Multiple sequence alignment - TraesCS1B01G084400

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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 TraesCS1B01G084400 chr1B 100.000 7767 0 0 1 7767 68936822 68944588 0.000000e+00 14344
1 TraesCS1B01G084400 chr1B 94.903 5415 272 4 1280 6693 656419489 656414078 0.000000e+00 8468
2 TraesCS1B01G084400 chr1B 91.518 1285 105 2 1 1281 533811575 533812859 0.000000e+00 1766
3 TraesCS1B01G084400 chr1B 88.354 1288 142 5 1 1281 510814675 510813389 0.000000e+00 1541
4 TraesCS1B01G084400 chr1B 94.366 71 4 0 6723 6793 533812852 533812922 8.240000e-20 110
5 TraesCS1B01G084400 chr1B 98.361 61 1 0 6721 6781 33827765 33827825 2.960000e-19 108
6 TraesCS1B01G084400 chr6B 96.283 5407 198 3 1280 6686 680314797 680320200 0.000000e+00 8868
7 TraesCS1B01G084400 chr6B 91.485 5414 446 11 1282 6691 461952452 461957854 0.000000e+00 7430
8 TraesCS1B01G084400 chr6B 95.320 1282 53 3 4 1282 478884227 478882950 0.000000e+00 2028
9 TraesCS1B01G084400 chr7B 96.138 5412 174 8 1280 6691 679614674 679609298 0.000000e+00 8804
10 TraesCS1B01G084400 chr7B 97.018 4393 128 2 1280 5672 614304237 614308626 0.000000e+00 7384
11 TraesCS1B01G084400 chr7B 89.261 1285 133 3 1 1281 74304280 74302997 0.000000e+00 1604
12 TraesCS1B01G084400 chr7B 97.015 67 1 1 6721 6786 730377291 730377357 2.290000e-20 111
13 TraesCS1B01G084400 chr7B 89.157 83 5 4 6723 6802 74303004 74302923 4.960000e-17 100
14 TraesCS1B01G084400 chr1D 89.791 5417 538 12 1280 6686 443437759 443432348 0.000000e+00 6926
15 TraesCS1B01G084400 chr1D 89.434 5423 544 16 1281 6689 28241120 28235713 0.000000e+00 6813
16 TraesCS1B01G084400 chr1D 90.339 383 23 8 7385 7767 48884310 48884678 2.520000e-134 490
17 TraesCS1B01G084400 chr1D 82.387 511 25 29 6850 7317 48883475 48883963 1.220000e-102 385
18 TraesCS1B01G084400 chr3B 96.265 4230 134 3 2464 6692 732068556 732064350 0.000000e+00 6914
19 TraesCS1B01G084400 chr3B 96.708 486 16 0 1280 1765 732093742 732093257 0.000000e+00 809
20 TraesCS1B01G084400 chr5D 90.847 4086 374 0 1280 5365 556036942 556041027 0.000000e+00 5474
21 TraesCS1B01G084400 chr2D 89.884 4132 407 9 1280 5403 501685852 501689980 0.000000e+00 5304
22 TraesCS1B01G084400 chr1A 83.339 5438 859 37 1280 6696 17871829 17877240 0.000000e+00 4979
23 TraesCS1B01G084400 chr1A 83.577 3014 472 18 3690 6691 568725690 568722688 0.000000e+00 2802
24 TraesCS1B01G084400 chr1A 87.475 495 34 13 7275 7767 48783887 48784355 5.300000e-151 545
25 TraesCS1B01G084400 chr1A 80.903 288 22 12 6883 7156 48783599 48783867 6.150000e-46 196
26 TraesCS1B01G084400 chr7D 87.193 4232 528 10 1553 5776 452995605 452991380 0.000000e+00 4800
27 TraesCS1B01G084400 chr2B 92.332 1278 95 1 4 1278 115905326 115904049 0.000000e+00 1814
28 TraesCS1B01G084400 chr2B 89.650 1285 126 5 1 1281 751294006 751292725 0.000000e+00 1629
29 TraesCS1B01G084400 chr2B 91.026 78 6 1 6723 6799 751291560 751291483 3.830000e-18 104
30 TraesCS1B01G084400 chr2B 91.026 78 6 1 6723 6799 751292074 751291997 3.830000e-18 104
31 TraesCS1B01G084400 chr2B 91.026 78 6 1 6723 6799 751292732 751292655 3.830000e-18 104
32 TraesCS1B01G084400 chr6A 86.973 1282 158 6 5 1281 511536377 511537654 0.000000e+00 1434
33 TraesCS1B01G084400 chr6A 86.739 1282 161 6 5 1281 97342668 97341391 0.000000e+00 1417
34 TraesCS1B01G084400 chr6A 91.026 78 4 3 6723 6799 543213945 543214020 1.380000e-17 102
35 TraesCS1B01G084400 chr4A 86.693 1285 159 10 5 1281 494000389 494001669 0.000000e+00 1415
36 TraesCS1B01G084400 chr4B 87.500 88 7 4 6721 6806 12822435 12822520 1.780000e-16 99


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 TraesCS1B01G084400 chr1B 68936822 68944588 7766 False 14344.00 14344 100.000 1 7767 1 chr1B.!!$F2 7766
1 TraesCS1B01G084400 chr1B 656414078 656419489 5411 True 8468.00 8468 94.903 1280 6693 1 chr1B.!!$R2 5413
2 TraesCS1B01G084400 chr1B 510813389 510814675 1286 True 1541.00 1541 88.354 1 1281 1 chr1B.!!$R1 1280
3 TraesCS1B01G084400 chr1B 533811575 533812922 1347 False 938.00 1766 92.942 1 6793 2 chr1B.!!$F3 6792
4 TraesCS1B01G084400 chr6B 680314797 680320200 5403 False 8868.00 8868 96.283 1280 6686 1 chr6B.!!$F2 5406
5 TraesCS1B01G084400 chr6B 461952452 461957854 5402 False 7430.00 7430 91.485 1282 6691 1 chr6B.!!$F1 5409
6 TraesCS1B01G084400 chr6B 478882950 478884227 1277 True 2028.00 2028 95.320 4 1282 1 chr6B.!!$R1 1278
7 TraesCS1B01G084400 chr7B 679609298 679614674 5376 True 8804.00 8804 96.138 1280 6691 1 chr7B.!!$R1 5411
8 TraesCS1B01G084400 chr7B 614304237 614308626 4389 False 7384.00 7384 97.018 1280 5672 1 chr7B.!!$F1 4392
9 TraesCS1B01G084400 chr7B 74302923 74304280 1357 True 852.00 1604 89.209 1 6802 2 chr7B.!!$R2 6801
10 TraesCS1B01G084400 chr1D 443432348 443437759 5411 True 6926.00 6926 89.791 1280 6686 1 chr1D.!!$R2 5406
11 TraesCS1B01G084400 chr1D 28235713 28241120 5407 True 6813.00 6813 89.434 1281 6689 1 chr1D.!!$R1 5408
12 TraesCS1B01G084400 chr1D 48883475 48884678 1203 False 437.50 490 86.363 6850 7767 2 chr1D.!!$F1 917
13 TraesCS1B01G084400 chr3B 732064350 732068556 4206 True 6914.00 6914 96.265 2464 6692 1 chr3B.!!$R1 4228
14 TraesCS1B01G084400 chr5D 556036942 556041027 4085 False 5474.00 5474 90.847 1280 5365 1 chr5D.!!$F1 4085
15 TraesCS1B01G084400 chr2D 501685852 501689980 4128 False 5304.00 5304 89.884 1280 5403 1 chr2D.!!$F1 4123
16 TraesCS1B01G084400 chr1A 17871829 17877240 5411 False 4979.00 4979 83.339 1280 6696 1 chr1A.!!$F1 5416
17 TraesCS1B01G084400 chr1A 568722688 568725690 3002 True 2802.00 2802 83.577 3690 6691 1 chr1A.!!$R1 3001
18 TraesCS1B01G084400 chr1A 48783599 48784355 756 False 370.50 545 84.189 6883 7767 2 chr1A.!!$F2 884
19 TraesCS1B01G084400 chr7D 452991380 452995605 4225 True 4800.00 4800 87.193 1553 5776 1 chr7D.!!$R1 4223
20 TraesCS1B01G084400 chr2B 115904049 115905326 1277 True 1814.00 1814 92.332 4 1278 1 chr2B.!!$R1 1274
21 TraesCS1B01G084400 chr2B 751291483 751294006 2523 True 485.25 1629 90.682 1 6799 4 chr2B.!!$R2 6798
22 TraesCS1B01G084400 chr6A 511536377 511537654 1277 False 1434.00 1434 86.973 5 1281 1 chr6A.!!$F1 1276
23 TraesCS1B01G084400 chr6A 97341391 97342668 1277 True 1417.00 1417 86.739 5 1281 1 chr6A.!!$R1 1276
24 TraesCS1B01G084400 chr4A 494000389 494001669 1280 False 1415.00 1415 86.693 5 1281 1 chr4A.!!$F1 1276

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
407 411 1.347707 CAAGGCCTACAGACACTTGGA 59.652 52.381 5.16 0.0 35.96 3.53 F
1169 1185 0.889306 ACTCGGGAGTTCTTTCCTCG 59.111 55.000 0.00 0.0 38.83 4.63 F
1616 1657 1.423161 AGCCTTGGAGAGAAGCAAACT 59.577 47.619 0.00 0.0 0.00 2.66 F
3288 3332 1.485066 TCCCGAAGCCTCTCCATAAAC 59.515 52.381 0.00 0.0 0.00 2.01 F
4386 4464 0.468226 AGCCACGGAACTCTTGAACA 59.532 50.000 0.00 0.0 0.00 3.18 F
4787 4876 0.323302 TAAAGGCAGATGACGCACCA 59.677 50.000 0.00 0.0 0.00 4.17 F
6706 6805 0.172352 AAAACTGGGCACACACAACG 59.828 50.000 0.00 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 1997 0.390603 TGACCGTGCCAAGATAACCG 60.391 55.000 0.00 0.00 0.00 4.44 R
2201 2245 1.133606 GTTTTGGTGGAGGGTCCTTCA 60.134 52.381 3.03 0.00 37.46 3.02 R
3540 3604 0.320073 CTTCTCGGTGCGGGTTAACA 60.320 55.000 8.10 0.00 0.00 2.41 R
4481 4559 0.982673 CGACTGAATCGTGTTCGGTC 59.017 55.000 23.37 23.37 46.25 4.79 R
6285 6382 2.572095 TTCGATCAGCGGGCGTCAAT 62.572 55.000 0.00 0.00 41.33 2.57 R
6715 6814 0.670854 GCCACAAGTCCTCGAGAACC 60.671 60.000 15.71 0.55 0.00 3.62 R
7637 8096 3.313524 TCGCCCAGCAGCTTGAGA 61.314 61.111 0.00 0.00 0.00 3.27 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
23 24 2.014857 CTCCTTCCGTACGATCACTCA 58.985 52.381 18.76 0.00 0.00 3.41
55 56 2.103432 TGTCGCTTCAACAGGGTTTCTA 59.897 45.455 0.00 0.00 36.78 2.10
185 186 2.551270 TGACTTCTTGGCCTGGTATCT 58.449 47.619 3.32 0.00 0.00 1.98
259 260 7.483691 CACATGATCATAATGTTGTCACAACTG 59.516 37.037 21.23 11.26 36.10 3.16
320 321 3.009143 GGGTGGAACTACATCTGGAAGTT 59.991 47.826 1.28 1.28 36.20 2.66
354 355 7.399245 TCAGAAAATGAAGATCAATGCATGA 57.601 32.000 0.00 0.03 37.45 3.07
407 411 1.347707 CAAGGCCTACAGACACTTGGA 59.652 52.381 5.16 0.00 35.96 3.53
471 478 4.210331 ACTCATTCCATGCCTTGATAACC 58.790 43.478 0.00 0.00 0.00 2.85
637 646 1.846007 TATTTGGCGGATTTGGCAGT 58.154 45.000 0.00 0.00 45.81 4.40
762 774 4.589374 ACTACGGAGGAGATCATTAAAGGG 59.411 45.833 0.00 0.00 0.00 3.95
1045 1060 3.070446 ACAACATTCTGACTTACCGGTGA 59.930 43.478 19.93 8.52 0.00 4.02
1153 1169 6.215495 AGATCAAAGCACTTCTAGGTACTC 57.785 41.667 0.00 0.00 41.75 2.59
1161 1177 3.377798 CACTTCTAGGTACTCGGGAGTTC 59.622 52.174 6.65 1.70 42.54 3.01
1169 1185 0.889306 ACTCGGGAGTTCTTTCCTCG 59.111 55.000 0.00 0.00 38.83 4.63
1371 1412 3.770388 GTCACTAAGAAGCTAGGGGTCTT 59.230 47.826 3.27 3.27 0.00 3.01
1387 1428 2.355108 GGTCTTGTCAAGCCAGCTATCA 60.355 50.000 16.57 0.00 0.00 2.15
1464 1505 4.467082 TGGCCTGATTACATGCTGAATTTT 59.533 37.500 3.32 0.00 37.69 1.82
1539 1580 2.254546 ACTGAACGAGAATTGTGGCA 57.745 45.000 0.00 0.00 29.05 4.92
1601 1642 5.131642 TCCATTATCACATGAGAGAAGCCTT 59.868 40.000 0.00 0.00 0.00 4.35
1616 1657 1.423161 AGCCTTGGAGAGAAGCAAACT 59.577 47.619 0.00 0.00 0.00 2.66
1619 1660 3.683802 CCTTGGAGAGAAGCAAACTGAT 58.316 45.455 0.00 0.00 0.00 2.90
1781 1824 2.810274 CCATCCATGGCGATCTTTACAG 59.190 50.000 6.96 0.00 41.75 2.74
1953 1997 6.467677 AGTGCCATATAGACCACATTATCAC 58.532 40.000 0.00 0.00 0.00 3.06
1957 2001 6.464222 CCATATAGACCACATTATCACGGTT 58.536 40.000 0.00 0.00 0.00 4.44
2201 2245 3.555966 GTTTCATCCGGGAGAATTCCAT 58.444 45.455 0.00 0.00 45.98 3.41
2337 2381 3.062763 CAACACGCTCTTTCTGAGTCAT 58.937 45.455 0.00 0.00 44.41 3.06
2343 2387 3.734597 CGCTCTTTCTGAGTCATGAGAGG 60.735 52.174 20.30 11.87 44.41 3.69
2437 2481 2.639065 TGCCGAATAGGGATGTTCAAC 58.361 47.619 0.00 0.00 41.48 3.18
2512 2556 7.279615 TCCACGACCAATTAGATGTATCAATT 58.720 34.615 0.00 0.00 0.00 2.32
2534 2578 2.069273 GCTCTAACACACGCTCAATGT 58.931 47.619 0.00 0.00 0.00 2.71
2690 2734 4.410400 CCCTCCAAGTGGCCGACC 62.410 72.222 0.00 0.00 34.44 4.79
3117 3161 4.641989 ACTGATATGATCAAAAGTGCCACC 59.358 41.667 0.00 0.00 39.11 4.61
3137 3181 3.329520 ACCTGTAATTCTACCCACAGCAA 59.670 43.478 0.00 0.00 37.63 3.91
3288 3332 1.485066 TCCCGAAGCCTCTCCATAAAC 59.515 52.381 0.00 0.00 0.00 2.01
3540 3604 7.994334 TGGTGTAAAGTATGGTAAAAGTTCACT 59.006 33.333 0.00 0.00 0.00 3.41
3705 3771 3.255642 ACCGCACATGAATAGTTTTTGCT 59.744 39.130 0.00 0.00 0.00 3.91
3786 3852 2.568090 GCGTCCGGGTACGAAAGA 59.432 61.111 18.90 0.00 45.68 2.52
3814 3880 6.338214 TGCTCTTCGCTAATAATCTCATCT 57.662 37.500 0.00 0.00 40.11 2.90
4051 4129 4.851558 CGCTGATAAAAACCTGCAGTAAAC 59.148 41.667 13.81 0.00 0.00 2.01
4131 4209 2.646930 CGGGGTATAGGGTTTGGAAAC 58.353 52.381 0.00 0.00 38.17 2.78
4167 4245 3.004734 GCTTGTGTCACTTTAACTGGCAT 59.995 43.478 4.27 0.00 0.00 4.40
4381 4459 1.878656 CTCGGAGCCACGGAACTCTT 61.879 60.000 0.00 0.00 33.29 2.85
4386 4464 0.468226 AGCCACGGAACTCTTGAACA 59.532 50.000 0.00 0.00 0.00 3.18
4709 4787 1.472878 GGAATTGTTTCTTCGCCCTCC 59.527 52.381 0.00 0.00 32.16 4.30
4787 4876 0.323302 TAAAGGCAGATGACGCACCA 59.677 50.000 0.00 0.00 0.00 4.17
4962 5051 4.100653 CCTGAAGGATCTCATGTGAGCTTA 59.899 45.833 12.29 0.00 38.62 3.09
5007 5096 3.066064 TGCTCACACGCATACAAAGTTTT 59.934 39.130 0.00 0.00 34.44 2.43
5028 5118 9.088987 AGTTTTGTTAAAATCTCCCATACACAT 57.911 29.630 0.00 0.00 32.22 3.21
5149 5241 7.411372 CGCCAAACATAAGCGTTTTGATTATTT 60.411 33.333 0.00 0.00 44.65 1.40
5569 5666 3.721172 ATGGTCGCTCCCCCATCCT 62.721 63.158 0.00 0.00 36.76 3.24
5865 5962 0.464452 AGCCCGGAGTAGCACAATAC 59.536 55.000 0.73 0.00 0.00 1.89
5976 6073 3.643320 TGGCAGACTCGATTAAGATCCAT 59.357 43.478 0.00 0.00 0.00 3.41
6105 6202 2.335681 TCCACCACACTTCATCCCTA 57.664 50.000 0.00 0.00 0.00 3.53
6285 6382 5.277974 GCTCTCAAATTCTGCTACAAACACA 60.278 40.000 0.00 0.00 0.00 3.72
6332 6429 4.947147 ACGCGGGTTGCCACATGT 62.947 61.111 12.47 0.00 42.08 3.21
6360 6457 1.482182 AGCGCATTAGTGATGGTCTGA 59.518 47.619 11.47 0.00 36.21 3.27
6692 6791 3.710086 TTTAGGGTTTGGGGGAAAACT 57.290 42.857 0.40 0.00 39.51 2.66
6696 6795 1.752198 GTTTGGGGGAAAACTGGGC 59.248 57.895 0.00 0.00 37.13 5.36
6697 6796 1.051556 GTTTGGGGGAAAACTGGGCA 61.052 55.000 0.00 0.00 37.13 5.36
6698 6797 1.051556 TTTGGGGGAAAACTGGGCAC 61.052 55.000 0.00 0.00 0.00 5.01
6699 6798 2.200092 GGGGGAAAACTGGGCACA 59.800 61.111 0.00 0.00 0.00 4.57
6700 6799 2.207229 GGGGGAAAACTGGGCACAC 61.207 63.158 0.00 0.00 0.00 3.82
6701 6800 1.456705 GGGGAAAACTGGGCACACA 60.457 57.895 0.00 0.00 0.00 3.72
6702 6801 1.739667 GGGAAAACTGGGCACACAC 59.260 57.895 0.00 0.00 0.00 3.82
6703 6802 1.040339 GGGAAAACTGGGCACACACA 61.040 55.000 0.00 0.00 0.00 3.72
6704 6803 0.820871 GGAAAACTGGGCACACACAA 59.179 50.000 0.00 0.00 0.00 3.33
6705 6804 1.470805 GGAAAACTGGGCACACACAAC 60.471 52.381 0.00 0.00 0.00 3.32
6706 6805 0.172352 AAAACTGGGCACACACAACG 59.828 50.000 0.00 0.00 0.00 4.10
6707 6806 0.963355 AAACTGGGCACACACAACGT 60.963 50.000 0.00 0.00 0.00 3.99
6719 6818 2.594529 CACAACGTGCTATGTGGTTC 57.405 50.000 9.73 0.00 42.46 3.62
6720 6819 2.143122 CACAACGTGCTATGTGGTTCT 58.857 47.619 9.73 0.00 42.46 3.01
6721 6820 2.157668 CACAACGTGCTATGTGGTTCTC 59.842 50.000 9.73 0.00 42.46 2.87
6760 6859 7.042321 CCTCTCGACTGTAACTCTATAACTCTG 60.042 44.444 0.00 0.00 0.00 3.35
6783 6883 4.624604 GCAATAAACTCCCTTTACCCTCGA 60.625 45.833 0.00 0.00 0.00 4.04
6786 6886 3.697619 AACTCCCTTTACCCTCGAAAG 57.302 47.619 0.00 0.00 34.32 2.62
6787 6887 2.617658 ACTCCCTTTACCCTCGAAAGT 58.382 47.619 0.00 0.00 32.94 2.66
6795 6895 6.072838 CCCTTTACCCTCGAAAGTAAAAGAAC 60.073 42.308 16.24 0.00 37.83 3.01
6799 6899 6.373186 ACCCTCGAAAGTAAAAGAACAAAG 57.627 37.500 0.00 0.00 0.00 2.77
6800 6900 5.884232 ACCCTCGAAAGTAAAAGAACAAAGT 59.116 36.000 0.00 0.00 0.00 2.66
6802 6902 7.718314 ACCCTCGAAAGTAAAAGAACAAAGTAT 59.282 33.333 0.00 0.00 0.00 2.12
6804 6904 9.382244 CCTCGAAAGTAAAAGAACAAAGTATTG 57.618 33.333 0.00 0.00 42.46 1.90
6805 6905 9.382244 CTCGAAAGTAAAAGAACAAAGTATTGG 57.618 33.333 0.00 0.00 41.01 3.16
6806 6906 8.895737 TCGAAAGTAAAAGAACAAAGTATTGGT 58.104 29.630 0.00 0.00 39.82 3.67
6814 6914 8.500753 AAAGAACAAAGTATTGGTATATGCGA 57.499 30.769 0.00 0.00 36.33 5.10
6815 6915 7.715265 AGAACAAAGTATTGGTATATGCGAG 57.285 36.000 0.00 0.00 36.33 5.03
6817 6917 8.418662 AGAACAAAGTATTGGTATATGCGAGTA 58.581 33.333 0.00 0.00 36.33 2.59
6818 6918 7.941795 ACAAAGTATTGGTATATGCGAGTAC 57.058 36.000 1.47 1.47 41.01 2.73
6819 6919 7.723324 ACAAAGTATTGGTATATGCGAGTACT 58.277 34.615 0.00 0.00 41.01 2.73
6820 6920 7.866393 ACAAAGTATTGGTATATGCGAGTACTC 59.134 37.037 13.18 13.18 41.01 2.59
6821 6921 7.520451 AAGTATTGGTATATGCGAGTACTCA 57.480 36.000 22.37 5.18 0.00 3.41
6822 6922 7.147143 AGTATTGGTATATGCGAGTACTCAG 57.853 40.000 22.37 15.32 0.00 3.35
6823 6923 4.848562 TTGGTATATGCGAGTACTCAGG 57.151 45.455 22.37 8.43 0.00 3.86
6824 6924 3.154710 TGGTATATGCGAGTACTCAGGG 58.845 50.000 22.37 7.72 0.00 4.45
6825 6925 3.155501 GGTATATGCGAGTACTCAGGGT 58.844 50.000 22.37 7.81 0.00 4.34
6826 6926 3.190953 GGTATATGCGAGTACTCAGGGTC 59.809 52.174 22.37 6.44 0.00 4.46
6827 6927 2.730934 TATGCGAGTACTCAGGGTCT 57.269 50.000 22.37 3.61 0.00 3.85
6828 6928 1.107114 ATGCGAGTACTCAGGGTCTG 58.893 55.000 22.37 5.58 0.00 3.51
6832 6932 2.671632 GCGAGTACTCAGGGTCTGAAAC 60.672 54.545 22.37 1.60 40.18 2.78
6863 6963 1.346395 ACCACGAACCATCTGCTTACA 59.654 47.619 0.00 0.00 0.00 2.41
6879 6979 2.038814 TACATGGCCGACGCATGGAT 62.039 55.000 16.47 3.27 36.38 3.41
6881 6981 1.301716 ATGGCCGACGCATGGATAC 60.302 57.895 0.00 0.00 36.38 2.24
6901 7001 0.606401 CGTTCCACCCAGCTGTTCAT 60.606 55.000 13.81 0.00 0.00 2.57
6914 7014 0.255604 TGTTCATGTGCCCGATCCAT 59.744 50.000 0.00 0.00 0.00 3.41
6916 7016 0.179020 TTCATGTGCCCGATCCATCC 60.179 55.000 0.00 0.00 0.00 3.51
6917 7017 1.148949 CATGTGCCCGATCCATCCA 59.851 57.895 0.00 0.00 0.00 3.41
6918 7018 0.887836 CATGTGCCCGATCCATCCAG 60.888 60.000 0.00 0.00 0.00 3.86
6974 7086 4.948576 ACGCACATACGTGTCGAA 57.051 50.000 11.53 0.00 46.28 3.71
7071 7188 2.385091 CCGCGTTTCCTACCGTTGG 61.385 63.158 4.92 0.00 0.00 3.77
7217 7348 4.404654 CCGCAAAAGCGAGCACCC 62.405 66.667 11.83 0.00 34.88 4.61
7218 7349 4.741781 CGCAAAAGCGAGCACCCG 62.742 66.667 3.45 0.00 34.88 5.28
7231 7394 1.071471 CACCCGTCACTGCCTTTCT 59.929 57.895 0.00 0.00 0.00 2.52
7232 7395 1.071471 ACCCGTCACTGCCTTTCTG 59.929 57.895 0.00 0.00 0.00 3.02
7233 7396 2.328099 CCCGTCACTGCCTTTCTGC 61.328 63.158 0.00 0.00 0.00 4.26
7234 7397 2.328099 CCGTCACTGCCTTTCTGCC 61.328 63.158 0.00 0.00 0.00 4.85
7235 7398 2.328099 CGTCACTGCCTTTCTGCCC 61.328 63.158 0.00 0.00 0.00 5.36
7236 7399 1.073897 GTCACTGCCTTTCTGCCCT 59.926 57.895 0.00 0.00 0.00 5.19
7237 7400 1.073722 TCACTGCCTTTCTGCCCTG 59.926 57.895 0.00 0.00 0.00 4.45
7238 7401 2.282745 ACTGCCTTTCTGCCCTGC 60.283 61.111 0.00 0.00 0.00 4.85
7239 7402 2.035312 CTGCCTTTCTGCCCTGCT 59.965 61.111 0.00 0.00 0.00 4.24
7240 7403 2.034687 TGCCTTTCTGCCCTGCTC 59.965 61.111 0.00 0.00 0.00 4.26
7241 7404 2.354343 GCCTTTCTGCCCTGCTCT 59.646 61.111 0.00 0.00 0.00 4.09
7326 7492 2.125673 CCGCACTCCCTACCGTTG 60.126 66.667 0.00 0.00 0.00 4.10
7329 7495 2.955881 GCACTCCCTACCGTTGCCT 61.956 63.158 0.00 0.00 0.00 4.75
7337 7503 3.166490 TACCGTTGCCTCGCCACAA 62.166 57.895 0.00 0.00 0.00 3.33
7338 7504 4.025401 CCGTTGCCTCGCCACAAC 62.025 66.667 0.00 0.00 42.15 3.32
7409 7850 0.413434 TCTCATCTCCCACCTCACCA 59.587 55.000 0.00 0.00 0.00 4.17
7411 7852 0.984230 TCATCTCCCACCTCACCAAC 59.016 55.000 0.00 0.00 0.00 3.77
7412 7853 0.987294 CATCTCCCACCTCACCAACT 59.013 55.000 0.00 0.00 0.00 3.16
7428 7869 2.139731 AACTCTCTCTCCCGGTCGGT 62.140 60.000 8.67 0.00 0.00 4.69
7434 7875 2.045242 CTCCCGGTCGGTCTCAGA 60.045 66.667 8.67 0.00 0.00 3.27
7435 7876 2.360852 TCCCGGTCGGTCTCAGAC 60.361 66.667 8.67 0.00 37.86 3.51
7436 7877 2.361357 CCCGGTCGGTCTCAGACT 60.361 66.667 4.40 0.00 38.58 3.24
7452 7893 0.613292 GACTCTCAGCTCACTCCCCA 60.613 60.000 0.00 0.00 0.00 4.96
7528 7975 2.672996 AATGGCCACGCTCACCAC 60.673 61.111 8.16 0.00 35.99 4.16
7571 8021 2.224329 CCTCAGCATCATCCTCTTCCTG 60.224 54.545 0.00 0.00 0.00 3.86
7574 8024 1.141254 AGCATCATCCTCTTCCTGCTG 59.859 52.381 0.00 0.00 38.45 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.900546 AGTTTCCCTTCTGAGTGATCGT 59.099 45.455 0.00 0.00 0.00 3.73
23 24 1.416401 TGAAGCGACAGTTTCCCTTCT 59.584 47.619 5.53 0.00 36.86 2.85
55 56 5.374921 TGCACCATTGTCATCCAAAAATTT 58.625 33.333 0.00 0.00 36.44 1.82
259 260 1.281899 GCAGTACTCGAAGCACCATC 58.718 55.000 0.00 0.00 0.00 3.51
320 321 1.982226 TCATTTTCTGAGGAACCCCGA 59.018 47.619 0.00 0.00 37.58 5.14
354 355 4.345859 TTTAGTTCCCGTCACACATCTT 57.654 40.909 0.00 0.00 0.00 2.40
407 411 2.049063 GACAGGTTGAGCGCGTCT 60.049 61.111 8.43 5.17 0.00 4.18
471 478 1.198408 AGCATTCGTGCATGTGAACAG 59.802 47.619 5.68 1.84 37.25 3.16
637 646 2.610976 CGTGGGTCAAGTCATTACGGAA 60.611 50.000 0.00 0.00 0.00 4.30
762 774 1.173913 CCTCCCCGGTTGACATTTTC 58.826 55.000 0.00 0.00 0.00 2.29
785 797 2.677228 CCCCTTGGTCTGGCGATT 59.323 61.111 0.00 0.00 0.00 3.34
840 852 2.743928 GACAGAGCCACCTTGCCG 60.744 66.667 0.00 0.00 0.00 5.69
845 857 1.002888 CATCAACTGACAGAGCCACCT 59.997 52.381 10.08 0.00 0.00 4.00
1056 1072 4.802876 AGACAAAGCTTCAAAAGAGTCG 57.197 40.909 0.00 0.00 0.00 4.18
1153 1169 2.450609 TTTCGAGGAAAGAACTCCCG 57.549 50.000 0.00 0.00 35.95 5.14
1371 1412 1.901833 TGACTGATAGCTGGCTTGACA 59.098 47.619 0.00 0.00 0.00 3.58
1387 1428 2.149578 GCTTGCACTCTGAATGTGACT 58.850 47.619 1.63 0.00 37.60 3.41
1539 1580 1.367840 GTGACGCTCTGGACCACTT 59.632 57.895 0.00 0.00 0.00 3.16
1601 1642 3.055530 GGAGATCAGTTTGCTTCTCTCCA 60.056 47.826 10.70 0.00 43.11 3.86
1770 1813 1.990799 TGACGGTGCTGTAAAGATCG 58.009 50.000 0.00 0.00 0.00 3.69
1953 1997 0.390603 TGACCGTGCCAAGATAACCG 60.391 55.000 0.00 0.00 0.00 4.44
1957 2001 2.700371 AGATGATGACCGTGCCAAGATA 59.300 45.455 0.00 0.00 0.00 1.98
2201 2245 1.133606 GTTTTGGTGGAGGGTCCTTCA 60.134 52.381 3.03 0.00 37.46 3.02
2512 2556 3.056821 ACATTGAGCGTGTGTTAGAGCTA 60.057 43.478 0.00 0.00 40.39 3.32
2519 2563 4.994852 ACATACTAACATTGAGCGTGTGTT 59.005 37.500 0.00 5.43 39.26 3.32
2534 2578 2.112998 CTCCCGACCCCAACATACTAA 58.887 52.381 0.00 0.00 0.00 2.24
2690 2734 5.070446 TGAATGCTACTATACCCAAGTCAGG 59.930 44.000 0.00 0.00 0.00 3.86
3117 3161 5.163622 CCAATTGCTGTGGGTAGAATTACAG 60.164 44.000 0.00 0.00 42.51 2.74
3254 3298 3.500680 GCTTCGGGACAAAGTGTTAATCA 59.499 43.478 0.00 0.00 0.00 2.57
3288 3332 4.399004 AGACTCAATGAGATTCTTCGGG 57.601 45.455 18.20 0.00 32.86 5.14
3540 3604 0.320073 CTTCTCGGTGCGGGTTAACA 60.320 55.000 8.10 0.00 0.00 2.41
3612 3678 3.250280 CGAAGCTATACTAGTTCGGCTGA 59.750 47.826 0.00 0.00 36.55 4.26
3705 3771 2.024846 ACGATGAGGAGGAGGAAGAAGA 60.025 50.000 0.00 0.00 0.00 2.87
3814 3880 6.821160 TCACCAATCGTTTGAGATGCTTTATA 59.179 34.615 7.79 0.00 34.60 0.98
4131 4209 4.627035 TGACACAAGCGATGAACATAGAAG 59.373 41.667 0.00 0.00 0.00 2.85
4167 4245 7.283354 CGGATCCTCAGCTACTATTATCACATA 59.717 40.741 10.75 0.00 0.00 2.29
4381 4459 2.971660 TTTGGACTCGACAGTGTTCA 57.028 45.000 0.00 0.00 30.63 3.18
4386 4464 2.494073 GAGGAGATTTGGACTCGACAGT 59.506 50.000 0.00 0.00 35.49 3.55
4481 4559 0.982673 CGACTGAATCGTGTTCGGTC 59.017 55.000 23.37 23.37 46.25 4.79
4640 4718 3.116300 CTGATTATGACCGTCTCGTTGG 58.884 50.000 0.00 0.00 0.00 3.77
4709 4787 1.602851 AGAGGTATTGTCGGATCGTCG 59.397 52.381 0.00 0.00 0.00 5.12
4787 4876 8.458573 TTTCGGCAATATTTTCACCATATACT 57.541 30.769 0.00 0.00 0.00 2.12
5007 5096 6.726379 TGGATGTGTATGGGAGATTTTAACA 58.274 36.000 0.00 0.00 0.00 2.41
5028 5118 1.922447 ACATTCCCCATAGTGCTTGGA 59.078 47.619 0.00 0.00 36.26 3.53
5569 5666 2.745698 CTCAGGTGCTGCAGTGGA 59.254 61.111 16.64 5.28 0.00 4.02
5865 5962 3.902881 AGATTAGGGCACTCAGAACTG 57.097 47.619 0.00 0.00 0.00 3.16
5976 6073 5.958380 TGAGGTAGATAAGCCTTTGAGAAGA 59.042 40.000 0.00 0.00 34.81 2.87
6105 6202 6.734281 GGGTTATGGATCTACCCTATAACCTT 59.266 42.308 20.16 0.00 46.55 3.50
6285 6382 2.572095 TTCGATCAGCGGGCGTCAAT 62.572 55.000 0.00 0.00 41.33 2.57
6332 6429 2.584970 CTAATGCGCTTCGGCCGA 60.585 61.111 27.28 27.28 37.76 5.54
6360 6457 5.555017 CTCCATCGGAACCATCTTCATATT 58.445 41.667 0.00 0.00 0.00 1.28
6699 6798 1.871039 GAACCACATAGCACGTTGTGT 59.129 47.619 15.03 1.03 41.27 3.72
6700 6799 2.143122 AGAACCACATAGCACGTTGTG 58.857 47.619 10.48 10.48 42.25 3.33
6701 6800 2.413837 GAGAACCACATAGCACGTTGT 58.586 47.619 0.00 0.00 0.00 3.32
6702 6801 1.390123 CGAGAACCACATAGCACGTTG 59.610 52.381 0.00 0.00 0.00 4.10
6703 6802 1.271379 TCGAGAACCACATAGCACGTT 59.729 47.619 0.00 0.00 0.00 3.99
6704 6803 0.885879 TCGAGAACCACATAGCACGT 59.114 50.000 0.00 0.00 0.00 4.49
6705 6804 1.550065 CTCGAGAACCACATAGCACG 58.450 55.000 6.58 0.00 0.00 5.34
6706 6805 1.476891 TCCTCGAGAACCACATAGCAC 59.523 52.381 15.71 0.00 0.00 4.40
6707 6806 1.476891 GTCCTCGAGAACCACATAGCA 59.523 52.381 15.71 0.00 0.00 3.49
6708 6807 1.751924 AGTCCTCGAGAACCACATAGC 59.248 52.381 15.71 0.00 0.00 2.97
6709 6808 3.193691 ACAAGTCCTCGAGAACCACATAG 59.806 47.826 15.71 0.00 0.00 2.23
6710 6809 3.056821 CACAAGTCCTCGAGAACCACATA 60.057 47.826 15.71 0.00 0.00 2.29
6711 6810 1.971357 ACAAGTCCTCGAGAACCACAT 59.029 47.619 15.71 0.00 0.00 3.21
6712 6811 1.068588 CACAAGTCCTCGAGAACCACA 59.931 52.381 15.71 0.00 0.00 4.17
6713 6812 1.605712 CCACAAGTCCTCGAGAACCAC 60.606 57.143 15.71 4.87 0.00 4.16
6714 6813 0.679505 CCACAAGTCCTCGAGAACCA 59.320 55.000 15.71 0.00 0.00 3.67
6715 6814 0.670854 GCCACAAGTCCTCGAGAACC 60.671 60.000 15.71 0.55 0.00 3.62
6716 6815 0.670854 GGCCACAAGTCCTCGAGAAC 60.671 60.000 15.71 2.88 0.00 3.01
6717 6816 0.832135 AGGCCACAAGTCCTCGAGAA 60.832 55.000 15.71 0.00 0.00 2.87
6718 6817 1.228894 AGGCCACAAGTCCTCGAGA 60.229 57.895 15.71 0.00 0.00 4.04
6719 6818 1.216710 GAGGCCACAAGTCCTCGAG 59.783 63.158 5.01 5.13 39.43 4.04
6720 6819 3.377656 GAGGCCACAAGTCCTCGA 58.622 61.111 5.01 0.00 39.43 4.04
6760 6859 3.626217 CGAGGGTAAAGGGAGTTTATTGC 59.374 47.826 0.00 0.00 33.11 3.56
6795 6895 7.865889 TGAGTACTCGCATATACCAATACTTTG 59.134 37.037 17.85 0.00 0.00 2.77
6799 6899 6.323266 CCTGAGTACTCGCATATACCAATAC 58.677 44.000 17.85 0.00 0.00 1.89
6800 6900 5.417894 CCCTGAGTACTCGCATATACCAATA 59.582 44.000 17.85 0.00 0.00 1.90
6802 6902 3.572682 CCCTGAGTACTCGCATATACCAA 59.427 47.826 17.85 0.00 0.00 3.67
6804 6904 3.155501 ACCCTGAGTACTCGCATATACC 58.844 50.000 17.85 0.00 0.00 2.73
6805 6905 4.073549 AGACCCTGAGTACTCGCATATAC 58.926 47.826 17.85 6.35 0.00 1.47
6806 6906 4.072839 CAGACCCTGAGTACTCGCATATA 58.927 47.826 17.85 0.00 32.44 0.86
6810 6910 0.037734 TCAGACCCTGAGTACTCGCA 59.962 55.000 17.85 1.17 35.39 5.10
6811 6911 1.174783 TTCAGACCCTGAGTACTCGC 58.825 55.000 17.85 5.12 41.75 5.03
6812 6912 2.094649 GGTTTCAGACCCTGAGTACTCG 60.095 54.545 17.85 12.12 41.75 4.18
6813 6913 3.596310 GGTTTCAGACCCTGAGTACTC 57.404 52.381 16.32 16.32 41.75 2.59
6833 6933 2.282110 TTCGTGGTGCCACCCATG 60.282 61.111 12.25 5.36 43.49 3.66
6835 6935 4.572571 GGTTCGTGGTGCCACCCA 62.573 66.667 12.25 0.00 43.49 4.51
6836 6936 3.860930 ATGGTTCGTGGTGCCACCC 62.861 63.158 12.25 11.07 43.49 4.61
6837 6937 2.282180 ATGGTTCGTGGTGCCACC 60.282 61.111 7.01 7.01 43.49 4.61
6838 6938 1.302511 AGATGGTTCGTGGTGCCAC 60.303 57.895 11.13 11.13 43.01 5.01
6839 6939 1.302431 CAGATGGTTCGTGGTGCCA 60.302 57.895 0.00 0.00 36.64 4.92
6840 6940 2.690778 GCAGATGGTTCGTGGTGCC 61.691 63.158 0.00 0.00 0.00 5.01
6842 6942 1.732259 GTAAGCAGATGGTTCGTGGTG 59.268 52.381 0.00 0.00 37.00 4.17
6844 6944 2.093306 TGTAAGCAGATGGTTCGTGG 57.907 50.000 0.00 0.00 37.00 4.94
6845 6945 2.352651 CCATGTAAGCAGATGGTTCGTG 59.647 50.000 0.00 5.34 40.08 4.35
6846 6946 2.632377 CCATGTAAGCAGATGGTTCGT 58.368 47.619 0.00 0.00 40.08 3.85
6847 6947 1.331756 GCCATGTAAGCAGATGGTTCG 59.668 52.381 0.00 0.00 45.42 3.95
6848 6948 1.678101 GGCCATGTAAGCAGATGGTTC 59.322 52.381 0.00 0.00 45.42 3.62
6863 6963 1.301716 GTATCCATGCGTCGGCCAT 60.302 57.895 2.24 0.00 38.85 4.40
6879 6979 1.412453 AACAGCTGGGTGGAACGGTA 61.412 55.000 19.93 0.00 38.12 4.02
6881 6981 1.966451 GAACAGCTGGGTGGAACGG 60.966 63.158 19.93 0.00 38.12 4.44
6901 7001 2.910360 CTGGATGGATCGGGCACA 59.090 61.111 0.00 0.00 0.00 4.57
6916 7016 4.504916 CTGGGCGAGGTCGAGCTG 62.505 72.222 23.97 14.96 43.02 4.24
6918 7018 4.500116 GACTGGGCGAGGTCGAGC 62.500 72.222 6.48 6.48 43.02 5.03
7104 7223 1.566563 GTCTGCTGTTGCTGTCACG 59.433 57.895 0.00 0.00 40.48 4.35
7105 7224 1.835483 CGGTCTGCTGTTGCTGTCAC 61.835 60.000 0.00 0.00 40.48 3.67
7106 7225 1.595109 CGGTCTGCTGTTGCTGTCA 60.595 57.895 0.00 0.00 40.48 3.58
7210 7341 3.537206 AAGGCAGTGACGGGTGCTC 62.537 63.158 0.00 0.00 39.76 4.26
7211 7342 3.120086 AAAGGCAGTGACGGGTGCT 62.120 57.895 0.00 0.00 39.76 4.40
7215 7346 2.328099 GCAGAAAGGCAGTGACGGG 61.328 63.158 0.00 0.00 0.00 5.28
7216 7347 2.328099 GGCAGAAAGGCAGTGACGG 61.328 63.158 0.00 0.00 43.51 4.79
7217 7348 2.328099 GGGCAGAAAGGCAGTGACG 61.328 63.158 0.00 0.00 46.44 4.35
7218 7349 1.073897 AGGGCAGAAAGGCAGTGAC 59.926 57.895 0.00 0.00 46.44 3.67
7231 7394 4.405671 GCAGAGCAGAGCAGGGCA 62.406 66.667 0.00 0.00 0.00 5.36
7233 7396 4.486503 GGGCAGAGCAGAGCAGGG 62.487 72.222 0.00 0.00 0.00 4.45
7234 7397 4.486503 GGGGCAGAGCAGAGCAGG 62.487 72.222 0.00 0.00 0.00 4.85
7235 7398 4.834453 CGGGGCAGAGCAGAGCAG 62.834 72.222 0.00 0.00 0.00 4.24
7238 7401 4.527583 GAGCGGGGCAGAGCAGAG 62.528 72.222 1.31 0.00 35.48 3.35
7263 7426 3.721706 CAGAGTGGTGGGGGAGCC 61.722 72.222 0.00 0.00 0.00 4.70
7311 7477 2.436115 GGCAACGGTAGGGAGTGC 60.436 66.667 0.00 0.00 0.00 4.40
7313 7479 2.348888 CGAGGCAACGGTAGGGAGT 61.349 63.158 0.00 0.00 46.39 3.85
7409 7850 1.378778 CCGACCGGGAGAGAGAGTT 60.379 63.158 6.32 0.00 38.47 3.01
7411 7852 1.820481 GACCGACCGGGAGAGAGAG 60.820 68.421 13.43 0.00 39.97 3.20
7412 7853 2.254737 GAGACCGACCGGGAGAGAGA 62.255 65.000 13.43 0.00 39.97 3.10
7428 7869 2.617788 GGAGTGAGCTGAGAGTCTGAGA 60.618 54.545 11.18 0.00 0.00 3.27
7434 7875 0.902516 GTGGGGAGTGAGCTGAGAGT 60.903 60.000 0.00 0.00 0.00 3.24
7435 7876 1.896694 GTGGGGAGTGAGCTGAGAG 59.103 63.158 0.00 0.00 0.00 3.20
7436 7877 1.979155 CGTGGGGAGTGAGCTGAGA 60.979 63.158 0.00 0.00 0.00 3.27
7452 7893 0.608130 TTACATGAGCTGGAGTGCGT 59.392 50.000 0.00 0.00 38.13 5.24
7528 7975 4.825679 GGAGGGGAGGGGAGGTGG 62.826 77.778 0.00 0.00 0.00 4.61
7637 8096 3.313524 TCGCCCAGCAGCTTGAGA 61.314 61.111 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.