Multiple sequence alignment - TraesCS6B01G313400

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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 TraesCS6B01G313400 chr6B 100.000 3664 0 0 1 3664 561286978 561283315 0.000000e+00 6767.0
1 TraesCS6B01G313400 chr6D 91.365 3173 126 55 494 3620 374121570 374118500 0.000000e+00 4205.0
2 TraesCS6B01G313400 chr6D 86.197 355 23 11 1 341 374122055 374121713 9.670000e-96 361.0
3 TraesCS6B01G313400 chr6D 97.619 42 1 0 3608 3649 374114524 374114483 5.080000e-09 73.1
4 TraesCS6B01G313400 chr6D 77.622 143 9 6 347 475 374121676 374121543 8.490000e-07 65.8
5 TraesCS6B01G313400 chr6A 86.812 2889 187 84 494 3308 516254373 516251605 0.000000e+00 3046.0
6 TraesCS6B01G313400 chr6A 91.057 492 18 11 1 474 516254829 516254346 3.080000e-180 641.0
7 TraesCS6B01G313400 chr6A 95.751 353 14 1 3298 3649 516223313 516222961 5.310000e-158 568.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G313400 chr6B 561283315 561286978 3663 True 6767.000 6767 100.00000 1 3664 1 chr6B.!!$R1 3663
1 TraesCS6B01G313400 chr6D 374114483 374122055 7572 True 1176.225 4205 88.20075 1 3649 4 chr6D.!!$R1 3648
2 TraesCS6B01G313400 chr6A 516251605 516254829 3224 True 1843.500 3046 88.93450 1 3308 2 chr6A.!!$R2 3307

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
661 741 0.032678 CGTCCCAGAATCCATCCGAG 59.967 60.0 0.0 0.0 0.0 4.63 F
1105 1211 0.107831 TGCGTTACCTGTTCCTGCTT 59.892 50.0 0.0 0.0 0.0 3.91 F
1485 1605 0.249073 GTCAGATCGGGGTGTCATCG 60.249 60.0 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2210 0.034896 TCGAAGCCTGGAACCAACTC 59.965 55.0 0.0 0.0 0.0 3.01 R
2558 2717 0.107831 CAACGTCTTTCTGGGGGACA 59.892 55.0 0.0 0.0 0.0 4.02 R
2664 2823 0.467290 ATCACCACCACCACAACCAC 60.467 55.0 0.0 0.0 0.0 4.16 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
23 24 0.109723 TGTACAGCCCTGGGTTGTTC 59.890 55.000 35.33 30.06 44.47 3.18
56 59 1.806542 CAACGTTCCATGGGTTCTCAG 59.193 52.381 13.02 0.00 0.00 3.35
73 83 3.696051 TCTCAGCCCAAATTGTAGATTGC 59.304 43.478 0.00 0.00 0.00 3.56
187 198 3.516586 TGTTGAGGGAGTGGTATTCTGA 58.483 45.455 0.00 0.00 0.00 3.27
211 222 1.963338 GGTGAGCTGTGTGGCACTC 60.963 63.158 19.83 16.03 35.11 3.51
324 339 2.158986 CCAGATTGAAGACGGCATCTCT 60.159 50.000 0.00 0.00 36.27 3.10
406 456 6.567050 TCAACGATTTTTACTCGCCTACTAT 58.433 36.000 0.00 0.00 39.71 2.12
407 457 7.706159 TCAACGATTTTTACTCGCCTACTATA 58.294 34.615 0.00 0.00 39.71 1.31
408 458 7.859377 TCAACGATTTTTACTCGCCTACTATAG 59.141 37.037 0.00 0.00 39.71 1.31
439 503 5.182950 TGCGTTCATTCCTTACATTTGTCAT 59.817 36.000 0.00 0.00 0.00 3.06
440 504 6.372937 TGCGTTCATTCCTTACATTTGTCATA 59.627 34.615 0.00 0.00 0.00 2.15
442 506 7.625395 GCGTTCATTCCTTACATTTGTCATACA 60.625 37.037 0.00 0.00 0.00 2.29
443 507 8.397906 CGTTCATTCCTTACATTTGTCATACAT 58.602 33.333 0.00 0.00 0.00 2.29
446 510 9.040939 TCATTCCTTACATTTGTCATACATACG 57.959 33.333 0.00 0.00 0.00 3.06
447 511 7.780008 TTCCTTACATTTGTCATACATACGG 57.220 36.000 0.00 0.00 0.00 4.02
448 512 6.880484 TCCTTACATTTGTCATACATACGGT 58.120 36.000 0.00 0.00 0.00 4.83
449 513 6.759356 TCCTTACATTTGTCATACATACGGTG 59.241 38.462 0.00 0.00 0.00 4.94
450 514 6.018262 CCTTACATTTGTCATACATACGGTGG 60.018 42.308 0.00 0.00 0.00 4.61
451 515 3.625764 ACATTTGTCATACATACGGTGGC 59.374 43.478 0.00 0.00 0.00 5.01
452 516 3.336138 TTTGTCATACATACGGTGGCA 57.664 42.857 0.00 0.00 0.00 4.92
453 517 2.595124 TGTCATACATACGGTGGCAG 57.405 50.000 0.00 0.00 0.00 4.85
454 518 1.138069 TGTCATACATACGGTGGCAGG 59.862 52.381 0.00 0.00 0.00 4.85
455 519 1.411246 GTCATACATACGGTGGCAGGA 59.589 52.381 0.00 0.00 0.00 3.86
456 520 2.112190 TCATACATACGGTGGCAGGAA 58.888 47.619 0.00 0.00 0.00 3.36
457 521 2.502130 TCATACATACGGTGGCAGGAAA 59.498 45.455 0.00 0.00 0.00 3.13
458 522 3.055021 TCATACATACGGTGGCAGGAAAA 60.055 43.478 0.00 0.00 0.00 2.29
459 523 2.279935 ACATACGGTGGCAGGAAAAA 57.720 45.000 0.00 0.00 0.00 1.94
460 524 1.883926 ACATACGGTGGCAGGAAAAAC 59.116 47.619 0.00 0.00 0.00 2.43
461 525 1.883275 CATACGGTGGCAGGAAAAACA 59.117 47.619 0.00 0.00 0.00 2.83
462 526 1.600023 TACGGTGGCAGGAAAAACAG 58.400 50.000 0.00 0.00 0.00 3.16
463 527 1.007387 CGGTGGCAGGAAAAACAGC 60.007 57.895 0.00 0.00 0.00 4.40
464 528 1.455383 CGGTGGCAGGAAAAACAGCT 61.455 55.000 0.00 0.00 0.00 4.24
465 529 1.616159 GGTGGCAGGAAAAACAGCTA 58.384 50.000 0.00 0.00 0.00 3.32
466 530 1.960689 GGTGGCAGGAAAAACAGCTAA 59.039 47.619 0.00 0.00 0.00 3.09
467 531 2.029918 GGTGGCAGGAAAAACAGCTAAG 60.030 50.000 0.00 0.00 0.00 2.18
468 532 2.029918 GTGGCAGGAAAAACAGCTAAGG 60.030 50.000 0.00 0.00 0.00 2.69
469 533 1.546029 GGCAGGAAAAACAGCTAAGGG 59.454 52.381 0.00 0.00 0.00 3.95
470 534 2.514803 GCAGGAAAAACAGCTAAGGGA 58.485 47.619 0.00 0.00 0.00 4.20
471 535 2.890945 GCAGGAAAAACAGCTAAGGGAA 59.109 45.455 0.00 0.00 0.00 3.97
472 536 3.320826 GCAGGAAAAACAGCTAAGGGAAA 59.679 43.478 0.00 0.00 0.00 3.13
473 537 4.202212 GCAGGAAAAACAGCTAAGGGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
474 538 5.683770 GCAGGAAAAACAGCTAAGGGAAAAA 60.684 40.000 0.00 0.00 0.00 1.94
501 565 2.100749 AGAAAAGAACAAAACGGCAGGG 59.899 45.455 0.00 0.00 0.00 4.45
510 574 1.744320 AAACGGCAGGGAAAACAGCC 61.744 55.000 0.00 0.00 43.61 4.85
521 585 2.171659 GGAAAACAGCCAAGGGGAAAAA 59.828 45.455 0.00 0.00 35.59 1.94
531 595 2.803203 GGGGAAAAATACCCTCGCC 58.197 57.895 0.00 0.00 46.03 5.54
573 646 3.041940 CGTCGCCTTGACCGCTTT 61.042 61.111 0.00 0.00 45.23 3.51
598 678 5.163322 CCCTAGGATATCTATCTACCGTCGT 60.163 48.000 11.48 0.00 33.28 4.34
609 689 0.594602 TACCGTCGTTGTCTCCAGTG 59.405 55.000 0.00 0.00 0.00 3.66
613 693 2.544277 CCGTCGTTGTCTCCAGTGTAAA 60.544 50.000 0.00 0.00 0.00 2.01
618 698 4.919168 TCGTTGTCTCCAGTGTAAATAACG 59.081 41.667 10.87 10.87 39.51 3.18
628 708 2.343544 GTGTAAATAACGTCGCTTCGCT 59.656 45.455 0.00 0.00 0.00 4.93
629 709 2.988493 TGTAAATAACGTCGCTTCGCTT 59.012 40.909 0.00 0.00 0.00 4.68
630 710 2.782198 AAATAACGTCGCTTCGCTTC 57.218 45.000 0.00 0.00 0.00 3.86
631 711 0.638746 AATAACGTCGCTTCGCTTCG 59.361 50.000 0.00 0.00 0.00 3.79
632 712 1.740043 ATAACGTCGCTTCGCTTCGC 61.740 55.000 0.00 0.00 0.00 4.70
633 713 2.791396 TAACGTCGCTTCGCTTCGCT 62.791 55.000 0.00 0.00 0.00 4.93
635 715 2.805353 GTCGCTTCGCTTCGCTGA 60.805 61.111 0.00 0.00 0.00 4.26
637 717 2.807045 CGCTTCGCTTCGCTGACT 60.807 61.111 0.00 0.00 0.00 3.41
638 718 2.783064 CGCTTCGCTTCGCTGACTC 61.783 63.158 0.00 0.00 0.00 3.36
639 719 2.783064 GCTTCGCTTCGCTGACTCG 61.783 63.158 0.00 0.00 0.00 4.18
640 720 2.783064 CTTCGCTTCGCTGACTCGC 61.783 63.158 0.00 0.00 0.00 5.03
641 721 3.268965 TTCGCTTCGCTGACTCGCT 62.269 57.895 0.00 0.00 0.00 4.93
642 722 3.243892 CGCTTCGCTGACTCGCTC 61.244 66.667 0.00 0.00 0.00 5.03
649 729 2.487428 CTGACTCGCTCGTCCCAG 59.513 66.667 0.61 0.00 32.97 4.45
660 740 0.396556 TCGTCCCAGAATCCATCCGA 60.397 55.000 0.00 0.00 0.00 4.55
661 741 0.032678 CGTCCCAGAATCCATCCGAG 59.967 60.000 0.00 0.00 0.00 4.63
662 742 1.123928 GTCCCAGAATCCATCCGAGT 58.876 55.000 0.00 0.00 0.00 4.18
663 743 1.123077 TCCCAGAATCCATCCGAGTG 58.877 55.000 0.00 0.00 0.00 3.51
683 763 0.892755 AATAACCACCGTCAGCGAGA 59.107 50.000 0.00 0.00 41.33 4.04
687 767 0.878961 ACCACCGTCAGCGAGAAAAC 60.879 55.000 0.00 0.00 41.33 2.43
691 771 1.329599 ACCGTCAGCGAGAAAACAAAC 59.670 47.619 0.00 0.00 41.33 2.93
696 777 3.240631 GTCAGCGAGAAAACAAACAAAGC 59.759 43.478 0.00 0.00 0.00 3.51
699 780 2.535574 GCGAGAAAACAAACAAAGCCAG 59.464 45.455 0.00 0.00 0.00 4.85
700 781 3.115554 CGAGAAAACAAACAAAGCCAGG 58.884 45.455 0.00 0.00 0.00 4.45
747 831 4.216687 TCACGTCCTTCTCTTCTTCTTCTC 59.783 45.833 0.00 0.00 0.00 2.87
799 895 1.873698 TCCGGCGCCACTAATTAATC 58.126 50.000 28.98 0.00 0.00 1.75
806 902 2.348872 CGCCACTAATTAATCGCAGCTG 60.349 50.000 10.11 10.11 0.00 4.24
807 903 2.614057 GCCACTAATTAATCGCAGCTGT 59.386 45.455 16.64 0.00 0.00 4.40
808 904 3.807622 GCCACTAATTAATCGCAGCTGTA 59.192 43.478 16.64 4.31 0.00 2.74
809 905 4.318831 GCCACTAATTAATCGCAGCTGTAC 60.319 45.833 16.64 0.00 0.00 2.90
810 906 4.085055 CCACTAATTAATCGCAGCTGTACG 60.085 45.833 16.64 11.56 0.00 3.67
811 907 3.489785 ACTAATTAATCGCAGCTGTACGC 59.510 43.478 16.64 0.00 39.57 4.42
812 908 1.934589 ATTAATCGCAGCTGTACGCA 58.065 45.000 16.64 2.36 42.61 5.24
813 909 1.277326 TTAATCGCAGCTGTACGCAG 58.723 50.000 16.64 5.38 45.23 5.18
824 920 1.080093 GTACGCAGCAGTAGCACCA 60.080 57.895 0.00 0.00 45.49 4.17
958 1061 2.092049 TCGTCCTAGATCCAACAGCCTA 60.092 50.000 0.00 0.00 0.00 3.93
1036 1142 3.997400 CTCCCGCTCCTCCTCGTCA 62.997 68.421 0.00 0.00 0.00 4.35
1092 1198 0.174845 CCTTCATCTCCGGTGCGTTA 59.825 55.000 0.00 0.00 0.00 3.18
1105 1211 0.107831 TGCGTTACCTGTTCCTGCTT 59.892 50.000 0.00 0.00 0.00 3.91
1107 1213 1.068474 CGTTACCTGTTCCTGCTTCG 58.932 55.000 0.00 0.00 0.00 3.79
1111 1217 2.037136 CCTGTTCCTGCTTCGGCTG 61.037 63.158 0.00 0.00 42.37 4.85
1112 1218 1.302033 CTGTTCCTGCTTCGGCTGT 60.302 57.895 0.00 0.00 42.37 4.40
1113 1219 0.886490 CTGTTCCTGCTTCGGCTGTT 60.886 55.000 0.00 0.00 42.37 3.16
1116 1222 0.465460 TTCCTGCTTCGGCTGTTTGT 60.465 50.000 0.00 0.00 42.37 2.83
1119 1225 0.662619 CTGCTTCGGCTGTTTGTTCA 59.337 50.000 0.00 0.00 42.37 3.18
1120 1226 1.267806 CTGCTTCGGCTGTTTGTTCAT 59.732 47.619 0.00 0.00 42.37 2.57
1130 1236 1.001487 TGTTTGTTCATTGCTGCCTCG 60.001 47.619 0.00 0.00 0.00 4.63
1132 1238 0.874390 TTGTTCATTGCTGCCTCGAC 59.126 50.000 0.00 0.00 0.00 4.20
1136 1242 2.034879 CATTGCTGCCTCGACCGTT 61.035 57.895 0.00 0.00 0.00 4.44
1137 1243 1.302511 ATTGCTGCCTCGACCGTTT 60.303 52.632 0.00 0.00 0.00 3.60
1142 1248 3.774702 GCCTCGACCGTTTGCGTC 61.775 66.667 0.00 0.00 36.15 5.19
1143 1249 2.049433 CCTCGACCGTTTGCGTCT 60.049 61.111 0.00 0.00 36.15 4.18
1144 1250 1.663702 CCTCGACCGTTTGCGTCTT 60.664 57.895 0.00 0.00 36.15 3.01
1150 1256 2.170985 CGTTTGCGTCTTGCCTCG 59.829 61.111 0.00 0.00 45.60 4.63
1183 1289 0.599204 TTCTGTTCTGACGGGTTCGC 60.599 55.000 0.00 0.00 40.63 4.70
1188 1294 4.351938 CTGACGGGTTCGCCGTGA 62.352 66.667 10.42 1.11 44.16 4.35
1290 1405 0.978907 TACGTTTCCTTCCACCTCCC 59.021 55.000 0.00 0.00 0.00 4.30
1291 1406 0.767060 ACGTTTCCTTCCACCTCCCT 60.767 55.000 0.00 0.00 0.00 4.20
1351 1466 3.007506 TGCTGGTTTCGGAGTTTGATCTA 59.992 43.478 0.00 0.00 0.00 1.98
1359 1474 7.094762 GGTTTCGGAGTTTGATCTAGAATTTGT 60.095 37.037 0.00 0.00 0.00 2.83
1435 1555 0.459899 TGTCGATTCCCTGATCCGTG 59.540 55.000 0.00 0.00 0.00 4.94
1480 1600 1.605451 TGTCGTCAGATCGGGGTGT 60.605 57.895 0.00 0.00 0.00 4.16
1485 1605 0.249073 GTCAGATCGGGGTGTCATCG 60.249 60.000 0.00 0.00 0.00 3.84
1486 1606 0.395173 TCAGATCGGGGTGTCATCGA 60.395 55.000 0.00 0.00 37.33 3.59
1487 1607 0.676184 CAGATCGGGGTGTCATCGAT 59.324 55.000 0.00 0.00 44.83 3.59
1488 1608 1.069204 CAGATCGGGGTGTCATCGATT 59.931 52.381 0.00 0.00 42.65 3.34
1517 1637 2.000447 GCGGTCATTGAACTGTAGACC 59.000 52.381 0.00 0.00 44.05 3.85
1531 1654 8.421784 TGAACTGTAGACCATGAGGAATAATAC 58.578 37.037 0.00 0.00 38.69 1.89
1563 1686 0.608130 GAGGGAACATTTTGGTGGCC 59.392 55.000 0.00 0.00 0.00 5.36
1570 1693 0.667184 CATTTTGGTGGCCGAGTTGC 60.667 55.000 0.00 0.00 0.00 4.17
1611 1736 0.981183 TGGGGTGCTACGAGTTGAAT 59.019 50.000 0.00 0.00 0.00 2.57
1621 1746 1.003580 ACGAGTTGAATGCAGGGATGT 59.996 47.619 0.00 0.00 0.00 3.06
1643 1768 2.037251 GGGCTGTAGCTTTCCGATGATA 59.963 50.000 3.63 0.00 41.70 2.15
1657 1786 5.230182 TCCGATGATATTCTTCACCGATTG 58.770 41.667 0.00 0.00 34.42 2.67
1702 1831 3.504863 GACTAGTCCGCGTTTCATGTTA 58.495 45.455 12.13 0.00 0.00 2.41
1713 1842 3.840209 CGTTTCATGTTATTCGCACTGTG 59.160 43.478 2.76 2.76 0.00 3.66
1944 2093 1.377987 TTGTCCGGTAAGGCATGCC 60.378 57.895 30.12 30.12 40.77 4.40
2048 2207 5.242393 AGCATACTTCTGCAAGTTTCATTGT 59.758 36.000 0.00 0.00 40.16 2.71
2051 2210 4.675510 ACTTCTGCAAGTTTCATTGTGTG 58.324 39.130 0.00 0.00 40.16 3.82
2101 2260 1.166531 ACCAAACACTTCGAGGCAGC 61.167 55.000 0.00 0.00 0.00 5.25
2102 2261 1.576421 CAAACACTTCGAGGCAGCC 59.424 57.895 1.84 1.84 0.00 4.85
2103 2262 1.600916 AAACACTTCGAGGCAGCCC 60.601 57.895 8.22 0.00 0.00 5.19
2129 2288 8.221944 CCCCCAAAGTACATATTTTGGTATCTA 58.778 37.037 19.04 0.00 45.91 1.98
2144 2303 9.787435 TTTTGGTATCTACTGTTCACTAAACAT 57.213 29.630 0.00 0.00 46.53 2.71
2146 2305 9.865321 TTGGTATCTACTGTTCACTAAACATAC 57.135 33.333 0.00 0.00 46.53 2.39
2148 2307 8.693625 GGTATCTACTGTTCACTAAACATACCT 58.306 37.037 9.05 0.00 46.53 3.08
2149 2308 9.517609 GTATCTACTGTTCACTAAACATACCTG 57.482 37.037 0.00 0.00 46.53 4.00
2150 2309 6.395629 TCTACTGTTCACTAAACATACCTGC 58.604 40.000 0.00 0.00 46.53 4.85
2151 2310 4.968259 ACTGTTCACTAAACATACCTGCA 58.032 39.130 0.00 0.00 46.53 4.41
2152 2311 5.560724 ACTGTTCACTAAACATACCTGCAT 58.439 37.500 0.00 0.00 46.53 3.96
2153 2312 6.707290 ACTGTTCACTAAACATACCTGCATA 58.293 36.000 0.00 0.00 46.53 3.14
2154 2313 7.338710 ACTGTTCACTAAACATACCTGCATAT 58.661 34.615 0.00 0.00 46.53 1.78
2155 2314 7.495934 ACTGTTCACTAAACATACCTGCATATC 59.504 37.037 0.00 0.00 46.53 1.63
2156 2315 7.334858 TGTTCACTAAACATACCTGCATATCA 58.665 34.615 0.00 0.00 42.95 2.15
2253 2412 5.684704 ACATACATCTACCCATGTTGAAGG 58.315 41.667 0.00 0.00 38.07 3.46
2420 2579 0.531657 TCAAGGAATTTGCATGCCCG 59.468 50.000 16.68 0.00 36.70 6.13
2558 2717 3.071167 AGTTAGGTCTTTCTTGCGAAGGT 59.929 43.478 0.00 0.00 0.00 3.50
2664 2823 5.091261 AGTAGCATTGTTCTTCCAGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2665 2824 4.532521 AGTAGCATTGTTCTTCCAGTAGGT 59.467 41.667 0.00 0.00 35.89 3.08
2696 2857 5.949952 GGTGGTGGTGATACCTTTATTTCTT 59.050 40.000 0.00 0.00 41.43 2.52
3018 3180 8.778059 TGACAATTGGTTTCCCTATCTATAAGT 58.222 33.333 10.83 0.00 0.00 2.24
3022 3184 6.824958 TGGTTTCCCTATCTATAAGTTGCT 57.175 37.500 0.00 0.00 0.00 3.91
3095 3257 8.695456 AGACAAATTTTGTAGTCACTGGATTTT 58.305 29.630 14.49 0.00 45.52 1.82
3106 3270 5.812642 AGTCACTGGATTTTAGATAAGTGCG 59.187 40.000 0.00 0.00 35.98 5.34
3167 3331 8.122472 CCAATCTGTGGGAAGTAGTTAAAATT 57.878 34.615 0.00 0.00 44.64 1.82
3308 3472 5.000591 CCACTGTTATCACAACACCATGTA 58.999 41.667 0.00 0.00 30.36 2.29
3411 3575 5.581479 CAGAGTCTGGAGATTTGATTGTCTG 59.419 44.000 12.67 0.00 0.00 3.51
3454 3618 7.018635 TCGTAGTTGGGTTTTGAAACTAAAG 57.981 36.000 6.57 0.00 38.89 1.85
3508 3672 9.455847 CAAACTTATCTCCTTTGTCTTTTGAAG 57.544 33.333 0.00 0.00 0.00 3.02
3640 7792 5.614308 CACTTATGTGGAGGCATCTATTCA 58.386 41.667 0.00 0.00 40.33 2.57
3649 7801 6.648725 GTGGAGGCATCTATTCAGAAGATTAC 59.351 42.308 0.00 0.00 33.50 1.89
3650 7802 6.169800 GGAGGCATCTATTCAGAAGATTACC 58.830 44.000 0.00 0.00 33.50 2.85
3651 7803 5.788450 AGGCATCTATTCAGAAGATTACCG 58.212 41.667 0.00 0.00 34.44 4.02
3652 7804 5.540337 AGGCATCTATTCAGAAGATTACCGA 59.460 40.000 0.00 0.00 34.44 4.69
3653 7805 6.042093 AGGCATCTATTCAGAAGATTACCGAA 59.958 38.462 0.00 0.00 34.44 4.30
3654 7806 6.706270 GGCATCTATTCAGAAGATTACCGAAA 59.294 38.462 0.00 0.00 33.50 3.46
3655 7807 7.226720 GGCATCTATTCAGAAGATTACCGAAAA 59.773 37.037 0.00 0.00 33.50 2.29
3656 7808 8.612619 GCATCTATTCAGAAGATTACCGAAAAA 58.387 33.333 0.00 0.00 33.50 1.94
3658 7810 8.718102 TCTATTCAGAAGATTACCGAAAAAGG 57.282 34.615 0.00 0.00 37.30 3.11
3659 7811 5.622770 TTCAGAAGATTACCGAAAAAGGC 57.377 39.130 0.00 0.00 33.69 4.35
3660 7812 4.906618 TCAGAAGATTACCGAAAAAGGCT 58.093 39.130 0.00 0.00 33.69 4.58
3661 7813 5.313712 TCAGAAGATTACCGAAAAAGGCTT 58.686 37.500 0.00 0.00 33.69 4.35
3662 7814 5.768164 TCAGAAGATTACCGAAAAAGGCTTT 59.232 36.000 6.68 6.68 33.69 3.51
3663 7815 6.072673 TCAGAAGATTACCGAAAAAGGCTTTC 60.073 38.462 13.76 0.41 33.69 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.354101 ACCCATGGAACGTTGGTAGA 58.646 50.000 15.22 0.00 33.08 2.59
38 41 0.321653 GCTGAGAACCCATGGAACGT 60.322 55.000 15.22 0.00 0.00 3.99
187 198 4.221422 ACACAGCTCACCGCACGT 62.221 61.111 0.00 0.00 42.61 4.49
211 222 6.682746 AGCTTGATGTGGTAGTATATCTTCG 58.317 40.000 0.00 0.00 0.00 3.79
288 303 0.110295 TCTGGCAGCTGGCTGTTTTA 59.890 50.000 36.39 19.60 45.24 1.52
324 339 2.037251 CCTTCGTCTTCTGTTGGAGGAA 59.963 50.000 0.00 0.00 35.81 3.36
439 503 3.075884 GTTTTTCCTGCCACCGTATGTA 58.924 45.455 0.00 0.00 0.00 2.29
440 504 1.883926 GTTTTTCCTGCCACCGTATGT 59.116 47.619 0.00 0.00 0.00 2.29
442 506 2.159382 CTGTTTTTCCTGCCACCGTAT 58.841 47.619 0.00 0.00 0.00 3.06
443 507 1.600023 CTGTTTTTCCTGCCACCGTA 58.400 50.000 0.00 0.00 0.00 4.02
444 508 1.734388 GCTGTTTTTCCTGCCACCGT 61.734 55.000 0.00 0.00 0.00 4.83
445 509 1.007387 GCTGTTTTTCCTGCCACCG 60.007 57.895 0.00 0.00 0.00 4.94
446 510 1.616159 TAGCTGTTTTTCCTGCCACC 58.384 50.000 0.00 0.00 0.00 4.61
447 511 2.029918 CCTTAGCTGTTTTTCCTGCCAC 60.030 50.000 0.00 0.00 0.00 5.01
448 512 2.238521 CCTTAGCTGTTTTTCCTGCCA 58.761 47.619 0.00 0.00 0.00 4.92
449 513 1.546029 CCCTTAGCTGTTTTTCCTGCC 59.454 52.381 0.00 0.00 0.00 4.85
450 514 2.514803 TCCCTTAGCTGTTTTTCCTGC 58.485 47.619 0.00 0.00 0.00 4.85
451 515 5.529581 TTTTCCCTTAGCTGTTTTTCCTG 57.470 39.130 0.00 0.00 0.00 3.86
472 536 6.310467 GCCGTTTTGTTCTTTTCTCTCTTTTT 59.690 34.615 0.00 0.00 0.00 1.94
473 537 5.805486 GCCGTTTTGTTCTTTTCTCTCTTTT 59.195 36.000 0.00 0.00 0.00 2.27
474 538 5.105917 TGCCGTTTTGTTCTTTTCTCTCTTT 60.106 36.000 0.00 0.00 0.00 2.52
475 539 4.398044 TGCCGTTTTGTTCTTTTCTCTCTT 59.602 37.500 0.00 0.00 0.00 2.85
476 540 3.945285 TGCCGTTTTGTTCTTTTCTCTCT 59.055 39.130 0.00 0.00 0.00 3.10
477 541 4.282873 CTGCCGTTTTGTTCTTTTCTCTC 58.717 43.478 0.00 0.00 0.00 3.20
478 542 3.066760 CCTGCCGTTTTGTTCTTTTCTCT 59.933 43.478 0.00 0.00 0.00 3.10
479 543 3.372060 CCTGCCGTTTTGTTCTTTTCTC 58.628 45.455 0.00 0.00 0.00 2.87
480 544 2.100749 CCCTGCCGTTTTGTTCTTTTCT 59.899 45.455 0.00 0.00 0.00 2.52
481 545 2.100087 TCCCTGCCGTTTTGTTCTTTTC 59.900 45.455 0.00 0.00 0.00 2.29
482 546 2.104170 TCCCTGCCGTTTTGTTCTTTT 58.896 42.857 0.00 0.00 0.00 2.27
483 547 1.770294 TCCCTGCCGTTTTGTTCTTT 58.230 45.000 0.00 0.00 0.00 2.52
484 548 1.770294 TTCCCTGCCGTTTTGTTCTT 58.230 45.000 0.00 0.00 0.00 2.52
485 549 1.770294 TTTCCCTGCCGTTTTGTTCT 58.230 45.000 0.00 0.00 0.00 3.01
486 550 2.198406 GTTTTCCCTGCCGTTTTGTTC 58.802 47.619 0.00 0.00 0.00 3.18
487 551 1.550976 TGTTTTCCCTGCCGTTTTGTT 59.449 42.857 0.00 0.00 0.00 2.83
488 552 1.136110 CTGTTTTCCCTGCCGTTTTGT 59.864 47.619 0.00 0.00 0.00 2.83
489 553 1.851658 CTGTTTTCCCTGCCGTTTTG 58.148 50.000 0.00 0.00 0.00 2.44
490 554 0.104120 GCTGTTTTCCCTGCCGTTTT 59.896 50.000 0.00 0.00 0.00 2.43
491 555 1.739667 GCTGTTTTCCCTGCCGTTT 59.260 52.632 0.00 0.00 0.00 3.60
492 556 2.200337 GGCTGTTTTCCCTGCCGTT 61.200 57.895 0.00 0.00 39.26 4.44
501 565 3.552132 TTTTTCCCCTTGGCTGTTTTC 57.448 42.857 0.00 0.00 0.00 2.29
521 585 0.759436 ATCTTCACCGGCGAGGGTAT 60.759 55.000 9.30 0.00 46.96 2.73
531 595 3.559655 TGTCTTGTGTTTGATCTTCACCG 59.440 43.478 10.95 5.13 0.00 4.94
573 646 5.070180 CGACGGTAGATAGATATCCTAGGGA 59.930 48.000 9.46 0.00 35.55 4.20
598 678 4.919168 CGACGTTATTTACACTGGAGACAA 59.081 41.667 0.00 0.00 42.06 3.18
628 708 2.176055 GACGAGCGAGTCAGCGAA 59.824 61.111 9.26 0.00 43.00 4.70
629 709 3.800863 GGACGAGCGAGTCAGCGA 61.801 66.667 14.73 0.00 42.62 4.93
630 710 4.838486 GGGACGAGCGAGTCAGCG 62.838 72.222 14.73 0.00 42.62 5.18
631 711 3.691744 CTGGGACGAGCGAGTCAGC 62.692 68.421 14.73 0.00 42.62 4.26
632 712 1.587043 TTCTGGGACGAGCGAGTCAG 61.587 60.000 14.73 6.87 42.62 3.51
633 713 0.965866 ATTCTGGGACGAGCGAGTCA 60.966 55.000 14.73 0.00 42.62 3.41
635 715 1.668101 GGATTCTGGGACGAGCGAGT 61.668 60.000 0.00 0.00 0.00 4.18
637 717 1.043116 ATGGATTCTGGGACGAGCGA 61.043 55.000 0.00 0.00 0.00 4.93
638 718 0.598680 GATGGATTCTGGGACGAGCG 60.599 60.000 0.00 0.00 0.00 5.03
639 719 0.250081 GGATGGATTCTGGGACGAGC 60.250 60.000 0.00 0.00 0.00 5.03
640 720 0.032678 CGGATGGATTCTGGGACGAG 59.967 60.000 0.00 0.00 0.00 4.18
641 721 0.396556 TCGGATGGATTCTGGGACGA 60.397 55.000 0.00 0.00 0.00 4.20
642 722 0.032678 CTCGGATGGATTCTGGGACG 59.967 60.000 0.00 0.00 32.27 4.79
649 729 4.511826 GTGGTTATTCACTCGGATGGATTC 59.488 45.833 0.00 0.00 34.98 2.52
660 740 1.671850 CGCTGACGGTGGTTATTCACT 60.672 52.381 0.00 0.00 37.75 3.41
661 741 0.719465 CGCTGACGGTGGTTATTCAC 59.281 55.000 0.00 0.00 36.95 3.18
662 742 0.604073 TCGCTGACGGTGGTTATTCA 59.396 50.000 0.00 0.00 40.63 2.57
663 743 1.135199 TCTCGCTGACGGTGGTTATTC 60.135 52.381 0.00 0.00 40.63 1.75
683 763 1.205893 TCGCCTGGCTTTGTTTGTTTT 59.794 42.857 17.92 0.00 0.00 2.43
687 767 1.208259 GTTTCGCCTGGCTTTGTTTG 58.792 50.000 17.92 0.00 0.00 2.93
691 771 1.592543 GTTTTGTTTCGCCTGGCTTTG 59.407 47.619 17.92 0.88 0.00 2.77
696 777 3.916439 GCGTTTTGTTTCGCCTGG 58.084 55.556 0.00 0.00 45.54 4.45
720 801 1.614413 AGAAGAGAAGGACGTGACCAC 59.386 52.381 0.00 0.00 0.00 4.16
747 831 1.304464 GGAACAGGAGGCAAAGGGG 60.304 63.158 0.00 0.00 0.00 4.79
784 880 1.660333 GCTGCGATTAATTAGTGGCGC 60.660 52.381 0.00 0.00 44.15 6.53
806 902 1.080093 TGGTGCTACTGCTGCGTAC 60.080 57.895 0.00 0.00 40.48 3.67
807 903 1.080093 GTGGTGCTACTGCTGCGTA 60.080 57.895 0.00 0.00 40.48 4.42
808 904 2.357517 GTGGTGCTACTGCTGCGT 60.358 61.111 0.00 0.00 40.48 5.24
809 905 3.121030 GGTGGTGCTACTGCTGCG 61.121 66.667 0.00 0.00 40.48 5.18
810 906 2.747855 GGGTGGTGCTACTGCTGC 60.748 66.667 0.00 0.00 40.48 5.25
811 907 2.434884 CGGGTGGTGCTACTGCTG 60.435 66.667 0.00 0.00 40.48 4.41
812 908 4.394712 GCGGGTGGTGCTACTGCT 62.395 66.667 0.00 0.00 40.48 4.24
814 910 4.778143 GGGCGGGTGGTGCTACTG 62.778 72.222 0.00 0.00 0.00 2.74
1068 1174 1.082206 ACCGGAGATGAAGGGGGAA 59.918 57.895 9.46 0.00 0.00 3.97
1092 1198 2.032681 GCCGAAGCAGGAACAGGT 59.967 61.111 0.00 0.00 39.53 4.00
1097 1203 0.465460 ACAAACAGCCGAAGCAGGAA 60.465 50.000 0.00 0.00 43.56 3.36
1105 1211 1.001487 CAGCAATGAACAAACAGCCGA 60.001 47.619 0.00 0.00 0.00 5.54
1107 1213 1.142474 GCAGCAATGAACAAACAGCC 58.858 50.000 0.00 0.00 0.00 4.85
1111 1217 1.266718 TCGAGGCAGCAATGAACAAAC 59.733 47.619 0.00 0.00 0.00 2.93
1112 1218 1.266718 GTCGAGGCAGCAATGAACAAA 59.733 47.619 0.00 0.00 0.00 2.83
1113 1219 0.874390 GTCGAGGCAGCAATGAACAA 59.126 50.000 0.00 0.00 0.00 2.83
1116 1222 1.741401 CGGTCGAGGCAGCAATGAA 60.741 57.895 0.00 0.00 0.00 2.57
1119 1225 1.302511 AAACGGTCGAGGCAGCAAT 60.303 52.632 0.00 0.00 0.00 3.56
1120 1226 2.110213 AAACGGTCGAGGCAGCAA 59.890 55.556 0.00 0.00 0.00 3.91
1130 1236 2.171489 GAGGCAAGACGCAAACGGTC 62.171 60.000 0.00 0.00 46.04 4.79
1132 1238 2.556287 GAGGCAAGACGCAAACGG 59.444 61.111 0.00 0.00 46.04 4.44
1183 1289 2.653890 CTCAAGCAAAACACATCACGG 58.346 47.619 0.00 0.00 0.00 4.94
1224 1331 3.900892 CGTGGTAGATCCGGCGCT 61.901 66.667 7.64 0.00 39.52 5.92
1290 1405 0.464373 AGCTCAGCGAGGAGAGAGAG 60.464 60.000 7.82 0.00 37.05 3.20
1291 1406 0.463654 GAGCTCAGCGAGGAGAGAGA 60.464 60.000 9.40 0.00 37.05 3.10
1351 1466 3.512724 CCAGCCCAATCTTCACAAATTCT 59.487 43.478 0.00 0.00 0.00 2.40
1359 1474 0.846427 AGGTCCCAGCCCAATCTTCA 60.846 55.000 0.00 0.00 0.00 3.02
1480 1600 1.000171 CCGCTGATCCTCAATCGATGA 60.000 52.381 0.00 0.00 37.17 2.92
1485 1605 2.540265 ATGACCGCTGATCCTCAATC 57.460 50.000 0.00 0.00 34.72 2.67
1486 1606 2.171237 TCAATGACCGCTGATCCTCAAT 59.829 45.455 0.00 0.00 0.00 2.57
1487 1607 1.554617 TCAATGACCGCTGATCCTCAA 59.445 47.619 0.00 0.00 0.00 3.02
1488 1608 1.194218 TCAATGACCGCTGATCCTCA 58.806 50.000 0.00 0.00 0.00 3.86
1531 1654 6.867662 AATGTTCCCTCAATCGCTATTTAG 57.132 37.500 0.00 0.00 0.00 1.85
1563 1686 3.731216 CACCGTAATCATCTAGCAACTCG 59.269 47.826 0.00 0.00 0.00 4.18
1570 1693 5.928839 CCAATTCCTCACCGTAATCATCTAG 59.071 44.000 0.00 0.00 0.00 2.43
1611 1736 1.913951 CTACAGCCCACATCCCTGCA 61.914 60.000 0.00 0.00 0.00 4.41
1621 1746 0.107703 CATCGGAAAGCTACAGCCCA 60.108 55.000 0.00 0.00 43.38 5.36
1657 1786 4.488879 GCAAACCATGTCAATTCCTCTTC 58.511 43.478 0.00 0.00 0.00 2.87
1660 1789 2.415893 CGGCAAACCATGTCAATTCCTC 60.416 50.000 0.00 0.00 31.20 3.71
1763 1892 7.575365 TCACGATTAATAAGCATGCAAGTATG 58.425 34.615 21.98 6.51 0.00 2.39
1944 2093 1.556911 AGGCTTCACTACCTGGACATG 59.443 52.381 0.00 0.00 34.07 3.21
2048 2207 0.550914 AAGCCTGGAACCAACTCACA 59.449 50.000 0.00 0.00 0.00 3.58
2051 2210 0.034896 TCGAAGCCTGGAACCAACTC 59.965 55.000 0.00 0.00 0.00 3.01
2253 2412 6.874288 ATAATAGATCAAGGCACTGAAAGC 57.126 37.500 0.00 0.00 40.86 3.51
2287 2446 6.072286 ACAATCTGAAAAGCACAAGTATGAGG 60.072 38.462 0.00 0.00 0.00 3.86
2369 2528 6.481644 CACAGCAGTCTTTAGGAGGATATTTC 59.518 42.308 0.00 0.00 0.00 2.17
2558 2717 0.107831 CAACGTCTTTCTGGGGGACA 59.892 55.000 0.00 0.00 0.00 4.02
2664 2823 0.467290 ATCACCACCACCACAACCAC 60.467 55.000 0.00 0.00 0.00 4.16
2665 2824 1.141185 TATCACCACCACCACAACCA 58.859 50.000 0.00 0.00 0.00 3.67
2669 2828 1.440618 AAGGTATCACCACCACCACA 58.559 50.000 0.00 0.00 41.95 4.17
2696 2857 6.424509 GCTCAACATCATTTGAAAAACATGGA 59.575 34.615 0.00 0.00 35.07 3.41
2933 3095 8.676401 CATGATGATTCACATACAACCAAACTA 58.324 33.333 0.00 0.00 39.56 2.24
3018 3180 1.774110 TGGCAAGAGAAAACCAGCAA 58.226 45.000 0.00 0.00 0.00 3.91
3022 3184 2.745968 ACCTTTGGCAAGAGAAAACCA 58.254 42.857 0.00 0.00 30.57 3.67
3095 3257 7.231925 TGGAGGTTATTCATACGCACTTATCTA 59.768 37.037 0.00 0.00 0.00 1.98
3106 3270 9.274206 GATCCTAGTTTTGGAGGTTATTCATAC 57.726 37.037 0.00 0.00 36.99 2.39
3411 3575 7.803724 ACTACGAATCAAGTATGGTTTTGAAC 58.196 34.615 0.00 0.00 36.93 3.18
3454 3618 3.685139 TCTCCAAACTCTGGTCATGAC 57.315 47.619 17.91 17.91 46.51 3.06
3508 3672 5.995897 CCATAGGGGTACTGTACATTTAAGC 59.004 44.000 18.79 0.58 0.00 3.09
3640 7792 6.255596 GAAAGCCTTTTTCGGTAATCTTCT 57.744 37.500 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.