Multiple sequence alignment - TraesCS3A01G516200

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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 TraesCS3A01G516200 chr3A 100.000 5316 0 0 1 5316 733926836 733921521 0.000000e+00 9817.0
1 TraesCS3A01G516200 chr3A 94.651 1290 63 3 1947 3236 710121900 710123183 0.000000e+00 1995.0
2 TraesCS3A01G516200 chr3A 92.678 478 27 7 1416 1890 474815984 474816456 0.000000e+00 682.0
3 TraesCS3A01G516200 chr3A 92.165 485 31 6 1414 1895 721334586 721335066 0.000000e+00 678.0
4 TraesCS3A01G516200 chr3A 91.959 485 30 8 1416 1895 676246656 676246176 0.000000e+00 671.0
5 TraesCS3A01G516200 chr3A 85.474 475 56 8 4448 4920 732435724 732435261 2.880000e-132 483.0
6 TraesCS3A01G516200 chr3A 89.655 116 11 1 5001 5115 732435261 732435146 4.290000e-31 147.0
7 TraesCS3A01G516200 chr3A 100.000 28 0 0 3238 3265 733871465 733871438 1.000000e-02 52.8
8 TraesCS3A01G516200 chr7A 93.732 1420 63 1 1843 3236 95227215 95228634 0.000000e+00 2106.0
9 TraesCS3A01G516200 chr7A 93.662 1420 63 2 1843 3236 95234391 95235809 0.000000e+00 2098.0
10 TraesCS3A01G516200 chr7A 93.053 1425 73 3 1843 3241 690773910 690772486 0.000000e+00 2060.0
11 TraesCS3A01G516200 chr7A 92.181 486 31 6 1413 1895 690774382 690773901 0.000000e+00 680.0
12 TraesCS3A01G516200 chr7A 80.412 97 12 4 327 417 534134551 534134646 3.440000e-07 67.6
13 TraesCS3A01G516200 chr7A 77.358 106 16 5 85 184 708312139 708312036 7.440000e-04 56.5
14 TraesCS3A01G516200 chr6A 93.601 1422 64 3 1843 3238 104450176 104451596 0.000000e+00 2097.0
15 TraesCS3A01G516200 chr6A 93.446 1419 65 3 1845 3236 602742783 602741366 0.000000e+00 2080.0
16 TraesCS3A01G516200 chr6A 85.863 481 48 10 4448 4920 192044 191576 1.330000e-135 494.0
17 TraesCS3A01G516200 chr6A 80.299 335 42 12 5001 5314 191576 191245 1.150000e-56 231.0
18 TraesCS3A01G516200 chr6A 75.909 220 35 15 431 636 420946415 420946200 4.380000e-16 97.1
19 TraesCS3A01G516200 chrUn 93.592 1420 64 2 1843 3236 82679985 82678567 0.000000e+00 2093.0
20 TraesCS3A01G516200 chrUn 88.627 1187 94 19 3267 4444 42250614 42251768 0.000000e+00 1406.0
21 TraesCS3A01G516200 chrUn 84.439 784 84 22 1 775 42248951 42249705 0.000000e+00 737.0
22 TraesCS3A01G516200 chrUn 83.801 642 37 22 800 1398 42249898 42250515 1.010000e-151 547.0
23 TraesCS3A01G516200 chrUn 82.819 454 31 15 800 1224 42243656 42244091 3.910000e-96 363.0
24 TraesCS3A01G516200 chrUn 82.488 217 22 6 3459 3675 42263320 42263520 5.470000e-40 176.0
25 TraesCS3A01G516200 chrUn 82.979 141 14 4 802 932 42216393 42216533 9.350000e-23 119.0
26 TraesCS3A01G516200 chr2A 93.399 1424 61 5 1843 3236 770409020 770407600 0.000000e+00 2078.0
27 TraesCS3A01G516200 chr2A 92.479 1436 54 5 1843 3236 101860922 101862345 0.000000e+00 2004.0
28 TraesCS3A01G516200 chr2A 88.774 1354 84 25 1418 2713 720493125 720491782 0.000000e+00 1596.0
29 TraesCS3A01G516200 chr2A 92.197 487 31 6 1412 1895 101860449 101860931 0.000000e+00 682.0
30 TraesCS3A01G516200 chr5A 92.978 1424 74 5 1843 3240 694534353 694532930 0.000000e+00 2052.0
31 TraesCS3A01G516200 chr5A 98.046 870 16 1 4446 5315 549341576 549342444 0.000000e+00 1511.0
32 TraesCS3A01G516200 chr5A 87.131 474 50 7 4449 4920 522979870 522979406 1.310000e-145 527.0
33 TraesCS3A01G516200 chr5A 92.241 116 8 1 5001 5115 522979406 522979291 4.260000e-36 163.0
34 TraesCS3A01G516200 chr5A 89.655 116 11 1 5001 5115 559502118 559502003 4.290000e-31 147.0
35 TraesCS3A01G516200 chr4A 90.131 1449 81 19 1845 3236 597036339 597037782 0.000000e+00 1827.0
36 TraesCS3A01G516200 chr4A 89.599 1423 91 21 1845 3238 69990473 69991867 0.000000e+00 1755.0
37 TraesCS3A01G516200 chr4A 87.948 1087 89 20 1415 2469 605365102 605366178 0.000000e+00 1243.0
38 TraesCS3A01G516200 chr4A 74.725 364 46 33 137 484 737414544 737414211 2.600000e-23 121.0
39 TraesCS3A01G516200 chr3D 90.769 1235 72 16 3235 4450 604291619 604290408 0.000000e+00 1611.0
40 TraesCS3A01G516200 chr3D 85.934 782 90 17 1 772 604293196 604292425 0.000000e+00 817.0
41 TraesCS3A01G516200 chr3D 84.923 650 31 16 800 1418 604292229 604291616 3.540000e-166 595.0
42 TraesCS3A01G516200 chr3D 86.345 476 49 7 4449 4916 445343835 445343368 6.140000e-139 505.0
43 TraesCS3A01G516200 chr3D 85.655 481 54 8 4449 4920 457836909 457837383 4.780000e-135 492.0
44 TraesCS3A01G516200 chr3D 76.440 191 33 11 450 636 356951991 356951809 5.670000e-15 93.5
45 TraesCS3A01G516200 chr1B 86.908 1352 134 22 1418 2727 650100201 650098851 0.000000e+00 1476.0
46 TraesCS3A01G516200 chr1B 87.527 465 48 6 4450 4913 317554319 317554774 3.650000e-146 529.0
47 TraesCS3A01G516200 chr1B 85.417 480 45 11 4449 4920 518872953 518873415 4.820000e-130 475.0
48 TraesCS3A01G516200 chr1B 73.763 465 69 35 230 657 558503501 558503949 3.340000e-27 134.0
49 TraesCS3A01G516200 chr7B 84.755 1102 78 28 1888 2929 474477613 474478684 0.000000e+00 1022.0
50 TraesCS3A01G516200 chr7B 77.500 160 29 6 420 574 527959656 527959813 7.330000e-14 89.8
51 TraesCS3A01G516200 chr1A 91.909 482 29 9 1418 1895 100043916 100043441 0.000000e+00 665.0
52 TraesCS3A01G516200 chr1A 87.368 475 48 8 4449 4920 589899254 589899719 7.840000e-148 534.0
53 TraesCS3A01G516200 chr1A 92.437 119 8 1 4998 5115 589899716 589899834 9.160000e-38 169.0
54 TraesCS3A01G516200 chr5B 86.469 473 53 7 4450 4920 660468949 660468486 4.750000e-140 508.0
55 TraesCS3A01G516200 chr5B 82.578 419 27 21 800 1193 710737838 710738235 1.430000e-85 327.0
56 TraesCS3A01G516200 chr5B 91.379 116 9 1 5001 5115 660468486 660468371 1.980000e-34 158.0
57 TraesCS3A01G516200 chr5B 81.915 188 24 5 243 420 349375130 349374943 3.320000e-32 150.0
58 TraesCS3A01G516200 chr4D 85.802 486 53 10 4442 4920 492912206 492912682 7.950000e-138 501.0
59 TraesCS3A01G516200 chr1D 86.325 468 46 9 4449 4911 48772542 48772088 1.330000e-135 494.0
60 TraesCS3A01G516200 chr1D 75.966 233 40 13 152 371 10291599 10291370 7.280000e-19 106.0
61 TraesCS3A01G516200 chr4B 84.583 480 54 13 4450 4920 442418342 442418810 4.850000e-125 459.0
62 TraesCS3A01G516200 chr4B 82.738 336 36 12 4998 5314 442418807 442419139 4.050000e-71 279.0
63 TraesCS3A01G516200 chr6B 84.760 479 48 11 4450 4920 187643168 187643629 1.740000e-124 457.0
64 TraesCS3A01G516200 chr6B 81.250 144 19 5 280 417 3721340 3721199 5.630000e-20 110.0
65 TraesCS3A01G516200 chr3B 85.011 467 43 12 4449 4913 697147635 697148076 2.920000e-122 449.0
66 TraesCS3A01G516200 chr3B 74.334 413 80 19 131 524 188861012 188861417 9.220000e-33 152.0
67 TraesCS3A01G516200 chr3B 89.916 119 11 1 4998 5115 709107359 709107477 9.220000e-33 152.0
68 TraesCS3A01G516200 chr3B 77.778 171 31 5 342 507 620659118 620658950 1.220000e-16 99.0
69 TraesCS3A01G516200 chr2B 79.800 401 48 18 800 1193 776627469 776627095 1.470000e-65 261.0
70 TraesCS3A01G516200 chr2B 80.282 213 33 7 235 438 131604396 131604608 9.220000e-33 152.0
71 TraesCS3A01G516200 chr7D 83.077 130 13 7 244 366 544785198 544785325 5.630000e-20 110.0
72 TraesCS3A01G516200 chr2D 84.211 114 9 7 416 523 485666683 485666573 9.420000e-18 102.0
73 TraesCS3A01G516200 chr2D 74.257 303 36 28 284 572 32732864 32732590 7.330000e-14 89.8


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 TraesCS3A01G516200 chr3A 733921521 733926836 5315 True 9817.000000 9817 100.000000 1 5316 1 chr3A.!!$R3 5315
1 TraesCS3A01G516200 chr3A 710121900 710123183 1283 False 1995.000000 1995 94.651000 1947 3236 1 chr3A.!!$F2 1289
2 TraesCS3A01G516200 chr3A 732435146 732435724 578 True 315.000000 483 87.564500 4448 5115 2 chr3A.!!$R4 667
3 TraesCS3A01G516200 chr7A 95227215 95228634 1419 False 2106.000000 2106 93.732000 1843 3236 1 chr7A.!!$F1 1393
4 TraesCS3A01G516200 chr7A 95234391 95235809 1418 False 2098.000000 2098 93.662000 1843 3236 1 chr7A.!!$F2 1393
5 TraesCS3A01G516200 chr7A 690772486 690774382 1896 True 1370.000000 2060 92.617000 1413 3241 2 chr7A.!!$R2 1828
6 TraesCS3A01G516200 chr6A 104450176 104451596 1420 False 2097.000000 2097 93.601000 1843 3238 1 chr6A.!!$F1 1395
7 TraesCS3A01G516200 chr6A 602741366 602742783 1417 True 2080.000000 2080 93.446000 1845 3236 1 chr6A.!!$R2 1391
8 TraesCS3A01G516200 chr6A 191245 192044 799 True 362.500000 494 83.081000 4448 5314 2 chr6A.!!$R3 866
9 TraesCS3A01G516200 chrUn 82678567 82679985 1418 True 2093.000000 2093 93.592000 1843 3236 1 chrUn.!!$R1 1393
10 TraesCS3A01G516200 chrUn 42248951 42251768 2817 False 896.666667 1406 85.622333 1 4444 3 chrUn.!!$F4 4443
11 TraesCS3A01G516200 chr2A 770407600 770409020 1420 True 2078.000000 2078 93.399000 1843 3236 1 chr2A.!!$R2 1393
12 TraesCS3A01G516200 chr2A 720491782 720493125 1343 True 1596.000000 1596 88.774000 1418 2713 1 chr2A.!!$R1 1295
13 TraesCS3A01G516200 chr2A 101860449 101862345 1896 False 1343.000000 2004 92.338000 1412 3236 2 chr2A.!!$F1 1824
14 TraesCS3A01G516200 chr5A 694532930 694534353 1423 True 2052.000000 2052 92.978000 1843 3240 1 chr5A.!!$R2 1397
15 TraesCS3A01G516200 chr5A 549341576 549342444 868 False 1511.000000 1511 98.046000 4446 5315 1 chr5A.!!$F1 869
16 TraesCS3A01G516200 chr5A 522979291 522979870 579 True 345.000000 527 89.686000 4449 5115 2 chr5A.!!$R3 666
17 TraesCS3A01G516200 chr4A 597036339 597037782 1443 False 1827.000000 1827 90.131000 1845 3236 1 chr4A.!!$F2 1391
18 TraesCS3A01G516200 chr4A 69990473 69991867 1394 False 1755.000000 1755 89.599000 1845 3238 1 chr4A.!!$F1 1393
19 TraesCS3A01G516200 chr4A 605365102 605366178 1076 False 1243.000000 1243 87.948000 1415 2469 1 chr4A.!!$F3 1054
20 TraesCS3A01G516200 chr3D 604290408 604293196 2788 True 1007.666667 1611 87.208667 1 4450 3 chr3D.!!$R3 4449
21 TraesCS3A01G516200 chr1B 650098851 650100201 1350 True 1476.000000 1476 86.908000 1418 2727 1 chr1B.!!$R1 1309
22 TraesCS3A01G516200 chr7B 474477613 474478684 1071 False 1022.000000 1022 84.755000 1888 2929 1 chr7B.!!$F1 1041
23 TraesCS3A01G516200 chr1A 589899254 589899834 580 False 351.500000 534 89.902500 4449 5115 2 chr1A.!!$F1 666
24 TraesCS3A01G516200 chr5B 660468371 660468949 578 True 333.000000 508 88.924000 4450 5115 2 chr5B.!!$R2 665
25 TraesCS3A01G516200 chr4B 442418342 442419139 797 False 369.000000 459 83.660500 4450 5314 2 chr4B.!!$F1 864

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
971 1207 0.243907 TGTTTCGCCTTCTCCTCTCG 59.756 55.000 0.0 0.0 0.0 4.04 F
1390 1665 1.170919 AGTTGAGCTTGCACTGCCAG 61.171 55.000 7.2 0.0 0.0 4.85 F
2600 2986 1.600636 CAAGCCAAAGACGGAGCCA 60.601 57.895 0.0 0.0 0.0 4.75 F
3354 3909 0.036010 AATTGTCCAGGTCCAGCTCG 60.036 55.000 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2346 1.606601 CTGAGTCTCCACCCCGTCA 60.607 63.158 0.00 0.0 0.0 4.35 R
2996 3466 1.334960 CGGCACATTTCAGCGAAGTTT 60.335 47.619 0.00 0.0 0.0 2.66 R
3874 4430 0.038618 ATATGCGCGGCTACGATGAA 60.039 50.000 8.83 0.0 44.6 2.57 R
4728 5301 2.747396 TTGCCATGGAAATTGCTGTC 57.253 45.000 18.40 0.0 0.0 3.51 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
388 393 4.931002 ACATTTGTGGCTTGATTACAATGC 59.069 37.500 0.00 0.00 34.63 3.56
577 610 9.934190 ACATTAAACATTTTTCAAATGCTTGAC 57.066 25.926 8.77 0.00 41.34 3.18
689 723 8.106247 TCTAAATTTTGTGTAGACATGGGAAC 57.894 34.615 0.00 0.00 30.13 3.62
731 766 7.315142 ACACATTCAATATCGTTCAAATGCTT 58.685 30.769 0.00 0.00 0.00 3.91
732 767 7.274033 ACACATTCAATATCGTTCAAATGCTTG 59.726 33.333 0.00 0.00 0.00 4.01
735 770 5.639757 TCAATATCGTTCAAATGCTTGGTG 58.360 37.500 0.00 0.00 33.01 4.17
742 777 7.015226 TCGTTCAAATGCTTGGTGAATATAG 57.985 36.000 3.28 0.00 34.04 1.31
743 778 6.597672 TCGTTCAAATGCTTGGTGAATATAGT 59.402 34.615 3.28 0.00 34.04 2.12
744 779 7.120579 TCGTTCAAATGCTTGGTGAATATAGTT 59.879 33.333 3.28 0.00 34.04 2.24
781 816 9.437045 CTTTTATGGAAAGTGTTTTTCAAATGC 57.563 29.630 2.52 0.00 39.92 3.56
783 818 8.729805 TTATGGAAAGTGTTTTTCAAATGCTT 57.270 26.923 2.52 0.00 35.47 3.91
784 819 6.419980 TGGAAAGTGTTTTTCAAATGCTTG 57.580 33.333 2.52 0.00 28.72 4.01
785 820 5.353678 TGGAAAGTGTTTTTCAAATGCTTGG 59.646 36.000 2.52 0.00 28.72 3.61
789 824 5.971763 AGTGTTTTTCAAATGCTTGGTGTA 58.028 33.333 0.00 0.00 33.01 2.90
792 827 7.651704 AGTGTTTTTCAAATGCTTGGTGTATAC 59.348 33.333 0.00 0.00 33.01 1.47
793 828 7.436673 GTGTTTTTCAAATGCTTGGTGTATACA 59.563 33.333 0.08 0.08 33.01 2.29
794 829 7.436673 TGTTTTTCAAATGCTTGGTGTATACAC 59.563 33.333 25.00 25.00 45.72 2.90
808 1029 4.802039 GTGTATACACATTTCGTCGTGGAT 59.198 41.667 27.37 0.00 45.75 3.41
917 1153 4.168101 ACATTTCAACTCCAGAGACCCTA 58.832 43.478 0.70 0.00 0.00 3.53
966 1202 1.377333 CCCCTGTTTCGCCTTCTCC 60.377 63.158 0.00 0.00 0.00 3.71
971 1207 0.243907 TGTTTCGCCTTCTCCTCTCG 59.756 55.000 0.00 0.00 0.00 4.04
1056 1299 3.117171 CTGCGACTGCTCCTGCAC 61.117 66.667 0.00 0.00 45.31 4.57
1057 1300 4.687215 TGCGACTGCTCCTGCACC 62.687 66.667 0.00 0.00 45.31 5.01
1058 1301 4.687215 GCGACTGCTCCTGCACCA 62.687 66.667 0.00 0.00 45.31 4.17
1059 1302 2.433838 CGACTGCTCCTGCACCAG 60.434 66.667 0.00 0.00 45.31 4.00
1060 1303 2.745492 GACTGCTCCTGCACCAGC 60.745 66.667 5.33 5.33 45.31 4.85
1061 1304 4.341783 ACTGCTCCTGCACCAGCC 62.342 66.667 9.22 0.00 45.31 4.85
1065 1308 4.767255 CTCCTGCACCAGCCGTCC 62.767 72.222 0.00 0.00 41.13 4.79
1313 1587 1.380246 TTGTCCATGCATCCCAGCC 60.380 57.895 0.00 0.00 0.00 4.85
1339 1613 6.199043 ACTTTATTCATACGCTTCGATTCG 57.801 37.500 0.00 0.00 0.00 3.34
1346 1620 2.209838 ACGCTTCGATTCGATGTCAT 57.790 45.000 19.30 6.43 35.23 3.06
1348 1622 2.119457 CGCTTCGATTCGATGTCATCA 58.881 47.619 19.30 0.00 35.23 3.07
1390 1665 1.170919 AGTTGAGCTTGCACTGCCAG 61.171 55.000 7.20 0.00 0.00 4.85
1449 1725 2.034221 GCGCCCCAGGAAGAACTT 59.966 61.111 0.00 0.00 0.00 2.66
1496 1773 4.544001 AAAAACGGTCCAGTCGCA 57.456 50.000 0.00 0.00 0.00 5.10
1497 1774 3.015516 AAAAACGGTCCAGTCGCAT 57.984 47.368 0.00 0.00 0.00 4.73
1828 2107 3.640407 ACTCGCCTGTGCCCACAT 61.640 61.111 1.04 0.00 41.01 3.21
2133 2483 2.285743 AACTCTCCCTCCCCCAGC 60.286 66.667 0.00 0.00 0.00 4.85
2297 2652 2.338620 CTCGAGGGCGTGTTGACA 59.661 61.111 3.91 0.00 38.98 3.58
2600 2986 1.600636 CAAGCCAAAGACGGAGCCA 60.601 57.895 0.00 0.00 0.00 4.75
2908 3378 2.124942 CAAGGAGGAGAAGGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
2996 3466 7.643569 ATGTGCTATGTAATGAAAATCCACA 57.356 32.000 0.00 0.00 34.51 4.17
3005 3475 4.853924 ATGAAAATCCACAAACTTCGCT 57.146 36.364 0.00 0.00 0.00 4.93
3006 3476 3.963665 TGAAAATCCACAAACTTCGCTG 58.036 40.909 0.00 0.00 0.00 5.18
3007 3477 3.629855 TGAAAATCCACAAACTTCGCTGA 59.370 39.130 0.00 0.00 0.00 4.26
3008 3478 4.097135 TGAAAATCCACAAACTTCGCTGAA 59.903 37.500 0.00 0.00 0.00 3.02
3009 3479 4.647424 AAATCCACAAACTTCGCTGAAA 57.353 36.364 0.00 0.00 0.00 2.69
3010 3480 4.853924 AATCCACAAACTTCGCTGAAAT 57.146 36.364 0.00 0.00 0.00 2.17
3011 3481 3.624326 TCCACAAACTTCGCTGAAATG 57.376 42.857 0.00 0.00 0.00 2.32
3012 3482 2.948979 TCCACAAACTTCGCTGAAATGT 59.051 40.909 0.00 0.00 0.00 2.71
3013 3483 3.044986 CCACAAACTTCGCTGAAATGTG 58.955 45.455 15.88 15.88 34.00 3.21
3014 3484 2.468777 CACAAACTTCGCTGAAATGTGC 59.531 45.455 13.16 0.00 30.30 4.57
3029 3509 2.535934 TGTGCCGAAATTTATCGTGC 57.464 45.000 0.00 0.00 41.16 5.34
3056 3536 3.366476 CCGAAATTTATCGTGTTTGGCCA 60.366 43.478 0.00 0.00 41.16 5.36
3113 3593 7.703298 ACTTCTTTTATTTTAAAACGTGCCC 57.297 32.000 1.97 0.00 0.00 5.36
3118 3598 1.964552 TTTTAAAACGTGCCCGAGGA 58.035 45.000 0.00 0.00 37.88 3.71
3173 3655 0.534873 CCCAGGCCCAATTTTTACGG 59.465 55.000 0.00 0.00 0.00 4.02
3177 3659 1.587568 GCCCAATTTTTACGGCGGT 59.412 52.632 13.24 1.39 0.00 5.68
3271 3809 3.057033 AGTTGAGCAAGCAATTGACCATC 60.057 43.478 10.34 0.61 0.00 3.51
3272 3810 2.516906 TGAGCAAGCAATTGACCATCA 58.483 42.857 10.34 3.32 0.00 3.07
3290 3845 6.567050 ACCATCAAGTAATTGCTAATTGCTG 58.433 36.000 10.99 0.00 41.97 4.41
3349 3904 2.039746 CCTACACAATTGTCCAGGTCCA 59.960 50.000 20.20 0.00 37.15 4.02
3350 3905 2.276732 ACACAATTGTCCAGGTCCAG 57.723 50.000 8.48 0.00 0.00 3.86
3351 3906 0.883833 CACAATTGTCCAGGTCCAGC 59.116 55.000 8.48 0.00 0.00 4.85
3353 3908 1.271597 ACAATTGTCCAGGTCCAGCTC 60.272 52.381 4.92 0.00 0.00 4.09
3354 3909 0.036010 AATTGTCCAGGTCCAGCTCG 60.036 55.000 0.00 0.00 0.00 5.03
3365 3920 2.151202 GTCCAGCTCGACCATTTTTCA 58.849 47.619 0.00 0.00 0.00 2.69
3370 3925 4.168760 CAGCTCGACCATTTTTCAAATCC 58.831 43.478 0.00 0.00 0.00 3.01
3416 3972 5.957842 AAAATCAATAGTCTTTCACCGCA 57.042 34.783 0.00 0.00 0.00 5.69
3433 3989 0.659417 GCATCGCTCATGGCAAATCG 60.659 55.000 0.00 0.00 41.91 3.34
3435 3991 0.816825 ATCGCTCATGGCAAATCGCT 60.817 50.000 0.00 0.00 41.91 4.93
3449 4005 0.109551 ATCGCTGCAGATACGGATCG 60.110 55.000 20.43 8.92 37.15 3.69
3530 4086 4.210093 CGCGCCCACGGGTATGTA 62.210 66.667 0.00 0.00 46.24 2.29
3531 4087 2.424302 GCGCCCACGGGTATGTAT 59.576 61.111 3.54 0.00 40.57 2.29
3532 4088 1.959226 GCGCCCACGGGTATGTATG 60.959 63.158 3.54 0.00 40.57 2.39
3533 4089 1.444250 CGCCCACGGGTATGTATGT 59.556 57.895 3.54 0.00 37.65 2.29
3539 4095 4.069304 CCCACGGGTATGTATGTAATTGG 58.931 47.826 0.00 0.00 0.00 3.16
3552 4108 4.471904 TGTAATTGGGTTTGTTGTTGCA 57.528 36.364 0.00 0.00 0.00 4.08
3557 4113 2.898705 TGGGTTTGTTGTTGCATGAAC 58.101 42.857 0.00 0.00 34.84 3.18
3562 4118 4.504097 GGTTTGTTGTTGCATGAACTTCTC 59.496 41.667 0.00 0.25 35.37 2.87
3587 4143 6.890268 CCTTCATATGATCCATCATCCATGTT 59.110 38.462 6.17 0.00 43.72 2.71
3588 4144 7.396339 CCTTCATATGATCCATCATCCATGTTT 59.604 37.037 6.17 0.00 43.72 2.83
3592 4148 8.803235 CATATGATCCATCATCCATGTTTCTTT 58.197 33.333 5.29 0.00 43.72 2.52
3593 4149 6.704289 TGATCCATCATCCATGTTTCTTTC 57.296 37.500 0.00 0.00 0.00 2.62
3595 4151 6.320418 TGATCCATCATCCATGTTTCTTTCTG 59.680 38.462 0.00 0.00 0.00 3.02
3602 4158 6.314648 TCATCCATGTTTCTTTCTGAATCGAG 59.685 38.462 0.00 0.00 34.24 4.04
3662 4218 1.486726 AGCCTTCTACACCATGCCTAC 59.513 52.381 0.00 0.00 0.00 3.18
3766 4322 3.678056 ACTAATCCAAAGACTCGTGCA 57.322 42.857 0.00 0.00 0.00 4.57
3768 4324 4.579869 ACTAATCCAAAGACTCGTGCATT 58.420 39.130 0.00 0.00 0.00 3.56
3869 4425 9.807649 GTAATTAAAAGCTCATTTGGACATCAT 57.192 29.630 0.00 0.00 0.00 2.45
3871 4427 5.988310 AAAAGCTCATTTGGACATCATCA 57.012 34.783 0.00 0.00 0.00 3.07
3873 4429 5.769484 AAGCTCATTTGGACATCATCATC 57.231 39.130 0.00 0.00 0.00 2.92
3874 4430 5.050126 AGCTCATTTGGACATCATCATCT 57.950 39.130 0.00 0.00 0.00 2.90
3876 4432 5.531659 AGCTCATTTGGACATCATCATCTTC 59.468 40.000 0.00 0.00 0.00 2.87
3886 4448 3.288809 TCATCATCTTCATCGTAGCCG 57.711 47.619 0.00 0.00 0.00 5.52
3901 4463 0.937304 AGCCGCGCATATACTTTGTG 59.063 50.000 8.75 0.00 0.00 3.33
3948 4510 2.731451 ACGTGATCGGAATATCAATGCG 59.269 45.455 0.00 0.00 37.61 4.73
4023 4585 0.321564 TTGGCAAGGATGTCGACCTG 60.322 55.000 14.12 3.88 37.85 4.00
4038 4600 0.972983 ACCTGGAGTCCCTCATCACG 60.973 60.000 6.74 0.00 31.08 4.35
4040 4602 2.303549 CTGGAGTCCCTCATCACGCC 62.304 65.000 6.74 0.00 33.33 5.68
4095 4657 2.572290 GACTGGTAAGCCACAACAAGT 58.428 47.619 0.00 0.00 40.46 3.16
4385 4950 2.225167 GGTGGTTGGAGGTTTTGGGATA 60.225 50.000 0.00 0.00 0.00 2.59
4552 5118 4.884668 TGGTCAGATTACTCTTTCGGTT 57.115 40.909 0.00 0.00 0.00 4.44
4559 5125 6.816640 TCAGATTACTCTTTCGGTTACATTGG 59.183 38.462 0.00 0.00 0.00 3.16
4693 5266 6.035650 ACATTATCAAAGACATGGTCGTTACG 59.964 38.462 0.00 0.00 37.67 3.18
4728 5301 4.696877 TGTATCAATGCACCAAGTCTCAAG 59.303 41.667 0.00 0.00 0.00 3.02
4897 5471 0.453390 GCCGGCAGAAGATTTCCAAG 59.547 55.000 24.80 0.00 0.00 3.61
4913 5487 4.270245 TCCAAGGCAAATTGAAATGGAC 57.730 40.909 9.09 0.00 30.90 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.671279 AAAATGATGAAAACCAAGAAAGAAACT 57.329 25.926 0.00 0.00 0.00 2.66
53 55 8.190784 CCGAGGAACAAGCAAAGAAAAATATAT 58.809 33.333 0.00 0.00 0.00 0.86
57 59 4.099419 ACCGAGGAACAAGCAAAGAAAAAT 59.901 37.500 0.00 0.00 0.00 1.82
68 70 7.761704 CCATATATTCATAGACCGAGGAACAAG 59.238 40.741 0.00 0.00 0.00 3.16
71 73 7.093902 TGACCATATATTCATAGACCGAGGAAC 60.094 40.741 0.00 0.00 0.00 3.62
373 378 6.591062 TGAATTTGAAGCATTGTAATCAAGCC 59.409 34.615 0.00 0.00 36.97 4.35
670 704 4.171878 TGGTTCCCATGTCTACACAAAA 57.828 40.909 0.00 0.00 35.64 2.44
679 713 5.011023 ACAGAAAGAAAATGGTTCCCATGTC 59.989 40.000 0.00 0.00 44.40 3.06
709 743 6.753279 ACCAAGCATTTGAACGATATTGAATG 59.247 34.615 0.00 0.00 36.36 2.67
713 747 5.639757 TCACCAAGCATTTGAACGATATTG 58.360 37.500 0.00 0.00 36.36 1.90
716 750 5.895636 ATTCACCAAGCATTTGAACGATA 57.104 34.783 0.00 0.00 36.36 2.92
719 753 6.785191 ACTATATTCACCAAGCATTTGAACG 58.215 36.000 0.00 0.00 36.36 3.95
720 754 8.986477 AAACTATATTCACCAAGCATTTGAAC 57.014 30.769 0.00 0.00 36.36 3.18
758 793 8.610896 CAAGCATTTGAAAAACACTTTCCATAA 58.389 29.630 0.00 0.00 36.36 1.90
772 807 6.641169 TGTGTATACACCAAGCATTTGAAA 57.359 33.333 28.67 6.64 45.88 2.69
775 810 6.251163 CGAAATGTGTATACACCAAGCATTTG 59.749 38.462 28.67 17.40 45.88 2.32
776 811 6.072175 ACGAAATGTGTATACACCAAGCATTT 60.072 34.615 28.67 24.82 45.88 2.32
777 812 5.414454 ACGAAATGTGTATACACCAAGCATT 59.586 36.000 28.67 19.28 45.88 3.56
779 814 4.320023 ACGAAATGTGTATACACCAAGCA 58.680 39.130 28.67 13.50 45.88 3.91
780 815 4.491924 CGACGAAATGTGTATACACCAAGC 60.492 45.833 28.67 16.48 45.88 4.01
781 816 4.624024 ACGACGAAATGTGTATACACCAAG 59.376 41.667 28.67 18.51 45.88 3.61
783 818 3.921630 CACGACGAAATGTGTATACACCA 59.078 43.478 28.67 18.62 45.88 4.17
784 819 3.305094 CCACGACGAAATGTGTATACACC 59.695 47.826 28.67 14.85 45.88 4.16
785 820 4.168014 TCCACGACGAAATGTGTATACAC 58.832 43.478 25.99 25.99 46.59 2.90
789 824 2.607635 GCATCCACGACGAAATGTGTAT 59.392 45.455 0.00 0.00 34.28 2.29
792 827 0.247262 CGCATCCACGACGAAATGTG 60.247 55.000 0.00 5.05 35.87 3.21
793 828 1.358725 CCGCATCCACGACGAAATGT 61.359 55.000 0.00 0.00 34.06 2.71
794 829 1.348250 CCGCATCCACGACGAAATG 59.652 57.895 0.00 3.25 34.06 2.32
795 830 1.079405 ACCGCATCCACGACGAAAT 60.079 52.632 0.00 0.00 34.06 2.17
796 831 2.024868 CACCGCATCCACGACGAAA 61.025 57.895 0.00 0.00 34.06 3.46
894 1128 3.008485 AGGGTCTCTGGAGTTGAAATGTC 59.992 47.826 0.00 0.00 0.00 3.06
917 1153 1.409427 GGCTGGCTAGTTGTAGACGAT 59.591 52.381 0.00 0.00 37.04 3.73
1035 1278 4.427661 AGGAGCAGTCGCAGTCGC 62.428 66.667 0.00 0.00 42.27 5.19
1077 1320 4.379243 AAGAGCGCAGACGGGGTG 62.379 66.667 11.47 0.00 40.57 4.61
1078 1321 4.070552 GAAGAGCGCAGACGGGGT 62.071 66.667 11.47 0.00 40.57 4.95
1229 1487 0.034476 GAGGAGATGCGGCATGATGA 59.966 55.000 21.98 0.00 0.00 2.92
1313 1587 7.939910 CGAATCGAAGCGTATGAATAAAGTTAG 59.060 37.037 0.00 0.00 0.00 2.34
1339 1613 2.860062 GCTGCAAACAGTGATGACATC 58.140 47.619 8.59 8.59 46.30 3.06
1375 1650 0.170561 CAATCTGGCAGTGCAAGCTC 59.829 55.000 18.61 0.00 28.00 4.09
1390 1665 9.604626 GAGCAATTATCAATTACAGTAGCAATC 57.395 33.333 0.00 0.00 0.00 2.67
1487 1764 3.083349 CCTGGGGATGCGACTGGA 61.083 66.667 0.00 0.00 0.00 3.86
1496 1773 0.718408 AAAATTGGGCTCCTGGGGAT 59.282 50.000 0.00 0.00 0.00 3.85
1497 1774 0.041090 GAAAATTGGGCTCCTGGGGA 59.959 55.000 0.00 0.00 0.00 4.81
1510 1787 3.068064 CCCAGGCCGGCGAAAATT 61.068 61.111 22.54 0.00 0.00 1.82
1743 2021 4.828296 GGAGGGGAGGCGTCGGTA 62.828 72.222 0.00 0.00 0.00 4.02
1996 2346 1.606601 CTGAGTCTCCACCCCGTCA 60.607 63.158 0.00 0.00 0.00 4.35
2133 2483 4.147322 GTGATTGTCGGCGGCGTG 62.147 66.667 31.06 4.09 0.00 5.34
2297 2652 2.762459 TTGCCGCCCTCGAGGTAT 60.762 61.111 29.25 0.00 38.26 2.73
2939 3409 8.478775 AACTAATCTAAAGGAAAAACTGGCTT 57.521 30.769 0.00 0.00 0.00 4.35
2994 3464 2.543653 GGCACATTTCAGCGAAGTTTGT 60.544 45.455 0.00 0.00 0.00 2.83
2996 3466 1.334960 CGGCACATTTCAGCGAAGTTT 60.335 47.619 0.00 0.00 0.00 2.66
3005 3475 5.092105 CACGATAAATTTCGGCACATTTCA 58.908 37.500 4.68 0.00 43.33 2.69
3006 3476 4.027702 GCACGATAAATTTCGGCACATTTC 60.028 41.667 4.68 0.00 43.33 2.17
3007 3477 3.857093 GCACGATAAATTTCGGCACATTT 59.143 39.130 4.68 0.00 43.33 2.32
3008 3478 3.128589 AGCACGATAAATTTCGGCACATT 59.871 39.130 12.41 0.00 43.33 2.71
3009 3479 2.682856 AGCACGATAAATTTCGGCACAT 59.317 40.909 12.41 0.00 43.33 3.21
3010 3480 2.080693 AGCACGATAAATTTCGGCACA 58.919 42.857 12.41 0.00 43.33 4.57
3011 3481 2.825086 AGCACGATAAATTTCGGCAC 57.175 45.000 12.41 0.60 43.33 5.01
3012 3482 2.159448 CCAAGCACGATAAATTTCGGCA 60.159 45.455 12.41 0.00 43.33 5.69
3013 3483 2.450160 CCAAGCACGATAAATTTCGGC 58.550 47.619 4.68 5.10 43.33 5.54
3014 3484 2.450160 GCCAAGCACGATAAATTTCGG 58.550 47.619 4.68 0.00 43.33 4.30
3029 3509 3.757745 ACACGATAAATTTCGGCCAAG 57.242 42.857 2.24 0.00 43.33 3.61
3056 3536 7.364970 AGTTCGGCTTAAACACGATAAATTTT 58.635 30.769 0.00 0.00 36.43 1.82
3334 3889 1.457346 GAGCTGGACCTGGACAATTG 58.543 55.000 3.24 3.24 0.00 2.32
3345 3900 2.151202 TGAAAAATGGTCGAGCTGGAC 58.849 47.619 19.63 19.63 36.18 4.02
3349 3904 4.082125 AGGATTTGAAAAATGGTCGAGCT 58.918 39.130 16.64 0.00 0.00 4.09
3350 3905 4.440839 AGGATTTGAAAAATGGTCGAGC 57.559 40.909 7.89 7.89 0.00 5.03
3351 3906 6.088824 CAGAAGGATTTGAAAAATGGTCGAG 58.911 40.000 0.00 0.00 0.00 4.04
3353 3908 5.772521 ACAGAAGGATTTGAAAAATGGTCG 58.227 37.500 0.00 0.00 0.00 4.79
3354 3909 7.886338 ACTACAGAAGGATTTGAAAAATGGTC 58.114 34.615 0.00 0.00 0.00 4.02
3393 3948 6.325919 TGCGGTGAAAGACTATTGATTTTT 57.674 33.333 0.00 0.00 0.00 1.94
3394 3949 5.957842 TGCGGTGAAAGACTATTGATTTT 57.042 34.783 0.00 0.00 0.00 1.82
3395 3950 5.220662 CGATGCGGTGAAAGACTATTGATTT 60.221 40.000 0.00 0.00 0.00 2.17
3396 3951 4.271049 CGATGCGGTGAAAGACTATTGATT 59.729 41.667 0.00 0.00 0.00 2.57
3397 3952 3.804325 CGATGCGGTGAAAGACTATTGAT 59.196 43.478 0.00 0.00 0.00 2.57
3433 3989 1.552348 GCACGATCCGTATCTGCAGC 61.552 60.000 9.47 0.00 38.32 5.25
3435 3991 1.299089 CGCACGATCCGTATCTGCA 60.299 57.895 11.03 0.00 38.32 4.41
3529 4085 6.161855 TGCAACAACAAACCCAATTACATA 57.838 33.333 0.00 0.00 0.00 2.29
3530 4086 5.028549 TGCAACAACAAACCCAATTACAT 57.971 34.783 0.00 0.00 0.00 2.29
3531 4087 4.471904 TGCAACAACAAACCCAATTACA 57.528 36.364 0.00 0.00 0.00 2.41
3532 4088 5.053145 TCATGCAACAACAAACCCAATTAC 58.947 37.500 0.00 0.00 0.00 1.89
3533 4089 5.282055 TCATGCAACAACAAACCCAATTA 57.718 34.783 0.00 0.00 0.00 1.40
3539 4095 4.432712 AGAAGTTCATGCAACAACAAACC 58.567 39.130 5.50 1.06 37.48 3.27
3552 4108 7.384524 TGGATCATATGAAGGAGAAGTTCAT 57.615 36.000 9.99 3.95 44.86 2.57
3557 4113 7.049133 GGATGATGGATCATATGAAGGAGAAG 58.951 42.308 9.99 0.00 46.84 2.85
3562 4118 6.424032 ACATGGATGATGGATCATATGAAGG 58.576 40.000 9.99 0.00 46.84 3.46
3587 4143 4.252971 ACGGAACTCGATTCAGAAAGAA 57.747 40.909 12.10 0.00 42.43 2.52
3588 4144 3.936372 ACGGAACTCGATTCAGAAAGA 57.064 42.857 12.10 0.00 42.43 2.52
3592 4148 1.808343 TCGAACGGAACTCGATTCAGA 59.192 47.619 12.10 1.70 40.25 3.27
3593 4149 2.257974 TCGAACGGAACTCGATTCAG 57.742 50.000 8.98 7.63 40.25 3.02
3715 4271 9.092322 GCGATAACAACGAATGTATATCAAAAG 57.908 33.333 17.08 9.53 42.99 2.27
3732 4288 9.168451 TCTTTGGATTAGTTTATGCGATAACAA 57.832 29.630 0.00 0.00 0.00 2.83
3739 4295 5.291128 ACGAGTCTTTGGATTAGTTTATGCG 59.709 40.000 0.00 0.00 0.00 4.73
3766 4322 3.118738 GGACTCACCGAATACCTGACAAT 60.119 47.826 0.00 0.00 0.00 2.71
3768 4324 1.822990 GGACTCACCGAATACCTGACA 59.177 52.381 0.00 0.00 0.00 3.58
3869 4425 0.317854 CGCGGCTACGATGAAGATGA 60.318 55.000 0.00 0.00 44.60 2.92
3871 4427 1.661821 GCGCGGCTACGATGAAGAT 60.662 57.895 8.83 0.00 44.60 2.40
3873 4429 0.663269 TATGCGCGGCTACGATGAAG 60.663 55.000 8.83 0.00 44.60 3.02
3874 4430 0.038618 ATATGCGCGGCTACGATGAA 60.039 50.000 8.83 0.00 44.60 2.57
3876 4432 0.914551 GTATATGCGCGGCTACGATG 59.085 55.000 8.83 0.00 44.60 3.84
3886 4448 5.456497 TCGTTACTACACAAAGTATATGCGC 59.544 40.000 0.00 0.00 32.16 6.09
4038 4600 4.570663 CCATCCTCGACGTCGGGC 62.571 72.222 35.05 0.00 38.81 6.13
4040 4602 3.350909 TTGCCATCCTCGACGTCGG 62.351 63.158 35.05 24.95 40.29 4.79
4086 4648 6.073819 TGACAGATAACATCGAACTTGTTGTG 60.074 38.462 12.09 9.31 37.81 3.33
4095 4657 4.693566 GGTTTGGTGACAGATAACATCGAA 59.306 41.667 0.00 0.00 44.54 3.71
4533 5099 7.201530 CCAATGTAACCGAAAGAGTAATCTGAC 60.202 40.741 0.00 0.00 0.00 3.51
4559 5125 8.131731 GCTTTCCCTTGAACTCATAACATTATC 58.868 37.037 0.00 0.00 0.00 1.75
4693 5266 6.751888 GGTGCATTGATACATTTGGAAAGTAC 59.248 38.462 0.00 0.00 0.00 2.73
4728 5301 2.747396 TTGCCATGGAAATTGCTGTC 57.253 45.000 18.40 0.00 0.00 3.51
4897 5471 6.691508 AGTTTCTAGTCCATTTCAATTTGCC 58.308 36.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.