Multiple sequence alignment - TraesCS3A01G385500

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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 TraesCS3A01G385500 chr3A 100.000 9966 0 0 1 9966 635094302 635104267 0.000000e+00 18404.0
1 TraesCS3A01G385500 chr3B 96.280 9328 252 30 37 9333 654474236 654483499 0.000000e+00 15215.0
2 TraesCS3A01G385500 chr3B 90.476 273 25 1 1 272 654473737 654474009 9.520000e-95 359.0
3 TraesCS3A01G385500 chr3B 87.931 290 24 6 9568 9847 654484089 654484377 2.070000e-86 331.0
4 TraesCS3A01G385500 chr3B 92.857 42 1 2 4234 4275 737781619 737781658 1.080000e-04 60.2
5 TraesCS3A01G385500 chr3D 98.332 4376 69 2 4674 9049 495572750 495577121 0.000000e+00 7673.0
6 TraesCS3A01G385500 chr3D 94.909 4655 132 31 1 4614 495568162 495572752 0.000000e+00 7186.0
7 TraesCS3A01G385500 chr3D 84.696 1052 130 17 7769 8812 576690823 576689795 0.000000e+00 1022.0
8 TraesCS3A01G385500 chr3D 88.642 405 35 6 9569 9962 495579827 495580231 5.410000e-132 483.0
9 TraesCS3A01G385500 chr3D 92.500 200 15 0 9366 9565 495579571 495579770 4.560000e-73 287.0
10 TraesCS3A01G385500 chr3D 92.908 141 10 0 6670 6810 576690961 576690821 1.310000e-48 206.0
11 TraesCS3A01G385500 chr3D 93.902 82 5 0 9193 9274 495579485 495579566 3.780000e-24 124.0
12 TraesCS3A01G385500 chr7D 86.265 1063 122 15 7756 8812 39315994 39317038 0.000000e+00 1133.0
13 TraesCS3A01G385500 chr7D 93.706 143 9 0 6669 6811 39315833 39315975 2.180000e-51 215.0
14 TraesCS3A01G385500 chr7D 94.565 92 5 0 6669 6760 5479209 5479118 1.040000e-29 143.0
15 TraesCS3A01G385500 chr7D 80.000 150 25 4 4189 4337 638681497 638681352 1.370000e-18 106.0
16 TraesCS3A01G385500 chr2D 84.402 1045 120 17 7773 8808 4478918 4479928 0.000000e+00 987.0
17 TraesCS3A01G385500 chr2D 90.991 111 10 0 6701 6811 4478777 4478887 6.240000e-32 150.0
18 TraesCS3A01G385500 chr6B 90.184 326 29 3 7832 8155 11168835 11168511 1.200000e-113 422.0
19 TraesCS3A01G385500 chr6B 95.105 143 7 0 6669 6811 11169786 11169644 1.010000e-54 226.0
20 TraesCS3A01G385500 chr6B 84.615 65 8 2 4241 4305 40435209 40435271 8.360000e-06 63.9
21 TraesCS3A01G385500 chr6A 81.699 153 20 6 4189 4338 519597396 519597543 4.890000e-23 121.0
22 TraesCS3A01G385500 chr2B 96.875 32 1 0 8404 8435 94211050 94211081 5.000000e-03 54.7
23 TraesCS3A01G385500 chr1A 90.244 41 4 0 4165 4205 463042702 463042662 5.000000e-03 54.7


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 TraesCS3A01G385500 chr3A 635094302 635104267 9965 False 18404.000000 18404 100.000000 1 9966 1 chr3A.!!$F1 9965
1 TraesCS3A01G385500 chr3B 654473737 654484377 10640 False 5301.666667 15215 91.562333 1 9847 3 chr3B.!!$F2 9846
2 TraesCS3A01G385500 chr3D 495568162 495580231 12069 False 3150.600000 7673 93.657000 1 9962 5 chr3D.!!$F1 9961
3 TraesCS3A01G385500 chr3D 576689795 576690961 1166 True 614.000000 1022 88.802000 6670 8812 2 chr3D.!!$R1 2142
4 TraesCS3A01G385500 chr7D 39315833 39317038 1205 False 674.000000 1133 89.985500 6669 8812 2 chr7D.!!$F1 2143
5 TraesCS3A01G385500 chr2D 4478777 4479928 1151 False 568.500000 987 87.696500 6701 8808 2 chr2D.!!$F1 2107
6 TraesCS3A01G385500 chr6B 11168511 11169786 1275 True 324.000000 422 92.644500 6669 8155 2 chr6B.!!$R1 1486

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
814 1303 0.099968 CCGAATTCCTAGTCGCGACA 59.900 55.000 37.85 23.27 40.30 4.35 F
1034 1524 0.034616 CGATCAGGATGCCTTCTCCC 59.965 60.000 0.00 0.00 34.76 4.30 F
1521 2011 2.042842 TGGCTACTCCTGTTGGGACAA 61.043 52.381 0.00 0.00 39.58 3.18 F
2431 2946 1.329256 TTGAGCTCCTAGATACCGGC 58.671 55.000 12.15 0.00 0.00 6.13 F
3187 3702 0.037326 TGTCTGATGGAGCAACCGAC 60.037 55.000 0.00 0.00 42.61 4.79 F
4153 4668 0.319211 GGTTTAAAAGGCCCACGTGC 60.319 55.000 10.91 0.00 0.00 5.34 F
5120 5646 3.525537 CGACAGCCAATGTATTCAGTCT 58.474 45.455 0.00 0.00 44.17 3.24 F
5684 6210 2.376518 TCCATTGGAGGAAGCACTTTCT 59.623 45.455 0.00 0.00 36.03 2.52 F
6390 6916 6.439487 TCTCTAGGTTGATTCTTCTCCTGAT 58.561 40.000 0.00 0.00 32.29 2.90 F
7084 7610 3.605634 TCTCATCAACAAATACACCCCG 58.394 45.455 0.00 0.00 0.00 5.73 F
8540 9787 0.598065 GTGATGTTGGTGCCTGAACC 59.402 55.000 0.00 0.00 40.94 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2429 0.110486 AAACTGAAGGGACCACGCAT 59.890 50.000 0.00 0.00 0.00 4.73 R
1915 2430 0.534203 GAAACTGAAGGGACCACGCA 60.534 55.000 0.00 0.00 0.00 5.24 R
2594 3109 1.406614 GGCACCTTGATCAGTCTCCAG 60.407 57.143 0.00 0.00 0.00 3.86 R
3446 3961 1.717791 GCATCTGCTTATGTGCGGCA 61.718 55.000 0.00 0.00 39.06 5.69 R
5133 5659 1.063642 TGTCGAGGGATCTGGATCAGT 60.064 52.381 11.93 0.00 39.54 3.41 R
5305 5831 1.445582 CTAGTCCCCGTGTGCGTTC 60.446 63.158 0.00 0.00 36.15 3.95 R
6737 7263 1.069227 GCCACCACGAGAATTGTCAAC 60.069 52.381 3.24 0.00 0.00 3.18 R
7084 7610 5.053145 AGTTGTGTCAGTGATGAAGAAGTC 58.947 41.667 0.00 0.00 0.00 3.01 R
8350 9597 4.007659 CCAGTTGTTTGTCCCAGGTATAC 58.992 47.826 0.00 0.00 0.00 1.47 R
8880 10127 0.176680 CTACCCTGCGCATTCTGAGT 59.823 55.000 12.24 4.93 0.00 3.41 R
9589 13459 0.037605 CCCCGTTCTAACTGTTCGCT 60.038 55.000 0.00 0.00 0.00 4.93 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 29 6.959361 ACATTTGTTAGAACACATCTGTCAC 58.041 36.000 0.00 0.00 39.30 3.67
71 72 1.332065 CATACACACAACCACGCAACA 59.668 47.619 0.00 0.00 0.00 3.33
83 84 2.186160 CGCAACAACTGGAGTGCCA 61.186 57.895 0.00 0.00 43.47 4.92
84 85 1.723608 CGCAACAACTGGAGTGCCAA 61.724 55.000 0.00 0.00 45.41 4.52
86 87 1.102154 CAACAACTGGAGTGCCAACA 58.898 50.000 0.00 0.00 45.41 3.33
101 102 2.284952 GCCAACAAAGTGCATCACAAAC 59.715 45.455 0.00 0.00 36.74 2.93
120 121 0.530650 CGCGAGGCAGGTGATACAAT 60.531 55.000 0.00 0.00 0.00 2.71
171 636 7.529880 AAATTACCGATTACGTCTAAACAGG 57.470 36.000 0.00 0.00 37.88 4.00
232 697 6.846283 CGACAATAAATTAGGAAATCGTGAGC 59.154 38.462 0.00 0.00 0.00 4.26
263 728 7.308770 CGATACAGACATTATTGCCCATTCAAT 60.309 37.037 0.00 0.00 39.70 2.57
278 743 7.343057 TGCCCATTCAATAACATAAATACCACA 59.657 33.333 0.00 0.00 0.00 4.17
296 761 9.682465 AATACCACATATTATCGCTAGACTAGA 57.318 33.333 13.91 0.00 31.28 2.43
297 762 7.997773 ACCACATATTATCGCTAGACTAGAA 57.002 36.000 13.91 0.71 0.00 2.10
298 763 8.046294 ACCACATATTATCGCTAGACTAGAAG 57.954 38.462 13.91 6.40 0.00 2.85
299 764 7.666388 ACCACATATTATCGCTAGACTAGAAGT 59.334 37.037 13.91 0.52 0.00 3.01
300 765 8.516234 CCACATATTATCGCTAGACTAGAAGTT 58.484 37.037 13.91 4.38 0.00 2.66
318 783 7.569639 AGAAGTTAACCTTTTCTTTCCTGTC 57.430 36.000 0.88 0.00 32.03 3.51
347 812 3.102204 CGTTCCCCCTAAAAGGAGACTA 58.898 50.000 0.00 0.00 42.68 2.59
348 813 3.132467 CGTTCCCCCTAAAAGGAGACTAG 59.868 52.174 0.00 0.00 42.68 2.57
354 819 5.191921 CCCCCTAAAAGGAGACTAGTTCATT 59.808 44.000 0.00 0.00 42.68 2.57
413 878 2.896801 GCATCGCATTAGGCACCCG 61.897 63.158 0.00 0.00 45.17 5.28
479 944 2.652095 TAACTTGAGCGACCGGGGG 61.652 63.158 6.32 0.00 0.00 5.40
500 965 2.201022 CCTCCCGTCTACCCATCCG 61.201 68.421 0.00 0.00 0.00 4.18
502 967 0.754217 CTCCCGTCTACCCATCCGAA 60.754 60.000 0.00 0.00 0.00 4.30
523 988 2.094234 ACCAATAATTCAAACTGGCGCC 60.094 45.455 22.73 22.73 0.00 6.53
527 992 0.883833 AATTCAAACTGGCGCCTGAG 59.116 50.000 36.36 24.74 0.00 3.35
566 1031 0.886490 CAGAGAACACCTGCACACCC 60.886 60.000 0.00 0.00 0.00 4.61
567 1032 1.148273 GAGAACACCTGCACACCCA 59.852 57.895 0.00 0.00 0.00 4.51
568 1033 1.152963 AGAACACCTGCACACCCAC 60.153 57.895 0.00 0.00 0.00 4.61
569 1034 1.453015 GAACACCTGCACACCCACA 60.453 57.895 0.00 0.00 0.00 4.17
570 1035 1.724582 GAACACCTGCACACCCACAC 61.725 60.000 0.00 0.00 0.00 3.82
571 1036 2.906897 CACCTGCACACCCACACC 60.907 66.667 0.00 0.00 0.00 4.16
663 1134 2.292794 ATACGTAGCACCGCCACCAG 62.293 60.000 0.08 0.00 0.00 4.00
811 1300 0.935366 GCTCCGAATTCCTAGTCGCG 60.935 60.000 0.00 0.00 40.30 5.87
813 1302 0.379669 TCCGAATTCCTAGTCGCGAC 59.620 55.000 31.30 31.30 40.30 5.19
814 1303 0.099968 CCGAATTCCTAGTCGCGACA 59.900 55.000 37.85 23.27 40.30 4.35
815 1304 1.468565 CCGAATTCCTAGTCGCGACAA 60.469 52.381 37.85 24.62 40.30 3.18
816 1305 2.460918 CGAATTCCTAGTCGCGACAAT 58.539 47.619 37.85 25.65 34.94 2.71
817 1306 2.468040 CGAATTCCTAGTCGCGACAATC 59.532 50.000 37.85 19.51 34.94 2.67
818 1307 2.510768 ATTCCTAGTCGCGACAATCC 57.489 50.000 37.85 13.90 0.00 3.01
819 1308 0.458669 TTCCTAGTCGCGACAATCCC 59.541 55.000 37.85 13.11 0.00 3.85
820 1309 0.681887 TCCTAGTCGCGACAATCCCA 60.682 55.000 37.85 15.68 0.00 4.37
821 1310 0.527817 CCTAGTCGCGACAATCCCAC 60.528 60.000 37.85 12.15 0.00 4.61
1034 1524 0.034616 CGATCAGGATGCCTTCTCCC 59.965 60.000 0.00 0.00 34.76 4.30
1421 1911 6.041637 TGCATCCGTAAGTCTATGGTCTTAAT 59.958 38.462 0.00 0.00 35.85 1.40
1424 1914 9.627395 CATCCGTAAGTCTATGGTCTTAATAAG 57.373 37.037 0.00 0.00 35.85 1.73
1426 1916 9.064706 TCCGTAAGTCTATGGTCTTAATAAGAG 57.935 37.037 2.48 0.00 38.41 2.85
1427 1917 8.848182 CCGTAAGTCTATGGTCTTAATAAGAGT 58.152 37.037 2.48 0.00 38.41 3.24
1509 1999 2.596904 TATTTGGCGTCTGGCTACTC 57.403 50.000 0.00 0.00 42.94 2.59
1521 2011 2.042842 TGGCTACTCCTGTTGGGACAA 61.043 52.381 0.00 0.00 39.58 3.18
1554 2044 3.699038 TCAAGGAACACCTGTTTTTGGAG 59.301 43.478 12.59 0.00 38.56 3.86
1598 2088 8.578151 CCATGTTCTTAGAATCCTAGTAGTACC 58.422 40.741 0.00 0.00 0.00 3.34
1624 2128 6.594788 TTATTTTCGGGAGTACTGTACACT 57.405 37.500 19.27 1.65 0.00 3.55
1625 2129 3.928727 TTTCGGGAGTACTGTACACTG 57.071 47.619 19.27 15.47 0.00 3.66
1675 2186 3.334691 TGTTACATGAGCTTAGTGGTGC 58.665 45.455 0.00 0.00 0.00 5.01
1776 2287 4.155644 CCTCTGAACTTCTGCTTCCAAATC 59.844 45.833 0.00 0.00 0.00 2.17
2136 2651 4.404640 AGCCATGGTATTGATTCATCAGG 58.595 43.478 14.67 0.00 38.19 3.86
2137 2652 3.508793 GCCATGGTATTGATTCATCAGGG 59.491 47.826 14.67 0.00 38.19 4.45
2395 2910 1.428869 GTGGCTCCCTCATGGATACT 58.571 55.000 0.00 0.00 44.07 2.12
2431 2946 1.329256 TTGAGCTCCTAGATACCGGC 58.671 55.000 12.15 0.00 0.00 6.13
2452 2967 5.136105 GGCCAACTTCATCCTGATATCTTT 58.864 41.667 0.00 0.00 0.00 2.52
2535 3050 7.179516 TGAACCCAGTCATACTACTGTATTCAA 59.820 37.037 13.46 3.62 44.45 2.69
2594 3109 7.644986 AATATTCTATCTAGTCAAACGCAGC 57.355 36.000 0.00 0.00 0.00 5.25
2625 3140 1.118838 CAAGGTGCCACCAAGGAAAA 58.881 50.000 17.80 0.00 41.95 2.29
2848 3363 6.207221 ACAACAACATATTGAATGCTGAGTCA 59.793 34.615 0.00 0.00 39.30 3.41
3187 3702 0.037326 TGTCTGATGGAGCAACCGAC 60.037 55.000 0.00 0.00 42.61 4.79
3252 3767 2.166459 CCTTACTCGTCAAGCCTGATGA 59.834 50.000 7.03 7.03 43.85 2.92
4070 4585 4.147321 TCCTCTTTCTGCTCTGCAATTTT 58.853 39.130 0.00 0.00 38.41 1.82
4153 4668 0.319211 GGTTTAAAAGGCCCACGTGC 60.319 55.000 10.91 0.00 0.00 5.34
4623 5143 9.979578 TTCTGTTTGTTTGCATAGTATTGAATT 57.020 25.926 0.00 0.00 0.00 2.17
4634 5154 7.284261 TGCATAGTATTGAATTGGAAATTCGGA 59.716 33.333 7.90 1.19 0.00 4.55
5100 5620 7.348201 CGAAATTAAGAATTCCAGAGATTCCG 58.652 38.462 0.65 0.00 0.00 4.30
5120 5646 3.525537 CGACAGCCAATGTATTCAGTCT 58.474 45.455 0.00 0.00 44.17 3.24
5121 5647 4.441495 CCGACAGCCAATGTATTCAGTCTA 60.441 45.833 0.00 0.00 44.17 2.59
5122 5648 5.109210 CGACAGCCAATGTATTCAGTCTAA 58.891 41.667 0.00 0.00 44.17 2.10
5123 5649 5.755375 CGACAGCCAATGTATTCAGTCTAAT 59.245 40.000 0.00 0.00 44.17 1.73
5124 5650 6.258727 CGACAGCCAATGTATTCAGTCTAATT 59.741 38.462 0.00 0.00 44.17 1.40
5125 5651 7.517417 CGACAGCCAATGTATTCAGTCTAATTC 60.517 40.741 0.00 0.00 44.17 2.17
5133 5659 3.793797 TTCAGTCTAATTCATCGCGGA 57.206 42.857 6.13 0.00 0.00 5.54
5552 6078 6.317642 TGGCTTTAATTATGCGTCAGTAACAT 59.682 34.615 5.32 0.00 0.00 2.71
5684 6210 2.376518 TCCATTGGAGGAAGCACTTTCT 59.623 45.455 0.00 0.00 36.03 2.52
6227 6753 7.872113 ACTCTTCTCTGAAATTGAAAACACT 57.128 32.000 0.00 0.00 0.00 3.55
6315 6841 6.699575 ATGAGGGAATATTTTTGGAAGTCG 57.300 37.500 0.00 0.00 0.00 4.18
6390 6916 6.439487 TCTCTAGGTTGATTCTTCTCCTGAT 58.561 40.000 0.00 0.00 32.29 2.90
6623 7149 8.246180 CAGACAATTCTAACCACAAAAGCATAT 58.754 33.333 0.00 0.00 0.00 1.78
6737 7263 8.136057 AGCAACTATAAATTCTTCTGACGATG 57.864 34.615 0.00 0.00 0.00 3.84
7084 7610 3.605634 TCTCATCAACAAATACACCCCG 58.394 45.455 0.00 0.00 0.00 5.73
7222 7748 4.327982 TGCACTGGCTATATCTGAAGAC 57.672 45.455 0.00 0.00 41.91 3.01
7384 7910 9.952188 GAAAAGGATCATAGCCTATTAAACAAC 57.048 33.333 0.00 0.00 33.76 3.32
8350 9597 5.180117 CGGGATAATTGATTACTTGAGGCAG 59.820 44.000 0.00 0.00 0.00 4.85
8540 9787 0.598065 GTGATGTTGGTGCCTGAACC 59.402 55.000 0.00 0.00 40.94 3.62
8544 9791 3.521531 TGATGTTGGTGCCTGAACCTATA 59.478 43.478 0.00 0.00 41.16 1.31
8545 9792 3.627395 TGTTGGTGCCTGAACCTATAG 57.373 47.619 0.00 0.00 41.16 1.31
8564 9811 7.068839 ACCTATAGTGAACTCTTGAGTATGGTG 59.931 40.741 3.52 0.00 0.00 4.17
8782 10029 2.026641 GTGATTGGCATGCACATACCT 58.973 47.619 21.36 0.00 32.96 3.08
8819 10066 3.849574 TGTTGATGATCCTAGGGTGGAAA 59.150 43.478 9.46 0.00 39.85 3.13
8880 10127 8.155821 TGGTAATAAAACTGTCGAAAATGACA 57.844 30.769 0.00 0.00 46.15 3.58
8897 10144 1.376424 CACTCAGAATGCGCAGGGT 60.376 57.895 18.32 4.88 34.76 4.34
9115 10367 7.332557 TCCGTTAATTGCTAGAAGATGGTTTA 58.667 34.615 0.00 0.00 0.00 2.01
9196 10452 1.804151 GTGCATTAGCGAACCTGAACA 59.196 47.619 0.00 0.00 46.23 3.18
9203 10459 3.626028 AGCGAACCTGAACAATTTCAC 57.374 42.857 0.00 0.00 36.79 3.18
9309 12818 4.853924 ACAAAATCGGAAAGTGAGCAAT 57.146 36.364 0.00 0.00 0.00 3.56
9327 12836 3.489398 GCAATGTCTAGACTACGACCAGG 60.489 52.174 23.01 4.67 0.00 4.45
9350 12888 1.100510 GGGGGCGGCTAAAGTAAAAG 58.899 55.000 9.56 0.00 0.00 2.27
9364 12902 9.760077 GCTAAAGTAAAAGGTATATAGTCTGCA 57.240 33.333 0.00 0.00 0.00 4.41
9393 12931 8.896320 TCATATTAAAATTAGGCGTCTTGCTA 57.104 30.769 0.00 0.00 45.43 3.49
9435 12984 2.203422 CCCTGTTTGCCCAACGGA 60.203 61.111 6.32 0.00 43.78 4.69
9443 12992 0.034337 TTGCCCAACGGACACTCTAC 59.966 55.000 0.00 0.00 0.00 2.59
9478 13027 0.179032 TGTCACTGGCACCGTTGAAT 60.179 50.000 0.00 0.00 0.00 2.57
9494 13308 1.066215 TGAATAGCATCACGCACCACT 60.066 47.619 0.00 0.00 46.13 4.00
9566 13383 5.688814 TCCATCAAGATGACAGATCTGTT 57.311 39.130 28.46 14.70 45.05 3.16
9589 13459 9.825109 TGTTCCATACACTATCGAAATGAAATA 57.175 29.630 0.00 0.00 0.00 1.40
9599 13469 5.856126 TCGAAATGAAATAGCGAACAGTT 57.144 34.783 0.00 0.00 30.72 3.16
9605 13475 5.756950 TGAAATAGCGAACAGTTAGAACG 57.243 39.130 0.00 0.00 0.00 3.95
9642 13512 6.102897 ACTTAGGGAATCTCCAACGATATG 57.897 41.667 0.00 0.00 38.64 1.78
9665 13535 5.068329 TGCATGAAAACAGACACACCAAATA 59.932 36.000 0.00 0.00 0.00 1.40
9668 13538 5.527951 TGAAAACAGACACACCAAATATGC 58.472 37.500 0.00 0.00 0.00 3.14
9669 13539 5.068329 TGAAAACAGACACACCAAATATGCA 59.932 36.000 0.00 0.00 0.00 3.96
9715 13595 2.933287 AGCCGACCATCCAACCCA 60.933 61.111 0.00 0.00 0.00 4.51
9716 13596 2.750237 GCCGACCATCCAACCCAC 60.750 66.667 0.00 0.00 0.00 4.61
9745 13625 9.605955 CGTCAAATAAAAACTGACATGACATTA 57.394 29.630 0.00 0.00 39.56 1.90
9840 13720 1.231068 GGGCACATCCATGTCCCAT 59.769 57.895 16.42 0.00 40.48 4.00
9869 13749 2.789409 GGGACCACACTTTAGCTGAT 57.211 50.000 0.00 0.00 0.00 2.90
9892 13772 7.769970 TGATCAAAGTCATCTATTGTGCATGTA 59.230 33.333 0.00 0.00 0.00 2.29
9901 13781 6.225981 TCTATTGTGCATGTACAGTGATCT 57.774 37.500 19.69 4.84 0.00 2.75
9932 13813 2.283086 TGCTCACTTAACACAACGAACG 59.717 45.455 0.00 0.00 0.00 3.95
9939 13820 6.013085 CACTTAACACAACGAACGGAATATG 58.987 40.000 0.00 0.00 0.00 1.78
9942 13823 3.921677 ACACAACGAACGGAATATGACT 58.078 40.909 0.00 0.00 0.00 3.41
9951 13832 5.175126 CGAACGGAATATGACTGGTTACATC 59.825 44.000 0.00 0.00 0.00 3.06
9963 13844 8.675705 TGACTGGTTACATCCATTACATAATG 57.324 34.615 4.87 4.87 42.00 1.90
9964 13845 8.490311 TGACTGGTTACATCCATTACATAATGA 58.510 33.333 12.30 1.06 44.40 2.57
9965 13846 9.507329 GACTGGTTACATCCATTACATAATGAT 57.493 33.333 12.30 3.04 44.40 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.490217 CAGCGGTGAGGTAGTCCG 59.510 66.667 9.50 0.00 45.94 4.79
71 72 1.750778 CACTTTGTTGGCACTCCAGTT 59.249 47.619 0.00 0.00 44.53 3.16
83 84 2.192624 GCGTTTGTGATGCACTTTGTT 58.807 42.857 0.00 0.00 40.14 2.83
84 85 1.838913 GCGTTTGTGATGCACTTTGT 58.161 45.000 0.00 0.00 40.14 2.83
86 87 0.660488 TCGCGTTTGTGATGCACTTT 59.340 45.000 5.77 0.00 40.43 2.66
101 102 0.530650 ATTGTATCACCTGCCTCGCG 60.531 55.000 0.00 0.00 0.00 5.87
171 636 2.663852 CGGACGGTGTGTGTTCCC 60.664 66.667 0.00 0.00 0.00 3.97
232 697 4.085055 GGCAATAATGTCTGTATCGTCACG 60.085 45.833 0.00 0.00 0.00 4.35
285 750 7.314393 AGAAAAGGTTAACTTCTAGTCTAGCG 58.686 38.462 5.42 0.00 38.85 4.26
290 755 8.775527 CAGGAAAGAAAAGGTTAACTTCTAGTC 58.224 37.037 5.42 7.94 38.85 2.59
291 756 8.272889 ACAGGAAAGAAAAGGTTAACTTCTAGT 58.727 33.333 5.42 0.00 38.85 2.57
292 757 8.678593 ACAGGAAAGAAAAGGTTAACTTCTAG 57.321 34.615 5.42 0.00 38.85 2.43
293 758 8.269317 TGACAGGAAAGAAAAGGTTAACTTCTA 58.731 33.333 5.42 0.00 38.85 2.10
294 759 7.116736 TGACAGGAAAGAAAAGGTTAACTTCT 58.883 34.615 5.42 4.26 38.85 2.85
295 760 7.329588 TGACAGGAAAGAAAAGGTTAACTTC 57.670 36.000 5.42 1.87 38.85 3.01
296 761 7.147897 CCTTGACAGGAAAGAAAAGGTTAACTT 60.148 37.037 5.42 0.00 44.19 2.66
297 762 6.321435 CCTTGACAGGAAAGAAAAGGTTAACT 59.679 38.462 5.42 0.00 44.19 2.24
298 763 6.504398 CCTTGACAGGAAAGAAAAGGTTAAC 58.496 40.000 0.00 0.00 44.19 2.01
299 764 6.709018 CCTTGACAGGAAAGAAAAGGTTAA 57.291 37.500 0.00 0.00 44.19 2.01
318 783 7.564137 TCCTTTTAGGGGGAACGAATCCTTG 62.564 48.000 10.93 0.00 40.37 3.61
331 796 5.959583 ATGAACTAGTCTCCTTTTAGGGG 57.040 43.478 0.00 0.00 37.13 4.79
377 842 5.666913 GCGATGCATTGTCAGTTTTGATTTG 60.667 40.000 15.45 0.00 35.39 2.32
413 878 2.288729 GGTGGTTTCGTGTACCTTTCAC 59.711 50.000 0.00 0.00 36.60 3.18
479 944 1.075450 ATGGGTAGACGGGAGGGAC 60.075 63.158 0.00 0.00 0.00 4.46
500 965 3.612423 GCGCCAGTTTGAATTATTGGTTC 59.388 43.478 0.00 0.00 0.00 3.62
502 967 2.094234 GGCGCCAGTTTGAATTATTGGT 60.094 45.455 24.80 0.00 0.00 3.67
523 988 1.007964 CCTAGCCGTGCGATCTCAG 60.008 63.158 0.00 0.00 0.00 3.35
566 1031 1.024579 GTATTCCTGGCGGTGGTGTG 61.025 60.000 0.00 0.00 0.00 3.82
567 1032 1.298667 GTATTCCTGGCGGTGGTGT 59.701 57.895 0.00 0.00 0.00 4.16
568 1033 1.813753 CGTATTCCTGGCGGTGGTG 60.814 63.158 0.00 0.00 0.00 4.17
569 1034 2.582436 CGTATTCCTGGCGGTGGT 59.418 61.111 0.00 0.00 0.00 4.16
570 1035 2.869503 AAGCGTATTCCTGGCGGTGG 62.870 60.000 0.00 0.00 36.46 4.61
571 1036 1.024579 AAAGCGTATTCCTGGCGGTG 61.025 55.000 0.00 0.00 36.46 4.94
803 1292 0.527817 GGTGGGATTGTCGCGACTAG 60.528 60.000 36.27 0.00 31.21 2.57
811 1300 0.183731 GATCTGGGGGTGGGATTGTC 59.816 60.000 0.00 0.00 0.00 3.18
813 1302 1.149174 CGATCTGGGGGTGGGATTG 59.851 63.158 0.00 0.00 0.00 2.67
814 1303 1.004230 TCGATCTGGGGGTGGGATT 59.996 57.895 0.00 0.00 0.00 3.01
815 1304 1.460305 CTCGATCTGGGGGTGGGAT 60.460 63.158 0.00 0.00 0.00 3.85
816 1305 2.041922 CTCGATCTGGGGGTGGGA 60.042 66.667 0.00 0.00 0.00 4.37
817 1306 2.041922 TCTCGATCTGGGGGTGGG 60.042 66.667 0.00 0.00 0.00 4.61
818 1307 2.801631 GCTCTCGATCTGGGGGTGG 61.802 68.421 0.00 0.00 0.00 4.61
819 1308 1.743321 GAGCTCTCGATCTGGGGGTG 61.743 65.000 6.43 0.00 0.00 4.61
820 1309 1.456705 GAGCTCTCGATCTGGGGGT 60.457 63.158 6.43 0.00 0.00 4.95
821 1310 2.206536 GGAGCTCTCGATCTGGGGG 61.207 68.421 14.64 0.00 0.00 5.40
864 1353 3.641925 GAGAGAGGGACGGACGGGT 62.642 68.421 0.00 0.00 0.00 5.28
865 1354 2.829458 GAGAGAGGGACGGACGGG 60.829 72.222 0.00 0.00 0.00 5.28
974 1464 2.734591 GTCAGACAGGGACGCACA 59.265 61.111 0.00 0.00 0.00 4.57
1034 1524 1.875364 GAAGCTTACGTACGGGCGG 60.875 63.158 21.06 7.73 35.98 6.13
1073 1563 1.134340 CCGATAAAACCCACCCGATCA 60.134 52.381 0.00 0.00 0.00 2.92
1180 1670 3.204597 ACGAACAGCGAAACAAACAAA 57.795 38.095 0.00 0.00 44.57 2.83
1181 1671 2.904011 ACGAACAGCGAAACAAACAA 57.096 40.000 0.00 0.00 44.57 2.83
1182 1672 2.904011 AACGAACAGCGAAACAAACA 57.096 40.000 0.00 0.00 44.57 2.83
1311 1801 2.956987 GGCACAGCAACGCTCAAT 59.043 55.556 0.00 0.00 36.40 2.57
1424 1914 9.776158 CCTATCATGTCGTCAAGTATAATACTC 57.224 37.037 0.00 0.00 38.26 2.59
1426 1916 9.343103 CACCTATCATGTCGTCAAGTATAATAC 57.657 37.037 0.00 0.00 0.00 1.89
1427 1917 9.292195 TCACCTATCATGTCGTCAAGTATAATA 57.708 33.333 0.00 0.00 0.00 0.98
1428 1918 8.178313 TCACCTATCATGTCGTCAAGTATAAT 57.822 34.615 0.00 0.00 0.00 1.28
1434 1924 4.748892 AGTTCACCTATCATGTCGTCAAG 58.251 43.478 0.00 0.00 0.00 3.02
1509 1999 0.250727 ACACCGATTGTCCCAACAGG 60.251 55.000 0.00 0.00 36.57 4.00
1521 2011 1.697432 TGTTCCTTGAAGGACACCGAT 59.303 47.619 14.62 0.00 45.78 4.18
1554 2044 5.538118 ACATGGGCAACTAAACTAAAAAGC 58.462 37.500 0.00 0.00 0.00 3.51
1598 2088 8.411683 AGTGTACAGTACTCCCGAAAATAATAG 58.588 37.037 12.07 0.00 0.00 1.73
1675 2186 3.926616 ACCAGTGGATTCTACAAAGTCG 58.073 45.455 18.40 0.00 0.00 4.18
1706 2217 7.940850 AGTGCAAAATAAGTTACTGTGTCAAT 58.059 30.769 0.00 0.00 0.00 2.57
1776 2287 1.834188 AGTTCCAGCGTAAATTGGGG 58.166 50.000 0.00 0.00 35.13 4.96
1834 2345 4.081972 TCAGCACTACAAGAATCTCCAGTC 60.082 45.833 0.00 0.00 0.00 3.51
1913 2428 0.981183 AACTGAAGGGACCACGCATA 59.019 50.000 0.00 0.00 0.00 3.14
1914 2429 0.110486 AAACTGAAGGGACCACGCAT 59.890 50.000 0.00 0.00 0.00 4.73
1915 2430 0.534203 GAAACTGAAGGGACCACGCA 60.534 55.000 0.00 0.00 0.00 5.24
1916 2431 1.566018 CGAAACTGAAGGGACCACGC 61.566 60.000 0.00 0.00 0.00 5.34
2078 2593 5.105146 AGCAAGAATCACTACAGGTAAGGAG 60.105 44.000 0.00 0.00 0.00 3.69
2136 2651 3.382546 CCATTCCATCTCACCATTTGTCC 59.617 47.826 0.00 0.00 0.00 4.02
2137 2652 3.181483 GCCATTCCATCTCACCATTTGTC 60.181 47.826 0.00 0.00 0.00 3.18
2277 2792 5.104776 AGCTATAAGAGAATGGTGCACAGAA 60.105 40.000 20.43 3.64 0.00 3.02
2358 2873 3.686691 GCCACCTGAGAAATAAGGAGCAT 60.687 47.826 0.00 0.00 0.00 3.79
2365 2880 2.505819 GAGGGAGCCACCTGAGAAATAA 59.494 50.000 0.82 0.00 42.10 1.40
2395 2910 4.285517 AGCTCAATTTCCTCTTCAGAGTCA 59.714 41.667 3.15 0.00 40.48 3.41
2452 2967 5.499313 TGCTCCATAAATTCATCACTGACA 58.501 37.500 0.00 0.00 0.00 3.58
2535 3050 4.509122 GGATGGGAATATTAGCACCACCAT 60.509 45.833 0.00 0.00 39.96 3.55
2594 3109 1.406614 GGCACCTTGATCAGTCTCCAG 60.407 57.143 0.00 0.00 0.00 3.86
2625 3140 4.889409 AGATGACATTACCGGCATCAAAAT 59.111 37.500 16.60 0.00 39.57 1.82
3252 3767 5.012354 GGATCCATTGCATTTCCCATATTGT 59.988 40.000 6.95 0.00 0.00 2.71
3446 3961 1.717791 GCATCTGCTTATGTGCGGCA 61.718 55.000 0.00 0.00 39.06 5.69
4111 4626 9.901172 AACCAAAAAGGAGGTAGTAACATATAG 57.099 33.333 0.00 0.00 41.22 1.31
4153 4668 7.194607 ACATTGGTCAAATTATCTAGCGATG 57.805 36.000 0.00 0.00 37.29 3.84
4623 5143 2.099592 GCTCATGCATTCCGAATTTCCA 59.900 45.455 0.00 0.00 39.41 3.53
5100 5620 7.280876 TGAATTAGACTGAATACATTGGCTGTC 59.719 37.037 0.00 0.00 39.39 3.51
5120 5646 3.026630 GGATCAGTCCGCGATGAATTA 57.973 47.619 8.23 0.00 34.13 1.40
5121 5647 1.871080 GGATCAGTCCGCGATGAATT 58.129 50.000 8.23 0.00 34.13 2.17
5122 5648 3.595691 GGATCAGTCCGCGATGAAT 57.404 52.632 8.23 0.00 34.13 2.57
5133 5659 1.063642 TGTCGAGGGATCTGGATCAGT 60.064 52.381 11.93 0.00 39.54 3.41
5305 5831 1.445582 CTAGTCCCCGTGTGCGTTC 60.446 63.158 0.00 0.00 36.15 3.95
5684 6210 4.453480 AATTCTTCTTTGACCCTCACCA 57.547 40.909 0.00 0.00 0.00 4.17
5986 6512 8.525290 TCAATAGATGAGTATCTGAACACAGA 57.475 34.615 0.00 0.00 43.41 3.41
6315 6841 4.142600 CCTTTCTTGTGCAAGCATACTACC 60.143 45.833 7.03 0.00 38.28 3.18
6390 6916 3.702792 TGTCAAAAACTCAACCCTTGGA 58.297 40.909 0.00 0.00 0.00 3.53
6623 7149 2.451490 AGAACTCAGCTCATTCTCCGA 58.549 47.619 0.00 0.00 0.00 4.55
6737 7263 1.069227 GCCACCACGAGAATTGTCAAC 60.069 52.381 3.24 0.00 0.00 3.18
7084 7610 5.053145 AGTTGTGTCAGTGATGAAGAAGTC 58.947 41.667 0.00 0.00 0.00 3.01
7222 7748 5.105635 TGCAGCTTCAGAATAAATTCCTTGG 60.106 40.000 0.00 0.00 37.51 3.61
7384 7910 8.713737 ATTCCTCATATGATAATGACGATGTG 57.286 34.615 5.72 0.00 32.51 3.21
8167 9414 5.108385 ACTCAACGAAAACTATTTGCAGG 57.892 39.130 0.00 0.00 0.00 4.85
8335 9582 5.070446 CCAGGTATACTGCCTCAAGTAATCA 59.930 44.000 2.25 0.00 46.14 2.57
8350 9597 4.007659 CCAGTTGTTTGTCCCAGGTATAC 58.992 47.826 0.00 0.00 0.00 1.47
8517 9764 1.955778 TCAGGCACCAACATCACAAAG 59.044 47.619 0.00 0.00 0.00 2.77
8540 9787 6.920758 GCACCATACTCAAGAGTTCACTATAG 59.079 42.308 8.17 0.00 42.54 1.31
8544 9791 3.324846 TGCACCATACTCAAGAGTTCACT 59.675 43.478 8.17 0.00 42.54 3.41
8545 9792 3.664107 TGCACCATACTCAAGAGTTCAC 58.336 45.455 8.17 0.00 42.54 3.18
8579 9826 7.942341 TCAACCATATTTTCCAGTAAGACAAGT 59.058 33.333 0.00 0.00 0.00 3.16
8782 10029 8.464404 GGATCATCAACAAAGATCATTTCTTCA 58.536 33.333 0.00 0.00 44.09 3.02
8880 10127 0.176680 CTACCCTGCGCATTCTGAGT 59.823 55.000 12.24 4.93 0.00 3.41
8897 10144 0.391228 TATGGAAAGATGCGCGGCTA 59.609 50.000 8.83 0.00 0.00 3.93
9115 10367 9.778741 CATATGGGTTACACACATCTAATAACT 57.221 33.333 0.00 0.00 37.83 2.24
9133 10385 7.577303 AGAAACAATCTCATGTACATATGGGT 58.423 34.615 8.32 0.00 30.46 4.51
9233 12742 9.953697 AGTGTCTTCTACTATGATTCGTAATTC 57.046 33.333 0.00 0.00 0.00 2.17
9309 12818 1.064906 CCCCTGGTCGTAGTCTAGACA 60.065 57.143 24.44 8.16 39.01 3.41
9327 12836 4.191015 CTTTAGCCGCCCCCTCCC 62.191 72.222 0.00 0.00 0.00 4.30
9364 12902 9.950680 CAAGACGCCTAATTTTAATATGAACAT 57.049 29.630 0.00 0.00 0.00 2.71
9375 12913 7.694886 GTCTTAATAGCAAGACGCCTAATTTT 58.305 34.615 0.65 0.00 43.55 1.82
9393 12931 7.444487 GGAGGTGTTTCTTTGTGTAGTCTTAAT 59.556 37.037 0.00 0.00 0.00 1.40
9395 12933 6.285990 GGAGGTGTTTCTTTGTGTAGTCTTA 58.714 40.000 0.00 0.00 0.00 2.10
9396 12934 5.123936 GGAGGTGTTTCTTTGTGTAGTCTT 58.876 41.667 0.00 0.00 0.00 3.01
9435 12984 4.931914 TCCTAGCTTAAGGTGTAGAGTGT 58.068 43.478 17.34 0.00 37.91 3.55
9443 12992 4.872691 CAGTGACAATCCTAGCTTAAGGTG 59.127 45.833 17.34 7.20 37.91 4.00
9478 13027 0.108662 CTCAGTGGTGCGTGATGCTA 60.109 55.000 0.00 0.00 46.63 3.49
9494 13308 0.179137 GGTGTCGCGATGTGATCTCA 60.179 55.000 14.06 0.00 0.00 3.27
9522 13336 0.327924 ATTGCCCTTCGGTGACATCA 59.672 50.000 0.00 0.00 0.00 3.07
9523 13337 0.734889 CATTGCCCTTCGGTGACATC 59.265 55.000 0.00 0.00 0.00 3.06
9524 13338 0.038166 ACATTGCCCTTCGGTGACAT 59.962 50.000 0.00 0.00 0.00 3.06
9565 13382 8.988934 GCTATTTCATTTCGATAGTGTATGGAA 58.011 33.333 0.00 0.00 32.20 3.53
9566 13383 7.328493 CGCTATTTCATTTCGATAGTGTATGGA 59.672 37.037 0.00 0.00 32.15 3.41
9589 13459 0.037605 CCCCGTTCTAACTGTTCGCT 60.038 55.000 0.00 0.00 0.00 4.93
9599 13469 3.461085 AGTACTCTATCCACCCCGTTCTA 59.539 47.826 0.00 0.00 0.00 2.10
9605 13475 3.141649 TCCCTAAGTACTCTATCCACCCC 59.858 52.174 0.00 0.00 0.00 4.95
9642 13512 3.435105 TTGGTGTGTCTGTTTTCATGC 57.565 42.857 0.00 0.00 0.00 4.06
9716 13596 6.086765 GTCATGTCAGTTTTTATTTGACGCAG 59.913 38.462 0.00 0.00 43.12 5.18
9745 13625 8.823220 ATGCAAAAGTTCCCAATACTAATACT 57.177 30.769 0.00 0.00 0.00 2.12
9794 13674 5.290386 CCGGTGAAGATTTAGACTATGGTC 58.710 45.833 0.00 0.00 42.41 4.02
9798 13678 3.709653 TGGCCGGTGAAGATTTAGACTAT 59.290 43.478 1.90 0.00 0.00 2.12
9828 13708 5.537811 CCACAAGGACATGGGACATGGAT 62.538 52.174 13.19 0.00 40.00 3.41
9869 13749 6.878389 TGTACATGCACAATAGATGACTTTGA 59.122 34.615 0.00 0.00 0.00 2.69
9901 13781 5.997129 TGTGTTAAGTGAGCATTGATCTTGA 59.003 36.000 3.27 0.00 0.00 3.02
9932 13813 7.936847 TGTAATGGATGTAACCAGTCATATTCC 59.063 37.037 0.00 0.00 43.49 3.01
9939 13820 8.902540 TCATTATGTAATGGATGTAACCAGTC 57.097 34.615 11.64 0.00 43.49 3.51


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

AutoCloner maintained by Alex Coulton.