Multiple sequence alignment - TraesCS3D01G176700

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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 TraesCS3D01G176700 chr3D 100.000 5402 0 0 1 5402 157770429 157775830 0.000000e+00 9976.0
1 TraesCS3D01G176700 chr3D 95.041 121 3 2 3653 3770 529507564 529507444 2.570000e-43 187.0
2 TraesCS3D01G176700 chr3A 96.157 3513 100 19 283 3770 170238188 170234686 0.000000e+00 5707.0
3 TraesCS3D01G176700 chr3A 96.534 1385 46 2 3767 5149 170234310 170232926 0.000000e+00 2290.0
4 TraesCS3D01G176700 chr3A 97.251 291 8 0 1 291 170245120 170244830 1.350000e-135 494.0
5 TraesCS3D01G176700 chr3A 94.203 138 6 2 5151 5288 170232761 170232626 5.480000e-50 209.0
6 TraesCS3D01G176700 chr3A 96.667 60 1 1 5288 5346 170220991 170220932 1.240000e-16 99.0
7 TraesCS3D01G176700 chr3B 92.927 1937 93 16 1604 3523 229300955 229302864 0.000000e+00 2778.0
8 TraesCS3D01G176700 chr3B 93.936 1583 69 14 1 1576 229299314 229300876 0.000000e+00 2366.0
9 TraesCS3D01G176700 chr3B 90.339 1004 62 19 4156 5137 229305235 229306225 0.000000e+00 1284.0
10 TraesCS3D01G176700 chr3B 93.750 272 13 3 3767 4034 229304897 229305168 6.520000e-109 405.0
11 TraesCS3D01G176700 chr3B 92.593 108 6 2 3546 3652 229304491 229304597 2.610000e-33 154.0
12 TraesCS3D01G176700 chr4B 85.572 402 33 13 2423 2814 250707985 250708371 1.090000e-106 398.0
13 TraesCS3D01G176700 chr4B 89.655 58 2 4 4019 4073 644289486 644289430 2.700000e-08 71.3
14 TraesCS3D01G176700 chr4A 84.171 398 38 13 2423 2812 336023977 336024357 3.980000e-96 363.0
15 TraesCS3D01G176700 chr6D 85.185 351 29 15 2472 2814 158227112 158226777 6.700000e-89 339.0
16 TraesCS3D01G176700 chr6D 95.745 47 2 0 4022 4068 405119640 405119594 5.800000e-10 76.8
17 TraesCS3D01G176700 chr6D 92.308 52 3 1 2314 2365 158228183 158228133 7.510000e-09 73.1
18 TraesCS3D01G176700 chrUn 95.041 121 3 2 3653 3770 425346485 425346365 2.570000e-43 187.0
19 TraesCS3D01G176700 chr5D 95.763 118 2 2 3653 3767 503295539 503295656 2.570000e-43 187.0
20 TraesCS3D01G176700 chr5D 95.763 118 2 2 3653 3767 512412910 512413027 2.570000e-43 187.0
21 TraesCS3D01G176700 chr5D 94.000 50 1 2 4026 4073 272146031 272145982 2.090000e-09 75.0
22 TraesCS3D01G176700 chr5D 95.122 41 2 0 1612 1652 496087125 496087165 1.260000e-06 65.8
23 TraesCS3D01G176700 chr5D 96.970 33 1 0 1611 1643 496087021 496087053 7.560000e-04 56.5
24 TraesCS3D01G176700 chr1D 95.763 118 2 2 3653 3767 254438699 254438816 2.570000e-43 187.0
25 TraesCS3D01G176700 chr1D 95.041 121 3 2 3653 3770 273914661 273914541 2.570000e-43 187.0
26 TraesCS3D01G176700 chr1D 95.041 121 3 2 3653 3770 491425270 491425150 2.570000e-43 187.0
27 TraesCS3D01G176700 chr1A 95.041 121 3 2 3653 3770 554474644 554474524 2.570000e-43 187.0
28 TraesCS3D01G176700 chr6A 94.118 51 2 1 4018 4068 614304657 614304706 5.800000e-10 76.8
29 TraesCS3D01G176700 chr6A 95.652 46 2 0 4023 4068 4785913 4785868 2.090000e-09 75.0
30 TraesCS3D01G176700 chr4D 90.741 54 3 2 4022 4073 80976635 80976582 2.700000e-08 71.3
31 TraesCS3D01G176700 chr1B 88.333 60 5 2 4009 4068 5947027 5947084 2.700000e-08 71.3
32 TraesCS3D01G176700 chr5A 89.091 55 6 0 4014 4068 21412558 21412504 9.710000e-08 69.4


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 TraesCS3D01G176700 chr3D 157770429 157775830 5401 False 9976.000000 9976 100.000000 1 5402 1 chr3D.!!$F1 5401
1 TraesCS3D01G176700 chr3A 170232626 170238188 5562 True 2735.333333 5707 95.631333 283 5288 3 chr3A.!!$R3 5005
2 TraesCS3D01G176700 chr3B 229299314 229306225 6911 False 1397.400000 2778 92.709000 1 5137 5 chr3B.!!$F1 5136
3 TraesCS3D01G176700 chr6D 158226777 158228183 1406 True 206.050000 339 88.746500 2314 2814 2 chr6D.!!$R2 500

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
791 799 0.250901 AAATGGACAAGGCTCGCTGT 60.251 50.000 0.00 0.0 0.00 4.40 F
1532 1549 0.251474 TTGCCTGCTTGCAGGAAGAT 60.251 50.000 36.96 0.0 45.00 2.40 F
2122 2190 2.869233 TGCAGCTTCCTCAACAAAAC 57.131 45.000 0.00 0.0 0.00 2.43 F
2542 3567 1.139654 TGTGCTTGAGCTTCAGTGACT 59.860 47.619 4.44 0.0 42.66 3.41 F
4093 7158 1.882623 CTCCTGTTGCCTTCCTTCAAC 59.117 52.381 0.00 0.0 41.99 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1815 1.338105 TGATCAAGAGTTCCGTGCCAG 60.338 52.381 0.00 0.00 0.00 4.85 R
2519 3544 2.038164 TCACTGAAGCTCAAGCACAGAT 59.962 45.455 24.81 13.08 44.21 2.90 R
3722 6389 0.179084 CGATCCTAGCGGAAAAGGCA 60.179 55.000 0.00 0.00 44.02 4.75 R
4116 7181 0.824109 ATTGCGATCCTCTTGTCCGA 59.176 50.000 0.00 0.00 0.00 4.55 R
5294 8538 0.037590 TGGTTATGTCAGCCCGCTTT 59.962 50.000 0.00 0.00 0.00 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.562182 TCCCTCTATGTCTAATCACGCA 58.438 45.455 0.00 0.00 0.00 5.24
36 37 2.353889 GTCTAATCACGCACGGAGACTA 59.646 50.000 0.00 0.00 32.41 2.59
63 64 6.020360 GCGATGGAAATAAGAAGAATTGCAAC 60.020 38.462 0.00 0.00 0.00 4.17
141 142 1.129998 CAAAGACTGCTGATTGGCGAG 59.870 52.381 0.00 0.00 34.52 5.03
161 162 4.027621 CGAGATGTTGCGATGTGTAAGTAC 60.028 45.833 0.00 0.00 0.00 2.73
328 329 8.408043 AGAATGATGACCAGTGTGATTTTTAA 57.592 30.769 0.00 0.00 0.00 1.52
362 363 1.067142 GTGTTACACAGCGGAGATCCA 60.067 52.381 10.96 0.00 34.08 3.41
412 413 9.382244 GCAAAACTTATGTATAATGAACCGATC 57.618 33.333 0.00 0.00 0.00 3.69
525 526 5.836705 TCCTGGATTATTTGTGGGAATTGA 58.163 37.500 0.00 0.00 0.00 2.57
529 530 6.736581 TGGATTATTTGTGGGAATTGACCTA 58.263 36.000 0.00 0.00 0.00 3.08
689 695 4.654262 ACAACGGGTAGATGTTAGATCCAT 59.346 41.667 0.00 0.00 31.36 3.41
691 697 5.215252 ACGGGTAGATGTTAGATCCATTG 57.785 43.478 0.00 0.00 0.00 2.82
747 755 0.749454 CAGCACCTATTGGCCCAGTC 60.749 60.000 0.00 0.00 36.63 3.51
791 799 0.250901 AAATGGACAAGGCTCGCTGT 60.251 50.000 0.00 0.00 0.00 4.40
830 840 8.943594 AAAAAGGACCCAGTTTACATGTTATA 57.056 30.769 2.30 0.00 0.00 0.98
952 962 2.116366 GCACAAAGCGAACGAACAATT 58.884 42.857 0.00 0.00 0.00 2.32
1050 1060 1.925972 GGAAGGGAGGTGGGAGCTT 60.926 63.158 0.00 0.00 0.00 3.74
1313 1323 1.081892 CACCAACAATCCTGCGAGAG 58.918 55.000 0.00 0.00 0.00 3.20
1427 1438 1.540363 CCATACGTACCAGCCACATCC 60.540 57.143 0.00 0.00 0.00 3.51
1428 1439 0.387929 ATACGTACCAGCCACATCCG 59.612 55.000 0.00 0.00 0.00 4.18
1430 1441 1.226974 CGTACCAGCCACATCCGAG 60.227 63.158 0.00 0.00 0.00 4.63
1431 1442 1.898154 GTACCAGCCACATCCGAGT 59.102 57.895 0.00 0.00 0.00 4.18
1432 1443 0.460284 GTACCAGCCACATCCGAGTG 60.460 60.000 0.00 0.00 39.21 3.51
1494 1511 5.565509 TGAATGCCTTGTGTCTGGTTATTA 58.434 37.500 0.00 0.00 0.00 0.98
1507 1524 9.698617 GTGTCTGGTTATTATGTTCGTTTATTC 57.301 33.333 0.00 0.00 0.00 1.75
1526 1543 1.370900 GAACGTTGCCTGCTTGCAG 60.371 57.895 5.00 15.02 43.21 4.41
1532 1549 0.251474 TTGCCTGCTTGCAGGAAGAT 60.251 50.000 36.96 0.00 45.00 2.40
1602 1657 4.278419 GCCCAAAACTCATGTTCACTAACT 59.722 41.667 0.00 0.00 36.51 2.24
1603 1658 5.221244 GCCCAAAACTCATGTTCACTAACTT 60.221 40.000 0.00 0.00 36.51 2.66
1604 1659 6.208644 CCCAAAACTCATGTTCACTAACTTG 58.791 40.000 0.00 0.00 40.41 3.16
1605 1660 6.208644 CCAAAACTCATGTTCACTAACTTGG 58.791 40.000 0.00 0.00 39.82 3.61
1747 1815 4.024218 GCATGATGTCATTTCTCTAGGTGC 60.024 45.833 0.00 0.00 33.61 5.01
1883 1951 7.612065 TGCTCTTAGGCTCTTTGGTATATAA 57.388 36.000 0.00 0.00 0.00 0.98
1926 1994 3.472283 TCATGTTTGTGCTGCCATTTT 57.528 38.095 0.00 0.00 0.00 1.82
1999 2067 7.275888 TCAATAGGTTGTGATGGATTTATGC 57.724 36.000 0.00 0.00 36.69 3.14
2080 2148 4.216902 TGCTGTTCTGAATGTTTGGATGAG 59.783 41.667 0.00 0.00 0.00 2.90
2122 2190 2.869233 TGCAGCTTCCTCAACAAAAC 57.131 45.000 0.00 0.00 0.00 2.43
2468 2542 4.846779 TTCACTGGAATTGTTGGTAAGC 57.153 40.909 0.00 0.00 0.00 3.09
2507 3532 6.639632 AGTGTTGTGCTGATTACATCTTTT 57.360 33.333 0.00 0.00 0.00 2.27
2525 3550 9.520204 ACATCTTTTTAGTTGTGAAAATCTGTG 57.480 29.630 0.00 0.00 0.00 3.66
2542 3567 1.139654 TGTGCTTGAGCTTCAGTGACT 59.860 47.619 4.44 0.00 42.66 3.41
2588 3631 3.744660 AGTTCTTGGGTCTACTTGCTTG 58.255 45.455 0.00 0.00 0.00 4.01
2716 3763 8.028354 CCAATGTATCACAAGATTTTGCAAGTA 58.972 33.333 0.00 0.00 37.85 2.24
2951 4013 4.495349 CGAGAGGAATAAGTTTGCTGCATG 60.495 45.833 1.84 0.00 0.00 4.06
3279 4341 5.525378 CCACAAAGCATGATACTCTTACTCC 59.475 44.000 0.00 0.00 0.00 3.85
3280 4342 6.344500 CACAAAGCATGATACTCTTACTCCT 58.656 40.000 0.00 0.00 0.00 3.69
3281 4343 6.820656 CACAAAGCATGATACTCTTACTCCTT 59.179 38.462 0.00 0.00 0.00 3.36
3722 6389 4.295905 TCCTATTGGGTATCTGTTCCCT 57.704 45.455 0.00 0.00 43.74 4.20
3729 6397 2.291605 GGGTATCTGTTCCCTGCCTTTT 60.292 50.000 0.00 0.00 40.48 2.27
3778 6839 6.638096 TTCCATATCCATGTATTGCAAGTG 57.362 37.500 4.94 1.22 0.00 3.16
3840 6901 4.154015 TGCGGAACACATTTCATTACTGAG 59.846 41.667 0.00 0.00 31.68 3.35
3882 6943 2.663826 TTTTTGCCACCACTTGTCAC 57.336 45.000 0.00 0.00 0.00 3.67
3919 6980 6.697019 GTGCCATGTATGAATACCATTTGTTC 59.303 38.462 0.00 0.00 36.71 3.18
3926 6987 6.916360 ATGAATACCATTTGTTCCAAGTGT 57.084 33.333 0.00 0.00 29.34 3.55
4093 7158 1.882623 CTCCTGTTGCCTTCCTTCAAC 59.117 52.381 0.00 0.00 41.99 3.18
4116 7181 9.976511 CAACATATTCCAAGCAGATGAATTAAT 57.023 29.630 0.00 0.00 31.55 1.40
4118 7183 8.509690 ACATATTCCAAGCAGATGAATTAATCG 58.490 33.333 0.00 0.00 31.55 3.34
4134 7199 0.824109 ATCGGACAAGAGGATCGCAA 59.176 50.000 0.00 0.00 42.67 4.85
4138 7203 2.359900 GGACAAGAGGATCGCAATGTT 58.640 47.619 0.00 0.00 42.67 2.71
4139 7204 2.749621 GGACAAGAGGATCGCAATGTTT 59.250 45.455 0.00 0.00 42.67 2.83
4151 7217 6.038271 GGATCGCAATGTTTAGGACTACAAAT 59.962 38.462 0.00 0.00 0.00 2.32
4516 7585 2.837498 TGTATGAATGGTCGATGCTGG 58.163 47.619 0.00 0.00 0.00 4.85
4705 7775 5.703978 ATTCACATTGTCCGTCAATTGAA 57.296 34.783 10.35 18.01 43.33 2.69
4767 7837 5.048224 CACTTGCTCTTTGTTCATCAATCCT 60.048 40.000 0.00 0.00 35.84 3.24
4813 7886 2.549754 CCTTACACACTGCTTGTTCTGG 59.450 50.000 0.00 0.00 35.67 3.86
4860 7934 5.499004 TGCCTAGGATTACTCTTTGTGTT 57.501 39.130 14.75 0.00 0.00 3.32
4917 7998 5.817296 TCTCATGGAATTATCAACCTTCACG 59.183 40.000 0.00 0.00 0.00 4.35
5059 8140 8.559536 TCTCACCATAAAAATTCGCTTATCATC 58.440 33.333 0.00 0.00 0.00 2.92
5084 8165 5.639931 GGATAGTGACTCTTTCCTTGTTCAC 59.360 44.000 6.73 0.00 39.89 3.18
5139 8220 7.614124 AAGGAAAAGTAAACGTGTGAAGTAA 57.386 32.000 0.00 0.00 0.00 2.24
5149 8230 7.542534 AAACGTGTGAAGTAACAAAGATACA 57.457 32.000 0.00 0.00 0.00 2.29
5166 8410 2.930826 ACAAGGTGTTTCACGGATCT 57.069 45.000 0.00 0.00 34.83 2.75
5167 8411 2.767505 ACAAGGTGTTTCACGGATCTC 58.232 47.619 0.00 0.00 34.83 2.75
5175 8419 1.910580 TTCACGGATCTCCCCCAAGC 61.911 60.000 0.00 0.00 0.00 4.01
5190 8434 2.487762 CCCAAGCTTGCAATTAAGTCGA 59.512 45.455 21.43 0.00 0.00 4.20
5192 8436 3.155998 CAAGCTTGCAATTAAGTCGACG 58.844 45.455 14.65 0.00 0.00 5.12
5242 8486 2.734079 CACGTGCTTCCTCTTTCTCTTC 59.266 50.000 0.82 0.00 0.00 2.87
5247 8491 3.906846 TGCTTCCTCTTTCTCTTCCTCTT 59.093 43.478 0.00 0.00 0.00 2.85
5288 8532 3.738482 GTTGCACGCAACGAACATA 57.262 47.368 18.23 0.00 45.24 2.29
5289 8533 1.314581 GTTGCACGCAACGAACATAC 58.685 50.000 18.23 0.00 45.24 2.39
5290 8534 0.938008 TTGCACGCAACGAACATACA 59.062 45.000 0.00 0.00 0.00 2.29
5291 8535 0.233590 TGCACGCAACGAACATACAC 59.766 50.000 0.00 0.00 0.00 2.90
5292 8536 0.511221 GCACGCAACGAACATACACT 59.489 50.000 0.00 0.00 0.00 3.55
5293 8537 1.070175 GCACGCAACGAACATACACTT 60.070 47.619 0.00 0.00 0.00 3.16
5294 8538 2.156117 GCACGCAACGAACATACACTTA 59.844 45.455 0.00 0.00 0.00 2.24
5295 8539 3.363182 GCACGCAACGAACATACACTTAA 60.363 43.478 0.00 0.00 0.00 1.85
5296 8540 4.763874 CACGCAACGAACATACACTTAAA 58.236 39.130 0.00 0.00 0.00 1.52
5297 8541 4.838642 CACGCAACGAACATACACTTAAAG 59.161 41.667 0.00 0.00 0.00 1.85
5298 8542 3.838550 CGCAACGAACATACACTTAAAGC 59.161 43.478 0.00 0.00 0.00 3.51
5299 8543 3.838550 GCAACGAACATACACTTAAAGCG 59.161 43.478 0.00 0.00 0.00 4.68
5300 8544 4.391358 CAACGAACATACACTTAAAGCGG 58.609 43.478 0.00 0.00 0.00 5.52
5301 8545 2.997986 ACGAACATACACTTAAAGCGGG 59.002 45.455 0.00 0.00 0.00 6.13
5302 8546 2.222953 CGAACATACACTTAAAGCGGGC 60.223 50.000 0.00 0.00 0.00 6.13
5303 8547 2.781681 ACATACACTTAAAGCGGGCT 57.218 45.000 0.00 0.00 0.00 5.19
5304 8548 2.356135 ACATACACTTAAAGCGGGCTG 58.644 47.619 0.00 0.00 0.00 4.85
5305 8549 2.027561 ACATACACTTAAAGCGGGCTGA 60.028 45.455 0.00 0.00 0.00 4.26
5306 8550 2.088950 TACACTTAAAGCGGGCTGAC 57.911 50.000 0.00 0.00 0.00 3.51
5307 8551 0.107831 ACACTTAAAGCGGGCTGACA 59.892 50.000 0.00 0.00 0.00 3.58
5308 8552 1.271379 ACACTTAAAGCGGGCTGACAT 60.271 47.619 0.00 0.00 0.00 3.06
5309 8553 2.027561 ACACTTAAAGCGGGCTGACATA 60.028 45.455 0.00 0.00 0.00 2.29
5310 8554 3.006940 CACTTAAAGCGGGCTGACATAA 58.993 45.455 0.00 0.00 0.00 1.90
5311 8555 3.007635 ACTTAAAGCGGGCTGACATAAC 58.992 45.455 0.00 0.00 0.00 1.89
5312 8556 2.032680 TAAAGCGGGCTGACATAACC 57.967 50.000 0.00 0.00 0.00 2.85
5313 8557 0.037590 AAAGCGGGCTGACATAACCA 59.962 50.000 0.00 0.00 0.00 3.67
5314 8558 0.255890 AAGCGGGCTGACATAACCAT 59.744 50.000 0.00 0.00 0.00 3.55
5315 8559 0.179045 AGCGGGCTGACATAACCATC 60.179 55.000 0.00 0.00 0.00 3.51
5316 8560 0.463654 GCGGGCTGACATAACCATCA 60.464 55.000 0.00 0.00 0.00 3.07
5317 8561 1.815408 GCGGGCTGACATAACCATCAT 60.815 52.381 0.00 0.00 0.00 2.45
5318 8562 2.146342 CGGGCTGACATAACCATCATC 58.854 52.381 0.00 0.00 0.00 2.92
5319 8563 2.224378 CGGGCTGACATAACCATCATCT 60.224 50.000 0.00 0.00 0.00 2.90
5320 8564 3.406764 GGGCTGACATAACCATCATCTC 58.593 50.000 0.00 0.00 0.00 2.75
5321 8565 3.406764 GGCTGACATAACCATCATCTCC 58.593 50.000 0.00 0.00 0.00 3.71
5322 8566 3.072184 GGCTGACATAACCATCATCTCCT 59.928 47.826 0.00 0.00 0.00 3.69
5323 8567 4.314121 GCTGACATAACCATCATCTCCTC 58.686 47.826 0.00 0.00 0.00 3.71
5324 8568 4.040217 GCTGACATAACCATCATCTCCTCT 59.960 45.833 0.00 0.00 0.00 3.69
5325 8569 5.454471 GCTGACATAACCATCATCTCCTCTT 60.454 44.000 0.00 0.00 0.00 2.85
5326 8570 5.922053 TGACATAACCATCATCTCCTCTTG 58.078 41.667 0.00 0.00 0.00 3.02
5327 8571 5.426509 TGACATAACCATCATCTCCTCTTGT 59.573 40.000 0.00 0.00 0.00 3.16
5328 8572 6.070021 TGACATAACCATCATCTCCTCTTGTT 60.070 38.462 0.00 0.00 0.00 2.83
5329 8573 6.118170 ACATAACCATCATCTCCTCTTGTTG 58.882 40.000 0.00 0.00 0.00 3.33
5330 8574 4.916041 AACCATCATCTCCTCTTGTTGA 57.084 40.909 0.00 0.00 0.00 3.18
5331 8575 5.447778 AACCATCATCTCCTCTTGTTGAT 57.552 39.130 0.00 0.00 0.00 2.57
5332 8576 5.033589 ACCATCATCTCCTCTTGTTGATC 57.966 43.478 0.00 0.00 0.00 2.92
5333 8577 4.056740 CCATCATCTCCTCTTGTTGATCG 58.943 47.826 0.00 0.00 0.00 3.69
5334 8578 3.808466 TCATCTCCTCTTGTTGATCGG 57.192 47.619 0.00 0.00 0.00 4.18
5335 8579 2.432146 TCATCTCCTCTTGTTGATCGGG 59.568 50.000 0.00 0.00 0.00 5.14
5336 8580 2.231716 TCTCCTCTTGTTGATCGGGA 57.768 50.000 0.00 0.00 0.00 5.14
5337 8581 2.536066 TCTCCTCTTGTTGATCGGGAA 58.464 47.619 0.00 0.00 0.00 3.97
5338 8582 2.497675 TCTCCTCTTGTTGATCGGGAAG 59.502 50.000 0.00 0.00 0.00 3.46
5339 8583 2.497675 CTCCTCTTGTTGATCGGGAAGA 59.502 50.000 0.00 0.00 0.00 2.87
5340 8584 2.233922 TCCTCTTGTTGATCGGGAAGAC 59.766 50.000 0.00 0.00 0.00 3.01
5341 8585 2.234908 CCTCTTGTTGATCGGGAAGACT 59.765 50.000 0.00 0.00 0.00 3.24
5342 8586 3.307059 CCTCTTGTTGATCGGGAAGACTT 60.307 47.826 0.00 0.00 0.00 3.01
5343 8587 3.926616 TCTTGTTGATCGGGAAGACTTC 58.073 45.455 6.66 6.66 0.00 3.01
5363 8607 4.252971 TCCACGAGGAACTTAGTTTCTG 57.747 45.455 11.10 6.04 42.23 3.02
5364 8608 2.737252 CCACGAGGAACTTAGTTTCTGC 59.263 50.000 11.10 2.18 41.55 4.26
5365 8609 3.390135 CACGAGGAACTTAGTTTCTGCA 58.610 45.455 11.10 0.00 41.55 4.41
5366 8610 3.997021 CACGAGGAACTTAGTTTCTGCAT 59.003 43.478 11.10 0.00 41.55 3.96
5367 8611 5.168569 CACGAGGAACTTAGTTTCTGCATA 58.831 41.667 11.10 0.00 41.55 3.14
5368 8612 5.062308 CACGAGGAACTTAGTTTCTGCATAC 59.938 44.000 11.10 0.00 41.55 2.39
5369 8613 5.168569 CGAGGAACTTAGTTTCTGCATACA 58.831 41.667 11.10 0.00 41.55 2.29
5370 8614 5.637810 CGAGGAACTTAGTTTCTGCATACAA 59.362 40.000 11.10 0.00 41.55 2.41
5371 8615 6.401153 CGAGGAACTTAGTTTCTGCATACAAC 60.401 42.308 11.10 0.00 41.55 3.32
5372 8616 6.534634 AGGAACTTAGTTTCTGCATACAACT 58.465 36.000 4.91 9.52 29.06 3.16
5373 8617 6.998673 AGGAACTTAGTTTCTGCATACAACTT 59.001 34.615 4.91 0.00 29.06 2.66
5374 8618 8.154856 AGGAACTTAGTTTCTGCATACAACTTA 58.845 33.333 4.91 2.26 29.06 2.24
5375 8619 8.780249 GGAACTTAGTTTCTGCATACAACTTAA 58.220 33.333 9.79 3.96 32.88 1.85
5381 8625 8.335532 AGTTTCTGCATACAACTTAATTAGCA 57.664 30.769 0.00 0.00 0.00 3.49
5382 8626 8.454106 AGTTTCTGCATACAACTTAATTAGCAG 58.546 33.333 11.03 11.03 46.94 4.24
5383 8627 7.921786 TTCTGCATACAACTTAATTAGCAGT 57.078 32.000 14.86 2.39 46.01 4.40
5384 8628 7.921786 TCTGCATACAACTTAATTAGCAGTT 57.078 32.000 14.86 7.55 46.01 3.16
5393 8637 8.832487 CAACTTAATTAGCAGTTGCATCTAAG 57.168 34.615 14.18 9.43 42.52 2.18
5394 8638 8.668353 CAACTTAATTAGCAGTTGCATCTAAGA 58.332 33.333 14.18 0.00 42.52 2.10
5395 8639 8.430801 ACTTAATTAGCAGTTGCATCTAAGAG 57.569 34.615 6.90 0.00 45.16 2.85
5396 8640 7.497249 ACTTAATTAGCAGTTGCATCTAAGAGG 59.503 37.037 6.90 0.00 45.16 3.69
5397 8641 4.826274 TTAGCAGTTGCATCTAAGAGGT 57.174 40.909 6.90 0.00 45.16 3.85
5398 8642 2.983229 AGCAGTTGCATCTAAGAGGTG 58.017 47.619 6.90 0.00 45.16 4.00
5399 8643 2.304180 AGCAGTTGCATCTAAGAGGTGT 59.696 45.455 6.90 0.00 45.16 4.16
5400 8644 3.077359 GCAGTTGCATCTAAGAGGTGTT 58.923 45.455 0.00 0.00 41.59 3.32
5401 8645 3.126000 GCAGTTGCATCTAAGAGGTGTTC 59.874 47.826 0.00 0.00 41.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.395311 TTCCATCGCCTAGTCTCCGT 60.395 55.000 0.00 0.00 0.00 4.69
36 37 5.221126 GCAATTCTTCTTATTTCCATCGCCT 60.221 40.000 0.00 0.00 0.00 5.52
75 76 2.357034 AGCAACTACGGCCACACG 60.357 61.111 2.24 0.00 40.31 4.49
136 137 1.349627 CACATCGCAACATCTCGCC 59.650 57.895 0.00 0.00 0.00 5.54
141 142 7.464830 AATAGTACTTACACATCGCAACATC 57.535 36.000 0.00 0.00 0.00 3.06
179 180 6.548441 GCACACGGCCATATAAATTACTTA 57.452 37.500 2.24 0.00 36.11 2.24
328 329 2.103432 TGTAACACTTCACATGGTCCGT 59.897 45.455 0.00 0.00 0.00 4.69
412 413 8.774890 ATCTTTCATCCATGAATAGAGATTCG 57.225 34.615 2.83 0.00 45.30 3.34
443 444 5.790593 AGAACATAGGCTTACAACGAGAAA 58.209 37.500 0.00 0.00 0.00 2.52
490 491 2.748058 ATCCAGGAAAACCGCACGCT 62.748 55.000 0.00 0.00 0.00 5.07
491 492 1.862602 AATCCAGGAAAACCGCACGC 61.863 55.000 0.00 0.00 0.00 5.34
559 560 9.672673 ATGCTCCTATATACAGCGAATTTAAAT 57.327 29.630 0.00 0.00 35.81 1.40
563 564 7.986085 AAATGCTCCTATATACAGCGAATTT 57.014 32.000 0.00 4.18 35.81 1.82
642 647 6.943899 AAGCCCAAATTTGTAGGGAAAATA 57.056 33.333 16.73 0.00 45.80 1.40
648 653 4.617298 CGTTGTAAGCCCAAATTTGTAGGG 60.617 45.833 16.73 11.97 45.68 3.53
689 695 8.613060 TTTGCAAAATATGATTAAACTGGCAA 57.387 26.923 10.02 0.00 34.93 4.52
719 727 4.455606 GCCAATAGGTGCTGATTACTCTT 58.544 43.478 0.00 0.00 37.19 2.85
747 755 5.352569 CCATTAGAGAAACTGCCACAAGTAG 59.647 44.000 0.00 0.00 0.00 2.57
810 820 6.238925 GGCAATATAACATGTAAACTGGGTCC 60.239 42.308 0.00 0.00 0.00 4.46
914 924 1.564622 CTGCGTCGGAGTGTTGTTG 59.435 57.895 5.47 0.00 0.00 3.33
915 925 2.244651 GCTGCGTCGGAGTGTTGTT 61.245 57.895 15.54 0.00 0.00 2.83
916 926 2.661866 GCTGCGTCGGAGTGTTGT 60.662 61.111 15.54 0.00 0.00 3.32
944 954 3.234386 GCCTTTTTCTCGGAATTGTTCG 58.766 45.455 0.00 0.00 0.00 3.95
952 962 0.591170 CGCTTTGCCTTTTTCTCGGA 59.409 50.000 0.00 0.00 0.00 4.55
1410 1421 0.680601 TCGGATGTGGCTGGTACGTA 60.681 55.000 0.00 0.00 0.00 3.57
1427 1438 4.303086 ACGACTAATATTCCACCACTCG 57.697 45.455 0.00 0.00 0.00 4.18
1428 1439 6.630444 TCTACGACTAATATTCCACCACTC 57.370 41.667 0.00 0.00 0.00 3.51
1430 1441 8.142551 AGAAATCTACGACTAATATTCCACCAC 58.857 37.037 0.00 0.00 0.00 4.16
1431 1442 8.246430 AGAAATCTACGACTAATATTCCACCA 57.754 34.615 0.00 0.00 0.00 4.17
1507 1524 2.427410 GCAAGCAGGCAACGTTCG 60.427 61.111 0.00 0.00 46.39 3.95
1526 1543 8.623903 TCATTGCAATTATACAGTTCATCTTCC 58.376 33.333 9.83 0.00 0.00 3.46
1566 1583 5.772672 TGAGTTTTGGGCACATACTTGTTAT 59.227 36.000 5.79 0.00 32.34 1.89
1602 1657 2.835764 AGATAGTAAACGACCTGCCCAA 59.164 45.455 0.00 0.00 0.00 4.12
1603 1658 2.463752 AGATAGTAAACGACCTGCCCA 58.536 47.619 0.00 0.00 0.00 5.36
1604 1659 3.195661 CAAGATAGTAAACGACCTGCCC 58.804 50.000 0.00 0.00 0.00 5.36
1605 1660 3.118884 TCCAAGATAGTAAACGACCTGCC 60.119 47.826 0.00 0.00 0.00 4.85
1747 1815 1.338105 TGATCAAGAGTTCCGTGCCAG 60.338 52.381 0.00 0.00 0.00 4.85
1895 1963 6.403527 GCAGCACAAACATGATAGAATACACA 60.404 38.462 0.00 0.00 0.00 3.72
1907 1975 3.560481 TGAAAAATGGCAGCACAAACATG 59.440 39.130 0.00 0.00 0.00 3.21
2080 2148 6.292328 GCAAACAGTAAAAAGAATGGTTCAGC 60.292 38.462 0.00 0.00 0.00 4.26
2122 2190 2.205074 CAGGACGCTGCTAATGTAAGG 58.795 52.381 0.00 0.00 0.00 2.69
2468 2542 6.582295 GCACAACACTAAAACATGGTAAGATG 59.418 38.462 0.00 0.00 0.00 2.90
2507 3532 6.691754 TCAAGCACAGATTTTCACAACTAA 57.308 33.333 0.00 0.00 0.00 2.24
2519 3544 2.038164 TCACTGAAGCTCAAGCACAGAT 59.962 45.455 24.81 13.08 44.21 2.90
2525 3550 2.160822 TGAGTCACTGAAGCTCAAGC 57.839 50.000 0.00 0.00 36.46 4.01
2542 3567 4.898320 TCTGAAAGCAGCTTACAGAATGA 58.102 39.130 8.45 0.00 42.01 2.57
2603 3650 3.563808 GGCATGTGAGTGAAAGTGTTGTA 59.436 43.478 0.00 0.00 0.00 2.41
2610 3657 2.163010 GGACATGGCATGTGAGTGAAAG 59.837 50.000 35.82 5.19 45.03 2.62
2724 3786 9.494271 GATAATATATCCAGAGAAAGTGCACAA 57.506 33.333 21.04 0.00 0.00 3.33
2726 3788 8.930760 GTGATAATATATCCAGAGAAAGTGCAC 58.069 37.037 9.40 9.40 0.00 4.57
2951 4013 3.072944 ACAGAAGCAAAGAGATCTGCAC 58.927 45.455 0.00 0.00 42.34 4.57
3722 6389 0.179084 CGATCCTAGCGGAAAAGGCA 60.179 55.000 0.00 0.00 44.02 4.75
3751 6419 9.365906 ACTTGCAATACATGGATATGGAAAATA 57.634 29.630 0.00 0.00 38.66 1.40
3778 6839 5.470437 GGTGGGAGAAGTTATAAGCAATAGC 59.530 44.000 0.00 0.00 42.56 2.97
3840 6901 6.603940 AATTATCCTGTAGCCTCTGAGATC 57.396 41.667 6.17 0.00 0.00 2.75
3876 6937 2.837498 CACTCCATGTGTCAGTGACAA 58.163 47.619 27.03 17.08 44.49 3.18
4063 7128 5.397142 AAGGCAACAGGAGAAAAATGATC 57.603 39.130 0.00 0.00 41.41 2.92
4093 7158 7.966753 CCGATTAATTCATCTGCTTGGAATATG 59.033 37.037 0.00 0.00 31.40 1.78
4116 7181 0.824109 ATTGCGATCCTCTTGTCCGA 59.176 50.000 0.00 0.00 0.00 4.55
4118 7183 2.029838 ACATTGCGATCCTCTTGTCC 57.970 50.000 0.00 0.00 0.00 4.02
4516 7585 6.633500 TGTATGCATAGGCTTGATAAAACC 57.367 37.500 6.67 0.00 41.91 3.27
4653 7723 7.964604 ACAACTGTCCTAGAACTGAAATAAC 57.035 36.000 0.00 0.00 0.00 1.89
4813 7886 7.042797 TGAGCCTAGCCAAAAATTATTCATC 57.957 36.000 0.00 0.00 0.00 2.92
4917 7998 5.119279 CCACATCGCTAGTATCAATTGCTAC 59.881 44.000 10.77 10.77 0.00 3.58
5038 8119 6.898041 TCCGATGATAAGCGAATTTTTATGG 58.102 36.000 0.00 0.00 0.00 2.74
5048 8129 4.072839 AGTCACTATCCGATGATAAGCGA 58.927 43.478 0.00 0.00 33.13 4.93
5059 8140 4.457834 ACAAGGAAAGAGTCACTATCCG 57.542 45.455 0.00 0.00 35.31 4.18
5084 8165 5.248640 TGAATTAGAGTTCTTGGCTCCTTG 58.751 41.667 0.00 0.00 33.69 3.61
5139 8220 4.274950 CCGTGAAACACCTTGTATCTTTGT 59.725 41.667 0.00 0.00 35.74 2.83
5149 8230 1.003233 GGGAGATCCGTGAAACACCTT 59.997 52.381 0.00 0.00 35.74 3.50
5166 8410 2.178580 CTTAATTGCAAGCTTGGGGGA 58.821 47.619 27.10 0.00 0.00 4.81
5167 8411 1.901833 ACTTAATTGCAAGCTTGGGGG 59.098 47.619 27.10 2.64 0.00 5.40
5175 8419 1.396996 CCCCGTCGACTTAATTGCAAG 59.603 52.381 14.70 0.00 0.00 4.01
5190 8434 2.789323 ATTAGGTATCAGGTCCCCGT 57.211 50.000 0.00 0.00 0.00 5.28
5192 8436 5.648330 AGAAAATTAGGTATCAGGTCCCC 57.352 43.478 0.00 0.00 0.00 4.81
5200 8444 6.535508 ACGTGCTCTGAAGAAAATTAGGTATC 59.464 38.462 0.00 0.00 0.00 2.24
5242 8486 4.450053 CAAGGATGAGAAGCCTAAAGAGG 58.550 47.826 0.00 0.00 46.93 3.69
5247 8491 2.505819 GGACCAAGGATGAGAAGCCTAA 59.494 50.000 0.00 0.00 33.20 2.69
5288 8532 0.107831 TGTCAGCCCGCTTTAAGTGT 59.892 50.000 4.77 0.00 0.00 3.55
5289 8533 1.453155 ATGTCAGCCCGCTTTAAGTG 58.547 50.000 0.00 0.00 0.00 3.16
5290 8534 3.007635 GTTATGTCAGCCCGCTTTAAGT 58.992 45.455 0.00 0.00 0.00 2.24
5291 8535 2.354821 GGTTATGTCAGCCCGCTTTAAG 59.645 50.000 0.00 0.00 0.00 1.85
5292 8536 2.290387 TGGTTATGTCAGCCCGCTTTAA 60.290 45.455 0.00 0.00 0.00 1.52
5293 8537 1.279558 TGGTTATGTCAGCCCGCTTTA 59.720 47.619 0.00 0.00 0.00 1.85
5294 8538 0.037590 TGGTTATGTCAGCCCGCTTT 59.962 50.000 0.00 0.00 0.00 3.51
5295 8539 0.255890 ATGGTTATGTCAGCCCGCTT 59.744 50.000 0.00 0.00 0.00 4.68
5296 8540 0.179045 GATGGTTATGTCAGCCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
5297 8541 0.463654 TGATGGTTATGTCAGCCCGC 60.464 55.000 0.00 0.00 0.00 6.13
5298 8542 2.146342 GATGATGGTTATGTCAGCCCG 58.854 52.381 0.00 0.00 0.00 6.13
5299 8543 3.406764 GAGATGATGGTTATGTCAGCCC 58.593 50.000 0.00 0.00 31.42 5.19
5300 8544 3.072184 AGGAGATGATGGTTATGTCAGCC 59.928 47.826 0.00 0.00 31.42 4.85
5301 8545 4.040217 AGAGGAGATGATGGTTATGTCAGC 59.960 45.833 0.00 0.00 0.00 4.26
5302 8546 5.804944 AGAGGAGATGATGGTTATGTCAG 57.195 43.478 0.00 0.00 0.00 3.51
5303 8547 5.426509 ACAAGAGGAGATGATGGTTATGTCA 59.573 40.000 0.00 0.00 0.00 3.58
5304 8548 5.923204 ACAAGAGGAGATGATGGTTATGTC 58.077 41.667 0.00 0.00 0.00 3.06
5305 8549 5.965033 ACAAGAGGAGATGATGGTTATGT 57.035 39.130 0.00 0.00 0.00 2.29
5306 8550 6.351711 TCAACAAGAGGAGATGATGGTTATG 58.648 40.000 0.00 0.00 0.00 1.90
5307 8551 6.566079 TCAACAAGAGGAGATGATGGTTAT 57.434 37.500 0.00 0.00 0.00 1.89
5308 8552 6.566079 ATCAACAAGAGGAGATGATGGTTA 57.434 37.500 0.00 0.00 30.00 2.85
5309 8553 4.916041 TCAACAAGAGGAGATGATGGTT 57.084 40.909 0.00 0.00 0.00 3.67
5310 8554 4.442612 CGATCAACAAGAGGAGATGATGGT 60.443 45.833 0.00 0.00 31.24 3.55
5311 8555 4.056740 CGATCAACAAGAGGAGATGATGG 58.943 47.826 0.00 0.00 31.24 3.51
5312 8556 4.056740 CCGATCAACAAGAGGAGATGATG 58.943 47.826 0.00 0.00 31.24 3.07
5313 8557 3.070734 CCCGATCAACAAGAGGAGATGAT 59.929 47.826 0.00 0.00 33.64 2.45
5314 8558 2.432146 CCCGATCAACAAGAGGAGATGA 59.568 50.000 0.00 0.00 0.00 2.92
5315 8559 2.432146 TCCCGATCAACAAGAGGAGATG 59.568 50.000 0.00 0.00 0.00 2.90
5316 8560 2.752030 TCCCGATCAACAAGAGGAGAT 58.248 47.619 0.00 0.00 0.00 2.75
5317 8561 2.231716 TCCCGATCAACAAGAGGAGA 57.768 50.000 0.00 0.00 0.00 3.71
5318 8562 2.497675 TCTTCCCGATCAACAAGAGGAG 59.502 50.000 0.00 0.00 0.00 3.69
5319 8563 2.233922 GTCTTCCCGATCAACAAGAGGA 59.766 50.000 0.00 0.00 0.00 3.71
5320 8564 2.234908 AGTCTTCCCGATCAACAAGAGG 59.765 50.000 0.00 0.00 0.00 3.69
5321 8565 3.601443 AGTCTTCCCGATCAACAAGAG 57.399 47.619 0.00 0.00 0.00 2.85
5322 8566 3.306780 GGAAGTCTTCCCGATCAACAAGA 60.307 47.826 19.59 0.00 44.30 3.02
5323 8567 3.003480 GGAAGTCTTCCCGATCAACAAG 58.997 50.000 19.59 0.00 44.30 3.16
5324 8568 3.053831 GGAAGTCTTCCCGATCAACAA 57.946 47.619 19.59 0.00 44.30 2.83
5325 8569 2.762535 GGAAGTCTTCCCGATCAACA 57.237 50.000 19.59 0.00 44.30 3.33
5342 8586 3.554337 GCAGAAACTAAGTTCCTCGTGGA 60.554 47.826 1.10 1.10 41.36 4.02
5343 8587 2.737252 GCAGAAACTAAGTTCCTCGTGG 59.263 50.000 0.00 0.00 0.00 4.94
5344 8588 3.390135 TGCAGAAACTAAGTTCCTCGTG 58.610 45.455 0.00 0.00 0.00 4.35
5345 8589 3.746045 TGCAGAAACTAAGTTCCTCGT 57.254 42.857 0.00 0.00 0.00 4.18
5346 8590 5.168569 TGTATGCAGAAACTAAGTTCCTCG 58.831 41.667 0.00 0.00 0.00 4.63
5347 8591 6.651225 AGTTGTATGCAGAAACTAAGTTCCTC 59.349 38.462 9.11 0.00 32.48 3.71
5348 8592 6.534634 AGTTGTATGCAGAAACTAAGTTCCT 58.465 36.000 9.11 0.00 32.48 3.36
5349 8593 6.803154 AGTTGTATGCAGAAACTAAGTTCC 57.197 37.500 9.11 0.00 32.48 3.62
5355 8599 9.443323 TGCTAATTAAGTTGTATGCAGAAACTA 57.557 29.630 10.76 0.00 33.09 2.24
5356 8600 8.335532 TGCTAATTAAGTTGTATGCAGAAACT 57.664 30.769 5.81 5.81 35.70 2.66
5357 8601 8.237267 ACTGCTAATTAAGTTGTATGCAGAAAC 58.763 33.333 19.84 0.00 46.40 2.78
5358 8602 8.335532 ACTGCTAATTAAGTTGTATGCAGAAA 57.664 30.769 19.84 0.00 46.40 2.52
5359 8603 7.921786 ACTGCTAATTAAGTTGTATGCAGAA 57.078 32.000 19.84 0.00 46.40 3.02
5360 8604 7.751732 CAACTGCTAATTAAGTTGTATGCAGA 58.248 34.615 19.84 0.00 46.40 4.26
5361 8605 7.959718 CAACTGCTAATTAAGTTGTATGCAG 57.040 36.000 16.81 15.53 45.30 4.41
5369 8613 8.792830 TCTTAGATGCAACTGCTAATTAAGTT 57.207 30.769 6.76 0.00 42.66 2.66
5370 8614 7.497249 CCTCTTAGATGCAACTGCTAATTAAGT 59.503 37.037 6.76 0.00 42.66 2.24
5371 8615 7.497249 ACCTCTTAGATGCAACTGCTAATTAAG 59.503 37.037 6.76 0.65 42.66 1.85
5372 8616 7.280876 CACCTCTTAGATGCAACTGCTAATTAA 59.719 37.037 6.76 0.00 42.66 1.40
5373 8617 6.763135 CACCTCTTAGATGCAACTGCTAATTA 59.237 38.462 6.76 0.00 42.66 1.40
5374 8618 5.587844 CACCTCTTAGATGCAACTGCTAATT 59.412 40.000 6.76 0.00 42.66 1.40
5375 8619 5.121811 CACCTCTTAGATGCAACTGCTAAT 58.878 41.667 6.76 0.00 42.66 1.73
5376 8620 4.020218 ACACCTCTTAGATGCAACTGCTAA 60.020 41.667 6.76 4.44 42.66 3.09
5377 8621 3.515502 ACACCTCTTAGATGCAACTGCTA 59.484 43.478 6.76 0.00 42.66 3.49
5378 8622 2.304180 ACACCTCTTAGATGCAACTGCT 59.696 45.455 6.76 0.00 42.66 4.24
5379 8623 2.704572 ACACCTCTTAGATGCAACTGC 58.295 47.619 6.76 0.00 42.50 4.40
5380 8624 4.935885 GAACACCTCTTAGATGCAACTG 57.064 45.455 6.76 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.