Multiple sequence alignment - TraesCS7A01G177300

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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 TraesCS7A01G177300 chr7A 100.000 3394 0 0 1 3394 130401703 130398310 0.000000e+00 6268.0
1 TraesCS7A01G177300 chr7A 98.529 68 1 0 2599 2666 130399072 130399005 1.650000e-23 121.0
2 TraesCS7A01G177300 chr7A 98.529 68 1 0 2632 2699 130399105 130399038 1.650000e-23 121.0
3 TraesCS7A01G177300 chr7A 97.143 35 1 0 2599 2633 130399039 130399005 3.660000e-05 60.2
4 TraesCS7A01G177300 chr7A 97.143 35 1 0 2665 2699 130399105 130399071 3.660000e-05 60.2
5 TraesCS7A01G177300 chr7B 89.553 2575 137 49 173 2633 93068868 93066312 0.000000e+00 3144.0
6 TraesCS7A01G177300 chr7B 93.602 719 41 1 2676 3394 93066335 93065622 0.000000e+00 1068.0
7 TraesCS7A01G177300 chr7D 91.667 2112 93 35 595 2633 131652709 131650608 0.000000e+00 2848.0
8 TraesCS7A01G177300 chr7D 91.172 725 35 3 2671 3394 131650636 131649940 0.000000e+00 957.0
9 TraesCS7A01G177300 chr7D 91.124 338 25 5 253 587 131653649 131653314 1.440000e-123 453.0
10 TraesCS7A01G177300 chr7D 91.373 255 20 2 1 254 131654203 131653950 6.970000e-92 348.0
11 TraesCS7A01G177300 chr7D 97.143 35 1 0 2632 2666 131650642 131650608 3.660000e-05 60.2
12 TraesCS7A01G177300 chr1B 86.466 1692 160 34 757 2425 537771291 537772936 0.000000e+00 1792.0
13 TraesCS7A01G177300 chr1B 86.438 1460 145 31 1029 2447 60109090 60107643 0.000000e+00 1550.0
14 TraesCS7A01G177300 chr1B 87.060 966 107 8 1493 2447 60473811 60474769 0.000000e+00 1075.0
15 TraesCS7A01G177300 chr1B 90.000 240 18 3 1192 1426 60473260 60473498 4.250000e-79 305.0
16 TraesCS7A01G177300 chr1B 78.904 365 41 24 798 1141 60456595 60456944 7.380000e-52 215.0
17 TraesCS7A01G177300 chr1D 86.528 1685 151 37 757 2417 400792245 400793877 0.000000e+00 1784.0
18 TraesCS7A01G177300 chr1D 88.601 965 94 6 1493 2447 40598009 40598967 0.000000e+00 1158.0
19 TraesCS7A01G177300 chr1D 87.413 429 37 9 1026 1449 40597393 40597809 8.520000e-131 477.0
20 TraesCS7A01G177300 chr1A 86.313 1695 161 34 757 2430 497083099 497084743 0.000000e+00 1779.0
21 TraesCS7A01G177300 chr1A 85.826 1531 162 31 954 2447 39872189 39870677 0.000000e+00 1574.0
22 TraesCS7A01G177300 chr1A 82.993 147 23 2 379 523 448636297 448636151 7.640000e-27 132.0
23 TraesCS7A01G177300 chr2A 75.779 289 57 13 2671 2953 543312931 543313212 2.120000e-27 134.0


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 TraesCS7A01G177300 chr7A 130398310 130401703 3393 True 1326.08 6268 98.2688 1 3394 5 chr7A.!!$R1 3393
1 TraesCS7A01G177300 chr7B 93065622 93068868 3246 True 2106.00 3144 91.5775 173 3394 2 chr7B.!!$R1 3221
2 TraesCS7A01G177300 chr7D 131649940 131654203 4263 True 933.24 2848 92.4958 1 3394 5 chr7D.!!$R1 3393
3 TraesCS7A01G177300 chr1B 537771291 537772936 1645 False 1792.00 1792 86.4660 757 2425 1 chr1B.!!$F2 1668
4 TraesCS7A01G177300 chr1B 60107643 60109090 1447 True 1550.00 1550 86.4380 1029 2447 1 chr1B.!!$R1 1418
5 TraesCS7A01G177300 chr1B 60473260 60474769 1509 False 690.00 1075 88.5300 1192 2447 2 chr1B.!!$F3 1255
6 TraesCS7A01G177300 chr1D 400792245 400793877 1632 False 1784.00 1784 86.5280 757 2417 1 chr1D.!!$F1 1660
7 TraesCS7A01G177300 chr1D 40597393 40598967 1574 False 817.50 1158 88.0070 1026 2447 2 chr1D.!!$F2 1421
8 TraesCS7A01G177300 chr1A 497083099 497084743 1644 False 1779.00 1779 86.3130 757 2430 1 chr1A.!!$F1 1673
9 TraesCS7A01G177300 chr1A 39870677 39872189 1512 True 1574.00 1574 85.8260 954 2447 1 chr1A.!!$R1 1493

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
718 1646 0.374758 CAAATCATGCTGTCGACCGG 59.625 55.0 14.12 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 4044 0.921347 CCGATTAGTCGCCAACTTCG 59.079 55.0 1.48 0.0 46.32 3.79 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
36 37 7.551035 TGTTTGCGGGTAATAATTAATACGT 57.449 32.000 4.92 0.00 0.00 3.57
40 41 7.225784 TGCGGGTAATAATTAATACGTCCTA 57.774 36.000 0.00 0.00 0.00 2.94
69 70 4.074970 CCCTGAGTAAACTGAAATGCACT 58.925 43.478 0.00 0.00 0.00 4.40
72 73 5.009010 CCTGAGTAAACTGAAATGCACTTGT 59.991 40.000 0.00 0.00 0.00 3.16
75 76 2.124011 AACTGAAATGCACTTGTGCG 57.876 45.000 18.99 7.67 37.69 5.34
89 90 4.120646 CTTGTGCGTGTTCAAGTCTTAG 57.879 45.455 0.00 0.00 37.04 2.18
95 96 4.151798 GCGTGTTCAAGTCTTAGAAATGC 58.848 43.478 0.00 0.00 0.00 3.56
107 108 4.107051 AAATGCGGCGCTGAGTGC 62.107 61.111 33.26 9.96 38.45 4.40
123 124 2.165437 GAGTGCACTACTTCCTCCAGAG 59.835 54.545 21.73 0.00 40.53 3.35
136 137 8.017418 ACTTCCTCCAGAGAGAAATATAAGTG 57.983 38.462 0.00 0.00 43.39 3.16
144 145 3.139077 GAGAAATATAAGTGGGGCACGG 58.861 50.000 0.00 0.00 39.64 4.94
158 159 1.610886 GGCACGGGTTTCTAGCTCTTT 60.611 52.381 0.00 0.00 0.00 2.52
160 161 2.930682 GCACGGGTTTCTAGCTCTTTAG 59.069 50.000 0.00 0.00 0.00 1.85
162 163 4.174762 CACGGGTTTCTAGCTCTTTAGTC 58.825 47.826 0.00 0.00 0.00 2.59
230 232 7.321745 AGTAATTCCATTCAACGAAGAATCC 57.678 36.000 0.00 0.00 36.13 3.01
293 595 8.717821 TCTAGTCAAATTGATAACAGAAAACCG 58.282 33.333 0.00 0.00 0.00 4.44
319 621 7.310664 CGCCCGAAAAGAAGTATACTGATATA 58.689 38.462 6.06 0.00 0.00 0.86
321 623 8.923683 GCCCGAAAAGAAGTATACTGATATAAC 58.076 37.037 6.06 0.00 0.00 1.89
328 630 6.946583 AGAAGTATACTGATATAACTCGCCCA 59.053 38.462 6.06 0.00 0.00 5.36
333 635 4.215908 ACTGATATAACTCGCCCAAGAGA 58.784 43.478 0.62 0.00 40.57 3.10
337 639 2.579207 TAACTCGCCCAAGAGATTCG 57.421 50.000 0.62 0.00 40.57 3.34
406 716 2.629137 AGAAGCATGACATTTGCCAACA 59.371 40.909 0.00 0.00 41.06 3.33
412 723 5.996513 AGCATGACATTTGCCAACATTTTTA 59.003 32.000 0.00 0.00 41.06 1.52
413 724 6.655848 AGCATGACATTTGCCAACATTTTTAT 59.344 30.769 0.00 0.00 41.06 1.40
414 725 6.743627 GCATGACATTTGCCAACATTTTTATG 59.256 34.615 0.00 0.00 33.95 1.90
426 738 7.674564 CCAACATTTTTATGGCAATTACTTCG 58.325 34.615 0.00 0.00 0.00 3.79
449 761 2.971330 ACACCCATGGCAATTTCTTCAA 59.029 40.909 6.09 0.00 0.00 2.69
457 769 6.016943 CCATGGCAATTTCTTCAAAACACATT 60.017 34.615 0.00 0.00 0.00 2.71
495 807 8.922931 AACAAGGGATTTTGCTATGAAATTTT 57.077 26.923 0.00 0.00 0.00 1.82
557 887 1.089481 GCGAATGTCATCCCAGCGAA 61.089 55.000 0.00 0.00 0.00 4.70
577 907 2.967362 ACGTTCGCTGAATCATTACCA 58.033 42.857 0.00 0.00 0.00 3.25
587 917 9.168451 TCGCTGAATCATTACCATTTAACTTTA 57.832 29.630 0.00 0.00 0.00 1.85
588 918 9.950680 CGCTGAATCATTACCATTTAACTTTAT 57.049 29.630 0.00 0.00 0.00 1.40
608 1535 8.903820 ACTTTATTATGATTTCTTTCCCTTCCG 58.096 33.333 0.00 0.00 0.00 4.30
611 1538 2.711542 TGATTTCTTTCCCTTCCGCTC 58.288 47.619 0.00 0.00 0.00 5.03
622 1549 2.551071 CCCTTCCGCTCTCTTTGTCTTT 60.551 50.000 0.00 0.00 0.00 2.52
623 1550 2.739379 CCTTCCGCTCTCTTTGTCTTTC 59.261 50.000 0.00 0.00 0.00 2.62
637 1564 9.103861 CTCTTTGTCTTTCTATTAGGATGGAAC 57.896 37.037 0.00 0.00 33.16 3.62
663 1590 7.165812 CGTGTAACTTTTGAAGAAAATCTGGTG 59.834 37.037 0.00 0.00 30.59 4.17
668 1595 2.151202 TGAAGAAAATCTGGTGCGACC 58.849 47.619 0.00 0.00 39.22 4.79
718 1646 0.374758 CAAATCATGCTGTCGACCGG 59.625 55.000 14.12 0.00 0.00 5.28
728 1656 3.807538 TCGACCGGTACAGCGAGC 61.808 66.667 7.34 0.00 0.00 5.03
795 1724 2.033577 CGCGCGCCATAAAATAAGTGTA 60.034 45.455 27.72 0.00 0.00 2.90
824 1753 3.565764 TGATTCCATCTTAGCCACTGG 57.434 47.619 0.00 0.00 0.00 4.00
891 1820 1.082104 CGGAAAGCGCAAGAACACC 60.082 57.895 11.47 1.87 43.02 4.16
928 1880 4.215399 CGAGCTGGGTCTTGTTTCAAATTA 59.785 41.667 0.00 0.00 0.00 1.40
933 1885 5.606505 TGGGTCTTGTTTCAAATTAAAGGC 58.393 37.500 0.00 0.00 0.00 4.35
934 1886 5.365314 TGGGTCTTGTTTCAAATTAAAGGCT 59.635 36.000 0.00 0.00 0.00 4.58
935 1887 5.926542 GGGTCTTGTTTCAAATTAAAGGCTC 59.073 40.000 0.00 0.00 0.00 4.70
936 1888 6.239317 GGGTCTTGTTTCAAATTAAAGGCTCT 60.239 38.462 0.00 0.00 0.00 4.09
937 1889 6.863645 GGTCTTGTTTCAAATTAAAGGCTCTC 59.136 38.462 0.00 0.00 0.00 3.20
1148 2119 2.031012 CAAGCTCCAGGCACGTCA 59.969 61.111 0.00 0.00 44.79 4.35
1200 2198 5.962433 TCTTCGTCGTCCTAGATTGATTTT 58.038 37.500 0.00 0.00 0.00 1.82
1313 2325 1.738099 GCTGGTCACGTCGATGCTT 60.738 57.895 4.06 0.00 0.00 3.91
1316 2328 1.738099 GGTCACGTCGATGCTTGCT 60.738 57.895 4.06 0.00 0.00 3.91
1366 2378 1.168714 GAGGCCAAGGACATCAACAC 58.831 55.000 5.01 0.00 0.00 3.32
1417 2429 0.747283 CCGCAGAGGAGGTACGTACT 60.747 60.000 24.07 11.06 45.00 2.73
1449 2466 0.679505 CACGGTGTCCCTTCTCTTCA 59.320 55.000 0.00 0.00 0.00 3.02
1994 3321 2.260434 GAGAAGTACACCGCGCCA 59.740 61.111 0.00 0.00 0.00 5.69
2159 3486 1.000283 CTACGCATCCAGGATGACTCC 60.000 57.143 30.90 13.28 42.09 3.85
2201 3528 1.140312 TGGATATCTCCACCAAGGCC 58.860 55.000 2.05 0.00 46.95 5.19
2295 3622 1.509463 GTGTATGAGCCCGTCGACA 59.491 57.895 17.16 0.00 0.00 4.35
2401 3728 4.467795 CCTCAACTCCCAATAGACAAGAGA 59.532 45.833 0.00 0.00 0.00 3.10
2420 3751 5.529791 AGAGAACGATTCGAAAGAGAACAA 58.470 37.500 13.95 0.00 43.69 2.83
2428 3759 6.400091 CGATTCGAAAGAGAACAAAGACGAAT 60.400 38.462 0.00 0.00 46.51 3.34
2476 3836 6.476053 GGACCGATCTAGAGTTGTAATGTTTC 59.524 42.308 0.00 0.00 0.00 2.78
2579 3939 4.940654 TGCAAGTCGGATCAAACAATATCA 59.059 37.500 0.00 0.00 0.00 2.15
2585 3945 4.335315 TCGGATCAAACAATATCAGGCAAC 59.665 41.667 0.00 0.00 0.00 4.17
2625 3985 9.612620 ATCAGCTTTAAGATTTTTACGAAGTTG 57.387 29.630 0.00 0.00 37.78 3.16
2626 3986 8.073768 TCAGCTTTAAGATTTTTACGAAGTTGG 58.926 33.333 0.00 0.00 37.78 3.77
2627 3987 6.861572 AGCTTTAAGATTTTTACGAAGTTGGC 59.138 34.615 0.00 0.00 37.78 4.52
2628 3988 6.183359 GCTTTAAGATTTTTACGAAGTTGGCG 60.183 38.462 0.00 0.00 37.78 5.69
2629 3989 6.542574 TTAAGATTTTTACGAAGTTGGCGA 57.457 33.333 0.00 0.00 37.78 5.54
2630 3990 4.400036 AGATTTTTACGAAGTTGGCGAC 57.600 40.909 0.00 0.00 37.78 5.19
2631 3991 4.062991 AGATTTTTACGAAGTTGGCGACT 58.937 39.130 0.18 0.18 37.78 4.18
2632 3992 5.232463 AGATTTTTACGAAGTTGGCGACTA 58.768 37.500 8.05 0.00 37.78 2.59
2633 3993 5.873164 AGATTTTTACGAAGTTGGCGACTAT 59.127 36.000 8.05 0.00 37.78 2.12
2634 3994 5.520022 TTTTTACGAAGTTGGCGACTATC 57.480 39.130 8.05 7.31 37.78 2.08
2635 3995 3.853831 TTACGAAGTTGGCGACTATCA 57.146 42.857 8.05 0.00 37.78 2.15
2636 3996 2.279582 ACGAAGTTGGCGACTATCAG 57.720 50.000 8.05 2.83 37.78 2.90
2637 3997 0.924090 CGAAGTTGGCGACTATCAGC 59.076 55.000 8.05 0.00 37.72 4.26
2638 3998 1.469940 CGAAGTTGGCGACTATCAGCT 60.470 52.381 8.05 0.00 37.72 4.24
2639 3999 2.622436 GAAGTTGGCGACTATCAGCTT 58.378 47.619 8.05 0.00 37.72 3.74
2640 4000 2.770164 AGTTGGCGACTATCAGCTTT 57.230 45.000 5.34 0.00 36.65 3.51
2641 4001 3.887621 AGTTGGCGACTATCAGCTTTA 57.112 42.857 5.34 0.00 36.65 1.85
2642 4002 4.202245 AGTTGGCGACTATCAGCTTTAA 57.798 40.909 5.34 0.00 36.65 1.52
2643 4003 4.184629 AGTTGGCGACTATCAGCTTTAAG 58.815 43.478 5.34 0.00 36.65 1.85
2644 4004 4.081642 AGTTGGCGACTATCAGCTTTAAGA 60.082 41.667 5.34 0.00 36.65 2.10
2645 4005 4.672587 TGGCGACTATCAGCTTTAAGAT 57.327 40.909 0.00 0.00 0.00 2.40
2646 4006 5.023533 TGGCGACTATCAGCTTTAAGATT 57.976 39.130 0.00 0.00 0.00 2.40
2647 4007 5.428253 TGGCGACTATCAGCTTTAAGATTT 58.572 37.500 0.00 0.00 0.00 2.17
2648 4008 5.880332 TGGCGACTATCAGCTTTAAGATTTT 59.120 36.000 0.00 0.00 0.00 1.82
2649 4009 6.374333 TGGCGACTATCAGCTTTAAGATTTTT 59.626 34.615 0.00 0.00 0.00 1.94
2650 4010 7.551262 TGGCGACTATCAGCTTTAAGATTTTTA 59.449 33.333 0.00 0.00 0.00 1.52
2651 4011 7.851472 GGCGACTATCAGCTTTAAGATTTTTAC 59.149 37.037 0.00 0.00 0.00 2.01
2652 4012 7.579450 GCGACTATCAGCTTTAAGATTTTTACG 59.421 37.037 0.00 0.00 0.00 3.18
2653 4013 8.804743 CGACTATCAGCTTTAAGATTTTTACGA 58.195 33.333 0.00 0.00 0.00 3.43
2658 4018 9.612620 ATCAGCTTTAAGATTTTTACGAAGTTG 57.387 29.630 0.00 0.00 37.78 3.16
2659 4019 8.073768 TCAGCTTTAAGATTTTTACGAAGTTGG 58.926 33.333 0.00 0.00 37.78 3.77
2660 4020 6.861572 AGCTTTAAGATTTTTACGAAGTTGGC 59.138 34.615 0.00 0.00 37.78 4.52
2661 4021 6.183359 GCTTTAAGATTTTTACGAAGTTGGCG 60.183 38.462 0.00 0.00 37.78 5.69
2662 4022 6.542574 TTAAGATTTTTACGAAGTTGGCGA 57.457 33.333 0.00 0.00 37.78 5.54
2663 4023 4.400036 AGATTTTTACGAAGTTGGCGAC 57.600 40.909 0.00 0.00 37.78 5.19
2664 4024 4.062991 AGATTTTTACGAAGTTGGCGACT 58.937 39.130 0.18 0.18 37.78 4.18
2665 4025 5.232463 AGATTTTTACGAAGTTGGCGACTA 58.768 37.500 8.05 0.00 37.78 2.59
2666 4026 5.873164 AGATTTTTACGAAGTTGGCGACTAT 59.127 36.000 8.05 0.00 37.78 2.12
2667 4027 5.520022 TTTTTACGAAGTTGGCGACTATC 57.480 39.130 8.05 7.31 37.78 2.08
2668 4028 3.853831 TTACGAAGTTGGCGACTATCA 57.146 42.857 8.05 0.00 37.78 2.15
2669 4029 2.736144 ACGAAGTTGGCGACTATCAA 57.264 45.000 8.05 0.00 37.78 2.57
2670 4030 2.334838 ACGAAGTTGGCGACTATCAAC 58.665 47.619 8.05 0.00 37.78 3.18
2678 4038 6.663944 GTTGGCGACTATCAACTTTAAGAT 57.336 37.500 0.00 0.00 39.85 2.40
2679 4039 7.073342 GTTGGCGACTATCAACTTTAAGATT 57.927 36.000 0.00 0.00 39.85 2.40
2680 4040 7.527457 GTTGGCGACTATCAACTTTAAGATTT 58.473 34.615 0.00 0.00 39.85 2.17
2681 4041 7.681939 TGGCGACTATCAACTTTAAGATTTT 57.318 32.000 0.00 0.00 0.00 1.82
2682 4042 8.106247 TGGCGACTATCAACTTTAAGATTTTT 57.894 30.769 0.00 0.00 0.00 1.94
2683 4043 9.221933 TGGCGACTATCAACTTTAAGATTTTTA 57.778 29.630 0.00 0.00 0.00 1.52
2684 4044 9.486857 GGCGACTATCAACTTTAAGATTTTTAC 57.513 33.333 0.00 0.00 0.00 2.01
2685 4045 9.195831 GCGACTATCAACTTTAAGATTTTTACG 57.804 33.333 0.00 0.00 0.00 3.18
2705 4065 6.954254 TACGAAGTTGGCGACTAATCGGTG 62.954 50.000 25.06 6.28 44.72 4.94
2712 4072 1.217882 CGACTAATCGGTGGAATGGC 58.782 55.000 0.00 0.00 44.99 4.40
2726 4086 1.961394 GAATGGCATGGCTGATCATGT 59.039 47.619 21.08 0.00 44.54 3.21
2727 4087 2.963599 ATGGCATGGCTGATCATGTA 57.036 45.000 21.08 0.00 44.54 2.29
2746 4106 5.745312 TGTAGTCCATCTCACTCAAACAT 57.255 39.130 0.00 0.00 0.00 2.71
2748 4108 4.897509 AGTCCATCTCACTCAAACATCA 57.102 40.909 0.00 0.00 0.00 3.07
2755 4115 3.692593 TCTCACTCAAACATCATGCATGG 59.307 43.478 25.97 13.66 36.72 3.66
2761 4121 4.283337 TCAAACATCATGCATGGAAGGAT 58.717 39.130 25.97 9.34 36.72 3.24
2762 4122 4.098807 TCAAACATCATGCATGGAAGGATG 59.901 41.667 25.97 21.80 40.78 3.51
2934 4294 4.646492 GGGGTTCTCACTAAAATGATGCAT 59.354 41.667 0.00 0.00 0.00 3.96
2935 4295 5.450965 GGGGTTCTCACTAAAATGATGCATG 60.451 44.000 2.46 0.00 0.00 4.06
3005 4365 4.020307 TGATGACATGAGCAACTACTTCCA 60.020 41.667 0.00 0.00 0.00 3.53
3139 4499 8.424918 GGGTAATTTCTCATCAGTAGAAGATGA 58.575 37.037 5.82 5.82 46.96 2.92
3148 4508 8.347004 TCATCAGTAGAAGATGATCTATCCAC 57.653 38.462 0.00 0.00 44.98 4.02
3149 4509 8.169393 TCATCAGTAGAAGATGATCTATCCACT 58.831 37.037 0.00 0.00 44.98 4.00
3150 4510 7.994425 TCAGTAGAAGATGATCTATCCACTC 57.006 40.000 0.00 0.00 36.40 3.51
3151 4511 7.754624 TCAGTAGAAGATGATCTATCCACTCT 58.245 38.462 0.00 0.00 36.40 3.24
3152 4512 8.885346 TCAGTAGAAGATGATCTATCCACTCTA 58.115 37.037 0.00 0.00 36.40 2.43
3153 4513 9.685276 CAGTAGAAGATGATCTATCCACTCTAT 57.315 37.037 0.00 0.00 36.40 1.98
3154 4514 9.905713 AGTAGAAGATGATCTATCCACTCTATC 57.094 37.037 0.00 0.00 36.40 2.08
3155 4515 9.679661 GTAGAAGATGATCTATCCACTCTATCA 57.320 37.037 0.00 0.00 36.40 2.15
3160 4520 9.081204 AGATGATCTATCCACTCTATCATATGC 57.919 37.037 0.00 0.00 37.40 3.14
3161 4521 7.594351 TGATCTATCCACTCTATCATATGCC 57.406 40.000 0.00 0.00 0.00 4.40
3162 4522 6.264067 TGATCTATCCACTCTATCATATGCCG 59.736 42.308 0.00 0.00 0.00 5.69
3163 4523 5.755849 TCTATCCACTCTATCATATGCCGA 58.244 41.667 0.00 0.00 0.00 5.54
3164 4524 6.368805 TCTATCCACTCTATCATATGCCGAT 58.631 40.000 0.00 0.00 0.00 4.18
3165 4525 7.518188 TCTATCCACTCTATCATATGCCGATA 58.482 38.462 0.00 0.00 0.00 2.92
3349 4732 3.056393 TGGTACTCAAATCCACTACCACG 60.056 47.826 0.00 0.00 33.43 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 5.911280 CACAAGTGCATTTCAGTTTACTCAG 59.089 40.000 0.00 0.00 36.23 3.35
50 51 5.820131 CACAAGTGCATTTCAGTTTACTCA 58.180 37.500 0.00 0.00 36.23 3.41
69 70 3.787785 TCTAAGACTTGAACACGCACAA 58.212 40.909 0.00 0.00 0.00 3.33
72 73 4.319477 GCATTTCTAAGACTTGAACACGCA 60.319 41.667 0.00 0.00 0.00 5.24
75 76 4.712763 CCGCATTTCTAAGACTTGAACAC 58.287 43.478 0.00 0.00 0.00 3.32
89 90 2.099062 CACTCAGCGCCGCATTTC 59.901 61.111 13.36 0.00 0.00 2.17
107 108 5.930837 ATTTCTCTCTGGAGGAAGTAGTG 57.069 43.478 0.00 0.00 40.09 2.74
123 124 3.139077 CCGTGCCCCACTTATATTTCTC 58.861 50.000 0.00 0.00 31.34 2.87
136 137 2.437895 GCTAGAAACCCGTGCCCC 60.438 66.667 0.00 0.00 0.00 5.80
144 145 5.047235 TGGTCAGACTAAAGAGCTAGAAACC 60.047 44.000 0.00 0.00 33.63 3.27
158 159 4.509970 CACAATGTTCGTTTGGTCAGACTA 59.490 41.667 0.00 0.00 0.00 2.59
160 161 3.064820 ACACAATGTTCGTTTGGTCAGAC 59.935 43.478 0.00 0.00 0.00 3.51
162 163 3.691049 ACACAATGTTCGTTTGGTCAG 57.309 42.857 0.00 0.00 0.00 3.51
289 591 2.592287 TTCTTTTCGGGCGCGGTT 60.592 55.556 23.74 0.00 0.00 4.44
293 595 2.284417 CAGTATACTTCTTTTCGGGCGC 59.716 50.000 1.56 0.00 0.00 6.53
319 621 0.108138 CCGAATCTCTTGGGCGAGTT 60.108 55.000 0.00 0.00 32.83 3.01
321 623 1.227380 CCCGAATCTCTTGGGCGAG 60.227 63.158 0.00 0.00 35.82 5.03
328 630 1.276421 CACACCTGTCCCGAATCTCTT 59.724 52.381 0.00 0.00 0.00 2.85
333 635 0.472471 AACACACACCTGTCCCGAAT 59.528 50.000 0.00 0.00 0.00 3.34
337 639 0.463116 AACGAACACACACCTGTCCC 60.463 55.000 0.00 0.00 0.00 4.46
406 716 7.544217 GGTGTTCGAAGTAATTGCCATAAAAAT 59.456 33.333 0.00 0.00 0.00 1.82
412 723 2.752903 GGGTGTTCGAAGTAATTGCCAT 59.247 45.455 0.00 0.00 0.00 4.40
413 724 2.156098 GGGTGTTCGAAGTAATTGCCA 58.844 47.619 0.00 0.00 0.00 4.92
414 725 2.156098 TGGGTGTTCGAAGTAATTGCC 58.844 47.619 0.00 0.00 0.00 4.52
417 728 2.752903 GCCATGGGTGTTCGAAGTAATT 59.247 45.455 15.13 0.00 0.00 1.40
419 730 1.072489 TGCCATGGGTGTTCGAAGTAA 59.928 47.619 15.13 0.00 0.00 2.24
420 731 0.687920 TGCCATGGGTGTTCGAAGTA 59.312 50.000 15.13 0.00 0.00 2.24
421 732 0.179004 TTGCCATGGGTGTTCGAAGT 60.179 50.000 15.13 0.00 0.00 3.01
422 733 1.176527 ATTGCCATGGGTGTTCGAAG 58.823 50.000 15.13 0.00 0.00 3.79
426 738 3.006752 TGAAGAAATTGCCATGGGTGTTC 59.993 43.478 15.13 0.00 0.00 3.18
557 887 2.967362 TGGTAATGATTCAGCGAACGT 58.033 42.857 0.00 0.00 0.00 3.99
587 917 5.449553 AGCGGAAGGGAAAGAAATCATAAT 58.550 37.500 0.00 0.00 0.00 1.28
588 918 4.855340 AGCGGAAGGGAAAGAAATCATAA 58.145 39.130 0.00 0.00 0.00 1.90
590 920 3.054065 AGAGCGGAAGGGAAAGAAATCAT 60.054 43.478 0.00 0.00 0.00 2.45
591 921 2.305927 AGAGCGGAAGGGAAAGAAATCA 59.694 45.455 0.00 0.00 0.00 2.57
593 923 2.573915 AGAGAGCGGAAGGGAAAGAAAT 59.426 45.455 0.00 0.00 0.00 2.17
596 926 1.645710 AAGAGAGCGGAAGGGAAAGA 58.354 50.000 0.00 0.00 0.00 2.52
608 1535 7.440856 CCATCCTAATAGAAAGACAAAGAGAGC 59.559 40.741 0.00 0.00 0.00 4.09
611 1538 9.103861 GTTCCATCCTAATAGAAAGACAAAGAG 57.896 37.037 0.00 0.00 0.00 2.85
622 1549 7.414222 AAGTTACACGTTCCATCCTAATAGA 57.586 36.000 0.00 0.00 0.00 1.98
623 1550 8.388103 CAAAAGTTACACGTTCCATCCTAATAG 58.612 37.037 0.00 0.00 0.00 1.73
637 1564 7.165812 CACCAGATTTTCTTCAAAAGTTACACG 59.834 37.037 0.00 0.00 34.92 4.49
718 1646 1.139947 GAGTCCCTGCTCGCTGTAC 59.860 63.158 0.00 0.00 0.00 2.90
728 1656 0.969894 ACCAACTTCTCGAGTCCCTG 59.030 55.000 13.13 6.37 37.72 4.45
737 1665 2.418334 GGGTACCGATGACCAACTTCTC 60.418 54.545 5.65 0.00 40.86 2.87
804 1733 2.421952 GCCAGTGGCTAAGATGGAATCA 60.422 50.000 27.48 0.00 46.03 2.57
928 1880 0.908198 CTAGCAGTGGGAGAGCCTTT 59.092 55.000 0.00 0.00 0.00 3.11
933 1885 1.680735 CTAGTGCTAGCAGTGGGAGAG 59.319 57.143 31.09 18.01 0.00 3.20
934 1886 1.769026 CTAGTGCTAGCAGTGGGAGA 58.231 55.000 31.09 12.83 0.00 3.71
1148 2119 0.894141 AGACAATCGAGCTGCAGACT 59.106 50.000 20.43 14.36 0.00 3.24
1200 2198 5.939457 TCAAACACAATACACGTCACAAAA 58.061 33.333 0.00 0.00 0.00 2.44
1994 3321 2.361610 CCCCATTTGGCGCAGTCT 60.362 61.111 10.83 0.00 0.00 3.24
2201 3528 1.769098 CGATGAGCGCCTCCATGTTG 61.769 60.000 2.29 0.00 0.00 3.33
2295 3622 2.622452 CCTCTTCATTGGTGCCCTCATT 60.622 50.000 0.00 0.00 0.00 2.57
2309 3636 1.301716 GTGAGCCAACGCCTCTTCA 60.302 57.895 0.00 0.00 34.57 3.02
2401 3728 5.332355 CGTCTTTGTTCTCTTTCGAATCGTT 60.332 40.000 1.52 0.00 0.00 3.85
2420 3751 6.018669 GCATAGCAGCTAGTTTTATTCGTCTT 60.019 38.462 8.43 0.00 0.00 3.01
2451 3787 5.517322 ACATTACAACTCTAGATCGGTCC 57.483 43.478 0.00 0.00 0.00 4.46
2536 3896 3.942748 GCATCCATCGTTTTAGGTGGTAA 59.057 43.478 0.00 0.00 33.47 2.85
2579 3939 5.748402 TGATAATCATGAGACAAGTTGCCT 58.252 37.500 1.81 0.00 0.00 4.75
2585 3945 9.322773 TCTTAAAGCTGATAATCATGAGACAAG 57.677 33.333 0.09 0.00 0.00 3.16
2602 3962 6.861572 GCCAACTTCGTAAAAATCTTAAAGCT 59.138 34.615 0.00 0.00 0.00 3.74
2620 3980 2.770164 AAGCTGATAGTCGCCAACTT 57.230 45.000 0.00 0.00 39.55 2.66
2621 3981 2.770164 AAAGCTGATAGTCGCCAACT 57.230 45.000 0.00 0.00 42.33 3.16
2622 3982 4.181578 TCTTAAAGCTGATAGTCGCCAAC 58.818 43.478 0.00 0.00 0.00 3.77
2623 3983 4.465632 TCTTAAAGCTGATAGTCGCCAA 57.534 40.909 0.00 0.00 0.00 4.52
2624 3984 4.672587 ATCTTAAAGCTGATAGTCGCCA 57.327 40.909 0.00 0.00 0.00 5.69
2625 3985 5.993106 AAATCTTAAAGCTGATAGTCGCC 57.007 39.130 0.00 0.00 0.00 5.54
2626 3986 7.579450 CGTAAAAATCTTAAAGCTGATAGTCGC 59.421 37.037 0.00 0.00 0.00 5.19
2627 3987 8.804743 TCGTAAAAATCTTAAAGCTGATAGTCG 58.195 33.333 0.00 0.00 0.00 4.18
2632 3992 9.612620 CAACTTCGTAAAAATCTTAAAGCTGAT 57.387 29.630 0.00 0.00 0.00 2.90
2633 3993 8.073768 CCAACTTCGTAAAAATCTTAAAGCTGA 58.926 33.333 0.00 0.00 0.00 4.26
2634 3994 7.148967 GCCAACTTCGTAAAAATCTTAAAGCTG 60.149 37.037 0.00 0.00 0.00 4.24
2635 3995 6.861572 GCCAACTTCGTAAAAATCTTAAAGCT 59.138 34.615 0.00 0.00 0.00 3.74
2636 3996 6.183359 CGCCAACTTCGTAAAAATCTTAAAGC 60.183 38.462 0.00 0.00 0.00 3.51
2637 3997 7.059147 GTCGCCAACTTCGTAAAAATCTTAAAG 59.941 37.037 0.00 0.00 0.00 1.85
2638 3998 6.852345 GTCGCCAACTTCGTAAAAATCTTAAA 59.148 34.615 0.00 0.00 0.00 1.52
2639 3999 6.203338 AGTCGCCAACTTCGTAAAAATCTTAA 59.797 34.615 0.00 0.00 33.03 1.85
2640 4000 5.697633 AGTCGCCAACTTCGTAAAAATCTTA 59.302 36.000 0.00 0.00 33.03 2.10
2641 4001 4.514066 AGTCGCCAACTTCGTAAAAATCTT 59.486 37.500 0.00 0.00 33.03 2.40
2642 4002 4.062991 AGTCGCCAACTTCGTAAAAATCT 58.937 39.130 0.00 0.00 33.03 2.40
2643 4003 4.400036 AGTCGCCAACTTCGTAAAAATC 57.600 40.909 0.00 0.00 33.03 2.17
2644 4004 5.640357 TGATAGTCGCCAACTTCGTAAAAAT 59.360 36.000 0.00 0.00 39.55 1.82
2645 4005 4.989797 TGATAGTCGCCAACTTCGTAAAAA 59.010 37.500 0.00 0.00 39.55 1.94
2646 4006 4.558178 TGATAGTCGCCAACTTCGTAAAA 58.442 39.130 0.00 0.00 39.55 1.52
2647 4007 4.177165 TGATAGTCGCCAACTTCGTAAA 57.823 40.909 0.00 0.00 39.55 2.01
2648 4008 3.853831 TGATAGTCGCCAACTTCGTAA 57.146 42.857 0.00 0.00 39.55 3.18
2649 4009 3.504863 GTTGATAGTCGCCAACTTCGTA 58.495 45.455 0.00 0.00 39.55 3.43
2650 4010 2.334838 GTTGATAGTCGCCAACTTCGT 58.665 47.619 0.00 0.00 39.55 3.85
2655 4015 6.663944 ATCTTAAAGTTGATAGTCGCCAAC 57.336 37.500 0.00 0.00 42.02 3.77
2656 4016 7.681939 AAATCTTAAAGTTGATAGTCGCCAA 57.318 32.000 0.00 0.00 0.00 4.52
2657 4017 7.681939 AAAATCTTAAAGTTGATAGTCGCCA 57.318 32.000 0.00 0.00 0.00 5.69
2658 4018 9.486857 GTAAAAATCTTAAAGTTGATAGTCGCC 57.513 33.333 0.00 0.00 0.00 5.54
2659 4019 9.195831 CGTAAAAATCTTAAAGTTGATAGTCGC 57.804 33.333 0.00 0.00 0.00 5.19
2667 4027 8.476925 GCCAACTTCGTAAAAATCTTAAAGTTG 58.523 33.333 14.83 14.83 45.75 3.16
2668 4028 7.377662 CGCCAACTTCGTAAAAATCTTAAAGTT 59.622 33.333 0.00 0.00 36.27 2.66
2669 4029 6.854381 CGCCAACTTCGTAAAAATCTTAAAGT 59.146 34.615 0.00 0.00 0.00 2.66
2670 4030 7.059147 GTCGCCAACTTCGTAAAAATCTTAAAG 59.941 37.037 0.00 0.00 0.00 1.85
2671 4031 6.852345 GTCGCCAACTTCGTAAAAATCTTAAA 59.148 34.615 0.00 0.00 0.00 1.52
2672 4032 6.203338 AGTCGCCAACTTCGTAAAAATCTTAA 59.797 34.615 0.00 0.00 33.03 1.85
2673 4033 5.697633 AGTCGCCAACTTCGTAAAAATCTTA 59.302 36.000 0.00 0.00 33.03 2.10
2674 4034 4.514066 AGTCGCCAACTTCGTAAAAATCTT 59.486 37.500 0.00 0.00 33.03 2.40
2675 4035 4.062991 AGTCGCCAACTTCGTAAAAATCT 58.937 39.130 0.00 0.00 33.03 2.40
2676 4036 4.400036 AGTCGCCAACTTCGTAAAAATC 57.600 40.909 0.00 0.00 33.03 2.17
2677 4037 5.927954 TTAGTCGCCAACTTCGTAAAAAT 57.072 34.783 0.00 0.00 39.55 1.82
2678 4038 5.388682 CGATTAGTCGCCAACTTCGTAAAAA 60.389 40.000 0.00 0.00 41.49 1.94
2679 4039 4.090354 CGATTAGTCGCCAACTTCGTAAAA 59.910 41.667 0.00 0.00 41.49 1.52
2680 4040 3.609373 CGATTAGTCGCCAACTTCGTAAA 59.391 43.478 0.00 0.00 41.49 2.01
2681 4041 3.173599 CGATTAGTCGCCAACTTCGTAA 58.826 45.455 0.00 0.00 41.49 3.18
2682 4042 2.478370 CCGATTAGTCGCCAACTTCGTA 60.478 50.000 1.48 0.00 46.32 3.43
2683 4043 1.625616 CGATTAGTCGCCAACTTCGT 58.374 50.000 0.00 0.00 41.49 3.85
2684 4044 0.921347 CCGATTAGTCGCCAACTTCG 59.079 55.000 1.48 0.00 46.32 3.79
2685 4045 1.659098 CACCGATTAGTCGCCAACTTC 59.341 52.381 1.48 0.00 46.32 3.01
2705 4065 1.272490 CATGATCAGCCATGCCATTCC 59.728 52.381 0.09 0.00 37.68 3.01
2712 4072 3.480505 TGGACTACATGATCAGCCATG 57.519 47.619 0.00 0.00 46.90 3.66
2726 4086 6.343703 CATGATGTTTGAGTGAGATGGACTA 58.656 40.000 0.00 0.00 0.00 2.59
2727 4087 4.897509 TGATGTTTGAGTGAGATGGACT 57.102 40.909 0.00 0.00 0.00 3.85
2746 4106 7.464273 AGTATATTTCATCCTTCCATGCATGA 58.536 34.615 28.31 11.26 0.00 3.07
2748 4108 7.946219 TCAAGTATATTTCATCCTTCCATGCAT 59.054 33.333 0.00 0.00 0.00 3.96
2761 4121 7.867921 ACACCAACCCTATCAAGTATATTTCA 58.132 34.615 0.00 0.00 0.00 2.69
2762 4122 7.444487 GGACACCAACCCTATCAAGTATATTTC 59.556 40.741 0.00 0.00 0.00 2.17
2893 4253 3.118738 ACCCCTACATGCGAAGAGTTTAG 60.119 47.826 0.00 0.00 0.00 1.85
2934 4294 0.179040 GACAAAACTCCCGACCCACA 60.179 55.000 0.00 0.00 0.00 4.17
2935 4295 0.108019 AGACAAAACTCCCGACCCAC 59.892 55.000 0.00 0.00 0.00 4.61
3005 4365 3.636764 GACACCATGACAAAGTCCCTTTT 59.363 43.478 0.00 0.00 30.60 2.27
3016 4376 0.464036 GATAGCGGGACACCATGACA 59.536 55.000 0.00 0.00 36.13 3.58
3139 4499 6.368805 TCGGCATATGATAGAGTGGATAGAT 58.631 40.000 6.97 0.00 0.00 1.98
3140 4500 5.755849 TCGGCATATGATAGAGTGGATAGA 58.244 41.667 6.97 0.00 0.00 1.98
3141 4501 6.647334 ATCGGCATATGATAGAGTGGATAG 57.353 41.667 6.97 0.00 0.00 2.08
3142 4502 8.712228 ATTATCGGCATATGATAGAGTGGATA 57.288 34.615 6.97 0.00 30.49 2.59
3143 4503 7.609097 ATTATCGGCATATGATAGAGTGGAT 57.391 36.000 6.97 0.00 30.49 3.41
3144 4504 8.414003 GTTATTATCGGCATATGATAGAGTGGA 58.586 37.037 6.97 0.00 30.49 4.02
3145 4505 8.197439 TGTTATTATCGGCATATGATAGAGTGG 58.803 37.037 6.97 0.00 30.49 4.00
3146 4506 9.025020 GTGTTATTATCGGCATATGATAGAGTG 57.975 37.037 6.97 0.00 30.49 3.51
3147 4507 8.198109 GGTGTTATTATCGGCATATGATAGAGT 58.802 37.037 6.97 0.00 30.49 3.24
3148 4508 8.197439 TGGTGTTATTATCGGCATATGATAGAG 58.803 37.037 6.97 0.00 30.49 2.43
3149 4509 8.073467 TGGTGTTATTATCGGCATATGATAGA 57.927 34.615 6.97 2.27 30.49 1.98
3150 4510 8.893219 ATGGTGTTATTATCGGCATATGATAG 57.107 34.615 6.97 0.00 30.49 2.08
3151 4511 9.325198 GAATGGTGTTATTATCGGCATATGATA 57.675 33.333 6.97 0.00 0.00 2.15
3152 4512 8.049117 AGAATGGTGTTATTATCGGCATATGAT 58.951 33.333 6.97 0.00 0.00 2.45
3153 4513 7.394016 AGAATGGTGTTATTATCGGCATATGA 58.606 34.615 6.97 0.00 0.00 2.15
3154 4514 7.550551 AGAGAATGGTGTTATTATCGGCATATG 59.449 37.037 0.00 0.00 34.39 1.78
3155 4515 7.624549 AGAGAATGGTGTTATTATCGGCATAT 58.375 34.615 0.00 0.00 34.39 1.78
3156 4516 7.004555 AGAGAATGGTGTTATTATCGGCATA 57.995 36.000 0.00 0.00 34.39 3.14
3157 4517 5.869579 AGAGAATGGTGTTATTATCGGCAT 58.130 37.500 0.00 0.00 34.39 4.40
3158 4518 5.290493 AGAGAATGGTGTTATTATCGGCA 57.710 39.130 0.00 0.00 34.39 5.69
3159 4519 7.148407 CCATAAGAGAATGGTGTTATTATCGGC 60.148 40.741 0.00 0.00 41.38 5.54
3160 4520 8.094548 TCCATAAGAGAATGGTGTTATTATCGG 58.905 37.037 2.98 0.00 45.67 4.18
3161 4521 8.926710 GTCCATAAGAGAATGGTGTTATTATCG 58.073 37.037 2.98 0.00 45.67 2.92
3162 4522 9.220767 GGTCCATAAGAGAATGGTGTTATTATC 57.779 37.037 2.98 0.00 45.67 1.75
3163 4523 8.723365 TGGTCCATAAGAGAATGGTGTTATTAT 58.277 33.333 2.98 0.00 45.67 1.28
3164 4524 8.096621 TGGTCCATAAGAGAATGGTGTTATTA 57.903 34.615 2.98 0.00 45.67 0.98
3165 4525 6.969043 TGGTCCATAAGAGAATGGTGTTATT 58.031 36.000 2.98 0.00 45.67 1.40
3282 4665 3.065371 CGAGGCAACAACCAAAGATATCC 59.935 47.826 0.00 0.00 41.41 2.59
3349 4732 3.048337 TCCACGTACATTTCCAAGTCC 57.952 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.