Multiple sequence alignment - TraesCS1A01G188400

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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 TraesCS1A01G188400 chr1A 100.000 2198 0 0 1 2198 340248645 340250842 0.000000e+00 4060.0
1 TraesCS1A01G188400 chr1B 92.163 689 35 7 687 1369 352529798 352530473 0.000000e+00 955.0
2 TraesCS1A01G188400 chr1B 87.815 714 39 21 4 684 352527160 352527858 0.000000e+00 793.0
3 TraesCS1A01G188400 chr1B 96.970 33 1 0 1518 1550 349351387 349351355 3.050000e-04 56.5
4 TraesCS1A01G188400 chr1D 93.186 587 23 7 825 1408 260402550 260401978 0.000000e+00 846.0
5 TraesCS1A01G188400 chr1D 88.379 697 48 18 1 683 260404058 260403381 0.000000e+00 808.0
6 TraesCS1A01G188400 chr1D 84.006 669 75 13 1498 2142 260401845 260401185 4.010000e-172 614.0
7 TraesCS1A01G188400 chr1D 92.810 153 11 0 679 831 260403073 260402921 2.840000e-54 222.0
8 TraesCS1A01G188400 chr5A 91.667 48 1 3 1513 1560 471728070 471728114 1.820000e-06 63.9
9 TraesCS1A01G188400 chr5A 100.000 30 0 0 1522 1551 566216500 566216471 3.050000e-04 56.5
10 TraesCS1A01G188400 chr6D 100.000 31 0 0 1523 1553 7222603 7222573 8.480000e-05 58.4
11 TraesCS1A01G188400 chr6B 90.909 44 3 1 1507 1550 23635173 23635215 8.480000e-05 58.4
12 TraesCS1A01G188400 chr6A 94.737 38 1 1 1513 1550 16236078 16236042 8.480000e-05 58.4
13 TraesCS1A01G188400 chr7B 100.000 29 0 0 1523 1551 697489815 697489787 1.000000e-03 54.7
14 TraesCS1A01G188400 chr4B 92.105 38 2 1 1513 1550 51003003 51003039 4.000000e-03 52.8
15 TraesCS1A01G188400 chr3A 100.000 28 0 0 1523 1550 552536326 552536353 4.000000e-03 52.8


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 TraesCS1A01G188400 chr1A 340248645 340250842 2197 False 4060.0 4060 100.00000 1 2198 1 chr1A.!!$F1 2197
1 TraesCS1A01G188400 chr1B 352527160 352530473 3313 False 874.0 955 89.98900 4 1369 2 chr1B.!!$F1 1365
2 TraesCS1A01G188400 chr1D 260401185 260404058 2873 True 622.5 846 89.59525 1 2142 4 chr1D.!!$R1 2141

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
684 2658 0.030908 GGTCGCGAGTTATCTCAGGG 59.969 60.0 10.24 3.42 40.44 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 4404 0.106894 GAGGTTCTAGGGCCCGATTG 59.893 60.0 18.44 8.12 0.0 2.67 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
69 70 4.152580 GGAAGAACAGTGAAGAAATCGTCC 59.847 45.833 0.00 0.00 0.00 4.79
87 88 3.785859 GATGGTGCGGCTCCAGGA 61.786 66.667 25.69 6.04 38.42 3.86
113 115 1.913951 ATGGCACGGGAATCTGCAGA 61.914 55.000 20.79 20.79 34.90 4.26
114 116 1.817099 GGCACGGGAATCTGCAGAG 60.817 63.158 22.96 10.43 34.90 3.35
115 117 1.219124 GCACGGGAATCTGCAGAGA 59.781 57.895 22.96 0.00 33.31 3.10
116 118 0.809241 GCACGGGAATCTGCAGAGAG 60.809 60.000 22.96 12.86 33.31 3.20
117 119 0.820226 CACGGGAATCTGCAGAGAGA 59.180 55.000 22.96 0.00 0.00 3.10
118 120 0.820871 ACGGGAATCTGCAGAGAGAC 59.179 55.000 22.96 11.71 0.00 3.36
119 121 1.110442 CGGGAATCTGCAGAGAGACT 58.890 55.000 22.96 1.08 0.00 3.24
239 249 1.329906 GCTCCATGCTTGATCGTTCTG 59.670 52.381 0.22 0.00 38.95 3.02
244 254 3.374988 CCATGCTTGATCGTTCTGCTTTA 59.625 43.478 0.22 0.00 0.00 1.85
251 272 6.074569 GCTTGATCGTTCTGCTTTATAGAGAC 60.075 42.308 0.00 0.00 0.00 3.36
252 273 5.833082 TGATCGTTCTGCTTTATAGAGACC 58.167 41.667 0.00 0.00 0.00 3.85
253 274 5.594725 TGATCGTTCTGCTTTATAGAGACCT 59.405 40.000 0.00 0.00 0.00 3.85
301 323 1.765904 TGGTAACTGGACAGCAGTCAA 59.234 47.619 11.67 0.00 41.91 3.18
339 361 4.004196 AGTACAGGGTGTAAAAGACTGC 57.996 45.455 0.00 0.00 34.21 4.40
377 414 1.203928 CGTGCTCGATCCATTGAGAC 58.796 55.000 1.00 3.24 40.12 3.36
391 428 5.417266 TCCATTGAGACGATGAGATCTATCC 59.583 44.000 0.00 0.00 0.00 2.59
397 434 5.569355 AGACGATGAGATCTATCCATCAGT 58.431 41.667 18.10 16.08 35.79 3.41
398 435 5.415389 AGACGATGAGATCTATCCATCAGTG 59.585 44.000 18.10 8.36 35.79 3.66
478 515 1.493861 CTTGCATCCCTCTCTCTCCA 58.506 55.000 0.00 0.00 0.00 3.86
487 524 4.290942 TCCCTCTCTCTCCAAAAGTATCC 58.709 47.826 0.00 0.00 0.00 2.59
492 529 5.087323 TCTCTCTCCAAAAGTATCCACAGT 58.913 41.667 0.00 0.00 0.00 3.55
518 555 7.804614 TTGGAAATAACGCATGTTAATCAAC 57.195 32.000 0.00 0.00 43.43 3.18
618 655 1.737793 CGCCAACAACTATCCCAAGTC 59.262 52.381 0.00 0.00 0.00 3.01
645 682 1.005037 GACACGGATGGCAGTGACA 60.005 57.895 0.00 0.00 41.89 3.58
684 2658 0.030908 GGTCGCGAGTTATCTCAGGG 59.969 60.000 10.24 3.42 40.44 4.45
685 2659 1.022735 GTCGCGAGTTATCTCAGGGA 58.977 55.000 10.24 5.36 40.44 4.20
721 2695 0.464554 GGACAAGGCAGCCTATGACC 60.465 60.000 16.56 19.26 37.86 4.02
734 2708 4.599241 AGCCTATGACCCTAAATGCACTAT 59.401 41.667 0.00 0.00 0.00 2.12
766 2740 2.342279 CACACCGGTCACCGTCAT 59.658 61.111 16.87 0.00 46.80 3.06
823 2803 1.625315 TGAGCTAGGACACAGCACATT 59.375 47.619 0.00 0.00 41.66 2.71
867 3224 3.390967 TCATATCAGGAAATCAAGGCGGA 59.609 43.478 0.00 0.00 0.00 5.54
873 3230 0.938008 GAAATCAAGGCGGATCGGAC 59.062 55.000 4.16 0.19 0.00 4.79
1133 3490 2.503061 CCCGAGGCTGGTGATCAG 59.497 66.667 0.00 0.00 46.03 2.90
1200 3557 2.291209 TGGCCTTCATGTTGTGATGT 57.709 45.000 3.32 0.00 36.54 3.06
1201 3558 1.887854 TGGCCTTCATGTTGTGATGTG 59.112 47.619 3.32 0.00 36.54 3.21
1202 3559 2.161855 GGCCTTCATGTTGTGATGTGA 58.838 47.619 0.00 0.00 36.54 3.58
1203 3560 2.095059 GGCCTTCATGTTGTGATGTGAC 60.095 50.000 0.00 0.00 36.54 3.67
1204 3561 2.413239 GCCTTCATGTTGTGATGTGACG 60.413 50.000 0.00 0.00 36.54 4.35
1205 3562 2.160219 CCTTCATGTTGTGATGTGACGG 59.840 50.000 0.00 0.00 36.54 4.79
1206 3563 1.155889 TCATGTTGTGATGTGACGGC 58.844 50.000 0.00 0.00 0.00 5.68
1207 3564 0.179217 CATGTTGTGATGTGACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
1208 3565 1.298157 ATGTTGTGATGTGACGGCGG 61.298 55.000 13.24 0.00 0.00 6.13
1209 3566 1.959226 GTTGTGATGTGACGGCGGT 60.959 57.895 13.24 0.00 0.00 5.68
1210 3567 1.958715 TTGTGATGTGACGGCGGTG 60.959 57.895 13.24 0.00 0.00 4.94
1211 3568 2.048597 GTGATGTGACGGCGGTGA 60.049 61.111 13.24 0.00 0.00 4.02
1212 3569 1.447838 GTGATGTGACGGCGGTGAT 60.448 57.895 13.24 0.00 0.00 3.06
1246 3604 4.168291 GCTTGCCCCTCTCCTCGG 62.168 72.222 0.00 0.00 0.00 4.63
1250 3608 3.787001 GCCCCTCTCCTCGGTTGG 61.787 72.222 0.00 0.00 0.00 3.77
1261 3619 0.670546 CTCGGTTGGTGTTCGATGCT 60.671 55.000 0.00 0.00 32.32 3.79
1299 3661 6.808008 TCTTCTTTTCTTGAGCCTTGTATG 57.192 37.500 0.00 0.00 0.00 2.39
1300 3662 6.299141 TCTTCTTTTCTTGAGCCTTGTATGT 58.701 36.000 0.00 0.00 0.00 2.29
1301 3663 7.450074 TCTTCTTTTCTTGAGCCTTGTATGTA 58.550 34.615 0.00 0.00 0.00 2.29
1302 3664 8.103305 TCTTCTTTTCTTGAGCCTTGTATGTAT 58.897 33.333 0.00 0.00 0.00 2.29
1316 3678 7.872993 GCCTTGTATGTATCTGTAATAAGCTCA 59.127 37.037 0.00 0.00 0.00 4.26
1333 3695 3.954904 AGCTCACGGTAGTTGAGATGTAT 59.045 43.478 4.30 0.00 31.61 2.29
1380 3744 5.564550 AGCTTGGACTTTGATGTTAGATGT 58.435 37.500 0.00 0.00 0.00 3.06
1408 3772 2.290260 TGGTGTGGTAGAGGCAATGAAG 60.290 50.000 0.00 0.00 0.00 3.02
1409 3773 2.290323 GGTGTGGTAGAGGCAATGAAGT 60.290 50.000 0.00 0.00 0.00 3.01
1410 3774 2.744202 GTGTGGTAGAGGCAATGAAGTG 59.256 50.000 0.00 0.00 0.00 3.16
1411 3775 2.637382 TGTGGTAGAGGCAATGAAGTGA 59.363 45.455 0.00 0.00 0.00 3.41
1412 3776 3.072330 TGTGGTAGAGGCAATGAAGTGAA 59.928 43.478 0.00 0.00 0.00 3.18
1413 3777 4.072131 GTGGTAGAGGCAATGAAGTGAAA 58.928 43.478 0.00 0.00 0.00 2.69
1414 3778 4.702131 GTGGTAGAGGCAATGAAGTGAAAT 59.298 41.667 0.00 0.00 0.00 2.17
1415 3779 5.183904 GTGGTAGAGGCAATGAAGTGAAATT 59.816 40.000 0.00 0.00 0.00 1.82
1416 3780 6.374333 GTGGTAGAGGCAATGAAGTGAAATTA 59.626 38.462 0.00 0.00 0.00 1.40
1417 3781 6.945435 TGGTAGAGGCAATGAAGTGAAATTAA 59.055 34.615 0.00 0.00 0.00 1.40
1418 3782 7.094377 TGGTAGAGGCAATGAAGTGAAATTAAC 60.094 37.037 0.00 0.00 0.00 2.01
1419 3783 5.942872 AGAGGCAATGAAGTGAAATTAACG 58.057 37.500 0.00 0.00 0.00 3.18
1420 3784 5.473504 AGAGGCAATGAAGTGAAATTAACGT 59.526 36.000 0.00 0.00 0.00 3.99
1421 3785 5.699839 AGGCAATGAAGTGAAATTAACGTC 58.300 37.500 0.00 0.00 0.00 4.34
1422 3786 5.240623 AGGCAATGAAGTGAAATTAACGTCA 59.759 36.000 1.70 1.70 39.72 4.35
1423 3787 6.071952 AGGCAATGAAGTGAAATTAACGTCAT 60.072 34.615 6.15 6.15 44.95 3.06
1424 3788 6.033831 GGCAATGAAGTGAAATTAACGTCATG 59.966 38.462 11.70 8.00 43.13 3.07
1425 3789 6.033831 GCAATGAAGTGAAATTAACGTCATGG 59.966 38.462 11.70 10.20 43.13 3.66
1426 3790 6.817765 ATGAAGTGAAATTAACGTCATGGT 57.182 33.333 10.45 0.00 42.59 3.55
1427 3791 6.627395 TGAAGTGAAATTAACGTCATGGTT 57.373 33.333 0.00 0.00 32.26 3.67
1428 3792 6.664515 TGAAGTGAAATTAACGTCATGGTTC 58.335 36.000 0.00 0.00 32.26 3.62
1429 3793 6.261158 TGAAGTGAAATTAACGTCATGGTTCA 59.739 34.615 0.00 0.00 32.26 3.18
1430 3794 6.817765 AGTGAAATTAACGTCATGGTTCAT 57.182 33.333 0.00 0.00 0.00 2.57
1431 3795 6.842163 AGTGAAATTAACGTCATGGTTCATC 58.158 36.000 0.00 0.00 0.00 2.92
1432 3796 6.655003 AGTGAAATTAACGTCATGGTTCATCT 59.345 34.615 0.00 0.00 0.00 2.90
1433 3797 7.822334 AGTGAAATTAACGTCATGGTTCATCTA 59.178 33.333 0.00 0.00 0.00 1.98
1434 3798 8.116753 GTGAAATTAACGTCATGGTTCATCTAG 58.883 37.037 0.00 0.00 0.00 2.43
1435 3799 6.604735 AATTAACGTCATGGTTCATCTAGC 57.395 37.500 0.00 0.00 0.00 3.42
1436 3800 2.209838 ACGTCATGGTTCATCTAGCG 57.790 50.000 0.00 0.00 0.00 4.26
1437 3801 1.202417 ACGTCATGGTTCATCTAGCGG 60.202 52.381 0.00 0.00 0.00 5.52
1438 3802 1.067060 CGTCATGGTTCATCTAGCGGA 59.933 52.381 0.00 0.00 0.00 5.54
1457 3821 5.655532 AGCGGAATTTCTTGGACTAGTAGTA 59.344 40.000 1.88 0.00 0.00 1.82
1520 3958 8.103305 ACATATTTCTCTTGAAGTAGGCTTTCA 58.897 33.333 0.00 0.00 32.07 2.69
1523 3961 5.091261 TCTCTTGAAGTAGGCTTTCATCC 57.909 43.478 2.65 0.00 34.61 3.51
1524 3962 4.080863 TCTCTTGAAGTAGGCTTTCATCCC 60.081 45.833 2.65 0.00 34.61 3.85
1525 3963 3.054361 TCTTGAAGTAGGCTTTCATCCCC 60.054 47.826 2.65 0.00 34.61 4.81
1526 3964 1.209504 TGAAGTAGGCTTTCATCCCCG 59.790 52.381 0.00 0.00 34.61 5.73
1532 3970 1.215423 AGGCTTTCATCCCCGCTTTAT 59.785 47.619 0.00 0.00 0.00 1.40
1564 4002 5.643664 CAACCATCACATCCATACAACAAG 58.356 41.667 0.00 0.00 0.00 3.16
1565 4003 5.178096 ACCATCACATCCATACAACAAGA 57.822 39.130 0.00 0.00 0.00 3.02
1566 4004 5.188434 ACCATCACATCCATACAACAAGAG 58.812 41.667 0.00 0.00 0.00 2.85
1567 4005 5.188434 CCATCACATCCATACAACAAGAGT 58.812 41.667 0.00 0.00 0.00 3.24
1568 4006 5.065602 CCATCACATCCATACAACAAGAGTG 59.934 44.000 0.00 0.00 0.00 3.51
1577 4019 2.627945 ACAACAAGAGTGCACGAAGAA 58.372 42.857 12.01 0.00 0.00 2.52
1584 4026 3.391049 AGAGTGCACGAAGAAAGTAACC 58.609 45.455 12.01 0.00 0.00 2.85
1589 4031 3.004629 TGCACGAAGAAAGTAACCGAGTA 59.995 43.478 0.00 0.00 0.00 2.59
1591 4033 5.106197 TGCACGAAGAAAGTAACCGAGTATA 60.106 40.000 0.00 0.00 0.00 1.47
1592 4034 5.975939 GCACGAAGAAAGTAACCGAGTATAT 59.024 40.000 0.00 0.00 0.00 0.86
1596 4038 7.148018 ACGAAGAAAGTAACCGAGTATATTGGA 60.148 37.037 0.00 0.00 36.15 3.53
1601 4043 6.026947 AGTAACCGAGTATATTGGAGCATC 57.973 41.667 0.00 0.00 36.15 3.91
1613 4055 0.110056 GGAGCATCAGCACAAACACG 60.110 55.000 0.00 0.00 45.49 4.49
1614 4056 0.110056 GAGCATCAGCACAAACACGG 60.110 55.000 0.00 0.00 45.49 4.94
1615 4057 1.730547 GCATCAGCACAAACACGGC 60.731 57.895 0.00 0.00 41.58 5.68
1616 4058 1.440850 CATCAGCACAAACACGGCG 60.441 57.895 4.80 4.80 0.00 6.46
1617 4059 1.596752 ATCAGCACAAACACGGCGA 60.597 52.632 16.62 0.00 0.00 5.54
1618 4060 1.163420 ATCAGCACAAACACGGCGAA 61.163 50.000 16.62 0.00 0.00 4.70
1685 4127 1.301244 CTCAAGCACACTGAGGCGT 60.301 57.895 0.00 0.00 34.54 5.68
1688 4130 0.319900 CAAGCACACTGAGGCGTAGT 60.320 55.000 0.00 0.00 34.54 2.73
1700 4142 2.589890 GCGTAGTAAGTCGGCATGG 58.410 57.895 0.00 0.00 0.00 3.66
1715 4157 4.783621 TGGGGCAGCAGTCATCGC 62.784 66.667 0.00 0.00 0.00 4.58
1718 4160 3.558411 GGCAGCAGTCATCGCGTC 61.558 66.667 5.77 0.00 0.00 5.19
1720 4162 2.125952 CAGCAGTCATCGCGTCCA 60.126 61.111 5.77 0.00 0.00 4.02
1723 4165 2.580470 GCAGTCATCGCGTCCATCG 61.580 63.158 5.77 0.00 43.12 3.84
1736 4178 1.963855 CCATCGTGTCGCCAAACCA 60.964 57.895 0.00 0.00 0.00 3.67
1740 4182 0.533085 TCGTGTCGCCAAACCAATCA 60.533 50.000 0.00 0.00 0.00 2.57
1741 4183 0.521291 CGTGTCGCCAAACCAATCAT 59.479 50.000 0.00 0.00 0.00 2.45
1751 4193 3.635373 CCAAACCAATCATGATCCCTCTG 59.365 47.826 9.06 2.93 0.00 3.35
1756 4198 3.474600 CAATCATGATCCCTCTGTCCAC 58.525 50.000 9.06 0.00 0.00 4.02
1760 4202 4.496540 TCATGATCCCTCTGTCCACATAT 58.503 43.478 0.00 0.00 0.00 1.78
1761 4203 4.909695 TCATGATCCCTCTGTCCACATATT 59.090 41.667 0.00 0.00 0.00 1.28
1769 4211 5.491070 CCTCTGTCCACATATTGAGTTTCA 58.509 41.667 0.00 0.00 0.00 2.69
1784 4226 4.821260 TGAGTTTCAGTGCTGCAAGAATAA 59.179 37.500 16.33 3.81 34.07 1.40
1787 4229 6.572519 AGTTTCAGTGCTGCAAGAATAAAAA 58.427 32.000 16.33 4.31 34.07 1.94
1812 4255 3.388552 TGAAGATAGAGTCAGAGGCCA 57.611 47.619 5.01 0.00 0.00 5.36
1813 4256 3.295093 TGAAGATAGAGTCAGAGGCCAG 58.705 50.000 5.01 0.00 0.00 4.85
1827 4270 0.394488 GGCCAGCCTAAGAAAGACCC 60.394 60.000 0.00 0.00 0.00 4.46
1845 4288 2.026262 ACCCGCTCAATAACCATCTTGT 60.026 45.455 0.00 0.00 0.00 3.16
1850 4293 4.328983 CGCTCAATAACCATCTTGTTACGT 59.671 41.667 0.00 0.00 33.78 3.57
1878 4321 1.156736 CAGGGTCCAAACTAACGCTG 58.843 55.000 5.37 5.37 45.87 5.18
1894 4354 1.680651 CTGCACGTCTCCTCCTCCT 60.681 63.158 0.00 0.00 0.00 3.69
1905 4365 2.237392 CTCCTCCTCCTAGTTTGGTTGG 59.763 54.545 0.00 0.00 0.00 3.77
1908 4368 0.698818 CCTCCTAGTTTGGTTGGCCT 59.301 55.000 3.32 0.00 35.27 5.19
1911 4371 2.572104 CTCCTAGTTTGGTTGGCCTAGT 59.428 50.000 3.32 0.00 35.27 2.57
1923 4383 5.217393 GGTTGGCCTAGTTTTAAAGAAACG 58.783 41.667 3.32 0.00 35.42 3.60
1924 4384 5.217393 GTTGGCCTAGTTTTAAAGAAACGG 58.783 41.667 3.32 0.00 35.42 4.44
1925 4385 4.716794 TGGCCTAGTTTTAAAGAAACGGA 58.283 39.130 3.32 0.00 35.42 4.69
1926 4386 4.758165 TGGCCTAGTTTTAAAGAAACGGAG 59.242 41.667 3.32 0.00 35.42 4.63
1927 4387 4.379186 GGCCTAGTTTTAAAGAAACGGAGC 60.379 45.833 0.00 0.00 35.42 4.70
1944 4404 2.137528 GCTAGGTCTGAGGCCTCCC 61.138 68.421 29.95 22.75 37.54 4.30
1946 4406 0.325671 CTAGGTCTGAGGCCTCCCAA 60.326 60.000 29.95 12.39 37.54 4.12
1973 4433 3.118519 GCCCTAGAACCTCACGGATAAAA 60.119 47.826 0.00 0.00 0.00 1.52
1986 4446 7.334921 CCTCACGGATAAAACACCAAAGTAATA 59.665 37.037 0.00 0.00 0.00 0.98
1991 4451 6.183360 GGATAAAACACCAAAGTAATAGCGCT 60.183 38.462 17.26 17.26 0.00 5.92
1995 4455 1.339631 ACCAAAGTAATAGCGCTGCCA 60.340 47.619 22.90 0.00 0.00 4.92
2024 4484 1.341531 GTATGAGTCCATGTCTCCGGG 59.658 57.143 0.00 0.00 34.31 5.73
2045 4505 1.847798 TAGCACAAAGGGGGCACGAT 61.848 55.000 0.00 0.00 0.00 3.73
2060 4520 2.520536 CGATCCATCCCCAGGGTCC 61.521 68.421 4.22 0.00 32.44 4.46
2083 4543 2.859165 TGTTTGATCACCTCTGTCCC 57.141 50.000 0.00 0.00 0.00 4.46
2120 4580 5.271598 TCTCCCAACAATTGCCATAGAAAT 58.728 37.500 5.05 0.00 0.00 2.17
2125 4585 6.642131 CCCAACAATTGCCATAGAAATATTCG 59.358 38.462 5.05 0.00 34.02 3.34
2153 4613 2.990941 GCATGATATTGCCAAGACACG 58.009 47.619 0.00 0.00 36.60 4.49
2154 4614 2.287188 GCATGATATTGCCAAGACACGG 60.287 50.000 0.00 0.00 36.60 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.091885 AGATTCCCGTGCCATAAACCAT 60.092 45.455 0.00 0.00 0.00 3.55
93 94 0.179048 CTGCAGATTCCCGTGCCATA 60.179 55.000 8.42 0.00 39.04 2.74
113 115 0.636101 ATGCCCCTCTCTCAGTCTCT 59.364 55.000 0.00 0.00 0.00 3.10
114 116 0.752054 CATGCCCCTCTCTCAGTCTC 59.248 60.000 0.00 0.00 0.00 3.36
115 117 0.042431 ACATGCCCCTCTCTCAGTCT 59.958 55.000 0.00 0.00 0.00 3.24
116 118 0.177604 CACATGCCCCTCTCTCAGTC 59.822 60.000 0.00 0.00 0.00 3.51
117 119 1.908340 GCACATGCCCCTCTCTCAGT 61.908 60.000 0.00 0.00 34.31 3.41
118 120 1.153208 GCACATGCCCCTCTCTCAG 60.153 63.158 0.00 0.00 34.31 3.35
119 121 1.276859 ATGCACATGCCCCTCTCTCA 61.277 55.000 0.49 0.00 41.18 3.27
120 122 0.761187 TATGCACATGCCCCTCTCTC 59.239 55.000 0.49 0.00 41.18 3.20
153 155 3.371063 TGGGTGACGCTCGTCCTC 61.371 66.667 18.23 10.83 43.97 3.71
251 272 1.884067 GCCCACAGAAACAAGAGGAGG 60.884 57.143 0.00 0.00 0.00 4.30
252 273 1.202806 TGCCCACAGAAACAAGAGGAG 60.203 52.381 0.00 0.00 0.00 3.69
253 274 0.843309 TGCCCACAGAAACAAGAGGA 59.157 50.000 0.00 0.00 0.00 3.71
301 323 6.407202 CCTGTACTTTGGCTAGTCTAATTGT 58.593 40.000 0.00 0.00 0.00 2.71
339 361 1.065102 CGGAAGGAGCAGCAATTGATG 59.935 52.381 19.22 19.22 34.00 3.07
350 372 1.590259 GATCGAGCACGGAAGGAGC 60.590 63.158 3.11 0.00 40.21 4.70
353 375 0.179073 AATGGATCGAGCACGGAAGG 60.179 55.000 1.84 0.00 40.21 3.46
487 524 5.879237 ACATGCGTTATTTCCAATACTGTG 58.121 37.500 0.00 0.00 0.00 3.66
492 529 9.509855 GTTGATTAACATGCGTTATTTCCAATA 57.490 29.630 0.00 0.00 37.44 1.90
618 655 1.909376 CCATCCGTGTCTGTCTTACG 58.091 55.000 0.00 0.00 37.55 3.18
663 700 0.656259 CTGAGATAACTCGCGACCGA 59.344 55.000 3.71 0.00 45.25 4.69
664 701 0.317103 CCTGAGATAACTCGCGACCG 60.317 60.000 3.71 0.00 45.25 4.79
684 2658 2.034685 GTCCTTTCACTGCCTTTGGTTC 59.965 50.000 0.00 0.00 0.00 3.62
685 2659 2.031870 GTCCTTTCACTGCCTTTGGTT 58.968 47.619 0.00 0.00 0.00 3.67
734 2708 5.067273 ACCGGTGTGTGATCTGAAATTAAA 58.933 37.500 6.12 0.00 0.00 1.52
766 2740 0.476771 GTTTCCCTTCCCACTCCACA 59.523 55.000 0.00 0.00 0.00 4.17
873 3230 4.514577 CTAGTGGAGGGCACGCCG 62.515 72.222 3.61 0.00 39.76 6.46
1099 3456 3.272334 GCGCATCATGGTCCGTCC 61.272 66.667 0.30 0.00 0.00 4.79
1101 3458 4.856801 GGGCGCATCATGGTCCGT 62.857 66.667 10.83 0.00 0.00 4.69
1133 3490 3.082579 ATGTCCTCTTCCCGCGAGC 62.083 63.158 8.23 0.00 0.00 5.03
1192 3549 1.958715 CACCGCCGTCACATCACAA 60.959 57.895 0.00 0.00 0.00 3.33
1198 3555 2.276853 TACCATCACCGCCGTCACA 61.277 57.895 0.00 0.00 0.00 3.58
1200 3557 0.680601 TAGTACCATCACCGCCGTCA 60.681 55.000 0.00 0.00 0.00 4.35
1201 3558 0.672342 ATAGTACCATCACCGCCGTC 59.328 55.000 0.00 0.00 0.00 4.79
1202 3559 0.387929 CATAGTACCATCACCGCCGT 59.612 55.000 0.00 0.00 0.00 5.68
1203 3560 0.387929 ACATAGTACCATCACCGCCG 59.612 55.000 0.00 0.00 0.00 6.46
1204 3561 1.138266 ACACATAGTACCATCACCGCC 59.862 52.381 0.00 0.00 0.00 6.13
1205 3562 2.201732 CACACATAGTACCATCACCGC 58.798 52.381 0.00 0.00 0.00 5.68
1206 3563 2.201732 GCACACATAGTACCATCACCG 58.798 52.381 0.00 0.00 0.00 4.94
1207 3564 2.170607 AGGCACACATAGTACCATCACC 59.829 50.000 0.00 0.00 35.98 4.02
1208 3565 3.198068 CAGGCACACATAGTACCATCAC 58.802 50.000 0.00 0.00 35.98 3.06
1209 3566 2.419990 GCAGGCACACATAGTACCATCA 60.420 50.000 0.00 0.00 35.98 3.07
1210 3567 2.158900 AGCAGGCACACATAGTACCATC 60.159 50.000 0.00 0.00 35.98 3.51
1211 3568 1.839994 AGCAGGCACACATAGTACCAT 59.160 47.619 0.00 0.00 35.98 3.55
1212 3569 1.275666 AGCAGGCACACATAGTACCA 58.724 50.000 0.00 0.00 35.98 3.25
1246 3604 3.250040 ACAACTTAGCATCGAACACCAAC 59.750 43.478 0.00 0.00 0.00 3.77
1250 3608 5.331532 GCAAAAACAACTTAGCATCGAACAC 60.332 40.000 0.00 0.00 0.00 3.32
1261 3619 9.705290 AAGAAAAGAAGAAGCAAAAACAACTTA 57.295 25.926 0.00 0.00 0.00 2.24
1299 3661 6.968250 ACTACCGTGAGCTTATTACAGATAC 58.032 40.000 0.00 0.00 0.00 2.24
1300 3662 7.283807 TCAACTACCGTGAGCTTATTACAGATA 59.716 37.037 0.00 0.00 0.00 1.98
1301 3663 6.096423 TCAACTACCGTGAGCTTATTACAGAT 59.904 38.462 0.00 0.00 0.00 2.90
1302 3664 5.416639 TCAACTACCGTGAGCTTATTACAGA 59.583 40.000 0.00 0.00 0.00 3.41
1316 3678 8.008513 ACATCTTAATACATCTCAACTACCGT 57.991 34.615 0.00 0.00 0.00 4.83
1349 3713 1.606668 CAAAGTCCAAGCTACGCCAAA 59.393 47.619 0.00 0.00 0.00 3.28
1380 3744 5.069518 TGCCTCTACCACACCAGTATATA 57.930 43.478 0.00 0.00 0.00 0.86
1408 3772 6.842163 AGATGAACCATGACGTTAATTTCAC 58.158 36.000 0.00 0.00 0.00 3.18
1409 3773 7.201609 GCTAGATGAACCATGACGTTAATTTCA 60.202 37.037 0.00 0.00 0.00 2.69
1410 3774 7.126398 GCTAGATGAACCATGACGTTAATTTC 58.874 38.462 0.00 0.00 0.00 2.17
1411 3775 6.238103 CGCTAGATGAACCATGACGTTAATTT 60.238 38.462 0.00 0.00 0.00 1.82
1412 3776 5.234329 CGCTAGATGAACCATGACGTTAATT 59.766 40.000 0.00 0.00 0.00 1.40
1413 3777 4.745125 CGCTAGATGAACCATGACGTTAAT 59.255 41.667 0.00 0.00 0.00 1.40
1414 3778 4.109766 CGCTAGATGAACCATGACGTTAA 58.890 43.478 0.00 0.00 0.00 2.01
1415 3779 3.490249 CCGCTAGATGAACCATGACGTTA 60.490 47.826 0.00 0.00 0.00 3.18
1416 3780 2.540515 CGCTAGATGAACCATGACGTT 58.459 47.619 0.00 0.00 0.00 3.99
1417 3781 1.202417 CCGCTAGATGAACCATGACGT 60.202 52.381 0.00 0.00 0.00 4.34
1418 3782 1.067060 TCCGCTAGATGAACCATGACG 59.933 52.381 0.00 0.00 0.00 4.35
1419 3783 2.890808 TCCGCTAGATGAACCATGAC 57.109 50.000 0.00 0.00 0.00 3.06
1420 3784 4.422073 AATTCCGCTAGATGAACCATGA 57.578 40.909 0.00 0.00 0.00 3.07
1421 3785 4.818546 AGAAATTCCGCTAGATGAACCATG 59.181 41.667 0.00 0.00 0.00 3.66
1422 3786 5.041191 AGAAATTCCGCTAGATGAACCAT 57.959 39.130 0.00 0.00 0.00 3.55
1423 3787 4.487714 AGAAATTCCGCTAGATGAACCA 57.512 40.909 0.00 0.00 0.00 3.67
1424 3788 4.035675 CCAAGAAATTCCGCTAGATGAACC 59.964 45.833 0.00 0.00 0.00 3.62
1425 3789 4.876107 TCCAAGAAATTCCGCTAGATGAAC 59.124 41.667 0.00 0.00 0.00 3.18
1426 3790 4.876107 GTCCAAGAAATTCCGCTAGATGAA 59.124 41.667 0.00 0.00 0.00 2.57
1427 3791 4.162320 AGTCCAAGAAATTCCGCTAGATGA 59.838 41.667 0.00 0.00 0.00 2.92
1428 3792 4.446371 AGTCCAAGAAATTCCGCTAGATG 58.554 43.478 0.00 0.00 0.00 2.90
1429 3793 4.762289 AGTCCAAGAAATTCCGCTAGAT 57.238 40.909 0.00 0.00 0.00 1.98
1430 3794 4.710375 ACTAGTCCAAGAAATTCCGCTAGA 59.290 41.667 0.00 0.00 0.00 2.43
1431 3795 5.012328 ACTAGTCCAAGAAATTCCGCTAG 57.988 43.478 0.00 0.00 0.00 3.42
1432 3796 5.655532 ACTACTAGTCCAAGAAATTCCGCTA 59.344 40.000 0.00 0.00 0.00 4.26
1433 3797 3.983044 ACTAGTCCAAGAAATTCCGCT 57.017 42.857 0.00 0.00 0.00 5.52
1434 3798 4.756502 ACTACTAGTCCAAGAAATTCCGC 58.243 43.478 0.00 0.00 0.00 5.54
1435 3799 8.818057 CAAATACTACTAGTCCAAGAAATTCCG 58.182 37.037 0.00 0.00 0.00 4.30
1436 3800 9.668497 ACAAATACTACTAGTCCAAGAAATTCC 57.332 33.333 0.00 0.00 0.00 3.01
1506 3944 1.209504 CGGGGATGAAAGCCTACTTCA 59.790 52.381 0.00 0.00 46.10 3.02
1510 3948 0.107165 AAGCGGGGATGAAAGCCTAC 60.107 55.000 0.00 0.00 46.10 3.18
1511 3949 0.623723 AAAGCGGGGATGAAAGCCTA 59.376 50.000 0.00 0.00 46.10 3.93
1532 3970 7.658525 ATGGATGTGATGGTTGCTTTATTTA 57.341 32.000 0.00 0.00 0.00 1.40
1544 3982 5.065602 CACTCTTGTTGTATGGATGTGATGG 59.934 44.000 0.00 0.00 0.00 3.51
1553 3991 2.412870 TCGTGCACTCTTGTTGTATGG 58.587 47.619 16.19 0.00 0.00 2.74
1564 4002 2.155155 CGGTTACTTTCTTCGTGCACTC 59.845 50.000 16.19 0.00 0.00 3.51
1565 4003 2.132762 CGGTTACTTTCTTCGTGCACT 58.867 47.619 16.19 0.00 0.00 4.40
1566 4004 2.129607 TCGGTTACTTTCTTCGTGCAC 58.870 47.619 6.82 6.82 0.00 4.57
1567 4005 2.223876 ACTCGGTTACTTTCTTCGTGCA 60.224 45.455 0.00 0.00 0.00 4.57
1568 4006 2.401351 ACTCGGTTACTTTCTTCGTGC 58.599 47.619 0.00 0.00 0.00 5.34
1577 4019 5.864418 TGCTCCAATATACTCGGTTACTT 57.136 39.130 0.00 0.00 0.00 2.24
1584 4026 3.677121 GTGCTGATGCTCCAATATACTCG 59.323 47.826 0.00 0.00 40.48 4.18
1589 4031 4.018490 TGTTTGTGCTGATGCTCCAATAT 58.982 39.130 0.00 0.00 40.48 1.28
1591 4033 2.029649 GTGTTTGTGCTGATGCTCCAAT 60.030 45.455 0.00 0.00 40.48 3.16
1592 4034 1.337703 GTGTTTGTGCTGATGCTCCAA 59.662 47.619 0.00 0.00 40.48 3.53
1596 4038 1.951510 CCGTGTTTGTGCTGATGCT 59.048 52.632 0.00 0.00 40.48 3.79
1601 4043 0.524392 TTTTCGCCGTGTTTGTGCTG 60.524 50.000 0.00 0.00 0.00 4.41
1652 4094 2.358737 GAGGCACCGACCACTTGG 60.359 66.667 0.00 0.00 42.17 3.61
1653 4095 1.227823 TTGAGGCACCGACCACTTG 60.228 57.895 0.00 0.00 0.00 3.16
1654 4096 1.071471 CTTGAGGCACCGACCACTT 59.929 57.895 0.00 0.00 0.00 3.16
1655 4097 2.743718 CTTGAGGCACCGACCACT 59.256 61.111 0.00 0.00 0.00 4.00
1656 4098 3.050275 GCTTGAGGCACCGACCAC 61.050 66.667 0.00 0.00 41.35 4.16
1665 4107 3.978272 CCTCAGTGTGCTTGAGGC 58.022 61.111 8.23 0.00 42.10 4.70
1674 4116 1.467734 CGACTTACTACGCCTCAGTGT 59.532 52.381 0.00 0.00 40.62 3.55
1675 4117 1.202154 CCGACTTACTACGCCTCAGTG 60.202 57.143 0.00 0.00 0.00 3.66
1676 4118 1.093159 CCGACTTACTACGCCTCAGT 58.907 55.000 0.00 0.00 0.00 3.41
1677 4119 0.248539 GCCGACTTACTACGCCTCAG 60.249 60.000 0.00 0.00 0.00 3.35
1685 4127 0.978667 TGCCCCATGCCGACTTACTA 60.979 55.000 0.00 0.00 40.16 1.82
1688 4130 2.589540 CTGCCCCATGCCGACTTA 59.410 61.111 0.00 0.00 40.16 2.24
1718 4160 1.511318 TTGGTTTGGCGACACGATGG 61.511 55.000 0.00 0.00 42.67 3.51
1720 4162 0.802494 GATTGGTTTGGCGACACGAT 59.198 50.000 0.00 0.00 42.67 3.73
1723 4165 1.539388 TCATGATTGGTTTGGCGACAC 59.461 47.619 0.00 0.00 42.67 3.67
1727 4169 1.067516 GGGATCATGATTGGTTTGGCG 59.932 52.381 10.14 0.00 0.00 5.69
1729 4171 3.635373 CAGAGGGATCATGATTGGTTTGG 59.365 47.826 10.14 0.00 0.00 3.28
1736 4178 3.117745 TGTGGACAGAGGGATCATGATT 58.882 45.455 10.14 0.00 0.00 2.57
1740 4182 4.909695 TCAATATGTGGACAGAGGGATCAT 59.090 41.667 0.00 0.00 0.00 2.45
1741 4183 4.297768 TCAATATGTGGACAGAGGGATCA 58.702 43.478 0.00 0.00 0.00 2.92
1751 4193 4.697352 AGCACTGAAACTCAATATGTGGAC 59.303 41.667 0.00 0.00 0.00 4.02
1756 4198 4.690184 TGCAGCACTGAAACTCAATATG 57.310 40.909 0.81 0.00 0.00 1.78
1760 4202 2.642427 TCTTGCAGCACTGAAACTCAA 58.358 42.857 0.00 0.00 0.00 3.02
1761 4203 2.330440 TCTTGCAGCACTGAAACTCA 57.670 45.000 0.00 0.00 0.00 3.41
1787 4229 5.337975 GGCCTCTGACTCTATCTTCAAGTTT 60.338 44.000 0.00 0.00 0.00 2.66
1788 4230 4.161377 GGCCTCTGACTCTATCTTCAAGTT 59.839 45.833 0.00 0.00 0.00 2.66
1790 4232 3.703556 TGGCCTCTGACTCTATCTTCAAG 59.296 47.826 3.32 0.00 0.00 3.02
1793 4235 2.035832 GCTGGCCTCTGACTCTATCTTC 59.964 54.545 3.32 0.00 0.00 2.87
1794 4236 2.038659 GCTGGCCTCTGACTCTATCTT 58.961 52.381 3.32 0.00 0.00 2.40
1796 4238 0.678950 GGCTGGCCTCTGACTCTATC 59.321 60.000 3.32 0.00 0.00 2.08
1803 4246 1.556911 CTTTCTTAGGCTGGCCTCTGA 59.443 52.381 18.06 13.70 44.43 3.27
1804 4247 1.556911 TCTTTCTTAGGCTGGCCTCTG 59.443 52.381 18.06 11.68 44.43 3.35
1812 4255 0.537653 GAGCGGGTCTTTCTTAGGCT 59.462 55.000 0.00 0.00 0.00 4.58
1813 4256 0.249398 TGAGCGGGTCTTTCTTAGGC 59.751 55.000 8.82 0.00 0.00 3.93
1827 4270 4.328983 ACGTAACAAGATGGTTATTGAGCG 59.671 41.667 0.00 0.00 35.83 5.03
1850 4293 1.338890 TTTGGACCCTGTGGACGACA 61.339 55.000 0.00 0.00 34.81 4.35
1878 4321 0.394625 ACTAGGAGGAGGAGACGTGC 60.395 60.000 0.00 0.00 0.00 5.34
1889 4349 0.698818 AGGCCAACCAAACTAGGAGG 59.301 55.000 5.01 0.00 39.06 4.30
1894 4354 7.061688 TCTTTAAAACTAGGCCAACCAAACTA 58.938 34.615 5.01 0.00 39.06 2.24
1905 4365 4.454847 AGCTCCGTTTCTTTAAAACTAGGC 59.545 41.667 0.00 0.00 0.00 3.93
1908 4368 6.762333 ACCTAGCTCCGTTTCTTTAAAACTA 58.238 36.000 0.00 0.00 0.00 2.24
1911 4371 5.699458 CAGACCTAGCTCCGTTTCTTTAAAA 59.301 40.000 0.00 0.00 0.00 1.52
1923 4383 1.075600 AGGCCTCAGACCTAGCTCC 60.076 63.158 0.00 0.00 35.10 4.70
1924 4384 1.112916 GGAGGCCTCAGACCTAGCTC 61.113 65.000 33.29 8.80 37.77 4.09
1925 4385 1.075600 GGAGGCCTCAGACCTAGCT 60.076 63.158 33.29 0.00 37.77 3.32
1926 4386 2.137528 GGGAGGCCTCAGACCTAGC 61.138 68.421 33.29 13.59 37.77 3.42
1927 4387 0.325671 TTGGGAGGCCTCAGACCTAG 60.326 60.000 33.29 0.00 37.77 3.02
1944 4404 0.106894 GAGGTTCTAGGGCCCGATTG 59.893 60.000 18.44 8.12 0.00 2.67
1946 4406 1.049289 GTGAGGTTCTAGGGCCCGAT 61.049 60.000 18.44 1.33 0.00 4.18
1973 4433 1.737793 GCAGCGCTATTACTTTGGTGT 59.262 47.619 10.99 0.00 0.00 4.16
1986 4446 2.046507 CCTCTTCTTGGCAGCGCT 60.047 61.111 2.64 2.64 0.00 5.92
1991 4451 2.501723 GACTCATACCCTCTTCTTGGCA 59.498 50.000 0.00 0.00 0.00 4.92
1995 4455 4.366267 ACATGGACTCATACCCTCTTCTT 58.634 43.478 0.00 0.00 31.33 2.52
2024 4484 1.376609 CGTGCCCCCTTTGTGCTATC 61.377 60.000 0.00 0.00 0.00 2.08
2045 4505 1.913321 ATCAGGACCCTGGGGATGGA 61.913 60.000 18.88 9.66 43.75 3.41
2060 4520 3.937706 GGACAGAGGTGATCAAACATCAG 59.062 47.826 0.00 0.00 33.35 2.90
2120 4580 2.346766 ATCATGCCTTGTGCCGAATA 57.653 45.000 0.00 0.00 40.16 1.75
2125 4585 2.144482 GCAATATCATGCCTTGTGCC 57.856 50.000 0.00 0.00 40.49 5.01


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

AutoCloner maintained by Alex Coulton.