Multiple sequence alignment - TraesCS1B01G138300

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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 TraesCS1B01G138300 chr1B 100.000 4011 0 0 1 4011 178511776 178515786 0.000000e+00 7408.0
1 TraesCS1B01G138300 chr1A 95.901 2293 66 10 376 2656 127758088 127760364 0.000000e+00 3688.0
2 TraesCS1B01G138300 chr1A 94.354 673 22 7 2650 3320 127760428 127761086 0.000000e+00 1018.0
3 TraesCS1B01G138300 chr1A 95.668 277 10 1 3318 3592 127761273 127761549 1.020000e-120 444.0
4 TraesCS1B01G138300 chr1A 88.451 381 17 5 3651 4010 127761545 127761919 6.160000e-118 435.0
5 TraesCS1B01G138300 chr1A 88.301 359 10 8 1 355 127757769 127758099 6.240000e-108 401.0
6 TraesCS1B01G138300 chr1A 96.035 227 9 0 376 602 445845242 445845468 1.760000e-98 370.0
7 TraesCS1B01G138300 chr1A 94.681 94 1 3 273 363 445845165 445845257 4.180000e-30 143.0
8 TraesCS1B01G138300 chr1A 100.000 49 0 0 3585 3633 16555396 16555444 1.540000e-14 91.6
9 TraesCS1B01G138300 chr1A 100.000 32 0 0 2589 2620 361357547 361357516 4.330000e-05 60.2
10 TraesCS1B01G138300 chr1A 100.000 32 0 0 1 32 445845135 445845166 4.330000e-05 60.2
11 TraesCS1B01G138300 chr1A 90.476 42 2 2 2580 2620 91162189 91162229 2.000000e-03 54.7
12 TraesCS1B01G138300 chr1D 95.880 1529 52 6 376 1898 116546818 116548341 0.000000e+00 2464.0
13 TraesCS1B01G138300 chr1D 96.224 768 16 6 1894 2656 116548453 116549212 0.000000e+00 1245.0
14 TraesCS1B01G138300 chr1D 96.484 512 14 3 2650 3158 116549276 116549786 0.000000e+00 843.0
15 TraesCS1B01G138300 chr1D 95.714 280 8 4 80 355 116546550 116546829 7.910000e-122 448.0
16 TraesCS1B01G138300 chr1D 96.356 247 9 0 3346 3592 116562836 116563082 1.340000e-109 407.0
17 TraesCS1B01G138300 chr1D 96.444 225 6 2 3651 3873 116563078 116563302 1.760000e-98 370.0
18 TraesCS1B01G138300 chr1D 92.381 105 3 1 3906 4010 116563413 116563512 1.160000e-30 145.0
19 TraesCS1B01G138300 chr1D 94.667 75 1 1 3265 3336 116549789 116549863 3.280000e-21 113.0
20 TraesCS1B01G138300 chr1D 96.667 60 1 1 1 60 116546494 116546552 9.170000e-17 99.0
21 TraesCS1B01G138300 chr1D 100.000 29 0 0 2592 2620 289395148 289395120 2.000000e-03 54.7
22 TraesCS1B01G138300 chr7D 95.265 359 12 5 1 355 595752073 595751716 7.530000e-157 564.0
23 TraesCS1B01G138300 chr7D 96.476 227 8 0 376 602 588776074 588776300 3.780000e-100 375.0
24 TraesCS1B01G138300 chr7D 96.476 227 8 0 376 602 595751727 595751501 3.780000e-100 375.0
25 TraesCS1B01G138300 chr7D 91.860 86 3 3 273 355 588776001 588776085 2.530000e-22 117.0
26 TraesCS1B01G138300 chr7D 100.000 32 0 0 1 32 588775971 588776002 4.330000e-05 60.2
27 TraesCS1B01G138300 chr7A 92.515 334 15 8 273 602 694281391 694281718 1.690000e-128 470.0
28 TraesCS1B01G138300 chr7A 100.000 32 0 0 1 32 694281361 694281392 4.330000e-05 60.2
29 TraesCS1B01G138300 chr5D 96.916 227 7 0 376 602 86778106 86777880 8.130000e-102 381.0
30 TraesCS1B01G138300 chr3D 96.476 227 8 0 376 602 220219283 220219057 3.780000e-100 375.0
31 TraesCS1B01G138300 chr3D 97.872 47 1 0 3588 3634 430148151 430148105 9.240000e-12 82.4
32 TraesCS1B01G138300 chr3D 100.000 32 0 0 1 32 220219386 220219355 4.330000e-05 60.2
33 TraesCS1B01G138300 chr5A 96.053 228 8 1 376 602 24002923 24002696 1.760000e-98 370.0
34 TraesCS1B01G138300 chr5A 91.667 96 2 4 273 363 24003002 24002908 1.170000e-25 128.0
35 TraesCS1B01G138300 chr5A 92.683 41 1 2 2580 2619 445263674 445263713 1.560000e-04 58.4
36 TraesCS1B01G138300 chr5A 100.000 29 0 0 2592 2620 670825940 670825912 2.000000e-03 54.7
37 TraesCS1B01G138300 chr2D 92.135 89 7 0 136 224 175825114 175825026 4.210000e-25 126.0
38 TraesCS1B01G138300 chr2D 94.340 53 3 0 3581 3633 340594110 340594162 9.240000e-12 82.4
39 TraesCS1B01G138300 chr2D 90.476 42 2 2 2580 2620 630467903 630467943 2.000000e-03 54.7
40 TraesCS1B01G138300 chr6A 93.023 86 2 3 273 355 455873097 455873013 5.440000e-24 122.0
41 TraesCS1B01G138300 chr6A 100.000 32 0 0 1 32 455873127 455873096 4.330000e-05 60.2
42 TraesCS1B01G138300 chr2A 93.827 81 5 0 140 220 67713361 67713281 5.440000e-24 122.0
43 TraesCS1B01G138300 chr2A 92.683 82 6 0 139 220 67978670 67978589 7.040000e-23 119.0
44 TraesCS1B01G138300 chr2A 94.444 54 3 0 3581 3634 551528448 551528501 2.570000e-12 84.2
45 TraesCS1B01G138300 chr4D 90.217 92 9 0 139 230 502014144 502014053 1.960000e-23 121.0
46 TraesCS1B01G138300 chr4D 95.556 45 2 0 3589 3633 275112345 275112301 5.560000e-09 73.1
47 TraesCS1B01G138300 chr4D 96.970 33 1 0 2588 2620 87716654 87716622 5.600000e-04 56.5
48 TraesCS1B01G138300 chrUn 91.860 86 3 3 273 355 70734511 70734595 2.530000e-22 117.0
49 TraesCS1B01G138300 chrUn 100.000 32 0 0 1 32 70734481 70734512 4.330000e-05 60.2
50 TraesCS1B01G138300 chr4B 89.888 89 9 0 136 224 103809582 103809494 9.110000e-22 115.0
51 TraesCS1B01G138300 chr4B 88.764 89 10 0 140 228 19727485 19727397 4.240000e-20 110.0
52 TraesCS1B01G138300 chr6D 88.764 89 7 3 140 225 24823423 24823335 5.480000e-19 106.0
53 TraesCS1B01G138300 chr3A 97.872 47 1 0 3587 3633 644582923 644582969 9.240000e-12 82.4
54 TraesCS1B01G138300 chr2B 95.833 48 2 0 3586 3633 250686544 250686497 1.200000e-10 78.7
55 TraesCS1B01G138300 chr7B 89.831 59 4 2 3577 3633 727632948 727633006 1.550000e-09 75.0
56 TraesCS1B01G138300 chr6B 89.831 59 5 1 3576 3633 705385794 705385852 1.550000e-09 75.0


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 TraesCS1B01G138300 chr1B 178511776 178515786 4010 False 7408.000000 7408 100.000000 1 4011 1 chr1B.!!$F1 4010
1 TraesCS1B01G138300 chr1A 127757769 127761919 4150 False 1197.200000 3688 92.535000 1 4010 5 chr1A.!!$F3 4009
2 TraesCS1B01G138300 chr1D 116546494 116549863 3369 False 868.666667 2464 95.939333 1 3336 6 chr1D.!!$F1 3335
3 TraesCS1B01G138300 chr1D 116562836 116563512 676 False 307.333333 407 95.060333 3346 4010 3 chr1D.!!$F2 664
4 TraesCS1B01G138300 chr7D 595751501 595752073 572 True 469.500000 564 95.870500 1 602 2 chr7D.!!$R1 601

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
479 484 0.035056 AGTAACTGTGATGCCAGGGC 60.035 55.0 2.62 2.62 42.35 5.19 F
1669 1679 0.394488 TGGAGTCCCGCAAAACAACA 60.394 50.0 6.74 0.00 34.29 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2233 0.039764 TCCCCACAACAAACCACACA 59.960 50.0 0.0 0.0 0.0 3.72 R
3351 3745 1.018910 TGCAGCCATCGATCATGTTG 58.981 50.0 0.0 0.0 0.0 3.33 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
53 54 3.931907 TCCCCATGTGATTACCTTGAG 57.068 47.619 0.00 0.00 0.00 3.02
331 336 7.224362 CCATTTGTTACAAGTTTTGAGCATGAA 59.776 33.333 0.00 0.00 0.00 2.57
343 348 4.350368 TGAGCATGAAACTGAACCTGTA 57.650 40.909 0.00 0.00 0.00 2.74
344 349 4.910195 TGAGCATGAAACTGAACCTGTAT 58.090 39.130 0.00 0.00 0.00 2.29
345 350 6.048732 TGAGCATGAAACTGAACCTGTATA 57.951 37.500 0.00 0.00 0.00 1.47
346 351 6.653020 TGAGCATGAAACTGAACCTGTATAT 58.347 36.000 0.00 0.00 0.00 0.86
347 352 7.791029 TGAGCATGAAACTGAACCTGTATATA 58.209 34.615 0.00 0.00 0.00 0.86
348 353 8.432013 TGAGCATGAAACTGAACCTGTATATAT 58.568 33.333 0.00 0.00 0.00 0.86
349 354 9.929180 GAGCATGAAACTGAACCTGTATATATA 57.071 33.333 0.00 0.00 0.00 0.86
474 479 3.879295 ACATGCATAGTAACTGTGATGCC 59.121 43.478 0.00 0.49 43.26 4.40
479 484 0.035056 AGTAACTGTGATGCCAGGGC 60.035 55.000 2.62 2.62 42.35 5.19
522 527 4.079500 TGCAGGTCCCCATGTCAAATTATA 60.080 41.667 0.00 0.00 0.00 0.98
543 548 9.936329 ATTATACAGTTAGGTTGAATTCCCATT 57.064 29.630 2.27 0.00 0.00 3.16
576 581 3.037549 GGATGGGATATAGGCCTCTGAG 58.962 54.545 9.68 0.00 0.00 3.35
603 608 7.864108 TCTTTCAGAGAAACATCTTTTGTGA 57.136 32.000 0.00 0.00 38.99 3.58
669 674 8.213679 ACTATGTATCATTATGCCAGTCAAACT 58.786 33.333 0.00 0.00 0.00 2.66
799 804 8.065473 TGAATTGACCACAGCAAATATATGTT 57.935 30.769 0.00 0.00 0.00 2.71
921 930 4.408270 AGTGAATCTGTCCTGCTGTCATAT 59.592 41.667 0.00 0.00 0.00 1.78
926 935 4.910195 TCTGTCCTGCTGTCATATGTTTT 58.090 39.130 1.90 0.00 0.00 2.43
981 991 9.651913 GATCAAGTCCATTTTCCTATAGAGATC 57.348 37.037 0.00 0.00 0.00 2.75
983 993 7.287927 TCAAGTCCATTTTCCTATAGAGATCGT 59.712 37.037 0.00 0.00 0.00 3.73
1021 1031 2.089980 AGCAGCTGTATTTCTGGCAAG 58.910 47.619 16.64 0.00 0.00 4.01
1028 1038 3.221771 TGTATTTCTGGCAAGCACAACT 58.778 40.909 0.00 0.00 0.00 3.16
1047 1057 6.536582 CACAACTAGCTAGTTTCATATGCAGT 59.463 38.462 31.90 21.15 43.57 4.40
1091 1101 3.192844 CCTGTTGAATCAGAAGCAAGCAT 59.807 43.478 0.00 0.00 37.61 3.79
1133 1143 6.316390 CCTTTACTGATAGACCACATGGAAAC 59.684 42.308 4.53 0.00 38.94 2.78
1161 1171 4.552378 GCTCATCTCGAGATTGCAATTGAC 60.552 45.833 30.03 15.61 45.45 3.18
1236 1246 1.602311 GCTTGGATCGATTGCCTCAT 58.398 50.000 0.00 0.00 0.00 2.90
1246 1256 5.131594 TCGATTGCCTCATATCTCAGAAG 57.868 43.478 0.00 0.00 0.00 2.85
1430 1440 4.136796 CTGTCATTGTCAAGGAAGGAACA 58.863 43.478 0.67 0.00 0.00 3.18
1446 1456 4.275810 AGGAACATCCACATTCTCCATTG 58.724 43.478 0.00 0.00 39.61 2.82
1485 1495 2.103537 ATACGGTAGGTTGTGTTGCC 57.896 50.000 0.00 0.00 0.00 4.52
1657 1667 4.385825 TGTAACTGACACAAATGGAGTCC 58.614 43.478 0.73 0.73 31.20 3.85
1669 1679 0.394488 TGGAGTCCCGCAAAACAACA 60.394 50.000 6.74 0.00 34.29 3.33
1720 1730 7.009179 TGTCTTCAGTTCCATGATTACTTCT 57.991 36.000 0.00 0.00 0.00 2.85
1722 1732 6.876257 GTCTTCAGTTCCATGATTACTTCTGT 59.124 38.462 0.00 0.00 0.00 3.41
1780 1790 5.412640 TCTACTGTCTCTCTCTGTAAGACG 58.587 45.833 0.00 0.00 38.67 4.18
1784 1794 4.891260 TGTCTCTCTCTGTAAGACGTGTA 58.109 43.478 0.00 0.00 38.67 2.90
1787 1797 5.638657 GTCTCTCTCTGTAAGACGTGTAGAA 59.361 44.000 0.00 0.00 38.67 2.10
1789 1799 6.879993 TCTCTCTCTGTAAGACGTGTAGAAAT 59.120 38.462 0.00 0.00 38.67 2.17
1790 1800 7.390996 TCTCTCTCTGTAAGACGTGTAGAAATT 59.609 37.037 0.00 0.00 38.67 1.82
1791 1801 7.306213 TCTCTCTGTAAGACGTGTAGAAATTG 58.694 38.462 0.00 0.00 38.67 2.32
1794 1804 6.509656 TCTGTAAGACGTGTAGAAATTGTGT 58.490 36.000 0.00 0.00 38.67 3.72
1795 1805 6.982141 TCTGTAAGACGTGTAGAAATTGTGTT 59.018 34.615 0.00 0.00 38.67 3.32
1796 1806 8.136800 TCTGTAAGACGTGTAGAAATTGTGTTA 58.863 33.333 0.00 0.00 38.67 2.41
1831 1843 5.874810 TGTCACCTTTCTGTGCTATTATGAC 59.125 40.000 0.00 0.00 36.17 3.06
1832 1844 5.294552 GTCACCTTTCTGTGCTATTATGACC 59.705 44.000 0.00 0.00 36.17 4.02
1841 1853 3.713288 TGCTATTATGACCGCACAGTAC 58.287 45.455 0.00 0.00 0.00 2.73
1865 1877 7.284074 ACGATAACATAAATGGGGTAATGTGA 58.716 34.615 0.00 0.00 33.04 3.58
1878 1890 5.066505 GGGGTAATGTGAACACAATCTGATC 59.933 44.000 11.60 0.00 45.41 2.92
2014 2142 4.507710 CAGCCTCTGAGTTGCTATGTTTA 58.492 43.478 7.90 0.00 32.44 2.01
2093 2221 1.064166 CACTTCAGGATGGCCCTTGAT 60.064 52.381 0.00 0.00 44.85 2.57
2105 2233 1.541588 GCCCTTGATTGTTTCTTCGCT 59.458 47.619 0.00 0.00 0.00 4.93
2212 2340 0.175760 TTCCCGTGCTGCAGTATCTC 59.824 55.000 16.64 0.00 0.00 2.75
2341 2469 2.223641 CGCATTGATATGTTGCTGCCTT 60.224 45.455 0.00 0.00 34.23 4.35
2437 2565 5.633830 ATGCCTTGAGAACATACAAGTTG 57.366 39.130 0.00 0.00 40.98 3.16
2516 2644 0.106918 TGGAACAAACAAGGAGCGGT 60.107 50.000 0.00 0.00 31.92 5.68
2581 2710 7.770662 TCCTATCTACTCCCTCATTCACTATT 58.229 38.462 0.00 0.00 0.00 1.73
2582 2711 8.901841 TCCTATCTACTCCCTCATTCACTATTA 58.098 37.037 0.00 0.00 0.00 0.98
2583 2712 8.962679 CCTATCTACTCCCTCATTCACTATTAC 58.037 40.741 0.00 0.00 0.00 1.89
2584 2713 9.521841 CTATCTACTCCCTCATTCACTATTACA 57.478 37.037 0.00 0.00 0.00 2.41
2585 2714 8.783660 ATCTACTCCCTCATTCACTATTACAA 57.216 34.615 0.00 0.00 0.00 2.41
2586 2715 8.008513 TCTACTCCCTCATTCACTATTACAAC 57.991 38.462 0.00 0.00 0.00 3.32
2587 2716 6.875972 ACTCCCTCATTCACTATTACAACT 57.124 37.500 0.00 0.00 0.00 3.16
2652 2784 6.535274 AGAACACAATAAAACGTGTCTACC 57.465 37.500 0.00 0.00 45.37 3.18
2681 2882 4.985538 TCTTGATTTAAAGCCTGAGGTGT 58.014 39.130 0.00 0.00 0.00 4.16
2808 3009 3.100817 CAAATGGCTCAAGATAAACGCG 58.899 45.455 3.53 3.53 0.00 6.01
2852 3053 1.139058 GATAGACAGTGGCCCGACAAT 59.861 52.381 0.00 0.00 0.00 2.71
2878 3079 3.059099 CCATTGGCTTTGGGCGTT 58.941 55.556 0.00 0.00 42.94 4.84
2972 3173 0.257039 ATGTCCCTGATGTGGCTTCC 59.743 55.000 0.00 0.00 0.00 3.46
3040 3243 3.836562 ACGGGCCCTTATATTATCGAACT 59.163 43.478 22.43 0.00 0.00 3.01
3073 3276 5.063186 GCTGTCTGATTACTGTCTCATTGTG 59.937 44.000 0.00 0.00 0.00 3.33
3168 3373 1.895707 CTGATGGCAATCCTCCCGC 60.896 63.158 0.00 0.00 31.15 6.13
3217 3422 9.713713 GGTTAATAGCCATTTGTTTTTCCTTTA 57.286 29.630 0.00 0.00 0.00 1.85
3337 3731 9.429600 GCTACGTACAATGTATTTTATGGTTTC 57.570 33.333 0.00 0.00 0.00 2.78
3340 3734 8.455682 ACGTACAATGTATTTTATGGTTTCTGG 58.544 33.333 0.00 0.00 0.00 3.86
3351 3745 1.004745 TGGTTTCTGGAAGGAGATGGC 59.995 52.381 0.00 0.00 0.00 4.40
3376 3770 1.311859 GATCGATGGCTGCAATCCAA 58.688 50.000 11.32 0.61 37.13 3.53
3439 3833 1.303309 GCCGATCATTCCCTGAACTG 58.697 55.000 0.00 0.00 37.44 3.16
3522 3918 0.740868 CATGCAGTACCCAGACCACG 60.741 60.000 0.00 0.00 0.00 4.94
3584 3980 3.448686 CTTCTATTTGCGGATGACTCGT 58.551 45.455 0.00 0.00 0.00 4.18
3592 3988 3.961182 TGCGGATGACTCGTTTATACTC 58.039 45.455 0.00 0.00 0.00 2.59
3593 3989 3.243301 TGCGGATGACTCGTTTATACTCC 60.243 47.826 0.00 0.00 0.00 3.85
3594 3990 3.004524 GCGGATGACTCGTTTATACTCCT 59.995 47.826 0.00 0.00 0.00 3.69
3595 3991 4.499357 GCGGATGACTCGTTTATACTCCTT 60.499 45.833 0.00 0.00 0.00 3.36
3596 3992 5.213675 CGGATGACTCGTTTATACTCCTTC 58.786 45.833 0.00 0.00 0.00 3.46
3597 3993 5.530712 GGATGACTCGTTTATACTCCTTCC 58.469 45.833 0.00 0.00 0.00 3.46
3598 3994 4.627611 TGACTCGTTTATACTCCTTCCG 57.372 45.455 0.00 0.00 0.00 4.30
3599 3995 4.012374 TGACTCGTTTATACTCCTTCCGT 58.988 43.478 0.00 0.00 0.00 4.69
3600 3996 4.460382 TGACTCGTTTATACTCCTTCCGTT 59.540 41.667 0.00 0.00 0.00 4.44
3601 3997 4.991472 ACTCGTTTATACTCCTTCCGTTC 58.009 43.478 0.00 0.00 0.00 3.95
3602 3998 4.704057 ACTCGTTTATACTCCTTCCGTTCT 59.296 41.667 0.00 0.00 0.00 3.01
3603 3999 5.882557 ACTCGTTTATACTCCTTCCGTTCTA 59.117 40.000 0.00 0.00 0.00 2.10
3604 4000 6.375455 ACTCGTTTATACTCCTTCCGTTCTAA 59.625 38.462 0.00 0.00 0.00 2.10
3605 4001 7.094205 ACTCGTTTATACTCCTTCCGTTCTAAA 60.094 37.037 0.00 0.00 0.00 1.85
3606 4002 7.601856 TCGTTTATACTCCTTCCGTTCTAAAA 58.398 34.615 0.00 0.00 0.00 1.52
3607 4003 8.253113 TCGTTTATACTCCTTCCGTTCTAAAAT 58.747 33.333 0.00 0.00 0.00 1.82
3608 4004 9.520204 CGTTTATACTCCTTCCGTTCTAAAATA 57.480 33.333 0.00 0.00 0.00 1.40
3613 4009 7.419711 ACTCCTTCCGTTCTAAAATAGATGA 57.580 36.000 0.00 0.00 34.22 2.92
3614 4010 7.266400 ACTCCTTCCGTTCTAAAATAGATGAC 58.734 38.462 0.00 0.00 34.22 3.06
3615 4011 6.579865 TCCTTCCGTTCTAAAATAGATGACC 58.420 40.000 0.00 0.00 34.22 4.02
3616 4012 5.758784 CCTTCCGTTCTAAAATAGATGACCC 59.241 44.000 0.00 0.00 34.22 4.46
3617 4013 5.943349 TCCGTTCTAAAATAGATGACCCA 57.057 39.130 0.00 0.00 34.22 4.51
3618 4014 6.302535 TCCGTTCTAAAATAGATGACCCAA 57.697 37.500 0.00 0.00 34.22 4.12
3619 4015 6.110707 TCCGTTCTAAAATAGATGACCCAAC 58.889 40.000 0.00 0.00 34.22 3.77
3620 4016 6.070424 TCCGTTCTAAAATAGATGACCCAACT 60.070 38.462 0.00 0.00 34.22 3.16
3621 4017 6.598064 CCGTTCTAAAATAGATGACCCAACTT 59.402 38.462 0.00 0.00 34.22 2.66
3622 4018 7.120726 CCGTTCTAAAATAGATGACCCAACTTT 59.879 37.037 0.00 0.00 34.22 2.66
3623 4019 7.962918 CGTTCTAAAATAGATGACCCAACTTTG 59.037 37.037 0.00 0.00 34.22 2.77
3624 4020 8.793592 GTTCTAAAATAGATGACCCAACTTTGT 58.206 33.333 0.00 0.00 34.22 2.83
3626 4022 9.444600 TCTAAAATAGATGACCCAACTTTGTAC 57.555 33.333 0.00 0.00 0.00 2.90
3627 4023 9.449719 CTAAAATAGATGACCCAACTTTGTACT 57.550 33.333 0.00 0.00 0.00 2.73
3629 4025 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3630 4026 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
3631 4027 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
3632 4028 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
3633 4029 6.935208 AGATGACCCAACTTTGTACTAACTTC 59.065 38.462 0.00 0.00 0.00 3.01
3634 4030 5.370679 TGACCCAACTTTGTACTAACTTCC 58.629 41.667 0.00 0.00 0.00 3.46
3635 4031 5.104444 TGACCCAACTTTGTACTAACTTCCA 60.104 40.000 0.00 0.00 0.00 3.53
3636 4032 5.128205 ACCCAACTTTGTACTAACTTCCAC 58.872 41.667 0.00 0.00 0.00 4.02
3637 4033 5.127491 CCCAACTTTGTACTAACTTCCACA 58.873 41.667 0.00 0.00 0.00 4.17
3638 4034 5.238650 CCCAACTTTGTACTAACTTCCACAG 59.761 44.000 0.00 0.00 0.00 3.66
3639 4035 6.053005 CCAACTTTGTACTAACTTCCACAGA 58.947 40.000 0.00 0.00 0.00 3.41
3640 4036 6.202954 CCAACTTTGTACTAACTTCCACAGAG 59.797 42.308 0.00 0.00 31.40 3.35
3641 4037 5.298347 ACTTTGTACTAACTTCCACAGAGC 58.702 41.667 0.00 0.00 28.85 4.09
3642 4038 4.948341 TTGTACTAACTTCCACAGAGCA 57.052 40.909 0.00 0.00 0.00 4.26
3643 4039 4.948341 TGTACTAACTTCCACAGAGCAA 57.052 40.909 0.00 0.00 0.00 3.91
3644 4040 5.483685 TGTACTAACTTCCACAGAGCAAT 57.516 39.130 0.00 0.00 0.00 3.56
3645 4041 5.865085 TGTACTAACTTCCACAGAGCAATT 58.135 37.500 0.00 0.00 0.00 2.32
3646 4042 6.296026 TGTACTAACTTCCACAGAGCAATTT 58.704 36.000 0.00 0.00 0.00 1.82
3647 4043 7.446769 TGTACTAACTTCCACAGAGCAATTTA 58.553 34.615 0.00 0.00 0.00 1.40
3648 4044 7.934665 TGTACTAACTTCCACAGAGCAATTTAA 59.065 33.333 0.00 0.00 0.00 1.52
3649 4045 7.817418 ACTAACTTCCACAGAGCAATTTAAA 57.183 32.000 0.00 0.00 0.00 1.52
3650 4046 8.232913 ACTAACTTCCACAGAGCAATTTAAAA 57.767 30.769 0.00 0.00 0.00 1.52
3651 4047 8.860088 ACTAACTTCCACAGAGCAATTTAAAAT 58.140 29.630 0.00 0.00 0.00 1.82
3869 4265 1.302949 GCCTGCAATGGTGGGAGTA 59.697 57.895 0.00 0.00 0.00 2.59
3877 4332 0.902531 ATGGTGGGAGTAGACCGTTG 59.097 55.000 0.00 0.00 34.69 4.10
3946 4420 7.121315 GCTATCAACAGGAGGAAAGTAATTGTT 59.879 37.037 0.00 0.00 0.00 2.83
3947 4421 6.633500 TCAACAGGAGGAAAGTAATTGTTG 57.367 37.500 7.84 7.84 43.02 3.33
3948 4422 5.009610 TCAACAGGAGGAAAGTAATTGTTGC 59.990 40.000 9.00 0.00 42.01 4.17
3949 4423 4.729868 ACAGGAGGAAAGTAATTGTTGCT 58.270 39.130 0.00 0.00 0.00 3.91
3950 4424 5.140454 ACAGGAGGAAAGTAATTGTTGCTT 58.860 37.500 0.00 0.00 37.18 3.91
3963 4437 8.846211 AGTAATTGTTGCTTTGCTTTAGAGTTA 58.154 29.630 0.00 0.00 0.00 2.24
3967 4441 5.048083 TGTTGCTTTGCTTTAGAGTTATGGG 60.048 40.000 0.00 0.00 0.00 4.00
3984 4458 1.375013 GGTCAACCCATACGCGTGT 60.375 57.895 24.59 13.76 0.00 4.49
4010 4484 4.559153 CAATGTCAGTGTTCAAAATCCCC 58.441 43.478 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.517285 TCTGACTAAAGAACATCATGGGC 58.483 43.478 0.00 0.00 0.00 5.36
123 124 5.661458 AGGTAGTACTTGTGAATCATTCCG 58.339 41.667 0.00 0.00 0.00 4.30
253 255 8.220755 ACAACATTCTCTAGCAACTTAAAACA 57.779 30.769 0.00 0.00 0.00 2.83
373 378 9.836864 GGATTGCTCACCAATACATATATATCA 57.163 33.333 0.00 0.00 44.02 2.15
459 464 1.209504 GCCCTGGCATCACAGTTACTA 59.790 52.381 2.58 0.00 41.49 1.82
474 479 2.288457 CCGTGTATAGATGTGAGCCCTG 60.288 54.545 0.00 0.00 0.00 4.45
479 484 4.045104 GCAAGTCCGTGTATAGATGTGAG 58.955 47.826 0.00 0.00 0.00 3.51
522 527 7.027874 TCTAATGGGAATTCAACCTAACTGT 57.972 36.000 7.93 0.00 0.00 3.55
543 548 7.189794 CCTATATCCCATCCTACCAGTTTCTA 58.810 42.308 0.00 0.00 0.00 2.10
576 581 9.178427 CACAAAAGATGTTTCTCTGAAAGATTC 57.822 33.333 4.59 0.00 41.38 2.52
603 608 7.469537 AAGCAGGAACGAATAGCTAGTATAT 57.530 36.000 0.00 0.00 34.66 0.86
618 623 4.390297 GTCACTTGTCAGATAAGCAGGAAC 59.610 45.833 6.82 0.00 0.00 3.62
695 700 5.648960 TGTGTACAGTCACCATAATACGAGA 59.351 40.000 0.00 0.00 37.51 4.04
937 946 1.376295 CCAAGGCCAGGCAATTTGC 60.376 57.895 15.19 13.04 44.08 3.68
981 991 4.686091 TGCTTTGACTTAAGACAGATGACG 59.314 41.667 10.09 0.00 0.00 4.35
983 993 4.692625 GCTGCTTTGACTTAAGACAGATGA 59.307 41.667 10.09 0.00 34.27 2.92
1021 1031 5.294306 TGCATATGAAACTAGCTAGTTGTGC 59.706 40.000 33.97 31.46 45.17 4.57
1028 1038 6.639563 TGAACACTGCATATGAAACTAGCTA 58.360 36.000 6.97 0.00 0.00 3.32
1047 1057 1.202794 TGAGCAGCCATCAACTGAACA 60.203 47.619 0.00 0.00 37.32 3.18
1091 1101 8.160765 TCAGTAAAGGGTGATTATCTGTTTCAA 58.839 33.333 0.00 0.00 0.00 2.69
1101 1111 6.670464 TGTGGTCTATCAGTAAAGGGTGATTA 59.330 38.462 0.00 0.00 35.08 1.75
1133 1143 3.243334 TGCAATCTCGAGATGAGCAGTAG 60.243 47.826 34.14 17.92 44.86 2.57
1161 1171 1.108776 CAACATCATCCCTTGGGCTG 58.891 55.000 3.28 3.28 0.00 4.85
1236 1246 4.641094 GTCTCCGAAGAACCTTCTGAGATA 59.359 45.833 23.63 8.73 37.65 1.98
1246 1256 3.576648 CAGTAGTTGTCTCCGAAGAACC 58.423 50.000 0.00 0.00 31.93 3.62
1297 1307 3.056304 GAGCACGATTAGCATCTCTTCC 58.944 50.000 0.00 0.00 0.00 3.46
1430 1440 5.184479 CACTCAAACAATGGAGAATGTGGAT 59.816 40.000 0.00 0.00 35.17 3.41
1434 1444 3.828451 CCCACTCAAACAATGGAGAATGT 59.172 43.478 0.00 0.00 35.33 2.71
1446 1456 5.163794 CGTATAACCAATGACCCACTCAAAC 60.164 44.000 0.00 0.00 30.60 2.93
1485 1495 3.130340 GCCAGTAGAGAAGAGGAAGAGTG 59.870 52.174 0.00 0.00 0.00 3.51
1657 1667 2.058057 GGTAAGCATGTTGTTTTGCGG 58.942 47.619 0.00 0.00 43.61 5.69
1669 1679 2.582636 ACCTGGGATTTCTGGTAAGCAT 59.417 45.455 0.00 0.00 37.24 3.79
1720 1730 8.602472 ACAGGCATATAAATTTAAAAGGGACA 57.398 30.769 1.21 0.00 0.00 4.02
1722 1732 9.930158 ACTACAGGCATATAAATTTAAAAGGGA 57.070 29.630 1.21 0.00 0.00 4.20
1787 1797 8.357402 GGTGACAAATAGAGGTTTAACACAATT 58.643 33.333 0.00 0.00 32.83 2.32
1789 1799 7.057894 AGGTGACAAATAGAGGTTTAACACAA 58.942 34.615 0.00 0.00 32.83 3.33
1790 1800 6.597562 AGGTGACAAATAGAGGTTTAACACA 58.402 36.000 0.00 0.00 32.83 3.72
1791 1801 7.506328 AAGGTGACAAATAGAGGTTTAACAC 57.494 36.000 0.00 0.00 0.00 3.32
1794 1804 7.996644 ACAGAAAGGTGACAAATAGAGGTTTAA 59.003 33.333 0.00 0.00 0.00 1.52
1795 1805 7.444183 CACAGAAAGGTGACAAATAGAGGTTTA 59.556 37.037 0.00 0.00 41.32 2.01
1796 1806 6.263168 CACAGAAAGGTGACAAATAGAGGTTT 59.737 38.462 0.00 0.00 41.32 3.27
1831 1843 5.333035 CCATTTATGTTATCGTACTGTGCGG 60.333 44.000 17.81 0.32 0.00 5.69
1832 1844 5.333035 CCCATTTATGTTATCGTACTGTGCG 60.333 44.000 12.16 12.16 0.00 5.34
1841 1853 7.737972 TCACATTACCCCATTTATGTTATCG 57.262 36.000 0.00 0.00 0.00 2.92
2014 2142 4.142026 GGGTGCACCTCAGTTTAAAACTTT 60.142 41.667 33.91 0.00 36.40 2.66
2093 2221 1.745232 ACCACACAGCGAAGAAACAA 58.255 45.000 0.00 0.00 0.00 2.83
2105 2233 0.039764 TCCCCACAACAAACCACACA 59.960 50.000 0.00 0.00 0.00 3.72
2212 2340 8.969121 TTATGAAACACATAAATGAGTTGCAG 57.031 30.769 15.97 0.00 45.64 4.41
2341 2469 4.502415 TCATTAGGGAGATTATGCAGGGA 58.498 43.478 0.00 0.00 0.00 4.20
2437 2565 3.121227 CGTTACGGGACTTCTTCGTTTTC 60.121 47.826 0.00 0.00 38.19 2.29
2504 2632 2.099098 CAGAAACAAACCGCTCCTTGTT 59.901 45.455 2.21 2.21 45.35 2.83
2516 2644 3.633525 ACAGCATCTTCAGCAGAAACAAA 59.366 39.130 0.00 0.00 34.16 2.83
2547 2675 3.373877 GGGAGTAGATAGGAGTGTGGGAA 60.374 52.174 0.00 0.00 0.00 3.97
2637 2769 9.798994 CAAGAGTAATAGGTAGACACGTTTTAT 57.201 33.333 0.00 0.00 0.00 1.40
2652 2784 9.050601 CCTCAGGCTTTAAATCAAGAGTAATAG 57.949 37.037 8.31 0.00 0.00 1.73
2808 3009 4.666253 TTGCAGAGGGGGCACAGC 62.666 66.667 0.00 0.00 41.75 4.40
2878 3079 1.152984 CCCTGTTGTCACTGTGGCA 60.153 57.895 11.65 11.65 0.00 4.92
2997 3198 5.163893 CCGTACATTGTGTCCACTATTTCAC 60.164 44.000 0.00 0.00 0.00 3.18
3007 3208 1.747745 GGGCCCGTACATTGTGTCC 60.748 63.158 5.69 0.00 0.00 4.02
3040 3243 2.839486 AATCAGACAGCGAAGAACCA 57.161 45.000 0.00 0.00 0.00 3.67
3081 3284 4.770795 ACCTGAATTACCATCTTCGGAAG 58.229 43.478 11.54 11.54 30.76 3.46
3168 3373 4.727507 TCTCTAGCCAGTCTGCTAAAAG 57.272 45.455 0.00 1.93 42.93 2.27
3217 3422 7.550597 TCTGATCAGCATCTGGTATTTAGAT 57.449 36.000 18.36 0.00 35.34 1.98
3337 3731 2.022195 CATGTTGCCATCTCCTTCCAG 58.978 52.381 0.00 0.00 0.00 3.86
3340 3734 2.547211 CGATCATGTTGCCATCTCCTTC 59.453 50.000 0.00 0.00 0.00 3.46
3351 3745 1.018910 TGCAGCCATCGATCATGTTG 58.981 50.000 0.00 0.00 0.00 3.33
3376 3770 2.679837 CGCCAGCACTATCAATCAACTT 59.320 45.455 0.00 0.00 0.00 2.66
3439 3833 4.381411 AGGAGAACAACAGCAGAAGTAAC 58.619 43.478 0.00 0.00 0.00 2.50
3592 3988 5.758784 GGGTCATCTATTTTAGAACGGAAGG 59.241 44.000 0.00 0.00 38.50 3.46
3593 3989 6.346096 TGGGTCATCTATTTTAGAACGGAAG 58.654 40.000 0.00 0.00 38.50 3.46
3594 3990 6.302535 TGGGTCATCTATTTTAGAACGGAA 57.697 37.500 0.00 0.00 38.50 4.30
3595 3991 5.943349 TGGGTCATCTATTTTAGAACGGA 57.057 39.130 0.00 0.00 38.50 4.69
3596 3992 6.113411 AGTTGGGTCATCTATTTTAGAACGG 58.887 40.000 0.00 0.00 38.50 4.44
3597 3993 7.611213 AAGTTGGGTCATCTATTTTAGAACG 57.389 36.000 0.00 0.00 38.50 3.95
3598 3994 8.793592 ACAAAGTTGGGTCATCTATTTTAGAAC 58.206 33.333 0.00 0.00 38.50 3.01
3599 3995 8.934023 ACAAAGTTGGGTCATCTATTTTAGAA 57.066 30.769 0.00 0.00 38.50 2.10
3600 3996 9.444600 GTACAAAGTTGGGTCATCTATTTTAGA 57.555 33.333 0.00 0.00 39.50 2.10
3601 3997 9.449719 AGTACAAAGTTGGGTCATCTATTTTAG 57.550 33.333 0.00 0.00 0.00 1.85
3603 3999 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3604 4000 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
3605 4001 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
3606 4002 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
3607 4003 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
3608 4004 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
3609 4005 6.148976 GGAAGTTAGTACAAAGTTGGGTCATC 59.851 42.308 0.00 0.00 0.00 2.92
3610 4006 6.002082 GGAAGTTAGTACAAAGTTGGGTCAT 58.998 40.000 0.00 0.00 0.00 3.06
3611 4007 5.104444 TGGAAGTTAGTACAAAGTTGGGTCA 60.104 40.000 0.00 0.00 0.00 4.02
3612 4008 5.237996 GTGGAAGTTAGTACAAAGTTGGGTC 59.762 44.000 0.00 0.00 0.00 4.46
3613 4009 5.128205 GTGGAAGTTAGTACAAAGTTGGGT 58.872 41.667 0.00 0.00 0.00 4.51
3614 4010 5.127491 TGTGGAAGTTAGTACAAAGTTGGG 58.873 41.667 0.00 0.00 0.00 4.12
3615 4011 6.053005 TCTGTGGAAGTTAGTACAAAGTTGG 58.947 40.000 0.00 0.00 0.00 3.77
3616 4012 6.292919 GCTCTGTGGAAGTTAGTACAAAGTTG 60.293 42.308 0.00 0.00 0.00 3.16
3617 4013 5.758784 GCTCTGTGGAAGTTAGTACAAAGTT 59.241 40.000 0.00 0.00 0.00 2.66
3618 4014 5.163343 TGCTCTGTGGAAGTTAGTACAAAGT 60.163 40.000 0.00 0.00 0.00 2.66
3619 4015 5.297547 TGCTCTGTGGAAGTTAGTACAAAG 58.702 41.667 0.00 0.00 0.00 2.77
3620 4016 5.284861 TGCTCTGTGGAAGTTAGTACAAA 57.715 39.130 0.00 0.00 0.00 2.83
3621 4017 4.948341 TGCTCTGTGGAAGTTAGTACAA 57.052 40.909 0.00 0.00 0.00 2.41
3622 4018 4.948341 TTGCTCTGTGGAAGTTAGTACA 57.052 40.909 0.00 0.00 0.00 2.90
3623 4019 6.803154 AAATTGCTCTGTGGAAGTTAGTAC 57.197 37.500 0.00 0.00 32.82 2.73
3624 4020 8.911918 TTTAAATTGCTCTGTGGAAGTTAGTA 57.088 30.769 4.60 0.00 37.70 1.82
3625 4021 7.817418 TTTAAATTGCTCTGTGGAAGTTAGT 57.183 32.000 4.60 0.00 37.70 2.24
3631 4027 9.995003 ACAAATATTTTAAATTGCTCTGTGGAA 57.005 25.926 0.00 0.00 0.00 3.53
3632 4028 9.638239 GACAAATATTTTAAATTGCTCTGTGGA 57.362 29.630 0.00 0.00 0.00 4.02
3633 4029 9.643693 AGACAAATATTTTAAATTGCTCTGTGG 57.356 29.630 0.00 0.00 0.00 4.17
3635 4031 9.143631 GCAGACAAATATTTTAAATTGCTCTGT 57.856 29.630 19.30 9.43 35.62 3.41
3636 4032 9.362539 AGCAGACAAATATTTTAAATTGCTCTG 57.637 29.630 16.92 16.92 33.29 3.35
3637 4033 9.362539 CAGCAGACAAATATTTTAAATTGCTCT 57.637 29.630 14.54 0.80 36.15 4.09
3638 4034 9.357652 TCAGCAGACAAATATTTTAAATTGCTC 57.642 29.630 14.54 0.00 36.15 4.26
3639 4035 9.880157 ATCAGCAGACAAATATTTTAAATTGCT 57.120 25.926 12.82 12.82 38.57 3.91
3640 4036 9.910511 CATCAGCAGACAAATATTTTAAATTGC 57.089 29.630 0.00 5.14 0.00 3.56
3647 4043 9.985730 TTCTTTTCATCAGCAGACAAATATTTT 57.014 25.926 0.00 0.00 0.00 1.82
3649 4045 9.582431 CATTCTTTTCATCAGCAGACAAATATT 57.418 29.630 0.00 0.00 0.00 1.28
3650 4046 7.705325 GCATTCTTTTCATCAGCAGACAAATAT 59.295 33.333 0.00 0.00 0.00 1.28
3651 4047 7.031372 GCATTCTTTTCATCAGCAGACAAATA 58.969 34.615 0.00 0.00 0.00 1.40
3652 4048 5.867716 GCATTCTTTTCATCAGCAGACAAAT 59.132 36.000 0.00 0.00 0.00 2.32
3653 4049 5.221283 TGCATTCTTTTCATCAGCAGACAAA 60.221 36.000 0.00 0.00 0.00 2.83
3654 4050 4.278919 TGCATTCTTTTCATCAGCAGACAA 59.721 37.500 0.00 0.00 0.00 3.18
3710 4106 0.955178 CATCTGACCCGAGCTCGTAT 59.045 55.000 32.41 21.01 37.74 3.06
3877 4332 4.394920 TCAATAAGATGCGGAAACAACCTC 59.605 41.667 0.00 0.00 0.00 3.85
3946 4420 4.662278 ACCCATAACTCTAAAGCAAAGCA 58.338 39.130 0.00 0.00 0.00 3.91
3947 4421 4.700213 TGACCCATAACTCTAAAGCAAAGC 59.300 41.667 0.00 0.00 0.00 3.51
3948 4422 6.349363 GGTTGACCCATAACTCTAAAGCAAAG 60.349 42.308 0.00 0.00 0.00 2.77
3949 4423 5.475564 GGTTGACCCATAACTCTAAAGCAAA 59.524 40.000 0.00 0.00 0.00 3.68
3950 4424 5.007682 GGTTGACCCATAACTCTAAAGCAA 58.992 41.667 0.00 0.00 0.00 3.91
3967 4441 0.869730 AAACACGCGTATGGGTTGAC 59.130 50.000 13.44 0.00 39.58 3.18
3984 4458 5.523188 GGATTTTGAACACTGACATTGCAAA 59.477 36.000 1.71 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.