Multiple sequence alignment - TraesCS2A01G020000

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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 TraesCS2A01G020000 chr2A 100.000 3494 0 0 1 3494 9315547 9319040 0.000000e+00 6453
1 TraesCS2A01G020000 chr2A 88.063 2798 199 55 557 3247 8788190 8785421 0.000000e+00 3192
2 TraesCS2A01G020000 chr2A 88.063 2798 199 55 557 3247 8797988 8795219 0.000000e+00 3192
3 TraesCS2A01G020000 chr2A 88.040 2801 200 56 554 3247 9668016 9670788 0.000000e+00 3192
4 TraesCS2A01G020000 chr2A 82.072 1824 268 32 705 2472 8790872 8789052 0.000000e+00 1502
5 TraesCS2A01G020000 chr2A 82.072 1824 268 32 705 2472 8800670 8798850 0.000000e+00 1502
6 TraesCS2A01G020000 chr2A 82.018 1824 269 31 705 2472 9665337 9667157 0.000000e+00 1496
7 TraesCS2A01G020000 chr2A 89.501 581 41 7 2035 2596 9364592 9365171 0.000000e+00 717
8 TraesCS2A01G020000 chr2A 86.727 663 53 16 2637 3266 9365166 9365826 0.000000e+00 704
9 TraesCS2A01G020000 chr2B 91.343 2472 160 30 284 2718 13499683 13497229 0.000000e+00 3330
10 TraesCS2A01G020000 chr2B 92.521 1805 103 11 714 2497 13716007 13717800 0.000000e+00 2556
11 TraesCS2A01G020000 chr2B 90.647 417 28 7 2599 3009 13717807 13718218 8.530000e-151 544
12 TraesCS2A01G020000 chr2B 85.159 283 32 8 2811 3087 13497198 13496920 7.380000e-72 281
13 TraesCS2A01G020000 chr2B 81.283 187 18 9 1 171 13505578 13505393 6.080000e-28 135
14 TraesCS2A01G020000 chr2B 83.117 154 15 5 1 143 13501046 13500893 2.830000e-26 130
15 TraesCS2A01G020000 chr2D 93.072 1963 106 16 957 2904 10089797 10091744 0.000000e+00 2844
16 TraesCS2A01G020000 chr2D 93.113 1902 101 16 957 2843 10171644 10169758 0.000000e+00 2760
17 TraesCS2A01G020000 chr2D 84.236 1865 236 42 705 2520 10070302 10072157 0.000000e+00 1762
18 TraesCS2A01G020000 chr2D 83.800 1500 225 12 991 2472 10176250 10174751 0.000000e+00 1408
19 TraesCS2A01G020000 chr2D 84.511 962 83 20 1 935 10172550 10171628 0.000000e+00 891
20 TraesCS2A01G020000 chr2D 85.748 856 67 27 2 816 10087974 10088815 0.000000e+00 854
21 TraesCS2A01G020000 chr2D 85.124 363 44 6 3094 3450 10091745 10092103 2.560000e-96 363
22 TraesCS2A01G020000 chr2D 95.294 85 4 0 525 609 10070187 10070271 6.080000e-28 135


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 TraesCS2A01G020000 chr2A 9315547 9319040 3493 False 6453.000000 6453 100.000000 1 3494 1 chr2A.!!$F1 3493
1 TraesCS2A01G020000 chr2A 8785421 8790872 5451 True 2347.000000 3192 85.067500 557 3247 2 chr2A.!!$R1 2690
2 TraesCS2A01G020000 chr2A 8795219 8800670 5451 True 2347.000000 3192 85.067500 557 3247 2 chr2A.!!$R2 2690
3 TraesCS2A01G020000 chr2A 9665337 9670788 5451 False 2344.000000 3192 85.029000 554 3247 2 chr2A.!!$F3 2693
4 TraesCS2A01G020000 chr2A 9364592 9365826 1234 False 710.500000 717 88.114000 2035 3266 2 chr2A.!!$F2 1231
5 TraesCS2A01G020000 chr2B 13716007 13718218 2211 False 1550.000000 2556 91.584000 714 3009 2 chr2B.!!$F1 2295
6 TraesCS2A01G020000 chr2B 13496920 13501046 4126 True 1247.000000 3330 86.539667 1 3087 3 chr2B.!!$R2 3086
7 TraesCS2A01G020000 chr2D 10169758 10176250 6492 True 1686.333333 2760 87.141333 1 2843 3 chr2D.!!$R1 2842
8 TraesCS2A01G020000 chr2D 10087974 10092103 4129 False 1353.666667 2844 87.981333 2 3450 3 chr2D.!!$F2 3448
9 TraesCS2A01G020000 chr2D 10070187 10072157 1970 False 948.500000 1762 89.765000 525 2520 2 chr2D.!!$F1 1995

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
140 177 0.037326 TGAGGTCGATTGTGCCAGAC 60.037 55.0 0.00 0.0 0.00 3.51 F
299 1431 0.324738 AGACCATCTCTCCAGCGGAA 60.325 55.0 0.00 0.0 0.00 4.30 F
1571 8515 0.395686 TTGCAAGCTGAGACTGCTCT 59.604 50.0 8.68 0.0 41.84 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 8504 0.034476 CAGCACCAAGAGCAGTCTCA 59.966 55.0 0.00 0.0 41.81 3.27 R
2051 8995 0.038343 CCCACTTGTCAAATTGGCCG 60.038 55.0 0.00 0.0 35.33 6.13 R
2730 9704 0.109723 CCCAACCCGAAGAACTTCCA 59.890 55.0 8.66 0.0 36.27 3.53 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
28 31 8.862325 TTAAATCTTGGCTGAACATAGAAGAA 57.138 30.769 0.00 0.00 0.00 2.52
59 62 4.584325 AGTGTGGCATACATCAAAAACTGT 59.416 37.500 16.92 0.00 42.24 3.55
94 112 4.385405 GCCGCAGCTCAGGACAGT 62.385 66.667 8.11 0.00 35.50 3.55
124 151 1.471684 GCTTGGCATCAAGGAGTTGAG 59.528 52.381 8.02 0.00 45.96 3.02
131 158 3.866651 CATCAAGGAGTTGAGGTCGATT 58.133 45.455 0.00 0.00 45.96 3.34
136 173 1.079503 GAGTTGAGGTCGATTGTGCC 58.920 55.000 0.00 0.00 0.00 5.01
137 174 0.396435 AGTTGAGGTCGATTGTGCCA 59.604 50.000 0.00 0.00 0.00 4.92
138 175 0.798776 GTTGAGGTCGATTGTGCCAG 59.201 55.000 0.00 0.00 0.00 4.85
139 176 0.684535 TTGAGGTCGATTGTGCCAGA 59.315 50.000 0.00 0.00 0.00 3.86
140 177 0.037326 TGAGGTCGATTGTGCCAGAC 60.037 55.000 0.00 0.00 0.00 3.51
141 178 1.078759 GAGGTCGATTGTGCCAGACG 61.079 60.000 0.00 0.00 34.68 4.18
162 199 1.988406 GGCTCTAGGTGTTCCCGGT 60.988 63.158 0.00 0.00 38.74 5.28
223 260 0.667487 TGCCGTCGCTTTTCTCTCTG 60.667 55.000 0.00 0.00 35.36 3.35
291 1423 3.137533 GCATAAAGCCAGACCATCTCTC 58.862 50.000 0.00 0.00 37.23 3.20
299 1431 0.324738 AGACCATCTCTCCAGCGGAA 60.325 55.000 0.00 0.00 0.00 4.30
324 1456 5.007724 GCAATAGCCATGTTAGTCCTTGTAC 59.992 44.000 0.00 0.00 33.58 2.90
335 1467 6.883217 TGTTAGTCCTTGTACTAGTCGATTCT 59.117 38.462 0.00 0.00 33.62 2.40
341 1473 7.441760 GTCCTTGTACTAGTCGATTCTGATAGA 59.558 40.741 0.00 0.00 0.00 1.98
350 1482 3.005261 TCGATTCTGATAGAAGCCTCAGC 59.995 47.826 1.72 0.00 37.33 4.26
367 1500 5.947228 CTCAGCAAAGAGGTTAATGTTGA 57.053 39.130 0.00 0.00 33.06 3.18
370 1503 7.288810 TCAGCAAAGAGGTTAATGTTGAAAT 57.711 32.000 0.00 0.00 31.44 2.17
399 1532 1.268079 GTCCAACAGAAGAAGCAAGCC 59.732 52.381 0.00 0.00 0.00 4.35
404 1537 2.024414 ACAGAAGAAGCAAGCCGTTTT 58.976 42.857 0.00 0.00 0.00 2.43
408 1541 0.954452 AGAAGCAAGCCGTTTTCTGG 59.046 50.000 0.00 0.00 0.00 3.86
432 1565 1.525077 GGCAGGTCGTGAAACACCA 60.525 57.895 0.00 0.00 39.48 4.17
435 1568 2.147958 GCAGGTCGTGAAACACCATTA 58.852 47.619 0.00 0.00 39.48 1.90
444 1577 5.937540 TCGTGAAACACCATTATCTGTCAAT 59.062 36.000 0.00 0.00 35.74 2.57
447 1580 7.472543 GTGAAACACCATTATCTGTCAATACC 58.527 38.462 0.00 0.00 36.32 2.73
448 1581 7.120579 GTGAAACACCATTATCTGTCAATACCA 59.879 37.037 0.00 0.00 36.32 3.25
453 1586 7.094377 ACACCATTATCTGTCAATACCACAAAC 60.094 37.037 0.00 0.00 0.00 2.93
457 1590 3.750371 TCTGTCAATACCACAAACAGGG 58.250 45.455 0.00 0.00 38.27 4.45
470 1603 5.669477 CACAAACAGGGGAAAAATTCTGAA 58.331 37.500 0.00 0.00 0.00 3.02
471 1604 6.290605 CACAAACAGGGGAAAAATTCTGAAT 58.709 36.000 0.00 0.00 0.00 2.57
472 1605 7.441017 CACAAACAGGGGAAAAATTCTGAATA 58.559 34.615 2.85 0.00 0.00 1.75
475 1608 9.154847 CAAACAGGGGAAAAATTCTGAATATTC 57.845 33.333 8.60 8.60 0.00 1.75
481 1614 6.473455 GGGAAAAATTCTGAATATTCTGTGCG 59.527 38.462 16.24 1.08 0.00 5.34
552 1686 1.029681 GTCTCCGGGTTTGCAAAGTT 58.970 50.000 13.26 0.00 0.00 2.66
576 1710 1.615392 GCAGGGTCACTTTCATGCTTT 59.385 47.619 0.00 0.00 0.00 3.51
589 1723 3.058450 TCATGCTTTGAAATGTTTGCCG 58.942 40.909 0.00 0.00 0.00 5.69
604 1738 2.752807 GCCGGGCAGGAAAGGGATA 61.753 63.158 15.62 0.00 45.00 2.59
612 1746 3.136626 GGCAGGAAAGGGATATACACTGT 59.863 47.826 0.00 0.00 29.82 3.55
720 6676 4.473444 TGACCATTTTTCTCTGCTCCTTT 58.527 39.130 0.00 0.00 0.00 3.11
824 7665 6.075519 CGTCTCTTTCGGTTTATACAATCTCG 60.076 42.308 0.00 0.00 0.00 4.04
865 7706 3.691498 AGAAAAGAAAAACACGGCTTCG 58.309 40.909 0.00 0.00 40.22 3.79
894 7736 7.875554 GGAGAAATAAGATGAAGACCCATAGTC 59.124 40.741 0.00 0.00 46.71 2.59
981 7903 5.952526 TCAGATATATGTAAACCGAGCGA 57.047 39.130 0.00 0.00 0.00 4.93
988 7910 0.525882 GTAAACCGAGCGAGCTCTCC 60.526 60.000 20.97 2.47 40.69 3.71
1064 7996 3.654806 AGATCCATATCTTTCCTGGTGGG 59.345 47.826 0.00 0.00 39.55 4.61
1065 7997 2.858644 TCCATATCTTTCCTGGTGGGT 58.141 47.619 0.00 0.00 36.25 4.51
1113 8045 1.380650 AACCGAGGAGGAGAGGCTC 60.381 63.158 6.34 6.34 45.00 4.70
1129 8061 3.832237 CTCCACAGCCTGCAACGGT 62.832 63.158 0.00 0.00 0.00 4.83
1155 8087 2.380410 GCGGCTTCATGTCGTCGTT 61.380 57.895 11.33 0.00 46.81 3.85
1259 8191 6.518493 GGTATTACACCCTCGATATGTTCAA 58.482 40.000 2.17 0.00 42.07 2.69
1547 8491 4.394300 GGAGATGGAACTTGTGATGAACTG 59.606 45.833 0.00 0.00 0.00 3.16
1571 8515 0.395686 TTGCAAGCTGAGACTGCTCT 59.604 50.000 8.68 0.00 41.84 4.09
1596 8540 2.019249 GCTGCTGATCATTTGGCTGTA 58.981 47.619 0.00 0.00 0.00 2.74
1668 8612 4.209307 TGTATGCAACGATGAAAGGGTA 57.791 40.909 0.00 0.00 0.00 3.69
1687 8631 2.550830 ACGCAACCACTTCTCTCAAT 57.449 45.000 0.00 0.00 0.00 2.57
1719 8663 9.965824 TTTTTCAATGGAGATGTTCTTAAAGAC 57.034 29.630 0.00 0.00 0.00 3.01
1921 8865 1.005340 CTCTGACAAGATCGCAAGCC 58.995 55.000 0.00 0.00 37.18 4.35
2051 8995 0.672342 GCATCAATGGCCATGGAGAC 59.328 55.000 26.79 17.49 0.00 3.36
2064 9008 0.109532 TGGAGACGGCCAATTTGACA 59.890 50.000 2.24 0.00 34.31 3.58
2166 9110 1.203287 GCAGCCCTCAGGAATTTGAAC 59.797 52.381 0.00 0.00 33.47 3.18
2236 9180 2.195727 TGGTGGAGCCAACATATCTCA 58.804 47.619 2.46 0.00 45.94 3.27
2237 9181 2.171237 TGGTGGAGCCAACATATCTCAG 59.829 50.000 2.46 0.00 45.94 3.35
2376 9332 2.420372 GAGGCTTCGAGGGAAATTCAAC 59.580 50.000 0.00 0.00 0.00 3.18
2579 9552 2.353803 GCAGAGTAGGTACAGGTTGTGG 60.354 54.545 0.00 0.00 0.00 4.17
2582 9555 0.035725 GTAGGTACAGGTTGTGGGCC 60.036 60.000 0.00 0.00 0.00 5.80
2600 9573 1.066787 GCCGAGAGCCTTAGACTGTTT 60.067 52.381 0.00 0.00 34.35 2.83
2653 9626 8.902806 TCTTCTTTTTGAGCAACTCTGAAATAA 58.097 29.630 0.00 0.00 28.26 1.40
2730 9704 3.832615 ACTGTACGGGTCAGAAGTTTT 57.167 42.857 6.65 0.00 36.81 2.43
2759 9734 2.112279 TCGGGTTGGGGATATTAGCT 57.888 50.000 0.00 0.00 0.00 3.32
2878 9855 1.757118 CATGATACCACTGGACGAGGT 59.243 52.381 0.71 0.00 39.99 3.85
2932 9911 5.221106 CCTGATATCAACGGTCAATGCATTT 60.221 40.000 9.83 0.00 0.00 2.32
3062 10044 5.997746 CCAACTTCAATAGTGAGACCTTTCA 59.002 40.000 0.00 0.00 37.12 2.69
3063 10045 6.486657 CCAACTTCAATAGTGAGACCTTTCAA 59.513 38.462 0.00 0.00 37.12 2.69
3087 10095 4.270325 GGTTCTACAGTGTGACAAGTCAAC 59.730 45.833 5.88 6.05 41.85 3.18
3097 10106 3.737266 GTGACAAGTCAACCATGCATTTG 59.263 43.478 4.20 0.00 41.85 2.32
3171 10188 2.966516 AGTAGAACCGATCCCCAATCTC 59.033 50.000 0.00 0.00 31.68 2.75
3202 10219 5.183713 TCGTTCTCGGGAAGAAGTGTTTATA 59.816 40.000 0.00 0.00 44.66 0.98
3203 10220 5.865552 CGTTCTCGGGAAGAAGTGTTTATAA 59.134 40.000 0.00 0.00 44.66 0.98
3288 10305 1.410004 GACACGGACTATCCCCATCA 58.590 55.000 0.00 0.00 31.13 3.07
3291 10308 2.368875 ACACGGACTATCCCCATCAATC 59.631 50.000 0.00 0.00 31.13 2.67
3353 10371 4.347096 CGGCAGTCGTTGTTACCA 57.653 55.556 0.00 0.00 0.00 3.25
3354 10372 2.835605 CGGCAGTCGTTGTTACCAT 58.164 52.632 0.00 0.00 0.00 3.55
3355 10373 1.999048 CGGCAGTCGTTGTTACCATA 58.001 50.000 0.00 0.00 0.00 2.74
3356 10374 1.924524 CGGCAGTCGTTGTTACCATAG 59.075 52.381 0.00 0.00 0.00 2.23
3357 10375 2.673043 CGGCAGTCGTTGTTACCATAGT 60.673 50.000 0.00 0.00 0.00 2.12
3360 10378 3.585862 CAGTCGTTGTTACCATAGTGCT 58.414 45.455 0.00 0.00 0.00 4.40
3363 10381 1.060553 CGTTGTTACCATAGTGCTGCG 59.939 52.381 0.00 0.00 0.00 5.18
3365 10383 1.081556 TGTTACCATAGTGCTGCGCG 61.082 55.000 0.00 0.00 0.00 6.86
3389 10407 4.035102 GAGGGGAGGCGCAAAGGT 62.035 66.667 10.83 0.00 0.00 3.50
3390 10408 3.978571 GAGGGGAGGCGCAAAGGTC 62.979 68.421 10.83 0.00 0.00 3.85
3398 10416 3.777925 CGCAAAGGTCGGTGCTCG 61.778 66.667 0.00 0.00 38.66 5.03
3399 10417 4.090057 GCAAAGGTCGGTGCTCGC 62.090 66.667 0.00 0.00 37.78 5.03
3400 10418 3.423154 CAAAGGTCGGTGCTCGCC 61.423 66.667 0.00 0.00 39.05 5.54
3428 10446 2.343758 GTGCTCCCTGCGAGTTCA 59.656 61.111 0.00 0.00 46.63 3.18
3431 10449 2.266055 CTCCCTGCGAGTTCACCC 59.734 66.667 0.00 0.00 33.51 4.61
3433 10451 1.831652 CTCCCTGCGAGTTCACCCTT 61.832 60.000 0.00 0.00 33.51 3.95
3435 10453 0.537371 CCCTGCGAGTTCACCCTTTT 60.537 55.000 0.00 0.00 0.00 2.27
3437 10455 0.875059 CTGCGAGTTCACCCTTTTCC 59.125 55.000 0.00 0.00 0.00 3.13
3439 10457 1.866925 CGAGTTCACCCTTTTCCGC 59.133 57.895 0.00 0.00 0.00 5.54
3440 10458 0.882927 CGAGTTCACCCTTTTCCGCA 60.883 55.000 0.00 0.00 0.00 5.69
3450 10468 3.056607 ACCCTTTTCCGCATTTGAATCTG 60.057 43.478 0.00 0.00 0.00 2.90
3451 10469 3.193267 CCCTTTTCCGCATTTGAATCTGA 59.807 43.478 0.00 0.00 0.00 3.27
3452 10470 4.142093 CCCTTTTCCGCATTTGAATCTGAT 60.142 41.667 0.00 0.00 0.00 2.90
3453 10471 5.067674 CCCTTTTCCGCATTTGAATCTGATA 59.932 40.000 0.00 0.00 0.00 2.15
3454 10472 6.239120 CCCTTTTCCGCATTTGAATCTGATAT 60.239 38.462 0.00 0.00 0.00 1.63
3455 10473 6.639686 CCTTTTCCGCATTTGAATCTGATATG 59.360 38.462 0.00 0.00 0.00 1.78
3456 10474 5.694231 TTCCGCATTTGAATCTGATATGG 57.306 39.130 0.00 0.00 0.00 2.74
3457 10475 4.717877 TCCGCATTTGAATCTGATATGGT 58.282 39.130 0.00 0.00 0.00 3.55
3458 10476 5.132502 TCCGCATTTGAATCTGATATGGTT 58.867 37.500 0.00 0.00 0.00 3.67
3459 10477 5.593909 TCCGCATTTGAATCTGATATGGTTT 59.406 36.000 0.00 0.00 0.00 3.27
3460 10478 5.916883 CCGCATTTGAATCTGATATGGTTTC 59.083 40.000 0.00 0.00 0.00 2.78
3461 10479 6.459985 CCGCATTTGAATCTGATATGGTTTCA 60.460 38.462 0.00 0.00 0.00 2.69
3462 10480 6.635641 CGCATTTGAATCTGATATGGTTTCAG 59.364 38.462 0.00 0.00 41.61 3.02
3463 10481 7.486647 GCATTTGAATCTGATATGGTTTCAGT 58.513 34.615 0.00 0.00 41.13 3.41
3464 10482 7.434307 GCATTTGAATCTGATATGGTTTCAGTG 59.566 37.037 0.00 0.00 41.13 3.66
3465 10483 8.464404 CATTTGAATCTGATATGGTTTCAGTGT 58.536 33.333 0.00 0.00 41.13 3.55
3466 10484 7.615582 TTGAATCTGATATGGTTTCAGTGTC 57.384 36.000 0.00 1.53 41.13 3.67
3467 10485 6.950842 TGAATCTGATATGGTTTCAGTGTCT 58.049 36.000 0.00 0.00 41.13 3.41
3468 10486 6.820152 TGAATCTGATATGGTTTCAGTGTCTG 59.180 38.462 0.00 0.00 41.13 3.51
3469 10487 5.745312 TCTGATATGGTTTCAGTGTCTGT 57.255 39.130 1.07 0.00 41.13 3.41
3470 10488 6.850752 TCTGATATGGTTTCAGTGTCTGTA 57.149 37.500 1.07 0.00 41.13 2.74
3471 10489 7.423844 TCTGATATGGTTTCAGTGTCTGTAT 57.576 36.000 1.07 0.00 41.13 2.29
3472 10490 7.851228 TCTGATATGGTTTCAGTGTCTGTATT 58.149 34.615 1.07 0.00 41.13 1.89
3473 10491 8.321353 TCTGATATGGTTTCAGTGTCTGTATTT 58.679 33.333 1.07 0.00 41.13 1.40
3474 10492 8.267620 TGATATGGTTTCAGTGTCTGTATTTG 57.732 34.615 0.00 0.00 32.61 2.32
3475 10493 7.882791 TGATATGGTTTCAGTGTCTGTATTTGT 59.117 33.333 0.00 0.00 32.61 2.83
3476 10494 6.560253 ATGGTTTCAGTGTCTGTATTTGTC 57.440 37.500 0.00 0.00 32.61 3.18
3477 10495 4.509970 TGGTTTCAGTGTCTGTATTTGTCG 59.490 41.667 0.00 0.00 32.61 4.35
3478 10496 4.455124 GTTTCAGTGTCTGTATTTGTCGC 58.545 43.478 0.00 0.00 32.61 5.19
3479 10497 3.378911 TCAGTGTCTGTATTTGTCGCA 57.621 42.857 0.00 0.00 32.61 5.10
3480 10498 3.723260 TCAGTGTCTGTATTTGTCGCAA 58.277 40.909 0.00 0.00 32.61 4.85
3481 10499 3.493129 TCAGTGTCTGTATTTGTCGCAAC 59.507 43.478 0.00 0.00 32.61 4.17
3482 10500 3.494626 CAGTGTCTGTATTTGTCGCAACT 59.505 43.478 0.00 0.00 0.00 3.16
3483 10501 3.494626 AGTGTCTGTATTTGTCGCAACTG 59.505 43.478 0.00 0.00 0.00 3.16
3484 10502 3.493129 GTGTCTGTATTTGTCGCAACTGA 59.507 43.478 0.00 0.00 0.00 3.41
3485 10503 4.025229 GTGTCTGTATTTGTCGCAACTGAA 60.025 41.667 0.00 0.00 0.00 3.02
3486 10504 4.754618 TGTCTGTATTTGTCGCAACTGAAT 59.245 37.500 0.00 0.00 0.00 2.57
3487 10505 5.238432 TGTCTGTATTTGTCGCAACTGAATT 59.762 36.000 0.00 0.00 0.00 2.17
3488 10506 6.142817 GTCTGTATTTGTCGCAACTGAATTT 58.857 36.000 0.00 0.00 0.00 1.82
3489 10507 6.303259 GTCTGTATTTGTCGCAACTGAATTTC 59.697 38.462 0.00 0.00 0.00 2.17
3490 10508 6.017523 TCTGTATTTGTCGCAACTGAATTTCA 60.018 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 31 1.416030 TGTATGCCACACTGACACTGT 59.584 47.619 0.00 0.00 30.04 3.55
87 105 1.446016 AGCCCCTGTTTTACTGTCCT 58.554 50.000 0.00 0.00 0.00 3.85
88 106 1.886542 CAAGCCCCTGTTTTACTGTCC 59.113 52.381 0.00 0.00 0.00 4.02
91 109 0.603065 GCCAAGCCCCTGTTTTACTG 59.397 55.000 0.00 0.00 0.00 2.74
92 110 0.187361 TGCCAAGCCCCTGTTTTACT 59.813 50.000 0.00 0.00 0.00 2.24
93 111 1.204704 GATGCCAAGCCCCTGTTTTAC 59.795 52.381 0.00 0.00 0.00 2.01
94 112 1.203112 TGATGCCAAGCCCCTGTTTTA 60.203 47.619 0.00 0.00 0.00 1.52
124 151 2.100631 CCGTCTGGCACAATCGACC 61.101 63.158 0.00 0.00 38.70 4.79
136 173 2.042843 ACCTAGAGCCCCCGTCTG 60.043 66.667 0.00 0.00 0.00 3.51
137 174 2.042843 CACCTAGAGCCCCCGTCT 60.043 66.667 0.00 0.00 0.00 4.18
138 175 1.957765 GAACACCTAGAGCCCCCGTC 61.958 65.000 0.00 0.00 0.00 4.79
139 176 1.988406 GAACACCTAGAGCCCCCGT 60.988 63.158 0.00 0.00 0.00 5.28
140 177 2.732619 GGAACACCTAGAGCCCCCG 61.733 68.421 0.00 0.00 0.00 5.73
141 178 2.376165 GGGAACACCTAGAGCCCCC 61.376 68.421 0.00 0.00 35.85 5.40
149 186 0.971386 GAGTTGACCGGGAACACCTA 59.029 55.000 17.94 0.00 36.97 3.08
162 199 5.057149 GCTGAAGAACTAAGTTGGAGTTGA 58.943 41.667 0.00 0.00 37.27 3.18
223 260 1.790623 CAATGCTTGCTTGCTGTTGAC 59.209 47.619 11.35 0.00 34.05 3.18
291 1423 0.820891 ATGGCTATTGCTTCCGCTGG 60.821 55.000 0.00 0.00 39.59 4.85
299 1431 4.202441 CAAGGACTAACATGGCTATTGCT 58.798 43.478 0.00 0.00 39.59 3.91
302 1434 6.561519 AGTACAAGGACTAACATGGCTATT 57.438 37.500 0.00 0.00 0.00 1.73
303 1435 6.839657 ACTAGTACAAGGACTAACATGGCTAT 59.160 38.462 0.00 0.00 31.57 2.97
304 1436 6.192773 ACTAGTACAAGGACTAACATGGCTA 58.807 40.000 0.00 0.00 31.57 3.93
309 1441 7.556996 AGAATCGACTAGTACAAGGACTAACAT 59.443 37.037 0.00 0.00 31.57 2.71
324 1456 5.471797 TGAGGCTTCTATCAGAATCGACTAG 59.528 44.000 0.00 0.00 33.13 2.57
335 1467 3.118482 CCTCTTTGCTGAGGCTTCTATCA 60.118 47.826 7.77 0.00 45.84 2.15
350 1482 8.792633 TCCAGTATTTCAACATTAACCTCTTTG 58.207 33.333 0.00 0.00 0.00 2.77
386 1519 2.291741 CAGAAAACGGCTTGCTTCTTCT 59.708 45.455 0.00 0.00 0.00 2.85
399 1532 2.650778 GCCAAGGGCCAGAAAACG 59.349 61.111 6.18 0.00 44.06 3.60
411 1544 0.307760 GTGTTTCACGACCTGCCAAG 59.692 55.000 0.00 0.00 0.00 3.61
412 1545 1.098712 GGTGTTTCACGACCTGCCAA 61.099 55.000 0.00 0.00 34.83 4.52
432 1565 6.603201 CCCTGTTTGTGGTATTGACAGATAAT 59.397 38.462 3.56 0.00 39.97 1.28
435 1568 4.335416 CCCTGTTTGTGGTATTGACAGAT 58.665 43.478 3.56 0.00 39.97 2.90
444 1577 5.069781 CAGAATTTTTCCCCTGTTTGTGGTA 59.930 40.000 0.00 0.00 0.00 3.25
447 1580 5.275067 TCAGAATTTTTCCCCTGTTTGTG 57.725 39.130 0.00 0.00 0.00 3.33
448 1581 5.948742 TTCAGAATTTTTCCCCTGTTTGT 57.051 34.783 0.00 0.00 0.00 2.83
453 1586 7.977853 CACAGAATATTCAGAATTTTTCCCCTG 59.022 37.037 17.56 6.18 0.00 4.45
457 1590 7.029563 ACGCACAGAATATTCAGAATTTTTCC 58.970 34.615 17.56 0.00 0.00 3.13
465 1598 4.805719 GTCATGACGCACAGAATATTCAGA 59.194 41.667 17.56 0.00 0.00 3.27
466 1599 5.075670 GTCATGACGCACAGAATATTCAG 57.924 43.478 17.56 11.95 0.00 3.02
481 1614 1.664965 GATAGCCGCCCGTCATGAC 60.665 63.158 16.21 16.21 0.00 3.06
552 1686 2.905075 CATGAAAGTGACCCTGCGATA 58.095 47.619 0.00 0.00 0.00 2.92
576 1710 1.664873 CTGCCCGGCAAACATTTCA 59.335 52.632 14.45 0.00 38.41 2.69
589 1723 2.711547 AGTGTATATCCCTTTCCTGCCC 59.288 50.000 0.00 0.00 0.00 5.36
604 1738 3.097342 ACCTTCTACGGGACAGTGTAT 57.903 47.619 0.00 0.00 0.00 2.29
612 1746 2.097825 GCTACTCAACCTTCTACGGGA 58.902 52.381 0.00 0.00 0.00 5.14
614 1748 3.587797 TTGCTACTCAACCTTCTACGG 57.412 47.619 0.00 0.00 0.00 4.02
660 6603 5.585820 TTGAACTTTCAACCCCTTAACAC 57.414 39.130 0.07 0.00 41.88 3.32
661 6604 6.014499 TGTTTTGAACTTTCAACCCCTTAACA 60.014 34.615 3.84 8.19 45.99 2.41
709 6665 4.727507 TGCTAGTCTAAAAGGAGCAGAG 57.272 45.455 0.00 0.00 38.20 3.35
720 6676 5.695424 TCTAGTGACCTCTGCTAGTCTAA 57.305 43.478 0.00 0.00 35.14 2.10
824 7665 9.535270 CTTTTCTTTGATCGAAGAGTTGAATAC 57.465 33.333 21.87 0.00 43.63 1.89
837 7678 5.331532 GCCGTGTTTTTCTTTTCTTTGATCG 60.332 40.000 0.00 0.00 0.00 3.69
865 7706 5.051153 GGGTCTTCATCTTATTTCTCCGTC 58.949 45.833 0.00 0.00 0.00 4.79
894 7736 0.035630 CAGAGGACTTGCCCAAGGAG 60.036 60.000 12.22 0.00 42.53 3.69
981 7903 3.603532 CATGTATGTGTGTTGGAGAGCT 58.396 45.455 0.00 0.00 0.00 4.09
988 7910 8.450578 AATATTACCTCCATGTATGTGTGTTG 57.549 34.615 0.00 0.00 0.00 3.33
1064 7996 1.681793 TCCGCTGCTTCAGGTATCTAC 59.318 52.381 0.00 0.00 31.21 2.59
1065 7997 1.681793 GTCCGCTGCTTCAGGTATCTA 59.318 52.381 0.00 0.00 31.21 1.98
1113 8045 2.906897 AACCGTTGCAGGCTGTGG 60.907 61.111 17.16 14.82 33.69 4.17
1129 8061 0.321564 ACATGAAGCCGCAGTAGCAA 60.322 50.000 0.00 0.00 42.27 3.91
1155 8087 2.060383 CCGGTCATCTGCCTCCTCA 61.060 63.158 0.00 0.00 0.00 3.86
1259 8191 1.674441 CATCTTCATGTGCTCGGCAAT 59.326 47.619 0.00 0.00 41.47 3.56
1394 8338 1.601419 GGTGTTCTGCATGCTGCCAT 61.601 55.000 20.33 0.00 44.23 4.40
1523 8467 3.251479 TCATCACAAGTTCCATCTCCG 57.749 47.619 0.00 0.00 0.00 4.63
1547 8491 0.888285 AGTCTCAGCTTGCAACAGGC 60.888 55.000 0.00 0.00 45.13 4.85
1560 8504 0.034476 CAGCACCAAGAGCAGTCTCA 59.966 55.000 0.00 0.00 41.81 3.27
1571 8515 1.546923 CCAAATGATCAGCAGCACCAA 59.453 47.619 0.09 0.00 0.00 3.67
1596 8540 1.451387 GGGACCGACGATTGGCAAT 60.451 57.895 13.54 13.54 0.00 3.56
1668 8612 2.550830 ATTGAGAGAAGTGGTTGCGT 57.449 45.000 0.00 0.00 0.00 5.24
1687 8631 9.447157 AAGAACATCTCCATTGAAAAACAAAAA 57.553 25.926 0.00 0.00 42.03 1.94
1719 8663 2.753452 TCTTAGGGTCTCTACACTTGCG 59.247 50.000 0.00 0.00 35.04 4.85
1921 8865 0.478507 AGGGGTTCTGTGGTTCCAAG 59.521 55.000 0.00 0.00 0.00 3.61
2051 8995 0.038343 CCCACTTGTCAAATTGGCCG 60.038 55.000 0.00 0.00 35.33 6.13
2064 9008 1.901591 CAGACATGAAGCACCCACTT 58.098 50.000 0.00 0.00 0.00 3.16
2166 9110 5.122869 CCCATACACTGAGATGTTTGTCTTG 59.877 44.000 0.00 0.00 31.74 3.02
2232 9176 1.076438 TCACCCTCCTGAGACTGAGA 58.924 55.000 0.00 0.00 0.00 3.27
2233 9177 1.930251 TTCACCCTCCTGAGACTGAG 58.070 55.000 0.00 0.00 0.00 3.35
2234 9178 2.630889 ATTCACCCTCCTGAGACTGA 57.369 50.000 0.00 0.00 0.00 3.41
2235 9179 4.826274 TTTATTCACCCTCCTGAGACTG 57.174 45.455 0.00 0.00 0.00 3.51
2236 9180 4.785376 ACATTTATTCACCCTCCTGAGACT 59.215 41.667 0.00 0.00 0.00 3.24
2237 9181 4.878397 CACATTTATTCACCCTCCTGAGAC 59.122 45.833 0.00 0.00 0.00 3.36
2582 9555 3.056465 AGGAAAACAGTCTAAGGCTCTCG 60.056 47.826 0.00 0.00 0.00 4.04
2591 9564 8.215050 TGGTATTTCAGAAAGGAAAACAGTCTA 58.785 33.333 1.28 0.00 39.94 2.59
2624 9597 5.647658 TCAGAGTTGCTCAAAAAGAAGAACA 59.352 36.000 0.00 0.00 32.06 3.18
2625 9598 6.124088 TCAGAGTTGCTCAAAAAGAAGAAC 57.876 37.500 0.00 0.00 32.06 3.01
2626 9599 6.757897 TTCAGAGTTGCTCAAAAAGAAGAA 57.242 33.333 0.00 0.00 32.06 2.52
2730 9704 0.109723 CCCAACCCGAAGAACTTCCA 59.890 55.000 8.66 0.00 36.27 3.53
2784 9761 3.243873 TGCTTTCTCACTGGTCAGTACAG 60.244 47.826 3.06 3.58 40.20 2.74
2849 9826 5.418840 GTCCAGTGGTATCATGGAAATTGTT 59.581 40.000 9.54 0.00 44.45 2.83
2850 9827 4.949856 GTCCAGTGGTATCATGGAAATTGT 59.050 41.667 9.54 0.00 44.45 2.71
2869 9846 4.800023 TCAGGATATCTTTACCTCGTCCA 58.200 43.478 2.05 0.00 31.06 4.02
3019 10000 0.321298 GCCTGGCTCTTGGTTTCGTA 60.321 55.000 12.43 0.00 0.00 3.43
3062 10044 4.161565 TGACTTGTCACACTGTAGAACCTT 59.838 41.667 0.00 0.00 0.00 3.50
3063 10045 3.704566 TGACTTGTCACACTGTAGAACCT 59.295 43.478 0.00 0.00 0.00 3.50
3087 10095 2.078392 GCTTCCCAAACAAATGCATGG 58.922 47.619 0.00 0.00 0.00 3.66
3097 10106 4.767409 AGAAATACTCCTTGCTTCCCAAAC 59.233 41.667 0.00 0.00 31.94 2.93
3171 10188 0.661187 TTCCCGAGAACGAACGAACG 60.661 55.000 0.14 0.00 42.66 3.95
3202 10219 0.607489 AGCGCCTCATGCTTGAAGTT 60.607 50.000 2.29 0.00 40.48 2.66
3203 10220 1.002868 AGCGCCTCATGCTTGAAGT 60.003 52.632 2.29 0.00 40.48 3.01
3210 10227 1.009222 GCATTACAGCGCCTCATGC 60.009 57.895 2.29 9.81 33.92 4.06
3213 10230 0.250234 AAGAGCATTACAGCGCCTCA 59.750 50.000 2.29 0.00 40.15 3.86
3278 10295 2.089408 AGTGGGAGGATTGATGGGGATA 60.089 50.000 0.00 0.00 0.00 2.59
3288 10305 2.971598 CGGCCACAGTGGGAGGATT 61.972 63.158 21.77 0.00 38.19 3.01
3421 10439 0.882927 TGCGGAAAAGGGTGAACTCG 60.883 55.000 0.00 0.00 0.00 4.18
3428 10446 3.056607 CAGATTCAAATGCGGAAAAGGGT 60.057 43.478 0.00 0.00 0.00 4.34
3431 10449 6.639686 CCATATCAGATTCAAATGCGGAAAAG 59.360 38.462 0.00 0.00 0.00 2.27
3433 10451 5.593909 ACCATATCAGATTCAAATGCGGAAA 59.406 36.000 0.00 0.00 0.00 3.13
3435 10453 4.717877 ACCATATCAGATTCAAATGCGGA 58.282 39.130 0.00 0.00 0.00 5.54
3437 10455 6.497437 TGAAACCATATCAGATTCAAATGCG 58.503 36.000 0.00 0.00 0.00 4.73
3439 10457 8.464404 ACACTGAAACCATATCAGATTCAAATG 58.536 33.333 10.27 0.00 45.74 2.32
3440 10458 8.585471 ACACTGAAACCATATCAGATTCAAAT 57.415 30.769 10.27 0.00 45.74 2.32
3450 10468 8.268850 ACAAATACAGACACTGAAACCATATC 57.731 34.615 5.76 0.00 35.18 1.63
3451 10469 7.064609 CGACAAATACAGACACTGAAACCATAT 59.935 37.037 5.76 0.00 35.18 1.78
3452 10470 6.367695 CGACAAATACAGACACTGAAACCATA 59.632 38.462 5.76 0.00 35.18 2.74
3453 10471 5.179368 CGACAAATACAGACACTGAAACCAT 59.821 40.000 5.76 0.00 35.18 3.55
3454 10472 4.509970 CGACAAATACAGACACTGAAACCA 59.490 41.667 5.76 0.00 35.18 3.67
3455 10473 4.610680 GCGACAAATACAGACACTGAAACC 60.611 45.833 5.76 0.00 35.18 3.27
3456 10474 4.025229 TGCGACAAATACAGACACTGAAAC 60.025 41.667 5.76 0.00 35.18 2.78
3457 10475 4.123506 TGCGACAAATACAGACACTGAAA 58.876 39.130 5.76 0.00 35.18 2.69
3458 10476 3.723260 TGCGACAAATACAGACACTGAA 58.277 40.909 5.76 0.00 35.18 3.02
3459 10477 3.378911 TGCGACAAATACAGACACTGA 57.621 42.857 5.76 0.00 35.18 3.41
3460 10478 3.494626 AGTTGCGACAAATACAGACACTG 59.505 43.478 6.90 0.00 37.52 3.66
3461 10479 3.494626 CAGTTGCGACAAATACAGACACT 59.505 43.478 6.90 0.00 0.00 3.55
3462 10480 3.493129 TCAGTTGCGACAAATACAGACAC 59.507 43.478 6.90 0.00 0.00 3.67
3463 10481 3.723260 TCAGTTGCGACAAATACAGACA 58.277 40.909 6.90 0.00 0.00 3.41
3464 10482 4.725556 TTCAGTTGCGACAAATACAGAC 57.274 40.909 6.90 0.00 0.00 3.51
3465 10483 5.940192 AATTCAGTTGCGACAAATACAGA 57.060 34.783 6.90 0.00 0.00 3.41
3466 10484 6.142139 TGAAATTCAGTTGCGACAAATACAG 58.858 36.000 6.90 0.00 0.00 2.74
3467 10485 6.017523 TCTGAAATTCAGTTGCGACAAATACA 60.018 34.615 20.91 8.64 44.58 2.29
3468 10486 6.370593 TCTGAAATTCAGTTGCGACAAATAC 58.629 36.000 20.91 5.06 44.58 1.89
3469 10487 6.552859 TCTGAAATTCAGTTGCGACAAATA 57.447 33.333 20.91 0.00 44.58 1.40
3470 10488 5.437289 TCTGAAATTCAGTTGCGACAAAT 57.563 34.783 20.91 2.97 44.58 2.32
3471 10489 4.891627 TCTGAAATTCAGTTGCGACAAA 57.108 36.364 20.91 0.42 44.58 2.83


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

AutoCloner maintained by Alex Coulton.