Multiple sequence alignment - TraesCS4A01G348700

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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 TraesCS4A01G348700 chr4A 100.000 5518 0 0 1 5518 625963221 625957704 0.000000e+00 10190.0
1 TraesCS4A01G348700 chr4A 78.916 1347 258 19 3153 4491 626074497 626073169 0.000000e+00 891.0
2 TraesCS4A01G348700 chr4A 77.835 1358 262 29 3149 4491 695981533 695980200 0.000000e+00 804.0
3 TraesCS4A01G348700 chr4A 76.359 1582 301 43 2923 4490 626049158 626047636 0.000000e+00 782.0
4 TraesCS4A01G348700 chr4A 77.556 1350 254 36 3147 4481 695805584 695806899 0.000000e+00 769.0
5 TraesCS4A01G348700 chr4A 80.315 762 126 11 3733 4491 626013149 626012409 6.250000e-154 555.0
6 TraesCS4A01G348700 chr4A 91.549 142 12 0 2216 2357 625960958 625960817 4.360000e-46 196.0
7 TraesCS4A01G348700 chr4A 91.549 142 12 0 2264 2405 625961006 625960865 4.360000e-46 196.0
8 TraesCS4A01G348700 chr4A 96.667 90 3 0 5079 5168 644038470 644038559 3.440000e-32 150.0
9 TraesCS4A01G348700 chr4A 96.667 90 3 0 5079 5168 644075073 644075162 3.440000e-32 150.0
10 TraesCS4A01G348700 chr5D 91.721 3515 149 63 1634 5080 543270096 543273536 0.000000e+00 4748.0
11 TraesCS4A01G348700 chr5D 77.186 1521 294 31 2981 4490 543100163 543101641 0.000000e+00 837.0
12 TraesCS4A01G348700 chr5D 76.803 1539 303 40 2974 4491 542109499 542111004 0.000000e+00 815.0
13 TraesCS4A01G348700 chr5D 79.941 673 114 14 2974 3641 543235972 543236628 5.000000e-130 475.0
14 TraesCS4A01G348700 chr5D 78.897 725 130 15 2923 3638 543213821 543214531 2.330000e-128 470.0
15 TraesCS4A01G348700 chr5D 90.164 366 27 6 5161 5518 543273534 543273898 8.370000e-128 468.0
16 TraesCS4A01G348700 chr5D 96.407 167 6 0 1468 1634 360981539 360981373 5.440000e-70 276.0
17 TraesCS4A01G348700 chr4D 97.816 1648 22 2 1 1634 507482409 507480762 0.000000e+00 2832.0
18 TraesCS4A01G348700 chr2B 97.570 1646 26 3 3 1634 773878803 773880448 0.000000e+00 2806.0
19 TraesCS4A01G348700 chr2B 96.512 86 3 0 5078 5163 583156235 583156320 5.760000e-30 143.0
20 TraesCS4A01G348700 chr7B 97.027 1648 34 5 1 1634 503191597 503189951 0.000000e+00 2758.0
21 TraesCS4A01G348700 chr7B 94.857 175 8 1 1462 1635 504460329 504460155 7.040000e-69 272.0
22 TraesCS4A01G348700 chr7D 96.541 1648 39 7 1 1634 413375601 413373958 0.000000e+00 2712.0
23 TraesCS4A01G348700 chr7D 92.118 203 8 1 1440 1634 268833761 268833963 4.210000e-71 279.0
24 TraesCS4A01G348700 chr6D 96.972 1222 21 4 1 1208 36111096 36109877 0.000000e+00 2037.0
25 TraesCS4A01G348700 chr6D 91.647 431 27 6 1205 1634 36109205 36108783 6.160000e-164 588.0
26 TraesCS4A01G348700 chr5B 92.593 1431 70 17 2264 3679 684744243 684745652 0.000000e+00 2023.0
27 TraesCS4A01G348700 chr5B 94.970 994 42 4 3681 4671 684745713 684746701 0.000000e+00 1552.0
28 TraesCS4A01G348700 chr5B 95.223 963 38 5 3681 4640 684772454 684771497 0.000000e+00 1517.0
29 TraesCS4A01G348700 chr5B 91.512 754 27 8 1634 2354 684743632 684744381 0.000000e+00 1003.0
30 TraesCS4A01G348700 chr5B 77.991 1354 264 25 3149 4491 557254074 557252744 0.000000e+00 819.0
31 TraesCS4A01G348700 chr5B 77.934 1355 267 25 3147 4491 684089445 684090777 0.000000e+00 817.0
32 TraesCS4A01G348700 chr5B 76.796 1517 298 32 2985 4490 684604494 684605967 0.000000e+00 802.0
33 TraesCS4A01G348700 chr5B 78.018 1342 250 25 3153 4490 684611200 684612500 0.000000e+00 802.0
34 TraesCS4A01G348700 chr5B 76.617 1531 302 37 2975 4481 684879974 684881472 0.000000e+00 793.0
35 TraesCS4A01G348700 chr5B 94.444 378 16 3 4704 5080 684746691 684747064 1.330000e-160 577.0
36 TraesCS4A01G348700 chr5B 94.231 364 9 3 5165 5518 684771398 684771037 3.760000e-151 545.0
37 TraesCS4A01G348700 chr5B 85.081 496 71 3 3156 3650 557350331 557350824 2.290000e-138 503.0
38 TraesCS4A01G348700 chr5B 87.228 368 28 12 5161 5518 684747062 684747420 8.610000e-108 401.0
39 TraesCS4A01G348700 chr5B 98.876 89 1 0 4989 5077 684771490 684771402 5.720000e-35 159.0
40 TraesCS4A01G348700 chr5B 90.110 91 9 0 2974 3064 684611052 684611142 9.710000e-23 119.0
41 TraesCS4A01G348700 chr5B 87.379 103 5 5 5419 5518 556963222 556963319 1.620000e-20 111.0
42 TraesCS4A01G348700 chr5B 92.647 68 5 0 5326 5393 556963154 556963221 1.270000e-16 99.0
43 TraesCS4A01G348700 chr5B 100.000 32 0 0 4460 4491 684606117 684606148 5.970000e-05 60.2
44 TraesCS4A01G348700 chr1B 96.119 773 22 3 353 1118 602263751 602264522 0.000000e+00 1254.0
45 TraesCS4A01G348700 chr1B 97.500 360 9 0 1 360 602263095 602263454 2.820000e-172 616.0
46 TraesCS4A01G348700 chr1A 96.823 661 13 2 984 1636 516714019 516713359 0.000000e+00 1098.0
47 TraesCS4A01G348700 chr1A 76.812 552 111 12 3753 4297 591148535 591147994 1.500000e-75 294.0
48 TraesCS4A01G348700 chrUn 98.728 393 5 0 107 499 479635157 479635549 0.000000e+00 699.0
49 TraesCS4A01G348700 chr1D 77.467 537 104 12 3753 4282 492641184 492640658 6.940000e-79 305.0
50 TraesCS4A01G348700 chr1D 95.050 101 5 0 5076 5176 408530646 408530746 5.720000e-35 159.0
51 TraesCS4A01G348700 chr3B 94.350 177 9 1 1460 1635 758575676 758575852 2.530000e-68 270.0
52 TraesCS4A01G348700 chr3A 89.952 209 12 2 1442 1641 77482557 77482349 1.520000e-65 261.0
53 TraesCS4A01G348700 chr2A 77.492 311 32 19 1694 1968 412387801 412388109 9.570000e-33 152.0
54 TraesCS4A01G348700 chr2A 94.792 96 3 2 5077 5171 686840778 686840872 1.240000e-31 148.0
55 TraesCS4A01G348700 chr6A 77.419 310 33 19 1694 1968 416959159 416958852 3.440000e-32 150.0
56 TraesCS4A01G348700 chr4B 94.737 95 5 0 5070 5164 624024901 624024995 1.240000e-31 148.0
57 TraesCS4A01G348700 chr7A 93.878 98 4 2 5072 5167 111835229 111835326 4.450000e-31 147.0
58 TraesCS4A01G348700 chr6B 93.069 101 6 1 5067 5167 12465858 12465759 4.450000e-31 147.0
59 TraesCS4A01G348700 chr2D 93.069 101 6 1 5077 5176 536428539 536428439 4.450000e-31 147.0


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 TraesCS4A01G348700 chr4A 625957704 625963221 5517 True 3527.333333 10190 94.3660 1 5518 3 chr4A.!!$R5 5517
1 TraesCS4A01G348700 chr4A 626073169 626074497 1328 True 891.000000 891 78.9160 3153 4491 1 chr4A.!!$R3 1338
2 TraesCS4A01G348700 chr4A 695980200 695981533 1333 True 804.000000 804 77.8350 3149 4491 1 chr4A.!!$R4 1342
3 TraesCS4A01G348700 chr4A 626047636 626049158 1522 True 782.000000 782 76.3590 2923 4490 1 chr4A.!!$R2 1567
4 TraesCS4A01G348700 chr4A 695805584 695806899 1315 False 769.000000 769 77.5560 3147 4481 1 chr4A.!!$F3 1334
5 TraesCS4A01G348700 chr4A 626012409 626013149 740 True 555.000000 555 80.3150 3733 4491 1 chr4A.!!$R1 758
6 TraesCS4A01G348700 chr5D 543270096 543273898 3802 False 2608.000000 4748 90.9425 1634 5518 2 chr5D.!!$F5 3884
7 TraesCS4A01G348700 chr5D 543100163 543101641 1478 False 837.000000 837 77.1860 2981 4490 1 chr5D.!!$F2 1509
8 TraesCS4A01G348700 chr5D 542109499 542111004 1505 False 815.000000 815 76.8030 2974 4491 1 chr5D.!!$F1 1517
9 TraesCS4A01G348700 chr5D 543235972 543236628 656 False 475.000000 475 79.9410 2974 3641 1 chr5D.!!$F4 667
10 TraesCS4A01G348700 chr5D 543213821 543214531 710 False 470.000000 470 78.8970 2923 3638 1 chr5D.!!$F3 715
11 TraesCS4A01G348700 chr4D 507480762 507482409 1647 True 2832.000000 2832 97.8160 1 1634 1 chr4D.!!$R1 1633
12 TraesCS4A01G348700 chr2B 773878803 773880448 1645 False 2806.000000 2806 97.5700 3 1634 1 chr2B.!!$F2 1631
13 TraesCS4A01G348700 chr7B 503189951 503191597 1646 True 2758.000000 2758 97.0270 1 1634 1 chr7B.!!$R1 1633
14 TraesCS4A01G348700 chr7D 413373958 413375601 1643 True 2712.000000 2712 96.5410 1 1634 1 chr7D.!!$R1 1633
15 TraesCS4A01G348700 chr6D 36108783 36111096 2313 True 1312.500000 2037 94.3095 1 1634 2 chr6D.!!$R1 1633
16 TraesCS4A01G348700 chr5B 684743632 684747420 3788 False 1111.200000 2023 92.1494 1634 5518 5 chr5B.!!$F7 3884
17 TraesCS4A01G348700 chr5B 557252744 557254074 1330 True 819.000000 819 77.9910 3149 4491 1 chr5B.!!$R1 1342
18 TraesCS4A01G348700 chr5B 684089445 684090777 1332 False 817.000000 817 77.9340 3147 4491 1 chr5B.!!$F2 1344
19 TraesCS4A01G348700 chr5B 684879974 684881472 1498 False 793.000000 793 76.6170 2975 4481 1 chr5B.!!$F3 1506
20 TraesCS4A01G348700 chr5B 684771037 684772454 1417 True 740.333333 1517 96.1100 3681 5518 3 chr5B.!!$R2 1837
21 TraesCS4A01G348700 chr5B 684611052 684612500 1448 False 460.500000 802 84.0640 2974 4490 2 chr5B.!!$F6 1516
22 TraesCS4A01G348700 chr5B 684604494 684606148 1654 False 431.100000 802 88.3980 2985 4491 2 chr5B.!!$F5 1506
23 TraesCS4A01G348700 chr1B 602263095 602264522 1427 False 935.000000 1254 96.8095 1 1118 2 chr1B.!!$F1 1117
24 TraesCS4A01G348700 chr1A 516713359 516714019 660 True 1098.000000 1098 96.8230 984 1636 1 chr1A.!!$R1 652
25 TraesCS4A01G348700 chr1A 591147994 591148535 541 True 294.000000 294 76.8120 3753 4297 1 chr1A.!!$R2 544
26 TraesCS4A01G348700 chr1D 492640658 492641184 526 True 305.000000 305 77.4670 3753 4282 1 chr1D.!!$R1 529

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
176 177 5.029807 TCACAACTACCATTGTCACAAGA 57.970 39.130 0.00 0.0 40.89 3.02 F
1087 1401 0.890542 GCTGATGCTGAACCACCACA 60.891 55.000 0.00 0.0 36.03 4.17 F
2220 3269 0.037697 TAGCATTGTTCGTCGCCTGT 60.038 50.000 0.00 0.0 0.00 4.00 F
2881 3955 0.596083 CTGAGCTCTTGGGCGATACG 60.596 60.000 16.19 0.0 37.29 3.06 F
2905 3979 0.966179 TGTCGAAGAAGCTGCAGGTA 59.034 50.000 20.51 0.0 39.69 3.08 F
3581 4679 1.070175 CGTTTTGACCGTCATGTCCAC 60.070 52.381 1.09 0.0 34.25 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 2756 0.109723 CACACCGGGGAAAGGAAGAA 59.890 55.000 12.96 0.00 0.00 2.52 R
2231 3280 0.098025 GGTCTCTGAGACGAGAAGCG 59.902 60.000 26.53 0.00 45.96 4.68 R
3730 4894 0.389426 CTTGGCTTTCACCTGCATGC 60.389 55.000 11.82 11.82 0.00 4.06 R
3813 4985 2.124151 GGCGGCCTCATTCACCAT 60.124 61.111 12.87 0.00 0.00 3.55 R
4398 5583 2.223525 CCTTCCTACGATCCGTGAGAAC 60.224 54.545 1.93 0.00 41.39 3.01 R
4948 6245 0.948623 TGAACAGTTCGCACGATGGG 60.949 55.000 8.80 0.00 0.00 4.00 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
176 177 5.029807 TCACAACTACCATTGTCACAAGA 57.970 39.130 0.00 0.00 40.89 3.02
293 294 9.894783 GATGAGATTAAAATCATCCTTGACATG 57.105 33.333 16.80 0.00 43.92 3.21
1087 1401 0.890542 GCTGATGCTGAACCACCACA 60.891 55.000 0.00 0.00 36.03 4.17
1331 2327 7.377131 GTCAATCTGTTTTCTTGTTTGCTACTC 59.623 37.037 0.00 0.00 0.00 2.59
1507 2511 2.710096 ACCGGAATTGATTGGATCGT 57.290 45.000 9.46 0.00 0.00 3.73
1531 2535 3.701532 TCCGCTTGACAAAAATCGTTT 57.298 38.095 0.00 0.00 0.00 3.60
1636 2640 2.733956 GGAAACATGGCAACTATGGGA 58.266 47.619 0.00 0.00 37.61 4.37
1712 2723 3.845259 GCGTCCGTCATGGCCCTA 61.845 66.667 0.00 0.00 37.80 3.53
1744 2755 5.163395 CCCAATCCAAGGTCTTCTACTCTAC 60.163 48.000 0.00 0.00 0.00 2.59
1745 2756 5.659079 CCAATCCAAGGTCTTCTACTCTACT 59.341 44.000 0.00 0.00 0.00 2.57
1746 2757 6.155393 CCAATCCAAGGTCTTCTACTCTACTT 59.845 42.308 0.00 0.00 0.00 2.24
1779 2793 2.810400 CGGTGTGACCCTGTTTCTGAAT 60.810 50.000 0.00 0.00 33.75 2.57
1785 2799 2.746362 GACCCTGTTTCTGAATCTGCAG 59.254 50.000 7.63 7.63 37.24 4.41
1843 2864 0.322997 TACGGGTTGCCATTTCAGGG 60.323 55.000 0.00 0.00 0.00 4.45
1951 2973 2.046023 CATCTGGCAAGGCGTGGA 60.046 61.111 1.91 0.00 0.00 4.02
1974 2996 1.368731 CGCGTGTGATTTGCAACGT 60.369 52.632 0.00 0.00 35.18 3.99
2047 3069 2.725815 GCACGCTGTTCGGTTTGC 60.726 61.111 0.00 0.00 43.86 3.68
2141 3190 4.054780 TGATTCTTACGTACCATGGAGC 57.945 45.455 21.47 9.51 0.00 4.70
2220 3269 0.037697 TAGCATTGTTCGTCGCCTGT 60.038 50.000 0.00 0.00 0.00 4.00
2231 3280 2.125512 CGCCTGTACTCTGGTGCC 60.126 66.667 0.00 0.00 36.63 5.01
2363 3412 0.689623 ACCTGAACAGAAGAGGCCTG 59.310 55.000 12.00 0.00 37.64 4.85
2508 3557 4.637771 TCGTCAGCCTCGAGATGA 57.362 55.556 15.71 14.75 33.38 2.92
2509 3558 2.398803 TCGTCAGCCTCGAGATGAG 58.601 57.895 15.71 11.16 44.83 2.90
2531 3580 0.984230 CTCAAGGTAGGTGGCCTCAA 59.016 55.000 3.32 0.00 34.81 3.02
2537 3586 3.460825 AGGTAGGTGGCCTCAATTTCTA 58.539 45.455 3.32 0.00 34.61 2.10
2547 3596 4.510571 GCCTCAATTTCTACTTAACCCGA 58.489 43.478 0.00 0.00 0.00 5.14
2550 3599 5.155278 TCAATTTCTACTTAACCCGAGCA 57.845 39.130 0.00 0.00 0.00 4.26
2567 3616 4.201910 CCGAGCATACGATTCACCAATTTT 60.202 41.667 0.00 0.00 35.09 1.82
2716 3777 3.459598 AGGGCAAGATATGGAAACTGCTA 59.540 43.478 0.00 0.00 0.00 3.49
2779 3840 3.272334 CTTGCGACCTATGGCGGC 61.272 66.667 0.00 0.00 30.86 6.53
2881 3955 0.596083 CTGAGCTCTTGGGCGATACG 60.596 60.000 16.19 0.00 37.29 3.06
2898 3972 1.006102 CGGTGGTGTCGAAGAAGCT 60.006 57.895 0.00 0.00 39.69 3.74
2899 3973 1.284982 CGGTGGTGTCGAAGAAGCTG 61.285 60.000 0.00 0.00 39.69 4.24
2900 3974 1.569479 GGTGGTGTCGAAGAAGCTGC 61.569 60.000 0.00 0.00 39.69 5.25
2905 3979 0.966179 TGTCGAAGAAGCTGCAGGTA 59.034 50.000 20.51 0.00 39.69 3.08
2909 3983 2.163815 TCGAAGAAGCTGCAGGTAGTAC 59.836 50.000 20.51 11.02 0.00 2.73
3091 4168 2.040813 ACACTGCCATCATCAACCTTCT 59.959 45.455 0.00 0.00 0.00 2.85
3092 4169 3.087031 CACTGCCATCATCAACCTTCTT 58.913 45.455 0.00 0.00 0.00 2.52
3100 4177 2.751259 TCATCAACCTTCTTCATGCAGC 59.249 45.455 0.00 0.00 0.00 5.25
3125 4211 2.325761 CGATCGTTTCTTTCCTCGTGT 58.674 47.619 7.03 0.00 0.00 4.49
3126 4212 2.090658 CGATCGTTTCTTTCCTCGTGTG 59.909 50.000 7.03 0.00 0.00 3.82
3127 4213 1.860676 TCGTTTCTTTCCTCGTGTGG 58.139 50.000 0.00 0.00 0.00 4.17
3128 4214 1.137479 TCGTTTCTTTCCTCGTGTGGT 59.863 47.619 0.00 0.00 0.00 4.16
3129 4215 1.937899 CGTTTCTTTCCTCGTGTGGTT 59.062 47.619 0.00 0.00 0.00 3.67
3130 4216 3.125316 CGTTTCTTTCCTCGTGTGGTTA 58.875 45.455 0.00 0.00 0.00 2.85
3131 4217 3.556775 CGTTTCTTTCCTCGTGTGGTTAA 59.443 43.478 0.00 0.00 0.00 2.01
3212 4308 1.600916 GGGCGTTCTGCTTTCTGGT 60.601 57.895 0.00 0.00 45.43 4.00
3312 4408 3.064958 CAGCGACTTCGAGGACAAGTATA 59.935 47.826 0.00 0.00 43.02 1.47
3314 4410 4.023878 AGCGACTTCGAGGACAAGTATATC 60.024 45.833 0.00 0.00 43.02 1.63
3581 4679 1.070175 CGTTTTGACCGTCATGTCCAC 60.070 52.381 1.09 0.00 34.25 4.02
3673 4771 4.321601 CGTCTGTCCCCAAAAATATTTGCA 60.322 41.667 0.39 0.00 43.73 4.08
3710 4874 8.542953 ACGTAAGACTTAACTTTAACCTTTTCG 58.457 33.333 0.00 0.00 43.62 3.46
3711 4875 8.755018 CGTAAGACTTAACTTTAACCTTTTCGA 58.245 33.333 0.00 0.00 43.02 3.71
3720 4884 8.617290 AACTTTAACCTTTTCGATCTGTGTAT 57.383 30.769 0.00 0.00 0.00 2.29
3730 4894 8.741101 TTTTCGATCTGTGTATTTTTCCATTG 57.259 30.769 0.00 0.00 0.00 2.82
3776 4948 3.000041 GGATGTGTTGACAATCGCTACA 59.000 45.455 0.00 0.00 35.11 2.74
3942 5114 1.800805 GGCGGTGATACCTGATCATG 58.199 55.000 0.00 0.00 46.34 3.07
3998 5170 3.257393 CGCTCTTGTTGCTATCTTCACT 58.743 45.455 0.00 0.00 0.00 3.41
4001 5173 4.692625 GCTCTTGTTGCTATCTTCACTGAA 59.307 41.667 0.00 0.00 0.00 3.02
4210 5382 1.274728 CCCCTCATCTGATCTAAGCGG 59.725 57.143 0.00 0.00 0.00 5.52
4536 5721 3.325870 TGACAATAGTCCTTTGACAGCG 58.674 45.455 0.00 0.00 44.33 5.18
4640 5930 8.668510 AGATGTACGAGCAGAATTTAATTGAT 57.331 30.769 0.00 0.00 0.00 2.57
4682 5979 8.099364 TGAATTTTGTTTCTCAGGTCATAGAC 57.901 34.615 0.00 0.00 0.00 2.59
4779 6076 1.475034 GGGTTTCTGTGACTGAGCACA 60.475 52.381 8.87 8.87 45.80 4.57
4944 6241 5.818336 TCGAAAACTATCAGAAAACCACACA 59.182 36.000 0.00 0.00 0.00 3.72
4948 6245 9.394477 GAAAACTATCAGAAAACCACACATAAC 57.606 33.333 0.00 0.00 0.00 1.89
4957 6254 0.732571 CCACACATAACCCATCGTGC 59.267 55.000 0.00 0.00 32.53 5.34
4969 6266 1.201954 CCATCGTGCGAACTGTTCATG 60.202 52.381 19.56 14.02 0.00 3.07
4987 6284 6.430616 TGTTCATGTATTCAGCTGATTTGTCA 59.569 34.615 19.04 12.71 0.00 3.58
5080 6377 5.618561 CCGAGTGAGCTGTTAAAATTGTAC 58.381 41.667 0.00 0.00 0.00 2.90
5081 6378 5.408604 CCGAGTGAGCTGTTAAAATTGTACT 59.591 40.000 0.00 0.00 0.00 2.73
5082 6379 6.401153 CCGAGTGAGCTGTTAAAATTGTACTC 60.401 42.308 0.00 0.00 0.00 2.59
5083 6380 6.401153 CGAGTGAGCTGTTAAAATTGTACTCC 60.401 42.308 0.00 0.00 0.00 3.85
5084 6381 5.705905 AGTGAGCTGTTAAAATTGTACTCCC 59.294 40.000 0.00 0.00 0.00 4.30
5085 6382 5.705905 GTGAGCTGTTAAAATTGTACTCCCT 59.294 40.000 0.00 0.00 0.00 4.20
5086 6383 5.938125 TGAGCTGTTAAAATTGTACTCCCTC 59.062 40.000 0.00 0.00 0.00 4.30
5087 6384 5.254115 AGCTGTTAAAATTGTACTCCCTCC 58.746 41.667 0.00 0.00 0.00 4.30
5088 6385 4.094442 GCTGTTAAAATTGTACTCCCTCCG 59.906 45.833 0.00 0.00 0.00 4.63
5089 6386 5.231702 TGTTAAAATTGTACTCCCTCCGT 57.768 39.130 0.00 0.00 0.00 4.69
5090 6387 6.357579 TGTTAAAATTGTACTCCCTCCGTA 57.642 37.500 0.00 0.00 0.00 4.02
5091 6388 6.767456 TGTTAAAATTGTACTCCCTCCGTAA 58.233 36.000 0.00 0.00 0.00 3.18
5092 6389 7.222872 TGTTAAAATTGTACTCCCTCCGTAAA 58.777 34.615 0.00 0.00 0.00 2.01
5093 6390 7.173047 TGTTAAAATTGTACTCCCTCCGTAAAC 59.827 37.037 0.00 0.00 0.00 2.01
5094 6391 5.494390 AAATTGTACTCCCTCCGTAAACT 57.506 39.130 0.00 0.00 0.00 2.66
5095 6392 6.610075 AAATTGTACTCCCTCCGTAAACTA 57.390 37.500 0.00 0.00 0.00 2.24
5096 6393 6.610075 AATTGTACTCCCTCCGTAAACTAA 57.390 37.500 0.00 0.00 0.00 2.24
5097 6394 6.803366 ATTGTACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
5098 6395 7.902920 ATTGTACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
5099 6396 7.902920 TTGTACTCCCTCCGTAAACTAATAT 57.097 36.000 0.00 0.00 0.00 1.28
5100 6397 8.995027 TTGTACTCCCTCCGTAAACTAATATA 57.005 34.615 0.00 0.00 0.00 0.86
5101 6398 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
5102 6399 9.420118 TGTACTCCCTCCGTAAACTAATATAAA 57.580 33.333 0.00 0.00 0.00 1.40
5105 6402 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
5106 6403 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
5107 6404 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
5108 6405 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
5109 6406 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
5127 6424 9.918630 AAAGCGTTTAGATTACTACTTTAGTGA 57.081 29.630 0.00 0.00 39.81 3.41
5129 6426 9.733219 AGCGTTTAGATTACTACTTTAGTGATC 57.267 33.333 9.14 9.14 46.38 2.92
5137 6434 9.733219 GATTACTACTTTAGTGATCTAAACGCT 57.267 33.333 9.68 0.00 44.10 5.07
5138 6435 9.733219 ATTACTACTTTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
5139 6436 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
5140 6437 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
5141 6438 6.952935 ACTTTAGTGATCTAAACGCTCTTG 57.047 37.500 0.00 0.00 40.05 3.02
5142 6439 6.456501 ACTTTAGTGATCTAAACGCTCTTGT 58.543 36.000 0.00 0.00 40.05 3.16
5143 6440 7.600065 ACTTTAGTGATCTAAACGCTCTTGTA 58.400 34.615 0.00 0.00 40.05 2.41
5144 6441 8.251721 ACTTTAGTGATCTAAACGCTCTTGTAT 58.748 33.333 0.00 0.00 40.05 2.29
5145 6442 8.997621 TTTAGTGATCTAAACGCTCTTGTATT 57.002 30.769 0.00 0.00 40.05 1.89
5147 6444 9.731819 TTAGTGATCTAAACGCTCTTGTATTAG 57.268 33.333 0.00 0.00 33.79 1.73
5148 6445 7.773149 AGTGATCTAAACGCTCTTGTATTAGT 58.227 34.615 0.00 0.00 0.00 2.24
5149 6446 8.251721 AGTGATCTAAACGCTCTTGTATTAGTT 58.748 33.333 0.00 0.00 0.00 2.24
5150 6447 8.870879 GTGATCTAAACGCTCTTGTATTAGTTT 58.129 33.333 0.00 0.00 36.11 2.66
5153 6450 9.865321 ATCTAAACGCTCTTGTATTAGTTTACA 57.135 29.630 0.00 0.00 34.29 2.41
5154 6451 9.865321 TCTAAACGCTCTTGTATTAGTTTACAT 57.135 29.630 0.00 0.00 34.29 2.29
5157 6454 8.644318 AACGCTCTTGTATTAGTTTACATAGG 57.356 34.615 0.00 0.00 32.39 2.57
5158 6455 7.208080 ACGCTCTTGTATTAGTTTACATAGGG 58.792 38.462 0.00 0.00 36.07 3.53
5159 6456 7.069085 ACGCTCTTGTATTAGTTTACATAGGGA 59.931 37.037 13.52 0.00 34.94 4.20
5160 6457 7.595502 CGCTCTTGTATTAGTTTACATAGGGAG 59.404 40.741 0.00 0.00 34.16 4.30
5161 6458 8.422566 GCTCTTGTATTAGTTTACATAGGGAGT 58.577 37.037 0.00 0.00 32.39 3.85
5243 6540 4.898861 ACTGCCCAAAGAAATTAGAAACCA 59.101 37.500 0.00 0.00 0.00 3.67
5295 6602 5.589452 AGCTGGAGAGATTTCATGACATTTC 59.411 40.000 0.00 0.00 0.00 2.17
5328 6635 4.764823 TCTGAAAAGAGTGTGGTGTTTTGT 59.235 37.500 0.00 0.00 0.00 2.83
5383 6692 4.019174 CTCAAGCATGTACCCCAAGATTT 58.981 43.478 0.00 0.00 0.00 2.17
5437 6746 7.093727 TGCCTTTTCCAATCGAATATGGTTTAA 60.094 33.333 13.10 5.95 37.94 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 9.553064 CCTCTTAAGCACAATATAATGAGAAGT 57.447 33.333 0.00 0.00 0.00 3.01
176 177 3.555966 CTTCACCAGTTCCTTCCACTTT 58.444 45.455 0.00 0.00 0.00 2.66
464 770 1.358787 TGCCAGTTCATCTTTCCCCAT 59.641 47.619 0.00 0.00 0.00 4.00
1087 1401 6.378280 AGTGTTTCAAGTCCTCTGAATTTTGT 59.622 34.615 0.00 0.00 0.00 2.83
1507 2511 3.181495 ACGATTTTTGTCAAGCGGAAACA 60.181 39.130 0.00 0.00 39.87 2.83
1531 2535 4.816126 ACAGCAGGGGTATACATCTCTAA 58.184 43.478 5.01 0.00 0.00 2.10
1636 2640 1.999071 GAGAGCGAGACGATGCCTGT 61.999 60.000 0.00 0.00 0.00 4.00
1712 2723 3.976701 CTTGGATTGGGCGAGCCGT 62.977 63.158 8.14 0.00 36.85 5.68
1744 2755 0.400594 ACACCGGGGAAAGGAAGAAG 59.599 55.000 12.96 0.00 0.00 2.85
1745 2756 0.109723 CACACCGGGGAAAGGAAGAA 59.890 55.000 12.96 0.00 0.00 2.52
1746 2757 0.765135 TCACACCGGGGAAAGGAAGA 60.765 55.000 12.96 0.00 0.00 2.87
1785 2799 3.177920 CAGACAGTCGCTCGCAGC 61.178 66.667 0.00 0.00 38.02 5.25
1865 2887 3.798337 AGCAAAGCAAACGTTGAATTCAG 59.202 39.130 8.41 0.49 37.44 3.02
1951 2973 2.945984 CAAATCACACGCGCCAGT 59.054 55.556 5.73 0.00 0.00 4.00
1974 2996 2.034066 CCCTGAAAGAAGCCGGCA 59.966 61.111 31.54 4.35 34.07 5.69
2220 3269 1.890894 GAGAAGCGGCACCAGAGTA 59.109 57.895 1.45 0.00 0.00 2.59
2231 3280 0.098025 GGTCTCTGAGACGAGAAGCG 59.902 60.000 26.53 0.00 45.96 4.68
2329 3378 1.609072 TCAGGTGTGTGAGACGAGAAG 59.391 52.381 0.00 0.00 0.00 2.85
2508 3557 0.984995 GGCCACCTACCTTGAGTTCT 59.015 55.000 0.00 0.00 0.00 3.01
2509 3558 0.984995 AGGCCACCTACCTTGAGTTC 59.015 55.000 5.01 0.00 31.87 3.01
2531 3580 5.068198 TCGTATGCTCGGGTTAAGTAGAAAT 59.932 40.000 0.00 0.00 0.00 2.17
2537 3586 3.131577 TGAATCGTATGCTCGGGTTAAGT 59.868 43.478 0.00 0.00 0.00 2.24
2547 3596 8.023128 GCATATAAAATTGGTGAATCGTATGCT 58.977 33.333 0.00 0.00 38.26 3.79
2881 3955 1.569479 GCAGCTTCTTCGACACCACC 61.569 60.000 0.00 0.00 0.00 4.61
2898 3972 1.271379 CCACTGAACGTACTACCTGCA 59.729 52.381 0.00 0.00 0.00 4.41
2899 3973 1.271656 ACCACTGAACGTACTACCTGC 59.728 52.381 0.00 0.00 0.00 4.85
2900 3974 2.555325 TGACCACTGAACGTACTACCTG 59.445 50.000 0.00 0.00 0.00 4.00
2905 3979 4.117685 GTTTTCTGACCACTGAACGTACT 58.882 43.478 0.00 0.00 34.61 2.73
2909 3983 4.349663 TTTGTTTTCTGACCACTGAACG 57.650 40.909 0.00 0.00 34.61 3.95
3091 4168 1.149964 CGATCGCTGAGCTGCATGAA 61.150 55.000 0.26 0.00 0.00 2.57
3092 4169 1.590792 CGATCGCTGAGCTGCATGA 60.591 57.895 0.26 0.00 0.00 3.07
3100 4177 2.600867 GAGGAAAGAAACGATCGCTGAG 59.399 50.000 16.60 0.00 0.00 3.35
3126 4212 5.867174 GCATGTGAAACTGGGTTAATTAACC 59.133 40.000 31.35 31.35 46.09 2.85
3127 4213 6.687604 AGCATGTGAAACTGGGTTAATTAAC 58.312 36.000 18.30 18.30 38.04 2.01
3128 4214 6.909550 AGCATGTGAAACTGGGTTAATTAA 57.090 33.333 0.00 0.00 38.04 1.40
3129 4215 6.686630 CAAGCATGTGAAACTGGGTTAATTA 58.313 36.000 0.00 0.00 38.04 1.40
3130 4216 5.540911 CAAGCATGTGAAACTGGGTTAATT 58.459 37.500 0.00 0.00 38.04 1.40
3131 4217 4.561326 GCAAGCATGTGAAACTGGGTTAAT 60.561 41.667 0.00 0.00 38.04 1.40
3212 4308 2.449518 TTCCCTGTGCCTGGTGGA 60.450 61.111 0.00 0.00 34.57 4.02
3312 4408 3.008049 ACTCTTTTAGAGGCAACACCGAT 59.992 43.478 8.44 0.00 46.45 4.18
3314 4410 2.480419 CACTCTTTTAGAGGCAACACCG 59.520 50.000 8.44 0.00 46.45 4.94
3611 4709 6.176896 TGAGATATAAGACTCGAGGATCTGG 58.823 44.000 18.41 0.00 36.11 3.86
3710 4874 6.019318 GCATGCAATGGAAAAATACACAGATC 60.019 38.462 14.21 0.00 46.86 2.75
3711 4875 5.813672 GCATGCAATGGAAAAATACACAGAT 59.186 36.000 14.21 0.00 46.86 2.90
3712 4876 5.170021 GCATGCAATGGAAAAATACACAGA 58.830 37.500 14.21 0.00 46.86 3.41
3720 4884 2.367894 TCACCTGCATGCAATGGAAAAA 59.632 40.909 27.64 8.88 46.70 1.94
3730 4894 0.389426 CTTGGCTTTCACCTGCATGC 60.389 55.000 11.82 11.82 0.00 4.06
3776 4948 2.284995 GAGAGCCCAGGTGTCCCT 60.285 66.667 0.00 0.00 44.02 4.20
3813 4985 2.124151 GGCGGCCTCATTCACCAT 60.124 61.111 12.87 0.00 0.00 3.55
3942 5114 4.232310 GGCAGTCATCTTCCTGGC 57.768 61.111 0.00 0.00 45.29 4.85
4019 5191 2.369394 CTGGGAACAATGGTAGCCTTC 58.631 52.381 0.00 0.00 42.06 3.46
4398 5583 2.223525 CCTTCCTACGATCCGTGAGAAC 60.224 54.545 1.93 0.00 41.39 3.01
4536 5721 5.529060 ACCAAACTGTCTGTTCAATCTCTTC 59.471 40.000 0.00 0.00 38.03 2.87
4682 5979 8.957028 CATAATATGCAAAAGTTGGATTACACG 58.043 33.333 0.17 0.00 42.07 4.49
4780 6077 9.807649 GAAAATTGCATTTATACACATCCTTCT 57.192 29.630 0.00 0.00 0.00 2.85
4781 6078 9.585099 TGAAAATTGCATTTATACACATCCTTC 57.415 29.630 0.00 0.00 0.00 3.46
4944 6241 1.066430 ACAGTTCGCACGATGGGTTAT 60.066 47.619 0.00 0.00 0.00 1.89
4948 6245 0.948623 TGAACAGTTCGCACGATGGG 60.949 55.000 8.80 0.00 0.00 4.00
4957 6254 4.627035 TCAGCTGAATACATGAACAGTTCG 59.373 41.667 15.67 0.00 33.57 3.95
4969 6266 7.141363 ACTGTTTTGACAAATCAGCTGAATAC 58.859 34.615 27.52 8.12 40.29 1.89
5080 6377 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
5081 6378 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
5082 6379 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
5083 6380 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
5101 6398 9.918630 TCACTAAAGTAGTAATCTAAACGCTTT 57.081 29.630 0.00 0.00 37.23 3.51
5103 6400 9.733219 GATCACTAAAGTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 37.23 5.07
5104 6401 9.733219 AGATCACTAAAGTAGTAATCTAAACGC 57.267 33.333 0.03 0.00 41.03 4.84
5110 6407 9.733219 GCGTTTAGATCACTAAAGTAGTAATCT 57.267 33.333 6.37 6.37 44.17 2.40
5111 6408 9.733219 AGCGTTTAGATCACTAAAGTAGTAATC 57.267 33.333 0.00 0.00 45.42 1.75
5112 6409 9.733219 GAGCGTTTAGATCACTAAAGTAGTAAT 57.267 33.333 0.00 0.00 45.42 1.89
5113 6410 8.954350 AGAGCGTTTAGATCACTAAAGTAGTAA 58.046 33.333 0.00 0.00 45.42 2.24
5114 6411 8.503458 AGAGCGTTTAGATCACTAAAGTAGTA 57.497 34.615 0.00 0.00 45.42 1.82
5115 6412 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
5116 6413 7.755822 ACAAGAGCGTTTAGATCACTAAAGTAG 59.244 37.037 0.00 0.00 45.42 2.57
5117 6414 7.600065 ACAAGAGCGTTTAGATCACTAAAGTA 58.400 34.615 0.00 0.00 45.42 2.24
5118 6415 6.456501 ACAAGAGCGTTTAGATCACTAAAGT 58.543 36.000 0.00 0.00 45.42 2.66
5119 6416 6.952935 ACAAGAGCGTTTAGATCACTAAAG 57.047 37.500 0.00 0.00 45.42 1.85
5120 6417 8.997621 AATACAAGAGCGTTTAGATCACTAAA 57.002 30.769 0.00 0.00 43.52 1.85
5121 6418 9.731819 CTAATACAAGAGCGTTTAGATCACTAA 57.268 33.333 0.00 0.00 37.82 2.24
5122 6419 8.900781 ACTAATACAAGAGCGTTTAGATCACTA 58.099 33.333 0.00 0.00 37.82 2.74
5123 6420 7.773149 ACTAATACAAGAGCGTTTAGATCACT 58.227 34.615 0.00 0.00 37.82 3.41
5124 6421 7.988904 ACTAATACAAGAGCGTTTAGATCAC 57.011 36.000 0.00 0.00 37.82 3.06
5125 6422 8.997621 AAACTAATACAAGAGCGTTTAGATCA 57.002 30.769 0.00 0.00 37.82 2.92
5127 6424 9.865321 TGTAAACTAATACAAGAGCGTTTAGAT 57.135 29.630 0.00 0.00 33.02 1.98
5128 6425 9.865321 ATGTAAACTAATACAAGAGCGTTTAGA 57.135 29.630 0.00 0.00 39.12 2.10
5131 6428 9.095065 CCTATGTAAACTAATACAAGAGCGTTT 57.905 33.333 0.00 0.00 39.12 3.60
5132 6429 7.709613 CCCTATGTAAACTAATACAAGAGCGTT 59.290 37.037 0.00 0.00 39.12 4.84
5133 6430 7.069085 TCCCTATGTAAACTAATACAAGAGCGT 59.931 37.037 0.00 0.00 39.12 5.07
5134 6431 7.431249 TCCCTATGTAAACTAATACAAGAGCG 58.569 38.462 0.00 0.00 39.12 5.03
5135 6432 8.422566 ACTCCCTATGTAAACTAATACAAGAGC 58.577 37.037 0.00 0.00 39.12 4.09
5154 6451 8.591072 CCGGACATCTAAATAAATTACTCCCTA 58.409 37.037 0.00 0.00 0.00 3.53
5155 6452 7.072076 ACCGGACATCTAAATAAATTACTCCCT 59.928 37.037 9.46 0.00 0.00 4.20
5156 6453 7.222161 ACCGGACATCTAAATAAATTACTCCC 58.778 38.462 9.46 0.00 0.00 4.30
5157 6454 8.672823 AACCGGACATCTAAATAAATTACTCC 57.327 34.615 9.46 0.00 0.00 3.85
5214 6511 9.892130 TTTCTAATTTCTTTGGGCAGTTTTAAA 57.108 25.926 0.00 0.00 0.00 1.52
5243 6540 9.010029 CCTTATATTGTGTGTTTTCCTGTAGTT 57.990 33.333 0.00 0.00 0.00 2.24
5295 6602 7.137426 CCACACTCTTTTCAGATTTGAGAAAG 58.863 38.462 11.38 11.38 35.41 2.62
5383 6692 6.072563 GGTATTTGTTTTAGAGCGGGTTACAA 60.073 38.462 0.00 0.00 0.00 2.41
5462 6771 6.134040 AGCTAGGAGACTACGAAATAACAC 57.866 41.667 0.00 0.00 43.67 3.32


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

AutoCloner maintained by Alex Coulton.