Multiple sequence alignment - TraesCS1D01G358900

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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 TraesCS1D01G358900 chr1D 100.000 3431 0 0 1 3431 442427013 442423583 0.000000e+00 6336
1 TraesCS1D01G358900 chr1A 91.023 2562 123 33 902 3431 536293260 536295746 0.000000e+00 3358
2 TraesCS1D01G358900 chr1A 94.419 215 12 0 3215 3429 497523122 497523336 7.100000e-87 331
3 TraesCS1D01G358900 chr1A 93.171 205 14 0 1 205 536288737 536288941 5.560000e-78 302
4 TraesCS1D01G358900 chr1A 92.453 106 3 4 688 792 536288939 536289040 2.760000e-31 147
5 TraesCS1D01G358900 chr1B 87.979 1905 135 27 915 2744 601008904 601007019 0.000000e+00 2163
6 TraesCS1D01G358900 chr1B 91.076 818 41 6 1471 2280 602233677 602234470 0.000000e+00 1077
7 TraesCS1D01G358900 chr1B 86.922 497 45 5 1 490 601011087 601010604 1.080000e-149 540
8 TraesCS1D01G358900 chr1B 82.952 393 29 14 962 1354 602233290 602233644 1.540000e-83 320
9 TraesCS1D01G358900 chr1B 95.135 185 9 0 3247 3431 33838837 33838653 3.350000e-75 292
10 TraesCS1D01G358900 chr1B 95.294 170 8 0 719 888 602231550 602231719 1.570000e-68 270
11 TraesCS1D01G358900 chr1B 94.186 172 9 1 709 880 601009081 601008911 9.440000e-66 261
12 TraesCS1D01G358900 chr4D 98.598 214 3 0 3218 3431 118377424 118377637 2.500000e-101 379
13 TraesCS1D01G358900 chr2D 96.774 217 7 0 3215 3431 121783910 121784126 2.520000e-96 363
14 TraesCS1D01G358900 chr2A 96.729 214 7 0 3218 3431 677394657 677394870 1.170000e-94 357
15 TraesCS1D01G358900 chr2A 85.902 305 38 5 2481 2783 421251606 421251907 1.540000e-83 320
16 TraesCS1D01G358900 chr2B 84.118 340 50 3 2481 2816 238629326 238629665 3.300000e-85 326
17 TraesCS1D01G358900 chr6A 94.393 214 7 1 3218 3431 123535306 123535098 1.190000e-84 324
18 TraesCS1D01G358900 chr3A 89.720 214 22 0 3218 3431 501935157 501935370 1.210000e-69 274
19 TraesCS1D01G358900 chr7D 88.785 214 24 0 3217 3430 84324418 84324631 2.630000e-66 263
20 TraesCS1D01G358900 chr5D 80.692 347 55 10 2481 2825 525592274 525591938 3.400000e-65 259


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 TraesCS1D01G358900 chr1D 442423583 442427013 3430 True 6336.000000 6336 100.000000 1 3431 1 chr1D.!!$R1 3430
1 TraesCS1D01G358900 chr1A 536293260 536295746 2486 False 3358.000000 3358 91.023000 902 3431 1 chr1A.!!$F2 2529
2 TraesCS1D01G358900 chr1B 601007019 601011087 4068 True 988.000000 2163 89.695667 1 2744 3 chr1B.!!$R2 2743
3 TraesCS1D01G358900 chr1B 602231550 602234470 2920 False 555.666667 1077 89.774000 719 2280 3 chr1B.!!$F1 1561

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
208 209 0.038159 GTTCAGAGGGACGACCACAG 60.038 60.0 6.2 0.0 43.89 3.66 F
863 2175 0.103208 AACAGAGATCCGACGATGGC 59.897 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1094 3922 1.002251 GGATCTCGATCACCACGTCTC 60.002 57.143 8.97 0.0 39.54 3.36 R
2746 5649 0.248866 GCCGGGCACAATATTTTCGG 60.249 55.000 15.62 0.0 39.07 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
40 41 4.767255 CCACAGCAGGACGCCTCC 62.767 72.222 0.00 0.00 44.04 4.30
84 85 2.033194 GTCTAGCCGTGTGCAACCC 61.033 63.158 0.00 0.00 44.83 4.11
116 117 2.513897 GGGACATGCTACCGTGGC 60.514 66.667 0.00 0.00 35.11 5.01
141 142 5.769662 TGGAAGACAATGTGTTTTCTAGCAT 59.230 36.000 10.40 0.00 40.21 3.79
143 144 5.633830 AGACAATGTGTTTTCTAGCATGG 57.366 39.130 0.00 0.00 0.00 3.66
146 147 4.826733 ACAATGTGTTTTCTAGCATGGACA 59.173 37.500 0.00 0.00 0.00 4.02
157 158 0.168788 GCATGGACATGAACACGGTG 59.831 55.000 15.99 6.58 41.20 4.94
163 164 0.944386 ACATGAACACGGTGAGTTGC 59.056 50.000 16.29 0.00 0.00 4.17
176 177 3.123621 GGTGAGTTGCGTCATTCTAACTG 59.876 47.826 0.00 0.00 33.83 3.16
194 195 3.579709 ACTGACGCAGACTATTGTTCAG 58.420 45.455 12.77 4.92 36.85 3.02
208 209 0.038159 GTTCAGAGGGACGACCACAG 60.038 60.000 6.20 0.00 43.89 3.66
211 212 4.436998 GAGGGACGACCACAGCCG 62.437 72.222 6.20 0.00 43.89 5.52
219 220 2.906897 ACCACAGCCGTTGCCAAG 60.907 61.111 0.00 0.00 38.69 3.61
228 229 1.491563 CGTTGCCAAGCTACACGAC 59.508 57.895 0.00 0.00 34.26 4.34
229 230 1.218875 CGTTGCCAAGCTACACGACA 61.219 55.000 0.00 0.00 34.26 4.35
230 231 1.156736 GTTGCCAAGCTACACGACAT 58.843 50.000 0.00 0.00 34.70 3.06
231 232 1.535462 GTTGCCAAGCTACACGACATT 59.465 47.619 0.00 0.00 34.70 2.71
232 233 1.890876 TGCCAAGCTACACGACATTT 58.109 45.000 0.00 0.00 0.00 2.32
233 234 2.226330 TGCCAAGCTACACGACATTTT 58.774 42.857 0.00 0.00 0.00 1.82
234 235 2.621055 TGCCAAGCTACACGACATTTTT 59.379 40.909 0.00 0.00 0.00 1.94
235 236 3.234386 GCCAAGCTACACGACATTTTTC 58.766 45.455 0.00 0.00 0.00 2.29
236 237 3.304391 GCCAAGCTACACGACATTTTTCA 60.304 43.478 0.00 0.00 0.00 2.69
244 245 7.172532 AGCTACACGACATTTTTCAAAGTGATA 59.827 33.333 2.11 0.00 31.05 2.15
307 308 2.564975 GACTTTCTCGTCCGCCGA 59.435 61.111 0.00 0.00 45.00 5.54
329 330 3.120086 AAGCTGGAGCACAACCGGT 62.120 57.895 0.00 0.00 45.16 5.28
342 343 1.135689 CAACCGGTATGTGCTTTCAGC 60.136 52.381 8.00 0.00 42.82 4.26
362 363 5.536538 TCAGCATAAGATGAAGACCGAGTAT 59.463 40.000 0.00 0.00 37.20 2.12
425 433 2.020720 CTCATCTCGAGCTACTGTGGT 58.979 52.381 7.81 0.00 34.18 4.16
450 458 2.562738 CCCACCCCTGAATTCAACTTTC 59.437 50.000 9.88 0.00 0.00 2.62
462 470 6.545666 TGAATTCAACTTTCAGACTAGCCAAA 59.454 34.615 5.45 0.00 0.00 3.28
465 473 5.003804 TCAACTTTCAGACTAGCCAAATCC 58.996 41.667 0.00 0.00 0.00 3.01
467 475 4.583871 ACTTTCAGACTAGCCAAATCCTG 58.416 43.478 0.00 0.00 0.00 3.86
471 479 2.768527 CAGACTAGCCAAATCCTGAGGA 59.231 50.000 2.43 2.43 35.55 3.71
480 488 3.503748 CCAAATCCTGAGGACACAGTTTC 59.496 47.826 1.77 0.00 32.98 2.78
490 498 2.955660 GGACACAGTTTCCAATTCCACA 59.044 45.455 0.35 0.00 32.82 4.17
491 499 3.243401 GGACACAGTTTCCAATTCCACAC 60.243 47.826 0.35 0.00 32.82 3.82
540 1456 9.325198 TCACATTAATGACGTATAGAAAGCAAT 57.675 29.630 22.16 0.00 0.00 3.56
542 1458 8.774586 ACATTAATGACGTATAGAAAGCAATCC 58.225 33.333 22.16 0.00 0.00 3.01
543 1459 8.773645 CATTAATGACGTATAGAAAGCAATCCA 58.226 33.333 10.04 0.00 0.00 3.41
546 1462 2.864343 ACGTATAGAAAGCAATCCACGC 59.136 45.455 0.00 0.00 0.00 5.34
559 1476 4.348656 CAATCCACGCAGAAGAAATCATG 58.651 43.478 0.00 0.00 0.00 3.07
566 1483 5.521372 CACGCAGAAGAAATCATGAGATGTA 59.479 40.000 0.09 0.00 33.90 2.29
594 1519 7.871853 TGAAGTTACAGTAAGATTGGAAAAGC 58.128 34.615 0.00 0.00 0.00 3.51
595 1520 7.719633 TGAAGTTACAGTAAGATTGGAAAAGCT 59.280 33.333 0.00 0.00 0.00 3.74
599 1524 8.780249 GTTACAGTAAGATTGGAAAAGCTTGTA 58.220 33.333 0.00 0.00 0.00 2.41
601 1526 8.409358 ACAGTAAGATTGGAAAAGCTTGTAAT 57.591 30.769 0.00 0.00 0.00 1.89
604 1529 8.515414 AGTAAGATTGGAAAAGCTTGTAATCAC 58.485 33.333 18.96 12.92 0.00 3.06
605 1530 6.272822 AGATTGGAAAAGCTTGTAATCACC 57.727 37.500 18.96 6.29 0.00 4.02
606 1531 5.774690 AGATTGGAAAAGCTTGTAATCACCA 59.225 36.000 18.96 8.34 0.00 4.17
609 1534 4.518970 TGGAAAAGCTTGTAATCACCAGAC 59.481 41.667 0.00 0.00 0.00 3.51
610 1535 4.378459 GGAAAAGCTTGTAATCACCAGACG 60.378 45.833 0.00 0.00 0.00 4.18
611 1536 2.386661 AGCTTGTAATCACCAGACGG 57.613 50.000 0.00 0.00 38.77 4.79
613 1538 2.501723 AGCTTGTAATCACCAGACGGAT 59.498 45.455 0.00 0.00 35.59 4.18
615 1540 2.863401 TGTAATCACCAGACGGATCG 57.137 50.000 0.00 0.00 35.59 3.69
617 1542 1.107945 TAATCACCAGACGGATCGCA 58.892 50.000 0.00 0.00 35.59 5.10
619 1544 2.635229 ATCACCAGACGGATCGCAGC 62.635 60.000 0.00 0.00 35.59 5.25
621 1546 2.279120 CCAGACGGATCGCAGCTC 60.279 66.667 0.00 0.00 0.00 4.09
623 1548 1.299014 CAGACGGATCGCAGCTCTC 60.299 63.158 0.00 0.00 0.00 3.20
624 1549 1.750780 AGACGGATCGCAGCTCTCA 60.751 57.895 0.00 0.00 0.00 3.27
625 1550 1.587613 GACGGATCGCAGCTCTCAC 60.588 63.158 0.00 0.00 0.00 3.51
626 1551 2.653448 CGGATCGCAGCTCTCACG 60.653 66.667 0.00 0.00 0.00 4.35
627 1552 2.492090 GGATCGCAGCTCTCACGT 59.508 61.111 0.00 0.00 0.00 4.49
628 1553 1.587613 GGATCGCAGCTCTCACGTC 60.588 63.158 0.00 0.00 0.00 4.34
630 1555 0.865218 GATCGCAGCTCTCACGTCAG 60.865 60.000 0.00 0.00 0.00 3.51
631 1556 1.590610 ATCGCAGCTCTCACGTCAGT 61.591 55.000 0.00 0.00 0.00 3.41
632 1557 1.799519 CGCAGCTCTCACGTCAGTC 60.800 63.158 0.00 0.00 0.00 3.51
633 1558 1.287191 GCAGCTCTCACGTCAGTCA 59.713 57.895 0.00 0.00 0.00 3.41
634 1559 1.006314 GCAGCTCTCACGTCAGTCAC 61.006 60.000 0.00 0.00 0.00 3.67
635 1560 0.387878 CAGCTCTCACGTCAGTCACC 60.388 60.000 0.00 0.00 0.00 4.02
636 1561 0.538516 AGCTCTCACGTCAGTCACCT 60.539 55.000 0.00 0.00 0.00 4.00
637 1562 0.315568 GCTCTCACGTCAGTCACCTT 59.684 55.000 0.00 0.00 0.00 3.50
638 1563 1.667467 GCTCTCACGTCAGTCACCTTC 60.667 57.143 0.00 0.00 0.00 3.46
641 1566 0.469331 TCACGTCAGTCACCTTCCCT 60.469 55.000 0.00 0.00 0.00 4.20
643 1568 1.374758 CGTCAGTCACCTTCCCTGC 60.375 63.158 0.00 0.00 0.00 4.85
644 1569 1.754745 GTCAGTCACCTTCCCTGCA 59.245 57.895 0.00 0.00 0.00 4.41
646 1571 0.397941 TCAGTCACCTTCCCTGCAAG 59.602 55.000 0.00 0.00 0.00 4.01
647 1572 1.073897 AGTCACCTTCCCTGCAAGC 59.926 57.895 0.00 0.00 0.00 4.01
648 1573 1.973812 GTCACCTTCCCTGCAAGCC 60.974 63.158 0.00 0.00 0.00 4.35
649 1574 2.115910 CACCTTCCCTGCAAGCCA 59.884 61.111 0.00 0.00 0.00 4.75
651 1576 2.115910 CCTTCCCTGCAAGCCACA 59.884 61.111 0.00 0.00 0.00 4.17
652 1577 1.304713 CCTTCCCTGCAAGCCACAT 60.305 57.895 0.00 0.00 0.00 3.21
654 1579 2.221906 CTTCCCTGCAAGCCACATGC 62.222 60.000 0.00 0.00 44.08 4.06
655 1580 3.766691 CCCTGCAAGCCACATGCC 61.767 66.667 0.00 0.00 43.16 4.40
656 1581 3.766691 CCTGCAAGCCACATGCCC 61.767 66.667 0.00 0.00 43.16 5.36
658 1583 4.617556 TGCAAGCCACATGCCCCA 62.618 61.111 0.00 0.00 43.16 4.96
659 1584 3.078836 GCAAGCCACATGCCCCAT 61.079 61.111 0.00 0.00 42.71 4.00
660 1585 2.897207 CAAGCCACATGCCCCATG 59.103 61.111 3.80 3.80 46.18 3.66
661 1586 2.364579 AAGCCACATGCCCCATGG 60.365 61.111 4.14 4.14 45.16 3.66
684 1788 4.234574 GCCACCACTATTAGTTTTGCAAC 58.765 43.478 0.00 0.00 0.00 4.17
685 1789 4.022329 GCCACCACTATTAGTTTTGCAACT 60.022 41.667 0.00 0.00 45.73 3.16
686 1790 5.182380 GCCACCACTATTAGTTTTGCAACTA 59.818 40.000 0.00 0.00 41.81 2.24
695 1799 6.472686 TTAGTTTTGCAACTAACCCATTGT 57.527 33.333 9.81 0.00 46.32 2.71
697 1801 5.739959 AGTTTTGCAACTAACCCATTGTTT 58.260 33.333 9.81 0.00 41.81 2.83
698 1802 5.815222 AGTTTTGCAACTAACCCATTGTTTC 59.185 36.000 9.81 0.00 41.81 2.78
699 1803 5.344743 TTTGCAACTAACCCATTGTTTCA 57.655 34.783 0.00 0.00 38.42 2.69
701 1805 5.543507 TGCAACTAACCCATTGTTTCAAT 57.456 34.783 0.00 0.00 38.42 2.57
702 1806 5.923204 TGCAACTAACCCATTGTTTCAATT 58.077 33.333 0.00 0.00 38.42 2.32
704 1808 6.825721 TGCAACTAACCCATTGTTTCAATTTT 59.174 30.769 0.00 0.00 38.42 1.82
705 1809 7.987458 TGCAACTAACCCATTGTTTCAATTTTA 59.013 29.630 0.00 0.00 38.42 1.52
706 1810 8.279800 GCAACTAACCCATTGTTTCAATTTTAC 58.720 33.333 0.00 0.00 38.42 2.01
707 1811 8.769891 CAACTAACCCATTGTTTCAATTTTACC 58.230 33.333 0.00 0.00 38.42 2.85
717 2029 9.974980 ATTGTTTCAATTTTACCGTACAGAAAT 57.025 25.926 0.00 0.00 0.00 2.17
722 2034 7.586747 TCAATTTTACCGTACAGAAATGAACC 58.413 34.615 0.00 0.00 0.00 3.62
814 2126 8.125978 TCAGCCAATTAAAGACTTCAATCAAT 57.874 30.769 0.00 0.00 0.00 2.57
854 2166 3.440522 GGGTTTGCTAACAACAGAGATCC 59.559 47.826 13.00 0.00 34.87 3.36
863 2175 0.103208 AACAGAGATCCGACGATGGC 59.897 55.000 0.00 0.00 0.00 4.40
881 2193 1.206523 GCTGTAAATCCGACGGCTAC 58.793 55.000 9.66 10.86 44.34 3.58
885 2197 3.544684 TGTAAATCCGACGGCTACTCTA 58.455 45.455 9.66 0.00 0.00 2.43
886 2198 3.947196 TGTAAATCCGACGGCTACTCTAA 59.053 43.478 9.66 0.00 0.00 2.10
887 2199 4.581824 TGTAAATCCGACGGCTACTCTAAT 59.418 41.667 9.66 0.00 0.00 1.73
888 2200 3.919223 AATCCGACGGCTACTCTAATC 57.081 47.619 9.66 0.00 0.00 1.75
889 2201 2.634815 TCCGACGGCTACTCTAATCT 57.365 50.000 9.66 0.00 0.00 2.40
890 2202 2.492012 TCCGACGGCTACTCTAATCTC 58.508 52.381 9.66 0.00 0.00 2.75
891 2203 2.104451 TCCGACGGCTACTCTAATCTCT 59.896 50.000 9.66 0.00 0.00 3.10
892 2204 3.323115 TCCGACGGCTACTCTAATCTCTA 59.677 47.826 9.66 0.00 0.00 2.43
893 2205 4.063689 CCGACGGCTACTCTAATCTCTAA 58.936 47.826 0.00 0.00 0.00 2.10
894 2206 4.696402 CCGACGGCTACTCTAATCTCTAAT 59.304 45.833 0.00 0.00 0.00 1.73
895 2207 5.391097 CCGACGGCTACTCTAATCTCTAATG 60.391 48.000 0.00 0.00 0.00 1.90
896 2208 5.391097 CGACGGCTACTCTAATCTCTAATGG 60.391 48.000 0.00 0.00 0.00 3.16
897 2209 4.767928 ACGGCTACTCTAATCTCTAATGGG 59.232 45.833 0.00 0.00 0.00 4.00
903 2215 6.694445 ACTCTAATCTCTAATGGGAATGGG 57.306 41.667 0.00 0.00 0.00 4.00
1366 4215 2.035155 TCGGCTCCTTCGTCTCCA 59.965 61.111 0.00 0.00 0.00 3.86
1398 4247 4.457496 CAGGACATGGACGGCGCT 62.457 66.667 6.90 0.00 0.00 5.92
1509 4361 3.998672 GGCCAGACCGTCGTCCAA 61.999 66.667 0.00 0.00 40.12 3.53
1570 4422 2.676121 CCCCGCTGGAATGCAACA 60.676 61.111 0.00 0.00 35.39 3.33
1635 4502 3.615562 GAGCTCGCACAAACGACGC 62.616 63.158 0.00 0.00 37.09 5.19
1685 4552 2.270986 CCCTGTTGAAGGTGCTGGC 61.271 63.158 0.00 0.00 45.78 4.85
1800 4667 1.445095 GGCGCTCAGGATCACAGAT 59.555 57.895 7.64 0.00 0.00 2.90
1849 4719 3.036084 ACTGGTTCGCTTGCGACG 61.036 61.111 17.53 8.81 0.00 5.12
2139 5017 4.047059 GTGCAATGCCTGTGCGCT 62.047 61.111 9.73 0.00 46.55 5.92
2290 5168 3.726557 TTGAGATGGATTGGCAGACTT 57.273 42.857 0.00 0.00 0.00 3.01
2383 5262 6.462073 TTCTCGTGTGCTATTTGTAAGTTC 57.538 37.500 0.00 0.00 0.00 3.01
2384 5263 4.927425 TCTCGTGTGCTATTTGTAAGTTCC 59.073 41.667 0.00 0.00 0.00 3.62
2385 5264 4.890088 TCGTGTGCTATTTGTAAGTTCCT 58.110 39.130 0.00 0.00 0.00 3.36
2409 5288 8.981647 CCTTTGAATGAAAGTAAAGTGGATTTG 58.018 33.333 0.00 0.00 39.71 2.32
2410 5289 9.748708 CTTTGAATGAAAGTAAAGTGGATTTGA 57.251 29.630 0.00 0.00 36.96 2.69
2442 5322 9.513906 AGAAGAAGAAAATAAGAAGAAGAAGGG 57.486 33.333 0.00 0.00 0.00 3.95
2444 5324 7.178573 AGAAGAAAATAAGAAGAAGAAGGGGG 58.821 38.462 0.00 0.00 0.00 5.40
2472 5368 1.202348 CGCCGAAGACAGAGATGATGT 60.202 52.381 0.00 0.00 0.00 3.06
2647 5550 1.468520 GCTTGATTGCTCTGCGGTTTA 59.531 47.619 0.00 0.00 0.00 2.01
2746 5649 9.780186 AATCCTAGTAATTAGAGTTGTAATGGC 57.220 33.333 0.00 0.00 0.00 4.40
2763 5666 0.248866 GGCCGAAAATATTGTGCCCG 60.249 55.000 0.00 0.00 32.74 6.13
2867 5770 2.434331 CGGGGAAGAAGGTTGGCA 59.566 61.111 0.00 0.00 0.00 4.92
2976 5879 4.580167 TGATATTTGTAAGCCATGTCCAGC 59.420 41.667 0.00 0.00 0.00 4.85
3012 5915 4.795970 AAACTCTTAACAGTGAGCAACG 57.204 40.909 0.00 0.00 33.92 4.10
3016 5919 2.800544 TCTTAACAGTGAGCAACGAAGC 59.199 45.455 0.00 0.00 0.00 3.86
3026 5929 2.662156 GAGCAACGAAGCTGTAGTACAC 59.338 50.000 10.83 0.00 46.75 2.90
3060 5963 1.087501 GACATCAAAACCGCCTCCTC 58.912 55.000 0.00 0.00 0.00 3.71
3063 5966 1.200020 CATCAAAACCGCCTCCTCAAC 59.800 52.381 0.00 0.00 0.00 3.18
3064 5967 0.472471 TCAAAACCGCCTCCTCAACT 59.528 50.000 0.00 0.00 0.00 3.16
3065 5968 0.875059 CAAAACCGCCTCCTCAACTC 59.125 55.000 0.00 0.00 0.00 3.01
3066 5969 0.472471 AAAACCGCCTCCTCAACTCA 59.528 50.000 0.00 0.00 0.00 3.41
3067 5970 0.693049 AAACCGCCTCCTCAACTCAT 59.307 50.000 0.00 0.00 0.00 2.90
3068 5971 0.036010 AACCGCCTCCTCAACTCATG 60.036 55.000 0.00 0.00 0.00 3.07
3069 5972 1.817099 CCGCCTCCTCAACTCATGC 60.817 63.158 0.00 0.00 0.00 4.06
3070 5973 1.078918 CGCCTCCTCAACTCATGCA 60.079 57.895 0.00 0.00 0.00 3.96
3071 5974 1.088340 CGCCTCCTCAACTCATGCAG 61.088 60.000 0.00 0.00 0.00 4.41
3072 5975 1.375098 GCCTCCTCAACTCATGCAGC 61.375 60.000 0.00 0.00 0.00 5.25
3073 5976 0.747283 CCTCCTCAACTCATGCAGCC 60.747 60.000 0.00 0.00 0.00 4.85
3074 5977 0.252479 CTCCTCAACTCATGCAGCCT 59.748 55.000 0.00 0.00 0.00 4.58
3075 5978 0.251354 TCCTCAACTCATGCAGCCTC 59.749 55.000 0.00 0.00 0.00 4.70
3076 5979 0.747283 CCTCAACTCATGCAGCCTCC 60.747 60.000 0.00 0.00 0.00 4.30
3077 5980 1.078918 TCAACTCATGCAGCCTCCG 60.079 57.895 0.00 0.00 0.00 4.63
3078 5981 2.437359 AACTCATGCAGCCTCCGC 60.437 61.111 0.00 0.00 0.00 5.54
3079 5982 3.984193 AACTCATGCAGCCTCCGCC 62.984 63.158 0.00 0.00 34.57 6.13
3080 5983 4.172512 CTCATGCAGCCTCCGCCT 62.173 66.667 0.00 0.00 34.57 5.52
3081 5984 4.166888 TCATGCAGCCTCCGCCTC 62.167 66.667 0.00 0.00 34.57 4.70
3084 5987 4.777854 TGCAGCCTCCGCCTCCTA 62.778 66.667 0.00 0.00 34.57 2.94
3085 5988 3.470888 GCAGCCTCCGCCTCCTAA 61.471 66.667 0.00 0.00 34.57 2.69
3086 5989 3.031417 GCAGCCTCCGCCTCCTAAA 62.031 63.158 0.00 0.00 34.57 1.85
3087 5990 1.144936 CAGCCTCCGCCTCCTAAAG 59.855 63.158 0.00 0.00 34.57 1.85
3088 5991 1.001760 AGCCTCCGCCTCCTAAAGA 59.998 57.895 0.00 0.00 34.57 2.52
3089 5992 0.617820 AGCCTCCGCCTCCTAAAGAA 60.618 55.000 0.00 0.00 34.57 2.52
3090 5993 0.179070 GCCTCCGCCTCCTAAAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
3151 6054 1.043816 ACTGGTATGCCTCATCTCCG 58.956 55.000 0.16 0.00 35.27 4.63
3152 6055 0.319728 CTGGTATGCCTCATCTCCGG 59.680 60.000 0.16 0.00 35.27 5.14
3318 6221 5.396324 CCACCAACTATGTGCCTAATGACTA 60.396 44.000 0.00 0.00 32.30 2.59
3349 6252 4.815308 GCACTGATTGTCTGATAAGCTCAT 59.185 41.667 4.13 0.00 32.10 2.90
3363 6266 7.362662 TGATAAGCTCATGAAAACAGTGAAAC 58.637 34.615 0.00 0.00 0.00 2.78
3383 6286 1.903404 GACAAGTTGGGCCCACCTG 60.903 63.158 28.70 23.58 41.11 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.767255 GTCCTGCTGTGGGCCGAG 62.767 72.222 0.00 0.00 40.92 4.63
40 41 0.300789 GTTTCCGCTTTAGATCGGCG 59.699 55.000 0.00 0.00 44.91 6.46
56 57 4.091939 GGCTAGACGGGCGGGTTT 62.092 66.667 0.00 0.00 0.00 3.27
63 64 3.583276 TTGCACACGGCTAGACGGG 62.583 63.158 21.34 21.34 45.15 5.28
91 92 1.153188 TAGCATGTCCCATGTGCCG 60.153 57.895 6.13 0.00 39.62 5.69
112 113 1.609208 ACACATTGTCTTCCAGCCAC 58.391 50.000 0.00 0.00 0.00 5.01
113 114 2.363306 AACACATTGTCTTCCAGCCA 57.637 45.000 0.00 0.00 0.00 4.75
114 115 3.319122 AGAAAACACATTGTCTTCCAGCC 59.681 43.478 0.00 0.00 0.00 4.85
116 117 5.239306 TGCTAGAAAACACATTGTCTTCCAG 59.761 40.000 0.00 0.00 0.00 3.86
141 142 0.756294 ACTCACCGTGTTCATGTCCA 59.244 50.000 0.00 0.00 0.00 4.02
143 144 1.069906 GCAACTCACCGTGTTCATGTC 60.070 52.381 0.00 0.00 0.00 3.06
146 147 0.531974 ACGCAACTCACCGTGTTCAT 60.532 50.000 0.00 0.00 36.18 2.57
157 158 4.569801 GTCAGTTAGAATGACGCAACTC 57.430 45.455 0.00 0.00 37.88 3.01
176 177 3.182967 CCTCTGAACAATAGTCTGCGTC 58.817 50.000 0.00 0.00 0.00 5.19
194 195 4.436998 CGGCTGTGGTCGTCCCTC 62.437 72.222 0.00 0.00 35.65 4.30
208 209 2.561373 GTGTAGCTTGGCAACGGC 59.439 61.111 0.00 0.00 42.51 5.68
211 212 1.156736 ATGTCGTGTAGCTTGGCAAC 58.843 50.000 0.00 0.00 0.00 4.17
219 220 5.507077 TCACTTTGAAAAATGTCGTGTAGC 58.493 37.500 0.00 0.00 0.00 3.58
307 308 0.536006 GGTTGTGCTCCAGCTTGAGT 60.536 55.000 15.66 0.00 42.66 3.41
338 339 3.701542 ACTCGGTCTTCATCTTATGCTGA 59.298 43.478 0.00 0.00 0.00 4.26
342 343 8.735315 ACAGATATACTCGGTCTTCATCTTATG 58.265 37.037 0.00 0.00 0.00 1.90
362 363 1.105457 CGACGGGGTTACCACAGATA 58.895 55.000 3.92 0.00 40.22 1.98
425 433 3.596046 AGTTGAATTCAGGGGTGGGATAA 59.404 43.478 8.41 0.00 0.00 1.75
450 458 2.768527 TCCTCAGGATTTGGCTAGTCTG 59.231 50.000 0.00 0.00 0.00 3.51
453 461 2.237392 GTGTCCTCAGGATTTGGCTAGT 59.763 50.000 0.00 0.00 32.73 2.57
456 464 1.004044 CTGTGTCCTCAGGATTTGGCT 59.996 52.381 0.00 0.00 32.73 4.75
462 470 2.338809 TGGAAACTGTGTCCTCAGGAT 58.661 47.619 17.64 0.00 39.48 3.24
465 473 3.503748 GGAATTGGAAACTGTGTCCTCAG 59.496 47.826 17.64 0.00 40.80 3.35
467 475 3.253432 GTGGAATTGGAAACTGTGTCCTC 59.747 47.826 17.64 7.30 36.03 3.71
471 479 2.357637 CGTGTGGAATTGGAAACTGTGT 59.642 45.455 0.00 0.00 0.00 3.72
526 1442 2.863740 TGCGTGGATTGCTTTCTATACG 59.136 45.455 0.00 0.00 0.00 3.06
540 1456 3.055891 TCTCATGATTTCTTCTGCGTGGA 60.056 43.478 0.00 0.00 0.00 4.02
542 1458 4.331992 ACATCTCATGATTTCTTCTGCGTG 59.668 41.667 0.00 0.00 0.00 5.34
543 1459 4.511527 ACATCTCATGATTTCTTCTGCGT 58.488 39.130 0.00 0.00 0.00 5.24
577 1494 8.514594 TGATTACAAGCTTTTCCAATCTTACTG 58.485 33.333 0.00 0.00 0.00 2.74
578 1495 8.515414 GTGATTACAAGCTTTTCCAATCTTACT 58.485 33.333 0.00 0.00 0.00 2.24
589 1514 3.502211 CCGTCTGGTGATTACAAGCTTTT 59.498 43.478 0.00 0.00 0.00 2.27
590 1515 3.074412 CCGTCTGGTGATTACAAGCTTT 58.926 45.455 0.00 0.00 0.00 3.51
593 1518 2.380084 TCCGTCTGGTGATTACAAGC 57.620 50.000 0.00 0.00 36.30 4.01
594 1519 3.116300 CGATCCGTCTGGTGATTACAAG 58.884 50.000 0.00 0.00 36.30 3.16
595 1520 2.737359 GCGATCCGTCTGGTGATTACAA 60.737 50.000 0.00 0.00 36.30 2.41
599 1524 0.179100 CTGCGATCCGTCTGGTGATT 60.179 55.000 0.00 0.00 36.30 2.57
601 1526 2.885113 CTGCGATCCGTCTGGTGA 59.115 61.111 0.00 0.00 36.30 4.02
604 1529 2.279120 GAGCTGCGATCCGTCTGG 60.279 66.667 0.00 0.00 0.00 3.86
605 1530 1.299014 GAGAGCTGCGATCCGTCTG 60.299 63.158 0.00 0.00 0.00 3.51
606 1531 1.750780 TGAGAGCTGCGATCCGTCT 60.751 57.895 0.00 0.00 0.00 4.18
609 1534 2.653448 CGTGAGAGCTGCGATCCG 60.653 66.667 0.00 0.00 0.00 4.18
610 1535 1.587613 GACGTGAGAGCTGCGATCC 60.588 63.158 0.00 0.00 0.00 3.36
611 1536 0.865218 CTGACGTGAGAGCTGCGATC 60.865 60.000 0.00 0.00 0.00 3.69
613 1538 2.188849 GACTGACGTGAGAGCTGCGA 62.189 60.000 9.65 0.00 0.00 5.10
615 1540 1.006314 GTGACTGACGTGAGAGCTGC 61.006 60.000 9.65 0.00 0.00 5.25
617 1542 0.538516 AGGTGACTGACGTGAGAGCT 60.539 55.000 9.65 0.00 41.13 4.09
619 1544 1.068194 GGAAGGTGACTGACGTGAGAG 60.068 57.143 9.65 0.00 42.68 3.20
621 1546 0.038159 GGGAAGGTGACTGACGTGAG 60.038 60.000 0.00 0.00 42.68 3.51
623 1548 0.319900 CAGGGAAGGTGACTGACGTG 60.320 60.000 0.00 0.00 42.68 4.49
624 1549 2.050269 CAGGGAAGGTGACTGACGT 58.950 57.895 0.00 0.00 42.68 4.34
625 1550 1.374758 GCAGGGAAGGTGACTGACG 60.375 63.158 0.00 0.00 42.68 4.35
626 1551 0.108585 TTGCAGGGAAGGTGACTGAC 59.891 55.000 0.00 0.00 42.68 3.51
627 1552 0.397941 CTTGCAGGGAAGGTGACTGA 59.602 55.000 0.00 0.00 42.68 3.41
628 1553 1.239968 GCTTGCAGGGAAGGTGACTG 61.240 60.000 0.00 0.00 42.68 3.51
630 1555 1.973812 GGCTTGCAGGGAAGGTGAC 60.974 63.158 0.00 0.00 0.00 3.67
631 1556 2.436109 GGCTTGCAGGGAAGGTGA 59.564 61.111 0.00 0.00 0.00 4.02
632 1557 2.115910 TGGCTTGCAGGGAAGGTG 59.884 61.111 0.00 0.00 0.00 4.00
633 1558 2.085343 ATGTGGCTTGCAGGGAAGGT 62.085 55.000 0.00 0.00 0.00 3.50
634 1559 1.304713 ATGTGGCTTGCAGGGAAGG 60.305 57.895 0.00 0.00 0.00 3.46
635 1560 1.888018 CATGTGGCTTGCAGGGAAG 59.112 57.895 0.00 0.00 0.00 3.46
636 1561 2.277591 GCATGTGGCTTGCAGGGAA 61.278 57.895 0.00 0.00 39.90 3.97
637 1562 2.677524 GCATGTGGCTTGCAGGGA 60.678 61.111 0.00 0.00 39.90 4.20
638 1563 3.766691 GGCATGTGGCTTGCAGGG 61.767 66.667 0.00 0.00 41.95 4.45
641 1566 3.908904 ATGGGGCATGTGGCTTGCA 62.909 57.895 6.52 0.00 41.95 4.08
643 1568 2.727392 CCATGGGGCATGTGGCTTG 61.727 63.158 2.85 2.90 44.01 4.01
644 1569 2.364579 CCATGGGGCATGTGGCTT 60.365 61.111 2.85 0.00 44.01 4.35
655 1580 0.850100 TAATAGTGGTGGCCCATGGG 59.150 55.000 27.87 27.87 44.35 4.00
656 1581 1.494721 ACTAATAGTGGTGGCCCATGG 59.505 52.381 4.14 4.14 44.35 3.66
658 1583 4.023291 CAAAACTAATAGTGGTGGCCCAT 58.977 43.478 0.00 0.00 44.35 4.00
659 1584 3.426615 CAAAACTAATAGTGGTGGCCCA 58.573 45.455 0.00 0.00 38.87 5.36
660 1585 2.165641 GCAAAACTAATAGTGGTGGCCC 59.834 50.000 0.00 0.00 0.00 5.80
661 1586 2.823154 TGCAAAACTAATAGTGGTGGCC 59.177 45.455 0.00 0.00 0.00 5.36
666 1770 6.207810 TGGGTTAGTTGCAAAACTAATAGTGG 59.792 38.462 12.84 0.00 44.28 4.00
669 1773 8.303876 ACAATGGGTTAGTTGCAAAACTAATAG 58.696 33.333 12.84 5.11 44.28 1.73
674 1778 5.351948 AACAATGGGTTAGTTGCAAAACT 57.648 34.783 12.48 5.25 38.15 2.66
675 1779 5.582665 TGAAACAATGGGTTAGTTGCAAAAC 59.417 36.000 0.00 2.65 39.29 2.43
677 1781 5.344743 TGAAACAATGGGTTAGTTGCAAA 57.655 34.783 0.00 0.00 39.29 3.68
684 1788 7.149307 ACGGTAAAATTGAAACAATGGGTTAG 58.851 34.615 0.00 0.00 39.29 2.34
685 1789 7.052142 ACGGTAAAATTGAAACAATGGGTTA 57.948 32.000 0.00 0.00 39.29 2.85
686 1790 5.919755 ACGGTAAAATTGAAACAATGGGTT 58.080 33.333 0.00 0.00 42.98 4.11
687 1791 5.538849 ACGGTAAAATTGAAACAATGGGT 57.461 34.783 0.00 0.00 0.00 4.51
689 1793 7.364200 TCTGTACGGTAAAATTGAAACAATGG 58.636 34.615 0.64 0.00 0.00 3.16
691 1795 9.974980 ATTTCTGTACGGTAAAATTGAAACAAT 57.025 25.926 0.64 0.00 0.00 2.71
693 1797 8.622157 TCATTTCTGTACGGTAAAATTGAAACA 58.378 29.630 0.64 0.00 0.00 2.83
694 1798 9.453325 TTCATTTCTGTACGGTAAAATTGAAAC 57.547 29.630 0.64 0.00 0.00 2.78
695 1799 9.453325 GTTCATTTCTGTACGGTAAAATTGAAA 57.547 29.630 9.03 6.15 0.00 2.69
697 1801 7.571613 CGGTTCATTTCTGTACGGTAAAATTGA 60.572 37.037 0.64 0.00 0.00 2.57
698 1802 6.521821 CGGTTCATTTCTGTACGGTAAAATTG 59.478 38.462 0.64 0.00 0.00 2.32
699 1803 6.604930 CGGTTCATTTCTGTACGGTAAAATT 58.395 36.000 0.64 0.00 0.00 1.82
701 1805 4.083908 GCGGTTCATTTCTGTACGGTAAAA 60.084 41.667 0.64 0.00 0.00 1.52
702 1806 3.432933 GCGGTTCATTTCTGTACGGTAAA 59.567 43.478 0.64 2.08 0.00 2.01
704 1808 2.029200 TGCGGTTCATTTCTGTACGGTA 60.029 45.455 0.64 0.00 0.00 4.02
705 1809 1.270412 TGCGGTTCATTTCTGTACGGT 60.270 47.619 0.64 0.00 0.00 4.83
706 1810 1.434555 TGCGGTTCATTTCTGTACGG 58.565 50.000 0.00 0.00 0.00 4.02
707 1811 2.222213 TGTTGCGGTTCATTTCTGTACG 59.778 45.455 0.00 0.00 0.00 3.67
717 2029 4.966787 GGGCCCTGTTGCGGTTCA 62.967 66.667 17.04 0.00 0.00 3.18
814 2126 3.787676 CGCGCGTGATTTGCTGGA 61.788 61.111 24.19 0.00 0.00 3.86
834 2146 3.994392 TCGGATCTCTGTTGTTAGCAAAC 59.006 43.478 0.00 0.00 36.22 2.93
854 2166 0.852777 CGGATTTACAGCCATCGTCG 59.147 55.000 0.00 0.00 0.00 5.12
863 2175 2.358267 AGAGTAGCCGTCGGATTTACAG 59.642 50.000 17.49 0.00 0.00 2.74
881 2193 6.942163 TCCCATTCCCATTAGAGATTAGAG 57.058 41.667 0.00 0.00 0.00 2.43
1028 3853 1.316706 CCTCGTCTTCTTCCGCCTCT 61.317 60.000 0.00 0.00 0.00 3.69
1081 3909 4.131088 GTCTCCCGGGAGCGTGTC 62.131 72.222 40.97 24.28 41.71 3.67
1094 3922 1.002251 GGATCTCGATCACCACGTCTC 60.002 57.143 8.97 0.00 39.54 3.36
1138 3966 4.699522 GGCGCAACGGAAGAGGGT 62.700 66.667 10.83 0.00 0.00 4.34
1243 4071 2.448705 GCTGAGCGAAGAAGCCGAC 61.449 63.158 0.00 0.00 38.01 4.79
1354 4182 3.760035 GGCGCTGGAGACGAAGGA 61.760 66.667 7.64 0.00 0.00 3.36
1381 4230 4.457496 AGCGCCGTCCATGTCCTG 62.457 66.667 2.29 0.00 0.00 3.86
1382 4231 4.457496 CAGCGCCGTCCATGTCCT 62.457 66.667 2.29 0.00 0.00 3.85
1398 4247 3.422303 GCGTCGTCAAGCATGCCA 61.422 61.111 15.66 0.00 0.00 4.92
1501 4353 2.737376 GACCGCCAGTTGGACGAC 60.737 66.667 13.86 6.52 37.05 4.34
1570 4422 1.067295 TTGTTGATGCTGGAGGAGGT 58.933 50.000 0.00 0.00 0.00 3.85
1970 4840 3.118454 GTGTGTCGTCCATGGCGG 61.118 66.667 22.59 11.18 0.00 6.13
1982 4852 2.505819 AGGTGAAACAAGGAGAGTGTGT 59.494 45.455 0.00 0.00 39.98 3.72
2290 5168 3.085533 CCTCCAGACGAGAGAAGAAGAA 58.914 50.000 0.00 0.00 41.63 2.52
2383 5262 8.981647 CAAATCCACTTTACTTTCATTCAAAGG 58.018 33.333 0.00 0.00 45.35 3.11
2384 5263 9.748708 TCAAATCCACTTTACTTTCATTCAAAG 57.251 29.630 0.00 0.00 46.36 2.77
2442 5322 3.431725 CTTCGGCGTTGCTTCCCC 61.432 66.667 6.85 0.00 0.00 4.81
2444 5324 1.901650 CTGTCTTCGGCGTTGCTTCC 61.902 60.000 6.85 0.00 0.00 3.46
2445 5325 0.944311 TCTGTCTTCGGCGTTGCTTC 60.944 55.000 6.85 0.00 0.00 3.86
2446 5326 0.946221 CTCTGTCTTCGGCGTTGCTT 60.946 55.000 6.85 0.00 0.00 3.91
2451 5347 1.107114 ATCATCTCTGTCTTCGGCGT 58.893 50.000 6.85 0.00 0.00 5.68
2452 5348 1.202348 ACATCATCTCTGTCTTCGGCG 60.202 52.381 0.00 0.00 0.00 6.46
2746 5649 0.248866 GCCGGGCACAATATTTTCGG 60.249 55.000 15.62 0.00 39.07 4.30
2828 5731 2.027605 CACCACGACGTCACAGCT 59.972 61.111 17.16 0.00 0.00 4.24
2829 5732 3.036084 CCACCACGACGTCACAGC 61.036 66.667 17.16 0.00 0.00 4.40
2830 5733 1.371758 CTCCACCACGACGTCACAG 60.372 63.158 17.16 5.25 0.00 3.66
2831 5734 2.725641 CTCCACCACGACGTCACA 59.274 61.111 17.16 0.00 0.00 3.58
2832 5735 2.049433 CCTCCACCACGACGTCAC 60.049 66.667 17.16 0.00 0.00 3.67
2867 5770 1.543896 ATGTTGTGCCCCCTACCCT 60.544 57.895 0.00 0.00 0.00 4.34
2912 5815 8.154649 ACAAGTTCAAGTCAAATAGTAACCAG 57.845 34.615 0.00 0.00 0.00 4.00
3060 5963 2.758089 GCGGAGGCTGCATGAGTTG 61.758 63.158 6.86 0.00 35.55 3.16
3072 5975 1.486211 TCTTCTTTAGGAGGCGGAGG 58.514 55.000 0.00 0.00 0.00 4.30
3073 5976 3.611766 TTTCTTCTTTAGGAGGCGGAG 57.388 47.619 0.00 0.00 0.00 4.63
3074 5977 4.360951 TTTTTCTTCTTTAGGAGGCGGA 57.639 40.909 0.00 0.00 0.00 5.54
3100 6003 0.761802 GGGATGCAGAGGAACCCTAG 59.238 60.000 0.00 0.00 37.75 3.02
3151 6054 1.144057 CCATGGCTCTACGTCCACC 59.856 63.158 0.00 0.00 34.81 4.61
3152 6055 0.103208 CTCCATGGCTCTACGTCCAC 59.897 60.000 6.96 0.00 34.81 4.02
3297 6200 5.234329 CGTTAGTCATTAGGCACATAGTTGG 59.766 44.000 0.00 0.00 0.00 3.77
3318 6221 3.062763 CAGACAATCAGTGCTCTTCGTT 58.937 45.455 0.00 0.00 0.00 3.85
3349 6252 5.957842 ACTTGTCAGTTTCACTGTTTTCA 57.042 34.783 3.87 0.00 46.03 2.69
3363 6266 1.903404 GGTGGGCCCAACTTGTCAG 60.903 63.158 33.79 0.00 0.00 3.51
3392 6295 3.572539 CACACAAGCACGCCACGT 61.573 61.111 0.00 0.00 42.36 4.49
3394 6297 2.899838 TCCACACAAGCACGCCAC 60.900 61.111 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.