Multiple sequence alignment - TraesCS4B01G106400

Loading Multiple Alignment...

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 TraesCS4B01G106400 chr4B 100.000 4429 0 0 1 4429 115849000 115844572 0.000000e+00 8179.0
1 TraesCS4B01G106400 chr4B 80.125 1444 208 45 2032 3431 115880767 115879359 0.000000e+00 1003.0
2 TraesCS4B01G106400 chr4B 79.625 800 101 36 700 1459 115881982 115881205 6.570000e-143 518.0
3 TraesCS4B01G106400 chr4D 90.767 1982 104 33 629 2564 81974674 81972726 0.000000e+00 2573.0
4 TraesCS4B01G106400 chr4D 92.762 1202 49 9 2563 3738 81972602 81971413 0.000000e+00 1703.0
5 TraesCS4B01G106400 chr4D 80.236 1442 206 44 2032 3431 81986389 81984985 0.000000e+00 1011.0
6 TraesCS4B01G106400 chr4D 91.052 637 45 4 1 636 81980413 81979788 0.000000e+00 850.0
7 TraesCS4B01G106400 chr4D 78.778 622 76 34 875 1459 81987588 81986986 2.520000e-97 366.0
8 TraesCS4B01G106400 chr4D 87.500 224 13 7 3761 3983 81971324 81971115 1.230000e-60 244.0
9 TraesCS4B01G106400 chr4D 81.229 293 28 10 4153 4421 81970834 81970545 1.250000e-50 211.0
10 TraesCS4B01G106400 chr4D 79.670 182 27 9 37 211 93079200 93079378 6.020000e-24 122.0
11 TraesCS4B01G106400 chr4A 90.702 1667 85 32 221 1845 491918390 491916752 0.000000e+00 2156.0
12 TraesCS4B01G106400 chr4A 90.517 1044 74 9 1842 2869 491916724 491915690 0.000000e+00 1356.0
13 TraesCS4B01G106400 chr4A 80.525 1448 201 53 2029 3431 492031610 492030199 0.000000e+00 1037.0
14 TraesCS4B01G106400 chr4A 95.491 377 17 0 3088 3464 491915454 491915078 1.760000e-168 603.0
15 TraesCS4B01G106400 chr4A 82.529 601 58 27 700 1263 492032843 492032253 6.660000e-133 484.0
16 TraesCS4B01G106400 chr4A 87.539 321 21 8 4114 4429 491914392 491914086 1.960000e-93 353.0
17 TraesCS4B01G106400 chr4A 94.470 217 11 1 2922 3137 491915663 491915447 2.550000e-87 333.0
18 TraesCS4B01G106400 chr4A 90.052 191 4 3 3554 3734 491915089 491914904 2.660000e-57 233.0
19 TraesCS4B01G106400 chr4A 86.164 159 13 3 3826 3976 491914765 491914608 3.540000e-36 163.0
20 TraesCS4B01G106400 chr1D 83.467 1742 178 56 1972 3633 452626901 452625190 0.000000e+00 1520.0
21 TraesCS4B01G106400 chr1D 76.557 1156 145 66 517 1615 452628003 452626917 6.570000e-143 518.0
22 TraesCS4B01G106400 chr1A 83.555 1733 172 55 1972 3633 547393308 547391618 0.000000e+00 1517.0
23 TraesCS4B01G106400 chr1A 83.451 1130 125 32 1981 3073 547414008 547412904 0.000000e+00 994.0
24 TraesCS4B01G106400 chr1A 76.578 935 126 51 510 1425 547417856 547416996 1.140000e-115 427.0
25 TraesCS4B01G106400 chr1A 82.700 474 50 19 812 1274 547396007 547395555 4.150000e-105 392.0
26 TraesCS4B01G106400 chr1A 79.688 192 17 9 1432 1605 547395388 547395201 7.780000e-23 119.0
27 TraesCS4B01G106400 chr5B 87.928 1284 115 12 2222 3483 608202829 608204094 0.000000e+00 1476.0
28 TraesCS4B01G106400 chr5B 87.713 822 71 12 1966 2771 608343323 608344130 0.000000e+00 931.0
29 TraesCS4B01G106400 chr5B 88.518 479 44 3 3006 3483 608344126 608344594 1.790000e-158 569.0
30 TraesCS4B01G106400 chr5B 78.492 716 79 38 896 1570 608199695 608200376 2.480000e-107 399.0
31 TraesCS4B01G106400 chr5B 80.340 529 68 20 1091 1615 608088758 608089254 7.000000e-98 368.0
32 TraesCS4B01G106400 chr5B 76.462 650 74 39 967 1570 608340621 608341237 3.370000e-71 279.0
33 TraesCS4B01G106400 chr5B 84.980 253 26 9 1629 1877 608089122 608089366 3.420000e-61 246.0
34 TraesCS4B01G106400 chr5B 88.525 122 8 2 3764 3880 608204237 608204357 4.620000e-30 143.0
35 TraesCS4B01G106400 chr5B 87.179 78 8 2 565 641 608340430 608340506 2.190000e-13 87.9
36 TraesCS4B01G106400 chr5D 87.073 967 93 13 2538 3483 493121956 493122911 0.000000e+00 1064.0
37 TraesCS4B01G106400 chr5D 90.519 559 46 4 1934 2491 493121405 493121957 0.000000e+00 732.0
38 TraesCS4B01G106400 chr5D 79.226 698 76 41 859 1518 493120453 493121119 5.300000e-114 422.0
39 TraesCS4B01G106400 chr5D 83.333 324 37 11 1119 1435 299832762 299833075 2.610000e-72 283.0
40 TraesCS4B01G106400 chr5D 86.473 207 22 6 1698 1902 493121126 493121328 5.770000e-54 222.0
41 TraesCS4B01G106400 chr5D 79.695 197 11 16 434 625 493120236 493120408 1.010000e-21 115.0
42 TraesCS4B01G106400 chr1B 83.482 896 92 31 2775 3633 622707286 622706410 0.000000e+00 784.0
43 TraesCS4B01G106400 chr1B 83.851 805 90 22 1972 2756 622708147 622707363 0.000000e+00 730.0
44 TraesCS4B01G106400 chr1B 78.436 844 104 50 812 1605 622709060 622708245 3.100000e-131 479.0
45 TraesCS4B01G106400 chr5A 88.530 558 58 5 1934 2491 616070053 616070604 0.000000e+00 671.0
46 TraesCS4B01G106400 chr5A 86.974 499 45 8 2538 3016 616070603 616071101 1.080000e-150 544.0
47 TraesCS4B01G106400 chr5A 79.714 700 71 40 859 1518 616069099 616069767 1.460000e-119 440.0
48 TraesCS4B01G106400 chr5A 82.965 317 38 10 1119 1433 397249879 397250181 5.640000e-69 272.0
49 TraesCS4B01G106400 chr5A 86.111 252 22 8 1629 1877 616048183 616048424 4.390000e-65 259.0
50 TraesCS4B01G106400 chr5A 86.473 207 22 6 1698 1902 616069774 616069976 5.770000e-54 222.0
51 TraesCS4B01G106400 chr3B 82.609 184 19 12 25 200 225180141 225179963 2.760000e-32 150.0
52 TraesCS4B01G106400 chr3A 83.234 167 19 8 41 200 64291109 64290945 1.280000e-30 145.0
53 TraesCS4B01G106400 chr2B 83.226 155 22 4 42 193 9718126 9717973 5.970000e-29 139.0
54 TraesCS4B01G106400 chr2B 82.530 166 20 8 42 200 414573071 414572908 2.150000e-28 137.0
55 TraesCS4B01G106400 chr7B 81.657 169 27 4 35 200 339685609 339685442 2.150000e-28 137.0
56 TraesCS4B01G106400 chr6B 82.635 167 17 11 42 200 693321354 693321192 2.150000e-28 137.0
57 TraesCS4B01G106400 chr7A 80.702 171 29 4 32 200 203515046 203515214 3.600000e-26 130.0
58 TraesCS4B01G106400 chr6A 84.874 119 16 2 4303 4420 53941580 53941697 7.780000e-23 119.0


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 TraesCS4B01G106400 chr4B 115844572 115849000 4428 True 8179.000000 8179 100.000000 1 4429 1 chr4B.!!$R1 4428
1 TraesCS4B01G106400 chr4B 115879359 115881982 2623 True 760.500000 1003 79.875000 700 3431 2 chr4B.!!$R2 2731
2 TraesCS4B01G106400 chr4D 81970545 81974674 4129 True 1182.750000 2573 88.064500 629 4421 4 chr4D.!!$R2 3792
3 TraesCS4B01G106400 chr4D 81979788 81980413 625 True 850.000000 850 91.052000 1 636 1 chr4D.!!$R1 635
4 TraesCS4B01G106400 chr4D 81984985 81987588 2603 True 688.500000 1011 79.507000 875 3431 2 chr4D.!!$R3 2556
5 TraesCS4B01G106400 chr4A 492030199 492032843 2644 True 760.500000 1037 81.527000 700 3431 2 chr4A.!!$R2 2731
6 TraesCS4B01G106400 chr4A 491914086 491918390 4304 True 742.428571 2156 90.705000 221 4429 7 chr4A.!!$R1 4208
7 TraesCS4B01G106400 chr1D 452625190 452628003 2813 True 1019.000000 1520 80.012000 517 3633 2 chr1D.!!$R1 3116
8 TraesCS4B01G106400 chr1A 547412904 547417856 4952 True 710.500000 994 80.014500 510 3073 2 chr1A.!!$R2 2563
9 TraesCS4B01G106400 chr1A 547391618 547396007 4389 True 676.000000 1517 81.981000 812 3633 3 chr1A.!!$R1 2821
10 TraesCS4B01G106400 chr5B 608199695 608204357 4662 False 672.666667 1476 84.981667 896 3880 3 chr5B.!!$F2 2984
11 TraesCS4B01G106400 chr5B 608340430 608344594 4164 False 466.725000 931 84.968000 565 3483 4 chr5B.!!$F3 2918
12 TraesCS4B01G106400 chr5B 608088758 608089366 608 False 307.000000 368 82.660000 1091 1877 2 chr5B.!!$F1 786
13 TraesCS4B01G106400 chr5D 493120236 493122911 2675 False 511.000000 1064 84.597200 434 3483 5 chr5D.!!$F2 3049
14 TraesCS4B01G106400 chr1B 622706410 622709060 2650 True 664.333333 784 81.923000 812 3633 3 chr1B.!!$R1 2821
15 TraesCS4B01G106400 chr5A 616069099 616071101 2002 False 469.250000 671 85.422750 859 3016 4 chr5A.!!$F3 2157

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
47 49 0.179062 CTGCTGGTCATGCTACTCCC 60.179 60.0 0.0 0.0 0.00 4.30 F
710 742 1.124780 CCACATATACCACACGGGGA 58.875 55.0 0.0 0.0 42.91 4.81 F
1875 8832 0.036010 CAGTTGCCGACCTCCTCATT 60.036 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1456 2.028385 GTGTCTTTCACCATACCCGTCT 60.028 50.000 0.0 0.0 40.84 4.18 R
2209 9351 0.608035 TTCCCGTTGATGGTGAAGCC 60.608 55.000 0.0 0.0 37.90 4.35 R
3526 11173 1.272212 TGCACATCTCACGACTAGCAA 59.728 47.619 0.0 0.0 0.00 3.91 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
28 29 6.225703 TCGACGAGTAGTATAGCTGATTTC 57.774 41.667 0.00 0.00 0.00 2.17
47 49 0.179062 CTGCTGGTCATGCTACTCCC 60.179 60.000 0.00 0.00 0.00 4.30
62 64 4.041321 GCTACTCCCCCGTTCCTAAATATT 59.959 45.833 0.00 0.00 0.00 1.28
63 65 4.701651 ACTCCCCCGTTCCTAAATATTC 57.298 45.455 0.00 0.00 0.00 1.75
66 68 3.070015 TCCCCCGTTCCTAAATATTCGTC 59.930 47.826 0.00 0.00 0.00 4.20
67 69 3.070590 CCCCCGTTCCTAAATATTCGTCT 59.929 47.826 0.00 0.00 0.00 4.18
86 88 9.831737 ATTCGTCTTTTTGAGATTTGAACATAG 57.168 29.630 0.00 0.00 36.61 2.23
131 133 8.236084 ACACGTATTTTAGAGTGTACATTCAC 57.764 34.615 19.24 7.49 44.79 3.18
150 152 5.681337 TCACTCATTTTGTTTCGTATGCA 57.319 34.783 0.00 0.00 0.00 3.96
157 159 6.581919 TCATTTTGTTTCGTATGCAGTTCATG 59.418 34.615 0.00 0.00 36.63 3.07
200 202 6.774170 ACTTATTTTTAGAAACGGTGGGAGTT 59.226 34.615 0.00 0.00 0.00 3.01
211 213 1.954382 GGTGGGAGTTCTTTGTTGGAC 59.046 52.381 0.00 0.00 0.00 4.02
334 336 4.755123 ACAATAGAACTGAAAACCGACAGG 59.245 41.667 0.00 0.00 45.13 4.00
374 376 7.358600 CGATACAGACTACGTACTGAATCTCTC 60.359 44.444 17.37 6.06 37.54 3.20
375 377 4.877251 ACAGACTACGTACTGAATCTCTCC 59.123 45.833 17.37 0.00 37.54 3.71
392 394 2.698797 TCTCCGAGGAAACACTGAAACT 59.301 45.455 0.00 0.00 0.00 2.66
393 395 2.802816 CTCCGAGGAAACACTGAAACTG 59.197 50.000 0.00 0.00 0.00 3.16
560 576 1.671379 GGGGAGGACGCTGTTGTTC 60.671 63.158 0.00 0.00 0.00 3.18
710 742 1.124780 CCACATATACCACACGGGGA 58.875 55.000 0.00 0.00 42.91 4.81
805 849 2.543653 CCGCCTTGTCCAAGAAAAACAG 60.544 50.000 8.59 0.00 40.79 3.16
927 983 5.255397 TCCTCACCAAAATCTACAACCAT 57.745 39.130 0.00 0.00 0.00 3.55
1295 1456 3.179048 CACAATTGCATCTCGTAGTCGA 58.821 45.455 5.05 0.00 44.12 4.20
1335 1519 4.635223 ACACGTGGATCAATGGATAGATG 58.365 43.478 21.57 0.00 32.67 2.90
1517 4807 8.023021 TCATATTGGCTTCTAGTTACAGTCAT 57.977 34.615 0.00 0.00 0.00 3.06
1519 4809 9.197694 CATATTGGCTTCTAGTTACAGTCATAC 57.802 37.037 0.00 0.00 0.00 2.39
1521 4811 7.949690 TTGGCTTCTAGTTACAGTCATACTA 57.050 36.000 0.00 0.00 0.00 1.82
1522 4812 7.330900 TGGCTTCTAGTTACAGTCATACTAC 57.669 40.000 0.00 0.00 0.00 2.73
1523 4813 7.117397 TGGCTTCTAGTTACAGTCATACTACT 58.883 38.462 0.00 0.00 0.00 2.57
1524 4814 8.270030 TGGCTTCTAGTTACAGTCATACTACTA 58.730 37.037 0.00 0.00 0.00 1.82
1533 4823 9.953697 GTTACAGTCATACTACTAAATCCTGAG 57.046 37.037 0.00 0.00 0.00 3.35
1555 4845 4.648762 AGCTGTCAGTGCTACTAGATTGAT 59.351 41.667 0.00 0.00 39.21 2.57
1636 4926 5.576774 TCACGACACAACACTGATCATTATC 59.423 40.000 0.00 0.00 0.00 1.75
1680 4970 7.921041 TTATAGTCATCCTGATTCCTGAACT 57.079 36.000 0.00 0.00 0.00 3.01
1684 4974 5.250313 AGTCATCCTGATTCCTGAACTCTTT 59.750 40.000 0.00 0.00 0.00 2.52
1720 5021 9.610705 GGTATTAGATCGATACCTACATACAGA 57.389 37.037 23.38 0.00 43.64 3.41
1840 8766 8.415950 ACAATCATATGGTTTTGGACTGTTAA 57.584 30.769 0.00 0.00 0.00 2.01
1859 8816 7.285401 ACTGTTAATTTTCCATGTTCTGTCAGT 59.715 33.333 0.00 0.00 0.00 3.41
1875 8832 0.036010 CAGTTGCCGACCTCCTCATT 60.036 55.000 0.00 0.00 0.00 2.57
1876 8833 1.207089 CAGTTGCCGACCTCCTCATTA 59.793 52.381 0.00 0.00 0.00 1.90
1884 8867 7.727578 TGCCGACCTCCTCATTAATTATATA 57.272 36.000 0.00 0.00 0.00 0.86
2097 9239 1.436336 CGACCATGTACTCCCGGTC 59.564 63.158 0.00 11.31 43.73 4.79
2209 9351 2.388890 GATCGGGGATGGGCAGTCAG 62.389 65.000 0.00 0.00 0.00 3.51
2466 9762 0.693049 CAGGACTTGGTGCTACCCTT 59.307 55.000 3.33 0.00 37.50 3.95
2584 10009 2.164219 ACGACATATTTTTGCAGGCTGG 59.836 45.455 17.64 0.00 0.00 4.85
2615 10066 4.988540 TGTGTGACTAATTACTGTGTGCTC 59.011 41.667 0.00 0.00 0.00 4.26
2712 10165 5.179742 TGCAAAATACGAACAAGGTACGATT 59.820 36.000 0.00 0.00 0.00 3.34
2758 10225 7.601705 ATCTTGGTAAATATTGTTGGATGGG 57.398 36.000 0.00 0.00 0.00 4.00
2779 10304 4.161565 GGGACACTGAACATCCTGTACATA 59.838 45.833 0.00 0.00 32.70 2.29
2851 10378 0.820891 CACCAAGCCAGTGCAAGAGT 60.821 55.000 0.00 0.00 41.13 3.24
2855 10382 1.952296 CAAGCCAGTGCAAGAGTTCTT 59.048 47.619 0.00 0.00 41.13 2.52
2976 10516 2.537560 CGAGATGACCAATGGCGGC 61.538 63.158 0.00 0.00 0.00 6.53
3416 11042 1.523032 CCTGCGCTGCATCATGAGA 60.523 57.895 9.73 0.00 38.13 3.27
3431 11057 6.453943 CATCATGAGAATGGACGAGTAGATT 58.546 40.000 0.09 0.00 0.00 2.40
3442 11068 5.128827 TGGACGAGTAGATTGCCTCTTATTT 59.871 40.000 0.00 0.00 35.28 1.40
3495 11142 3.378339 CTTGAGAAGCACAAGCCAAAAG 58.622 45.455 0.00 0.00 43.56 2.27
3526 11173 2.099592 TCCCTCGCGTAATAATCGTGTT 59.900 45.455 5.77 0.00 39.38 3.32
3704 11380 5.351465 TGGCGTCAAATCAGTTCTTCTATTC 59.649 40.000 0.00 0.00 0.00 1.75
3739 11417 7.043565 TCTTGAATGCAGAAAGCTTTTCTTTT 58.956 30.769 14.05 4.29 44.58 2.27
3740 11418 7.550196 TCTTGAATGCAGAAAGCTTTTCTTTTT 59.450 29.630 14.05 5.34 44.58 1.94
3741 11419 7.007313 TGAATGCAGAAAGCTTTTCTTTTTG 57.993 32.000 14.05 6.75 44.58 2.44
3743 11421 6.990341 ATGCAGAAAGCTTTTCTTTTTGTT 57.010 29.167 14.05 0.00 44.34 2.83
3744 11422 8.491331 AATGCAGAAAGCTTTTCTTTTTGTTA 57.509 26.923 14.05 1.30 44.34 2.41
3746 11424 8.130307 TGCAGAAAGCTTTTCTTTTTGTTATC 57.870 30.769 14.05 0.00 44.34 1.75
3805 11577 4.223320 ACCAAATAAGTCGCAAGTGTTG 57.777 40.909 0.00 0.00 39.48 3.33
3897 11674 2.741486 TAGGCGTCAACAAGGGTGCC 62.741 60.000 0.00 0.00 42.76 5.01
3911 11688 0.458669 GGTGCCTCATCTTTGCATGG 59.541 55.000 0.00 0.00 37.34 3.66
3912 11689 0.179119 GTGCCTCATCTTTGCATGGC 60.179 55.000 0.00 0.00 37.34 4.40
3913 11690 1.324740 TGCCTCATCTTTGCATGGCC 61.325 55.000 0.00 0.00 39.60 5.36
3914 11691 1.324740 GCCTCATCTTTGCATGGCCA 61.325 55.000 8.56 8.56 34.81 5.36
3916 11693 1.760613 CCTCATCTTTGCATGGCCAAT 59.239 47.619 10.96 0.00 0.00 3.16
3917 11694 2.483013 CCTCATCTTTGCATGGCCAATG 60.483 50.000 10.96 7.33 39.49 2.82
3918 11695 2.429250 CTCATCTTTGCATGGCCAATGA 59.571 45.455 10.96 11.85 38.72 2.57
3919 11696 2.429250 TCATCTTTGCATGGCCAATGAG 59.571 45.455 10.96 3.95 38.72 2.90
3920 11697 1.927487 TCTTTGCATGGCCAATGAGT 58.073 45.000 10.96 0.00 38.72 3.41
3922 11699 3.018856 TCTTTGCATGGCCAATGAGTAG 58.981 45.455 10.96 3.50 38.72 2.57
4002 11844 0.667453 TTAACGCCAACGAAAACCCC 59.333 50.000 0.00 0.00 43.93 4.95
4065 11907 8.553459 AAAATAGTGTGAATAGTGTCTTGGAG 57.447 34.615 0.00 0.00 0.00 3.86
4066 11908 6.859112 ATAGTGTGAATAGTGTCTTGGAGT 57.141 37.500 0.00 0.00 0.00 3.85
4067 11909 7.956328 ATAGTGTGAATAGTGTCTTGGAGTA 57.044 36.000 0.00 0.00 0.00 2.59
4069 11911 7.062749 AGTGTGAATAGTGTCTTGGAGTAAA 57.937 36.000 0.00 0.00 0.00 2.01
4070 11912 7.680730 AGTGTGAATAGTGTCTTGGAGTAAAT 58.319 34.615 0.00 0.00 0.00 1.40
4073 11915 9.431887 TGTGAATAGTGTCTTGGAGTAAATAAC 57.568 33.333 0.00 0.00 0.00 1.89
4097 11949 7.522374 ACAATATTTTTGTTTGTTTGCAACGT 58.478 26.923 0.00 0.00 33.82 3.99
4106 11959 2.767505 TGTTTGCAACGTTGGGTTTTT 58.232 38.095 28.33 0.00 36.49 1.94
4107 11960 3.921677 TGTTTGCAACGTTGGGTTTTTA 58.078 36.364 28.33 0.00 36.49 1.52
4109 11962 4.935808 TGTTTGCAACGTTGGGTTTTTATT 59.064 33.333 28.33 0.00 36.49 1.40
4111 11964 3.458189 TGCAACGTTGGGTTTTTATTGG 58.542 40.909 28.33 0.00 36.49 3.16
4112 11965 2.222213 GCAACGTTGGGTTTTTATTGGC 59.778 45.455 28.33 6.54 36.49 4.52
4125 12040 6.476053 GGTTTTTATTGGCGACTGTTTTTGTA 59.524 34.615 0.00 0.00 0.00 2.41
4126 12041 7.010275 GGTTTTTATTGGCGACTGTTTTTGTAA 59.990 33.333 0.00 0.00 0.00 2.41
4127 12042 8.381387 GTTTTTATTGGCGACTGTTTTTGTAAA 58.619 29.630 0.00 0.00 0.00 2.01
4128 12043 7.687005 TTTATTGGCGACTGTTTTTGTAAAG 57.313 32.000 0.00 0.00 0.00 1.85
4183 12111 2.034879 CGCGTCCCTCAACTTGCAT 61.035 57.895 0.00 0.00 0.00 3.96
4187 12115 0.524862 GTCCCTCAACTTGCATGCTG 59.475 55.000 20.33 14.00 0.00 4.41
4196 12124 4.337836 TCAACTTGCATGCTGTACTCAAAA 59.662 37.500 20.33 0.00 0.00 2.44
4234 12162 9.143155 GGTAGGGACAAATGAATATTAACCATT 57.857 33.333 0.00 0.00 32.46 3.16
4265 12193 6.421485 ACTTGATCTAATGTGCCAGATCTTT 58.579 36.000 11.63 0.00 44.94 2.52
4282 12231 1.667724 CTTTCGATGCTGGTAGGCAAG 59.332 52.381 0.00 0.00 45.68 4.01
4283 12232 0.613260 TTCGATGCTGGTAGGCAAGT 59.387 50.000 0.00 0.00 45.68 3.16
4343 12308 5.244626 AGGTCCTCAAACATTTTCAAGGATG 59.755 40.000 0.00 0.00 35.50 3.51
4344 12309 5.011023 GGTCCTCAAACATTTTCAAGGATGT 59.989 40.000 0.00 0.00 38.08 3.06
4345 12310 6.152379 GTCCTCAAACATTTTCAAGGATGTC 58.848 40.000 0.00 0.00 35.55 3.06
4346 12311 5.832595 TCCTCAAACATTTTCAAGGATGTCA 59.167 36.000 0.00 0.00 35.55 3.58
4347 12312 6.494491 TCCTCAAACATTTTCAAGGATGTCAT 59.506 34.615 0.00 0.00 35.55 3.06
4348 12313 6.588756 CCTCAAACATTTTCAAGGATGTCATG 59.411 38.462 0.00 0.00 35.55 3.07
4349 12314 7.053316 TCAAACATTTTCAAGGATGTCATGT 57.947 32.000 0.00 0.00 35.55 3.21
4350 12315 8.175925 TCAAACATTTTCAAGGATGTCATGTA 57.824 30.769 0.00 0.00 35.55 2.29
4351 12316 8.298854 TCAAACATTTTCAAGGATGTCATGTAG 58.701 33.333 0.00 0.00 35.55 2.74
4352 12317 6.764308 ACATTTTCAAGGATGTCATGTAGG 57.236 37.500 0.00 0.00 31.07 3.18
4353 12318 6.248433 ACATTTTCAAGGATGTCATGTAGGT 58.752 36.000 0.00 0.00 31.07 3.08
4369 12334 7.278868 GTCATGTAGGTCCTTGAACTATGAAAG 59.721 40.741 0.00 0.00 34.19 2.62
4374 12339 4.562963 GGTCCTTGAACTATGAAAGTCGGT 60.563 45.833 0.00 0.00 37.50 4.69
4380 12345 7.010552 CCTTGAACTATGAAAGTCGGTATTCAG 59.989 40.741 0.00 0.00 38.80 3.02
4387 12352 2.526888 AGTCGGTATTCAGGTCCTCA 57.473 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.179062 GGGAGTAGCATGACCAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
47 49 6.673154 AAAAGACGAATATTTAGGAACGGG 57.327 37.500 0.00 0.00 0.00 5.28
62 64 8.495949 GTCTATGTTCAAATCTCAAAAAGACGA 58.504 33.333 0.00 0.00 36.65 4.20
63 65 8.499162 AGTCTATGTTCAAATCTCAAAAAGACG 58.501 33.333 0.00 0.00 36.65 4.18
97 99 9.793252 ACACTCTAAAATACGTGTATATTCGTT 57.207 29.630 0.00 0.00 38.69 3.85
121 123 7.022055 ACGAAACAAAATGAGTGAATGTACA 57.978 32.000 0.00 0.00 0.00 2.90
124 126 6.582295 GCATACGAAACAAAATGAGTGAATGT 59.418 34.615 0.00 0.00 0.00 2.71
125 127 6.581919 TGCATACGAAACAAAATGAGTGAATG 59.418 34.615 0.00 0.00 0.00 2.67
131 133 6.142139 TGAACTGCATACGAAACAAAATGAG 58.858 36.000 0.00 0.00 0.00 2.90
133 135 6.363088 ACATGAACTGCATACGAAACAAAATG 59.637 34.615 0.00 0.00 34.82 2.32
140 142 7.609760 ATTCTAACATGAACTGCATACGAAA 57.390 32.000 0.00 0.00 34.82 3.46
192 194 2.932261 AGTCCAACAAAGAACTCCCAC 58.068 47.619 0.00 0.00 0.00 4.61
193 195 4.781775 TTAGTCCAACAAAGAACTCCCA 57.218 40.909 0.00 0.00 0.00 4.37
200 202 7.873719 TGTGAATCTTTTAGTCCAACAAAGA 57.126 32.000 0.00 0.00 40.07 2.52
293 295 7.780064 TCTATTGTTCTCTCCAGAAGATTCAG 58.220 38.462 0.00 0.00 39.45 3.02
334 336 0.601311 GTATCGGATGGCTGACCTGC 60.601 60.000 0.00 0.00 36.63 4.85
349 351 7.095523 GGAGAGATTCAGTACGTAGTCTGTATC 60.096 44.444 17.70 17.70 43.93 2.24
374 376 2.287915 CACAGTTTCAGTGTTTCCTCGG 59.712 50.000 0.00 0.00 27.13 4.63
375 377 3.194861 TCACAGTTTCAGTGTTTCCTCG 58.805 45.455 0.00 0.00 38.16 4.63
436 442 1.597302 CTGCATCTGCCGGATCAGG 60.597 63.158 5.05 7.64 41.18 3.86
560 576 1.630244 CCGAGAAAACCAGCTGCGAG 61.630 60.000 8.66 0.00 0.00 5.03
659 685 0.970937 CGTGACCAAGGGGCTAGAGA 60.971 60.000 0.00 0.00 37.90 3.10
805 849 0.250770 AGCGGGGAAAGAAGTTGGAC 60.251 55.000 0.00 0.00 0.00 4.02
903 952 5.070001 TGGTTGTAGATTTTGGTGAGGAAG 58.930 41.667 0.00 0.00 0.00 3.46
1059 1159 4.758674 TCCAGAGCTTCAAAATCAGACAAG 59.241 41.667 0.00 0.00 0.00 3.16
1295 1456 2.028385 GTGTCTTTCACCATACCCGTCT 60.028 50.000 0.00 0.00 40.84 4.18
1335 1519 4.708726 AGCAGAACATGGCAAGTTAATC 57.291 40.909 8.23 0.00 0.00 1.75
1511 4801 7.144661 CAGCTCAGGATTTAGTAGTATGACTG 58.855 42.308 0.00 0.00 0.00 3.51
1517 4807 6.701145 CTGACAGCTCAGGATTTAGTAGTA 57.299 41.667 0.00 0.00 40.46 1.82
1533 4823 4.377839 TCAATCTAGTAGCACTGACAGC 57.622 45.455 1.25 0.00 0.00 4.40
1555 4845 4.342951 ACGGGCACTTGCTGTATATAGTTA 59.657 41.667 0.38 0.00 41.70 2.24
1676 4966 9.436957 TCTAATACCATTGACAGAAAAGAGTTC 57.563 33.333 0.00 0.00 0.00 3.01
1680 4970 8.474831 TCGATCTAATACCATTGACAGAAAAGA 58.525 33.333 0.00 0.00 0.00 2.52
1684 4974 8.304596 GGTATCGATCTAATACCATTGACAGAA 58.695 37.037 20.91 0.00 45.36 3.02
1720 5021 6.266103 CCATGGCAATAAGATATGGACACTTT 59.734 38.462 0.00 0.00 40.52 2.66
1840 8766 4.262164 GGCAACTGACAGAACATGGAAAAT 60.262 41.667 10.08 0.00 0.00 1.82
1859 8816 3.644966 AATTAATGAGGAGGTCGGCAA 57.355 42.857 0.00 0.00 0.00 4.52
1892 8875 6.828785 ACTGCCGGAATCTTTGATTATAAACT 59.171 34.615 5.05 0.00 0.00 2.66
1976 9115 8.149973 AGCAGAAAAGATAAACTACGAAAACA 57.850 30.769 0.00 0.00 0.00 2.83
2097 9239 2.175184 CTTTGCACTCGCCGGTGAAG 62.175 60.000 20.06 15.31 39.34 3.02
2209 9351 0.608035 TTCCCGTTGATGGTGAAGCC 60.608 55.000 0.00 0.00 37.90 4.35
2400 9683 1.004277 TGGAGGTACCCTGAACATTGC 59.996 52.381 8.74 0.00 38.00 3.56
2424 9712 7.487189 CCTGCAGAAAAATGACAATTTAGCTAG 59.513 37.037 17.39 0.00 34.84 3.42
2426 9717 6.015180 TCCTGCAGAAAAATGACAATTTAGCT 60.015 34.615 17.39 0.00 34.84 3.32
2430 9721 6.165700 AGTCCTGCAGAAAAATGACAATTT 57.834 33.333 17.39 0.00 37.61 1.82
2466 9762 3.364167 CCTTTTTCGGTTTCGCGACATTA 60.364 43.478 9.15 0.00 36.13 1.90
2558 9857 6.202762 CAGCCTGCAAAAATATGTCGTAGATA 59.797 38.462 0.00 0.00 40.67 1.98
2559 9858 5.008019 CAGCCTGCAAAAATATGTCGTAGAT 59.992 40.000 0.00 0.00 40.67 1.98
2584 10009 8.651588 CACAGTAATTAGTCACACAATTCTCTC 58.348 37.037 0.00 0.00 0.00 3.20
2615 10066 1.605753 CATGGCCTGATCATGTGAGG 58.394 55.000 3.32 0.00 37.72 3.86
2779 10304 8.724229 GCATCCAAATTTCTTAGCTGAAAAATT 58.276 29.630 0.00 0.00 39.08 1.82
2851 10378 3.394274 TGTGTTGAGGGAGATGGAAAGAA 59.606 43.478 0.00 0.00 0.00 2.52
2855 10382 5.715439 AATATGTGTTGAGGGAGATGGAA 57.285 39.130 0.00 0.00 0.00 3.53
3115 10733 7.229306 AGCAGATTTCAACATTCAGTCTAAACA 59.771 33.333 0.00 0.00 0.00 2.83
3416 11042 3.034635 AGAGGCAATCTACTCGTCCATT 58.965 45.455 0.00 0.00 36.10 3.16
3431 11057 5.127194 AGAGACACACGATAAATAAGAGGCA 59.873 40.000 0.00 0.00 0.00 4.75
3442 11068 7.210718 TCTTAAAACAGAGAGACACACGATA 57.789 36.000 0.00 0.00 0.00 2.92
3490 11134 4.610680 CGCGAGGGAAGTTTTCTACTTTTG 60.611 45.833 0.00 0.00 47.00 2.44
3495 11142 2.075979 ACGCGAGGGAAGTTTTCTAC 57.924 50.000 15.93 0.00 0.00 2.59
3512 11159 5.228635 ACGACTAGCAAACACGATTATTACG 59.771 40.000 0.00 0.00 0.00 3.18
3526 11173 1.272212 TGCACATCTCACGACTAGCAA 59.728 47.619 0.00 0.00 0.00 3.91
3641 11304 2.279741 CACGCTGTACTATTGTGCCAT 58.720 47.619 0.00 0.00 0.00 4.40
3650 11313 3.431912 CACAGAAATTGCACGCTGTACTA 59.568 43.478 8.92 0.00 39.40 1.82
3655 11318 2.124011 AACACAGAAATTGCACGCTG 57.876 45.000 0.00 0.00 34.65 5.18
3753 11431 9.145865 GGAAAATTTGTGAAGTTGTCAGTTTAA 57.854 29.630 0.00 0.00 36.74 1.52
3758 11436 5.232838 GCAGGAAAATTTGTGAAGTTGTCAG 59.767 40.000 0.00 0.00 36.74 3.51
3759 11437 5.105392 AGCAGGAAAATTTGTGAAGTTGTCA 60.105 36.000 0.00 0.00 0.00 3.58
3897 11674 2.429250 TCATTGGCCATGCAAAGATGAG 59.571 45.455 6.09 0.00 32.13 2.90
3918 11695 2.895404 TCCCGCAAGTTGAGTTACTACT 59.105 45.455 7.16 0.00 36.26 2.57
3919 11696 3.308438 TCCCGCAAGTTGAGTTACTAC 57.692 47.619 7.16 0.00 0.00 2.73
3920 11697 4.339872 TTTCCCGCAAGTTGAGTTACTA 57.660 40.909 7.16 0.00 0.00 1.82
3922 11699 4.694037 AGTATTTCCCGCAAGTTGAGTTAC 59.306 41.667 7.16 0.87 0.00 2.50
3978 11777 4.497173 GGGTTTTCGTTGGCGTTAACTTAA 60.497 41.667 3.71 0.00 39.49 1.85
3985 11784 2.836793 CGGGGTTTTCGTTGGCGTT 61.837 57.895 0.00 0.00 39.49 4.84
3986 11785 3.281395 CGGGGTTTTCGTTGGCGT 61.281 61.111 0.00 0.00 39.49 5.68
3994 11836 1.894223 GAAGTCGACGCGGGGTTTTC 61.894 60.000 12.47 5.10 0.00 2.29
4039 11881 9.653287 CTCCAAGACACTATTCACACTATTTTA 57.347 33.333 0.00 0.00 0.00 1.52
4088 11940 4.332819 CCAATAAAAACCCAACGTTGCAAA 59.667 37.500 22.93 3.74 33.93 3.68
4089 11941 3.871594 CCAATAAAAACCCAACGTTGCAA 59.128 39.130 22.93 0.00 33.93 4.08
4090 11942 3.458189 CCAATAAAAACCCAACGTTGCA 58.542 40.909 22.93 1.68 33.93 4.08
4091 11943 2.222213 GCCAATAAAAACCCAACGTTGC 59.778 45.455 22.93 2.62 33.93 4.17
4097 11949 2.959707 ACAGTCGCCAATAAAAACCCAA 59.040 40.909 0.00 0.00 0.00 4.12
4106 11959 6.621316 TCTTTACAAAAACAGTCGCCAATA 57.379 33.333 0.00 0.00 0.00 1.90
4107 11960 5.508200 TCTTTACAAAAACAGTCGCCAAT 57.492 34.783 0.00 0.00 0.00 3.16
4109 11962 4.966965 TTCTTTACAAAAACAGTCGCCA 57.033 36.364 0.00 0.00 0.00 5.69
4169 12097 0.111061 ACAGCATGCAAGTTGAGGGA 59.889 50.000 21.98 0.00 42.53 4.20
4183 12111 5.835113 AAAAGAGCTTTTTGAGTACAGCA 57.165 34.783 2.54 0.00 39.52 4.41
4187 12115 8.451748 CCTACCATAAAAGAGCTTTTTGAGTAC 58.548 37.037 12.83 0.00 42.22 2.73
4196 12124 5.514500 TTGTCCCTACCATAAAAGAGCTT 57.486 39.130 0.00 0.00 0.00 3.74
4234 12162 3.691118 GCACATTAGATCAAGTTGGAGCA 59.309 43.478 2.34 0.00 0.00 4.26
4265 12193 0.108186 CACTTGCCTACCAGCATCGA 60.108 55.000 0.00 0.00 43.64 3.59
4282 12231 9.790344 TCACTCTATATTTCTACTAGGGTACAC 57.210 37.037 0.00 0.00 0.00 2.90
4343 12308 6.222038 TCATAGTTCAAGGACCTACATGAC 57.778 41.667 0.00 0.00 0.00 3.06
4344 12309 6.867519 TTCATAGTTCAAGGACCTACATGA 57.132 37.500 0.00 0.00 0.00 3.07
4345 12310 7.106239 ACTTTCATAGTTCAAGGACCTACATG 58.894 38.462 0.00 0.00 31.29 3.21
4346 12311 7.259088 ACTTTCATAGTTCAAGGACCTACAT 57.741 36.000 0.00 0.00 31.29 2.29
4347 12312 6.571731 CGACTTTCATAGTTCAAGGACCTACA 60.572 42.308 0.00 0.00 37.17 2.74
4348 12313 5.805994 CGACTTTCATAGTTCAAGGACCTAC 59.194 44.000 0.00 0.00 37.17 3.18
4349 12314 5.105473 CCGACTTTCATAGTTCAAGGACCTA 60.105 44.000 0.00 0.00 37.17 3.08
4350 12315 4.322801 CCGACTTTCATAGTTCAAGGACCT 60.323 45.833 0.00 0.00 37.17 3.85
4351 12316 3.933332 CCGACTTTCATAGTTCAAGGACC 59.067 47.826 0.00 0.00 37.17 4.46
4352 12317 4.566987 ACCGACTTTCATAGTTCAAGGAC 58.433 43.478 0.00 0.00 37.17 3.85
4353 12318 4.884668 ACCGACTTTCATAGTTCAAGGA 57.115 40.909 0.00 0.00 37.17 3.36
4357 12322 6.070995 ACCTGAATACCGACTTTCATAGTTCA 60.071 38.462 0.00 0.00 37.17 3.18
4369 12334 3.056035 ACTTTGAGGACCTGAATACCGAC 60.056 47.826 0.00 0.00 0.00 4.79
4374 12339 4.530553 TGCTACACTTTGAGGACCTGAATA 59.469 41.667 0.00 0.00 0.00 1.75
4380 12345 2.808543 CACTTGCTACACTTTGAGGACC 59.191 50.000 0.00 0.00 0.00 4.46
4387 12352 4.708177 AGATGACACACTTGCTACACTTT 58.292 39.130 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.