Multiple sequence alignment - TraesCS5B01G447800

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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 TraesCS5B01G447800 chr5B 100.000 8392 0 0 1 8392 619846368 619854759 0.000000e+00 15498
1 TraesCS5B01G447800 chr5B 89.515 2823 253 17 1927 4725 619100612 619103415 0.000000e+00 3533
2 TraesCS5B01G447800 chr5B 90.163 2582 227 12 1303 3863 619131142 619133717 0.000000e+00 3336
3 TraesCS5B01G447800 chr5B 89.814 2582 233 13 1303 3863 619184328 619186900 0.000000e+00 3284
4 TraesCS5B01G447800 chr5B 92.020 1767 106 11 5550 7307 619592328 619594068 0.000000e+00 2449
5 TraesCS5B01G447800 chr5B 83.622 2595 389 26 1746 4336 619298429 619300991 0.000000e+00 2405
6 TraesCS5B01G447800 chr5B 89.259 1741 144 24 1 1721 619462960 619464677 0.000000e+00 2139
7 TraesCS5B01G447800 chr5B 86.883 1944 206 24 2850 4787 619037607 619039507 0.000000e+00 2132
8 TraesCS5B01G447800 chr5B 86.895 1923 202 24 2792 4707 619062545 619064424 0.000000e+00 2109
9 TraesCS5B01G447800 chr5B 92.184 1497 106 8 4917 6405 619610168 619611661 0.000000e+00 2106
10 TraesCS5B01G447800 chr5B 85.850 2007 224 34 2792 4793 619064420 619066371 0.000000e+00 2078
11 TraesCS5B01G447800 chr5B 88.573 1514 147 13 242 1733 619099094 619100603 0.000000e+00 1814
12 TraesCS5B01G447800 chr5B 90.846 1289 100 9 447 1724 619224812 619226093 0.000000e+00 1711
13 TraesCS5B01G447800 chr5B 90.824 1286 100 9 447 1721 619166276 619167554 0.000000e+00 1705
14 TraesCS5B01G447800 chr5B 83.644 1822 270 17 1538 3353 619113621 619115420 0.000000e+00 1688
15 TraesCS5B01G447800 chr5B 83.333 1824 267 23 1536 3352 619076999 619078792 0.000000e+00 1650
16 TraesCS5B01G447800 chr5B 90.503 1253 99 10 484 1724 619217172 619218416 0.000000e+00 1637
17 TraesCS5B01G447800 chr5B 90.408 1251 103 7 484 1724 619163480 619164723 0.000000e+00 1629
18 TraesCS5B01G447800 chr5B 88.786 1079 102 11 242 1303 619123278 619124354 0.000000e+00 1304
19 TraesCS5B01G447800 chr5B 90.668 868 58 9 6402 7268 619762685 619763530 0.000000e+00 1133
20 TraesCS5B01G447800 chr5B 82.328 1194 175 25 1173 2342 619072723 619073904 0.000000e+00 1003
21 TraesCS5B01G447800 chr5B 82.116 1191 185 17 1173 2342 619109371 619110554 0.000000e+00 994
22 TraesCS5B01G447800 chr5B 86.775 862 100 7 1 849 619059109 619059969 0.000000e+00 948
23 TraesCS5B01G447800 chr5B 82.375 1078 163 20 1279 2337 619288486 619289555 0.000000e+00 913
24 TraesCS5B01G447800 chr5B 81.827 1084 169 21 1279 2342 619275838 619276913 0.000000e+00 885
25 TraesCS5B01G447800 chr5B 82.914 954 144 14 1173 2113 619286582 619287529 0.000000e+00 841
26 TraesCS5B01G447800 chr5B 90.881 636 41 1 4917 5552 619550092 619550710 0.000000e+00 837
27 TraesCS5B01G447800 chr5B 96.096 333 13 0 4792 5124 619220813 619221145 2.060000e-150 544
28 TraesCS5B01G447800 chr5B 86.623 456 31 16 1 451 619165296 619165726 2.120000e-130 477
29 TraesCS5B01G447800 chr5B 86.623 456 31 16 1 451 619222360 619222790 2.120000e-130 477
30 TraesCS5B01G447800 chr5B 90.625 256 12 8 1 255 619161858 619162102 6.280000e-86 329
31 TraesCS5B01G447800 chr5B 90.625 256 12 8 1 255 619215552 619215796 6.280000e-86 329
32 TraesCS5B01G447800 chr5D 97.422 3995 87 5 1 3984 499217812 499221801 0.000000e+00 6793
33 TraesCS5B01G447800 chr5D 92.135 3751 260 18 836 4580 499030408 499034129 0.000000e+00 5260
34 TraesCS5B01G447800 chr5D 97.431 2491 57 3 4025 6509 499221801 499224290 0.000000e+00 4239
35 TraesCS5B01G447800 chr5D 94.804 1867 78 10 6539 8392 499224286 499226146 0.000000e+00 2892
36 TraesCS5B01G447800 chr5D 90.237 1895 177 8 3042 4932 499092899 499094789 0.000000e+00 2468
37 TraesCS5B01G447800 chr5D 89.954 1742 120 31 1 1724 499056560 499058264 0.000000e+00 2196
38 TraesCS5B01G447800 chr5D 88.718 1755 187 9 3042 4793 499052677 499054423 0.000000e+00 2134
39 TraesCS5B01G447800 chr5D 89.271 1743 132 32 1 1724 499050884 499052590 0.000000e+00 2132
40 TraesCS5B01G447800 chr5D 91.452 1088 52 15 6222 7307 499108814 499109862 0.000000e+00 1456
41 TraesCS5B01G447800 chr5D 82.776 1196 170 25 1173 2342 499065782 499066967 0.000000e+00 1035
42 TraesCS5B01G447800 chr5D 92.564 659 41 3 5569 6219 499095106 499095764 0.000000e+00 939
43 TraesCS5B01G447800 chr5D 95.195 333 16 0 4792 5124 499054973 499055305 2.070000e-145 527
44 TraesCS5B01G447800 chr5A 94.875 3649 140 18 4698 8333 623489302 623492916 0.000000e+00 5659
45 TraesCS5B01G447800 chr5A 93.366 2442 133 13 4871 7307 623473264 623475681 0.000000e+00 3585
46 TraesCS5B01G447800 chr5A 92.845 2432 146 12 2365 4793 623321666 623324072 0.000000e+00 3502
47 TraesCS5B01G447800 chr5A 90.052 1739 138 20 1 1721 623469651 623471372 0.000000e+00 2220
48 TraesCS5B01G447800 chr5A 90.663 1660 151 4 3042 4699 623487484 623489141 0.000000e+00 2204
49 TraesCS5B01G447800 chr5A 90.278 1656 107 27 96 1721 623485763 623487394 0.000000e+00 2117
50 TraesCS5B01G447800 chr5A 92.447 1377 100 4 836 2210 623319392 623320766 0.000000e+00 1964
51 TraesCS5B01G447800 chr5A 81.041 749 108 25 4702 5431 691994582 691993849 4.400000e-157 566
52 TraesCS5B01G447800 chr7B 82.769 3099 469 39 1542 4611 711459873 711456811 0.000000e+00 2704
53 TraesCS5B01G447800 chr7B 80.628 2803 357 111 4650 7330 711456733 711453995 0.000000e+00 1997
54 TraesCS5B01G447800 chr7D 82.334 3102 480 43 1542 4611 617094021 617090956 0.000000e+00 2630
55 TraesCS5B01G447800 chr7D 82.112 2292 285 77 4650 6847 617090881 617088621 0.000000e+00 1845
56 TraesCS5B01G447800 chr7D 92.424 132 10 0 7199 7330 617088096 617087965 1.110000e-43 189
57 TraesCS5B01G447800 chr7A 82.093 2284 291 74 4650 6847 709968695 709966444 0.000000e+00 1844
58 TraesCS5B01G447800 chr7A 81.545 233 25 9 7114 7330 709966036 709965806 8.660000e-40 176
59 TraesCS5B01G447800 chr4B 90.557 646 40 9 6450 7095 286459589 286460213 0.000000e+00 835


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 TraesCS5B01G447800 chr5B 619846368 619854759 8391 False 15498.000000 15498 100.000000 1 8392 1 chr5B.!!$F12 8391
1 TraesCS5B01G447800 chr5B 619131142 619133717 2575 False 3336.000000 3336 90.163000 1303 3863 1 chr5B.!!$F3 2560
2 TraesCS5B01G447800 chr5B 619184328 619186900 2572 False 3284.000000 3284 89.814000 1303 3863 1 chr5B.!!$F4 2560
3 TraesCS5B01G447800 chr5B 619099094 619103415 4321 False 2673.500000 3533 89.044000 242 4725 2 chr5B.!!$F15 4483
4 TraesCS5B01G447800 chr5B 619592328 619594068 1740 False 2449.000000 2449 92.020000 5550 7307 1 chr5B.!!$F9 1757
5 TraesCS5B01G447800 chr5B 619298429 619300991 2562 False 2405.000000 2405 83.622000 1746 4336 1 chr5B.!!$F6 2590
6 TraesCS5B01G447800 chr5B 619462960 619464677 1717 False 2139.000000 2139 89.259000 1 1721 1 chr5B.!!$F7 1720
7 TraesCS5B01G447800 chr5B 619037607 619039507 1900 False 2132.000000 2132 86.883000 2850 4787 1 chr5B.!!$F1 1937
8 TraesCS5B01G447800 chr5B 619610168 619611661 1493 False 2106.000000 2106 92.184000 4917 6405 1 chr5B.!!$F10 1488
9 TraesCS5B01G447800 chr5B 619059109 619066371 7262 False 1711.666667 2109 86.506667 1 4793 3 chr5B.!!$F13 4792
10 TraesCS5B01G447800 chr5B 619109371 619115420 6049 False 1341.000000 1688 82.880000 1173 3353 2 chr5B.!!$F16 2180
11 TraesCS5B01G447800 chr5B 619072723 619078792 6069 False 1326.500000 1650 82.830500 1173 3352 2 chr5B.!!$F14 2179
12 TraesCS5B01G447800 chr5B 619123278 619124354 1076 False 1304.000000 1304 88.786000 242 1303 1 chr5B.!!$F2 1061
13 TraesCS5B01G447800 chr5B 619762685 619763530 845 False 1133.000000 1133 90.668000 6402 7268 1 chr5B.!!$F11 866
14 TraesCS5B01G447800 chr5B 619161858 619167554 5696 False 1035.000000 1705 89.620000 1 1724 4 chr5B.!!$F17 1723
15 TraesCS5B01G447800 chr5B 619215552 619226093 10541 False 939.600000 1711 90.938600 1 5124 5 chr5B.!!$F18 5123
16 TraesCS5B01G447800 chr5B 619275838 619276913 1075 False 885.000000 885 81.827000 1279 2342 1 chr5B.!!$F5 1063
17 TraesCS5B01G447800 chr5B 619286582 619289555 2973 False 877.000000 913 82.644500 1173 2337 2 chr5B.!!$F19 1164
18 TraesCS5B01G447800 chr5B 619550092 619550710 618 False 837.000000 837 90.881000 4917 5552 1 chr5B.!!$F8 635
19 TraesCS5B01G447800 chr5D 499030408 499034129 3721 False 5260.000000 5260 92.135000 836 4580 1 chr5D.!!$F1 3744
20 TraesCS5B01G447800 chr5D 499217812 499226146 8334 False 4641.333333 6793 96.552333 1 8392 3 chr5D.!!$F6 8391
21 TraesCS5B01G447800 chr5D 499050884 499058264 7380 False 1747.250000 2196 90.784500 1 5124 4 chr5D.!!$F4 5123
22 TraesCS5B01G447800 chr5D 499092899 499095764 2865 False 1703.500000 2468 91.400500 3042 6219 2 chr5D.!!$F5 3177
23 TraesCS5B01G447800 chr5D 499108814 499109862 1048 False 1456.000000 1456 91.452000 6222 7307 1 chr5D.!!$F3 1085
24 TraesCS5B01G447800 chr5D 499065782 499066967 1185 False 1035.000000 1035 82.776000 1173 2342 1 chr5D.!!$F2 1169
25 TraesCS5B01G447800 chr5A 623485763 623492916 7153 False 3326.666667 5659 91.938667 96 8333 3 chr5A.!!$F3 8237
26 TraesCS5B01G447800 chr5A 623469651 623475681 6030 False 2902.500000 3585 91.709000 1 7307 2 chr5A.!!$F2 7306
27 TraesCS5B01G447800 chr5A 623319392 623324072 4680 False 2733.000000 3502 92.646000 836 4793 2 chr5A.!!$F1 3957
28 TraesCS5B01G447800 chr5A 691993849 691994582 733 True 566.000000 566 81.041000 4702 5431 1 chr5A.!!$R1 729
29 TraesCS5B01G447800 chr7B 711453995 711459873 5878 True 2350.500000 2704 81.698500 1542 7330 2 chr7B.!!$R1 5788
30 TraesCS5B01G447800 chr7D 617087965 617094021 6056 True 1554.666667 2630 85.623333 1542 7330 3 chr7D.!!$R1 5788
31 TraesCS5B01G447800 chr7A 709965806 709968695 2889 True 1010.000000 1844 81.819000 4650 7330 2 chr7A.!!$R1 2680
32 TraesCS5B01G447800 chr4B 286459589 286460213 624 False 835.000000 835 90.557000 6450 7095 1 chr4B.!!$F1 645

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
734 5945 0.035317 ATGTTGCGCAGGAGTCTTGA 59.965 50.000 11.31 0.0 0.00 3.02 F
1922 9161 0.886490 GCGTATCAAGGGATGGGCAG 60.886 60.000 0.00 0.0 34.84 4.85 F
3224 15905 1.002792 ACTCGCGCTTCAAAACTTTCC 60.003 47.619 5.56 0.0 0.00 3.13 F
3866 16557 0.323725 GTGGGGCACTCACATTGGAT 60.324 55.000 3.05 0.0 35.39 3.41 F
5304 20997 1.257936 CGTACAAAATGGGCGATCGAG 59.742 52.381 21.57 0.0 0.00 4.04 F
5877 21711 0.741326 TGACACTAGCATCGCTCCTC 59.259 55.000 0.00 0.0 40.44 3.71 F
5946 21792 1.004745 TGGCCTTCCTTGACTTCCATC 59.995 52.381 3.32 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 14634 0.100682 CAGCATGCCATCTTCACTGC 59.899 55.000 15.66 0.00 0.0 4.40 R
3673 16364 1.228124 CCCTCGCCAACTTCAACCA 60.228 57.895 0.00 0.00 0.0 3.67 R
5102 20527 2.173569 AGGGTTGCAAGACAGTTCTCTT 59.826 45.455 0.00 0.00 0.0 2.85 R
5633 21463 1.266718 TGACAAAACGCTGAGCATTCC 59.733 47.619 4.88 0.00 0.0 3.01 R
7038 26414 0.725784 GCACGTGCACACAACTATGC 60.726 55.000 34.52 10.16 42.4 3.14 R
7163 26714 3.450096 TGTGGGATCAGATCAGAGTCTTG 59.550 47.826 12.66 0.00 0.0 3.02 R
7737 27312 5.171339 AGCTCAAGAGTTGGTATCATGTT 57.829 39.130 0.00 0.00 0.0 2.71 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
40 3479 6.462768 GGCTTGATTTATAAATGGTGGCATCA 60.463 38.462 15.39 1.35 0.00 3.07
321 4955 4.589908 GATGGTTGATGGGTACTTCTTGT 58.410 43.478 0.00 0.00 0.00 3.16
384 5023 0.254462 TTGCCCATAGGTTGCATCGA 59.746 50.000 0.00 0.00 34.51 3.59
435 5074 5.248640 TCTTGGTTGCTCTATTTCTTCTGG 58.751 41.667 0.00 0.00 0.00 3.86
471 5664 2.178580 GGCATTTCATCACCCCTTCAA 58.821 47.619 0.00 0.00 0.00 2.69
570 5776 2.159170 GGTGAAGCTTCTACGCTCTGAT 60.159 50.000 26.09 0.00 39.86 2.90
734 5945 0.035317 ATGTTGCGCAGGAGTCTTGA 59.965 50.000 11.31 0.00 0.00 3.02
800 6012 1.745653 GATTCAACTGGCCAGGTAAGC 59.254 52.381 35.42 23.55 0.00 3.09
909 6292 6.262273 ACGAATTGTTGATTTGAGGTGTAACT 59.738 34.615 0.00 0.00 33.43 2.24
1284 8480 7.335924 TCAACAATATACTTTACAAGGCCACTC 59.664 37.037 5.01 0.00 0.00 3.51
1401 8618 6.348498 TGCATACATACTTGCACTACATTCT 58.652 36.000 0.00 0.00 43.54 2.40
1882 9121 2.956333 CGAAAAGGACAGGAAAAAGGGT 59.044 45.455 0.00 0.00 0.00 4.34
1922 9161 0.886490 GCGTATCAAGGGATGGGCAG 60.886 60.000 0.00 0.00 34.84 4.85
2069 9364 4.497291 TGTGTTGAAGTTTACAGGGAGT 57.503 40.909 0.00 0.00 0.00 3.85
2132 9427 2.124529 TGCTTGCCGGTGTTGTCA 60.125 55.556 1.90 0.00 0.00 3.58
2598 14634 6.824305 AGAAAAGGATGAGTACATGTTTGG 57.176 37.500 2.30 0.00 36.82 3.28
2638 15061 5.390991 GCTGCCAGTAAGAATACTCAACAAC 60.391 44.000 0.00 0.00 40.44 3.32
2839 15493 4.152284 AGATCAAGGGATTCCGGTTTAC 57.848 45.455 0.00 0.00 38.33 2.01
2845 15504 2.172082 AGGGATTCCGGTTTACCTAAGC 59.828 50.000 8.24 0.00 38.33 3.09
2901 15560 6.271566 GCTCGATGATCTGCATATCTATTCA 58.728 40.000 12.72 0.00 37.34 2.57
2930 15593 5.024118 ACATAGCTTGGTAAGTACTCCTGT 58.976 41.667 0.00 0.00 0.00 4.00
3224 15905 1.002792 ACTCGCGCTTCAAAACTTTCC 60.003 47.619 5.56 0.00 0.00 3.13
3440 16125 1.679944 GGGCAGATGAAGCTAGCAACA 60.680 52.381 18.83 16.21 0.00 3.33
3567 16257 4.081476 TCAGCAGGATATGGGATGATTACG 60.081 45.833 0.00 0.00 0.00 3.18
3673 16364 2.566746 AGAAGATGATGTTGAGGGGGT 58.433 47.619 0.00 0.00 0.00 4.95
3691 16382 1.228124 TGGTTGAAGTTGGCGAGGG 60.228 57.895 0.00 0.00 0.00 4.30
3734 16425 5.006746 GCCATCAACAAGGTCTAGAAATACG 59.993 44.000 0.00 0.00 0.00 3.06
3866 16557 0.323725 GTGGGGCACTCACATTGGAT 60.324 55.000 3.05 0.00 35.39 3.41
4873 20250 6.191657 ACATTTATATGATCCTGGCACTGA 57.808 37.500 0.00 0.00 35.65 3.41
4875 20252 7.062322 ACATTTATATGATCCTGGCACTGAAA 58.938 34.615 0.00 0.00 35.65 2.69
5102 20527 5.049060 CGGATAAACACAAGGATGAAACACA 60.049 40.000 0.00 0.00 0.00 3.72
5304 20997 1.257936 CGTACAAAATGGGCGATCGAG 59.742 52.381 21.57 0.00 0.00 4.04
5321 21122 1.929836 CGAGTATGAAGAACCTGCTGC 59.070 52.381 0.00 0.00 0.00 5.25
5633 21463 0.759346 GCCTCACCTATACACCAGGG 59.241 60.000 0.00 0.00 37.51 4.45
5675 21509 3.281727 TCCTCTTGTTGCTTGACACTT 57.718 42.857 0.00 0.00 0.00 3.16
5877 21711 0.741326 TGACACTAGCATCGCTCCTC 59.259 55.000 0.00 0.00 40.44 3.71
5946 21792 1.004745 TGGCCTTCCTTGACTTCCATC 59.995 52.381 3.32 0.00 0.00 3.51
6187 22098 2.147436 GAGCTCCTTTCCGCTCTATG 57.853 55.000 0.87 0.00 46.87 2.23
6513 25353 4.727507 TGAGAAGGTAGCATTCAGTCTC 57.272 45.455 0.00 0.00 0.00 3.36
6516 25356 5.163468 TGAGAAGGTAGCATTCAGTCTCATC 60.163 44.000 0.00 0.00 36.12 2.92
6518 25358 3.378512 AGGTAGCATTCAGTCTCATCCA 58.621 45.455 0.00 0.00 0.00 3.41
6520 25360 4.040217 AGGTAGCATTCAGTCTCATCCATC 59.960 45.833 0.00 0.00 0.00 3.51
6523 25363 5.883685 AGCATTCAGTCTCATCCATCTTA 57.116 39.130 0.00 0.00 0.00 2.10
6526 25366 6.935771 AGCATTCAGTCTCATCCATCTTATTC 59.064 38.462 0.00 0.00 0.00 1.75
6563 25455 2.098934 ACATTCTCTGCTGCTCTCTACG 59.901 50.000 0.00 0.00 0.00 3.51
6752 25911 1.168714 GCAACTTCCCCACATCAGTC 58.831 55.000 0.00 0.00 0.00 3.51
6857 26080 3.185880 TCCCAGGTAAGCAAGTACTCT 57.814 47.619 0.00 0.00 0.00 3.24
6965 26317 5.154222 GCAACTACACTTGGCTAAAATGAC 58.846 41.667 1.31 0.00 0.00 3.06
6966 26318 5.278266 GCAACTACACTTGGCTAAAATGACA 60.278 40.000 1.31 0.00 0.00 3.58
6967 26319 6.570378 GCAACTACACTTGGCTAAAATGACAT 60.570 38.462 1.31 0.00 0.00 3.06
6969 26321 7.611213 ACTACACTTGGCTAAAATGACATAC 57.389 36.000 1.31 0.00 0.00 2.39
7038 26414 8.665643 ATTGAGCTATTTTCTCAGAATCAGAG 57.334 34.615 0.00 0.00 41.10 3.35
7046 26422 7.606858 TTTTCTCAGAATCAGAGCATAGTTG 57.393 36.000 0.00 0.00 33.15 3.16
7163 26714 6.610741 ATCGGATCTGCTGTTATCTTTTTC 57.389 37.500 0.00 0.00 0.00 2.29
7330 26897 1.077212 AAGCCATCGATGCCAAGCT 60.077 52.632 20.25 18.83 0.00 3.74
7333 26900 2.719979 CATCGATGCCAAGCTGCC 59.280 61.111 13.37 0.00 0.00 4.85
7353 26923 6.109156 TGCCTAAGTTAACTGAAGACATGA 57.891 37.500 9.34 0.00 0.00 3.07
7432 27002 4.832248 TCTGAAGTTATTACAGGCTGGTG 58.168 43.478 20.34 0.00 33.19 4.17
7455 27025 7.227314 GGTGACATGAATCTTTATGTGCATCTA 59.773 37.037 0.00 0.00 37.63 1.98
7509 27079 1.210478 TGGAGGGAACATGCTCTTAGC 59.790 52.381 0.00 0.00 42.82 3.09
7591 27162 8.685838 ATCCTAGTAAACAGCAACTGTAAAAA 57.314 30.769 0.00 0.00 44.62 1.94
7951 27528 0.954452 GAACCCAACTCTGCACCTTG 59.046 55.000 0.00 0.00 0.00 3.61
7990 27567 7.448161 TCTCTTTCATGTATCAGCTTTTCCAAA 59.552 33.333 0.00 0.00 0.00 3.28
7993 27570 7.945033 TTCATGTATCAGCTTTTCCAAAAAC 57.055 32.000 0.00 0.00 0.00 2.43
7995 27572 5.860941 TGTATCAGCTTTTCCAAAAACCA 57.139 34.783 0.00 0.00 0.00 3.67
8003 27580 5.822519 AGCTTTTCCAAAAACCAAATCTTCC 59.177 36.000 0.00 0.00 0.00 3.46
8007 27584 2.799978 CCAAAAACCAAATCTTCCGTGC 59.200 45.455 0.00 0.00 0.00 5.34
8021 27598 2.034879 CGTGCTGGCCCTGTTACTG 61.035 63.158 0.00 0.00 0.00 2.74
8037 27614 9.010029 CCCTGTTACTGTGTTAGTTAATTCAAT 57.990 33.333 0.00 0.00 40.89 2.57
8038 27615 9.825972 CCTGTTACTGTGTTAGTTAATTCAATG 57.174 33.333 0.00 0.00 40.89 2.82
8064 27643 8.859236 ATGCATAAGAACATAGCAAGATACAT 57.141 30.769 0.00 0.00 38.85 2.29
8162 27742 7.713764 AAATTTCCCTTGAAAAACAGATTCG 57.286 32.000 0.00 0.00 43.37 3.34
8235 27815 5.659079 ACTACAAACAAATCAAAACTCCCCA 59.341 36.000 0.00 0.00 0.00 4.96
8255 27835 4.198530 CCACAAAAGGGAAAGCAAACAAT 58.801 39.130 0.00 0.00 0.00 2.71
8286 27866 2.950309 ACCGCATACAGACTACGAAGAT 59.050 45.455 0.00 0.00 0.00 2.40
8356 27937 1.512926 CCACACTCAGGAAGAAACGG 58.487 55.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 3479 8.491950 GTTTCAAAATACACAAACACAAACAGT 58.508 29.630 0.00 0.00 0.00 3.55
264 4896 1.984297 GAACGGAGTGAGAGCGTTAAC 59.016 52.381 0.00 0.00 45.00 2.01
384 5023 0.112412 ACAAAAATGGGGAGAGGCGT 59.888 50.000 0.00 0.00 0.00 5.68
435 5074 0.941542 TGCCAAGTACACAAAGCGAC 59.058 50.000 0.00 0.00 0.00 5.19
471 5664 5.209818 TCACAGTAAGTCGGATTCAAACT 57.790 39.130 0.00 0.00 0.00 2.66
533 5730 4.620982 CTTCACCCAGATTGAAACCAAAC 58.379 43.478 0.00 0.00 32.61 2.93
542 5739 2.932614 CGTAGAAGCTTCACCCAGATTG 59.067 50.000 27.57 6.40 0.00 2.67
734 5945 2.813754 CACGATTCACCACCACAGAAAT 59.186 45.455 0.00 0.00 0.00 2.17
800 6012 1.230212 GTGGGGAGGGGGCAATAAG 59.770 63.158 0.00 0.00 0.00 1.73
909 6292 9.594478 TCAAATTACGAAATCAAGAGTATAGCA 57.406 29.630 0.00 0.00 0.00 3.49
1096 6479 3.006659 GCAATGTTGCGGAAACTACAA 57.993 42.857 1.53 0.00 45.11 2.41
1121 6504 6.995686 TGACCGTGTAATTTGCTAATATGGAT 59.004 34.615 7.20 0.00 0.00 3.41
1269 6667 2.851195 ACACAGAGTGGCCTTGTAAAG 58.149 47.619 3.32 0.00 39.97 1.85
1284 8480 5.281727 TGATTATGCTCGCTTACTACACAG 58.718 41.667 0.00 0.00 0.00 3.66
1401 8618 7.581213 AAATATTGGACACACTGAAAGAACA 57.419 32.000 0.00 0.00 37.43 3.18
1574 8811 1.761784 TGTTCTTTTGCAGCCAATGGT 59.238 42.857 0.00 0.00 0.00 3.55
1882 9121 4.034626 CGCCCAAATTTGACACATCGTATA 59.965 41.667 19.86 0.00 0.00 1.47
1922 9161 2.219458 GCCTTCCTTATAGCCGGAAAC 58.781 52.381 5.05 0.00 38.72 2.78
2069 9364 0.387929 CCGCCAACCGATCTAGCTAA 59.612 55.000 0.00 0.00 40.02 3.09
2132 9427 4.082026 GCCACTGCTCAAATTAATGGAACT 60.082 41.667 0.00 0.00 33.53 3.01
2598 14634 0.100682 CAGCATGCCATCTTCACTGC 59.899 55.000 15.66 0.00 0.00 4.40
2638 15061 9.730705 TTGAAATCTGAATTATATAGAGCCCAG 57.269 33.333 0.00 0.00 0.00 4.45
2839 15493 2.961062 CCATTCCTTGATTGGGCTTAGG 59.039 50.000 0.00 0.00 31.67 2.69
2845 15504 2.181975 ACAAGCCATTCCTTGATTGGG 58.818 47.619 8.71 0.00 43.79 4.12
2901 15560 4.281898 ACTTACCAAGCTATGTCGGTTT 57.718 40.909 0.00 0.00 32.81 3.27
2957 15620 9.786105 CAAGCAATTGTAACATGTGTTCATATA 57.214 29.630 7.40 0.00 39.31 0.86
2958 15621 7.276218 GCAAGCAATTGTAACATGTGTTCATAT 59.724 33.333 7.40 0.00 39.31 1.78
2959 15622 6.585702 GCAAGCAATTGTAACATGTGTTCATA 59.414 34.615 7.40 0.00 39.31 2.15
3440 16125 2.160417 CGCCGCTTGAGATTTCTTCTTT 59.840 45.455 0.00 0.00 33.74 2.52
3567 16257 1.753073 CTCTGGGAAATGGGTTGCATC 59.247 52.381 0.00 0.00 0.00 3.91
3673 16364 1.228124 CCCTCGCCAACTTCAACCA 60.228 57.895 0.00 0.00 0.00 3.67
3691 16382 1.464997 GCGAGGTCCTTGAAACATGTC 59.535 52.381 10.67 0.00 0.00 3.06
3734 16425 5.618056 TTTCTTCACAAGCATCTGATGAC 57.382 39.130 21.30 12.02 0.00 3.06
3866 16557 1.361204 TGGCTTCTCCTGAATGACCA 58.639 50.000 0.00 0.00 35.26 4.02
4623 19247 9.492973 CACAATATGATGGTAGTGATTCACATA 57.507 33.333 18.57 6.48 36.74 2.29
4629 19253 5.766670 CAGGCACAATATGATGGTAGTGATT 59.233 40.000 0.00 0.00 0.00 2.57
4873 20250 3.845781 TTCTGACCTGCTTGAGAGTTT 57.154 42.857 0.00 0.00 0.00 2.66
4875 20252 2.902486 TCATTCTGACCTGCTTGAGAGT 59.098 45.455 0.00 0.00 0.00 3.24
5102 20527 2.173569 AGGGTTGCAAGACAGTTCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
5321 21122 5.220340 GGATGATTTTGAAGAAATGCTTGCG 60.220 40.000 0.00 0.00 36.83 4.85
5529 21355 8.608844 TTCTTAACCTTCTCATCTGAAAGTTC 57.391 34.615 0.00 0.00 33.97 3.01
5633 21463 1.266718 TGACAAAACGCTGAGCATTCC 59.733 47.619 4.88 0.00 0.00 3.01
5675 21509 3.415212 CCCTGAGAAAAGATGCACAGAA 58.585 45.455 0.00 0.00 0.00 3.02
5877 21711 1.823295 CACCTGGTACCCCATCTCG 59.177 63.158 10.07 0.00 40.90 4.04
5946 21792 3.562973 ACATGCAGACAAGTTCAGAACAG 59.437 43.478 15.85 9.75 0.00 3.16
5998 21853 3.573491 GCGACGCCATAAGCACCC 61.573 66.667 9.14 0.00 44.04 4.61
6121 21976 4.202367 GCATAGTATTTACCTCCTGGCAGT 60.202 45.833 14.43 0.00 36.63 4.40
6187 22098 2.803492 GCCGATTGTATCCCTGACTGTC 60.803 54.545 0.00 0.00 0.00 3.51
6516 25356 9.955102 TGAATAAGATGGATGAGAATAAGATGG 57.045 33.333 0.00 0.00 0.00 3.51
6523 25363 9.504708 GAGAATGTGAATAAGATGGATGAGAAT 57.495 33.333 0.00 0.00 0.00 2.40
6526 25366 7.095144 GCAGAGAATGTGAATAAGATGGATGAG 60.095 40.741 0.00 0.00 0.00 2.90
6752 25911 1.389609 GCATTGGCTGGGGATCTGTG 61.390 60.000 0.00 0.00 36.96 3.66
6857 26080 6.100279 AGAGTGTTGATAGGGATATCTGCAAA 59.900 38.462 2.05 0.00 0.00 3.68
6966 26318 9.654663 GGAACAAAATCTACTGTCAACTAGTAT 57.345 33.333 0.00 0.00 30.83 2.12
6967 26319 8.092687 GGGAACAAAATCTACTGTCAACTAGTA 58.907 37.037 0.00 0.00 0.00 1.82
6969 26321 6.934645 TGGGAACAAAATCTACTGTCAACTAG 59.065 38.462 0.00 0.00 37.44 2.57
7026 26400 5.291371 CACACAACTATGCTCTGATTCTGAG 59.709 44.000 14.37 14.37 33.52 3.35
7038 26414 0.725784 GCACGTGCACACAACTATGC 60.726 55.000 34.52 10.16 42.40 3.14
7107 26650 4.427312 GTGCATTGGATTCTGATTTGTCC 58.573 43.478 0.00 0.00 0.00 4.02
7109 26652 3.507233 ACGTGCATTGGATTCTGATTTGT 59.493 39.130 0.00 0.00 0.00 2.83
7163 26714 3.450096 TGTGGGATCAGATCAGAGTCTTG 59.550 47.826 12.66 0.00 0.00 3.02
7330 26897 6.109156 TCATGTCTTCAGTTAACTTAGGCA 57.891 37.500 18.87 18.87 0.00 4.75
7333 26900 8.777865 TTGGATCATGTCTTCAGTTAACTTAG 57.222 34.615 5.07 6.77 0.00 2.18
7374 26944 5.711976 CCAGAATTTATATAGGGCCCAGTTG 59.288 44.000 27.56 4.11 0.00 3.16
7432 27002 9.608617 CAATAGATGCACATAAAGATTCATGTC 57.391 33.333 0.00 0.00 33.12 3.06
7455 27025 8.971073 CCTGATGTTTTTAATCCTCCTTACAAT 58.029 33.333 0.00 0.00 0.00 2.71
7509 27079 7.120579 TGTTTACTAAAGATTATGCACCCACTG 59.879 37.037 0.00 0.00 0.00 3.66
7516 27086 7.857456 TCCCTCTGTTTACTAAAGATTATGCA 58.143 34.615 0.00 0.00 0.00 3.96
7730 27305 9.470399 TCAAGAGTTGGTATCATGTTACTAGTA 57.530 33.333 12.51 0.00 0.00 1.82
7737 27312 5.171339 AGCTCAAGAGTTGGTATCATGTT 57.829 39.130 0.00 0.00 0.00 2.71
7951 27528 2.278854 GAAAGAGATCAGCTGACAGGC 58.721 52.381 20.97 9.03 0.00 4.85
7990 27567 1.613437 CCAGCACGGAAGATTTGGTTT 59.387 47.619 0.00 0.00 36.56 3.27
7993 27570 1.508088 GCCAGCACGGAAGATTTGG 59.492 57.895 0.00 0.00 36.56 3.28
7995 27572 1.678970 GGGCCAGCACGGAAGATTT 60.679 57.895 4.39 0.00 36.56 2.17
8003 27580 2.034879 CAGTAACAGGGCCAGCACG 61.035 63.158 6.18 0.00 0.00 5.34
8007 27584 2.038557 ACTAACACAGTAACAGGGCCAG 59.961 50.000 6.18 0.00 34.98 4.85
8037 27614 7.933033 TGTATCTTGCTATGTTCTTATGCATCA 59.067 33.333 0.19 0.00 33.50 3.07
8038 27615 8.315391 TGTATCTTGCTATGTTCTTATGCATC 57.685 34.615 0.19 0.00 33.50 3.91
8039 27616 8.859236 ATGTATCTTGCTATGTTCTTATGCAT 57.141 30.769 3.79 3.79 33.50 3.96
8040 27617 8.562052 CAATGTATCTTGCTATGTTCTTATGCA 58.438 33.333 0.00 0.00 0.00 3.96
8064 27643 9.376075 TGTGAAAATAAAGCTTGTGAAATTCAA 57.624 25.926 0.00 0.00 0.00 2.69
8086 27665 3.332783 TCCCTCCTACTGACTAGTTGTGA 59.667 47.826 0.00 0.00 38.36 3.58
8162 27742 6.932356 TTCTTAAGCTGATTGTGATGATCC 57.068 37.500 0.00 0.00 0.00 3.36
8235 27815 6.043127 AGGATATTGTTTGCTTTCCCTTTTGT 59.957 34.615 0.00 0.00 0.00 2.83
8255 27835 5.567430 AGTCTGTATGCGGTGTATAGGATA 58.433 41.667 0.00 0.00 0.00 2.59
8286 27866 3.084536 TGTAATGCTCTGGGATTGCAA 57.915 42.857 0.00 0.00 41.11 4.08


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

AutoCloner maintained by Alex Coulton.