Multiple sequence alignment - TraesCS3A01G170800

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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 TraesCS3A01G170800 chr3A 100.000 4612 0 0 1 4612 179538680 179534069 0.000000e+00 8517.0
1 TraesCS3A01G170800 chr3A 85.577 104 11 3 4374 4475 387293106 387293005 6.310000e-19 106.0
2 TraesCS3A01G170800 chr3B 92.745 3432 136 47 1 3372 222244843 222248221 0.000000e+00 4854.0
3 TraesCS3A01G170800 chr3B 93.276 937 46 6 3372 4293 222248248 222249182 0.000000e+00 1365.0
4 TraesCS3A01G170800 chr3B 90.244 246 16 2 4363 4605 803062443 803062203 9.630000e-82 315.0
5 TraesCS3A01G170800 chr3B 82.192 219 21 9 4379 4594 86069547 86069750 6.130000e-39 172.0
6 TraesCS3A01G170800 chr3D 88.391 2300 166 59 1 2267 151436844 151439075 0.000000e+00 2675.0
7 TraesCS3A01G170800 chr3D 92.649 1850 82 18 2297 4095 151439075 151440921 0.000000e+00 2614.0
8 TraesCS3A01G170800 chr3D 95.902 122 5 0 4086 4207 151440944 151441065 1.010000e-46 198.0
9 TraesCS3A01G170800 chr3D 97.059 68 2 0 4249 4316 151441394 151441461 1.050000e-21 115.0
10 TraesCS3A01G170800 chr3D 94.366 71 4 0 4193 4263 151441085 151441155 4.880000e-20 110.0
11 TraesCS3A01G170800 chr3D 97.368 38 1 0 1299 1336 429303004 429303041 1.070000e-06 65.8
12 TraesCS3A01G170800 chr1B 85.039 762 61 23 1506 2243 602238771 602239503 0.000000e+00 726.0
13 TraesCS3A01G170800 chr1B 82.838 437 42 12 1506 1933 66928310 66928722 1.220000e-95 361.0
14 TraesCS3A01G170800 chr1B 97.368 38 1 0 1299 1336 327570802 327570839 1.070000e-06 65.8
15 TraesCS3A01G170800 chr6B 81.681 464 74 11 1017 1476 434184514 434184970 4.360000e-100 375.0
16 TraesCS3A01G170800 chr6A 81.545 466 71 14 1017 1476 389758286 389758742 2.030000e-98 370.0
17 TraesCS3A01G170800 chr5B 91.935 248 17 1 4363 4607 594140045 594139798 1.230000e-90 344.0
18 TraesCS3A01G170800 chr2A 81.963 438 45 13 1506 1933 719360142 719360555 1.590000e-89 340.0
19 TraesCS3A01G170800 chr2A 85.124 242 22 6 4368 4604 717937943 717938175 7.710000e-58 235.0
20 TraesCS3A01G170800 chrUn 90.795 239 14 2 4372 4607 444040671 444040438 3.460000e-81 313.0
21 TraesCS3A01G170800 chr1D 89.558 249 17 3 4363 4607 487280320 487280077 1.610000e-79 307.0
22 TraesCS3A01G170800 chr6D 88.077 260 20 5 4358 4612 24320639 24320892 9.700000e-77 298.0
23 TraesCS3A01G170800 chr1A 87.550 249 22 3 4363 4607 534169289 534169532 3.510000e-71 279.0
24 TraesCS3A01G170800 chr5A 85.542 249 23 6 4363 4607 436617137 436616898 9.910000e-62 248.0
25 TraesCS3A01G170800 chr7A 86.364 198 15 4 1563 1760 165443491 165443306 6.050000e-49 206.0
26 TraesCS3A01G170800 chr7A 76.871 294 30 19 1762 2036 165391371 165391097 1.040000e-26 132.0
27 TraesCS3A01G170800 chr7D 97.368 38 1 0 1299 1336 619809261 619809298 1.070000e-06 65.8


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 TraesCS3A01G170800 chr3A 179534069 179538680 4611 True 8517.0 8517 100.0000 1 4612 1 chr3A.!!$R1 4611
1 TraesCS3A01G170800 chr3B 222244843 222249182 4339 False 3109.5 4854 93.0105 1 4293 2 chr3B.!!$F2 4292
2 TraesCS3A01G170800 chr3D 151436844 151441461 4617 False 1142.4 2675 93.6734 1 4316 5 chr3D.!!$F2 4315
3 TraesCS3A01G170800 chr1B 602238771 602239503 732 False 726.0 726 85.0390 1506 2243 1 chr1B.!!$F3 737

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
490 515 0.179045 AGACTTTGTCTTGCGTGCCT 60.179 50.0 0.0 0.0 40.28 4.75 F
491 516 0.235926 GACTTTGTCTTGCGTGCCTC 59.764 55.0 0.0 0.0 0.00 4.70 F
606 631 0.326238 TGGGGTTCCTCCGAGCTTAT 60.326 55.0 0.0 0.0 37.00 1.73 F
608 633 0.533085 GGGTTCCTCCGAGCTTATGC 60.533 60.0 0.0 0.0 37.00 3.14 F
936 1015 0.680618 CATGGCAAATGGGTGTGTGT 59.319 50.0 0.0 0.0 0.00 3.72 F
2015 2126 0.964860 TGGACATTCAACATGCCCGG 60.965 55.0 0.0 0.0 0.00 5.73 F
3261 3392 0.107800 CGTCTCCTCGGTGGACTCTA 60.108 60.0 0.0 0.0 40.56 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1639 0.457853 TCTCGCGCCTGAACATGTAC 60.458 55.000 0.00 0.00 0.00 2.90 R
2288 2414 0.605589 AAACACTAGCTTCCCACGGC 60.606 55.000 0.00 0.00 0.00 5.68 R
2501 2632 1.073548 GGCTTCCACCACCGGTAAA 59.926 57.895 6.87 0.00 32.11 2.01 R
2513 2644 2.514824 GCGGTCATCAGGGCTTCC 60.515 66.667 0.00 0.00 0.00 3.46 R
2832 2963 0.037326 TGCGGCTGTTTCCTCAGTAG 60.037 55.000 0.00 0.00 37.70 2.57 R
3387 3545 0.253327 GAAGACCAGGAGGCCGAAAT 59.747 55.000 0.00 0.00 39.06 2.17 R
4247 4492 1.108776 CCTGAAATGCATCCCACCAG 58.891 55.000 0.00 3.44 0.00 4.00 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
33 34 2.444351 GAGATTTGCCTTCGAATTGCG 58.556 47.619 13.20 0.00 42.69 4.85
159 160 0.179234 TGCACACTTCTGGAAACCGA 59.821 50.000 0.00 0.00 0.00 4.69
291 294 4.564769 GCTTCACAGGATAGAAAACTCTCG 59.435 45.833 0.00 0.00 0.00 4.04
314 317 1.076332 CAGCGGCAACAGTAGGTAAC 58.924 55.000 1.45 0.00 0.00 2.50
376 383 7.642194 TCAAACAGTAGTTAATCTTTTGTTGCG 59.358 33.333 0.00 0.00 36.84 4.85
429 436 6.644592 TCTTGCCGTAAATCCATTTTTCTTTG 59.355 34.615 0.00 0.00 0.00 2.77
430 437 5.848406 TGCCGTAAATCCATTTTTCTTTGT 58.152 33.333 0.00 0.00 0.00 2.83
490 515 0.179045 AGACTTTGTCTTGCGTGCCT 60.179 50.000 0.00 0.00 40.28 4.75
491 516 0.235926 GACTTTGTCTTGCGTGCCTC 59.764 55.000 0.00 0.00 0.00 4.70
545 570 4.047125 CACATGGCCCCTCCCGTT 62.047 66.667 0.00 0.00 0.00 4.44
576 601 1.216710 CTTGACGACCTGCCTCTCC 59.783 63.158 0.00 0.00 0.00 3.71
583 608 2.045536 CCTGCCTCTCCCTTGTGC 60.046 66.667 0.00 0.00 0.00 4.57
590 615 0.607489 CTCTCCCTTGTGCTTGTGGG 60.607 60.000 0.00 0.00 40.95 4.61
591 616 1.604593 CTCCCTTGTGCTTGTGGGG 60.605 63.158 0.00 0.00 40.05 4.96
594 619 1.463553 CCCTTGTGCTTGTGGGGTTC 61.464 60.000 0.00 0.00 36.15 3.62
595 620 1.463553 CCTTGTGCTTGTGGGGTTCC 61.464 60.000 0.00 0.00 0.00 3.62
596 621 0.468029 CTTGTGCTTGTGGGGTTCCT 60.468 55.000 0.00 0.00 0.00 3.36
597 622 0.467290 TTGTGCTTGTGGGGTTCCTC 60.467 55.000 0.00 0.00 0.00 3.71
598 623 1.603739 GTGCTTGTGGGGTTCCTCC 60.604 63.158 0.00 0.00 0.00 4.30
599 624 2.359975 GCTTGTGGGGTTCCTCCG 60.360 66.667 0.00 0.00 37.00 4.63
600 625 2.890766 GCTTGTGGGGTTCCTCCGA 61.891 63.158 0.00 0.00 37.00 4.55
601 626 1.296715 CTTGTGGGGTTCCTCCGAG 59.703 63.158 0.00 0.00 37.00 4.63
603 628 3.003763 GTGGGGTTCCTCCGAGCT 61.004 66.667 0.00 0.00 37.00 4.09
604 629 2.203938 TGGGGTTCCTCCGAGCTT 60.204 61.111 0.00 0.00 37.00 3.74
605 630 1.079621 TGGGGTTCCTCCGAGCTTA 59.920 57.895 0.00 0.00 37.00 3.09
606 631 0.326238 TGGGGTTCCTCCGAGCTTAT 60.326 55.000 0.00 0.00 37.00 1.73
608 633 0.533085 GGGTTCCTCCGAGCTTATGC 60.533 60.000 0.00 0.00 37.00 3.14
609 634 0.876342 GGTTCCTCCGAGCTTATGCG 60.876 60.000 0.00 0.00 45.42 4.73
610 635 1.227263 TTCCTCCGAGCTTATGCGC 60.227 57.895 0.00 0.00 45.42 6.09
611 636 1.676678 TTCCTCCGAGCTTATGCGCT 61.677 55.000 9.73 0.00 45.42 5.92
612 637 1.227380 CCTCCGAGCTTATGCGCTT 60.227 57.895 9.73 4.59 45.42 4.68
615 640 2.053638 CGAGCTTATGCGCTTGCG 60.054 61.111 9.73 10.90 45.42 4.85
616 641 2.351661 GAGCTTATGCGCTTGCGC 60.352 61.111 29.59 29.59 45.42 6.09
617 642 2.817423 GAGCTTATGCGCTTGCGCT 61.817 57.895 33.96 23.38 45.42 5.92
618 643 2.100991 GCTTATGCGCTTGCGCTT 59.899 55.556 33.96 29.96 43.34 4.68
619 644 2.219562 GCTTATGCGCTTGCGCTTG 61.220 57.895 33.96 22.73 43.34 4.01
620 645 1.584483 CTTATGCGCTTGCGCTTGG 60.584 57.895 33.96 22.05 43.34 3.61
621 646 2.257286 CTTATGCGCTTGCGCTTGGT 62.257 55.000 33.96 21.45 43.34 3.67
623 648 2.526091 TATGCGCTTGCGCTTGGTTG 62.526 55.000 33.96 0.00 43.34 3.77
625 650 3.964875 CGCTTGCGCTTGGTTGGT 61.965 61.111 9.73 0.00 0.00 3.67
626 651 2.050077 GCTTGCGCTTGGTTGGTC 60.050 61.111 9.73 0.00 0.00 4.02
627 652 2.644992 CTTGCGCTTGGTTGGTCC 59.355 61.111 9.73 0.00 0.00 4.46
646 696 1.146485 CATGGAGCCTCTGCCTCTG 59.854 63.158 0.00 0.00 38.69 3.35
656 706 2.184323 CTGCCTCTGTCTCGCAGTA 58.816 57.895 0.00 0.00 43.98 2.74
842 904 3.360340 GAAGCTGCCGCAACTGCT 61.360 61.111 2.05 0.00 45.52 4.24
932 1011 1.714541 TGTTCATGGCAAATGGGTGT 58.285 45.000 0.00 0.00 0.00 4.16
934 1013 1.344114 GTTCATGGCAAATGGGTGTGT 59.656 47.619 0.00 0.00 0.00 3.72
935 1014 0.967662 TCATGGCAAATGGGTGTGTG 59.032 50.000 0.00 0.00 0.00 3.82
936 1015 0.680618 CATGGCAAATGGGTGTGTGT 59.319 50.000 0.00 0.00 0.00 3.72
958 1037 1.001633 TGGGTTAGCTCAACTTCGTCC 59.998 52.381 0.00 0.00 37.30 4.79
983 1062 1.065998 TGCAGGTGGATTAACCGGTAC 60.066 52.381 8.00 0.00 45.53 3.34
1491 1570 3.414700 CTCAACGCGGTGCTGTCC 61.415 66.667 21.87 0.00 0.00 4.02
1517 1602 4.332543 AGAAGACGGGGCTGGGGA 62.333 66.667 0.00 0.00 0.00 4.81
1518 1603 3.090532 GAAGACGGGGCTGGGGAT 61.091 66.667 0.00 0.00 0.00 3.85
1519 1604 2.614013 AAGACGGGGCTGGGGATT 60.614 61.111 0.00 0.00 0.00 3.01
1520 1605 2.610532 GAAGACGGGGCTGGGGATTC 62.611 65.000 0.00 0.00 0.00 2.52
1521 1606 4.547367 GACGGGGCTGGGGATTCG 62.547 72.222 0.00 0.00 0.00 3.34
1530 1615 2.403132 CTGGGGATTCGGGAGATGCC 62.403 65.000 0.00 0.00 39.57 4.40
1896 1985 3.247173 GGCGATGAACTGAGCTAAATCTG 59.753 47.826 0.00 0.00 0.00 2.90
2013 2124 1.255882 TGTGGACATTCAACATGCCC 58.744 50.000 0.00 0.00 0.00 5.36
2015 2126 0.964860 TGGACATTCAACATGCCCGG 60.965 55.000 0.00 0.00 0.00 5.73
2088 2199 7.531857 TTTTGGTGATAAGTCTTTTGGCATA 57.468 32.000 0.00 0.00 0.00 3.14
2094 2205 8.736244 GGTGATAAGTCTTTTGGCATACTTTAA 58.264 33.333 9.38 0.00 34.23 1.52
2198 2316 2.135933 GTAAGTTCTCACGCTTGCAGT 58.864 47.619 0.00 0.00 0.00 4.40
2288 2414 8.768957 ATCATTCTAAATCATATGGTGTCTCG 57.231 34.615 2.13 0.00 0.00 4.04
2290 2416 4.883083 TCTAAATCATATGGTGTCTCGCC 58.117 43.478 2.13 0.00 34.12 5.54
2315 2441 5.880332 GTGGGAAGCTAGTGTTTCATCATTA 59.120 40.000 0.00 0.00 35.50 1.90
2316 2442 6.374333 GTGGGAAGCTAGTGTTTCATCATTAA 59.626 38.462 0.00 0.00 35.50 1.40
2427 2558 4.469586 TGCAGGTGGTGAAGTATCTGATTA 59.530 41.667 0.00 0.00 0.00 1.75
2501 2632 1.123077 TAGCAGCATTCCGAGGTCAT 58.877 50.000 0.00 0.00 0.00 3.06
2528 2659 1.077429 GGTGGAAGCCCTGATGACC 60.077 63.158 0.00 0.00 0.00 4.02
2579 2710 2.285977 GAAGTTGGTGACACGTTCCTT 58.714 47.619 0.00 0.00 42.67 3.36
2587 2718 3.596214 GTGACACGTTCCTTCATATGGT 58.404 45.455 2.13 0.00 0.00 3.55
2832 2963 1.596477 GGCATGACTCCGCTGGATC 60.596 63.158 0.00 0.00 0.00 3.36
2861 2992 3.561213 CAGCCGCAGACAGCATCG 61.561 66.667 0.00 0.00 46.13 3.84
3026 3157 0.753111 AGATTTTCCTCCATGCGGGC 60.753 55.000 0.00 0.00 36.21 6.13
3090 3221 5.244178 ACAAGAACGACCTCATTCTCTAGTT 59.756 40.000 0.00 0.00 34.01 2.24
3177 3308 0.532573 GGCGAGACATCTCAAGGTCA 59.467 55.000 9.49 0.00 43.00 4.02
3180 3311 2.417924 GCGAGACATCTCAAGGTCATGT 60.418 50.000 9.49 0.00 43.00 3.21
3257 3388 2.876219 GACGTCTCCTCGGTGGAC 59.124 66.667 8.70 0.00 40.56 4.02
3261 3392 0.107800 CGTCTCCTCGGTGGACTCTA 60.108 60.000 0.00 0.00 40.56 2.43
3314 3445 3.543537 CCGCTGAGGCAGAGGTAT 58.456 61.111 8.77 0.00 44.47 2.73
3387 3545 2.179427 TGAAGCCTGAATCTCCTTCGA 58.821 47.619 0.00 0.00 37.18 3.71
3488 3646 1.450848 CAGTGCGGTGATCAGGCAT 60.451 57.895 20.60 9.92 39.14 4.40
3551 3709 1.127567 AGTACCTTGGCACTGGAGCA 61.128 55.000 12.05 0.00 35.83 4.26
3665 3837 2.083774 CACCGCCTGATGCTTAAAAGA 58.916 47.619 0.00 0.00 38.05 2.52
3706 3884 1.068194 CAGACAGACGACTTCAGTCCC 60.068 57.143 1.25 0.00 40.77 4.46
3720 3898 2.441375 TCAGTCCCCATTGTTTGAGTCA 59.559 45.455 0.00 0.00 0.00 3.41
3735 3913 3.738982 TGAGTCAATGTGGTGTTACTGG 58.261 45.455 0.00 0.00 0.00 4.00
3740 3918 2.185004 ATGTGGTGTTACTGGTGAGC 57.815 50.000 0.00 0.00 0.00 4.26
3743 3921 1.057275 TGGTGTTACTGGTGAGCCCA 61.057 55.000 0.00 0.00 42.51 5.36
3806 3984 5.458015 GGTTACAATGTTAGTGTGCCTTTC 58.542 41.667 0.00 0.00 0.00 2.62
3851 4029 5.914033 AGAGCATGATTTGGAAATGAATGG 58.086 37.500 0.00 0.00 0.00 3.16
3956 4134 2.915349 CATAGTGCTCACCTCTGCATT 58.085 47.619 0.00 0.00 41.45 3.56
4005 4183 5.803967 GCAGATTTGTCAATCATTCTTCACC 59.196 40.000 0.00 0.00 41.37 4.02
4036 4214 8.829612 CCTGCTGTTATTCTTTTCATTTTGTTT 58.170 29.630 0.00 0.00 0.00 2.83
4188 4399 8.792830 TTGAGAAGATGTATCTTTTAAGGGTG 57.207 34.615 8.41 0.00 46.47 4.61
4300 4798 6.968263 TTTGTCTAGAGAGATCGATGGAAT 57.032 37.500 0.54 0.00 33.14 3.01
4312 4810 6.540995 AGATCGATGGAATGGAAATCAGATT 58.459 36.000 0.54 0.00 33.78 2.40
4316 4814 8.158169 TCGATGGAATGGAAATCAGATTAAAG 57.842 34.615 0.00 0.00 0.00 1.85
4317 4815 7.992608 TCGATGGAATGGAAATCAGATTAAAGA 59.007 33.333 0.00 0.00 0.00 2.52
4318 4816 8.790718 CGATGGAATGGAAATCAGATTAAAGAT 58.209 33.333 0.00 0.00 0.00 2.40
4326 4824 9.973661 TGGAAATCAGATTAAAGATAAAGGTCA 57.026 29.630 0.00 0.00 0.00 4.02
4331 4829 9.620259 ATCAGATTAAAGATAAAGGTCAGGAAC 57.380 33.333 0.00 0.00 0.00 3.62
4332 4830 8.826765 TCAGATTAAAGATAAAGGTCAGGAACT 58.173 33.333 0.00 0.00 43.88 3.01
4333 4831 9.103861 CAGATTAAAGATAAAGGTCAGGAACTC 57.896 37.037 0.00 0.00 34.60 3.01
4334 4832 9.052365 AGATTAAAGATAAAGGTCAGGAACTCT 57.948 33.333 0.00 0.00 34.60 3.24
4335 4833 9.320352 GATTAAAGATAAAGGTCAGGAACTCTC 57.680 37.037 0.00 0.00 34.60 3.20
4336 4834 6.943899 AAAGATAAAGGTCAGGAACTCTCT 57.056 37.500 0.00 0.00 34.60 3.10
4337 4835 6.943899 AAGATAAAGGTCAGGAACTCTCTT 57.056 37.500 0.00 0.00 34.60 2.85
4338 4836 6.538945 AGATAAAGGTCAGGAACTCTCTTC 57.461 41.667 0.00 0.00 34.60 2.87
4339 4837 6.260663 AGATAAAGGTCAGGAACTCTCTTCT 58.739 40.000 0.00 0.00 34.60 2.85
4340 4838 4.615588 AAAGGTCAGGAACTCTCTTCTG 57.384 45.455 0.00 0.00 34.60 3.02
4341 4839 3.534357 AGGTCAGGAACTCTCTTCTGA 57.466 47.619 0.00 0.00 34.60 3.27
4342 4840 3.850752 AGGTCAGGAACTCTCTTCTGAA 58.149 45.455 0.00 0.00 37.90 3.02
4343 4841 4.424842 AGGTCAGGAACTCTCTTCTGAAT 58.575 43.478 0.00 0.00 37.90 2.57
4344 4842 4.466015 AGGTCAGGAACTCTCTTCTGAATC 59.534 45.833 0.00 0.00 37.90 2.52
4345 4843 4.466015 GGTCAGGAACTCTCTTCTGAATCT 59.534 45.833 0.00 0.00 37.90 2.40
4346 4844 5.046663 GGTCAGGAACTCTCTTCTGAATCTT 60.047 44.000 0.00 0.00 37.90 2.40
4347 4845 5.868801 GTCAGGAACTCTCTTCTGAATCTTG 59.131 44.000 0.00 0.00 37.90 3.02
4348 4846 5.777223 TCAGGAACTCTCTTCTGAATCTTGA 59.223 40.000 0.00 0.00 34.60 3.02
4349 4847 6.268617 TCAGGAACTCTCTTCTGAATCTTGAA 59.731 38.462 0.00 0.00 34.60 2.69
4350 4848 6.933521 CAGGAACTCTCTTCTGAATCTTGAAA 59.066 38.462 0.00 0.00 34.60 2.69
4351 4849 7.443575 CAGGAACTCTCTTCTGAATCTTGAAAA 59.556 37.037 0.00 0.00 34.60 2.29
4352 4850 7.995488 AGGAACTCTCTTCTGAATCTTGAAAAA 59.005 33.333 0.00 0.00 0.00 1.94
4367 4865 2.596338 AAAAACACCTCCCCCGCG 60.596 61.111 0.00 0.00 0.00 6.46
4368 4866 3.424780 AAAAACACCTCCCCCGCGT 62.425 57.895 4.92 0.00 0.00 6.01
4369 4867 3.837570 AAAACACCTCCCCCGCGTC 62.838 63.158 4.92 0.00 0.00 5.19
4409 4907 2.029221 GGAACCCTAGATCGCGCC 59.971 66.667 0.00 0.00 0.00 6.53
4410 4908 2.354773 GAACCCTAGATCGCGCCG 60.355 66.667 0.00 0.00 0.00 6.46
4411 4909 4.587189 AACCCTAGATCGCGCCGC 62.587 66.667 0.00 0.00 0.00 6.53
4440 4938 4.806339 CCCTCCCGCCTCCTCCTT 62.806 72.222 0.00 0.00 0.00 3.36
4441 4939 3.157949 CCTCCCGCCTCCTCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
4442 4940 3.157949 CTCCCGCCTCCTCCTTCC 61.158 72.222 0.00 0.00 0.00 3.46
4443 4941 3.684628 TCCCGCCTCCTCCTTCCT 61.685 66.667 0.00 0.00 0.00 3.36
4444 4942 3.157949 CCCGCCTCCTCCTTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
4445 4943 2.364317 CCGCCTCCTCCTTCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
4446 4944 2.726351 CCGCCTCCTCCTTCCTCAC 61.726 68.421 0.00 0.00 0.00 3.51
4447 4945 2.726351 CGCCTCCTCCTTCCTCACC 61.726 68.421 0.00 0.00 0.00 4.02
4448 4946 2.726351 GCCTCCTCCTTCCTCACCG 61.726 68.421 0.00 0.00 0.00 4.94
4449 4947 2.726351 CCTCCTCCTTCCTCACCGC 61.726 68.421 0.00 0.00 0.00 5.68
4450 4948 2.683933 TCCTCCTTCCTCACCGCC 60.684 66.667 0.00 0.00 0.00 6.13
4451 4949 4.148825 CCTCCTTCCTCACCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
4452 4950 4.821589 CTCCTTCCTCACCGCCGC 62.822 72.222 0.00 0.00 0.00 6.53
4510 5008 3.917760 CGGGGCATCCTCGTCCTC 61.918 72.222 0.00 0.00 0.00 3.71
4511 5009 3.551407 GGGGCATCCTCGTCCTCC 61.551 72.222 0.00 0.00 0.00 4.30
4512 5010 3.551407 GGGCATCCTCGTCCTCCC 61.551 72.222 0.00 0.00 0.00 4.30
4513 5011 3.917760 GGCATCCTCGTCCTCCCG 61.918 72.222 0.00 0.00 0.00 5.14
4514 5012 4.593864 GCATCCTCGTCCTCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
4515 5013 4.271816 CATCCTCGTCCTCCCGCG 62.272 72.222 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.160137 GCAAATCTCGTTCTGGCTGT 58.840 50.000 0.00 0.00 0.00 4.40
33 34 6.396829 CAAAGAGGATAATGATTTGGACCC 57.603 41.667 0.00 0.00 0.00 4.46
159 160 0.995024 ACAGCCAGGAATGCCTTAGT 59.005 50.000 0.00 0.00 43.90 2.24
291 294 2.047274 TACTGTTGCCGCTGCCTC 60.047 61.111 0.00 0.00 36.33 4.70
314 317 1.318576 AGAAACAAGCGAGTTTGGGG 58.681 50.000 13.13 0.00 41.48 4.96
376 383 0.102844 TGCAGGCACAAGTTTTGCTC 59.897 50.000 13.40 4.50 40.07 4.26
429 436 2.044620 ATCCCTCCCTCCCCCAAC 59.955 66.667 0.00 0.00 0.00 3.77
430 437 2.044450 CATCCCTCCCTCCCCCAA 59.956 66.667 0.00 0.00 0.00 4.12
490 515 2.232208 TCAAGCGCAGAATTCAGAGAGA 59.768 45.455 11.47 0.00 0.00 3.10
491 516 2.614779 TCAAGCGCAGAATTCAGAGAG 58.385 47.619 11.47 0.33 0.00 3.20
545 570 0.109723 CGTCAAGGGGAAAGGGAACA 59.890 55.000 0.00 0.00 0.00 3.18
576 601 1.463553 GGAACCCCACAAGCACAAGG 61.464 60.000 0.00 0.00 0.00 3.61
583 608 1.296715 CTCGGAGGAACCCCACAAG 59.703 63.158 0.00 0.00 34.64 3.16
590 615 0.876342 CGCATAAGCTCGGAGGAACC 60.876 60.000 7.20 0.00 39.10 3.62
591 616 1.491505 GCGCATAAGCTCGGAGGAAC 61.492 60.000 0.30 0.00 39.10 3.62
594 619 2.419198 AGCGCATAAGCTCGGAGG 59.581 61.111 11.47 0.00 45.67 4.30
610 635 2.644992 GGACCAACCAAGCGCAAG 59.355 61.111 11.47 0.00 38.79 4.01
611 636 2.909965 GGGACCAACCAAGCGCAA 60.910 61.111 11.47 0.00 41.20 4.85
612 637 3.505790 ATGGGACCAACCAAGCGCA 62.506 57.895 11.47 0.00 45.13 6.09
615 640 0.967380 CTCCATGGGACCAACCAAGC 60.967 60.000 13.02 0.00 45.13 4.01
616 641 0.967380 GCTCCATGGGACCAACCAAG 60.967 60.000 13.02 0.00 45.13 3.61
617 642 1.076549 GCTCCATGGGACCAACCAA 59.923 57.895 13.02 0.00 45.13 3.67
618 643 2.763215 GCTCCATGGGACCAACCA 59.237 61.111 13.02 0.00 46.24 3.67
619 644 2.043953 GGCTCCATGGGACCAACC 60.044 66.667 13.02 0.89 38.08 3.77
620 645 1.077429 GAGGCTCCATGGGACCAAC 60.077 63.158 21.66 13.29 0.00 3.77
621 646 1.229951 AGAGGCTCCATGGGACCAA 60.230 57.895 21.66 0.00 0.00 3.67
623 648 2.914289 CAGAGGCTCCATGGGACC 59.086 66.667 13.02 13.79 0.00 4.46
625 650 3.092511 GGCAGAGGCTCCATGGGA 61.093 66.667 13.02 0.00 40.87 4.37
626 651 3.095163 AGGCAGAGGCTCCATGGG 61.095 66.667 13.02 3.69 40.87 4.00
646 696 0.249238 CATGGGAGCTACTGCGAGAC 60.249 60.000 0.00 0.00 45.42 3.36
781 841 5.776358 AGCAATTATGGAAGGGGTTATCAA 58.224 37.500 0.00 0.00 0.00 2.57
842 904 1.872388 TCGAACATCAAAGCAACGGA 58.128 45.000 0.00 0.00 0.00 4.69
844 906 3.454042 TGATCGAACATCAAAGCAACG 57.546 42.857 0.00 0.00 0.00 4.10
932 1011 1.488812 AGTTGAGCTAACCCACACACA 59.511 47.619 0.00 0.00 40.24 3.72
934 1013 2.805295 CGAAGTTGAGCTAACCCACACA 60.805 50.000 0.00 0.00 40.24 3.72
935 1014 1.798813 CGAAGTTGAGCTAACCCACAC 59.201 52.381 0.00 0.00 40.24 3.82
936 1015 1.414919 ACGAAGTTGAGCTAACCCACA 59.585 47.619 0.00 0.00 37.78 4.17
958 1037 2.420022 CGGTTAATCCACCTGCAGAAAG 59.580 50.000 17.39 0.15 34.22 2.62
988 1067 1.050988 TCCTCCATGGACTGCTAGCC 61.051 60.000 11.44 0.00 40.56 3.93
991 1070 0.636647 TCCTCCTCCATGGACTGCTA 59.363 55.000 11.44 0.00 40.56 3.49
995 1074 1.697291 GGGATTCCTCCTCCATGGACT 60.697 57.143 11.44 0.00 40.56 3.85
997 1076 0.346574 TGGGATTCCTCCTCCATGGA 59.653 55.000 15.27 15.27 43.86 3.41
1401 1480 3.066814 GTCACGCCGTACTCCCCT 61.067 66.667 0.00 0.00 0.00 4.79
1491 1570 4.148825 CCGTCTTCTCCTGCCGGG 62.149 72.222 2.18 0.00 35.11 5.73
1497 1576 2.685380 CCAGCCCCGTCTTCTCCT 60.685 66.667 0.00 0.00 0.00 3.69
1522 1607 3.806667 AGCAGCAGGGGCATCTCC 61.807 66.667 0.00 0.00 44.61 3.71
1554 1639 0.457853 TCTCGCGCCTGAACATGTAC 60.458 55.000 0.00 0.00 0.00 2.90
1650 1735 4.075854 TGGTACGCAGCGGCATCA 62.076 61.111 21.15 10.24 41.24 3.07
1896 1985 7.761704 TCTCACAAACTAGCAACTAATCTCATC 59.238 37.037 0.00 0.00 0.00 2.92
1935 2031 5.294552 GTGCGCTATTATTCTCAGGTTTCTT 59.705 40.000 9.73 0.00 0.00 2.52
2013 2124 1.503542 GCAGAATCACAACCTGCCG 59.496 57.895 0.00 0.00 45.38 5.69
2095 2206 7.973388 GCAAACAGAGCACCATTACAATAATAA 59.027 33.333 0.00 0.00 0.00 1.40
2096 2207 7.339212 AGCAAACAGAGCACCATTACAATAATA 59.661 33.333 0.00 0.00 0.00 0.98
2288 2414 0.605589 AAACACTAGCTTCCCACGGC 60.606 55.000 0.00 0.00 0.00 5.68
2290 2416 2.163818 TGAAACACTAGCTTCCCACG 57.836 50.000 0.00 0.00 0.00 4.94
2315 2441 4.523943 TGAACCTGATACTGCAGCAAAATT 59.476 37.500 15.27 0.00 34.56 1.82
2316 2442 4.081406 TGAACCTGATACTGCAGCAAAAT 58.919 39.130 15.27 2.08 34.56 1.82
2427 2558 2.365617 AGTTGACGATATCGAAGGCCAT 59.634 45.455 30.75 7.00 43.02 4.40
2501 2632 1.073548 GGCTTCCACCACCGGTAAA 59.926 57.895 6.87 0.00 32.11 2.01
2513 2644 2.514824 GCGGTCATCAGGGCTTCC 60.515 66.667 0.00 0.00 0.00 3.46
2528 2659 3.197265 TGATACAAGTGATGGTGATGCG 58.803 45.455 0.00 0.00 0.00 4.73
2579 2710 4.030216 TGAAGCCAGTCAGTACCATATGA 58.970 43.478 3.65 0.00 0.00 2.15
2587 2718 3.501349 AGAGTTCTGAAGCCAGTCAGTA 58.499 45.455 8.92 0.00 44.56 2.74
2825 2956 3.791245 CTGTTTCCTCAGTAGATCCAGC 58.209 50.000 0.00 0.00 0.00 4.85
2832 2963 0.037326 TGCGGCTGTTTCCTCAGTAG 60.037 55.000 0.00 0.00 37.70 2.57
2861 2992 4.584325 AGCTCCTTGATGAGTATCTCAGAC 59.416 45.833 5.71 3.56 44.08 3.51
2864 2995 4.540715 TCAGCTCCTTGATGAGTATCTCA 58.459 43.478 1.92 1.92 44.99 3.27
3042 3173 1.986378 CGTTCTCGTTCTTTCGCTGAT 59.014 47.619 0.00 0.00 0.00 2.90
3047 3178 3.040795 TGTTCTCGTTCTCGTTCTTTCG 58.959 45.455 0.00 0.00 38.33 3.46
3161 3292 4.825422 TGAACATGACCTTGAGATGTCTC 58.175 43.478 0.00 3.07 43.15 3.36
3177 3308 1.091771 CGAAGCGGCCATCTGAACAT 61.092 55.000 2.24 0.00 0.00 2.71
3261 3392 0.917533 ACATGGCTCCAGCTCTTGAT 59.082 50.000 0.00 0.00 41.70 2.57
3314 3445 0.768221 ACAGGGAGCTCACCTTGGAA 60.768 55.000 13.73 0.00 40.60 3.53
3387 3545 0.253327 GAAGACCAGGAGGCCGAAAT 59.747 55.000 0.00 0.00 39.06 2.17
3488 3646 8.089625 TCAGAGATCCATATTTCTTTGGTGTA 57.910 34.615 0.00 0.00 34.48 2.90
3551 3709 2.820178 GAGGTTGAATCCCCCAATTGT 58.180 47.619 4.43 0.00 0.00 2.71
3720 3898 2.504367 GCTCACCAGTAACACCACATT 58.496 47.619 0.00 0.00 0.00 2.71
3735 3913 4.342862 TGATTAGCTATCTTGGGCTCAC 57.657 45.455 0.00 0.00 39.65 3.51
3806 3984 1.001633 AGTTACACTTACCAGCCCACG 59.998 52.381 0.00 0.00 0.00 4.94
3873 4051 1.202463 CGGAGAACTCATCTGGCGATT 60.202 52.381 4.23 0.00 38.96 3.34
3907 4085 7.643528 TGCAGATGTATAACGAATCATTCTC 57.356 36.000 0.00 0.00 0.00 2.87
3960 4138 7.791029 TCTGCACCTTCATGTAGACATTATAA 58.209 34.615 0.12 0.00 36.53 0.98
3961 4139 7.360113 TCTGCACCTTCATGTAGACATTATA 57.640 36.000 0.12 0.00 36.53 0.98
4005 4183 4.022935 TGAAAAGAATAACAGCAGGCACAG 60.023 41.667 0.00 0.00 0.00 3.66
4036 4214 9.316730 ACAAAAACAAGTACACGTCTTCTTATA 57.683 29.630 0.00 0.00 0.00 0.98
4037 4215 8.120465 CACAAAAACAAGTACACGTCTTCTTAT 58.880 33.333 0.00 0.00 0.00 1.73
4059 4237 2.739913 GCCGACACAGCTTTATACACAA 59.260 45.455 0.00 0.00 0.00 3.33
4118 4328 3.439129 GGTAGTTGAAATCAAGGAACCGG 59.561 47.826 0.00 0.00 36.39 5.28
4247 4492 1.108776 CCTGAAATGCATCCCACCAG 58.891 55.000 0.00 3.44 0.00 4.00
4300 4798 9.973661 TGACCTTTATCTTTAATCTGATTTCCA 57.026 29.630 8.38 0.00 0.00 3.53
4312 4810 8.437274 AAGAGAGTTCCTGACCTTTATCTTTA 57.563 34.615 0.00 0.00 0.00 1.85
4316 4814 6.153680 TCAGAAGAGAGTTCCTGACCTTTATC 59.846 42.308 0.00 0.00 31.45 1.75
4317 4815 6.019748 TCAGAAGAGAGTTCCTGACCTTTAT 58.980 40.000 0.00 0.00 31.45 1.40
4318 4816 5.394738 TCAGAAGAGAGTTCCTGACCTTTA 58.605 41.667 0.00 0.00 31.45 1.85
4319 4817 4.227197 TCAGAAGAGAGTTCCTGACCTTT 58.773 43.478 0.00 0.00 31.45 3.11
4320 4818 3.850752 TCAGAAGAGAGTTCCTGACCTT 58.149 45.455 0.00 0.00 31.45 3.50
4321 4819 3.534357 TCAGAAGAGAGTTCCTGACCT 57.466 47.619 0.00 0.00 31.45 3.85
4322 4820 4.466015 AGATTCAGAAGAGAGTTCCTGACC 59.534 45.833 0.00 0.00 35.63 4.02
4323 4821 5.659440 AGATTCAGAAGAGAGTTCCTGAC 57.341 43.478 0.00 0.00 35.63 3.51
4324 4822 5.777223 TCAAGATTCAGAAGAGAGTTCCTGA 59.223 40.000 0.00 0.00 34.25 3.86
4325 4823 6.035368 TCAAGATTCAGAAGAGAGTTCCTG 57.965 41.667 0.00 0.00 0.00 3.86
4326 4824 6.678568 TTCAAGATTCAGAAGAGAGTTCCT 57.321 37.500 0.00 0.00 0.00 3.36
4327 4825 7.736447 TTTTCAAGATTCAGAAGAGAGTTCC 57.264 36.000 0.00 0.00 0.00 3.62
4350 4848 2.596338 CGCGGGGGAGGTGTTTTT 60.596 61.111 0.00 0.00 0.00 1.94
4351 4849 3.837570 GACGCGGGGGAGGTGTTTT 62.838 63.158 12.47 0.00 0.00 2.43
4352 4850 4.324991 GACGCGGGGGAGGTGTTT 62.325 66.667 12.47 0.00 0.00 2.83
4388 4886 1.807495 CGCGATCTAGGGTTCCCTCC 61.807 65.000 14.24 2.17 37.64 4.30
4389 4887 1.660917 CGCGATCTAGGGTTCCCTC 59.339 63.158 14.24 0.00 37.64 4.30
4390 4888 2.499827 GCGCGATCTAGGGTTCCCT 61.500 63.158 12.10 15.19 40.06 4.20
4391 4889 2.029221 GCGCGATCTAGGGTTCCC 59.971 66.667 12.10 0.00 0.00 3.97
4392 4890 2.029221 GGCGCGATCTAGGGTTCC 59.971 66.667 12.10 0.00 0.00 3.62
4393 4891 2.354773 CGGCGCGATCTAGGGTTC 60.355 66.667 12.10 0.00 0.00 3.62
4394 4892 4.587189 GCGGCGCGATCTAGGGTT 62.587 66.667 19.09 0.00 0.00 4.11
4423 4921 4.806339 AAGGAGGAGGCGGGAGGG 62.806 72.222 0.00 0.00 0.00 4.30
4424 4922 3.157949 GAAGGAGGAGGCGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
4425 4923 3.157949 GGAAGGAGGAGGCGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
4426 4924 3.680920 GAGGAAGGAGGAGGCGGGA 62.681 68.421 0.00 0.00 0.00 5.14
4427 4925 3.157949 GAGGAAGGAGGAGGCGGG 61.158 72.222 0.00 0.00 0.00 6.13
4428 4926 2.364317 TGAGGAAGGAGGAGGCGG 60.364 66.667 0.00 0.00 0.00 6.13
4429 4927 2.726351 GGTGAGGAAGGAGGAGGCG 61.726 68.421 0.00 0.00 0.00 5.52
4430 4928 2.726351 CGGTGAGGAAGGAGGAGGC 61.726 68.421 0.00 0.00 0.00 4.70
4431 4929 2.726351 GCGGTGAGGAAGGAGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
4432 4930 2.726351 GGCGGTGAGGAAGGAGGAG 61.726 68.421 0.00 0.00 0.00 3.69
4433 4931 2.683933 GGCGGTGAGGAAGGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
4434 4932 4.148825 CGGCGGTGAGGAAGGAGG 62.149 72.222 0.00 0.00 0.00 4.30
4435 4933 4.821589 GCGGCGGTGAGGAAGGAG 62.822 72.222 9.78 0.00 0.00 3.69
4493 4991 3.917760 GAGGACGAGGATGCCCCG 61.918 72.222 0.00 0.00 40.87 5.73
4494 4992 3.551407 GGAGGACGAGGATGCCCC 61.551 72.222 0.00 0.00 0.00 5.80
4495 4993 3.551407 GGGAGGACGAGGATGCCC 61.551 72.222 0.00 0.00 0.00 5.36
4496 4994 3.917760 CGGGAGGACGAGGATGCC 61.918 72.222 0.00 0.00 35.47 4.40
4497 4995 4.593864 GCGGGAGGACGAGGATGC 62.594 72.222 0.00 0.00 35.47 3.91
4498 4996 4.271816 CGCGGGAGGACGAGGATG 62.272 72.222 0.00 0.00 35.47 3.51
4523 5021 4.322385 GTGTTGACCCGCGCCAAC 62.322 66.667 21.89 21.89 42.04 3.77


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

AutoCloner maintained by Alex Coulton.