Multiple sequence alignment - TraesCS6A01G361500

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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 TraesCS6A01G361500 chr6A 100.000 3956 0 0 1 3956 591903407 591899452 0.000000e+00 7306.0
1 TraesCS6A01G361500 chr6D 92.012 3330 142 56 1 3264 445004316 445001045 0.000000e+00 4562.0
2 TraesCS6A01G361500 chr6D 93.624 643 38 1 3314 3956 444958390 444957751 0.000000e+00 957.0
3 TraesCS6A01G361500 chr6D 93.468 643 39 1 3314 3956 444933938 444933299 0.000000e+00 952.0
4 TraesCS6A01G361500 chr6D 93.468 643 39 1 3314 3956 444953160 444952521 0.000000e+00 952.0
5 TraesCS6A01G361500 chr6D 93.468 643 39 1 3314 3956 444966146 444965507 0.000000e+00 952.0
6 TraesCS6A01G361500 chr6D 93.468 643 39 1 3314 3956 444987584 444986945 0.000000e+00 952.0
7 TraesCS6A01G361500 chr6D 93.468 643 39 1 3314 3956 444995338 444994699 0.000000e+00 952.0
8 TraesCS6A01G361500 chr6D 93.313 643 40 1 3314 3956 444955769 444955130 0.000000e+00 946.0
9 TraesCS6A01G361500 chr6D 93.313 643 40 1 3314 3956 444960969 444960330 0.000000e+00 946.0
10 TraesCS6A01G361500 chr6B 90.220 2679 162 43 175 2813 669497612 669494994 0.000000e+00 3404.0
11 TraesCS6A01G361500 chr6B 90.140 2566 163 37 274 2810 669998240 670000744 0.000000e+00 3254.0
12 TraesCS6A01G361500 chr6B 89.983 1188 82 14 2805 3956 670000781 670001967 0.000000e+00 1500.0
13 TraesCS6A01G361500 chr6B 92.200 1000 69 5 1819 2810 670020070 670021068 0.000000e+00 1406.0
14 TraesCS6A01G361500 chr6B 88.764 801 54 13 3160 3956 670022173 670022941 0.000000e+00 948.0
15 TraesCS6A01G361500 chr6B 87.019 832 46 24 3160 3956 669494283 669493479 0.000000e+00 881.0
16 TraesCS6A01G361500 chr6B 88.769 650 48 12 1191 1827 670019023 670019660 0.000000e+00 773.0
17 TraesCS6A01G361500 chr6B 92.711 343 17 5 2808 3147 669494957 669494620 4.590000e-134 488.0
18 TraesCS6A01G361500 chr6B 92.581 310 21 2 2805 3114 670021105 670021412 1.010000e-120 444.0
19 TraesCS6A01G361500 chr6B 92.241 232 14 3 175 404 670018753 670018982 3.810000e-85 326.0
20 TraesCS6A01G361500 chr6B 85.294 136 14 1 41 176 389903902 389904031 6.900000e-28 135.0
21 TraesCS6A01G361500 chr1A 85.465 172 18 4 5 176 86606388 86606552 5.260000e-39 172.0
22 TraesCS6A01G361500 chr4A 82.482 137 16 4 41 176 713998672 713998543 3.230000e-21 113.0
23 TraesCS6A01G361500 chr2D 83.465 127 15 2 46 172 445889823 445889703 3.230000e-21 113.0
24 TraesCS6A01G361500 chr2D 82.243 107 12 4 41 147 6967188 6967287 7.040000e-13 86.1
25 TraesCS6A01G361500 chr2D 97.368 38 1 0 4 41 638287274 638287237 9.180000e-07 65.8
26 TraesCS6A01G361500 chr7A 82.000 100 12 5 33 129 101466812 101466716 3.280000e-11 80.5
27 TraesCS6A01G361500 chr3D 87.324 71 8 1 41 111 442402308 442402377 3.280000e-11 80.5
28 TraesCS6A01G361500 chr2A 100.000 38 0 0 4 41 171607751 171607714 1.970000e-08 71.3
29 TraesCS6A01G361500 chr3A 97.500 40 0 1 3 41 613498606 613498645 2.550000e-07 67.6
30 TraesCS6A01G361500 chr5B 80.682 88 13 3 33 117 62026759 62026673 9.180000e-07 65.8
31 TraesCS6A01G361500 chr5B 97.368 38 1 0 4 41 382378710 382378673 9.180000e-07 65.8
32 TraesCS6A01G361500 chr5A 97.368 38 1 0 1 38 687951479 687951516 9.180000e-07 65.8
33 TraesCS6A01G361500 chr7D 95.000 40 2 0 1 40 160428151 160428190 3.300000e-06 63.9
34 TraesCS6A01G361500 chrUn 79.167 96 14 5 25 116 233088653 233088560 1.190000e-05 62.1


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 TraesCS6A01G361500 chr6A 591899452 591903407 3955 True 7306.00 7306 100.000000 1 3956 1 chr6A.!!$R1 3955
1 TraesCS6A01G361500 chr6D 445001045 445004316 3271 True 4562.00 4562 92.012000 1 3264 1 chr6D.!!$R5 3263
2 TraesCS6A01G361500 chr6D 444933299 444933938 639 True 952.00 952 93.468000 3314 3956 1 chr6D.!!$R1 642
3 TraesCS6A01G361500 chr6D 444965507 444966146 639 True 952.00 952 93.468000 3314 3956 1 chr6D.!!$R2 642
4 TraesCS6A01G361500 chr6D 444986945 444987584 639 True 952.00 952 93.468000 3314 3956 1 chr6D.!!$R3 642
5 TraesCS6A01G361500 chr6D 444994699 444995338 639 True 952.00 952 93.468000 3314 3956 1 chr6D.!!$R4 642
6 TraesCS6A01G361500 chr6D 444952521 444960969 8448 True 950.25 957 93.429500 3314 3956 4 chr6D.!!$R6 642
7 TraesCS6A01G361500 chr6B 669998240 670001967 3727 False 2377.00 3254 90.061500 274 3956 2 chr6B.!!$F2 3682
8 TraesCS6A01G361500 chr6B 669493479 669497612 4133 True 1591.00 3404 89.983333 175 3956 3 chr6B.!!$R1 3781
9 TraesCS6A01G361500 chr6B 670018753 670022941 4188 False 779.40 1406 90.911000 175 3956 5 chr6B.!!$F3 3781

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
867 919 0.179092 CAAATACTCGGGTCCGGTCC 60.179 60.0 9.52 9.52 40.25 4.46 F
994 1046 0.250166 GTGTGGCTACGGTTCCTGTT 60.250 55.0 0.00 0.00 0.00 3.16 F
2346 2838 0.320683 GGTCATGGCAAAGGCAAACC 60.321 55.0 0.00 10.99 42.43 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2936 0.320247 AGCTTGAAGTGAGCACGAGG 60.320 55.0 0.0 0.0 42.56 4.63 R
2583 3076 1.431488 CGATGCCCATGTCTTCCACG 61.431 60.0 0.0 0.0 0.00 4.94 R
3682 7580 0.755698 TGTAGCTAGAGGAAGGCGGG 60.756 60.0 0.0 0.0 0.00 6.13 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 9.816354 AAGAATAGAATTAGAGAGCTTTGAGAC 57.184 33.333 0.00 0.00 0.00 3.36
74 75 9.762933 AATAGAATTAGAGAGCTTTGAGACATC 57.237 33.333 0.00 0.00 0.00 3.06
83 84 1.726791 CTTTGAGACATCGTTGACCCG 59.273 52.381 0.00 0.00 0.00 5.28
155 156 7.864379 GTGGGTTCTTTAAAACTAAAACTAGGC 59.136 37.037 0.00 0.00 0.00 3.93
169 170 8.755977 ACTAAAACTAGGCAGCTTAGTGTTATA 58.244 33.333 21.77 8.31 34.64 0.98
223 225 3.370527 GCCCCACTCTTACATGCTTCTAA 60.371 47.826 0.00 0.00 0.00 2.10
271 277 2.826979 ACATACGAGTACAGTCGCTG 57.173 50.000 6.38 7.11 44.06 5.18
283 289 2.870411 ACAGTCGCTGGTACAAAAGTTC 59.130 45.455 10.80 0.00 38.70 3.01
303 309 6.899114 AGTTCGAACCTTGAACACATAAATC 58.101 36.000 24.22 0.00 46.34 2.17
354 362 8.370940 ACATATGTTTATCATCGAAGACCTGAT 58.629 33.333 1.41 4.07 42.51 2.90
363 371 1.000145 GAAGACCTGATCGTTTCGCC 59.000 55.000 0.00 0.00 0.00 5.54
368 376 1.699656 CCTGATCGTTTCGCCTGCAG 61.700 60.000 6.78 6.78 0.00 4.41
373 382 0.602638 TCGTTTCGCCTGCAGACATT 60.603 50.000 17.39 0.00 0.00 2.71
387 396 1.002087 AGACATTCGAAACGGAAGGCT 59.998 47.619 0.00 0.00 31.25 4.58
388 397 1.804748 GACATTCGAAACGGAAGGCTT 59.195 47.619 0.00 0.00 31.25 4.35
408 417 5.220854 GGCTTTTAACGTCAGATGCACATAT 60.221 40.000 0.00 0.00 0.00 1.78
409 418 6.018262 GGCTTTTAACGTCAGATGCACATATA 60.018 38.462 0.00 0.00 0.00 0.86
410 419 7.065894 GCTTTTAACGTCAGATGCACATATAG 58.934 38.462 0.00 0.00 0.00 1.31
411 420 7.254455 GCTTTTAACGTCAGATGCACATATAGT 60.254 37.037 0.00 0.00 0.00 2.12
412 421 7.694388 TTTAACGTCAGATGCACATATAGTC 57.306 36.000 0.00 0.00 0.00 2.59
431 440 3.118811 AGTCCAGATTAGCTTCACTCAGC 60.119 47.826 0.00 0.00 40.44 4.26
463 476 1.042559 AACAGGTTGGTTGGCTGGTG 61.043 55.000 0.00 0.00 0.00 4.17
569 603 5.590530 ACAGACTTGACCATCTATCACTC 57.409 43.478 0.00 0.00 0.00 3.51
586 620 2.983136 CACTCGAGATATAAAGCAGCCG 59.017 50.000 21.68 0.00 0.00 5.52
587 621 1.989165 CTCGAGATATAAAGCAGCCGC 59.011 52.381 6.58 0.00 38.99 6.53
598 632 0.679002 AGCAGCCGCACTCATTCATT 60.679 50.000 0.00 0.00 42.27 2.57
599 633 0.248377 GCAGCCGCACTCATTCATTC 60.248 55.000 0.00 0.00 38.36 2.67
600 634 1.089112 CAGCCGCACTCATTCATTCA 58.911 50.000 0.00 0.00 0.00 2.57
601 635 1.674441 CAGCCGCACTCATTCATTCAT 59.326 47.619 0.00 0.00 0.00 2.57
602 636 1.674441 AGCCGCACTCATTCATTCATG 59.326 47.619 0.00 0.00 0.00 3.07
603 637 1.862815 GCCGCACTCATTCATTCATGC 60.863 52.381 0.00 0.00 0.00 4.06
606 640 2.713011 GCACTCATTCATTCATGCGAC 58.287 47.619 0.00 0.00 0.00 5.19
607 641 2.096335 GCACTCATTCATTCATGCGACA 59.904 45.455 0.00 0.00 0.00 4.35
608 642 3.426560 GCACTCATTCATTCATGCGACAA 60.427 43.478 0.00 0.00 0.00 3.18
609 643 4.093514 CACTCATTCATTCATGCGACAAC 58.906 43.478 0.00 0.00 0.00 3.32
610 644 3.752747 ACTCATTCATTCATGCGACAACA 59.247 39.130 0.00 0.00 0.00 3.33
632 668 9.727627 CAACAAAAGATATAGAAAATCTCCAGC 57.272 33.333 0.00 0.00 32.48 4.85
637 673 6.613233 AGATATAGAAAATCTCCAGCGTACG 58.387 40.000 11.84 11.84 0.00 3.67
638 674 4.650754 ATAGAAAATCTCCAGCGTACGT 57.349 40.909 17.90 0.00 0.00 3.57
640 676 3.767278 AGAAAATCTCCAGCGTACGTAC 58.233 45.455 17.90 15.90 0.00 3.67
641 677 2.573941 AAATCTCCAGCGTACGTACC 57.426 50.000 19.67 12.32 0.00 3.34
643 679 1.466856 ATCTCCAGCGTACGTACCAA 58.533 50.000 19.67 0.00 0.00 3.67
644 680 1.246649 TCTCCAGCGTACGTACCAAA 58.753 50.000 19.67 1.05 0.00 3.28
821 868 5.646467 TTTGTTTGTCAGTTACTACTCGC 57.354 39.130 0.00 0.00 30.26 5.03
823 870 2.991866 GTTTGTCAGTTACTACTCGCCC 59.008 50.000 0.00 0.00 30.26 6.13
824 871 2.211250 TGTCAGTTACTACTCGCCCT 57.789 50.000 0.00 0.00 30.26 5.19
825 872 2.522185 TGTCAGTTACTACTCGCCCTT 58.478 47.619 0.00 0.00 30.26 3.95
828 875 1.101331 AGTTACTACTCGCCCTTCCG 58.899 55.000 0.00 0.00 0.00 4.30
867 919 0.179092 CAAATACTCGGGTCCGGTCC 60.179 60.000 9.52 9.52 40.25 4.46
893 945 5.534654 CCCTGGTTCTATTCACTCAAAAACA 59.465 40.000 0.00 0.00 0.00 2.83
894 946 6.209391 CCCTGGTTCTATTCACTCAAAAACAT 59.791 38.462 0.00 0.00 0.00 2.71
895 947 7.393234 CCCTGGTTCTATTCACTCAAAAACATA 59.607 37.037 0.00 0.00 0.00 2.29
896 948 8.960591 CCTGGTTCTATTCACTCAAAAACATAT 58.039 33.333 0.00 0.00 0.00 1.78
994 1046 0.250166 GTGTGGCTACGGTTCCTGTT 60.250 55.000 0.00 0.00 0.00 3.16
1008 1060 0.883833 CCTGTTGCACAATGGAGGAC 59.116 55.000 0.00 0.00 0.00 3.85
1031 1083 0.537188 TTGCTCGCCTTCTTCCCTAG 59.463 55.000 0.00 0.00 0.00 3.02
1106 1158 2.789208 CACCATGCTTAATCTGTTGCG 58.211 47.619 0.00 0.00 0.00 4.85
1208 1261 5.178096 TGAGCTTCATTTATGAGAACCCA 57.822 39.130 0.00 0.00 38.19 4.51
1218 1271 2.602257 TGAGAACCCACATCTATGCG 57.398 50.000 0.00 0.00 0.00 4.73
1232 1285 2.083774 CTATGCGCTTGGTTGGAAAGA 58.916 47.619 9.73 0.00 0.00 2.52
1293 1346 7.040892 TGTGATGAATTCTTTGAGTTCTCCTTG 60.041 37.037 7.05 0.00 31.12 3.61
1303 1356 9.273016 TCTTTGAGTTCTCCTTGTAAATGTTAG 57.727 33.333 0.00 0.00 0.00 2.34
1305 1358 8.833231 TTGAGTTCTCCTTGTAAATGTTAGAG 57.167 34.615 0.00 0.00 0.00 2.43
1308 1361 5.401531 TCTCCTTGTAAATGTTAGAGCGT 57.598 39.130 0.00 0.00 0.00 5.07
1381 1434 4.537135 ACGATATTGGGAATACATCGCT 57.463 40.909 0.00 0.00 41.39 4.93
1499 1553 4.891260 TGATCGCGATCTACCTTCTACTA 58.109 43.478 39.74 19.26 38.60 1.82
1502 1556 4.639334 TCGCGATCTACCTTCTACTACAT 58.361 43.478 3.71 0.00 0.00 2.29
1617 1674 7.503521 TGAGCTTTCACATATGTTTGTACAA 57.496 32.000 5.37 3.59 37.91 2.41
1730 1802 4.732647 GCGTGAAGATACATGGAACTACGA 60.733 45.833 13.10 0.00 0.00 3.43
1764 1836 5.916883 CACGGTCTTGTATATAAGGTTACCG 59.083 44.000 25.89 25.89 44.50 4.02
1784 1856 8.969267 GTTACCGTCTGTATTTCTCATCATAAG 58.031 37.037 0.00 0.00 0.00 1.73
1785 1857 7.113658 ACCGTCTGTATTTCTCATCATAAGT 57.886 36.000 0.00 0.00 0.00 2.24
1786 1858 8.234136 ACCGTCTGTATTTCTCATCATAAGTA 57.766 34.615 0.00 0.00 0.00 2.24
1787 1859 8.136165 ACCGTCTGTATTTCTCATCATAAGTAC 58.864 37.037 0.00 0.00 0.00 2.73
1843 2333 7.764443 ACTCTATTTGCACATATACACGAGTTT 59.236 33.333 6.10 0.00 0.00 2.66
1849 2339 5.105269 TGCACATATACACGAGTTTCCCTAA 60.105 40.000 0.00 0.00 0.00 2.69
1926 2418 4.954970 ACACCAACCGCAGCCCTG 62.955 66.667 0.00 0.00 0.00 4.45
1972 2464 4.686839 GATATCATCGATGTCGTCCTCA 57.313 45.455 24.09 3.45 40.80 3.86
1988 2480 1.283029 CCTCATTGATGGTCACAGGGT 59.717 52.381 0.00 0.00 0.00 4.34
2010 2502 2.852449 TCAACATGCGGTTTTGACCTA 58.148 42.857 0.00 0.00 37.72 3.08
2112 2604 5.554437 TGTCAGTACCTTTTACATGTCCA 57.446 39.130 0.00 0.00 0.00 4.02
2346 2838 0.320683 GGTCATGGCAAAGGCAAACC 60.321 55.000 0.00 10.99 42.43 3.27
2359 2851 3.334583 GGCAAACCTGTATCTCACTCA 57.665 47.619 0.00 0.00 0.00 3.41
2444 2936 3.293262 GACGACGACAATGAGATAGAGC 58.707 50.000 0.00 0.00 0.00 4.09
2462 2954 1.905922 GCCTCGTGCTCACTTCAAGC 61.906 60.000 0.00 0.00 40.26 4.01
2583 3076 1.692411 AGGAAAGGTTCAAGTGTGCC 58.308 50.000 0.00 0.00 0.00 5.01
2694 3188 7.446001 TGTTTTCAATATGCACACATCTGTA 57.554 32.000 0.00 0.00 37.74 2.74
2911 3459 8.865590 TTTAGGACTAAAATGTTGTTTGCTTC 57.134 30.769 2.20 0.00 32.64 3.86
3022 3570 3.004734 GTGGGTCATGTTCTTCCAAAGTG 59.995 47.826 0.00 0.00 0.00 3.16
3091 3640 9.308318 AGCATTGTAGAAATTTAAACGTTTTGT 57.692 25.926 20.19 1.51 0.00 2.83
3092 3641 9.562752 GCATTGTAGAAATTTAAACGTTTTGTC 57.437 29.630 20.19 6.06 0.00 3.18
3129 3678 5.064325 TCTCTCATTTTTGTCTCGATGCATG 59.936 40.000 2.46 0.00 0.00 4.06
3130 3679 4.095334 TCTCATTTTTGTCTCGATGCATGG 59.905 41.667 2.46 2.00 0.00 3.66
3131 3680 3.758023 TCATTTTTGTCTCGATGCATGGT 59.242 39.130 2.46 0.00 0.00 3.55
3132 3681 4.940654 TCATTTTTGTCTCGATGCATGGTA 59.059 37.500 2.46 0.00 0.00 3.25
3133 3682 5.589855 TCATTTTTGTCTCGATGCATGGTAT 59.410 36.000 2.46 0.00 0.00 2.73
3134 3683 6.765512 TCATTTTTGTCTCGATGCATGGTATA 59.234 34.615 2.46 0.00 0.00 1.47
3135 3684 7.445096 TCATTTTTGTCTCGATGCATGGTATAT 59.555 33.333 2.46 0.00 0.00 0.86
3136 3685 8.720562 CATTTTTGTCTCGATGCATGGTATATA 58.279 33.333 2.46 0.00 0.00 0.86
3137 3686 7.889589 TTTTGTCTCGATGCATGGTATATAG 57.110 36.000 2.46 0.00 0.00 1.31
3138 3687 6.590234 TTGTCTCGATGCATGGTATATAGT 57.410 37.500 2.46 0.00 0.00 2.12
3139 3688 7.696992 TTGTCTCGATGCATGGTATATAGTA 57.303 36.000 2.46 0.00 0.00 1.82
3140 3689 7.321745 TGTCTCGATGCATGGTATATAGTAG 57.678 40.000 2.46 0.00 0.00 2.57
3141 3690 7.110155 TGTCTCGATGCATGGTATATAGTAGA 58.890 38.462 2.46 0.00 0.00 2.59
3142 3691 7.065923 TGTCTCGATGCATGGTATATAGTAGAC 59.934 40.741 2.46 9.71 0.00 2.59
3143 3692 7.281324 GTCTCGATGCATGGTATATAGTAGACT 59.719 40.741 2.46 0.00 0.00 3.24
3144 3693 7.829706 TCTCGATGCATGGTATATAGTAGACTT 59.170 37.037 2.46 0.00 0.00 3.01
3145 3694 8.349568 TCGATGCATGGTATATAGTAGACTTT 57.650 34.615 2.46 0.00 0.00 2.66
3194 4469 4.016444 TGCCAATACCTGAAGAAATCCAC 58.984 43.478 0.00 0.00 0.00 4.02
3204 4479 2.779755 AGAAATCCACGGTGCATACA 57.220 45.000 1.68 0.00 0.00 2.29
3264 4540 9.986157 TTCCTAATTAGAGTACCAGTTCTAGAA 57.014 33.333 14.28 0.00 0.00 2.10
3265 4541 9.986157 TCCTAATTAGAGTACCAGTTCTAGAAA 57.014 33.333 14.28 0.00 0.00 2.52
3338 4634 5.794687 TTGCTTCATAACACCATTCTACG 57.205 39.130 0.00 0.00 0.00 3.51
3348 4644 8.957028 CATAACACCATTCTACGCATAAAATTG 58.043 33.333 0.00 0.00 0.00 2.32
3413 4709 4.067192 CCATCCATCGATGCAGAAATACA 58.933 43.478 20.25 0.00 44.00 2.29
3465 4761 2.699954 CAACACCTCGAATAGTTGCCT 58.300 47.619 9.61 0.00 35.51 4.75
3522 4818 0.323725 ATTCAAACCGCCCATCAGCT 60.324 50.000 0.00 0.00 0.00 4.24
3528 4824 3.200593 CGCCCATCAGCTGCAGAC 61.201 66.667 20.43 9.11 0.00 3.51
3529 4825 3.200593 GCCCATCAGCTGCAGACG 61.201 66.667 20.43 7.24 0.00 4.18
3662 4981 0.110238 CTTCAACGACATTGCACCGG 60.110 55.000 0.00 0.00 38.29 5.28
3666 4985 3.430862 CGACATTGCACCGGTGGG 61.431 66.667 34.58 12.47 40.11 4.61
3682 7580 2.566529 GGCGTGCTAACAAAGGGC 59.433 61.111 0.00 0.00 0.00 5.19
3770 7668 1.758936 CCCATCTCTGCAAGCATCAA 58.241 50.000 0.00 0.00 0.00 2.57
3783 7681 1.795170 GCATCAAACACGCCACCTGT 61.795 55.000 0.00 0.00 0.00 4.00
3859 12987 0.391130 TCCCCGAGTCTTTTGATGCG 60.391 55.000 0.00 0.00 0.00 4.73
3904 13032 0.443869 CTGAACCGACAATGGAAGCG 59.556 55.000 0.00 0.00 0.00 4.68
3951 13079 2.259204 CACATTTGTGCCGCCTGG 59.741 61.111 0.00 0.00 39.39 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.417719 GGTCAACGATGTCTCAAAGCT 58.582 47.619 0.00 0.00 0.00 3.74
71 72 4.685447 TTGACCGGGTCAACGATG 57.315 55.556 33.05 0.00 45.88 3.84
83 84 2.178912 TGAGTCACCCGATTTTGACC 57.821 50.000 0.00 0.00 42.73 4.02
155 156 7.231722 AGGTACATCCTCTATAACACTAAGCTG 59.768 40.741 0.00 0.00 44.42 4.24
271 277 5.163733 TGTTCAAGGTTCGAACTTTTGTACC 60.164 40.000 29.23 22.39 42.63 3.34
283 289 8.116753 GTCTATGATTTATGTGTTCAAGGTTCG 58.883 37.037 0.00 0.00 0.00 3.95
303 309 8.085296 GTGTATCTGTTTCCTAGGATGTCTATG 58.915 40.741 13.57 0.11 0.00 2.23
354 362 0.602638 AATGTCTGCAGGCGAAACGA 60.603 50.000 14.71 0.00 0.00 3.85
363 371 1.428448 TCCGTTTCGAATGTCTGCAG 58.572 50.000 7.63 7.63 0.00 4.41
368 376 1.439679 AGCCTTCCGTTTCGAATGTC 58.560 50.000 0.00 0.00 0.00 3.06
373 382 2.221517 CGTTAAAAGCCTTCCGTTTCGA 59.778 45.455 0.00 0.00 0.00 3.71
387 396 7.223971 GGACTATATGTGCATCTGACGTTAAAA 59.776 37.037 0.00 0.00 36.96 1.52
388 397 6.700081 GGACTATATGTGCATCTGACGTTAAA 59.300 38.462 0.00 0.00 36.96 1.52
408 417 4.098654 GCTGAGTGAAGCTAATCTGGACTA 59.901 45.833 0.00 0.00 40.20 2.59
409 418 3.118811 GCTGAGTGAAGCTAATCTGGACT 60.119 47.826 0.00 0.00 40.20 3.85
410 419 3.194062 GCTGAGTGAAGCTAATCTGGAC 58.806 50.000 0.00 0.00 40.20 4.02
411 420 3.533606 GCTGAGTGAAGCTAATCTGGA 57.466 47.619 0.00 0.00 40.20 3.86
463 476 0.954452 CACTGAGTTGACTTTGGCCC 59.046 55.000 0.00 0.00 0.00 5.80
516 536 3.059834 GCTAACGCATGCTGTTCAAAATG 59.940 43.478 24.21 5.89 35.78 2.32
569 603 1.457303 GTGCGGCTGCTTTATATCTCG 59.543 52.381 20.27 0.00 43.34 4.04
586 620 2.096335 TGTCGCATGAATGAATGAGTGC 59.904 45.455 0.00 0.00 0.00 4.40
587 621 4.093514 GTTGTCGCATGAATGAATGAGTG 58.906 43.478 0.00 0.00 0.00 3.51
598 632 7.841915 TTCTATATCTTTTGTTGTCGCATGA 57.158 32.000 0.00 0.00 0.00 3.07
599 633 8.894409 TTTTCTATATCTTTTGTTGTCGCATG 57.106 30.769 0.00 0.00 0.00 4.06
600 634 9.722056 GATTTTCTATATCTTTTGTTGTCGCAT 57.278 29.630 0.00 0.00 0.00 4.73
601 635 8.946085 AGATTTTCTATATCTTTTGTTGTCGCA 58.054 29.630 0.00 0.00 0.00 5.10
602 636 9.427127 GAGATTTTCTATATCTTTTGTTGTCGC 57.573 33.333 0.00 0.00 32.64 5.19
603 637 9.922305 GGAGATTTTCTATATCTTTTGTTGTCG 57.078 33.333 0.00 0.00 32.64 4.35
606 640 9.727627 GCTGGAGATTTTCTATATCTTTTGTTG 57.272 33.333 0.00 0.00 32.64 3.33
607 641 8.616076 CGCTGGAGATTTTCTATATCTTTTGTT 58.384 33.333 0.00 0.00 32.64 2.83
608 642 7.770897 ACGCTGGAGATTTTCTATATCTTTTGT 59.229 33.333 0.00 0.00 32.64 2.83
609 643 8.147642 ACGCTGGAGATTTTCTATATCTTTTG 57.852 34.615 0.00 0.00 32.64 2.44
610 644 9.262358 GTACGCTGGAGATTTTCTATATCTTTT 57.738 33.333 0.00 0.00 32.64 2.27
632 668 7.005380 CAGTTTTCTTGTATTTGGTACGTACG 58.995 38.462 18.98 15.01 36.01 3.67
637 673 7.506328 ACTCCAGTTTTCTTGTATTTGGTAC 57.494 36.000 0.00 0.00 0.00 3.34
638 674 9.059260 GTTACTCCAGTTTTCTTGTATTTGGTA 57.941 33.333 0.00 0.00 0.00 3.25
640 676 8.076178 CAGTTACTCCAGTTTTCTTGTATTTGG 58.924 37.037 0.00 0.00 0.00 3.28
641 677 8.621286 ACAGTTACTCCAGTTTTCTTGTATTTG 58.379 33.333 0.00 0.00 0.00 2.32
643 679 7.773690 ACACAGTTACTCCAGTTTTCTTGTATT 59.226 33.333 0.00 0.00 0.00 1.89
644 680 7.280356 ACACAGTTACTCCAGTTTTCTTGTAT 58.720 34.615 0.00 0.00 0.00 2.29
779 817 8.560576 AACAAAAGTTATACATAATGATGCGC 57.439 30.769 0.00 0.00 36.43 6.09
821 868 0.978146 AGAGGATGGTGTCGGAAGGG 60.978 60.000 0.00 0.00 0.00 3.95
823 870 2.009042 GCAAGAGGATGGTGTCGGAAG 61.009 57.143 0.00 0.00 0.00 3.46
824 871 0.036388 GCAAGAGGATGGTGTCGGAA 60.036 55.000 0.00 0.00 0.00 4.30
825 872 1.596934 GCAAGAGGATGGTGTCGGA 59.403 57.895 0.00 0.00 0.00 4.55
828 875 1.134371 GTAGGGCAAGAGGATGGTGTC 60.134 57.143 0.00 0.00 0.00 3.67
867 919 4.826274 TTGAGTGAATAGAACCAGGGAG 57.174 45.455 0.00 0.00 0.00 4.30
994 1046 1.811965 CAATTCGTCCTCCATTGTGCA 59.188 47.619 0.00 0.00 0.00 4.57
1106 1158 7.130303 AGAAAGTAATCGTTACCTTTGAAGC 57.870 36.000 0.00 0.00 36.81 3.86
1182 1235 6.459298 GGGTTCTCATAAATGAAGCTCATGTG 60.459 42.308 0.00 0.00 37.15 3.21
1183 1236 5.591877 GGGTTCTCATAAATGAAGCTCATGT 59.408 40.000 0.00 0.00 37.15 3.21
1184 1237 5.591472 TGGGTTCTCATAAATGAAGCTCATG 59.409 40.000 0.00 0.00 37.15 3.07
1185 1238 5.591877 GTGGGTTCTCATAAATGAAGCTCAT 59.408 40.000 0.00 0.00 39.09 2.90
1208 1261 1.065491 TCCAACCAAGCGCATAGATGT 60.065 47.619 11.47 0.00 0.00 3.06
1264 1317 8.302438 GGAGAACTCAAAGAATTCATCACAAAT 58.698 33.333 8.44 0.00 0.00 2.32
1265 1318 7.503566 AGGAGAACTCAAAGAATTCATCACAAA 59.496 33.333 8.44 0.00 0.00 2.83
1266 1319 7.000472 AGGAGAACTCAAAGAATTCATCACAA 59.000 34.615 8.44 0.00 0.00 3.33
1273 1326 9.617975 CATTTACAAGGAGAACTCAAAGAATTC 57.382 33.333 0.00 0.00 0.00 2.17
1293 1346 5.857822 AGGAAACACGCTCTAACATTTAC 57.142 39.130 0.00 0.00 0.00 2.01
1303 1356 3.066203 TCTTGGAAAAAGGAAACACGCTC 59.934 43.478 0.00 0.00 0.00 5.03
1305 1358 3.066203 TCTCTTGGAAAAAGGAAACACGC 59.934 43.478 0.00 0.00 0.00 5.34
1308 1361 6.129179 ACATCTCTCTTGGAAAAAGGAAACA 58.871 36.000 0.00 0.00 0.00 2.83
1381 1434 1.634702 GGCATAATTTGGCGCGAAAA 58.365 45.000 21.44 14.90 41.53 2.29
1468 1521 3.416119 AGATCGCGATCAAGTTTCGTA 57.584 42.857 41.16 4.72 40.22 3.43
1469 1522 2.279582 AGATCGCGATCAAGTTTCGT 57.720 45.000 41.16 21.69 40.22 3.85
1470 1523 2.468040 GGTAGATCGCGATCAAGTTTCG 59.532 50.000 41.16 0.00 40.22 3.46
1471 1524 3.707793 AGGTAGATCGCGATCAAGTTTC 58.292 45.455 41.16 25.93 40.22 2.78
1784 1856 7.137426 CCTATGTGATTGTAAGTCCTACGTAC 58.863 42.308 0.00 0.00 34.39 3.67
1785 1857 6.830324 ACCTATGTGATTGTAAGTCCTACGTA 59.170 38.462 0.00 0.00 32.65 3.57
1786 1858 5.655532 ACCTATGTGATTGTAAGTCCTACGT 59.344 40.000 0.00 0.00 32.65 3.57
1787 1859 6.145338 ACCTATGTGATTGTAAGTCCTACG 57.855 41.667 0.00 0.00 32.65 3.51
1972 2464 4.018506 TGTTGATACCCTGTGACCATCAAT 60.019 41.667 0.00 0.00 37.78 2.57
1988 2480 3.840890 GGTCAAAACCGCATGTTGATA 57.159 42.857 0.00 0.00 37.23 2.15
2144 2636 0.758123 TCCAGTGACATGTCTGTGCA 59.242 50.000 25.55 7.41 35.14 4.57
2145 2637 1.802960 CTTCCAGTGACATGTCTGTGC 59.197 52.381 25.55 13.27 35.14 4.57
2146 2638 3.062763 GTCTTCCAGTGACATGTCTGTG 58.937 50.000 25.55 20.58 35.14 3.66
2147 2639 2.037772 GGTCTTCCAGTGACATGTCTGT 59.962 50.000 25.55 10.73 38.67 3.41
2191 2683 1.917336 GCACCATCCGGGAAAGGGTA 61.917 60.000 19.37 0.00 41.15 3.69
2274 2766 3.326747 GCCAATCTACGGTAGGCAATAG 58.673 50.000 14.82 1.85 44.59 1.73
2346 2838 5.089970 TCCAACCAATGAGTGAGATACAG 57.910 43.478 0.00 0.00 0.00 2.74
2349 2841 4.777366 TGTCTCCAACCAATGAGTGAGATA 59.223 41.667 0.00 0.00 30.06 1.98
2355 2847 3.117512 ACCTTTGTCTCCAACCAATGAGT 60.118 43.478 0.00 0.00 0.00 3.41
2359 2851 2.158667 ACGACCTTTGTCTCCAACCAAT 60.159 45.455 0.00 0.00 39.47 3.16
2444 2936 0.320247 AGCTTGAAGTGAGCACGAGG 60.320 55.000 0.00 0.00 42.56 4.63
2462 2954 4.058797 GGTGTGAACCCGAACCAG 57.941 61.111 0.00 0.00 32.69 4.00
2583 3076 1.431488 CGATGCCCATGTCTTCCACG 61.431 60.000 0.00 0.00 0.00 4.94
2678 3172 9.875691 ATAAATATCGTACAGATGTGTGCATAT 57.124 29.630 11.50 9.88 39.13 1.78
2694 3188 5.701224 ACCCCACCATTTGATAAATATCGT 58.299 37.500 0.00 0.00 35.48 3.73
2906 3454 5.810587 GTGTCCTAGTTGATTTATCGAAGCA 59.189 40.000 0.00 0.00 0.00 3.91
2911 3459 5.018539 TGGGTGTCCTAGTTGATTTATCG 57.981 43.478 0.00 0.00 0.00 2.92
3022 3570 7.044798 AGAGTGCAAATGACTACTCCTAAATC 58.955 38.462 0.00 0.00 40.21 2.17
3084 3632 6.739550 AGAGAAAACTACAAAACGACAAAACG 59.260 34.615 0.00 0.00 39.31 3.60
3086 3634 7.808672 TGAGAGAAAACTACAAAACGACAAAA 58.191 30.769 0.00 0.00 0.00 2.44
3090 3639 8.836959 AAAATGAGAGAAAACTACAAAACGAC 57.163 30.769 0.00 0.00 0.00 4.34
3091 3640 9.284594 CAAAAATGAGAGAAAACTACAAAACGA 57.715 29.630 0.00 0.00 0.00 3.85
3092 3641 9.072294 ACAAAAATGAGAGAAAACTACAAAACG 57.928 29.630 0.00 0.00 0.00 3.60
3194 4469 1.674359 TAGCCCAAATGTATGCACCG 58.326 50.000 0.00 0.00 0.00 4.94
3204 4479 4.971939 ACAAAAATGCAGTTAGCCCAAAT 58.028 34.783 0.00 0.00 44.83 2.32
3269 4545 8.621286 CGCAGAAAGTATTTACCTTGGATATTT 58.379 33.333 0.00 0.00 39.27 1.40
3272 4548 6.880484 TCGCAGAAAGTATTTACCTTGGATA 58.120 36.000 0.00 0.00 39.27 2.59
3274 4550 5.155278 TCGCAGAAAGTATTTACCTTGGA 57.845 39.130 0.00 0.00 39.27 3.53
3275 4551 4.201822 GCTCGCAGAAAGTATTTACCTTGG 60.202 45.833 0.00 0.00 39.27 3.61
3276 4552 4.631813 AGCTCGCAGAAAGTATTTACCTTG 59.368 41.667 0.00 0.00 39.27 3.61
3338 4634 9.730420 ATTAATACGGTGTCTTCAATTTTATGC 57.270 29.630 0.00 0.00 0.00 3.14
3348 4644 7.118680 TGGTCAAAGAATTAATACGGTGTCTTC 59.881 37.037 0.00 0.00 0.00 2.87
3382 4678 2.086610 TCGATGGATGGAGATCACCA 57.913 50.000 14.63 14.63 44.41 4.17
3413 4709 1.808945 CTTCATTTGGAGCTTCGCACT 59.191 47.619 0.00 0.00 0.00 4.40
3529 4825 2.562876 GGCCCTATCGACGGAGGAC 61.563 68.421 15.79 6.43 34.46 3.85
3662 4981 1.579429 CCTTTGTTAGCACGCCCAC 59.421 57.895 0.00 0.00 0.00 4.61
3666 4985 2.566529 GGCCCTTTGTTAGCACGC 59.433 61.111 0.00 0.00 0.00 5.34
3682 7580 0.755698 TGTAGCTAGAGGAAGGCGGG 60.756 60.000 0.00 0.00 0.00 6.13
3770 7668 2.264005 TAATTCACAGGTGGCGTGTT 57.736 45.000 0.00 0.00 35.79 3.32
3783 7681 1.805943 CATGATCGCCCGCATAATTCA 59.194 47.619 0.00 0.00 0.00 2.57
3859 12987 5.391312 TGCCAAAGAAAGCTTCTATTTCC 57.609 39.130 0.00 0.00 39.61 3.13
3904 13032 2.178273 GCGGCACCATTTTCGGAC 59.822 61.111 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.