Multiple sequence alignment - TraesCS5B01G389900

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 TraesCS5B01G389900 chr5B 100.000 7451 0 0 1 7451 569142191 569149641 0.000000e+00 13760.0
1 TraesCS5B01G389900 chr5B 96.746 7498 173 23 1 7451 569243368 569250841 0.000000e+00 12429.0
2 TraesCS5B01G389900 chr5B 84.318 5127 688 73 1228 6271 454865659 454870752 0.000000e+00 4907.0
3 TraesCS5B01G389900 chr5B 90.452 398 27 5 1219 1614 569249287 569249675 1.430000e-141 514.0
4 TraesCS5B01G389900 chr5B 90.201 398 28 5 1219 1614 569148073 569148461 6.670000e-140 508.0
5 TraesCS5B01G389900 chrUn 86.423 5119 603 49 1219 6271 111007462 111002370 0.000000e+00 5518.0
6 TraesCS5B01G389900 chrUn 86.084 1660 193 24 4645 6273 356304155 356302503 0.000000e+00 1751.0
7 TraesCS5B01G389900 chrUn 88.305 838 52 33 6272 7094 67087726 67086920 0.000000e+00 963.0
8 TraesCS5B01G389900 chrUn 88.305 838 52 33 6272 7094 307431908 307432714 0.000000e+00 963.0
9 TraesCS5B01G389900 chrUn 84.367 403 47 10 1219 1615 111002761 111002369 1.520000e-101 381.0
10 TraesCS5B01G389900 chrUn 90.775 271 25 0 948 1218 67087992 67087722 5.500000e-96 363.0
11 TraesCS5B01G389900 chrUn 90.775 271 25 0 948 1218 307431642 307431912 5.500000e-96 363.0
12 TraesCS5B01G389900 chr1A 85.235 5127 640 72 1215 6271 3915032 3920111 0.000000e+00 5166.0
13 TraesCS5B01G389900 chr1A 92.500 920 68 1 1 919 527021979 527022898 0.000000e+00 1315.0
14 TraesCS5B01G389900 chr1A 86.374 844 60 22 6272 7094 559979070 559978261 0.000000e+00 870.0
15 TraesCS5B01G389900 chr1A 84.752 846 53 35 6272 7094 559886660 559885868 0.000000e+00 778.0
16 TraesCS5B01G389900 chr1A 91.447 456 29 4 6272 6720 559941626 559941174 1.060000e-172 617.0
17 TraesCS5B01G389900 chr1A 90.282 319 26 3 6776 7094 559941177 559940864 5.380000e-111 412.0
18 TraesCS5B01G389900 chr1A 89.963 269 27 0 948 1216 559886926 559886658 1.540000e-91 348.0
19 TraesCS5B01G389900 chr1A 89.299 271 29 0 948 1218 559941892 559941622 2.570000e-89 340.0
20 TraesCS5B01G389900 chr1A 88.476 269 31 0 948 1216 559979336 559979068 7.210000e-85 326.0
21 TraesCS5B01G389900 chr4A 84.070 5135 689 79 1219 6271 634259665 634264752 0.000000e+00 4831.0
22 TraesCS5B01G389900 chr4A 83.817 5135 719 78 1219 6271 664327763 664332867 0.000000e+00 4776.0
23 TraesCS5B01G389900 chr4A 85.474 1783 216 31 4523 6271 634300876 634302649 0.000000e+00 1818.0
24 TraesCS5B01G389900 chr4A 85.137 1783 222 31 4523 6271 634281823 634283596 0.000000e+00 1784.0
25 TraesCS5B01G389900 chr4B 83.268 5122 748 65 1219 6272 83843442 83848522 0.000000e+00 4610.0
26 TraesCS5B01G389900 chr3B 83.966 4665 664 39 1670 6271 467425053 467429696 0.000000e+00 4394.0
27 TraesCS5B01G389900 chr4D 86.474 3327 410 18 1219 4539 418527977 418524685 0.000000e+00 3615.0
28 TraesCS5B01G389900 chr4D 85.959 3333 432 24 1219 4539 435204070 435200762 0.000000e+00 3530.0
29 TraesCS5B01G389900 chr4D 87.620 1777 185 20 4523 6271 418524672 418522903 0.000000e+00 2030.0
30 TraesCS5B01G389900 chr4D 84.500 400 47 9 1219 1614 418523291 418522903 1.520000e-101 381.0
31 TraesCS5B01G389900 chr1D 84.198 2430 315 47 3888 6273 17342548 17340144 0.000000e+00 2296.0
32 TraesCS5B01G389900 chr1D 93.391 923 59 2 1 922 223389188 223388267 0.000000e+00 1365.0
33 TraesCS5B01G389900 chr1D 92.188 704 52 3 222 924 223349175 223348474 0.000000e+00 992.0
34 TraesCS5B01G389900 chr5D 85.489 2219 299 20 1216 3425 431883938 431886142 0.000000e+00 2292.0
35 TraesCS5B01G389900 chr5D 90.682 719 31 14 6404 7094 462670009 462670719 0.000000e+00 924.0
36 TraesCS5B01G389900 chr5D 85.863 771 61 28 6272 7035 462746636 462747365 0.000000e+00 776.0
37 TraesCS5B01G389900 chr5D 91.144 271 24 0 948 1218 462669709 462669979 1.180000e-97 368.0
38 TraesCS5B01G389900 chr5D 91.144 271 24 0 948 1218 462746370 462746640 1.180000e-97 368.0
39 TraesCS5B01G389900 chr5D 82.353 255 32 5 7198 7451 462670848 462671090 7.580000e-50 209.0
40 TraesCS5B01G389900 chr5D 84.444 135 15 2 6960 7094 462896901 462897029 2.180000e-25 128.0
41 TraesCS5B01G389900 chr5D 79.459 185 28 5 6272 6447 462895881 462896064 1.020000e-23 122.0
42 TraesCS5B01G389900 chr5D 82.653 98 11 3 7103 7196 487170806 487170901 1.720000e-11 82.4
43 TraesCS5B01G389900 chr3D 87.932 1765 192 15 4523 6271 445867435 445865676 0.000000e+00 2060.0
44 TraesCS5B01G389900 chr3D 85.000 400 46 10 1219 1614 445866065 445865676 1.950000e-105 394.0
45 TraesCS5B01G389900 chr3D 85.057 87 10 2 7111 7196 551242501 551242417 1.330000e-12 86.1
46 TraesCS5B01G389900 chr1B 88.206 1399 157 7 4879 6272 66379979 66378584 0.000000e+00 1663.0
47 TraesCS5B01G389900 chr1B 94.009 918 54 1 1 918 340425077 340424161 0.000000e+00 1389.0
48 TraesCS5B01G389900 chr1B 85.393 89 10 2 7110 7197 415738388 415738302 1.030000e-13 89.8
49 TraesCS5B01G389900 chr1B 83.908 87 11 2 7111 7196 415738303 415738387 6.200000e-11 80.5
50 TraesCS5B01G389900 chr5A 86.988 1245 156 4 4536 5774 307105436 307106680 0.000000e+00 1397.0
51 TraesCS5B01G389900 chr5A 85.683 915 65 27 6552 7411 582654403 582655306 0.000000e+00 904.0
52 TraesCS5B01G389900 chr5A 91.855 221 16 2 6272 6491 582653196 582653415 2.610000e-79 307.0
53 TraesCS5B01G389900 chr5A 86.029 272 25 5 948 1218 582652941 582653200 5.690000e-71 279.0
54 TraesCS5B01G389900 chr7D 93.580 919 57 2 2 919 88213688 88214605 0.000000e+00 1369.0
55 TraesCS5B01G389900 chr2D 94.882 762 38 1 1 761 467114236 467113475 0.000000e+00 1190.0
56 TraesCS5B01G389900 chr7A 84.458 637 72 11 4353 4962 113339065 113338429 2.970000e-168 603.0
57 TraesCS5B01G389900 chr2B 85.714 91 9 3 7111 7200 161464992 161464905 7.960000e-15 93.5
58 TraesCS5B01G389900 chr2B 84.043 94 12 2 7111 7203 740308682 740308591 3.700000e-13 87.9
59 TraesCS5B01G389900 chr6B 83.908 87 11 2 7111 7196 718384572 718384656 6.200000e-11 80.5


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 TraesCS5B01G389900 chr5B 569142191 569149641 7450 False 7134.000000 13760 95.100500 1 7451 2 chr5B.!!$F2 7450
1 TraesCS5B01G389900 chr5B 569243368 569250841 7473 False 6471.500000 12429 93.599000 1 7451 2 chr5B.!!$F3 7450
2 TraesCS5B01G389900 chr5B 454865659 454870752 5093 False 4907.000000 4907 84.318000 1228 6271 1 chr5B.!!$F1 5043
3 TraesCS5B01G389900 chrUn 111002369 111007462 5093 True 2949.500000 5518 85.395000 1219 6271 2 chrUn.!!$R3 5052
4 TraesCS5B01G389900 chrUn 356302503 356304155 1652 True 1751.000000 1751 86.084000 4645 6273 1 chrUn.!!$R1 1628
5 TraesCS5B01G389900 chrUn 67086920 67087992 1072 True 663.000000 963 89.540000 948 7094 2 chrUn.!!$R2 6146
6 TraesCS5B01G389900 chrUn 307431642 307432714 1072 False 663.000000 963 89.540000 948 7094 2 chrUn.!!$F1 6146
7 TraesCS5B01G389900 chr1A 3915032 3920111 5079 False 5166.000000 5166 85.235000 1215 6271 1 chr1A.!!$F1 5056
8 TraesCS5B01G389900 chr1A 527021979 527022898 919 False 1315.000000 1315 92.500000 1 919 1 chr1A.!!$F2 918
9 TraesCS5B01G389900 chr1A 559978261 559979336 1075 True 598.000000 870 87.425000 948 7094 2 chr1A.!!$R3 6146
10 TraesCS5B01G389900 chr1A 559885868 559886926 1058 True 563.000000 778 87.357500 948 7094 2 chr1A.!!$R1 6146
11 TraesCS5B01G389900 chr1A 559940864 559941892 1028 True 456.333333 617 90.342667 948 7094 3 chr1A.!!$R2 6146
12 TraesCS5B01G389900 chr4A 634259665 634264752 5087 False 4831.000000 4831 84.070000 1219 6271 1 chr4A.!!$F1 5052
13 TraesCS5B01G389900 chr4A 664327763 664332867 5104 False 4776.000000 4776 83.817000 1219 6271 1 chr4A.!!$F4 5052
14 TraesCS5B01G389900 chr4A 634300876 634302649 1773 False 1818.000000 1818 85.474000 4523 6271 1 chr4A.!!$F3 1748
15 TraesCS5B01G389900 chr4A 634281823 634283596 1773 False 1784.000000 1784 85.137000 4523 6271 1 chr4A.!!$F2 1748
16 TraesCS5B01G389900 chr4B 83843442 83848522 5080 False 4610.000000 4610 83.268000 1219 6272 1 chr4B.!!$F1 5053
17 TraesCS5B01G389900 chr3B 467425053 467429696 4643 False 4394.000000 4394 83.966000 1670 6271 1 chr3B.!!$F1 4601
18 TraesCS5B01G389900 chr4D 435200762 435204070 3308 True 3530.000000 3530 85.959000 1219 4539 1 chr4D.!!$R1 3320
19 TraesCS5B01G389900 chr4D 418522903 418527977 5074 True 2008.666667 3615 86.198000 1219 6271 3 chr4D.!!$R2 5052
20 TraesCS5B01G389900 chr1D 17340144 17342548 2404 True 2296.000000 2296 84.198000 3888 6273 1 chr1D.!!$R1 2385
21 TraesCS5B01G389900 chr1D 223388267 223389188 921 True 1365.000000 1365 93.391000 1 922 1 chr1D.!!$R3 921
22 TraesCS5B01G389900 chr1D 223348474 223349175 701 True 992.000000 992 92.188000 222 924 1 chr1D.!!$R2 702
23 TraesCS5B01G389900 chr5D 431883938 431886142 2204 False 2292.000000 2292 85.489000 1216 3425 1 chr5D.!!$F1 2209
24 TraesCS5B01G389900 chr5D 462746370 462747365 995 False 572.000000 776 88.503500 948 7035 2 chr5D.!!$F4 6087
25 TraesCS5B01G389900 chr5D 462669709 462671090 1381 False 500.333333 924 88.059667 948 7451 3 chr5D.!!$F3 6503
26 TraesCS5B01G389900 chr3D 445865676 445867435 1759 True 1227.000000 2060 86.466000 1219 6271 2 chr3D.!!$R2 5052
27 TraesCS5B01G389900 chr1B 66378584 66379979 1395 True 1663.000000 1663 88.206000 4879 6272 1 chr1B.!!$R1 1393
28 TraesCS5B01G389900 chr1B 340424161 340425077 916 True 1389.000000 1389 94.009000 1 918 1 chr1B.!!$R2 917
29 TraesCS5B01G389900 chr5A 307105436 307106680 1244 False 1397.000000 1397 86.988000 4536 5774 1 chr5A.!!$F1 1238
30 TraesCS5B01G389900 chr5A 582652941 582655306 2365 False 496.666667 904 87.855667 948 7411 3 chr5A.!!$F2 6463
31 TraesCS5B01G389900 chr7D 88213688 88214605 917 False 1369.000000 1369 93.580000 2 919 1 chr7D.!!$F1 917
32 TraesCS5B01G389900 chr2D 467113475 467114236 761 True 1190.000000 1190 94.882000 1 761 1 chr2D.!!$R1 760
33 TraesCS5B01G389900 chr7A 113338429 113339065 636 True 603.000000 603 84.458000 4353 4962 1 chr7A.!!$R1 609

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
903 907 0.035630 ATCACAACAGCTCTCCTGCC 60.036 55.0 0.00 0.00 45.78 4.85 F
1437 1458 0.105778 TGATCGTGCACTTGTGGACA 59.894 50.0 21.56 11.43 0.00 4.02 F
1667 1698 0.179076 TCGATCATGCCGATGCTTGT 60.179 50.0 6.03 0.00 41.89 3.16 F
2193 2224 1.014352 AAATATGCTTGACGGCGGTC 58.986 50.0 16.90 16.90 43.71 4.79 F
3526 3561 0.320858 TGTTTACGGCGCCATCTTCA 60.321 50.0 28.98 16.33 0.00 3.02 F
4498 4553 0.249073 CGATTCGGTGCTCCCTGTAG 60.249 60.0 0.00 0.00 0.00 2.74 F
4526 4581 0.385751 GAAGACGATGCTCCCGATCA 59.614 55.0 0.00 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2224 1.071471 ACCAACTGAAGAGCACCGG 59.929 57.895 0.00 0.0 0.00 5.28 R
3237 3268 0.814010 GCACCGATTCCGCACCTTAT 60.814 55.000 0.00 0.0 0.00 1.73 R
3396 3427 1.525995 CCCACGCCACTTGTGTCTT 60.526 57.895 0.00 0.0 34.84 3.01 R
3712 3747 0.827507 ATTTCCTGCGCACCTTTGGT 60.828 50.000 5.66 0.0 35.62 3.67 R
4866 4948 0.039437 TTCGACCTCAACTCTGACGC 60.039 55.000 0.00 0.0 0.00 5.19 R
6105 6226 2.029073 CGAGTGCACGGTCAAGGT 59.971 61.111 12.01 0.0 0.00 3.50 R
7330 10875 1.476488 CAAAAATTAGAGGGGCCGGTG 59.524 52.381 1.90 0.0 0.00 4.94 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
71 72 4.527816 TGCTCATTTATGGGATAATTGGCC 59.472 41.667 0.00 0.00 30.34 5.36
174 175 3.261818 AACCCCTCTGTTAGTGACTCT 57.738 47.619 0.00 0.00 0.00 3.24
462 463 0.037232 GGTCTCGAAAGGTGTGGGAG 60.037 60.000 0.00 0.00 0.00 4.30
671 673 5.417580 TCAACAAAAAGGAACAACTAGTGCT 59.582 36.000 0.00 0.00 0.00 4.40
782 786 8.506196 AGATGGTAATCCTATTTAGTTGCCTA 57.494 34.615 0.00 0.00 32.77 3.93
890 894 8.514594 CCTTACTTCTGCTTAATGAAATCACAA 58.485 33.333 0.00 0.00 0.00 3.33
903 907 0.035630 ATCACAACAGCTCTCCTGCC 60.036 55.000 0.00 0.00 45.78 4.85
910 914 0.532573 CAGCTCTCCTGCCGTCTTTA 59.467 55.000 0.00 0.00 34.21 1.85
937 941 5.906113 AAAAATTGTCTACACACACCACA 57.094 34.783 0.00 0.00 29.76 4.17
1007 1012 6.441088 ACTTTCAAAGTTAGAGATGGAGGT 57.559 37.500 0.00 0.00 39.04 3.85
1105 1110 1.857348 AGGGCTTACTTTGGGGGCT 60.857 57.895 0.00 0.00 0.00 5.19
1129 1134 4.182433 TGTGCGGGTTGTGCTCCA 62.182 61.111 0.00 0.00 0.00 3.86
1135 1140 1.150536 GGGTTGTGCTCCAAGTCCA 59.849 57.895 0.00 0.00 32.51 4.02
1143 1148 3.264193 TGTGCTCCAAGTCCATCAAGTAT 59.736 43.478 0.00 0.00 0.00 2.12
1419 1440 2.423446 GCCATCCTAGCGTCCCTG 59.577 66.667 0.00 0.00 0.00 4.45
1420 1441 2.134287 GCCATCCTAGCGTCCCTGA 61.134 63.158 0.00 0.00 0.00 3.86
1421 1442 1.476007 GCCATCCTAGCGTCCCTGAT 61.476 60.000 0.00 0.00 0.00 2.90
1422 1443 0.605589 CCATCCTAGCGTCCCTGATC 59.394 60.000 0.00 0.00 0.00 2.92
1425 1446 1.101635 TCCTAGCGTCCCTGATCGTG 61.102 60.000 0.00 0.00 0.00 4.35
1427 1448 2.004808 CTAGCGTCCCTGATCGTGCA 62.005 60.000 0.00 0.00 0.00 4.57
1429 1450 2.573869 CGTCCCTGATCGTGCACT 59.426 61.111 16.19 0.00 0.00 4.40
1430 1451 1.079819 CGTCCCTGATCGTGCACTT 60.080 57.895 16.19 1.52 0.00 3.16
1431 1452 1.354337 CGTCCCTGATCGTGCACTTG 61.354 60.000 16.19 0.00 0.00 3.16
1432 1453 0.320771 GTCCCTGATCGTGCACTTGT 60.321 55.000 16.19 0.00 0.00 3.16
1433 1454 0.320683 TCCCTGATCGTGCACTTGTG 60.321 55.000 16.19 0.00 0.00 3.33
1434 1455 1.300971 CCCTGATCGTGCACTTGTGG 61.301 60.000 16.19 10.11 0.00 4.17
1435 1456 0.320683 CCTGATCGTGCACTTGTGGA 60.321 55.000 16.19 4.42 0.00 4.02
1436 1457 0.792640 CTGATCGTGCACTTGTGGAC 59.207 55.000 16.19 14.06 0.00 4.02
1437 1458 0.105778 TGATCGTGCACTTGTGGACA 59.894 50.000 21.56 11.43 0.00 4.02
1464 1485 2.680913 GCGCCTTGATCGTGCACTT 61.681 57.895 16.19 1.52 36.73 3.16
1495 1516 3.391665 GATCGGGTCAGGGCACAGG 62.392 68.421 0.00 0.00 0.00 4.00
1502 1523 1.202891 GGTCAGGGCACAGGTAAAACT 60.203 52.381 0.00 0.00 0.00 2.66
1568 1596 7.605410 AGAAACTACTGACGAAACTGAAAAA 57.395 32.000 0.00 0.00 0.00 1.94
1667 1698 0.179076 TCGATCATGCCGATGCTTGT 60.179 50.000 6.03 0.00 41.89 3.16
1957 1988 2.023223 GCCATTGTTGTTGCTGCGG 61.023 57.895 0.00 0.00 0.00 5.69
2050 2081 2.281484 GCAAGAACAGGGTGCCGA 60.281 61.111 0.00 0.00 31.94 5.54
2193 2224 1.014352 AAATATGCTTGACGGCGGTC 58.986 50.000 16.90 16.90 43.71 4.79
2300 2331 3.947841 GTTGCCAACGACGCTGCA 61.948 61.111 0.00 0.00 0.00 4.41
2586 2617 3.203710 ACAATGATCACCAGGTCATCCAT 59.796 43.478 0.13 0.00 34.14 3.41
3202 3233 2.699321 CAGAAGATGGAGCTCCTCATCA 59.301 50.000 32.28 13.40 36.82 3.07
3237 3268 2.288666 GCCGAAATCCAGCATGTTCTA 58.711 47.619 0.00 0.00 0.00 2.10
3396 3427 1.661509 CTGCAGACAACGACGCTGA 60.662 57.895 8.42 0.00 0.00 4.26
3526 3561 0.320858 TGTTTACGGCGCCATCTTCA 60.321 50.000 28.98 16.33 0.00 3.02
3712 3747 1.336440 CCCTTCACATGCACGAAACAA 59.664 47.619 0.00 0.00 0.00 2.83
3819 3854 0.878523 CGGTTCAGCAGAAACACCGA 60.879 55.000 13.81 0.00 41.66 4.69
3999 4035 2.203070 GCCGTGAATGAGCCGGAT 60.203 61.111 5.05 0.00 44.41 4.18
4087 4142 1.562017 TGCACGCGCTTTATCGATAA 58.438 45.000 13.85 13.85 39.64 1.75
4103 4158 0.249911 ATAATGCGGCCTCGTCCTTC 60.250 55.000 0.00 0.00 38.89 3.46
4240 4295 4.383861 CAGCCGCTCCTGTGCTCA 62.384 66.667 0.00 0.00 31.77 4.26
4498 4553 0.249073 CGATTCGGTGCTCCCTGTAG 60.249 60.000 0.00 0.00 0.00 2.74
4526 4581 0.385751 GAAGACGATGCTCCCGATCA 59.614 55.000 0.00 0.00 0.00 2.92
4533 4588 2.887568 GCTCCCGATCACGCACAG 60.888 66.667 0.00 0.00 38.29 3.66
4534 4589 2.887568 CTCCCGATCACGCACAGC 60.888 66.667 0.00 0.00 38.29 4.40
4654 4736 1.194121 GCCAGCAAAATGGTTCCCCT 61.194 55.000 0.00 0.00 42.75 4.79
4886 4968 1.402984 GCGTCAGAGTTGAGGTCGAAT 60.403 52.381 0.00 0.00 40.46 3.34
5173 5271 0.699399 ACTCCTCCTCCGTGAGAAGA 59.301 55.000 2.84 0.00 34.11 2.87
5192 5293 3.771216 AGAAGTTTTCCACTGCCATCAT 58.229 40.909 0.00 0.00 35.12 2.45
5341 5442 3.270877 CTTGGGGACGATCGAGAAAAAT 58.729 45.455 24.34 0.00 0.00 1.82
6209 6336 8.823818 CGGGTTATATGACGAAAAAGAAACTAT 58.176 33.333 0.00 0.00 0.00 2.12
6788 10040 6.263842 TCAGAATGATCTTGCACTTGTTCTTT 59.736 34.615 0.00 0.00 42.56 2.52
7330 10875 1.938657 TACTCAGAGTGCTGCCGAGC 61.939 60.000 13.84 0.00 46.44 5.03
7376 10923 3.740141 GCCGTCCGATTTCAGAGGATTAA 60.740 47.826 0.00 0.00 36.34 1.40
7377 10924 4.439057 CCGTCCGATTTCAGAGGATTAAA 58.561 43.478 0.00 0.00 36.34 1.52
7378 10925 4.873827 CCGTCCGATTTCAGAGGATTAAAA 59.126 41.667 0.00 0.00 36.34 1.52
7379 10926 5.353123 CCGTCCGATTTCAGAGGATTAAAAA 59.647 40.000 0.00 0.00 36.34 1.94
7380 10927 6.038271 CCGTCCGATTTCAGAGGATTAAAAAT 59.962 38.462 0.00 0.00 36.34 1.82
7381 10928 7.225931 CCGTCCGATTTCAGAGGATTAAAAATA 59.774 37.037 0.00 0.00 36.34 1.40
7382 10929 8.609176 CGTCCGATTTCAGAGGATTAAAAATAA 58.391 33.333 0.00 0.00 36.34 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
474 475 2.424601 CAATGATCGTTGTCCTGCCATT 59.575 45.455 17.93 0.00 0.00 3.16
671 673 3.067040 TCGGATTCGGTTTATGATCGTCA 59.933 43.478 0.00 0.00 36.95 4.35
782 786 1.073199 AGCAGTTACCGGCTTTGCT 59.927 52.632 15.14 15.14 39.17 3.91
823 827 2.662309 GGTCAGTGACCCGAGGTTA 58.338 57.895 29.13 0.00 46.19 2.85
926 930 1.271652 TGTCCTTTGTGTGGTGTGTGT 60.272 47.619 0.00 0.00 0.00 3.72
937 941 1.322442 GGCTCTGCTTTGTCCTTTGT 58.678 50.000 0.00 0.00 0.00 2.83
1092 1097 1.462928 CCACCAGCCCCCAAAGTAA 59.537 57.895 0.00 0.00 0.00 2.24
1135 1140 1.888215 CGGCCTGCATCATACTTGAT 58.112 50.000 0.00 0.00 43.51 2.57
1166 1171 3.770040 CCACGCCCATGGACTCGA 61.770 66.667 15.22 0.00 43.02 4.04
1419 1440 0.512952 GTGTCCACAAGTGCACGATC 59.487 55.000 12.01 0.14 0.00 3.69
1420 1441 0.884704 GGTGTCCACAAGTGCACGAT 60.885 55.000 12.01 1.15 33.09 3.73
1421 1442 1.522806 GGTGTCCACAAGTGCACGA 60.523 57.895 12.01 0.00 33.09 4.35
1422 1443 2.881266 CGGTGTCCACAAGTGCACG 61.881 63.158 12.01 0.00 33.09 5.34
1425 1446 3.660111 GGCGGTGTCCACAAGTGC 61.660 66.667 0.00 0.00 0.00 4.40
1427 1448 1.600636 CATGGCGGTGTCCACAAGT 60.601 57.895 0.00 0.00 39.25 3.16
1429 1450 2.282110 CCATGGCGGTGTCCACAA 60.282 61.111 0.00 0.00 39.25 3.33
1495 1516 7.618139 GCGACTCGGTTTAGTTAGAAGTTTTAC 60.618 40.741 0.00 0.00 0.00 2.01
1502 1523 3.829948 CTGCGACTCGGTTTAGTTAGAA 58.170 45.455 0.00 0.00 0.00 2.10
1568 1596 5.623169 TGTTTAGGGTTTTAGGTGTCGATT 58.377 37.500 0.00 0.00 0.00 3.34
1641 1672 1.821272 ATCGGCATGATCGAGGAGACT 60.821 52.381 14.90 0.00 40.09 3.24
1667 1698 2.433145 GACTGCAGCAGCTACGCA 60.433 61.111 23.05 7.19 42.74 5.24
1957 1988 2.668457 CCAACTGTGAATCAGAGTACGC 59.332 50.000 13.56 0.00 46.27 4.42
2050 2081 3.349006 CACGCGCAAGAGCACCTT 61.349 61.111 5.73 0.00 42.78 3.50
2193 2224 1.071471 ACCAACTGAAGAGCACCGG 59.929 57.895 0.00 0.00 0.00 5.28
2300 2331 1.904865 TGGACGCAACCGGAGTACT 60.905 57.895 9.46 0.00 39.22 2.73
2586 2617 1.214325 CTCATCGTGGGCGTGTACA 59.786 57.895 0.00 0.00 39.49 2.90
2834 2865 5.046910 GTTCATCACATGGACGTCAAATT 57.953 39.130 18.91 0.00 0.00 1.82
3202 3233 2.959484 CGGCCCGGCATATGATCCT 61.959 63.158 12.58 0.00 0.00 3.24
3237 3268 0.814010 GCACCGATTCCGCACCTTAT 60.814 55.000 0.00 0.00 0.00 1.73
3396 3427 1.525995 CCCACGCCACTTGTGTCTT 60.526 57.895 0.00 0.00 34.84 3.01
3526 3561 2.092914 GGCACACTAGGACTAGGCAAAT 60.093 50.000 10.81 0.00 37.49 2.32
3712 3747 0.827507 ATTTCCTGCGCACCTTTGGT 60.828 50.000 5.66 0.00 35.62 3.67
3999 4035 3.573772 CTGCGGCGGAGAGTTCACA 62.574 63.158 24.84 0.00 0.00 3.58
4087 4142 4.514577 CGAAGGACGAGGCCGCAT 62.515 66.667 7.44 0.00 45.77 4.73
4251 4306 3.000080 GCTCGTCCTTCGCACAACG 62.000 63.158 0.00 0.00 45.62 4.10
4439 4494 0.950555 GAATCGTGCAGCCAGTGTGA 60.951 55.000 0.00 0.00 0.00 3.58
4498 4553 2.002127 CATCGTCTTCTCGCCAAGC 58.998 57.895 0.00 0.00 0.00 4.01
4533 4588 2.657944 CGATGAGAGAGGCTGCGC 60.658 66.667 0.00 0.00 0.00 6.09
4534 4589 3.114650 TCGATGAGAGAGGCTGCG 58.885 61.111 0.00 0.00 0.00 5.18
4654 4736 0.455464 CGTCGTCAACATCTGCGGTA 60.455 55.000 0.00 0.00 0.00 4.02
4866 4948 0.039437 TTCGACCTCAACTCTGACGC 60.039 55.000 0.00 0.00 0.00 5.19
4902 4984 1.612726 GGAGCAGAGCTTGTTGATGGT 60.613 52.381 0.00 0.00 39.88 3.55
4909 4991 0.540923 GGATGAGGAGCAGAGCTTGT 59.459 55.000 0.00 0.00 39.88 3.16
4912 4994 1.108727 CGAGGATGAGGAGCAGAGCT 61.109 60.000 0.00 0.00 43.88 4.09
5173 5271 2.489329 CGATGATGGCAGTGGAAAACTT 59.511 45.455 0.00 0.00 36.83 2.66
5725 5827 2.443390 GGCCTTGCCCATGCTGAT 60.443 61.111 0.00 0.00 44.06 2.90
5922 6028 4.759782 CACCCACTTTCGTATTCATCTCT 58.240 43.478 0.00 0.00 0.00 3.10
6105 6226 2.029073 CGAGTGCACGGTCAAGGT 59.971 61.111 12.01 0.00 0.00 3.50
7330 10875 1.476488 CAAAAATTAGAGGGGCCGGTG 59.524 52.381 1.90 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.