Multiple sequence alignment - TraesCS1A01G320000

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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 TraesCS1A01G320000 chr1A 100.000 3385 0 0 1 3385 510671493 510674877 0.000000e+00 6252.0
1 TraesCS1A01G320000 chr1A 87.793 811 61 16 1256 2038 510803509 510804309 0.000000e+00 915.0
2 TraesCS1A01G320000 chr1A 87.411 421 50 3 2036 2455 510804487 510804905 6.570000e-132 481.0
3 TraesCS1A01G320000 chr1A 90.079 252 24 1 999 1250 510803178 510803428 3.260000e-85 326.0
4 TraesCS1A01G320000 chr1B 88.554 2953 194 54 92 2968 558283583 558286467 0.000000e+00 3448.0
5 TraesCS1A01G320000 chr1B 86.359 1085 86 28 999 2029 558495621 558496697 0.000000e+00 1127.0
6 TraesCS1A01G320000 chr1D 89.905 2199 124 38 1223 3376 413730653 413732798 0.000000e+00 2741.0
7 TraesCS1A01G320000 chr1D 89.232 1198 64 11 42 1231 413728524 413729664 0.000000e+00 1437.0
8 TraesCS1A01G320000 chr1D 86.063 574 53 11 1488 2043 413778604 413779168 2.910000e-165 592.0
9 TraesCS1A01G320000 chr1D 85.876 531 47 6 999 1501 413772205 413772735 1.070000e-149 540.0
10 TraesCS1A01G320000 chr1D 97.778 45 1 0 1 45 354442363 354442407 1.010000e-10 78.7
11 TraesCS1A01G320000 chr1D 88.710 62 3 3 1 61 277020195 277020253 4.690000e-09 73.1
12 TraesCS1A01G320000 chr7A 78.479 1078 169 43 968 1994 25006379 25007444 0.000000e+00 647.0
13 TraesCS1A01G320000 chr7A 80.941 425 67 9 2035 2455 25007666 25008080 1.170000e-84 324.0
14 TraesCS1A01G320000 chr7A 82.891 339 58 0 1650 1988 24627557 24627895 4.240000e-79 305.0
15 TraesCS1A01G320000 chr7A 80.516 349 54 12 2069 2408 26838641 26838298 4.330000e-64 255.0
16 TraesCS1A01G320000 chr4A 78.131 1038 173 32 1000 1994 708916783 708915757 8.030000e-171 610.0
17 TraesCS1A01G320000 chr4A 79.032 744 119 25 1299 2011 710413610 710412873 3.060000e-130 475.0
18 TraesCS1A01G320000 chr4A 81.449 345 64 0 1650 1994 708299780 708299436 1.990000e-72 283.0
19 TraesCS1A01G320000 chr4A 80.415 337 54 9 2069 2397 710412602 710412270 2.610000e-61 246.0
20 TraesCS1A01G320000 chr7D 82.891 339 58 0 1650 1988 23510430 23510768 4.240000e-79 305.0
21 TraesCS1A01G320000 chr7D 81.200 250 43 4 2141 2388 23511000 23511247 7.410000e-47 198.0
22 TraesCS1A01G320000 chr7D 94.231 52 3 0 1 52 396828491 396828440 2.800000e-11 80.5
23 TraesCS1A01G320000 chrUn 79.009 424 77 8 2035 2455 90117326 90116912 2.570000e-71 279.0
24 TraesCS1A01G320000 chr3D 80.415 337 55 9 2845 3176 267785696 267786026 2.610000e-61 246.0
25 TraesCS1A01G320000 chr2B 79.245 318 52 11 2845 3156 369436541 369436850 3.420000e-50 209.0
26 TraesCS1A01G320000 chr3B 73.786 515 117 5 103 610 245357004 245357507 1.600000e-43 187.0
27 TraesCS1A01G320000 chr2D 76.440 191 38 5 395 583 174391780 174391965 2.780000e-16 97.1
28 TraesCS1A01G320000 chr5B 91.935 62 4 1 512 572 18950569 18950508 6.020000e-13 86.1
29 TraesCS1A01G320000 chr6D 97.872 47 1 0 1 47 202441518 202441564 7.780000e-12 82.4
30 TraesCS1A01G320000 chr7B 91.525 59 3 2 1 58 445583161 445583104 2.800000e-11 80.5
31 TraesCS1A01G320000 chr4D 96.000 50 1 1 1 49 252363044 252362995 2.800000e-11 80.5
32 TraesCS1A01G320000 chr4D 96.000 50 1 1 1 49 252628146 252628097 2.800000e-11 80.5
33 TraesCS1A01G320000 chr4B 88.525 61 5 1 1 61 108914048 108913990 4.690000e-09 73.1
34 TraesCS1A01G320000 chr3A 88.525 61 5 1 1 61 430204350 430204408 4.690000e-09 73.1
35 TraesCS1A01G320000 chr6A 100.000 38 0 0 2189 2226 445776081 445776118 1.690000e-08 71.3
36 TraesCS1A01G320000 chr2A 86.538 52 7 0 513 564 51001856 51001805 1.310000e-04 58.4
37 TraesCS1A01G320000 chr5D 100.000 28 0 0 534 561 59607162 59607189 6.000000e-03 52.8


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 TraesCS1A01G320000 chr1A 510671493 510674877 3384 False 6252.0 6252 100.000000 1 3385 1 chr1A.!!$F1 3384
1 TraesCS1A01G320000 chr1A 510803178 510804905 1727 False 574.0 915 88.427667 999 2455 3 chr1A.!!$F2 1456
2 TraesCS1A01G320000 chr1B 558283583 558286467 2884 False 3448.0 3448 88.554000 92 2968 1 chr1B.!!$F1 2876
3 TraesCS1A01G320000 chr1B 558495621 558496697 1076 False 1127.0 1127 86.359000 999 2029 1 chr1B.!!$F2 1030
4 TraesCS1A01G320000 chr1D 413728524 413732798 4274 False 2089.0 2741 89.568500 42 3376 2 chr1D.!!$F5 3334
5 TraesCS1A01G320000 chr1D 413778604 413779168 564 False 592.0 592 86.063000 1488 2043 1 chr1D.!!$F4 555
6 TraesCS1A01G320000 chr1D 413772205 413772735 530 False 540.0 540 85.876000 999 1501 1 chr1D.!!$F3 502
7 TraesCS1A01G320000 chr7A 25006379 25008080 1701 False 485.5 647 79.710000 968 2455 2 chr7A.!!$F2 1487
8 TraesCS1A01G320000 chr4A 708915757 708916783 1026 True 610.0 610 78.131000 1000 1994 1 chr4A.!!$R2 994
9 TraesCS1A01G320000 chr4A 710412270 710413610 1340 True 360.5 475 79.723500 1299 2397 2 chr4A.!!$R3 1098
10 TraesCS1A01G320000 chr7D 23510430 23511247 817 False 251.5 305 82.045500 1650 2388 2 chr7D.!!$F1 738

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
26 27 0.172578 TAGTGTCGCGTTAGCAGCAT 59.827 50.0 5.77 0.0 45.49 3.79 F
1444 2577 0.337082 TCCAGTTCGAGGGGTATGGA 59.663 55.0 0.00 0.0 34.54 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2720 0.034616 GAATCCTCCCTCGAGCCATG 59.965 60.0 6.99 0.00 34.49 3.66 R
3284 4803 0.764890 AAATCAGGCCGGCTAGCATA 59.235 50.0 28.56 6.65 0.00 3.14 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
18 19 3.307829 CTGATCGTAGTGTCGCGTT 57.692 52.632 5.77 0.00 0.00 4.84
19 20 2.447089 CTGATCGTAGTGTCGCGTTA 57.553 50.000 5.77 0.00 0.00 3.18
20 21 2.364128 CTGATCGTAGTGTCGCGTTAG 58.636 52.381 5.77 0.00 0.00 2.34
21 22 1.110876 GATCGTAGTGTCGCGTTAGC 58.889 55.000 5.77 0.00 40.74 3.09
22 23 0.448990 ATCGTAGTGTCGCGTTAGCA 59.551 50.000 5.77 0.00 45.49 3.49
23 24 0.179207 TCGTAGTGTCGCGTTAGCAG 60.179 55.000 5.77 0.00 45.49 4.24
24 25 1.730593 CGTAGTGTCGCGTTAGCAGC 61.731 60.000 5.77 0.00 45.49 5.25
25 26 0.731514 GTAGTGTCGCGTTAGCAGCA 60.732 55.000 5.77 0.00 45.49 4.41
26 27 0.172578 TAGTGTCGCGTTAGCAGCAT 59.827 50.000 5.77 0.00 45.49 3.79
27 28 1.078759 AGTGTCGCGTTAGCAGCATC 61.079 55.000 5.77 0.00 45.49 3.91
28 29 1.809619 TGTCGCGTTAGCAGCATCC 60.810 57.895 5.77 0.00 45.49 3.51
29 30 1.519455 GTCGCGTTAGCAGCATCCT 60.519 57.895 5.77 0.00 45.49 3.24
30 31 1.519234 TCGCGTTAGCAGCATCCTG 60.519 57.895 5.77 0.00 45.49 3.86
164 167 1.151899 TGGAGCCACCAACCCTAGT 60.152 57.895 0.00 0.00 46.75 2.57
182 185 0.532115 GTGGATCCAAGCGCCATTTT 59.468 50.000 18.20 0.00 33.66 1.82
185 188 0.451783 GATCCAAGCGCCATTTTCGT 59.548 50.000 2.29 0.00 0.00 3.85
221 224 1.142748 GCTGGATGGAGTCTGACCG 59.857 63.158 3.76 0.00 0.00 4.79
247 250 4.444081 CGGACTCCTCCCGGGACT 62.444 72.222 22.63 1.26 43.05 3.85
262 265 2.158900 CGGGACTGATAGAAAGCCATGT 60.159 50.000 0.00 0.00 0.00 3.21
339 342 8.831297 GATCAGGAGATCTTGGAGTTGTATCCA 61.831 44.444 0.00 0.00 45.27 3.41
370 373 2.216148 CCGGAGAAGGCCAGAGATT 58.784 57.895 5.01 0.00 0.00 2.40
391 394 2.434774 GGAACGAAGCTTGGGGGT 59.565 61.111 13.38 0.00 0.00 4.95
447 450 7.808672 CGGGATACGGATAGAGATGAATATAC 58.191 42.308 0.00 0.00 39.75 1.47
469 472 1.202769 GGGGTTGTGGTGGGCTAGTA 61.203 60.000 0.00 0.00 0.00 1.82
498 501 4.680237 CGAAGACGCACCTGGGCA 62.680 66.667 0.00 0.00 0.00 5.36
652 661 4.275196 CGGACTTATATGGAGTGTTCGAGA 59.725 45.833 0.00 0.00 0.00 4.04
662 671 1.009389 GTGTTCGAGAAGTCCGGCTG 61.009 60.000 0.00 0.00 0.00 4.85
671 680 0.905357 AAGTCCGGCTGTAGATGCTT 59.095 50.000 0.00 0.00 0.00 3.91
687 696 8.183536 TGTAGATGCTTTAACATGTGCTAATTG 58.816 33.333 0.00 0.00 29.13 2.32
732 741 1.985473 TGCATGTTCTTTGCTCTGGT 58.015 45.000 0.00 0.00 40.77 4.00
877 886 2.575694 CTGTCTCCCAGTTCATCTCG 57.424 55.000 0.00 0.00 36.37 4.04
914 923 2.754946 TTTCCTACATGTCCCGTGTC 57.245 50.000 0.00 0.00 35.12 3.67
939 948 6.237942 CGTATGAGCATTTGTACTGAAAGAGG 60.238 42.308 0.00 0.00 37.43 3.69
947 956 1.832366 GTACTGAAAGAGGGAGGGGAC 59.168 57.143 0.00 0.00 37.43 4.46
992 1015 4.818534 TTCAGATTCTTCTGTGCAACAC 57.181 40.909 0.00 0.00 45.67 3.32
993 1016 4.077300 TCAGATTCTTCTGTGCAACACT 57.923 40.909 0.00 0.00 45.67 3.55
994 1017 3.811497 TCAGATTCTTCTGTGCAACACTG 59.189 43.478 0.00 0.00 45.67 3.66
995 1018 2.551459 AGATTCTTCTGTGCAACACTGC 59.449 45.455 0.00 0.00 45.67 4.40
1153 1179 1.032657 CCCTGTCATCGACCTCGTCT 61.033 60.000 0.00 0.00 40.80 4.18
1220 1246 1.742761 CGGTCAGCCATCAAGTCATT 58.257 50.000 0.00 0.00 34.09 2.57
1221 1247 2.086869 CGGTCAGCCATCAAGTCATTT 58.913 47.619 0.00 0.00 34.09 2.32
1314 2429 4.096532 TCGTATCTTCTTGCAGGTCAGTAG 59.903 45.833 0.00 0.00 0.00 2.57
1322 2437 1.601419 GCAGGTCAGTAGCCACGGTA 61.601 60.000 0.00 0.00 0.00 4.02
1444 2577 0.337082 TCCAGTTCGAGGGGTATGGA 59.663 55.000 0.00 0.00 34.54 3.41
1504 2637 1.115467 CTGACCGCCTCTACCTCAAT 58.885 55.000 0.00 0.00 0.00 2.57
1581 2717 1.303317 GGTGGCCGACCTCACAAAT 60.303 57.895 14.93 0.00 42.25 2.32
1582 2718 0.893727 GGTGGCCGACCTCACAAATT 60.894 55.000 14.93 0.00 42.25 1.82
1583 2719 0.958822 GTGGCCGACCTCACAAATTT 59.041 50.000 0.00 0.00 36.63 1.82
1584 2720 1.068541 GTGGCCGACCTCACAAATTTC 60.069 52.381 0.00 0.00 36.63 2.17
1585 2721 1.243902 GGCCGACCTCACAAATTTCA 58.756 50.000 0.00 0.00 0.00 2.69
1586 2722 1.818674 GGCCGACCTCACAAATTTCAT 59.181 47.619 0.00 0.00 0.00 2.57
1587 2723 2.415893 GGCCGACCTCACAAATTTCATG 60.416 50.000 0.00 0.00 0.00 3.07
1588 2724 2.415893 GCCGACCTCACAAATTTCATGG 60.416 50.000 0.00 0.00 0.00 3.66
1589 2725 2.415893 CCGACCTCACAAATTTCATGGC 60.416 50.000 0.00 0.00 0.00 4.40
1590 2726 2.489329 CGACCTCACAAATTTCATGGCT 59.511 45.455 0.00 0.00 0.00 4.75
1591 2727 3.426695 CGACCTCACAAATTTCATGGCTC 60.427 47.826 0.00 0.00 0.00 4.70
1592 2728 2.489329 ACCTCACAAATTTCATGGCTCG 59.511 45.455 0.00 0.00 0.00 5.03
1593 2729 2.749076 CCTCACAAATTTCATGGCTCGA 59.251 45.455 0.00 0.00 0.00 4.04
1594 2730 3.181503 CCTCACAAATTTCATGGCTCGAG 60.182 47.826 8.45 8.45 0.00 4.04
1595 2731 2.749076 TCACAAATTTCATGGCTCGAGG 59.251 45.455 15.58 0.00 0.00 4.63
1596 2732 2.094675 ACAAATTTCATGGCTCGAGGG 58.905 47.619 15.58 0.00 0.00 4.30
1597 2733 2.290896 ACAAATTTCATGGCTCGAGGGA 60.291 45.455 15.58 0.00 0.00 4.20
1598 2734 2.338577 AATTTCATGGCTCGAGGGAG 57.661 50.000 15.58 0.00 43.46 4.30
1599 2735 0.471617 ATTTCATGGCTCGAGGGAGG 59.528 55.000 15.58 0.00 40.80 4.30
1600 2736 0.617535 TTTCATGGCTCGAGGGAGGA 60.618 55.000 15.58 0.00 40.80 3.71
1601 2737 0.399091 TTCATGGCTCGAGGGAGGAT 60.399 55.000 15.58 0.00 40.80 3.24
1602 2738 0.399091 TCATGGCTCGAGGGAGGATT 60.399 55.000 15.58 0.00 40.80 3.01
1756 2974 6.668541 ACTTGACGATGATGATTACTTTGG 57.331 37.500 0.00 0.00 0.00 3.28
1892 3110 3.381590 CAGTCCTTATGGTCGATGACAGA 59.618 47.826 0.00 0.00 33.68 3.41
1895 3113 3.381590 TCCTTATGGTCGATGACAGAGTG 59.618 47.826 0.00 0.00 33.68 3.51
2011 3232 9.893305 GGTACGCTTGCAAAATAAATCTATATT 57.107 29.630 0.00 0.00 0.00 1.28
2122 3582 1.912043 ACCTCTTGGACTGATGAAGGG 59.088 52.381 0.00 0.00 37.04 3.95
2138 3598 3.563808 TGAAGGGTCAATCTTTTGTGACG 59.436 43.478 0.00 0.00 44.19 4.35
2179 3639 4.568072 TCTTTAAGAGCCCTATGCACAA 57.432 40.909 0.00 0.00 44.83 3.33
2339 3799 5.049612 GGACTACTTTGCCAGAAGTTACAAC 60.050 44.000 3.07 0.00 40.24 3.32
2515 3986 7.920682 ACTTCCTTTGTTCAATAACACATGTTC 59.079 33.333 0.00 0.00 45.18 3.18
2519 3990 8.137437 CCTTTGTTCAATAACACATGTTCTCTT 58.863 33.333 0.00 0.00 45.18 2.85
2527 3998 3.412386 ACACATGTTCTCTTGGTTAGCC 58.588 45.455 0.00 0.00 0.00 3.93
2554 4048 7.495606 TGGTCTACATATGCAGATTTACACTTG 59.504 37.037 8.89 0.00 0.00 3.16
2586 4080 9.462606 AGTAAATCCAGAAACAAAATACTAGGG 57.537 33.333 0.00 0.00 0.00 3.53
2587 4081 7.718334 AAATCCAGAAACAAAATACTAGGGG 57.282 36.000 0.00 0.00 0.00 4.79
2588 4082 5.187621 TCCAGAAACAAAATACTAGGGGG 57.812 43.478 0.00 0.00 0.00 5.40
2628 4138 8.418662 TGTCTTGTAACATACATGGTATACTCC 58.581 37.037 2.25 0.00 38.68 3.85
2666 4176 6.488006 GGCAAAGAGGTAACATGATCATATGT 59.512 38.462 8.15 1.47 42.82 2.29
2667 4177 7.358066 GCAAAGAGGTAACATGATCATATGTG 58.642 38.462 8.15 0.00 40.24 3.21
2764 4277 1.168714 GGCAAGTCATCTCCCACAAC 58.831 55.000 0.00 0.00 0.00 3.32
2819 4332 6.053632 TCTGTCATGATGAGTACCAAACAT 57.946 37.500 0.00 0.00 0.00 2.71
2833 4346 5.806654 ACCAAACATAGCAAAACCTCAAT 57.193 34.783 0.00 0.00 0.00 2.57
2847 4360 7.566709 CAAAACCTCAATTGCAATGTTTCTAC 58.433 34.615 19.83 0.00 0.00 2.59
2880 4393 1.786441 AGGTGGTGGGGAAAATTCTCA 59.214 47.619 0.00 0.00 0.00 3.27
2921 4435 0.109919 GCTCTTGCCCGTTTTTACCG 60.110 55.000 0.00 0.00 0.00 4.02
2938 4452 0.449786 CCGTGTTGCAGTTGTTGTCA 59.550 50.000 0.00 0.00 0.00 3.58
2944 4458 1.024271 TGCAGTTGTTGTCAGCCTTC 58.976 50.000 0.00 0.00 0.00 3.46
2963 4477 5.181245 GCCTTCTGTGCTGTCAAAAGTTATA 59.819 40.000 0.00 0.00 0.00 0.98
3002 4516 4.850680 ACTTACCAAGTGACCAAACAAGA 58.149 39.130 0.00 0.00 41.01 3.02
3018 4532 9.912634 ACCAAACAAGATACAATATGAAAAGTG 57.087 29.630 0.00 0.00 0.00 3.16
3031 4545 3.892284 TGAAAAGTGGAGCTTGGTTACA 58.108 40.909 0.00 0.00 37.52 2.41
3035 4549 6.547880 TGAAAAGTGGAGCTTGGTTACAATTA 59.452 34.615 0.00 0.00 37.52 1.40
3037 4551 4.980573 AGTGGAGCTTGGTTACAATTACA 58.019 39.130 0.00 0.00 35.73 2.41
3038 4552 5.381757 AGTGGAGCTTGGTTACAATTACAA 58.618 37.500 0.00 0.00 35.73 2.41
3055 4569 8.342634 ACAATTACAACAACTCACAGTATCAAC 58.657 33.333 0.00 0.00 0.00 3.18
3056 4570 6.519353 TTACAACAACTCACAGTATCAACG 57.481 37.500 0.00 0.00 0.00 4.10
3081 4595 5.404968 GCACAATGTAGCAAAAAGTAATGCA 59.595 36.000 0.00 0.00 44.95 3.96
3083 4597 7.360269 GCACAATGTAGCAAAAAGTAATGCAAT 60.360 33.333 0.00 0.00 44.95 3.56
3131 4646 1.488527 GCGGGCAATCGACTAGTAAG 58.511 55.000 0.00 0.00 0.00 2.34
3135 4650 3.548415 CGGGCAATCGACTAGTAAGAGAC 60.548 52.174 0.00 0.00 0.00 3.36
3138 4653 5.452077 GGGCAATCGACTAGTAAGAGACAAT 60.452 44.000 0.00 0.00 0.00 2.71
3230 4745 2.263077 GTGATGTGGTAGTCAAGCTCG 58.737 52.381 0.00 0.00 0.00 5.03
3235 4754 0.679505 TGGTAGTCAAGCTCGCAACT 59.320 50.000 0.00 0.00 0.00 3.16
3248 4767 0.785979 CGCAACTGCAAAAAGGATGC 59.214 50.000 2.12 0.00 44.08 3.91
3294 4813 1.608590 CCCCAAAACATATGCTAGCCG 59.391 52.381 13.29 0.36 0.00 5.52
3304 4823 0.106519 ATGCTAGCCGGCCTGATTTT 60.107 50.000 26.15 4.77 0.00 1.82
3313 4832 3.434637 CCGGCCTGATTTTATTTTCACG 58.565 45.455 0.00 0.00 0.00 4.35
3367 4886 2.351726 GTCAAGCCGGTTACTAGCAATG 59.648 50.000 1.90 0.00 0.00 2.82
3376 4895 4.608951 GGTTACTAGCAATGGAGACGTAG 58.391 47.826 0.00 0.00 0.00 3.51
3377 4896 2.873133 ACTAGCAATGGAGACGTAGC 57.127 50.000 0.00 0.00 0.00 3.58
3378 4897 2.100197 ACTAGCAATGGAGACGTAGCA 58.900 47.619 0.00 0.00 0.00 3.49
3379 4898 2.159226 ACTAGCAATGGAGACGTAGCAC 60.159 50.000 0.00 0.00 0.00 4.40
3380 4899 0.608130 AGCAATGGAGACGTAGCACA 59.392 50.000 0.00 0.00 0.00 4.57
3381 4900 0.721718 GCAATGGAGACGTAGCACAC 59.278 55.000 0.00 0.00 0.00 3.82
3382 4901 1.939381 GCAATGGAGACGTAGCACACA 60.939 52.381 0.00 0.00 0.00 3.72
3383 4902 2.412870 CAATGGAGACGTAGCACACAA 58.587 47.619 0.00 0.00 0.00 3.33
3384 4903 3.002791 CAATGGAGACGTAGCACACAAT 58.997 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.364128 CTAACGCGACACTACGATCAG 58.636 52.381 15.93 0.00 35.09 2.90
1 2 1.530441 GCTAACGCGACACTACGATCA 60.530 52.381 15.93 0.00 35.09 2.92
2 3 1.110876 GCTAACGCGACACTACGATC 58.889 55.000 15.93 0.00 35.09 3.69
3 4 0.448990 TGCTAACGCGACACTACGAT 59.551 50.000 15.93 0.00 39.65 3.73
4 5 0.179207 CTGCTAACGCGACACTACGA 60.179 55.000 15.93 0.00 39.65 3.43
5 6 1.730593 GCTGCTAACGCGACACTACG 61.731 60.000 15.93 0.00 39.65 3.51
6 7 0.731514 TGCTGCTAACGCGACACTAC 60.732 55.000 15.93 0.00 39.65 2.73
7 8 0.172578 ATGCTGCTAACGCGACACTA 59.827 50.000 15.93 0.00 39.65 2.74
8 9 1.078759 GATGCTGCTAACGCGACACT 61.079 55.000 15.93 0.00 39.65 3.55
9 10 1.345176 GATGCTGCTAACGCGACAC 59.655 57.895 15.93 0.00 39.65 3.67
10 11 1.809619 GGATGCTGCTAACGCGACA 60.810 57.895 15.93 4.24 39.65 4.35
11 12 1.519455 AGGATGCTGCTAACGCGAC 60.519 57.895 15.93 0.00 39.65 5.19
12 13 1.519234 CAGGATGCTGCTAACGCGA 60.519 57.895 15.93 0.00 39.65 5.87
13 14 3.009140 CAGGATGCTGCTAACGCG 58.991 61.111 3.53 3.53 39.65 6.01
24 25 0.532573 ACGACCACTACTGCAGGATG 59.467 55.000 19.93 12.53 40.87 3.51
25 26 1.267121 AACGACCACTACTGCAGGAT 58.733 50.000 19.93 0.00 0.00 3.24
26 27 1.045407 AAACGACCACTACTGCAGGA 58.955 50.000 19.93 9.06 0.00 3.86
27 28 2.334838 GTAAACGACCACTACTGCAGG 58.665 52.381 19.93 2.50 0.00 4.85
40 41 2.421424 GCTCCTAGTCGAAGGTAAACGA 59.579 50.000 3.11 0.00 37.91 3.85
147 150 1.299976 CACTAGGGTTGGTGGCTCC 59.700 63.158 0.00 0.00 32.61 4.70
157 160 1.972660 GCGCTTGGATCCACTAGGGT 61.973 60.000 23.98 0.00 38.11 4.34
162 165 0.323725 AAATGGCGCTTGGATCCACT 60.324 50.000 15.91 0.00 31.94 4.00
164 167 0.817013 GAAAATGGCGCTTGGATCCA 59.183 50.000 11.44 11.44 0.00 3.41
182 185 0.107214 GGAATCCATTGCCTCCACGA 60.107 55.000 0.00 0.00 0.00 4.35
185 188 0.396139 GCAGGAATCCATTGCCTCCA 60.396 55.000 0.61 0.00 31.79 3.86
221 224 2.913060 AGGAGTCCGCCCTATCGC 60.913 66.667 2.76 0.00 30.92 4.58
247 250 3.824133 CCATCCACATGGCTTTCTATCA 58.176 45.455 0.00 0.00 43.55 2.15
262 265 1.755621 CGAGGAGGAGATGACCATCCA 60.756 57.143 6.40 0.00 38.58 3.41
339 342 3.535561 CTTCTCCGGCATAACAGACAAT 58.464 45.455 0.00 0.00 0.00 2.71
364 367 1.546476 AGCTTCGTTCCGACAATCTCT 59.454 47.619 0.00 0.00 34.89 3.10
370 373 1.301401 CCCAAGCTTCGTTCCGACA 60.301 57.895 0.00 0.00 34.89 4.35
391 394 2.901338 AGCCACTCCACTCTACTACA 57.099 50.000 0.00 0.00 0.00 2.74
469 472 0.387202 CGTCTTCGGATCCAGCTCAT 59.613 55.000 13.41 0.00 0.00 2.90
498 501 2.552591 CGGATATGGAGAGGTAGGACGT 60.553 54.545 0.00 0.00 0.00 4.34
504 507 2.696526 AAGGCGGATATGGAGAGGTA 57.303 50.000 0.00 0.00 0.00 3.08
574 578 0.327924 CCAACTGCACCCCTCATACA 59.672 55.000 0.00 0.00 0.00 2.29
622 626 5.163301 ACACTCCATATAAGTCCGATTGCTT 60.163 40.000 0.00 0.00 0.00 3.91
652 661 0.905357 AAGCATCTACAGCCGGACTT 59.095 50.000 5.05 0.00 0.00 3.01
662 671 8.184192 ACAATTAGCACATGTTAAAGCATCTAC 58.816 33.333 8.42 0.00 0.00 2.59
671 680 6.000840 TGGAGTGACAATTAGCACATGTTAA 58.999 36.000 0.00 0.00 37.48 2.01
732 741 5.697178 TGTAACGCAGCTAAAGTGTGAATTA 59.303 36.000 0.00 0.00 0.00 1.40
804 813 3.003480 GACGGATCTTGGAACTTGGAAG 58.997 50.000 0.00 0.00 0.00 3.46
805 814 2.637872 AGACGGATCTTGGAACTTGGAA 59.362 45.455 0.00 0.00 0.00 3.53
806 815 2.233922 GAGACGGATCTTGGAACTTGGA 59.766 50.000 0.00 0.00 34.34 3.53
807 816 2.234908 AGAGACGGATCTTGGAACTTGG 59.765 50.000 0.00 0.00 34.34 3.61
808 817 3.056536 TCAGAGACGGATCTTGGAACTTG 60.057 47.826 0.00 0.00 34.34 3.16
809 818 3.165875 TCAGAGACGGATCTTGGAACTT 58.834 45.455 0.00 0.00 34.34 2.66
810 819 2.808919 TCAGAGACGGATCTTGGAACT 58.191 47.619 0.00 0.00 34.34 3.01
875 884 0.457443 AGCTCGAAGATCATGCACGA 59.543 50.000 0.00 0.00 33.89 4.35
876 885 1.284657 AAGCTCGAAGATCATGCACG 58.715 50.000 0.00 0.00 33.89 5.34
877 886 3.486542 GGAAAAGCTCGAAGATCATGCAC 60.487 47.826 0.00 0.00 33.89 4.57
914 923 6.237942 CCTCTTTCAGTACAAATGCTCATACG 60.238 42.308 0.00 0.00 0.00 3.06
939 948 1.285078 AGCACAAAATAGGTCCCCTCC 59.715 52.381 0.00 0.00 34.61 4.30
947 956 3.689161 TGTCCGATTCAGCACAAAATAGG 59.311 43.478 0.00 0.00 0.00 2.57
988 1011 2.162681 GCTTCCCATAGTTGCAGTGTT 58.837 47.619 0.00 0.00 0.00 3.32
989 1012 1.073763 TGCTTCCCATAGTTGCAGTGT 59.926 47.619 0.00 0.00 0.00 3.55
990 1013 1.825090 TGCTTCCCATAGTTGCAGTG 58.175 50.000 0.00 0.00 0.00 3.66
991 1014 2.584835 TTGCTTCCCATAGTTGCAGT 57.415 45.000 0.00 0.00 35.02 4.40
992 1015 2.165030 CCTTTGCTTCCCATAGTTGCAG 59.835 50.000 0.00 0.00 35.02 4.41
993 1016 2.170166 CCTTTGCTTCCCATAGTTGCA 58.830 47.619 0.00 0.00 0.00 4.08
994 1017 1.478105 CCCTTTGCTTCCCATAGTTGC 59.522 52.381 0.00 0.00 0.00 4.17
995 1018 2.755103 GTCCCTTTGCTTCCCATAGTTG 59.245 50.000 0.00 0.00 0.00 3.16
1153 1179 3.353836 GCCGTGCTTCGAAAGGCA 61.354 61.111 21.22 15.74 46.48 4.75
1200 1226 0.745845 ATGACTTGATGGCTGACCGC 60.746 55.000 0.00 0.00 39.70 5.68
1213 1239 4.677182 ACCATAAAGAGGCCAAATGACTT 58.323 39.130 5.01 0.00 0.00 3.01
1220 1246 6.129414 TGTTACTTACCATAAAGAGGCCAA 57.871 37.500 5.01 0.00 0.00 4.52
1221 1247 5.765576 TGTTACTTACCATAAAGAGGCCA 57.234 39.130 5.01 0.00 0.00 5.36
1322 2437 2.166870 TGTTGTCCATTACCGCGTCTAT 59.833 45.455 4.92 0.00 0.00 1.98
1444 2577 1.006102 CGAGCTCACCCAGTCGTTT 60.006 57.895 15.40 0.00 0.00 3.60
1504 2637 1.620739 GCTCATCCTCTGGCTCCACA 61.621 60.000 0.00 0.00 0.00 4.17
1567 2700 2.415893 CCATGAAATTTGTGAGGTCGGC 60.416 50.000 0.00 0.00 0.00 5.54
1579 2715 1.133976 CCTCCCTCGAGCCATGAAATT 60.134 52.381 6.99 0.00 34.49 1.82
1581 2717 0.617535 TCCTCCCTCGAGCCATGAAA 60.618 55.000 6.99 0.00 34.49 2.69
1582 2718 0.399091 ATCCTCCCTCGAGCCATGAA 60.399 55.000 6.99 0.00 34.49 2.57
1583 2719 0.399091 AATCCTCCCTCGAGCCATGA 60.399 55.000 6.99 1.01 34.49 3.07
1584 2720 0.034616 GAATCCTCCCTCGAGCCATG 59.965 60.000 6.99 0.00 34.49 3.66
1585 2721 1.467678 CGAATCCTCCCTCGAGCCAT 61.468 60.000 6.99 0.00 37.23 4.40
1586 2722 2.127869 CGAATCCTCCCTCGAGCCA 61.128 63.158 6.99 0.00 37.23 4.75
1587 2723 1.677637 AACGAATCCTCCCTCGAGCC 61.678 60.000 6.99 0.00 38.43 4.70
1588 2724 0.528684 CAACGAATCCTCCCTCGAGC 60.529 60.000 6.99 0.00 38.43 5.03
1589 2725 1.103803 TCAACGAATCCTCCCTCGAG 58.896 55.000 5.13 5.13 38.43 4.04
1590 2726 0.815734 GTCAACGAATCCTCCCTCGA 59.184 55.000 0.00 0.00 38.43 4.04
1591 2727 0.818296 AGTCAACGAATCCTCCCTCG 59.182 55.000 0.00 0.00 40.87 4.63
1592 2728 1.825474 TCAGTCAACGAATCCTCCCTC 59.175 52.381 0.00 0.00 0.00 4.30
1593 2729 1.938585 TCAGTCAACGAATCCTCCCT 58.061 50.000 0.00 0.00 0.00 4.20
1594 2730 2.168521 TGATCAGTCAACGAATCCTCCC 59.831 50.000 0.00 0.00 0.00 4.30
1595 2731 3.526931 TGATCAGTCAACGAATCCTCC 57.473 47.619 0.00 0.00 0.00 4.30
1596 2732 4.437239 ACATGATCAGTCAACGAATCCTC 58.563 43.478 0.00 0.00 38.01 3.71
1597 2733 4.081476 TGACATGATCAGTCAACGAATCCT 60.081 41.667 19.31 0.00 42.57 3.24
1598 2734 4.183865 TGACATGATCAGTCAACGAATCC 58.816 43.478 19.31 0.00 42.57 3.01
1756 2974 1.911057 CTTCTCCCCAAAGTGTTCCC 58.089 55.000 0.00 0.00 0.00 3.97
1892 3110 0.400594 GAACTTGTAGGCCACCCACT 59.599 55.000 5.01 0.00 0.00 4.00
1895 3113 0.690762 TGAGAACTTGTAGGCCACCC 59.309 55.000 5.01 0.00 0.00 4.61
2011 3232 6.452494 TTCACCAAACAATACTTTTTCCGA 57.548 33.333 0.00 0.00 0.00 4.55
2122 3582 3.878086 TCTGCGTCACAAAAGATTGAC 57.122 42.857 0.00 0.00 38.94 3.18
2138 3598 4.333690 AGATCCCATTGCTCATTATCTGC 58.666 43.478 0.00 0.00 0.00 4.26
2172 3632 1.333619 GTTTGTCACGACCTTGTGCAT 59.666 47.619 0.00 0.00 39.73 3.96
2339 3799 4.022329 ACCATTTTCCCTTCAGTAAAAGCG 60.022 41.667 0.00 0.00 0.00 4.68
2455 3918 5.694910 CAGGGGTGTAACGATACATGAATAC 59.305 44.000 8.88 0.00 43.60 1.89
2456 3919 5.599242 TCAGGGGTGTAACGATACATGAATA 59.401 40.000 8.88 0.00 43.60 1.75
2457 3920 4.407621 TCAGGGGTGTAACGATACATGAAT 59.592 41.667 8.88 0.00 43.60 2.57
2458 3921 3.770388 TCAGGGGTGTAACGATACATGAA 59.230 43.478 8.88 0.00 43.60 2.57
2492 3963 7.502226 AGAGAACATGTGTTATTGAACAAAGGA 59.498 33.333 0.00 0.00 46.99 3.36
2515 3986 2.832129 TGTAGACCAGGCTAACCAAGAG 59.168 50.000 0.00 0.00 39.06 2.85
2519 3990 3.071023 GCATATGTAGACCAGGCTAACCA 59.929 47.826 4.29 0.00 39.06 3.67
2527 3998 7.212976 AGTGTAAATCTGCATATGTAGACCAG 58.787 38.462 23.58 12.33 39.51 4.00
2586 4080 8.978539 GTTACAAGACAAATTCAGATTTTTCCC 58.021 33.333 0.00 0.00 34.12 3.97
2587 4081 9.528018 TGTTACAAGACAAATTCAGATTTTTCC 57.472 29.630 0.00 0.00 34.12 3.13
2628 4138 4.520492 ACCTCTTTGCCAAACTTCATACAG 59.480 41.667 0.00 0.00 0.00 2.74
2666 4176 8.402472 CAAGATGTACTTCAAGGTAAAAACACA 58.598 33.333 11.02 0.00 36.61 3.72
2667 4177 8.403236 ACAAGATGTACTTCAAGGTAAAAACAC 58.597 33.333 11.02 0.00 36.61 3.32
2764 4277 7.220030 AGTGACCAATATTTAGGCTATGTCTG 58.780 38.462 0.00 0.00 0.00 3.51
2819 4332 5.212532 ACATTGCAATTGAGGTTTTGCTA 57.787 34.783 9.83 2.23 46.50 3.49
2833 4346 8.033038 CCTAGTAGTACTGTAGAAACATTGCAA 58.967 37.037 13.29 0.00 34.37 4.08
2847 4360 3.288964 CCACCACCTCCTAGTAGTACTG 58.711 54.545 13.29 3.27 0.00 2.74
2880 4393 7.005709 AGCTTGGTACTTATTACAGAGTTGT 57.994 36.000 0.00 0.00 41.39 3.32
2921 4435 1.548986 GCTGACAACAACTGCAACAC 58.451 50.000 0.00 0.00 33.57 3.32
2938 4452 1.952296 CTTTTGACAGCACAGAAGGCT 59.048 47.619 0.00 0.00 43.77 4.58
2981 4495 6.485313 TGTATCTTGTTTGGTCACTTGGTAAG 59.515 38.462 0.00 0.00 0.00 2.34
3001 4515 7.067494 ACCAAGCTCCACTTTTCATATTGTATC 59.933 37.037 0.00 0.00 36.04 2.24
3002 4516 6.891908 ACCAAGCTCCACTTTTCATATTGTAT 59.108 34.615 0.00 0.00 36.04 2.29
3018 4532 5.699097 TGTTGTAATTGTAACCAAGCTCC 57.301 39.130 0.00 0.00 33.17 4.70
3021 4535 6.416750 GTGAGTTGTTGTAATTGTAACCAAGC 59.583 38.462 0.00 0.00 33.17 4.01
3031 4545 7.307751 CCGTTGATACTGTGAGTTGTTGTAATT 60.308 37.037 0.00 0.00 0.00 1.40
3035 4549 3.807622 CCGTTGATACTGTGAGTTGTTGT 59.192 43.478 0.00 0.00 0.00 3.32
3037 4551 2.806244 GCCGTTGATACTGTGAGTTGTT 59.194 45.455 0.00 0.00 0.00 2.83
3038 4552 2.224185 TGCCGTTGATACTGTGAGTTGT 60.224 45.455 0.00 0.00 0.00 3.32
3055 4569 3.011949 ACTTTTTGCTACATTGTGCCG 57.988 42.857 0.00 0.00 0.00 5.69
3056 4570 5.163963 GCATTACTTTTTGCTACATTGTGCC 60.164 40.000 0.00 0.00 35.95 5.01
3081 4595 7.383102 ACGAGTTTGAGCAATTATTCAGATT 57.617 32.000 0.00 0.00 0.00 2.40
3083 4597 7.602644 AGTTACGAGTTTGAGCAATTATTCAGA 59.397 33.333 0.00 0.00 0.00 3.27
3103 4617 1.213094 CGATTGCCCGCCTAGTTACG 61.213 60.000 0.00 0.00 0.00 3.18
3144 4659 9.667107 CTCACTTGATTTAGTATCTGGGTTTAA 57.333 33.333 0.00 0.00 0.00 1.52
3147 4662 7.259088 ACTCACTTGATTTAGTATCTGGGTT 57.741 36.000 0.00 0.00 0.00 4.11
3159 4674 9.136323 ACTCCAGAAATTTTACTCACTTGATTT 57.864 29.630 0.00 0.00 0.00 2.17
3179 4694 5.235186 CGGTTTGAGCTTCATTATACTCCAG 59.765 44.000 0.00 0.00 0.00 3.86
3230 4745 1.150827 GGCATCCTTTTTGCAGTTGC 58.849 50.000 0.00 0.00 41.95 4.17
3235 4754 4.343526 TCTGTTTTAGGCATCCTTTTTGCA 59.656 37.500 0.00 0.00 41.95 4.08
3273 4792 2.666317 GGCTAGCATATGTTTTGGGGT 58.334 47.619 18.24 0.00 0.00 4.95
3284 4803 0.764890 AAATCAGGCCGGCTAGCATA 59.235 50.000 28.56 6.65 0.00 3.14
3294 4813 6.645003 AGAAAACGTGAAAATAAAATCAGGCC 59.355 34.615 0.00 0.00 35.44 5.19
3304 4823 8.899771 AGAGAAGGAAAAGAAAACGTGAAAATA 58.100 29.630 0.00 0.00 0.00 1.40
3313 4832 8.988064 ACAAAAAGAGAGAAGGAAAAGAAAAC 57.012 30.769 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.