Multiple sequence alignment - TraesCS6D01G401400

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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 TraesCS6D01G401400 chr6D 100.000 2585 0 0 1 2585 470619692 470617108 0.000000e+00 4774.0
1 TraesCS6D01G401400 chr6D 84.496 129 17 3 1845 1971 175148879 175148752 9.710000e-25 124.0
2 TraesCS6D01G401400 chr6D 80.986 142 24 3 1830 1969 218412642 218412782 2.720000e-20 110.0
3 TraesCS6D01G401400 chr6D 90.909 44 4 0 1023 1066 31867061 31867104 2.780000e-05 60.2
4 TraesCS6D01G401400 chr6B 91.486 1656 101 13 789 2429 720514544 720516174 0.000000e+00 2241.0
5 TraesCS6D01G401400 chr6B 89.655 87 9 0 1891 1977 20150922 20151008 7.560000e-21 111.0
6 TraesCS6D01G401400 chr6A 92.662 1431 63 17 789 2215 615448049 615446657 0.000000e+00 2023.0
7 TraesCS6D01G401400 chr6A 96.429 224 8 0 2206 2429 615443850 615443627 1.130000e-98 370.0
8 TraesCS6D01G401400 chr6A 94.340 106 6 0 2480 2585 615443638 615443533 2.060000e-36 163.0
9 TraesCS6D01G401400 chr6A 83.815 173 13 10 602 762 615448304 615448135 1.600000e-32 150.0
10 TraesCS6D01G401400 chr6A 79.577 142 25 4 1830 1969 297652933 297653072 5.890000e-17 99.0
11 TraesCS6D01G401400 chr7D 95.479 553 22 3 27 576 22559969 22559417 0.000000e+00 880.0
12 TraesCS6D01G401400 chr7D 95.479 553 21 4 27 576 611776271 611776822 0.000000e+00 880.0
13 TraesCS6D01G401400 chr7D 96.552 58 1 1 2423 2479 47480602 47480545 7.620000e-16 95.3
14 TraesCS6D01G401400 chr5D 95.479 553 22 3 27 576 66014538 66013986 0.000000e+00 880.0
15 TraesCS6D01G401400 chr5D 95.479 553 22 3 27 576 473997298 473997850 0.000000e+00 880.0
16 TraesCS6D01G401400 chr5D 83.333 132 19 3 1845 1974 504232271 504232141 4.520000e-23 119.0
17 TraesCS6D01G401400 chr4D 95.479 553 22 3 27 576 506361100 506360548 0.000000e+00 880.0
18 TraesCS6D01G401400 chr4D 96.491 57 0 2 2423 2479 227305431 227305377 2.740000e-15 93.5
19 TraesCS6D01G401400 chr4D 96.875 32 1 0 1 32 173972768 173972737 1.000000e-03 54.7
20 TraesCS6D01G401400 chr3D 95.479 553 22 3 27 576 599276393 599275841 0.000000e+00 880.0
21 TraesCS6D01G401400 chr2D 95.479 553 22 3 27 576 56881889 56881337 0.000000e+00 880.0
22 TraesCS6D01G401400 chr2D 95.479 553 22 3 27 576 621338311 621337759 0.000000e+00 880.0
23 TraesCS6D01G401400 chr2D 95.463 551 24 1 27 576 33039552 33039002 0.000000e+00 878.0
24 TraesCS6D01G401400 chr2D 96.875 32 1 0 1 32 8035736 8035705 1.000000e-03 54.7
25 TraesCS6D01G401400 chr4A 83.459 133 14 6 1845 1973 668280736 668280608 1.630000e-22 117.0
26 TraesCS6D01G401400 chr7A 82.400 125 19 3 1845 1967 538577909 538578032 3.520000e-19 106.0
27 TraesCS6D01G401400 chr1D 96.667 60 2 0 2420 2479 60310696 60310637 1.640000e-17 100.0
28 TraesCS6D01G401400 chr5B 96.610 59 1 1 2424 2481 392048035 392047977 2.120000e-16 97.1
29 TraesCS6D01G401400 chr7B 95.082 61 1 2 2420 2479 351906979 351907038 7.620000e-16 95.3
30 TraesCS6D01G401400 chr3B 95.000 60 2 1 2421 2479 821308350 821308291 2.740000e-15 93.5
31 TraesCS6D01G401400 chr3B 90.909 66 2 4 2416 2479 416805569 416805506 4.580000e-13 86.1
32 TraesCS6D01G401400 chr1B 92.424 66 4 1 2411 2475 42060481 42060546 2.740000e-15 93.5
33 TraesCS6D01G401400 chr2B 86.842 76 7 3 2408 2483 154526719 154526647 5.930000e-12 82.4
34 TraesCS6D01G401400 chr2B 96.875 32 1 0 1 32 657726532 657726501 1.000000e-03 54.7
35 TraesCS6D01G401400 chr2B 96.875 32 1 0 1 32 763158847 763158816 1.000000e-03 54.7
36 TraesCS6D01G401400 chr5A 100.000 28 0 0 5 32 35837167 35837194 5.000000e-03 52.8
37 TraesCS6D01G401400 chr1A 100.000 28 0 0 5 32 512001044 512001071 5.000000e-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 TraesCS6D01G401400 chr6D 470617108 470619692 2584 True 4774.0 4774 100.0000 1 2585 1 chr6D.!!$R2 2584
1 TraesCS6D01G401400 chr6B 720514544 720516174 1630 False 2241.0 2241 91.4860 789 2429 1 chr6B.!!$F2 1640
2 TraesCS6D01G401400 chr6A 615443533 615448304 4771 True 676.5 2023 91.8115 602 2585 4 chr6A.!!$R1 1983
3 TraesCS6D01G401400 chr7D 22559417 22559969 552 True 880.0 880 95.4790 27 576 1 chr7D.!!$R1 549
4 TraesCS6D01G401400 chr7D 611776271 611776822 551 False 880.0 880 95.4790 27 576 1 chr7D.!!$F1 549
5 TraesCS6D01G401400 chr5D 66013986 66014538 552 True 880.0 880 95.4790 27 576 1 chr5D.!!$R1 549
6 TraesCS6D01G401400 chr5D 473997298 473997850 552 False 880.0 880 95.4790 27 576 1 chr5D.!!$F1 549
7 TraesCS6D01G401400 chr4D 506360548 506361100 552 True 880.0 880 95.4790 27 576 1 chr4D.!!$R3 549
8 TraesCS6D01G401400 chr3D 599275841 599276393 552 True 880.0 880 95.4790 27 576 1 chr3D.!!$R1 549
9 TraesCS6D01G401400 chr2D 56881337 56881889 552 True 880.0 880 95.4790 27 576 1 chr2D.!!$R3 549
10 TraesCS6D01G401400 chr2D 621337759 621338311 552 True 880.0 880 95.4790 27 576 1 chr2D.!!$R4 549
11 TraesCS6D01G401400 chr2D 33039002 33039552 550 True 878.0 878 95.4630 27 576 1 chr2D.!!$R2 549

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
764 787 0.457166 CGGTTTGTGGCATGCATCTG 60.457 55.0 21.36 3.98 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 5188 1.167851 TGTGCTAATGCTTCAGCCAC 58.832 50.0 0.0 0.0 41.18 5.01 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
29 30 3.952535 CTTGGTTTCAAGCACACTACAC 58.047 45.455 0.00 0.00 43.10 2.90
30 31 2.992593 TGGTTTCAAGCACACTACACA 58.007 42.857 0.00 0.00 0.00 3.72
201 202 7.654568 TCTTCGACTGTATTGACTTACAAAGA 58.345 34.615 0.00 0.00 42.03 2.52
242 243 2.160813 ACATTTTACACGATCGCCCAAC 59.839 45.455 16.60 0.00 0.00 3.77
445 446 3.428870 CACAGTACGGAATGACAACAGTC 59.571 47.826 0.04 0.00 39.90 3.51
449 450 3.040147 ACGGAATGACAACAGTCGATT 57.960 42.857 0.00 0.00 41.27 3.34
458 459 6.130298 TGACAACAGTCGATTTGAACAATT 57.870 33.333 10.36 0.00 35.00 2.32
576 579 9.896645 ATAAGGAAGCGAATACATCATATGATT 57.103 29.630 15.74 9.89 31.21 2.57
577 580 7.840342 AGGAAGCGAATACATCATATGATTC 57.160 36.000 15.74 10.55 31.21 2.52
578 581 7.389232 AGGAAGCGAATACATCATATGATTCA 58.611 34.615 15.74 6.94 31.86 2.57
579 582 7.548427 AGGAAGCGAATACATCATATGATTCAG 59.452 37.037 15.74 7.64 31.86 3.02
580 583 7.332926 GGAAGCGAATACATCATATGATTCAGT 59.667 37.037 15.74 12.90 31.86 3.41
581 584 7.592439 AGCGAATACATCATATGATTCAGTG 57.408 36.000 15.74 8.47 31.86 3.66
582 585 6.592994 AGCGAATACATCATATGATTCAGTGG 59.407 38.462 15.74 8.12 31.86 4.00
583 586 6.183360 GCGAATACATCATATGATTCAGTGGG 60.183 42.308 15.74 5.53 31.86 4.61
584 587 6.183360 CGAATACATCATATGATTCAGTGGGC 60.183 42.308 15.74 4.57 31.86 5.36
585 588 4.719026 ACATCATATGATTCAGTGGGCT 57.281 40.909 15.74 0.00 31.21 5.19
586 589 4.395625 ACATCATATGATTCAGTGGGCTG 58.604 43.478 15.74 4.91 37.05 4.85
587 590 4.141321 ACATCATATGATTCAGTGGGCTGT 60.141 41.667 15.74 5.54 37.04 4.40
588 591 5.072193 ACATCATATGATTCAGTGGGCTGTA 59.928 40.000 15.74 0.00 37.04 2.74
589 592 5.628797 TCATATGATTCAGTGGGCTGTAA 57.371 39.130 0.00 0.00 43.05 2.41
590 593 5.614308 TCATATGATTCAGTGGGCTGTAAG 58.386 41.667 0.00 0.00 43.05 2.34
591 594 5.130975 TCATATGATTCAGTGGGCTGTAAGT 59.869 40.000 0.00 0.00 43.05 2.24
592 595 6.326323 TCATATGATTCAGTGGGCTGTAAGTA 59.674 38.462 0.00 0.00 43.05 2.24
593 596 4.202245 TGATTCAGTGGGCTGTAAGTAC 57.798 45.455 0.00 0.00 43.05 2.73
594 597 3.580895 TGATTCAGTGGGCTGTAAGTACA 59.419 43.478 0.00 0.00 43.05 2.90
595 598 4.041075 TGATTCAGTGGGCTGTAAGTACAA 59.959 41.667 0.00 0.00 43.05 2.41
596 599 3.396260 TCAGTGGGCTGTAAGTACAAC 57.604 47.619 0.00 0.00 43.05 3.32
597 600 2.969950 TCAGTGGGCTGTAAGTACAACT 59.030 45.455 0.00 0.00 43.05 3.16
598 601 3.389983 TCAGTGGGCTGTAAGTACAACTT 59.610 43.478 0.00 0.00 43.05 2.66
599 602 4.134563 CAGTGGGCTGTAAGTACAACTTT 58.865 43.478 0.00 0.00 34.97 2.66
600 603 4.024048 CAGTGGGCTGTAAGTACAACTTTG 60.024 45.833 0.00 0.00 34.97 2.77
622 625 3.186613 GGAACAACTCTTTAGTGCTTCGG 59.813 47.826 0.00 0.00 35.62 4.30
666 670 2.009774 GTGCCTAACGTGATTGCATCT 58.990 47.619 5.74 0.00 34.04 2.90
669 673 3.871006 TGCCTAACGTGATTGCATCTTAG 59.129 43.478 0.00 0.00 0.00 2.18
679 683 6.238184 CGTGATTGCATCTTAGCTAATTGTGA 60.238 38.462 6.64 0.90 34.99 3.58
684 688 6.283694 TGCATCTTAGCTAATTGTGACCTAG 58.716 40.000 6.64 0.00 34.99 3.02
685 689 6.098266 TGCATCTTAGCTAATTGTGACCTAGA 59.902 38.462 6.64 0.00 34.99 2.43
686 690 6.986817 GCATCTTAGCTAATTGTGACCTAGAA 59.013 38.462 6.64 0.00 0.00 2.10
687 691 7.042389 GCATCTTAGCTAATTGTGACCTAGAAC 60.042 40.741 6.64 0.00 0.00 3.01
689 693 7.321153 TCTTAGCTAATTGTGACCTAGAACAC 58.679 38.462 6.64 10.76 37.51 3.32
690 694 4.833390 AGCTAATTGTGACCTAGAACACC 58.167 43.478 13.70 1.90 36.35 4.16
691 695 4.532521 AGCTAATTGTGACCTAGAACACCT 59.467 41.667 13.70 3.61 36.35 4.00
692 696 5.720041 AGCTAATTGTGACCTAGAACACCTA 59.280 40.000 13.70 5.67 36.35 3.08
693 697 6.384305 AGCTAATTGTGACCTAGAACACCTAT 59.616 38.462 13.70 7.18 36.35 2.57
694 698 6.480320 GCTAATTGTGACCTAGAACACCTATG 59.520 42.308 13.70 5.22 36.35 2.23
695 699 3.887621 TGTGACCTAGAACACCTATGC 57.112 47.619 13.70 0.00 36.35 3.14
696 700 3.441101 TGTGACCTAGAACACCTATGCT 58.559 45.455 13.70 0.00 36.35 3.79
697 701 3.447586 TGTGACCTAGAACACCTATGCTC 59.552 47.826 13.70 0.00 36.35 4.26
698 702 2.688446 TGACCTAGAACACCTATGCTCG 59.312 50.000 0.00 0.00 0.00 5.03
699 703 2.950309 GACCTAGAACACCTATGCTCGA 59.050 50.000 0.00 0.00 0.00 4.04
700 704 2.952978 ACCTAGAACACCTATGCTCGAG 59.047 50.000 8.45 8.45 0.00 4.04
701 705 2.952978 CCTAGAACACCTATGCTCGAGT 59.047 50.000 15.13 0.00 0.00 4.18
702 706 3.381908 CCTAGAACACCTATGCTCGAGTT 59.618 47.826 15.13 4.75 0.00 3.01
703 707 3.963428 AGAACACCTATGCTCGAGTTT 57.037 42.857 15.13 4.37 0.00 2.66
704 708 3.589988 AGAACACCTATGCTCGAGTTTG 58.410 45.455 15.13 5.09 0.00 2.93
710 714 2.271800 CTATGCTCGAGTTTGACCACC 58.728 52.381 15.13 0.00 0.00 4.61
762 785 0.808125 TACGGTTTGTGGCATGCATC 59.192 50.000 21.36 12.03 0.00 3.91
763 786 0.895100 ACGGTTTGTGGCATGCATCT 60.895 50.000 21.36 0.00 0.00 2.90
764 787 0.457166 CGGTTTGTGGCATGCATCTG 60.457 55.000 21.36 3.98 0.00 2.90
766 789 1.818060 GGTTTGTGGCATGCATCTGTA 59.182 47.619 21.36 0.00 0.00 2.74
768 791 3.631686 GGTTTGTGGCATGCATCTGTATA 59.368 43.478 21.36 0.00 0.00 1.47
769 792 4.279169 GGTTTGTGGCATGCATCTGTATAT 59.721 41.667 21.36 0.00 0.00 0.86
770 793 5.217393 GTTTGTGGCATGCATCTGTATATG 58.783 41.667 21.36 0.00 0.00 1.78
771 794 3.414269 TGTGGCATGCATCTGTATATGG 58.586 45.455 21.36 0.00 0.00 2.74
772 795 2.751259 GTGGCATGCATCTGTATATGGG 59.249 50.000 21.36 0.00 0.00 4.00
773 796 2.376181 TGGCATGCATCTGTATATGGGT 59.624 45.455 21.36 0.00 0.00 4.51
774 797 2.751259 GGCATGCATCTGTATATGGGTG 59.249 50.000 21.36 0.00 0.00 4.61
801 883 5.007430 CGATTGACCATGATCTCAGGAAAAG 59.993 44.000 0.00 0.00 0.00 2.27
812 894 2.941720 CTCAGGAAAAGCATAGCTCACC 59.058 50.000 0.00 0.00 38.25 4.02
825 908 3.352611 AGCTCACCCATATACCTCCTT 57.647 47.619 0.00 0.00 0.00 3.36
936 1042 3.502164 CCATGGAGATGGGTCAACC 57.498 57.895 5.56 0.00 45.11 3.77
949 1055 4.864704 GGGTCAACCAATTAAGAAGCAA 57.135 40.909 0.89 0.00 39.85 3.91
950 1056 5.208463 GGGTCAACCAATTAAGAAGCAAA 57.792 39.130 0.89 0.00 39.85 3.68
951 1057 5.793817 GGGTCAACCAATTAAGAAGCAAAT 58.206 37.500 0.89 0.00 39.85 2.32
952 1058 6.930731 GGGTCAACCAATTAAGAAGCAAATA 58.069 36.000 0.89 0.00 39.85 1.40
953 1059 7.035612 GGGTCAACCAATTAAGAAGCAAATAG 58.964 38.462 0.89 0.00 39.85 1.73
954 1060 7.309805 GGGTCAACCAATTAAGAAGCAAATAGT 60.310 37.037 0.89 0.00 39.85 2.12
955 1061 7.755373 GGTCAACCAATTAAGAAGCAAATAGTC 59.245 37.037 0.00 0.00 35.64 2.59
972 1078 1.180029 GTCTAGGCCTCCAACGTACA 58.820 55.000 9.68 0.00 0.00 2.90
1032 1138 0.471211 TCACCACCGTCTCCTCCTTT 60.471 55.000 0.00 0.00 0.00 3.11
1037 1146 1.344763 CACCGTCTCCTCCTTTGTCTT 59.655 52.381 0.00 0.00 0.00 3.01
1038 1147 1.619332 ACCGTCTCCTCCTTTGTCTTC 59.381 52.381 0.00 0.00 0.00 2.87
1039 1148 1.618837 CCGTCTCCTCCTTTGTCTTCA 59.381 52.381 0.00 0.00 0.00 3.02
1087 1196 3.858868 GAAGTCTCACACGCCGCCA 62.859 63.158 0.00 0.00 0.00 5.69
1145 1254 1.295792 GTCAAGAAGTTGTGCACCGA 58.704 50.000 15.69 0.00 34.98 4.69
1189 1298 0.941463 CTCCATGATCACGCGCTACC 60.941 60.000 5.73 0.00 0.00 3.18
1393 1502 1.880601 GACACTCGACAAGCTGTGCG 61.881 60.000 0.00 0.00 34.14 5.34
1394 1503 1.951130 CACTCGACAAGCTGTGCGT 60.951 57.895 0.00 0.00 0.00 5.24
1395 1504 1.227263 ACTCGACAAGCTGTGCGTT 60.227 52.632 0.00 0.00 0.00 4.84
1455 1564 2.254546 TCAACAAGGAGTCGCATGTT 57.745 45.000 0.00 2.13 36.49 2.71
1464 1573 1.461127 GAGTCGCATGTTGAGTGGAAC 59.539 52.381 0.00 0.00 0.00 3.62
1496 1605 1.000866 GCCAAGGGGAAGCCAAGAT 59.999 57.895 0.00 0.00 35.59 2.40
1497 1606 1.325476 GCCAAGGGGAAGCCAAGATG 61.325 60.000 0.00 0.00 35.59 2.90
1570 1679 1.503818 GGAGGCGCTCGTCAACAAAA 61.504 55.000 7.64 0.00 0.00 2.44
1618 1727 6.896021 AAACTCACTGAGTACTAGCTGTTA 57.104 37.500 12.22 0.00 42.59 2.41
1639 1750 9.719279 CTGTTATTACGTTTTTGGTTAGTTTCA 57.281 29.630 0.00 0.00 0.00 2.69
1689 1800 9.590451 TTAGTTTCCTTGGTTATGTAATACGAG 57.410 33.333 0.00 0.00 0.00 4.18
1876 1987 4.202253 TGCTAAACTTCTTGAGCACTCAGA 60.202 41.667 0.00 0.00 39.93 3.27
1908 2019 8.000709 AGTAATATGGTCATTGGATTGACATGT 58.999 33.333 0.00 0.00 46.32 3.21
1942 2053 9.448438 GTTAAGATTAATTGAATTTGCCCCTTT 57.552 29.630 0.00 0.00 0.00 3.11
2004 2115 3.930229 GGTTTTGTTTTCTTTGTCGGCTT 59.070 39.130 0.00 0.00 0.00 4.35
2115 2226 6.423302 CCAGACTCTACATAACAAGATGCATC 59.577 42.308 19.37 19.37 0.00 3.91
2192 2312 6.868826 ACTAAGATGGAGGAGATTCTATCCA 58.131 40.000 17.91 17.91 45.48 3.41
2395 5338 0.396974 GGCCCAACATAGGATTGCCA 60.397 55.000 0.00 0.00 34.69 4.92
2401 5344 3.260380 CCAACATAGGATTGCCACCAAAA 59.740 43.478 0.00 0.00 36.29 2.44
2450 5393 3.505464 TTTTTCGAAACGGAGGCAAAA 57.495 38.095 10.79 0.00 0.00 2.44
2451 5394 2.766970 TTTCGAAACGGAGGCAAAAG 57.233 45.000 6.47 0.00 0.00 2.27
2452 5395 1.956297 TTCGAAACGGAGGCAAAAGA 58.044 45.000 0.00 0.00 0.00 2.52
2453 5396 2.178912 TCGAAACGGAGGCAAAAGAT 57.821 45.000 0.00 0.00 0.00 2.40
2454 5397 2.500229 TCGAAACGGAGGCAAAAGATT 58.500 42.857 0.00 0.00 0.00 2.40
2455 5398 2.882137 TCGAAACGGAGGCAAAAGATTT 59.118 40.909 0.00 0.00 0.00 2.17
2456 5399 2.979813 CGAAACGGAGGCAAAAGATTTG 59.020 45.455 0.00 0.00 0.00 2.32
2457 5400 2.438868 AACGGAGGCAAAAGATTTGC 57.561 45.000 17.18 17.18 44.22 3.68
2470 5413 8.931385 GCAAAAGATTTGCCTCATCTATTAAA 57.069 30.769 15.12 0.00 39.38 1.52
2471 5414 9.538508 GCAAAAGATTTGCCTCATCTATTAAAT 57.461 29.630 15.12 0.00 39.38 1.40
2476 5419 9.525826 AGATTTGCCTCATCTATTAAATAAGGG 57.474 33.333 0.00 0.00 0.00 3.95
2477 5420 9.520515 GATTTGCCTCATCTATTAAATAAGGGA 57.479 33.333 0.00 0.00 0.00 4.20
2478 5421 8.924511 TTTGCCTCATCTATTAAATAAGGGAG 57.075 34.615 0.00 0.00 0.00 4.30
2479 5422 7.020827 TGCCTCATCTATTAAATAAGGGAGG 57.979 40.000 0.00 0.00 41.73 4.30
2480 5423 6.012508 TGCCTCATCTATTAAATAAGGGAGGG 60.013 42.308 0.00 0.00 39.74 4.30
2481 5424 6.215636 GCCTCATCTATTAAATAAGGGAGGGA 59.784 42.308 0.00 0.00 39.74 4.20
2482 5425 7.257053 GCCTCATCTATTAAATAAGGGAGGGAA 60.257 40.741 0.00 0.00 39.74 3.97
2483 5426 8.669571 CCTCATCTATTAAATAAGGGAGGGAAA 58.330 37.037 0.00 0.00 36.59 3.13
2505 5448 8.956426 GGAAATATTTATCAAGACACCTCAACA 58.044 33.333 0.00 0.00 0.00 3.33
2538 5481 0.108329 ATTACGAACGCTCCAGGGTG 60.108 55.000 0.00 0.00 41.23 4.61
2572 5515 9.528018 GCTTCAAGCTATCAGGACTATATAATC 57.472 37.037 0.71 0.00 38.45 1.75
2576 5519 9.258826 CAAGCTATCAGGACTATATAATCATGC 57.741 37.037 1.13 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.293122 TGCTTGAAACCAAGAATGACCG 59.707 45.455 9.13 0.00 42.71 4.79
1 2 3.068024 TGTGCTTGAAACCAAGAATGACC 59.932 43.478 9.13 0.00 42.71 4.02
2 3 4.044426 GTGTGCTTGAAACCAAGAATGAC 58.956 43.478 9.13 0.00 42.71 3.06
3 4 3.953612 AGTGTGCTTGAAACCAAGAATGA 59.046 39.130 9.13 0.00 42.71 2.57
4 5 4.311816 AGTGTGCTTGAAACCAAGAATG 57.688 40.909 9.13 0.00 42.71 2.67
6 7 4.095782 GTGTAGTGTGCTTGAAACCAAGAA 59.904 41.667 9.13 0.00 42.71 2.52
7 8 3.625764 GTGTAGTGTGCTTGAAACCAAGA 59.374 43.478 9.13 0.00 42.71 3.02
8 9 3.376859 TGTGTAGTGTGCTTGAAACCAAG 59.623 43.478 0.00 0.00 42.90 3.61
9 10 3.348119 TGTGTAGTGTGCTTGAAACCAA 58.652 40.909 0.00 0.00 0.00 3.67
10 11 2.942376 CTGTGTAGTGTGCTTGAAACCA 59.058 45.455 0.00 0.00 0.00 3.67
11 12 3.202906 TCTGTGTAGTGTGCTTGAAACC 58.797 45.455 0.00 0.00 0.00 3.27
12 13 4.094294 TGTTCTGTGTAGTGTGCTTGAAAC 59.906 41.667 0.00 0.00 0.00 2.78
13 14 4.257731 TGTTCTGTGTAGTGTGCTTGAAA 58.742 39.130 0.00 0.00 0.00 2.69
14 15 3.867857 TGTTCTGTGTAGTGTGCTTGAA 58.132 40.909 0.00 0.00 0.00 2.69
15 16 3.118775 ACTGTTCTGTGTAGTGTGCTTGA 60.119 43.478 0.00 0.00 0.00 3.02
16 17 3.198068 ACTGTTCTGTGTAGTGTGCTTG 58.802 45.455 0.00 0.00 0.00 4.01
17 18 3.133003 AGACTGTTCTGTGTAGTGTGCTT 59.867 43.478 0.00 0.00 0.00 3.91
18 19 2.695666 AGACTGTTCTGTGTAGTGTGCT 59.304 45.455 0.00 0.00 0.00 4.40
19 20 2.797156 CAGACTGTTCTGTGTAGTGTGC 59.203 50.000 0.00 0.00 43.95 4.57
30 31 0.106708 TTTGGAGCGCAGACTGTTCT 59.893 50.000 11.47 1.35 0.00 3.01
165 166 0.252284 AGTCGAAGATGGTCCCCTGT 60.252 55.000 0.00 0.00 40.67 4.00
242 243 3.731652 TTGGTTGGTGCTCTTTTGATG 57.268 42.857 0.00 0.00 0.00 3.07
329 330 4.468510 TCCGTAGTCAAGTTCCCATATGTT 59.531 41.667 1.24 0.00 0.00 2.71
445 446 6.143758 CAGTGTACCCAAAATTGTTCAAATCG 59.856 38.462 0.00 0.00 0.00 3.34
449 450 5.449314 CGTCAGTGTACCCAAAATTGTTCAA 60.449 40.000 0.00 0.00 0.00 2.69
458 459 1.538634 CGGTTCGTCAGTGTACCCAAA 60.539 52.381 0.00 0.00 0.00 3.28
549 552 9.896645 ATCATATGATGTATTCGCTTCCTTATT 57.103 29.630 17.51 0.00 32.68 1.40
576 579 3.389983 AAGTTGTACTTACAGCCCACTGA 59.610 43.478 0.00 0.00 40.62 3.41
577 580 3.740115 AAGTTGTACTTACAGCCCACTG 58.260 45.455 0.00 0.00 39.38 3.66
578 581 4.134563 CAAAGTTGTACTTACAGCCCACT 58.865 43.478 0.00 0.00 37.47 4.00
579 582 3.252458 CCAAAGTTGTACTTACAGCCCAC 59.748 47.826 0.00 0.00 37.47 4.61
580 583 3.136809 TCCAAAGTTGTACTTACAGCCCA 59.863 43.478 0.00 0.00 37.47 5.36
581 584 3.746940 TCCAAAGTTGTACTTACAGCCC 58.253 45.455 0.00 0.00 37.47 5.19
582 585 4.577283 TGTTCCAAAGTTGTACTTACAGCC 59.423 41.667 0.00 0.00 37.47 4.85
583 586 5.744666 TGTTCCAAAGTTGTACTTACAGC 57.255 39.130 0.00 0.00 37.47 4.40
584 587 7.280205 AGAGTTGTTCCAAAGTTGTACTTACAG 59.720 37.037 0.00 0.00 37.47 2.74
585 588 7.107542 AGAGTTGTTCCAAAGTTGTACTTACA 58.892 34.615 0.00 0.00 37.47 2.41
586 589 7.549615 AGAGTTGTTCCAAAGTTGTACTTAC 57.450 36.000 0.00 0.00 37.47 2.34
587 590 8.570068 AAAGAGTTGTTCCAAAGTTGTACTTA 57.430 30.769 0.00 0.00 37.47 2.24
588 591 7.462571 AAAGAGTTGTTCCAAAGTTGTACTT 57.537 32.000 0.00 0.00 40.80 2.24
589 592 7.827729 ACTAAAGAGTTGTTCCAAAGTTGTACT 59.172 33.333 0.00 0.00 28.61 2.73
590 593 7.908601 CACTAAAGAGTTGTTCCAAAGTTGTAC 59.091 37.037 0.00 0.00 31.73 2.90
591 594 7.414762 GCACTAAAGAGTTGTTCCAAAGTTGTA 60.415 37.037 0.00 0.00 31.73 2.41
592 595 6.625081 GCACTAAAGAGTTGTTCCAAAGTTGT 60.625 38.462 0.00 0.00 31.73 3.32
593 596 5.743872 GCACTAAAGAGTTGTTCCAAAGTTG 59.256 40.000 0.00 0.00 31.73 3.16
594 597 5.652452 AGCACTAAAGAGTTGTTCCAAAGTT 59.348 36.000 0.00 0.00 31.73 2.66
595 598 5.193679 AGCACTAAAGAGTTGTTCCAAAGT 58.806 37.500 0.00 0.00 31.73 2.66
596 599 5.757850 AGCACTAAAGAGTTGTTCCAAAG 57.242 39.130 0.00 0.00 31.73 2.77
597 600 5.220777 CGAAGCACTAAAGAGTTGTTCCAAA 60.221 40.000 0.00 0.00 31.73 3.28
598 601 4.272504 CGAAGCACTAAAGAGTTGTTCCAA 59.727 41.667 0.00 0.00 31.73 3.53
599 602 3.807622 CGAAGCACTAAAGAGTTGTTCCA 59.192 43.478 0.00 0.00 31.73 3.53
600 603 3.186613 CCGAAGCACTAAAGAGTTGTTCC 59.813 47.826 0.00 0.00 31.73 3.62
666 670 6.212791 AGGTGTTCTAGGTCACAATTAGCTAA 59.787 38.462 8.99 8.99 36.43 3.09
669 673 4.833390 AGGTGTTCTAGGTCACAATTAGC 58.167 43.478 15.92 0.00 36.43 3.09
679 683 2.952978 CTCGAGCATAGGTGTTCTAGGT 59.047 50.000 0.00 0.00 33.85 3.08
684 688 3.368236 GTCAAACTCGAGCATAGGTGTTC 59.632 47.826 13.61 0.00 32.80 3.18
685 689 3.326747 GTCAAACTCGAGCATAGGTGTT 58.673 45.455 13.61 0.00 0.00 3.32
686 690 2.353803 GGTCAAACTCGAGCATAGGTGT 60.354 50.000 13.61 0.00 33.55 4.16
687 691 2.271800 GGTCAAACTCGAGCATAGGTG 58.728 52.381 13.61 1.92 33.55 4.00
689 693 2.271800 GTGGTCAAACTCGAGCATAGG 58.728 52.381 13.61 0.00 44.54 2.57
690 694 2.271800 GGTGGTCAAACTCGAGCATAG 58.728 52.381 13.61 0.00 44.54 2.23
691 695 1.066430 GGGTGGTCAAACTCGAGCATA 60.066 52.381 13.61 0.00 44.54 3.14
692 696 0.321653 GGGTGGTCAAACTCGAGCAT 60.322 55.000 13.61 0.00 44.54 3.79
693 697 1.070786 GGGTGGTCAAACTCGAGCA 59.929 57.895 13.61 0.00 40.92 4.26
694 698 3.967715 GGGTGGTCAAACTCGAGC 58.032 61.111 13.61 0.00 0.00 5.03
698 702 2.140717 CACTAACGGGTGGTCAAACTC 58.859 52.381 0.00 0.00 33.95 3.01
699 703 1.812708 GCACTAACGGGTGGTCAAACT 60.813 52.381 7.36 0.00 37.65 2.66
700 704 0.589708 GCACTAACGGGTGGTCAAAC 59.410 55.000 7.36 0.00 37.65 2.93
701 705 0.470766 AGCACTAACGGGTGGTCAAA 59.529 50.000 4.74 0.00 43.20 2.69
702 706 2.138595 AGCACTAACGGGTGGTCAA 58.861 52.632 4.74 0.00 43.20 3.18
703 707 3.879844 AGCACTAACGGGTGGTCA 58.120 55.556 4.74 0.00 43.20 4.02
710 714 2.092211 GTCAAATGTCGAGCACTAACGG 59.908 50.000 0.00 0.00 0.00 4.44
746 769 0.604578 ACAGATGCATGCCACAAACC 59.395 50.000 16.68 0.00 0.00 3.27
762 785 5.171476 GGTCAATCGATCACCCATATACAG 58.829 45.833 13.38 0.00 0.00 2.74
763 786 4.591072 TGGTCAATCGATCACCCATATACA 59.409 41.667 19.16 1.64 0.00 2.29
764 787 5.147330 TGGTCAATCGATCACCCATATAC 57.853 43.478 19.16 1.06 0.00 1.47
766 789 4.286808 TCATGGTCAATCGATCACCCATAT 59.713 41.667 19.16 7.62 34.27 1.78
768 791 2.439135 TCATGGTCAATCGATCACCCAT 59.561 45.455 19.16 16.49 34.27 4.00
769 792 1.836802 TCATGGTCAATCGATCACCCA 59.163 47.619 19.16 15.23 34.27 4.51
770 793 2.620251 TCATGGTCAATCGATCACCC 57.380 50.000 19.16 10.86 34.27 4.61
771 794 3.993081 GAGATCATGGTCAATCGATCACC 59.007 47.826 16.36 16.36 34.27 4.02
772 795 4.625028 TGAGATCATGGTCAATCGATCAC 58.375 43.478 9.06 0.00 34.27 3.06
773 796 4.262335 CCTGAGATCATGGTCAATCGATCA 60.262 45.833 9.06 0.96 37.36 2.92
774 797 4.021632 TCCTGAGATCATGGTCAATCGATC 60.022 45.833 9.06 0.00 35.54 3.69
801 883 3.118592 GGAGGTATATGGGTGAGCTATGC 60.119 52.174 0.00 0.00 0.00 3.14
812 894 2.563179 CGGAGGTGAAGGAGGTATATGG 59.437 54.545 0.00 0.00 0.00 2.74
933 1039 9.178758 CCTAGACTATTTGCTTCTTAATTGGTT 57.821 33.333 0.00 0.00 0.00 3.67
934 1040 7.283354 GCCTAGACTATTTGCTTCTTAATTGGT 59.717 37.037 0.00 0.00 0.00 3.67
935 1041 7.255277 GGCCTAGACTATTTGCTTCTTAATTGG 60.255 40.741 0.00 0.00 0.00 3.16
936 1042 7.500559 AGGCCTAGACTATTTGCTTCTTAATTG 59.499 37.037 1.29 0.00 0.00 2.32
937 1043 7.578203 AGGCCTAGACTATTTGCTTCTTAATT 58.422 34.615 1.29 0.00 0.00 1.40
938 1044 7.142995 AGGCCTAGACTATTTGCTTCTTAAT 57.857 36.000 1.29 0.00 0.00 1.40
939 1045 6.408206 GGAGGCCTAGACTATTTGCTTCTTAA 60.408 42.308 4.42 0.00 0.00 1.85
940 1046 5.070580 GGAGGCCTAGACTATTTGCTTCTTA 59.929 44.000 4.42 0.00 0.00 2.10
941 1047 4.141597 GGAGGCCTAGACTATTTGCTTCTT 60.142 45.833 4.42 0.00 0.00 2.52
942 1048 3.389656 GGAGGCCTAGACTATTTGCTTCT 59.610 47.826 4.42 0.00 0.00 2.85
943 1049 3.134804 TGGAGGCCTAGACTATTTGCTTC 59.865 47.826 4.42 0.00 0.00 3.86
944 1050 3.115390 TGGAGGCCTAGACTATTTGCTT 58.885 45.455 4.42 0.00 0.00 3.91
945 1051 2.764269 TGGAGGCCTAGACTATTTGCT 58.236 47.619 4.42 0.00 0.00 3.91
946 1052 3.206964 GTTGGAGGCCTAGACTATTTGC 58.793 50.000 4.42 0.00 0.00 3.68
947 1053 3.118738 ACGTTGGAGGCCTAGACTATTTG 60.119 47.826 4.42 0.00 0.00 2.32
948 1054 3.105283 ACGTTGGAGGCCTAGACTATTT 58.895 45.455 4.42 0.00 0.00 1.40
949 1055 2.748388 ACGTTGGAGGCCTAGACTATT 58.252 47.619 4.42 0.00 0.00 1.73
950 1056 2.456073 ACGTTGGAGGCCTAGACTAT 57.544 50.000 4.42 0.00 0.00 2.12
951 1057 2.025981 TGTACGTTGGAGGCCTAGACTA 60.026 50.000 4.42 0.00 0.00 2.59
952 1058 1.272313 TGTACGTTGGAGGCCTAGACT 60.272 52.381 4.42 0.00 0.00 3.24
953 1059 1.180029 TGTACGTTGGAGGCCTAGAC 58.820 55.000 4.42 3.61 0.00 2.59
954 1060 1.927487 TTGTACGTTGGAGGCCTAGA 58.073 50.000 4.42 0.00 0.00 2.43
955 1061 2.936498 CAATTGTACGTTGGAGGCCTAG 59.064 50.000 4.42 0.00 0.00 3.02
972 1078 2.030007 CCGATGCACAAACTGTCCAATT 60.030 45.455 0.00 0.00 0.00 2.32
1032 1138 0.179233 CGACGACGACGATGAAGACA 60.179 55.000 15.32 0.00 42.66 3.41
1037 1146 1.690283 GAGGACGACGACGACGATGA 61.690 60.000 25.15 0.00 42.66 2.92
1038 1147 1.296722 GAGGACGACGACGACGATG 60.297 63.158 25.15 8.06 42.66 3.84
1039 1148 2.459442 GGAGGACGACGACGACGAT 61.459 63.158 25.15 10.97 42.66 3.73
1189 1298 2.116736 TTTGCGCCTTTGCTCTCGTG 62.117 55.000 4.18 0.00 35.36 4.35
1239 1348 1.612442 AAGGAGCTTGGCGGAGGTA 60.612 57.895 0.00 0.00 0.00 3.08
1393 1502 1.454201 GGGAGCTGAACCTTGCTAAC 58.546 55.000 0.00 0.00 39.91 2.34
1394 1503 0.328258 GGGGAGCTGAACCTTGCTAA 59.672 55.000 0.00 0.00 39.91 3.09
1395 1504 1.562672 GGGGGAGCTGAACCTTGCTA 61.563 60.000 0.00 0.00 39.91 3.49
1455 1564 0.827925 ACCTCTCGCAGTTCCACTCA 60.828 55.000 0.00 0.00 0.00 3.41
1496 1605 0.952280 GGAGACATCGTCGGCTATCA 59.048 55.000 0.00 0.00 37.67 2.15
1497 1606 0.952280 TGGAGACATCGTCGGCTATC 59.048 55.000 0.00 0.00 37.67 2.08
1595 1704 5.793030 AACAGCTAGTACTCAGTGAGTTT 57.207 39.130 29.84 20.14 40.28 2.66
1639 1750 5.813513 AAGATGCCCAAAAGACAGAAAAT 57.186 34.783 0.00 0.00 0.00 1.82
1684 1795 6.784176 TGCACGTATGAATTTACTACTCGTA 58.216 36.000 0.00 0.00 0.00 3.43
1685 1796 5.643664 TGCACGTATGAATTTACTACTCGT 58.356 37.500 0.00 0.00 0.00 4.18
1686 1797 6.563398 TTGCACGTATGAATTTACTACTCG 57.437 37.500 0.00 0.00 0.00 4.18
1687 1798 6.846283 GCATTGCACGTATGAATTTACTACTC 59.154 38.462 3.15 0.00 0.00 2.59
1688 1799 6.315144 TGCATTGCACGTATGAATTTACTACT 59.685 34.615 7.38 0.00 31.71 2.57
1689 1800 6.482835 TGCATTGCACGTATGAATTTACTAC 58.517 36.000 7.38 0.00 31.71 2.73
1876 1987 6.575244 TCCAATGACCATATTACTCCAACT 57.425 37.500 0.00 0.00 0.00 3.16
2183 2303 6.783708 AGTCTTCGACTCTTTGGATAGAAT 57.216 37.500 0.00 0.00 38.71 2.40
2192 2312 2.162008 GCGGAGTAGTCTTCGACTCTTT 59.838 50.000 0.00 0.00 44.73 2.52
2252 5188 1.167851 TGTGCTAATGCTTCAGCCAC 58.832 50.000 0.00 0.00 41.18 5.01
2395 5338 5.943416 TCCATTCACATATTCTCGTTTTGGT 59.057 36.000 0.00 0.00 0.00 3.67
2430 5373 3.128938 TCTTTTGCCTCCGTTTCGAAAAA 59.871 39.130 13.10 0.00 0.00 1.94
2431 5374 2.683867 TCTTTTGCCTCCGTTTCGAAAA 59.316 40.909 13.10 0.00 0.00 2.29
2432 5375 2.290464 TCTTTTGCCTCCGTTTCGAAA 58.710 42.857 6.47 6.47 0.00 3.46
2433 5376 1.956297 TCTTTTGCCTCCGTTTCGAA 58.044 45.000 0.00 0.00 0.00 3.71
2434 5377 2.178912 ATCTTTTGCCTCCGTTTCGA 57.821 45.000 0.00 0.00 0.00 3.71
2435 5378 2.979813 CAAATCTTTTGCCTCCGTTTCG 59.020 45.455 0.00 0.00 0.00 3.46
2436 5379 2.731451 GCAAATCTTTTGCCTCCGTTTC 59.269 45.455 12.74 0.00 39.38 2.78
2437 5380 2.754472 GCAAATCTTTTGCCTCCGTTT 58.246 42.857 12.74 0.00 39.38 3.60
2438 5381 2.438868 GCAAATCTTTTGCCTCCGTT 57.561 45.000 12.74 0.00 39.38 4.44
2445 5388 8.931385 TTTAATAGATGAGGCAAATCTTTTGC 57.069 30.769 14.88 14.88 44.22 3.68
2450 5393 9.525826 CCCTTATTTAATAGATGAGGCAAATCT 57.474 33.333 7.08 7.08 38.03 2.40
2451 5394 9.520515 TCCCTTATTTAATAGATGAGGCAAATC 57.479 33.333 0.00 0.00 30.94 2.17
2452 5395 9.525826 CTCCCTTATTTAATAGATGAGGCAAAT 57.474 33.333 0.00 0.00 30.94 2.32
2453 5396 7.944554 CCTCCCTTATTTAATAGATGAGGCAAA 59.055 37.037 10.56 0.00 30.94 3.68
2454 5397 7.461749 CCTCCCTTATTTAATAGATGAGGCAA 58.538 38.462 10.56 0.00 30.94 4.52
2455 5398 6.012508 CCCTCCCTTATTTAATAGATGAGGCA 60.013 42.308 14.72 0.00 36.40 4.75
2456 5399 6.215636 TCCCTCCCTTATTTAATAGATGAGGC 59.784 42.308 14.72 0.00 36.40 4.70
2457 5400 7.814693 TCCCTCCCTTATTTAATAGATGAGG 57.185 40.000 13.86 13.86 37.26 3.86
2471 5414 9.009675 TGTCTTGATAAATATTTCCCTCCCTTA 57.990 33.333 3.39 0.00 0.00 2.69
2472 5415 7.780271 GTGTCTTGATAAATATTTCCCTCCCTT 59.220 37.037 3.39 0.00 0.00 3.95
2473 5416 7.290813 GTGTCTTGATAAATATTTCCCTCCCT 58.709 38.462 3.39 0.00 0.00 4.20
2474 5417 6.490381 GGTGTCTTGATAAATATTTCCCTCCC 59.510 42.308 3.39 0.00 0.00 4.30
2475 5418 7.290813 AGGTGTCTTGATAAATATTTCCCTCC 58.709 38.462 3.39 0.00 0.00 4.30
2476 5419 7.993183 TGAGGTGTCTTGATAAATATTTCCCTC 59.007 37.037 3.39 7.41 34.29 4.30
2477 5420 7.872138 TGAGGTGTCTTGATAAATATTTCCCT 58.128 34.615 3.39 0.00 0.00 4.20
2478 5421 8.406297 GTTGAGGTGTCTTGATAAATATTTCCC 58.594 37.037 3.39 0.00 0.00 3.97
2479 5422 8.956426 TGTTGAGGTGTCTTGATAAATATTTCC 58.044 33.333 3.39 0.00 0.00 3.13
2482 5425 9.520515 ACTTGTTGAGGTGTCTTGATAAATATT 57.479 29.630 0.00 0.00 0.00 1.28
2483 5426 9.520515 AACTTGTTGAGGTGTCTTGATAAATAT 57.479 29.630 0.00 0.00 0.00 1.28
2484 5427 8.783093 CAACTTGTTGAGGTGTCTTGATAAATA 58.217 33.333 7.66 0.00 38.32 1.40
2485 5428 7.651808 CAACTTGTTGAGGTGTCTTGATAAAT 58.348 34.615 7.66 0.00 38.32 1.40
2486 5429 6.459573 GCAACTTGTTGAGGTGTCTTGATAAA 60.460 38.462 16.57 0.00 45.28 1.40
2487 5430 5.008613 GCAACTTGTTGAGGTGTCTTGATAA 59.991 40.000 16.57 0.00 45.28 1.75
2488 5431 4.515191 GCAACTTGTTGAGGTGTCTTGATA 59.485 41.667 16.57 0.00 45.28 2.15
2489 5432 3.316308 GCAACTTGTTGAGGTGTCTTGAT 59.684 43.478 16.57 0.00 45.28 2.57
2490 5433 2.682856 GCAACTTGTTGAGGTGTCTTGA 59.317 45.455 16.57 0.00 45.28 3.02
2505 5448 5.387279 CGTTCGTAATATGTTTGGCAACTT 58.613 37.500 0.00 0.00 33.58 2.66
2559 5502 8.671987 ACTGTAAGGCATGATTATATAGTCCT 57.328 34.615 0.00 0.00 39.30 3.85


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

AutoCloner maintained by Alex Coulton.