Multiple sequence alignment - TraesCS4D01G054400

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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 TraesCS4D01G054400 chr4D 100.000 3788 0 0 1 3788 30216873 30213086 0.000000e+00 6996.0
1 TraesCS4D01G054400 chr4A 94.245 2676 136 10 879 3548 572835993 572838656 0.000000e+00 4072.0
2 TraesCS4D01G054400 chr4A 88.520 331 27 6 1 321 572834876 572835205 1.280000e-104 390.0
3 TraesCS4D01G054400 chr4A 78.405 514 32 24 322 758 572835241 572835752 1.040000e-65 261.0
4 TraesCS4D01G054400 chr4A 92.000 175 11 3 3582 3755 572838658 572838830 3.780000e-60 243.0
5 TraesCS4D01G054400 chr4B 94.162 2364 101 10 899 3253 43107197 43104862 0.000000e+00 3567.0
6 TraesCS4D01G054400 chr4B 84.615 637 53 17 1 616 43108714 43108102 3.260000e-165 592.0
7 TraesCS4D01G054400 chr4B 88.142 253 24 5 3299 3551 43104862 43104616 2.860000e-76 296.0
8 TraesCS4D01G054400 chr4B 83.478 115 6 5 652 758 43108018 43107909 1.120000e-15 95.3
9 TraesCS4D01G054400 chr4B 100.000 28 0 0 3585 3612 43104614 43104587 7.000000e-03 52.8


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 TraesCS4D01G054400 chr4D 30213086 30216873 3787 True 6996.00 6996 100.0000 1 3788 1 chr4D.!!$R1 3787
1 TraesCS4D01G054400 chr4A 572834876 572838830 3954 False 1241.50 4072 88.2925 1 3755 4 chr4A.!!$F1 3754
2 TraesCS4D01G054400 chr4B 43104587 43108714 4127 True 920.62 3567 90.0794 1 3612 5 chr4B.!!$R1 3611

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
132 136 0.753262 CATGCCCGCTACCTAGAGTT 59.247 55.0 0.00 0.0 0.0 3.01 F
1294 2031 0.252479 CTGCTGCAACTCCATCCTCT 59.748 55.0 3.02 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2636 0.820891 CATCCTCCCCGAAGCCATTG 60.821 60.0 0.00 0.0 0.00 2.82 R
2946 3684 0.773014 TGGGTCCATATGCCCTGATG 59.227 55.0 16.69 0.0 45.06 3.07 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
25 26 5.966636 TGATTAACGGACAATCAATCGAG 57.033 39.130 6.23 0.00 38.98 4.04
31 32 3.262420 CGGACAATCAATCGAGAAACCT 58.738 45.455 0.00 0.00 0.00 3.50
44 45 4.062293 CGAGAAACCTAACAATGACCACA 58.938 43.478 0.00 0.00 0.00 4.17
48 49 6.805713 AGAAACCTAACAATGACCACAAAAG 58.194 36.000 0.00 0.00 0.00 2.27
51 52 6.783708 ACCTAACAATGACCACAAAAGAAA 57.216 33.333 0.00 0.00 0.00 2.52
52 53 7.176589 ACCTAACAATGACCACAAAAGAAAA 57.823 32.000 0.00 0.00 0.00 2.29
54 55 7.763985 ACCTAACAATGACCACAAAAGAAAAAG 59.236 33.333 0.00 0.00 0.00 2.27
127 131 1.524961 CCAACATGCCCGCTACCTA 59.475 57.895 0.00 0.00 0.00 3.08
132 136 0.753262 CATGCCCGCTACCTAGAGTT 59.247 55.000 0.00 0.00 0.00 3.01
165 169 2.892852 CAAGAAGGAAGAACAATGCCCA 59.107 45.455 0.00 0.00 0.00 5.36
211 215 2.398498 CCTCGCCGATCAATAGAACTG 58.602 52.381 0.00 0.00 0.00 3.16
224 228 4.974645 ATAGAACTGTCACCCAGAAACA 57.025 40.909 0.00 0.00 44.49 2.83
231 235 1.903404 CACCCAGAAACAGCCCACC 60.903 63.158 0.00 0.00 0.00 4.61
233 237 1.077265 CCCAGAAACAGCCCACCAT 59.923 57.895 0.00 0.00 0.00 3.55
287 301 6.177610 TCGATATTTGGCCACTTTTAGAAGT 58.822 36.000 3.88 0.00 46.85 3.01
307 321 5.675684 AGTTTTTGACATGGTTTTCACCT 57.324 34.783 0.00 0.00 44.61 4.00
309 323 5.046663 AGTTTTTGACATGGTTTTCACCTGT 60.047 36.000 0.00 0.00 44.61 4.00
385 435 9.725019 ATTTTTGGAAGGAAACCAATTAAGATC 57.275 29.630 0.00 0.00 45.09 2.75
387 437 4.947388 TGGAAGGAAACCAATTAAGATCCG 59.053 41.667 0.00 0.00 34.25 4.18
409 459 3.071874 TCGATTGAAGCCAAATGGAGT 57.928 42.857 2.98 0.00 35.67 3.85
423 473 6.337356 CCAAATGGAGTAACTTTTGTTGTGT 58.663 36.000 0.00 0.00 39.39 3.72
424 474 6.255453 CCAAATGGAGTAACTTTTGTTGTGTG 59.745 38.462 0.00 0.00 39.39 3.82
426 476 5.968528 TGGAGTAACTTTTGTTGTGTGTT 57.031 34.783 0.00 0.00 43.41 3.32
429 490 5.969435 GGAGTAACTTTTGTTGTGTGTTAGC 59.031 40.000 0.00 0.00 43.41 3.09
467 528 2.803451 ACGAGCGCAATTGAACAAAAA 58.197 38.095 11.47 0.00 0.00 1.94
469 530 2.533535 CGAGCGCAATTGAACAAAAACA 59.466 40.909 11.47 0.00 0.00 2.83
528 589 4.702831 CCATGCACCTGTGTATACATGTA 58.297 43.478 9.18 8.27 34.49 2.29
533 614 9.002600 CATGCACCTGTGTATACATGTATAAAT 57.997 33.333 23.88 5.66 34.49 1.40
616 697 5.008619 TCACACATCAAAATGCAACAACT 57.991 34.783 0.00 0.00 36.26 3.16
631 732 2.086869 ACAACTAGTGCCATGCATGTC 58.913 47.619 24.58 13.73 41.91 3.06
639 740 2.125326 CCATGCATGTCCAGCCCAG 61.125 63.158 24.58 2.77 0.00 4.45
650 751 1.006281 TCCAGCCCAGAATGCAAATCT 59.994 47.619 0.00 0.00 31.97 2.40
654 784 4.100498 CCAGCCCAGAATGCAAATCTTTAT 59.900 41.667 2.82 0.00 31.97 1.40
682 814 9.683069 ATCATCAAAAACATCAAACTTAGACAC 57.317 29.630 0.00 0.00 0.00 3.67
759 899 8.879759 AGTATCGTACACATTCATAAAACAAGG 58.120 33.333 0.00 0.00 0.00 3.61
761 901 7.731882 TCGTACACATTCATAAAACAAGGAA 57.268 32.000 0.00 0.00 0.00 3.36
762 902 8.330466 TCGTACACATTCATAAAACAAGGAAT 57.670 30.769 0.00 0.00 0.00 3.01
779 919 8.036273 ACAAGGAATGTAATAAGTACCAAACG 57.964 34.615 0.00 0.00 41.63 3.60
780 920 7.662669 ACAAGGAATGTAATAAGTACCAAACGT 59.337 33.333 0.00 0.00 41.63 3.99
781 921 7.838771 AGGAATGTAATAAGTACCAAACGTC 57.161 36.000 0.00 0.00 30.94 4.34
783 923 7.548075 AGGAATGTAATAAGTACCAAACGTCAG 59.452 37.037 0.00 0.00 30.94 3.51
785 925 6.100404 TGTAATAAGTACCAAACGTCAGGT 57.900 37.500 15.18 15.18 41.89 4.00
786 926 7.225784 TGTAATAAGTACCAAACGTCAGGTA 57.774 36.000 13.36 13.36 39.31 3.08
799 939 1.545841 TCAGGTACGAGCACATGACT 58.454 50.000 0.00 0.00 34.53 3.41
800 940 2.718563 TCAGGTACGAGCACATGACTA 58.281 47.619 0.00 0.00 34.53 2.59
801 941 2.422479 TCAGGTACGAGCACATGACTAC 59.578 50.000 0.00 0.00 34.53 2.73
803 943 3.090037 AGGTACGAGCACATGACTACTT 58.910 45.455 0.00 0.00 0.00 2.24
804 944 3.128938 AGGTACGAGCACATGACTACTTC 59.871 47.826 0.00 0.00 0.00 3.01
805 945 2.264109 ACGAGCACATGACTACTTCG 57.736 50.000 0.00 2.70 0.00 3.79
806 946 1.810755 ACGAGCACATGACTACTTCGA 59.189 47.619 0.00 0.00 0.00 3.71
808 948 2.594654 CGAGCACATGACTACTTCGAAC 59.405 50.000 0.00 0.00 0.00 3.95
810 950 3.318017 AGCACATGACTACTTCGAACAC 58.682 45.455 0.00 0.00 0.00 3.32
823 1476 3.624326 TCGAACACTTTTGATGGCAAG 57.376 42.857 0.00 0.00 35.04 4.01
828 1481 5.746245 CGAACACTTTTGATGGCAAGTTTAA 59.254 36.000 0.00 0.00 35.04 1.52
829 1482 6.291585 CGAACACTTTTGATGGCAAGTTTAAC 60.292 38.462 0.00 0.00 35.04 2.01
830 1483 5.040635 ACACTTTTGATGGCAAGTTTAACG 58.959 37.500 0.00 0.00 35.04 3.18
831 1484 5.163602 ACACTTTTGATGGCAAGTTTAACGA 60.164 36.000 0.00 0.00 35.04 3.85
832 1485 5.920273 CACTTTTGATGGCAAGTTTAACGAT 59.080 36.000 0.00 0.00 35.04 3.73
834 1487 5.957842 TTTGATGGCAAGTTTAACGATCT 57.042 34.783 0.00 0.00 35.04 2.75
835 1488 4.944962 TGATGGCAAGTTTAACGATCTG 57.055 40.909 0.00 0.00 0.00 2.90
836 1489 4.574892 TGATGGCAAGTTTAACGATCTGA 58.425 39.130 0.00 0.00 0.00 3.27
837 1490 4.631377 TGATGGCAAGTTTAACGATCTGAG 59.369 41.667 0.00 0.00 0.00 3.35
838 1491 4.002906 TGGCAAGTTTAACGATCTGAGT 57.997 40.909 0.00 0.00 0.00 3.41
839 1492 5.142061 TGGCAAGTTTAACGATCTGAGTA 57.858 39.130 0.00 0.00 0.00 2.59
841 1494 5.580691 TGGCAAGTTTAACGATCTGAGTATG 59.419 40.000 0.00 0.00 0.00 2.39
842 1495 5.493735 GCAAGTTTAACGATCTGAGTATGC 58.506 41.667 0.00 0.00 0.00 3.14
843 1496 5.502544 GCAAGTTTAACGATCTGAGTATGCC 60.503 44.000 0.00 0.00 0.00 4.40
844 1497 5.339008 AGTTTAACGATCTGAGTATGCCA 57.661 39.130 0.00 0.00 0.00 4.92
846 1499 5.581085 AGTTTAACGATCTGAGTATGCCAAC 59.419 40.000 0.00 0.00 0.00 3.77
847 1500 3.895232 AACGATCTGAGTATGCCAACT 57.105 42.857 0.00 0.00 0.00 3.16
848 1501 3.895232 ACGATCTGAGTATGCCAACTT 57.105 42.857 0.00 0.00 0.00 2.66
849 1502 4.207891 ACGATCTGAGTATGCCAACTTT 57.792 40.909 0.00 0.00 0.00 2.66
850 1503 5.339008 ACGATCTGAGTATGCCAACTTTA 57.661 39.130 0.00 0.00 0.00 1.85
851 1504 5.730550 ACGATCTGAGTATGCCAACTTTAA 58.269 37.500 0.00 0.00 0.00 1.52
852 1505 5.581085 ACGATCTGAGTATGCCAACTTTAAC 59.419 40.000 0.00 0.00 0.00 2.01
854 1507 6.237942 CGATCTGAGTATGCCAACTTTAACTG 60.238 42.308 0.00 0.00 0.00 3.16
855 1508 6.109156 TCTGAGTATGCCAACTTTAACTGA 57.891 37.500 0.00 0.00 0.00 3.41
856 1509 5.932303 TCTGAGTATGCCAACTTTAACTGAC 59.068 40.000 0.00 0.00 0.00 3.51
857 1510 5.616270 TGAGTATGCCAACTTTAACTGACA 58.384 37.500 0.00 0.00 0.00 3.58
858 1511 6.058833 TGAGTATGCCAACTTTAACTGACAA 58.941 36.000 0.00 0.00 0.00 3.18
859 1512 6.204688 TGAGTATGCCAACTTTAACTGACAAG 59.795 38.462 0.00 0.00 0.00 3.16
861 1514 7.221450 AGTATGCCAACTTTAACTGACAAGTA 58.779 34.615 0.00 0.00 34.77 2.24
863 1516 6.312399 TGCCAACTTTAACTGACAAGTATG 57.688 37.500 0.00 0.00 34.77 2.39
865 1518 6.714810 TGCCAACTTTAACTGACAAGTATGAT 59.285 34.615 0.00 0.00 34.77 2.45
944 1670 7.723616 ACACGAATCCATGATTTCCCATTTATA 59.276 33.333 0.00 0.00 31.89 0.98
945 1671 8.575589 CACGAATCCATGATTTCCCATTTATAA 58.424 33.333 0.00 0.00 31.89 0.98
952 1678 7.308589 CCATGATTTCCCATTTATAAGTCGACC 60.309 40.741 13.01 0.00 0.00 4.79
1107 1844 1.826921 GACATCGCCTCTCCCCGTA 60.827 63.158 0.00 0.00 0.00 4.02
1294 2031 0.252479 CTGCTGCAACTCCATCCTCT 59.748 55.000 3.02 0.00 0.00 3.69
1303 2040 1.074926 TCCATCCTCTGCTCCCTCC 60.075 63.158 0.00 0.00 0.00 4.30
1887 2624 2.037901 ACATGGAGTGCGATGATCTCT 58.962 47.619 0.00 0.00 34.69 3.10
1893 2630 3.494048 GGAGTGCGATGATCTCTGGATTT 60.494 47.826 0.00 0.00 31.46 2.17
1899 2636 2.048444 TGATCTCTGGATTTGCAGCC 57.952 50.000 0.00 0.00 31.46 4.85
1995 2732 0.038251 TTACTGGTGTGCTCTCTGCG 60.038 55.000 0.00 0.00 46.63 5.18
2139 2876 2.954318 GTTGCTTGATGAGGCATACCAT 59.046 45.455 0.00 0.00 38.30 3.55
2208 2945 0.674581 CTCTTCTTGGTGCATGCCGA 60.675 55.000 16.68 0.60 0.00 5.54
2334 3071 3.031013 GGTTGGGGATTGGATAAAGGTG 58.969 50.000 0.00 0.00 0.00 4.00
2361 3098 6.238648 GGAAGTTAGGAAGTTGATGAAGGAA 58.761 40.000 0.00 0.00 0.00 3.36
2421 3158 2.544685 CTTAACGGTGAGCTCCATGAG 58.455 52.381 12.15 0.74 0.00 2.90
2655 3392 2.489938 TACGCCTGGCAAAGAATCTT 57.510 45.000 20.29 0.00 0.00 2.40
2685 3422 4.582240 TGTGTAGATTGCCACAATTTCACA 59.418 37.500 15.24 15.24 38.56 3.58
2736 3473 7.971168 CGATTAGTGATTGTAAGAGACAGAACT 59.029 37.037 0.00 0.00 39.88 3.01
2826 3563 3.130869 TGCTGCATTCATTTATGGTGGAC 59.869 43.478 0.00 0.00 0.00 4.02
2829 3566 5.682990 GCTGCATTCATTTATGGTGGACATT 60.683 40.000 0.00 0.00 41.03 2.71
2906 3644 4.987408 TGATACCAAATGCACTTGATGG 57.013 40.909 9.94 6.50 37.19 3.51
2940 3678 2.749076 TGATTCGGTGATTTTGAGGCAG 59.251 45.455 0.00 0.00 0.00 4.85
2946 3684 3.010420 GGTGATTTTGAGGCAGTCTACC 58.990 50.000 0.00 0.00 0.00 3.18
2981 3719 4.141824 TGGACCCAATTCCACAAGAAAAAC 60.142 41.667 0.00 0.00 41.00 2.43
3054 3793 2.416566 CCTCGAACAGTGATGTCTGAGG 60.417 54.545 11.92 11.92 38.63 3.86
3096 3835 4.932200 AGAAAGACTGTACATGCTGCTTAC 59.068 41.667 0.00 0.67 0.00 2.34
3116 3855 4.650972 ACAGGAGCACCCTTGTAATAAA 57.349 40.909 0.00 0.00 44.85 1.40
3207 3946 4.576463 GTGTCAGTTTCTTGTTGGTCTGAT 59.424 41.667 0.00 0.00 35.07 2.90
3364 4103 2.875296 TGGCTATTTCAGTTTGGCAGT 58.125 42.857 0.00 0.00 0.00 4.40
3369 4108 4.455877 GCTATTTCAGTTTGGCAGTACTGT 59.544 41.667 23.44 12.29 41.87 3.55
3371 4110 5.852282 ATTTCAGTTTGGCAGTACTGTTT 57.148 34.783 23.44 11.83 41.87 2.83
3372 4111 6.952773 ATTTCAGTTTGGCAGTACTGTTTA 57.047 33.333 23.44 8.09 41.87 2.01
3458 4197 2.151881 TGACAATGCCACAATGTTGC 57.848 45.000 2.17 2.17 26.67 4.17
3498 4237 3.811497 TGCAGTCATCTGAACAAGTTGAG 59.189 43.478 10.54 0.00 43.76 3.02
3501 4240 5.180868 GCAGTCATCTGAACAAGTTGAGAAT 59.819 40.000 10.54 0.00 43.76 2.40
3510 4249 7.173218 TCTGAACAAGTTGAGAATTACATGGTC 59.827 37.037 10.54 0.00 30.09 4.02
3511 4250 6.998074 TGAACAAGTTGAGAATTACATGGTCT 59.002 34.615 10.54 0.00 32.51 3.85
3513 4252 7.907214 ACAAGTTGAGAATTACATGGTCTAC 57.093 36.000 10.54 0.00 0.00 2.59
3524 4263 2.505819 ACATGGTCTACTGATTCCCCAC 59.494 50.000 0.00 0.00 0.00 4.61
3542 4282 6.366340 TCCCCACAAGTAATACTTTGAACAA 58.634 36.000 2.41 0.00 36.03 2.83
3548 4288 9.347934 CACAAGTAATACTTTGAACAACAACAA 57.652 29.630 2.41 0.00 36.03 2.83
3551 4291 8.905103 AGTAATACTTTGAACAACAACAACAC 57.095 30.769 0.00 0.00 38.29 3.32
3552 4292 7.971722 AGTAATACTTTGAACAACAACAACACC 59.028 33.333 0.00 0.00 38.29 4.16
3553 4293 4.592485 ACTTTGAACAACAACAACACCA 57.408 36.364 0.00 0.00 38.29 4.17
3554 4294 4.555262 ACTTTGAACAACAACAACACCAG 58.445 39.130 0.00 0.00 38.29 4.00
3555 4295 2.645730 TGAACAACAACAACACCAGC 57.354 45.000 0.00 0.00 0.00 4.85
3556 4296 1.889170 TGAACAACAACAACACCAGCA 59.111 42.857 0.00 0.00 0.00 4.41
3557 4297 2.094803 TGAACAACAACAACACCAGCAG 60.095 45.455 0.00 0.00 0.00 4.24
3558 4298 1.544724 ACAACAACAACACCAGCAGT 58.455 45.000 0.00 0.00 0.00 4.40
3559 4299 2.717390 ACAACAACAACACCAGCAGTA 58.283 42.857 0.00 0.00 0.00 2.74
3560 4300 3.287222 ACAACAACAACACCAGCAGTAT 58.713 40.909 0.00 0.00 0.00 2.12
3561 4301 3.315191 ACAACAACAACACCAGCAGTATC 59.685 43.478 0.00 0.00 0.00 2.24
3562 4302 2.504367 ACAACAACACCAGCAGTATCC 58.496 47.619 0.00 0.00 0.00 2.59
3563 4303 2.106511 ACAACAACACCAGCAGTATCCT 59.893 45.455 0.00 0.00 0.00 3.24
3564 4304 3.149196 CAACAACACCAGCAGTATCCTT 58.851 45.455 0.00 0.00 0.00 3.36
3565 4305 3.059352 ACAACACCAGCAGTATCCTTC 57.941 47.619 0.00 0.00 0.00 3.46
3566 4306 2.371841 ACAACACCAGCAGTATCCTTCA 59.628 45.455 0.00 0.00 0.00 3.02
3567 4307 3.181445 ACAACACCAGCAGTATCCTTCAA 60.181 43.478 0.00 0.00 0.00 2.69
3568 4308 3.788227 ACACCAGCAGTATCCTTCAAA 57.212 42.857 0.00 0.00 0.00 2.69
3569 4309 3.679389 ACACCAGCAGTATCCTTCAAAG 58.321 45.455 0.00 0.00 0.00 2.77
3571 4311 2.644798 ACCAGCAGTATCCTTCAAAGGT 59.355 45.455 8.60 0.00 46.54 3.50
3572 4312 3.074538 ACCAGCAGTATCCTTCAAAGGTT 59.925 43.478 8.60 3.40 46.54 3.50
3573 4313 4.288626 ACCAGCAGTATCCTTCAAAGGTTA 59.711 41.667 8.60 2.45 46.54 2.85
3574 4314 5.222048 ACCAGCAGTATCCTTCAAAGGTTAA 60.222 40.000 8.60 0.00 46.54 2.01
3575 4315 5.710099 CCAGCAGTATCCTTCAAAGGTTAAA 59.290 40.000 8.60 0.00 46.54 1.52
3576 4316 6.208599 CCAGCAGTATCCTTCAAAGGTTAAAA 59.791 38.462 8.60 0.00 46.54 1.52
3577 4317 7.255801 CCAGCAGTATCCTTCAAAGGTTAAAAA 60.256 37.037 8.60 0.00 46.54 1.94
3627 4367 2.756760 CAGCAAACTGGCACCTGAATAT 59.243 45.455 0.01 0.00 40.48 1.28
3667 4407 2.355115 CCCAGGGCCTAACACCAC 59.645 66.667 5.28 0.00 0.00 4.16
3669 4409 2.746277 CAGGGCCTAACACCACGC 60.746 66.667 5.28 0.00 0.00 5.34
3678 4418 0.312416 TAACACCACGCATGTTTGGC 59.688 50.000 13.10 0.00 40.68 4.52
3682 4422 0.881118 ACCACGCATGTTTGGCTAAG 59.119 50.000 13.10 0.00 36.20 2.18
3711 4451 3.326880 GGGGTTCAAAGTCTCACTCCTTA 59.673 47.826 0.00 0.00 0.00 2.69
3728 4468 3.534747 TCCTTACCTAGTCACCCAGGTAT 59.465 47.826 6.72 0.00 44.79 2.73
3741 4482 2.168313 CCCAGGTATTGTGAATTTGCCC 59.832 50.000 0.00 0.00 0.00 5.36
3755 4496 1.243342 TTGCCCGCATTCTTGTCTGG 61.243 55.000 0.00 0.00 0.00 3.86
3756 4497 3.056313 GCCCGCATTCTTGTCTGGC 62.056 63.158 0.00 0.00 0.00 4.85
3757 4498 2.753966 CCCGCATTCTTGTCTGGCG 61.754 63.158 0.00 0.00 46.61 5.69
3761 4502 2.704725 GCATTCTTGTCTGGCGAAAA 57.295 45.000 0.00 0.00 0.00 2.29
3762 4503 2.319472 GCATTCTTGTCTGGCGAAAAC 58.681 47.619 0.00 0.00 0.00 2.43
3763 4504 2.922335 GCATTCTTGTCTGGCGAAAACC 60.922 50.000 0.00 0.00 0.00 3.27
3764 4505 1.314730 TTCTTGTCTGGCGAAAACCC 58.685 50.000 0.00 0.00 0.00 4.11
3765 4506 0.181587 TCTTGTCTGGCGAAAACCCA 59.818 50.000 0.00 0.00 0.00 4.51
3766 4507 1.028905 CTTGTCTGGCGAAAACCCAA 58.971 50.000 0.00 0.00 30.66 4.12
3767 4508 1.001378 CTTGTCTGGCGAAAACCCAAG 60.001 52.381 0.00 0.00 30.66 3.61
3768 4509 1.285950 GTCTGGCGAAAACCCAAGC 59.714 57.895 0.00 0.00 30.66 4.01
3769 4510 1.150536 TCTGGCGAAAACCCAAGCT 59.849 52.632 0.00 0.00 30.66 3.74
3770 4511 0.467290 TCTGGCGAAAACCCAAGCTT 60.467 50.000 0.00 0.00 30.66 3.74
3771 4512 0.318955 CTGGCGAAAACCCAAGCTTG 60.319 55.000 19.93 19.93 30.66 4.01
3772 4513 1.664649 GGCGAAAACCCAAGCTTGC 60.665 57.895 21.43 6.76 0.00 4.01
3773 4514 1.363807 GCGAAAACCCAAGCTTGCT 59.636 52.632 21.43 4.96 0.00 3.91
3774 4515 0.940991 GCGAAAACCCAAGCTTGCTG 60.941 55.000 21.43 15.75 0.00 4.41
3775 4516 0.385390 CGAAAACCCAAGCTTGCTGT 59.615 50.000 21.43 16.40 0.00 4.40
3776 4517 1.606668 CGAAAACCCAAGCTTGCTGTA 59.393 47.619 21.43 0.00 0.00 2.74
3777 4518 2.604614 CGAAAACCCAAGCTTGCTGTAC 60.605 50.000 21.43 12.71 0.00 2.90
3778 4519 2.364972 AAACCCAAGCTTGCTGTACT 57.635 45.000 21.43 8.17 0.00 2.73
3779 4520 1.609208 AACCCAAGCTTGCTGTACTG 58.391 50.000 21.43 5.31 0.00 2.74
3780 4521 0.764890 ACCCAAGCTTGCTGTACTGA 59.235 50.000 21.43 0.00 0.00 3.41
3781 4522 1.160137 CCCAAGCTTGCTGTACTGAC 58.840 55.000 21.43 0.00 0.00 3.51
3782 4523 1.160137 CCAAGCTTGCTGTACTGACC 58.840 55.000 21.43 0.00 0.00 4.02
3783 4524 1.543208 CCAAGCTTGCTGTACTGACCA 60.543 52.381 21.43 0.00 0.00 4.02
3784 4525 2.221169 CAAGCTTGCTGTACTGACCAA 58.779 47.619 14.65 0.00 0.00 3.67
3785 4526 2.816087 CAAGCTTGCTGTACTGACCAAT 59.184 45.455 14.65 0.00 0.00 3.16
3786 4527 3.146104 AGCTTGCTGTACTGACCAATT 57.854 42.857 3.61 0.00 0.00 2.32
3787 4528 3.077359 AGCTTGCTGTACTGACCAATTC 58.923 45.455 3.61 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.262420 AGGTTTCTCGATTGATTGTCCG 58.738 45.455 0.00 0.00 0.00 4.79
25 26 6.801575 TCTTTTGTGGTCATTGTTAGGTTTC 58.198 36.000 0.00 0.00 0.00 2.78
31 32 9.712305 TTTCTTTTTCTTTTGTGGTCATTGTTA 57.288 25.926 0.00 0.00 0.00 2.41
127 131 2.365617 TCTTGAAGGCGTCTCAAACTCT 59.634 45.455 1.41 0.00 0.00 3.24
132 136 1.691976 TCCTTCTTGAAGGCGTCTCAA 59.308 47.619 21.16 0.00 39.80 3.02
187 191 0.673985 CTATTGATCGGCGAGGGTCA 59.326 55.000 17.22 11.90 0.00 4.02
211 215 1.150536 TGGGCTGTTTCTGGGTGAC 59.849 57.895 0.00 0.00 0.00 3.67
224 228 1.002134 CAAGGTTCGATGGTGGGCT 60.002 57.895 0.00 0.00 0.00 5.19
231 235 1.543429 GCCCTATCCCAAGGTTCGATG 60.543 57.143 0.00 0.00 34.56 3.84
233 237 1.342672 GGCCCTATCCCAAGGTTCGA 61.343 60.000 0.00 0.00 34.56 3.71
287 301 5.413309 ACAGGTGAAAACCATGTCAAAAA 57.587 34.783 0.00 0.00 0.00 1.94
383 433 2.620251 TTGGCTTCAATCGATCGGAT 57.380 45.000 16.41 4.75 36.78 4.18
384 434 2.394930 TTTGGCTTCAATCGATCGGA 57.605 45.000 16.41 1.35 0.00 4.55
385 435 2.287188 CCATTTGGCTTCAATCGATCGG 60.287 50.000 16.41 0.00 0.00 4.18
387 437 3.629398 ACTCCATTTGGCTTCAATCGATC 59.371 43.478 0.00 0.00 34.44 3.69
409 459 4.142665 TGCGCTAACACACAACAAAAGTTA 60.143 37.500 9.73 0.00 0.00 2.24
423 473 0.238025 TACGTCGTCTTGCGCTAACA 59.762 50.000 9.73 0.00 41.07 2.41
424 474 1.252015 CATACGTCGTCTTGCGCTAAC 59.748 52.381 9.73 2.92 41.07 2.34
426 476 0.248336 CCATACGTCGTCTTGCGCTA 60.248 55.000 9.73 0.00 41.07 4.26
429 490 1.186030 GTACCATACGTCGTCTTGCG 58.814 55.000 0.00 0.00 43.01 4.85
449 510 4.713854 ATGTTTTTGTTCAATTGCGCTC 57.286 36.364 9.73 0.00 0.00 5.03
453 514 9.286946 TGAATTTGAATGTTTTTGTTCAATTGC 57.713 25.926 0.00 0.00 42.12 3.56
467 528 9.598517 TTTTAGCACTCTTTTGAATTTGAATGT 57.401 25.926 0.00 0.00 0.00 2.71
505 566 2.036958 TGTATACACAGGTGCATGGC 57.963 50.000 0.08 0.00 0.00 4.40
616 697 0.749091 GCTGGACATGCATGGCACTA 60.749 55.000 32.84 17.59 43.04 2.74
631 732 1.481871 AGATTTGCATTCTGGGCTGG 58.518 50.000 0.00 0.00 0.00 4.85
654 784 9.897744 GTCTAAGTTTGATGTTTTTGATGATGA 57.102 29.630 0.00 0.00 0.00 2.92
718 850 7.634817 GTGTACGATACTTTGATTTGTGTATGC 59.365 37.037 0.00 0.00 0.00 3.14
758 898 7.201582 CCTGACGTTTGGTACTTATTACATTCC 60.202 40.741 0.00 0.00 31.46 3.01
759 899 7.332678 ACCTGACGTTTGGTACTTATTACATTC 59.667 37.037 11.02 0.00 34.36 2.67
761 901 6.704310 ACCTGACGTTTGGTACTTATTACAT 58.296 36.000 11.02 0.00 34.36 2.29
762 902 6.100404 ACCTGACGTTTGGTACTTATTACA 57.900 37.500 11.02 0.00 34.36 2.41
779 919 1.202582 AGTCATGTGCTCGTACCTGAC 59.797 52.381 12.89 12.89 42.71 3.51
780 920 1.545841 AGTCATGTGCTCGTACCTGA 58.454 50.000 0.00 0.00 0.00 3.86
781 921 2.423892 AGTAGTCATGTGCTCGTACCTG 59.576 50.000 0.00 0.00 0.00 4.00
783 923 3.436496 GAAGTAGTCATGTGCTCGTACC 58.564 50.000 0.00 0.00 0.00 3.34
785 925 3.004862 TCGAAGTAGTCATGTGCTCGTA 58.995 45.455 0.00 0.00 0.00 3.43
786 926 1.810755 TCGAAGTAGTCATGTGCTCGT 59.189 47.619 0.00 0.00 0.00 4.18
787 927 2.544480 TCGAAGTAGTCATGTGCTCG 57.456 50.000 0.00 0.00 0.00 5.03
788 928 3.365220 GTGTTCGAAGTAGTCATGTGCTC 59.635 47.826 0.00 0.00 0.00 4.26
790 930 3.318017 AGTGTTCGAAGTAGTCATGTGC 58.682 45.455 0.00 0.00 0.00 4.57
791 931 5.907197 AAAGTGTTCGAAGTAGTCATGTG 57.093 39.130 0.00 0.00 0.00 3.21
792 932 6.046593 TCAAAAGTGTTCGAAGTAGTCATGT 58.953 36.000 0.00 0.00 0.00 3.21
793 933 6.525121 TCAAAAGTGTTCGAAGTAGTCATG 57.475 37.500 0.00 0.00 0.00 3.07
794 934 6.147821 CCATCAAAAGTGTTCGAAGTAGTCAT 59.852 38.462 0.00 0.00 0.00 3.06
796 936 5.614887 GCCATCAAAAGTGTTCGAAGTAGTC 60.615 44.000 0.00 0.00 0.00 2.59
797 937 4.213482 GCCATCAAAAGTGTTCGAAGTAGT 59.787 41.667 0.00 0.00 0.00 2.73
798 938 4.213270 TGCCATCAAAAGTGTTCGAAGTAG 59.787 41.667 0.00 0.00 0.00 2.57
799 939 4.130857 TGCCATCAAAAGTGTTCGAAGTA 58.869 39.130 0.00 0.00 0.00 2.24
800 940 2.948979 TGCCATCAAAAGTGTTCGAAGT 59.051 40.909 0.00 0.00 0.00 3.01
801 941 3.624326 TGCCATCAAAAGTGTTCGAAG 57.376 42.857 0.00 0.00 0.00 3.79
803 943 2.948979 ACTTGCCATCAAAAGTGTTCGA 59.051 40.909 0.00 0.00 35.34 3.71
804 944 3.354089 ACTTGCCATCAAAAGTGTTCG 57.646 42.857 0.00 0.00 35.34 3.95
805 945 6.291585 CGTTAAACTTGCCATCAAAAGTGTTC 60.292 38.462 0.00 0.00 36.75 3.18
806 946 5.518487 CGTTAAACTTGCCATCAAAAGTGTT 59.482 36.000 0.00 0.00 36.75 3.32
808 948 5.277825 TCGTTAAACTTGCCATCAAAAGTG 58.722 37.500 0.00 0.00 36.75 3.16
810 950 6.306356 CAGATCGTTAAACTTGCCATCAAAAG 59.694 38.462 0.00 0.00 0.00 2.27
823 1476 5.581085 AGTTGGCATACTCAGATCGTTAAAC 59.419 40.000 0.00 0.00 0.00 2.01
828 1481 3.895232 AAGTTGGCATACTCAGATCGT 57.105 42.857 0.00 0.00 0.00 3.73
829 1482 5.812642 AGTTAAAGTTGGCATACTCAGATCG 59.187 40.000 0.00 0.00 0.00 3.69
830 1483 6.818644 TCAGTTAAAGTTGGCATACTCAGATC 59.181 38.462 0.00 0.00 0.00 2.75
831 1484 6.595716 GTCAGTTAAAGTTGGCATACTCAGAT 59.404 38.462 0.00 0.00 0.00 2.90
832 1485 5.932303 GTCAGTTAAAGTTGGCATACTCAGA 59.068 40.000 0.00 0.00 0.00 3.27
834 1487 5.616270 TGTCAGTTAAAGTTGGCATACTCA 58.384 37.500 0.00 0.00 0.00 3.41
835 1488 6.204882 ACTTGTCAGTTAAAGTTGGCATACTC 59.795 38.462 0.00 0.00 32.75 2.59
836 1489 6.062095 ACTTGTCAGTTAAAGTTGGCATACT 58.938 36.000 0.00 0.00 32.75 2.12
837 1490 6.313744 ACTTGTCAGTTAAAGTTGGCATAC 57.686 37.500 0.00 0.00 32.75 2.39
838 1491 7.880713 TCATACTTGTCAGTTAAAGTTGGCATA 59.119 33.333 0.00 0.00 37.74 3.14
839 1492 6.714810 TCATACTTGTCAGTTAAAGTTGGCAT 59.285 34.615 0.00 0.00 37.74 4.40
841 1494 6.554334 TCATACTTGTCAGTTAAAGTTGGC 57.446 37.500 0.00 0.00 37.74 4.52
861 1514 9.620660 GTTCGGATTTGTGTTTAAAGTTATCAT 57.379 29.630 0.00 0.00 0.00 2.45
863 1516 7.799914 ACGTTCGGATTTGTGTTTAAAGTTATC 59.200 33.333 0.00 0.00 0.00 1.75
865 1518 7.014092 ACGTTCGGATTTGTGTTTAAAGTTA 57.986 32.000 0.00 0.00 0.00 2.24
868 1521 5.112937 CGAACGTTCGGATTTGTGTTTAAAG 59.887 40.000 36.53 7.98 46.30 1.85
869 1522 4.962751 CGAACGTTCGGATTTGTGTTTAAA 59.037 37.500 36.53 0.00 46.30 1.52
870 1523 4.516359 CGAACGTTCGGATTTGTGTTTAA 58.484 39.130 36.53 0.00 46.30 1.52
872 1525 2.976729 CGAACGTTCGGATTTGTGTTT 58.023 42.857 36.53 0.00 46.30 2.83
894 1620 4.586306 AAAGTTTGGACCCCGATAGATT 57.414 40.909 0.00 0.00 39.76 2.40
897 1623 5.005094 TGTTTAAAGTTTGGACCCCGATAG 58.995 41.667 0.00 0.00 0.00 2.08
1090 1827 2.125961 GTACGGGGAGAGGCGATGT 61.126 63.158 0.00 0.00 0.00 3.06
1179 1916 2.438614 GCGAGGGAAAGGAAGGCC 60.439 66.667 0.00 0.00 0.00 5.19
1566 2303 2.931969 CGCATAGCAAGTGATCAGAACA 59.068 45.455 0.00 0.00 0.00 3.18
1729 2466 2.181021 CACCGCGTACTCCCAGAC 59.819 66.667 4.92 0.00 0.00 3.51
1887 2624 1.597989 GCCATTGGCTGCAAATCCA 59.402 52.632 20.66 0.00 46.69 3.41
1899 2636 0.820891 CATCCTCCCCGAAGCCATTG 60.821 60.000 0.00 0.00 0.00 2.82
2011 2748 2.224867 ACCTGAAACCCTCATCAACCAG 60.225 50.000 0.00 0.00 32.14 4.00
2048 2785 2.297315 GGCATCATCTGATACTCACGGA 59.703 50.000 0.00 0.00 32.63 4.69
2050 2787 3.375782 TGGCATCATCTGATACTCACG 57.624 47.619 0.00 0.00 32.63 4.35
2139 2876 4.103153 ACCTTCATCTCTTCAACCACAAGA 59.897 41.667 0.00 0.00 0.00 3.02
2208 2945 4.703575 CCAAGATCAACATGACCATGAACT 59.296 41.667 16.07 0.00 41.20 3.01
2334 3071 2.467566 TCAACTTCCTAACTTCCGCC 57.532 50.000 0.00 0.00 0.00 6.13
2361 3098 5.264395 CCAGGAGTAGTTTGGATTCCATTT 58.736 41.667 6.15 0.00 33.76 2.32
2451 3188 2.981859 TCCCGTAAATCTCAGCCTTC 57.018 50.000 0.00 0.00 0.00 3.46
2640 3377 2.154462 ACACGAAGATTCTTTGCCAGG 58.846 47.619 12.72 4.27 0.00 4.45
2655 3392 2.546368 GTGGCAATCTACACAAACACGA 59.454 45.455 0.00 0.00 37.54 4.35
2685 3422 8.517056 CGGTTATAAACACCAGAAAATACCTTT 58.483 33.333 0.64 0.00 33.36 3.11
2801 3538 4.499188 CCACCATAAATGAATGCAGCAGAG 60.499 45.833 0.00 0.00 0.00 3.35
2806 3543 4.987408 TGTCCACCATAAATGAATGCAG 57.013 40.909 0.00 0.00 0.00 4.41
2826 3563 7.062605 GTGCATGGACACTTCAAATCTTTAATG 59.937 37.037 13.07 0.00 37.58 1.90
2829 3566 5.534278 TGTGCATGGACACTTCAAATCTTTA 59.466 36.000 16.89 0.00 41.30 1.85
2906 3644 1.600957 CCGAATCACATCACATCTGGC 59.399 52.381 0.00 0.00 0.00 4.85
2940 3678 2.906389 TCCATATGCCCTGATGGTAGAC 59.094 50.000 0.00 0.00 42.82 2.59
2946 3684 0.773014 TGGGTCCATATGCCCTGATG 59.227 55.000 16.69 0.00 45.06 3.07
3054 3793 1.537202 CTAACTGAACCACTGCCAAGC 59.463 52.381 0.00 0.00 0.00 4.01
3207 3946 4.021807 TGCTTGTCTACGAAACCTGATGTA 60.022 41.667 0.00 0.00 0.00 2.29
3273 4012 2.486472 AAGAGGTCCACAGATGCAAG 57.514 50.000 0.00 0.00 0.00 4.01
3280 4019 5.543507 ATTATCTGCTAAGAGGTCCACAG 57.456 43.478 0.00 0.00 35.37 3.66
3319 4058 7.194607 TGCTTAGTCAAATTTCTCAGACTTG 57.805 36.000 12.53 8.53 41.27 3.16
3383 4122 4.559862 ATGGAGAGGTTTACTGACTTGG 57.440 45.455 0.00 0.00 0.00 3.61
3397 4136 5.819901 GTCCTTGAAAATCTGGTATGGAGAG 59.180 44.000 0.00 0.00 0.00 3.20
3398 4137 5.339200 GGTCCTTGAAAATCTGGTATGGAGA 60.339 44.000 0.00 0.00 0.00 3.71
3466 4205 2.161012 CAGATGACTGCAATTGAGCGTT 59.839 45.455 10.34 0.00 37.33 4.84
3467 4206 1.736126 CAGATGACTGCAATTGAGCGT 59.264 47.619 10.34 1.84 37.33 5.07
3498 4237 5.998363 GGGGAATCAGTAGACCATGTAATTC 59.002 44.000 0.00 0.00 0.00 2.17
3501 4240 4.163458 GTGGGGAATCAGTAGACCATGTAA 59.837 45.833 0.00 0.00 0.00 2.41
3510 4249 7.125792 AGTATTACTTGTGGGGAATCAGTAG 57.874 40.000 0.00 0.00 0.00 2.57
3511 4250 7.504926 AAGTATTACTTGTGGGGAATCAGTA 57.495 36.000 8.27 0.00 37.00 2.74
3513 4252 6.884295 TCAAAGTATTACTTGTGGGGAATCAG 59.116 38.462 9.78 0.00 38.66 2.90
3524 4263 9.347934 TGTTGTTGTTGTTCAAAGTATTACTTG 57.652 29.630 9.78 5.10 38.66 3.16
3542 4282 2.504367 GGATACTGCTGGTGTTGTTGT 58.496 47.619 0.00 0.00 0.00 3.32
3576 4316 9.783081 AAGAAAATGCAGAAGGATATTGTTTTT 57.217 25.926 0.00 0.00 0.00 1.94
3577 4317 9.783081 AAAGAAAATGCAGAAGGATATTGTTTT 57.217 25.926 0.00 0.00 0.00 2.43
3578 4318 9.211485 CAAAGAAAATGCAGAAGGATATTGTTT 57.789 29.630 0.00 0.00 0.00 2.83
3579 4319 8.587608 TCAAAGAAAATGCAGAAGGATATTGTT 58.412 29.630 0.00 0.00 0.00 2.83
3580 4320 8.031277 GTCAAAGAAAATGCAGAAGGATATTGT 58.969 33.333 0.00 0.00 0.00 2.71
3581 4321 8.030692 TGTCAAAGAAAATGCAGAAGGATATTG 58.969 33.333 0.00 0.00 0.00 1.90
3582 4322 8.125978 TGTCAAAGAAAATGCAGAAGGATATT 57.874 30.769 0.00 0.00 0.00 1.28
3583 4323 7.630082 GCTGTCAAAGAAAATGCAGAAGGATAT 60.630 37.037 0.00 0.00 0.00 1.63
3627 4367 6.983890 GGGTGACTTCTCAATTAAAGCAAAAA 59.016 34.615 0.00 0.00 0.00 1.94
3649 4389 2.121689 TGGTGTTAGGCCCTGGGT 60.122 61.111 15.56 0.00 0.00 4.51
3667 4407 2.532531 CTGACTTAGCCAAACATGCG 57.467 50.000 0.00 0.00 0.00 4.73
3678 4418 2.859165 TTGAACCCCAGCTGACTTAG 57.141 50.000 17.39 0.00 0.00 2.18
3682 4422 1.202818 AGACTTTGAACCCCAGCTGAC 60.203 52.381 17.39 1.71 0.00 3.51
3692 4432 5.216614 AGGTAAGGAGTGAGACTTTGAAC 57.783 43.478 0.00 0.00 0.00 3.18
3696 4436 5.477637 GTGACTAGGTAAGGAGTGAGACTTT 59.522 44.000 0.00 0.00 0.00 2.66
3728 4468 1.617850 AGAATGCGGGCAAATTCACAA 59.382 42.857 9.04 0.00 35.63 3.33
3741 4482 0.516877 TTTCGCCAGACAAGAATGCG 59.483 50.000 0.00 0.00 46.09 4.73
3755 4496 0.940991 CAGCAAGCTTGGGTTTTCGC 60.941 55.000 27.10 10.64 0.00 4.70
3756 4497 0.385390 ACAGCAAGCTTGGGTTTTCG 59.615 50.000 27.10 8.66 0.00 3.46
3757 4498 2.623416 AGTACAGCAAGCTTGGGTTTTC 59.377 45.455 27.10 9.80 0.00 2.29
3758 4499 2.362077 CAGTACAGCAAGCTTGGGTTTT 59.638 45.455 27.10 6.44 0.00 2.43
3759 4500 1.956477 CAGTACAGCAAGCTTGGGTTT 59.044 47.619 27.10 9.71 0.00 3.27
3760 4501 1.142870 TCAGTACAGCAAGCTTGGGTT 59.857 47.619 27.10 0.00 0.00 4.11
3761 4502 0.764890 TCAGTACAGCAAGCTTGGGT 59.235 50.000 27.10 11.21 0.00 4.51
3762 4503 1.160137 GTCAGTACAGCAAGCTTGGG 58.840 55.000 27.10 3.84 0.00 4.12
3763 4504 1.160137 GGTCAGTACAGCAAGCTTGG 58.840 55.000 27.10 14.26 0.00 3.61
3764 4505 1.882912 TGGTCAGTACAGCAAGCTTG 58.117 50.000 22.44 22.44 0.00 4.01
3765 4506 2.638480 TTGGTCAGTACAGCAAGCTT 57.362 45.000 0.00 0.00 30.35 3.74
3766 4507 2.867109 ATTGGTCAGTACAGCAAGCT 57.133 45.000 0.00 0.00 37.20 3.74
3767 4508 3.477899 GAATTGGTCAGTACAGCAAGC 57.522 47.619 0.00 0.00 37.20 4.01


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

AutoCloner maintained by Alex Coulton.