Multiple sequence alignment - TraesCS3D01G299500

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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 TraesCS3D01G299500 chr3D 100.000 5136 0 0 1 5136 414631217 414636352 0.000000e+00 9485.0
1 TraesCS3D01G299500 chr3D 96.154 52 2 0 2794 2845 108242116 108242167 9.160000e-13 86.1
2 TraesCS3D01G299500 chr3D 82.716 81 13 1 658 738 148067725 148067646 2.570000e-08 71.3
3 TraesCS3D01G299500 chr3B 93.631 2795 123 24 2256 5034 540460774 540463529 0.000000e+00 4124.0
4 TraesCS3D01G299500 chr3B 94.851 1515 69 6 737 2250 540459180 540460686 0.000000e+00 2357.0
5 TraesCS3D01G299500 chr3B 88.050 636 49 18 41 661 540458549 540459172 0.000000e+00 728.0
6 TraesCS3D01G299500 chr3B 94.643 112 5 1 5023 5134 540465027 540465137 6.840000e-39 172.0
7 TraesCS3D01G299500 chr3A 92.435 2300 129 14 2843 5134 535808922 535806660 0.000000e+00 3241.0
8 TraesCS3D01G299500 chr3A 95.889 900 37 0 1343 2242 535812273 535811374 0.000000e+00 1458.0
9 TraesCS3D01G299500 chr3A 94.646 579 29 1 767 1345 535821147 535820571 0.000000e+00 896.0
10 TraesCS3D01G299500 chr3A 91.896 617 22 10 56 662 535821741 535821143 0.000000e+00 837.0
11 TraesCS3D01G299500 chr3A 89.640 222 21 2 2240 2461 535810796 535810577 1.090000e-71 281.0
12 TraesCS3D01G299500 chr7D 78.840 638 124 9 3361 3991 154208975 154209608 2.210000e-113 420.0
13 TraesCS3D01G299500 chr7D 90.667 75 4 3 666 738 141811651 141811578 4.230000e-16 97.1
14 TraesCS3D01G299500 chr5A 75.953 341 65 11 1880 2210 657651613 657651946 5.320000e-35 159.0
15 TraesCS3D01G299500 chr5A 96.154 52 2 0 2794 2845 59701100 59701049 9.160000e-13 86.1
16 TraesCS3D01G299500 chr5D 76.431 297 60 9 3464 3755 530414294 530414003 8.910000e-33 152.0
17 TraesCS3D01G299500 chr5B 76.364 275 57 7 3464 3734 669593188 669592918 1.930000e-29 141.0
18 TraesCS3D01G299500 chr5B 87.342 79 9 1 2843 2921 490224178 490224101 7.080000e-14 89.8
19 TraesCS3D01G299500 chr4D 92.754 69 5 0 2842 2910 19348996 19349064 3.270000e-17 100.0
20 TraesCS3D01G299500 chr4D 94.737 57 2 1 685 741 372844610 372844555 2.550000e-13 87.9
21 TraesCS3D01G299500 chr4D 94.231 52 3 0 2794 2845 465124022 465124073 4.260000e-11 80.5
22 TraesCS3D01G299500 chr4D 92.593 54 3 1 685 738 380693973 380693921 5.510000e-10 76.8
23 TraesCS3D01G299500 chr2D 92.754 69 5 0 2843 2911 71386504 71386572 3.270000e-17 100.0
24 TraesCS3D01G299500 chr2D 88.158 76 9 0 2843 2918 215833227 215833302 1.970000e-14 91.6
25 TraesCS3D01G299500 chr2D 96.296 54 1 1 685 738 512036 511984 2.550000e-13 87.9
26 TraesCS3D01G299500 chr2D 96.154 52 2 0 2794 2845 71386571 71386520 9.160000e-13 86.1
27 TraesCS3D01G299500 chr2D 96.154 52 2 0 2794 2845 291856846 291856795 9.160000e-13 86.1
28 TraesCS3D01G299500 chr7B 92.647 68 5 0 2843 2910 151405778 151405845 1.180000e-16 99.0
29 TraesCS3D01G299500 chr7B 96.296 54 1 1 685 738 278476503 278476451 2.550000e-13 87.9
30 TraesCS3D01G299500 chr7B 96.154 52 2 0 2794 2845 13309649 13309700 9.160000e-13 86.1
31 TraesCS3D01G299500 chr7B 94.340 53 3 0 2793 2845 61851955 61851903 1.190000e-11 82.4
32 TraesCS3D01G299500 chr6D 92.647 68 5 0 2843 2910 418957054 418956987 1.180000e-16 99.0
33 TraesCS3D01G299500 chr6D 96.154 52 2 0 2794 2845 418956987 418957038 9.160000e-13 86.1
34 TraesCS3D01G299500 chr6D 96.078 51 2 0 2794 2844 418957161 418957111 3.300000e-12 84.2
35 TraesCS3D01G299500 chr1A 91.304 69 6 0 2843 2911 559234289 559234357 1.520000e-15 95.3
36 TraesCS3D01G299500 chr2A 96.296 54 1 1 685 738 152240398 152240450 2.550000e-13 87.9
37 TraesCS3D01G299500 chr4B 93.220 59 3 1 680 738 376153227 376153170 9.160000e-13 86.1
38 TraesCS3D01G299500 chr4A 94.545 55 2 1 685 739 439049551 439049604 3.300000e-12 84.2


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 TraesCS3D01G299500 chr3D 414631217 414636352 5135 False 9485.00 9485 100.000000 1 5136 1 chr3D.!!$F2 5135
1 TraesCS3D01G299500 chr3B 540458549 540465137 6588 False 1845.25 4124 92.793750 41 5134 4 chr3B.!!$F1 5093
2 TraesCS3D01G299500 chr3A 535806660 535812273 5613 True 1660.00 3241 92.654667 1343 5134 3 chr3A.!!$R1 3791
3 TraesCS3D01G299500 chr3A 535820571 535821741 1170 True 866.50 896 93.271000 56 1345 2 chr3A.!!$R2 1289
4 TraesCS3D01G299500 chr7D 154208975 154209608 633 False 420.00 420 78.840000 3361 3991 1 chr7D.!!$F1 630

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
861 892 0.865769 AACTGTGCGGATCGTTTCAC 59.134 50.0 0.0 0.0 0.00 3.18 F
2340 3033 0.312729 GTGTGTTTTTGGCTACCCCG 59.687 55.0 0.0 0.0 35.87 5.73 F
2699 4584 0.918983 ATTTCTCGCCCCATCTTGGA 59.081 50.0 0.0 0.0 40.96 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2766 4651 0.105408 ACGCGAACCTACCACAAACT 59.895 50.0 15.93 0.00 0.00 2.66 R
3991 5982 0.529119 CGGTCGGCGGTAGCTTTAAT 60.529 55.0 7.21 0.00 44.37 1.40 R
4503 6497 0.870393 ACTGAGTTGTTGCGCATCTG 59.130 50.0 12.75 12.11 0.00 2.90 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
71 72 4.853743 GCATAGTAAGCTTTTTGTGCAGTC 59.146 41.667 19.56 0.00 0.00 3.51
110 111 5.300752 CAATACCCAGTACTGAATAGGCAG 58.699 45.833 24.68 4.54 41.63 4.85
112 113 3.182152 ACCCAGTACTGAATAGGCAGTT 58.818 45.455 24.68 0.00 46.42 3.16
113 114 4.359105 ACCCAGTACTGAATAGGCAGTTA 58.641 43.478 24.68 0.00 46.42 2.24
116 117 4.372656 CAGTACTGAATAGGCAGTTAGGC 58.627 47.826 18.45 0.00 46.42 3.93
117 118 4.030913 AGTACTGAATAGGCAGTTAGGCA 58.969 43.478 0.00 0.00 46.42 4.75
118 119 3.268023 ACTGAATAGGCAGTTAGGCAC 57.732 47.619 0.00 0.00 46.42 5.01
120 121 4.030913 ACTGAATAGGCAGTTAGGCACTA 58.969 43.478 0.00 0.00 46.42 2.74
121 122 4.141914 ACTGAATAGGCAGTTAGGCACTAC 60.142 45.833 0.00 0.00 46.42 2.73
122 123 4.030913 TGAATAGGCAGTTAGGCACTACT 58.969 43.478 0.00 0.00 42.67 2.57
123 124 5.205821 TGAATAGGCAGTTAGGCACTACTA 58.794 41.667 0.00 0.00 42.67 1.82
124 125 5.839063 TGAATAGGCAGTTAGGCACTACTAT 59.161 40.000 0.00 0.00 42.67 2.12
125 126 5.730296 ATAGGCAGTTAGGCACTACTATG 57.270 43.478 0.00 0.00 42.67 2.23
126 127 3.375699 AGGCAGTTAGGCACTACTATGT 58.624 45.455 0.00 0.00 42.67 2.29
127 128 3.775316 AGGCAGTTAGGCACTACTATGTT 59.225 43.478 0.00 0.00 42.67 2.71
251 253 1.668751 TGACAACGACTTCACCAAAGC 59.331 47.619 0.00 0.00 38.67 3.51
270 272 3.334691 AGCGTAGACATTGCAAAAGCTA 58.665 40.909 1.71 2.24 0.00 3.32
292 294 4.749245 AAGAGCTTGTTAATGTTCACCG 57.251 40.909 0.00 0.00 0.00 4.94
381 383 4.068599 AGCTGAGCTTAGACTTTTTCCAC 58.931 43.478 10.16 0.00 33.89 4.02
383 385 4.307432 CTGAGCTTAGACTTTTTCCACGA 58.693 43.478 0.00 0.00 0.00 4.35
396 398 5.565592 TTTTCCACGATCATGAAGGATTG 57.434 39.130 0.00 0.00 35.24 2.67
406 408 4.272489 TCATGAAGGATTGGATGTTGGAC 58.728 43.478 0.00 0.00 0.00 4.02
411 413 6.493166 TGAAGGATTGGATGTTGGACTAATT 58.507 36.000 0.00 0.00 0.00 1.40
431 443 7.822334 ACTAATTTGACAATGACCTCGACAATA 59.178 33.333 0.00 0.00 0.00 1.90
539 566 2.136026 AGTTGTTCCTCTCAACCCCTT 58.864 47.619 5.38 0.00 44.02 3.95
560 589 5.067936 CCTTCAGTCAACTCTACGGTATGAT 59.932 44.000 0.00 0.00 0.00 2.45
690 720 7.861629 AGAGAGAGAGAGAGAAAGTCTATTCA 58.138 38.462 0.00 0.00 34.71 2.57
691 721 8.497745 AGAGAGAGAGAGAGAAAGTCTATTCAT 58.502 37.037 0.00 0.00 34.71 2.57
692 722 8.682936 AGAGAGAGAGAGAAAGTCTATTCATC 57.317 38.462 0.00 0.00 34.71 2.92
693 723 8.274322 AGAGAGAGAGAGAAAGTCTATTCATCA 58.726 37.037 0.00 0.00 34.71 3.07
694 724 9.071276 GAGAGAGAGAGAAAGTCTATTCATCAT 57.929 37.037 0.00 0.00 34.71 2.45
695 725 9.425248 AGAGAGAGAGAAAGTCTATTCATCATT 57.575 33.333 0.00 0.00 34.71 2.57
696 726 9.683069 GAGAGAGAGAAAGTCTATTCATCATTC 57.317 37.037 0.00 0.00 34.71 2.67
697 727 9.199645 AGAGAGAGAAAGTCTATTCATCATTCA 57.800 33.333 0.00 0.00 34.71 2.57
698 728 9.467258 GAGAGAGAAAGTCTATTCATCATTCAG 57.533 37.037 0.00 0.00 34.71 3.02
699 729 8.423349 AGAGAGAAAGTCTATTCATCATTCAGG 58.577 37.037 0.00 0.00 34.71 3.86
700 730 8.316497 AGAGAAAGTCTATTCATCATTCAGGA 57.684 34.615 0.00 0.00 31.71 3.86
701 731 8.936787 AGAGAAAGTCTATTCATCATTCAGGAT 58.063 33.333 0.00 0.00 31.71 3.24
702 732 8.905660 AGAAAGTCTATTCATCATTCAGGATG 57.094 34.615 0.00 0.00 44.78 3.51
703 733 7.444792 AGAAAGTCTATTCATCATTCAGGATGC 59.555 37.037 0.00 0.00 43.44 3.91
704 734 6.183810 AGTCTATTCATCATTCAGGATGCA 57.816 37.500 0.00 0.00 43.44 3.96
705 735 6.231951 AGTCTATTCATCATTCAGGATGCAG 58.768 40.000 0.00 0.00 43.44 4.41
706 736 6.042897 AGTCTATTCATCATTCAGGATGCAGA 59.957 38.462 0.00 0.00 43.44 4.26
707 737 6.709397 GTCTATTCATCATTCAGGATGCAGAA 59.291 38.462 0.00 0.00 43.44 3.02
708 738 7.390996 GTCTATTCATCATTCAGGATGCAGAAT 59.609 37.037 11.19 11.19 43.44 2.40
709 739 8.599792 TCTATTCATCATTCAGGATGCAGAATA 58.400 33.333 4.55 11.93 43.44 1.75
710 740 9.227777 CTATTCATCATTCAGGATGCAGAATAA 57.772 33.333 4.55 0.00 43.44 1.40
711 741 7.506328 TTCATCATTCAGGATGCAGAATAAG 57.494 36.000 4.55 0.00 43.44 1.73
712 742 6.598503 TCATCATTCAGGATGCAGAATAAGT 58.401 36.000 4.55 0.00 43.44 2.24
713 743 7.058525 TCATCATTCAGGATGCAGAATAAGTT 58.941 34.615 4.55 0.00 43.44 2.66
714 744 8.212995 TCATCATTCAGGATGCAGAATAAGTTA 58.787 33.333 4.55 0.00 43.44 2.24
715 745 9.011095 CATCATTCAGGATGCAGAATAAGTTAT 57.989 33.333 4.55 0.00 38.35 1.89
716 746 8.985315 TCATTCAGGATGCAGAATAAGTTATT 57.015 30.769 7.87 7.87 35.64 1.40
717 747 9.060347 TCATTCAGGATGCAGAATAAGTTATTC 57.940 33.333 22.80 22.80 39.06 1.75
718 748 9.064706 CATTCAGGATGCAGAATAAGTTATTCT 57.935 33.333 25.91 25.91 45.02 2.40
719 749 9.638176 ATTCAGGATGCAGAATAAGTTATTCTT 57.362 29.630 28.07 17.96 43.71 2.52
720 750 8.668510 TCAGGATGCAGAATAAGTTATTCTTC 57.331 34.615 28.07 24.63 43.71 2.87
721 751 8.267183 TCAGGATGCAGAATAAGTTATTCTTCA 58.733 33.333 28.46 28.46 46.81 3.02
765 795 9.520515 AACTTGTCATCAACTATTCTAACCATT 57.479 29.630 0.00 0.00 0.00 3.16
799 830 7.027778 ACAGGAATGAACAAAAGTTAGTGAC 57.972 36.000 0.00 0.00 0.00 3.67
861 892 0.865769 AACTGTGCGGATCGTTTCAC 59.134 50.000 0.00 0.00 0.00 3.18
989 1020 7.609532 AGTCCAATTCCATTTCTAAGAACAGAG 59.390 37.037 0.00 0.00 0.00 3.35
1107 1138 1.246056 ACGTCGTGGCCTACAGCTTA 61.246 55.000 3.32 0.00 43.05 3.09
1121 1152 1.470098 CAGCTTAGCCACCATCAACAC 59.530 52.381 0.00 0.00 0.00 3.32
1122 1153 1.073763 AGCTTAGCCACCATCAACACA 59.926 47.619 0.00 0.00 0.00 3.72
1132 1163 1.152860 ATCAACACAACCACGGCCA 60.153 52.632 2.24 0.00 0.00 5.36
1133 1164 1.172180 ATCAACACAACCACGGCCAG 61.172 55.000 2.24 0.00 0.00 4.85
1497 1528 2.125793 GTGAAGTCGTACGCCCCC 60.126 66.667 11.24 0.51 0.00 5.40
1598 1629 4.436998 CGTGGTGTCCCGCCTCTC 62.437 72.222 0.00 0.00 38.04 3.20
1610 1641 1.444553 GCCTCTCAGTGTTCGTCGG 60.445 63.158 0.00 0.00 0.00 4.79
1652 1683 3.257561 CGATCAGCTCGTTGGCGG 61.258 66.667 0.00 0.00 42.56 6.13
1995 2026 1.065709 TCCGACATTAAGAAGGCCACC 60.066 52.381 5.01 0.00 0.00 4.61
2142 2173 4.208686 GAGGACCGGCGCTTCGAT 62.209 66.667 7.64 0.00 0.00 3.59
2210 2241 1.537638 CATCGTCCCTCTCATCGGTAG 59.462 57.143 0.00 0.00 0.00 3.18
2340 3033 0.312729 GTGTGTTTTTGGCTACCCCG 59.687 55.000 0.00 0.00 35.87 5.73
2361 3054 6.310224 CCCCGCAAGAAAAATATGTACAAAAG 59.690 38.462 0.00 0.00 43.02 2.27
2362 3055 7.087639 CCCGCAAGAAAAATATGTACAAAAGA 58.912 34.615 0.00 0.00 43.02 2.52
2467 4344 7.443259 AAATGGTGTAGTGGTAAACATGTAC 57.557 36.000 0.00 0.00 0.00 2.90
2468 4345 5.548181 TGGTGTAGTGGTAAACATGTACA 57.452 39.130 0.00 0.00 32.22 2.90
2469 4346 5.543714 TGGTGTAGTGGTAAACATGTACAG 58.456 41.667 0.00 0.00 34.15 2.74
2470 4347 5.070714 TGGTGTAGTGGTAAACATGTACAGT 59.929 40.000 0.00 2.23 34.15 3.55
2471 4348 6.267242 TGGTGTAGTGGTAAACATGTACAGTA 59.733 38.462 0.00 1.25 34.15 2.74
2502 4379 1.077716 CCAGTCGGGGGATTGAACC 60.078 63.158 0.00 0.00 0.00 3.62
2518 4395 2.550606 TGAACCCACATACTCAAAACGC 59.449 45.455 0.00 0.00 0.00 4.84
2577 4454 4.022475 GCGAGTTTCGAAACAATATGAGC 58.978 43.478 35.29 24.77 43.74 4.26
2675 4553 8.728833 CCTGGTATTTTCTAGTATCTACGGTAG 58.271 40.741 8.91 8.91 0.00 3.18
2677 4555 9.632638 TGGTATTTTCTAGTATCTACGGTAGTT 57.367 33.333 14.45 9.22 0.00 2.24
2699 4584 0.918983 ATTTCTCGCCCCATCTTGGA 59.081 50.000 0.00 0.00 40.96 3.53
2715 4600 7.388437 CCATCTTGGAAATTCTTTGGATTTCA 58.612 34.615 11.87 0.00 40.96 2.69
2766 4651 4.478699 CGTTGTCCAGTCGTTATTGTAGA 58.521 43.478 0.00 0.00 0.00 2.59
2782 4667 4.247267 TGTAGAGTTTGTGGTAGGTTCG 57.753 45.455 0.00 0.00 0.00 3.95
2809 4694 1.580059 TGGTACTCCCTCCATTCCAC 58.420 55.000 0.00 0.00 0.00 4.02
2813 4698 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
2818 4703 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
2819 4704 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
2821 4706 1.202177 CCATTCCACAATGTAGTGCGC 60.202 52.381 0.00 0.00 38.22 6.09
2825 4710 2.032634 CACAATGTAGTGCGCCCGT 61.033 57.895 4.18 0.00 32.04 5.28
2955 4937 9.168451 TCTGTTGTAAGTCAATTTGTTCAGTAA 57.832 29.630 0.00 0.00 38.38 2.24
2980 4965 8.913487 ATGATGCTGAGTTTTGTATATCATCA 57.087 30.769 0.00 0.00 40.99 3.07
2981 4966 8.913487 TGATGCTGAGTTTTGTATATCATCAT 57.087 30.769 0.00 0.00 34.66 2.45
2982 4967 8.996271 TGATGCTGAGTTTTGTATATCATCATC 58.004 33.333 9.68 9.68 41.91 2.92
3135 5121 7.369551 ACATGGCAGGATTCATATTTGAAAT 57.630 32.000 5.99 0.00 44.70 2.17
3168 5154 5.710409 TCCTGGGACCCTCTTTATTAAAG 57.290 43.478 13.00 9.48 39.88 1.85
3308 5295 8.649841 CATATTTACAAATGACCAGTTTGCTTG 58.350 33.333 0.00 0.00 39.55 4.01
3703 5694 1.607628 CCGGAGTACGCTTGTAGCTAT 59.392 52.381 0.00 0.00 39.60 2.97
3764 5755 1.366854 CGTCCTCGAGATCGTGACCA 61.367 60.000 15.71 0.00 38.21 4.02
3772 5763 2.277969 GAGATCGTGACCAGTAGACGA 58.722 52.381 0.00 0.00 45.42 4.20
3886 5877 2.996734 CTTGCCATGGCGGGGTTT 60.997 61.111 30.87 0.00 45.51 3.27
4007 5998 2.011222 CCAAATTAAAGCTACCGCCGA 58.989 47.619 0.00 0.00 36.60 5.54
4012 6003 1.876497 TAAAGCTACCGCCGACCGTT 61.876 55.000 0.00 0.00 36.60 4.44
4030 6021 3.495453 CCGTTCCTCCTAAGAAACCAACA 60.495 47.826 0.00 0.00 0.00 3.33
4241 6234 2.300152 CACGTGACCCTGGCTATCATAT 59.700 50.000 10.90 0.00 0.00 1.78
4242 6235 2.563179 ACGTGACCCTGGCTATCATATC 59.437 50.000 0.00 0.00 0.00 1.63
4243 6236 2.562738 CGTGACCCTGGCTATCATATCA 59.437 50.000 0.00 0.00 0.00 2.15
4244 6237 3.196469 CGTGACCCTGGCTATCATATCAT 59.804 47.826 0.00 0.00 0.00 2.45
4245 6238 4.402474 CGTGACCCTGGCTATCATATCATA 59.598 45.833 0.00 0.00 0.00 2.15
4403 6396 6.516739 TGCCGTGGATTATGATTTTGTTTA 57.483 33.333 0.00 0.00 0.00 2.01
4444 6437 7.719633 ACCTATCTTAGTGTTTGTTTGACATGT 59.280 33.333 0.00 0.00 0.00 3.21
4503 6497 8.794335 AATCCTGAAAGACTAACCTTTGATAC 57.206 34.615 0.00 0.00 36.58 2.24
4520 6515 2.162319 TACAGATGCGCAACAACTCA 57.838 45.000 17.11 0.00 0.00 3.41
4527 6522 1.069296 TGCGCAACAACTCAGTAATGC 60.069 47.619 8.16 0.40 0.00 3.56
4715 6716 4.894784 TCCACTTGGACTAACTTAGCTTG 58.105 43.478 0.00 0.00 39.78 4.01
4726 6727 7.148239 GGACTAACTTAGCTTGCATATGTTTGT 60.148 37.037 4.29 9.66 32.86 2.83
4833 6834 2.508300 TGAAACCCCCTTATCTAGCCAC 59.492 50.000 0.00 0.00 0.00 5.01
4835 6836 0.648301 ACCCCCTTATCTAGCCACCT 59.352 55.000 0.00 0.00 0.00 4.00
4855 6856 1.086696 ATTTTCTGCATCACGGTCCG 58.913 50.000 10.48 10.48 0.00 4.79
4869 6870 1.135972 CGGTCCGTTCATGAGCTTTTG 60.136 52.381 8.01 0.00 0.00 2.44
4978 6979 9.037737 CATATTTTAAAGCAATGTTGGAGGATG 57.962 33.333 0.00 0.00 0.00 3.51
5043 8553 7.337942 ACTCTCTTGACTGAAATCTTGTGTTTT 59.662 33.333 0.00 0.00 0.00 2.43
5056 8566 4.344679 TCTTGTGTTTTGCCCTCATGATTT 59.655 37.500 0.00 0.00 0.00 2.17
5134 8644 8.936864 CGTCAACTAGAATTTCTTTGAATAGGT 58.063 33.333 12.79 0.00 28.49 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.396022 AGCTTACTATGCACATAACTTATTTGT 57.604 29.630 0.00 0.00 0.00 2.83
39 40 8.576442 ACAAAAAGCTTACTATGCACATAACTT 58.424 29.630 0.00 0.00 0.00 2.66
45 46 4.037327 TGCACAAAAAGCTTACTATGCACA 59.963 37.500 18.94 7.71 36.94 4.57
110 111 7.325694 TCCTTTACAACATAGTAGTGCCTAAC 58.674 38.462 0.00 0.00 0.00 2.34
112 113 7.484993 TTCCTTTACAACATAGTAGTGCCTA 57.515 36.000 0.00 0.00 0.00 3.93
113 114 6.368779 TTCCTTTACAACATAGTAGTGCCT 57.631 37.500 0.00 0.00 0.00 4.75
116 117 7.707035 CCTAGCTTCCTTTACAACATAGTAGTG 59.293 40.741 0.00 0.00 0.00 2.74
117 118 7.633116 GCCTAGCTTCCTTTACAACATAGTAGT 60.633 40.741 0.00 0.00 0.00 2.73
118 119 6.702282 GCCTAGCTTCCTTTACAACATAGTAG 59.298 42.308 0.00 0.00 0.00 2.57
120 121 5.189934 AGCCTAGCTTCCTTTACAACATAGT 59.810 40.000 0.00 0.00 33.89 2.12
121 122 5.675538 AGCCTAGCTTCCTTTACAACATAG 58.324 41.667 0.00 0.00 33.89 2.23
122 123 5.693769 AGCCTAGCTTCCTTTACAACATA 57.306 39.130 0.00 0.00 33.89 2.29
123 124 4.576330 AGCCTAGCTTCCTTTACAACAT 57.424 40.909 0.00 0.00 33.89 2.71
124 125 4.367039 AAGCCTAGCTTCCTTTACAACA 57.633 40.909 0.00 0.00 46.77 3.33
270 272 4.578928 ACGGTGAACATTAACAAGCTCTTT 59.421 37.500 0.00 0.00 0.00 2.52
381 383 4.023450 CCAACATCCAATCCTTCATGATCG 60.023 45.833 0.00 0.00 0.00 3.69
383 385 4.891756 GTCCAACATCCAATCCTTCATGAT 59.108 41.667 0.00 0.00 0.00 2.45
396 398 7.029563 GTCATTGTCAAATTAGTCCAACATCC 58.970 38.462 0.00 0.00 0.00 3.51
406 408 6.480524 TTGTCGAGGTCATTGTCAAATTAG 57.519 37.500 0.00 0.00 0.00 1.73
411 413 6.313658 CAGAATATTGTCGAGGTCATTGTCAA 59.686 38.462 0.00 0.00 0.00 3.18
431 443 8.853126 TGATCTTCAACTTTTCATTGTCAGAAT 58.147 29.630 0.00 0.00 0.00 2.40
539 566 5.678871 GCAATCATACCGTAGAGTTGACTGA 60.679 44.000 0.00 0.00 0.00 3.41
560 589 7.846644 AAAATGTCTGAGTCAAAATTTGCAA 57.153 28.000 0.00 0.00 0.00 4.08
607 637 8.110271 TCACAAAGTTTACACATGGGGATATAA 58.890 33.333 0.00 0.00 0.00 0.98
664 694 8.988060 TGAATAGACTTTCTCTCTCTCTCTCTA 58.012 37.037 0.00 0.00 0.00 2.43
665 695 7.861629 TGAATAGACTTTCTCTCTCTCTCTCT 58.138 38.462 0.00 0.00 0.00 3.10
666 696 8.682936 ATGAATAGACTTTCTCTCTCTCTCTC 57.317 38.462 0.00 0.00 0.00 3.20
667 697 8.274322 TGATGAATAGACTTTCTCTCTCTCTCT 58.726 37.037 0.00 0.00 0.00 3.10
669 699 9.425248 AATGATGAATAGACTTTCTCTCTCTCT 57.575 33.333 0.00 0.00 0.00 3.10
670 700 9.683069 GAATGATGAATAGACTTTCTCTCTCTC 57.317 37.037 0.00 0.00 0.00 3.20
671 701 9.199645 TGAATGATGAATAGACTTTCTCTCTCT 57.800 33.333 0.00 0.00 0.00 3.10
672 702 9.467258 CTGAATGATGAATAGACTTTCTCTCTC 57.533 37.037 0.00 0.00 0.00 3.20
673 703 8.423349 CCTGAATGATGAATAGACTTTCTCTCT 58.577 37.037 0.00 0.00 0.00 3.10
674 704 8.420222 TCCTGAATGATGAATAGACTTTCTCTC 58.580 37.037 0.00 0.00 0.00 3.20
675 705 8.316497 TCCTGAATGATGAATAGACTTTCTCT 57.684 34.615 0.00 0.00 0.00 3.10
676 706 8.991026 CATCCTGAATGATGAATAGACTTTCTC 58.009 37.037 0.00 0.00 43.94 2.87
677 707 7.444792 GCATCCTGAATGATGAATAGACTTTCT 59.555 37.037 5.26 0.00 43.94 2.52
678 708 7.228108 TGCATCCTGAATGATGAATAGACTTTC 59.772 37.037 5.26 0.00 43.94 2.62
679 709 7.058525 TGCATCCTGAATGATGAATAGACTTT 58.941 34.615 5.26 0.00 43.94 2.66
680 710 6.598503 TGCATCCTGAATGATGAATAGACTT 58.401 36.000 5.26 0.00 43.94 3.01
681 711 6.042897 TCTGCATCCTGAATGATGAATAGACT 59.957 38.462 5.26 0.00 43.94 3.24
682 712 6.228995 TCTGCATCCTGAATGATGAATAGAC 58.771 40.000 5.26 0.00 43.94 2.59
683 713 6.429521 TCTGCATCCTGAATGATGAATAGA 57.570 37.500 5.26 3.07 43.94 1.98
684 714 7.689446 ATTCTGCATCCTGAATGATGAATAG 57.311 36.000 5.26 1.04 43.94 1.73
685 715 9.227777 CTTATTCTGCATCCTGAATGATGAATA 57.772 33.333 8.70 1.94 43.94 1.75
686 716 7.724506 ACTTATTCTGCATCCTGAATGATGAAT 59.275 33.333 8.70 2.77 43.94 2.57
687 717 7.058525 ACTTATTCTGCATCCTGAATGATGAA 58.941 34.615 8.70 0.00 43.94 2.57
688 718 6.598503 ACTTATTCTGCATCCTGAATGATGA 58.401 36.000 8.70 0.00 43.94 2.92
689 719 6.879276 ACTTATTCTGCATCCTGAATGATG 57.121 37.500 8.70 0.00 44.02 3.07
690 720 9.584008 AATAACTTATTCTGCATCCTGAATGAT 57.416 29.630 8.70 0.00 39.19 2.45
691 721 8.985315 AATAACTTATTCTGCATCCTGAATGA 57.015 30.769 8.70 1.10 39.19 2.57
722 752 9.838339 ATGACAAGTTATAAGATTACCTTCAGG 57.162 33.333 0.00 0.00 42.17 3.86
841 872 2.063266 GTGAAACGATCCGCACAGTTA 58.937 47.619 0.00 0.00 0.00 2.24
842 873 0.865769 GTGAAACGATCCGCACAGTT 59.134 50.000 0.00 0.00 0.00 3.16
844 875 0.670546 AGGTGAAACGATCCGCACAG 60.671 55.000 0.00 0.00 38.12 3.66
845 876 0.604073 TAGGTGAAACGATCCGCACA 59.396 50.000 0.00 0.00 38.12 4.57
853 884 2.549349 GGCTCCAAAGTAGGTGAAACGA 60.549 50.000 0.00 0.00 38.12 3.85
989 1020 2.237392 AGACCCAACATCTTACTGCTCC 59.763 50.000 0.00 0.00 0.00 4.70
1045 1076 0.249531 ATCATCGCTGAGCAGAGCAG 60.250 55.000 4.88 0.00 39.07 4.24
1101 1132 1.470098 GTGTTGATGGTGGCTAAGCTG 59.530 52.381 0.00 0.00 0.00 4.24
1107 1138 0.106268 TGGTTGTGTTGATGGTGGCT 60.106 50.000 0.00 0.00 0.00 4.75
1550 1581 0.527817 GATCCACACGGTCACGATCC 60.528 60.000 0.00 0.00 44.60 3.36
1585 1616 2.100879 AACACTGAGAGGCGGGACAC 62.101 60.000 0.00 0.00 0.00 3.67
1597 1628 3.998672 GGGGCCGACGAACACTGA 61.999 66.667 0.00 0.00 0.00 3.41
1652 1683 2.434185 TCATGTTGACGGCCGAGC 60.434 61.111 35.90 23.41 0.00 5.03
1666 1697 2.358247 GTTGGTGCGACCCGTCAT 60.358 61.111 3.33 0.00 37.50 3.06
1720 1751 3.537874 GCCGGCGAGGACATAGGT 61.538 66.667 12.58 0.00 45.00 3.08
1874 1905 6.649557 CCTGTACCTGGAGTTGTAGTAAAAAG 59.350 42.308 0.00 0.00 0.00 2.27
1995 2026 0.934496 TTGTGCCGTCGAAGTTCTTG 59.066 50.000 0.56 0.00 0.00 3.02
2127 2158 4.508128 TCATCGAAGCGCCGGTCC 62.508 66.667 2.29 0.00 0.00 4.46
2251 2862 4.584743 ACAAACCCATTCAAGAAGGAGAAC 59.415 41.667 0.00 0.00 0.00 3.01
2254 2947 4.401925 AGACAAACCCATTCAAGAAGGAG 58.598 43.478 0.00 0.00 0.00 3.69
2269 2962 4.398358 GCCCAATACCTTTCCTAGACAAAC 59.602 45.833 0.00 0.00 0.00 2.93
2340 3033 9.255304 TGGTTCTTTTGTACATATTTTTCTTGC 57.745 29.630 0.00 0.00 0.00 4.01
2427 3122 7.625828 ACACCATTTTACTGCTTATTACTCC 57.374 36.000 0.00 0.00 0.00 3.85
2483 4360 1.683441 GTTCAATCCCCCGACTGGT 59.317 57.895 0.00 0.00 0.00 4.00
2502 4379 4.092968 GTCCTTAGCGTTTTGAGTATGTGG 59.907 45.833 0.00 0.00 0.00 4.17
2518 4395 1.153823 CCTCCGCACGTGTCCTTAG 60.154 63.158 18.38 7.84 0.00 2.18
2638 4516 8.262933 ACTAGAAAATACCAGGTAAATACGCTT 58.737 33.333 2.53 0.00 0.00 4.68
2648 4526 7.065504 ACCGTAGATACTAGAAAATACCAGGT 58.934 38.462 0.00 0.00 0.00 4.00
2649 4527 7.521871 ACCGTAGATACTAGAAAATACCAGG 57.478 40.000 0.00 0.00 0.00 4.45
2650 4528 9.282569 ACTACCGTAGATACTAGAAAATACCAG 57.717 37.037 12.66 0.00 0.00 4.00
2662 4540 7.519649 GCGAGAAATACAACTACCGTAGATACT 60.520 40.741 12.66 0.04 0.00 2.12
2675 4553 2.919228 AGATGGGGCGAGAAATACAAC 58.081 47.619 0.00 0.00 0.00 3.32
2677 4555 2.421388 CCAAGATGGGGCGAGAAATACA 60.421 50.000 0.00 0.00 32.67 2.29
2699 4584 6.916360 TGGCTACTGAAATCCAAAGAATTT 57.084 33.333 0.00 0.00 40.26 1.82
2715 4600 4.880164 TGATACTCCTAGGTTTGGCTACT 58.120 43.478 9.08 0.00 0.00 2.57
2766 4651 0.105408 ACGCGAACCTACCACAAACT 59.895 50.000 15.93 0.00 0.00 2.66
2782 4667 1.653151 GAGGGAGTACCATTCAACGC 58.347 55.000 0.00 0.00 43.89 4.84
2809 4694 2.784596 CACGGGCGCACTACATTG 59.215 61.111 8.62 0.00 0.00 2.82
2831 4716 9.042008 TGACCATAAATTTAACTTAGATCTCGC 57.958 33.333 0.00 0.00 0.00 5.03
2883 4865 3.463944 CCTCTTTTCCACAACGTAGTGT 58.536 45.455 0.00 0.00 45.00 3.55
2890 4872 4.906618 TGATACTCCCTCTTTTCCACAAC 58.093 43.478 0.00 0.00 0.00 3.32
2955 4937 8.913487 TGATGATATACAAAACTCAGCATCAT 57.087 30.769 0.00 0.00 35.90 2.45
3116 5102 9.688592 CCTAAAGATTTCAAATATGAATCCTGC 57.311 33.333 0.00 0.00 44.70 4.85
3135 5121 3.056201 GGTCCCAGGATACCCTAAAGA 57.944 52.381 0.00 0.00 42.02 2.52
3168 5154 9.143631 ACATATTTCTGCAAATTTAGCTGTTTC 57.856 29.630 0.00 0.00 33.95 2.78
3295 5282 3.782889 ACAAAGTCAAGCAAACTGGTC 57.217 42.857 0.00 0.00 0.00 4.02
3330 5317 4.606210 AGTTGTTACAAAGTGAACCCCTT 58.394 39.130 0.00 0.00 0.00 3.95
3703 5694 2.117051 TCAGTCTCCCTCGTAGCTCTA 58.883 52.381 0.00 0.00 0.00 2.43
3886 5877 1.075542 GTTTGGCGTCATCATCGTCA 58.924 50.000 0.00 0.00 41.07 4.35
3914 5905 4.283403 GCACGCCAAGCCAAGCAA 62.283 61.111 0.00 0.00 0.00 3.91
3991 5982 0.529119 CGGTCGGCGGTAGCTTTAAT 60.529 55.000 7.21 0.00 44.37 1.40
4007 5998 2.332117 TGGTTTCTTAGGAGGAACGGT 58.668 47.619 0.00 0.00 41.54 4.83
4012 6003 5.534654 CACAAATGTTGGTTTCTTAGGAGGA 59.465 40.000 0.00 0.00 34.12 3.71
4056 6047 6.881065 TGTGCTAAAGTAAGAGCTCAATGAAT 59.119 34.615 17.77 0.27 38.76 2.57
4166 6157 4.088648 GGTGAAGTGCGAACAAATAATCG 58.911 43.478 0.00 0.00 41.81 3.34
4243 6236 9.965824 CCAACACATTCAAAAGTCTTAACTTAT 57.034 29.630 0.00 0.00 45.07 1.73
4244 6237 7.918562 GCCAACACATTCAAAAGTCTTAACTTA 59.081 33.333 0.00 0.00 45.07 2.24
4329 6322 9.367160 TCACTCAGTTAGGTGATTGATATATCA 57.633 33.333 11.49 11.49 37.52 2.15
4503 6497 0.870393 ACTGAGTTGTTGCGCATCTG 59.130 50.000 12.75 12.11 0.00 2.90
4520 6515 3.776969 TCCTTCATCCACTCAGCATTACT 59.223 43.478 0.00 0.00 0.00 2.24
4527 6522 7.826252 TCTCTTTAAAATCCTTCATCCACTCAG 59.174 37.037 0.00 0.00 0.00 3.35
4664 6665 3.498397 CCACACCTTAGATGTTGTCACAC 59.502 47.826 0.00 0.00 35.03 3.82
4715 6716 2.094675 AGAGGCACCACAAACATATGC 58.905 47.619 1.58 0.00 35.51 3.14
4726 6727 0.545309 AGGAGTAAGCAGAGGCACCA 60.545 55.000 0.00 0.00 44.61 4.17
4813 6814 2.158652 GGTGGCTAGATAAGGGGGTTTC 60.159 54.545 0.00 0.00 0.00 2.78
4820 6821 5.703130 GCAGAAAATAGGTGGCTAGATAAGG 59.297 44.000 0.00 0.00 0.00 2.69
4833 6834 2.614057 GGACCGTGATGCAGAAAATAGG 59.386 50.000 0.00 0.00 0.00 2.57
4835 6836 2.276201 CGGACCGTGATGCAGAAAATA 58.724 47.619 5.48 0.00 0.00 1.40
4944 6945 9.927668 AACATTGCTTTAAAATATGTGCTAGTT 57.072 25.926 9.12 3.78 30.43 2.24
4957 6958 5.185635 CCTCATCCTCCAACATTGCTTTAAA 59.814 40.000 0.00 0.00 0.00 1.52
4978 6979 3.142174 GCACATTGTAGCCCTTATCCTC 58.858 50.000 0.00 0.00 0.00 3.71
5043 8553 3.937778 TCAGATCAAATCATGAGGGCA 57.062 42.857 0.09 0.00 42.53 5.36


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

AutoCloner maintained by Alex Coulton.