01G424000 chr1D 478517520 478518870 1350 False 597.666667 856 94.146667 1 1501 3 chr1D.!!$F5 1500
4 TraesCS1D01G424000 chr1D 478578234 478580562 2328 False 431.600000 1112 92.563000 653 1522 3 chr1D.!!$F6 869
5 TraesCS1D01G424000 chr1D 478499847 478502013 2166 False 256.950000 658 93.805250 653 1522 4 chr1D.!!$F3 869
6 TraesCS1D01G424000 chr1A 574727343 574728495 1152 False 619.550000 1153 93.604000 676 1525 2 chr1A.!!$F1 849
7 TraesCS1D01G424000 chr1A 60359483 60360028 545 True 590.000000 590 86.703000 1592 2122 1 chr1A.!!$R1 530
8 TraesCS1D01G424000 chr1A 574681529 574682206 677 True 540.000000 540 81.373000 813 1517 1 chr1A.!!$R3 704
9 TraesCS1D01G424000 chr1B 666571540 666572086 546 True 508.000000 508 83.571000 963 1517 1 chr1B.!!$R1 554
10 TraesCS1D01G424000 chr5B 537901154 537901695 541 False 329.000000 329 78.300000 1588 2122 1 chr5B.!!$F1 534

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
552 556 0.396435 ACCTCCACGTCAAATGCTGA 59.604 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 3728 0.110823 GACGCGGTTTACAAGCTGTG 60.111 55.0 12.47 0.0 0.0 3.66 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
98 100 2.801388 CGGATGTCATCACGATCCG 58.199 57.895 14.72 5.58 46.38 4.18
208 210 1.705002 AATCGATTGGGATGGGGCGA 61.705 55.000 10.50 0.00 0.00 5.54
369 371 0.602638 CTTGGCCCATTCGCGCTATA 60.603 55.000 5.56 0.00 0.00 1.31
381 383 2.292292 TCGCGCTATAACAGTATGCTGA 59.708 45.455 18.40 0.00 45.28 4.26
484 487 5.531287 GGCACGGTAGATTTGGAAGATTTAT 59.469 40.000 0.00 0.00 0.00 1.40
552 556 0.396435 ACCTCCACGTCAAATGCTGA 59.604 50.000 0.00 0.00 0.00 4.26
648 942 2.940410 ACAGTACAAACAGGTTGGTTCG 59.060 45.455 2.51 0.00 41.97 3.95
649 943 3.199677 CAGTACAAACAGGTTGGTTCGA 58.800 45.455 2.51 0.00 41.97 3.71
674 968 5.163814 GCACTTATCCGGATTGATATGAAGC 60.164 44.000 24.71 11.92 0.00 3.86
1255 3150 1.212688 TCTACATGACCATGGCCAAGG 59.787 52.381 25.43 25.43 42.91 3.61
1526 3699 8.885722 CAAATAAATTGGATGTTTCTTCCATGG 58.114 33.333 4.97 4.97 42.69 3.66
1527 3700 7.976414 ATAAATTGGATGTTTCTTCCATGGA 57.024 32.000 11.44 11.44 42.69 3.41
1528 3701 6.684897 AAATTGGATGTTTCTTCCATGGAA 57.315 33.333 25.53 25.53 42.69 3.53
1529 3702 6.684897 AATTGGATGTTTCTTCCATGGAAA 57.315 33.333 26.87 13.13 42.69 3.13
1530 3703 6.684897 ATTGGATGTTTCTTCCATGGAAAA 57.315 33.333 26.87 19.70 42.69 2.29
1531 3704 5.726980 TGGATGTTTCTTCCATGGAAAAG 57.273 39.130 26.87 17.02 38.35 2.27
1532 3705 5.147032 TGGATGTTTCTTCCATGGAAAAGT 58.853 37.500 26.87 11.49 38.35 2.66
1533 3706 5.010922 TGGATGTTTCTTCCATGGAAAAGTG 59.989 40.000 26.87 15.77 38.35 3.16
1534 3707 5.011023 GGATGTTTCTTCCATGGAAAAGTGT 59.989 40.000 26.87 12.21 34.97 3.55
1535 3708 5.930837 TGTTTCTTCCATGGAAAAGTGTT 57.069 34.783 26.87 0.00 34.97 3.32
1536 3709 5.901552 TGTTTCTTCCATGGAAAAGTGTTC 58.098 37.500 26.87 13.93 34.97 3.18
1537 3710 4.829064 TTCTTCCATGGAAAAGTGTTCG 57.171 40.909 26.87 13.33 33.34 3.95
1538 3711 3.815809 TCTTCCATGGAAAAGTGTTCGT 58.184 40.909 26.87 0.00 33.34 3.85
1539 3712 4.204012 TCTTCCATGGAAAAGTGTTCGTT 58.796 39.130 26.87 0.00 33.34 3.85
1540 3713 4.642885 TCTTCCATGGAAAAGTGTTCGTTT 59.357 37.500 26.87 0.00 33.34 3.60
1541 3714 4.561735 TCCATGGAAAAGTGTTCGTTTC 57.438 40.909 13.46 0.00 39.85 2.78
1542 3715 3.948473 TCCATGGAAAAGTGTTCGTTTCA 59.052 39.130 13.46 0.00 41.41 2.69
1543 3716 4.399618 TCCATGGAAAAGTGTTCGTTTCAA 59.600 37.500 13.46 0.00 41.41 2.69
1544 3717 5.068460 TCCATGGAAAAGTGTTCGTTTCAAT 59.932 36.000 13.46 1.39 41.41 2.57
1545 3718 5.402270 CCATGGAAAAGTGTTCGTTTCAATC 59.598 40.000 5.56 0.00 41.41 2.67
1546 3719 4.593157 TGGAAAAGTGTTCGTTTCAATCG 58.407 39.130 8.32 0.00 41.41 3.34
1547 3720 3.972502 GGAAAAGTGTTCGTTTCAATCGG 59.027 43.478 8.32 0.00 41.41 4.18
1548 3721 2.681152 AAGTGTTCGTTTCAATCGGC 57.319 45.000 0.00 0.00 0.00 5.54
1549 3722 1.878953 AGTGTTCGTTTCAATCGGCT 58.121 45.000 0.00 0.00 0.00 5.52
1550 3723 1.531149 AGTGTTCGTTTCAATCGGCTG 59.469 47.619 0.00 0.00 0.00 4.85
1551 3724 1.529438 GTGTTCGTTTCAATCGGCTGA 59.471 47.619 0.00 0.00 0.00 4.26
1552 3725 2.159627 GTGTTCGTTTCAATCGGCTGAT 59.840 45.455 0.90 0.90 35.98 2.90
1553 3726 2.811431 TGTTCGTTTCAATCGGCTGATT 59.189 40.909 15.26 15.26 45.70 2.57
1554 3727 3.252215 TGTTCGTTTCAATCGGCTGATTT 59.748 39.130 18.34 1.34 42.14 2.17
1555 3728 3.740044 TCGTTTCAATCGGCTGATTTC 57.260 42.857 18.34 8.36 42.14 2.17
1556 3729 3.070748 TCGTTTCAATCGGCTGATTTCA 58.929 40.909 18.34 5.34 42.14 2.69
1557 3730 3.120338 TCGTTTCAATCGGCTGATTTCAC 60.120 43.478 18.34 13.17 42.14 3.18
1558 3731 3.364864 CGTTTCAATCGGCTGATTTCACA 60.365 43.478 18.34 0.37 42.14 3.58
1559 3732 4.161333 GTTTCAATCGGCTGATTTCACAG 58.839 43.478 18.34 7.09 42.14 3.66
1570 3743 4.466828 CTGATTTCACAGCTTGTAAACCG 58.533 43.478 0.00 0.00 0.00 4.44
1571 3744 2.766970 TTTCACAGCTTGTAAACCGC 57.233 45.000 0.00 0.00 0.00 5.68
1572 3745 0.584396 TTCACAGCTTGTAAACCGCG 59.416 50.000 0.00 0.00 0.00 6.46
1573 3746 0.531090 TCACAGCTTGTAAACCGCGT 60.531 50.000 4.92 0.00 0.00 6.01
1574 3747 0.110823 CACAGCTTGTAAACCGCGTC 60.111 55.000 4.92 0.00 0.00 5.19
1575 3748 1.226030 ACAGCTTGTAAACCGCGTCC 61.226 55.000 4.92 0.00 0.00 4.79
1576 3749 0.949105 CAGCTTGTAAACCGCGTCCT 60.949 55.000 4.92 0.00 0.00 3.85
1577 3750 0.949105 AGCTTGTAAACCGCGTCCTG 60.949 55.000 4.92 0.00 0.00 3.86
1578 3751 1.495951 CTTGTAAACCGCGTCCTGC 59.504 57.895 4.92 0.00 41.47 4.85
1616 3789 3.649986 GCACCACGTGTCCTGTGC 61.650 66.667 24.83 24.83 46.09 4.57
1618 3791 4.602259 ACCACGTGTCCTGTGCGG 62.602 66.667 15.65 0.00 36.01 5.69
1620 3793 4.293648 CACGTGTCCTGTGCGGGA 62.294 66.667 7.58 0.00 0.00 5.14
1655 3828 1.133450 TCCCAGCCTTATCTACTCGCT 60.133 52.381 0.00 0.00 0.00 4.93
1711 3884 0.388520 TTCATCCTCACGCGACACTG 60.389 55.000 15.93 0.00 0.00 3.66
1713 3886 2.640302 ATCCTCACGCGACACTGCT 61.640 57.895 15.93 0.00 0.00 4.24
1762 3951 0.396417 CACCACCAACCAAGGAACCA 60.396 55.000 0.00 0.00 0.00 3.67
1815 4004 3.902112 CTGCCCCAACACCACCCT 61.902 66.667 0.00 0.00 0.00 4.34
1851 4040 1.679898 GAAGCAGCCACCCTACTGT 59.320 57.895 0.00 0.00 36.26 3.55
1856 4045 1.209504 GCAGCCACCCTACTGTCATAA 59.790 52.381 0.00 0.00 36.26 1.90
1861 4052 3.055385 GCCACCCTACTGTCATAACTCAA 60.055 47.826 0.00 0.00 0.00 3.02
1919 4112 0.731514 ACACCGACAATGCTACGACG 60.732 55.000 0.00 0.00 0.00 5.12
1988 4182 4.070552 GTTCCCGCTCGCCACTCT 62.071 66.667 0.00 0.00 0.00 3.24
2040 4235 2.981560 GCACCATTGCTGTGACGGG 61.982 63.158 0.00 0.00 46.17 5.28
2096 4292 2.818487 CTGCGTTGCAACACGACCA 61.818 57.895 28.01 14.86 43.15 4.02
2102 4300 0.105964 TTGCAACACGACCAGCTACT 59.894 50.000 0.00 0.00 0.00 2.57
2122 4320 3.241530 TGGAAGAGGCTGCGGTGT 61.242 61.111 0.00 0.00 0.00 4.16
2123 4321 2.435059 GGAAGAGGCTGCGGTGTC 60.435 66.667 0.00 0.00 0.00 3.67
2124 4322 2.811317 GAAGAGGCTGCGGTGTCG 60.811 66.667 0.00 0.00 39.81 4.35
2159 4357 4.717629 CTCTGGCGGCGTTGACGA 62.718 66.667 9.37 0.00 43.02 4.20
2160 4358 4.717629 TCTGGCGGCGTTGACGAG 62.718 66.667 9.37 0.00 43.02 4.18
2165 4363 3.767230 CGGCGTTGACGAGCACTG 61.767 66.667 7.85 0.00 43.02 3.66
2166 4364 4.077188 GGCGTTGACGAGCACTGC 62.077 66.667 7.85 0.00 43.02 4.40
2167 4365 3.337889 GCGTTGACGAGCACTGCA 61.338 61.111 7.85 0.00 43.02 4.41
2168 4366 2.671177 GCGTTGACGAGCACTGCAT 61.671 57.895 7.85 0.00 43.02 3.96
2169 4367 1.131218 CGTTGACGAGCACTGCATG 59.869 57.895 3.30 0.00 43.02 4.06
2170 4368 1.560004 CGTTGACGAGCACTGCATGT 61.560 55.000 3.30 0.53 43.02 3.21
2171 4369 0.164647 GTTGACGAGCACTGCATGTC 59.835 55.000 15.22 15.22 36.17 3.06
2172 4370 0.249826 TTGACGAGCACTGCATGTCA 60.250 50.000 18.97 18.97 40.92 3.58
2174 4372 1.964290 GACGAGCACTGCATGTCAGC 61.964 60.000 16.54 5.50 46.76 4.26
2175 4373 1.740664 CGAGCACTGCATGTCAGCT 60.741 57.895 14.56 9.66 46.76 4.24
2176 4374 1.296755 CGAGCACTGCATGTCAGCTT 61.297 55.000 14.56 3.70 46.76 3.74
2177 4375 0.447011 GAGCACTGCATGTCAGCTTC 59.553 55.000 14.56 8.05 46.76 3.86
2178 4376 1.134075 GCACTGCATGTCAGCTTCG 59.866 57.895 14.56 5.18 46.76 3.79
2179 4377 1.134075 CACTGCATGTCAGCTTCGC 59.866 57.895 14.56 0.00 46.76 4.70
2180 4378 1.301953 ACTGCATGTCAGCTTCGCA 60.302 52.632 14.56 0.00 46.76 5.10
2181 4379 1.424240 CTGCATGTCAGCTTCGCAG 59.576 57.895 4.55 0.00 43.55 5.18
2190 4388 4.527157 GCTTCGCAGCGTCATGGC 62.527 66.667 15.93 9.26 35.91 4.40
2191 4389 3.869272 CTTCGCAGCGTCATGGCC 61.869 66.667 15.93 0.00 0.00 5.36
2199 4397 3.945434 CGTCATGGCCGCTGCATC 61.945 66.667 1.55 0.00 40.13 3.91
2200 4398 3.945434 GTCATGGCCGCTGCATCG 61.945 66.667 2.26 2.26 40.13 3.84
2206 4404 4.527157 GCCGCTGCATCGCAACTC 62.527 66.667 4.01 0.00 38.41 3.01
2207 4405 3.869272 CCGCTGCATCGCAACTCC 61.869 66.667 4.01 0.00 38.41 3.85
2208 4406 4.214383 CGCTGCATCGCAACTCCG 62.214 66.667 0.00 0.00 38.41 4.63
2209 4407 3.869272 GCTGCATCGCAACTCCGG 61.869 66.667 0.00 0.00 38.41 5.14
2210 4408 3.869272 CTGCATCGCAACTCCGGC 61.869 66.667 0.00 0.00 38.41 6.13
2260 4458 4.796231 GGTCGACGACCGCTGCAT 62.796 66.667 29.82 0.00 43.14 3.96
2261 4459 3.248171 GTCGACGACCGCTGCATC 61.248 66.667 17.25 0.00 38.37 3.91
2262 4460 4.829518 TCGACGACCGCTGCATCG 62.830 66.667 18.40 18.40 43.97 3.84
2272 4470 4.457496 CTGCATCGCACCTCCGGT 62.457 66.667 0.00 0.00 35.62 5.28
2345 4543 2.308344 CAGCTCTGCGTCATCATGG 58.692 57.895 0.00 0.00 0.00 3.66
2346 4544 1.523258 AGCTCTGCGTCATCATGGC 60.523 57.895 0.00 0.00 0.00 4.40
2347 4545 2.541120 GCTCTGCGTCATCATGGCC 61.541 63.158 0.00 0.00 0.00 5.36
2348 4546 2.202919 TCTGCGTCATCATGGCCG 60.203 61.111 0.00 0.00 0.00 6.13
2349 4547 3.945434 CTGCGTCATCATGGCCGC 61.945 66.667 13.66 13.66 45.92 6.53
2350 4548 4.471908 TGCGTCATCATGGCCGCT 62.472 61.111 19.05 0.00 45.90 5.52
2351 4549 3.945434 GCGTCATCATGGCCGCTG 61.945 66.667 13.37 0.00 42.66 5.18
2352 4550 3.945434 CGTCATCATGGCCGCTGC 61.945 66.667 0.00 0.00 0.00 5.25
2353 4551 2.825387 GTCATCATGGCCGCTGCA 60.825 61.111 1.55 0.00 40.13 4.41
2354 4552 2.191513 GTCATCATGGCCGCTGCAT 61.192 57.895 1.55 0.00 40.13 3.96
2355 4553 1.895231 TCATCATGGCCGCTGCATC 60.895 57.895 1.55 0.00 40.13 3.91
2356 4554 2.976350 ATCATGGCCGCTGCATCG 60.976 61.111 2.26 2.26 40.13 3.84
2390 4588 2.103538 GGCGTCCGCTTCATCGTA 59.896 61.111 11.82 0.00 41.60 3.43
2391 4589 1.944676 GGCGTCCGCTTCATCGTAG 60.945 63.158 11.82 0.00 41.60 3.51
2392 4590 2.577785 GCGTCCGCTTCATCGTAGC 61.578 63.158 4.10 0.00 38.26 3.58
2393 4591 1.064296 CGTCCGCTTCATCGTAGCT 59.936 57.895 0.00 0.00 36.49 3.32
2394 4592 0.930742 CGTCCGCTTCATCGTAGCTC 60.931 60.000 0.00 0.00 36.49 4.09
2395 4593 0.595310 GTCCGCTTCATCGTAGCTCC 60.595 60.000 0.00 0.00 36.49 4.70
2396 4594 1.658717 CCGCTTCATCGTAGCTCCG 60.659 63.158 0.00 0.00 36.49 4.63
2397 4595 1.658717 CGCTTCATCGTAGCTCCGG 60.659 63.158 0.00 0.00 36.49 5.14
2398 4596 1.951631 GCTTCATCGTAGCTCCGGC 60.952 63.158 0.00 0.00 35.74 6.13
2399 4597 1.658717 CTTCATCGTAGCTCCGGCG 60.659 63.158 0.00 0.00 44.37 6.46
2400 4598 3.133767 TTCATCGTAGCTCCGGCGG 62.134 63.158 22.51 22.51 44.37 6.13
2414 4612 3.740397 GCGGCTGCTGCATCACAA 61.740 61.111 27.51 0.00 41.91 3.33
2415 4613 2.177531 CGGCTGCTGCATCACAAC 59.822 61.111 17.89 0.00 41.91 3.32
2416 4614 2.330372 CGGCTGCTGCATCACAACT 61.330 57.895 17.89 0.00 41.91 3.16
2417 4615 1.505353 GGCTGCTGCATCACAACTC 59.495 57.895 17.89 0.00 41.91 3.01
2418 4616 1.505353 GCTGCTGCATCACAACTCC 59.495 57.895 11.11 0.00 39.41 3.85
2419 4617 1.792301 CTGCTGCATCACAACTCCG 59.208 57.895 1.31 0.00 0.00 4.63
2420 4618 1.642037 CTGCTGCATCACAACTCCGG 61.642 60.000 1.31 0.00 0.00 5.14
2421 4619 3.044059 GCTGCATCACAACTCCGGC 62.044 63.158 0.00 0.00 0.00 6.13
2422 4620 2.741985 TGCATCACAACTCCGGCG 60.742 61.111 0.00 0.00 0.00 6.46
2423 4621 4.166011 GCATCACAACTCCGGCGC 62.166 66.667 0.00 0.00 0.00 6.53
2424 4622 3.499737 CATCACAACTCCGGCGCC 61.500 66.667 19.07 19.07 0.00 6.53
2425 4623 3.706373 ATCACAACTCCGGCGCCT 61.706 61.111 26.68 1.35 0.00 5.52
2426 4624 2.355986 ATCACAACTCCGGCGCCTA 61.356 57.895 26.68 11.82 0.00 3.93
2427 4625 2.573609 ATCACAACTCCGGCGCCTAC 62.574 60.000 26.68 0.00 0.00 3.18
2428 4626 3.307906 ACAACTCCGGCGCCTACA 61.308 61.111 26.68 6.78 0.00 2.74
2429 4627 2.047655 CAACTCCGGCGCCTACAA 60.048 61.111 26.68 5.78 0.00 2.41
2430 4628 2.100631 CAACTCCGGCGCCTACAAG 61.101 63.158 26.68 17.61 0.00 3.16
2431 4629 3.310860 AACTCCGGCGCCTACAAGG 62.311 63.158 26.68 18.19 38.80 3.61
2440 4638 2.821366 CCTACAAGGCCGCTGCTG 60.821 66.667 7.72 0.00 37.74 4.41
2441 4639 3.503363 CTACAAGGCCGCTGCTGC 61.503 66.667 7.57 7.57 37.74 5.25
2458 4656 4.124351 CCGTGCTGGGCATGCTTG 62.124 66.667 18.92 9.06 43.41 4.01
2459 4657 4.124351 CGTGCTGGGCATGCTTGG 62.124 66.667 18.92 8.67 41.91 3.61
2460 4658 2.677524 GTGCTGGGCATGCTTGGA 60.678 61.111 18.92 6.44 41.91 3.53
2461 4659 2.361992 TGCTGGGCATGCTTGGAG 60.362 61.111 18.92 9.28 31.71 3.86
2462 4660 3.834799 GCTGGGCATGCTTGGAGC 61.835 66.667 18.92 15.10 42.82 4.70
2463 4661 3.515286 CTGGGCATGCTTGGAGCG 61.515 66.667 18.92 0.00 46.26 5.03
2465 4663 4.802051 GGGCATGCTTGGAGCGGA 62.802 66.667 18.92 0.00 46.26 5.54
2466 4664 3.512516 GGCATGCTTGGAGCGGAC 61.513 66.667 18.92 0.00 46.26 4.79
2467 4665 2.747460 GCATGCTTGGAGCGGACA 60.747 61.111 11.37 0.00 46.26 4.02
2468 4666 2.758089 GCATGCTTGGAGCGGACAG 61.758 63.158 11.37 0.00 46.26 3.51
2469 4667 1.376424 CATGCTTGGAGCGGACAGT 60.376 57.895 0.00 0.00 46.26 3.55
2470 4668 1.376424 ATGCTTGGAGCGGACAGTG 60.376 57.895 0.00 0.00 46.26 3.66
2471 4669 2.743928 GCTTGGAGCGGACAGTGG 60.744 66.667 0.00 0.00 0.00 4.00
2472 4670 2.046892 CTTGGAGCGGACAGTGGG 60.047 66.667 0.00 0.00 0.00 4.61
2473 4671 4.329545 TTGGAGCGGACAGTGGGC 62.330 66.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
369 371 2.037251 AGGTTGACGTCAGCATACTGTT 59.963 45.455 29.72 8.95 44.77 3.16
569 573 4.683400 CGCAGAGACCAACCAATATTACCT 60.683 45.833 0.00 0.00 0.00 3.08
648 942 5.724328 TCATATCAATCCGGATAAGTGCTC 58.276 41.667 19.48 0.00 33.73 4.26
649 943 5.745312 TCATATCAATCCGGATAAGTGCT 57.255 39.130 19.48 6.79 33.73 4.40
674 968 7.816031 ACTTGGAAAAGCTGTCATGAAATAATG 59.184 33.333 0.00 0.00 0.00 1.90
1215 3110 0.106708 GTCTGGTGCAGGTGTTGAGA 59.893 55.000 0.00 0.00 31.51 3.27
1525 3698 3.972502 CCGATTGAAACGAACACTTTTCC 59.027 43.478 0.00 0.00 31.76 3.13
1526 3699 3.420904 GCCGATTGAAACGAACACTTTTC 59.579 43.478 0.00 0.00 33.15 2.29
1527 3700 3.066203 AGCCGATTGAAACGAACACTTTT 59.934 39.130 0.00 0.00 0.00 2.27
1528 3701 2.616842 AGCCGATTGAAACGAACACTTT 59.383 40.909 0.00 0.00 0.00 2.66
1529 3702 2.032030 CAGCCGATTGAAACGAACACTT 60.032 45.455 0.00 0.00 0.00 3.16
1530 3703 1.531149 CAGCCGATTGAAACGAACACT 59.469 47.619 0.00 0.00 0.00 3.55
1531 3704 1.529438 TCAGCCGATTGAAACGAACAC 59.471 47.619 0.00 0.00 0.00 3.32
1532 3705 1.872388 TCAGCCGATTGAAACGAACA 58.128 45.000 0.00 0.00 0.00 3.18
1533 3706 3.471495 AATCAGCCGATTGAAACGAAC 57.529 42.857 0.00 0.00 40.45 3.95
1534 3707 3.500299 TGAAATCAGCCGATTGAAACGAA 59.500 39.130 0.00 0.00 41.12 3.85
1535 3708 3.070748 TGAAATCAGCCGATTGAAACGA 58.929 40.909 0.00 0.00 41.12 3.85
1536 3709 3.163594 GTGAAATCAGCCGATTGAAACG 58.836 45.455 0.00 0.00 41.12 3.60
1537 3710 4.159377 TGTGAAATCAGCCGATTGAAAC 57.841 40.909 0.00 0.00 41.12 2.78
1538 3711 4.424061 CTGTGAAATCAGCCGATTGAAA 57.576 40.909 0.00 0.00 41.12 2.69
1548 3721 4.466828 CGGTTTACAAGCTGTGAAATCAG 58.533 43.478 0.00 0.00 38.35 2.90
1549 3722 3.304391 GCGGTTTACAAGCTGTGAAATCA 60.304 43.478 0.00 0.00 27.45 2.57
1550 3723 3.234386 GCGGTTTACAAGCTGTGAAATC 58.766 45.455 0.00 0.00 27.45 2.17
1551 3724 2.350388 CGCGGTTTACAAGCTGTGAAAT 60.350 45.455 0.00 0.00 27.45 2.17
1552 3725 1.003331 CGCGGTTTACAAGCTGTGAAA 60.003 47.619 0.00 0.00 27.45 2.69
1553 3726 0.584396 CGCGGTTTACAAGCTGTGAA 59.416 50.000 0.00 0.00 0.00 3.18
1554 3727 0.531090 ACGCGGTTTACAAGCTGTGA 60.531 50.000 12.47 0.00 0.00 3.58
1555 3728 0.110823 GACGCGGTTTACAAGCTGTG 60.111 55.000 12.47 0.00 0.00 3.66
1556 3729 1.226030 GGACGCGGTTTACAAGCTGT 61.226 55.000 12.47 0.00 0.00 4.40
1557 3730 0.949105 AGGACGCGGTTTACAAGCTG 60.949 55.000 12.47 0.00 0.00 4.24
1558 3731 0.949105 CAGGACGCGGTTTACAAGCT 60.949 55.000 12.47 0.00 0.00 3.74
1559 3732 1.495951 CAGGACGCGGTTTACAAGC 59.504 57.895 12.47 0.00 0.00 4.01
1560 3733 1.495951 GCAGGACGCGGTTTACAAG 59.504 57.895 12.47 0.00 0.00 3.16
1561 3734 3.645286 GCAGGACGCGGTTTACAA 58.355 55.556 12.47 0.00 0.00 2.41
1580 3753 3.337889 CACAGGACACGTGGTGCG 61.338 66.667 21.57 8.10 43.57 5.34
1581 3754 3.649986 GCACAGGACACGTGGTGC 61.650 66.667 24.83 24.83 36.98 5.01
1582 3755 3.337889 CGCACAGGACACGTGGTG 61.338 66.667 21.57 18.12 39.75 4.17
1585 3758 4.000557 GTGCGCACAGGACACGTG 62.001 66.667 34.52 15.48 41.21 4.49
1616 3789 4.016706 GGAGTGGTGGTGGTCCCG 62.017 72.222 0.00 0.00 35.15 5.14
1618 3791 1.299976 GATGGAGTGGTGGTGGTCC 59.700 63.158 0.00 0.00 0.00 4.46
1620 3793 2.231380 GGGATGGAGTGGTGGTGGT 61.231 63.158 0.00 0.00 0.00 4.16
1655 3828 0.253610 ACGGGTGGAGAAAACACACA 59.746 50.000 0.00 0.00 42.28 3.72
1711 3884 1.323412 TCGATGGCCTCTTCTCTAGC 58.677 55.000 3.32 0.00 0.00 3.42
1713 3886 2.520069 GGATCGATGGCCTCTTCTCTA 58.480 52.381 0.54 0.00 0.00 2.43
1779 3968 4.238514 GCAGAGTAGCATTATAAGGTCGG 58.761 47.826 0.00 0.00 0.00 4.79
1782 3971 3.328050 GGGGCAGAGTAGCATTATAAGGT 59.672 47.826 0.00 0.00 35.83 3.50
1815 4004 1.610363 TCGCCCTATGTTTGCAACAA 58.390 45.000 0.00 0.00 45.86 2.83
1851 4040 3.064958 CGGCTACGACTCTTGAGTTATGA 59.935 47.826 4.67 0.00 44.60 2.15
1856 4045 1.507174 GCGGCTACGACTCTTGAGT 59.493 57.895 2.59 2.59 44.60 3.41
1906 4099 1.373748 AACCGCGTCGTAGCATTGT 60.374 52.632 4.92 0.00 36.85 2.71
1987 4181 1.022735 GGATTGCAGCATGGAGTGAG 58.977 55.000 0.00 0.00 38.09 3.51
1988 4182 0.328926 TGGATTGCAGCATGGAGTGA 59.671 50.000 0.00 0.00 38.09 3.41
2040 4235 1.144936 CGGAGTTGAGGGAGATGGC 59.855 63.158 0.00 0.00 0.00 4.40
2090 4286 2.093106 CTTCCACTAGTAGCTGGTCGT 58.907 52.381 14.60 0.00 0.00 4.34
2096 4292 2.383855 CAGCCTCTTCCACTAGTAGCT 58.616 52.381 0.00 0.00 0.00 3.32
2102 4300 1.609501 ACCGCAGCCTCTTCCACTA 60.610 57.895 0.00 0.00 0.00 2.74
2142 4340 4.717629 TCGTCAACGCCGCCAGAG 62.718 66.667 0.00 0.00 39.60 3.35
2143 4341 4.717629 CTCGTCAACGCCGCCAGA 62.718 66.667 0.00 0.00 39.60 3.86
2148 4346 3.767230 CAGTGCTCGTCAACGCCG 61.767 66.667 0.00 0.00 39.60 6.46
2149 4347 4.077188 GCAGTGCTCGTCAACGCC 62.077 66.667 8.18 0.00 39.60 5.68
2150 4348 2.671177 ATGCAGTGCTCGTCAACGC 61.671 57.895 17.60 0.00 39.60 4.84
2151 4349 1.131218 CATGCAGTGCTCGTCAACG 59.869 57.895 17.60 0.00 41.45 4.10
2152 4350 0.164647 GACATGCAGTGCTCGTCAAC 59.835 55.000 23.98 5.98 33.18 3.18
2153 4351 0.249826 TGACATGCAGTGCTCGTCAA 60.250 50.000 27.26 16.25 37.43 3.18
2154 4352 0.668401 CTGACATGCAGTGCTCGTCA 60.668 55.000 27.39 27.39 39.85 4.35
2155 4353 1.964290 GCTGACATGCAGTGCTCGTC 61.964 60.000 22.84 22.84 46.62 4.20
2156 4354 2.031516 GCTGACATGCAGTGCTCGT 61.032 57.895 17.60 13.07 46.62 4.18
2157 4355 1.296755 AAGCTGACATGCAGTGCTCG 61.297 55.000 17.60 9.69 46.62 5.03
2158 4356 0.447011 GAAGCTGACATGCAGTGCTC 59.553 55.000 17.60 6.27 46.62 4.26
2159 4357 1.296755 CGAAGCTGACATGCAGTGCT 61.297 55.000 17.60 7.81 46.62 4.40
2160 4358 1.134075 CGAAGCTGACATGCAGTGC 59.866 57.895 8.58 8.58 46.62 4.40
2174 4372 3.869272 GGCCATGACGCTGCGAAG 61.869 66.667 30.47 14.06 0.00 3.79
2182 4380 3.945434 GATGCAGCGGCCATGACG 61.945 66.667 6.32 0.00 40.13 4.35
2183 4381 3.945434 CGATGCAGCGGCCATGAC 61.945 66.667 18.26 0.00 40.13 3.06
2189 4387 4.527157 GAGTTGCGATGCAGCGGC 62.527 66.667 27.22 18.26 44.23 6.53
2190 4388 3.869272 GGAGTTGCGATGCAGCGG 61.869 66.667 27.22 8.00 44.23 5.52
2191 4389 4.214383 CGGAGTTGCGATGCAGCG 62.214 66.667 22.00 22.00 44.23 5.18
2192 4390 3.869272 CCGGAGTTGCGATGCAGC 61.869 66.667 0.00 0.00 40.61 5.25
2193 4391 3.869272 GCCGGAGTTGCGATGCAG 61.869 66.667 5.05 0.00 40.61 4.41
2244 4442 3.248171 GATGCAGCGGTCGTCGAC 61.248 66.667 17.16 17.16 42.43 4.20
2245 4443 4.829518 CGATGCAGCGGTCGTCGA 62.830 66.667 18.26 0.00 43.45 4.20
2327 4525 1.773054 GCCATGATGACGCAGAGCTG 61.773 60.000 0.00 0.00 0.00 4.24
2328 4526 1.523258 GCCATGATGACGCAGAGCT 60.523 57.895 0.00 0.00 0.00 4.09
2329 4527 2.541120 GGCCATGATGACGCAGAGC 61.541 63.158 0.00 0.00 0.00 4.09
2330 4528 2.242572 CGGCCATGATGACGCAGAG 61.243 63.158 2.24 0.00 0.00 3.35
2331 4529 2.202919 CGGCCATGATGACGCAGA 60.203 61.111 2.24 0.00 0.00 4.26
2335 4533 3.945434 GCAGCGGCCATGATGACG 61.945 66.667 2.24 0.00 0.00 4.35
2336 4534 2.126417 GATGCAGCGGCCATGATGAC 62.126 60.000 6.32 0.00 40.13 3.06
2337 4535 1.895231 GATGCAGCGGCCATGATGA 60.895 57.895 6.32 0.00 40.13 2.92
2338 4536 2.643272 GATGCAGCGGCCATGATG 59.357 61.111 6.32 0.00 40.13 3.07
2339 4537 2.976350 CGATGCAGCGGCCATGAT 60.976 61.111 18.26 0.00 40.13 2.45
2373 4571 1.944676 CTACGATGAAGCGGACGCC 60.945 63.158 13.63 0.00 43.17 5.68
2374 4572 2.577785 GCTACGATGAAGCGGACGC 61.578 63.158 8.91 8.91 42.33 5.19
2375 4573 0.930742 GAGCTACGATGAAGCGGACG 60.931 60.000 0.00 0.00 44.87 4.79
2376 4574 0.595310 GGAGCTACGATGAAGCGGAC 60.595 60.000 0.00 0.00 44.87 4.79
2377 4575 1.734137 GGAGCTACGATGAAGCGGA 59.266 57.895 0.00 0.00 44.87 5.54
2378 4576 1.658717 CGGAGCTACGATGAAGCGG 60.659 63.158 14.92 0.00 44.87 5.52
2379 4577 1.658717 CCGGAGCTACGATGAAGCG 60.659 63.158 22.92 0.00 44.87 4.68
2380 4578 1.951631 GCCGGAGCTACGATGAAGC 60.952 63.158 22.92 10.76 40.40 3.86
2381 4579 1.658717 CGCCGGAGCTACGATGAAG 60.659 63.158 22.92 3.02 36.60 3.02
2382 4580 2.411701 CGCCGGAGCTACGATGAA 59.588 61.111 22.92 0.00 36.60 2.57
2383 4581 3.592814 CCGCCGGAGCTACGATGA 61.593 66.667 22.92 0.00 36.60 2.92
2397 4595 3.740397 TTGTGATGCAGCAGCCGC 61.740 61.111 4.06 6.20 41.13 6.53
2398 4596 2.177531 GTTGTGATGCAGCAGCCG 59.822 61.111 4.06 0.00 41.13 5.52
2399 4597 1.505353 GAGTTGTGATGCAGCAGCC 59.495 57.895 4.06 0.00 41.13 4.85
2400 4598 1.505353 GGAGTTGTGATGCAGCAGC 59.495 57.895 4.06 2.87 42.57 5.25
2401 4599 1.642037 CCGGAGTTGTGATGCAGCAG 61.642 60.000 4.06 0.00 0.00 4.24
2402 4600 1.672030 CCGGAGTTGTGATGCAGCA 60.672 57.895 0.00 0.00 0.00 4.41
2403 4601 3.044059 GCCGGAGTTGTGATGCAGC 62.044 63.158 5.05 0.00 0.00 5.25
2404 4602 2.743752 CGCCGGAGTTGTGATGCAG 61.744 63.158 5.05 0.00 0.00 4.41
2405 4603 2.741985 CGCCGGAGTTGTGATGCA 60.742 61.111 5.05 0.00 0.00 3.96
2406 4604 4.166011 GCGCCGGAGTTGTGATGC 62.166 66.667 5.05 0.00 0.00 3.91
2407 4605 2.572095 TAGGCGCCGGAGTTGTGATG 62.572 60.000 23.20 0.00 0.00 3.07
2408 4606 2.355986 TAGGCGCCGGAGTTGTGAT 61.356 57.895 23.20 0.95 0.00 3.06
2409 4607 2.992689 TAGGCGCCGGAGTTGTGA 60.993 61.111 23.20 0.00 0.00 3.58
2410 4608 2.813908 GTAGGCGCCGGAGTTGTG 60.814 66.667 23.20 0.00 0.00 3.33
2411 4609 2.781595 CTTGTAGGCGCCGGAGTTGT 62.782 60.000 23.20 3.61 0.00 3.32
2412 4610 2.047655 TTGTAGGCGCCGGAGTTG 60.048 61.111 23.20 0.00 0.00 3.16
2413 4611 2.264794 CTTGTAGGCGCCGGAGTT 59.735 61.111 23.20 5.39 0.00 3.01
2414 4612 3.771160 CCTTGTAGGCGCCGGAGT 61.771 66.667 23.20 5.85 0.00 3.85
2423 4621 2.821366 CAGCAGCGGCCTTGTAGG 60.821 66.667 4.82 0.00 42.56 3.18
2424 4622 3.503363 GCAGCAGCGGCCTTGTAG 61.503 66.667 6.19 0.00 42.56 2.74
2441 4639 4.124351 CAAGCATGCCCAGCACGG 62.124 66.667 15.66 0.00 43.04 4.94
2442 4640 4.124351 CCAAGCATGCCCAGCACG 62.124 66.667 15.66 0.00 43.04 5.34
2443 4641 2.677524 TCCAAGCATGCCCAGCAC 60.678 61.111 15.66 0.00 43.04 4.40
2444 4642 2.361992 CTCCAAGCATGCCCAGCA 60.362 61.111 15.66 0.00 44.86 4.41
2445 4643 3.834799 GCTCCAAGCATGCCCAGC 61.835 66.667 15.66 12.73 41.89 4.85
2446 4644 3.515286 CGCTCCAAGCATGCCCAG 61.515 66.667 15.66 6.25 42.58 4.45
2448 4646 4.802051 TCCGCTCCAAGCATGCCC 62.802 66.667 15.66 0.00 42.58 5.36
2449 4647 3.512516 GTCCGCTCCAAGCATGCC 61.513 66.667 15.66 0.00 42.58 4.40
2450 4648 2.747460 TGTCCGCTCCAAGCATGC 60.747 61.111 10.51 10.51 42.58 4.06
2451 4649 1.376424 ACTGTCCGCTCCAAGCATG 60.376 57.895 0.00 0.00 42.58 4.06
2452 4650 1.376424 CACTGTCCGCTCCAAGCAT 60.376 57.895 0.00 0.00 42.58 3.79
2453 4651 2.031012 CACTGTCCGCTCCAAGCA 59.969 61.111 0.00 0.00 42.58 3.91
2454 4652 2.743928 CCACTGTCCGCTCCAAGC 60.744 66.667 0.00 0.00 38.02 4.01
2455 4653 2.046892 CCCACTGTCCGCTCCAAG 60.047 66.667 0.00 0.00 0.00 3.61
2456 4654 4.329545 GCCCACTGTCCGCTCCAA 62.330 66.667 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.