Multiple sequence alignment - TraesCS2B01G057900

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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 TraesCS2B01G057900 chr2B 100.000 4478 0 0 1 4478 28270903 28275380 0.000000e+00 8270.0
1 TraesCS2B01G057900 chr2B 96.299 2864 62 15 1060 3904 28292180 28295018 0.000000e+00 4662.0
2 TraesCS2B01G057900 chr2B 99.177 486 4 0 3993 4478 28295534 28296019 0.000000e+00 876.0
3 TraesCS2B01G057900 chr2B 83.851 644 102 1 2837 3480 28339962 28340603 2.960000e-171 612.0
4 TraesCS2B01G057900 chr2B 87.384 539 57 4 1036 1570 28331659 28332190 3.830000e-170 608.0
5 TraesCS2B01G057900 chr2B 87.194 531 57 4 1036 1562 28349232 28349755 1.070000e-165 593.0
6 TraesCS2B01G057900 chr2B 83.410 434 72 0 2101 2534 28357704 28358137 1.940000e-108 403.0
7 TraesCS2B01G057900 chr2B 90.411 73 1 3 659 727 28271493 28271563 1.720000e-14 91.6
8 TraesCS2B01G057900 chr2B 90.411 73 1 3 591 661 28271561 28271629 1.720000e-14 91.6
9 TraesCS2B01G057900 chr2A 90.773 1940 152 11 1883 3798 17931149 17933085 0.000000e+00 2566.0
10 TraesCS2B01G057900 chr2A 89.386 1743 84 24 39 1709 17929061 17930774 0.000000e+00 2100.0
11 TraesCS2B01G057900 chr2A 84.254 724 77 16 839 1561 17892983 17893670 0.000000e+00 671.0
12 TraesCS2B01G057900 chr2A 87.743 514 57 4 1060 1570 17981456 17981966 2.980000e-166 595.0
13 TraesCS2B01G057900 chr2A 85.323 511 67 3 3972 4475 17933234 17933743 5.130000e-144 521.0
14 TraesCS2B01G057900 chr2A 83.180 434 73 0 2101 2534 17984449 17984882 9.030000e-107 398.0
15 TraesCS2B01G057900 chr2A 91.667 72 1 2 591 661 17929677 17929744 1.330000e-15 95.3
16 TraesCS2B01G057900 chr2D 90.904 1814 126 17 2022 3802 16016309 16018116 0.000000e+00 2399.0
17 TraesCS2B01G057900 chr2D 90.462 975 40 22 659 1585 16015296 16016265 0.000000e+00 1236.0
18 TraesCS2B01G057900 chr2D 86.120 634 86 1 2835 3468 16129869 16130500 0.000000e+00 682.0
19 TraesCS2B01G057900 chr2D 87.681 552 57 4 1015 1562 16232552 16233096 2.270000e-177 632.0
20 TraesCS2B01G057900 chr2D 86.456 539 62 4 1036 1570 16124676 16125207 8.350000e-162 580.0
21 TraesCS2B01G057900 chr2D 85.417 528 67 2 3957 4474 16018269 16018796 1.420000e-149 540.0
22 TraesCS2B01G057900 chr2D 83.410 434 72 0 2101 2534 16236991 16237424 1.940000e-108 403.0
23 TraesCS2B01G057900 chr2D 83.688 282 36 4 1603 1881 590806264 590806538 1.600000e-64 257.0
24 TraesCS2B01G057900 chr5A 86.219 283 31 7 1604 1881 389765285 389765564 2.620000e-77 300.0
25 TraesCS2B01G057900 chr3D 85.765 281 38 2 1603 1881 599370586 599370306 3.390000e-76 296.0
26 TraesCS2B01G057900 chr3D 82.986 288 25 11 1613 1881 56395649 56395367 5.790000e-59 239.0
27 TraesCS2B01G057900 chr7B 85.818 275 27 9 1611 1879 610857560 610857292 9.480000e-72 281.0
28 TraesCS2B01G057900 chr7B 83.453 278 38 7 1604 1879 611043567 611043296 7.440000e-63 252.0
29 TraesCS2B01G057900 chr7B 84.397 141 21 1 1883 2023 611043256 611043117 2.170000e-28 137.0
30 TraesCS2B01G057900 chr7B 97.619 42 1 0 1 42 481688441 481688400 6.210000e-09 73.1
31 TraesCS2B01G057900 chr7A 84.155 284 38 6 1602 1881 10626011 10625731 7.380000e-68 268.0
32 TraesCS2B01G057900 chr5D 82.500 280 45 3 1605 1881 546348606 546348884 4.480000e-60 243.0
33 TraesCS2B01G057900 chr7D 87.943 141 12 5 1883 2021 519601540 519601403 1.290000e-35 161.0
34 TraesCS2B01G057900 chr7D 87.943 141 12 5 1883 2021 519602904 519603041 1.290000e-35 161.0
35 TraesCS2B01G057900 chr4A 85.156 128 19 0 1883 2010 692563599 692563472 1.010000e-26 132.0
36 TraesCS2B01G057900 chr1B 97.619 42 1 0 1 42 19991040 19991081 6.210000e-09 73.1
37 TraesCS2B01G057900 chr1B 92.857 42 3 0 543 584 35441545 35441586 1.340000e-05 62.1


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 TraesCS2B01G057900 chr2B 28270903 28275380 4477 False 2817.733333 8270 93.607333 1 4478 3 chr2B.!!$F5 4477
1 TraesCS2B01G057900 chr2B 28292180 28296019 3839 False 2769.000000 4662 97.738000 1060 4478 2 chr2B.!!$F6 3418
2 TraesCS2B01G057900 chr2B 28339962 28340603 641 False 612.000000 612 83.851000 2837 3480 1 chr2B.!!$F2 643
3 TraesCS2B01G057900 chr2B 28331659 28332190 531 False 608.000000 608 87.384000 1036 1570 1 chr2B.!!$F1 534
4 TraesCS2B01G057900 chr2B 28349232 28349755 523 False 593.000000 593 87.194000 1036 1562 1 chr2B.!!$F3 526
5 TraesCS2B01G057900 chr2A 17929061 17933743 4682 False 1320.575000 2566 89.287250 39 4475 4 chr2A.!!$F2 4436
6 TraesCS2B01G057900 chr2A 17892983 17893670 687 False 671.000000 671 84.254000 839 1561 1 chr2A.!!$F1 722
7 TraesCS2B01G057900 chr2A 17981456 17984882 3426 False 496.500000 595 85.461500 1060 2534 2 chr2A.!!$F3 1474
8 TraesCS2B01G057900 chr2D 16015296 16018796 3500 False 1391.666667 2399 88.927667 659 4474 3 chr2D.!!$F4 3815
9 TraesCS2B01G057900 chr2D 16129869 16130500 631 False 682.000000 682 86.120000 2835 3468 1 chr2D.!!$F2 633
10 TraesCS2B01G057900 chr2D 16124676 16125207 531 False 580.000000 580 86.456000 1036 1570 1 chr2D.!!$F1 534
11 TraesCS2B01G057900 chr2D 16232552 16237424 4872 False 517.500000 632 85.545500 1015 2534 2 chr2D.!!$F5 1519

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
468 489 0.032952 GTGGTGCGAGTGGTGTTAGA 59.967 55.0 0.0 0.0 0.0 2.10 F
638 659 0.103208 GTGCGACGAGGATGAGGATT 59.897 55.0 0.0 0.0 0.0 3.01 F
978 1047 0.107017 CCAGCGACCAATCCCTCATT 60.107 55.0 0.0 0.0 0.0 2.57 F
980 1049 0.179073 AGCGACCAATCCCTCATTCG 60.179 55.0 0.0 0.0 0.0 3.34 F
981 1050 0.179084 GCGACCAATCCCTCATTCGA 60.179 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 6843 0.263765 ACCCCGGACCTGCTATTCTA 59.736 55.000 0.73 0.0 0.00 2.10 R
2220 7130 2.676748 TGTGGCCTTGTTTCCTGAAAT 58.323 42.857 3.32 0.0 32.36 2.17 R
2503 7413 4.298626 ACTGAGCCTTAATATGGTCTCCA 58.701 43.478 11.24 0.0 38.19 3.86 R
2504 7414 4.965200 ACTGAGCCTTAATATGGTCTCC 57.035 45.455 11.24 0.0 31.46 3.71 R
3759 8713 4.503714 CCCACCAGAGGCTCTTTAATTA 57.496 45.455 15.90 0.0 0.00 1.40 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
94 95 5.779241 AGATCTCCCTGATGTTTTGGTAA 57.221 39.130 0.00 0.00 35.14 2.85
141 162 8.302515 TCACTATACCCTACGAAAAGAATCTT 57.697 34.615 0.00 0.00 0.00 2.40
151 172 5.936054 ACGAAAAGAATCTTGATCTTGCAG 58.064 37.500 0.00 0.00 37.22 4.41
231 252 5.765182 ACGGAATTGATCAAGACAAGTCTTT 59.235 36.000 14.54 0.00 46.95 2.52
258 279 3.524541 ACAGAAAGCAACTTGCCTTTTG 58.475 40.909 10.25 11.31 46.52 2.44
283 304 1.884579 ACTCGGTCGTTTCTCTAAGCA 59.115 47.619 0.00 0.00 0.00 3.91
290 311 4.547532 GTCGTTTCTCTAAGCACTCTTCA 58.452 43.478 0.00 0.00 33.85 3.02
293 314 4.985409 CGTTTCTCTAAGCACTCTTCAACT 59.015 41.667 0.00 0.00 33.85 3.16
307 328 2.702592 TCAACTTGTTTCCACTCCGT 57.297 45.000 0.00 0.00 0.00 4.69
337 358 6.348498 TGATGTGTCGGTAATGAATCAGAAT 58.652 36.000 0.00 0.00 0.00 2.40
356 377 6.157820 TCAGAATTCCCATGTATCAAGTGGTA 59.842 38.462 0.65 0.00 0.00 3.25
357 378 6.828273 CAGAATTCCCATGTATCAAGTGGTAA 59.172 38.462 0.65 0.00 0.00 2.85
370 391 1.992557 AGTGGTAATGGTGGTGGTGAT 59.007 47.619 0.00 0.00 0.00 3.06
468 489 0.032952 GTGGTGCGAGTGGTGTTAGA 59.967 55.000 0.00 0.00 0.00 2.10
509 530 1.377536 GCAGGAGCACTTGGAAGATC 58.622 55.000 0.00 0.00 41.58 2.75
530 551 3.569701 TCTCAAGGAGTTTTGGCATGTTC 59.430 43.478 0.00 0.00 0.00 3.18
531 552 2.293122 TCAAGGAGTTTTGGCATGTTCG 59.707 45.455 0.00 0.00 0.00 3.95
532 553 0.598065 AGGAGTTTTGGCATGTTCGC 59.402 50.000 0.00 0.00 0.00 4.70
579 600 3.649986 GCGAGTTGTGTTGCCGCT 61.650 61.111 0.00 0.00 42.24 5.52
580 601 2.249309 CGAGTTGTGTTGCCGCTG 59.751 61.111 0.00 0.00 0.00 5.18
581 602 2.639286 GAGTTGTGTTGCCGCTGG 59.361 61.111 0.00 0.00 0.00 4.85
582 603 1.891919 GAGTTGTGTTGCCGCTGGA 60.892 57.895 0.00 0.00 0.00 3.86
583 604 2.117941 GAGTTGTGTTGCCGCTGGAC 62.118 60.000 0.00 0.00 0.00 4.02
584 605 3.276091 TTGTGTTGCCGCTGGACG 61.276 61.111 0.00 0.00 43.15 4.79
585 606 4.539083 TGTGTTGCCGCTGGACGT 62.539 61.111 0.00 0.00 41.42 4.34
586 607 3.712881 GTGTTGCCGCTGGACGTC 61.713 66.667 7.13 7.13 41.42 4.34
587 608 4.228567 TGTTGCCGCTGGACGTCA 62.229 61.111 18.91 2.63 41.42 4.35
588 609 3.414700 GTTGCCGCTGGACGTCAG 61.415 66.667 18.91 13.54 46.03 3.51
589 610 3.923864 TTGCCGCTGGACGTCAGT 61.924 61.111 18.91 0.00 45.08 3.41
590 611 3.454587 TTGCCGCTGGACGTCAGTT 62.455 57.895 18.91 0.00 45.08 3.16
591 612 3.414700 GCCGCTGGACGTCAGTTG 61.415 66.667 18.91 9.43 45.08 3.16
592 613 3.414700 CCGCTGGACGTCAGTTGC 61.415 66.667 18.91 13.59 45.08 4.17
593 614 3.414700 CGCTGGACGTCAGTTGCC 61.415 66.667 18.91 0.00 45.08 4.52
594 615 3.414700 GCTGGACGTCAGTTGCCG 61.415 66.667 18.91 0.00 45.08 5.69
595 616 2.738521 CTGGACGTCAGTTGCCGG 60.739 66.667 18.91 0.00 38.64 6.13
596 617 4.980805 TGGACGTCAGTTGCCGGC 62.981 66.667 22.73 22.73 0.00 6.13
597 618 4.681978 GGACGTCAGTTGCCGGCT 62.682 66.667 29.70 3.84 31.24 5.52
598 619 2.665185 GACGTCAGTTGCCGGCTT 60.665 61.111 29.70 10.65 0.00 4.35
599 620 2.954753 GACGTCAGTTGCCGGCTTG 61.955 63.158 29.70 22.09 0.00 4.01
602 623 4.577677 TCAGTTGCCGGCTTGCCA 62.578 61.111 29.70 2.88 0.00 4.92
622 643 4.681978 AAGAGACGGGCGGTGTGC 62.682 66.667 1.11 0.00 45.38 4.57
638 659 0.103208 GTGCGACGAGGATGAGGATT 59.897 55.000 0.00 0.00 0.00 3.01
719 744 4.580580 GGATGAGGAGTGAAGTTTGTGTTT 59.419 41.667 0.00 0.00 0.00 2.83
758 783 7.208080 ACGTAAGATTCTGTTGTAGTTGAAGT 58.792 34.615 0.00 0.00 43.62 3.01
759 784 7.709613 ACGTAAGATTCTGTTGTAGTTGAAGTT 59.290 33.333 0.00 0.00 43.62 2.66
787 832 1.546476 GGTCAGTGAGGACGAAGACAT 59.454 52.381 0.00 0.00 38.70 3.06
797 842 4.227197 AGGACGAAGACATGAGGGATAAT 58.773 43.478 0.00 0.00 0.00 1.28
978 1047 0.107017 CCAGCGACCAATCCCTCATT 60.107 55.000 0.00 0.00 0.00 2.57
979 1048 1.303309 CAGCGACCAATCCCTCATTC 58.697 55.000 0.00 0.00 0.00 2.67
980 1049 0.179073 AGCGACCAATCCCTCATTCG 60.179 55.000 0.00 0.00 0.00 3.34
981 1050 0.179084 GCGACCAATCCCTCATTCGA 60.179 55.000 0.00 0.00 0.00 3.71
1080 1152 0.687757 CTCCACAGGCAGCCCTAGTA 60.688 60.000 8.22 0.00 40.33 1.82
1113 1185 0.318441 TCTTCTGCCCACTTCTCGTG 59.682 55.000 0.00 0.00 43.41 4.35
1506 1578 1.815421 GAAGATCGCCACCACGCAT 60.815 57.895 0.00 0.00 0.00 4.73
1565 1637 0.587285 CGCGAGAACGAGGTAGCTAT 59.413 55.000 0.00 0.00 42.66 2.97
1908 6351 6.811665 TGAACTTCAAGACATGTTCTATACGG 59.188 38.462 0.00 0.00 39.38 4.02
1983 6843 2.871096 TAAAGCGACATTGGAGGGTT 57.129 45.000 0.00 0.00 0.00 4.11
2465 7375 1.913317 CGATGACAGCGACTTCATCA 58.087 50.000 7.46 5.17 45.78 3.07
2495 7405 4.213270 TGCTTTCCATTCAACAAGAGTACG 59.787 41.667 0.00 0.00 0.00 3.67
2503 7413 7.036220 CCATTCAACAAGAGTACGATCTTACT 58.964 38.462 11.41 11.41 37.43 2.24
2504 7414 7.009631 CCATTCAACAAGAGTACGATCTTACTG 59.990 40.741 15.99 6.16 37.43 2.74
2633 7562 8.923683 GTTGACTAAGTCTATACAAAAGTGTCC 58.076 37.037 0.00 0.00 34.87 4.02
3703 8657 2.831526 TCAGCAATACTCAGCACTACCA 59.168 45.455 0.00 0.00 0.00 3.25
3759 8713 6.006275 ACATTGCTTACTTCCATAGGTCAT 57.994 37.500 0.00 0.00 0.00 3.06
3902 8923 8.908786 TTTTGATAGATCTCTCTCTCTCTCTC 57.091 38.462 0.00 0.00 32.66 3.20
3903 8924 7.862274 TTGATAGATCTCTCTCTCTCTCTCT 57.138 40.000 0.00 0.00 32.66 3.10
3904 8925 7.473735 TGATAGATCTCTCTCTCTCTCTCTC 57.526 44.000 0.00 0.00 32.66 3.20
3905 8926 6.438741 TGATAGATCTCTCTCTCTCTCTCTCC 59.561 46.154 0.00 0.00 32.66 3.71
3906 8927 3.906846 AGATCTCTCTCTCTCTCTCTCCC 59.093 52.174 0.00 0.00 0.00 4.30
3907 8928 3.421394 TCTCTCTCTCTCTCTCTCCCT 57.579 52.381 0.00 0.00 0.00 4.20
3908 8929 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
3909 8930 2.370189 CTCTCTCTCTCTCTCTCCCTCC 59.630 59.091 0.00 0.00 0.00 4.30
3910 8931 1.421646 CTCTCTCTCTCTCTCCCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
3911 8932 1.010793 TCTCTCTCTCTCTCCCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
3912 8933 1.421646 CTCTCTCTCTCTCCCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
3913 8934 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
3914 8935 0.996762 TCTCTCTCTCCCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
3915 8936 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
3916 8937 0.996762 TCTCTCTCCCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
3917 8938 2.015726 TCTCTCCCTCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
3918 8939 3.430497 TCTCCCTCCCTCCCTCCG 61.430 72.222 0.00 0.00 0.00 4.63
3919 8940 3.756783 CTCCCTCCCTCCCTCCGT 61.757 72.222 0.00 0.00 0.00 4.69
3920 8941 3.742248 CTCCCTCCCTCCCTCCGTC 62.742 73.684 0.00 0.00 0.00 4.79
3921 8942 4.862823 CCCTCCCTCCCTCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
3922 8943 4.862823 CCTCCCTCCCTCCGTCCC 62.863 77.778 0.00 0.00 0.00 4.46
3923 8944 3.756783 CTCCCTCCCTCCGTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
3924 8945 3.742248 CTCCCTCCCTCCGTCCCTC 62.742 73.684 0.00 0.00 0.00 4.30
3925 8946 4.862823 CCCTCCCTCCGTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
3926 8947 4.862823 CCTCCCTCCGTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
3927 8948 3.756783 CTCCCTCCGTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
3928 8949 3.742248 CTCCCTCCGTCCCTCCCTC 62.742 73.684 0.00 0.00 0.00 4.30
3929 8950 4.862823 CCCTCCGTCCCTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
3931 8952 4.444081 CTCCGTCCCTCCCTCCGT 62.444 72.222 0.00 0.00 0.00 4.69
3935 8956 4.077180 GTCCCTCCCTCCGTCCCT 62.077 72.222 0.00 0.00 0.00 4.20
3955 8976 1.010793 TCCCTCCCTCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
3957 8978 2.412591 CCTCCCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
3958 8979 2.370189 CCTCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
3959 8980 3.312890 CTCCCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
3960 8981 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
3961 8982 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
3962 8983 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
3963 8984 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
3964 8985 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
3965 8986 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3966 8987 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3967 8988 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3968 8989 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3969 8990 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
3970 8991 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
4234 9737 0.609662 CTTTTGGTGCCCTCCATTGG 59.390 55.000 0.00 0.00 37.33 3.16
4235 9738 0.105246 TTTTGGTGCCCTCCATTGGT 60.105 50.000 1.86 0.00 37.33 3.67
4236 9739 0.831288 TTTGGTGCCCTCCATTGGTG 60.831 55.000 1.86 0.00 37.33 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.694137 GGCTTACTAGGTAATTTAGATGTGTAG 57.306 37.037 0.00 0.00 0.00 2.74
26 27 9.204337 TGGCTTACTAGGTAATTTAGATGTGTA 57.796 33.333 0.00 0.00 0.00 2.90
27 28 8.086143 TGGCTTACTAGGTAATTTAGATGTGT 57.914 34.615 0.00 0.00 0.00 3.72
28 29 9.561069 AATGGCTTACTAGGTAATTTAGATGTG 57.439 33.333 0.00 0.00 0.00 3.21
60 61 2.520120 AGGGAGATCTAGGTCCATGTCA 59.480 50.000 0.00 0.00 34.14 3.58
106 127 8.712285 TCGTAGGGTATAGTGAAAATGAAAAG 57.288 34.615 0.00 0.00 0.00 2.27
121 142 8.024145 AGATCAAGATTCTTTTCGTAGGGTAT 57.976 34.615 0.00 0.00 0.00 2.73
141 162 5.481122 TCCCAAAATGAATTCTGCAAGATCA 59.519 36.000 7.05 0.00 46.36 2.92
151 172 7.800155 TTTTTCCAACTCCCAAAATGAATTC 57.200 32.000 0.00 0.00 0.00 2.17
209 230 7.446001 AGAAAGACTTGTCTTGATCAATTCC 57.554 36.000 15.61 0.57 0.00 3.01
231 252 3.181487 GGCAAGTTGCTTTCTGTTCAAGA 60.181 43.478 26.16 0.00 44.28 3.02
258 279 3.828060 AGAGAAACGACCGAGTAGTTC 57.172 47.619 0.00 0.00 30.73 3.01
283 304 4.200092 GGAGTGGAAACAAGTTGAAGAGT 58.800 43.478 10.54 0.00 46.06 3.24
290 311 6.938030 TCATAAATACGGAGTGGAAACAAGTT 59.062 34.615 0.00 0.00 45.73 2.66
293 314 6.882140 ACATCATAAATACGGAGTGGAAACAA 59.118 34.615 0.00 0.00 45.73 2.83
307 328 9.771534 TGATTCATTACCGACACATCATAAATA 57.228 29.630 0.00 0.00 0.00 1.40
337 358 5.044476 ACCATTACCACTTGATACATGGGAA 60.044 40.000 0.00 0.00 40.66 3.97
356 377 0.612732 CTGCCATCACCACCACCATT 60.613 55.000 0.00 0.00 0.00 3.16
357 378 1.000521 CTGCCATCACCACCACCAT 60.001 57.895 0.00 0.00 0.00 3.55
468 489 4.836825 CAGACACCATGACTTAGGACATT 58.163 43.478 0.00 0.00 0.00 2.71
499 520 5.182760 CCAAAACTCCTTGAGATCTTCCAAG 59.817 44.000 14.43 14.43 39.43 3.61
504 525 4.104383 TGCCAAAACTCCTTGAGATCTT 57.896 40.909 0.00 0.00 33.32 2.40
509 530 3.610114 CGAACATGCCAAAACTCCTTGAG 60.610 47.826 0.00 0.00 35.52 3.02
530 551 1.350193 ACTCAGCTTCGTTATGTGCG 58.650 50.000 0.00 0.00 0.00 5.34
531 552 2.726066 GCAACTCAGCTTCGTTATGTGC 60.726 50.000 0.00 0.00 0.00 4.57
532 553 2.738846 AGCAACTCAGCTTCGTTATGTG 59.261 45.455 0.00 0.00 43.70 3.21
544 565 2.289820 TCGCCGTATACTAGCAACTCAG 59.710 50.000 13.28 0.00 0.00 3.35
584 605 4.043200 GGCAAGCCGGCAACTGAC 62.043 66.667 31.54 21.11 40.76 3.51
592 613 3.058160 CTCTTGGTGGCAAGCCGG 61.058 66.667 6.60 0.00 39.42 6.13
593 614 2.032528 TCTCTTGGTGGCAAGCCG 59.967 61.111 6.60 0.00 39.42 5.52
594 615 2.328099 CGTCTCTTGGTGGCAAGCC 61.328 63.158 3.61 3.61 32.52 4.35
595 616 2.328099 CCGTCTCTTGGTGGCAAGC 61.328 63.158 0.00 0.00 32.52 4.01
596 617 1.672356 CCCGTCTCTTGGTGGCAAG 60.672 63.158 0.00 0.00 0.00 4.01
597 618 2.429930 CCCGTCTCTTGGTGGCAA 59.570 61.111 0.00 0.00 0.00 4.52
598 619 4.329545 GCCCGTCTCTTGGTGGCA 62.330 66.667 0.00 0.00 41.76 4.92
602 623 4.003788 CACCGCCCGTCTCTTGGT 62.004 66.667 0.00 0.00 0.00 3.67
622 643 1.678627 ACTGAATCCTCATCCTCGTCG 59.321 52.381 0.00 0.00 0.00 5.12
626 647 4.751767 ACTTCACTGAATCCTCATCCTC 57.248 45.455 0.00 0.00 0.00 3.71
638 659 4.439974 GGCATTGAACACAAACTTCACTGA 60.440 41.667 3.47 0.00 32.65 3.41
719 744 2.486592 TCTTACGTCGATGAGCACTTGA 59.513 45.455 12.58 0.00 0.00 3.02
758 783 2.115427 TCCTCACTGACCTCACACAAA 58.885 47.619 0.00 0.00 0.00 2.83
759 784 1.412710 GTCCTCACTGACCTCACACAA 59.587 52.381 0.00 0.00 0.00 3.33
787 832 5.394883 GGTGACGTCTTGTAATTATCCCTCA 60.395 44.000 17.92 0.00 0.00 3.86
797 842 3.462483 ACATGTGGTGACGTCTTGTAA 57.538 42.857 17.92 0.04 0.00 2.41
885 954 0.620030 TCCAGCAAGAGCAAGGCATA 59.380 50.000 0.00 0.00 45.49 3.14
978 1047 2.602878 GCTGTTCAGTTTACGGATCGA 58.397 47.619 0.00 0.00 0.00 3.59
979 1048 1.659098 GGCTGTTCAGTTTACGGATCG 59.341 52.381 1.78 0.00 0.00 3.69
980 1049 2.695359 TGGCTGTTCAGTTTACGGATC 58.305 47.619 1.78 0.00 0.00 3.36
981 1050 2.851263 TGGCTGTTCAGTTTACGGAT 57.149 45.000 1.78 0.00 0.00 4.18
1010 1079 2.963854 CGTGGAGGCTATGCTGCG 60.964 66.667 0.00 0.00 0.00 5.18
1080 1152 2.726821 CAGAAGAGCAGGAGAGAGACT 58.273 52.381 0.00 0.00 0.00 3.24
1506 1578 2.368875 GACCTTCTTGTTGGTGAGGAGA 59.631 50.000 0.00 0.00 36.59 3.71
1565 1637 6.127647 GGTGCTATCAAAATCAAGTTGATGGA 60.128 38.462 18.94 16.05 43.11 3.41
1637 1866 7.227512 ACGAGAAATGGATGGCTAGATAAAAAG 59.772 37.037 0.00 0.00 0.00 2.27
1983 6843 0.263765 ACCCCGGACCTGCTATTCTA 59.736 55.000 0.73 0.00 0.00 2.10
2220 7130 2.676748 TGTGGCCTTGTTTCCTGAAAT 58.323 42.857 3.32 0.00 32.36 2.17
2465 7375 5.021033 TGTTGAATGGAAAGCAACACATT 57.979 34.783 0.00 0.00 44.73 2.71
2495 7405 7.038658 AGCCTTAATATGGTCTCCAGTAAGATC 60.039 40.741 13.44 0.00 36.75 2.75
2503 7413 4.298626 ACTGAGCCTTAATATGGTCTCCA 58.701 43.478 11.24 0.00 38.19 3.86
2504 7414 4.965200 ACTGAGCCTTAATATGGTCTCC 57.035 45.455 11.24 0.00 31.46 3.71
3759 8713 4.503714 CCCACCAGAGGCTCTTTAATTA 57.496 45.455 15.90 0.00 0.00 1.40
3887 8908 3.309296 GAGGGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
3889 8910 2.408565 GGAGGGAGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
3890 8911 1.421646 GGGAGGGAGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
3891 8912 1.010793 AGGGAGGGAGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
3892 8913 1.421646 GAGGGAGGGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
3893 8914 1.518367 GAGGGAGGGAGAGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
3894 8915 0.478507 GGAGGGAGGGAGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
3895 8916 0.996762 GGGAGGGAGGGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
3896 8917 0.998945 AGGGAGGGAGGGAGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
3897 8918 0.996762 GAGGGAGGGAGGGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
3898 8919 1.541672 GAGGGAGGGAGGGAGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
3899 8920 2.015726 GGAGGGAGGGAGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
3900 8921 2.612251 GGAGGGAGGGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
3901 8922 3.430497 CGGAGGGAGGGAGGGAGA 61.430 72.222 0.00 0.00 0.00 3.71
3902 8923 3.742248 GACGGAGGGAGGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
3903 8924 3.752167 GACGGAGGGAGGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
3904 8925 4.862823 GGACGGAGGGAGGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
3905 8926 4.862823 GGGACGGAGGGAGGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
3906 8927 3.742248 GAGGGACGGAGGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
3907 8928 3.752167 GAGGGACGGAGGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
3908 8929 4.862823 GGAGGGACGGAGGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
3909 8930 4.862823 GGGAGGGACGGAGGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
3910 8931 3.742248 GAGGGAGGGACGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
3911 8932 3.752167 GAGGGAGGGACGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
3912 8933 4.862823 GGAGGGAGGGACGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
3914 8935 4.444081 ACGGAGGGAGGGACGGAG 62.444 72.222 0.00 0.00 0.00 4.63
3915 8936 4.437587 GACGGAGGGAGGGACGGA 62.438 72.222 0.00 0.00 0.00 4.69
3918 8939 4.077180 AGGGACGGAGGGAGGGAC 62.077 72.222 0.00 0.00 0.00 4.46
3919 8940 3.752167 GAGGGACGGAGGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
3920 8941 4.862823 GGAGGGACGGAGGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
3921 8942 4.862823 GGGAGGGACGGAGGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
3922 8943 3.742248 GAGGGAGGGACGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
3923 8944 3.752167 GAGGGAGGGACGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
3924 8945 4.862823 GGAGGGAGGGACGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
3925 8946 4.862823 GGGAGGGAGGGACGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
3926 8947 3.742248 GAGGGAGGGAGGGACGGAG 62.742 73.684 0.00 0.00 0.00 4.63
3927 8948 3.752167 GAGGGAGGGAGGGACGGA 61.752 72.222 0.00 0.00 0.00 4.69
3928 8949 3.742248 GAGAGGGAGGGAGGGACGG 62.742 73.684 0.00 0.00 0.00 4.79
3929 8950 2.123640 GAGAGGGAGGGAGGGACG 60.124 72.222 0.00 0.00 0.00 4.79
3930 8951 1.231928 GAGAGAGGGAGGGAGGGAC 59.768 68.421 0.00 0.00 0.00 4.46
3931 8952 0.996762 GAGAGAGAGGGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
3935 8956 1.010793 AGAGAGAGAGAGAGGGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
3955 8976 0.550914 GGCTGGGAGAGAGAGAGAGA 59.449 60.000 0.00 0.00 0.00 3.10
3957 8978 0.033601 GTGGCTGGGAGAGAGAGAGA 60.034 60.000 0.00 0.00 0.00 3.10
3958 8979 0.033208 AGTGGCTGGGAGAGAGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
3959 8980 1.299939 TAGTGGCTGGGAGAGAGAGA 58.700 55.000 0.00 0.00 0.00 3.10
3960 8981 2.151502 TTAGTGGCTGGGAGAGAGAG 57.848 55.000 0.00 0.00 0.00 3.20
3961 8982 2.392662 CATTAGTGGCTGGGAGAGAGA 58.607 52.381 0.00 0.00 0.00 3.10
3962 8983 1.415659 CCATTAGTGGCTGGGAGAGAG 59.584 57.143 0.00 0.00 39.01 3.20
3963 8984 1.500474 CCATTAGTGGCTGGGAGAGA 58.500 55.000 0.00 0.00 39.01 3.10
3969 8990 0.911769 TCAGTCCCATTAGTGGCTGG 59.088 55.000 10.60 0.00 44.62 4.85
3970 8991 2.092753 ACATCAGTCCCATTAGTGGCTG 60.093 50.000 0.00 2.34 44.62 4.85
3983 9004 3.864583 GCACTTCAGATCAGACATCAGTC 59.135 47.826 0.00 0.00 45.31 3.51
3988 9009 4.822685 AAGAGCACTTCAGATCAGACAT 57.177 40.909 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.