Multiple sequence alignment - TraesCS1A01G234600

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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 TraesCS1A01G234600 chr1A 100.000 5799 0 0 1 5799 410151973 410157771 0.000000e+00 10709.0
1 TraesCS1A01G234600 chr1A 100.000 28 0 0 2530 2557 494028053 494028080 1.100000e-02 52.8
2 TraesCS1A01G234600 chr1B 92.621 4689 200 67 1175 5799 441388707 441384101 0.000000e+00 6608.0
3 TraesCS1A01G234600 chr1B 90.312 1218 82 16 1 1210 441389891 441388702 0.000000e+00 1563.0
4 TraesCS1A01G234600 chr1D 91.371 3326 136 49 1 3256 326913360 326910116 0.000000e+00 4412.0
5 TraesCS1A01G234600 chr1D 95.303 1895 68 14 3286 5175 326909898 326908020 0.000000e+00 2987.0
6 TraesCS1A01G234600 chr1D 91.653 611 36 3 5203 5799 326908023 326907414 0.000000e+00 832.0
7 TraesCS1A01G234600 chr7D 91.717 1002 76 6 3710 4705 635517896 635516896 0.000000e+00 1384.0
8 TraesCS1A01G234600 chr7D 78.222 450 38 18 1085 1495 635520423 635519995 3.490000e-57 233.0
9 TraesCS1A01G234600 chr7D 97.059 34 1 0 2137 2170 635519461 635519428 2.260000e-04 58.4
10 TraesCS1A01G234600 chr7A 91.420 1014 76 5 3691 4694 730504558 730505570 0.000000e+00 1380.0
11 TraesCS1A01G234600 chr7A 78.049 656 97 17 372 1012 730501139 730501762 2.550000e-98 370.0
12 TraesCS1A01G234600 chr7A 88.679 106 9 2 1086 1191 730527577 730527679 6.100000e-25 126.0
13 TraesCS1A01G234600 chr7A 84.466 103 6 3 1079 1181 730501805 730501897 6.190000e-15 93.5
14 TraesCS1A01G234600 chr7A 100.000 36 0 0 2135 2170 730502992 730503027 3.750000e-07 67.6
15 TraesCS1A01G234600 chr7B 88.525 1037 107 9 3680 4706 740260978 740262012 0.000000e+00 1245.0
16 TraesCS1A01G234600 chr7B 92.794 569 38 3 4138 4705 740301807 740302373 0.000000e+00 821.0
17 TraesCS1A01G234600 chr7B 89.943 527 52 1 4176 4702 740239657 740240182 0.000000e+00 678.0
18 TraesCS1A01G234600 chr7B 88.822 501 49 4 3691 4185 740238691 740239190 4.970000e-170 608.0
19 TraesCS1A01G234600 chr7B 89.069 494 39 7 3691 4174 740763887 740764375 2.990000e-167 599.0
20 TraesCS1A01G234600 chr7B 88.664 494 41 7 3691 4174 740723026 740723514 6.470000e-164 588.0
21 TraesCS1A01G234600 chr7B 79.109 943 97 62 1085 1977 740720389 740721281 5.080000e-155 558.0
22 TraesCS1A01G234600 chr7B 79.076 693 62 34 1082 1741 740286751 740287393 3.260000e-107 399.0
23 TraesCS1A01G234600 chr7B 77.076 554 72 23 372 909 740254586 740255100 9.580000e-68 268.0
24 TraesCS1A01G234600 chr7B 81.433 307 22 13 1085 1360 740758176 740758478 9.780000e-53 219.0
25 TraesCS1A01G234600 chr7B 81.818 143 7 9 3442 3573 740238155 740238289 1.030000e-17 102.0
26 TraesCS1A01G234600 chr7B 92.063 63 3 1 2494 2556 740300701 740300761 2.880000e-13 87.9
27 TraesCS1A01G234600 chr7B 92.063 63 3 1 2494 2556 740721954 740722014 2.880000e-13 87.9
28 TraesCS1A01G234600 chr7B 96.154 52 2 0 1085 1136 740255907 740255958 1.040000e-12 86.1
29 TraesCS1A01G234600 chr7B 96.078 51 2 0 2506 2556 740237709 740237759 3.720000e-12 84.2
30 TraesCS1A01G234600 chr7B 100.000 34 0 0 2137 2170 740240861 740240894 4.850000e-06 63.9
31 TraesCS1A01G234600 chr7B 100.000 34 0 0 2137 2170 740721402 740721435 4.850000e-06 63.9
32 TraesCS1A01G234600 chr3D 73.624 872 190 27 3769 4623 575759765 575758917 3.400000e-77 300.0
33 TraesCS1A01G234600 chr3D 82.955 176 28 2 4448 4622 578242883 578242709 2.160000e-34 158.0


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 TraesCS1A01G234600 chr1A 410151973 410157771 5798 False 10709.000000 10709 100.000000 1 5799 1 chr1A.!!$F1 5798
1 TraesCS1A01G234600 chr1B 441384101 441389891 5790 True 4085.500000 6608 91.466500 1 5799 2 chr1B.!!$R1 5798
2 TraesCS1A01G234600 chr1D 326907414 326913360 5946 True 2743.666667 4412 92.775667 1 5799 3 chr1D.!!$R1 5798
3 TraesCS1A01G234600 chr7D 635516896 635520423 3527 True 558.466667 1384 88.999333 1085 4705 3 chr7D.!!$R1 3620
4 TraesCS1A01G234600 chr7A 730501139 730505570 4431 False 477.775000 1380 88.483750 372 4694 4 chr7A.!!$F2 4322
5 TraesCS1A01G234600 chr7B 740260978 740262012 1034 False 1245.000000 1245 88.525000 3680 4706 1 chr7B.!!$F1 1026
6 TraesCS1A01G234600 chr7B 740300701 740302373 1672 False 454.450000 821 92.428500 2494 4705 2 chr7B.!!$F7 2211
7 TraesCS1A01G234600 chr7B 740286751 740287393 642 False 399.000000 399 79.076000 1082 1741 1 chr7B.!!$F2 659
8 TraesCS1A01G234600 chr7B 740720389 740723514 3125 False 324.450000 588 89.959000 1085 4174 4 chr7B.!!$F8 3089
9 TraesCS1A01G234600 chr7B 740237709 740240894 3185 False 307.220000 678 91.332200 2137 4702 5 chr7B.!!$F5 2565
10 TraesCS1A01G234600 chr3D 575758917 575759765 848 True 300.000000 300 73.624000 3769 4623 1 chr3D.!!$R1 854

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
551 554 0.237235 CAACAAGGCTTCGCGCTTTA 59.763 50.000 5.56 0.00 35.52 1.85 F
2085 2445 0.106569 TGCCATGCTAATCACCCAGG 60.107 55.000 0.00 0.00 0.00 4.45 F
3094 3723 0.040157 TGCACAGTACGTCACGGTAC 60.040 55.000 0.35 1.89 42.41 3.34 F
3096 3725 0.592637 CACAGTACGTCACGGTACCA 59.407 55.000 13.54 0.00 42.95 3.25 F
3097 3726 1.001487 CACAGTACGTCACGGTACCAA 60.001 52.381 13.54 0.00 42.95 3.67 F
3099 3728 1.267806 CAGTACGTCACGGTACCAACT 59.732 52.381 13.54 0.45 42.95 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2513 0.108615 CTAGGGCGACACTGTCAAGG 60.109 60.000 9.84 0.00 32.09 3.61 R
3389 4221 0.025898 GGCCGATTCGCGACTTAAAC 59.974 55.000 9.15 0.00 44.57 2.01 R
4695 6776 0.656259 CTACGTACGCAGCTAGCTCA 59.344 55.000 16.15 0.00 42.61 4.26 R
4710 6791 1.297664 ACGGACACTAGCTAGCTACG 58.702 55.000 20.67 21.95 0.00 3.51 R
4714 6795 2.030981 GGACATACGGACACTAGCTAGC 60.031 54.545 20.91 6.62 0.00 3.42 R
5084 7264 3.526931 TGTATCTTGGAGCTAGTGTGC 57.473 47.619 0.00 0.00 0.00 4.57 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
33 34 7.749666 TCTATGGCAATTCCTAATAAAGCTCT 58.250 34.615 0.00 0.00 35.26 4.09
35 36 7.666063 ATGGCAATTCCTAATAAAGCTCTTT 57.334 32.000 0.00 0.27 34.66 2.52
174 176 8.740123 TTAAAGTGGTTCAAGTAATTCTGTGA 57.260 30.769 0.00 0.00 0.00 3.58
241 243 9.844790 ACACAAATGTTCTTATGACACATATTG 57.155 29.630 0.00 15.19 34.46 1.90
321 323 8.824756 TCAATATAGATCCCACTATGAGGTAC 57.175 38.462 0.00 0.00 35.19 3.34
322 324 8.398743 TCAATATAGATCCCACTATGAGGTACA 58.601 37.037 0.00 0.00 35.19 2.90
323 325 8.690884 CAATATAGATCCCACTATGAGGTACAG 58.309 40.741 0.00 0.00 35.19 2.74
324 326 4.544564 AGATCCCACTATGAGGTACAGT 57.455 45.455 0.00 0.00 0.00 3.55
325 327 5.664815 AGATCCCACTATGAGGTACAGTA 57.335 43.478 0.00 0.00 0.00 2.74
326 328 5.636123 AGATCCCACTATGAGGTACAGTAG 58.364 45.833 0.00 0.00 0.00 2.57
327 329 4.875578 TCCCACTATGAGGTACAGTAGT 57.124 45.455 0.00 0.00 0.00 2.73
328 330 5.981494 TCCCACTATGAGGTACAGTAGTA 57.019 43.478 0.00 0.00 0.00 1.82
329 331 6.331577 TCCCACTATGAGGTACAGTAGTAA 57.668 41.667 0.00 0.00 30.67 2.24
330 332 6.919158 TCCCACTATGAGGTACAGTAGTAAT 58.081 40.000 0.00 0.00 30.67 1.89
363 365 2.158449 GTGACGAAAGGCTTCTGATGTG 59.842 50.000 0.00 0.00 42.42 3.21
364 366 1.129437 GACGAAAGGCTTCTGATGTGC 59.871 52.381 0.00 0.00 34.96 4.57
378 380 4.125703 CTGATGTGCTACTCCAAATCTCC 58.874 47.826 0.00 0.00 31.93 3.71
394 396 3.343941 TCTCCTTAAATTGACCGTGGG 57.656 47.619 0.00 0.00 0.00 4.61
443 446 7.919091 TCCTTTGTATATATGTCACTTCACGAC 59.081 37.037 0.00 0.00 0.00 4.34
487 490 2.158959 CCGTAGCGCCAGTTCTTCG 61.159 63.158 2.29 0.00 0.00 3.79
489 492 1.674611 CGTAGCGCCAGTTCTTCGTG 61.675 60.000 2.29 0.00 0.00 4.35
490 493 0.666577 GTAGCGCCAGTTCTTCGTGT 60.667 55.000 2.29 0.00 0.00 4.49
551 554 0.237235 CAACAAGGCTTCGCGCTTTA 59.763 50.000 5.56 0.00 35.52 1.85
653 657 3.861276 AAGACGTGAACATATCCGACA 57.139 42.857 0.00 0.00 0.00 4.35
659 663 1.546923 TGAACATATCCGACACCACGT 59.453 47.619 0.00 0.00 0.00 4.49
696 700 5.765182 ACCTAGAAACTTCACTTTCATGGTG 59.235 40.000 0.00 0.00 36.99 4.17
858 873 2.047179 GAGAAGGGGGTGACGCAC 60.047 66.667 1.14 0.00 46.93 5.34
997 1021 4.740822 GCCCCGTTGTGGCCTCAT 62.741 66.667 8.61 0.00 43.33 2.90
1022 1046 7.378181 TCAGAAAAGAAACAACAAGAGCTTTT 58.622 30.769 0.00 0.00 38.01 2.27
1121 1164 0.391661 TTGCCTCCATGTTCGCTCTC 60.392 55.000 0.00 0.00 0.00 3.20
1136 1179 2.587194 CTCGCATTGCTCCTCGGG 60.587 66.667 7.12 0.00 0.00 5.14
1283 1410 9.100895 GCTTAGAAGATAGTAATACGTACGTTG 57.899 37.037 27.92 0.00 37.81 4.10
1334 1610 2.850695 AGCTAGGTAAGGTAGCCAGT 57.149 50.000 0.00 0.00 43.44 4.00
1335 1611 2.668625 AGCTAGGTAAGGTAGCCAGTC 58.331 52.381 0.00 0.00 43.44 3.51
1381 1657 0.250513 AATCTCTCTCCCACCAACGC 59.749 55.000 0.00 0.00 0.00 4.84
1490 1778 3.006940 CAGTCGCATGGTAAAGCCTAAA 58.993 45.455 0.00 0.00 38.35 1.85
1514 1804 3.827898 CCGCCGGTCTCACTCTCC 61.828 72.222 1.90 0.00 0.00 3.71
1560 1852 5.815581 TGGGAGCACAGTAACTTTTCATAT 58.184 37.500 0.00 0.00 0.00 1.78
1630 1927 7.038659 CACTAAAATAGTCAGGAGTCTTGGAG 58.961 42.308 1.97 0.00 36.76 3.86
1713 2015 5.618395 GTGTAATCGACCTTCGTTGTTTTTC 59.382 40.000 0.00 0.00 41.35 2.29
1729 2031 7.414762 CGTTGTTTTTCTCTAGGGAAGAAAACA 60.415 37.037 22.85 22.85 40.04 2.83
1819 2128 4.923415 AGGGGAAACATTGAAAGAGGTAG 58.077 43.478 0.00 0.00 0.00 3.18
1820 2129 4.017126 GGGGAAACATTGAAAGAGGTAGG 58.983 47.826 0.00 0.00 0.00 3.18
1821 2130 4.263771 GGGGAAACATTGAAAGAGGTAGGA 60.264 45.833 0.00 0.00 0.00 2.94
1892 2201 9.543783 AACGATATTTCTAGGATAGTTTCAACC 57.456 33.333 0.00 0.00 40.38 3.77
1915 2228 8.429493 ACCGTTTAACTATAAACCAATCTAGC 57.571 34.615 6.02 0.00 45.27 3.42
1964 2277 3.930634 AAGCTTGCAAATGAAGTCTCC 57.069 42.857 0.00 0.00 0.00 3.71
2073 2400 1.093159 CTCTTTCTCCAGTGCCATGC 58.907 55.000 0.00 0.00 0.00 4.06
2082 2442 1.027357 CAGTGCCATGCTAATCACCC 58.973 55.000 0.00 0.00 0.00 4.61
2085 2445 0.106569 TGCCATGCTAATCACCCAGG 60.107 55.000 0.00 0.00 0.00 4.45
2108 2491 6.701145 GAAGTTTTTCTTCTTCTTCCCTGT 57.299 37.500 0.00 0.00 46.36 4.00
2110 2493 7.569639 AAGTTTTTCTTCTTCTTCCCTGTAC 57.430 36.000 0.00 0.00 0.00 2.90
2234 2618 2.738521 CTGAACCACCCGTCGCTG 60.739 66.667 0.00 0.00 0.00 5.18
2248 2632 2.092838 CGTCGCTGACCATCTTTTTCTC 59.907 50.000 3.65 0.00 0.00 2.87
2249 2633 2.416893 GTCGCTGACCATCTTTTTCTCC 59.583 50.000 0.00 0.00 0.00 3.71
2342 2734 0.745468 GTCCGGTGGTCCTACTCATC 59.255 60.000 0.00 0.00 0.00 2.92
2375 2767 0.321653 ACCGCCACTGTTCCATTCTC 60.322 55.000 0.00 0.00 0.00 2.87
2399 2791 8.948853 TCTAAGTTTAACGAAAATGATTGCTG 57.051 30.769 0.00 0.00 0.00 4.41
2400 2792 8.020819 TCTAAGTTTAACGAAAATGATTGCTGG 58.979 33.333 0.00 0.00 0.00 4.85
2401 2793 6.084326 AGTTTAACGAAAATGATTGCTGGT 57.916 33.333 0.00 0.00 0.00 4.00
2431 2823 9.733219 GCTAGTTATAGTAACTAACTCACTTGG 57.267 37.037 9.95 0.00 39.50 3.61
2556 3174 2.430332 CCAAGTTTGGTCTGCCTGAAAA 59.570 45.455 2.66 0.00 43.43 2.29
2621 3242 0.537143 TGCTAGTGGTTGGCACTTGG 60.537 55.000 0.00 0.00 38.49 3.61
2662 3283 3.187700 GAGGATTAAGTGGCGTGTACTG 58.812 50.000 0.00 0.00 0.00 2.74
2708 3329 4.113354 GTGAGCTAGACCGTTAATTGGAG 58.887 47.826 0.00 0.00 0.00 3.86
2867 3493 4.402829 GCATGAGGTCTCTACTCTCCATA 58.597 47.826 0.00 0.00 35.98 2.74
2877 3505 8.691797 GGTCTCTACTCTCCATATATTCATTCC 58.308 40.741 0.00 0.00 0.00 3.01
2878 3506 9.474313 GTCTCTACTCTCCATATATTCATTCCT 57.526 37.037 0.00 0.00 0.00 3.36
2949 3577 2.586648 CCCCCTACAATATTCCTGGC 57.413 55.000 0.00 0.00 0.00 4.85
2998 3626 0.320073 TGCCGTGCAAGTACTACACC 60.320 55.000 18.41 9.53 34.76 4.16
3004 3632 4.691685 CCGTGCAAGTACTACACCATTTAA 59.308 41.667 18.41 0.00 0.00 1.52
3015 3643 6.431722 ACTACACCATTTAAGCCATACCATT 58.568 36.000 0.00 0.00 0.00 3.16
3016 3644 6.895204 ACTACACCATTTAAGCCATACCATTT 59.105 34.615 0.00 0.00 0.00 2.32
3017 3645 5.976458 ACACCATTTAAGCCATACCATTTG 58.024 37.500 0.00 0.00 0.00 2.32
3018 3646 5.719085 ACACCATTTAAGCCATACCATTTGA 59.281 36.000 0.00 0.00 0.00 2.69
3019 3647 6.383726 ACACCATTTAAGCCATACCATTTGAT 59.616 34.615 0.00 0.00 0.00 2.57
3020 3648 7.092935 ACACCATTTAAGCCATACCATTTGATT 60.093 33.333 0.00 0.00 0.00 2.57
3021 3649 7.225145 CACCATTTAAGCCATACCATTTGATTG 59.775 37.037 0.00 0.00 0.00 2.67
3022 3650 6.707161 CCATTTAAGCCATACCATTTGATTGG 59.293 38.462 0.00 0.00 42.82 3.16
3024 3652 2.138596 GCCATACCATTTGATTGGCG 57.861 50.000 0.00 0.00 42.97 5.69
3025 3653 1.680735 GCCATACCATTTGATTGGCGA 59.319 47.619 0.00 0.00 42.97 5.54
3045 3673 5.493735 GCGATTGCATTCTTAAGAGTACAC 58.506 41.667 5.12 0.00 42.15 2.90
3089 3718 5.492854 CATAATTGATGCACAGTACGTCAC 58.507 41.667 0.00 0.00 32.91 3.67
3090 3719 1.414378 TTGATGCACAGTACGTCACG 58.586 50.000 0.00 0.00 32.91 4.35
3091 3720 0.388006 TGATGCACAGTACGTCACGG 60.388 55.000 0.35 0.00 0.00 4.94
3092 3721 0.388134 GATGCACAGTACGTCACGGT 60.388 55.000 0.35 0.00 35.80 4.83
3093 3722 0.883153 ATGCACAGTACGTCACGGTA 59.117 50.000 0.35 0.00 33.43 4.02
3094 3723 0.040157 TGCACAGTACGTCACGGTAC 60.040 55.000 0.35 1.89 42.41 3.34
3095 3724 0.730494 GCACAGTACGTCACGGTACC 60.730 60.000 0.35 0.16 42.95 3.34
3096 3725 0.592637 CACAGTACGTCACGGTACCA 59.407 55.000 13.54 0.00 42.95 3.25
3097 3726 1.001487 CACAGTACGTCACGGTACCAA 60.001 52.381 13.54 0.00 42.95 3.67
3099 3728 1.267806 CAGTACGTCACGGTACCAACT 59.732 52.381 13.54 0.45 42.95 3.16
3100 3729 2.483877 CAGTACGTCACGGTACCAACTA 59.516 50.000 13.54 0.00 42.95 2.24
3108 3737 3.575256 TCACGGTACCAACTATCAAGTGT 59.425 43.478 13.54 0.00 35.62 3.55
3112 3741 4.251268 GGTACCAACTATCAAGTGTGACC 58.749 47.826 7.15 0.00 36.31 4.02
3120 3749 5.794894 ACTATCAAGTGTGACCCTTTACTG 58.205 41.667 0.00 0.00 36.31 2.74
3173 3804 6.319911 GCAAATCAGCTAGGGTAAAAGATTCT 59.680 38.462 0.00 0.00 0.00 2.40
3257 4075 8.391106 GCCAAAGCTATATATTTATCCAGTTCG 58.609 37.037 0.00 0.00 35.50 3.95
3277 4095 7.435192 CAGTTCGTTTAAATTTTCTCCTTGCTT 59.565 33.333 0.00 0.00 0.00 3.91
3405 4237 3.986128 ACATTGTTTAAGTCGCGAATCG 58.014 40.909 12.06 0.00 40.15 3.34
3550 4702 1.269778 GCCAACAGGTCAAAAGGCTTC 60.270 52.381 0.00 0.00 39.02 3.86
3589 4852 1.597937 CGCCGCCATTCTTGCTTATTC 60.598 52.381 0.00 0.00 0.00 1.75
3596 4859 5.402398 GCCATTCTTGCTTATTCGTTTCTT 58.598 37.500 0.00 0.00 0.00 2.52
3599 4862 7.095649 GCCATTCTTGCTTATTCGTTTCTTTTT 60.096 33.333 0.00 0.00 0.00 1.94
3688 5274 6.528072 GTGCTAGCTTGGTGTGAATAATTTTC 59.472 38.462 17.23 0.00 0.00 2.29
3693 5281 7.260603 AGCTTGGTGTGAATAATTTTCTATGC 58.739 34.615 0.00 0.00 0.00 3.14
3697 5285 4.976116 GTGTGAATAATTTTCTATGCGGCC 59.024 41.667 0.00 0.00 0.00 6.13
3750 5342 7.739498 AACTAACCAAAGTTACATGTACCTG 57.261 36.000 4.68 0.80 37.93 4.00
3752 5344 4.367039 ACCAAAGTTACATGTACCTGCT 57.633 40.909 4.68 0.00 0.00 4.24
3754 5346 5.871834 ACCAAAGTTACATGTACCTGCTTA 58.128 37.500 4.68 0.00 0.00 3.09
4694 6775 3.132289 CGTCTACCCCATTAGCTTCTGAA 59.868 47.826 0.00 0.00 0.00 3.02
4695 6776 4.202264 CGTCTACCCCATTAGCTTCTGAAT 60.202 45.833 0.00 0.00 0.00 2.57
4811 6974 5.049405 GCACATTATGTATTGTACAGGGCTC 60.049 44.000 0.00 0.00 42.77 4.70
4959 7137 3.678915 TCATGCATTTGATACGCACAG 57.321 42.857 0.00 0.00 38.73 3.66
5109 7289 5.980116 CACACTAGCTCCAAGATACATGTAC 59.020 44.000 7.96 2.64 0.00 2.90
5114 7294 7.780745 ACTAGCTCCAAGATACATGTACTAGTT 59.219 37.037 16.74 8.98 34.49 2.24
5147 7327 7.554118 ACAATTAATCACATCCCACTACAGAAG 59.446 37.037 0.00 0.00 0.00 2.85
5149 7329 5.505181 AATCACATCCCACTACAGAAGTT 57.495 39.130 0.00 0.00 35.76 2.66
5205 7411 6.311935 TGGTACATGAGCTCGTAAATAAACAC 59.688 38.462 8.44 0.00 0.00 3.32
5241 7447 1.153229 GTAACGGGTGGCCCAGATC 60.153 63.158 0.00 0.00 45.83 2.75
5249 7455 0.811616 GTGGCCCAGATCGATGTCAC 60.812 60.000 0.54 2.02 0.00 3.67
5281 7487 3.342370 ATTCGCGCGTGCTCTGAGA 62.342 57.895 30.98 3.31 39.65 3.27
5289 7495 2.283173 TGCTCTGAGAGGCACGGA 60.283 61.111 12.01 0.00 33.23 4.69
5323 7540 1.529865 CGCACGATGTAGACGATCCTA 59.470 52.381 0.00 0.00 34.70 2.94
5340 7557 5.470098 CGATCCTACCCATACCATTTTCTTG 59.530 44.000 0.00 0.00 0.00 3.02
5341 7558 5.789574 TCCTACCCATACCATTTTCTTGT 57.210 39.130 0.00 0.00 0.00 3.16
5361 7578 7.175104 TCTTGTTTTACTGCTCCCAAATCTAT 58.825 34.615 0.00 0.00 0.00 1.98
5437 7659 1.784525 GCAGTAGGTATCATCCGTGC 58.215 55.000 0.00 0.00 0.00 5.34
5467 7689 3.373130 TGGATACGTATATCTCGCCGAAG 59.627 47.826 8.34 0.00 37.85 3.79
5537 7759 5.421374 ACCCACAGTGAAGATAAGTAGTACC 59.579 44.000 0.62 0.00 0.00 3.34
5541 7763 5.657302 ACAGTGAAGATAAGTAGTACCCCTG 59.343 44.000 0.00 0.00 0.00 4.45
5581 7803 8.585471 AGAAAATGGTGAGTGTGAATTGATAT 57.415 30.769 0.00 0.00 0.00 1.63
5646 7868 9.875691 ATTTATTCCAAGGAATTTTCAAGTAGC 57.124 29.630 18.65 0.00 41.55 3.58
5685 7910 2.906047 GCTAGCCAGCTAACCGATG 58.094 57.895 2.29 0.00 44.93 3.84
5709 7934 2.419297 GCGGATGAGGATTTGACAGACT 60.419 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 297 9.256228 GTACCTCATAGTGGGATCTATATTGAA 57.744 37.037 0.00 0.00 0.00 2.69
296 298 8.398743 TGTACCTCATAGTGGGATCTATATTGA 58.601 37.037 0.00 0.00 0.00 2.57
297 299 8.595362 TGTACCTCATAGTGGGATCTATATTG 57.405 38.462 0.00 0.00 0.00 1.90
298 300 8.402683 ACTGTACCTCATAGTGGGATCTATATT 58.597 37.037 0.00 0.00 0.00 1.28
299 301 7.945278 ACTGTACCTCATAGTGGGATCTATAT 58.055 38.462 0.00 0.00 0.00 0.86
321 323 9.286946 CGTCACTCTACCTTTTAATTACTACTG 57.713 37.037 0.00 0.00 0.00 2.74
322 324 9.236006 TCGTCACTCTACCTTTTAATTACTACT 57.764 33.333 0.00 0.00 0.00 2.57
323 325 9.846248 TTCGTCACTCTACCTTTTAATTACTAC 57.154 33.333 0.00 0.00 0.00 2.73
325 327 9.420551 CTTTCGTCACTCTACCTTTTAATTACT 57.579 33.333 0.00 0.00 0.00 2.24
326 328 8.654215 CCTTTCGTCACTCTACCTTTTAATTAC 58.346 37.037 0.00 0.00 0.00 1.89
327 329 7.332678 GCCTTTCGTCACTCTACCTTTTAATTA 59.667 37.037 0.00 0.00 0.00 1.40
328 330 6.148976 GCCTTTCGTCACTCTACCTTTTAATT 59.851 38.462 0.00 0.00 0.00 1.40
329 331 5.642491 GCCTTTCGTCACTCTACCTTTTAAT 59.358 40.000 0.00 0.00 0.00 1.40
330 332 4.992951 GCCTTTCGTCACTCTACCTTTTAA 59.007 41.667 0.00 0.00 0.00 1.52
363 365 7.201741 GGTCAATTTAAGGAGATTTGGAGTAGC 60.202 40.741 0.00 0.00 0.00 3.58
364 366 7.011482 CGGTCAATTTAAGGAGATTTGGAGTAG 59.989 40.741 0.00 0.00 0.00 2.57
378 380 6.693315 ATGAATACCCACGGTCAATTTAAG 57.307 37.500 0.00 0.00 37.09 1.85
443 446 3.226347 GTCGGCTTCGATGTTCTTTTTG 58.774 45.455 0.00 0.00 45.21 2.44
487 490 5.984233 TGAAGTTGACATGACTTACACAC 57.016 39.130 0.00 0.00 37.46 3.82
489 492 6.038271 ACCTTTGAAGTTGACATGACTTACAC 59.962 38.462 0.00 0.00 37.46 2.90
490 493 6.119536 ACCTTTGAAGTTGACATGACTTACA 58.880 36.000 0.00 0.00 37.46 2.41
551 554 8.866956 CCGACATAACTTACGTAAGAAGAATTT 58.133 33.333 35.60 22.16 43.62 1.82
659 663 2.225382 TCTAGGTCAATGACGGGTCA 57.775 50.000 7.35 3.69 44.59 4.02
696 700 0.034186 TTGGACTCCACCCATGATGC 60.034 55.000 0.00 0.00 30.78 3.91
740 744 4.032960 TCATTCATAGTGGCACCAAACT 57.967 40.909 15.27 0.00 0.00 2.66
858 873 0.804933 GACTACCTAGGCCGTTTGCG 60.805 60.000 9.30 0.00 42.61 4.85
926 950 0.605319 TGGTCCAATCCACTCGCAAC 60.605 55.000 0.00 0.00 31.96 4.17
997 1021 6.515272 AAGCTCTTGTTGTTTCTTTTCTGA 57.485 33.333 0.00 0.00 0.00 3.27
1022 1046 5.360999 TGTGTGTCTTTCTTTCTCTCTCTCA 59.639 40.000 0.00 0.00 0.00 3.27
1067 1097 4.383552 GCCATTCTCTTTCTCTCTGGCTAA 60.384 45.833 3.51 0.00 43.34 3.09
1331 1607 1.809619 CGTACACCATGGCCGACTG 60.810 63.158 13.04 4.49 0.00 3.51
1333 1609 3.192922 GCGTACACCATGGCCGAC 61.193 66.667 13.04 6.03 0.00 4.79
1334 1610 3.025189 ATGCGTACACCATGGCCGA 62.025 57.895 13.04 0.00 0.00 5.54
1335 1611 2.513666 ATGCGTACACCATGGCCG 60.514 61.111 13.04 10.42 0.00 6.13
1509 1799 1.863267 GGACGCATCAAGATGGAGAG 58.137 55.000 11.66 0.00 39.16 3.20
1514 1804 1.259770 CATGACGGACGCATCAAGATG 59.740 52.381 5.70 5.70 41.60 2.90
1615 1912 3.477210 ACAAACTCCAAGACTCCTGAC 57.523 47.619 0.00 0.00 0.00 3.51
1713 2015 5.707298 TCTTGCAATGTTTTCTTCCCTAGAG 59.293 40.000 0.00 0.00 33.51 2.43
1729 2031 3.074412 CGGAACACCTACTTCTTGCAAT 58.926 45.455 0.00 0.00 0.00 3.56
1788 2090 6.773976 TTCAATGTTTCCCCTAGCAAATAG 57.226 37.500 0.00 0.00 0.00 1.73
1789 2091 6.951198 TCTTTCAATGTTTCCCCTAGCAAATA 59.049 34.615 0.00 0.00 0.00 1.40
1790 2092 5.779771 TCTTTCAATGTTTCCCCTAGCAAAT 59.220 36.000 0.00 0.00 0.00 2.32
1794 2096 3.696548 CCTCTTTCAATGTTTCCCCTAGC 59.303 47.826 0.00 0.00 0.00 3.42
1799 2101 4.918588 TCCTACCTCTTTCAATGTTTCCC 58.081 43.478 0.00 0.00 0.00 3.97
1800 2102 5.561679 ACTCCTACCTCTTTCAATGTTTCC 58.438 41.667 0.00 0.00 0.00 3.13
1819 2128 3.703052 TCCTCGTGGAAAACCTATACTCC 59.297 47.826 3.14 0.00 39.87 3.85
1820 2129 4.996788 TCCTCGTGGAAAACCTATACTC 57.003 45.455 3.14 0.00 39.87 2.59
1892 2201 9.309516 TCAGCTAGATTGGTTTATAGTTAAACG 57.690 33.333 0.00 0.00 45.38 3.60
1906 2215 4.576216 AGTGTACGATCAGCTAGATTGG 57.424 45.455 14.25 7.17 41.68 3.16
1915 2228 3.511699 TGCTGCTTTAGTGTACGATCAG 58.488 45.455 0.00 0.00 0.00 2.90
1964 2277 1.158434 GCATGCCCACCAAACATTTG 58.842 50.000 6.36 0.00 37.90 2.32
2073 2400 6.901081 AAGAAAAACTTCCTGGGTGATTAG 57.099 37.500 0.00 0.00 32.91 1.73
2108 2491 0.665298 TGCATGCACAACTTTGCGTA 59.335 45.000 18.46 0.00 46.20 4.42
2110 2493 0.436913 CATGCATGCACAACTTTGCG 59.563 50.000 25.37 0.00 46.20 4.85
2130 2513 0.108615 CTAGGGCGACACTGTCAAGG 60.109 60.000 9.84 0.00 32.09 3.61
2234 2618 7.148000 CCAAAGGAATAGGAGAAAAAGATGGTC 60.148 40.741 0.00 0.00 0.00 4.02
2248 2632 0.814010 CCGCGGACCAAAGGAATAGG 60.814 60.000 24.07 0.00 0.00 2.57
2249 2633 0.177141 TCCGCGGACCAAAGGAATAG 59.823 55.000 27.28 0.00 0.00 1.73
2273 2657 3.729526 AAAACGTCAAGATGCGATGAG 57.270 42.857 0.00 0.00 0.00 2.90
2342 2734 1.066587 GCGGTACTGGCTAGCTGAG 59.933 63.158 15.72 13.18 0.00 3.35
2375 2767 7.807907 ACCAGCAATCATTTTCGTTAAACTTAG 59.192 33.333 0.00 0.00 0.00 2.18
2399 2791 7.714703 AGTTAGTTACTATAACTAGCAGCACC 58.285 38.462 18.76 2.78 40.74 5.01
2400 2792 8.404000 TGAGTTAGTTACTATAACTAGCAGCAC 58.596 37.037 18.76 10.44 42.17 4.40
2401 2793 8.404000 GTGAGTTAGTTACTATAACTAGCAGCA 58.596 37.037 18.76 14.59 42.17 4.41
2431 2823 7.312657 TCAGTTGCACTTTGAAGATATGATC 57.687 36.000 0.00 0.00 0.00 2.92
2457 2849 1.270147 GGCGTCATGTACCATAGGTCC 60.270 57.143 0.00 0.00 37.09 4.46
2586 3204 5.526846 CCACTAGCAGTACCACTACTACTAC 59.473 48.000 0.00 0.00 30.38 2.73
2587 3205 5.190528 ACCACTAGCAGTACCACTACTACTA 59.809 44.000 0.00 0.00 30.38 1.82
2588 3206 4.018597 ACCACTAGCAGTACCACTACTACT 60.019 45.833 0.00 0.00 32.24 2.57
2609 3227 2.617274 GCTCGACCAAGTGCCAACC 61.617 63.158 0.00 0.00 0.00 3.77
2621 3242 2.492484 TCCTCTTAACTTCCTGCTCGAC 59.508 50.000 0.00 0.00 0.00 4.20
2662 3283 5.050769 CGTGCATGACAAAGTACTCCATATC 60.051 44.000 0.00 0.00 0.00 1.63
2708 3329 2.028337 GGCTGCTCCTAGCTACGC 59.972 66.667 0.00 0.00 42.97 4.42
2867 3493 6.028780 AGGAAGCCTAGCTAGGAATGAATAT 58.971 40.000 38.74 16.51 46.63 1.28
2949 3577 5.961272 AGTTGGATTTATTAAACAAGCGGG 58.039 37.500 0.00 0.00 0.00 6.13
2998 3626 7.718272 CCAATCAAATGGTATGGCTTAAATG 57.282 36.000 0.00 0.00 35.65 2.32
3015 3643 3.872511 AAGAATGCAATCGCCAATCAA 57.127 38.095 0.00 0.00 37.32 2.57
3016 3644 4.639755 TCTTAAGAATGCAATCGCCAATCA 59.360 37.500 1.68 0.00 37.32 2.57
3017 3645 5.173774 TCTTAAGAATGCAATCGCCAATC 57.826 39.130 1.68 0.00 37.32 2.67
3018 3646 4.641989 ACTCTTAAGAATGCAATCGCCAAT 59.358 37.500 6.63 0.00 37.32 3.16
3019 3647 4.009675 ACTCTTAAGAATGCAATCGCCAA 58.990 39.130 6.63 0.00 37.32 4.52
3020 3648 3.609853 ACTCTTAAGAATGCAATCGCCA 58.390 40.909 6.63 0.00 37.32 5.69
3021 3649 4.570772 TGTACTCTTAAGAATGCAATCGCC 59.429 41.667 6.63 0.00 37.32 5.54
3022 3650 5.493735 GTGTACTCTTAAGAATGCAATCGC 58.506 41.667 6.28 0.00 39.24 4.58
3023 3651 5.288712 ACGTGTACTCTTAAGAATGCAATCG 59.711 40.000 6.28 9.34 0.00 3.34
3024 3652 6.648725 ACGTGTACTCTTAAGAATGCAATC 57.351 37.500 6.28 0.00 0.00 2.67
3025 3653 7.275779 CAGTACGTGTACTCTTAAGAATGCAAT 59.724 37.037 6.28 1.48 43.98 3.56
3089 3718 3.924686 GTCACACTTGATAGTTGGTACCG 59.075 47.826 7.57 0.00 33.11 4.02
3090 3719 4.251268 GGTCACACTTGATAGTTGGTACC 58.749 47.826 4.43 4.43 33.11 3.34
3091 3720 4.020485 AGGGTCACACTTGATAGTTGGTAC 60.020 45.833 0.00 0.00 33.11 3.34
3092 3721 4.164981 AGGGTCACACTTGATAGTTGGTA 58.835 43.478 0.00 0.00 33.11 3.25
3093 3722 2.979678 AGGGTCACACTTGATAGTTGGT 59.020 45.455 0.00 0.00 33.11 3.67
3094 3723 3.703001 AGGGTCACACTTGATAGTTGG 57.297 47.619 0.00 0.00 33.11 3.77
3095 3724 6.147821 CAGTAAAGGGTCACACTTGATAGTTG 59.852 42.308 0.00 0.00 33.11 3.16
3096 3725 6.042781 TCAGTAAAGGGTCACACTTGATAGTT 59.957 38.462 0.00 0.00 33.11 2.24
3097 3726 5.542635 TCAGTAAAGGGTCACACTTGATAGT 59.457 40.000 0.00 0.00 33.11 2.12
3099 3728 6.428083 TTCAGTAAAGGGTCACACTTGATA 57.572 37.500 0.00 0.00 33.11 2.15
3100 3729 4.974645 TCAGTAAAGGGTCACACTTGAT 57.025 40.909 0.00 0.00 33.11 2.57
3112 3741 8.979534 ACTAACTCTACCCTAATTCAGTAAAGG 58.020 37.037 0.00 0.00 0.00 3.11
3120 3749 7.124750 TGGTACCAACTAACTCTACCCTAATTC 59.875 40.741 13.60 0.00 0.00 2.17
3173 3804 4.955811 TGAACTTTGACTAGCTTCCAGA 57.044 40.909 0.00 0.00 0.00 3.86
3257 4075 6.761242 ACCACAAGCAAGGAGAAAATTTAAAC 59.239 34.615 0.00 0.00 0.00 2.01
3259 4077 6.478512 ACCACAAGCAAGGAGAAAATTTAA 57.521 33.333 0.00 0.00 0.00 1.52
3260 4078 6.294508 GCTACCACAAGCAAGGAGAAAATTTA 60.295 38.462 0.00 0.00 42.30 1.40
3261 4079 5.509670 GCTACCACAAGCAAGGAGAAAATTT 60.510 40.000 0.00 0.00 42.30 1.82
3262 4080 4.021981 GCTACCACAAGCAAGGAGAAAATT 60.022 41.667 0.00 0.00 42.30 1.82
3263 4081 3.507622 GCTACCACAAGCAAGGAGAAAAT 59.492 43.478 0.00 0.00 42.30 1.82
3357 4189 1.112113 AGTCACGAGTTGGTGTCACT 58.888 50.000 2.35 0.00 39.00 3.41
3358 4190 1.209128 CAGTCACGAGTTGGTGTCAC 58.791 55.000 0.00 0.00 39.00 3.67
3389 4221 0.025898 GGCCGATTCGCGACTTAAAC 59.974 55.000 9.15 0.00 44.57 2.01
3405 4237 1.623811 TGTCTCTAGACTTTGGTGGCC 59.376 52.381 11.22 0.00 44.99 5.36
3550 4702 1.395954 CGATGCATGAACACACAGAGG 59.604 52.381 2.46 0.00 0.00 3.69
3610 4873 6.312180 CCGTGATGACATGTGATGGAATATAG 59.688 42.308 1.15 0.00 33.60 1.31
3688 5274 0.037697 TATTACAGCCGGCCGCATAG 60.038 55.000 26.15 11.70 41.38 2.23
3693 5281 2.762745 ACTAATTATTACAGCCGGCCG 58.237 47.619 26.15 21.04 0.00 6.13
3697 5285 8.122952 CCTTCAGAAAACTAATTATTACAGCCG 58.877 37.037 0.00 0.00 0.00 5.52
4510 6591 1.066430 TGGTTGTAGATCCTGGCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
4573 6654 2.441348 TAGGTCTCGATGGCGCCA 60.441 61.111 34.80 34.80 37.46 5.69
4694 6775 1.264557 CTACGTACGCAGCTAGCTCAT 59.735 52.381 16.15 5.67 42.61 2.90
4695 6776 0.656259 CTACGTACGCAGCTAGCTCA 59.344 55.000 16.15 0.00 42.61 4.26
4710 6791 1.297664 ACGGACACTAGCTAGCTACG 58.702 55.000 20.67 21.95 0.00 3.51
4714 6795 2.030981 GGACATACGGACACTAGCTAGC 60.031 54.545 20.91 6.62 0.00 3.42
4858 7025 3.728845 ACACTACTACAGCAAACCACTG 58.271 45.455 0.00 0.00 41.08 3.66
4959 7137 4.235360 AGTTCTACTTACGCACACATGTC 58.765 43.478 0.00 0.00 0.00 3.06
5084 7264 3.526931 TGTATCTTGGAGCTAGTGTGC 57.473 47.619 0.00 0.00 0.00 4.57
5109 7289 9.559958 GATGTGATTAATTGTGTTTCCAACTAG 57.440 33.333 0.00 0.00 0.00 2.57
5114 7294 5.777223 TGGGATGTGATTAATTGTGTTTCCA 59.223 36.000 0.00 0.00 0.00 3.53
5147 7327 8.181573 TGTCCATGCGATTCTTTCTTATTTAAC 58.818 33.333 0.00 0.00 0.00 2.01
5149 7329 7.857734 TGTCCATGCGATTCTTTCTTATTTA 57.142 32.000 0.00 0.00 0.00 1.40
5165 7346 1.949525 GTACCATGTCCATGTCCATGC 59.050 52.381 13.63 1.25 37.67 4.06
5201 7382 3.857038 ACGTGTCCGGCTGGTGTT 61.857 61.111 12.43 0.00 38.78 3.32
5241 7447 2.105128 GGGGAGCTCGTGACATCG 59.895 66.667 7.83 0.00 0.00 3.84
5249 7455 4.951963 GAATCGCGGGGGAGCTCG 62.952 72.222 6.13 0.00 34.40 5.03
5281 7487 1.747367 CTCTCTCGAGTCCGTGCCT 60.747 63.158 13.13 0.00 37.05 4.75
5289 7495 2.041686 GTGCGTCCCTCTCTCGAGT 61.042 63.158 13.13 0.00 35.43 4.18
5323 7540 7.666623 CAGTAAAACAAGAAAATGGTATGGGT 58.333 34.615 0.00 0.00 0.00 4.51
5340 7557 8.910351 ATAGATAGATTTGGGAGCAGTAAAAC 57.090 34.615 0.00 0.00 0.00 2.43
5361 7578 9.494271 GTTGACAGAATAATCCAAGCATATAGA 57.506 33.333 0.00 0.00 0.00 1.98
5437 7659 5.789021 CGAGATATACGTATCCACAGAAACG 59.211 44.000 12.24 3.83 37.94 3.60
5499 7721 2.358737 GGGTTGCACAGGGACGAG 60.359 66.667 0.00 0.00 0.00 4.18
5523 7745 7.932683 AAATAGCAGGGGTACTACTTATCTT 57.067 36.000 0.00 0.00 0.00 2.40
5555 7777 6.713762 TCAATTCACACTCACCATTTTCTT 57.286 33.333 0.00 0.00 0.00 2.52
5581 7803 8.533569 TTATCATCCGGAGCAGTATATCATTA 57.466 34.615 11.34 0.00 0.00 1.90
5584 7806 6.381133 ACATTATCATCCGGAGCAGTATATCA 59.619 38.462 11.34 0.00 0.00 2.15
5645 7867 5.305386 AGCCCCATTTCAGGAATTAATTAGC 59.695 40.000 0.00 0.00 0.00 3.09
5646 7868 6.983906 AGCCCCATTTCAGGAATTAATTAG 57.016 37.500 0.00 0.00 0.00 1.73
5659 7884 3.847621 GCTGGCTAGCCCCATTTC 58.152 61.111 30.81 9.47 44.33 2.17
5685 7910 1.134401 TGTCAAATCCTCATCCGCCTC 60.134 52.381 0.00 0.00 0.00 4.70
5709 7934 7.095695 GCTCCTGTAGCCATTTAAAACATAA 57.904 36.000 0.00 0.00 46.25 1.90


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

AutoCloner maintained by Alex Coulton.