Multiple sequence alignment - TraesCS1D01G390100

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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 TraesCS1D01G390100 chr1D 100.000 4954 0 0 1 4954 461540106 461535153 0.000000e+00 9149.0
1 TraesCS1D01G390100 chr1D 97.254 947 23 3 4 947 60170869 60171815 0.000000e+00 1602.0
2 TraesCS1D01G390100 chr1D 96.938 947 26 2 4 947 205133750 205134696 0.000000e+00 1585.0
3 TraesCS1D01G390100 chr1D 96.938 947 26 2 4 947 247504811 247505757 0.000000e+00 1585.0
4 TraesCS1D01G390100 chr1D 93.349 872 45 3 4095 4954 325507743 325506873 0.000000e+00 1277.0
5 TraesCS1D01G390100 chr1D 92.661 872 52 2 4095 4954 414900506 414899635 0.000000e+00 1245.0
6 TraesCS1D01G390100 chr1D 82.904 1398 194 24 958 2336 461752744 461751373 0.000000e+00 1216.0
7 TraesCS1D01G390100 chr1D 95.963 322 11 1 3780 4099 461487539 461487218 5.680000e-144 521.0
8 TraesCS1D01G390100 chr1D 87.003 377 42 5 1000 1374 461422929 461422558 7.670000e-113 418.0
9 TraesCS1D01G390100 chr1D 82.283 508 22 12 3279 3778 461488051 461487604 1.300000e-100 377.0
10 TraesCS1D01G390100 chr1B 94.179 2113 77 18 955 3058 634564753 634566828 0.000000e+00 3179.0
11 TraesCS1D01G390100 chr1B 92.431 872 53 7 4095 4954 87739283 87740153 0.000000e+00 1232.0
12 TraesCS1D01G390100 chr1B 83.095 1396 194 28 961 2336 634687366 634685993 0.000000e+00 1232.0
13 TraesCS1D01G390100 chr1B 86.388 742 27 19 3056 3783 634599850 634600531 0.000000e+00 743.0
14 TraesCS1D01G390100 chr1B 91.385 325 18 3 3779 4099 634600576 634600894 2.120000e-118 436.0
15 TraesCS1D01G390100 chr1B 91.358 324 18 3 3780 4099 634419038 634418721 7.620000e-118 435.0
16 TraesCS1D01G390100 chr1B 87.978 366 39 3 1000 1364 634313687 634313326 1.270000e-115 427.0
17 TraesCS1D01G390100 chr1B 91.026 234 11 4 3550 3783 634419297 634419074 1.730000e-79 307.0
18 TraesCS1D01G390100 chr1B 87.500 64 0 1 3366 3429 634419431 634419376 3.200000e-07 67.6
19 TraesCS1D01G390100 chrUn 94.937 1422 45 8 958 2358 1068303 1066888 0.000000e+00 2202.0
20 TraesCS1D01G390100 chrUn 88.308 325 17 9 3780 4099 218154380 218154688 2.180000e-98 370.0
21 TraesCS1D01G390100 chrUn 88.308 325 17 9 3780 4099 246423989 246423681 2.180000e-98 370.0
22 TraesCS1D01G390100 chrUn 87.462 327 10 5 3447 3772 218148908 218149204 1.020000e-91 348.0
23 TraesCS1D01G390100 chrUn 87.462 327 10 5 3447 3772 246429461 246429165 1.020000e-91 348.0
24 TraesCS1D01G390100 chrUn 93.478 46 3 0 4054 4099 478319186 478319231 8.900000e-08 69.4
25 TraesCS1D01G390100 chr2D 96.832 947 27 2 4 947 73125925 73126871 0.000000e+00 1580.0
26 TraesCS1D01G390100 chr2D 96.406 946 29 4 10 950 621749744 621748799 0.000000e+00 1554.0
27 TraesCS1D01G390100 chr2D 93.922 872 40 3 4095 4954 352201246 352200376 0.000000e+00 1304.0
28 TraesCS1D01G390100 chr2D 95.477 597 25 2 4358 4954 29142547 29143141 0.000000e+00 952.0
29 TraesCS1D01G390100 chr6D 96.512 946 31 2 4 947 57790196 57791141 0.000000e+00 1563.0
30 TraesCS1D01G390100 chr7D 96.515 947 28 4 4 947 497561852 497560908 0.000000e+00 1561.0
31 TraesCS1D01G390100 chr7D 94.037 872 39 3 4095 4954 107051487 107052357 0.000000e+00 1310.0
32 TraesCS1D01G390100 chr3D 96.603 942 29 2 4 942 613712217 613711276 0.000000e+00 1559.0
33 TraesCS1D01G390100 chr3D 96.304 947 32 2 4 947 584700445 584701391 0.000000e+00 1552.0
34 TraesCS1D01G390100 chr7B 93.578 872 44 2 4095 4954 587871779 587870908 0.000000e+00 1290.0
35 TraesCS1D01G390100 chr7B 93.671 869 41 4 4098 4954 587702922 587702056 0.000000e+00 1288.0
36 TraesCS1D01G390100 chr7B 93.463 872 45 2 4095 4954 587853935 587853064 0.000000e+00 1284.0
37 TraesCS1D01G390100 chr7B 93.471 873 44 3 4095 4954 740176902 740176030 0.000000e+00 1284.0
38 TraesCS1D01G390100 chr7B 93.349 872 46 2 4095 4954 587813688 587812817 0.000000e+00 1279.0
39 TraesCS1D01G390100 chr7B 93.127 873 47 3 4095 4954 740392000 740391128 0.000000e+00 1267.0
40 TraesCS1D01G390100 chr7B 94.057 774 34 2 4193 4954 456503486 456504259 0.000000e+00 1164.0
41 TraesCS1D01G390100 chr2B 93.471 873 44 5 4095 4954 785737300 785736428 0.000000e+00 1284.0
42 TraesCS1D01G390100 chr5D 94.917 787 24 3 4095 4869 553023330 553022548 0.000000e+00 1218.0
43 TraesCS1D01G390100 chr1A 82.378 1396 211 24 958 2336 552976572 552975195 0.000000e+00 1182.0
44 TraesCS1D01G390100 chr1A 81.701 1399 209 32 958 2336 553047290 553045919 0.000000e+00 1122.0
45 TraesCS1D01G390100 chr1A 90.596 319 20 6 3788 4099 552952368 552952053 9.920000e-112 414.0
46 TraesCS1D01G390100 chr1A 85.372 376 52 1 1000 1375 552908583 552908211 2.160000e-103 387.0
47 TraesCS1D01G390100 chr1A 79.843 511 25 17 3279 3778 552952852 552952409 8.060000e-78 302.0
48 TraesCS1D01G390100 chr1A 88.889 108 6 4 1409 1513 553133611 553133507 1.450000e-25 128.0


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 TraesCS1D01G390100 chr1D 461535153 461540106 4953 True 9149.000000 9149 100.000000 1 4954 1 chr1D.!!$R4 4953
1 TraesCS1D01G390100 chr1D 60170869 60171815 946 False 1602.000000 1602 97.254000 4 947 1 chr1D.!!$F1 943
2 TraesCS1D01G390100 chr1D 205133750 205134696 946 False 1585.000000 1585 96.938000 4 947 1 chr1D.!!$F2 943
3 TraesCS1D01G390100 chr1D 247504811 247505757 946 False 1585.000000 1585 96.938000 4 947 1 chr1D.!!$F3 943
4 TraesCS1D01G390100 chr1D 325506873 325507743 870 True 1277.000000 1277 93.349000 4095 4954 1 chr1D.!!$R1 859
5 TraesCS1D01G390100 chr1D 414899635 414900506 871 True 1245.000000 1245 92.661000 4095 4954 1 chr1D.!!$R2 859
6 TraesCS1D01G390100 chr1D 461751373 461752744 1371 True 1216.000000 1216 82.904000 958 2336 1 chr1D.!!$R5 1378
7 TraesCS1D01G390100 chr1D 461487218 461488051 833 True 449.000000 521 89.123000 3279 4099 2 chr1D.!!$R6 820
8 TraesCS1D01G390100 chr1B 634564753 634566828 2075 False 3179.000000 3179 94.179000 955 3058 1 chr1B.!!$F2 2103
9 TraesCS1D01G390100 chr1B 87739283 87740153 870 False 1232.000000 1232 92.431000 4095 4954 1 chr1B.!!$F1 859
10 TraesCS1D01G390100 chr1B 634685993 634687366 1373 True 1232.000000 1232 83.095000 961 2336 1 chr1B.!!$R2 1375
11 TraesCS1D01G390100 chr1B 634599850 634600894 1044 False 589.500000 743 88.886500 3056 4099 2 chr1B.!!$F3 1043
12 TraesCS1D01G390100 chr1B 634418721 634419431 710 True 269.866667 435 89.961333 3366 4099 3 chr1B.!!$R3 733
13 TraesCS1D01G390100 chrUn 1066888 1068303 1415 True 2202.000000 2202 94.937000 958 2358 1 chrUn.!!$R1 1400
14 TraesCS1D01G390100 chr2D 73125925 73126871 946 False 1580.000000 1580 96.832000 4 947 1 chr2D.!!$F2 943
15 TraesCS1D01G390100 chr2D 621748799 621749744 945 True 1554.000000 1554 96.406000 10 950 1 chr2D.!!$R2 940
16 TraesCS1D01G390100 chr2D 352200376 352201246 870 True 1304.000000 1304 93.922000 4095 4954 1 chr2D.!!$R1 859
17 TraesCS1D01G390100 chr2D 29142547 29143141 594 False 952.000000 952 95.477000 4358 4954 1 chr2D.!!$F1 596
18 TraesCS1D01G390100 chr6D 57790196 57791141 945 False 1563.000000 1563 96.512000 4 947 1 chr6D.!!$F1 943
19 TraesCS1D01G390100 chr7D 497560908 497561852 944 True 1561.000000 1561 96.515000 4 947 1 chr7D.!!$R1 943
20 TraesCS1D01G390100 chr7D 107051487 107052357 870 False 1310.000000 1310 94.037000 4095 4954 1 chr7D.!!$F1 859
21 TraesCS1D01G390100 chr3D 613711276 613712217 941 True 1559.000000 1559 96.603000 4 942 1 chr3D.!!$R1 938
22 TraesCS1D01G390100 chr3D 584700445 584701391 946 False 1552.000000 1552 96.304000 4 947 1 chr3D.!!$F1 943
23 TraesCS1D01G390100 chr7B 587870908 587871779 871 True 1290.000000 1290 93.578000 4095 4954 1 chr7B.!!$R4 859
24 TraesCS1D01G390100 chr7B 587702056 587702922 866 True 1288.000000 1288 93.671000 4098 4954 1 chr7B.!!$R1 856
25 TraesCS1D01G390100 chr7B 587853064 587853935 871 True 1284.000000 1284 93.463000 4095 4954 1 chr7B.!!$R3 859
26 TraesCS1D01G390100 chr7B 740176030 740176902 872 True 1284.000000 1284 93.471000 4095 4954 1 chr7B.!!$R5 859
27 TraesCS1D01G390100 chr7B 587812817 587813688 871 True 1279.000000 1279 93.349000 4095 4954 1 chr7B.!!$R2 859
28 TraesCS1D01G390100 chr7B 740391128 740392000 872 True 1267.000000 1267 93.127000 4095 4954 1 chr7B.!!$R6 859
29 TraesCS1D01G390100 chr7B 456503486 456504259 773 False 1164.000000 1164 94.057000 4193 4954 1 chr7B.!!$F1 761
30 TraesCS1D01G390100 chr2B 785736428 785737300 872 True 1284.000000 1284 93.471000 4095 4954 1 chr2B.!!$R1 859
31 TraesCS1D01G390100 chr5D 553022548 553023330 782 True 1218.000000 1218 94.917000 4095 4869 1 chr5D.!!$R1 774
32 TraesCS1D01G390100 chr1A 552975195 552976572 1377 True 1182.000000 1182 82.378000 958 2336 1 chr1A.!!$R2 1378
33 TraesCS1D01G390100 chr1A 553045919 553047290 1371 True 1122.000000 1122 81.701000 958 2336 1 chr1A.!!$R3 1378
34 TraesCS1D01G390100 chr1A 552952053 552952852 799 True 358.000000 414 85.219500 3279 4099 2 chr1A.!!$R5 820

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
939 944 0.611896 CCGGGTGCATCCTCCTTTTT 60.612 55.0 15.59 0.0 36.25 1.94 F
2157 2213 0.035630 AAGCAGCTCCATGGTCACTC 60.036 55.0 12.58 0.0 0.00 3.51 F
3434 3500 0.033504 AGATCACACACGGTTCGCTT 59.966 50.0 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 2791 0.103026 CTTCATGGCAGGATCGACGA 59.897 55.0 1.35 0.0 0.0 4.20 R
3543 3613 0.035439 CCACGATACCAAAGCCCAGT 60.035 55.0 0.00 0.0 0.0 4.00 R
4462 4637 0.106708 AAAGCAGAACACCTCGCTCA 59.893 50.0 0.00 0.0 34.3 4.26 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
379 381 2.058675 CCGTCTTGGGAGGAACTGT 58.941 57.895 0.00 0.00 41.55 3.55
420 422 1.335132 GGATGGTGGGCTCCGAGTAA 61.335 60.000 0.00 0.00 0.00 2.24
462 464 4.947147 GGTTGCCAGGTGGTGCGA 62.947 66.667 0.00 0.00 37.57 5.10
612 614 1.900498 GCTTGGCAAGGTCTGTGCT 60.900 57.895 27.25 0.00 41.88 4.40
715 717 1.338107 CCGGTATGTGGCTAGGATGA 58.662 55.000 0.00 0.00 0.00 2.92
774 776 3.516300 TCTGTTTGGTATTAGGCTCGGAA 59.484 43.478 0.00 0.00 0.00 4.30
803 805 0.911769 CACTGCATCAAGGGGGTAGA 59.088 55.000 0.00 0.00 0.00 2.59
849 851 1.491668 TGGCTTCGGGCTTACTGATA 58.508 50.000 1.83 0.00 41.46 2.15
939 944 0.611896 CCGGGTGCATCCTCCTTTTT 60.612 55.000 15.59 0.00 36.25 1.94
940 945 1.340600 CCGGGTGCATCCTCCTTTTTA 60.341 52.381 15.59 0.00 36.25 1.52
986 991 1.343069 GTTATCGGGCTGGATCTCCT 58.657 55.000 0.00 0.00 36.82 3.69
1023 1028 2.155279 GCAAAGAGGTCCAGGAAGAAC 58.845 52.381 0.00 0.00 0.00 3.01
1242 1247 1.664321 ATAACGAGCTCCGCTTCCGT 61.664 55.000 8.47 0.00 39.98 4.69
1629 1645 3.755628 GGCGACCTCACCAGCGTA 61.756 66.667 0.00 0.00 0.00 4.42
1724 1740 2.190578 GGTGGATGCGGAAGGGAG 59.809 66.667 0.00 0.00 0.00 4.30
1917 1942 2.644555 ATACCGCCAGCATGTCGGAC 62.645 60.000 19.24 0.00 45.53 4.79
2004 2036 5.404466 TCCAAATCAATGGGTTGAATGAC 57.596 39.130 8.15 0.00 46.67 3.06
2036 2068 2.083167 TACGATGTGGAAAACCGGAC 57.917 50.000 9.46 0.00 0.00 4.79
2157 2213 0.035630 AAGCAGCTCCATGGTCACTC 60.036 55.000 12.58 0.00 0.00 3.51
2158 2214 0.908656 AGCAGCTCCATGGTCACTCT 60.909 55.000 12.58 2.28 0.00 3.24
2159 2215 0.461693 GCAGCTCCATGGTCACTCTC 60.462 60.000 12.58 0.00 0.00 3.20
2160 2216 0.900421 CAGCTCCATGGTCACTCTCA 59.100 55.000 12.58 0.00 0.00 3.27
2161 2217 0.901124 AGCTCCATGGTCACTCTCAC 59.099 55.000 12.58 0.00 0.00 3.51
2162 2218 0.901124 GCTCCATGGTCACTCTCACT 59.099 55.000 12.58 0.00 0.00 3.41
2347 2410 9.069078 CAATTCATTTGCTTTCATGTACTAGTG 57.931 33.333 5.39 0.00 0.00 2.74
2348 2411 7.744087 TTCATTTGCTTTCATGTACTAGTGT 57.256 32.000 5.39 0.00 0.00 3.55
2349 2412 7.132694 TCATTTGCTTTCATGTACTAGTGTG 57.867 36.000 5.39 2.07 0.00 3.82
2350 2413 5.940192 TTTGCTTTCATGTACTAGTGTGG 57.060 39.130 5.39 0.00 0.00 4.17
2351 2414 4.882842 TGCTTTCATGTACTAGTGTGGA 57.117 40.909 5.39 0.00 0.00 4.02
2352 2415 4.566004 TGCTTTCATGTACTAGTGTGGAC 58.434 43.478 5.39 0.00 0.00 4.02
2417 2480 7.537306 CAGATCCGTGTTTTTGGTAATAAGTTG 59.463 37.037 0.00 0.00 0.00 3.16
2452 2515 7.233348 TGGGATTATATTTCATTTCTCTTGGCC 59.767 37.037 0.00 0.00 0.00 5.36
2453 2516 7.233348 GGGATTATATTTCATTTCTCTTGGCCA 59.767 37.037 0.00 0.00 0.00 5.36
2454 2517 8.810041 GGATTATATTTCATTTCTCTTGGCCAT 58.190 33.333 6.09 0.00 0.00 4.40
2455 2518 9.635520 GATTATATTTCATTTCTCTTGGCCATG 57.364 33.333 6.09 9.88 0.00 3.66
2456 2519 3.598019 TTTCATTTCTCTTGGCCATGC 57.402 42.857 6.09 0.00 0.00 4.06
2457 2520 1.097232 TCATTTCTCTTGGCCATGCG 58.903 50.000 6.09 3.77 0.00 4.73
2458 2521 1.097232 CATTTCTCTTGGCCATGCGA 58.903 50.000 6.09 6.77 0.00 5.10
2459 2522 1.679680 CATTTCTCTTGGCCATGCGAT 59.320 47.619 6.09 0.00 0.00 4.58
2460 2523 1.097232 TTTCTCTTGGCCATGCGATG 58.903 50.000 6.09 0.44 0.00 3.84
2461 2524 1.378882 TTCTCTTGGCCATGCGATGC 61.379 55.000 6.09 0.00 0.00 3.91
2478 2541 2.697761 GCGTCTGGAGCCTACACGA 61.698 63.158 8.85 0.00 32.08 4.35
2501 2564 3.655814 CGAAATTCACGTACAACCGTTTG 59.344 43.478 0.00 0.00 39.45 2.93
2583 2646 7.650834 TTAAAGTGCAAAATCTACATTTGGC 57.349 32.000 0.00 0.00 45.92 4.52
2601 2664 1.589716 GCTGGCTGTGCAGTAAAGGG 61.590 60.000 0.00 0.00 0.00 3.95
2699 2762 5.981315 GGAAGATACCGTCGATCACATTTTA 59.019 40.000 0.00 0.00 0.00 1.52
2705 2769 5.556470 ACCGTCGATCACATTTTATTTTCG 58.444 37.500 0.00 0.00 0.00 3.46
2727 2791 1.024579 CCGTTGCTCCTTTGGCGTAT 61.025 55.000 0.00 0.00 0.00 3.06
2755 2819 2.846206 TCCTGCCATGAAGGTTAGACAT 59.154 45.455 12.56 0.00 40.61 3.06
2846 2910 5.083821 TCCTTTTTCCTCGGGATTTTCATT 58.916 37.500 0.00 0.00 0.00 2.57
2875 2939 0.179119 ACACGTGCGGTAGATTAGGC 60.179 55.000 17.22 0.00 0.00 3.93
2930 2994 6.090628 CACCAATTTGTCAACATTAATTCCCG 59.909 38.462 0.00 0.00 0.00 5.14
2955 3019 3.037549 TCCAAAGCTTTTGGTGTTGGAT 58.962 40.909 9.53 0.00 39.60 3.41
2990 3054 5.048013 GGAACCCTCCAAAACATCTAACTTG 60.048 44.000 0.00 0.00 41.96 3.16
3006 3070 4.470334 AACTTGTTGCAACATGGAGTTT 57.530 36.364 35.06 23.36 38.74 2.66
3036 3100 3.082548 TGCTCTCGTACTGCTAGTTCTT 58.917 45.455 0.00 0.00 0.00 2.52
3038 3102 3.127203 GCTCTCGTACTGCTAGTTCTTGA 59.873 47.826 0.00 0.00 0.00 3.02
3136 3200 2.669569 CCACTGAACACCGGCCAG 60.670 66.667 0.00 6.79 0.00 4.85
3152 3216 3.217626 GGCCAGAAAATGTCCATAGGAG 58.782 50.000 0.00 0.00 29.39 3.69
3174 3238 0.250793 CCACGTTGGCTGGTGGTATA 59.749 55.000 12.14 0.00 46.79 1.47
3175 3239 1.134220 CCACGTTGGCTGGTGGTATAT 60.134 52.381 12.14 0.00 46.79 0.86
3176 3240 2.103432 CCACGTTGGCTGGTGGTATATA 59.897 50.000 12.14 0.00 46.79 0.86
3177 3241 3.244422 CCACGTTGGCTGGTGGTATATAT 60.244 47.826 12.14 0.00 46.79 0.86
3194 3258 2.880963 TATGTTCCACATCATCGCGA 57.119 45.000 13.09 13.09 39.88 5.87
3200 3264 2.147150 TCCACATCATCGCGACAAAAA 58.853 42.857 12.93 0.00 0.00 1.94
3214 3278 5.084722 GCGACAAAAATCAAGATGACTGAG 58.915 41.667 0.00 0.00 0.00 3.35
3276 3340 4.753186 TCTCTTTCTTTCTCCCTAGGTGT 58.247 43.478 8.29 0.00 0.00 4.16
3297 3361 5.637810 GTGTCATCCAATCTTTTCGTGAGTA 59.362 40.000 0.00 0.00 0.00 2.59
3311 3375 2.424557 GTGAGTACCGTGTCAGAGAGA 58.575 52.381 0.00 0.00 0.00 3.10
3431 3497 1.778334 TTCAGATCACACACGGTTCG 58.222 50.000 0.00 0.00 0.00 3.95
3432 3498 0.666274 TCAGATCACACACGGTTCGC 60.666 55.000 0.00 0.00 0.00 4.70
3434 3500 0.033504 AGATCACACACGGTTCGCTT 59.966 50.000 0.00 0.00 0.00 4.68
3436 3502 1.263217 GATCACACACGGTTCGCTTTT 59.737 47.619 0.00 0.00 0.00 2.27
3437 3503 1.088306 TCACACACGGTTCGCTTTTT 58.912 45.000 0.00 0.00 0.00 1.94
3438 3504 1.062880 TCACACACGGTTCGCTTTTTC 59.937 47.619 0.00 0.00 0.00 2.29
3439 3505 1.063469 CACACACGGTTCGCTTTTTCT 59.937 47.619 0.00 0.00 0.00 2.52
3440 3506 1.741145 ACACACGGTTCGCTTTTTCTT 59.259 42.857 0.00 0.00 0.00 2.52
3441 3507 2.162809 ACACACGGTTCGCTTTTTCTTT 59.837 40.909 0.00 0.00 0.00 2.52
3442 3508 2.781646 CACACGGTTCGCTTTTTCTTTC 59.218 45.455 0.00 0.00 0.00 2.62
3443 3509 2.681344 ACACGGTTCGCTTTTTCTTTCT 59.319 40.909 0.00 0.00 0.00 2.52
3444 3510 3.242641 ACACGGTTCGCTTTTTCTTTCTC 60.243 43.478 0.00 0.00 0.00 2.87
3445 3511 2.289820 ACGGTTCGCTTTTTCTTTCTCC 59.710 45.455 0.00 0.00 0.00 3.71
3446 3512 2.350484 CGGTTCGCTTTTTCTTTCTCCC 60.350 50.000 0.00 0.00 0.00 4.30
3447 3513 2.885266 GGTTCGCTTTTTCTTTCTCCCT 59.115 45.455 0.00 0.00 0.00 4.20
3448 3514 4.070009 GGTTCGCTTTTTCTTTCTCCCTA 58.930 43.478 0.00 0.00 0.00 3.53
3449 3515 4.154375 GGTTCGCTTTTTCTTTCTCCCTAG 59.846 45.833 0.00 0.00 0.00 3.02
3450 3516 3.939066 TCGCTTTTTCTTTCTCCCTAGG 58.061 45.455 0.06 0.06 0.00 3.02
3451 3517 3.326880 TCGCTTTTTCTTTCTCCCTAGGT 59.673 43.478 8.29 0.00 0.00 3.08
3452 3518 3.437049 CGCTTTTTCTTTCTCCCTAGGTG 59.563 47.826 8.29 0.00 0.00 4.00
3453 3519 3.191581 GCTTTTTCTTTCTCCCTAGGTGC 59.808 47.826 8.29 0.00 0.00 5.01
3454 3520 3.434940 TTTTCTTTCTCCCTAGGTGCC 57.565 47.619 8.29 0.00 0.00 5.01
3455 3521 2.038863 TTCTTTCTCCCTAGGTGCCA 57.961 50.000 8.29 0.00 0.00 4.92
3456 3522 2.270434 TCTTTCTCCCTAGGTGCCAT 57.730 50.000 8.29 0.00 0.00 4.40
3457 3523 3.414759 TCTTTCTCCCTAGGTGCCATA 57.585 47.619 8.29 0.00 0.00 2.74
3458 3524 3.941629 TCTTTCTCCCTAGGTGCCATAT 58.058 45.455 8.29 0.00 0.00 1.78
3494 3564 0.463295 CATGGAGAAGAGCCACGCAT 60.463 55.000 0.00 0.00 38.44 4.73
3525 3595 2.558313 GAGCTGCTTTGTGCGTCC 59.442 61.111 2.53 0.00 46.63 4.79
3526 3596 2.203195 AGCTGCTTTGTGCGTCCA 60.203 55.556 0.00 0.00 46.63 4.02
3527 3597 2.050985 GCTGCTTTGTGCGTCCAC 60.051 61.111 0.00 0.00 46.63 4.02
3535 3605 3.972227 GTGCGTCCACAATCTGCT 58.028 55.556 0.00 0.00 41.67 4.24
3536 3606 1.790387 GTGCGTCCACAATCTGCTC 59.210 57.895 0.00 0.00 41.67 4.26
3537 3607 0.950555 GTGCGTCCACAATCTGCTCA 60.951 55.000 0.00 0.00 41.67 4.26
3538 3608 0.250252 TGCGTCCACAATCTGCTCAA 60.250 50.000 0.00 0.00 0.00 3.02
3539 3609 0.874390 GCGTCCACAATCTGCTCAAA 59.126 50.000 0.00 0.00 0.00 2.69
3540 3610 1.266718 GCGTCCACAATCTGCTCAAAA 59.733 47.619 0.00 0.00 0.00 2.44
3541 3611 2.666619 GCGTCCACAATCTGCTCAAAAG 60.667 50.000 0.00 0.00 0.00 2.27
3542 3612 2.807967 CGTCCACAATCTGCTCAAAAGA 59.192 45.455 0.00 0.00 0.00 2.52
3543 3613 3.250762 CGTCCACAATCTGCTCAAAAGAA 59.749 43.478 0.00 0.00 0.00 2.52
3544 3614 4.540824 GTCCACAATCTGCTCAAAAGAAC 58.459 43.478 0.00 0.00 0.00 3.01
3545 3615 4.276926 GTCCACAATCTGCTCAAAAGAACT 59.723 41.667 0.00 0.00 0.00 3.01
3546 3616 4.276678 TCCACAATCTGCTCAAAAGAACTG 59.723 41.667 0.00 0.00 0.00 3.16
3547 3617 4.543692 CACAATCTGCTCAAAAGAACTGG 58.456 43.478 0.00 0.00 0.00 4.00
3548 3618 3.571401 ACAATCTGCTCAAAAGAACTGGG 59.429 43.478 0.00 0.00 0.00 4.45
3559 3629 2.403252 AGAACTGGGCTTTGGTATCG 57.597 50.000 0.00 0.00 0.00 2.92
3576 3651 1.019673 TCGTGGCAGGATCGTAGTAC 58.980 55.000 5.66 0.00 0.00 2.73
3577 3652 0.736636 CGTGGCAGGATCGTAGTACA 59.263 55.000 0.00 0.00 0.00 2.90
3578 3653 1.268589 CGTGGCAGGATCGTAGTACAG 60.269 57.143 0.00 0.00 0.00 2.74
3579 3654 1.749634 GTGGCAGGATCGTAGTACAGT 59.250 52.381 0.38 0.00 0.00 3.55
3580 3655 2.947652 GTGGCAGGATCGTAGTACAGTA 59.052 50.000 0.38 0.00 0.00 2.74
3602 3677 4.890158 TGCTGACCTTTACAGAGAATCA 57.110 40.909 0.00 0.00 37.82 2.57
3647 3730 2.814280 TCTCTCACGTGAAGTTTCCC 57.186 50.000 20.49 0.00 0.00 3.97
3683 3766 1.071605 CCGAGCTGAAAGTGTAGCAC 58.928 55.000 0.00 0.00 42.29 4.40
3702 3785 1.694696 ACAGGTCAAAGGGAGAGACAC 59.305 52.381 0.00 0.00 34.04 3.67
3732 3815 4.895297 CCCTGGCAACCACTGATAAAATAT 59.105 41.667 0.00 0.00 0.00 1.28
3782 3933 2.268298 CTGGGTAGTAACATGCACGAC 58.732 52.381 0.00 0.00 0.00 4.34
3812 3963 1.131618 GCAAATTAAAGCGCCGGTCG 61.132 55.000 2.29 12.98 42.12 4.79
4158 4321 6.940298 CCAAGTAGATAACCAAGTCCAGAAAA 59.060 38.462 0.00 0.00 0.00 2.29
4172 4335 6.365520 AGTCCAGAAAAGTAGTGTTGGAATT 58.634 36.000 0.00 0.00 36.56 2.17
4283 4446 1.154197 CAGATATGCTGGCCGTCATG 58.846 55.000 16.99 1.42 41.07 3.07
4317 4480 1.793134 GCAGCATGGCCATGTAGAGC 61.793 60.000 39.08 31.80 40.80 4.09
4396 4571 2.308570 TGGAACATGACATGGCTAAGGT 59.691 45.455 19.39 0.00 33.60 3.50
4796 4973 1.949525 TGCTTCTTTTGGCAGTCTGAC 59.050 47.619 3.32 0.00 34.22 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.733593 GACGTGGCCAGTGACGAC 60.734 66.667 19.17 9.99 38.94 4.34
8 9 4.129737 CGATCCGACGTGGCCAGT 62.130 66.667 5.11 6.62 37.80 4.00
184 185 1.952133 CGAACACGCCGACCAAAGA 60.952 57.895 0.00 0.00 0.00 2.52
379 381 2.632996 ACAACATCTCTCCCTCGAACAA 59.367 45.455 0.00 0.00 0.00 2.83
386 388 1.842562 CCATCCACAACATCTCTCCCT 59.157 52.381 0.00 0.00 0.00 4.20
420 422 2.267006 CATCGCCACTGCTGGAGT 59.733 61.111 0.00 0.00 40.55 3.85
462 464 0.804364 TGACGCGGTAGATACAACGT 59.196 50.000 12.47 8.65 40.38 3.99
592 594 1.529010 CACAGACCTTGCCAAGCCA 60.529 57.895 0.00 0.00 0.00 4.75
715 717 0.767375 ACATCTAATGCCGGATGCCT 59.233 50.000 5.05 0.00 41.93 4.75
803 805 1.276421 AGGCAACATCTGTCGCTACTT 59.724 47.619 0.00 0.00 41.41 2.24
837 839 9.694137 CTTACAAAGTAGTATATCAGTAAGCCC 57.306 37.037 0.00 0.00 33.35 5.19
849 851 7.937394 AGCACAAAAGACCTTACAAAGTAGTAT 59.063 33.333 0.00 0.00 0.00 2.12
1242 1247 3.072468 CCTCGGCCCGACAGGTTA 61.072 66.667 0.00 0.00 38.26 2.85
1278 1283 4.033776 CGCAGGAAAGGGAGGCCA 62.034 66.667 5.01 0.00 0.00 5.36
1629 1645 3.703556 AGACTGAACCATCATGATCGACT 59.296 43.478 4.86 0.00 34.37 4.18
1917 1942 3.181447 ACACCTCATCATGGCCTATCAAG 60.181 47.826 3.32 0.00 0.00 3.02
2004 2036 2.349580 CACATCGTATGACACAAGCCTG 59.650 50.000 2.48 0.00 0.00 4.85
2036 2068 4.536364 AAACAGAAGACAACACGACATG 57.464 40.909 0.00 0.00 0.00 3.21
2347 2410 0.249911 GACCACAGTCCACAGTCCAC 60.250 60.000 0.00 0.00 37.00 4.02
2348 2411 0.689412 TGACCACAGTCCACAGTCCA 60.689 55.000 0.00 0.00 42.81 4.02
2349 2412 0.249911 GTGACCACAGTCCACAGTCC 60.250 60.000 0.00 0.00 42.81 3.85
2350 2413 0.753262 AGTGACCACAGTCCACAGTC 59.247 55.000 2.78 0.00 42.81 3.51
2351 2414 1.134401 CAAGTGACCACAGTCCACAGT 60.134 52.381 2.78 0.00 42.81 3.55
2352 2415 1.134401 ACAAGTGACCACAGTCCACAG 60.134 52.381 2.78 0.00 42.81 3.66
2452 2515 2.879070 GCTCCAGACGCATCGCATG 61.879 63.158 0.00 0.00 0.00 4.06
2453 2516 2.587194 GCTCCAGACGCATCGCAT 60.587 61.111 0.00 0.00 0.00 4.73
2454 2517 4.819761 GGCTCCAGACGCATCGCA 62.820 66.667 0.00 0.00 0.00 5.10
2455 2518 3.138930 TAGGCTCCAGACGCATCGC 62.139 63.158 0.00 0.00 0.00 4.58
2456 2519 1.299468 GTAGGCTCCAGACGCATCG 60.299 63.158 0.00 0.00 0.00 3.84
2457 2520 0.528684 GTGTAGGCTCCAGACGCATC 60.529 60.000 0.00 0.00 0.00 3.91
2458 2521 1.517832 GTGTAGGCTCCAGACGCAT 59.482 57.895 0.00 0.00 0.00 4.73
2459 2522 2.970639 GTGTAGGCTCCAGACGCA 59.029 61.111 0.00 0.00 0.00 5.24
2460 2523 2.202623 CGTGTAGGCTCCAGACGC 60.203 66.667 0.00 0.00 0.00 5.19
2461 2524 1.136984 GTCGTGTAGGCTCCAGACG 59.863 63.158 0.88 0.88 0.00 4.18
2478 2541 2.472816 ACGGTTGTACGTGAATTTCGT 58.527 42.857 0.00 12.65 46.64 3.85
2501 2564 4.899239 CGGATCAGGCCCGTGCTC 62.899 72.222 0.00 0.00 41.91 4.26
2583 2646 0.250901 ACCCTTTACTGCACAGCCAG 60.251 55.000 0.00 0.00 38.78 4.85
2601 2664 1.883084 GGCGATCGGATGTCCACAC 60.883 63.158 18.30 0.00 35.14 3.82
2634 2697 1.537202 GCTTGCAGTTTGGTCCTGTAG 59.463 52.381 0.00 0.00 32.41 2.74
2639 2702 1.527433 GGGAGCTTGCAGTTTGGTCC 61.527 60.000 15.94 15.94 44.78 4.46
2699 2762 1.892209 AGGAGCAACGGTTCGAAAAT 58.108 45.000 0.00 0.00 0.00 1.82
2705 2769 1.285950 GCCAAAGGAGCAACGGTTC 59.714 57.895 0.00 0.00 0.00 3.62
2727 2791 0.103026 CTTCATGGCAGGATCGACGA 59.897 55.000 1.35 0.00 0.00 4.20
2846 2910 2.465299 CGCACGTGTGGTTGTGGAA 61.465 57.895 21.32 0.00 36.61 3.53
2875 2939 0.601046 TTGACTTGCTCGCAGGACTG 60.601 55.000 8.06 0.00 0.00 3.51
2930 2994 3.801114 ACACCAAAAGCTTTGGAAGTC 57.199 42.857 25.14 0.00 42.06 3.01
2976 3040 6.479660 CCATGTTGCAACAAGTTAGATGTTTT 59.520 34.615 34.06 11.74 43.03 2.43
2990 3054 3.988379 TGAGAAACTCCATGTTGCAAC 57.012 42.857 22.83 22.83 39.13 4.17
3006 3070 3.428180 GCAGTACGAGAGCAATCTTGAGA 60.428 47.826 0.00 0.00 0.00 3.27
3036 3100 2.297701 GCTGTTGAACTGGGTTCTTCA 58.702 47.619 10.98 8.93 42.39 3.02
3038 3102 1.308998 CGCTGTTGAACTGGGTTCTT 58.691 50.000 10.38 0.00 42.39 2.52
3136 3200 4.332819 CGTGGAACTCCTATGGACATTTTC 59.667 45.833 0.00 0.00 36.82 2.29
3152 3216 3.030652 CACCAGCCAACGTGGAAC 58.969 61.111 8.04 0.00 40.96 3.62
3194 3258 6.994496 TCAGACTCAGTCATCTTGATTTTTGT 59.006 34.615 7.77 0.00 34.60 2.83
3200 3264 5.735285 TGTTCAGACTCAGTCATCTTGAT 57.265 39.130 7.77 0.00 34.60 2.57
3276 3340 5.175859 GGTACTCACGAAAAGATTGGATGA 58.824 41.667 0.00 0.00 0.00 2.92
3297 3361 1.202952 ACCTCTTCTCTCTGACACGGT 60.203 52.381 0.00 0.00 0.00 4.83
3311 3375 5.625150 ACAACTTTCTCTATGCAACCTCTT 58.375 37.500 0.00 0.00 0.00 2.85
3431 3497 3.191581 GCACCTAGGGAGAAAGAAAAAGC 59.808 47.826 14.81 0.00 0.00 3.51
3432 3498 3.759086 GGCACCTAGGGAGAAAGAAAAAG 59.241 47.826 14.81 0.00 0.00 2.27
3434 3500 2.714250 TGGCACCTAGGGAGAAAGAAAA 59.286 45.455 14.81 0.00 0.00 2.29
3436 3502 2.038863 TGGCACCTAGGGAGAAAGAA 57.961 50.000 14.81 0.00 0.00 2.52
3437 3503 2.270434 ATGGCACCTAGGGAGAAAGA 57.730 50.000 14.81 0.00 0.00 2.52
3438 3504 3.244700 CCATATGGCACCTAGGGAGAAAG 60.245 52.174 14.81 0.00 0.00 2.62
3439 3505 2.711009 CCATATGGCACCTAGGGAGAAA 59.289 50.000 14.81 0.00 0.00 2.52
3440 3506 2.338809 CCATATGGCACCTAGGGAGAA 58.661 52.381 14.81 0.00 0.00 2.87
3441 3507 2.030027 CCATATGGCACCTAGGGAGA 57.970 55.000 14.81 0.00 0.00 3.71
3453 3519 1.142465 AGAGCTTCACCTGCCATATGG 59.858 52.381 18.07 18.07 38.53 2.74
3454 3520 2.492012 GAGAGCTTCACCTGCCATATG 58.508 52.381 0.00 0.00 0.00 1.78
3455 3521 1.419387 GGAGAGCTTCACCTGCCATAT 59.581 52.381 0.00 0.00 0.00 1.78
3456 3522 0.833287 GGAGAGCTTCACCTGCCATA 59.167 55.000 0.00 0.00 0.00 2.74
3457 3523 1.203441 TGGAGAGCTTCACCTGCCAT 61.203 55.000 0.00 0.00 0.00 4.40
3458 3524 1.203441 ATGGAGAGCTTCACCTGCCA 61.203 55.000 0.00 0.00 0.00 4.92
3482 3548 3.060020 GCATGCATGCGTGGCTCTT 62.060 57.895 34.64 1.72 44.67 2.85
3494 3564 1.303806 AGCTCCACACATGCATGCA 60.304 52.632 26.53 25.04 0.00 3.96
3525 3595 4.543692 CCAGTTCTTTTGAGCAGATTGTG 58.456 43.478 0.00 0.00 31.68 3.33
3526 3596 3.571401 CCCAGTTCTTTTGAGCAGATTGT 59.429 43.478 0.00 0.00 31.68 2.71
3527 3597 3.613432 GCCCAGTTCTTTTGAGCAGATTG 60.613 47.826 0.00 0.00 31.68 2.67
3528 3598 2.560105 GCCCAGTTCTTTTGAGCAGATT 59.440 45.455 0.00 0.00 31.68 2.40
3529 3599 2.165998 GCCCAGTTCTTTTGAGCAGAT 58.834 47.619 0.00 0.00 31.68 2.90
3530 3600 1.143684 AGCCCAGTTCTTTTGAGCAGA 59.856 47.619 0.00 0.00 31.68 4.26
3531 3601 1.613836 AGCCCAGTTCTTTTGAGCAG 58.386 50.000 0.00 0.00 31.68 4.24
3532 3602 2.071778 AAGCCCAGTTCTTTTGAGCA 57.928 45.000 0.00 0.00 31.68 4.26
3533 3603 2.546584 CCAAAGCCCAGTTCTTTTGAGC 60.547 50.000 0.00 0.00 31.94 4.26
3534 3604 2.695147 ACCAAAGCCCAGTTCTTTTGAG 59.305 45.455 0.00 0.00 31.94 3.02
3535 3605 2.745968 ACCAAAGCCCAGTTCTTTTGA 58.254 42.857 0.00 0.00 31.94 2.69
3536 3606 4.615912 CGATACCAAAGCCCAGTTCTTTTG 60.616 45.833 0.00 0.00 31.94 2.44
3537 3607 3.506067 CGATACCAAAGCCCAGTTCTTTT 59.494 43.478 0.00 0.00 31.94 2.27
3538 3608 3.081804 CGATACCAAAGCCCAGTTCTTT 58.918 45.455 0.00 0.00 34.37 2.52
3539 3609 2.039879 ACGATACCAAAGCCCAGTTCTT 59.960 45.455 0.00 0.00 0.00 2.52
3540 3610 1.628846 ACGATACCAAAGCCCAGTTCT 59.371 47.619 0.00 0.00 0.00 3.01
3541 3611 1.737793 CACGATACCAAAGCCCAGTTC 59.262 52.381 0.00 0.00 0.00 3.01
3542 3612 1.613255 CCACGATACCAAAGCCCAGTT 60.613 52.381 0.00 0.00 0.00 3.16
3543 3613 0.035439 CCACGATACCAAAGCCCAGT 60.035 55.000 0.00 0.00 0.00 4.00
3544 3614 1.376609 GCCACGATACCAAAGCCCAG 61.377 60.000 0.00 0.00 0.00 4.45
3545 3615 1.377987 GCCACGATACCAAAGCCCA 60.378 57.895 0.00 0.00 0.00 5.36
3546 3616 1.376609 CTGCCACGATACCAAAGCCC 61.377 60.000 0.00 0.00 0.00 5.19
3547 3617 1.376609 CCTGCCACGATACCAAAGCC 61.377 60.000 0.00 0.00 0.00 4.35
3548 3618 0.392461 TCCTGCCACGATACCAAAGC 60.392 55.000 0.00 0.00 0.00 3.51
3559 3629 1.749634 ACTGTACTACGATCCTGCCAC 59.250 52.381 0.00 0.00 0.00 5.01
3576 3651 5.330455 TCTCTGTAAAGGTCAGCATACTG 57.670 43.478 0.00 0.00 45.95 2.74
3577 3652 6.155221 TGATTCTCTGTAAAGGTCAGCATACT 59.845 38.462 0.00 0.00 33.48 2.12
3578 3653 6.341316 TGATTCTCTGTAAAGGTCAGCATAC 58.659 40.000 0.00 0.00 33.48 2.39
3579 3654 6.381133 TCTGATTCTCTGTAAAGGTCAGCATA 59.619 38.462 0.00 0.00 33.35 3.14
3580 3655 5.188555 TCTGATTCTCTGTAAAGGTCAGCAT 59.811 40.000 0.00 0.00 33.35 3.79
3602 3677 3.181454 CCACCACCGCCTTATTATTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
3683 3766 1.694150 TGTGTCTCTCCCTTTGACCTG 59.306 52.381 0.00 0.00 0.00 4.00
3702 3785 0.890683 GTGGTTGCCAGGGAGAAATG 59.109 55.000 0.00 0.00 32.34 2.32
3732 3815 7.147776 GCTAGATTGTCCTACCCTTTACAGTAA 60.148 40.741 0.00 0.00 0.00 2.24
3782 3933 5.497597 GCGCTTTAATTTGCTTTCGAATCTG 60.498 40.000 0.00 0.00 0.00 2.90
3812 3963 4.380980 GCTTTCTATAGCCCCCGC 57.619 61.111 0.00 0.00 35.06 6.13
4038 4201 0.960861 GTTGTACTTCTGGGCCTGGC 60.961 60.000 11.05 11.05 0.00 4.85
4082 4245 1.868997 CATTGCCCGTGTCAGTGAC 59.131 57.895 16.68 16.68 0.00 3.67
4144 4307 4.772886 ACACTACTTTTCTGGACTTGGT 57.227 40.909 0.00 0.00 0.00 3.67
4158 4321 5.699458 CGTTCACCTTAATTCCAACACTACT 59.301 40.000 0.00 0.00 0.00 2.57
4172 4335 5.879669 TGACCGATGTCATCGTTCACCTTA 61.880 45.833 25.94 8.19 46.79 2.69
4317 4480 4.370049 TCGACTAGATGAGGAACTAGACG 58.630 47.826 15.36 15.36 46.80 4.18
4356 4519 9.857656 ATGTTCCATGAATAGAATAGTGTCATT 57.142 29.630 0.00 0.00 0.00 2.57
4462 4637 0.106708 AAAGCAGAACACCTCGCTCA 59.893 50.000 0.00 0.00 34.30 4.26
4796 4973 1.806623 CGGTATTTCCTCTTGGCCTCG 60.807 57.143 3.32 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.