Multiple sequence alignment - TraesCS2D01G310600

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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 TraesCS2D01G310600 chr2D 100.000 3269 0 0 1 3269 398779047 398782315 0.000000e+00 6037
1 TraesCS2D01G310600 chr2B 96.857 2450 39 18 828 3269 472898326 472900745 0.000000e+00 4063
2 TraesCS2D01G310600 chr2B 92.469 571 28 8 1 563 472896924 472897487 0.000000e+00 802
3 TraesCS2D01G310600 chr2B 98.507 67 1 0 556 622 472898245 472898311 5.730000e-23 119
4 TraesCS2D01G310600 chr2A 92.438 2301 109 40 828 3101 536623482 536625744 0.000000e+00 3225
5 TraesCS2D01G310600 chr2A 90.469 682 33 7 1 666 536622838 536623503 0.000000e+00 870
6 TraesCS2D01G310600 chr2A 97.076 171 5 0 661 831 65400328 65400498 4.130000e-74 289
7 TraesCS2D01G310600 chr4D 89.914 1398 128 9 999 2386 502412811 502411417 0.000000e+00 1788
8 TraesCS2D01G310600 chr4B 89.899 1386 133 4 999 2377 646659675 646658290 0.000000e+00 1777
9 TraesCS2D01G310600 chr5A 89.561 1389 137 5 999 2379 685538674 685537286 0.000000e+00 1755
10 TraesCS2D01G310600 chr5B 92.611 203 13 2 634 835 428847144 428847345 1.150000e-74 291
11 TraesCS2D01G310600 chr7B 96.045 177 6 1 663 839 129222272 129222447 1.480000e-73 287
12 TraesCS2D01G310600 chr7B 95.506 178 6 2 663 838 134048620 134048443 1.920000e-72 283
13 TraesCS2D01G310600 chr7B 93.229 192 8 5 650 840 472508904 472508717 8.930000e-71 278
14 TraesCS2D01G310600 chr7A 96.532 173 6 0 662 834 143050264 143050436 1.480000e-73 287
15 TraesCS2D01G310600 chr7A 97.059 170 5 0 661 830 426576422 426576591 1.480000e-73 287
16 TraesCS2D01G310600 chr4A 96.532 173 6 0 657 829 546625021 546624849 1.480000e-73 287
17 TraesCS2D01G310600 chr6B 96.000 175 7 0 663 837 460493634 460493460 5.340000e-73 285


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 TraesCS2D01G310600 chr2D 398779047 398782315 3268 False 6037.000000 6037 100.000000 1 3269 1 chr2D.!!$F1 3268
1 TraesCS2D01G310600 chr2B 472896924 472900745 3821 False 1661.333333 4063 95.944333 1 3269 3 chr2B.!!$F1 3268
2 TraesCS2D01G310600 chr2A 536622838 536625744 2906 False 2047.500000 3225 91.453500 1 3101 2 chr2A.!!$F2 3100
3 TraesCS2D01G310600 chr4D 502411417 502412811 1394 True 1788.000000 1788 89.914000 999 2386 1 chr4D.!!$R1 1387
4 TraesCS2D01G310600 chr4B 646658290 646659675 1385 True 1777.000000 1777 89.899000 999 2377 1 chr4B.!!$R1 1378
5 TraesCS2D01G310600 chr5A 685537286 685538674 1388 True 1755.000000 1755 89.561000 999 2379 1 chr5A.!!$R1 1380

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
701 1484 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.0 0.00 0.0 34.10 3.16 F
746 1529 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.0 7.38 0.0 33.79 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2762 2.972713 GCTCCAGGAGGGTATCATACAA 59.027 50.000 18.83 0.00 38.11 2.41 R
2745 3580 4.809958 ACTTCGATCAGAAATCTGCATCAG 59.190 41.667 5.53 6.95 43.46 2.90 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
78 79 4.946157 CCTGTCTTGGCTGTTTATTCTGAT 59.054 41.667 0.00 0.00 0.00 2.90
107 108 4.887655 GGTTTAGGGATTCTGGTTATGGTG 59.112 45.833 0.00 0.00 0.00 4.17
108 109 4.788925 TTAGGGATTCTGGTTATGGTGG 57.211 45.455 0.00 0.00 0.00 4.61
109 110 2.573463 AGGGATTCTGGTTATGGTGGT 58.427 47.619 0.00 0.00 0.00 4.16
152 154 1.339097 ACGACCTAGCTTGGTGAAGT 58.661 50.000 25.04 17.23 41.00 3.01
162 164 4.067896 AGCTTGGTGAAGTGTATTGTCAG 58.932 43.478 0.00 0.00 0.00 3.51
197 200 0.833834 AGAGGCACTGGTAGCACTGT 60.834 55.000 0.00 0.00 41.55 3.55
206 209 2.478894 CTGGTAGCACTGTGTTTTACCG 59.521 50.000 21.73 16.33 37.24 4.02
211 214 2.548057 AGCACTGTGTTTTACCGTGATG 59.452 45.455 9.86 0.00 44.42 3.07
217 220 2.546368 GTGTTTTACCGTGATGTGCTGA 59.454 45.455 0.00 0.00 0.00 4.26
220 223 4.083537 TGTTTTACCGTGATGTGCTGAATC 60.084 41.667 0.00 0.00 0.00 2.52
222 225 0.037326 ACCGTGATGTGCTGAATCGT 60.037 50.000 0.00 0.00 0.00 3.73
223 226 1.203758 ACCGTGATGTGCTGAATCGTA 59.796 47.619 0.00 0.00 0.00 3.43
226 229 2.028045 CGTGATGTGCTGAATCGTACAC 59.972 50.000 0.00 0.00 32.42 2.90
308 311 0.038159 GGGACACTGTTGAGAGACGG 60.038 60.000 0.00 0.00 0.00 4.79
322 325 0.321653 AGACGGTTGATTCTGCCCAC 60.322 55.000 0.00 0.00 0.00 4.61
383 386 8.837788 AACATGGTTACACTACCTAACTTAAC 57.162 34.615 0.00 0.00 39.04 2.01
384 387 7.965718 ACATGGTTACACTACCTAACTTAACA 58.034 34.615 0.00 0.00 39.04 2.41
385 388 8.431222 ACATGGTTACACTACCTAACTTAACAA 58.569 33.333 0.00 0.00 39.04 2.83
386 389 9.275398 CATGGTTACACTACCTAACTTAACAAA 57.725 33.333 0.00 0.00 39.04 2.83
388 391 9.328845 TGGTTACACTACCTAACTTAACAAAAG 57.671 33.333 0.00 0.00 39.04 2.27
389 392 9.330063 GGTTACACTACCTAACTTAACAAAAGT 57.670 33.333 0.00 0.00 35.23 2.66
391 394 7.797038 ACACTACCTAACTTAACAAAAGTGG 57.203 36.000 0.00 0.00 36.89 4.00
543 561 8.821686 AGATATTCCAGATAGTGATAGACCTG 57.178 38.462 0.00 0.00 0.00 4.00
632 1415 0.391793 TGCACGCCGATATGTTTCCA 60.392 50.000 0.00 0.00 0.00 3.53
657 1440 5.772393 TTTTCCTCTATTAGTTGGAGGCA 57.228 39.130 0.00 0.00 44.39 4.75
658 1441 5.975988 TTTCCTCTATTAGTTGGAGGCAT 57.024 39.130 0.00 0.00 44.39 4.40
659 1442 5.552870 TTCCTCTATTAGTTGGAGGCATC 57.447 43.478 0.00 0.00 44.39 3.91
660 1443 3.574396 TCCTCTATTAGTTGGAGGCATCG 59.426 47.826 0.00 0.00 44.39 3.84
661 1444 3.322254 CCTCTATTAGTTGGAGGCATCGT 59.678 47.826 0.00 0.00 39.87 3.73
662 1445 4.302455 CTCTATTAGTTGGAGGCATCGTG 58.698 47.826 0.00 0.00 0.00 4.35
663 1446 3.958147 TCTATTAGTTGGAGGCATCGTGA 59.042 43.478 0.00 0.00 0.00 4.35
664 1447 2.672961 TTAGTTGGAGGCATCGTGAG 57.327 50.000 0.00 0.00 0.00 3.51
665 1448 0.824109 TAGTTGGAGGCATCGTGAGG 59.176 55.000 0.00 0.00 0.00 3.86
666 1449 1.450312 GTTGGAGGCATCGTGAGGG 60.450 63.158 0.00 0.00 0.00 4.30
667 1450 3.329542 TTGGAGGCATCGTGAGGGC 62.330 63.158 0.00 0.00 37.98 5.19
668 1451 3.785859 GGAGGCATCGTGAGGGCA 61.786 66.667 10.68 0.00 40.30 5.36
669 1452 2.202987 GAGGCATCGTGAGGGCAG 60.203 66.667 10.68 0.00 40.30 4.85
670 1453 3.746949 GAGGCATCGTGAGGGCAGG 62.747 68.421 10.68 0.00 40.30 4.85
673 1456 3.790437 CATCGTGAGGGCAGGCCT 61.790 66.667 17.36 17.36 36.10 5.19
674 1457 3.790437 ATCGTGAGGGCAGGCCTG 61.790 66.667 29.34 29.34 36.10 4.85
688 1471 3.052082 CCTGGCGCAGTGGTGAAG 61.052 66.667 10.83 0.00 0.00 3.02
689 1472 2.281070 CTGGCGCAGTGGTGAAGT 60.281 61.111 10.83 0.00 0.00 3.01
690 1473 2.280797 TGGCGCAGTGGTGAAGTC 60.281 61.111 10.83 0.00 0.00 3.01
691 1474 3.050275 GGCGCAGTGGTGAAGTCC 61.050 66.667 10.83 0.00 0.00 3.85
692 1475 2.031163 GCGCAGTGGTGAAGTCCT 59.969 61.111 0.30 0.00 0.00 3.85
693 1476 2.029844 GCGCAGTGGTGAAGTCCTC 61.030 63.158 0.30 0.00 0.00 3.71
694 1477 1.374758 CGCAGTGGTGAAGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
695 1478 1.003233 GCAGTGGTGAAGTCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
696 1479 1.679898 CAGTGGTGAAGTCCTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
697 1480 1.127567 CAGTGGTGAAGTCCTCCCCA 61.128 60.000 0.00 0.00 0.00 4.96
698 1481 1.128188 AGTGGTGAAGTCCTCCCCAC 61.128 60.000 0.00 0.00 44.69 4.61
699 1482 1.128188 GTGGTGAAGTCCTCCCCACT 61.128 60.000 0.00 0.00 41.83 4.00
700 1483 0.401395 TGGTGAAGTCCTCCCCACTT 60.401 55.000 0.00 0.00 36.77 3.16
701 1484 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16
702 1485 0.765510 GTGAAGTCCTCCCCACTTGT 59.234 55.000 0.00 0.00 34.10 3.16
703 1486 0.764890 TGAAGTCCTCCCCACTTGTG 59.235 55.000 0.00 0.00 34.10 3.33
704 1487 0.606673 GAAGTCCTCCCCACTTGTGC 60.607 60.000 0.00 0.00 34.10 4.57
705 1488 2.034221 GTCCTCCCCACTTGTGCC 59.966 66.667 0.00 0.00 0.00 5.01
706 1489 2.449518 TCCTCCCCACTTGTGCCA 60.450 61.111 0.00 0.00 0.00 4.92
707 1490 2.081787 TCCTCCCCACTTGTGCCAA 61.082 57.895 0.00 0.00 0.00 4.52
708 1491 1.604593 CCTCCCCACTTGTGCCAAG 60.605 63.158 11.87 11.87 0.00 3.61
709 1492 1.455849 CTCCCCACTTGTGCCAAGA 59.544 57.895 18.22 0.00 0.00 3.02
710 1493 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
711 1494 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
712 1495 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
713 1496 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
714 1497 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
715 1498 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
716 1499 1.347707 CACTTGTGCCAAGAGGTCCTA 59.652 52.381 18.22 0.00 37.19 2.94
717 1500 1.625818 ACTTGTGCCAAGAGGTCCTAG 59.374 52.381 18.22 0.00 37.19 3.02
718 1501 0.984230 TTGTGCCAAGAGGTCCTAGG 59.016 55.000 0.82 0.82 37.19 3.02
719 1502 0.178903 TGTGCCAAGAGGTCCTAGGT 60.179 55.000 9.08 0.00 37.19 3.08
720 1503 0.984995 GTGCCAAGAGGTCCTAGGTT 59.015 55.000 9.08 0.00 37.19 3.50
721 1504 1.351350 GTGCCAAGAGGTCCTAGGTTT 59.649 52.381 9.08 0.00 37.19 3.27
722 1505 1.351017 TGCCAAGAGGTCCTAGGTTTG 59.649 52.381 9.08 7.11 37.19 2.93
723 1506 1.628846 GCCAAGAGGTCCTAGGTTTGA 59.371 52.381 9.08 0.00 37.19 2.69
724 1507 2.039879 GCCAAGAGGTCCTAGGTTTGAA 59.960 50.000 9.08 0.00 37.19 2.69
725 1508 3.676093 CCAAGAGGTCCTAGGTTTGAAC 58.324 50.000 9.08 0.00 0.00 3.18
737 1520 0.877743 GTTTGAACCAGCCTCTCTGC 59.122 55.000 0.00 0.00 41.50 4.26
738 1521 0.473755 TTTGAACCAGCCTCTCTGCA 59.526 50.000 0.00 0.00 41.50 4.41
739 1522 0.694771 TTGAACCAGCCTCTCTGCAT 59.305 50.000 0.00 0.00 41.50 3.96
740 1523 0.694771 TGAACCAGCCTCTCTGCATT 59.305 50.000 0.00 0.00 41.50 3.56
741 1524 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
742 1525 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
743 1526 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
744 1527 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
745 1528 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
746 1529 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
747 1530 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
748 1531 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
749 1532 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
765 1548 3.404773 GCAGGGGCAAGACTAGGT 58.595 61.111 0.00 0.00 40.72 3.08
766 1549 1.685820 GCAGGGGCAAGACTAGGTT 59.314 57.895 0.00 0.00 40.72 3.50
767 1550 0.393132 GCAGGGGCAAGACTAGGTTC 60.393 60.000 0.00 0.00 40.72 3.62
768 1551 0.253327 CAGGGGCAAGACTAGGTTCC 59.747 60.000 0.00 0.00 0.00 3.62
769 1552 0.119358 AGGGGCAAGACTAGGTTCCT 59.881 55.000 0.00 0.00 0.00 3.36
770 1553 1.365028 AGGGGCAAGACTAGGTTCCTA 59.635 52.381 0.00 0.00 0.00 2.94
771 1554 2.021936 AGGGGCAAGACTAGGTTCCTAT 60.022 50.000 0.00 0.00 0.00 2.57
772 1555 3.209152 AGGGGCAAGACTAGGTTCCTATA 59.791 47.826 0.00 0.00 0.00 1.31
773 1556 3.971971 GGGGCAAGACTAGGTTCCTATAA 59.028 47.826 0.00 0.00 0.00 0.98
774 1557 4.597940 GGGGCAAGACTAGGTTCCTATAAT 59.402 45.833 0.00 0.00 0.00 1.28
775 1558 5.280062 GGGGCAAGACTAGGTTCCTATAATC 60.280 48.000 0.00 0.00 0.00 1.75
776 1559 5.280062 GGGCAAGACTAGGTTCCTATAATCC 60.280 48.000 0.00 0.00 0.00 3.01
777 1560 5.280062 GGCAAGACTAGGTTCCTATAATCCC 60.280 48.000 0.00 0.00 0.00 3.85
778 1561 5.544562 GCAAGACTAGGTTCCTATAATCCCT 59.455 44.000 0.00 0.00 0.00 4.20
779 1562 6.295405 GCAAGACTAGGTTCCTATAATCCCTC 60.295 46.154 0.00 0.00 0.00 4.30
780 1563 6.806959 AGACTAGGTTCCTATAATCCCTCT 57.193 41.667 0.00 0.00 0.00 3.69
781 1564 6.796648 AGACTAGGTTCCTATAATCCCTCTC 58.203 44.000 0.00 0.00 0.00 3.20
782 1565 5.906254 ACTAGGTTCCTATAATCCCTCTCC 58.094 45.833 0.00 0.00 0.00 3.71
783 1566 4.852991 AGGTTCCTATAATCCCTCTCCA 57.147 45.455 0.00 0.00 0.00 3.86
784 1567 4.757692 AGGTTCCTATAATCCCTCTCCAG 58.242 47.826 0.00 0.00 0.00 3.86
785 1568 4.423960 AGGTTCCTATAATCCCTCTCCAGA 59.576 45.833 0.00 0.00 0.00 3.86
786 1569 4.528987 GGTTCCTATAATCCCTCTCCAGAC 59.471 50.000 0.00 0.00 0.00 3.51
787 1570 4.405756 TCCTATAATCCCTCTCCAGACC 57.594 50.000 0.00 0.00 0.00 3.85
788 1571 3.077695 TCCTATAATCCCTCTCCAGACCC 59.922 52.174 0.00 0.00 0.00 4.46
789 1572 2.424684 ATAATCCCTCTCCAGACCCC 57.575 55.000 0.00 0.00 0.00 4.95
790 1573 1.023719 TAATCCCTCTCCAGACCCCA 58.976 55.000 0.00 0.00 0.00 4.96
791 1574 0.621862 AATCCCTCTCCAGACCCCAC 60.622 60.000 0.00 0.00 0.00 4.61
792 1575 2.553438 ATCCCTCTCCAGACCCCACC 62.553 65.000 0.00 0.00 0.00 4.61
793 1576 2.452114 CCTCTCCAGACCCCACCT 59.548 66.667 0.00 0.00 0.00 4.00
794 1577 1.229658 CCTCTCCAGACCCCACCTT 60.230 63.158 0.00 0.00 0.00 3.50
795 1578 1.557269 CCTCTCCAGACCCCACCTTG 61.557 65.000 0.00 0.00 0.00 3.61
796 1579 0.838122 CTCTCCAGACCCCACCTTGT 60.838 60.000 0.00 0.00 0.00 3.16
797 1580 1.127567 TCTCCAGACCCCACCTTGTG 61.128 60.000 0.00 0.00 0.00 3.33
798 1581 1.385347 TCCAGACCCCACCTTGTGT 60.385 57.895 0.00 0.00 0.00 3.72
799 1582 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
806 1589 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
807 1590 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
808 1591 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
809 1592 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
810 1593 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
811 1594 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
812 1595 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
813 1596 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
814 1597 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
815 1598 0.253044 TGTGGGAGCTTCTATGCACC 59.747 55.000 0.00 0.00 41.84 5.01
816 1599 0.811616 GTGGGAGCTTCTATGCACCG 60.812 60.000 0.00 0.00 43.16 4.94
817 1600 1.227674 GGGAGCTTCTATGCACCGG 60.228 63.158 0.00 0.00 43.16 5.28
818 1601 1.227674 GGAGCTTCTATGCACCGGG 60.228 63.158 6.32 0.00 34.33 5.73
819 1602 1.522569 GAGCTTCTATGCACCGGGT 59.477 57.895 6.32 0.00 34.99 5.28
820 1603 0.530870 GAGCTTCTATGCACCGGGTC 60.531 60.000 6.32 0.00 34.99 4.46
821 1604 0.978146 AGCTTCTATGCACCGGGTCT 60.978 55.000 6.32 0.00 34.99 3.85
822 1605 0.811616 GCTTCTATGCACCGGGTCTG 60.812 60.000 6.32 0.00 0.00 3.51
823 1606 0.537188 CTTCTATGCACCGGGTCTGT 59.463 55.000 6.32 0.00 0.00 3.41
824 1607 0.535335 TTCTATGCACCGGGTCTGTC 59.465 55.000 6.32 0.00 0.00 3.51
825 1608 1.144057 CTATGCACCGGGTCTGTCC 59.856 63.158 6.32 0.00 0.00 4.02
826 1609 1.305802 TATGCACCGGGTCTGTCCT 60.306 57.895 6.32 0.00 36.25 3.85
1389 2179 1.003839 CCTTAGGCAGCGTGTGGAA 60.004 57.895 0.00 0.00 0.00 3.53
1473 2263 8.660295 TTACTGGTCTTATTAAGGAAGTCAGA 57.340 34.615 19.77 10.01 34.08 3.27
1524 2314 3.055530 ACATAGACCTGTTGGAGAGCAAG 60.056 47.826 0.00 0.00 37.04 4.01
1972 2762 3.181440 TGTTCACAGGCATCTTTCCTCTT 60.181 43.478 0.00 0.00 0.00 2.85
2412 3211 8.827832 TTGGATCATAGAAAAATCCATCTTGT 57.172 30.769 4.28 0.00 46.23 3.16
2425 3224 4.326826 TCCATCTTGTTCATGAACTGGAC 58.673 43.478 29.62 13.50 37.16 4.02
2611 3410 6.024049 GTCAGAGTTGTTAATGCTGTTATGC 58.976 40.000 0.00 0.00 0.00 3.14
2693 3528 5.416947 GTTCTGGGTCGTATGTTCTATTGT 58.583 41.667 0.00 0.00 0.00 2.71
2745 3580 2.456594 TTCGTCAGCCATGCGTTTGC 62.457 55.000 0.00 0.00 43.20 3.68
2827 3662 7.229707 AGAGTTGATGATGCTTAGTACTCGTAT 59.770 37.037 0.00 0.00 36.71 3.06
2830 3665 8.903723 GTTGATGATGCTTAGTACTCGTATAAC 58.096 37.037 0.00 0.00 0.00 1.89
2898 3734 9.031537 TGTTCTATACTGATTTGGTGAGACTTA 57.968 33.333 0.00 0.00 0.00 2.24
3084 3926 6.817765 TGTCTCAGGAACCATGTAAAATTC 57.182 37.500 0.00 0.00 0.00 2.17
3125 3967 7.050377 TCTCTTCTCAATTATAAGCACCCAAG 58.950 38.462 0.00 0.00 0.00 3.61
3198 4040 1.211457 GGTCATGTCATGGGCTTCTCT 59.789 52.381 12.90 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 8.665906 CATAACCAGAATCCCTAAACCCTAATA 58.334 37.037 0.00 0.00 0.00 0.98
162 164 6.975772 CAGTGCCTCTTATAACTCAGTAGAAC 59.024 42.308 0.00 0.00 0.00 3.01
197 200 2.839975 TCAGCACATCACGGTAAAACA 58.160 42.857 0.00 0.00 0.00 2.83
206 209 2.348666 GGTGTACGATTCAGCACATCAC 59.651 50.000 0.00 0.00 33.88 3.06
211 214 4.368315 TGATATGGTGTACGATTCAGCAC 58.632 43.478 11.45 0.00 44.09 4.40
308 311 1.336240 GCAACAGTGGGCAGAATCAAC 60.336 52.381 4.37 0.00 0.00 3.18
322 325 2.749621 GGTAATTCCCAGAGTGCAACAG 59.250 50.000 0.00 0.00 41.43 3.16
354 357 7.384477 AGTTAGGTAGTGTAACCATGTTCTTC 58.616 38.462 0.00 0.00 42.40 2.87
383 386 3.374220 TGCAAAGCTCATCCACTTTTG 57.626 42.857 0.00 0.00 33.92 2.44
384 387 3.322828 ACATGCAAAGCTCATCCACTTTT 59.677 39.130 0.00 0.00 33.92 2.27
385 388 2.895404 ACATGCAAAGCTCATCCACTTT 59.105 40.909 0.00 0.00 36.56 2.66
386 389 2.522185 ACATGCAAAGCTCATCCACTT 58.478 42.857 0.00 0.00 0.00 3.16
388 391 3.012518 ACTACATGCAAAGCTCATCCAC 58.987 45.455 0.00 0.00 0.00 4.02
389 392 3.354948 ACTACATGCAAAGCTCATCCA 57.645 42.857 0.00 0.00 0.00 3.41
390 393 3.249559 GCTACTACATGCAAAGCTCATCC 59.750 47.826 0.00 0.00 0.00 3.51
391 394 4.125703 AGCTACTACATGCAAAGCTCATC 58.874 43.478 6.62 0.00 39.23 2.92
434 444 1.679944 GCTCACCTTGCAGCTCCATAA 60.680 52.381 0.00 0.00 32.48 1.90
442 452 1.294659 GGAAGACGCTCACCTTGCAG 61.295 60.000 0.00 0.00 32.10 4.41
454 464 0.606401 AACTGCATGTGGGGAAGACG 60.606 55.000 0.00 0.00 0.00 4.18
644 1427 2.158900 CCTCACGATGCCTCCAACTAAT 60.159 50.000 0.00 0.00 0.00 1.73
645 1428 1.207089 CCTCACGATGCCTCCAACTAA 59.793 52.381 0.00 0.00 0.00 2.24
646 1429 0.824109 CCTCACGATGCCTCCAACTA 59.176 55.000 0.00 0.00 0.00 2.24
647 1430 1.599047 CCTCACGATGCCTCCAACT 59.401 57.895 0.00 0.00 0.00 3.16
648 1431 1.450312 CCCTCACGATGCCTCCAAC 60.450 63.158 0.00 0.00 0.00 3.77
649 1432 2.989639 CCCTCACGATGCCTCCAA 59.010 61.111 0.00 0.00 0.00 3.53
650 1433 3.785859 GCCCTCACGATGCCTCCA 61.786 66.667 0.00 0.00 0.00 3.86
651 1434 3.746949 CTGCCCTCACGATGCCTCC 62.747 68.421 0.00 0.00 0.00 4.30
652 1435 2.202987 CTGCCCTCACGATGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
653 1436 3.790437 CCTGCCCTCACGATGCCT 61.790 66.667 0.00 0.00 0.00 4.75
656 1439 3.790437 AGGCCTGCCCTCACGATG 61.790 66.667 3.11 0.00 41.21 3.84
657 1440 3.790437 CAGGCCTGCCCTCACGAT 61.790 66.667 22.33 0.00 44.09 3.73
671 1454 3.052082 CTTCACCACTGCGCCAGG 61.052 66.667 4.18 6.64 35.51 4.45
672 1455 2.281070 ACTTCACCACTGCGCCAG 60.281 61.111 4.18 4.99 37.52 4.85
673 1456 2.280797 GACTTCACCACTGCGCCA 60.281 61.111 4.18 0.00 0.00 5.69
674 1457 3.050275 GGACTTCACCACTGCGCC 61.050 66.667 4.18 0.00 0.00 6.53
675 1458 2.029844 GAGGACTTCACCACTGCGC 61.030 63.158 0.00 0.00 0.00 6.09
676 1459 1.374758 GGAGGACTTCACCACTGCG 60.375 63.158 0.00 0.00 0.00 5.18
677 1460 1.003233 GGGAGGACTTCACCACTGC 60.003 63.158 0.00 0.00 0.00 4.40
683 1466 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.000 0.00 0.00 31.05 3.18
684 1467 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.000 0.00 0.00 31.05 3.02
685 1468 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.000 2.00 0.00 31.05 3.01
686 1469 1.456287 GCACAAGTGGGGAGGACTT 59.544 57.895 2.00 0.00 33.82 3.01
687 1470 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
688 1471 2.034221 GGCACAAGTGGGGAGGAC 59.966 66.667 2.00 0.00 0.00 3.85
689 1472 2.449518 TGGCACAAGTGGGGAGGA 60.450 61.111 2.00 0.00 31.92 3.71
700 1483 0.178903 ACCTAGGACCTCTTGGCACA 60.179 55.000 17.98 0.00 41.23 4.57
701 1484 0.984995 AACCTAGGACCTCTTGGCAC 59.015 55.000 17.98 0.00 41.23 5.01
702 1485 1.351017 CAAACCTAGGACCTCTTGGCA 59.649 52.381 17.98 0.00 41.23 4.92
703 1486 1.628846 TCAAACCTAGGACCTCTTGGC 59.371 52.381 17.98 0.00 41.23 4.52
704 1487 3.559384 GGTTCAAACCTAGGACCTCTTGG 60.559 52.174 17.98 1.57 45.75 3.61
705 1488 3.676093 GGTTCAAACCTAGGACCTCTTG 58.324 50.000 17.98 10.32 45.75 3.02
718 1501 0.877743 GCAGAGAGGCTGGTTCAAAC 59.122 55.000 0.00 0.00 45.03 2.93
719 1502 0.473755 TGCAGAGAGGCTGGTTCAAA 59.526 50.000 0.00 0.00 45.03 2.69
720 1503 0.694771 ATGCAGAGAGGCTGGTTCAA 59.305 50.000 0.00 0.00 45.03 2.69
721 1504 0.694771 AATGCAGAGAGGCTGGTTCA 59.305 50.000 0.00 0.00 45.03 3.18
722 1505 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
723 1506 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
724 1507 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
725 1508 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
727 1510 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
728 1511 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
729 1512 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
730 1513 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
748 1531 0.393132 GAACCTAGTCTTGCCCCTGC 60.393 60.000 0.00 0.00 38.26 4.85
749 1532 0.253327 GGAACCTAGTCTTGCCCCTG 59.747 60.000 0.00 0.00 0.00 4.45
750 1533 0.119358 AGGAACCTAGTCTTGCCCCT 59.881 55.000 0.00 0.00 0.00 4.79
751 1534 1.875488 TAGGAACCTAGTCTTGCCCC 58.125 55.000 0.00 0.00 0.00 5.80
752 1535 5.280062 GGATTATAGGAACCTAGTCTTGCCC 60.280 48.000 6.72 0.00 31.45 5.36
753 1536 5.280062 GGGATTATAGGAACCTAGTCTTGCC 60.280 48.000 6.72 3.19 31.45 4.52
754 1537 5.544562 AGGGATTATAGGAACCTAGTCTTGC 59.455 44.000 6.72 0.00 31.45 4.01
755 1538 7.013834 AGAGGGATTATAGGAACCTAGTCTTG 58.986 42.308 6.72 0.00 31.45 3.02
756 1539 7.182017 AGAGGGATTATAGGAACCTAGTCTT 57.818 40.000 6.72 0.00 31.45 3.01
757 1540 6.240645 GGAGAGGGATTATAGGAACCTAGTCT 60.241 46.154 6.72 0.93 31.45 3.24
758 1541 5.953548 GGAGAGGGATTATAGGAACCTAGTC 59.046 48.000 6.72 4.93 31.45 2.59
759 1542 5.378985 TGGAGAGGGATTATAGGAACCTAGT 59.621 44.000 6.72 0.00 31.45 2.57
760 1543 5.905088 TGGAGAGGGATTATAGGAACCTAG 58.095 45.833 6.72 0.00 31.45 3.02
761 1544 5.620021 TCTGGAGAGGGATTATAGGAACCTA 59.380 44.000 2.93 2.93 0.00 3.08
762 1545 4.423960 TCTGGAGAGGGATTATAGGAACCT 59.576 45.833 0.00 0.00 0.00 3.50
763 1546 4.528987 GTCTGGAGAGGGATTATAGGAACC 59.471 50.000 0.00 0.00 0.00 3.62
764 1547 4.528987 GGTCTGGAGAGGGATTATAGGAAC 59.471 50.000 0.00 0.00 0.00 3.62
765 1548 4.450861 GGGTCTGGAGAGGGATTATAGGAA 60.451 50.000 0.00 0.00 0.00 3.36
766 1549 3.077695 GGGTCTGGAGAGGGATTATAGGA 59.922 52.174 0.00 0.00 0.00 2.94
767 1550 3.445987 GGGTCTGGAGAGGGATTATAGG 58.554 54.545 0.00 0.00 0.00 2.57
768 1551 3.181406 TGGGGTCTGGAGAGGGATTATAG 60.181 52.174 0.00 0.00 0.00 1.31
769 1552 2.801394 TGGGGTCTGGAGAGGGATTATA 59.199 50.000 0.00 0.00 0.00 0.98
770 1553 1.585592 TGGGGTCTGGAGAGGGATTAT 59.414 52.381 0.00 0.00 0.00 1.28
771 1554 1.023719 TGGGGTCTGGAGAGGGATTA 58.976 55.000 0.00 0.00 0.00 1.75
772 1555 0.621862 GTGGGGTCTGGAGAGGGATT 60.622 60.000 0.00 0.00 0.00 3.01
773 1556 1.003573 GTGGGGTCTGGAGAGGGAT 59.996 63.158 0.00 0.00 0.00 3.85
774 1557 2.450243 GTGGGGTCTGGAGAGGGA 59.550 66.667 0.00 0.00 0.00 4.20
775 1558 2.689034 GGTGGGGTCTGGAGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
776 1559 1.229658 AAGGTGGGGTCTGGAGAGG 60.230 63.158 0.00 0.00 0.00 3.69
777 1560 0.838122 ACAAGGTGGGGTCTGGAGAG 60.838 60.000 0.00 0.00 0.00 3.20
778 1561 1.127567 CACAAGGTGGGGTCTGGAGA 61.128 60.000 0.00 0.00 0.00 3.71
779 1562 1.376466 CACAAGGTGGGGTCTGGAG 59.624 63.158 0.00 0.00 0.00 3.86
780 1563 1.385347 ACACAAGGTGGGGTCTGGA 60.385 57.895 1.07 0.00 37.94 3.86
781 1564 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
782 1565 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
790 1573 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
791 1574 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
792 1575 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
793 1576 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
794 1577 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
795 1578 1.373570 GTGCATAGAAGCTCCCACAC 58.626 55.000 0.00 0.00 34.99 3.82
796 1579 0.253044 GGTGCATAGAAGCTCCCACA 59.747 55.000 0.00 0.00 41.18 4.17
797 1580 0.811616 CGGTGCATAGAAGCTCCCAC 60.812 60.000 0.00 0.00 43.42 4.61
798 1581 1.522092 CGGTGCATAGAAGCTCCCA 59.478 57.895 0.00 0.00 43.42 4.37
799 1582 1.227674 CCGGTGCATAGAAGCTCCC 60.228 63.158 0.00 0.00 43.42 4.30
800 1583 1.227674 CCCGGTGCATAGAAGCTCC 60.228 63.158 0.00 0.00 43.03 4.70
801 1584 0.530870 GACCCGGTGCATAGAAGCTC 60.531 60.000 0.00 0.00 34.99 4.09
802 1585 0.978146 AGACCCGGTGCATAGAAGCT 60.978 55.000 0.00 0.00 34.99 3.74
803 1586 0.811616 CAGACCCGGTGCATAGAAGC 60.812 60.000 0.00 0.00 0.00 3.86
804 1587 0.537188 ACAGACCCGGTGCATAGAAG 59.463 55.000 0.00 0.00 0.00 2.85
805 1588 0.535335 GACAGACCCGGTGCATAGAA 59.465 55.000 0.00 0.00 0.00 2.10
806 1589 1.327690 GGACAGACCCGGTGCATAGA 61.328 60.000 0.00 0.00 0.00 1.98
807 1590 1.144057 GGACAGACCCGGTGCATAG 59.856 63.158 0.00 0.00 0.00 2.23
808 1591 0.907704 AAGGACAGACCCGGTGCATA 60.908 55.000 0.00 0.00 40.05 3.14
809 1592 1.779061 AAAGGACAGACCCGGTGCAT 61.779 55.000 0.00 0.00 40.05 3.96
810 1593 1.122632 TAAAGGACAGACCCGGTGCA 61.123 55.000 0.00 0.00 40.05 4.57
811 1594 0.391263 CTAAAGGACAGACCCGGTGC 60.391 60.000 0.00 0.00 40.05 5.01
812 1595 0.974383 ACTAAAGGACAGACCCGGTG 59.026 55.000 0.00 0.00 40.05 4.94
813 1596 1.346722 CAACTAAAGGACAGACCCGGT 59.653 52.381 0.00 0.00 40.05 5.28
814 1597 1.338769 CCAACTAAAGGACAGACCCGG 60.339 57.143 0.00 0.00 40.05 5.73
815 1598 1.621814 TCCAACTAAAGGACAGACCCG 59.378 52.381 0.00 0.00 40.05 5.28
816 1599 2.027100 CCTCCAACTAAAGGACAGACCC 60.027 54.545 0.00 0.00 40.05 4.46
817 1600 2.615747 GCCTCCAACTAAAGGACAGACC 60.616 54.545 0.00 0.00 34.35 3.85
818 1601 2.038557 TGCCTCCAACTAAAGGACAGAC 59.961 50.000 0.00 0.00 34.35 3.51
819 1602 2.334977 TGCCTCCAACTAAAGGACAGA 58.665 47.619 0.00 0.00 34.35 3.41
820 1603 2.859165 TGCCTCCAACTAAAGGACAG 57.141 50.000 0.00 0.00 34.35 3.51
821 1604 2.354704 CGATGCCTCCAACTAAAGGACA 60.355 50.000 0.00 0.00 34.35 4.02
822 1605 2.280628 CGATGCCTCCAACTAAAGGAC 58.719 52.381 0.00 0.00 34.35 3.85
823 1606 1.906574 ACGATGCCTCCAACTAAAGGA 59.093 47.619 0.00 0.00 34.35 3.36
824 1607 2.009774 CACGATGCCTCCAACTAAAGG 58.990 52.381 0.00 0.00 35.65 3.11
825 1608 2.699954 ACACGATGCCTCCAACTAAAG 58.300 47.619 0.00 0.00 0.00 1.85
826 1609 2.851263 ACACGATGCCTCCAACTAAA 57.149 45.000 0.00 0.00 0.00 1.85
1389 2179 0.955919 GAAGTGCCGCTAACCTTGCT 60.956 55.000 0.00 0.00 0.00 3.91
1972 2762 2.972713 GCTCCAGGAGGGTATCATACAA 59.027 50.000 18.83 0.00 38.11 2.41
2412 3211 5.128499 ACAACAAATTGGTCCAGTTCATGAA 59.872 36.000 3.38 3.38 40.42 2.57
2425 3224 6.540189 TCCACCACATAAAAACAACAAATTGG 59.460 34.615 0.00 0.00 40.42 3.16
2611 3410 4.911390 AGACAGTAACTGAAAGGGAATGG 58.089 43.478 0.00 0.00 39.30 3.16
2745 3580 4.809958 ACTTCGATCAGAAATCTGCATCAG 59.190 41.667 5.53 6.95 43.46 2.90
2827 3662 2.902705 ACTGGCTTCGTTGTGAGTTA 57.097 45.000 0.00 0.00 0.00 2.24
2830 3665 1.000955 ACCTACTGGCTTCGTTGTGAG 59.999 52.381 0.00 0.00 36.63 3.51
2870 3706 8.543774 AGTCTCACCAAATCAGTATAGAACAAT 58.456 33.333 0.00 0.00 0.00 2.71
2871 3707 7.907389 AGTCTCACCAAATCAGTATAGAACAA 58.093 34.615 0.00 0.00 0.00 2.83
2921 3757 6.319405 AGCACATGTGAATGCATTCTTGTATA 59.681 34.615 33.23 16.39 44.59 1.47
3198 4040 1.135315 GTACGTCTCGGCGTTGCTA 59.865 57.895 6.85 0.00 43.04 3.49


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

AutoCloner maintained by Alex Coulton.