Multiple sequence alignment - TraesCS7B01G007000

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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 TraesCS7B01G007000 chr7B 100.000 4519 0 0 2190 6708 3855593 3851075 0.000000e+00 8346.0
1 TraesCS7B01G007000 chr7B 100.000 2089 0 0 1 2089 3857782 3855694 0.000000e+00 3858.0
2 TraesCS7B01G007000 chr7B 98.900 1000 11 0 1 1000 697360237 697359238 0.000000e+00 1786.0
3 TraesCS7B01G007000 chr7B 100.000 316 0 0 1140 1455 3854350 3854035 9.690000e-163 584.0
4 TraesCS7B01G007000 chr7B 100.000 316 0 0 3433 3748 3856643 3856328 9.690000e-163 584.0
5 TraesCS7B01G007000 chr7B 83.681 288 47 0 4783 5070 3886754 3886467 8.570000e-69 272.0
6 TraesCS7B01G007000 chr5B 97.472 1582 17 2 2190 3748 403747254 403745673 0.000000e+00 2678.0
7 TraesCS7B01G007000 chr5B 98.709 1007 13 0 1 1007 655842525 655841519 0.000000e+00 1788.0
8 TraesCS7B01G007000 chr5B 98.209 949 17 0 1141 2089 403749420 403748472 0.000000e+00 1659.0
9 TraesCS7B01G007000 chr5B 98.734 316 4 0 1140 1455 403745988 403745673 4.540000e-156 562.0
10 TraesCS7B01G007000 chr5B 97.778 315 7 0 3434 3748 403749420 403749106 1.650000e-150 544.0
11 TraesCS7B01G007000 chr5B 89.831 118 10 2 2572 2688 7050903 7050787 4.190000e-32 150.0
12 TraesCS7B01G007000 chr3B 97.408 1582 12 3 2190 3748 622772997 622774572 0.000000e+00 2667.0
13 TraesCS7B01G007000 chr3B 92.598 1459 69 12 2317 3748 279642642 279641196 0.000000e+00 2060.0
14 TraesCS7B01G007000 chr3B 98.423 951 14 1 1140 2089 622770829 622771779 0.000000e+00 1672.0
15 TraesCS7B01G007000 chr3B 93.619 956 45 10 1139 2089 279644864 279643920 0.000000e+00 1413.0
16 TraesCS7B01G007000 chr3B 83.333 972 128 21 2758 3704 672737107 672736145 0.000000e+00 867.0
17 TraesCS7B01G007000 chr3B 99.054 317 3 0 1140 1456 622774257 622774573 2.710000e-158 569.0
18 TraesCS7B01G007000 chr3B 98.738 317 4 0 3432 3748 622770828 622771144 1.260000e-156 564.0
19 TraesCS7B01G007000 chr3B 87.200 125 16 0 2564 2688 525629349 525629225 7.010000e-30 143.0
20 TraesCS7B01G007000 chr3B 96.875 64 2 0 2190 2253 279642706 279642643 2.560000e-19 108.0
21 TraesCS7B01G007000 chr7D 92.882 1728 78 19 4216 5923 63449319 63447617 0.000000e+00 2468.0
22 TraesCS7B01G007000 chr7D 85.876 2117 226 30 3749 5820 63455652 63453564 0.000000e+00 2185.0
23 TraesCS7B01G007000 chr7D 86.667 570 60 12 5970 6527 63453431 63452866 9.560000e-173 617.0
24 TraesCS7B01G007000 chr7D 94.146 205 12 0 3749 3953 63449524 63449320 5.050000e-81 313.0
25 TraesCS7B01G007000 chr7D 82.162 370 33 16 6331 6667 63447352 63446983 3.060000e-73 287.0
26 TraesCS7B01G007000 chr7D 94.798 173 8 1 5938 6109 63447634 63447462 1.110000e-67 268.0
27 TraesCS7B01G007000 chr7D 92.857 140 10 0 1001 1140 63449659 63449520 3.170000e-48 204.0
28 TraesCS7B01G007000 chr7D 87.143 140 15 1 1001 1140 63455784 63455648 9.010000e-34 156.0
29 TraesCS7B01G007000 chr7D 87.313 134 13 1 6534 6663 63452828 63452695 4.190000e-32 150.0
30 TraesCS7B01G007000 chr7D 98.684 76 1 0 6182 6257 63447451 63447376 1.170000e-27 135.0
31 TraesCS7B01G007000 chr7D 95.082 61 3 0 5822 5882 63453501 63453441 5.540000e-16 97.1
32 TraesCS7B01G007000 chr7A 92.820 1532 74 20 3749 5270 66249210 66247705 0.000000e+00 2187.0
33 TraesCS7B01G007000 chr7A 87.748 604 49 12 5938 6527 66237845 66237253 0.000000e+00 682.0
34 TraesCS7B01G007000 chr7A 94.460 361 18 2 5264 5624 66247417 66247059 7.600000e-154 555.0
35 TraesCS7B01G007000 chr7A 91.892 296 23 1 5619 5914 66238131 66237837 4.840000e-111 412.0
36 TraesCS7B01G007000 chr7A 82.971 276 46 1 4781 5056 66255277 66255003 1.440000e-61 248.0
37 TraesCS7B01G007000 chr7A 95.000 140 7 0 1001 1140 66249345 66249206 3.150000e-53 220.0
38 TraesCS7B01G007000 chr1B 92.735 1459 68 11 2317 3748 421536448 421537895 0.000000e+00 2073.0
39 TraesCS7B01G007000 chr1B 98.900 1000 11 0 1 1000 51091843 51090844 0.000000e+00 1786.0
40 TraesCS7B01G007000 chr1B 93.613 955 46 9 1139 2089 421534509 421535452 0.000000e+00 1411.0
41 TraesCS7B01G007000 chr1B 86.008 243 32 2 2316 2558 449257330 449257090 6.670000e-65 259.0
42 TraesCS7B01G007000 chr6B 92.329 1460 67 12 2317 3749 625291647 625293088 0.000000e+00 2034.0
43 TraesCS7B01G007000 chr6B 98.804 1003 12 0 1 1003 247019594 247020596 0.000000e+00 1786.0
44 TraesCS7B01G007000 chr6B 93.809 953 44 9 1141 2089 625289427 625290368 0.000000e+00 1419.0
45 TraesCS7B01G007000 chr6B 84.984 959 121 22 1141 2089 143472051 143471106 0.000000e+00 952.0
46 TraesCS7B01G007000 chr6B 89.776 626 59 5 1466 2089 214887549 214886927 0.000000e+00 797.0
47 TraesCS7B01G007000 chr6B 86.520 319 28 9 3434 3748 625289427 625289734 3.000000e-88 337.0
48 TraesCS7B01G007000 chr6B 96.875 64 2 0 2190 2253 625291583 625291646 2.560000e-19 108.0
49 TraesCS7B01G007000 chr4B 99.001 1001 10 0 1 1001 661636437 661635437 0.000000e+00 1794.0
50 TraesCS7B01G007000 chr4B 82.672 756 119 12 1320 2070 517436712 517435964 0.000000e+00 660.0
51 TraesCS7B01G007000 chr1A 99.000 1000 10 0 1 1000 413727162 413726163 0.000000e+00 1792.0
52 TraesCS7B01G007000 chr4A 99.000 1000 9 1 1 1000 336015356 336016354 0.000000e+00 1790.0
53 TraesCS7B01G007000 chr4A 98.900 1000 11 0 1 1000 16028671 16029670 0.000000e+00 1786.0
54 TraesCS7B01G007000 chr2A 99.000 1000 9 1 1 1000 456650270 456651268 0.000000e+00 1790.0
55 TraesCS7B01G007000 chr4D 85.181 830 113 8 2924 3748 44622758 44621934 0.000000e+00 843.0
56 TraesCS7B01G007000 chr4D 87.539 321 34 6 1140 1455 44622253 44621934 3.820000e-97 366.0
57 TraesCS7B01G007000 chr6A 87.923 621 73 2 1469 2089 548232180 548231562 0.000000e+00 730.0
58 TraesCS7B01G007000 chr6D 85.425 247 34 2 2312 2558 143480442 143480198 8.630000e-64 255.0
59 TraesCS7B01G007000 chr3D 85.366 246 34 2 2313 2558 299095162 299095405 3.100000e-63 254.0
60 TraesCS7B01G007000 chr3D 82.034 295 44 4 2790 3081 335657932 335658220 6.720000e-60 243.0
61 TraesCS7B01G007000 chr3D 81.695 295 44 5 2790 3081 335661590 335661877 3.130000e-58 237.0
62 TraesCS7B01G007000 chr3D 76.471 323 57 18 3393 3704 335659049 335659363 2.500000e-34 158.0
63 TraesCS7B01G007000 chr3D 76.543 324 55 19 3393 3704 335662723 335663037 2.500000e-34 158.0
64 TraesCS7B01G007000 chr3D 88.800 125 14 0 2564 2688 555430001 555430125 3.240000e-33 154.0
65 TraesCS7B01G007000 chr3D 88.800 125 14 0 2564 2688 555442277 555442401 3.240000e-33 154.0
66 TraesCS7B01G007000 chr3A 76.446 484 102 9 3065 3540 20306869 20306390 1.120000e-62 252.0
67 TraesCS7B01G007000 chrUn 100.000 54 0 0 2190 2243 417864642 417864695 4.280000e-17 100.0


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 TraesCS7B01G007000 chr7B 3851075 3857782 6707 True 3343.000000 8346 100.000000 1 6708 4 chr7B.!!$R3 6707
1 TraesCS7B01G007000 chr7B 697359238 697360237 999 True 1786.000000 1786 98.900000 1 1000 1 chr7B.!!$R2 999
2 TraesCS7B01G007000 chr5B 655841519 655842525 1006 True 1788.000000 1788 98.709000 1 1007 1 chr5B.!!$R2 1006
3 TraesCS7B01G007000 chr5B 403745673 403749420 3747 True 1360.750000 2678 98.048250 1140 3748 4 chr5B.!!$R3 2608
4 TraesCS7B01G007000 chr3B 622770828 622774573 3745 False 1368.000000 2667 98.405750 1140 3748 4 chr3B.!!$F1 2608
5 TraesCS7B01G007000 chr3B 279641196 279644864 3668 True 1193.666667 2060 94.364000 1139 3748 3 chr3B.!!$R3 2609
6 TraesCS7B01G007000 chr3B 672736145 672737107 962 True 867.000000 867 83.333000 2758 3704 1 chr3B.!!$R2 946
7 TraesCS7B01G007000 chr7D 63446983 63455784 8801 True 625.463636 2468 90.691818 1001 6667 11 chr7D.!!$R1 5666
8 TraesCS7B01G007000 chr7A 66247059 66249345 2286 True 987.333333 2187 94.093333 1001 5624 3 chr7A.!!$R3 4623
9 TraesCS7B01G007000 chr7A 66237253 66238131 878 True 547.000000 682 89.820000 5619 6527 2 chr7A.!!$R2 908
10 TraesCS7B01G007000 chr1B 51090844 51091843 999 True 1786.000000 1786 98.900000 1 1000 1 chr1B.!!$R1 999
11 TraesCS7B01G007000 chr1B 421534509 421537895 3386 False 1742.000000 2073 93.174000 1139 3748 2 chr1B.!!$F1 2609
12 TraesCS7B01G007000 chr6B 247019594 247020596 1002 False 1786.000000 1786 98.804000 1 1003 1 chr6B.!!$F1 1002
13 TraesCS7B01G007000 chr6B 625289427 625293088 3661 False 974.500000 2034 92.383250 1141 3749 4 chr6B.!!$F2 2608
14 TraesCS7B01G007000 chr6B 143471106 143472051 945 True 952.000000 952 84.984000 1141 2089 1 chr6B.!!$R1 948
15 TraesCS7B01G007000 chr6B 214886927 214887549 622 True 797.000000 797 89.776000 1466 2089 1 chr6B.!!$R2 623
16 TraesCS7B01G007000 chr4B 661635437 661636437 1000 True 1794.000000 1794 99.001000 1 1001 1 chr4B.!!$R2 1000
17 TraesCS7B01G007000 chr4B 517435964 517436712 748 True 660.000000 660 82.672000 1320 2070 1 chr4B.!!$R1 750
18 TraesCS7B01G007000 chr1A 413726163 413727162 999 True 1792.000000 1792 99.000000 1 1000 1 chr1A.!!$R1 999
19 TraesCS7B01G007000 chr4A 336015356 336016354 998 False 1790.000000 1790 99.000000 1 1000 1 chr4A.!!$F2 999
20 TraesCS7B01G007000 chr4A 16028671 16029670 999 False 1786.000000 1786 98.900000 1 1000 1 chr4A.!!$F1 999
21 TraesCS7B01G007000 chr2A 456650270 456651268 998 False 1790.000000 1790 99.000000 1 1000 1 chr2A.!!$F1 999
22 TraesCS7B01G007000 chr4D 44621934 44622758 824 True 604.500000 843 86.360000 1140 3748 2 chr4D.!!$R1 2608
23 TraesCS7B01G007000 chr6A 548231562 548232180 618 True 730.000000 730 87.923000 1469 2089 1 chr6A.!!$R1 620

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
665 666 3.616721 CCCGATCGGAGCCGGAAT 61.617 66.667 35.42 0.00 43.80 3.01 F
1168 1170 1.152984 CCAATATGGGCTGCCACGA 60.153 57.895 22.05 4.43 32.67 4.35 F
1940 1948 2.550699 TACATTGAGGGCTTGCGGGG 62.551 60.000 0.00 0.00 0.00 5.73 F
3751 4941 0.243907 AGTCTGGGTCGTGACATTCG 59.756 55.000 2.00 0.00 35.81 3.34 F
4877 11942 0.108472 CCTGAGCATGTTCGAGAGCA 60.108 55.000 5.02 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1886 1.912043 CTCAGGTTGGGGTTGAGATCT 59.088 52.381 0.00 0.00 40.54 2.75 R
2253 3378 6.605995 ACATAAGGCATCATGATATCCCAATG 59.394 38.462 21.66 21.66 0.00 2.82 R
3881 5071 1.078988 TCGATGTTAACCCGGCCAC 60.079 57.895 2.24 0.00 0.00 5.01 R
5275 12634 0.609662 CCTGGCCCAAATTCAAGTGG 59.390 55.000 0.00 0.00 34.44 4.00 R
5936 13303 0.036388 TGGACGCACTTGGGAATCTC 60.036 55.000 0.00 0.00 0.00 2.75 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
665 666 3.616721 CCCGATCGGAGCCGGAAT 61.617 66.667 35.42 0.00 43.80 3.01
1080 1081 3.198489 GCACTTCCAGCTAGCGCC 61.198 66.667 9.55 0.00 36.60 6.53
1113 1114 4.269523 GGTGGCAGCAGTGGACCA 62.270 66.667 12.58 0.00 0.00 4.02
1168 1170 1.152984 CCAATATGGGCTGCCACGA 60.153 57.895 22.05 4.43 32.67 4.35
1476 1483 5.416952 ACAATTTGGTATTCAGAGCCAAGAG 59.583 40.000 0.78 0.00 42.38 2.85
1878 1886 3.130633 GGAATGCGTACATCATGTGCTA 58.869 45.455 0.00 0.00 34.62 3.49
1940 1948 2.550699 TACATTGAGGGCTTGCGGGG 62.551 60.000 0.00 0.00 0.00 5.73
2253 3378 0.740737 ACAGCTGTGGTCTGCAAAAC 59.259 50.000 20.97 0.00 40.25 2.43
2439 3564 2.093500 TGTTCGGATCATGGAACTCTGG 60.093 50.000 18.38 0.00 42.28 3.86
3208 4368 1.338020 CTTTCAAGGACACTGGTTGGC 59.662 52.381 0.00 0.00 0.00 4.52
3461 4621 1.152984 CCAATATGGGCTGCCACGA 60.153 57.895 22.05 4.43 32.67 4.35
3749 4939 1.338107 TGAGTCTGGGTCGTGACATT 58.662 50.000 2.00 0.00 35.81 2.71
3750 4940 1.272490 TGAGTCTGGGTCGTGACATTC 59.728 52.381 2.00 0.00 35.81 2.67
3751 4941 0.243907 AGTCTGGGTCGTGACATTCG 59.756 55.000 2.00 0.00 35.81 3.34
3752 4942 0.736325 GTCTGGGTCGTGACATTCGG 60.736 60.000 2.00 0.00 33.75 4.30
3786 4976 1.463444 GACACCGGCAACTTATGTGTC 59.537 52.381 0.00 0.00 46.02 3.67
3935 5125 4.942761 ATGCAGTGTCCAAACATTTCTT 57.057 36.364 0.00 0.00 37.81 2.52
4039 5232 4.003648 ACATAGTTTAAGTGAGTGCAGCC 58.996 43.478 0.00 0.00 0.00 4.85
4084 5277 4.820744 CCATCCAAGGCACCCCGG 62.821 72.222 0.00 0.00 35.76 5.73
4195 5388 1.386533 GCTCCATGAACACCCAGATG 58.613 55.000 0.00 0.00 0.00 2.90
4300 11356 5.559227 TCATTTGATCAACTGATTAACGCG 58.441 37.500 20.93 3.53 34.37 6.01
4303 11359 2.093625 TGATCAACTGATTAACGCGCAC 59.906 45.455 5.73 0.00 34.37 5.34
4304 11360 1.503294 TCAACTGATTAACGCGCACA 58.497 45.000 5.73 0.00 0.00 4.57
4390 11446 3.872511 TGCAAGATGTATTTGGCCAAG 57.127 42.857 19.48 4.68 0.00 3.61
4391 11447 3.429492 TGCAAGATGTATTTGGCCAAGA 58.571 40.909 19.48 10.42 0.00 3.02
4399 11455 1.632589 ATTTGGCCAAGACCCTGTTC 58.367 50.000 19.48 0.00 0.00 3.18
4405 11461 1.226746 CCAAGACCCTGTTCGTGTTC 58.773 55.000 0.00 0.00 0.00 3.18
4408 11464 0.834612 AGACCCTGTTCGTGTTCCAA 59.165 50.000 0.00 0.00 0.00 3.53
4496 11552 2.762535 ACCCAGAATAGTGAACACCG 57.237 50.000 1.11 0.00 0.00 4.94
4508 11564 3.260884 AGTGAACACCGTCATATCTGGTT 59.739 43.478 1.11 0.00 32.48 3.67
4550 11606 5.755409 TTATAGTTCTCCCTCTGTTTGCA 57.245 39.130 0.00 0.00 0.00 4.08
4551 11607 4.640771 ATAGTTCTCCCTCTGTTTGCAA 57.359 40.909 0.00 0.00 0.00 4.08
4555 11611 1.494721 TCTCCCTCTGTTTGCAAAGGT 59.505 47.619 13.26 0.00 0.00 3.50
4592 11656 4.217754 TGAACATGCTTACCAACGAAAC 57.782 40.909 0.00 0.00 0.00 2.78
4601 11665 6.202937 TGCTTACCAACGAAACAATTAGTTG 58.797 36.000 7.34 7.34 45.90 3.16
4608 11672 7.988904 CAACGAAACAATTAGTTGGGTTAAA 57.011 32.000 2.81 0.00 43.94 1.52
4616 11680 6.555360 ACAATTAGTTGGGTTAAATTGGACCA 59.445 34.615 11.40 0.00 41.46 4.02
4631 11695 2.037511 TGGACCAAAGTACCCTACAACG 59.962 50.000 0.00 0.00 0.00 4.10
4649 11713 4.328983 ACAACGGTAACAATATCTCAAGCG 59.671 41.667 0.00 0.00 0.00 4.68
4650 11714 4.380841 ACGGTAACAATATCTCAAGCGA 57.619 40.909 0.00 0.00 0.00 4.93
4652 11716 3.182572 CGGTAACAATATCTCAAGCGAGC 59.817 47.826 0.00 0.00 39.30 5.03
4653 11717 3.182572 GGTAACAATATCTCAAGCGAGCG 59.817 47.826 0.00 0.00 39.30 5.03
4654 11718 1.858091 ACAATATCTCAAGCGAGCGG 58.142 50.000 0.00 0.00 39.30 5.52
4655 11719 1.137086 ACAATATCTCAAGCGAGCGGT 59.863 47.619 0.00 0.00 39.30 5.68
4656 11720 2.361119 ACAATATCTCAAGCGAGCGGTA 59.639 45.455 0.00 0.00 39.30 4.02
4657 11721 2.983136 CAATATCTCAAGCGAGCGGTAG 59.017 50.000 0.00 0.00 39.30 3.18
4658 11722 1.963172 TATCTCAAGCGAGCGGTAGA 58.037 50.000 0.00 0.00 39.30 2.59
4659 11723 1.103803 ATCTCAAGCGAGCGGTAGAA 58.896 50.000 0.00 0.00 39.30 2.10
4660 11724 0.885879 TCTCAAGCGAGCGGTAGAAA 59.114 50.000 0.00 0.00 39.30 2.52
4661 11725 1.271379 TCTCAAGCGAGCGGTAGAAAA 59.729 47.619 0.00 0.00 39.30 2.29
4662 11726 2.066262 CTCAAGCGAGCGGTAGAAAAA 58.934 47.619 0.00 0.00 31.00 1.94
4695 11759 6.489700 TCTGAAGCATGACTATTTTGGAAACA 59.510 34.615 0.00 0.00 39.83 2.83
4696 11760 7.177216 TCTGAAGCATGACTATTTTGGAAACAT 59.823 33.333 0.00 0.00 42.32 2.71
4711 11776 3.944015 GGAAACATTCCTCACAGATGGAG 59.056 47.826 1.86 0.00 46.57 3.86
4715 11780 3.204526 CATTCCTCACAGATGGAGAAGC 58.795 50.000 0.00 0.00 34.24 3.86
4718 11783 1.205655 CCTCACAGATGGAGAAGCGAA 59.794 52.381 0.00 0.00 34.24 4.70
4745 11810 5.138125 ACATGAACAAATAAAGTGGCCAG 57.862 39.130 5.11 0.00 0.00 4.85
4877 11942 0.108472 CCTGAGCATGTTCGAGAGCA 60.108 55.000 5.02 0.00 0.00 4.26
4928 11993 1.082756 CTGAGAAACCACAACGCGC 60.083 57.895 5.73 0.00 0.00 6.86
5083 12148 2.000447 GAGTCTCGGCAACCATGTTAC 59.000 52.381 0.00 0.00 0.00 2.50
5092 12157 1.670811 CAACCATGTTACCGATGCCTC 59.329 52.381 0.00 0.00 0.00 4.70
5093 12158 0.908910 ACCATGTTACCGATGCCTCA 59.091 50.000 0.00 0.00 0.00 3.86
5215 12280 4.954875 ACATCACTAGGCTCAAGAATAGC 58.045 43.478 0.00 0.00 39.33 2.97
5241 12307 8.428536 CAACAAAATTTCAACGTTCAGTGTTAA 58.571 29.630 0.00 0.00 0.00 2.01
5307 12666 2.701423 TGGGCCAGGTTTTAAAGGAAAC 59.299 45.455 0.00 0.00 38.49 2.78
5485 12852 8.483758 ACCTAAATATGGTTAGACTGATTTCGT 58.516 33.333 0.00 0.00 33.62 3.85
5718 13085 0.107945 CTGCAGTGAAGGTCCTAGCC 60.108 60.000 5.25 0.00 0.00 3.93
5737 13104 2.287547 GCCAAATGGGTGCATATACACG 60.288 50.000 0.90 0.00 41.65 4.49
5768 13135 0.394762 TTCTGGGGACTGCATGCATC 60.395 55.000 22.97 19.20 0.00 3.91
5795 13162 3.314357 GTGTGTACTTCCTTTGTGGGAAC 59.686 47.826 0.00 0.00 40.08 3.62
5876 13243 2.580962 TGTGGTTGATGCAAGCTACAA 58.419 42.857 10.22 0.00 41.66 2.41
5886 13253 1.069296 GCAAGCTACAAACACGCATGA 60.069 47.619 0.00 0.00 0.00 3.07
5894 13261 2.622942 ACAAACACGCATGAAAGTGGAT 59.377 40.909 16.82 6.36 42.25 3.41
5918 13285 1.341383 GGGCATCAGATTCCCAAGTGT 60.341 52.381 13.05 0.00 39.82 3.55
5921 13288 2.421424 GCATCAGATTCCCAAGTGTGTC 59.579 50.000 0.00 0.00 0.00 3.67
5922 13289 2.859165 TCAGATTCCCAAGTGTGTCC 57.141 50.000 0.00 0.00 0.00 4.02
5923 13290 2.338809 TCAGATTCCCAAGTGTGTCCT 58.661 47.619 0.00 0.00 0.00 3.85
5924 13291 2.711009 TCAGATTCCCAAGTGTGTCCTT 59.289 45.455 0.00 0.00 0.00 3.36
5925 13292 3.138283 TCAGATTCCCAAGTGTGTCCTTT 59.862 43.478 0.00 0.00 0.00 3.11
5926 13293 3.891366 CAGATTCCCAAGTGTGTCCTTTT 59.109 43.478 0.00 0.00 0.00 2.27
5927 13294 4.342092 CAGATTCCCAAGTGTGTCCTTTTT 59.658 41.667 0.00 0.00 0.00 1.94
5969 13336 1.857837 GCGTCCAACACCACAAATTTG 59.142 47.619 16.67 16.67 0.00 2.32
5990 13361 1.812571 GTCCATGTGTTCGGCTGATTT 59.187 47.619 0.00 0.00 0.00 2.17
5993 13364 0.168788 ATGTGTTCGGCTGATTTGCG 59.831 50.000 0.00 0.00 0.00 4.85
6031 13402 0.318762 AAGAGTGAACGGGTCAGAGC 59.681 55.000 0.00 0.00 36.74 4.09
6054 13425 5.179368 GCAAAAGAGACTAGTGCACACATAA 59.821 40.000 21.04 0.00 35.28 1.90
6063 13434 8.094548 AGACTAGTGCACACATAATTGACTTAA 58.905 33.333 21.04 0.00 0.00 1.85
6257 13629 6.127980 TGAGTAGGAGAATCTTCACAACTACG 60.128 42.308 0.00 0.00 35.84 3.51
6258 13630 5.944599 AGTAGGAGAATCTTCACAACTACGA 59.055 40.000 0.00 0.00 35.84 3.43
6259 13631 5.923733 AGGAGAATCTTCACAACTACGAT 57.076 39.130 0.00 0.00 33.73 3.73
6262 13634 5.746245 GGAGAATCTTCACAACTACGATCTG 59.254 44.000 0.00 0.00 33.73 2.90
6263 13635 5.105752 AGAATCTTCACAACTACGATCTGC 58.894 41.667 0.00 0.00 0.00 4.26
6290 13662 3.055819 ACCAGATAAGCGTTGACATGTCT 60.056 43.478 25.55 7.77 0.00 3.41
6294 13666 1.237285 AAGCGTTGACATGTCTGGCC 61.237 55.000 25.55 12.10 0.00 5.36
6295 13667 1.965930 GCGTTGACATGTCTGGCCA 60.966 57.895 25.55 4.71 0.00 5.36
6308 13680 0.037975 CTGGCCAACTGGTTGCATTC 60.038 55.000 7.01 0.00 39.16 2.67
6324 13696 2.005451 CATTCCCGTCAGAGCTTTGAG 58.995 52.381 7.29 2.31 0.00 3.02
6335 13707 1.153765 GCTTTGAGCCGGCCATTTC 60.154 57.895 26.15 15.26 34.48 2.17
6353 13725 5.349543 CCATTTCGGTAACTAGTTACACCAC 59.650 44.000 35.09 22.11 45.32 4.16
6357 13729 2.610433 GTAACTAGTTACACCACGCCC 58.390 52.381 31.74 9.07 43.55 6.13
6383 13756 2.593346 TGGTGTTTTGCGCAAAAGAT 57.407 40.000 40.26 0.00 40.53 2.40
6394 13767 6.572153 TTGCGCAAAAGATAAATAGCAATG 57.428 33.333 22.78 0.00 38.26 2.82
6516 13897 4.141482 ACACTTGGAAGAAGCTCCTTGTAA 60.141 41.667 0.00 0.00 36.35 2.41
6520 13901 5.755409 TGGAAGAAGCTCCTTGTAACATA 57.245 39.130 0.00 0.00 36.35 2.29
6521 13902 5.488341 TGGAAGAAGCTCCTTGTAACATAC 58.512 41.667 0.00 0.00 36.35 2.39
6522 13903 4.567159 GGAAGAAGCTCCTTGTAACATACG 59.433 45.833 0.00 0.00 32.21 3.06
6523 13904 4.803098 AGAAGCTCCTTGTAACATACGT 57.197 40.909 0.00 0.00 0.00 3.57
6524 13905 5.909621 AGAAGCTCCTTGTAACATACGTA 57.090 39.130 0.00 0.00 0.00 3.57
6525 13906 6.466885 AGAAGCTCCTTGTAACATACGTAT 57.533 37.500 1.14 1.14 0.00 3.06
6530 13944 8.053026 AGCTCCTTGTAACATACGTATATAGG 57.947 38.462 7.96 0.73 0.00 2.57
6532 13946 7.754027 GCTCCTTGTAACATACGTATATAGGTG 59.246 40.741 16.48 3.22 0.00 4.00
6668 14082 9.474313 AAATGGTATTCAAACACATACATACCT 57.526 29.630 7.49 0.00 37.90 3.08
6669 14083 7.857734 TGGTATTCAAACACATACATACCTG 57.142 36.000 7.49 0.00 37.90 4.00
6670 14084 7.625469 TGGTATTCAAACACATACATACCTGA 58.375 34.615 7.49 0.00 37.90 3.86
6671 14085 8.271458 TGGTATTCAAACACATACATACCTGAT 58.729 33.333 7.49 0.00 37.90 2.90
6672 14086 9.120538 GGTATTCAAACACATACATACCTGATT 57.879 33.333 0.00 0.00 35.30 2.57
6706 14120 9.599866 TTTGAGAAGAACATACATACATACCTG 57.400 33.333 0.00 0.00 0.00 4.00
6707 14121 8.533569 TGAGAAGAACATACATACATACCTGA 57.466 34.615 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
665 666 2.543802 CCGCTCGATGCCGTCTCTA 61.544 63.158 0.00 0.00 38.78 2.43
1080 1081 2.202797 CCTGATCTGGTCACGGCG 60.203 66.667 4.80 4.80 32.22 6.46
1087 1088 2.194388 CTGCTGCCACCTGATCTGGT 62.194 60.000 17.95 17.95 41.77 4.00
1113 1114 2.806244 GTTGAAGATGGCGTTGTACAGT 59.194 45.455 0.00 0.00 0.00 3.55
1168 1170 5.324409 CCAAGGCCCATGTTACATACATAT 58.676 41.667 0.00 0.00 45.71 1.78
1476 1483 3.005791 CAGGAAGTGGGTGGTGATTTTTC 59.994 47.826 0.00 0.00 0.00 2.29
1878 1886 1.912043 CTCAGGTTGGGGTTGAGATCT 59.088 52.381 0.00 0.00 40.54 2.75
1940 1948 2.983136 CGCACGACATCCTTGATATCTC 59.017 50.000 3.98 0.00 0.00 2.75
2253 3378 6.605995 ACATAAGGCATCATGATATCCCAATG 59.394 38.462 21.66 21.66 0.00 2.82
3208 4368 4.807834 GTGGACACACATGATACATCTGAG 59.192 45.833 0.00 0.00 46.90 3.35
3461 4621 5.324409 CCAAGGCCCATGTTACATACATAT 58.676 41.667 0.00 0.00 45.71 1.78
3749 4939 4.193334 CAGATGCCGAGTCGCCGA 62.193 66.667 7.12 0.00 0.00 5.54
3750 4940 4.193334 TCAGATGCCGAGTCGCCG 62.193 66.667 7.12 0.00 0.00 6.46
3751 4941 2.583593 GTCAGATGCCGAGTCGCC 60.584 66.667 7.12 0.00 0.00 5.54
3752 4942 2.161486 GTGTCAGATGCCGAGTCGC 61.161 63.158 7.12 3.40 0.00 5.19
3762 4952 2.027192 ACATAAGTTGCCGGTGTCAGAT 60.027 45.455 1.90 0.00 0.00 2.90
3765 4955 1.202710 ACACATAAGTTGCCGGTGTCA 60.203 47.619 1.90 0.00 38.20 3.58
3881 5071 1.078988 TCGATGTTAACCCGGCCAC 60.079 57.895 2.24 0.00 0.00 5.01
3935 5125 4.761739 CAGGTTTTTGAAGCCAGTCAGATA 59.238 41.667 0.00 0.00 33.65 1.98
4084 5277 1.219393 CCCTCGCTGGAAGTCCTTC 59.781 63.158 0.00 0.00 38.35 3.46
4098 5291 3.721370 ATGGCCATGTTCGCCCCTC 62.721 63.158 20.04 0.00 46.48 4.30
4118 5311 2.048503 AAGTACAGTGCCGCCGAC 60.049 61.111 0.00 0.00 0.00 4.79
4129 5322 2.400399 GCGTTGCTGTAGTCAAGTACA 58.600 47.619 0.00 0.00 0.00 2.90
4287 11343 0.162933 CGTGTGCGCGTTAATCAGTT 59.837 50.000 8.43 0.00 0.00 3.16
4295 11351 1.355971 AATATTCTCGTGTGCGCGTT 58.644 45.000 8.43 0.00 38.14 4.84
4300 11356 5.569059 CACCAAAGAAAATATTCTCGTGTGC 59.431 40.000 0.00 0.00 45.19 4.57
4303 11359 5.095490 GGCACCAAAGAAAATATTCTCGTG 58.905 41.667 0.00 8.11 45.19 4.35
4304 11360 4.764823 TGGCACCAAAGAAAATATTCTCGT 59.235 37.500 0.00 0.00 45.19 4.18
4390 11446 1.892209 ATTGGAACACGAACAGGGTC 58.108 50.000 0.00 0.00 39.29 4.46
4391 11447 1.953686 CAATTGGAACACGAACAGGGT 59.046 47.619 0.00 0.00 39.29 4.34
4399 11455 0.037590 TCTCCCCCAATTGGAACACG 59.962 55.000 26.60 8.37 39.29 4.49
4405 11461 2.834638 AGTCATTCTCCCCCAATTGG 57.165 50.000 18.21 18.21 0.00 3.16
4408 11464 2.173569 GCTGTAGTCATTCTCCCCCAAT 59.826 50.000 0.00 0.00 0.00 3.16
4496 11552 5.817816 CAGTTACCTCCAAACCAGATATGAC 59.182 44.000 0.00 0.00 0.00 3.06
4508 11564 2.656947 AGCTTTGCAGTTACCTCCAA 57.343 45.000 0.00 0.00 0.00 3.53
4592 11656 6.998802 TGGTCCAATTTAACCCAACTAATTG 58.001 36.000 0.00 0.00 37.59 2.32
4601 11665 4.221262 GGGTACTTTGGTCCAATTTAACCC 59.779 45.833 20.66 20.66 34.47 4.11
4606 11670 5.327737 TGTAGGGTACTTTGGTCCAATTT 57.672 39.130 4.80 0.00 0.00 1.82
4608 11672 4.659115 GTTGTAGGGTACTTTGGTCCAAT 58.341 43.478 4.80 0.00 0.00 3.16
4616 11680 4.953940 TGTTACCGTTGTAGGGTACTTT 57.046 40.909 0.00 0.00 38.23 2.66
4631 11695 3.182572 CGCTCGCTTGAGATATTGTTACC 59.817 47.826 0.00 0.00 42.66 2.85
4664 11728 9.011095 CCAAAATAGTCATGCTTCAGATATCAT 57.989 33.333 5.32 0.00 0.00 2.45
4665 11729 8.212995 TCCAAAATAGTCATGCTTCAGATATCA 58.787 33.333 5.32 0.00 0.00 2.15
4666 11730 8.613060 TCCAAAATAGTCATGCTTCAGATATC 57.387 34.615 0.00 0.00 0.00 1.63
4667 11731 8.985315 TTCCAAAATAGTCATGCTTCAGATAT 57.015 30.769 0.00 0.00 0.00 1.63
4668 11732 8.677300 GTTTCCAAAATAGTCATGCTTCAGATA 58.323 33.333 0.00 0.00 0.00 1.98
4669 11733 7.177216 TGTTTCCAAAATAGTCATGCTTCAGAT 59.823 33.333 0.00 0.00 0.00 2.90
4670 11734 6.489700 TGTTTCCAAAATAGTCATGCTTCAGA 59.510 34.615 0.00 0.00 0.00 3.27
4671 11735 6.680810 TGTTTCCAAAATAGTCATGCTTCAG 58.319 36.000 0.00 0.00 0.00 3.02
4672 11736 6.647334 TGTTTCCAAAATAGTCATGCTTCA 57.353 33.333 0.00 0.00 0.00 3.02
4695 11759 2.158986 CGCTTCTCCATCTGTGAGGAAT 60.159 50.000 0.00 0.00 32.57 3.01
4696 11760 1.205655 CGCTTCTCCATCTGTGAGGAA 59.794 52.381 0.00 0.00 32.57 3.36
4718 11783 8.153550 TGGCCACTTTATTTGTTCATGTATTTT 58.846 29.630 0.00 0.00 0.00 1.82
4745 11810 1.767759 AGGATACAAACTGCATGGCC 58.232 50.000 0.00 0.00 41.41 5.36
4831 11896 0.960364 GAAAGCAACCCATCGGAGCA 60.960 55.000 2.16 0.00 36.55 4.26
4877 11942 5.885912 ACTTGTCATAGTCACTTTTGTTGGT 59.114 36.000 0.00 0.00 0.00 3.67
4928 11993 4.376340 AAGAGTTGTGCCTTTTGAACAG 57.624 40.909 0.00 0.00 0.00 3.16
5092 12157 3.306917 TCATTGCCTGCTCATTTTGTG 57.693 42.857 0.00 0.00 0.00 3.33
5093 12158 4.222145 AGAATCATTGCCTGCTCATTTTGT 59.778 37.500 0.00 0.00 0.00 2.83
5215 12280 6.388259 ACACTGAACGTTGAAATTTTGTTG 57.612 33.333 5.00 0.00 0.00 3.33
5263 12329 9.717942 CCCAAATTCAAGTGGTATTGATTTTTA 57.282 29.630 6.59 0.00 39.17 1.52
5275 12634 0.609662 CCTGGCCCAAATTCAAGTGG 59.390 55.000 0.00 0.00 34.44 4.00
5324 12683 9.878599 ATTACATTTGAACTTAACTGAAACTCG 57.121 29.630 0.00 0.00 0.00 4.18
5485 12852 1.737838 CGGTCTCAAAGCCTGCATAA 58.262 50.000 0.00 0.00 0.00 1.90
5718 13085 2.357323 TGCGTGTATATGCACCCATTTG 59.643 45.455 17.01 4.47 43.60 2.32
5737 13104 1.515521 CCCCAGAAGTCCGTTTGTGC 61.516 60.000 0.00 0.00 0.00 4.57
5768 13135 4.201910 CCACAAAGGAAGTACACACAACAG 60.202 45.833 0.00 0.00 41.22 3.16
5795 13162 8.670135 TGTTTTGTAATTTCGGTACATAGGATG 58.330 33.333 0.00 0.00 31.72 3.51
5876 13243 1.068333 GCATCCACTTTCATGCGTGTT 60.068 47.619 5.68 0.00 36.33 3.32
5894 13261 2.192979 GGAATCTGATGCCCCGCA 59.807 61.111 2.94 0.00 44.86 5.69
5935 13302 0.744771 GGACGCACTTGGGAATCTCC 60.745 60.000 0.00 0.00 35.23 3.71
5936 13303 0.036388 TGGACGCACTTGGGAATCTC 60.036 55.000 0.00 0.00 0.00 2.75
5937 13304 0.400213 TTGGACGCACTTGGGAATCT 59.600 50.000 0.00 0.00 0.00 2.40
5938 13305 0.521735 GTTGGACGCACTTGGGAATC 59.478 55.000 0.00 0.00 0.00 2.52
5939 13306 0.179004 TGTTGGACGCACTTGGGAAT 60.179 50.000 0.00 0.00 0.00 3.01
5940 13307 1.098712 GTGTTGGACGCACTTGGGAA 61.099 55.000 0.00 0.00 34.30 3.97
5941 13308 1.525077 GTGTTGGACGCACTTGGGA 60.525 57.895 0.00 0.00 34.30 4.37
5942 13309 2.551912 GGTGTTGGACGCACTTGGG 61.552 63.158 0.00 0.00 37.07 4.12
5943 13310 1.821759 TGGTGTTGGACGCACTTGG 60.822 57.895 0.00 0.00 37.07 3.61
5944 13311 1.355210 GTGGTGTTGGACGCACTTG 59.645 57.895 0.00 0.00 37.07 3.16
5945 13312 0.678366 TTGTGGTGTTGGACGCACTT 60.678 50.000 0.00 0.00 37.07 3.16
5946 13313 0.678366 TTTGTGGTGTTGGACGCACT 60.678 50.000 0.00 0.00 37.07 4.40
5947 13314 0.383949 ATTTGTGGTGTTGGACGCAC 59.616 50.000 0.00 0.00 36.22 5.34
5948 13315 1.107114 AATTTGTGGTGTTGGACGCA 58.893 45.000 0.00 0.00 0.00 5.24
5969 13336 0.392998 ATCAGCCGAACACATGGACC 60.393 55.000 0.00 0.00 0.00 4.46
5993 13364 2.051345 CACAACCGACAAAGCCGC 60.051 61.111 0.00 0.00 0.00 6.53
6031 13402 6.785488 TTATGTGTGCACTAGTCTCTTTTG 57.215 37.500 19.41 0.00 0.00 2.44
6054 13425 7.225784 TGCACATAACACCATTTAAGTCAAT 57.774 32.000 0.00 0.00 0.00 2.57
6063 13434 4.161377 GGGGTATTTGCACATAACACCATT 59.839 41.667 9.99 0.00 0.00 3.16
6214 13586 9.029368 TCCTACTCAGATATTAGAATCACATGG 57.971 37.037 0.00 0.00 0.00 3.66
6257 13629 2.492012 CTTATCTGGTGGCTGCAGATC 58.508 52.381 20.43 9.32 37.01 2.75
6258 13630 1.476471 GCTTATCTGGTGGCTGCAGAT 60.476 52.381 20.43 2.39 38.91 2.90
6259 13631 0.107508 GCTTATCTGGTGGCTGCAGA 60.108 55.000 20.43 0.00 0.00 4.26
6262 13634 1.026718 AACGCTTATCTGGTGGCTGC 61.027 55.000 0.00 0.00 0.00 5.25
6263 13635 0.729116 CAACGCTTATCTGGTGGCTG 59.271 55.000 0.00 0.00 0.00 4.85
6290 13662 1.470996 GGAATGCAACCAGTTGGCCA 61.471 55.000 0.00 0.00 40.74 5.36
6294 13666 0.240945 GACGGGAATGCAACCAGTTG 59.759 55.000 16.77 6.15 43.14 3.16
6295 13667 0.179004 TGACGGGAATGCAACCAGTT 60.179 50.000 16.77 0.00 36.12 3.16
6308 13680 1.743252 GGCTCAAAGCTCTGACGGG 60.743 63.158 0.00 0.00 41.99 5.28
6335 13707 2.253603 GCGTGGTGTAACTAGTTACCG 58.746 52.381 32.75 28.67 43.47 4.02
6372 13745 5.042593 CCATTGCTATTTATCTTTTGCGCA 58.957 37.500 5.66 5.66 0.00 6.09
6383 13756 7.929941 TGTTACACATGACCATTGCTATTTA 57.070 32.000 0.00 0.00 0.00 1.40
6394 13767 3.562557 ACTTTCGGTTGTTACACATGACC 59.437 43.478 0.00 0.00 0.00 4.02
6409 13782 1.136110 ACAAAAAGCCACCACTTTCGG 59.864 47.619 0.00 0.00 38.92 4.30
6410 13783 2.577449 ACAAAAAGCCACCACTTTCG 57.423 45.000 0.00 0.00 38.92 3.46
6411 13784 6.918892 AAATTACAAAAAGCCACCACTTTC 57.081 33.333 0.00 0.00 38.92 2.62
6412 13785 7.331791 TGTAAATTACAAAAAGCCACCACTTT 58.668 30.769 2.97 0.00 36.20 2.66
6492 13873 3.391296 ACAAGGAGCTTCTTCCAAGTGTA 59.609 43.478 3.55 0.00 39.84 2.90
6516 13897 6.373774 GTGCCTAGTCACCTATATACGTATGT 59.626 42.308 18.37 13.99 0.00 2.29
6520 13901 4.983053 AGTGCCTAGTCACCTATATACGT 58.017 43.478 0.00 0.00 37.68 3.57
6521 13902 7.444629 TTTAGTGCCTAGTCACCTATATACG 57.555 40.000 0.00 0.00 37.68 3.06
6522 13903 9.245481 AGATTTAGTGCCTAGTCACCTATATAC 57.755 37.037 0.00 0.00 37.68 1.47
6523 13904 9.244292 CAGATTTAGTGCCTAGTCACCTATATA 57.756 37.037 0.00 0.00 37.68 0.86
6524 13905 7.310113 GCAGATTTAGTGCCTAGTCACCTATAT 60.310 40.741 0.00 0.00 37.68 0.86
6525 13906 6.015350 GCAGATTTAGTGCCTAGTCACCTATA 60.015 42.308 0.00 0.00 37.68 1.31
6530 13944 4.130286 AGCAGATTTAGTGCCTAGTCAC 57.870 45.455 0.00 0.00 42.24 3.67
6532 13946 5.017294 AGAAGCAGATTTAGTGCCTAGTC 57.983 43.478 0.00 0.00 42.24 2.59
6539 13953 8.539770 TTCTCTACAAAGAAGCAGATTTAGTG 57.460 34.615 0.00 0.00 31.71 2.74
6680 14094 9.599866 CAGGTATGTATGTATGTTCTTCTCAAA 57.400 33.333 0.00 0.00 0.00 2.69
6681 14095 8.977412 TCAGGTATGTATGTATGTTCTTCTCAA 58.023 33.333 0.00 0.00 0.00 3.02
6682 14096 8.533569 TCAGGTATGTATGTATGTTCTTCTCA 57.466 34.615 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.