Multiple sequence alignment - TraesCS3D01G398900

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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 TraesCS3D01G398900 chr3D 100.000 4312 0 0 1 4312 513887359 513891670 0.000000e+00 7963
1 TraesCS3D01G398900 chr3A 90.392 2217 109 35 1 2155 648858822 648860996 0.000000e+00 2819
2 TraesCS3D01G398900 chr3A 91.740 908 43 10 3076 3971 648862042 648862929 0.000000e+00 1232
3 TraesCS3D01G398900 chr3A 92.067 832 27 7 2272 3077 648861173 648861991 0.000000e+00 1134
4 TraesCS3D01G398900 chr3A 86.236 356 28 11 3975 4312 648863028 648863380 2.450000e-97 366
5 TraesCS3D01G398900 chr3A 91.667 108 5 2 2154 2257 648861078 648861185 3.470000e-31 147
6 TraesCS3D01G398900 chr3B 92.161 1518 61 25 1576 3077 676212414 676213889 0.000000e+00 2091
7 TraesCS3D01G398900 chr3B 90.019 1543 82 34 1 1511 676210902 676212404 0.000000e+00 1930
8 TraesCS3D01G398900 chr3B 88.793 696 41 9 3076 3746 676213941 676214624 0.000000e+00 819
9 TraesCS3D01G398900 chr3B 86.172 593 40 21 3747 4303 676214704 676215290 1.720000e-168 603
10 TraesCS3D01G398900 chr1D 85.784 204 29 0 3 206 356141875 356142078 2.610000e-52 217
11 TraesCS3D01G398900 chr1A 85.784 204 29 0 3 206 456931341 456931544 2.610000e-52 217
12 TraesCS3D01G398900 chr1B 85.294 204 30 0 3 206 478715537 478715740 1.210000e-50 211


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 TraesCS3D01G398900 chr3D 513887359 513891670 4311 False 7963.00 7963 100.00000 1 4312 1 chr3D.!!$F1 4311
1 TraesCS3D01G398900 chr3A 648858822 648863380 4558 False 1139.60 2819 90.42040 1 4312 5 chr3A.!!$F1 4311
2 TraesCS3D01G398900 chr3B 676210902 676215290 4388 False 1360.75 2091 89.28625 1 4303 4 chr3B.!!$F1 4302

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
782 851 0.178955 TACACGGGTTCCTCCTCACA 60.179 55.0 0.00 0.0 36.25 3.58 F
1527 1618 0.043183 TGGGGCTTCCTCTCATCTCA 59.957 55.0 0.00 0.0 36.20 3.27 F
2905 3128 0.744414 GAGCGGCTGCCAATGAACTA 60.744 55.0 20.29 0.0 44.31 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1836 0.806102 ATCGATGAAGGTTGTCGCGG 60.806 55.000 6.13 0.0 35.48 6.46 R
2928 3151 1.610038 CAGCTGGACACTGATTTGCAA 59.390 47.619 5.57 0.0 37.32 4.08 R
4069 4553 0.326264 ATGCCCTTGAGGTCACTGAC 59.674 55.000 0.00 0.0 38.26 3.51 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
31 32 3.878519 GAGGACGAGGGCGACGAG 61.879 72.222 0.00 0.00 41.64 4.18
371 375 4.952460 TCCTAGTCTGTAAGCGTGTTTTT 58.048 39.130 0.00 0.00 0.00 1.94
467 476 0.957395 CGACTGCCAGCTGACCATTT 60.957 55.000 17.39 2.03 0.00 2.32
488 497 7.308229 CCATTTCTTCATTATTCGTGGATCCTC 60.308 40.741 14.23 8.71 0.00 3.71
550 563 1.457346 CACTGATCCTGGGTTGCTTC 58.543 55.000 0.00 0.00 0.00 3.86
586 600 7.333174 TGCTCTGTTGATCGAAACATATTTGTA 59.667 33.333 3.26 0.00 39.25 2.41
621 639 9.051679 TGGTTAATACTACAATTCCATCATTCG 57.948 33.333 0.00 0.00 0.00 3.34
625 643 7.891183 ATACTACAATTCCATCATTCGTAGC 57.109 36.000 0.00 0.00 0.00 3.58
646 664 4.460382 AGCAGTATTGACCAAACATCCTTG 59.540 41.667 0.00 0.00 0.00 3.61
656 674 4.776837 ACCAAACATCCTTGCAAATATGGA 59.223 37.500 19.43 14.41 0.00 3.41
670 688 7.853299 TGCAAATATGGAGTACTACTTTGGTA 58.147 34.615 16.12 0.60 0.00 3.25
681 699 2.358322 ACTTTGGTAGTTGGGTGGTG 57.642 50.000 0.00 0.00 31.29 4.17
753 783 2.007360 TGCTTGTGTTGCAAAACTGG 57.993 45.000 20.26 13.29 37.51 4.00
754 784 0.652071 GCTTGTGTTGCAAAACTGGC 59.348 50.000 20.26 18.42 36.53 4.85
755 785 1.289276 CTTGTGTTGCAAAACTGGCC 58.711 50.000 20.26 0.00 36.53 5.36
757 787 1.769026 TGTGTTGCAAAACTGGCCTA 58.231 45.000 20.26 0.00 0.00 3.93
772 841 0.828677 GCCTACAGGATACACGGGTT 59.171 55.000 0.00 0.00 37.39 4.11
776 845 1.192428 ACAGGATACACGGGTTCCTC 58.808 55.000 15.84 2.95 34.43 3.71
777 846 0.464452 CAGGATACACGGGTTCCTCC 59.536 60.000 15.84 11.03 34.43 4.30
778 847 0.338814 AGGATACACGGGTTCCTCCT 59.661 55.000 13.70 11.76 41.41 3.69
779 848 0.751452 GGATACACGGGTTCCTCCTC 59.249 60.000 0.00 0.00 36.25 3.71
780 849 1.481871 GATACACGGGTTCCTCCTCA 58.518 55.000 0.00 0.00 36.25 3.86
781 850 1.136500 GATACACGGGTTCCTCCTCAC 59.864 57.143 0.00 0.00 36.25 3.51
782 851 0.178955 TACACGGGTTCCTCCTCACA 60.179 55.000 0.00 0.00 36.25 3.58
783 852 1.293498 CACGGGTTCCTCCTCACAG 59.707 63.158 0.00 0.00 36.25 3.66
784 853 1.913762 ACGGGTTCCTCCTCACAGG 60.914 63.158 0.00 0.00 36.46 4.00
785 854 1.913762 CGGGTTCCTCCTCACAGGT 60.914 63.158 0.00 0.00 36.53 4.00
786 855 1.481056 CGGGTTCCTCCTCACAGGTT 61.481 60.000 0.00 0.00 36.53 3.50
787 856 0.771755 GGGTTCCTCCTCACAGGTTT 59.228 55.000 0.00 0.00 36.53 3.27
788 857 1.145119 GGGTTCCTCCTCACAGGTTTT 59.855 52.381 0.00 0.00 36.53 2.43
789 858 2.424379 GGGTTCCTCCTCACAGGTTTTT 60.424 50.000 0.00 0.00 36.53 1.94
820 889 2.930019 CCTCACAGGTCTGGGCCA 60.930 66.667 5.85 5.85 33.05 5.36
875 949 0.321653 AAGCCCACCAAGTAGCGAAG 60.322 55.000 0.00 0.00 0.00 3.79
901 975 2.747855 CTGTCGGAGCCCAAAGCC 60.748 66.667 0.00 0.00 45.47 4.35
964 1042 3.585990 CGCCGCATCCAACCCATC 61.586 66.667 0.00 0.00 0.00 3.51
965 1043 3.585990 GCCGCATCCAACCCATCG 61.586 66.667 0.00 0.00 0.00 3.84
1030 1110 2.443016 CCCTCCTCCTCCGGACAG 60.443 72.222 0.00 0.00 0.00 3.51
1220 1306 1.348775 GGGGAGGATGACAAGGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
1263 1349 2.181777 GACGACGAGCTCATGGCA 59.818 61.111 15.40 0.00 44.79 4.92
1388 1474 1.271543 CCAGGTCAGCTTCCATTGTCA 60.272 52.381 7.36 0.00 0.00 3.58
1394 1480 2.294233 TCAGCTTCCATTGTCAAGTTGC 59.706 45.455 0.00 0.00 32.50 4.17
1395 1481 2.295349 CAGCTTCCATTGTCAAGTTGCT 59.705 45.455 0.00 0.00 0.00 3.91
1399 1485 2.507484 TCCATTGTCAAGTTGCTCTGG 58.493 47.619 0.00 2.97 0.00 3.86
1403 1489 1.131638 TGTCAAGTTGCTCTGGGAGT 58.868 50.000 0.00 0.00 31.39 3.85
1404 1490 1.202687 TGTCAAGTTGCTCTGGGAGTG 60.203 52.381 0.00 0.00 31.39 3.51
1405 1491 1.131638 TCAAGTTGCTCTGGGAGTGT 58.868 50.000 0.00 0.00 31.39 3.55
1406 1492 1.202687 TCAAGTTGCTCTGGGAGTGTG 60.203 52.381 0.00 0.00 31.39 3.82
1407 1493 0.536006 AAGTTGCTCTGGGAGTGTGC 60.536 55.000 0.00 0.00 31.39 4.57
1501 1592 0.320697 ACGGTGGACTTGTAGCTTCC 59.679 55.000 0.00 0.00 0.00 3.46
1519 1610 3.412408 GGGAGGTGGGGCTTCCTC 61.412 72.222 12.25 12.25 46.62 3.71
1520 1611 2.285743 GGAGGTGGGGCTTCCTCT 60.286 66.667 17.29 5.42 46.56 3.69
1521 1612 2.371259 GGAGGTGGGGCTTCCTCTC 61.371 68.421 17.29 11.49 46.56 3.20
1522 1613 1.613630 GAGGTGGGGCTTCCTCTCA 60.614 63.158 13.01 0.00 44.68 3.27
1523 1614 0.985490 GAGGTGGGGCTTCCTCTCAT 60.985 60.000 13.01 0.00 44.68 2.90
1524 1615 0.985490 AGGTGGGGCTTCCTCTCATC 60.985 60.000 0.00 0.00 36.20 2.92
1525 1616 0.985490 GGTGGGGCTTCCTCTCATCT 60.985 60.000 0.00 0.00 36.20 2.90
1526 1617 0.467804 GTGGGGCTTCCTCTCATCTC 59.532 60.000 0.00 0.00 36.20 2.75
1527 1618 0.043183 TGGGGCTTCCTCTCATCTCA 59.957 55.000 0.00 0.00 36.20 3.27
1528 1619 1.207791 GGGGCTTCCTCTCATCTCAA 58.792 55.000 0.00 0.00 0.00 3.02
1529 1620 1.561542 GGGGCTTCCTCTCATCTCAAA 59.438 52.381 0.00 0.00 0.00 2.69
1530 1621 2.174424 GGGGCTTCCTCTCATCTCAAAT 59.826 50.000 0.00 0.00 0.00 2.32
1531 1622 3.392616 GGGGCTTCCTCTCATCTCAAATA 59.607 47.826 0.00 0.00 0.00 1.40
1561 1652 2.785269 TGGCACTTCCCAGAATATCCAT 59.215 45.455 0.00 0.00 0.00 3.41
1568 1659 7.006509 CACTTCCCAGAATATCCATACCATTT 58.993 38.462 0.00 0.00 0.00 2.32
1613 1704 7.521099 CGCATTGCCTAATTGAGAGATTTATGT 60.521 37.037 2.41 0.00 0.00 2.29
1669 1766 9.720667 CACAACATCAACCAACAATATATGTAG 57.279 33.333 0.00 0.00 42.99 2.74
1694 1791 3.897239 TCATGGCGGACAGGATTTTATT 58.103 40.909 0.00 0.00 34.49 1.40
1737 1836 8.668353 TCAATCTATCATTGTTTCAGTTAGTGC 58.332 33.333 0.00 0.00 0.00 4.40
1774 1875 3.563808 TCGATGTCTTTGAACCCAAACAG 59.436 43.478 0.00 0.00 37.36 3.16
1836 1937 2.384382 CTTGCCATGTTCGTGTTTGAC 58.616 47.619 0.00 0.00 0.00 3.18
1837 1938 1.383523 TGCCATGTTCGTGTTTGACA 58.616 45.000 0.00 0.00 0.00 3.58
1926 2027 7.830739 ACCAACCAAATGTCTGATTCTTAATC 58.169 34.615 0.00 0.00 38.40 1.75
1929 2031 9.865321 CAACCAAATGTCTGATTCTTAATCATT 57.135 29.630 2.98 0.00 46.10 2.57
1988 2098 2.708325 AGCTCTTTCTCCACTCCTTTGT 59.292 45.455 0.00 0.00 0.00 2.83
1989 2099 2.810852 GCTCTTTCTCCACTCCTTTGTG 59.189 50.000 0.00 0.00 37.66 3.33
2007 2117 8.539544 TCCTTTGTGTGATAGTTTATCTCATCA 58.460 33.333 4.70 0.00 39.81 3.07
2010 2120 8.667076 TTGTGTGATAGTTTATCTCATCATGG 57.333 34.615 0.00 0.00 39.81 3.66
2195 2391 2.695359 GACGTGACCTAAATGGCTCAA 58.305 47.619 0.00 0.00 40.22 3.02
2348 2545 6.423905 AGAATGATCGGGTTATGTTTACATCG 59.576 38.462 0.00 0.00 37.76 3.84
2502 2699 5.356751 CCATTCGATCAAAGGATGTTGGTAA 59.643 40.000 0.00 0.00 32.67 2.85
2521 2718 5.251700 TGGTAACCAAATTGGCCCAAATAAT 59.748 36.000 12.67 0.00 42.67 1.28
2596 2819 1.243902 TGAATGCCTCCGTTTCCAAC 58.756 50.000 0.00 0.00 0.00 3.77
2697 2920 3.560068 AGCGAAAATTCTAGGGTAATGCG 59.440 43.478 0.00 0.00 0.00 4.73
2735 2958 5.847670 TTTGGCAAGTGTAACAAAACAAC 57.152 34.783 0.00 0.00 41.43 3.32
2745 2968 7.703328 AGTGTAACAAAACAACCTGTTATCAG 58.297 34.615 0.00 0.00 38.60 2.90
2905 3128 0.744414 GAGCGGCTGCCAATGAACTA 60.744 55.000 20.29 0.00 44.31 2.24
2924 3147 1.867363 ACGAGCCTCCAAGGTATTCT 58.133 50.000 0.00 0.00 37.80 2.40
2925 3148 2.188817 ACGAGCCTCCAAGGTATTCTT 58.811 47.619 0.00 0.00 37.80 2.52
2926 3149 2.572104 ACGAGCCTCCAAGGTATTCTTT 59.428 45.455 0.00 0.00 37.80 2.52
2927 3150 3.198872 CGAGCCTCCAAGGTATTCTTTC 58.801 50.000 0.00 0.00 37.80 2.62
2928 3151 3.118592 CGAGCCTCCAAGGTATTCTTTCT 60.119 47.826 0.00 0.00 37.80 2.52
2952 3175 3.411446 CAAATCAGTGTCCAGCTGGTTA 58.589 45.455 31.58 18.92 36.39 2.85
2969 3192 5.220416 GCTGGTTATACATGTCTGTTCGTTC 60.220 44.000 0.00 0.00 36.79 3.95
2996 3219 3.534554 AGAACAATACAGATCGCATGCA 58.465 40.909 19.57 5.34 0.00 3.96
3050 3273 5.007724 GCAATAACTAGTTATGTCACCCAGC 59.992 44.000 25.21 15.57 36.04 4.85
3056 3279 2.026822 AGTTATGTCACCCAGCTTCCAG 60.027 50.000 0.00 0.00 0.00 3.86
3077 3300 3.538634 GGTACCCAAGCTTAGGTGTAG 57.461 52.381 24.74 7.00 36.88 2.74
3176 3454 4.261741 GCATTGTCATATTCCCCATCACAC 60.262 45.833 0.00 0.00 0.00 3.82
3186 3464 2.719705 TCCCCATCACACCCTAAGTTTT 59.280 45.455 0.00 0.00 0.00 2.43
3187 3465 2.825532 CCCCATCACACCCTAAGTTTTG 59.174 50.000 0.00 0.00 0.00 2.44
3188 3466 3.499563 CCCCATCACACCCTAAGTTTTGA 60.500 47.826 0.00 0.00 0.00 2.69
3189 3467 3.758554 CCCATCACACCCTAAGTTTTGAG 59.241 47.826 0.00 0.00 0.00 3.02
3190 3468 4.398319 CCATCACACCCTAAGTTTTGAGT 58.602 43.478 0.00 0.00 0.00 3.41
3338 3620 6.321181 GCCCCTTTACAATGTTATCATCTTCA 59.679 38.462 0.00 0.00 32.56 3.02
3365 3647 1.149174 ACAGGTGCCAAGGTGTCTG 59.851 57.895 0.00 0.00 0.00 3.51
3372 3654 1.251251 GCCAAGGTGTCTGATTGCTT 58.749 50.000 0.00 0.00 0.00 3.91
3413 3695 1.332195 GGAGCTTATGCCCAATTCCC 58.668 55.000 0.00 0.00 40.80 3.97
3415 3697 1.959282 GAGCTTATGCCCAATTCCCTG 59.041 52.381 0.00 0.00 40.80 4.45
3450 3732 3.418684 AAACATACACAGGGTCTGTCC 57.581 47.619 0.00 0.00 43.43 4.02
3451 3733 2.327325 ACATACACAGGGTCTGTCCT 57.673 50.000 0.00 0.00 43.43 3.85
3452 3734 3.468071 ACATACACAGGGTCTGTCCTA 57.532 47.619 0.00 0.00 43.43 2.94
3453 3735 3.995636 ACATACACAGGGTCTGTCCTAT 58.004 45.455 0.00 0.00 43.43 2.57
3454 3736 5.138758 ACATACACAGGGTCTGTCCTATA 57.861 43.478 0.00 0.00 43.43 1.31
3455 3737 4.894114 ACATACACAGGGTCTGTCCTATAC 59.106 45.833 0.00 0.00 43.43 1.47
3456 3738 3.759815 ACACAGGGTCTGTCCTATACT 57.240 47.619 0.00 0.00 43.43 2.12
3457 3739 3.366396 ACACAGGGTCTGTCCTATACTG 58.634 50.000 0.00 0.00 43.43 2.74
3458 3740 2.101582 CACAGGGTCTGTCCTATACTGC 59.898 54.545 0.00 0.00 43.43 4.40
3511 3800 2.095919 GTCGCACACCATTGTAACCTTC 60.096 50.000 0.00 0.00 33.30 3.46
3595 3893 9.651718 CAAATTGGATCTACTTTTAAGCGATAC 57.348 33.333 0.00 0.00 0.00 2.24
3637 3935 7.971168 CCAAACTACTTTTCACATTTGTGTGTA 59.029 33.333 10.30 8.65 45.76 2.90
3722 4027 2.364632 TGGCACATGTTACATACAGGC 58.635 47.619 0.00 4.21 42.15 4.85
3737 4042 5.182190 ACATACAGGCTATCTATCTCGTGTG 59.818 44.000 0.00 0.00 0.00 3.82
3746 4134 2.608090 TCTATCTCGTGTGTGAGCTACG 59.392 50.000 0.00 0.00 39.04 3.51
3747 4135 1.166129 ATCTCGTGTGTGAGCTACGT 58.834 50.000 5.92 0.00 38.80 3.57
3748 4136 1.799544 TCTCGTGTGTGAGCTACGTA 58.200 50.000 5.92 0.00 38.80 3.57
3749 4137 1.462283 TCTCGTGTGTGAGCTACGTAC 59.538 52.381 5.92 0.00 38.80 3.67
3801 4189 2.610438 ACTGTGGAAAGGCAATGGAT 57.390 45.000 0.00 0.00 0.00 3.41
3802 4190 3.737559 ACTGTGGAAAGGCAATGGATA 57.262 42.857 0.00 0.00 0.00 2.59
3803 4191 4.255510 ACTGTGGAAAGGCAATGGATAT 57.744 40.909 0.00 0.00 0.00 1.63
3804 4192 4.210331 ACTGTGGAAAGGCAATGGATATC 58.790 43.478 0.00 0.00 0.00 1.63
3805 4193 4.079558 ACTGTGGAAAGGCAATGGATATCT 60.080 41.667 2.05 0.00 0.00 1.98
3892 4281 3.648179 GTTCATCAAACGCTCAGCTAG 57.352 47.619 0.00 0.00 0.00 3.42
3937 4326 5.126222 TCACCTGCAACAAGTTCACATTTTA 59.874 36.000 0.00 0.00 0.00 1.52
3941 4330 6.214191 TGCAACAAGTTCACATTTTAAGGA 57.786 33.333 0.00 0.00 0.00 3.36
3948 4337 8.695456 ACAAGTTCACATTTTAAGGATCAGTTT 58.305 29.630 0.00 0.00 0.00 2.66
3971 4360 8.950961 GTTTATTCAAACTTAACGGTTCAGAAC 58.049 33.333 8.94 4.52 40.78 3.01
3973 4362 5.728351 TCAAACTTAACGGTTCAGAACAG 57.272 39.130 15.36 13.38 0.00 3.16
3981 4465 4.240175 ACGGTTCAGAACAGACTAGTTC 57.760 45.455 19.03 8.76 46.35 3.01
4024 4508 4.693283 TGATGTTTGTATAAGAGCCCTCG 58.307 43.478 0.00 0.00 34.09 4.63
4085 4569 0.898320 ATCGTCAGTGACCTCAAGGG 59.102 55.000 17.57 1.85 40.27 3.95
4118 4602 2.481952 GTGCAGAGTTTAGTCAGCAAGG 59.518 50.000 6.27 0.00 40.25 3.61
4122 4606 4.493547 CAGAGTTTAGTCAGCAAGGAGAG 58.506 47.826 0.00 0.00 0.00 3.20
4135 4625 4.133078 GCAAGGAGAGATGGGAATTAGTG 58.867 47.826 0.00 0.00 0.00 2.74
4154 4644 8.657387 ATTAGTGTATCAGTGGACTATATGCT 57.343 34.615 0.00 0.00 0.00 3.79
4155 4645 6.338214 AGTGTATCAGTGGACTATATGCTG 57.662 41.667 0.00 0.00 0.00 4.41
4158 4648 5.833131 TGTATCAGTGGACTATATGCTGTGA 59.167 40.000 0.00 0.00 0.00 3.58
4159 4649 6.494835 TGTATCAGTGGACTATATGCTGTGAT 59.505 38.462 0.00 0.00 0.00 3.06
4160 4650 5.459536 TCAGTGGACTATATGCTGTGATC 57.540 43.478 0.00 0.00 0.00 2.92
4191 4701 4.473199 GTTTAACAAGCTCGAAACCATCC 58.527 43.478 0.00 0.00 0.00 3.51
4192 4702 1.534729 AACAAGCTCGAAACCATCCC 58.465 50.000 0.00 0.00 0.00 3.85
4203 4713 3.674138 CGAAACCATCCCTGAGCAAATTG 60.674 47.826 0.00 0.00 0.00 2.32
4225 4735 4.042809 TGGGTTTCATCACCTACAATCAGT 59.957 41.667 0.00 0.00 36.97 3.41
4229 4739 7.441458 GGGTTTCATCACCTACAATCAGTATAC 59.559 40.741 0.00 0.00 36.97 1.47
4236 4746 8.319057 TCACCTACAATCAGTATACATTTCCT 57.681 34.615 5.50 0.00 30.93 3.36
4299 4817 8.277713 GGAAACACAAATCATGAAATGTTCTTG 58.722 33.333 12.58 6.12 46.80 3.02
4303 4821 9.248291 ACACAAATCATGAAATGTTCTTGTTAC 57.752 29.630 12.58 0.00 46.80 2.50
4306 4824 9.681692 CAAATCATGAAATGTTCTTGTTACAGA 57.318 29.630 0.00 0.00 46.80 3.41
4307 4825 9.903682 AAATCATGAAATGTTCTTGTTACAGAG 57.096 29.630 0.00 0.00 46.80 3.35
4308 4826 7.439157 TCATGAAATGTTCTTGTTACAGAGG 57.561 36.000 0.00 0.00 46.80 3.69
4309 4827 5.689383 TGAAATGTTCTTGTTACAGAGGC 57.311 39.130 0.00 0.00 0.00 4.70
4310 4828 5.129634 TGAAATGTTCTTGTTACAGAGGCA 58.870 37.500 0.00 0.00 0.00 4.75
4311 4829 5.592282 TGAAATGTTCTTGTTACAGAGGCAA 59.408 36.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.043852 TCGTGCTCCTCCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
467 476 5.363868 ACAGAGGATCCACGAATAATGAAGA 59.636 40.000 15.82 0.00 33.66 2.87
488 497 2.726760 GCAACAGAGTCACGAACTACAG 59.273 50.000 0.00 0.00 38.74 2.74
621 639 5.186198 AGGATGTTTGGTCAATACTGCTAC 58.814 41.667 0.00 0.00 0.00 3.58
625 643 4.218200 TGCAAGGATGTTTGGTCAATACTG 59.782 41.667 0.00 0.00 0.00 2.74
646 664 8.366671 CTACCAAAGTAGTACTCCATATTTGC 57.633 38.462 2.58 0.00 41.03 3.68
687 712 6.353323 TCACTCAACTATTCCAGTGTCAAAA 58.647 36.000 0.00 0.00 37.63 2.44
718 743 0.254178 AGCAAGACATACAGCAGGGG 59.746 55.000 0.00 0.00 0.00 4.79
751 781 1.046472 CCCGTGTATCCTGTAGGCCA 61.046 60.000 5.01 0.00 34.44 5.36
753 783 0.828677 AACCCGTGTATCCTGTAGGC 59.171 55.000 0.00 0.00 34.44 3.93
754 784 1.411612 GGAACCCGTGTATCCTGTAGG 59.588 57.143 0.00 0.00 0.00 3.18
755 785 2.361438 GAGGAACCCGTGTATCCTGTAG 59.639 54.545 6.52 0.00 43.55 2.74
757 787 1.192428 GAGGAACCCGTGTATCCTGT 58.808 55.000 6.52 0.00 43.55 4.00
793 862 3.721706 CTGTGAGGAGGGTGCCCC 61.722 72.222 3.17 2.16 45.90 5.80
794 863 3.721706 CCTGTGAGGAGGGTGCCC 61.722 72.222 0.00 0.00 37.67 5.36
795 864 2.930562 ACCTGTGAGGAGGGTGCC 60.931 66.667 0.00 0.00 37.67 5.01
796 865 1.915769 AGACCTGTGAGGAGGGTGC 60.916 63.158 0.00 0.00 37.67 5.01
797 866 1.548357 CCAGACCTGTGAGGAGGGTG 61.548 65.000 0.00 0.00 37.67 4.61
798 867 1.229336 CCAGACCTGTGAGGAGGGT 60.229 63.158 0.00 0.00 37.67 4.34
964 1042 1.668101 CGGAGGAGGAAGGAAGGACG 61.668 65.000 0.00 0.00 0.00 4.79
965 1043 1.962321 GCGGAGGAGGAAGGAAGGAC 61.962 65.000 0.00 0.00 0.00 3.85
1196 1282 0.179000 CTTGTCATCCTCCCCTTCGG 59.821 60.000 0.00 0.00 0.00 4.30
1197 1283 0.179000 CCTTGTCATCCTCCCCTTCG 59.821 60.000 0.00 0.00 0.00 3.79
1198 1284 0.548510 CCCTTGTCATCCTCCCCTTC 59.451 60.000 0.00 0.00 0.00 3.46
1199 1285 0.121197 TCCCTTGTCATCCTCCCCTT 59.879 55.000 0.00 0.00 0.00 3.95
1200 1286 0.327000 CTCCCTTGTCATCCTCCCCT 60.327 60.000 0.00 0.00 0.00 4.79
1220 1306 1.109609 CCCCAGGTAGTTCTCGTACC 58.890 60.000 0.00 0.00 40.42 3.34
1359 1445 2.782222 GCTGACCTGGGCGACGATA 61.782 63.158 0.00 0.00 0.00 2.92
1388 1474 0.536006 GCACACTCCCAGAGCAACTT 60.536 55.000 0.00 0.00 32.04 2.66
1394 1480 2.046507 GGCAGCACACTCCCAGAG 60.047 66.667 0.00 0.00 35.52 3.35
1395 1481 3.640407 GGGCAGCACACTCCCAGA 61.640 66.667 0.00 0.00 39.82 3.86
1399 1485 1.363807 GTTTTGGGCAGCACACTCC 59.636 57.895 0.00 0.00 0.00 3.85
1403 1489 0.395586 ACTCTGTTTTGGGCAGCACA 60.396 50.000 0.00 0.00 34.21 4.57
1404 1490 0.031178 CACTCTGTTTTGGGCAGCAC 59.969 55.000 0.00 0.00 34.21 4.40
1405 1491 1.108727 CCACTCTGTTTTGGGCAGCA 61.109 55.000 0.00 0.00 34.21 4.41
1406 1492 1.109323 ACCACTCTGTTTTGGGCAGC 61.109 55.000 0.00 0.00 37.18 5.25
1407 1493 1.402787 AACCACTCTGTTTTGGGCAG 58.597 50.000 0.00 0.00 37.18 4.85
1507 1598 0.467804 GAGATGAGAGGAAGCCCCAC 59.532 60.000 0.00 0.00 37.41 4.61
1509 1600 1.207791 TTGAGATGAGAGGAAGCCCC 58.792 55.000 0.00 0.00 0.00 5.80
1510 1601 3.574354 ATTTGAGATGAGAGGAAGCCC 57.426 47.619 0.00 0.00 0.00 5.19
1511 1602 4.346418 TCCTATTTGAGATGAGAGGAAGCC 59.654 45.833 0.00 0.00 30.16 4.35
1512 1603 5.070313 ACTCCTATTTGAGATGAGAGGAAGC 59.930 44.000 0.00 0.00 36.22 3.86
1513 1604 6.729690 ACTCCTATTTGAGATGAGAGGAAG 57.270 41.667 0.00 0.00 36.22 3.46
1514 1605 7.358263 AGTACTCCTATTTGAGATGAGAGGAA 58.642 38.462 0.00 0.00 36.22 3.36
1515 1606 6.916909 AGTACTCCTATTTGAGATGAGAGGA 58.083 40.000 0.00 0.00 36.22 3.71
1516 1607 7.432869 CAAGTACTCCTATTTGAGATGAGAGG 58.567 42.308 0.00 0.00 36.22 3.69
1517 1608 7.432869 CCAAGTACTCCTATTTGAGATGAGAG 58.567 42.308 0.00 0.00 36.22 3.20
1518 1609 6.183360 GCCAAGTACTCCTATTTGAGATGAGA 60.183 42.308 0.00 0.00 36.22 3.27
1519 1610 5.988561 GCCAAGTACTCCTATTTGAGATGAG 59.011 44.000 0.00 0.00 36.22 2.90
1520 1611 5.425217 TGCCAAGTACTCCTATTTGAGATGA 59.575 40.000 0.00 0.00 36.22 2.92
1521 1612 5.525378 GTGCCAAGTACTCCTATTTGAGATG 59.475 44.000 0.00 0.00 36.22 2.90
1522 1613 5.426833 AGTGCCAAGTACTCCTATTTGAGAT 59.573 40.000 0.00 0.00 36.22 2.75
1523 1614 4.777896 AGTGCCAAGTACTCCTATTTGAGA 59.222 41.667 0.00 0.00 36.22 3.27
1524 1615 5.091261 AGTGCCAAGTACTCCTATTTGAG 57.909 43.478 0.00 0.00 38.37 3.02
1525 1616 5.488341 GAAGTGCCAAGTACTCCTATTTGA 58.512 41.667 0.00 0.00 0.00 2.69
1526 1617 4.636206 GGAAGTGCCAAGTACTCCTATTTG 59.364 45.833 0.00 0.00 36.34 2.32
1527 1618 4.324331 GGGAAGTGCCAAGTACTCCTATTT 60.324 45.833 0.00 0.00 38.95 1.40
1528 1619 3.200165 GGGAAGTGCCAAGTACTCCTATT 59.800 47.826 0.00 0.00 38.95 1.73
1529 1620 2.772515 GGGAAGTGCCAAGTACTCCTAT 59.227 50.000 0.00 0.00 38.95 2.57
1530 1621 2.185387 GGGAAGTGCCAAGTACTCCTA 58.815 52.381 0.00 0.00 38.95 2.94
1531 1622 0.984995 GGGAAGTGCCAAGTACTCCT 59.015 55.000 0.00 0.00 38.95 3.69
1561 1652 6.655003 CCTCTAAAGCTCAACTGAAAATGGTA 59.345 38.462 0.00 0.00 0.00 3.25
1568 1659 2.688507 CGCCTCTAAAGCTCAACTGAA 58.311 47.619 0.00 0.00 0.00 3.02
1613 1704 9.502091 ACACTAATTATGCTAGTTGACTTGAAA 57.498 29.630 0.00 0.00 0.00 2.69
1737 1836 0.806102 ATCGATGAAGGTTGTCGCGG 60.806 55.000 6.13 0.00 35.48 6.46
1774 1875 2.409948 AGAGGGTTAGTGCAAGATGC 57.590 50.000 0.00 0.00 45.29 3.91
1836 1937 4.381932 GGGGAAAGCAACATTCCATACTTG 60.382 45.833 7.53 0.00 46.69 3.16
1837 1938 3.769300 GGGGAAAGCAACATTCCATACTT 59.231 43.478 7.53 0.00 46.69 2.24
1929 2031 2.956132 TGGCTGACATGAAGGGAAAAA 58.044 42.857 0.00 0.00 0.00 1.94
1988 2098 7.933577 GGAACCATGATGAGATAAACTATCACA 59.066 37.037 0.00 0.00 39.48 3.58
1989 2099 8.316640 GGAACCATGATGAGATAAACTATCAC 57.683 38.462 0.00 0.00 37.65 3.06
2266 2463 9.699410 TGATCAAGATAAACAATTATTGTCCCT 57.301 29.630 11.24 3.85 44.59 4.20
2267 2464 9.736023 GTGATCAAGATAAACAATTATTGTCCC 57.264 33.333 11.24 1.73 44.59 4.46
2268 2465 9.736023 GGTGATCAAGATAAACAATTATTGTCC 57.264 33.333 11.24 0.00 44.59 4.02
2272 2469 9.754382 GCATGGTGATCAAGATAAACAATTATT 57.246 29.630 0.00 0.00 31.83 1.40
2273 2470 8.916062 TGCATGGTGATCAAGATAAACAATTAT 58.084 29.630 0.00 0.00 34.40 1.28
2274 2471 8.190122 GTGCATGGTGATCAAGATAAACAATTA 58.810 33.333 0.00 0.00 0.00 1.40
2275 2472 7.037438 GTGCATGGTGATCAAGATAAACAATT 58.963 34.615 0.00 0.00 0.00 2.32
2276 2473 6.379133 AGTGCATGGTGATCAAGATAAACAAT 59.621 34.615 0.00 0.00 0.00 2.71
2277 2474 5.711506 AGTGCATGGTGATCAAGATAAACAA 59.288 36.000 0.00 0.00 0.00 2.83
2278 2475 5.255687 AGTGCATGGTGATCAAGATAAACA 58.744 37.500 0.00 0.00 0.00 2.83
2279 2476 5.824904 AGTGCATGGTGATCAAGATAAAC 57.175 39.130 0.00 0.00 0.00 2.01
2280 2477 7.112122 AGTAAGTGCATGGTGATCAAGATAAA 58.888 34.615 0.00 0.00 0.00 1.40
2281 2478 6.653020 AGTAAGTGCATGGTGATCAAGATAA 58.347 36.000 0.00 0.00 0.00 1.75
2282 2479 6.127083 TGAGTAAGTGCATGGTGATCAAGATA 60.127 38.462 0.00 0.00 0.00 1.98
2283 2480 5.108187 AGTAAGTGCATGGTGATCAAGAT 57.892 39.130 0.00 0.00 0.00 2.40
2284 2481 4.020307 TGAGTAAGTGCATGGTGATCAAGA 60.020 41.667 0.00 0.00 0.00 3.02
2285 2482 4.256110 TGAGTAAGTGCATGGTGATCAAG 58.744 43.478 0.00 0.00 0.00 3.02
2348 2545 6.443792 ACTACCATGGAAATTGAAAACGAAC 58.556 36.000 21.47 0.00 0.00 3.95
2502 2699 3.848975 TGGATTATTTGGGCCAATTTGGT 59.151 39.130 21.65 5.59 40.46 3.67
2521 2718 6.721208 AGAAGCATACTGGAGAAAATTTTGGA 59.279 34.615 8.47 0.00 0.00 3.53
2596 2819 2.872245 TGCTCACCAAAAGAAGAGAACG 59.128 45.455 0.00 0.00 0.00 3.95
2735 2958 3.624777 AGCACCCATTTCTGATAACAGG 58.375 45.455 0.00 0.00 43.60 4.00
2896 3119 2.672961 TGGAGGCTCGTAGTTCATTG 57.327 50.000 8.69 0.00 0.00 2.82
2905 3128 1.867363 AGAATACCTTGGAGGCTCGT 58.133 50.000 8.69 3.15 39.63 4.18
2924 3147 3.243501 GCTGGACACTGATTTGCAAGAAA 60.244 43.478 0.00 0.00 0.00 2.52
2925 3148 2.294233 GCTGGACACTGATTTGCAAGAA 59.706 45.455 0.00 0.00 0.00 2.52
2926 3149 1.881973 GCTGGACACTGATTTGCAAGA 59.118 47.619 0.00 0.00 0.00 3.02
2927 3150 1.884579 AGCTGGACACTGATTTGCAAG 59.115 47.619 0.00 0.00 0.00 4.01
2928 3151 1.610038 CAGCTGGACACTGATTTGCAA 59.390 47.619 5.57 0.00 37.32 4.08
2952 3175 6.929049 TCTTTTCTGAACGAACAGACATGTAT 59.071 34.615 13.62 0.00 44.94 2.29
2969 3192 6.169419 TGCGATCTGTATTGTTCTTTTCTG 57.831 37.500 0.00 0.00 0.00 3.02
3015 3238 5.599999 ACTAGTTATTGCTGGAACTCGAT 57.400 39.130 0.00 0.00 37.16 3.59
3176 3454 3.503748 CAGCCAAGACTCAAAACTTAGGG 59.496 47.826 0.00 0.00 0.00 3.53
3186 3464 2.319844 TCAGAGTTCAGCCAAGACTCA 58.680 47.619 5.64 0.00 0.00 3.41
3187 3465 3.324993 CTTCAGAGTTCAGCCAAGACTC 58.675 50.000 0.00 0.00 0.00 3.36
3188 3466 2.549778 GCTTCAGAGTTCAGCCAAGACT 60.550 50.000 0.00 0.00 0.00 3.24
3189 3467 1.803555 GCTTCAGAGTTCAGCCAAGAC 59.196 52.381 0.00 0.00 0.00 3.01
3190 3468 2.175878 GCTTCAGAGTTCAGCCAAGA 57.824 50.000 0.00 0.00 0.00 3.02
3365 3647 5.120208 GCATGCCATGAAATCATAAGCAATC 59.880 40.000 18.51 12.09 43.43 2.67
3450 3732 4.711846 TGATGGCCCTGTATAGCAGTATAG 59.288 45.833 0.00 0.00 43.55 1.31
3451 3733 4.683643 TGATGGCCCTGTATAGCAGTATA 58.316 43.478 0.00 0.00 43.55 1.47
3452 3734 3.520696 TGATGGCCCTGTATAGCAGTAT 58.479 45.455 0.00 0.00 43.55 2.12
3453 3735 2.970987 TGATGGCCCTGTATAGCAGTA 58.029 47.619 0.00 0.00 43.55 2.74
3454 3736 1.806496 TGATGGCCCTGTATAGCAGT 58.194 50.000 0.00 0.00 43.55 4.40
3455 3737 2.303890 TGATGATGGCCCTGTATAGCAG 59.696 50.000 0.00 0.00 44.63 4.24
3456 3738 2.337849 TGATGATGGCCCTGTATAGCA 58.662 47.619 0.00 0.00 0.00 3.49
3457 3739 3.276857 CATGATGATGGCCCTGTATAGC 58.723 50.000 0.00 0.00 0.00 2.97
3458 3740 3.276857 GCATGATGATGGCCCTGTATAG 58.723 50.000 0.00 0.00 0.00 1.31
3595 3893 4.805219 AGTTTGGTAATAAAAAGGCGCTG 58.195 39.130 7.64 0.00 0.00 5.18
3637 3935 0.737804 TGACACAACGCAGCAAATGT 59.262 45.000 0.00 0.00 0.00 2.71
3722 4027 5.388994 CGTAGCTCACACACGAGATAGATAG 60.389 48.000 0.00 0.00 34.71 2.08
3737 4042 8.440833 AGAAAAATAAACATGTACGTAGCTCAC 58.559 33.333 0.00 0.00 0.00 3.51
3748 4136 9.362151 TCTTGGGAACTAGAAAAATAAACATGT 57.638 29.630 0.00 0.00 39.28 3.21
3749 4137 9.846248 CTCTTGGGAACTAGAAAAATAAACATG 57.154 33.333 0.00 0.00 41.64 3.21
3801 4189 9.599866 CACCTGTATGAATTTGTCAGTAAGATA 57.400 33.333 0.00 0.00 40.43 1.98
3802 4190 7.066284 GCACCTGTATGAATTTGTCAGTAAGAT 59.934 37.037 0.00 0.00 40.43 2.40
3803 4191 6.371548 GCACCTGTATGAATTTGTCAGTAAGA 59.628 38.462 0.00 0.00 40.43 2.10
3804 4192 6.403636 GGCACCTGTATGAATTTGTCAGTAAG 60.404 42.308 0.00 0.00 40.43 2.34
3805 4193 5.414454 GGCACCTGTATGAATTTGTCAGTAA 59.586 40.000 0.00 0.00 40.43 2.24
3858 4247 3.659786 TGATGAACGATAAATAGGGCCG 58.340 45.455 0.00 0.00 0.00 6.13
3892 4281 2.697751 ACTACTCCTGATGACATGCTCC 59.302 50.000 0.00 0.00 0.00 4.70
3948 4337 7.711772 TCTGTTCTGAACCGTTAAGTTTGAATA 59.288 33.333 17.26 0.00 30.75 1.75
3961 4350 4.238761 TGAACTAGTCTGTTCTGAACCG 57.761 45.455 17.26 11.46 44.63 4.44
3962 4351 7.148557 GCTATTTGAACTAGTCTGTTCTGAACC 60.149 40.741 17.26 2.90 44.63 3.62
3971 4360 8.932945 TCATGTTAGCTATTTGAACTAGTCTG 57.067 34.615 0.00 0.00 0.00 3.51
3981 4465 9.060347 ACATCAAGGTATCATGTTAGCTATTTG 57.940 33.333 14.27 13.29 30.06 2.32
4069 4553 0.326264 ATGCCCTTGAGGTCACTGAC 59.674 55.000 0.00 0.00 38.26 3.51
4094 4578 1.989165 GCTGACTAAACTCTGCACTCG 59.011 52.381 0.00 0.00 35.70 4.18
4102 4586 4.792521 TCTCTCCTTGCTGACTAAACTC 57.207 45.455 0.00 0.00 0.00 3.01
4109 4593 1.198713 TCCCATCTCTCCTTGCTGAC 58.801 55.000 0.00 0.00 0.00 3.51
4118 4602 7.151308 CACTGATACACTAATTCCCATCTCTC 58.849 42.308 0.00 0.00 0.00 3.20
4122 4606 5.992217 GTCCACTGATACACTAATTCCCATC 59.008 44.000 0.00 0.00 0.00 3.51
4135 4625 6.332735 TCACAGCATATAGTCCACTGATAC 57.667 41.667 0.00 0.00 32.67 2.24
4169 4679 4.473199 GGATGGTTTCGAGCTTGTTAAAC 58.527 43.478 8.97 8.97 0.00 2.01
4170 4680 3.504520 GGGATGGTTTCGAGCTTGTTAAA 59.495 43.478 0.00 0.00 0.00 1.52
4191 4701 3.258872 TGATGAAACCCAATTTGCTCAGG 59.741 43.478 0.00 0.00 0.00 3.86
4192 4702 4.240096 GTGATGAAACCCAATTTGCTCAG 58.760 43.478 0.00 0.00 0.00 3.35
4203 4713 4.589908 ACTGATTGTAGGTGATGAAACCC 58.410 43.478 0.00 0.00 41.54 4.11
4229 4739 6.426328 GGCAGAACAGATATGACTAGGAAATG 59.574 42.308 0.00 0.00 0.00 2.32
4236 4746 4.030216 TGTGGGCAGAACAGATATGACTA 58.970 43.478 0.00 0.00 0.00 2.59
4265 4775 7.006865 TCATGATTTGTGTTTCCATTTCCAT 57.993 32.000 0.00 0.00 0.00 3.41
4266 4776 6.416631 TCATGATTTGTGTTTCCATTTCCA 57.583 33.333 0.00 0.00 0.00 3.53
4267 4777 7.727331 TTTCATGATTTGTGTTTCCATTTCC 57.273 32.000 0.00 0.00 0.00 3.13
4269 4779 8.680039 ACATTTCATGATTTGTGTTTCCATTT 57.320 26.923 9.55 0.00 0.00 2.32
4271 4781 8.152246 AGAACATTTCATGATTTGTGTTTCCAT 58.848 29.630 10.75 0.00 30.70 3.41
4272 4782 7.499292 AGAACATTTCATGATTTGTGTTTCCA 58.501 30.769 10.75 0.00 30.70 3.53
4278 4796 9.247126 TGTAACAAGAACATTTCATGATTTGTG 57.753 29.630 10.75 4.32 34.54 3.33


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

AutoCloner maintained by Alex Coulton.