Multiple sequence alignment - TraesCS6D01G089100

Loading Multiple Alignment...

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 TraesCS6D01G089100 chr6D 100.000 3526 0 0 1 3526 54080186 54076661 0.000000e+00 6512.0
1 TraesCS6D01G089100 chr6D 93.407 91 0 1 3442 3526 264060136 264060046 2.860000e-26 130.0
2 TraesCS6D01G089100 chr6B 95.833 2040 52 14 1415 3446 117126623 117128637 0.000000e+00 3265.0
3 TraesCS6D01G089100 chr6B 94.368 1314 28 7 1 1314 117125354 117126621 0.000000e+00 1975.0
4 TraesCS6D01G089100 chr6B 93.933 890 27 6 1 890 116823466 116822604 0.000000e+00 1319.0
5 TraesCS6D01G089100 chr6B 91.244 217 15 4 3082 3297 116822611 116822398 3.440000e-75 292.0
6 TraesCS6D01G089100 chr6B 100.000 51 0 0 3330 3380 116822408 116822358 1.040000e-15 95.3
7 TraesCS6D01G089100 chr5A 94.041 1309 54 10 1415 2711 698332563 698331267 0.000000e+00 1964.0
8 TraesCS6D01G089100 chr5A 93.151 1314 50 12 4 1312 698333845 698332567 0.000000e+00 1892.0
9 TraesCS6D01G089100 chr5A 89.396 745 53 14 2709 3446 698331232 698330507 0.000000e+00 915.0
10 TraesCS6D01G089100 chr5A 78.520 1108 157 47 230 1314 698343627 698342578 0.000000e+00 652.0
11 TraesCS6D01G089100 chr5A 78.613 1038 146 37 1625 2629 698342324 698341330 5.000000e-173 617.0
12 TraesCS6D01G089100 chr5A 78.523 1043 136 40 286 1312 698349154 698348184 3.890000e-169 604.0
13 TraesCS6D01G089100 chr5A 81.714 700 71 26 2709 3393 698322951 698322294 6.700000e-147 531.0
14 TraesCS6D01G089100 chr5A 89.302 430 33 5 2249 2669 698326421 698325996 8.670000e-146 527.0
15 TraesCS6D01G089100 chr5A 76.505 1030 173 38 1625 2629 698347928 698346943 6.800000e-137 497.0
16 TraesCS6D01G089100 chr4B 92.722 1319 45 10 1 1314 657288344 657289616 0.000000e+00 1857.0
17 TraesCS6D01G089100 chr4B 92.095 1050 43 12 1415 2436 657289618 657290655 0.000000e+00 1443.0
18 TraesCS6D01G089100 chr4B 86.817 311 27 10 2471 2770 657290658 657290965 5.640000e-88 335.0
19 TraesCS6D01G089100 chr4B 79.747 395 38 16 2796 3177 657291330 657291695 7.560000e-62 248.0
20 TraesCS6D01G089100 chr4B 99.048 105 1 0 1314 1418 381290492 381290388 4.650000e-44 189.0
21 TraesCS6D01G089100 chr4B 91.667 84 6 1 3444 3526 396700934 396700851 8.000000e-22 115.0
22 TraesCS6D01G089100 chr4B 92.405 79 6 0 3368 3446 657295057 657295135 2.880000e-21 113.0
23 TraesCS6D01G089100 chr4D 94.631 1192 45 8 1588 2764 509452791 509451604 0.000000e+00 1829.0
24 TraesCS6D01G089100 chr4D 92.701 1096 37 5 224 1314 509454142 509453085 0.000000e+00 1541.0
25 TraesCS6D01G089100 chr4D 77.306 1106 155 46 230 1314 509458896 509457866 6.610000e-157 564.0
26 TraesCS6D01G089100 chr4D 92.464 345 25 1 3102 3446 509451567 509451224 3.160000e-135 492.0
27 TraesCS6D01G089100 chr4D 93.939 264 14 2 1415 1677 509453083 509452821 7.090000e-107 398.0
28 TraesCS6D01G089100 chr4D 83.529 170 15 7 392 549 69653505 69653673 2.840000e-31 147.0
29 TraesCS6D01G089100 chr4D 92.553 94 1 1 3439 3526 287304831 287304924 2.860000e-26 130.0
30 TraesCS6D01G089100 chr4D 92.308 91 1 1 3439 3523 300000000 300000090 1.330000e-24 124.0
31 TraesCS6D01G089100 chr4D 84.211 95 14 1 28 122 69652946 69653039 1.350000e-14 91.6
32 TraesCS6D01G089100 chr5B 89.916 1428 79 29 1415 2800 43905755 43904351 0.000000e+00 1779.0
33 TraesCS6D01G089100 chr5B 94.150 547 32 0 224 770 43906756 43906210 0.000000e+00 833.0
34 TraesCS6D01G089100 chr5B 85.386 609 54 19 2844 3443 43904355 43903773 1.810000e-167 599.0
35 TraesCS6D01G089100 chr5B 90.160 437 14 4 882 1314 43906168 43905757 3.100000e-150 542.0
36 TraesCS6D01G089100 chr5B 98.095 105 2 0 1314 1418 63371107 63371211 2.160000e-42 183.0
37 TraesCS6D01G089100 chr5B 92.857 84 5 1 3443 3526 163905023 163905105 1.720000e-23 121.0
38 TraesCS6D01G089100 chr5B 100.000 37 0 0 788 824 43906209 43906173 6.320000e-08 69.4
39 TraesCS6D01G089100 chr4A 79.775 445 60 16 286 710 716267870 716268304 2.660000e-76 296.0
40 TraesCS6D01G089100 chr4A 86.316 95 12 1 28 122 521845528 521845621 6.230000e-18 102.0
41 TraesCS6D01G089100 chrUn 99.048 105 1 0 1314 1418 407032220 407032324 4.650000e-44 189.0
42 TraesCS6D01G089100 chr5D 99.048 105 1 0 1314 1418 6233424 6233320 4.650000e-44 189.0
43 TraesCS6D01G089100 chr3B 99.048 105 1 0 1314 1418 201495827 201495931 4.650000e-44 189.0
44 TraesCS6D01G089100 chr2B 99.048 105 1 0 1314 1418 474937675 474937779 4.650000e-44 189.0
45 TraesCS6D01G089100 chr1D 99.048 105 1 0 1314 1418 254479802 254479906 4.650000e-44 189.0
46 TraesCS6D01G089100 chr1D 96.460 113 4 0 1314 1426 68404548 68404436 1.670000e-43 187.0
47 TraesCS6D01G089100 chr1D 93.407 91 0 1 3442 3526 48585029 48584939 2.860000e-26 130.0
48 TraesCS6D01G089100 chr3D 99.029 103 1 0 1314 1416 527409391 527409289 6.010000e-43 185.0
49 TraesCS6D01G089100 chr1A 94.253 87 4 1 3440 3526 365069610 365069525 7.940000e-27 132.0
50 TraesCS6D01G089100 chr1B 90.722 97 2 3 3436 3526 332086465 332086370 4.780000e-24 122.0
51 TraesCS6D01G089100 chr7D 87.387 111 6 3 3424 3526 344419183 344419073 1.720000e-23 121.0


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 TraesCS6D01G089100 chr6D 54076661 54080186 3525 True 6512.000000 6512 100.00000 1 3526 1 chr6D.!!$R1 3525
1 TraesCS6D01G089100 chr6B 117125354 117128637 3283 False 2620.000000 3265 95.10050 1 3446 2 chr6B.!!$F1 3445
2 TraesCS6D01G089100 chr6B 116822358 116823466 1108 True 568.766667 1319 95.05900 1 3380 3 chr6B.!!$R1 3379
3 TraesCS6D01G089100 chr5A 698330507 698333845 3338 True 1590.333333 1964 92.19600 4 3446 3 chr5A.!!$R2 3442
4 TraesCS6D01G089100 chr5A 698341330 698349154 7824 True 592.500000 652 78.04025 230 2629 4 chr5A.!!$R3 2399
5 TraesCS6D01G089100 chr5A 698322294 698326421 4127 True 529.000000 531 85.50800 2249 3393 2 chr5A.!!$R1 1144
6 TraesCS6D01G089100 chr4B 657288344 657295135 6791 False 799.200000 1857 88.75720 1 3446 5 chr4B.!!$F1 3445
7 TraesCS6D01G089100 chr4D 509451224 509458896 7672 True 964.800000 1829 90.20820 224 3446 5 chr4D.!!$R1 3222
8 TraesCS6D01G089100 chr5B 43903773 43906756 2983 True 764.480000 1779 91.92240 224 3443 5 chr5B.!!$R1 3219

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
982 5563 0.248336 CTATGTGCTGCAATGCGGTG 60.248 55.0 16.13 2.15 37.24 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 13098 1.386748 CATGTATATCGAAGGTGCGCG 59.613 52.381 0.0 0.0 0.0 6.86 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
104 105 6.889177 TGTGTGAATTCTATAAAATGGCTGGA 59.111 34.615 7.05 0.00 0.00 3.86
210 213 5.067273 TCTTTCTTGTCGGCCTTAATTTCA 58.933 37.500 0.00 0.00 0.00 2.69
211 214 5.710099 TCTTTCTTGTCGGCCTTAATTTCAT 59.290 36.000 0.00 0.00 0.00 2.57
212 215 5.975693 TTCTTGTCGGCCTTAATTTCATT 57.024 34.783 0.00 0.00 0.00 2.57
303 4836 0.519077 GAAAGCAGCGGAGGAAACTG 59.481 55.000 0.00 0.00 44.43 3.16
929 5510 2.242196 ACACCCATATTACAAGCCAGCT 59.758 45.455 0.00 0.00 0.00 4.24
975 5556 3.133464 GCCCGCTATGTGCTGCAA 61.133 61.111 2.77 0.00 40.11 4.08
976 5557 2.484062 GCCCGCTATGTGCTGCAAT 61.484 57.895 2.77 3.26 40.11 3.56
977 5558 1.357690 CCCGCTATGTGCTGCAATG 59.642 57.895 2.77 0.00 40.11 2.82
978 5559 1.298863 CCGCTATGTGCTGCAATGC 60.299 57.895 2.77 0.00 40.11 3.56
979 5560 1.653232 CGCTATGTGCTGCAATGCG 60.653 57.895 19.19 19.19 42.63 4.73
980 5561 1.298863 GCTATGTGCTGCAATGCGG 60.299 57.895 10.16 10.16 38.95 5.69
981 5562 1.996786 GCTATGTGCTGCAATGCGGT 61.997 55.000 16.13 0.00 37.24 5.68
982 5563 0.248336 CTATGTGCTGCAATGCGGTG 60.248 55.000 16.13 2.15 37.24 4.94
983 5564 1.655885 TATGTGCTGCAATGCGGTGG 61.656 55.000 16.13 0.00 37.24 4.61
996 5577 4.489771 GGTGGCCCGCTATGTGCT 62.490 66.667 0.00 0.00 40.11 4.40
997 5578 3.204827 GTGGCCCGCTATGTGCTG 61.205 66.667 0.00 0.00 40.11 4.41
1314 11505 1.153086 ATGGCATCCTTGGACTCGC 60.153 57.895 0.00 0.00 0.00 5.03
1315 11506 1.630126 ATGGCATCCTTGGACTCGCT 61.630 55.000 0.00 0.00 0.00 4.93
1318 11509 0.878086 GCATCCTTGGACTCGCTAGC 60.878 60.000 4.06 4.06 0.00 3.42
1319 11510 0.749649 CATCCTTGGACTCGCTAGCT 59.250 55.000 13.93 0.00 0.00 3.32
1320 11511 1.137872 CATCCTTGGACTCGCTAGCTT 59.862 52.381 13.93 0.00 0.00 3.74
1321 11512 0.818296 TCCTTGGACTCGCTAGCTTC 59.182 55.000 13.93 6.25 0.00 3.86
1322 11513 0.532573 CCTTGGACTCGCTAGCTTCA 59.467 55.000 13.93 0.00 0.00 3.02
1323 11514 1.137872 CCTTGGACTCGCTAGCTTCAT 59.862 52.381 13.93 0.00 0.00 2.57
1324 11515 2.468831 CTTGGACTCGCTAGCTTCATC 58.531 52.381 13.93 4.96 0.00 2.92
1325 11516 0.382158 TGGACTCGCTAGCTTCATCG 59.618 55.000 13.93 0.00 0.00 3.84
1326 11517 0.663688 GGACTCGCTAGCTTCATCGA 59.336 55.000 13.93 0.06 0.00 3.59
1328 11519 3.470520 CTCGCTAGCTTCATCGAGG 57.529 57.895 13.93 0.00 43.13 4.63
1329 11520 0.665835 CTCGCTAGCTTCATCGAGGT 59.334 55.000 13.93 0.00 43.13 3.85
1330 11521 1.066303 CTCGCTAGCTTCATCGAGGTT 59.934 52.381 13.93 0.00 43.13 3.50
1331 11522 2.290916 CTCGCTAGCTTCATCGAGGTTA 59.709 50.000 13.93 0.00 43.13 2.85
1332 11523 2.033049 TCGCTAGCTTCATCGAGGTTAC 59.967 50.000 13.93 0.00 0.00 2.50
1333 11524 2.745102 GCTAGCTTCATCGAGGTTACC 58.255 52.381 7.70 0.00 0.00 2.85
1334 11525 2.546162 GCTAGCTTCATCGAGGTTACCC 60.546 54.545 7.70 0.00 0.00 3.69
1335 11526 1.568504 AGCTTCATCGAGGTTACCCA 58.431 50.000 0.00 0.00 0.00 4.51
1336 11527 1.207329 AGCTTCATCGAGGTTACCCAC 59.793 52.381 0.00 0.00 0.00 4.61
1349 11540 4.571919 GGTTACCCACCAAATAAAAAGCC 58.428 43.478 0.00 0.00 46.42 4.35
1350 11541 4.285003 GGTTACCCACCAAATAAAAAGCCT 59.715 41.667 0.00 0.00 46.42 4.58
1351 11542 5.234752 GTTACCCACCAAATAAAAAGCCTG 58.765 41.667 0.00 0.00 0.00 4.85
1352 11543 3.313791 ACCCACCAAATAAAAAGCCTGT 58.686 40.909 0.00 0.00 0.00 4.00
1353 11544 3.714280 ACCCACCAAATAAAAAGCCTGTT 59.286 39.130 0.00 0.00 0.00 3.16
1354 11545 4.202315 ACCCACCAAATAAAAAGCCTGTTC 60.202 41.667 0.00 0.00 0.00 3.18
1355 11546 4.202305 CCCACCAAATAAAAAGCCTGTTCA 60.202 41.667 0.00 0.00 0.00 3.18
1356 11547 4.990426 CCACCAAATAAAAAGCCTGTTCAG 59.010 41.667 0.00 0.00 0.00 3.02
1357 11548 4.990426 CACCAAATAAAAAGCCTGTTCAGG 59.010 41.667 13.88 13.88 0.00 3.86
1358 11549 4.653801 ACCAAATAAAAAGCCTGTTCAGGT 59.346 37.500 18.42 4.79 0.00 4.00
1359 11550 5.836358 ACCAAATAAAAAGCCTGTTCAGGTA 59.164 36.000 18.42 4.97 0.00 3.08
1360 11551 6.015434 ACCAAATAAAAAGCCTGTTCAGGTAG 60.015 38.462 18.42 0.00 0.00 3.18
1361 11552 6.389906 CAAATAAAAAGCCTGTTCAGGTAGG 58.610 40.000 18.42 0.00 37.14 3.18
1365 11556 3.388841 CCTGTTCAGGTAGGCCGT 58.611 61.111 10.40 0.00 40.50 5.68
1366 11557 1.218316 CCTGTTCAGGTAGGCCGTC 59.782 63.158 10.40 0.00 40.50 4.79
1367 11558 1.258445 CCTGTTCAGGTAGGCCGTCT 61.258 60.000 10.40 0.00 40.50 4.18
1368 11559 1.471119 CTGTTCAGGTAGGCCGTCTA 58.529 55.000 0.00 0.00 40.50 2.59
1369 11560 1.822990 CTGTTCAGGTAGGCCGTCTAA 59.177 52.381 0.00 0.00 40.50 2.10
1370 11561 2.431057 CTGTTCAGGTAGGCCGTCTAAT 59.569 50.000 0.00 0.00 40.50 1.73
1371 11562 2.835764 TGTTCAGGTAGGCCGTCTAATT 59.164 45.455 0.00 0.00 40.50 1.40
1372 11563 3.118884 TGTTCAGGTAGGCCGTCTAATTC 60.119 47.826 0.00 0.00 40.50 2.17
1373 11564 3.028094 TCAGGTAGGCCGTCTAATTCT 57.972 47.619 0.00 0.00 40.50 2.40
1374 11565 2.957006 TCAGGTAGGCCGTCTAATTCTC 59.043 50.000 0.00 0.00 40.50 2.87
1375 11566 2.036089 CAGGTAGGCCGTCTAATTCTCC 59.964 54.545 0.00 0.00 40.50 3.71
1376 11567 1.000496 GGTAGGCCGTCTAATTCTCCG 60.000 57.143 0.00 0.00 0.00 4.63
1377 11568 1.000496 GTAGGCCGTCTAATTCTCCGG 60.000 57.143 0.00 0.00 43.22 5.14
1378 11569 0.396695 AGGCCGTCTAATTCTCCGGA 60.397 55.000 2.93 2.93 43.01 5.14
1379 11570 0.462789 GGCCGTCTAATTCTCCGGAA 59.537 55.000 5.23 0.00 43.01 4.30
1380 11571 1.134610 GGCCGTCTAATTCTCCGGAAA 60.135 52.381 5.23 3.39 43.01 3.13
1381 11572 2.202566 GCCGTCTAATTCTCCGGAAAG 58.797 52.381 5.23 0.00 43.01 2.62
1382 11573 2.822764 CCGTCTAATTCTCCGGAAAGG 58.177 52.381 5.23 0.00 43.01 3.11
1407 11598 9.642343 GGATTAGTTGAAATCCCCTAATAGTTT 57.358 33.333 4.57 0.00 46.28 2.66
1409 11600 9.642343 ATTAGTTGAAATCCCCTAATAGTTTCC 57.358 33.333 0.00 0.00 30.43 3.13
1410 11601 6.120220 AGTTGAAATCCCCTAATAGTTTCCG 58.880 40.000 0.00 0.00 0.00 4.30
1411 11602 4.457466 TGAAATCCCCTAATAGTTTCCGC 58.543 43.478 0.00 0.00 0.00 5.54
1412 11603 4.080243 TGAAATCCCCTAATAGTTTCCGCA 60.080 41.667 0.00 0.00 0.00 5.69
1413 11604 4.513406 AATCCCCTAATAGTTTCCGCAA 57.487 40.909 0.00 0.00 0.00 4.85
1414 11605 3.553828 TCCCCTAATAGTTTCCGCAAG 57.446 47.619 0.00 0.00 0.00 4.01
1415 11606 3.109151 TCCCCTAATAGTTTCCGCAAGA 58.891 45.455 0.00 0.00 43.02 3.02
1416 11607 3.134081 TCCCCTAATAGTTTCCGCAAGAG 59.866 47.826 0.00 0.00 43.02 2.85
1417 11608 2.872858 CCCTAATAGTTTCCGCAAGAGC 59.127 50.000 0.00 0.00 43.02 4.09
1517 11708 1.880941 AAGGAAAGGGCGTCCTCTAT 58.119 50.000 10.20 0.00 45.12 1.98
1691 12062 7.319142 ACTTTTCATTTGGTTCCAAACATTG 57.681 32.000 17.59 12.82 38.52 2.82
2098 12482 0.885196 GAAAATTACCCACGCCAGCA 59.115 50.000 0.00 0.00 0.00 4.41
2185 12577 3.895232 ACCGATAAGCATCACTGAACT 57.105 42.857 0.00 0.00 0.00 3.01
2504 12936 1.451028 GGCGCAGGAGCTTGAATCT 60.451 57.895 10.83 0.00 39.10 2.40
2527 12959 4.166523 GTCATCGATTCACGTCTCTGAAA 58.833 43.478 0.00 0.00 43.13 2.69
2652 13098 4.434713 AAATGTTGGCATACCGAGAAAC 57.565 40.909 0.00 0.00 39.70 2.78
2669 13117 1.484356 AACGCGCACCTTCGATATAC 58.516 50.000 5.73 0.00 0.00 1.47
2670 13118 0.382873 ACGCGCACCTTCGATATACA 59.617 50.000 5.73 0.00 0.00 2.29
2961 16775 4.329392 TCCTCTCACGGGGAAATTAAAAC 58.671 43.478 0.00 0.00 0.00 2.43
2969 16783 3.253921 CGGGGAAATTAAAACGACCAACT 59.746 43.478 0.00 0.00 0.00 3.16
3085 16912 4.095782 GTGGACTATTTTGTGTGTGTGTGT 59.904 41.667 0.00 0.00 0.00 3.72
3091 16918 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
3094 16921 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
3095 16922 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
3097 16924 1.950216 TGTGTGTGTGTGTGTGTTTGT 59.050 42.857 0.00 0.00 0.00 2.83
3099 16926 1.950216 TGTGTGTGTGTGTGTTTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
3100 16927 2.287248 TGTGTGTGTGTGTGTTTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
3145 16984 4.451435 CCATCTCAGTTATGTATGCTGCTG 59.549 45.833 0.00 0.00 0.00 4.41
3446 20528 8.534954 TTAGTCTGTGGCACTTCTAATATACT 57.465 34.615 19.83 7.10 0.00 2.12
3447 20529 7.045126 AGTCTGTGGCACTTCTAATATACTC 57.955 40.000 19.83 0.00 0.00 2.59
3448 20530 6.041069 AGTCTGTGGCACTTCTAATATACTCC 59.959 42.308 19.83 0.00 0.00 3.85
3449 20531 5.304614 TCTGTGGCACTTCTAATATACTCCC 59.695 44.000 19.83 0.00 0.00 4.30
3450 20532 5.216622 TGTGGCACTTCTAATATACTCCCT 58.783 41.667 19.83 0.00 0.00 4.20
3451 20533 5.304614 TGTGGCACTTCTAATATACTCCCTC 59.695 44.000 19.83 0.00 0.00 4.30
3452 20534 4.838986 TGGCACTTCTAATATACTCCCTCC 59.161 45.833 0.00 0.00 0.00 4.30
3453 20535 4.082136 GGCACTTCTAATATACTCCCTCCG 60.082 50.000 0.00 0.00 0.00 4.63
3454 20536 4.523558 GCACTTCTAATATACTCCCTCCGT 59.476 45.833 0.00 0.00 0.00 4.69
3455 20537 5.335819 GCACTTCTAATATACTCCCTCCGTC 60.336 48.000 0.00 0.00 0.00 4.79
3456 20538 5.183522 CACTTCTAATATACTCCCTCCGTCC 59.816 48.000 0.00 0.00 0.00 4.79
3457 20539 3.947868 TCTAATATACTCCCTCCGTCCG 58.052 50.000 0.00 0.00 0.00 4.79
3458 20540 1.920610 AATATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
3459 20541 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
3460 20542 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
3461 20543 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3462 20544 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3463 20545 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3464 20546 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3465 20547 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3466 20548 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3467 20549 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3468 20550 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3469 20551 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3470 20552 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3471 20553 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3472 20554 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3473 20555 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3474 20556 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3475 20557 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3476 20558 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3477 20559 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3478 20560 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3479 20561 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
3480 20562 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
3481 20563 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
3482 20564 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
3488 20570 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
3489 20571 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
3490 20572 5.424895 TGTCATCAAAATGGATAAAAGGGGG 59.575 40.000 0.00 0.00 33.42 5.40
3491 20573 5.425217 GTCATCAAAATGGATAAAAGGGGGT 59.575 40.000 0.00 0.00 33.42 4.95
3492 20574 5.424895 TCATCAAAATGGATAAAAGGGGGTG 59.575 40.000 0.00 0.00 33.42 4.61
3493 20575 4.757692 TCAAAATGGATAAAAGGGGGTGT 58.242 39.130 0.00 0.00 0.00 4.16
3494 20576 5.905088 TCAAAATGGATAAAAGGGGGTGTA 58.095 37.500 0.00 0.00 0.00 2.90
3495 20577 6.507568 TCAAAATGGATAAAAGGGGGTGTAT 58.492 36.000 0.00 0.00 0.00 2.29
3496 20578 6.609616 TCAAAATGGATAAAAGGGGGTGTATC 59.390 38.462 0.00 0.00 0.00 2.24
3497 20579 6.355588 AAATGGATAAAAGGGGGTGTATCT 57.644 37.500 0.00 0.00 0.00 1.98
3498 20580 7.474474 AAATGGATAAAAGGGGGTGTATCTA 57.526 36.000 0.00 0.00 0.00 1.98
3499 20581 6.704056 ATGGATAAAAGGGGGTGTATCTAG 57.296 41.667 0.00 0.00 0.00 2.43
3500 20582 5.795079 TGGATAAAAGGGGGTGTATCTAGA 58.205 41.667 0.00 0.00 0.00 2.43
3501 20583 5.605488 TGGATAAAAGGGGGTGTATCTAGAC 59.395 44.000 0.00 0.00 0.00 2.59
3502 20584 5.279356 GGATAAAAGGGGGTGTATCTAGACG 60.279 48.000 0.00 0.00 0.00 4.18
3503 20585 2.842645 AAGGGGGTGTATCTAGACGT 57.157 50.000 0.00 0.00 0.00 4.34
3504 20586 3.959495 AAGGGGGTGTATCTAGACGTA 57.041 47.619 0.00 0.00 0.00 3.57
3505 20587 4.466255 AAGGGGGTGTATCTAGACGTAT 57.534 45.455 0.00 0.00 0.00 3.06
3506 20588 4.466255 AGGGGGTGTATCTAGACGTATT 57.534 45.455 0.00 0.00 0.00 1.89
3507 20589 4.405548 AGGGGGTGTATCTAGACGTATTC 58.594 47.826 0.00 0.00 0.00 1.75
3508 20590 4.106019 AGGGGGTGTATCTAGACGTATTCT 59.894 45.833 0.00 0.00 38.51 2.40
3509 20591 5.311649 AGGGGGTGTATCTAGACGTATTCTA 59.688 44.000 0.00 0.00 35.55 2.10
3519 20601 4.839668 AGACGTATTCTAGGTGCATCTC 57.160 45.455 0.56 0.00 30.17 2.75
3520 20602 4.465886 AGACGTATTCTAGGTGCATCTCT 58.534 43.478 0.56 0.00 30.17 3.10
3521 20603 4.890581 AGACGTATTCTAGGTGCATCTCTT 59.109 41.667 0.56 0.00 30.17 2.85
3522 20604 5.361285 AGACGTATTCTAGGTGCATCTCTTT 59.639 40.000 0.56 0.00 30.17 2.52
3523 20605 5.978814 ACGTATTCTAGGTGCATCTCTTTT 58.021 37.500 0.56 0.00 0.00 2.27
3524 20606 6.407202 ACGTATTCTAGGTGCATCTCTTTTT 58.593 36.000 0.56 0.00 0.00 1.94
3525 20607 7.553334 ACGTATTCTAGGTGCATCTCTTTTTA 58.447 34.615 0.56 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 7.933577 CGATGGGCAGTGATATAATTATACCAT 59.066 37.037 15.95 15.95 36.61 3.55
733 5285 1.715019 TTGTTACCAGGTGGCAGCCT 61.715 55.000 14.15 7.94 39.99 4.58
744 5296 4.121317 CCGAGTGTTGTTAGTTGTTACCA 58.879 43.478 0.00 0.00 0.00 3.25
929 5510 1.024271 GCACCTTCAACTTGTCAGCA 58.976 50.000 0.00 0.00 0.00 4.41
987 5568 1.942712 GCGCATTGCAGCACATAGC 60.943 57.895 16.75 0.00 45.45 2.97
988 5569 4.297071 GCGCATTGCAGCACATAG 57.703 55.556 16.75 0.00 45.45 2.23
997 5578 1.345176 GTACGTCTCTGCGCATTGC 59.655 57.895 12.24 0.00 46.70 3.56
998 5579 0.458543 AGGTACGTCTCTGCGCATTG 60.459 55.000 12.24 7.04 34.88 2.82
999 5580 0.458543 CAGGTACGTCTCTGCGCATT 60.459 55.000 12.24 0.00 34.88 3.56
1051 5632 6.874134 ACATATTTAATCTCGTAGTGGCATCC 59.126 38.462 0.00 0.00 0.00 3.51
1328 11519 5.221561 ACAGGCTTTTTATTTGGTGGGTAAC 60.222 40.000 0.00 0.00 0.00 2.50
1329 11520 4.902448 ACAGGCTTTTTATTTGGTGGGTAA 59.098 37.500 0.00 0.00 0.00 2.85
1330 11521 4.484912 ACAGGCTTTTTATTTGGTGGGTA 58.515 39.130 0.00 0.00 0.00 3.69
1331 11522 3.313791 ACAGGCTTTTTATTTGGTGGGT 58.686 40.909 0.00 0.00 0.00 4.51
1332 11523 4.202305 TGAACAGGCTTTTTATTTGGTGGG 60.202 41.667 0.00 0.00 0.00 4.61
1333 11524 4.954875 TGAACAGGCTTTTTATTTGGTGG 58.045 39.130 0.00 0.00 0.00 4.61
1334 11525 4.990426 CCTGAACAGGCTTTTTATTTGGTG 59.010 41.667 7.95 0.00 42.44 4.17
1335 11526 5.213891 CCTGAACAGGCTTTTTATTTGGT 57.786 39.130 7.95 0.00 42.44 3.67
1349 11540 1.471119 TAGACGGCCTACCTGAACAG 58.529 55.000 0.00 0.00 0.00 3.16
1350 11541 1.927487 TTAGACGGCCTACCTGAACA 58.073 50.000 0.00 0.00 0.00 3.18
1351 11542 3.132467 AGAATTAGACGGCCTACCTGAAC 59.868 47.826 0.00 0.00 0.00 3.18
1352 11543 3.371965 AGAATTAGACGGCCTACCTGAA 58.628 45.455 0.00 0.00 0.00 3.02
1353 11544 2.957006 GAGAATTAGACGGCCTACCTGA 59.043 50.000 0.00 0.00 0.00 3.86
1354 11545 2.036089 GGAGAATTAGACGGCCTACCTG 59.964 54.545 0.00 0.00 0.00 4.00
1355 11546 2.317973 GGAGAATTAGACGGCCTACCT 58.682 52.381 0.00 0.00 0.00 3.08
1356 11547 1.000496 CGGAGAATTAGACGGCCTACC 60.000 57.143 0.00 0.00 0.00 3.18
1357 11548 1.000496 CCGGAGAATTAGACGGCCTAC 60.000 57.143 0.00 0.00 39.85 3.18
1358 11549 1.133699 TCCGGAGAATTAGACGGCCTA 60.134 52.381 0.00 0.00 45.58 3.93
1359 11550 0.396695 TCCGGAGAATTAGACGGCCT 60.397 55.000 0.00 0.00 45.58 5.19
1360 11551 0.462789 TTCCGGAGAATTAGACGGCC 59.537 55.000 3.34 0.00 45.58 6.13
1361 11552 2.202566 CTTTCCGGAGAATTAGACGGC 58.797 52.381 3.34 0.00 45.58 5.68
1363 11554 3.795623 TCCTTTCCGGAGAATTAGACG 57.204 47.619 3.34 0.00 36.69 4.18
1373 11564 5.190677 GGATTTCAACTAATCCTTTCCGGA 58.809 41.667 0.00 0.00 46.62 5.14
1374 11565 5.500645 GGATTTCAACTAATCCTTTCCGG 57.499 43.478 0.00 0.00 46.62 5.14
1383 11574 9.642343 GGAAACTATTAGGGGATTTCAACTAAT 57.358 33.333 0.00 0.00 38.99 1.73
1384 11575 7.771826 CGGAAACTATTAGGGGATTTCAACTAA 59.228 37.037 0.00 0.00 32.13 2.24
1385 11576 7.277396 CGGAAACTATTAGGGGATTTCAACTA 58.723 38.462 0.00 0.00 32.13 2.24
1386 11577 6.120220 CGGAAACTATTAGGGGATTTCAACT 58.880 40.000 0.00 0.00 32.13 3.16
1387 11578 5.220989 GCGGAAACTATTAGGGGATTTCAAC 60.221 44.000 0.00 0.00 32.13 3.18
1388 11579 4.885325 GCGGAAACTATTAGGGGATTTCAA 59.115 41.667 0.00 0.00 32.13 2.69
1389 11580 4.080243 TGCGGAAACTATTAGGGGATTTCA 60.080 41.667 0.00 0.00 32.13 2.69
1390 11581 4.457466 TGCGGAAACTATTAGGGGATTTC 58.543 43.478 0.00 0.00 0.00 2.17
1391 11582 4.513406 TGCGGAAACTATTAGGGGATTT 57.487 40.909 0.00 0.00 0.00 2.17
1392 11583 4.165372 TCTTGCGGAAACTATTAGGGGATT 59.835 41.667 0.00 0.00 0.00 3.01
1393 11584 3.714798 TCTTGCGGAAACTATTAGGGGAT 59.285 43.478 0.00 0.00 0.00 3.85
1394 11585 3.109151 TCTTGCGGAAACTATTAGGGGA 58.891 45.455 0.00 0.00 0.00 4.81
1395 11586 3.467803 CTCTTGCGGAAACTATTAGGGG 58.532 50.000 0.00 0.00 0.00 4.79
1396 11587 2.872858 GCTCTTGCGGAAACTATTAGGG 59.127 50.000 0.00 0.00 0.00 3.53
1410 11601 2.672996 TGCCTTTCCCGCTCTTGC 60.673 61.111 0.00 0.00 0.00 4.01
1411 11602 2.042831 CCTGCCTTTCCCGCTCTTG 61.043 63.158 0.00 0.00 0.00 3.02
1412 11603 2.352805 CCTGCCTTTCCCGCTCTT 59.647 61.111 0.00 0.00 0.00 2.85
1413 11604 4.416738 GCCTGCCTTTCCCGCTCT 62.417 66.667 0.00 0.00 0.00 4.09
1414 11605 3.927481 AAGCCTGCCTTTCCCGCTC 62.927 63.158 0.00 0.00 0.00 5.03
1415 11606 3.513750 AAAGCCTGCCTTTCCCGCT 62.514 57.895 0.00 0.00 39.55 5.52
1416 11607 2.991540 AAAGCCTGCCTTTCCCGC 60.992 61.111 0.00 0.00 39.55 6.13
1417 11608 2.964978 CAAAGCCTGCCTTTCCCG 59.035 61.111 0.00 0.00 41.75 5.14
1517 11708 1.594833 CGGATTGAAGTCCCCGACA 59.405 57.895 0.00 0.00 44.29 4.35
1691 12062 2.089201 CCTGGGGAAAAACGATGGTAC 58.911 52.381 0.00 0.00 0.00 3.34
2098 12482 2.072874 ATGTCCAGGTTGCTGGTGCT 62.073 55.000 0.00 0.00 44.53 4.40
2185 12577 9.845740 ATACACAAGACATGTTAGCCATTAATA 57.154 29.630 0.00 0.00 41.46 0.98
2504 12936 2.747446 TCAGAGACGTGAATCGATGACA 59.253 45.455 0.00 0.00 42.86 3.58
2527 12959 7.905604 TTTGTCTATGTCGATCTGAACATTT 57.094 32.000 9.59 0.00 0.00 2.32
2652 13098 1.386748 CATGTATATCGAAGGTGCGCG 59.613 52.381 0.00 0.00 0.00 6.86
2669 13117 7.592938 ACCAAGATTGTAAATACACACACATG 58.407 34.615 0.00 0.00 35.64 3.21
2670 13118 7.759489 ACCAAGATTGTAAATACACACACAT 57.241 32.000 0.00 0.00 35.64 3.21
2961 16775 5.243207 ACCCTAATTTTGTAGAGTTGGTCG 58.757 41.667 0.00 0.00 0.00 4.79
3085 16912 1.950216 ACACACACACAAACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
3091 16918 4.217334 AGAAATCACACACACACACAAACA 59.783 37.500 0.00 0.00 0.00 2.83
3094 16921 3.755905 ACAGAAATCACACACACACACAA 59.244 39.130 0.00 0.00 0.00 3.33
3095 16922 3.342719 ACAGAAATCACACACACACACA 58.657 40.909 0.00 0.00 0.00 3.72
3097 16924 2.607180 CGACAGAAATCACACACACACA 59.393 45.455 0.00 0.00 0.00 3.72
3099 16926 3.172229 TCGACAGAAATCACACACACA 57.828 42.857 0.00 0.00 0.00 3.72
3100 16927 4.377431 GGAATCGACAGAAATCACACACAC 60.377 45.833 0.00 0.00 0.00 3.82
3145 16984 3.931578 AGTGTGAACTGATCCAAGCTAC 58.068 45.455 0.00 0.00 0.00 3.58
3446 20528 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3447 20529 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3448 20530 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3449 20531 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3450 20532 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3451 20533 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3452 20534 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3453 20535 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3454 20536 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
3455 20537 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
3456 20538 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
3462 20544 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
3463 20545 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
3464 20546 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
3465 20547 6.070309 CCCCCTTTTATCCATTTTGATGACAA 60.070 38.462 0.00 0.00 0.00 3.18
3466 20548 5.424895 CCCCCTTTTATCCATTTTGATGACA 59.575 40.000 0.00 0.00 0.00 3.58
3467 20549 5.425217 ACCCCCTTTTATCCATTTTGATGAC 59.575 40.000 0.00 0.00 0.00 3.06
3468 20550 5.424895 CACCCCCTTTTATCCATTTTGATGA 59.575 40.000 0.00 0.00 0.00 2.92
3469 20551 5.189539 ACACCCCCTTTTATCCATTTTGATG 59.810 40.000 0.00 0.00 0.00 3.07
3470 20552 5.349690 ACACCCCCTTTTATCCATTTTGAT 58.650 37.500 0.00 0.00 0.00 2.57
3471 20553 4.757692 ACACCCCCTTTTATCCATTTTGA 58.242 39.130 0.00 0.00 0.00 2.69
3472 20554 6.611236 AGATACACCCCCTTTTATCCATTTTG 59.389 38.462 0.00 0.00 0.00 2.44
3473 20555 6.752091 AGATACACCCCCTTTTATCCATTTT 58.248 36.000 0.00 0.00 0.00 1.82
3474 20556 6.355588 AGATACACCCCCTTTTATCCATTT 57.644 37.500 0.00 0.00 0.00 2.32
3475 20557 6.855061 TCTAGATACACCCCCTTTTATCCATT 59.145 38.462 0.00 0.00 0.00 3.16
3476 20558 6.272558 GTCTAGATACACCCCCTTTTATCCAT 59.727 42.308 0.00 0.00 0.00 3.41
3477 20559 5.605488 GTCTAGATACACCCCCTTTTATCCA 59.395 44.000 0.00 0.00 0.00 3.41
3478 20560 5.279356 CGTCTAGATACACCCCCTTTTATCC 60.279 48.000 0.00 0.00 0.00 2.59
3479 20561 5.303845 ACGTCTAGATACACCCCCTTTTATC 59.696 44.000 0.00 0.00 0.00 1.75
3480 20562 5.214293 ACGTCTAGATACACCCCCTTTTAT 58.786 41.667 0.00 0.00 0.00 1.40
3481 20563 4.613437 ACGTCTAGATACACCCCCTTTTA 58.387 43.478 0.00 0.00 0.00 1.52
3482 20564 3.447950 ACGTCTAGATACACCCCCTTTT 58.552 45.455 0.00 0.00 0.00 2.27
3483 20565 3.111741 ACGTCTAGATACACCCCCTTT 57.888 47.619 0.00 0.00 0.00 3.11
3484 20566 2.842645 ACGTCTAGATACACCCCCTT 57.157 50.000 0.00 0.00 0.00 3.95
3485 20567 4.106019 AGAATACGTCTAGATACACCCCCT 59.894 45.833 0.00 0.00 33.56 4.79
3486 20568 4.405548 AGAATACGTCTAGATACACCCCC 58.594 47.826 0.00 0.00 33.56 5.40
3497 20579 5.622180 AGAGATGCACCTAGAATACGTCTA 58.378 41.667 0.00 0.00 37.84 2.59
3498 20580 4.465886 AGAGATGCACCTAGAATACGTCT 58.534 43.478 0.00 0.00 40.71 4.18
3499 20581 4.839668 AGAGATGCACCTAGAATACGTC 57.160 45.455 0.00 0.00 0.00 4.34
3500 20582 5.599999 AAAGAGATGCACCTAGAATACGT 57.400 39.130 0.00 0.00 0.00 3.57
3501 20583 6.910536 AAAAAGAGATGCACCTAGAATACG 57.089 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.