Multiple sequence alignment - TraesCS6B01G015100

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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 TraesCS6B01G015100 chr6B 100.000 3815 0 0 1 3815 9033513 9037327 0.000000e+00 7046.0
1 TraesCS6B01G015100 chr6B 89.368 1646 152 13 1376 3008 9058660 9060295 0.000000e+00 2049.0
2 TraesCS6B01G015100 chr6B 81.582 847 112 24 2994 3815 9060355 9061182 0.000000e+00 660.0
3 TraesCS6B01G015100 chr6B 84.000 575 65 16 2062 2612 9080352 9080923 9.390000e-146 527.0
4 TraesCS6B01G015100 chr6B 81.395 602 70 20 488 1058 9057530 9058120 1.620000e-123 453.0
5 TraesCS6B01G015100 chr6B 85.339 457 45 13 1503 1948 9079838 9080283 1.620000e-123 453.0
6 TraesCS6B01G015100 chr6D 88.264 2914 229 46 975 3815 4722543 4719670 0.000000e+00 3382.0
7 TraesCS6B01G015100 chr6D 92.285 998 57 11 6 988 4723552 4722560 0.000000e+00 1399.0
8 TraesCS6B01G015100 chr6D 78.251 1784 269 71 1326 3039 3713344 3715078 0.000000e+00 1035.0
9 TraesCS6B01G015100 chr6D 83.384 662 75 13 2062 2692 3726989 3727646 7.100000e-162 580.0
10 TraesCS6B01G015100 chr6D 83.515 643 74 20 2062 2690 3740058 3740682 4.280000e-159 571.0
11 TraesCS6B01G015100 chr6D 79.315 701 87 24 407 1058 3756523 3757214 4.520000e-119 438.0
12 TraesCS6B01G015100 chr6D 85.092 436 46 10 1503 1927 3739543 3739970 9.790000e-116 427.0
13 TraesCS6B01G015100 chr6D 78.064 661 74 30 629 1252 3712567 3713193 6.060000e-93 351.0
14 TraesCS6B01G015100 chr6D 78.421 570 88 22 2073 2610 3763844 3764410 4.720000e-89 339.0
15 TraesCS6B01G015100 chr6D 86.166 253 18 3 654 889 3725675 3725927 1.360000e-64 257.0
16 TraesCS6B01G015100 chr6D 85.075 268 21 7 640 889 3738716 3738982 4.890000e-64 255.0
17 TraesCS6B01G015100 chr6D 86.014 143 18 2 934 1075 3726006 3726147 6.600000e-33 152.0
18 TraesCS6B01G015100 chr6D 87.097 124 16 0 934 1057 3739061 3739184 1.430000e-29 141.0
19 TraesCS6B01G015100 chr6D 97.297 37 1 0 779 815 3725934 3725970 3.180000e-06 63.9
20 TraesCS6B01G015100 chr6D 97.297 37 1 0 779 815 3738989 3739025 3.180000e-06 63.9
21 TraesCS6B01G015100 chr6A 88.420 2418 224 26 1440 3815 3773594 3771191 0.000000e+00 2863.0
22 TraesCS6B01G015100 chr6A 84.975 1391 105 32 1 1372 3774895 3773590 0.000000e+00 1315.0
23 TraesCS6B01G015100 chr6A 85.635 724 78 14 1 713 3801126 3800418 0.000000e+00 737.0
24 TraesCS6B01G015100 chr6A 84.699 647 64 21 2062 2690 3747027 3746398 7.000000e-172 614.0
25 TraesCS6B01G015100 chr6A 84.716 458 49 12 1503 1949 3747542 3747095 4.520000e-119 438.0
26 TraesCS6B01G015100 chr6A 85.714 245 22 5 657 889 3748404 3748161 2.940000e-61 246.0
27 TraesCS6B01G015100 chr6A 88.710 124 14 0 934 1057 3748082 3747959 6.600000e-33 152.0
28 TraesCS6B01G015100 chrUn 78.015 1733 265 73 1326 2989 306428556 306430241 0.000000e+00 983.0
29 TraesCS6B01G015100 chrUn 78.064 661 74 30 629 1252 306427779 306428405 6.060000e-93 351.0
30 TraesCS6B01G015100 chrUn 81.111 270 28 8 3067 3317 371790579 371790844 1.080000e-45 195.0
31 TraesCS6B01G015100 chr1B 81.317 562 78 23 2069 2612 51106508 51107060 7.570000e-117 431.0
32 TraesCS6B01G015100 chr1B 80.992 363 50 13 1566 1919 51106152 51106504 1.750000e-68 270.0
33 TraesCS6B01G015100 chr1D 79.464 560 83 28 2069 2610 33639648 33640193 6.020000e-98 368.0
34 TraesCS6B01G015100 chr1D 81.918 365 53 9 1566 1919 33639282 33639644 2.880000e-76 296.0
35 TraesCS6B01G015100 chr1D 81.111 270 28 10 3067 3317 177261406 177261671 1.080000e-45 195.0
36 TraesCS6B01G015100 chr1D 94.231 52 3 0 3464 3515 270507868 270507817 3.160000e-11 80.5
37 TraesCS6B01G015100 chr1A 78.307 567 87 28 2069 2610 32261198 32261753 2.200000e-87 333.0
38 TraesCS6B01G015100 chr1A 80.863 371 48 16 1566 1919 32260830 32261194 1.750000e-68 270.0
39 TraesCS6B01G015100 chr5D 81.919 271 24 10 3067 3317 432406889 432406624 5.000000e-49 206.0
40 TraesCS6B01G015100 chr5D 80.000 270 29 10 3067 3317 503252947 503253210 3.920000e-40 176.0
41 TraesCS6B01G015100 chr4A 81.481 270 27 8 3067 3317 219304484 219304219 2.320000e-47 200.0
42 TraesCS6B01G015100 chr4A 74.211 190 37 12 3462 3644 611433198 611433382 6.840000e-08 69.4
43 TraesCS6B01G015100 chr3D 81.481 270 27 8 3067 3317 158931033 158931298 2.320000e-47 200.0
44 TraesCS6B01G015100 chr3D 94.828 58 3 0 3458 3515 79302437 79302380 1.460000e-14 91.6
45 TraesCS6B01G015100 chr3B 81.481 270 27 8 3067 3317 201555259 201554994 2.320000e-47 200.0
46 TraesCS6B01G015100 chr2B 73.222 239 54 9 3465 3698 410066326 410066093 1.140000e-10 78.7
47 TraesCS6B01G015100 chr7D 88.525 61 4 1 3458 3515 148127798 148127738 1.900000e-08 71.3
48 TraesCS6B01G015100 chr7D 85.965 57 8 0 3464 3520 611482321 611482377 1.140000e-05 62.1
49 TraesCS6B01G015100 chr7B 82.143 84 12 3 3461 3542 101480818 101480736 6.840000e-08 69.4


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 TraesCS6B01G015100 chr6B 9033513 9037327 3814 False 7046.000 7046 100.00000 1 3815 1 chr6B.!!$F1 3814
1 TraesCS6B01G015100 chr6B 9057530 9061182 3652 False 1054.000 2049 84.11500 488 3815 3 chr6B.!!$F2 3327
2 TraesCS6B01G015100 chr6B 9079838 9080923 1085 False 490.000 527 84.66950 1503 2612 2 chr6B.!!$F3 1109
3 TraesCS6B01G015100 chr6D 4719670 4723552 3882 True 2390.500 3382 90.27450 6 3815 2 chr6D.!!$R1 3809
4 TraesCS6B01G015100 chr6D 3712567 3715078 2511 False 693.000 1035 78.15750 629 3039 2 chr6D.!!$F3 2410
5 TraesCS6B01G015100 chr6D 3756523 3757214 691 False 438.000 438 79.31500 407 1058 1 chr6D.!!$F1 651
6 TraesCS6B01G015100 chr6D 3763844 3764410 566 False 339.000 339 78.42100 2073 2610 1 chr6D.!!$F2 537
7 TraesCS6B01G015100 chr6D 3738716 3740682 1966 False 291.580 571 87.61520 640 2690 5 chr6D.!!$F5 2050
8 TraesCS6B01G015100 chr6D 3725675 3727646 1971 False 263.225 580 88.21525 654 2692 4 chr6D.!!$F4 2038
9 TraesCS6B01G015100 chr6A 3771191 3774895 3704 True 2089.000 2863 86.69750 1 3815 2 chr6A.!!$R3 3814
10 TraesCS6B01G015100 chr6A 3800418 3801126 708 True 737.000 737 85.63500 1 713 1 chr6A.!!$R1 712
11 TraesCS6B01G015100 chr6A 3746398 3748404 2006 True 362.500 614 85.95975 657 2690 4 chr6A.!!$R2 2033
12 TraesCS6B01G015100 chrUn 306427779 306430241 2462 False 667.000 983 78.03950 629 2989 2 chrUn.!!$F2 2360
13 TraesCS6B01G015100 chr1B 51106152 51107060 908 False 350.500 431 81.15450 1566 2612 2 chr1B.!!$F1 1046
14 TraesCS6B01G015100 chr1D 33639282 33640193 911 False 332.000 368 80.69100 1566 2610 2 chr1D.!!$F2 1044
15 TraesCS6B01G015100 chr1A 32260830 32261753 923 False 301.500 333 79.58500 1566 2610 2 chr1A.!!$F1 1044

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
219 235 0.659957 GAGCATTGCCACTTCCGATC 59.340 55.0 4.7 0.0 0.0 3.69 F
1322 1762 0.181114 TGATCCATTCTTCTGCCCCG 59.819 55.0 0.0 0.0 0.0 5.73 F
1549 2110 0.033504 TGTGTCTCCTTGTTCTCGCC 59.966 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 2091 0.033504 GGCGAGAACAAGGAGACACA 59.966 55.000 0.0 0.0 0.0 3.72 R
2798 3608 0.958876 TGCCTAGACTTGCTCGACGA 60.959 55.000 0.0 0.0 0.0 4.20 R
3534 4445 1.071471 AAGTCACCAGCCAACGGAG 59.929 57.895 0.0 0.0 0.0 4.63 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
25 27 6.709397 CCCGATCTTACACTGTACATAGAGTA 59.291 42.308 0.00 0.00 0.00 2.59
39 41 8.910944 TGTACATAGAGTAGTGGAAGGAATTAC 58.089 37.037 0.00 0.00 32.19 1.89
51 53 3.004752 AGGAATTACAGGGATGTGTGC 57.995 47.619 0.00 0.00 31.46 4.57
70 74 1.202510 GCTGCCTGAAGATCTCATCGT 60.203 52.381 0.00 0.00 32.14 3.73
115 120 8.647796 AGTTTTACGATCATGGAGGATTACATA 58.352 33.333 0.00 0.00 0.00 2.29
145 154 2.379972 CATCCTCCTTCGAGTAGGTGT 58.620 52.381 3.11 0.00 36.63 4.16
147 156 0.733729 CCTCCTTCGAGTAGGTGTCG 59.266 60.000 3.11 0.00 38.84 4.35
167 176 0.688487 TTACTCACCGACAAAGGGGG 59.312 55.000 0.00 0.00 34.80 5.40
170 179 4.278513 CACCGACAAAGGGGGCCA 62.279 66.667 4.39 0.00 35.02 5.36
186 195 1.904771 CCATAGTTGCCACCCGAGA 59.095 57.895 0.00 0.00 0.00 4.04
215 231 2.093216 CGAGAGCATTGCCACTTCC 58.907 57.895 4.70 0.00 0.00 3.46
219 235 0.659957 GAGCATTGCCACTTCCGATC 59.340 55.000 4.70 0.00 0.00 3.69
226 242 1.737236 TGCCACTTCCGATCATTTTCG 59.263 47.619 0.00 0.00 38.83 3.46
265 281 4.774200 AGAAAAGCCAATCCAGCTATTGTT 59.226 37.500 8.13 0.00 40.49 2.83
274 290 7.765819 GCCAATCCAGCTATTGTTTAGAAATTT 59.234 33.333 8.13 0.00 35.48 1.82
312 329 8.500753 AAAAACGTAGAATTATATGAGTGGCA 57.499 30.769 6.32 0.00 0.00 4.92
328 345 5.825679 TGAGTGGCAGTTAAGTAATTGTTGT 59.174 36.000 0.00 0.00 0.00 3.32
361 378 9.739276 TTATCATCAGTGGATTTGAAGTAACTT 57.261 29.630 0.00 0.00 0.00 2.66
392 410 5.390567 GCGAGTTGTACTTGGTATTTCCTTG 60.391 44.000 0.00 0.00 37.07 3.61
397 415 8.194769 AGTTGTACTTGGTATTTCCTTGTTTTG 58.805 33.333 0.00 0.00 37.07 2.44
398 416 7.648039 TGTACTTGGTATTTCCTTGTTTTGT 57.352 32.000 0.00 0.00 37.07 2.83
399 417 7.484975 TGTACTTGGTATTTCCTTGTTTTGTG 58.515 34.615 0.00 0.00 37.07 3.33
421 439 4.414182 TGGGGGTATACTTGGTATTTCCTG 59.586 45.833 2.25 0.00 37.07 3.86
462 482 7.071572 TGGATCTCATCTGATGATTTACAGGAA 59.928 37.037 19.84 0.00 38.85 3.36
476 496 6.681729 TTTACAGGAACTAGAGTTGGACAT 57.318 37.500 0.00 0.00 38.56 3.06
636 679 7.664731 TGTAAGATAGGGATTAGAGAGGTAACG 59.335 40.741 0.00 0.00 46.39 3.18
940 1064 5.946972 TGACTATCATCCTAACTAGCTAGCC 59.053 44.000 20.91 0.00 0.00 3.93
950 1074 3.383698 ACTAGCTAGCCTGGTAGAACA 57.616 47.619 20.91 0.00 39.57 3.18
977 1101 7.855375 TCTCATTGTGATCTCCTCATAAACTT 58.145 34.615 0.00 0.00 38.32 2.66
1058 1218 3.055021 GCCTTTGGCCTCCTAGGTATATC 60.055 52.174 9.08 0.00 44.06 1.63
1059 1219 4.430441 CCTTTGGCCTCCTAGGTATATCT 58.570 47.826 9.08 0.00 37.80 1.98
1075 1303 8.596781 AGGTATATCTATGTCCACCTCAATAC 57.403 38.462 0.00 0.00 30.59 1.89
1088 1316 5.945784 CCACCTCAATACATCCTTCTCAAAA 59.054 40.000 0.00 0.00 0.00 2.44
1089 1317 6.127897 CCACCTCAATACATCCTTCTCAAAAC 60.128 42.308 0.00 0.00 0.00 2.43
1091 1319 7.824289 CACCTCAATACATCCTTCTCAAAACTA 59.176 37.037 0.00 0.00 0.00 2.24
1092 1320 8.383175 ACCTCAATACATCCTTCTCAAAACTAA 58.617 33.333 0.00 0.00 0.00 2.24
1093 1321 9.401058 CCTCAATACATCCTTCTCAAAACTAAT 57.599 33.333 0.00 0.00 0.00 1.73
1107 1335 9.932207 TCTCAAAACTAATAGTATTTTCGGACA 57.068 29.630 0.00 0.00 0.00 4.02
1109 1337 9.932207 TCAAAACTAATAGTATTTTCGGACAGA 57.068 29.630 0.00 0.00 0.00 3.41
1111 1339 8.943909 AAACTAATAGTATTTTCGGACAGAGG 57.056 34.615 0.00 0.00 0.00 3.69
1112 1340 7.052142 ACTAATAGTATTTTCGGACAGAGGG 57.948 40.000 0.00 0.00 0.00 4.30
1113 1341 6.837568 ACTAATAGTATTTTCGGACAGAGGGA 59.162 38.462 0.00 0.00 0.00 4.20
1114 1342 5.793030 ATAGTATTTTCGGACAGAGGGAG 57.207 43.478 0.00 0.00 0.00 4.30
1115 1343 3.442076 AGTATTTTCGGACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
1116 1344 4.607239 AGTATTTTCGGACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
1150 1378 7.454260 AAGAGTTCTTACTTATGGCCTTTTG 57.546 36.000 3.32 0.00 33.84 2.44
1157 1385 9.921637 TTCTTACTTATGGCCTTTTGTTTTATG 57.078 29.630 3.32 0.00 0.00 1.90
1223 1453 6.926630 TGCCAAAACTAATATTTCCACCTT 57.073 33.333 0.00 0.00 0.00 3.50
1278 1651 3.458189 GTGTAGTAGGGATGCATGTGAC 58.542 50.000 2.46 0.00 0.00 3.67
1292 1665 1.981256 TGTGACCCTTCCTCTTTTGC 58.019 50.000 0.00 0.00 0.00 3.68
1294 1667 0.889186 TGACCCTTCCTCTTTTGCGC 60.889 55.000 0.00 0.00 0.00 6.09
1319 1759 3.126831 CGTAGTGATCCATTCTTCTGCC 58.873 50.000 0.00 0.00 0.00 4.85
1322 1762 0.181114 TGATCCATTCTTCTGCCCCG 59.819 55.000 0.00 0.00 0.00 5.73
1323 1763 0.469917 GATCCATTCTTCTGCCCCGA 59.530 55.000 0.00 0.00 0.00 5.14
1389 1892 5.146482 CACATCAAGTGGCAAACAAAAAG 57.854 39.130 0.00 0.00 44.69 2.27
1403 1906 8.073167 GGCAAACAAAAAGAAAGTTGAGAAAAA 58.927 29.630 0.00 0.00 0.00 1.94
1530 2091 5.104859 TGGGGATTGTGTAACGTATGTACAT 60.105 40.000 13.93 13.93 42.39 2.29
1549 2110 0.033504 TGTGTCTCCTTGTTCTCGCC 59.966 55.000 0.00 0.00 0.00 5.54
1664 2278 5.941058 ACTCAACATCGTTTCTCTCTCTAGA 59.059 40.000 0.00 0.00 0.00 2.43
1694 2316 4.826733 TCACAAGAAACTAATGGTGCATGT 59.173 37.500 0.00 0.00 0.00 3.21
1698 2320 2.603075 AACTAATGGTGCATGTGGGT 57.397 45.000 0.00 0.00 0.00 4.51
1758 2400 3.235481 TCGACGCAGGGGTTCCAA 61.235 61.111 0.00 0.00 34.83 3.53
1940 2582 1.204941 GGTACTCGATTGCACCTCAGT 59.795 52.381 0.00 0.00 0.00 3.41
1952 2601 3.382865 TGCACCTCAGTTGCACATTTTTA 59.617 39.130 0.00 0.00 33.24 1.52
1998 2656 5.474532 GGCCTCTACATTGATTGATGCATAA 59.525 40.000 0.00 0.00 0.00 1.90
2004 2662 9.955208 TCTACATTGATTGATGCATAAAATCAC 57.045 29.630 25.82 10.18 39.40 3.06
2060 2727 8.352201 GTGGCTAACATAAAAATATGCTCATCA 58.648 33.333 0.00 0.00 0.00 3.07
2090 2757 0.970937 TCACGGCGAAGATCCTCCTT 60.971 55.000 16.62 0.00 0.00 3.36
2235 2902 2.202479 TCAGCGTCATCGTGAGCG 60.202 61.111 0.00 0.00 39.49 5.03
2255 2934 2.238521 GACTGAGCATCCTCCCTCTAG 58.761 57.143 0.00 0.00 37.29 2.43
2325 3053 2.357034 CGCCTTGTGGTGCGTACT 60.357 61.111 3.01 0.00 45.43 2.73
2495 3286 5.468540 ACTTCCCTTCTTTAATTGTTGGC 57.531 39.130 0.00 0.00 0.00 4.52
2514 3309 1.292992 CGTTGATCTGCATGCAGCTA 58.707 50.000 37.48 24.79 45.94 3.32
2594 3389 2.210144 AATGCCATGCCTACACCGGT 62.210 55.000 0.00 0.00 0.00 5.28
2615 3410 1.003355 CCAAGCAGGTGGACGATGT 60.003 57.895 0.00 0.00 41.65 3.06
2660 3470 1.804151 TGTCGTCAACATTGCTAAGCC 59.196 47.619 0.00 0.00 31.20 4.35
2709 3519 1.351017 ACACACAATCCCATCGAACCT 59.649 47.619 0.00 0.00 0.00 3.50
2724 3534 3.660571 CCTGGGATGCCACCACCA 61.661 66.667 0.00 0.00 33.63 4.17
2726 3536 1.978617 CTGGGATGCCACCACCAAC 60.979 63.158 0.00 0.00 33.63 3.77
2742 3552 4.250464 CACCAACGAAGGATAACAGCTTA 58.750 43.478 4.96 0.00 0.00 3.09
2752 3562 0.035439 TAACAGCTTAGCCTGCACCC 60.035 55.000 0.00 0.00 36.29 4.61
2771 3581 3.307906 CGTCGTGACCAAGGGGGA 61.308 66.667 0.00 0.00 41.15 4.81
2772 3582 2.874664 CGTCGTGACCAAGGGGGAA 61.875 63.158 0.00 0.00 41.15 3.97
2928 3738 2.485426 CACGTGAGCTTGTGATTTCCAT 59.515 45.455 10.90 0.00 38.36 3.41
2969 3779 5.023533 TGCTCGAGCCAGTTATTTTATCT 57.976 39.130 33.23 0.00 41.18 1.98
3050 3935 2.095110 TGCCATTTTCAGACGAAGCATG 60.095 45.455 0.00 0.00 31.28 4.06
3052 3937 2.489329 CCATTTTCAGACGAAGCATGGT 59.511 45.455 0.00 0.00 38.18 3.55
3055 3940 3.678056 TTTCAGACGAAGCATGGTAGT 57.322 42.857 0.00 1.20 31.28 2.73
3059 3944 3.195610 TCAGACGAAGCATGGTAGTGAAT 59.804 43.478 10.14 0.00 0.00 2.57
3140 4030 1.776034 GATGCGGCCACTCGAATTCC 61.776 60.000 2.24 0.00 0.00 3.01
3160 4050 1.197721 CAACCGAGATGCTTGAACACC 59.802 52.381 0.00 0.00 0.00 4.16
3165 4055 2.549754 CGAGATGCTTGAACACCACTTT 59.450 45.455 0.00 0.00 0.00 2.66
3259 4166 5.351948 TCATCGATACTGGGAAAATGTCA 57.648 39.130 0.00 0.00 0.00 3.58
3263 4170 8.156820 TCATCGATACTGGGAAAATGTCAATAT 58.843 33.333 0.00 0.00 0.00 1.28
3327 4234 4.594123 TGATAGTATCGATCCGGCAAAA 57.406 40.909 0.00 0.00 0.00 2.44
3376 4283 4.337145 TGTAAAGGGTTGTTGTGTTCTGT 58.663 39.130 0.00 0.00 0.00 3.41
3380 4287 2.026262 AGGGTTGTTGTGTTCTGTCTGT 60.026 45.455 0.00 0.00 0.00 3.41
3411 4318 7.175104 ACCTTTGATTCCAAGCAAGAGTATTA 58.825 34.615 0.00 0.00 35.54 0.98
3430 4337 5.560966 ATTATGACGGTGAATTGGAACAC 57.439 39.130 0.00 0.00 39.29 3.32
3519 4430 3.982316 TAGGCTCCTCGCGGTCGAA 62.982 63.158 6.13 0.00 44.98 3.71
3534 4445 4.103103 GAAAGCGCGTCCTTGCCC 62.103 66.667 8.43 0.00 0.00 5.36
3596 4507 3.011517 AGGGCCGACCAATCTGCT 61.012 61.111 0.00 0.00 43.89 4.24
3599 4510 2.184322 GCCGACCAATCTGCTCGA 59.816 61.111 0.00 0.00 32.64 4.04
3605 4516 0.035152 ACCAATCTGCTCGAATGGCA 60.035 50.000 9.66 0.00 45.02 4.92
3612 4523 2.579201 CTCGAATGGCACGGACCT 59.421 61.111 0.00 0.00 0.00 3.85
3661 4572 2.261671 GGACTGTCCGACGCACAT 59.738 61.111 11.71 0.00 0.00 3.21
3733 4653 1.039785 CGGGTGGCTCTGATCTCTCA 61.040 60.000 0.00 0.00 0.00 3.27
3738 4658 0.829333 GGCTCTGATCTCTCAAGGCA 59.171 55.000 0.00 0.00 36.26 4.75
3762 4682 5.581975 TCTCTGAGCCATATGATCTCTCAT 58.418 41.667 19.04 0.00 44.39 2.90
3770 4690 4.141892 CCATATGATCTCTCATGGCCTCTC 60.142 50.000 3.32 0.00 42.19 3.20
3771 4691 2.466547 TGATCTCTCATGGCCTCTCA 57.533 50.000 3.32 0.00 0.00 3.27
3784 4704 2.560105 GGCCTCTCAAAGCTGTTCAATT 59.440 45.455 0.00 0.00 0.00 2.32
3789 4709 5.266733 TCTCAAAGCTGTTCAATTTGCTT 57.733 34.783 0.00 0.00 46.11 3.91
3793 4713 3.375782 AGCTGTTCAATTTGCTTGGAC 57.624 42.857 0.00 0.00 42.85 4.02
3803 4723 2.038814 TTGCTTGGACGGCTCAGACA 62.039 55.000 0.00 0.00 0.00 3.41
3804 4724 1.078848 GCTTGGACGGCTCAGACAT 60.079 57.895 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.561212 CCACTACTCTATGTACAGTGTAAGATC 58.439 40.741 4.11 0.00 34.87 2.75
4 5 8.272889 TCCACTACTCTATGTACAGTGTAAGAT 58.727 37.037 4.11 3.12 34.87 2.40
25 27 3.852578 ACATCCCTGTAATTCCTTCCACT 59.147 43.478 0.00 0.00 32.49 4.00
39 41 2.044555 CAGGCAGCACACATCCCTG 61.045 63.158 0.00 0.00 37.35 4.45
51 53 2.864946 CAACGATGAGATCTTCAGGCAG 59.135 50.000 0.00 0.00 39.68 4.85
70 74 3.167485 ACTACCGTATCACCTTCACCAA 58.833 45.455 0.00 0.00 0.00 3.67
115 120 1.689273 GAAGGAGGATGCCGTACAGAT 59.311 52.381 0.00 0.00 0.00 2.90
145 154 1.000060 CCCTTTGTCGGTGAGTAACGA 60.000 52.381 0.00 0.00 36.68 3.85
147 156 1.609841 CCCCCTTTGTCGGTGAGTAAC 60.610 57.143 0.00 0.00 0.00 2.50
170 179 0.249398 GTGTCTCGGGTGGCAACTAT 59.751 55.000 0.97 0.00 37.61 2.12
186 195 2.665185 GCTCTCGCGTTTGGGTGT 60.665 61.111 5.77 0.00 0.00 4.16
192 201 1.965930 TGGCAATGCTCTCGCGTTT 60.966 52.632 5.77 0.00 42.52 3.60
205 214 2.161410 CGAAAATGATCGGAAGTGGCAA 59.839 45.455 0.00 0.00 39.12 4.52
215 231 5.237815 TGATATTCCTCCCGAAAATGATCG 58.762 41.667 0.00 0.00 42.37 3.69
219 235 6.767902 TCTTCTTGATATTCCTCCCGAAAATG 59.232 38.462 0.00 0.00 33.08 2.32
226 242 5.300539 GGCTTTTCTTCTTGATATTCCTCCC 59.699 44.000 0.00 0.00 0.00 4.30
265 281 4.280436 TGGAGCTCGGTCAAATTTCTAA 57.720 40.909 7.83 0.00 0.00 2.10
328 345 8.578448 TCAAATCCACTGATGATAACATTCAA 57.422 30.769 0.00 0.00 36.82 2.69
361 378 2.479837 CAAGTACAACTCGCAGGTGAA 58.520 47.619 8.00 0.00 33.95 3.18
392 410 3.770046 ACCAAGTATACCCCCACAAAAC 58.230 45.455 0.00 0.00 0.00 2.43
397 415 4.414514 AGGAAATACCAAGTATACCCCCAC 59.585 45.833 0.00 0.00 42.04 4.61
398 416 4.414182 CAGGAAATACCAAGTATACCCCCA 59.586 45.833 0.00 0.00 42.04 4.96
399 417 4.661709 TCAGGAAATACCAAGTATACCCCC 59.338 45.833 0.00 0.00 42.04 5.40
421 439 7.928167 AGATGAGATCCAAACCTTTTGTTTTTC 59.072 33.333 0.00 0.00 44.80 2.29
462 482 2.269940 AGGCCAATGTCCAACTCTAGT 58.730 47.619 5.01 0.00 0.00 2.57
636 679 6.238925 GCCTATCTTACACTCTTTCTCTCTCC 60.239 46.154 0.00 0.00 0.00 3.71
752 801 1.548719 CCTTATGGTGTGTGACTCCGA 59.451 52.381 0.00 0.00 34.63 4.55
950 1074 8.492782 AGTTTATGAGGAGATCACAATGAGATT 58.507 33.333 0.00 0.00 41.91 2.40
972 1096 8.568794 GCAAGATCTTAACTACCTTTGAAGTTT 58.431 33.333 7.86 0.00 37.19 2.66
977 1101 7.121168 CCATTGCAAGATCTTAACTACCTTTGA 59.879 37.037 7.86 0.00 0.00 2.69
1058 1218 5.815233 AGGATGTATTGAGGTGGACATAG 57.185 43.478 0.00 0.00 32.75 2.23
1059 1219 5.905331 AGAAGGATGTATTGAGGTGGACATA 59.095 40.000 0.00 0.00 32.75 2.29
1088 1316 6.837568 TCCCTCTGTCCGAAAATACTATTAGT 59.162 38.462 1.30 1.30 0.00 2.24
1089 1317 7.014422 ACTCCCTCTGTCCGAAAATACTATTAG 59.986 40.741 0.00 0.00 0.00 1.73
1091 1319 5.661759 ACTCCCTCTGTCCGAAAATACTATT 59.338 40.000 0.00 0.00 0.00 1.73
1092 1320 5.209659 ACTCCCTCTGTCCGAAAATACTAT 58.790 41.667 0.00 0.00 0.00 2.12
1093 1321 4.607239 ACTCCCTCTGTCCGAAAATACTA 58.393 43.478 0.00 0.00 0.00 1.82
1094 1322 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
1095 1323 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
1096 1324 4.607239 AGTACTCCCTCTGTCCGAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
1097 1325 3.442076 AGTACTCCCTCTGTCCGAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
1098 1326 2.885616 AGTACTCCCTCTGTCCGAAAA 58.114 47.619 0.00 0.00 0.00 2.29
1099 1327 2.599408 AGTACTCCCTCTGTCCGAAA 57.401 50.000 0.00 0.00 0.00 3.46
1100 1328 3.458857 AGATAGTACTCCCTCTGTCCGAA 59.541 47.826 0.00 0.00 0.00 4.30
1101 1329 3.047115 AGATAGTACTCCCTCTGTCCGA 58.953 50.000 0.00 0.00 0.00 4.55
1102 1330 3.495434 AGATAGTACTCCCTCTGTCCG 57.505 52.381 0.00 0.00 0.00 4.79
1103 1331 7.560626 TCTTAAAAGATAGTACTCCCTCTGTCC 59.439 40.741 0.00 0.00 0.00 4.02
1104 1332 8.522542 TCTTAAAAGATAGTACTCCCTCTGTC 57.477 38.462 0.00 0.00 0.00 3.51
1105 1333 8.117312 ACTCTTAAAAGATAGTACTCCCTCTGT 58.883 37.037 0.00 0.00 33.93 3.41
1106 1334 8.528044 ACTCTTAAAAGATAGTACTCCCTCTG 57.472 38.462 0.00 0.00 33.93 3.35
1107 1335 9.192642 GAACTCTTAAAAGATAGTACTCCCTCT 57.807 37.037 0.00 0.00 33.93 3.69
1108 1336 9.192642 AGAACTCTTAAAAGATAGTACTCCCTC 57.807 37.037 0.00 0.00 33.93 4.30
1109 1337 9.549984 AAGAACTCTTAAAAGATAGTACTCCCT 57.450 33.333 0.00 0.00 33.79 4.20
1223 1453 6.946340 TCTTGGATGCTCAGAATACTAACAA 58.054 36.000 0.00 0.00 0.00 2.83
1252 1581 2.384828 TGCATCCCTACTACACGTGAT 58.615 47.619 25.01 9.25 0.00 3.06
1253 1582 1.842052 TGCATCCCTACTACACGTGA 58.158 50.000 25.01 4.97 0.00 4.35
1257 1586 3.458189 GTCACATGCATCCCTACTACAC 58.542 50.000 0.00 0.00 0.00 2.90
1278 1651 0.606401 TCTGCGCAAAAGAGGAAGGG 60.606 55.000 13.05 0.00 0.00 3.95
1292 1665 2.120232 GAATGGATCACTACGTCTGCG 58.880 52.381 0.00 0.00 44.93 5.18
1294 1667 5.039984 CAGAAGAATGGATCACTACGTCTG 58.960 45.833 0.00 3.35 0.00 3.51
1319 1759 0.108963 TAATAAATGGCGGGGTCGGG 59.891 55.000 0.00 0.00 36.79 5.14
1322 1762 8.769891 CAAAAATAATTAATAAATGGCGGGGTC 58.230 33.333 0.00 0.00 0.00 4.46
1323 1763 8.268605 ACAAAAATAATTAATAAATGGCGGGGT 58.731 29.630 0.00 0.00 0.00 4.95
1389 1892 7.027760 ACTTTCGTTCCTTTTTCTCAACTTTC 58.972 34.615 0.00 0.00 0.00 2.62
1403 1906 6.238566 GCCTTTAGTTTACAACTTTCGTTCCT 60.239 38.462 0.00 0.00 42.81 3.36
1414 1917 8.915036 TGTAAATTGAAGGCCTTTAGTTTACAA 58.085 29.630 39.49 30.33 42.39 2.41
1530 2091 0.033504 GGCGAGAACAAGGAGACACA 59.966 55.000 0.00 0.00 0.00 3.72
1549 2110 2.097954 TGGTACATACGACAGTTAGCCG 59.902 50.000 0.00 0.00 0.00 5.52
1694 2316 4.794648 GCCTGCATGCCGTACCCA 62.795 66.667 16.68 0.00 0.00 4.51
1940 2582 5.278266 CCTCTTCCGAAGTAAAAATGTGCAA 60.278 40.000 8.01 0.00 0.00 4.08
1952 2601 5.116882 CCGAAAATTATCCTCTTCCGAAGT 58.883 41.667 8.01 0.00 0.00 3.01
1998 2656 8.846943 TGCGTGGATCTAATAATATGTGATTT 57.153 30.769 0.00 0.00 0.00 2.17
2055 2722 2.004733 CGTGAAGAGCTGCATTGATGA 58.995 47.619 1.02 0.00 0.00 2.92
2060 2727 2.393768 CGCCGTGAAGAGCTGCATT 61.394 57.895 1.02 0.00 0.00 3.56
2090 2757 1.434188 ACACACCCACATTCAGGAGA 58.566 50.000 0.00 0.00 0.00 3.71
2235 2902 2.158534 TCTAGAGGGAGGATGCTCAGTC 60.159 54.545 16.72 11.25 0.00 3.51
2255 2934 6.801539 TCATGGATCAACAAACTAACACTC 57.198 37.500 0.00 0.00 0.00 3.51
2300 3001 3.594775 CCACAAGGCGCTGCAACA 61.595 61.111 7.64 0.00 0.00 3.33
2325 3053 1.215382 CATGAACTCCACGCTCCGA 59.785 57.895 0.00 0.00 0.00 4.55
2455 3183 4.389077 GGAAGTTGAGTTACGATGAACTGG 59.611 45.833 6.81 0.00 39.79 4.00
2495 3286 1.004185 GTAGCTGCATGCAGATCAACG 60.004 52.381 44.02 22.21 46.30 4.10
2514 3309 1.339929 GCGAACCCAAGAATGTTTGGT 59.660 47.619 7.49 0.00 44.98 3.67
2594 3389 4.641645 CGTCCACCTGCTTGGGCA 62.642 66.667 5.26 0.00 41.84 5.36
2615 3410 2.582272 GGCACCTTGATGGCATCAA 58.418 52.632 33.82 33.82 46.30 2.57
2709 3519 2.117206 GTTGGTGGTGGCATCCCA 59.883 61.111 4.11 4.11 39.32 4.37
2724 3534 3.197983 AGGCTAAGCTGTTATCCTTCGTT 59.802 43.478 0.00 0.00 31.78 3.85
2726 3536 3.126831 CAGGCTAAGCTGTTATCCTTCG 58.873 50.000 0.00 0.00 33.26 3.79
2771 3581 2.952310 GCCTTCTCAACCTTGTCAACTT 59.048 45.455 0.00 0.00 0.00 2.66
2772 3582 2.092429 TGCCTTCTCAACCTTGTCAACT 60.092 45.455 0.00 0.00 0.00 3.16
2798 3608 0.958876 TGCCTAGACTTGCTCGACGA 60.959 55.000 0.00 0.00 0.00 4.20
2880 3690 5.011533 TGCATTTCTCTCCCTATAGCTTCTC 59.988 44.000 0.00 0.00 0.00 2.87
2928 3738 5.196341 AGCATCTAATGGAACGTCGATAA 57.804 39.130 0.00 0.00 0.00 1.75
2969 3779 7.114866 TGGACATACTAATGAATACGACCAA 57.885 36.000 0.00 0.00 36.54 3.67
3039 3924 3.895232 ATTCACTACCATGCTTCGTCT 57.105 42.857 0.00 0.00 0.00 4.18
3040 3925 5.348986 TCTAATTCACTACCATGCTTCGTC 58.651 41.667 0.00 0.00 0.00 4.20
3042 3927 5.277058 GCTTCTAATTCACTACCATGCTTCG 60.277 44.000 0.00 0.00 0.00 3.79
3109 3998 2.290008 TGGCCGCATCTCTAACAAGAAA 60.290 45.455 0.00 0.00 0.00 2.52
3160 4050 2.408050 ACACGCTGCTCTTAGAAAGTG 58.592 47.619 0.00 4.28 34.85 3.16
3165 4055 1.743958 GGTAGACACGCTGCTCTTAGA 59.256 52.381 0.00 0.00 0.00 2.10
3222 4129 7.800847 CAGTATCGATGATTCGCGAGATAATAT 59.199 37.037 9.59 0.00 45.10 1.28
3302 4209 3.319689 TGCCGGATCGATACTATCAAACA 59.680 43.478 5.05 0.00 0.00 2.83
3327 4234 7.174946 AGACGTAAATGACCATTTCATCAGTTT 59.825 33.333 10.85 0.72 44.86 2.66
3348 4255 3.375922 CACAACAACCCTTTACAAGACGT 59.624 43.478 0.00 0.00 0.00 4.34
3362 4269 5.796350 ACTTACAGACAGAACACAACAAC 57.204 39.130 0.00 0.00 0.00 3.32
3411 4318 1.804151 CGTGTTCCAATTCACCGTCAT 59.196 47.619 0.00 0.00 0.00 3.06
3430 4337 4.686091 TCAGTTCTTGCTCACAAATACTCG 59.314 41.667 0.00 0.00 34.74 4.18
3525 4436 2.359975 CCAACGGAGGGCAAGGAC 60.360 66.667 0.00 0.00 0.00 3.85
3534 4445 1.071471 AAGTCACCAGCCAACGGAG 59.929 57.895 0.00 0.00 0.00 4.63
3577 4488 2.124570 CAGATTGGTCGGCCCTGG 60.125 66.667 2.12 0.00 0.00 4.45
3586 4497 0.035152 TGCCATTCGAGCAGATTGGT 60.035 50.000 18.16 0.00 46.72 3.67
3589 4500 1.091771 CCGTGCCATTCGAGCAGATT 61.092 55.000 0.00 0.00 41.87 2.40
3596 4507 1.375396 CAAGGTCCGTGCCATTCGA 60.375 57.895 0.00 0.00 0.00 3.71
3599 4510 2.676471 GCCAAGGTCCGTGCCATT 60.676 61.111 0.00 0.00 0.00 3.16
3661 4572 2.350895 CCAATGACGGTGCCCTCA 59.649 61.111 0.00 0.00 0.00 3.86
3738 4658 5.581975 TGAGAGATCATATGGCTCAGAGAT 58.418 41.667 20.97 6.94 32.36 2.75
3751 4671 2.973710 TGAGAGGCCATGAGAGATCAT 58.026 47.619 5.01 0.00 0.00 2.45
3762 4682 0.473755 TGAACAGCTTTGAGAGGCCA 59.526 50.000 5.01 0.00 0.00 5.36
3770 4690 4.025480 GTCCAAGCAAATTGAACAGCTTTG 60.025 41.667 0.00 0.00 44.22 2.77
3771 4691 4.122046 GTCCAAGCAAATTGAACAGCTTT 58.878 39.130 0.00 0.00 44.22 3.51
3784 4704 1.301716 GTCTGAGCCGTCCAAGCAA 60.302 57.895 0.00 0.00 0.00 3.91
3789 4709 1.607801 CCAGATGTCTGAGCCGTCCA 61.608 60.000 11.47 0.00 46.59 4.02
3793 4713 2.584418 CGCCAGATGTCTGAGCCG 60.584 66.667 11.47 7.29 46.59 5.52


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

AutoCloner maintained by Alex Coulton.