Multiple sequence alignment - TraesCS2D01G297800

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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 TraesCS2D01G297800 chr2D 100.000 4001 0 0 1 4001 380088459 380092459 0.000000e+00 7389.0
1 TraesCS2D01G297800 chr2D 79.870 2459 446 39 305 2725 2774513 2776960 0.000000e+00 1753.0
2 TraesCS2D01G297800 chr2D 79.425 2367 424 43 370 2712 380078234 380080561 0.000000e+00 1615.0
3 TraesCS2D01G297800 chr2D 90.584 308 11 8 3694 4001 380081150 380081439 3.750000e-105 392.0
4 TraesCS2D01G297800 chr2D 77.645 501 67 29 2817 3279 380080639 380081132 3.070000e-66 263.0
5 TraesCS2D01G297800 chr2D 88.235 68 5 1 3416 3480 334331578 334331511 1.190000e-10 78.7
6 TraesCS2D01G297800 chr2A 94.605 3151 153 8 1 3134 515308520 515311670 0.000000e+00 4861.0
7 TraesCS2D01G297800 chr2A 80.361 2383 424 33 371 2728 16348156 16345793 0.000000e+00 1768.0
8 TraesCS2D01G297800 chr2A 79.382 2362 434 36 370 2712 515302471 515304798 0.000000e+00 1615.0
9 TraesCS2D01G297800 chr2A 81.181 1642 286 16 1101 2723 2819230 2817593 0.000000e+00 1299.0
10 TraesCS2D01G297800 chr2A 79.887 706 133 9 370 1069 2819997 2819295 3.570000e-140 508.0
11 TraesCS2D01G297800 chr2A 88.220 382 21 4 3644 4001 515312136 515312517 6.140000e-118 435.0
12 TraesCS2D01G297800 chr2A 73.858 941 224 19 1762 2688 754567819 754566887 4.920000e-94 355.0
13 TraesCS2D01G297800 chr2A 90.000 240 20 4 3177 3415 515311668 515311904 1.400000e-79 307.0
14 TraesCS2D01G297800 chr2A 76.636 214 47 2 925 1138 16350013 16349803 9.090000e-22 115.0
15 TraesCS2D01G297800 chr2B 80.268 2387 423 34 370 2723 9143765 9146136 0.000000e+00 1755.0
16 TraesCS2D01G297800 chr2B 80.008 2391 424 40 380 2746 451454166 451456526 0.000000e+00 1718.0
17 TraesCS2D01G297800 chr2B 83.583 1066 167 4 1665 2723 8321521 8320457 0.000000e+00 992.0
18 TraesCS2D01G297800 chr2B 76.825 1329 292 15 305 1622 8322923 8321600 0.000000e+00 734.0
19 TraesCS2D01G297800 chr2B 75.107 932 204 23 1774 2688 765296596 765295676 1.030000e-110 411.0
20 TraesCS2D01G297800 chr2B 88.720 328 17 2 3694 4001 451457111 451457438 2.260000e-102 383.0
21 TraesCS2D01G297800 chr2B 82.734 278 18 15 2978 3230 451456760 451457032 1.870000e-53 220.0
22 TraesCS2D01G297800 chr1D 73.418 948 208 33 1766 2679 6900013 6900950 8.350000e-82 315.0
23 TraesCS2D01G297800 chr5B 73.810 882 189 31 1774 2621 549549535 549550408 1.080000e-80 311.0
24 TraesCS2D01G297800 chr5B 85.333 75 6 3 3410 3480 572349909 572349982 5.550000e-09 73.1
25 TraesCS2D01G297800 chr7D 91.525 59 3 2 3393 3451 614654952 614654896 3.310000e-11 80.5
26 TraesCS2D01G297800 chr7D 86.567 67 7 2 3416 3480 25043197 25043131 5.550000e-09 73.1
27 TraesCS2D01G297800 chr4A 88.060 67 7 1 3415 3480 552149406 552149472 1.190000e-10 78.7
28 TraesCS2D01G297800 chr4A 85.333 75 7 2 3410 3480 683493808 683493882 1.540000e-09 75.0
29 TraesCS2D01G297800 chr6B 87.879 66 6 2 3416 3480 195461861 195461925 4.290000e-10 76.8
30 TraesCS2D01G297800 chr6B 87.324 71 4 3 3416 3481 214872003 214871933 4.290000e-10 76.8
31 TraesCS2D01G297800 chr7B 86.957 69 6 1 3415 3480 713303718 713303786 1.540000e-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 TraesCS2D01G297800 chr2D 380088459 380092459 4000 False 7389.000000 7389 100.000000 1 4001 1 chr2D.!!$F2 4000
1 TraesCS2D01G297800 chr2D 2774513 2776960 2447 False 1753.000000 1753 79.870000 305 2725 1 chr2D.!!$F1 2420
2 TraesCS2D01G297800 chr2D 380078234 380081439 3205 False 756.666667 1615 82.551333 370 4001 3 chr2D.!!$F3 3631
3 TraesCS2D01G297800 chr2A 515302471 515312517 10046 False 1804.500000 4861 88.051750 1 4001 4 chr2A.!!$F1 4000
4 TraesCS2D01G297800 chr2A 16345793 16350013 4220 True 941.500000 1768 78.498500 371 2728 2 chr2A.!!$R3 2357
5 TraesCS2D01G297800 chr2A 2817593 2819997 2404 True 903.500000 1299 80.534000 370 2723 2 chr2A.!!$R2 2353
6 TraesCS2D01G297800 chr2A 754566887 754567819 932 True 355.000000 355 73.858000 1762 2688 1 chr2A.!!$R1 926
7 TraesCS2D01G297800 chr2B 9143765 9146136 2371 False 1755.000000 1755 80.268000 370 2723 1 chr2B.!!$F1 2353
8 TraesCS2D01G297800 chr2B 8320457 8322923 2466 True 863.000000 992 80.204000 305 2723 2 chr2B.!!$R2 2418
9 TraesCS2D01G297800 chr2B 451454166 451457438 3272 False 773.666667 1718 83.820667 380 4001 3 chr2B.!!$F2 3621
10 TraesCS2D01G297800 chr2B 765295676 765296596 920 True 411.000000 411 75.107000 1774 2688 1 chr2B.!!$R1 914
11 TraesCS2D01G297800 chr1D 6900013 6900950 937 False 315.000000 315 73.418000 1766 2679 1 chr1D.!!$F1 913
12 TraesCS2D01G297800 chr5B 549549535 549550408 873 False 311.000000 311 73.810000 1774 2621 1 chr5B.!!$F1 847

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
887 6949 1.228367 CCCCTGGCAGATATGGTGC 60.228 63.158 17.94 0.0 40.42 5.01 F
1483 7590 0.249155 CCTTGGCAACTGCACTTGTG 60.249 55.000 3.76 0.0 44.36 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 8663 0.995024 CCAAACTCTCCACATCCCCT 59.005 55.0 0.0 0.0 0.0 4.79 R
3457 9719 0.032813 TCCCTCCGTCCCGAAATAGT 60.033 55.0 0.0 0.0 0.0 2.12 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
21 6071 4.104383 AGAACACAATGTTGGATGAGGT 57.896 40.909 0.00 0.00 41.28 3.85
22 6072 3.822735 AGAACACAATGTTGGATGAGGTG 59.177 43.478 0.00 0.00 41.28 4.00
30 6080 3.750371 TGTTGGATGAGGTGAACGAAAT 58.250 40.909 0.00 0.00 0.00 2.17
32 6082 5.496556 TGTTGGATGAGGTGAACGAAATAT 58.503 37.500 0.00 0.00 0.00 1.28
38 6088 8.673711 TGGATGAGGTGAACGAAATATAAAAAG 58.326 33.333 0.00 0.00 0.00 2.27
69 6119 4.641989 GGTTAGCCATCTTGTCACAATCAT 59.358 41.667 0.00 0.00 34.09 2.45
108 6161 2.226330 GTGCAACACATGGTCACCTAA 58.774 47.619 0.00 0.00 36.32 2.69
115 6168 4.532834 ACACATGGTCACCTAACACTTTT 58.467 39.130 0.00 0.00 0.00 2.27
120 6173 4.590918 TGGTCACCTAACACTTTTCACAA 58.409 39.130 0.00 0.00 0.00 3.33
125 6178 7.416326 GGTCACCTAACACTTTTCACAAATTCT 60.416 37.037 0.00 0.00 0.00 2.40
198 6251 3.802948 ATTAGGGATATCGATCACGGC 57.197 47.619 0.00 0.00 40.78 5.68
207 6260 6.797852 GATATCGATCACGGCCATAGAGGC 62.798 54.167 0.00 0.00 46.39 4.70
257 6310 4.498513 GGTGTTGCCCAGTGTTTTAAGTAC 60.499 45.833 0.00 0.00 0.00 2.73
329 6382 2.780714 CATGCATCTCTTCCTCATCCC 58.219 52.381 0.00 0.00 0.00 3.85
674 6736 2.433239 GGTCTACCCACACGAATACCAT 59.567 50.000 0.00 0.00 0.00 3.55
817 6879 7.881232 CTGGTATAAAACTAGGTTGGAACAAGA 59.119 37.037 0.00 0.00 36.88 3.02
887 6949 1.228367 CCCCTGGCAGATATGGTGC 60.228 63.158 17.94 0.00 40.42 5.01
954 7019 5.739070 GCTGAACTCGTCCATACCATATTGA 60.739 44.000 0.00 0.00 0.00 2.57
1282 7389 6.731292 TGAAAGGATTCTCCATAAGATCGA 57.269 37.500 0.00 0.00 39.61 3.59
1467 7574 1.039856 AATGTGCCGAAGTTTGCCTT 58.960 45.000 0.00 0.00 35.59 4.35
1482 7589 2.019897 GCCTTGGCAACTGCACTTGT 62.020 55.000 6.79 0.00 44.36 3.16
1483 7590 0.249155 CCTTGGCAACTGCACTTGTG 60.249 55.000 3.76 0.00 44.36 3.33
1494 7601 2.422479 CTGCACTTGTGCTGCATATTCT 59.578 45.455 23.53 0.00 43.61 2.40
1547 7654 9.438291 GAATGGTGAGATTATTAATGTGAAACG 57.562 33.333 0.00 0.00 42.39 3.60
1570 7677 4.094887 GGCAACAATGTGATGGTACTACAG 59.905 45.833 0.00 0.00 0.00 2.74
1671 7814 0.943673 TCGGCATATCAATTGGTGCG 59.056 50.000 18.41 15.07 38.43 5.34
1870 8013 2.507407 TGGTTCTGTATTCAAGGGGC 57.493 50.000 0.00 0.00 0.00 5.80
1935 8078 1.451067 CTTGCCAAGGAGAGAAGCAG 58.549 55.000 0.00 0.00 34.45 4.24
1959 8102 3.056250 TCAGAGCTGAAGTGAGGTCAATC 60.056 47.826 0.00 0.00 41.98 2.67
2013 8156 1.616159 TTGGCTTTTGTACTGAGGGC 58.384 50.000 0.00 0.00 0.00 5.19
2040 8183 2.755650 AGGTTGCTTGTCTACGAACAG 58.244 47.619 0.00 0.00 0.00 3.16
2049 8192 4.725556 TGTCTACGAACAGATGCAAAAC 57.274 40.909 0.00 0.00 0.00 2.43
2216 8371 5.046014 AGCCAGAGAACATACTTCTTGATGT 60.046 40.000 0.00 0.00 37.91 3.06
2389 8544 3.056678 CAGCTATGGCATGGTTTTGTTGA 60.057 43.478 10.98 0.00 41.70 3.18
2448 8627 6.983474 TGTACAACCAGTGATGATTATGTG 57.017 37.500 0.00 0.00 0.00 3.21
2484 8663 3.202906 AGTTGCAAGCAAACTACTCGAA 58.797 40.909 9.32 0.00 37.70 3.71
2523 8702 2.092968 GGTGGACAGCAATCTACATGGA 60.093 50.000 0.00 0.00 31.98 3.41
2789 8968 6.933514 AGCCTGGAATCCAAGAAAATAAAA 57.066 33.333 2.61 0.00 30.80 1.52
2799 8978 8.992835 ATCCAAGAAAATAAAAAGAGACATGC 57.007 30.769 0.00 0.00 0.00 4.06
2806 8985 8.748380 AAAATAAAAAGAGACATGCTAAGCAC 57.252 30.769 0.00 0.00 43.04 4.40
2892 9073 2.207590 TGCTAGCATTTCTGATCGCAG 58.792 47.619 14.93 0.00 34.93 5.18
3022 9230 0.744057 GAGCAGAGCTTCCCTTCAGC 60.744 60.000 0.00 0.00 39.88 4.26
3031 9239 2.275318 CTTCCCTTCAGCGATTGTCTC 58.725 52.381 0.00 0.00 0.00 3.36
3063 9277 2.162681 ACCAGTGGCAAGTTAGCATTC 58.837 47.619 9.78 0.00 35.83 2.67
3070 9284 3.894427 TGGCAAGTTAGCATTCCTGAAAA 59.106 39.130 0.00 0.00 35.83 2.29
3073 9287 6.036470 GGCAAGTTAGCATTCCTGAAAATAC 58.964 40.000 0.00 0.00 35.83 1.89
3074 9288 6.127619 GGCAAGTTAGCATTCCTGAAAATACT 60.128 38.462 0.00 0.00 35.83 2.12
3157 9414 4.923871 GTCGCTGACACTCTTTAAGATTGA 59.076 41.667 17.23 0.00 30.47 2.57
3246 9507 4.900635 AAAATGGATGCAAGTACGGATC 57.099 40.909 0.00 0.00 33.30 3.36
3255 9516 4.990257 TGCAAGTACGGATCTAGTACAAC 58.010 43.478 23.67 16.29 44.92 3.32
3288 9549 4.061357 TCGTTGTCTGTGTTGTATCCAA 57.939 40.909 0.00 0.00 0.00 3.53
3292 9553 6.876789 TCGTTGTCTGTGTTGTATCCAAATAT 59.123 34.615 0.00 0.00 30.94 1.28
3293 9554 7.389330 TCGTTGTCTGTGTTGTATCCAAATATT 59.611 33.333 0.00 0.00 30.94 1.28
3294 9555 8.661257 CGTTGTCTGTGTTGTATCCAAATATTA 58.339 33.333 0.00 0.00 30.94 0.98
3319 9580 5.154222 GTTTTTCTTCTTCCATTAGTGGCG 58.846 41.667 0.00 0.00 45.63 5.69
3321 9582 2.184533 TCTTCTTCCATTAGTGGCGGA 58.815 47.619 0.00 0.00 45.63 5.54
3326 9587 2.396590 TCCATTAGTGGCGGAAGTTC 57.603 50.000 0.00 0.00 45.63 3.01
3364 9625 9.725019 TGAAGAAAGAGAATTAATTAGTGAGCA 57.275 29.630 0.00 0.00 0.00 4.26
3398 9659 6.506500 AAAGACTGCAGAAGGTATGAAATG 57.493 37.500 23.35 0.00 0.00 2.32
3399 9660 4.521146 AGACTGCAGAAGGTATGAAATGG 58.479 43.478 23.35 0.00 0.00 3.16
3415 9677 6.729690 TGAAATGGTCAAAGGAAAACTGAT 57.270 33.333 0.00 0.00 31.51 2.90
3417 9679 7.657336 TGAAATGGTCAAAGGAAAACTGATAC 58.343 34.615 0.00 0.00 31.51 2.24
3418 9680 7.505585 TGAAATGGTCAAAGGAAAACTGATACT 59.494 33.333 0.00 0.00 31.51 2.12
3419 9681 7.454260 AATGGTCAAAGGAAAACTGATACTC 57.546 36.000 0.00 0.00 0.00 2.59
3420 9682 5.313712 TGGTCAAAGGAAAACTGATACTCC 58.686 41.667 0.00 0.00 0.00 3.85
3421 9683 4.700692 GGTCAAAGGAAAACTGATACTCCC 59.299 45.833 0.00 0.00 0.00 4.30
3422 9684 5.515008 GGTCAAAGGAAAACTGATACTCCCT 60.515 44.000 0.00 0.00 0.00 4.20
3423 9685 5.644206 GTCAAAGGAAAACTGATACTCCCTC 59.356 44.000 0.00 0.00 0.00 4.30
3424 9686 4.846168 AAGGAAAACTGATACTCCCTCC 57.154 45.455 0.00 0.00 0.00 4.30
3425 9687 2.766828 AGGAAAACTGATACTCCCTCCG 59.233 50.000 0.00 0.00 0.00 4.63
3426 9688 2.500504 GGAAAACTGATACTCCCTCCGT 59.499 50.000 0.00 0.00 0.00 4.69
3427 9689 3.430513 GGAAAACTGATACTCCCTCCGTC 60.431 52.174 0.00 0.00 0.00 4.79
3428 9690 1.777941 AACTGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3429 9691 0.106116 ACTGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
3430 9692 0.106167 CTGATACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
3431 9693 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
3432 9694 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
3433 9695 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
3434 9696 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3435 9697 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3436 9698 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3437 9699 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3438 9700 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3439 9701 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3440 9702 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3441 9703 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3442 9704 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3443 9705 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3444 9706 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3445 9707 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3446 9708 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3447 9709 4.083484 CGTCCCAAAATAAGTGTCTCAACC 60.083 45.833 0.00 0.00 0.00 3.77
3448 9710 5.070685 GTCCCAAAATAAGTGTCTCAACCT 58.929 41.667 0.00 0.00 0.00 3.50
3449 9711 5.535030 GTCCCAAAATAAGTGTCTCAACCTT 59.465 40.000 0.00 0.00 0.00 3.50
3450 9712 6.713450 GTCCCAAAATAAGTGTCTCAACCTTA 59.287 38.462 0.00 0.00 0.00 2.69
3451 9713 7.393515 GTCCCAAAATAAGTGTCTCAACCTTAT 59.606 37.037 0.00 0.00 33.74 1.73
3452 9714 7.947890 TCCCAAAATAAGTGTCTCAACCTTATT 59.052 33.333 0.00 0.00 38.77 1.40
3453 9715 8.585018 CCCAAAATAAGTGTCTCAACCTTATTT 58.415 33.333 9.60 9.60 42.65 1.40
3454 9716 9.981114 CCAAAATAAGTGTCTCAACCTTATTTT 57.019 29.630 17.25 17.25 45.35 1.82
3456 9718 9.981114 AAAATAAGTGTCTCAACCTTATTTTGG 57.019 29.630 20.15 0.00 44.43 3.28
3457 9719 8.934023 AATAAGTGTCTCAACCTTATTTTGGA 57.066 30.769 0.00 0.00 36.50 3.53
3458 9720 6.635030 AAGTGTCTCAACCTTATTTTGGAC 57.365 37.500 0.00 0.00 0.00 4.02
3459 9721 5.941788 AGTGTCTCAACCTTATTTTGGACT 58.058 37.500 0.00 0.00 31.11 3.85
3460 9722 7.074653 AGTGTCTCAACCTTATTTTGGACTA 57.925 36.000 0.00 0.00 31.11 2.59
3461 9723 7.690256 AGTGTCTCAACCTTATTTTGGACTAT 58.310 34.615 0.00 0.00 31.11 2.12
3462 9724 8.164070 AGTGTCTCAACCTTATTTTGGACTATT 58.836 33.333 0.00 0.00 31.11 1.73
3463 9725 8.793592 GTGTCTCAACCTTATTTTGGACTATTT 58.206 33.333 0.00 0.00 31.11 1.40
3464 9726 9.010029 TGTCTCAACCTTATTTTGGACTATTTC 57.990 33.333 0.00 0.00 31.11 2.17
3465 9727 8.175716 GTCTCAACCTTATTTTGGACTATTTCG 58.824 37.037 0.00 0.00 0.00 3.46
3466 9728 7.335924 TCTCAACCTTATTTTGGACTATTTCGG 59.664 37.037 0.00 0.00 0.00 4.30
3467 9729 6.376018 TCAACCTTATTTTGGACTATTTCGGG 59.624 38.462 0.00 0.00 0.00 5.14
3468 9730 6.069705 ACCTTATTTTGGACTATTTCGGGA 57.930 37.500 0.00 0.00 0.00 5.14
3469 9731 5.884232 ACCTTATTTTGGACTATTTCGGGAC 59.116 40.000 0.00 0.00 0.00 4.46
3483 9745 3.849002 GGGACGGAGGGAGTAAAAC 57.151 57.895 0.00 0.00 0.00 2.43
3492 9754 3.017442 GAGGGAGTAAAACCAGATTGGC 58.983 50.000 0.00 0.00 42.67 4.52
3496 9758 4.386424 GGGAGTAAAACCAGATTGGCCTAT 60.386 45.833 3.32 0.02 42.67 2.57
3506 9768 4.264253 CAGATTGGCCTATGACAGAACAA 58.736 43.478 3.77 0.00 0.00 2.83
3510 9772 3.808728 TGGCCTATGACAGAACAATAGC 58.191 45.455 3.32 0.00 0.00 2.97
3516 9778 2.079158 TGACAGAACAATAGCAGCAGC 58.921 47.619 0.00 0.00 42.56 5.25
3530 9792 2.064762 CAGCAGCTAAATAGGCTAGCG 58.935 52.381 9.00 0.00 45.32 4.26
3537 9799 1.379527 AAATAGGCTAGCGCACAACC 58.620 50.000 11.47 5.28 38.10 3.77
3539 9801 0.179073 ATAGGCTAGCGCACAACCTG 60.179 55.000 11.47 0.00 38.10 4.00
3552 9814 3.641648 CACAACCTGTGGTAGCAAATTG 58.358 45.455 0.00 0.00 44.27 2.32
3583 9845 1.610038 CTGCAATCAGTTGTTGAGGCA 59.390 47.619 0.00 6.26 43.55 4.75
3615 9877 5.827797 TCAACATGGTTATGGGATTCTTAGC 59.172 40.000 0.00 0.00 38.66 3.09
3617 9879 5.765510 ACATGGTTATGGGATTCTTAGCAA 58.234 37.500 0.00 0.00 38.66 3.91
3643 9962 8.031277 ACAAAAGATGAAGATAATTGGCACTTC 58.969 33.333 7.61 7.61 39.08 3.01
3649 9968 6.189859 TGAAGATAATTGGCACTTCCTCATT 58.810 36.000 11.01 0.00 38.22 2.57
3650 9969 6.319658 TGAAGATAATTGGCACTTCCTCATTC 59.680 38.462 11.01 7.97 38.22 2.67
3652 9971 2.905415 ATTGGCACTTCCTCATTCCA 57.095 45.000 0.00 0.00 35.26 3.53
3676 10003 4.611367 AGGTGGACTTGTATACTACTGCT 58.389 43.478 4.17 0.00 0.00 4.24
3679 10006 5.349809 GTGGACTTGTATACTACTGCTTCC 58.650 45.833 4.17 1.72 0.00 3.46
3727 10067 1.851304 GGCTCATCCCCAATTCAACA 58.149 50.000 0.00 0.00 0.00 3.33
3839 10179 0.804989 GGACCAGATTTGTTGAGCCG 59.195 55.000 0.00 0.00 0.00 5.52
3847 10187 2.739849 TTTGTTGAGCCGGGCGATGA 62.740 55.000 14.39 0.00 0.00 2.92
3939 10337 1.542547 GGGAAACAGGAGAAGTTGCGA 60.543 52.381 0.00 0.00 0.00 5.10
3942 10340 2.839486 AACAGGAGAAGTTGCGATGA 57.161 45.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.822735 CACCTCATCCAACATTGTGTTCT 59.177 43.478 0.00 0.00 38.77 3.01
2 3 3.831323 TCACCTCATCCAACATTGTGTT 58.169 40.909 0.00 0.00 42.08 3.32
21 6071 7.081349 CAGTGCACCTTTTTATATTTCGTTCA 58.919 34.615 14.63 0.00 0.00 3.18
22 6072 6.526674 CCAGTGCACCTTTTTATATTTCGTTC 59.473 38.462 14.63 0.00 0.00 3.95
30 6080 4.703093 GGCTAACCAGTGCACCTTTTTATA 59.297 41.667 14.63 0.00 35.26 0.98
32 6082 2.888414 GGCTAACCAGTGCACCTTTTTA 59.112 45.455 14.63 5.50 35.26 1.52
96 6149 4.578516 TGTGAAAAGTGTTAGGTGACCATG 59.421 41.667 3.63 0.00 0.00 3.66
97 6150 4.787551 TGTGAAAAGTGTTAGGTGACCAT 58.212 39.130 3.63 0.00 0.00 3.55
135 6188 5.782047 CCATCTTTGCAAAATCCAACACTA 58.218 37.500 13.84 0.00 0.00 2.74
148 6201 4.115270 TGGCATGCCATCTTTGCA 57.885 50.000 35.59 10.49 41.89 4.08
198 6251 1.007964 CGAGCACTCGCCTCTATGG 60.008 63.158 7.18 0.00 46.50 2.74
211 6264 1.271379 ACGTCATGGTAAAGTCGAGCA 59.729 47.619 0.00 0.00 0.00 4.26
215 6268 3.449322 CCAAACGTCATGGTAAAGTCG 57.551 47.619 11.25 0.00 33.08 4.18
257 6310 6.648879 TCAAGAAGTTTGGTTAGAATTGGG 57.351 37.500 0.00 0.00 0.00 4.12
329 6382 2.956333 AGGGACAAGAAAAACCCGAAAG 59.044 45.455 0.00 0.00 46.13 2.62
522 6575 0.984230 CTGGAGTTAGCTTGGGGACA 59.016 55.000 0.00 0.00 39.83 4.02
547 6600 7.998383 TGTAACTGGGTTATGATCATTTGCTAT 59.002 33.333 14.65 0.00 30.49 2.97
817 6879 1.144057 GGCGATTCAGACCCGTGAT 59.856 57.895 0.00 0.00 0.00 3.06
887 6949 3.265791 GCACCACTTGGATCTAACTCTG 58.734 50.000 1.14 0.00 38.94 3.35
954 7019 0.750850 CGTTCCATACCCCACTCGAT 59.249 55.000 0.00 0.00 0.00 3.59
1282 7389 3.203263 TCATCTAGCTCCCAGTCACTAGT 59.797 47.826 0.00 0.00 34.89 2.57
1482 7589 4.779696 TGACACCATAAGAATATGCAGCA 58.220 39.130 0.00 0.00 38.06 4.41
1483 7590 5.756195 TTGACACCATAAGAATATGCAGC 57.244 39.130 0.00 0.00 38.06 5.25
1494 7601 4.771577 ACAAAGCATCCATTGACACCATAA 59.228 37.500 0.00 0.00 0.00 1.90
1547 7654 4.006989 TGTAGTACCATCACATTGTTGCC 58.993 43.478 0.00 0.00 0.00 4.52
1570 7677 7.900782 TGTAAAGAGTGGCTTTGTTAGTATC 57.099 36.000 0.00 0.00 46.03 2.24
1671 7814 0.663153 AACCGCAGAAAGCAACACTC 59.337 50.000 0.00 0.00 46.13 3.51
1870 8013 3.942829 TGGCAGTGGAGTCATTTAGAAG 58.057 45.455 0.00 0.00 0.00 2.85
1898 8041 4.082026 GGCAAGCACCATCAAGTCTTTTAT 60.082 41.667 0.00 0.00 0.00 1.40
1935 8078 2.036475 TGACCTCACTTCAGCTCTGAAC 59.964 50.000 8.14 0.00 43.90 3.18
1959 8102 6.738832 AGATTGATATGCTGAATGAATCCG 57.261 37.500 0.00 0.00 0.00 4.18
2013 8156 4.034858 TCGTAGACAAGCAACCTACTATCG 59.965 45.833 0.00 0.00 32.73 2.92
2040 8183 3.896648 TCAAGAGAACGGTTTTGCATC 57.103 42.857 0.00 0.00 0.00 3.91
2216 8371 5.471797 TCTGCTATTTTCGGAACAAATGACA 59.528 36.000 0.00 0.00 0.00 3.58
2389 8544 7.119846 CGAGTTCCTCTTTCCTGATACAATTTT 59.880 37.037 0.00 0.00 0.00 1.82
2448 8627 2.946564 GCAACTTGCACAGGGAAATAC 58.053 47.619 8.97 0.00 44.26 1.89
2484 8663 0.995024 CCAAACTCTCCACATCCCCT 59.005 55.000 0.00 0.00 0.00 4.79
2523 8702 3.424703 CACCTGTTCCAAATGGACATCT 58.575 45.455 0.54 0.00 45.39 2.90
2679 8858 2.450476 GAGTGTGGATTCCCTGCAATT 58.550 47.619 0.00 0.00 0.00 2.32
2789 8968 4.252073 CTGAAGTGCTTAGCATGTCTCTT 58.748 43.478 11.03 8.49 41.91 2.85
2799 8978 5.239306 TCATGACAAAACCTGAAGTGCTTAG 59.761 40.000 0.00 0.00 0.00 2.18
2806 8985 6.808008 ATGTACTCATGACAAAACCTGAAG 57.192 37.500 0.00 0.00 32.51 3.02
2911 9095 2.841881 GGTCCAGGTACCCATCAACTAA 59.158 50.000 8.74 0.00 33.02 2.24
2936 9120 1.615392 GTTTGCCTGCCTCTTGTGAAT 59.385 47.619 0.00 0.00 0.00 2.57
2970 9154 3.672808 CAACCTGTCTTCATGAAGCTCT 58.327 45.455 27.45 8.19 38.28 4.09
3022 9230 4.332819 GGTATTTCAGGGTTGAGACAATCG 59.667 45.833 0.00 0.00 34.15 3.34
3031 9239 1.818674 GCCACTGGTATTTCAGGGTTG 59.181 52.381 0.00 0.00 36.48 3.77
3091 9327 9.687210 AATGATTGCTATGCATAAATACAACAG 57.313 29.630 8.00 0.00 38.76 3.16
3100 9356 6.774170 AGAGTCCAAATGATTGCTATGCATAA 59.226 34.615 8.00 0.00 38.76 1.90
3104 9361 4.577693 TGAGAGTCCAAATGATTGCTATGC 59.422 41.667 0.00 0.00 35.10 3.14
3246 9507 7.074507 ACGATCACTAGTCAAGTTGTACTAG 57.925 40.000 25.18 25.18 46.96 2.57
3255 9516 4.618912 CACAGACAACGATCACTAGTCAAG 59.381 45.833 0.00 0.00 0.00 3.02
3319 9580 3.596214 TCATCTAAACGGCAGAACTTCC 58.404 45.455 0.00 0.00 0.00 3.46
3321 9582 4.894784 TCTTCATCTAAACGGCAGAACTT 58.105 39.130 0.00 0.00 0.00 2.66
3326 9587 5.171476 TCTCTTTCTTCATCTAAACGGCAG 58.829 41.667 0.00 0.00 0.00 4.85
3364 9625 3.327757 TCTGCAGTCTTTACAGGGTTCAT 59.672 43.478 14.67 0.00 32.19 2.57
3366 9627 3.402628 TCTGCAGTCTTTACAGGGTTC 57.597 47.619 14.67 0.00 32.19 3.62
3398 9659 4.700692 GGGAGTATCAGTTTTCCTTTGACC 59.299 45.833 0.00 0.00 36.25 4.02
3399 9660 5.561679 AGGGAGTATCAGTTTTCCTTTGAC 58.438 41.667 0.00 0.00 36.25 3.18
3415 9677 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3417 9679 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3418 9680 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3419 9681 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3420 9682 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3421 9683 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3422 9684 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3423 9685 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3424 9686 4.083484 GGTTGAGACACTTATTTTGGGACG 60.083 45.833 0.00 0.00 0.00 4.79
3425 9687 5.070685 AGGTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
3426 9688 5.319043 AGGTTGAGACACTTATTTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
3427 9689 7.703058 ATAAGGTTGAGACACTTATTTTGGG 57.297 36.000 0.00 0.00 34.66 4.12
3432 9694 8.793592 GTCCAAAATAAGGTTGAGACACTTATT 58.206 33.333 0.00 0.00 44.73 1.40
3433 9695 8.164070 AGTCCAAAATAAGGTTGAGACACTTAT 58.836 33.333 0.00 0.00 38.64 1.73
3434 9696 7.514721 AGTCCAAAATAAGGTTGAGACACTTA 58.485 34.615 0.00 0.00 32.83 2.24
3435 9697 6.365520 AGTCCAAAATAAGGTTGAGACACTT 58.634 36.000 0.00 0.00 32.83 3.16
3436 9698 5.941788 AGTCCAAAATAAGGTTGAGACACT 58.058 37.500 0.00 0.00 32.83 3.55
3437 9699 7.923414 ATAGTCCAAAATAAGGTTGAGACAC 57.077 36.000 0.00 0.00 32.83 3.67
3438 9700 8.934023 AAATAGTCCAAAATAAGGTTGAGACA 57.066 30.769 0.00 0.00 32.83 3.41
3439 9701 8.175716 CGAAATAGTCCAAAATAAGGTTGAGAC 58.824 37.037 0.00 0.00 31.64 3.36
3440 9702 7.335924 CCGAAATAGTCCAAAATAAGGTTGAGA 59.664 37.037 0.00 0.00 0.00 3.27
3441 9703 7.415206 CCCGAAATAGTCCAAAATAAGGTTGAG 60.415 40.741 0.00 0.00 0.00 3.02
3442 9704 6.376018 CCCGAAATAGTCCAAAATAAGGTTGA 59.624 38.462 0.00 0.00 0.00 3.18
3443 9705 6.376018 TCCCGAAATAGTCCAAAATAAGGTTG 59.624 38.462 0.00 0.00 0.00 3.77
3444 9706 6.376299 GTCCCGAAATAGTCCAAAATAAGGTT 59.624 38.462 0.00 0.00 0.00 3.50
3445 9707 5.884232 GTCCCGAAATAGTCCAAAATAAGGT 59.116 40.000 0.00 0.00 0.00 3.50
3446 9708 5.007332 CGTCCCGAAATAGTCCAAAATAAGG 59.993 44.000 0.00 0.00 0.00 2.69
3447 9709 5.007332 CCGTCCCGAAATAGTCCAAAATAAG 59.993 44.000 0.00 0.00 0.00 1.73
3448 9710 4.877251 CCGTCCCGAAATAGTCCAAAATAA 59.123 41.667 0.00 0.00 0.00 1.40
3449 9711 4.161942 TCCGTCCCGAAATAGTCCAAAATA 59.838 41.667 0.00 0.00 0.00 1.40
3450 9712 3.054948 TCCGTCCCGAAATAGTCCAAAAT 60.055 43.478 0.00 0.00 0.00 1.82
3451 9713 2.302445 TCCGTCCCGAAATAGTCCAAAA 59.698 45.455 0.00 0.00 0.00 2.44
3452 9714 1.901159 TCCGTCCCGAAATAGTCCAAA 59.099 47.619 0.00 0.00 0.00 3.28
3453 9715 1.479323 CTCCGTCCCGAAATAGTCCAA 59.521 52.381 0.00 0.00 0.00 3.53
3454 9716 1.108776 CTCCGTCCCGAAATAGTCCA 58.891 55.000 0.00 0.00 0.00 4.02
3455 9717 0.388294 CCTCCGTCCCGAAATAGTCC 59.612 60.000 0.00 0.00 0.00 3.85
3456 9718 0.388294 CCCTCCGTCCCGAAATAGTC 59.612 60.000 0.00 0.00 0.00 2.59
3457 9719 0.032813 TCCCTCCGTCCCGAAATAGT 60.033 55.000 0.00 0.00 0.00 2.12
3458 9720 0.674534 CTCCCTCCGTCCCGAAATAG 59.325 60.000 0.00 0.00 0.00 1.73
3459 9721 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
3460 9722 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
3461 9723 0.251742 TTACTCCCTCCGTCCCGAAA 60.252 55.000 0.00 0.00 0.00 3.46
3462 9724 0.251742 TTTACTCCCTCCGTCCCGAA 60.252 55.000 0.00 0.00 0.00 4.30
3463 9725 0.251742 TTTTACTCCCTCCGTCCCGA 60.252 55.000 0.00 0.00 0.00 5.14
3464 9726 0.108472 GTTTTACTCCCTCCGTCCCG 60.108 60.000 0.00 0.00 0.00 5.14
3465 9727 0.251354 GGTTTTACTCCCTCCGTCCC 59.749 60.000 0.00 0.00 0.00 4.46
3466 9728 0.978907 TGGTTTTACTCCCTCCGTCC 59.021 55.000 0.00 0.00 0.00 4.79
3467 9729 1.897802 TCTGGTTTTACTCCCTCCGTC 59.102 52.381 0.00 0.00 0.00 4.79
3468 9730 2.019807 TCTGGTTTTACTCCCTCCGT 57.980 50.000 0.00 0.00 0.00 4.69
3469 9731 3.270877 CAATCTGGTTTTACTCCCTCCG 58.729 50.000 0.00 0.00 0.00 4.63
3470 9732 3.621558 CCAATCTGGTTTTACTCCCTCC 58.378 50.000 0.00 0.00 31.35 4.30
3471 9733 3.017442 GCCAATCTGGTTTTACTCCCTC 58.983 50.000 0.00 0.00 40.46 4.30
3472 9734 2.291605 GGCCAATCTGGTTTTACTCCCT 60.292 50.000 0.00 0.00 40.46 4.20
3473 9735 2.100197 GGCCAATCTGGTTTTACTCCC 58.900 52.381 0.00 0.00 40.46 4.30
3474 9736 3.087370 AGGCCAATCTGGTTTTACTCC 57.913 47.619 5.01 0.00 40.46 3.85
3475 9737 5.297029 GTCATAGGCCAATCTGGTTTTACTC 59.703 44.000 5.01 0.00 40.46 2.59
3476 9738 5.193679 GTCATAGGCCAATCTGGTTTTACT 58.806 41.667 5.01 0.00 40.46 2.24
3477 9739 4.947388 TGTCATAGGCCAATCTGGTTTTAC 59.053 41.667 5.01 0.00 40.46 2.01
3478 9740 5.045213 TCTGTCATAGGCCAATCTGGTTTTA 60.045 40.000 5.01 0.00 40.46 1.52
3479 9741 4.019174 CTGTCATAGGCCAATCTGGTTTT 58.981 43.478 5.01 0.00 40.46 2.43
3480 9742 3.266772 TCTGTCATAGGCCAATCTGGTTT 59.733 43.478 5.01 0.00 40.46 3.27
3481 9743 2.846206 TCTGTCATAGGCCAATCTGGTT 59.154 45.455 5.01 0.00 40.46 3.67
3482 9744 2.481441 TCTGTCATAGGCCAATCTGGT 58.519 47.619 5.01 0.00 40.46 4.00
3483 9745 3.209410 GTTCTGTCATAGGCCAATCTGG 58.791 50.000 5.01 0.00 41.55 3.86
3492 9754 4.445453 TGCTGCTATTGTTCTGTCATAGG 58.555 43.478 0.00 0.00 0.00 2.57
3496 9758 2.079158 GCTGCTGCTATTGTTCTGTCA 58.921 47.619 8.53 0.00 36.03 3.58
3510 9772 2.064762 CGCTAGCCTATTTAGCTGCTG 58.935 52.381 13.43 0.00 41.71 4.41
3516 9778 2.544267 GGTTGTGCGCTAGCCTATTTAG 59.456 50.000 9.73 0.00 44.33 1.85
3530 9792 1.028905 TTTGCTACCACAGGTTGTGC 58.971 50.000 3.72 0.00 46.51 4.57
3552 9814 3.959573 CTGATTGCAGTTAAGGCTAGC 57.040 47.619 6.04 6.04 37.37 3.42
3565 9827 2.029649 ACATGCCTCAACAACTGATTGC 60.030 45.455 0.00 0.00 39.66 3.56
3574 9836 4.241590 GTTGATTCAACATGCCTCAACA 57.758 40.909 21.75 0.76 43.16 3.33
3615 9877 7.816031 AGTGCCAATTATCTTCATCTTTTGTTG 59.184 33.333 0.00 0.00 0.00 3.33
3617 9879 7.472334 AGTGCCAATTATCTTCATCTTTTGT 57.528 32.000 0.00 0.00 0.00 2.83
3649 9968 6.290294 GTAGTATACAAGTCCACCTTTGGA 57.710 41.667 5.50 0.00 45.32 3.53
3650 9969 6.106673 CAGTAGTATACAAGTCCACCTTTGG 58.893 44.000 5.50 0.00 46.26 3.28
3652 9971 5.484290 AGCAGTAGTATACAAGTCCACCTTT 59.516 40.000 5.50 0.00 46.26 3.11
3661 9988 5.502153 ACTCGGAAGCAGTAGTATACAAG 57.498 43.478 5.50 0.00 46.26 3.16
3692 10027 2.513897 CCCGGACGGCTGAATTCC 60.514 66.667 0.73 0.00 0.00 3.01
3752 10092 3.285215 CCGCATCCTGCCTGCATC 61.285 66.667 0.00 0.00 41.12 3.91
3804 10144 3.392616 CTGGTCCCAAGCTTGAGGTATAT 59.607 47.826 28.05 0.00 0.00 0.86
3839 10179 4.424711 TGCCCACCTTCATCGCCC 62.425 66.667 0.00 0.00 0.00 6.13
3939 10337 0.753479 AGACCGGCGAGATCACTCAT 60.753 55.000 9.30 0.00 42.72 2.90
3942 10340 1.668101 GGAAGACCGGCGAGATCACT 61.668 60.000 9.30 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.