Multiple sequence alignment - TraesCS2B01G490600

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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 TraesCS2B01G490600 chr2B 100.000 3615 0 0 1 3615 688378107 688374493 0.000000e+00 6676.0
1 TraesCS2B01G490600 chr2B 86.582 1021 103 24 1777 2786 688240723 688239726 0.000000e+00 1096.0
2 TraesCS2B01G490600 chr2B 84.763 1096 103 24 745 1780 688242911 688241820 0.000000e+00 1040.0
3 TraesCS2B01G490600 chr2B 80.428 654 74 27 2967 3585 688431422 688430788 1.980000e-122 449.0
4 TraesCS2B01G490600 chr2B 95.480 177 8 0 566 742 256481650 256481826 2.120000e-72 283.0
5 TraesCS2B01G490600 chr2B 86.325 234 25 4 110 342 688243247 688243020 7.750000e-62 248.0
6 TraesCS2B01G490600 chr2B 86.170 94 10 2 425 517 247368629 247368538 8.260000e-17 99.0
7 TraesCS2B01G490600 chr2B 87.654 81 8 1 438 518 633391676 633391598 3.840000e-15 93.5
8 TraesCS2B01G490600 chr2A 94.552 2900 121 11 737 3609 711942678 711939789 0.000000e+00 4446.0
9 TraesCS2B01G490600 chr2A 85.756 1025 107 26 1777 2786 711882439 711881439 0.000000e+00 1048.0
10 TraesCS2B01G490600 chr2A 82.462 1129 155 19 536 1635 711885022 711883908 0.000000e+00 948.0
11 TraesCS2B01G490600 chr2A 79.460 667 83 34 2958 3588 711968937 711968289 1.200000e-114 424.0
12 TraesCS2B01G490600 chr2A 96.522 230 4 1 80 305 711953561 711953332 9.470000e-101 377.0
13 TraesCS2B01G490600 chr2A 91.667 240 14 2 336 575 711942910 711942677 9.680000e-86 327.0
14 TraesCS2B01G490600 chr2A 94.366 71 4 0 273 343 711885253 711885183 3.820000e-20 110.0
15 TraesCS2B01G490600 chr2D 93.793 1869 80 14 1757 3615 572695572 572693730 0.000000e+00 2776.0
16 TraesCS2B01G490600 chr2D 84.624 1743 193 35 536 2217 572684807 572683079 0.000000e+00 1664.0
17 TraesCS2B01G490600 chr2D 95.210 1023 29 3 754 1756 572697023 572696001 0.000000e+00 1600.0
18 TraesCS2B01G490600 chr2D 86.444 568 64 9 2227 2786 572682961 572682399 8.580000e-171 610.0
19 TraesCS2B01G490600 chr2D 89.706 408 21 8 177 575 572703803 572703408 5.390000e-138 501.0
20 TraesCS2B01G490600 chr2D 79.848 660 82 29 2956 3586 572732865 572732228 5.540000e-118 435.0
21 TraesCS2B01G490600 chr2D 82.051 234 19 4 110 343 572685099 572684889 1.030000e-40 178.0
22 TraesCS2B01G490600 chr5D 82.490 514 78 7 2958 3461 12872565 12873076 1.190000e-119 440.0
23 TraesCS2B01G490600 chr5D 87.805 82 7 1 431 512 546857278 546857356 3.840000e-15 93.5
24 TraesCS2B01G490600 chr7A 81.907 514 81 8 2958 3461 594163224 594163735 1.200000e-114 424.0
25 TraesCS2B01G490600 chr5B 80.619 485 82 7 2987 3461 670365612 670366094 7.380000e-97 364.0
26 TraesCS2B01G490600 chr5B 94.857 175 9 0 571 745 275370134 275369960 1.280000e-69 274.0
27 TraesCS2B01G490600 chr3B 96.471 170 6 0 573 742 755376108 755376277 7.640000e-72 281.0
28 TraesCS2B01G490600 chr5A 94.505 182 9 1 572 753 290391695 290391875 2.750000e-71 279.0
29 TraesCS2B01G490600 chr6D 95.882 170 7 0 573 742 72996953 72996784 3.560000e-70 276.0
30 TraesCS2B01G490600 chr6D 90.955 199 14 2 567 761 221865026 221864828 7.700000e-67 265.0
31 TraesCS2B01G490600 chr6D 85.714 91 8 4 430 517 343295720 343295808 1.380000e-14 91.6
32 TraesCS2B01G490600 chr1D 94.444 180 9 1 567 745 420065413 420065234 3.560000e-70 276.0
33 TraesCS2B01G490600 chr7B 94.382 178 8 2 571 748 551954760 551954935 4.600000e-69 272.0
34 TraesCS2B01G490600 chr4D 94.857 175 8 1 572 746 93338040 93338213 4.600000e-69 272.0
35 TraesCS2B01G490600 chr1B 90.805 87 2 5 429 513 85441624 85441706 1.060000e-20 111.0
36 TraesCS2B01G490600 chr1B 86.905 84 7 3 431 512 597156888 597156807 1.380000e-14 91.6
37 TraesCS2B01G490600 chr1A 86.747 83 10 1 431 513 330769319 330769238 1.380000e-14 91.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G490600 chr2B 688374493 688378107 3614 True 6676.000000 6676 100.0000 1 3615 1 chr2B.!!$R3 3614
1 TraesCS2B01G490600 chr2B 688239726 688243247 3521 True 794.666667 1096 85.8900 110 2786 3 chr2B.!!$R5 2676
2 TraesCS2B01G490600 chr2B 688430788 688431422 634 True 449.000000 449 80.4280 2967 3585 1 chr2B.!!$R4 618
3 TraesCS2B01G490600 chr2A 711939789 711942910 3121 True 2386.500000 4446 93.1095 336 3609 2 chr2A.!!$R4 3273
4 TraesCS2B01G490600 chr2A 711881439 711885253 3814 True 702.000000 1048 87.5280 273 2786 3 chr2A.!!$R3 2513
5 TraesCS2B01G490600 chr2A 711968289 711968937 648 True 424.000000 424 79.4600 2958 3588 1 chr2A.!!$R2 630
6 TraesCS2B01G490600 chr2D 572693730 572697023 3293 True 2188.000000 2776 94.5015 754 3615 2 chr2D.!!$R4 2861
7 TraesCS2B01G490600 chr2D 572682399 572685099 2700 True 817.333333 1664 84.3730 110 2786 3 chr2D.!!$R3 2676
8 TraesCS2B01G490600 chr2D 572732228 572732865 637 True 435.000000 435 79.8480 2956 3586 1 chr2D.!!$R2 630
9 TraesCS2B01G490600 chr5D 12872565 12873076 511 False 440.000000 440 82.4900 2958 3461 1 chr5D.!!$F1 503
10 TraesCS2B01G490600 chr7A 594163224 594163735 511 False 424.000000 424 81.9070 2958 3461 1 chr7A.!!$F1 503

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
104 105 0.030908 CGAGGTACGAGCTTCCATCC 59.969 60.0 0.0 0.0 45.77 3.51 F
934 1031 0.527565 GGATGCAGGCGTTTGATGTT 59.472 50.0 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1712 1.970640 AGGAATGAAAAGGTTGGGCAC 59.029 47.619 0.00 0.0 0.0 5.01 R
2864 4936 0.107831 AGTACTTGAGTTGCGGCCAA 59.892 50.000 2.24 0.0 0.0 4.52 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
17 18 4.308458 TCTCGTTGCCCACCACCG 62.308 66.667 0.00 0.00 0.00 4.94
76 77 4.506255 CGCCCCCAACCCTCCATC 62.506 72.222 0.00 0.00 0.00 3.51
77 78 3.023735 GCCCCCAACCCTCCATCT 61.024 66.667 0.00 0.00 0.00 2.90
78 79 1.696314 GCCCCCAACCCTCCATCTA 60.696 63.158 0.00 0.00 0.00 1.98
79 80 1.709994 GCCCCCAACCCTCCATCTAG 61.710 65.000 0.00 0.00 0.00 2.43
80 81 0.327576 CCCCCAACCCTCCATCTAGT 60.328 60.000 0.00 0.00 0.00 2.57
81 82 1.596496 CCCCAACCCTCCATCTAGTT 58.404 55.000 0.00 0.00 0.00 2.24
82 83 1.923148 CCCCAACCCTCCATCTAGTTT 59.077 52.381 0.00 0.00 0.00 2.66
83 84 2.311841 CCCCAACCCTCCATCTAGTTTT 59.688 50.000 0.00 0.00 0.00 2.43
84 85 3.245622 CCCCAACCCTCCATCTAGTTTTT 60.246 47.826 0.00 0.00 0.00 1.94
85 86 4.017126 CCCAACCCTCCATCTAGTTTTTC 58.983 47.826 0.00 0.00 0.00 2.29
86 87 3.689649 CCAACCCTCCATCTAGTTTTTCG 59.310 47.826 0.00 0.00 0.00 3.46
87 88 4.564821 CCAACCCTCCATCTAGTTTTTCGA 60.565 45.833 0.00 0.00 0.00 3.71
88 89 4.473477 ACCCTCCATCTAGTTTTTCGAG 57.527 45.455 0.00 0.00 0.00 4.04
89 90 3.197983 ACCCTCCATCTAGTTTTTCGAGG 59.802 47.826 0.00 0.00 36.08 4.63
90 91 3.197983 CCCTCCATCTAGTTTTTCGAGGT 59.802 47.826 0.00 0.00 34.80 3.85
91 92 4.404715 CCCTCCATCTAGTTTTTCGAGGTA 59.595 45.833 0.00 0.00 34.80 3.08
92 93 5.349809 CCTCCATCTAGTTTTTCGAGGTAC 58.650 45.833 0.00 0.00 32.47 3.34
93 94 4.990257 TCCATCTAGTTTTTCGAGGTACG 58.010 43.478 0.00 0.00 44.09 3.67
101 102 4.728409 TCGAGGTACGAGCTTCCA 57.272 55.556 0.00 0.00 46.45 3.53
102 103 3.186345 TCGAGGTACGAGCTTCCAT 57.814 52.632 0.00 0.00 46.45 3.41
103 104 1.022735 TCGAGGTACGAGCTTCCATC 58.977 55.000 0.00 0.00 46.45 3.51
104 105 0.030908 CGAGGTACGAGCTTCCATCC 59.969 60.000 0.00 0.00 45.77 3.51
105 106 1.112113 GAGGTACGAGCTTCCATCCA 58.888 55.000 0.00 0.00 0.00 3.41
106 107 1.689273 GAGGTACGAGCTTCCATCCAT 59.311 52.381 0.00 0.00 0.00 3.41
107 108 2.103263 GAGGTACGAGCTTCCATCCATT 59.897 50.000 0.00 0.00 0.00 3.16
108 109 2.103263 AGGTACGAGCTTCCATCCATTC 59.897 50.000 0.00 0.00 0.00 2.67
129 130 4.136796 TCACATTCTCCAAGTCCACAAAG 58.863 43.478 0.00 0.00 0.00 2.77
137 138 3.259876 TCCAAGTCCACAAAGCTATACGT 59.740 43.478 0.00 0.00 0.00 3.57
149 150 1.884579 GCTATACGTCGATTCCCTGGA 59.115 52.381 0.00 0.00 0.00 3.86
150 151 2.095161 GCTATACGTCGATTCCCTGGAG 60.095 54.545 0.00 0.00 0.00 3.86
151 152 2.068834 ATACGTCGATTCCCTGGAGT 57.931 50.000 0.00 0.00 0.00 3.85
152 153 1.100510 TACGTCGATTCCCTGGAGTG 58.899 55.000 0.00 0.00 0.00 3.51
175 176 3.005554 ACCATTCTTGATCTGCGAACAG 58.994 45.455 0.00 0.00 45.95 3.16
206 207 2.631160 TTTTTGAGAGGAGAACGGCA 57.369 45.000 0.00 0.00 0.00 5.69
226 227 5.169295 GGCACGAGGTCCATAATAGATAAC 58.831 45.833 0.00 0.00 0.00 1.89
238 240 7.039011 TCCATAATAGATAACGCTCACTTGGAT 60.039 37.037 0.00 0.00 0.00 3.41
247 249 2.615493 CGCTCACTTGGATGGTAGGTTT 60.615 50.000 0.00 0.00 0.00 3.27
331 333 2.750948 GTTCAGCGACAAGTGGAAGTA 58.249 47.619 0.00 0.00 0.00 2.24
371 373 6.998673 ACATACTCCCTAAGTTCCATAATTGC 59.001 38.462 0.00 0.00 39.55 3.56
392 394 3.848554 GCTGTTGTGCTTTTAGTTCGTCC 60.849 47.826 0.00 0.00 0.00 4.79
401 403 5.585445 TGCTTTTAGTTCGTCCAAAGTACAA 59.415 36.000 0.00 0.00 0.00 2.41
456 536 5.163794 CCCCATCCGTATCAAAATATAACGC 60.164 44.000 0.00 0.00 0.00 4.84
457 537 5.410132 CCCATCCGTATCAAAATATAACGCA 59.590 40.000 0.00 0.00 0.00 5.24
459 539 6.960992 CCATCCGTATCAAAATATAACGCATG 59.039 38.462 0.00 0.00 0.00 4.06
513 593 8.627403 CGTCTTATATTTTGGTACAGAGGTAGA 58.373 37.037 0.00 0.00 42.39 2.59
514 594 9.968870 GTCTTATATTTTGGTACAGAGGTAGAG 57.031 37.037 0.00 0.00 42.39 2.43
515 595 9.710818 TCTTATATTTTGGTACAGAGGTAGAGT 57.289 33.333 0.00 0.00 42.39 3.24
546 635 6.418057 AGTTTTAGGTGCCATTCAAAATGA 57.582 33.333 1.29 0.00 0.00 2.57
586 675 4.262678 GGCTGTCTTATACTCCCTCCATTC 60.263 50.000 0.00 0.00 0.00 2.67
598 687 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
600 689 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
603 692 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
620 709 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
632 721 8.902540 AGATTTCAACAAGTGACTACATACAA 57.097 30.769 0.00 0.00 35.39 2.41
634 723 9.944663 GATTTCAACAAGTGACTACATACAAAA 57.055 29.630 0.00 0.00 35.39 2.44
635 724 9.730420 ATTTCAACAAGTGACTACATACAAAAC 57.270 29.630 0.00 0.00 35.39 2.43
636 725 6.939627 TCAACAAGTGACTACATACAAAACG 58.060 36.000 0.00 0.00 0.00 3.60
638 727 7.278203 TCAACAAGTGACTACATACAAAACGAA 59.722 33.333 0.00 0.00 0.00 3.85
641 730 8.067784 ACAAGTGACTACATACAAAACGAAATG 58.932 33.333 0.00 0.00 0.00 2.32
642 731 7.956420 AGTGACTACATACAAAACGAAATGA 57.044 32.000 0.00 0.00 0.00 2.57
643 732 8.018677 AGTGACTACATACAAAACGAAATGAG 57.981 34.615 0.00 0.00 0.00 2.90
644 733 7.656137 AGTGACTACATACAAAACGAAATGAGT 59.344 33.333 0.00 0.00 0.00 3.41
646 735 7.654116 TGACTACATACAAAACGAAATGAGTGA 59.346 33.333 0.00 0.00 0.00 3.41
649 738 9.478019 CTACATACAAAACGAAATGAGTGAATC 57.522 33.333 0.00 0.00 0.00 2.52
651 740 9.214957 ACATACAAAACGAAATGAGTGAATCTA 57.785 29.630 0.00 0.00 0.00 1.98
652 741 9.478019 CATACAAAACGAAATGAGTGAATCTAC 57.522 33.333 0.00 0.00 0.00 2.59
653 742 7.490962 ACAAAACGAAATGAGTGAATCTACA 57.509 32.000 0.00 0.00 0.00 2.74
654 743 7.352739 ACAAAACGAAATGAGTGAATCTACAC 58.647 34.615 0.00 0.00 40.60 2.90
689 778 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
690 779 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
691 780 8.396390 GTCTATATACATCCGTATGTGGTAGTG 58.604 40.741 3.56 0.00 45.99 2.74
692 781 2.596904 ACATCCGTATGTGGTAGTGC 57.403 50.000 0.00 0.00 44.79 4.40
694 783 2.434336 ACATCCGTATGTGGTAGTGCAT 59.566 45.455 0.00 0.00 44.79 3.96
695 784 3.118408 ACATCCGTATGTGGTAGTGCATT 60.118 43.478 0.00 0.00 44.79 3.56
698 787 3.055747 TCCGTATGTGGTAGTGCATTTGA 60.056 43.478 0.00 0.00 0.00 2.69
710 799 8.855110 TGGTAGTGCATTTGAAATCTCTAAAAA 58.145 29.630 0.00 0.00 0.00 1.94
870 963 1.750778 ACTTTGGTGCTGTGAAACCAG 59.249 47.619 0.00 0.00 46.78 4.00
875 968 0.663153 GTGCTGTGAAACCAGGTCAC 59.337 55.000 4.71 4.71 44.67 3.67
892 985 2.935201 GTCACTGGCTCTTTGCTATCTG 59.065 50.000 0.00 0.00 42.39 2.90
915 1012 9.778741 TCTGCTCTTATATAGGGTTGTTTTATG 57.221 33.333 0.00 0.00 0.00 1.90
934 1031 0.527565 GGATGCAGGCGTTTGATGTT 59.472 50.000 0.00 0.00 0.00 2.71
996 1093 0.666274 TAAGCACGCTTCTGACACGG 60.666 55.000 7.71 0.00 37.47 4.94
1103 1200 3.119352 GGATTGTCATCTGGAAAGTTGCC 60.119 47.826 0.00 0.00 0.00 4.52
1233 1354 4.694509 ACTTCTGAACATGAGCAATCTGTC 59.305 41.667 0.00 0.00 0.00 3.51
1270 1391 9.010029 TCTTTGATATTAAGACCACTGGTTTTC 57.990 33.333 7.26 0.00 35.25 2.29
1374 1516 5.559148 ATCCTGAGATGGATGTTCCTAAC 57.441 43.478 0.00 0.00 44.48 2.34
1391 1533 3.620374 CCTAACTACATTGCAGCTGTCAG 59.380 47.826 16.64 5.84 0.00 3.51
1470 1612 6.575267 TCCAATGCATTCATGTTATTTCCAG 58.425 36.000 9.53 0.00 32.23 3.86
1607 1750 1.162698 CCTCAACATGGTGCTGTCAG 58.837 55.000 5.66 0.00 0.00 3.51
1824 3762 5.466819 TGTAAGTTCAGTGATGTACTTCCG 58.533 41.667 11.14 0.00 37.60 4.30
2113 4052 0.249868 GCTTGCAAGGGTGGTTTTCC 60.250 55.000 27.10 3.20 41.14 3.13
2128 4067 4.036262 TGGTTTTCCATGTCTCACTTTTCG 59.964 41.667 0.00 0.00 46.22 3.46
2139 4078 6.943981 TGTCTCACTTTTCGAAGTACAATTG 58.056 36.000 3.24 3.24 0.00 2.32
2183 4122 8.653191 TGGTAGTTCTTTCTTTTACTCCATGTA 58.347 33.333 0.00 0.00 0.00 2.29
2285 4334 4.207019 CGAAGACCATTTTTGTTGAAGTGC 59.793 41.667 0.00 0.00 0.00 4.40
2336 4390 5.009010 GTCGATATCATTTTTGCAGTCCCAT 59.991 40.000 3.12 0.00 0.00 4.00
2663 4723 9.757227 TCCTTGTTTTAGTGGTCAAATTTATTG 57.243 29.630 0.00 0.00 0.00 1.90
2815 4887 6.845302 TGAGCTTTATTGATGTGCTTTACTG 58.155 36.000 0.00 0.00 33.83 2.74
2818 4890 7.661040 AGCTTTATTGATGTGCTTTACTGTTT 58.339 30.769 0.00 0.00 0.00 2.83
2864 4936 3.411446 TCGACAGGCAAGTCAATTCAAT 58.589 40.909 10.12 0.00 38.43 2.57
2905 4977 7.100458 ACTCATTTTTACCATATCTGCAACC 57.900 36.000 0.00 0.00 0.00 3.77
2929 5001 9.492730 ACCTCCAAAGTAAATTATCCATTTCAT 57.507 29.630 0.00 0.00 36.43 2.57
3117 5197 0.317160 TGTTCTCGTTGAGCGTCCAT 59.683 50.000 0.00 0.00 42.13 3.41
3118 5198 0.716108 GTTCTCGTTGAGCGTCCATG 59.284 55.000 0.00 0.00 42.13 3.66
3127 5207 2.666317 TGAGCGTCCATGGATCTTCTA 58.334 47.619 19.62 6.58 0.00 2.10
3160 5240 4.260538 CGTAGTAGTCGTACACCATCTTCC 60.261 50.000 0.00 0.00 0.00 3.46
3185 5265 0.687354 TTCTCCTTGGCGAGCTTCTT 59.313 50.000 0.00 0.00 0.00 2.52
3191 5273 0.315886 TTGGCGAGCTTCTTGTACGA 59.684 50.000 0.00 0.00 0.00 3.43
3216 5298 8.645814 AACACATTCATGATTATATCCATGCT 57.354 30.769 0.00 0.03 39.82 3.79
3401 5521 3.106827 TGAACAGATCAGGTGGCTGATA 58.893 45.455 0.00 0.00 43.38 2.15
3435 5556 6.599445 AGGAGTTGATTAGCTGCAGAATATT 58.401 36.000 20.43 5.72 0.00 1.28
3484 5605 6.967767 CAGTAGTTCGAGATGTTACTTTCGAT 59.032 38.462 7.09 0.00 41.14 3.59
3485 5606 7.485277 CAGTAGTTCGAGATGTTACTTTCGATT 59.515 37.037 7.09 3.50 41.14 3.34
3486 5607 8.027771 AGTAGTTCGAGATGTTACTTTCGATTT 58.972 33.333 7.09 3.25 41.14 2.17
3487 5608 7.653767 AGTTCGAGATGTTACTTTCGATTTT 57.346 32.000 7.09 0.00 41.14 1.82
3488 5609 8.084590 AGTTCGAGATGTTACTTTCGATTTTT 57.915 30.769 7.09 0.00 41.14 1.94
3489 5610 8.009974 AGTTCGAGATGTTACTTTCGATTTTTG 58.990 33.333 7.09 0.00 41.14 2.44
3490 5611 7.646446 TCGAGATGTTACTTTCGATTTTTGA 57.354 32.000 0.00 0.00 37.18 2.69
3605 5727 4.113354 GGTGGAAAGTGCTACTCTAATCG 58.887 47.826 0.00 0.00 0.00 3.34
3612 5734 1.609072 TGCTACTCTAATCGCGAGCAT 59.391 47.619 16.66 5.98 35.12 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.308458 CGGTGGTGGGCAACGAGA 62.308 66.667 0.00 0.00 37.60 4.04
59 60 4.506255 GATGGAGGGTTGGGGGCG 62.506 72.222 0.00 0.00 0.00 6.13
60 61 1.696314 TAGATGGAGGGTTGGGGGC 60.696 63.158 0.00 0.00 0.00 5.80
61 62 0.327576 ACTAGATGGAGGGTTGGGGG 60.328 60.000 0.00 0.00 0.00 5.40
62 63 1.596496 AACTAGATGGAGGGTTGGGG 58.404 55.000 0.00 0.00 0.00 4.96
63 64 3.739401 AAAACTAGATGGAGGGTTGGG 57.261 47.619 0.00 0.00 0.00 4.12
64 65 3.689649 CGAAAAACTAGATGGAGGGTTGG 59.310 47.826 0.00 0.00 0.00 3.77
65 66 4.575885 TCGAAAAACTAGATGGAGGGTTG 58.424 43.478 0.00 0.00 0.00 3.77
66 67 4.323562 CCTCGAAAAACTAGATGGAGGGTT 60.324 45.833 0.00 0.00 36.73 4.11
67 68 3.197983 CCTCGAAAAACTAGATGGAGGGT 59.802 47.826 0.00 0.00 36.73 4.34
68 69 3.197983 ACCTCGAAAAACTAGATGGAGGG 59.802 47.826 17.49 6.03 42.96 4.30
69 70 4.473477 ACCTCGAAAAACTAGATGGAGG 57.527 45.455 14.18 14.18 43.97 4.30
70 71 5.035443 CGTACCTCGAAAAACTAGATGGAG 58.965 45.833 0.00 0.00 42.86 3.86
71 72 4.701651 TCGTACCTCGAAAAACTAGATGGA 59.298 41.667 0.00 0.00 45.98 3.41
72 73 4.990257 TCGTACCTCGAAAAACTAGATGG 58.010 43.478 0.00 0.00 45.98 3.51
84 85 1.022735 GATGGAAGCTCGTACCTCGA 58.977 55.000 0.00 0.00 46.83 4.04
85 86 0.030908 GGATGGAAGCTCGTACCTCG 59.969 60.000 0.00 0.00 41.41 4.63
86 87 1.112113 TGGATGGAAGCTCGTACCTC 58.888 55.000 0.00 0.00 0.00 3.85
87 88 1.794714 ATGGATGGAAGCTCGTACCT 58.205 50.000 0.00 0.00 0.00 3.08
88 89 2.158957 TGAATGGATGGAAGCTCGTACC 60.159 50.000 0.00 0.00 0.00 3.34
89 90 2.866762 GTGAATGGATGGAAGCTCGTAC 59.133 50.000 0.00 0.00 0.00 3.67
90 91 2.499693 TGTGAATGGATGGAAGCTCGTA 59.500 45.455 0.00 0.00 0.00 3.43
91 92 1.278985 TGTGAATGGATGGAAGCTCGT 59.721 47.619 0.00 0.00 0.00 4.18
92 93 2.028420 TGTGAATGGATGGAAGCTCG 57.972 50.000 0.00 0.00 0.00 5.03
93 94 4.205587 AGAATGTGAATGGATGGAAGCTC 58.794 43.478 0.00 0.00 0.00 4.09
94 95 4.205587 GAGAATGTGAATGGATGGAAGCT 58.794 43.478 0.00 0.00 0.00 3.74
95 96 3.317430 GGAGAATGTGAATGGATGGAAGC 59.683 47.826 0.00 0.00 0.00 3.86
96 97 4.529897 TGGAGAATGTGAATGGATGGAAG 58.470 43.478 0.00 0.00 0.00 3.46
97 98 4.589647 TGGAGAATGTGAATGGATGGAA 57.410 40.909 0.00 0.00 0.00 3.53
98 99 4.018141 ACTTGGAGAATGTGAATGGATGGA 60.018 41.667 0.00 0.00 0.00 3.41
99 100 4.275810 ACTTGGAGAATGTGAATGGATGG 58.724 43.478 0.00 0.00 0.00 3.51
100 101 4.337555 GGACTTGGAGAATGTGAATGGATG 59.662 45.833 0.00 0.00 0.00 3.51
101 102 4.018141 TGGACTTGGAGAATGTGAATGGAT 60.018 41.667 0.00 0.00 0.00 3.41
102 103 3.330405 TGGACTTGGAGAATGTGAATGGA 59.670 43.478 0.00 0.00 0.00 3.41
103 104 3.441572 GTGGACTTGGAGAATGTGAATGG 59.558 47.826 0.00 0.00 0.00 3.16
104 105 4.074259 TGTGGACTTGGAGAATGTGAATG 58.926 43.478 0.00 0.00 0.00 2.67
105 106 4.371624 TGTGGACTTGGAGAATGTGAAT 57.628 40.909 0.00 0.00 0.00 2.57
106 107 3.855255 TGTGGACTTGGAGAATGTGAA 57.145 42.857 0.00 0.00 0.00 3.18
107 108 3.855255 TTGTGGACTTGGAGAATGTGA 57.145 42.857 0.00 0.00 0.00 3.58
108 109 3.304928 GCTTTGTGGACTTGGAGAATGTG 60.305 47.826 0.00 0.00 0.00 3.21
129 130 1.884579 TCCAGGGAATCGACGTATAGC 59.115 52.381 0.00 0.00 0.00 2.97
137 138 0.976073 GGTCCACTCCAGGGAATCGA 60.976 60.000 0.00 0.00 35.88 3.59
149 150 2.679059 CGCAGATCAAGAATGGTCCACT 60.679 50.000 0.00 0.00 37.40 4.00
150 151 1.667724 CGCAGATCAAGAATGGTCCAC 59.332 52.381 0.00 0.00 37.40 4.02
151 152 1.554617 TCGCAGATCAAGAATGGTCCA 59.445 47.619 0.00 0.00 37.40 4.02
152 153 2.315925 TCGCAGATCAAGAATGGTCC 57.684 50.000 0.00 0.00 37.40 4.46
188 189 1.872237 CGTGCCGTTCTCCTCTCAAAA 60.872 52.381 0.00 0.00 0.00 2.44
199 200 0.108520 TTATGGACCTCGTGCCGTTC 60.109 55.000 0.00 0.00 0.00 3.95
203 204 3.963428 ATCTATTATGGACCTCGTGCC 57.037 47.619 0.00 0.00 0.00 5.01
206 207 4.765856 AGCGTTATCTATTATGGACCTCGT 59.234 41.667 0.00 0.00 0.00 4.18
212 213 6.266786 TCCAAGTGAGCGTTATCTATTATGGA 59.733 38.462 0.00 0.00 0.00 3.41
226 227 0.537188 ACCTACCATCCAAGTGAGCG 59.463 55.000 0.00 0.00 0.00 5.03
238 240 2.626785 TCTGACCCATCAAACCTACCA 58.373 47.619 0.00 0.00 33.30 3.25
371 373 3.311322 TGGACGAACTAAAAGCACAACAG 59.689 43.478 0.00 0.00 0.00 3.16
456 536 6.415702 CAGTTGAAATTGAACTGCAAACATG 58.584 36.000 11.98 0.00 42.78 3.21
457 537 6.592798 CAGTTGAAATTGAACTGCAAACAT 57.407 33.333 11.98 0.00 42.78 2.71
469 549 5.701029 AGACGTTTTTGCAGTTGAAATTG 57.299 34.783 0.00 0.00 0.00 2.32
475 555 8.213812 CCAAAATATAAGACGTTTTTGCAGTTG 58.786 33.333 13.03 6.40 37.60 3.16
480 560 8.730970 TGTACCAAAATATAAGACGTTTTTGC 57.269 30.769 13.03 3.83 37.60 3.68
487 567 8.627403 TCTACCTCTGTACCAAAATATAAGACG 58.373 37.037 0.00 0.00 0.00 4.18
513 593 6.862469 TGGCACCTAAAACTATGTACTACT 57.138 37.500 0.00 0.00 0.00 2.57
514 594 7.767198 TGAATGGCACCTAAAACTATGTACTAC 59.233 37.037 0.00 0.00 0.00 2.73
515 595 7.853299 TGAATGGCACCTAAAACTATGTACTA 58.147 34.615 0.00 0.00 0.00 1.82
516 596 6.717289 TGAATGGCACCTAAAACTATGTACT 58.283 36.000 0.00 0.00 0.00 2.73
546 635 7.667575 AGACAGCCGATAGATCCAAATATAT 57.332 36.000 0.00 0.00 39.76 0.86
562 651 1.614413 GGAGGGAGTATAAGACAGCCG 59.386 57.143 0.00 0.00 0.00 5.52
595 684 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
596 685 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
598 687 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
600 689 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
603 692 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
616 705 8.279800 TCATTTCGTTTTGTATGTAGTCACTTG 58.720 33.333 0.00 0.00 0.00 3.16
618 707 7.656137 ACTCATTTCGTTTTGTATGTAGTCACT 59.344 33.333 0.00 0.00 0.00 3.41
620 709 7.654116 TCACTCATTTCGTTTTGTATGTAGTCA 59.346 33.333 0.00 0.00 0.00 3.41
663 752 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
664 753 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
666 755 7.066645 GCACTACCACATACGGATGTATATAGA 59.933 40.741 22.62 5.04 44.82 1.98
668 757 6.660094 TGCACTACCACATACGGATGTATATA 59.340 38.462 14.23 5.36 44.82 0.86
671 760 3.639561 TGCACTACCACATACGGATGTAT 59.360 43.478 14.23 7.46 44.82 2.29
674 763 2.595124 TGCACTACCACATACGGATG 57.405 50.000 5.94 5.94 39.16 3.51
675 764 3.838244 AATGCACTACCACATACGGAT 57.162 42.857 0.00 0.00 0.00 4.18
677 766 3.266636 TCAAATGCACTACCACATACGG 58.733 45.455 0.00 0.00 0.00 4.02
685 774 9.346725 CTTTTTAGAGATTTCAAATGCACTACC 57.653 33.333 0.00 0.00 0.00 3.18
710 799 7.513091 ACTCCCTCCGTTCCTAAATATTTATCT 59.487 37.037 8.34 0.00 0.00 1.98
712 801 7.628501 ACTCCCTCCGTTCCTAAATATTTAT 57.371 36.000 8.34 0.00 0.00 1.40
713 802 8.006564 TCTACTCCCTCCGTTCCTAAATATTTA 58.993 37.037 7.66 7.66 0.00 1.40
714 803 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
715 804 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
818 907 7.441890 TGGAAAGCACGAAATGTAATCTTTA 57.558 32.000 0.00 0.00 0.00 1.85
892 985 9.740710 ATCCATAAAACAACCCTATATAAGAGC 57.259 33.333 0.00 0.00 0.00 4.09
915 1012 0.527565 AACATCAAACGCCTGCATCC 59.472 50.000 0.00 0.00 0.00 3.51
934 1031 2.353704 CGTCCTGTGGCTTAGATGAACA 60.354 50.000 0.00 0.00 0.00 3.18
996 1093 2.346545 GCGAAGAAGCAATGCCATTTTC 59.653 45.455 0.00 0.00 37.05 2.29
1103 1200 4.275443 GCCTCTCATAGCTTTTTGGATCAG 59.725 45.833 0.00 0.00 0.00 2.90
1270 1391 5.689514 CAGTGATTCTATTACGCTTCTGGAG 59.310 44.000 0.00 0.00 0.00 3.86
1374 1516 3.996363 TGTTACTGACAGCTGCAATGTAG 59.004 43.478 15.27 5.82 33.40 2.74
1391 1533 6.308766 GCAGACCAAATCATTGTTGATGTTAC 59.691 38.462 0.00 0.00 41.83 2.50
1470 1612 2.281276 GGGGTGTCGTGGTGGAAC 60.281 66.667 0.00 0.00 0.00 3.62
1570 1712 1.970640 AGGAATGAAAAGGTTGGGCAC 59.029 47.619 0.00 0.00 0.00 5.01
1824 3762 3.052036 TCGAACAAACGCCAGTAGTAAC 58.948 45.455 0.00 0.00 0.00 2.50
2113 4052 6.525121 TTGTACTTCGAAAAGTGAGACATG 57.475 37.500 0.00 0.00 45.37 3.21
2114 4053 7.226720 ACAATTGTACTTCGAAAAGTGAGACAT 59.773 33.333 9.97 0.00 45.37 3.06
2116 4055 6.945072 ACAATTGTACTTCGAAAAGTGAGAC 58.055 36.000 9.97 0.00 45.37 3.36
2128 4067 8.565416 ACAAGGTTTTAGCTACAATTGTACTTC 58.435 33.333 14.35 6.88 30.20 3.01
2139 4078 7.268199 ACTACCAAAACAAGGTTTTAGCTAC 57.732 36.000 6.75 0.00 40.54 3.58
2183 4122 6.172630 GGGAAATGGAGTTGCATTACAAATT 58.827 36.000 0.00 0.00 40.82 1.82
2249 4298 2.948979 TGGTCTTCGCATTCACAAAACT 59.051 40.909 0.00 0.00 0.00 2.66
2253 4302 4.582701 AAAATGGTCTTCGCATTCACAA 57.417 36.364 0.00 0.00 0.00 3.33
2285 4334 7.924103 AACGACAAAAGCAAATAAACTTAGG 57.076 32.000 0.00 0.00 0.00 2.69
2582 4638 6.372937 AGAAACTTGCTGAAATAACTAGCCTC 59.627 38.462 0.00 0.00 36.64 4.70
2663 4723 4.399219 GCTAATCCTATTGGGGAAAGTCC 58.601 47.826 0.00 0.00 39.02 3.85
2753 4815 6.421801 ACTGACAAATGCAGCTATTTTTCAAC 59.578 34.615 10.50 0.00 36.71 3.18
2815 4887 4.473199 GCAGGAACGATAAGGTTTGAAAC 58.527 43.478 0.00 0.00 0.00 2.78
2818 4890 2.617021 GGGCAGGAACGATAAGGTTTGA 60.617 50.000 0.00 0.00 0.00 2.69
2864 4936 0.107831 AGTACTTGAGTTGCGGCCAA 59.892 50.000 2.24 0.00 0.00 4.52
2929 5001 4.408921 CCATAGAGGGTGTAACATTCCAGA 59.591 45.833 0.00 0.00 39.98 3.86
2965 5037 5.914898 TGCTGCTAGATGAACTGTACTTA 57.085 39.130 0.00 0.00 0.00 2.24
3014 5088 9.997482 GCTGCATTTATTGATTTTGATTTGAAT 57.003 25.926 0.00 0.00 0.00 2.57
3033 5107 3.129988 GGTCTCATGCTTTTAGCTGCATT 59.870 43.478 6.52 0.00 46.29 3.56
3117 5197 1.107538 CCTCCGGCGTAGAAGATCCA 61.108 60.000 6.01 0.00 0.00 3.41
3118 5198 1.660917 CCTCCGGCGTAGAAGATCC 59.339 63.158 6.01 0.00 0.00 3.36
3160 5240 3.494336 CGCCAAGGAGAAGCTGCG 61.494 66.667 0.00 0.00 35.81 5.18
3185 5265 9.203421 GGATATAATCATGAATGTGTTCGTACA 57.797 33.333 0.00 0.00 37.15 2.90
3191 5273 8.645814 AGCATGGATATAATCATGAATGTGTT 57.354 30.769 17.55 0.00 42.25 3.32
3294 5394 3.531538 TGTTGAAGCGTCTTCACTCTTT 58.468 40.909 17.92 0.00 27.21 2.52
3401 5521 6.211184 CAGCTAATCAACTCCTCTCCAGATAT 59.789 42.308 0.00 0.00 0.00 1.63
3435 5556 7.124721 TGATACCAAATCAGGAATTCATGGAA 58.875 34.615 19.21 2.14 31.96 3.53
3453 5574 6.827251 AGTAACATCTCGAACTACTGATACCA 59.173 38.462 0.00 0.00 0.00 3.25
3486 5607 9.515020 GTTTCATTTTGTCAGTACTGATTCAAA 57.485 29.630 27.54 26.63 42.18 2.69
3487 5608 7.855409 CGTTTCATTTTGTCAGTACTGATTCAA 59.145 33.333 27.54 23.03 42.18 2.69
3488 5609 7.351981 CGTTTCATTTTGTCAGTACTGATTCA 58.648 34.615 27.54 18.82 42.18 2.57
3489 5610 6.797033 CCGTTTCATTTTGTCAGTACTGATTC 59.203 38.462 27.54 16.48 42.18 2.52
3490 5611 6.485313 TCCGTTTCATTTTGTCAGTACTGATT 59.515 34.615 27.54 8.77 42.18 2.57
3526 5648 0.666577 CGTTTCTTTCTCGACCGGCT 60.667 55.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.