Multiple sequence alignment - TraesCS5B01G022200

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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 TraesCS5B01G022200 chr5B 100.000 4356 0 0 1 4356 20815366 20811011 0.000000e+00 8045.0
1 TraesCS5B01G022200 chr5B 82.704 821 136 6 3540 4356 19591239 19592057 0.000000e+00 725.0
2 TraesCS5B01G022200 chr5B 83.871 744 117 3 3615 4356 19672630 19673372 0.000000e+00 706.0
3 TraesCS5B01G022200 chr5B 84.825 659 87 8 1022 1673 19575691 19576343 0.000000e+00 651.0
4 TraesCS5B01G022200 chr5B 84.067 659 88 11 1022 1673 19589857 19590505 1.720000e-173 619.0
5 TraesCS5B01G022200 chr5D 96.575 1343 43 3 3016 4356 28481120 28482461 0.000000e+00 2222.0
6 TraesCS5B01G022200 chr5D 95.856 748 25 1 932 1673 28480375 28481122 0.000000e+00 1205.0
7 TraesCS5B01G022200 chr5D 83.724 725 115 3 3634 4356 27432599 27433322 0.000000e+00 682.0
8 TraesCS5B01G022200 chr5D 82.032 807 138 7 3554 4356 27438366 27439169 0.000000e+00 680.0
9 TraesCS5B01G022200 chr5D 82.976 746 120 7 3615 4356 27459594 27460336 0.000000e+00 667.0
10 TraesCS5B01G022200 chr5D 83.752 677 102 4 1001 1673 27399154 27399826 6.150000e-178 634.0
11 TraesCS5B01G022200 chr5D 82.055 691 106 8 1001 1673 27436927 27437617 1.360000e-159 573.0
12 TraesCS5B01G022200 chr5D 82.535 647 83 13 3018 3649 27431839 27432470 3.830000e-150 542.0
13 TraesCS5B01G022200 chr5D 84.029 551 67 9 1131 1672 27458254 27458792 1.080000e-140 510.0
14 TraesCS5B01G022200 chr5D 84.600 500 71 6 3846 4341 27409444 27409941 3.910000e-135 492.0
15 TraesCS5B01G022200 chr5D 79.904 627 80 14 1063 1671 27278900 27279498 6.740000e-113 418.0
16 TraesCS5B01G022200 chr5D 82.639 432 61 9 3634 4061 27309372 27309793 1.910000e-98 370.0
17 TraesCS5B01G022200 chr5D 84.298 363 57 0 3018 3380 27279500 27279862 5.360000e-94 355.0
18 TraesCS5B01G022200 chr5D 85.256 312 40 5 4049 4356 27310143 27310452 2.530000e-82 316.0
19 TraesCS5B01G022200 chr5D 96.774 62 2 0 866 927 28480266 28480327 2.140000e-18 104.0
20 TraesCS5B01G022200 chr5A 95.902 1342 54 1 3016 4356 19106136 19107477 0.000000e+00 2172.0
21 TraesCS5B01G022200 chr5A 96.123 748 23 1 932 1673 19105391 19106138 0.000000e+00 1216.0
22 TraesCS5B01G022200 chr5A 90.083 605 32 9 2443 3022 396007085 396006484 0.000000e+00 760.0
23 TraesCS5B01G022200 chr5A 83.690 748 111 11 3615 4356 18710376 18711118 0.000000e+00 695.0
24 TraesCS5B01G022200 chr5A 82.999 747 118 9 3615 4356 18790347 18791089 0.000000e+00 667.0
25 TraesCS5B01G022200 chr5A 84.545 550 64 10 1131 1672 18788997 18789533 3.860000e-145 525.0
26 TraesCS5B01G022200 chr5A 96.000 50 2 0 878 927 19105294 19105343 1.000000e-11 82.4
27 TraesCS5B01G022200 chr2B 93.570 1322 31 17 1742 3015 45321018 45319703 0.000000e+00 1921.0
28 TraesCS5B01G022200 chr2B 92.740 1336 35 12 1739 3015 788845378 788846710 0.000000e+00 1873.0
29 TraesCS5B01G022200 chr2B 92.729 1334 30 17 1742 3015 651899052 651897726 0.000000e+00 1864.0
30 TraesCS5B01G022200 chr2B 91.692 1324 40 16 1742 3019 513477958 513476659 0.000000e+00 1772.0
31 TraesCS5B01G022200 chr2B 97.468 79 2 0 2937 3015 28337159 28337237 7.600000e-28 135.0
32 TraesCS5B01G022200 chr6B 93.403 1334 26 21 1742 3017 142607111 142605782 0.000000e+00 1919.0
33 TraesCS5B01G022200 chr6B 93.553 1303 49 12 1743 3015 647269744 647268447 0.000000e+00 1908.0
34 TraesCS5B01G022200 chr6B 91.473 1337 52 18 1742 3021 646400593 646399262 0.000000e+00 1781.0
35 TraesCS5B01G022200 chr6B 92.899 845 33 7 18 835 255012113 255012957 0.000000e+00 1203.0
36 TraesCS5B01G022200 chr6B 92.154 599 23 9 2443 3017 43926380 43925782 0.000000e+00 824.0
37 TraesCS5B01G022200 chr4B 91.907 1421 33 18 1672 3018 631500523 631499111 0.000000e+00 1912.0
38 TraesCS5B01G022200 chr4B 93.418 1018 24 12 2040 3017 657620336 657619322 0.000000e+00 1469.0
39 TraesCS5B01G022200 chr4B 92.782 1039 35 5 2022 3021 635757758 635756721 0.000000e+00 1467.0
40 TraesCS5B01G022200 chr4B 87.987 308 9 5 1674 1956 609502151 609501847 5.400000e-89 339.0
41 TraesCS5B01G022200 chr7B 92.836 1340 28 17 1739 3015 732683443 732684777 0.000000e+00 1881.0
42 TraesCS5B01G022200 chr7B 95.644 1056 21 8 1739 2774 26956358 26957408 0.000000e+00 1672.0
43 TraesCS5B01G022200 chr7B 94.549 1064 26 6 1739 2774 572426990 572428049 0.000000e+00 1615.0
44 TraesCS5B01G022200 chr7B 97.590 83 2 0 2934 3016 548740838 548740920 4.540000e-30 143.0
45 TraesCS5B01G022200 chr1B 92.163 1327 50 15 1672 2950 22865660 22864340 0.000000e+00 1825.0
46 TraesCS5B01G022200 chr1B 92.695 1013 28 9 2051 3018 22348382 22349393 0.000000e+00 1419.0
47 TraesCS5B01G022200 chr1B 81.424 646 78 19 3018 3649 631119117 631118500 1.410000e-134 490.0
48 TraesCS5B01G022200 chr1B 88.050 318 18 12 1671 1972 559228779 559228466 4.140000e-95 359.0
49 TraesCS5B01G022200 chr1B 86.687 323 43 0 1349 1671 631119441 631119119 4.140000e-95 359.0
50 TraesCS5B01G022200 chr1B 89.706 272 2 1 1674 1919 58175265 58174994 1.510000e-84 324.0
51 TraesCS5B01G022200 chr1B 86.306 314 15 12 1666 1954 22347641 22347951 2.530000e-82 316.0
52 TraesCS5B01G022200 chrUn 89.323 1433 40 21 1666 3015 261212666 261214068 0.000000e+00 1694.0
53 TraesCS5B01G022200 chrUn 91.883 1158 37 10 1669 2775 268063425 268062274 0.000000e+00 1565.0
54 TraesCS5B01G022200 chrUn 91.810 1160 35 12 1669 2775 358347083 358345931 0.000000e+00 1561.0
55 TraesCS5B01G022200 chrUn 90.552 688 30 7 1673 2329 318541839 318542522 0.000000e+00 878.0
56 TraesCS5B01G022200 chrUn 92.833 600 16 10 2443 3017 335391070 335391667 0.000000e+00 845.0
57 TraesCS5B01G022200 chrUn 92.550 604 16 13 2443 3020 363516089 363515489 0.000000e+00 839.0
58 TraesCS5B01G022200 chrUn 90.704 355 4 2 1674 2002 134960042 134960393 3.090000e-121 446.0
59 TraesCS5B01G022200 chrUn 88.041 393 10 4 1674 2032 478716360 478716749 8.650000e-117 431.0
60 TraesCS5B01G022200 chrUn 88.889 351 9 5 1673 1997 65781676 65782022 5.250000e-109 405.0
61 TraesCS5B01G022200 chrUn 88.535 314 7 2 1674 1961 472935910 472936220 1.930000e-93 353.0
62 TraesCS5B01G022200 chrUn 84.034 238 12 3 1674 1885 63127395 63127158 5.710000e-49 206.0
63 TraesCS5B01G022200 chrUn 97.753 89 2 0 1674 1762 94227909 94227997 2.100000e-33 154.0
64 TraesCS5B01G022200 chr7A 90.015 1312 74 13 1753 3015 137747569 137746266 0.000000e+00 1644.0
65 TraesCS5B01G022200 chr7A 89.831 1298 89 16 1753 3015 523507970 523506681 0.000000e+00 1626.0
66 TraesCS5B01G022200 chr4A 92.596 1040 38 12 2018 3022 667018520 667017485 0.000000e+00 1458.0
67 TraesCS5B01G022200 chr4A 92.399 592 24 10 2443 3017 407529942 407529355 0.000000e+00 824.0
68 TraesCS5B01G022200 chr4A 88.276 725 26 12 2339 3021 323249339 323250046 0.000000e+00 813.0
69 TraesCS5B01G022200 chr4A 86.195 297 12 4 1672 1942 705725685 705725392 1.180000e-75 294.0
70 TraesCS5B01G022200 chr4A 87.215 219 2 1 1673 1865 704312638 704312420 4.380000e-55 226.0
71 TraesCS5B01G022200 chr3A 92.679 601 16 12 2443 3017 658246325 658246923 0.000000e+00 841.0
72 TraesCS5B01G022200 chr3D 77.571 807 163 16 3558 4356 12808026 12807230 5.100000e-129 472.0
73 TraesCS5B01G022200 chr3D 78.788 660 120 15 1026 1672 12803568 12802916 4.030000e-115 425.0
74 TraesCS5B01G022200 chr3D 78.939 641 113 17 1046 1672 12809415 12808783 2.420000e-112 416.0
75 TraesCS5B01G022200 chr3D 77.479 706 139 17 3660 4356 12751368 12750674 5.250000e-109 405.0
76 TraesCS5B01G022200 chr3D 79.487 585 99 15 1002 1579 12722477 12723047 3.160000e-106 396.0
77 TraesCS5B01G022200 chr3D 76.590 739 152 17 3628 4356 12505214 12504487 1.900000e-103 387.0
78 TraesCS5B01G022200 chr3D 81.381 333 56 2 1346 1672 12554980 12554648 2.580000e-67 267.0
79 TraesCS5B01G022200 chr3D 74.439 579 126 19 3019 3586 12702945 12703512 3.390000e-56 230.0
80 TraesCS5B01G022200 chr1A 93.043 115 6 2 1674 1786 588363367 588363481 2.690000e-37 167.0


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 TraesCS5B01G022200 chr5B 20811011 20815366 4355 True 8045.000000 8045 100.000000 1 4356 1 chr5B.!!$R1 4355
1 TraesCS5B01G022200 chr5B 19672630 19673372 742 False 706.000000 706 83.871000 3615 4356 1 chr5B.!!$F2 741
2 TraesCS5B01G022200 chr5B 19589857 19592057 2200 False 672.000000 725 83.385500 1022 4356 2 chr5B.!!$F3 3334
3 TraesCS5B01G022200 chr5B 19575691 19576343 652 False 651.000000 651 84.825000 1022 1673 1 chr5B.!!$F1 651
4 TraesCS5B01G022200 chr5D 28480266 28482461 2195 False 1177.000000 2222 96.401667 866 4356 3 chr5D.!!$F7 3490
5 TraesCS5B01G022200 chr5D 27399154 27399826 672 False 634.000000 634 83.752000 1001 1673 1 chr5D.!!$F1 672
6 TraesCS5B01G022200 chr5D 27431839 27439169 7330 False 619.250000 682 82.586500 1001 4356 4 chr5D.!!$F5 3355
7 TraesCS5B01G022200 chr5D 27458254 27460336 2082 False 588.500000 667 83.502500 1131 4356 2 chr5D.!!$F6 3225
8 TraesCS5B01G022200 chr5D 27278900 27279862 962 False 386.500000 418 82.101000 1063 3380 2 chr5D.!!$F3 2317
9 TraesCS5B01G022200 chr5D 27309372 27310452 1080 False 343.000000 370 83.947500 3634 4356 2 chr5D.!!$F4 722
10 TraesCS5B01G022200 chr5A 19105294 19107477 2183 False 1156.800000 2172 96.008333 878 4356 3 chr5A.!!$F3 3478
11 TraesCS5B01G022200 chr5A 396006484 396007085 601 True 760.000000 760 90.083000 2443 3022 1 chr5A.!!$R1 579
12 TraesCS5B01G022200 chr5A 18710376 18711118 742 False 695.000000 695 83.690000 3615 4356 1 chr5A.!!$F1 741
13 TraesCS5B01G022200 chr5A 18788997 18791089 2092 False 596.000000 667 83.772000 1131 4356 2 chr5A.!!$F2 3225
14 TraesCS5B01G022200 chr2B 45319703 45321018 1315 True 1921.000000 1921 93.570000 1742 3015 1 chr2B.!!$R1 1273
15 TraesCS5B01G022200 chr2B 788845378 788846710 1332 False 1873.000000 1873 92.740000 1739 3015 1 chr2B.!!$F2 1276
16 TraesCS5B01G022200 chr2B 651897726 651899052 1326 True 1864.000000 1864 92.729000 1742 3015 1 chr2B.!!$R3 1273
17 TraesCS5B01G022200 chr2B 513476659 513477958 1299 True 1772.000000 1772 91.692000 1742 3019 1 chr2B.!!$R2 1277
18 TraesCS5B01G022200 chr6B 142605782 142607111 1329 True 1919.000000 1919 93.403000 1742 3017 1 chr6B.!!$R2 1275
19 TraesCS5B01G022200 chr6B 647268447 647269744 1297 True 1908.000000 1908 93.553000 1743 3015 1 chr6B.!!$R4 1272
20 TraesCS5B01G022200 chr6B 646399262 646400593 1331 True 1781.000000 1781 91.473000 1742 3021 1 chr6B.!!$R3 1279
21 TraesCS5B01G022200 chr6B 255012113 255012957 844 False 1203.000000 1203 92.899000 18 835 1 chr6B.!!$F1 817
22 TraesCS5B01G022200 chr6B 43925782 43926380 598 True 824.000000 824 92.154000 2443 3017 1 chr6B.!!$R1 574
23 TraesCS5B01G022200 chr4B 631499111 631500523 1412 True 1912.000000 1912 91.907000 1672 3018 1 chr4B.!!$R2 1346
24 TraesCS5B01G022200 chr4B 657619322 657620336 1014 True 1469.000000 1469 93.418000 2040 3017 1 chr4B.!!$R4 977
25 TraesCS5B01G022200 chr4B 635756721 635757758 1037 True 1467.000000 1467 92.782000 2022 3021 1 chr4B.!!$R3 999
26 TraesCS5B01G022200 chr7B 732683443 732684777 1334 False 1881.000000 1881 92.836000 1739 3015 1 chr7B.!!$F4 1276
27 TraesCS5B01G022200 chr7B 26956358 26957408 1050 False 1672.000000 1672 95.644000 1739 2774 1 chr7B.!!$F1 1035
28 TraesCS5B01G022200 chr7B 572426990 572428049 1059 False 1615.000000 1615 94.549000 1739 2774 1 chr7B.!!$F3 1035
29 TraesCS5B01G022200 chr1B 22864340 22865660 1320 True 1825.000000 1825 92.163000 1672 2950 1 chr1B.!!$R1 1278
30 TraesCS5B01G022200 chr1B 22347641 22349393 1752 False 867.500000 1419 89.500500 1666 3018 2 chr1B.!!$F1 1352
31 TraesCS5B01G022200 chr1B 631118500 631119441 941 True 424.500000 490 84.055500 1349 3649 2 chr1B.!!$R4 2300
32 TraesCS5B01G022200 chrUn 261212666 261214068 1402 False 1694.000000 1694 89.323000 1666 3015 1 chrUn.!!$F4 1349
33 TraesCS5B01G022200 chrUn 268062274 268063425 1151 True 1565.000000 1565 91.883000 1669 2775 1 chrUn.!!$R2 1106
34 TraesCS5B01G022200 chrUn 358345931 358347083 1152 True 1561.000000 1561 91.810000 1669 2775 1 chrUn.!!$R3 1106
35 TraesCS5B01G022200 chrUn 318541839 318542522 683 False 878.000000 878 90.552000 1673 2329 1 chrUn.!!$F5 656
36 TraesCS5B01G022200 chrUn 335391070 335391667 597 False 845.000000 845 92.833000 2443 3017 1 chrUn.!!$F6 574
37 TraesCS5B01G022200 chrUn 363515489 363516089 600 True 839.000000 839 92.550000 2443 3020 1 chrUn.!!$R4 577
38 TraesCS5B01G022200 chr7A 137746266 137747569 1303 True 1644.000000 1644 90.015000 1753 3015 1 chr7A.!!$R1 1262
39 TraesCS5B01G022200 chr7A 523506681 523507970 1289 True 1626.000000 1626 89.831000 1753 3015 1 chr7A.!!$R2 1262
40 TraesCS5B01G022200 chr4A 667017485 667018520 1035 True 1458.000000 1458 92.596000 2018 3022 1 chr4A.!!$R2 1004
41 TraesCS5B01G022200 chr4A 407529355 407529942 587 True 824.000000 824 92.399000 2443 3017 1 chr4A.!!$R1 574
42 TraesCS5B01G022200 chr4A 323249339 323250046 707 False 813.000000 813 88.276000 2339 3021 1 chr4A.!!$F1 682
43 TraesCS5B01G022200 chr3A 658246325 658246923 598 False 841.000000 841 92.679000 2443 3017 1 chr3A.!!$F1 574
44 TraesCS5B01G022200 chr3D 12802916 12809415 6499 True 437.666667 472 78.432667 1026 4356 3 chr3D.!!$R4 3330
45 TraesCS5B01G022200 chr3D 12750674 12751368 694 True 405.000000 405 77.479000 3660 4356 1 chr3D.!!$R3 696
46 TraesCS5B01G022200 chr3D 12722477 12723047 570 False 396.000000 396 79.487000 1002 1579 1 chr3D.!!$F2 577
47 TraesCS5B01G022200 chr3D 12504487 12505214 727 True 387.000000 387 76.590000 3628 4356 1 chr3D.!!$R1 728
48 TraesCS5B01G022200 chr3D 12702945 12703512 567 False 230.000000 230 74.439000 3019 3586 1 chr3D.!!$F1 567

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
927 955 0.250467 ATCACAGTGTGGCCACAGAC 60.250 55.0 38.55 26.89 44.39 3.51 F
1324 1413 0.178533 CAATACGTTTCCGGGCCCTA 59.821 55.0 22.43 4.58 38.78 3.53 F
1617 1731 0.671781 ACTCAGCGGACATCACTTGC 60.672 55.0 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2073 1.276989 CGGTACTAAAGGCTTGTCCCA 59.723 52.381 0.00 0.0 34.51 4.37 R
3188 3832 2.430694 GGCTTGTCACTTTCCAAAACCT 59.569 45.455 0.00 0.0 0.00 3.50 R
3525 4207 0.868406 GTTTCTGGACAGGTCAAGCG 59.132 55.000 1.41 0.0 30.64 4.68 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
17 18 3.041351 TGCGCCACAGCTACAACG 61.041 61.111 4.18 0.00 38.13 4.10
18 19 3.788766 GCGCCACAGCTACAACGG 61.789 66.667 0.00 0.00 36.60 4.44
19 20 2.048597 CGCCACAGCTACAACGGA 60.049 61.111 0.00 0.00 36.60 4.69
20 21 2.380410 CGCCACAGCTACAACGGAC 61.380 63.158 0.00 0.00 36.60 4.79
21 22 2.380410 GCCACAGCTACAACGGACG 61.380 63.158 0.00 0.00 35.50 4.79
22 23 1.736645 CCACAGCTACAACGGACGG 60.737 63.158 0.00 0.00 0.00 4.79
23 24 1.006571 CACAGCTACAACGGACGGT 60.007 57.895 0.00 0.00 0.00 4.83
24 25 1.006571 ACAGCTACAACGGACGGTG 60.007 57.895 8.38 8.38 39.06 4.94
25 26 1.736645 CAGCTACAACGGACGGTGG 60.737 63.158 14.72 0.36 37.09 4.61
26 27 2.205152 AGCTACAACGGACGGTGGT 61.205 57.895 14.72 6.62 37.09 4.16
120 121 1.760875 GCCCTACCAGACCCGATCA 60.761 63.158 0.00 0.00 0.00 2.92
122 123 1.424638 CCCTACCAGACCCGATCAAT 58.575 55.000 0.00 0.00 0.00 2.57
138 139 0.519519 CAATGCAAAGTACGGCCGAA 59.480 50.000 35.90 6.58 0.00 4.30
170 171 1.425412 CCCTAGGAACAACACGAACG 58.575 55.000 11.48 0.00 0.00 3.95
171 172 1.425412 CCTAGGAACAACACGAACGG 58.575 55.000 1.05 0.00 0.00 4.44
200 201 2.223433 ACCCTCGATCGAATCACGTAAC 60.223 50.000 19.92 0.00 43.13 2.50
202 203 3.249320 CCCTCGATCGAATCACGTAACTA 59.751 47.826 19.92 0.00 43.13 2.24
224 225 2.158959 GTCAGACGGGTTCGATGCG 61.159 63.158 0.00 0.00 40.11 4.73
228 229 3.636313 GACGGGTTCGATGCGGTGA 62.636 63.158 0.00 0.00 40.11 4.02
242 243 1.065928 GGTGACCTGGATCGCTACG 59.934 63.158 0.00 0.00 0.00 3.51
328 329 2.033550 CCAACAACGAATTCAAACGGGA 59.966 45.455 6.22 0.00 0.00 5.14
334 335 2.551032 ACGAATTCAAACGGGAAAGTCC 59.449 45.455 6.22 0.00 35.23 3.85
353 354 1.079543 CATCGCCCGGATCTCATCC 60.080 63.158 0.73 0.00 46.22 3.51
385 401 1.531840 GCGGCCTAGATCTCCTCCA 60.532 63.158 0.00 0.00 0.00 3.86
483 499 2.709125 CTTCCAAGGCCGTGTCGACA 62.709 60.000 15.76 15.76 0.00 4.35
619 635 1.830408 CCTCCTCCGAGTAGCCAGG 60.830 68.421 0.00 0.00 33.93 4.45
672 688 2.117156 GGAGAGTACGCCGCCACTA 61.117 63.158 6.29 0.00 0.00 2.74
703 719 3.483869 GGCGGCCTCCTCCTCATT 61.484 66.667 12.87 0.00 0.00 2.57
750 766 1.299976 GCCCAGAAACGACTCCCAT 59.700 57.895 0.00 0.00 0.00 4.00
754 770 0.389817 CAGAAACGACTCCCATCGCA 60.390 55.000 0.00 0.00 46.22 5.10
786 802 2.556287 CCGGCAGAAACTTGTCGC 59.444 61.111 0.00 0.00 44.34 5.19
835 863 2.967615 GCCTCGCTTACCCATCGC 60.968 66.667 0.00 0.00 0.00 4.58
836 864 2.280186 CCTCGCTTACCCATCGCC 60.280 66.667 0.00 0.00 0.00 5.54
837 865 2.797278 CCTCGCTTACCCATCGCCT 61.797 63.158 0.00 0.00 0.00 5.52
838 866 1.300233 CTCGCTTACCCATCGCCTC 60.300 63.158 0.00 0.00 0.00 4.70
839 867 2.280186 CGCTTACCCATCGCCTCC 60.280 66.667 0.00 0.00 0.00 4.30
840 868 2.908015 GCTTACCCATCGCCTCCA 59.092 61.111 0.00 0.00 0.00 3.86
841 869 1.227674 GCTTACCCATCGCCTCCAG 60.228 63.158 0.00 0.00 0.00 3.86
842 870 1.686325 GCTTACCCATCGCCTCCAGA 61.686 60.000 0.00 0.00 0.00 3.86
843 871 0.390860 CTTACCCATCGCCTCCAGAG 59.609 60.000 0.00 0.00 0.00 3.35
844 872 1.686325 TTACCCATCGCCTCCAGAGC 61.686 60.000 0.00 0.00 0.00 4.09
864 892 2.953020 CGCAAGCTTCTCAACTAGTCT 58.047 47.619 0.00 0.00 0.00 3.24
870 898 2.739379 GCTTCTCAACTAGTCTTGTGGC 59.261 50.000 0.00 0.00 0.00 5.01
927 955 0.250467 ATCACAGTGTGGCCACAGAC 60.250 55.000 38.55 26.89 44.39 3.51
970 1041 4.886163 TGACCATAGACTACATGGGGTTA 58.114 43.478 8.76 0.00 46.14 2.85
981 1052 6.970191 ACTACATGGGGTTAGCTTAAAGATT 58.030 36.000 0.00 0.00 0.00 2.40
985 1056 6.603599 ACATGGGGTTAGCTTAAAGATTTCTC 59.396 38.462 0.00 0.00 0.00 2.87
1182 1271 3.061848 GCCGCCTTGCTTGCCTTA 61.062 61.111 0.00 0.00 0.00 2.69
1324 1413 0.178533 CAATACGTTTCCGGGCCCTA 59.821 55.000 22.43 4.58 38.78 3.53
1326 1415 0.911053 ATACGTTTCCGGGCCCTAAA 59.089 50.000 22.43 17.29 38.78 1.85
1411 1505 6.212388 TCTGCTTTCCTTGAAGAATCTAGAGT 59.788 38.462 0.00 0.00 31.03 3.24
1522 1616 3.432186 CCTCTCTGGCATTCCATTTACGA 60.432 47.826 0.00 0.00 42.51 3.43
1617 1731 0.671781 ACTCAGCGGACATCACTTGC 60.672 55.000 0.00 0.00 0.00 4.01
1930 2073 2.963432 CACGAACCGGTGGTACTAAAT 58.037 47.619 8.52 0.00 33.12 1.40
2556 3072 5.046304 ACTTCATGCTCAAGCTAAACTCCTA 60.046 40.000 3.32 0.00 42.66 2.94
2753 3270 9.403583 AGTTAAGAGAGGTGATTAGAGACTAAG 57.596 37.037 0.00 0.00 0.00 2.18
2762 3279 8.816894 AGGTGATTAGAGACTAAGTCATCAAAA 58.183 33.333 0.00 0.00 34.60 2.44
3050 3694 1.543429 GGCCTCGTCCCTTGAATATGG 60.543 57.143 0.00 0.00 0.00 2.74
3062 3706 6.000219 CCCTTGAATATGGTTCCATCACTAG 59.000 44.000 7.67 7.23 0.00 2.57
3156 3800 5.136105 ACTTGAGAAGCTTGATTTGTCCTT 58.864 37.500 2.10 0.00 0.00 3.36
3188 3832 2.754552 GGCCACTCAATTGCATCAAGTA 59.245 45.455 0.00 0.00 0.00 2.24
3355 4020 9.855021 CTTCAAAGTCTTCTTAAAAACCTTTGA 57.145 29.630 7.59 7.59 36.78 2.69
3449 4117 0.314935 ATGCGCACAGGAAAAGTTGG 59.685 50.000 14.90 0.00 0.00 3.77
3525 4207 1.135460 GGAATTCAGCAGCTTGAGCAC 60.135 52.381 7.93 0.00 45.16 4.40
3682 4724 6.951198 AGAATCTGGTTTCTCTGAGACTAAGA 59.049 38.462 6.92 8.62 29.99 2.10
3716 4758 0.904649 TGGTGCGATCACAGAAGGAT 59.095 50.000 0.00 0.00 44.87 3.24
3778 4820 7.028962 TGTCTTCCAATAATTTGAAGATTGCG 58.971 34.615 11.32 0.00 34.52 4.85
3840 12649 3.930848 GGAGATTTTGCATCTTGCCAAAG 59.069 43.478 5.23 0.00 44.23 2.77
3953 12762 9.874205 CTGATTGGTTTTGGTATACATTTTCAT 57.126 29.630 5.01 0.00 0.00 2.57
4074 12883 0.609131 CTCACCGGGTCAATGCCTTT 60.609 55.000 6.32 0.00 0.00 3.11
4093 12902 2.834574 TGTTGCCGGCAAATATTACG 57.165 45.000 41.60 0.00 37.70 3.18
4140 12949 6.653989 ACTTTTCAGGAGTAATACCATCCAG 58.346 40.000 2.20 0.00 35.45 3.86
4168 12977 2.838202 AGCCTCCCGACTTCAAATCTTA 59.162 45.455 0.00 0.00 0.00 2.10
4202 13011 3.662759 ATCGGATTGGTGGGTACATTT 57.337 42.857 0.00 0.00 0.00 2.32
4291 13101 9.013490 GTGAAATTCCTCAATGTTTTCATATCG 57.987 33.333 0.00 0.00 39.94 2.92
4325 13135 5.880332 AGTTTCTTCTGCTCAGTAACAACAA 59.120 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.380410 CGTCCGTTGTAGCTGTGGC 61.380 63.158 0.00 0.00 39.06 5.01
7 8 1.736645 CCACCGTCCGTTGTAGCTG 60.737 63.158 0.00 0.00 0.00 4.24
8 9 2.205152 ACCACCGTCCGTTGTAGCT 61.205 57.895 0.00 0.00 0.00 3.32
9 10 2.025418 CACCACCGTCCGTTGTAGC 61.025 63.158 0.00 0.00 0.00 3.58
10 11 1.373748 CCACCACCGTCCGTTGTAG 60.374 63.158 0.00 0.00 0.00 2.74
11 12 2.735883 CCACCACCGTCCGTTGTA 59.264 61.111 0.00 0.00 0.00 2.41
12 13 4.922026 GCCACCACCGTCCGTTGT 62.922 66.667 0.00 0.00 0.00 3.32
13 14 4.619227 AGCCACCACCGTCCGTTG 62.619 66.667 0.00 0.00 0.00 4.10
14 15 4.619227 CAGCCACCACCGTCCGTT 62.619 66.667 0.00 0.00 0.00 4.44
63 64 0.742635 GCTGCTGGTCCTGTTAGCTC 60.743 60.000 15.19 0.34 38.25 4.09
99 100 1.950748 ATCGGGTCTGGTAGGGCTCT 61.951 60.000 0.00 0.00 0.00 4.09
120 121 1.240256 TTTCGGCCGTACTTTGCATT 58.760 45.000 27.15 0.00 0.00 3.56
122 123 0.308376 GTTTTCGGCCGTACTTTGCA 59.692 50.000 27.15 0.00 0.00 4.08
138 139 1.192428 CCTAGGGCTACCGTGAGTTT 58.808 55.000 0.00 0.00 43.47 2.66
170 171 0.386113 CGATCGAGGGTTTCTCTCCC 59.614 60.000 10.26 0.00 44.90 4.30
171 172 1.390565 TCGATCGAGGGTTTCTCTCC 58.609 55.000 15.15 0.00 40.30 3.71
200 201 1.399440 TCGAACCCGTCTGACGATTAG 59.601 52.381 29.93 21.42 46.05 1.73
202 203 0.815734 ATCGAACCCGTCTGACGATT 59.184 50.000 29.93 22.30 46.05 3.34
224 225 1.065928 CGTAGCGATCCAGGTCACC 59.934 63.158 0.00 0.00 0.00 4.02
228 229 2.423898 CCCACGTAGCGATCCAGGT 61.424 63.158 0.00 0.00 0.00 4.00
305 306 2.223618 CCGTTTGAATTCGTTGTTGGGT 60.224 45.455 0.04 0.00 0.00 4.51
328 329 2.325393 GATCCGGGCGATGGGACTTT 62.325 60.000 0.00 0.00 34.58 2.66
334 335 1.079543 GATGAGATCCGGGCGATGG 60.080 63.158 0.00 0.00 0.00 3.51
385 401 2.224523 TGGAAGGTTGTGAAAGATCGCT 60.225 45.455 0.00 0.00 36.99 4.93
583 599 1.457009 GGTTGTGGCCGGCTTTGTTA 61.457 55.000 28.56 4.31 0.00 2.41
619 635 4.947147 TGTGCGAGGTGTTGGGGC 62.947 66.667 0.00 0.00 0.00 5.80
642 658 4.180946 CTCTCCGACGCCGAGTGG 62.181 72.222 0.00 0.00 38.22 4.00
724 740 2.282180 GTTTCTGGGCCCTTGCGA 60.282 61.111 25.70 11.41 38.85 5.10
767 783 2.556287 GACAAGTTTCTGCCGGCG 59.444 61.111 23.90 16.91 0.00 6.46
843 871 1.391826 GACTAGTTGAGAAGCTTGCGC 59.608 52.381 2.10 0.00 0.00 6.09
844 872 2.953020 AGACTAGTTGAGAAGCTTGCG 58.047 47.619 2.10 0.00 0.00 4.85
845 873 4.061596 ACAAGACTAGTTGAGAAGCTTGC 58.938 43.478 2.10 0.00 36.61 4.01
846 874 4.450419 CCACAAGACTAGTTGAGAAGCTTG 59.550 45.833 2.10 13.71 37.84 4.01
847 875 4.636249 CCACAAGACTAGTTGAGAAGCTT 58.364 43.478 0.00 0.00 0.00 3.74
848 876 3.556004 GCCACAAGACTAGTTGAGAAGCT 60.556 47.826 0.00 0.00 0.00 3.74
849 877 2.739379 GCCACAAGACTAGTTGAGAAGC 59.261 50.000 0.00 0.00 0.00 3.86
850 878 3.993081 CAGCCACAAGACTAGTTGAGAAG 59.007 47.826 0.00 0.00 0.00 2.85
851 879 3.803715 GCAGCCACAAGACTAGTTGAGAA 60.804 47.826 0.00 0.00 0.00 2.87
852 880 2.289072 GCAGCCACAAGACTAGTTGAGA 60.289 50.000 0.00 0.00 0.00 3.27
853 881 2.072298 GCAGCCACAAGACTAGTTGAG 58.928 52.381 0.00 0.00 0.00 3.02
854 882 1.416030 TGCAGCCACAAGACTAGTTGA 59.584 47.619 0.00 0.00 0.00 3.18
855 883 1.802960 CTGCAGCCACAAGACTAGTTG 59.197 52.381 0.00 0.00 0.00 3.16
856 884 1.271054 CCTGCAGCCACAAGACTAGTT 60.271 52.381 8.66 0.00 0.00 2.24
857 885 0.322975 CCTGCAGCCACAAGACTAGT 59.677 55.000 8.66 0.00 0.00 2.57
858 886 1.023513 GCCTGCAGCCACAAGACTAG 61.024 60.000 8.66 0.00 34.35 2.57
859 887 1.003355 GCCTGCAGCCACAAGACTA 60.003 57.895 8.66 0.00 34.35 2.59
860 888 2.282040 GCCTGCAGCCACAAGACT 60.282 61.111 8.66 0.00 34.35 3.24
861 889 2.595463 TGCCTGCAGCCACAAGAC 60.595 61.111 8.66 0.00 42.71 3.01
862 890 2.595463 GTGCCTGCAGCCACAAGA 60.595 61.111 22.12 0.00 42.71 3.02
863 891 2.596631 AGTGCCTGCAGCCACAAG 60.597 61.111 27.69 5.82 42.71 3.16
864 892 2.595463 GAGTGCCTGCAGCCACAA 60.595 61.111 27.69 0.00 42.71 3.33
870 898 1.274728 AGACTAGTTGAGTGCCTGCAG 59.725 52.381 6.78 6.78 39.06 4.41
879 907 2.037772 ACCAGCCACAAGACTAGTTGAG 59.962 50.000 0.00 0.00 0.00 3.02
927 955 2.122729 TCCCAGTCCCAGTCCCAG 59.877 66.667 0.00 0.00 0.00 4.45
929 957 1.134438 AAAGTCCCAGTCCCAGTCCC 61.134 60.000 0.00 0.00 0.00 4.46
970 1041 9.953697 CACTATACTACGAGAAATCTTTAAGCT 57.046 33.333 0.00 0.00 0.00 3.74
981 1052 6.819397 AGCATATGCACTATACTACGAGAA 57.181 37.500 28.62 0.00 45.16 2.87
985 1056 5.103000 GGGAAGCATATGCACTATACTACG 58.897 45.833 28.62 0.00 45.16 3.51
1182 1271 2.039084 GTCACTTGTGATCCCCTTCTGT 59.961 50.000 6.74 0.00 0.00 3.41
1221 1310 2.487265 GCAATCATACCCTTCCCACGAT 60.487 50.000 0.00 0.00 0.00 3.73
1324 1413 6.074698 ACACCCATTGTAGTTATAGGCTTT 57.925 37.500 0.00 0.00 36.32 3.51
1411 1505 6.239217 ACAGTTCATGCTAAGATCCATGTA 57.761 37.500 8.83 0.00 39.74 2.29
1522 1616 3.513515 CCAAGCTGAGAAGGAACTCTACT 59.486 47.826 0.00 0.00 38.49 2.57
1617 1731 3.366374 GCAGCAAGGGTAGCTTTGTTAAG 60.366 47.826 16.83 3.24 41.14 1.85
1740 1882 5.509716 ACACGAATCGGTACTATTGATCA 57.490 39.130 7.80 0.00 0.00 2.92
1921 2064 3.646736 AGGCTTGTCCCATTTAGTACC 57.353 47.619 0.00 0.00 34.51 3.34
1922 2065 6.178324 ACTAAAGGCTTGTCCCATTTAGTAC 58.822 40.000 0.00 0.00 42.10 2.73
1923 2066 6.382919 ACTAAAGGCTTGTCCCATTTAGTA 57.617 37.500 0.00 0.00 42.10 1.82
1930 2073 1.276989 CGGTACTAAAGGCTTGTCCCA 59.723 52.381 0.00 0.00 34.51 4.37
2556 3072 9.004231 AGTAAGATGTCAATCCTATTAACCCTT 57.996 33.333 0.00 0.00 32.77 3.95
2586 3102 3.953612 TCTGCACTTGTTGTTTTCCTGAT 59.046 39.130 0.00 0.00 0.00 2.90
3050 3694 7.731054 AGATTGATAACTCCTAGTGATGGAAC 58.269 38.462 0.00 0.00 32.61 3.62
3062 3706 4.023365 GCATCCAGCAAGATTGATAACTCC 60.023 45.833 0.00 0.00 44.79 3.85
3156 3800 5.532406 GCAATTGAGTGGCCTAGATTATTCA 59.468 40.000 10.34 0.00 0.00 2.57
3188 3832 2.430694 GGCTTGTCACTTTCCAAAACCT 59.569 45.455 0.00 0.00 0.00 3.50
3355 4020 1.561542 AGGTCGAGGATTTCCAAGCAT 59.438 47.619 0.00 0.00 38.89 3.79
3481 4163 4.962362 CCTATAAAATTTGGCAAGGTCCCT 59.038 41.667 0.00 0.00 0.00 4.20
3525 4207 0.868406 GTTTCTGGACAGGTCAAGCG 59.132 55.000 1.41 0.00 30.64 4.68
3649 4547 5.868801 CAGAGAAACCAGATTCTTCAGAGAC 59.131 44.000 0.00 0.00 39.70 3.36
3682 4724 2.552315 CGCACCACCAAGTCTATTGTTT 59.448 45.455 0.00 0.00 0.00 2.83
3778 4820 3.022406 AGAAAGCCAATCTGAATCCAGC 58.978 45.455 0.00 0.00 40.20 4.85
3840 12649 2.428530 CAAGCTGGAAATAAAGGCCCTC 59.571 50.000 0.00 0.00 0.00 4.30
3921 12730 8.062065 TGTATACCAAAACCAATCAGGAAATC 57.938 34.615 0.00 0.00 41.22 2.17
3953 12762 0.904649 ATGTCGAGATCAGTTGCCCA 59.095 50.000 0.00 0.00 0.00 5.36
4074 12883 2.085320 ACGTAATATTTGCCGGCAACA 58.915 42.857 40.36 30.02 35.46 3.33
4093 12902 9.614792 AAGTTATTATTGGAGATGTCTAACCAC 57.385 33.333 0.00 0.00 31.87 4.16
4168 12977 7.416664 CCACCAATCCGATTTGAATAGACAATT 60.417 37.037 0.00 0.00 0.00 2.32
4186 12995 2.993937 TCGGAAATGTACCCACCAATC 58.006 47.619 0.00 0.00 0.00 2.67
4291 13101 8.131731 ACTGAGCAGAAGAAACTGTAATTTTTC 58.868 33.333 4.21 0.00 39.73 2.29
4325 13135 8.613922 AAATGTTGGGAATCTTCCTGATAAAT 57.386 30.769 8.78 0.00 46.72 1.40


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

AutoCloner maintained by Alex Coulton.