Multiple sequence alignment - TraesCS1D01G275200

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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 TraesCS1D01G275200 chr1D 100.000 2855 0 0 1 2855 370919225 370916371 0.000000e+00 5273.0
1 TraesCS1D01G275200 chr1D 74.272 206 40 9 315 519 326480219 326480026 1.100000e-09 75.0
2 TraesCS1D01G275200 chr1A 94.069 2057 75 20 740 2783 469663964 469661942 0.000000e+00 3079.0
3 TraesCS1D01G275200 chr1A 93.852 244 13 2 1 243 469665367 469665125 1.620000e-97 366.0
4 TraesCS1D01G275200 chr1A 80.412 194 21 6 95 288 461032708 461032532 6.420000e-27 132.0
5 TraesCS1D01G275200 chr1B 92.551 1423 65 18 572 1968 494241033 494239626 0.000000e+00 2002.0
6 TraesCS1D01G275200 chr1B 92.118 850 37 12 1996 2817 494237543 494236696 0.000000e+00 1171.0
7 TraesCS1D01G275200 chr1B 94.030 201 11 1 1 201 494241683 494241484 1.290000e-78 303.0
8 TraesCS1D01G275200 chr1B 86.772 189 18 2 298 486 494241244 494241063 1.340000e-48 204.0
9 TraesCS1D01G275200 chr1B 82.199 191 32 2 4 193 517898793 517898982 2.280000e-36 163.0
10 TraesCS1D01G275200 chr2B 82.759 203 26 8 1478 1674 785271228 785271427 3.780000e-39 172.0
11 TraesCS1D01G275200 chr2B 81.043 211 24 12 1478 1674 785278585 785278793 1.370000e-33 154.0
12 TraesCS1D01G275200 chr2B 100.000 35 0 0 2818 2852 699045674 699045708 6.600000e-07 65.8
13 TraesCS1D01G275200 chr2A 81.043 211 24 11 1478 1674 775272171 775271963 1.370000e-33 154.0
14 TraesCS1D01G275200 chr2D 80.095 211 26 11 1478 1674 649585907 649586115 2.970000e-30 143.0
15 TraesCS1D01G275200 chr7A 87.255 102 13 0 185 286 538823521 538823420 1.800000e-22 117.0
16 TraesCS1D01G275200 chr7A 86.792 53 7 0 469 521 375898805 375898857 3.070000e-05 60.2
17 TraesCS1D01G275200 chr3B 86.207 87 12 0 202 288 625886808 625886894 8.420000e-16 95.3
18 TraesCS1D01G275200 chr3B 97.297 37 1 0 2817 2853 39345749 39345713 2.370000e-06 63.9
19 TraesCS1D01G275200 chr5A 82.692 104 17 1 326 429 321714208 321714106 1.090000e-14 91.6
20 TraesCS1D01G275200 chr6D 100.000 37 0 0 2819 2855 68091027 68091063 5.100000e-08 69.4
21 TraesCS1D01G275200 chr6D 100.000 37 0 0 2819 2855 89300082 89300118 5.100000e-08 69.4
22 TraesCS1D01G275200 chr4B 90.385 52 5 0 468 519 388826702 388826651 5.100000e-08 69.4
23 TraesCS1D01G275200 chr3D 83.333 78 10 3 468 543 421702669 421702745 5.100000e-08 69.4
24 TraesCS1D01G275200 chr3D 97.297 37 1 0 2817 2853 19031461 19031497 2.370000e-06 63.9
25 TraesCS1D01G275200 chr5D 100.000 36 0 0 2820 2855 540120435 540120470 1.840000e-07 67.6
26 TraesCS1D01G275200 chr5D 97.297 37 0 1 2815 2851 368953128 368953093 8.540000e-06 62.1
27 TraesCS1D01G275200 chr6B 100.000 35 0 0 2819 2853 567499944 567499910 6.600000e-07 65.8
28 TraesCS1D01G275200 chr7D 94.737 38 2 0 325 362 186825172 186825135 3.070000e-05 60.2
29 TraesCS1D01G275200 chr7B 92.683 41 3 0 2813 2853 58245649 58245689 3.070000e-05 60.2
30 TraesCS1D01G275200 chr5B 97.143 35 1 0 326 360 271311995 271312029 3.070000e-05 60.2


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 TraesCS1D01G275200 chr1D 370916371 370919225 2854 True 5273.0 5273 100.00000 1 2855 1 chr1D.!!$R2 2854
1 TraesCS1D01G275200 chr1A 469661942 469665367 3425 True 1722.5 3079 93.96050 1 2783 2 chr1A.!!$R2 2782
2 TraesCS1D01G275200 chr1B 494236696 494241683 4987 True 920.0 2002 91.36775 1 2817 4 chr1B.!!$R1 2816

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
206 208 0.815734 ACCTAGTTGACCGACCATCG 59.184 55.0 0.00 0.00 40.07 3.84 F
675 1709 0.825425 TTGGAATTGGAGGTTGCGCA 60.825 50.0 5.66 5.66 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 2261 0.250553 TCAACGAAAAGGGATGCGGT 60.251 50.0 0.0 0.0 0.00 5.68 R
2443 5581 0.179092 GCAGCTTGCCATTTGATCCC 60.179 55.0 0.0 0.0 37.42 3.85 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
49 50 2.434336 CAGTCCACTTATCCCCGATCAA 59.566 50.000 0.00 0.00 0.00 2.57
59 60 1.063190 TCCCCGATCAAAGCTCTCCTA 60.063 52.381 0.00 0.00 0.00 2.94
126 128 9.926751 CATAGTATTTCTTGCACTGAACAATAG 57.073 33.333 1.27 0.00 0.00 1.73
196 198 3.491766 ATCCTCCCAGAACCTAGTTGA 57.508 47.619 0.00 0.00 0.00 3.18
206 208 0.815734 ACCTAGTTGACCGACCATCG 59.184 55.000 0.00 0.00 40.07 3.84
209 211 1.252215 TAGTTGACCGACCATCGCCA 61.252 55.000 0.00 0.00 38.82 5.69
226 228 3.138283 TCGCCAATATGAATTCTTCCCCT 59.862 43.478 7.05 0.00 0.00 4.79
257 259 8.785329 AAAAAGCAACCTTAGTTTTCATCAAA 57.215 26.923 0.00 0.00 32.45 2.69
258 260 7.770801 AAAGCAACCTTAGTTTTCATCAAAC 57.229 32.000 0.00 0.00 44.73 2.93
259 261 5.842907 AGCAACCTTAGTTTTCATCAAACC 58.157 37.500 0.00 0.00 45.42 3.27
260 262 4.988540 GCAACCTTAGTTTTCATCAAACCC 59.011 41.667 0.00 0.00 45.42 4.11
261 263 5.221441 GCAACCTTAGTTTTCATCAAACCCT 60.221 40.000 0.00 0.00 45.42 4.34
262 264 6.685368 GCAACCTTAGTTTTCATCAAACCCTT 60.685 38.462 0.00 0.00 45.42 3.95
263 265 6.650427 ACCTTAGTTTTCATCAAACCCTTC 57.350 37.500 0.00 0.00 45.42 3.46
264 266 5.538813 ACCTTAGTTTTCATCAAACCCTTCC 59.461 40.000 0.00 0.00 45.42 3.46
265 267 5.538433 CCTTAGTTTTCATCAAACCCTTCCA 59.462 40.000 0.00 0.00 45.42 3.53
266 268 6.294731 CCTTAGTTTTCATCAAACCCTTCCAG 60.295 42.308 0.00 0.00 45.42 3.86
267 269 4.803452 AGTTTTCATCAAACCCTTCCAGA 58.197 39.130 0.00 0.00 45.42 3.86
268 270 4.829492 AGTTTTCATCAAACCCTTCCAGAG 59.171 41.667 0.00 0.00 45.42 3.35
288 290 3.769300 GAGGGGTGAATTAAATGGTTGCT 59.231 43.478 0.00 0.00 0.00 3.91
291 1319 3.260632 GGGTGAATTAAATGGTTGCTGGT 59.739 43.478 0.00 0.00 0.00 4.00
295 1323 6.350949 GGTGAATTAAATGGTTGCTGGTGTAT 60.351 38.462 0.00 0.00 0.00 2.29
296 1324 7.096551 GTGAATTAAATGGTTGCTGGTGTATT 58.903 34.615 0.00 0.00 0.00 1.89
308 1336 2.233922 CTGGTGTATTTGTCCGTCTCCT 59.766 50.000 0.00 0.00 0.00 3.69
309 1337 3.433343 TGGTGTATTTGTCCGTCTCCTA 58.567 45.455 0.00 0.00 0.00 2.94
320 1348 1.202463 CCGTCTCCTAGCACAAGATGG 60.202 57.143 6.55 6.55 39.24 3.51
328 1356 3.323115 CCTAGCACAAGATGGAGAGCATA 59.677 47.826 0.00 0.00 0.00 3.14
332 1360 3.881688 GCACAAGATGGAGAGCATATTGT 59.118 43.478 0.00 0.00 42.82 2.71
349 1377 6.073331 GCATATTGTGAACTTCCTAGAGATGC 60.073 42.308 0.00 0.00 0.00 3.91
352 1380 5.016051 TGTGAACTTCCTAGAGATGCATC 57.984 43.478 19.37 19.37 0.00 3.91
361 1389 4.047822 CCTAGAGATGCATCGACAACTTC 58.952 47.826 20.67 10.95 0.00 3.01
378 1406 4.032960 ACTTCAAGATACCCATGCACAA 57.967 40.909 0.00 0.00 0.00 3.33
397 1425 4.216042 CACAAATGCAACCACTCAGTGATA 59.784 41.667 6.30 0.00 35.23 2.15
400 1428 5.571784 AATGCAACCACTCAGTGATAATG 57.428 39.130 6.30 0.61 35.23 1.90
459 1487 9.716531 TGAATTTTATATTTGAACAATGCACCA 57.283 25.926 0.00 0.00 0.00 4.17
462 1490 9.887629 ATTTTATATTTGAACAATGCACCATGA 57.112 25.926 0.00 0.00 0.00 3.07
463 1491 9.716531 TTTTATATTTGAACAATGCACCATGAA 57.283 25.926 0.00 0.00 0.00 2.57
464 1492 9.887629 TTTATATTTGAACAATGCACCATGAAT 57.112 25.926 0.00 0.00 0.00 2.57
466 1494 8.876275 ATATTTGAACAATGCACCATGAATAC 57.124 30.769 0.00 0.00 0.00 1.89
467 1495 5.718724 TTGAACAATGCACCATGAATACA 57.281 34.783 0.00 0.00 0.00 2.29
468 1496 5.918426 TGAACAATGCACCATGAATACAT 57.082 34.783 0.00 0.00 37.19 2.29
469 1497 6.283544 TGAACAATGCACCATGAATACATT 57.716 33.333 0.00 0.00 34.15 2.71
470 1498 6.699366 TGAACAATGCACCATGAATACATTT 58.301 32.000 0.00 0.00 34.15 2.32
471 1499 7.160049 TGAACAATGCACCATGAATACATTTT 58.840 30.769 0.00 0.00 34.15 1.82
529 1557 6.425721 TGTTTGAACTATGTAACTTTCTCCCG 59.574 38.462 0.00 0.00 0.00 5.14
531 1559 4.773674 TGAACTATGTAACTTTCTCCCGGA 59.226 41.667 0.73 0.00 0.00 5.14
541 1569 8.102047 TGTAACTTTCTCCCGGAATACATTTTA 58.898 33.333 0.73 0.00 33.53 1.52
547 1575 7.328277 TCTCCCGGAATACATTTTATGTTTG 57.672 36.000 0.73 0.00 41.63 2.93
548 1576 7.113437 TCTCCCGGAATACATTTTATGTTTGA 58.887 34.615 0.73 0.00 41.63 2.69
549 1577 7.612244 TCTCCCGGAATACATTTTATGTTTGAA 59.388 33.333 0.73 0.00 41.63 2.69
550 1578 7.540299 TCCCGGAATACATTTTATGTTTGAAC 58.460 34.615 0.73 0.00 41.63 3.18
551 1579 7.394923 TCCCGGAATACATTTTATGTTTGAACT 59.605 33.333 0.73 0.00 41.63 3.01
552 1580 8.032451 CCCGGAATACATTTTATGTTTGAACTT 58.968 33.333 0.73 0.00 41.63 2.66
553 1581 9.418045 CCGGAATACATTTTATGTTTGAACTTT 57.582 29.630 0.00 0.00 41.63 2.66
567 1595 7.703328 TGTTTGAACTTTGTATGTTTCTCTCC 58.297 34.615 0.00 0.00 0.00 3.71
568 1596 7.338196 TGTTTGAACTTTGTATGTTTCTCTCCA 59.662 33.333 0.00 0.00 0.00 3.86
569 1597 7.873719 TTGAACTTTGTATGTTTCTCTCCAA 57.126 32.000 0.00 0.00 0.00 3.53
570 1598 7.873719 TGAACTTTGTATGTTTCTCTCCAAA 57.126 32.000 0.00 0.00 0.00 3.28
571 1599 8.463930 TGAACTTTGTATGTTTCTCTCCAAAT 57.536 30.769 0.00 0.00 0.00 2.32
626 1654 8.755696 TGTTTTGCTTATTCATATTGTCCAAC 57.244 30.769 0.00 0.00 0.00 3.77
628 1656 6.993786 TTGCTTATTCATATTGTCCAACGA 57.006 33.333 0.00 0.00 0.00 3.85
631 1659 6.073819 TGCTTATTCATATTGTCCAACGATCG 60.074 38.462 14.88 14.88 0.00 3.69
633 1661 7.307160 GCTTATTCATATTGTCCAACGATCGAA 60.307 37.037 24.34 4.42 0.00 3.71
634 1662 5.712217 TTCATATTGTCCAACGATCGAAC 57.288 39.130 24.34 13.93 0.00 3.95
635 1663 4.116961 TCATATTGTCCAACGATCGAACC 58.883 43.478 24.34 5.17 0.00 3.62
636 1664 2.465860 ATTGTCCAACGATCGAACCA 57.534 45.000 24.34 7.80 0.00 3.67
647 1681 2.802247 CGATCGAACCACATGCATGTAT 59.198 45.455 30.92 19.70 39.39 2.29
673 1707 2.810439 TTTTGGAATTGGAGGTTGCG 57.190 45.000 0.00 0.00 0.00 4.85
675 1709 0.825425 TTGGAATTGGAGGTTGCGCA 60.825 50.000 5.66 5.66 0.00 6.09
682 1716 2.125512 GAGGTTGCGCAGACGGAT 60.126 61.111 11.31 2.19 40.25 4.18
686 1720 1.618837 AGGTTGCGCAGACGGATATAT 59.381 47.619 11.31 0.00 40.25 0.86
687 1721 2.037251 AGGTTGCGCAGACGGATATATT 59.963 45.455 11.31 0.00 40.25 1.28
689 1723 2.078849 TGCGCAGACGGATATATTGG 57.921 50.000 5.66 0.00 40.57 3.16
691 1725 1.067142 GCGCAGACGGATATATTGGGA 60.067 52.381 0.30 0.00 40.57 4.37
692 1726 2.607187 CGCAGACGGATATATTGGGAC 58.393 52.381 0.00 0.00 34.97 4.46
694 1728 2.607187 CAGACGGATATATTGGGACGC 58.393 52.381 0.00 0.00 0.00 5.19
695 1729 2.029380 CAGACGGATATATTGGGACGCA 60.029 50.000 0.00 0.00 0.00 5.24
696 1730 2.832129 AGACGGATATATTGGGACGCAT 59.168 45.455 0.00 0.00 0.00 4.73
711 1760 1.753141 ACGCATCGTGGACCTATAGGT 60.753 52.381 24.84 24.84 45.41 3.08
729 1778 6.817765 ATAGGTGGTCAAATTTGTACAGTG 57.182 37.500 17.47 0.00 0.00 3.66
730 1779 4.532834 AGGTGGTCAAATTTGTACAGTGT 58.467 39.130 17.47 0.00 0.00 3.55
731 1780 4.953579 AGGTGGTCAAATTTGTACAGTGTT 59.046 37.500 17.47 2.62 0.00 3.32
768 1817 1.982226 TGCTCTAAACCCTAGCCACAA 59.018 47.619 0.00 0.00 35.33 3.33
777 1826 3.956744 ACCCTAGCCACAAAAGATCTTC 58.043 45.455 8.78 0.00 0.00 2.87
785 1834 4.151883 CCACAAAAGATCTTCCCCTTCAA 58.848 43.478 8.78 0.00 0.00 2.69
786 1835 4.774200 CCACAAAAGATCTTCCCCTTCAAT 59.226 41.667 8.78 0.00 0.00 2.57
947 1996 1.207089 CTTCACCAGTTCGGCTCCATA 59.793 52.381 0.00 0.00 39.03 2.74
1060 2109 2.413765 CTCGCTCTTCTACCCCGC 59.586 66.667 0.00 0.00 0.00 6.13
1136 2185 2.048023 ACAAGCATGGATGTGGCCG 61.048 57.895 0.00 0.00 0.00 6.13
1139 2188 3.576356 GCATGGATGTGGCCGTCG 61.576 66.667 0.00 0.00 0.00 5.12
1154 2203 1.652563 GTCGTGCAAGAACCCAACC 59.347 57.895 3.20 0.00 0.00 3.77
1212 2261 2.594303 CGGTGGCAGCCAAGAACA 60.594 61.111 18.28 0.00 34.18 3.18
1229 2278 0.536460 ACACCGCATCCCTTTTCGTT 60.536 50.000 0.00 0.00 0.00 3.85
1421 2470 1.814772 CGCCCTCTAGCTCCATCCTG 61.815 65.000 0.00 0.00 0.00 3.86
1742 2791 3.714871 GAGCGACCTGGAGAGCAGC 62.715 68.421 0.00 0.00 0.00 5.25
1822 2871 2.881352 GCTCAGCTACGTGTCCGC 60.881 66.667 0.00 0.00 37.70 5.54
1868 2929 2.159212 TGCCTCGATTCATTTTGCCATG 60.159 45.455 0.00 0.00 0.00 3.66
1869 2930 2.159198 GCCTCGATTCATTTTGCCATGT 60.159 45.455 0.00 0.00 0.00 3.21
1870 2931 3.066621 GCCTCGATTCATTTTGCCATGTA 59.933 43.478 0.00 0.00 0.00 2.29
1871 2932 4.790766 GCCTCGATTCATTTTGCCATGTAG 60.791 45.833 0.00 0.00 0.00 2.74
1872 2933 4.336433 CCTCGATTCATTTTGCCATGTAGT 59.664 41.667 0.00 0.00 0.00 2.73
1873 2934 5.527214 CCTCGATTCATTTTGCCATGTAGTA 59.473 40.000 0.00 0.00 0.00 1.82
1903 2964 7.512992 ACTGTAGCAGCTCCAGATTAATTAAT 58.487 34.615 21.17 10.51 34.37 1.40
1957 3019 1.956620 GCGTTACTGCTCCTGCGAAC 61.957 60.000 0.00 0.00 43.34 3.95
2049 5166 3.726631 GAGCTGACGACGAGAGCGG 62.727 68.421 0.00 0.00 43.17 5.52
2084 5203 1.870901 CGGTACTACGTGCGCTTCC 60.871 63.158 9.73 0.00 0.00 3.46
2099 5218 1.474077 GCTTCCCAGTAATTGTGGCAG 59.526 52.381 3.59 3.51 33.24 4.85
2113 5232 2.202730 GCAGCCAGCGAGAGAGAC 60.203 66.667 0.00 0.00 0.00 3.36
2114 5233 2.101965 CAGCCAGCGAGAGAGACG 59.898 66.667 0.00 0.00 0.00 4.18
2189 5310 3.846896 GTGAACTCGACGTAACAGATCTG 59.153 47.826 21.37 21.37 0.00 2.90
2443 5581 4.351938 TCACGTTCGTGAGGGCCG 62.352 66.667 21.38 0.00 39.83 6.13
2524 5664 2.966309 GAAAGGAACGGTGCTGGCG 61.966 63.158 0.00 0.00 0.00 5.69
2783 5929 5.239963 CCTTTTTACCCTCGCTGTTTTTCTA 59.760 40.000 0.00 0.00 0.00 2.10
2784 5930 6.238814 CCTTTTTACCCTCGCTGTTTTTCTAA 60.239 38.462 0.00 0.00 0.00 2.10
2785 5931 6.696441 TTTTACCCTCGCTGTTTTTCTAAA 57.304 33.333 0.00 0.00 0.00 1.85
2824 5970 2.900122 GTACAGTGCGTACCGAGTAA 57.100 50.000 0.00 0.00 44.11 2.24
2825 5971 3.201726 GTACAGTGCGTACCGAGTAAA 57.798 47.619 0.00 0.00 44.11 2.01
2826 5972 3.762779 GTACAGTGCGTACCGAGTAAAT 58.237 45.455 0.00 0.00 44.11 1.40
2827 5973 3.308438 ACAGTGCGTACCGAGTAAATT 57.692 42.857 0.00 0.00 0.00 1.82
2828 5974 2.991190 ACAGTGCGTACCGAGTAAATTG 59.009 45.455 0.00 0.00 0.00 2.32
2829 5975 1.997606 AGTGCGTACCGAGTAAATTGC 59.002 47.619 0.00 0.00 0.00 3.56
2830 5976 1.727880 GTGCGTACCGAGTAAATTGCA 59.272 47.619 0.00 0.00 0.00 4.08
2831 5977 2.350498 GTGCGTACCGAGTAAATTGCAT 59.650 45.455 0.00 0.00 33.25 3.96
2832 5978 3.552699 GTGCGTACCGAGTAAATTGCATA 59.447 43.478 0.00 0.00 33.25 3.14
2833 5979 4.033129 GTGCGTACCGAGTAAATTGCATAA 59.967 41.667 0.00 0.00 33.25 1.90
2834 5980 4.630505 TGCGTACCGAGTAAATTGCATAAA 59.369 37.500 0.00 0.00 0.00 1.40
2835 5981 5.121925 TGCGTACCGAGTAAATTGCATAAAA 59.878 36.000 0.00 0.00 0.00 1.52
2836 5982 5.450066 GCGTACCGAGTAAATTGCATAAAAC 59.550 40.000 0.00 0.00 0.00 2.43
2837 5983 5.961263 CGTACCGAGTAAATTGCATAAAACC 59.039 40.000 0.00 0.00 0.00 3.27
2838 5984 5.968528 ACCGAGTAAATTGCATAAAACCA 57.031 34.783 0.00 0.00 0.00 3.67
2839 5985 5.705902 ACCGAGTAAATTGCATAAAACCAC 58.294 37.500 0.00 0.00 0.00 4.16
2840 5986 5.099575 CCGAGTAAATTGCATAAAACCACC 58.900 41.667 0.00 0.00 0.00 4.61
2841 5987 5.336055 CCGAGTAAATTGCATAAAACCACCA 60.336 40.000 0.00 0.00 0.00 4.17
2842 5988 5.571357 CGAGTAAATTGCATAAAACCACCAC 59.429 40.000 0.00 0.00 0.00 4.16
2843 5989 6.569610 CGAGTAAATTGCATAAAACCACCACT 60.570 38.462 0.00 0.00 0.00 4.00
2844 5990 7.061566 AGTAAATTGCATAAAACCACCACTT 57.938 32.000 0.00 0.00 0.00 3.16
2845 5991 7.505258 AGTAAATTGCATAAAACCACCACTTT 58.495 30.769 0.00 0.00 0.00 2.66
2846 5992 6.616774 AAATTGCATAAAACCACCACTTTG 57.383 33.333 0.00 0.00 0.00 2.77
2847 5993 5.543507 ATTGCATAAAACCACCACTTTGA 57.456 34.783 0.00 0.00 0.00 2.69
2848 5994 5.344743 TTGCATAAAACCACCACTTTGAA 57.655 34.783 0.00 0.00 0.00 2.69
2849 5995 4.942852 TGCATAAAACCACCACTTTGAAG 58.057 39.130 0.00 0.00 0.00 3.02
2850 5996 4.202202 TGCATAAAACCACCACTTTGAAGG 60.202 41.667 0.00 0.00 0.00 3.46
2851 5997 2.979814 AAAACCACCACTTTGAAGGC 57.020 45.000 0.00 0.00 0.00 4.35
2852 5998 2.159179 AAACCACCACTTTGAAGGCT 57.841 45.000 0.00 0.00 0.00 4.58
2853 5999 1.692411 AACCACCACTTTGAAGGCTC 58.308 50.000 0.00 0.00 0.00 4.70
2854 6000 0.535102 ACCACCACTTTGAAGGCTCG 60.535 55.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.637986 CACTGAATATCTAGTTTAGGAGAGCTT 58.362 37.037 0.00 0.00 0.00 3.74
59 60 9.614792 GGGTCAAATACACTGAATATCTAGTTT 57.385 33.333 0.00 0.00 0.00 2.66
126 128 6.620089 GCTTCACGGTATCCTTCTTTGTAAAC 60.620 42.308 0.00 0.00 0.00 2.01
144 146 3.726517 CACGCCCCTTGCTTCACG 61.727 66.667 0.00 0.00 38.05 4.35
196 198 0.756294 TCATATTGGCGATGGTCGGT 59.244 50.000 0.00 0.00 40.84 4.69
236 238 5.221441 GGGTTTGATGAAAACTAAGGTTGCT 60.221 40.000 0.00 0.00 46.27 3.91
237 239 4.988540 GGGTTTGATGAAAACTAAGGTTGC 59.011 41.667 0.00 0.00 46.27 4.17
238 240 6.405278 AGGGTTTGATGAAAACTAAGGTTG 57.595 37.500 0.00 0.00 46.27 3.77
240 242 5.538813 GGAAGGGTTTGATGAAAACTAAGGT 59.461 40.000 0.00 0.00 46.27 3.50
242 244 6.490040 TCTGGAAGGGTTTGATGAAAACTAAG 59.510 38.462 0.00 0.00 46.27 2.18
243 245 6.369629 TCTGGAAGGGTTTGATGAAAACTAA 58.630 36.000 0.00 0.00 46.27 2.24
244 246 5.947663 TCTGGAAGGGTTTGATGAAAACTA 58.052 37.500 0.00 0.00 46.27 2.24
245 247 4.803452 TCTGGAAGGGTTTGATGAAAACT 58.197 39.130 0.00 0.00 46.27 2.66
246 248 4.021981 CCTCTGGAAGGGTTTGATGAAAAC 60.022 45.833 0.00 0.00 46.32 2.43
247 249 4.151883 CCTCTGGAAGGGTTTGATGAAAA 58.848 43.478 0.00 0.00 42.03 2.29
248 250 3.766545 CCTCTGGAAGGGTTTGATGAAA 58.233 45.455 0.00 0.00 42.03 2.69
249 251 3.439857 CCTCTGGAAGGGTTTGATGAA 57.560 47.619 0.00 0.00 42.03 2.57
259 261 4.316025 TTTAATTCACCCCTCTGGAAGG 57.684 45.455 0.00 0.00 45.77 3.46
260 262 4.646492 CCATTTAATTCACCCCTCTGGAAG 59.354 45.833 0.00 0.00 38.00 3.46
261 263 4.045334 ACCATTTAATTCACCCCTCTGGAA 59.955 41.667 0.00 0.00 38.00 3.53
262 264 3.596046 ACCATTTAATTCACCCCTCTGGA 59.404 43.478 0.00 0.00 38.00 3.86
263 265 3.981212 ACCATTTAATTCACCCCTCTGG 58.019 45.455 0.00 0.00 41.37 3.86
264 266 4.381932 GCAACCATTTAATTCACCCCTCTG 60.382 45.833 0.00 0.00 0.00 3.35
265 267 3.769300 GCAACCATTTAATTCACCCCTCT 59.231 43.478 0.00 0.00 0.00 3.69
266 268 3.769300 AGCAACCATTTAATTCACCCCTC 59.231 43.478 0.00 0.00 0.00 4.30
267 269 3.515104 CAGCAACCATTTAATTCACCCCT 59.485 43.478 0.00 0.00 0.00 4.79
268 270 3.369366 CCAGCAACCATTTAATTCACCCC 60.369 47.826 0.00 0.00 0.00 4.95
277 279 5.047660 GGACAAATACACCAGCAACCATTTA 60.048 40.000 0.00 0.00 0.00 1.40
288 290 2.253610 AGGAGACGGACAAATACACCA 58.746 47.619 0.00 0.00 0.00 4.17
291 1319 3.093814 TGCTAGGAGACGGACAAATACA 58.906 45.455 0.00 0.00 0.00 2.29
295 1323 1.334160 TGTGCTAGGAGACGGACAAA 58.666 50.000 0.00 0.00 0.00 2.83
296 1324 1.272490 CTTGTGCTAGGAGACGGACAA 59.728 52.381 0.00 0.00 0.00 3.18
308 1336 5.163269 ACAATATGCTCTCCATCTTGTGCTA 60.163 40.000 6.35 0.00 44.62 3.49
309 1337 4.135306 CAATATGCTCTCCATCTTGTGCT 58.865 43.478 0.00 0.00 34.85 4.40
320 1348 6.810911 TCTAGGAAGTTCACAATATGCTCTC 58.189 40.000 5.01 0.00 0.00 3.20
328 1356 5.426689 TGCATCTCTAGGAAGTTCACAAT 57.573 39.130 5.01 0.00 0.00 2.71
332 1360 3.954258 TCGATGCATCTCTAGGAAGTTCA 59.046 43.478 23.73 0.00 0.00 3.18
349 1377 4.503910 TGGGTATCTTGAAGTTGTCGATG 58.496 43.478 0.00 0.00 0.00 3.84
352 1380 3.063997 GCATGGGTATCTTGAAGTTGTCG 59.936 47.826 0.00 0.00 0.00 4.35
361 1389 3.119065 TGCATTTGTGCATGGGTATCTTG 60.119 43.478 0.00 0.00 40.23 3.02
378 1406 5.012239 ACATTATCACTGAGTGGTTGCATT 58.988 37.500 13.33 0.00 33.87 3.56
391 1419 3.943381 CACACATGCTCCACATTATCACT 59.057 43.478 0.00 0.00 36.64 3.41
392 1420 3.065786 CCACACATGCTCCACATTATCAC 59.934 47.826 0.00 0.00 36.64 3.06
393 1421 3.054508 TCCACACATGCTCCACATTATCA 60.055 43.478 0.00 0.00 36.64 2.15
397 1425 2.097036 CATCCACACATGCTCCACATT 58.903 47.619 0.00 0.00 36.64 2.71
400 1428 1.805254 GCATCCACACATGCTCCAC 59.195 57.895 0.00 0.00 45.03 4.02
441 1469 8.476447 TGTATTCATGGTGCATTGTTCAAATAT 58.524 29.630 0.00 0.00 0.00 1.28
442 1470 7.834803 TGTATTCATGGTGCATTGTTCAAATA 58.165 30.769 0.00 0.00 0.00 1.40
443 1471 6.699366 TGTATTCATGGTGCATTGTTCAAAT 58.301 32.000 0.00 0.00 0.00 2.32
444 1472 6.094193 TGTATTCATGGTGCATTGTTCAAA 57.906 33.333 0.00 0.00 0.00 2.69
445 1473 5.718724 TGTATTCATGGTGCATTGTTCAA 57.281 34.783 0.00 0.00 0.00 2.69
446 1474 5.918426 ATGTATTCATGGTGCATTGTTCA 57.082 34.783 0.00 0.00 32.51 3.18
447 1475 7.599630 AAAATGTATTCATGGTGCATTGTTC 57.400 32.000 13.08 0.00 34.19 3.18
448 1476 9.100554 CATAAAATGTATTCATGGTGCATTGTT 57.899 29.630 13.08 11.79 34.19 2.83
449 1477 8.259411 ACATAAAATGTATTCATGGTGCATTGT 58.741 29.630 13.08 11.13 42.78 2.71
450 1478 8.651391 ACATAAAATGTATTCATGGTGCATTG 57.349 30.769 13.08 6.88 42.78 2.82
451 1479 9.669887 AAACATAAAATGTATTCATGGTGCATT 57.330 25.926 8.66 8.66 44.07 3.56
452 1480 9.100554 CAAACATAAAATGTATTCATGGTGCAT 57.899 29.630 0.00 0.00 44.07 3.96
453 1481 8.309656 TCAAACATAAAATGTATTCATGGTGCA 58.690 29.630 0.00 0.00 44.07 4.57
454 1482 8.700722 TCAAACATAAAATGTATTCATGGTGC 57.299 30.769 0.00 0.00 44.07 5.01
463 1491 8.934825 GGTGCATTGTTCAAACATAAAATGTAT 58.065 29.630 0.00 0.00 44.07 2.29
464 1492 7.928167 TGGTGCATTGTTCAAACATAAAATGTA 59.072 29.630 0.00 0.00 44.07 2.29
466 1494 7.187244 TGGTGCATTGTTCAAACATAAAATG 57.813 32.000 0.00 0.00 38.95 2.32
467 1495 7.660617 TCATGGTGCATTGTTCAAACATAAAAT 59.339 29.630 0.00 0.00 38.95 1.82
468 1496 6.988580 TCATGGTGCATTGTTCAAACATAAAA 59.011 30.769 0.00 0.00 38.95 1.52
469 1497 6.519382 TCATGGTGCATTGTTCAAACATAAA 58.481 32.000 0.00 0.00 38.95 1.40
470 1498 6.094193 TCATGGTGCATTGTTCAAACATAA 57.906 33.333 0.00 0.00 38.95 1.90
471 1499 5.718724 TCATGGTGCATTGTTCAAACATA 57.281 34.783 0.00 0.00 38.95 2.29
508 1536 4.773674 TCCGGGAGAAAGTTACATAGTTCA 59.226 41.667 0.00 0.00 0.00 3.18
520 1548 7.568199 ACATAAAATGTATTCCGGGAGAAAG 57.432 36.000 0.00 0.00 42.78 2.62
521 1549 7.948034 AACATAAAATGTATTCCGGGAGAAA 57.052 32.000 0.00 0.00 44.07 2.52
541 1569 8.352942 GGAGAGAAACATACAAAGTTCAAACAT 58.647 33.333 0.00 0.00 0.00 2.71
560 1588 9.921637 ACGCAAATAAAATTTATTTGGAGAGAA 57.078 25.926 33.82 0.00 42.23 2.87
561 1589 9.352784 CACGCAAATAAAATTTATTTGGAGAGA 57.647 29.630 33.82 0.00 42.23 3.10
562 1590 9.139174 ACACGCAAATAAAATTTATTTGGAGAG 57.861 29.630 33.82 22.82 42.23 3.20
563 1591 9.482627 AACACGCAAATAAAATTTATTTGGAGA 57.517 25.926 33.82 0.00 42.23 3.71
599 1627 9.941325 TTGGACAATATGAATAAGCAAAACAAT 57.059 25.926 0.00 0.00 0.00 2.71
619 1647 0.389757 TGTGGTTCGATCGTTGGACA 59.610 50.000 15.94 11.22 0.00 4.02
622 1650 0.096976 GCATGTGGTTCGATCGTTGG 59.903 55.000 15.94 0.00 0.00 3.77
626 1654 1.009078 ACATGCATGTGGTTCGATCG 58.991 50.000 30.92 9.36 40.03 3.69
628 1656 4.639755 TCAAATACATGCATGTGGTTCGAT 59.360 37.500 36.72 21.09 41.89 3.59
631 1659 5.565592 TCTCAAATACATGCATGTGGTTC 57.434 39.130 36.72 0.00 41.89 3.62
633 1661 6.534475 AAATCTCAAATACATGCATGTGGT 57.466 33.333 36.72 24.13 41.89 4.16
634 1662 6.256975 CCAAAATCTCAAATACATGCATGTGG 59.743 38.462 36.72 23.83 41.89 4.17
635 1663 7.036829 TCCAAAATCTCAAATACATGCATGTG 58.963 34.615 36.72 22.61 41.89 3.21
636 1664 7.172868 TCCAAAATCTCAAATACATGCATGT 57.827 32.000 33.20 33.20 44.48 3.21
647 1681 6.523840 CAACCTCCAATTCCAAAATCTCAAA 58.476 36.000 0.00 0.00 0.00 2.69
673 1707 2.607187 CGTCCCAATATATCCGTCTGC 58.393 52.381 0.00 0.00 0.00 4.26
675 1709 2.244695 TGCGTCCCAATATATCCGTCT 58.755 47.619 0.00 0.00 0.00 4.18
682 1716 1.964933 TCCACGATGCGTCCCAATATA 59.035 47.619 0.00 0.00 38.32 0.86
686 1720 2.047655 GTCCACGATGCGTCCCAA 60.048 61.111 0.00 0.00 38.32 4.12
687 1721 4.077184 GGTCCACGATGCGTCCCA 62.077 66.667 0.00 0.00 38.32 4.37
689 1723 0.956633 TATAGGTCCACGATGCGTCC 59.043 55.000 0.00 0.00 38.32 4.79
691 1725 0.959553 CCTATAGGTCCACGATGCGT 59.040 55.000 10.96 0.00 42.36 5.24
692 1726 3.794690 CCTATAGGTCCACGATGCG 57.205 57.895 10.96 0.00 0.00 4.73
711 1760 5.906113 ACAACACTGTACAAATTTGACCA 57.094 34.783 24.64 17.18 32.54 4.02
724 1773 2.769663 TCCAACAGGAGTACAACACTGT 59.230 45.455 0.00 0.80 45.34 3.55
768 1817 5.504853 GTGAGATTGAAGGGGAAGATCTTT 58.495 41.667 9.87 0.00 0.00 2.52
777 1826 3.615155 GAAGAAGGTGAGATTGAAGGGG 58.385 50.000 0.00 0.00 0.00 4.79
785 1834 3.111484 GAGGGAAGGAAGAAGGTGAGAT 58.889 50.000 0.00 0.00 0.00 2.75
786 1835 2.541466 GAGGGAAGGAAGAAGGTGAGA 58.459 52.381 0.00 0.00 0.00 3.27
947 1996 5.738909 CAACAGGAGTAGTTGGATGAAGAT 58.261 41.667 0.00 0.00 41.92 2.40
987 2036 3.895232 TGATGGGAAGTGTAGAAGAGC 57.105 47.619 0.00 0.00 0.00 4.09
988 2037 5.174395 CAGTTGATGGGAAGTGTAGAAGAG 58.826 45.833 0.00 0.00 0.00 2.85
995 2044 2.172505 TGTGACAGTTGATGGGAAGTGT 59.827 45.455 0.00 0.00 41.29 3.55
1060 2109 1.890041 TCGTTGTTGGCCGAGTTGG 60.890 57.895 0.00 0.00 42.50 3.77
1121 2170 2.124570 GACGGCCACATCCATGCT 60.125 61.111 2.24 0.00 0.00 3.79
1136 2185 1.652563 GGTTGGGTTCTTGCACGAC 59.347 57.895 0.00 0.00 0.00 4.34
1139 2188 2.130073 GAGCGGTTGGGTTCTTGCAC 62.130 60.000 0.00 0.00 0.00 4.57
1212 2261 0.250553 TCAACGAAAAGGGATGCGGT 60.251 50.000 0.00 0.00 0.00 5.68
1426 2475 2.360475 GTGCTGGAGGTGGCTTCC 60.360 66.667 0.00 0.00 35.20 3.46
1822 2871 2.809601 GTAGCACACGCAGTCGGG 60.810 66.667 0.00 0.00 41.61 5.14
1868 2929 5.125097 TGGAGCTGCTACAGTTTACTACTAC 59.875 44.000 11.31 0.00 34.56 2.73
1869 2930 5.258841 TGGAGCTGCTACAGTTTACTACTA 58.741 41.667 11.31 0.00 34.56 1.82
1870 2931 4.087182 TGGAGCTGCTACAGTTTACTACT 58.913 43.478 11.31 0.00 37.68 2.57
1871 2932 4.158025 TCTGGAGCTGCTACAGTTTACTAC 59.842 45.833 34.35 5.01 42.66 2.73
1872 2933 4.341487 TCTGGAGCTGCTACAGTTTACTA 58.659 43.478 34.35 16.61 42.66 1.82
1873 2934 3.165875 TCTGGAGCTGCTACAGTTTACT 58.834 45.455 34.35 0.00 42.66 2.24
1903 2964 3.170991 ACAACCAGAGGCTAGTACAGA 57.829 47.619 0.00 0.00 0.00 3.41
1957 3019 2.415512 GCGGGTTACAGCTTAGTTTCAG 59.584 50.000 0.00 0.00 0.00 3.02
1998 5115 1.799916 GCGTGCATGTTTTACCGGC 60.800 57.895 0.00 0.00 0.00 6.13
2005 5122 4.383602 GCGTCGGCGTGCATGTTT 62.384 61.111 12.58 0.00 40.81 2.83
2031 5148 2.276994 CGCTCTCGTCGTCAGCTC 60.277 66.667 13.72 0.00 0.00 4.09
2049 5166 2.202008 GTGTTACGTTGCTCGCGC 60.202 61.111 0.00 0.00 44.19 6.86
2052 5169 0.704551 GTACCGTGTTACGTTGCTCG 59.295 55.000 0.00 0.00 40.58 5.03
2084 5203 0.813184 CTGGCTGCCACAATTACTGG 59.187 55.000 19.30 0.18 0.00 4.00
2115 5234 3.834447 TTGTCCGGCTGTGACGACG 62.834 63.158 0.00 0.00 35.20 5.12
2116 5235 2.022129 CTTGTCCGGCTGTGACGAC 61.022 63.158 0.00 2.07 35.20 4.34
2117 5236 2.338620 CTTGTCCGGCTGTGACGA 59.661 61.111 0.00 6.75 35.20 4.20
2211 5332 2.286025 CACATCACATGTATGGCGACTG 59.714 50.000 0.00 0.00 42.70 3.51
2213 5334 2.541346 CTCACATCACATGTATGGCGAC 59.459 50.000 0.00 0.00 42.70 5.19
2361 5499 3.708734 CAACGTCGACGCCAACCC 61.709 66.667 35.92 0.00 44.43 4.11
2443 5581 0.179092 GCAGCTTGCCATTTGATCCC 60.179 55.000 0.00 0.00 37.42 3.85
2817 5963 5.099575 GGTGGTTTTATGCAATTTACTCGG 58.900 41.667 0.00 0.00 0.00 4.63
2818 5964 5.571357 GTGGTGGTTTTATGCAATTTACTCG 59.429 40.000 0.00 0.00 0.00 4.18
2819 5965 6.687604 AGTGGTGGTTTTATGCAATTTACTC 58.312 36.000 0.00 0.00 0.00 2.59
2820 5966 6.664428 AGTGGTGGTTTTATGCAATTTACT 57.336 33.333 0.00 0.00 0.00 2.24
2821 5967 7.439655 TCAAAGTGGTGGTTTTATGCAATTTAC 59.560 33.333 0.00 0.00 0.00 2.01
2822 5968 7.500992 TCAAAGTGGTGGTTTTATGCAATTTA 58.499 30.769 0.00 0.00 0.00 1.40
2823 5969 6.352516 TCAAAGTGGTGGTTTTATGCAATTT 58.647 32.000 0.00 0.00 0.00 1.82
2824 5970 5.923204 TCAAAGTGGTGGTTTTATGCAATT 58.077 33.333 0.00 0.00 0.00 2.32
2825 5971 5.543507 TCAAAGTGGTGGTTTTATGCAAT 57.456 34.783 0.00 0.00 0.00 3.56
2826 5972 5.344743 TTCAAAGTGGTGGTTTTATGCAA 57.655 34.783 0.00 0.00 0.00 4.08
2827 5973 4.202202 CCTTCAAAGTGGTGGTTTTATGCA 60.202 41.667 0.00 0.00 0.00 3.96
2828 5974 4.306600 CCTTCAAAGTGGTGGTTTTATGC 58.693 43.478 0.00 0.00 0.00 3.14
2829 5975 4.039124 AGCCTTCAAAGTGGTGGTTTTATG 59.961 41.667 0.00 0.00 0.00 1.90
2830 5976 4.223144 AGCCTTCAAAGTGGTGGTTTTAT 58.777 39.130 0.00 0.00 0.00 1.40
2831 5977 3.634910 GAGCCTTCAAAGTGGTGGTTTTA 59.365 43.478 0.00 0.00 0.00 1.52
2832 5978 2.430694 GAGCCTTCAAAGTGGTGGTTTT 59.569 45.455 0.00 0.00 0.00 2.43
2833 5979 2.031870 GAGCCTTCAAAGTGGTGGTTT 58.968 47.619 0.00 0.00 0.00 3.27
2834 5980 1.692411 GAGCCTTCAAAGTGGTGGTT 58.308 50.000 0.00 0.00 0.00 3.67
2835 5981 0.535102 CGAGCCTTCAAAGTGGTGGT 60.535 55.000 0.00 0.00 0.00 4.16
2836 5982 2.247790 CGAGCCTTCAAAGTGGTGG 58.752 57.895 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.