Multiple sequence alignment - TraesCS6B01G360700

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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 TraesCS6B01G360700 chr6B 100.000 3853 0 0 1 3853 632501795 632505647 0.000000e+00 7116.0
1 TraesCS6B01G360700 chr6B 91.206 887 65 8 1649 2535 632242725 632243598 0.000000e+00 1194.0
2 TraesCS6B01G360700 chr6B 92.099 848 37 14 3 840 638424679 638423852 0.000000e+00 1168.0
3 TraesCS6B01G360700 chr6B 83.306 1204 144 37 1648 2828 632787079 632788248 0.000000e+00 1057.0
4 TraesCS6B01G360700 chr6B 83.051 1180 138 41 1675 2831 632565259 632566399 0.000000e+00 1014.0
5 TraesCS6B01G360700 chr6B 92.045 704 55 1 3150 3853 365737380 365736678 0.000000e+00 989.0
6 TraesCS6B01G360700 chr6B 91.523 696 57 2 3150 3845 19544672 19543979 0.000000e+00 957.0
7 TraesCS6B01G360700 chr6B 82.322 379 41 20 999 1366 632786241 632786604 4.840000e-79 305.0
8 TraesCS6B01G360700 chr6B 83.962 318 37 11 524 836 719443184 719442876 3.770000e-75 292.0
9 TraesCS6B01G360700 chr6B 96.296 162 6 0 999 1160 632419983 632420144 2.280000e-67 267.0
10 TraesCS6B01G360700 chr6B 75.625 320 47 22 1194 1497 632564728 632565032 3.120000e-26 130.0
11 TraesCS6B01G360700 chr6A 92.098 1468 69 19 1395 2840 562813170 562814612 0.000000e+00 2025.0
12 TraesCS6B01G360700 chr6A 89.709 894 77 12 1646 2535 562704433 562705315 0.000000e+00 1127.0
13 TraesCS6B01G360700 chr6A 82.715 1186 149 34 1675 2840 562869208 562870357 0.000000e+00 1003.0
14 TraesCS6B01G360700 chr6A 82.738 1176 141 40 1673 2828 562920181 562921314 0.000000e+00 990.0
15 TraesCS6B01G360700 chr6A 83.366 1034 119 33 1831 2818 562796843 562797869 0.000000e+00 907.0
16 TraesCS6B01G360700 chr6A 88.525 366 23 12 999 1354 562812609 562812965 3.560000e-115 425.0
17 TraesCS6B01G360700 chr6A 96.296 162 6 0 999 1160 562794945 562795106 2.280000e-67 267.0
18 TraesCS6B01G360700 chr6A 92.655 177 9 3 999 1175 562918916 562919088 6.390000e-63 252.0
19 TraesCS6B01G360700 chr6A 91.860 172 10 1 2983 3150 562814704 562814875 1.790000e-58 237.0
20 TraesCS6B01G360700 chr6A 85.714 77 11 0 1420 1496 562795971 562796047 8.870000e-12 82.4
21 TraesCS6B01G360700 chr6A 84.706 85 9 2 1413 1497 562868928 562869008 8.870000e-12 82.4
22 TraesCS6B01G360700 chr6D 95.161 1178 46 7 1673 2840 419614588 419615764 0.000000e+00 1849.0
23 TraesCS6B01G360700 chr6D 90.244 861 75 6 1675 2535 419285944 419286795 0.000000e+00 1116.0
24 TraesCS6B01G360700 chr6D 83.632 1173 143 32 1673 2828 419748293 419749433 0.000000e+00 1057.0
25 TraesCS6B01G360700 chr6D 83.076 1164 153 29 1675 2831 419657292 419658418 0.000000e+00 1018.0
26 TraesCS6B01G360700 chr6D 84.038 946 118 18 1857 2782 419447742 419448674 0.000000e+00 880.0
27 TraesCS6B01G360700 chr6D 90.545 275 8 6 999 1255 419614314 419614588 7.920000e-92 348.0
28 TraesCS6B01G360700 chr6D 95.062 162 8 0 999 1160 419482543 419482704 4.940000e-64 255.0
29 TraesCS6B01G360700 chr6D 94.083 169 7 2 999 1167 419746991 419747156 1.780000e-63 254.0
30 TraesCS6B01G360700 chr6D 96.078 153 6 0 999 1151 419284401 419284553 2.300000e-62 250.0
31 TraesCS6B01G360700 chr6D 92.529 174 7 3 837 1004 419614098 419614271 1.070000e-60 244.0
32 TraesCS6B01G360700 chr6D 95.294 85 4 0 3066 3150 419616051 419616135 6.710000e-28 135.0
33 TraesCS6B01G360700 chr6D 74.909 275 41 17 1192 1450 419655403 419655665 2.450000e-17 100.0
34 TraesCS6B01G360700 chr6D 96.970 33 1 0 1333 1365 419484271 419484303 5.380000e-04 56.5
35 TraesCS6B01G360700 chr5A 93.993 849 30 12 3 836 650550118 650550960 0.000000e+00 1266.0
36 TraesCS6B01G360700 chr5A 91.841 429 35 0 3 431 647972662 647973090 1.980000e-167 599.0
37 TraesCS6B01G360700 chr5A 88.816 456 40 8 3 453 671513618 671514067 2.020000e-152 549.0
38 TraesCS6B01G360700 chr5B 89.692 844 64 17 3 836 58401213 58402043 0.000000e+00 1055.0
39 TraesCS6B01G360700 chr5B 91.335 704 59 2 3150 3853 653395954 653396655 0.000000e+00 961.0
40 TraesCS6B01G360700 chr5B 96.706 425 11 2 3 424 394619167 394618743 0.000000e+00 704.0
41 TraesCS6B01G360700 chr5B 94.000 300 14 3 541 836 394609989 394609690 5.870000e-123 451.0
42 TraesCS6B01G360700 chr1B 92.472 704 52 1 3150 3853 272403674 272402972 0.000000e+00 1005.0
43 TraesCS6B01G360700 chr1B 93.458 107 7 0 2859 2965 564918992 564919098 3.980000e-35 159.0
44 TraesCS6B01G360700 chr3B 92.045 704 54 2 3150 3853 592828952 592829653 0.000000e+00 989.0
45 TraesCS6B01G360700 chr3B 93.519 108 7 0 2858 2965 457968681 457968788 1.110000e-35 161.0
46 TraesCS6B01G360700 chr2B 91.977 698 56 0 3156 3853 163736645 163735948 0.000000e+00 979.0
47 TraesCS6B01G360700 chr2B 91.773 705 56 2 3150 3853 424512703 424513406 0.000000e+00 979.0
48 TraesCS6B01G360700 chr2B 90.845 284 19 5 559 836 733207507 733207789 1.310000e-99 374.0
49 TraesCS6B01G360700 chr7B 91.372 707 61 0 3147 3853 240024745 240025451 0.000000e+00 968.0
50 TraesCS6B01G360700 chr7B 86.747 332 33 9 511 836 746590619 746590945 3.660000e-95 359.0
51 TraesCS6B01G360700 chr7B 92.593 108 8 0 2858 2965 226219532 226219639 5.150000e-34 156.0
52 TraesCS6B01G360700 chr3D 91.348 705 59 2 3151 3853 467275625 467276329 0.000000e+00 963.0
53 TraesCS6B01G360700 chr3D 93.458 107 7 0 2859 2965 439679604 439679498 3.980000e-35 159.0
54 TraesCS6B01G360700 chr7D 83.117 847 95 40 3 836 534328875 534328064 0.000000e+00 728.0
55 TraesCS6B01G360700 chr7D 93.519 108 7 0 2858 2965 55400508 55400615 1.110000e-35 161.0
56 TraesCS6B01G360700 chr1D 94.550 422 23 0 3 424 408935385 408935806 0.000000e+00 652.0
57 TraesCS6B01G360700 chr2A 90.654 428 40 0 3 430 775306025 775306452 1.550000e-158 569.0
58 TraesCS6B01G360700 chr4D 89.575 259 23 4 580 836 361847188 361847444 3.710000e-85 326.0
59 TraesCS6B01G360700 chr5D 89.189 259 24 4 580 836 101752566 101752310 1.730000e-83 320.0
60 TraesCS6B01G360700 chr4B 93.578 109 6 1 2857 2965 636915231 636915338 1.110000e-35 161.0
61 TraesCS6B01G360700 chr4B 93.458 107 6 1 2859 2965 460273683 460273578 1.430000e-34 158.0
62 TraesCS6B01G360700 chr4A 93.458 107 7 0 2859 2965 660714405 660714299 3.980000e-35 159.0
63 TraesCS6B01G360700 chrUn 93.458 107 6 1 2859 2965 233406921 233406816 1.430000e-34 158.0


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 TraesCS6B01G360700 chr6B 632501795 632505647 3852 False 7116.000000 7116 100.000000 1 3853 1 chr6B.!!$F3 3852
1 TraesCS6B01G360700 chr6B 632242725 632243598 873 False 1194.000000 1194 91.206000 1649 2535 1 chr6B.!!$F1 886
2 TraesCS6B01G360700 chr6B 638423852 638424679 827 True 1168.000000 1168 92.099000 3 840 1 chr6B.!!$R3 837
3 TraesCS6B01G360700 chr6B 365736678 365737380 702 True 989.000000 989 92.045000 3150 3853 1 chr6B.!!$R2 703
4 TraesCS6B01G360700 chr6B 19543979 19544672 693 True 957.000000 957 91.523000 3150 3845 1 chr6B.!!$R1 695
5 TraesCS6B01G360700 chr6B 632786241 632788248 2007 False 681.000000 1057 82.814000 999 2828 2 chr6B.!!$F5 1829
6 TraesCS6B01G360700 chr6B 632564728 632566399 1671 False 572.000000 1014 79.338000 1194 2831 2 chr6B.!!$F4 1637
7 TraesCS6B01G360700 chr6A 562704433 562705315 882 False 1127.000000 1127 89.709000 1646 2535 1 chr6A.!!$F1 889
8 TraesCS6B01G360700 chr6A 562812609 562814875 2266 False 895.666667 2025 90.827667 999 3150 3 chr6A.!!$F3 2151
9 TraesCS6B01G360700 chr6A 562918916 562921314 2398 False 621.000000 990 87.696500 999 2828 2 chr6A.!!$F5 1829
10 TraesCS6B01G360700 chr6A 562868928 562870357 1429 False 542.700000 1003 83.710500 1413 2840 2 chr6A.!!$F4 1427
11 TraesCS6B01G360700 chr6A 562794945 562797869 2924 False 418.800000 907 88.458667 999 2818 3 chr6A.!!$F2 1819
12 TraesCS6B01G360700 chr6D 419447742 419448674 932 False 880.000000 880 84.038000 1857 2782 1 chr6D.!!$F1 925
13 TraesCS6B01G360700 chr6D 419284401 419286795 2394 False 683.000000 1116 93.161000 999 2535 2 chr6D.!!$F2 1536
14 TraesCS6B01G360700 chr6D 419746991 419749433 2442 False 655.500000 1057 88.857500 999 2828 2 chr6D.!!$F6 1829
15 TraesCS6B01G360700 chr6D 419614098 419616135 2037 False 644.000000 1849 93.382250 837 3150 4 chr6D.!!$F4 2313
16 TraesCS6B01G360700 chr6D 419655403 419658418 3015 False 559.000000 1018 78.992500 1192 2831 2 chr6D.!!$F5 1639
17 TraesCS6B01G360700 chr5A 650550118 650550960 842 False 1266.000000 1266 93.993000 3 836 1 chr5A.!!$F2 833
18 TraesCS6B01G360700 chr5B 58401213 58402043 830 False 1055.000000 1055 89.692000 3 836 1 chr5B.!!$F1 833
19 TraesCS6B01G360700 chr5B 653395954 653396655 701 False 961.000000 961 91.335000 3150 3853 1 chr5B.!!$F2 703
20 TraesCS6B01G360700 chr1B 272402972 272403674 702 True 1005.000000 1005 92.472000 3150 3853 1 chr1B.!!$R1 703
21 TraesCS6B01G360700 chr3B 592828952 592829653 701 False 989.000000 989 92.045000 3150 3853 1 chr3B.!!$F2 703
22 TraesCS6B01G360700 chr2B 163735948 163736645 697 True 979.000000 979 91.977000 3156 3853 1 chr2B.!!$R1 697
23 TraesCS6B01G360700 chr2B 424512703 424513406 703 False 979.000000 979 91.773000 3150 3853 1 chr2B.!!$F1 703
24 TraesCS6B01G360700 chr7B 240024745 240025451 706 False 968.000000 968 91.372000 3147 3853 1 chr7B.!!$F2 706
25 TraesCS6B01G360700 chr3D 467275625 467276329 704 False 963.000000 963 91.348000 3151 3853 1 chr3D.!!$F1 702
26 TraesCS6B01G360700 chr7D 534328064 534328875 811 True 728.000000 728 83.117000 3 836 1 chr7D.!!$R1 833

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
876 1000 0.390340 GTGTGAGCTCATCGCCTCAA 60.39 55.000 21.47 0.0 40.39 3.02 F
1898 5372 1.000163 CTCTACTACATGGGCGCGAAT 60.00 52.381 12.10 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 5846 1.444553 CGTGAAGAGGCGAGTGTCC 60.445 63.158 0.0 0.0 0.0 4.02 R
2959 6530 0.179161 CTCTCGCTACACTGGTTCGG 60.179 60.000 0.0 0.0 0.0 4.30 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
391 395 2.359850 GAACCGGACATGGCTGCA 60.360 61.111 9.46 0.00 0.00 4.41
496 580 2.583593 GCGTAGGCGAGCAGGAAG 60.584 66.667 0.00 0.00 41.33 3.46
497 581 2.885861 CGTAGGCGAGCAGGAAGT 59.114 61.111 0.00 0.00 41.33 3.01
500 584 1.609501 TAGGCGAGCAGGAAGTGGT 60.610 57.895 0.00 0.00 40.54 4.16
507 619 2.103042 GCAGGAAGTGGTGCTAGCG 61.103 63.158 10.77 0.00 36.71 4.26
583 696 3.217743 GGCGAGGCTAGCTACGGT 61.218 66.667 25.48 5.34 34.52 4.83
585 698 2.478890 GCGAGGCTAGCTACGGTGA 61.479 63.158 25.48 0.00 0.00 4.02
693 816 4.443739 CGGGTTTAGGCTGATACCATGTAA 60.444 45.833 13.99 0.00 32.20 2.41
714 837 5.490139 AAAGGATTATGCAACTCACGATG 57.510 39.130 0.00 0.00 0.00 3.84
876 1000 0.390340 GTGTGAGCTCATCGCCTCAA 60.390 55.000 21.47 0.00 40.39 3.02
915 1039 5.758296 GGCAGTAGTTAAATCCAATCGATCA 59.242 40.000 0.00 0.00 0.00 2.92
949 1076 5.971763 ACCATAGCTACAAAAGAGTGAGAG 58.028 41.667 0.00 0.00 0.00 3.20
967 1097 4.058817 GAGAGTTGGAGCGAGAAGAAAAA 58.941 43.478 0.00 0.00 0.00 1.94
968 1098 4.061596 AGAGTTGGAGCGAGAAGAAAAAG 58.938 43.478 0.00 0.00 0.00 2.27
986 1116 1.230324 AGACTCGCAAACTTCCAAGC 58.770 50.000 0.00 0.00 0.00 4.01
990 1120 2.049156 GCAAACTTCCAAGCGGGC 60.049 61.111 0.00 0.00 36.21 6.13
1036 1214 2.125269 GGTTCGCCGGCATGTACT 60.125 61.111 28.98 0.00 0.00 2.73
1061 1239 4.680237 CGTGGCGTCCCTCAAGCA 62.680 66.667 0.00 0.00 0.00 3.91
1171 1350 4.880164 ACCCTACCTAGCTAGTTCAATCA 58.120 43.478 19.31 0.00 0.00 2.57
1172 1351 4.650131 ACCCTACCTAGCTAGTTCAATCAC 59.350 45.833 19.31 0.00 0.00 3.06
1174 1353 5.305644 CCCTACCTAGCTAGTTCAATCACAT 59.694 44.000 19.31 0.00 0.00 3.21
1175 1354 6.183361 CCCTACCTAGCTAGTTCAATCACATT 60.183 42.308 19.31 0.00 0.00 2.71
1307 2292 9.139734 CCAGAAAAGTAGTACATACATACCCTA 57.860 37.037 2.52 0.00 36.79 3.53
1367 2423 6.970613 CCTTATTCTATTTTGTACCGGCAAAC 59.029 38.462 0.00 0.00 37.98 2.93
1401 2475 3.120477 CCTTGTAACGCGTCAAATAAGCA 60.120 43.478 14.44 0.00 32.19 3.91
1410 2579 4.527564 GCGTCAAATAAGCATATGTCCAC 58.472 43.478 4.29 0.00 32.19 4.02
1481 4011 9.944376 TGCATTAGTCAGTAGAAGTAGAAAATT 57.056 29.630 0.00 0.00 0.00 1.82
1499 4029 3.720949 ATTACGCATACGCAGGTAGAA 57.279 42.857 0.00 0.00 45.53 2.10
1531 4068 2.174639 AGGAACCATTGTCACTTCACCA 59.825 45.455 0.00 0.00 0.00 4.17
1555 4239 4.102210 CACCATCCTCAGTTCCACTCATAT 59.898 45.833 0.00 0.00 0.00 1.78
1560 4244 6.019656 TCCTCAGTTCCACTCATATACTCT 57.980 41.667 0.00 0.00 0.00 3.24
1563 4247 7.667635 TCCTCAGTTCCACTCATATACTCTATG 59.332 40.741 0.00 0.00 0.00 2.23
1593 5029 5.345702 TCATTTCGACGTTTATACCTGGAG 58.654 41.667 0.00 0.00 0.00 3.86
1594 5030 4.789012 TTTCGACGTTTATACCTGGAGT 57.211 40.909 0.00 0.00 0.00 3.85
1612 5053 9.838339 ACCTGGAGTAGTATTCATGAAATTAAG 57.162 33.333 13.09 1.50 0.00 1.85
1635 5076 6.787225 AGATCAGAACTAGTTAACGTGCTAG 58.213 40.000 8.42 15.92 40.21 3.42
1637 5078 7.551974 AGATCAGAACTAGTTAACGTGCTAGTA 59.448 37.037 20.59 10.78 44.84 1.82
1639 5080 8.048534 TCAGAACTAGTTAACGTGCTAGTAAT 57.951 34.615 20.59 13.16 44.84 1.89
1641 5082 9.778993 CAGAACTAGTTAACGTGCTAGTAATTA 57.221 33.333 20.59 4.36 44.84 1.40
1668 5110 5.153513 TGTATTTACTCCAACGTACGTGAC 58.846 41.667 23.57 8.06 0.00 3.67
1772 5217 3.088552 CGTTGCGGTTGATTAATTCGAC 58.911 45.455 0.00 0.00 37.94 4.20
1810 5267 1.134995 TCCATGCATGACGACAGAGTC 60.135 52.381 28.31 0.00 41.30 3.36
1827 5292 3.578716 AGAGTCCAAAGCTGCTGTTACTA 59.421 43.478 1.35 0.00 0.00 1.82
1898 5372 1.000163 CTCTACTACATGGGCGCGAAT 60.000 52.381 12.10 0.00 0.00 3.34
2348 5846 3.499737 GCGTGGGTCATCGGCTTG 61.500 66.667 0.00 0.00 0.00 4.01
2571 6080 2.866156 TGCCATTTTCAGATCGACGATC 59.134 45.455 26.72 26.72 39.17 3.69
2572 6081 2.097202 GCCATTTTCAGATCGACGATCG 60.097 50.000 27.27 22.05 43.17 3.69
2863 6434 1.823976 GCCACTAGCCCACTACTCC 59.176 63.158 0.00 0.00 34.35 3.85
2866 6437 1.404843 CACTAGCCCACTACTCCCTC 58.595 60.000 0.00 0.00 0.00 4.30
2867 6438 0.262285 ACTAGCCCACTACTCCCTCC 59.738 60.000 0.00 0.00 0.00 4.30
2868 6439 0.824182 CTAGCCCACTACTCCCTCCG 60.824 65.000 0.00 0.00 0.00 4.63
2870 6441 1.988406 GCCCACTACTCCCTCCGTT 60.988 63.158 0.00 0.00 0.00 4.44
2871 6442 1.551019 GCCCACTACTCCCTCCGTTT 61.551 60.000 0.00 0.00 0.00 3.60
2872 6443 1.856629 CCCACTACTCCCTCCGTTTA 58.143 55.000 0.00 0.00 0.00 2.01
2873 6444 2.181975 CCCACTACTCCCTCCGTTTAA 58.818 52.381 0.00 0.00 0.00 1.52
2874 6445 2.568509 CCCACTACTCCCTCCGTTTAAA 59.431 50.000 0.00 0.00 0.00 1.52
2877 6448 5.250982 CCACTACTCCCTCCGTTTAAAATT 58.749 41.667 0.00 0.00 0.00 1.82
2878 6449 6.408869 CCACTACTCCCTCCGTTTAAAATTA 58.591 40.000 0.00 0.00 0.00 1.40
2879 6450 6.314648 CCACTACTCCCTCCGTTTAAAATTAC 59.685 42.308 0.00 0.00 0.00 1.89
2880 6451 7.101700 CACTACTCCCTCCGTTTAAAATTACT 58.898 38.462 0.00 0.00 0.00 2.24
2881 6452 7.605309 CACTACTCCCTCCGTTTAAAATTACTT 59.395 37.037 0.00 0.00 0.00 2.24
2883 6454 6.301486 ACTCCCTCCGTTTAAAATTACTTGT 58.699 36.000 0.00 0.00 0.00 3.16
2884 6455 6.429078 ACTCCCTCCGTTTAAAATTACTTGTC 59.571 38.462 0.00 0.00 0.00 3.18
2885 6456 6.297582 TCCCTCCGTTTAAAATTACTTGTCA 58.702 36.000 0.00 0.00 0.00 3.58
2886 6457 6.205270 TCCCTCCGTTTAAAATTACTTGTCAC 59.795 38.462 0.00 0.00 0.00 3.67
2888 6459 7.419204 CCTCCGTTTAAAATTACTTGTCACAA 58.581 34.615 0.00 0.00 0.00 3.33
2889 6460 7.916450 CCTCCGTTTAAAATTACTTGTCACAAA 59.084 33.333 0.00 0.00 0.00 2.83
2890 6461 9.291664 CTCCGTTTAAAATTACTTGTCACAAAA 57.708 29.630 0.00 0.00 0.00 2.44
2960 6531 9.099454 ACATTCATTTTCTAGACGAGTAATTCC 57.901 33.333 0.00 0.00 0.00 3.01
2961 6532 7.751047 TTCATTTTCTAGACGAGTAATTCCG 57.249 36.000 0.00 0.00 0.00 4.30
2962 6533 7.092137 TCATTTTCTAGACGAGTAATTCCGA 57.908 36.000 0.00 0.00 0.00 4.55
2963 6534 7.541162 TCATTTTCTAGACGAGTAATTCCGAA 58.459 34.615 0.00 0.00 0.00 4.30
2964 6535 7.487189 TCATTTTCTAGACGAGTAATTCCGAAC 59.513 37.037 0.00 0.00 0.00 3.95
2965 6536 4.889832 TCTAGACGAGTAATTCCGAACC 57.110 45.455 0.00 0.00 0.00 3.62
2966 6537 4.264253 TCTAGACGAGTAATTCCGAACCA 58.736 43.478 0.00 0.00 0.00 3.67
2967 6538 3.505464 AGACGAGTAATTCCGAACCAG 57.495 47.619 0.00 0.00 0.00 4.00
2968 6539 2.824341 AGACGAGTAATTCCGAACCAGT 59.176 45.455 0.00 0.00 0.00 4.00
2969 6540 2.921754 GACGAGTAATTCCGAACCAGTG 59.078 50.000 0.00 0.00 0.00 3.66
2970 6541 2.298163 ACGAGTAATTCCGAACCAGTGT 59.702 45.455 0.00 0.00 0.00 3.55
2971 6542 3.507233 ACGAGTAATTCCGAACCAGTGTA 59.493 43.478 0.00 0.00 0.00 2.90
2972 6543 4.103357 CGAGTAATTCCGAACCAGTGTAG 58.897 47.826 0.00 0.00 0.00 2.74
2973 6544 3.858247 AGTAATTCCGAACCAGTGTAGC 58.142 45.455 0.00 0.00 0.00 3.58
2974 6545 1.722011 AATTCCGAACCAGTGTAGCG 58.278 50.000 0.00 0.00 0.00 4.26
2975 6546 0.892755 ATTCCGAACCAGTGTAGCGA 59.107 50.000 0.00 0.00 0.00 4.93
2976 6547 0.242825 TTCCGAACCAGTGTAGCGAG 59.757 55.000 0.00 0.00 0.00 5.03
2977 6548 0.607217 TCCGAACCAGTGTAGCGAGA 60.607 55.000 0.00 0.00 0.00 4.04
2978 6549 0.179161 CCGAACCAGTGTAGCGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
2979 6550 0.522180 CGAACCAGTGTAGCGAGAGT 59.478 55.000 0.00 0.00 0.00 3.24
2980 6551 1.736126 CGAACCAGTGTAGCGAGAGTA 59.264 52.381 0.00 0.00 0.00 2.59
2981 6552 2.223066 CGAACCAGTGTAGCGAGAGTAG 60.223 54.545 0.00 0.00 0.00 2.57
2991 6562 0.383737 GCGAGAGTAGCATCGACGAG 60.384 60.000 3.01 0.00 41.40 4.18
3006 6577 2.599082 CGACGAGTATGTCTGCCTTTTC 59.401 50.000 0.00 0.00 36.71 2.29
3014 6585 2.681421 CTGCCTTTTCCCCCTGGC 60.681 66.667 0.00 0.00 45.10 4.85
3017 6588 1.309688 GCCTTTTCCCCCTGGCATA 59.690 57.895 0.00 0.00 44.34 3.14
3064 6687 7.589574 TCATGCATGAAGATGAATTTTGTTG 57.410 32.000 26.87 0.00 33.08 3.33
3077 6700 6.287525 TGAATTTTGTTGTCCATTTTCCTCC 58.712 36.000 0.00 0.00 0.00 4.30
3111 6734 2.478709 CCTAGCGACGATCCTATCATGC 60.479 54.545 0.00 0.00 0.00 4.06
3124 6747 5.012893 TCCTATCATGCGACTATGTGAGAT 58.987 41.667 0.00 0.00 0.00 2.75
3214 6841 3.003482 CCGTTTTATGTTCGTTTGGGTCA 59.997 43.478 0.00 0.00 0.00 4.02
3387 7016 4.715983 GCATACATTGCCGGCTTG 57.284 55.556 29.70 25.80 46.15 4.01
3617 7248 2.750350 CACGGCCTCTTCCTTGGT 59.250 61.111 0.00 0.00 0.00 3.67
3658 7289 2.111878 CATGATCTCCACCCCGGC 59.888 66.667 0.00 0.00 33.14 6.13
3777 7408 3.529341 TTGGCTTGCTTCTCCGCGA 62.529 57.895 8.23 0.00 0.00 5.87
3803 7434 4.631234 TCTTTAGCCTCCTCCTTTGGATA 58.369 43.478 0.00 0.00 35.30 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.098200 CAAGGACGATGCATGCACAG 59.902 55.000 25.37 21.59 0.00 3.66
1 2 0.606130 ACAAGGACGATGCATGCACA 60.606 50.000 25.37 0.00 0.00 4.57
391 395 1.530655 CCCAGCCAAAACCGAACCT 60.531 57.895 0.00 0.00 0.00 3.50
455 531 4.598894 CCCGATCGCCCTGCTCTG 62.599 72.222 10.32 0.00 0.00 3.35
483 567 2.925170 ACCACTTCCTGCTCGCCT 60.925 61.111 0.00 0.00 0.00 5.52
484 568 2.743928 CACCACTTCCTGCTCGCC 60.744 66.667 0.00 0.00 0.00 5.54
486 570 0.459237 CTAGCACCACTTCCTGCTCG 60.459 60.000 0.00 0.00 42.86 5.03
488 572 1.298014 GCTAGCACCACTTCCTGCT 59.702 57.895 10.63 0.00 45.76 4.24
489 573 2.103042 CGCTAGCACCACTTCCTGC 61.103 63.158 16.45 0.00 0.00 4.85
490 574 1.448540 CCGCTAGCACCACTTCCTG 60.449 63.158 16.45 0.00 0.00 3.86
583 696 0.101579 TCGCAGATTATTCGCCGTCA 59.898 50.000 0.00 0.00 0.00 4.35
585 698 1.206745 CGTCGCAGATTATTCGCCGT 61.207 55.000 0.00 0.00 40.67 5.68
660 780 0.546598 CCTAAACCCGATTCCTGCCT 59.453 55.000 0.00 0.00 0.00 4.75
693 816 4.517285 ACATCGTGAGTTGCATAATCCTT 58.483 39.130 0.00 0.00 34.20 3.36
714 837 2.096417 GCGTATTGCACCCGATCAATAC 60.096 50.000 12.54 12.54 45.56 1.89
737 860 9.604569 TGGCTACCCTTTGTACTTATATATACA 57.395 33.333 0.00 0.00 0.00 2.29
938 1062 1.964223 TCGCTCCAACTCTCACTCTTT 59.036 47.619 0.00 0.00 0.00 2.52
939 1063 1.543802 CTCGCTCCAACTCTCACTCTT 59.456 52.381 0.00 0.00 0.00 2.85
949 1076 3.810386 AGTCTTTTTCTTCTCGCTCCAAC 59.190 43.478 0.00 0.00 0.00 3.77
967 1097 1.230324 GCTTGGAAGTTTGCGAGTCT 58.770 50.000 3.08 0.00 33.05 3.24
968 1098 3.755697 GCTTGGAAGTTTGCGAGTC 57.244 52.632 3.08 0.00 33.05 3.36
986 1116 2.885644 CCATCGTCGTCTTGCCCG 60.886 66.667 0.00 0.00 0.00 6.13
990 1120 1.959899 GCAGCACCATCGTCGTCTTG 61.960 60.000 0.00 0.00 0.00 3.02
1061 1239 2.283529 ACGAAGTGGCTCATCCCGT 61.284 57.895 0.00 0.00 42.51 5.28
1171 1350 1.399440 CGCATGAGCTAGCACAAATGT 59.601 47.619 18.89 0.00 39.10 2.71
1172 1351 1.858798 GCGCATGAGCTAGCACAAATG 60.859 52.381 18.89 14.12 39.10 2.32
1174 1353 0.954938 TGCGCATGAGCTAGCACAAA 60.955 50.000 22.25 0.00 39.10 2.83
1175 1354 1.375780 TGCGCATGAGCTAGCACAA 60.376 52.632 22.25 2.58 39.10 3.33
1313 2298 9.244799 TCAAGATGCATATGTTTACTAGTAACG 57.755 33.333 14.96 1.80 0.00 3.18
1385 2459 4.260620 GGACATATGCTTATTTGACGCGTT 60.261 41.667 15.53 0.00 0.00 4.84
1401 2475 0.464193 TGCTGCATGCGTGGACATAT 60.464 50.000 14.09 0.00 46.63 1.78
1410 2579 4.374399 TCCATATATAGATGCTGCATGCG 58.626 43.478 21.53 9.16 46.63 4.73
1484 4014 3.984508 TCTACTTCTACCTGCGTATGC 57.015 47.619 0.00 0.00 43.20 3.14
1499 4029 5.061721 ACAATGGTTCCTGGTTTTCTACT 57.938 39.130 0.00 0.00 0.00 2.57
1555 4239 5.753438 GTCGAAATGAACCATGCATAGAGTA 59.247 40.000 0.00 0.00 0.00 2.59
1560 4244 3.266636 ACGTCGAAATGAACCATGCATA 58.733 40.909 0.00 0.00 0.00 3.14
1563 4247 2.611974 AACGTCGAAATGAACCATGC 57.388 45.000 0.00 0.00 0.00 4.06
1612 5053 6.553524 ACTAGCACGTTAACTAGTTCTGATC 58.446 40.000 12.39 0.00 45.25 2.92
1639 5080 9.202273 ACGTACGTTGGAGTAAATACAAATTAA 57.798 29.630 16.72 0.00 31.92 1.40
1641 5082 7.384660 TCACGTACGTTGGAGTAAATACAAATT 59.615 33.333 20.23 0.00 31.92 1.82
1642 5083 6.867816 TCACGTACGTTGGAGTAAATACAAAT 59.132 34.615 20.23 0.00 31.92 2.32
1810 5267 4.216257 ACATGTTAGTAACAGCAGCTTTGG 59.784 41.667 19.87 4.94 45.95 3.28
1827 5292 1.532921 CGACGCAACAAACCACATGTT 60.533 47.619 0.00 0.00 41.50 2.71
2348 5846 1.444553 CGTGAAGAGGCGAGTGTCC 60.445 63.158 0.00 0.00 0.00 4.02
2714 6264 1.668151 GCCCTTGACACTGACGTCC 60.668 63.158 14.12 0.00 34.88 4.79
2854 6425 3.967332 TTTAAACGGAGGGAGTAGTGG 57.033 47.619 0.00 0.00 0.00 4.00
2857 6428 7.605309 ACAAGTAATTTTAAACGGAGGGAGTAG 59.395 37.037 0.00 0.00 0.00 2.57
2860 6431 6.428771 TGACAAGTAATTTTAAACGGAGGGAG 59.571 38.462 0.00 0.00 0.00 4.30
2861 6432 6.205270 GTGACAAGTAATTTTAAACGGAGGGA 59.795 38.462 0.00 0.00 0.00 4.20
2862 6433 6.016943 TGTGACAAGTAATTTTAAACGGAGGG 60.017 38.462 0.00 0.00 0.00 4.30
2863 6434 6.961576 TGTGACAAGTAATTTTAAACGGAGG 58.038 36.000 0.00 0.00 0.00 4.30
2934 6505 9.099454 GGAATTACTCGTCTAGAAAATGAATGT 57.901 33.333 0.00 0.00 0.00 2.71
2935 6506 8.269424 CGGAATTACTCGTCTAGAAAATGAATG 58.731 37.037 0.00 0.00 0.00 2.67
2936 6507 8.195436 TCGGAATTACTCGTCTAGAAAATGAAT 58.805 33.333 0.00 0.00 0.00 2.57
2937 6508 7.541162 TCGGAATTACTCGTCTAGAAAATGAA 58.459 34.615 0.00 0.00 0.00 2.57
2938 6509 7.092137 TCGGAATTACTCGTCTAGAAAATGA 57.908 36.000 0.00 0.00 0.00 2.57
2939 6510 7.254017 GGTTCGGAATTACTCGTCTAGAAAATG 60.254 40.741 0.00 0.00 0.00 2.32
2940 6511 6.755607 GGTTCGGAATTACTCGTCTAGAAAAT 59.244 38.462 0.00 0.00 0.00 1.82
2941 6512 6.095377 GGTTCGGAATTACTCGTCTAGAAAA 58.905 40.000 0.00 0.00 0.00 2.29
2942 6513 5.183713 TGGTTCGGAATTACTCGTCTAGAAA 59.816 40.000 0.00 0.00 0.00 2.52
2943 6514 4.701651 TGGTTCGGAATTACTCGTCTAGAA 59.298 41.667 0.00 0.00 0.00 2.10
2944 6515 4.264253 TGGTTCGGAATTACTCGTCTAGA 58.736 43.478 0.00 0.00 0.00 2.43
2945 6516 4.096081 ACTGGTTCGGAATTACTCGTCTAG 59.904 45.833 0.00 0.00 0.00 2.43
2946 6517 4.012374 ACTGGTTCGGAATTACTCGTCTA 58.988 43.478 0.00 0.00 0.00 2.59
2947 6518 2.824341 ACTGGTTCGGAATTACTCGTCT 59.176 45.455 0.00 0.00 0.00 4.18
2948 6519 2.921754 CACTGGTTCGGAATTACTCGTC 59.078 50.000 0.00 0.00 0.00 4.20
2949 6520 2.298163 ACACTGGTTCGGAATTACTCGT 59.702 45.455 0.00 0.00 0.00 4.18
2950 6521 2.955614 ACACTGGTTCGGAATTACTCG 58.044 47.619 0.00 0.00 0.00 4.18
2951 6522 3.864003 GCTACACTGGTTCGGAATTACTC 59.136 47.826 0.00 0.00 0.00 2.59
2952 6523 3.675228 CGCTACACTGGTTCGGAATTACT 60.675 47.826 0.00 0.00 0.00 2.24
2953 6524 2.601763 CGCTACACTGGTTCGGAATTAC 59.398 50.000 0.00 0.00 0.00 1.89
2954 6525 2.492881 TCGCTACACTGGTTCGGAATTA 59.507 45.455 0.00 0.00 0.00 1.40
2955 6526 1.274167 TCGCTACACTGGTTCGGAATT 59.726 47.619 0.00 0.00 0.00 2.17
2956 6527 0.892755 TCGCTACACTGGTTCGGAAT 59.107 50.000 0.00 0.00 0.00 3.01
2957 6528 0.242825 CTCGCTACACTGGTTCGGAA 59.757 55.000 0.00 0.00 0.00 4.30
2958 6529 0.607217 TCTCGCTACACTGGTTCGGA 60.607 55.000 0.00 0.00 0.00 4.55
2959 6530 0.179161 CTCTCGCTACACTGGTTCGG 60.179 60.000 0.00 0.00 0.00 4.30
2960 6531 0.522180 ACTCTCGCTACACTGGTTCG 59.478 55.000 0.00 0.00 0.00 3.95
2961 6532 2.478200 GCTACTCTCGCTACACTGGTTC 60.478 54.545 0.00 0.00 0.00 3.62
2962 6533 1.473278 GCTACTCTCGCTACACTGGTT 59.527 52.381 0.00 0.00 0.00 3.67
2963 6534 1.096416 GCTACTCTCGCTACACTGGT 58.904 55.000 0.00 0.00 0.00 4.00
2964 6535 1.095600 TGCTACTCTCGCTACACTGG 58.904 55.000 0.00 0.00 0.00 4.00
2965 6536 2.601029 CGATGCTACTCTCGCTACACTG 60.601 54.545 0.00 0.00 0.00 3.66
2966 6537 1.600013 CGATGCTACTCTCGCTACACT 59.400 52.381 0.00 0.00 0.00 3.55
2967 6538 1.598132 TCGATGCTACTCTCGCTACAC 59.402 52.381 0.00 0.00 34.94 2.90
2968 6539 1.598132 GTCGATGCTACTCTCGCTACA 59.402 52.381 0.00 0.00 34.94 2.74
2969 6540 1.397441 CGTCGATGCTACTCTCGCTAC 60.397 57.143 0.00 0.00 34.94 3.58
2970 6541 0.859882 CGTCGATGCTACTCTCGCTA 59.140 55.000 0.00 0.00 34.94 4.26
2971 6542 0.810426 TCGTCGATGCTACTCTCGCT 60.810 55.000 0.00 0.00 34.94 4.93
2972 6543 0.383737 CTCGTCGATGCTACTCTCGC 60.384 60.000 0.00 0.00 34.94 5.03
2973 6544 0.931702 ACTCGTCGATGCTACTCTCG 59.068 55.000 0.00 0.00 36.25 4.04
2974 6545 3.495377 ACATACTCGTCGATGCTACTCTC 59.505 47.826 0.00 0.00 0.00 3.20
2975 6546 3.468770 ACATACTCGTCGATGCTACTCT 58.531 45.455 0.00 0.00 0.00 3.24
2976 6547 3.495377 AGACATACTCGTCGATGCTACTC 59.505 47.826 0.00 0.00 40.98 2.59
2977 6548 3.248841 CAGACATACTCGTCGATGCTACT 59.751 47.826 0.00 0.00 40.98 2.57
2978 6549 3.546617 CAGACATACTCGTCGATGCTAC 58.453 50.000 0.00 0.00 40.98 3.58
2979 6550 2.031944 GCAGACATACTCGTCGATGCTA 60.032 50.000 0.00 0.00 40.98 3.49
2980 6551 1.268794 GCAGACATACTCGTCGATGCT 60.269 52.381 0.00 0.00 40.98 3.79
2981 6552 1.124462 GCAGACATACTCGTCGATGC 58.876 55.000 0.00 0.00 40.98 3.91
2991 6562 1.285078 AGGGGGAAAAGGCAGACATAC 59.715 52.381 0.00 0.00 0.00 2.39
3014 6585 4.192429 TCGATGGACCATGCACTATATG 57.808 45.455 12.99 0.00 0.00 1.78
3017 6588 2.353109 CGATCGATGGACCATGCACTAT 60.353 50.000 12.99 0.00 0.00 2.12
3033 6604 3.924686 TCATCTTCATGCATGATCGATCG 59.075 43.478 29.13 22.52 36.56 3.69
3064 6687 2.087646 GCTGACAGGAGGAAAATGGAC 58.912 52.381 4.26 0.00 0.00 4.02
3077 6700 1.066858 TCGCTAGGGAAAAGCTGACAG 60.067 52.381 7.09 0.00 37.85 3.51
3111 6734 5.755861 TCACTCTCACTATCTCACATAGTCG 59.244 44.000 0.00 0.00 32.93 4.18
3124 6747 2.732412 GCACTTGCTCACTCTCACTA 57.268 50.000 0.00 0.00 38.21 2.74
3154 6781 4.754667 GGTCGGCCCGTTGGAGTC 62.755 72.222 1.63 0.00 0.00 3.36
3172 6799 3.552684 CGGACAAATGCACCATCTGTTTT 60.553 43.478 0.00 0.00 23.93 2.43
3183 6810 4.222886 CGAACATAAAACGGACAAATGCA 58.777 39.130 0.00 0.00 0.00 3.96
3564 7195 0.874390 GCCGACATGCTCAAGTTCAA 59.126 50.000 0.00 0.00 0.00 2.69
3617 7248 1.044611 TGGATCTCAACACCGTGTCA 58.955 50.000 4.23 0.00 0.00 3.58
3639 7270 1.447643 CCGGGGTGGAGATCATGAC 59.552 63.158 0.00 0.00 42.00 3.06
3658 7289 1.647629 GCTCTCGCAAGCATGATGG 59.352 57.895 0.00 0.00 42.05 3.51
3725 7356 2.563427 GCGGAGAAGCAAGCCAAC 59.437 61.111 0.00 0.00 37.05 3.77
3777 7408 2.577772 AGGAGGAGGCTAAAGATGGT 57.422 50.000 0.00 0.00 0.00 3.55
3803 7434 2.159198 GCAAATGAACGCCTTCATGGAT 60.159 45.455 11.07 0.25 44.93 3.41


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

AutoCloner maintained by Alex Coulton.